[ECOLOG-L] Organic Agriculture
Lately, a lot of people in skeptical communities have been saying that not only does organic agriculture use more land than conventional, it's no better or even worse for the environment overall. What do those of you with expertise in agroecology think about this? Jane -- - Jane Shevtsov, Ph.D. Lecturer and DBER Fellow, UCLA co-founder, www.worldbeyondborders.org "Muad'Dib learned rapidly because his first training was in how to learn. And the first lesson of all was the basic trust that he *could* learn. It's shocking to find how many people do not believe they can learn, and how many more believe learning to be difficult." --Frank Herbert, *Dune*
Re: [ECOLOG-L] Request for Readings/Videos for Honors Course on Future of Human Civilization
I taught a similar seminar a few years ago that was built around David Brin's novel "Earth:. It's idea-dense science fiction that gives students a lot to sink their teeth into and provides a framework for discussing a lot of science. I also strongly recommend "The World in 2050" by Laurence C. Smith, which looks at big environmental and demographic trends. "Thinking in Systems" by Donella Meadows is also a good supplement. Hope that helps, Jane On Wed, Feb 1, 2017 at 6:53 PM, Neufeld, Howard S. <neufel...@appstate.edu> wrote: > Dear All – > > This semester I am teaching an experimental Honors seminar course to > juniors/seniors titled *The Future of Human Civilization: Climate Change, > Population Growth and the Possibilities for Sustainability*. > > > > I know the title may sound pretentious, but I purposely wanted to make it > provocative. The students are a mix of STEM and non-STEM majors. > > > > I would welcome suggestions for ancillary materials for the course. We > have a large number of primary journal articles and a large cadre of books, > including the updated *Limits to Growth*, *2050* and *2052* (yes those > are two books about the future!), Al Gore’s *The Future*, Oreskes & > Conway’s *Collapse of Western Civilization*, and Ron Scranton’s *How to > Die in the Anthropocene*. > > > > I almost included Diamond’s *Collapse*, which was high on the list, but I > didn’t think it had the proper perspective. I'm currently reading David > Biello's *The Unnatural World*. > > > > I’d be particularly interested in any high quality videos that pertain to > the course subject, plus further suggestions for readings. We opened with > Nick Bostrom’s article “*The Future of Humanity*” to set the stage for > the rest of the course, then followed up with the Ehrlichs’ recent PNAS > article on whether global civilization can avoid a collapse. Then we read > Schramski et al.’s article in PNAS on the analogy of Earth as a discharging > battery. > > > > Thanks! > > Howie Neufeld > > -- > Dr. Howard S. Neufeld, Professor > Director, Southern Appalachian Environmental Research and Education Center > (SAEREC) > Chair, Appalachian Interdisciplinary Atmospheric Research Group (AppalAIR) > > Mailing Address: >Department of Biology >572 Rivers St. >Appalachian State University >Boone, NC 28608 >Tel: 828-262-2683; Fax 828-262-2127 > > Websites: > Academic: http://biology.appstate.edu/faculty-staff/104 > Personal: http://www.appstate.edu/~neufeldhs/index.html > SAEREC: http://saerec.appstate.edu > AppalAIR: http://appalair.appstate.edu > Fall Colors: > Academic: http://biology.appstate.edu/fall-colors > Facebook: https://www.facebook.com/FallColorGuy > > -- - Jane Shevtsov, Ph.D. Lecturer and DBER Fellow, UCLA co-founder, www.worldbeyondborders.org "Muad'Dib learned rapidly because his first training was in how to learn. And the first lesson of all was the basic trust that he *could* learn. It's shocking to find how many people do not believe they can learn, and how many more believe learning to be difficult." --Frank Herbert, *Dune*
[ECOLOG-L] Math for Life Sciences Teaching Position at UCLA
and continue until the position is filled. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see: UC Nondiscrimination and Affirmative Action Policy (http://policy.ucop.edu/doc/4000376/NondiscrimAffirmAct). -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org "Muad'Dib learned rapidly because his first training was in how to learn. And the first lesson of all was the basic trust that he *could* learn. It's shocking to find how many people do not believe they can learn, and how many more believe learning to be difficult." --Frank Herbert, *Dune*
Re: [ECOLOG-L] Should Calculus Be Required of All Ecology/Biology Majors?
For the last four years, I have been working on a new Math for Life Scientists course at UCLA that our life sciences majors can take (along with a stats course) instead of the usual Calculus for Life Sciences sequence. This course dives right into dynamical modeling, with students learning how to write basic differential equation models on the first day, before we do any calculus, treating X' as just a piece of notation. (Most of our students took calculus in high school but this is not a requirement and we cover the essential concepts of calculus, which most students who took AP Calculus have very little understanding of.) During the two-course sequence, we teach the core concepts of calculus, including multivariable, and linear algebra, but our main focus is on making, simulating and analyzing differential equation models, including many ecological ones. Topics covered include state space, vector fields, trajectories, equilibria and stability (both graphical and linear), nullclines, bifurcations, oscillations and limit cycles, chaos and multivariable optimization, with models from ecology, physiology, and other subject areas including chemistry and physics. There's also a weekly computer lab that uses the free, Python-based program SageMath, so our students also learn basic programming. Student response has been tremendous, to the point where our main challenge now is keeping up with demand. (If you might be interested in teaching this course, please email me off-llist.) We've had many students seek out opportunities to learn more about modeling, get into research that uses it, ask for ways to stay involved with the course after finishing it (we started an undergraduate learning assistant program for the computer labs based on a combination of need and student enthusiasm) and request that a third quarter be added to the sequence. (This would probably cover stochastic and spatial models.) Basically, we're teaching nonlinear dynamics to biology freshmen and they love it. Some combination of this kind of modeling course and statistics would serve most students much better than calculus. Jane Shevtsov On Thu, Oct 20, 2016 at 8:30 PM, John Grady <jgra...@gmail.com> wrote: > Great conversation. I guess I'll add my two cents too. In my experience > (postdoc, macroecology) I deal regularly with calculus equations, but > really only insofar as I see them in a paper and need to understand what > they are trying to say. I'm not integrating many equations, and I suspect > the number of ecologists actually doing such work is somewhere near 1%. > Sure, the theory behind most ecology - from Lotka-Volterra to modern > statistical methods we use in R - is based on some amount of calculus, > probability theory or linear algebra. These are all great things to know, > but rarely of much actual use for the vast majority of practicing > ecologists. However, what I think *is* very useful, is knowing how read > and understand equations. To understand *dN/dt*, you should understand > what a derivative is and why its such an important concept. Likewise, > understanding integrals and limits are quite useful. A course designed to > give biologists a basic vocabulary in calculus - filled with real > biological examples - would be invaluable and not nearly so painful and > mostly pointless as the calculus many of us have taken. Those classes > basically consisted of pattern recognition (what kind of math problem is > this?), plugging in some algorithm you'll forget the next week, and then > chugging away at a solution that makes little sense. Most math taught today > is too abstract and mechanical to offer conceptual insight to biologists. > It goes in one ear and out the other. > > Theoretical and computational type ecologists could certainly benefit from > more learning, but I think a mandatory semester stressing conceptual and > reading competency in math would be sufficient for 90+ percent of biology > majors. The main challenge I suppose would be designing an appropriate > curriculum and getting the right instructor to teach it. > > John > > On Thu, Oct 20, 2016 at 6:17 PM, Loretta Fisher <loretta.fis...@gmail.com> > wrote: > >> Hello, all, >> >> What an interesting discussion. I am a master's student in ecology. I >> am also from a very rural area in Colorado that has poor public math >> education, and am a first generation college student from a low-income >> family. Calculus requirements were much of the reason I initially dropped >> out of my undergraduate schooling in an aerospace engineering program. >> When I finally returned to finish my undergraduate studies, I went to the >> humanities instead of the sciences, because I had completely lost my >> confidence in my quantitative abilities. It has taken me a long time to >> dev
[ECOLOG-L] Lynx-Hares Data
Does anyone have the actual data for the Canada lynx and snowshoe hare dataset that Elton studied? Thanks!
[ECOLOG-L] Culturing Acellular Slime Molds
Hi all, Does anyone here work with Physarum or similar slime molds? How do you prevent the cultures from getting moldy? Do you just transfer the organism to new medium every few days or are there other things that help? Thanks, Jane Shevtsov -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org Make no little plans. They have no magic to stir men's blood and probably themselves will not be realized. Make big plans; aim high in hope and work, remembering that a noble, logical diagram once recorded will never die, but long after we are gone will be a living thing, asserting itself with ever-growing insistency. --Daniel Burnham, architect of first skyscraper (1864-1912)
Re: [ECOLOG-L] advice for disabled student seeking grad program in wildlife biology?
Dear Laura, I also use a wheelchair because of cerebral palsy and earned a Ph.D. in ecology, combining both fieldwork and modeling, in 2012. (I'm currently a postdoc doing curriculum development.) I'll be happy to correspond off-list, but here are two main points that I want to make publicly so others can benefit. 1. Don't assume that having a physical disability means being unable to do field work, especially if the disability in question is a spinal cord injury. There are off-road powerchairs ( http://www.accesstr.com/All_Terrain_Wheelchairs_s/1513.htm) that maybe a grant could pay for. People with SCIs can usually paddle a kayak or canoe (possibly with a seat frame or paddle holder, but those are not hard to build). They can also rock climb with adaptive equipment ( https://www.nolimitstahoe.com/) and such equipment could be adapted to tree climbing for canopy work. Horseback riding ( http://www.grit.com/animals/horse-saddles-for-handicap-riders.aspx) can provide a way to reach field sites. Or how about a snowmobile? http://www.mobility-advisor.com/adaptive-snowmobiling.html The point is that there's a lot of room for creativity here! If your school has an outdoor recreation program, they may be able to help out. Plus, there's always the time-honored tactic of asking your friends to help out. I went to my field sites to get a feel for them and identify plants, but friends did much of the actual data and sample collection. The university also paid for a field and lab assistant. 2. There's always work to be done with theory, other people's data or data collected for you. (See Adventurers and Scientists for Conservation, http://www.adventurescience.org, for the latter.) Plus, depending on the student's intellectual tastes, there's modeling (dynamical and statistical), GIS, remote sensing and all that good stuff. (Ecologists are starting to use drones!) Definitely encourage your student to learn basic modeling, one or two programming languages (Python, R, Matlab, etc.) and basic GIS. She can branch out from there. Please email me if you want to correspond further. I'd also be happy to correspond with your student directly. Best, Jane On Tue, Apr 21, 2015 at 7:54 AM, Gough, Laura go...@uta.edu wrote: Dear all: A student has contacted me who wants to pursue graduate studies and an academic career in wildlife biology. Tragically, she fractured her back two years ago and is currently confined to a wheelchair. There is only a remote chance that she will be able to walk again. I am reaching out to the Ecolog community to see if any of you have ideas for how she can pursue her dream if she is not physically able to conduct field work. Please respond to me off-list. Thanks in advance, Laura Gough Laura Gough, Professor and Interim Chair Department of Biology University of Texas Arlington Arlington, TX 76019-0498 817-272-2872 go...@uta.edumailto:go...@uta.edu http://www.uta.edu/biology/gough/lab/index.htm -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org Make no little plans. They have no magic to stir men's blood and probably themselves will not be realized. Make big plans; aim high in hope and work, remembering that a noble, logical diagram once recorded will never die, but long after we are gone will be a living thing, asserting itself with ever-growing insistency. --Daniel Burnham, architect of first skyscraper (1864-1912)
Re: [ECOLOG-L] open source alternatives to MATLAB
I've used Octave and Sage. Octave is very, very close to Matlab. If you want to run Matlab code without buying Matlab, Octave is what you want. The graphics aren't as polished, but otherwise it seems like a solid piece of software. I've used it in my research to do metacommunity analysis. Sage is a very different animal, and I am absolutely in love with it. Why? First of all, the syntax. Sage is based on Python (although it incorporates other programs, like Octave and R) and retains Python's accessibility and clarity. How do you plot x^2? plot(x^2). If you want to specify a plotting range, use plot(x^2, (x,-5,5)) or whatever. You can create an animation in two lines, one of which is just the show() command. My Math for Life Scientists students (mostly lower-division bio students at UCLA) create slider-driven interactive plots on their first day in lab. I created a complex interactive that does dynamic simulation, vector fields, equilbria and nullclines 3 or 4 weeks after starting to use Sage. A student of mine put together some very useful network weight computation and visualization code in a weekend, about 3 weeks after he started using Sage. (He was moderately proficient in Matlab and knew a little R before starting; I knew the basics of those languages and had a working knowledge of C++ but was not an expert programmer by any means.) In no other programming environment that I have ever seen can you go so far so fast. The other great thing about Sage is that it will do pretty much anything. You can simulate differential equation models (much more easily than in Matlab or R.) You can do symbolic work, like in Mathematica or Maple. You can plot things. You can study networks. And you can do anything Python can do. If Sage doesn't do what you want but there's a Python library for it (and there usually is), you're good to go. (This is easiest on a Linux or Mac system; you may be able to install packages on the virtual machine that Sage runs on in Windows but I've never tried it.) And if you or your students are using Sage a lot, you can set up a server for them to use. Since you typically use Sage inside a web browser, this is indistinguishable from running it on your own computer and saves the trouble of installation. I'm happy to answer any Sage questions people may have. Jane Shevtsov On Sun, May 4, 2014 at 6:13 PM, Malcolm McCallum malcolm.mccallum.ta...@gmail.com wrote: On a whim, I did a google search for open source version of matlab and was shocked to see just how many supposed open equivalents there were! Does anyone know enough about these to evaluate which they think is the best or the pluses and minuses of these different free alternatives? GNU Octave (http://www.gnu.org/software/octave/) FreeMat (http://freemat.sourceforge.net/) Scilab (http://scilab.org/) Sage (http://www.sagemath.org) If you want to email me directly, I can post a follow up summary. M -- Malcolm L. McCallum, PHD, REP Department of Environmental Studies University of Illinois at Springfield Managing Editor, Herpetological Conservation and Biology “Nothing is more priceless and worthy of preservation than the rich array of animal life with which our country has been blessed. It is a many-faceted treasure, of value to scholars, scientists, and nature lovers alike, and it forms a vital part of the heritage we all share as Americans.” -President Richard Nixon upon signing the Endangered Species Act of 1973 into law. Peer pressure is designed to contain anyone with a sense of drive - Allan Nation 1880's: There's lots of good fish in the sea W.S. Gilbert 1990's: Many fish stocks depleted due to overfishing, habitat loss, and pollution. 2000: Marine reserves, ecosystem restoration, and pollution reduction MAY help restore populations. 2022: Soylent Green is People! The Seven Blunders of the World (Mohandas Gandhi) Wealth w/o work Pleasure w/o conscience Knowledge w/o character Commerce w/o morality Science w/o humanity Worship w/o sacrifice Politics w/o principle Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] Recent PhDs on Food Stamps - Overwhelmed with Replies
People from comfortable middle-class backgrounds don't know how to be poor. In grad school, other students were complaining about their assistantships, but it was more money than I had ever had. Since graduation, I've alternated between temporary full-time and half-time positions (reasonably well-paid, thanks to the University of California's very active unions, but in a very expensive city), but my family's support and the expectations shaped by my background have made it a good experience. As long as you avoid or minimize undergrad debt, coming from a low-income background can be an advantage in academia. Jane Shevtsov On Mon, Feb 10, 2014 at 10:45 PM, Cynthia O'Rourke c...@umbc.edu wrote: Jason touches on my primary concern with this situation, other than having a Ph.D. that might eventually enable me to do no better than tech position in the field that I love. Ecology, evolution, and to a broader extent the organismal sciences have been predominately white and middle-class fields ever since they stopped being exclusively white and upper-class fields. The current situation makes it insanity for anyone without a strong safety net to pursue a Ph.D. in evolutionary biology, which further limits the diversity of viewpoints that we can bring to our investigations and discussions. I think that will hinder the progress of evolutionary biology, and perhaps these other fields as well. On Mon, Feb 10, 2014 at 6:25 PM, Jason Hernandez jason.hernande...@yahoo.com wrote: I was one of those who responded offline to the original post. Rather than tell my story again here, I offer further thoughts. Steven Schwartz wrote (in part) Perhaps the question ought to be how much one is willing to sacrifice with the knowledge that you may never achieve your dream. My answer: more than I ever thought I would. But when my savings completely dry up, I have to pay the bills somehow, and if a job completely outside my chosen field finally presents itself, then the question becomes: which risk do I take? Do I risk becoming trapped in that other career track, taking me away from my dream as my degree recedes into the past? Or do I risk becoming a bum on the streets for love of a dream? Because that is the reality some of us face. Every day, I see announcements for really great experiences that are not only unpaid, but in many cases, require the intern to cover his/her own expenses. I don't really care about upward mobility; but if I don't have the money, I cannot be a part of those opportunities, no matter how wonderful they may be in terms of the work being done. Unfortunately, anyone interested particularly in tropical ecosystems will face this situation; I do not remember ever seeing an opening for a paid position in any project in a tropical country. If students coming in knew this, how many would still pursue that path? Who would do these internships, knowing that they essentially are preparing for a career as an intern? The urgency of the situation in the tropics needs quality work, but economic realities tend to turn aspiring researchers away from those parts of the world. Jason Hernandez M.S., East Carolina University -- Date:Sun, 9 Feb 2014 22:40:15 -0500 From:Steven Schwartz drstevenschwa...@aol.com Subject: Re: Recent PhDs on Food Stamps - Overwhelmed with Replies I=92ll add my two cents. The scarcity of positions is absolutely = nothing new. In the 1980=92s it was not unusual for there to be 300-400 = applicants or more for positions in any kind of organismal biology. It = was during that decade that doing a post-doc in ecology became the norm = as a holding place for the emerging cohort. I don=92t mean to plead a = sad tale, but I was a post-doc at a major lab, published many papers, = and later taught and taught before getting a tenure-track job after way = too many years. I stuck with it, through the tough times, when I = perhaps should have recognized my giving-up-time. I was financially = insecure most of the time but that was price I was willing to pay to = achieve my dream. Perhaps the question ought to be how much one is = willing to sacrifice with the knowledge that you may never achieve your = dream. This isn=92t fair and I, more than most, feel badly for all the = young scientists who won=92t get what they so badly want. And deserve. = But it just won=92t happen for any number of reasons which speak nothing = of the quality of the candidates passed over. As for the preponderance of adjunct or part-time faculty, one only has = to look at the corporate model of governance at most colleges and = universities to see where the real growth in higher education has been. = While the quality of education has been taking hits, the quality, = quantity, and salaries of administrators has been growing enormously
[ECOLOG-L] Summer Programs and the Quarter System
This time of year, I scan ECOLOG for summer opportunities for students I mentor. However, I end up having to discard many excellent programs, including the majority of REU positions, because they start a week or more before spring quarter ends at UCLA. The quarter system isn't that rare. For example, all University of California campuses other than Berkeley and Merced run on it. (I personally prefer semesters, but quarters are what we've got.) While some longer programs may require a may or early June start date, those lasting 8 or fewer weeks should be able to run from mid-June to August, allowing students on both quarter and semester systems to participate. I therefore issue a plea for program scheduling that considers the needs of students on the quarter system! -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org Those who say it cannot be done should not interfere with those who are doing it. --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] Why No Foundations Book for Evolution?
Thanks, Mitch. The Ridley reader looks close enough to what I was looking for that I just ordered it. (These days, it's generally possible to find the full text of papers that pique your interest online anyway.) I'd appreciate your list as well. BTW, if you haven't read the Applebaum book, it's a must-have. It's particularly strong on connections with the humanities. Best, Jane On Tue, Aug 27, 2013 at 10:24 PM, Mitch Cruzan cru...@pdx.edu wrote: Hi Jane, Some years ago I ran into the same problem when I taught a Foundations of Evolution graduate-level course. I ended up choosing my own collection of papers and it worked pretty well - I can send you my list if you want. You should also have a look at Ridley's Oxford Reader on evolution, but it is heavily annotated like the one you describe. Be aware that some of the classic papers by Fisher, Haldane, Wright, Kimura, and others are pretty math-heavy and incomprehensible for many students. Depending on the level of students, a text that provides excerpts from classic papers and interpretations might be just the thing you are looking for. Mitch Cruzan On 8/27/2013 9:24 PM, Jane Shevtsov wrote: Recently, while looking for some readings to use with students, I tried locating a book similar to Foundations of Ecology for evolution. To my surprise, the only things I was able to find were Appleman's Norton Critical Edition of Darwin, which is excellent but omits much of scientific importance, and Wetherington's Readings in the History of Evolutionary Theory, which is also very good but uses highly abridged selections and a much stronger editorial voice than the Foundations series. Have I missed something? If not, maybe someone will be moved to produce such a book! -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] Job: National Coordinator for the Landscape Conservation Cooperatives initiative, USFWS
The word nice used to mean foolish. Etymology is fascinating, but it's a mistake to think that historical meanings or sources of words constrain current meanings. See http://www.fallacyfiles.org/etymolog.html and http://en.wikipedia.org/wiki/Etymological_fallacy . Jane Shevtsov On Sun, May 26, 2013 at 10:44 PM, Wayne Tyson landr...@cox.net wrote: The etymology of the term landscape means to scrape the land. Not much to do with ecology. Yes, I know that the word has come to mean something else, but it interferes with public understanding of the fundamental opposition of landscaping with ecosystems. It may be futile, but I'm gonna keep on griping about it. WT - Original Message - From: David Inouye ino...@umd.edu To: ECOLOG-L@LISTSERV.UMD.EDU Sent: Thursday, May 16, 2013 7:31 AM Subject: [ECOLOG-L] Job: National Coordinator for the Landscape Conservation Cooperatives initiative, USFWS This is a heads up for those who might be interested in applying for the position of National Coordinator for the Landscape Conservation Cooperatives initiative. Doug Austen has announced his departure, and the FWS will shortly post the position in USA JOBS. We believe the posting will be only open for two weeks. The following infomation should be helpful in locating the position, but regular users of USAJobs will know that the published title might not match exactly what the position title is USFWS Title: National Landscape Conservation Coordinator OPM Title: Fish and Wildlife Administrator Series and Grade: GS-0480, Series 15 Duty Location: Washington, DC (Arlington, VA, is actual office location) - No virus found in this message. Checked by AVG - www.avg.com Version: 10.0.1432 / Virus Database: 3162/5828 - Release Date: 05/16/13 -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] Take the Train to ESA Minneapolis
As far as I'm concerned, the best reason for taking the train is that it's fun! You see fascinating places, meet new people and eat good food. What's not to like? Jane Shevtsov On May 2, 2013 5:33 PM, Reinmann, Andrew, Brett reinm...@bu.edu wrote: Hello Ecologgers, There is quite an interesting discussion in response to my post about taking the train to ESA, so I thought I would chime in. Paul is 100% correct, taking the train to ESA will have no mathematical impact on climate change. In fact, nothing that any one of us changes in our own lives will have an impact on climate change, and the same can be said for many other environmental issues. So then, why take the train to ESA? 1. Reduce the carbon footprint of science. While many of us have made changes to our liftestyles to reduce our carbon footprints, increased air travel has caused the carbon footprint of many scientists to surge to 2.5 x the American average (see Fox et al. 2009 in Frontiers, http://www.esajournals.org/doi/pdf/10.1890/09.WB.019). So, finding alternative means of travel to conferences will reduce our individual carbon footprints and that of the conferences we attend. 2. Symbolism. While some may shrug this off as meaningless, I would argue that symbolic activities set an example for others to follow and can have a cascade of effects that COULD make a mathematical contribution to the climate change equation. History has shown us that acts of symbolism work (think civil rights protests in the 1960s) and there is no reason to think that they cannot continue to bring about positivie change. 3. Demand alternatives to air travel. Admittedly, the passenger rail system in the U.S. is not what it should, or could be, given our wealth. Amtrak largely travels on tracks designed for and owned by freight train companies. As a result, they are not designed for high-speed train travel and freight trains almost always get the right of way. If train travel demand increases so will the resources and justification for investing in our passenger rail infrastructure. While bad train travel experiences, such as those described by McNeeley, do occur, I would challenge you to find a mode of long-distance travel that does not have its own share of frustrating experiences (flight delays, getting searched, traffic jams, etc.). I have traversed the country many times via train and I will add that a sleeping car might be ideal, but I have never had one and just make do with my reclining train seat. My back is still ok, though I am only 34! Telecommuting would certainly have a bigger impact on the footprint of conferences and this is something that perhaps we should move towards. However, when we do have to travel to conferences, taking the train is one way to reduce our environmental impact. Certainly train travel will not be feasible for everyone, so when flying is necessary consider taking a direct flight and purchasing carbon offsets through one of the many reputable programs available (e.g., Carbonfund.org and Terrapass.com). 'Scientist' is one of the most respected and trusted professions in the U.S. As such, we have a great ability and responsibility to lead by example. As with all societal issues, we cannot expect the world around to us to change if we, ourselves, are unwilling to. REMINDER: If you decide to take the train to ESA this year and/or buy carbon offsets for your travel please email me the details so I can help coordinate and tally up the numbers. Feel free to contact me if you want some tips for saving money on your train ticket. Thanks! -Andy Reinmann -- Andy Reinmann Ph.D. Candidate Biology Department Boston University 5 Cummington St Boston, MA 02215 From: Ecological Society of America: grants, jobs, news [ ECOLOG-L@LISTSERV.UMD.EDU] on behalf of Wayne Tyson [landr...@cox.net] Sent: Monday, April 29, 2013 12:28 AM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: Re: [ECOLOG-L] Take the Train to ESA Minneapolis Lou Ziegler once said that Nature has shrugged off countless species in the history of the earth, and she will shrug of Homo sapiens in the same way. When that happens, things can get back to normal. WT “In the heart of the city I have heard the wild geese crying on the pathways that lie over a vanished forest. Nature has not changed the force that drives them. Man, too, is a different expression of that natural force. He has fought his way from the sea’s depths to Palomar Mountain. He has mastered the plague. Now, in some final Armageddon, he confronts himself.” –Loren Eiseley, The Invisible Pyramid. “We need another and a wiser and perhaps a more mystical concept of animals. Remote from universal nature, and living by complicated artifice, man in civilization surveys the creature through the glass of his knowledge and sees thereby a feather magnified and the whole image in distortion. We patronize
Re: [ECOLOG-L] A response to EO Wislon's opinion about math
It's interesting that Kim is from Canada and Robert is from the UK, while David is from the US. I'm also from the US and I've never heard of a biology program that didn't require at least one term of calculus, although I've heard of such things having existed in the past. (BTW, I think linear algebra is also a very good option.) I don't know about Canadian universities, but in the UK, students start to specialize as early as 16, while in the US, specialization is at least nominally discouraged until the last 2-3 years of college. American science students usually take calculus in college; as far as I know, students in the UK tend to do so before college -- and may not do so at all if they study biology. For Oxford's biology program, math is not an entry requirement (http://www.biology.ox.ac.uk/admissions.html); students do take Quantitative Methods, but this is apparently statistics. I would be very surprised if any reputable US university allowed this, although the usefulness of the typical freshman calculus course is debatable. Could the difference in math requirements be a consequence of early vs. late specialization? Jane Shevtsov On Thu, Apr 11, 2013 at 8:26 AM, Kim Cuddington kcudd...@gmail.com wrote: Extremely limited or even no math requirements may be a more common feature of biology programs than you realize. For example, up until recently, my program required only a stats course. It is my understanding that this is an increasingly common approach for biology programs. Partially as a result of my efforts, all our biology students now require a math course, but it is not necessarily a calculus course (linear algebra is an option, and non-calculus physics for some reason). Don't get me wrong, I think linear algebra is equally necessary, but many of our ecology students opt for the easier algebra course. Students from another environmental campus program on campus require no math course at all. Therefore, when I explain concepts as basic as exponential growth in a 4th year ecology course, I also have to explain the meaning of a derivative. Needless to say, I find the situation ludicrous. Educated students in ANY science need to know what a derivative is, and educated citizens, regardless of what their university major, REALLY need to understand exponential population growth. Math is not an optional part of any education, let alone a science education, but I've seen it being treated that way at at several institutions. Kim Cuddington University of Waterloo (BTW this is a notoriously mathy school) -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] A response to E.O. Wilson's opinion about math
Some of you may be interested in a response I wrote on Google+, from the perspective of someone who does plenty of modeling. https://plus.google.com/u/0/109678189789435119043/posts/7mZ9iuhztKC Jane Shevtsov On Tue, Apr 9, 2013 at 7:56 PM, malcolm McCallum malcolm.mccal...@herpconbio.org wrote: I disagree. E.O. Wilson has written an essay that few seem to be actually reading. He is targeting specific audiences, and providing encouragement for those without math skills. He is not telling people to blow off math. See below. 1) This article is written with two specific audiences in mind: A) students interested in science but who find math very very difficult, and B) people who believe that if you are not a mathematical superstar you have no place in science. It is not concerning those who can do math well. NO, you do not need to have great math skills, it helps, a lot, but you can get around it. The audience is made clear in this paragraph: During my decades of teaching biology at Harvard, I watched sadly as bright undergraduates turned away from the possibility of a scientific career, fearing that, without strong math skills, they would fail. This mistaken assumption has deprived science of an immeasurable amount of sorely needed talent. It has created a hemorrhage of brain power we need to stanch. 2) He does not say math is not important, he says that the ability to form concepts is more important than math. Based on the comments on this listerve over the year, I believe we all agree here. I come to this based on this excerpt: Fortunately, exceptional mathematical fluency is required in only a few disciplines, such as particle physics, astrophysics and information theory. Far more important throughout the rest of science is the ability to form concepts, during which the researcher conjures images and processes by intuition. 3) He makes the point that math without conceptualization ability is basically useless, whereas when you combine the two it can be much better, but you must team up with a person who does have the skills, and these folks are everywhere happy to team up with you. I come to this based on this excerpt: Ideas in science emerge most readily when some part of the world is studied for its own sake. They follow from thorough, well-organized knowledge of all that is known or can be imagined of real entities and processes within that fragment of existence. When something new is encountered, the follow-up steps usually require mathematical and statistical methods to move the analysis forward. If that step proves too technically difficult for the person who made the discovery, a mathematician or statistician can be added as a collaborator. and from this excerpt: Call it Wilson's Principle No. 1: It is far easier for scientists to acquire needed collaboration from mathematicians and statisticians than it is for mathematicians and statisticians to find scientists able to make use of their equations. 4) He specifically tells people that if their math skills are not adequate, they better take more math. He is very clear on this in this excerpt: If your level of mathematical competence is low, plan to raise it, but meanwhile, know that you can do outstanding scientific work with what you have. 5) The entire point of this article is that just because you are poor in math, does not mean you are a poor scientist. You just have to pick your field properly. (I recall an environment chemist once telling me he has never needed to use any math higher than a simple regression, and he is at an R1 with quite a funded lab). To support this notion, I concluded this from the final paragraph: For aspiring scientists, a key first step is to find a subject that interests them deeply and focus on it. In doing so, they should keep in mind Wilson's Principle No. 2: For every scientist, there exists a discipline for which his or her level of mathematical competence is enough to achieve excellence. I have a feeling that a lot of people jumped to a conclusion before finishing reading the article, because nowhere does he say math is not necessary. He just says that if you need math, you must either attain the skills yourself, or find someone else who has the skills and can work with you. This is actually not only good and encouraging advice (because so many of us learn math late in life), it is also spot on accurate with how we do much science today. On Tue, Apr 9, 2013 at 8:22 PM, David Inouye ino...@umd.edu wrote: Don't Listen to E.O. Wilson Math can help you in almost any career. There's no reason to fear it. http://www.slate.com/articles/health_and_science/science/2013/04/e_o_wilson_is_wrong_about_math_and_science.html http://www.slate.com/articles/health_and_science/science/2013/04/e_o_wilson_is_wrong_about_math_and_science.html -- Malcolm L. McCallum Department of Molecular Biology and Biochemistry
Re: [ECOLOG-L] Livestock practice and ethics
When you say that Americans spend less than people in other countries on food, don't forget that we have to spend more on insurance and medical expenses. These things are either free or heavily subsidized in other wealthy countries. Also, the cost of housing varies greatly from place to place, but in many places, like Los Angeles, it can easily take up half of a person's income. Jane Shevtsov On Thu, Mar 28, 2013 at 1:21 PM, Yasmin J. Cardoza yjcar...@ncsu.eduwrote: Hello all, I am posting this on behalf of one of our students in animal science, Keena Mullen, with whom I shared this interesting discussion thread and she wishes to provide her insights on the topic. Her e-mail address is below if you wish to correspond to her directly. Cheers! Yasmin From: cefslist-ow...@lists.ncsu.edu [mailto:cefslist-ow...@lists.ncsu.edu] On Behalf Of Keena Mullen Sent: Thursday, March 28, 2013 9:12 AM To: Yasmin J. Cardoza Cc: CEFS List; Wilmer Pacheco-Dominguez; David Rosero Tapia; Santa Mendoza Benavides Subject: Re: [cefslist] FW: [ECOLOG-L] Livestock practice and ethics Hi all, Here is the response that I sent to Dr. Ganter last night. I received your post on the ECOLOG-list from Yasmin Cardoza at NCSU. I am a PhD candidate in Animal Science at North Carolina State University, and I would like to respond to your comments. I won't be able to address all of your questions, but I would like to give you some points to ponder. One of the major challenges that Animal Science faces is to produce animals more efficiently so that we can feed the ever-growing population with less land and resources. In order to do this, we have studied management strategies to increase production of food from animals. These strategies include those you mentioned - beak trimming, hormone usage, and mass rearing facilities. Many animal science programs around the country have a mandatory animal welfare/animal well-being class that undergraduate students take. In addition, research in recent years has focused on animal welfare and assessing the natural behaviors of livestock, so that we can more adequately allow these animals to express their natural behaviors. One example of this research is the work of Dr. Temple Grandin, with whom you may be familiar. Her work on cattle handling has greatly decreased the stress of cattle heading to slaughter and her recommendations are being put into place worldwide. Another major issue that Animal Science is dealing with in regards to increasing efficiency is that many consumers do not seem to care how their meat has been produced. I say this, because consumers in the United States spend very little of their income on food ( http://www.motherjones.com/blue-marble/2012/01/america-food-spending-less http://www.motherjones.com/blue-marble/2012/01/america-food-spending-less) relative to other countries. Consumers demand cheap meat, so we strive to come up with technologies to produce it more efficiently. Of course, there are people who are concerned about where their food comes from, and that growing segment of the population is demanding change. I work with pasture-based and organic dairies and I see the great future in the market for these operations - many are also Animal Welfare Approved. This label is one way that consumers can make choices on purchasing food that will affect change in animal production. Regarding the ag-gag laws, I would like for you to think for a moment from the side of a farmer. Let's say you own a company, and you have a suspicion that your employees are doing something terribly wrong, but they seem to be doing their job and you don't find any evidence that they are doing something punishable. Your company is expanding and you decide to hire on a few more people. The next thing you know, those bad things you had suspicions about are posted all over YouTube by one of your recent hires. Your reputation is ruined, and your company has a black mark because you hired in someone that you trusted and, instead of telling you what was going on, they video taped it for the whole world to see. My interpretation of the ag-gag laws is to prevent these types of untrustworthy people from being hired and destroying farms from the inside out. I agree, farmers should be more transparent about what they are doing to their livestock. I just think this can be accomplished by people visiting farms to learn about where their food comes from, rather than from a sensational YouTube video that may have been provoked by an animal rights detective. I know that this does not answer your posed questions, but I thought I might pass on some food for thought. https://mail.google.com/mail/u/0/images/cleardot.gif On Wed, Mar 27, 2013 at 4:20 PM, Yasmin J. Cardoza yjcar...@ncsu.edu wrote: I thought this might be of interest to some of you...it definitely got me thinking how little we usually think about this subject
Re: [ECOLOG-L] Gender issues
Let's not forget that the original comment that triggered this whole discussion was made by a woman! I don't think it was intended to be sexist. It's not sexist to say, In my experience, women tend to do X and would be better off doing Y. It may be accurate or inaccurate, but it's not sexist. Jane Shevtsov On Mon, Feb 18, 2013 at 12:40 PM, Leslie M. Adams leslie.ad...@comcast.netwrote: Now, I am the one who must speak up and voice my support for Yvette (and Chandreyee). While no slight may have been intended, as a female scientist I too experienced the responses Yvette cites - and especially the one recently posted by Dr. Olden - as belittling and dismissive. There is considerable gender bias in the fields of ecology and biology and it is important to object to it whenever it arises; whether intentional or not. Perhaps it is easy to counsel moving on when you are unaffected by this handicap personally, but to say that it is somehow unsuitable or inappropriate to address on this listserv is ridiculous and dismisses the tremendously damaging effect this bias has on many, many lives. It is also not lost on me that the issue of gender has somehow arisen in a discussion of the skills necessary for landing a job in ecology. I would suggest that this is no coincidence. Leslie M. Adams, Ph.D. Adjunct Professor of Plant Systematics Professional Training and Development University of New Hampshire http://home.comcast.net/~leslie.adams/ http://home.comcast.net/~leslie.adams/ Home Office: 603 / 659-6177 Adjunct Associate Professor of Environmental Sustainability School of Undergraduate Studies (online) University of Maryland University College Adjunct Professor of Life Sciences Department of Liberal Arts New Hampshire Institute of Art We can't solve problems by using the same kind of thinking we used when we created them. - Albert Einstein -Original Message- From: Ecological Society of America: grants, jobs, news [mailto:ECOLOG-L@LISTSERV.UMD.EDU] On Behalf Of Julian Olden Sent: Monday, February 18, 2013 1:04 PM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: Re: [ECOLOG-L] A Graduate Student#x2019;s Guide to Neces sary Skills for Landing a Job Hi Yvette, Apologies, but your interpretation of my suggestion is extremely misguided and flat-out wrong. My response was a cleaver way of saying that you can ignore the silly responses of particular ECO-LOGGERS (some of which have a track record of this behavior) by filtering your emails. Unfortunately your email has added fuel to a series of ECOLOG posts that have very little to do with the original premise of the Blickley et al. (2012). Let's all move on now. Cheers, Julian --- Julian D. Olden Freshwater Ecology Conservation Lab School of Aquatic and Fishery Sciences University of Washington, Seattle WA 98195 e: mailto:ol...@uw.edu ol...@uw.edu, t: (206) 616-3112 tel:%28206%29%20616-3112 tel:%28206%29%20616-3112 w: http://www.fish.washington.edu/research/oldenlab/ http://www.fish.washington.edu/research/oldenlab/ skype: goldenolden The face of the river . . . was not a book to be read once and thrown aside, for it had a new story to tell every day. Mark Twain On 2/18/13 7:37 AM, Yvette Dickinson mailto: yvette.dickin...@gmail.com yvette.dickin...@gmail.com wrote: Like Chandreyee Mitra I was surprised by the comment included in Clara's list: 7. ...i am somewhat exercised by your post because, IMO, too many young, especially, female, applicants don't bring much to the table that others don't already know or that cannot be readily duplicated or that is mostly generalist-oriented... This is a sentiment that I have heard before in other venues and find abhorrent. I initially chose not to comment on it here, but I do support Chandreyee's in her comment. However, I am disgusted by the response Chandreyee recieved. To be told to simply use your email filter and not worry your silly little head over such matters is offensive. The concerns Chandreyee raised are legitimate, and should be addressed with the gravity and respect they deserve. I would like to remind all readers of ESA's code of ethics, particularly principle g. Ecologists will not discriminate against others, in the course of their work on the basis of gender, sexual orientation, marital status, creed, religion, race, color, national origin, age, economic status, disability, or organizational affiliation. Yvette Dickinson -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
[ECOLOG-L] Grad Students Choosing Their Own Questions (was: Advice for 36 year old trying to get into M.S. program)
Having graduated last year from a research group in which all students had to choose their own questions, I disagree with Aaron's point to an extent that is difficult to express in civil terms. However, I will attempt to do so for the sake of any students reading this. Aaron writes that grad students shouldn't work on their own questions because, If you already have a certain skillset and can come up with your own research projects and successfully execute them, you do NOT need to be a student (at least in that lab). But having a project idea and having the skills to execute it are two entirely different things. (Also, I simply could not have asked some of the questions I ended up writing substantial portions of my dissertation on with only my undergraduate background.) You are in grad school to learn the knowledge and skills to formulate and answer this and future questions, to be educated rather than trained. Aaron routinely and quite justifiably rails against students and postdocs being used as technicians. Well, the only way to not be a technician is to find your own questions! Work on your advisor's questions enough to earn your keep if you're on an assistantship and to learn and participate in collaborations within your lab. The rest of the time, focus on your own questions -- and make sure, when contacting prospective advisors, that they will allow and support this. Is it possible that your advisor will take credit for your ideas? Yes, although they probably won't. But if you wait, you may well get scooped by someone else! I will go further. A master's degree earned entirely by working on someone else's questions is fine, but a Ph.D. is not. A Ph.D. is supposed to signify the ability to do original research and the only way to prove this ability is to do a project of your own. I think the Ph.D. degree should simply not be awarded to someone who hasn't done this. No matter how many papers such a student has their name on, they're still working at an MS level. The current trend, driven by funding, of grad students working entirely on their advisors' questions is a profoundly destructive one and must be checked. Jane Shevtsov On Wed, Jan 30, 2013 at 6:25 PM, Aaron T. Dossey bugoc...@gmail.com wrote: If you do for some reason (which I cannot currently imagine) to go to graduate school, here is some advice that will help you get the most out of it without putting the future of your career at risk: 1) pick a very HANDS-ON professor who spends a lot of time with his or her students and postdocs (eg: they spend lots of time in the lab) in a successful lab with a great reputation (lots of publications, with students and postdocs who have left it and have successful careers currently who can attribute it to having worked in that lab) and 2) insist that you ONLY will work on work that is from the professor's own ideas - from their grants and based on their ideas. Do not fall into the trap of working for a professor who expects you to come up with your own projects. You are there to learn from them primarily, and also to do parts of their research. If you already have a certain skillset and can come up with your own research projects and successfully execute them, you do NOT need to be a student (at least in that lab). Pick a lab and a professor who have a lot to offer you in the form of TRAINING, connections and projects likely to be very fruitful. IF and when you have your own ideas you want to pursue, keep a log book of those and save those for when you graduate and are on your own/independent. Otherwise, it can get ugly. Many professors will, to put it bluntly, steal credit and reward for your ideas and independent work. Might as well avoid that pitfall and keep everyone happy (and keep you learning) by doing whatever work originates from the professor - besides, it's their job to drive the research and come up with the ideas. Basically, pick a prof and lab who seems to have YOUR CAREER INTERESTS at heart and act like it. -- Aaron T. Dossey, Ph.D. Biochemistry and Molecular Biology Founder/Owner: All Things Bugs Capitalizing on Low-Crawling Fruit from Insect-Based Innovation http://allthingsbugs.com/about/people/ http://www.facebook.com/Allthingsbugs 1-352-281-3643 -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] Tree stump removal in sensitive area
The number of people killed by falling trees each year isn't really the information we need. That number could be low because few decayed trees kill (or severely injure) people or because there are few such trees in populated areas. What we really want to know is the probability that a decayed tree will fall on somebody (or come close) when it eventually falls, given that it is in an area frequented by people. We can guesstimate this by finding out what fraction of the time there are people in the tree's fall zone, adjusting for any inaccessible areas/directions. (Yes, this ignores things like weather, but that's what makes it a back-of-the envelope estimate.) Suppose there are no inaccessible areas around the tree and there are people near it about 1/4 of the time. Then the probability of a hit or near miss when the tree eventually falls is 1/4 -- quite substantial in my eyes. Adjusting for weather and time of day or treefall may reduce it to 5% or 10%, which is not small considering the stakes. Some might object to this calculation, saying that it could be used to justify the removal of any urban trees. But the chances of a randomly chosen urban tree falling in the near future are very small and we can generally detect the conditions that make a tree likely to fall. The estimate above only makes sense for a tree that we know is likely to fall in the near future. If you wanted to, you could multiply the probability by an estimate of the probability of the tree falling in the next ten years (or whatever the time horizon of interest is), which the calculation above assumes to be 100%. Jane Shevtsov On Sun, Jan 20, 2013 at 12:32 PM, Nirmalya Chatterjee buba...@gmail.comwrote: Sorry to contradict you here Wayne, but your argument is anecdotal and seems to be as straw-manly as GWPatton's - people who work in the Forest Service are likely to get injured by trees, (lethally or otherwise) from falling branches, trees etc. - there's a term for that - occupational hazard. That doesn't necessarily mean that the general populace has the same odds of facing such an injury. 2010 CDC data indicate 4.88% accidental deaths (at #5 reason), and ~80% of those were due to poisoning, accidental falling and motor vehicle related, that pushes other reasons to sub-1% levels. Wind related tree failures caused 31 deaths/year from 1995-2007. http://www.bama.ua.edu/~jcsenkbeil/gy4570/schmidlin%20tree%20fatalities.pdf . That's 407 people in 12 years, don't blame the trees here. Blame human carelessness, thoughtlessness and Nature's unmitigated fury (the last cannot be controlled). Trees would be the means here, not the cause. My point being, yes there are some activities which cause people to be injured - but this always begs the question of what the odds are. As for the irrational fear of urban people to dying from tree-related as related by GWPatton - in my anecdotal experience, yes such fears exist. And trees are easy to pin the blame on, they aren't vocal about it, and with urban areas heavily paved and a whole gamut of underground disturbances related to utility lines etc., it is expected trees don't really find the unfettered access to the soil to stabilize themselves as evolution and Nature intended. The solution lies in learning to think more holistically instead of knee-jerk reactions, which many tend to do. And talking to victims of tree-fall injuries or their family members to get your ideas about its dangers is not proper science, neither is hearing anecdotes from of the likes of you, both would be called biased sources. I am yet to hear families and victims of auto accidents stopping riding or driving cars (in significant numbers), post-accident. Or people stopping use of household poisons because some one they knew mistakenly drank rat poison. As scientists it behooves us to keep emotion out of science. NC On 19 January 2013 23:11, Wayne Tyson landr...@cox.net wrote: Ecolog: I know I won't convince Me that while public safety concerns about falling trees (and dropping branches) might sometimes be exaggerated, the truth is that trees do fall and break and people die from it, and it is only prudent to get the dangerous ones down before they fall down. Me's point is also irrational, on this basis, and using straw-man arguments does not advance the issue, it only adds an emotional component. He knows damned well I did not imply that every tree that falls is going to kill someone; thankfully, even in heavily-used areas such deaths are somewhat rare, but that does not mean that dangerous trees should not be removed. Talk to the families of the victims and tell them you stopped the tree that killed their loved one from being removed. In my area, a public protest prevented a severely leaning large tree that showed clear signs of root failure opposite the direction of the lean from being removed. Those people should have to face the families
Re: [ECOLOG-L] JOB: Asst/Assoc. Prof. Biology at Bethune-Cookman
This ad has some of the oddest requirements I've ever seen. The applicant must have normal manual dexterity and visual and auditory faculty? I understand ads specifying that a person must be able to lift 50 pounds, hike over rough terrain or even, as in this ad, get around campus, as these are meaningful job-related activities, but manual dexterity and sensory acuteness are just means to various ends. Would you turn down Geerat Vermeij because he's blind? It would be much better to think about what you want the person you hire to be able to do. Do you care about their ability to teach lab classes? Give effective lectures? Do research? Then say that. A person who doesn't have normal manual dexterity may have other ways of doing these things. Don't shut out qualified applicants with disabilities from the get-go. Jane Shevtsov On Mon, Jan 7, 2013 at 10:43 AM, Elizabeth Congdon congdo...@gmail.comwrote: Bethune-Cookman University has three openings in our Biology Department due to two retirements and restructuring. The full announcements can be seen on HigherEdJobs. You are also free to e-mail me. I joined the department in the fall of 2012. One of these positions will be responsible for our genetics course, one will be responsible for our anatomy/physiology courses, and one is open to any discipline specialty. JOB SUMMARY: The Department of Biology seeks to fill a 9-month, tenure-track position at the Associate Professor level beginning August 2013. Applicants should be interdisciplinary scholar-teachers with particular expertise in the biological sciences and a robust background in one or two STEM disciplines. The ideal applicant will also show strong potential for interaction across diverse disciplines represented in the College and demonstrated expertise in pedagogy, curriculum development, and/or assessment. Potential applicants should be prepared to collaborate with faculty from multiple departments to develop and apply for extramural funding. ESSENTIAL FUNCTIONS: The successful candidate will be expected to teach in a predominantly undergraduate environment in an introductory biology sequence and/or upper-division major's courses appropriate to the candidate's area of specialization. Research supervision and mentorship of undergraduate and students is desired. The successful candidate will be expected to promote the Department's research profile by establishing a dynamic and vigorous research program in any area of biology supported by external funding sources. Competitive salary and an excellent benefits program are available. To apply for the position, please send: a letter of application, which identifies the position sought; curriculum vitae (with contact information); a one-page statement of teaching philosophy; statement of scholarly, creative or research interest. Excellence in teaching, research and/or scholarly or creative production, and service are required. Official copies of graduate transcripts required. Three letters of recommendation should be sent directly from the referee. Send all information to: Human Resources. MINIMUM EDUCATION and EXPERIENCE: Qualifications: Ph.D. in Biology or a related field is required; teaching experience and post doctoral training preferred. Review of applications begins immediately and will continue until the position is filled. ENVIRONMENTAL/PHYSICAL CONDITIONS: - Working environment is a normal business office setting - Demands normal manual dexterity and visual and auditory faculty - Must be mobile throughout the campus - Nothing in the job description restricts the right to assign or reassign duties and responsibilities to this job at any time Application Information Postal Address: Elvira WolfordPHR, Assistant Director Human Resources Management Bethune-Cookman University 640 Dr. Mary McLeod Bethune Blvd Daytona Beach, FL 32114 Phone: 386-481-2049 Fax: 386-481-2052 Online App. Form: http://www4.cookman.edu/humanresources/application.html Email Address: h...@cookman.edu -- Dr. Elizabeth Congdon Biology Department Bethune-Cookman University Daytona Beach, Florida 32114 congd...@cookman.edu -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] Scholarly research training for ecology grad students
I'm a huge fan of Sigma Xi's brochures Honor in Science and The Responsible Researcher. (They also have a collection of articles on authorship issues.) They're not specific to any discipline but are excellent because they focus on ethics rather than complying with regulations. Jane Shevtsov On Mon, Oct 22, 2012 at 6:15 PM, Russell, Leland leland.russ...@wichita.edu wrote: Hi, I am writing to seek advice concerning resources for Scholarly Integrity Training that are ecological, evolutionary or organismal in their focus. We are required to implement Scholarly Integrity Training for our graduate students. Topics that we need to cover include publication practices and authorship, conflict of interest and commitment and data management and ownership. We are thinking of using the CITI Biomedical Responsible Conduct or Research Modules, but because we are a Biology Department it would be nice to complement these biomedically-focused modules with something from an ecological point of view. I have thought about trying to incorporate a discussion of the Ecological Society's Code of Ethics into our new graduate student orientation. However, any ideas about resources for Scholarly Integrity Training for ecologists would be appreciated. Thanks. Leland F. Leland Russell, Ph.D. Associate Professor Department of Biological Sciences Wichita State University -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] The Audacity of Graduate School -training grad students in teaching and outreach
and Molecular Biology Founder/Owner: All Things Bugs Capitalizing on Low-Crawling Fruit from Insect-Based Innovation http://allthingsbugs.com/about/people/ http://www.facebook.com/Allthingsbugs 1-352-281-3643 -- Aaron T. Dossey, Ph.D. Biochemistry and Molecular Biology Founder/Owner: All Things Bugs Capitalizing on Low-Crawling Fruit from Insect-Based Innovation http://allthingsbugs.com/about/people/ http://www.facebook.com/Allthingsbugs 1-352-281-3643 -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
[ECOLOG-L] FW: Announcing 2013 Switzer Fellowships
This may be of interest to ECOLOG members. ___ Greetings from the Robert and Patricia Switzer Foundation: We are pleased to announce that the application period for the 2013 Switzer Environmental Fellowships is now open! Switzer Fellowships are given to top graduate students in New England and California who are committed to a career in environmental improvement, and who demonstrate the potential for leadership in their chosen field. The Fellowship provides a one-year $15,000 cash award, as well as access to other Switzer grant programs and career support, and membership in the Switzer Fellowship Network, a vibrant community of over 500 Switzer Fellows and environmental leaders. (We invite you to check out Switzer Network News to see live podcast interviews with some of our Fellows working on a diverse set of issues.) The Switzer Fellowship is not intended to be a research fellowship. We fund individuals doing a wide variety of environmental work (e.g., science, law, policy, engineering). Leadership potential is a more significant factor in our evaluation than the specifics of a particular graduate research project, although we are interested in novel and applied approaches to contemporary issues. Please see the Call for Applications which describes the Fellowship program and its requirements. Please pass this on to eligible candidates and colleagues, and post to your financial aid or graduate student office bulletin boards! This year's application deadline is January 10, 2013. If you have any questions about the Fellowship Program guidelines or the online application process, please do not hesitate to contact any of the Switzer Foundation staff. Thank you, and we look forward to receiving your students' applications! Lissa Widoff, Executive Director - li...@switzernetwork.org Erin Lloyd, Program Officer - e...@switzernetwork.org Don Brackett, Administrative Officer - d...@switzernetwork.org Office: (207) 338-5654 (office hours 8:30 am - 5:00 pm Eastern time, Mon-Thurs, other hours available by appointment) The Robert and Patricia Switzer Foundation is a results-driven family foundation that invests in individuals and organizations that drive positive environmental change. Founded in 1986, the Foundation is a grant making organization that mobilizes leaders from diverse disciplines who focus on integrated solutions to environmental issues. Through the Switzer Environmental Fellowship Program and related grants, the Foundation supports a Network of over 500 Switzer Fellows who are leaders in the nonprofit, public policy, business, academic and government sectors working to solve today's environmental challenges. For more information see www.switzernetwork.org. -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] The Audacity of Graduate School
The author misses the fact that European Ph.D. programs are 3-4 years long because the students do, by and large, work as technicians. There are no classes. There is, in most cases, no opportunity or time to pick your own question (even within a large project), which is really the thing that distinguishes a Ph.D. from an M.S. in my mind. If some countries have programs that work differently, I'm interested in knowing about them, but from what I've read, American programs are better (aside from pay). Jane Shevtsov On Tue, Oct 16, 2012 at 5:03 PM, Aaron T. Dossey bugoc...@gmail.com wrote: Very well written article: http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2012_09_28/caredit.a1200108 -- Aaron T. Dossey, Ph.D. Biochemistry and Molecular Biology Founder/Owner: All Things Bugs Capitalizing on Low-Crawling Fruit from Insect-Based Innovation http://allthingsbugs.com/about/people/ http://www.facebook.com/Allthingsbugs 1-352-281-3643 -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] The Audacity of Graduate School - Reshuffling Graduate Training
Again, your mileage may vary. When I wrote my first paper in grad school, I automatically put my advsor's name on it. He thanked me but said that he hadn't made enough of a contribution to earn that credit. Only after he made substantial (albeit sometimes exasperating to me) contributions to the writing did we put his name on the manuscript. And all his students had to come up with their own questions -- with some help if necessary, but their own questions. A few dropped out because they couldn't do this, but most did well. The Brazilian system does sound good, although I'd add university funding for the first 1-2 years for the coming up with your own question part. Not everyone will do this well straight out of undergrad, especially if they're skipping the MS. But yes, having faculty be fully paid by their universities (what a concept!) will go a long way toward making my experience a lot more common and the type that leads to burn-out a lot less common. And it should be possible for grad students to be PIs. Jane Shevtsov On Tue, Oct 16, 2012 at 9:55 PM, Aaron T. Dossey bugoc...@gmail.com wrote: Ph.D. students and postdocs picking their own question has devolved into institutionalized intellectual property theft. Why do original research when you don't get credit or own the IP? Now days many grad students and postdocs/postechs/postemps are expected not only to do all of the experiments, but to do the ordering for the lab, WRITE GRANTS, write the papers and even come up with the ideas. HOWEVER, it is always expected that the faculty boss is senior corresponding author on all papers that their students/postdocs/property generate regardless of if those faculty bosses had anything to do with it or were even aware it was going on. They also must be PI on all grants, again regardless of their involvement in formulation, writing or submission of the grant. Most institutions forbid students and postdocs from being PI of any grant they write, so even if they want to pursue their own ideas, they must tack on the name of one of the gatekeeper faculty to have the right to submit it to federal agencies for funding. THAT is institutionalized intellectual property theft - similar to bribes that people must pay in third world countries to authorities for various things. Any scientist should always have an unlimited right to PI their own grants, petition their own government for research funding and publish their own work independently if the effort warrants it. Check out this article: http://www.sciencemag.org/content/325/5940/528.summary Brazil has a fantastic system, as I understand it. There, federal research grants do NOT contain any salary funding - for faculty, students or postdocs. Trainees (I use the term very loosely for the sake of discussion here) like students and postdocs write for their own fellowships, and faculty are paid their full salaries by the institutions. This accomplishes many nice things such as: 1) giving students and postdocs more freedom and control of their careers - if they work for an abusive boss, they can take their funding to another lab, 2) prevents faculty from obcessing over grants just to get higher salaries, 3) reduces the incentive for faculty to do NOTHING but try to get grants, since their salaries are covered and it probably means that more scientists can get funding, rather than a few faculty oligarchs soaking up all of the grants by design. On 10/17/2012 12:40 AM, Jane Shevtsov wrote: The author misses the fact that European Ph.D. programs are 3-4 years long because the students do, by and large, work as technicians. There are no classes. There is, in most cases, no opportunity or time to pick your own question (even within a large project), which is really the thing that distinguishes a Ph.D. from an M.S. in my mind. If some countries have programs that work differently, I'm interested in knowing about them, but from what I've read, American programs are better (aside from pay). Jane Shevtsov On Tue, Oct 16, 2012 at 5:03 PM, Aaron T. Dosseybugoc...@gmail.com wrote: Very well written article: http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2012_09_28/caredit.a1200108 -- Aaron T. Dossey, Ph.D. Biochemistry and Molecular Biology Founder/Owner: All Things Bugs Capitalizing on Low-Crawling Fruit from Insect-Based Innovation http://allthingsbugs.com/about/people/ http://www.facebook.com/Allthingsbugs 1-352-281-3643 -- Aaron T. Dossey, Ph.D. Biochemistry and Molecular Biology Founder/Owner: All Things Bugs Capitalizing on Low-Crawling Fruit from Insect-Based Innovation http://allthingsbugs.com/about/people/ http://www.facebook.com/Allthingsbugs 1-352-281-3643 -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who
Re: [ECOLOG-L] The Audacity of Graduate School
On Wed, Oct 17, 2012 at 6:40 AM, Aaron T. Dossey bugoc...@gmail.com wrote: When we graduate, we have more or less the same credentials as everyone else - a degree. There are many successful scientists without Ph.D.'s but many more with Ph.D.'s who are unemployed. Can you make a rough estimate of the relative frequencies of each. Also, to emphasize how little we get out of a Ph.D. (a lot is stolen from us), we don't get credit for our work or publications because the professor always gets credit for everything we do while in their lab as a student or postdoc (which is something I am fighting on other fronts - I call it institutionalized intellectual property theft). Isn't that taken care of by the first author/last author distinction? A PI may get some undeserved credit, but that's different from the student not getting credit. The paper is still cited as Student et al. Or are you talking about taking the student's idea outright? BTW, if you believe that grad students are employees to the point of needing a union and thinking of their advisor as their boss, I would point out that people who do creative work as employees rarely keep the rights to their work. Typically, the intellectual property belongs to their employer (work done for hire). Isn't it better to say that grad students are not employees? -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org “Those who say it cannot be done should not interfere with those who are doing it.” --attributed to Robert Heinlein, George Bernard Shaw and others
Re: [ECOLOG-L] a vision?
A fascinating question. The first thing that comes to my mind is that all students should learn the rudiments of systems thinking, at least at the level of Donella Meadows' book _Thinking in Systems_, and some should take it much further. The nationalism you mention is a potential source of serious problems. Geology and evolutionary biology (the history of life) tie in with mining and biodiversity but also provide a broader perspective that may be very salutary. Same for world history and geography -- useful for international business and working with tourists, but also providing a bit of perspective. None of this has to be at a very deep level. A freshman-level introductory course should be enough. As for languages, I think students should learn SOME widely used language. It's probably best to give them a few choices (English, French, Chinese, Arabic, and maybe Spanish or Portuguese come to mind), although English is likely to be a popular one. Jane Shevtsov On Tue, Jul 17, 2012 at 10:25 PM, David Duffy ddu...@hawaii.edu wrote: If you had a chance to found and direct a university in a developing, strongly nationalistic country dependent on oil, mining and its biodiversity (ecotourism, indigenous people), what would you have as its curriculum? The university would cover all three fields. How should they influence one another? How much would you involve expats? Would you insist everyone learn English as the lingua franca so their work could receive international attention? What should the role of the internet be? This is not an idle exercise or pie in the sky but one involving a country with serious social needs,willing to make an investment in its future, even in the face of present suffering. Thanks, David Duffy -- Pacific Cooperative Studies Unit Botany University of Hawaii 3190 Maile Way Honolulu Hawaii 96822 USA 1-808-956-8218 -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] How to chose a Master's Thesis in Biology
Hi Jeremy, You haven't told us the most important thing -- WHY you're doing a Master's and want to do a PhD. Answer that, and you'll be well on your way to picking a topic, with the rest being a matter of finding a specific question. I also highly recommend the book _On Becoming a Biologist_ by John Janovy, Jr. It is a very wise book that deals with these types of questions. Good luck, Jane Shevtsov On Thu, Jul 19, 2012 at 8:55 AM, Jeremy Fontaine fonta...@student.umass.edu wrote: Hello all, this upcoming Fall semester I will be attending the University of Massachusetts Lowell to obtain my Master's Degree in Biology with the possibility of a Biotechnology option. I want to do a Master's Thesis because I want to get my PHD later on, but I am really not sure what I want to do my master's thesis on. I completed my bachelors degree in Biology at the University of Massachusetts Amherst and learned a great deal. Some guidance or advice for the process of picking a thesis topic or how to approach the situation would be very helpful. Thank you, Jeremy -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Confronting climate deniers on college campuses - EOS Forum
Seriously? In my undegrad physics class, we did a problem that involved calculating the effect of a doubling of CO2 concentration on temperature, using only the fact that CO2 blocks long-wavelength infrared radiation -- stuff that was known to Arrhenius a hundred years ago. Even though this was just a textbook problem, I remember being struck by how close our prediction was to that generated by complex models. Saying There is no evidence that changes in CO2 levels have caused any sort of atmospheric warming is just denying basic physics -- or claiming that the climate system is so wonderfully balanced that some effect or other will exactly compensate for the increase in CO2. On a related note, I recommend that everyone read The Discovery of Global Warming by Spencer R. Weart. This is available both in book form and as a free online text. (http://www.aip.org/history/climate/index.htm) It's a great review of how we know what we know. Jane Shevtsov On Wed, Jul 4, 2012 at 3:18 PM, Robert Hamilton roberthamil...@alc.eduwrote: Actually this climate debate is more about hocus pocus than anything else. at least a it is. That climate change is occurring is undeniable, and the oddity would be no climate change occurring. The climate is going to change regardless. The issue of why is where the hocus pocus comes in. There is no evidence that changes in CO2 levels have caused any sort of atmospheric warming; none. It is a predicted outcome of climate models designed to show that CO2 can affect atmospheric temperatures. We know for a fact that atmospheric warming would cause CO2 levels to increase because all the various organisms would increase respiration rates. It is dubious to suggest that CO2 levels that we observe could have any influence on the greenhouse effect on earth given the overwhelming effect of water vapour, and the flux of water vapour, which in itself is substantially greater than the total effect of CO2, let alone the difference in CO2 past and present. Many of the things we do could cause climate change. The massive increase in runoff of freshwater from terrestrial systems; various drainings and fillings in of wetlands and floodplains, channeling if rivers along with rapid runoff through sewers and other means. A lot less standing water in the spring to ameliorate continental warming through the summer. Conversion of heat sinks like say Manhattan Island (via urbanization) into heat sources, possibly radiating more energy back than is input from the sun due to additional heat from things like air conditioners and automobiles, and this sort of thing occurs on a massive scale (like say Germany, which used to be a very moist deciduous forest) in the northern hemisphere. But such issues are not allowed to be investigated for the sake of the political hacks with their CO2 argument. There is no science to this process, and amazingly the public in general sees the weakness of the science. The thing of it is that what goes around comes around, and the truth will out in the end. If we are wrong about CO2 but right about human impacts the political hacks will blame us for being unscientific even though it is they that force us this way via the way they dispense power in the form of academic appointments and funding. A bit like CFCs causing the ozone hole. They could cause the ozone hole for sure, but do they actually cause it? Never seen any evidence of that. Could be that flying jet aircraft is causing the ozone hole, but political hacks don't want to go there! If it isn't CFCs, they will blame us for sure, because we are supposed to know for sure in their eyes in such situations. We are the scapegoat if they (we) are wrong). I suppose I am a denier because I reject politically motivated science, and that sort would shout me down, pull my hair and throw things at me if I were ever to present such heretical arguments to the public. But I don't need to. As the consequences of the CO2 based policies sink in, they will be revisited with a more skeptical eye. We move forward, but do bumble along, and that seems to work in general, although there are casualties along the way, and the way it looks now is Ecology will be one of those casualties, which is the real crime here IMHO. Rob Hamilton -Original Message- From: Ecological Society of America: grants, jobs, news on behalf of malcolm McCallum Sent: Tue 7/3/2012 10:07 PM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: Re: [ECOLOG-L] Confronting climate deniers on college campuses - EOS Forum society has never been trusting of scientists. However, the same could be said of business with identical survey mechanisms. So what. This isn't about a bunch of hocus pocus and its not about baseless opinions. ITs about the facts that exist. Period. As for track records of academics, virtually all of our discoveries were by academics. Very few were made by others. Do your homework. Malcolm On Tue
[ECOLOG-L] Explaining Positive Feedback Looks to the Public (was [ECOLOG-L] Confronting climate deniers on college campuses - EOS Forum)
Hi Dawn, You might take a look at Donella Meadows' excellent book _Thinking in Systems_. One of her examples of a positive feedback loop (vicious cycle) is how she and her brother used to fight when they were kids: he would push her, she pushed back harder, he pushed back harder yet, and soon an actual fight would break out. Jane Shevtsov On Thu, Jul 5, 2012 at 11:10 AM, Dawn Stover dsto...@hughes.net wrote: Water vapor is the most powerful greenhouse gas is a meme that has been around for at least 15 years (I first heard it from people in the automotive industry), although I thought it had run its course by now. There are plenty of websites that offer factual responses (one example is http://www.skepticalscience.com/Climate-change-Water-vapor-makes-for-a-wet-argument.html), but they often take the form of a counter-argument and thus are perceived as political. And too often they're a slog for non-scientists. As a science journalist, I'd love to hear some fresh ideas about how to show scientific concepts like positive feedback loop to the general public. (Journalism is all about showing, rather than telling.) Here are a few things to keep in mind: - Images and graphs are seen as less political than words. - Stories are more memorable than numbers. - Analogies and metaphors can be powerful. - Examples from everyday life can help make science relevant. - Humans tend to be interested in other humans. - Cultural affiliation affects how people perceive certain types of information and sources. - Humor is usually appreciated. - Journalists have a different role than educators and researchers. I enjoyed reading about the creative, respectful ways that some of you respond to individuals you meet. How can those approaches be applied to larger audiences? And which scientists out there are doing the best job of communicating with the general public about climate change? Dawn Stover Independent Writer Editor 1208 Snowden Road White Salmon, WA 98672 tel: 509 493 3652 email: dsto...@hughes.net web: www.dawnstover.com Contributing Editor, Bulletin of the Atomic Scientists Contributing Editor, Popular Science -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
[ECOLOG-L] invasive truffles
As much as I enjoy (and tend to agree with) Matt Chew's commentary on this list, I must express my disagreement with some of what he says below. On Wed, May 23, 2012 at 3:28 PM, Matt Chew anek...@gmail.com wrote: Labeling a fungus as an invader it is an absurd anthropomorphism. It is a further, even less supportable one to call a fungus invasive as if invading is an essential trait or characteristic of the taxon. While I was speaking casually, I don't think that using the word invasive implies an intrinsic characteristic any more than, say, successful does. A person's success in some endeavor is a function of both their traits and their environment; the same goes for invasiveness. Furthermore, there's no necessary anthropomorphism behind the word invasive. For example, doctors may speak of invasive cancers. No Chinese truffle found growing in Italy has ever been Chinese except in name, and possibly as a spore—unless a person knowingly moved it from Asia to Italy— in which case the motivation and volition were the person's, and the relevant action was translocation, not invasion. If there was ever any intention to invade anything as a result, it was only and entirely a person's intention. Why is volition relevant? Also, we often say that X (a fungus, a person, or whatever) is Chinese when its immediate ancestors are from China. Claiming this (or any) fungus causes problems violates any rational conception of causality. The problem discussed in the article (one species of truffle being mistaken for or misrepresented as another) is one of unethical conduct by truffle dealers and/or taxonomic error by dealers and or buyers. Truffles aren't causing anything. The article also describes Tuber indicum as becoming established in truffle orchards and, either by human error or competition, preventing the growth of the desired Tuber melanosporum. If that's not causality, I don't know what is. Careless metaphorical misconstruction and blaming organisms for arriving and persisting in unexpected places actively undermines ecological understanding, communication, effective research and appropriate conservation action. Is there any evidence that research is being undemined or that anyone is blaming organisms? I agree that many control/eradication efforts are thoroughly misguided. We should be interested in working out why any specific translocation event results in a viable population (or not)…unless ecology's primary purpose is to declare, We hate this change, so we hate this species! One of the reasons I highlighted this article is that it describes concrete harms arising from an exotic species, unlike the all-too-common we must get rid of this species because it's not from here or presentation of the cost of control efforts as a harm caused by the species. -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
[ECOLOG-L] Invasive Truffles
Now this is an invasive that causes problems! http://blogs.smithsonianmag.com/adventure/2012/05/truffle-trouble-in-europe-the-invader-without-flavor/ -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Ride the Train to ESA 2012 in Portland, OR!
I also plan to take the train from Los Angeles, largely because it's a beautiful route and train trips are fun. Jane On Wed, May 16, 2012 at 5:38 PM, Jorge Ramos jramo...@asu.edu wrote: Hello ESA 2012 participants, The ESA Student Section is happy to announce that one of its members, Andrew Reinman, will be riding the train from Boston, MA to to Portland, OR to attend the 2012 ESA annual meeting! He is doing this and inviting others to do it to help reduce the environmental footprint of the meeting. To read more about him, his initiative, and how to meet up with him at a train station, visit the link in the ESA Student Section website ( http://www.esa.org/students/section/node/457). You can also find his contact info in the ESA-SS website and on the ESA-SS Facebook page ( https://www.facebook.com/groups/4239397781/) Stay involved and make sure you keep an eye out for Andrew at your nearest train station! Jorge ESA-SS website: http://www.esa.org/students/section/ ESA-SS facebook: https://www.facebook.com/groups/4239397781/ ESA-SS twitter: @esa_students -- Jorge Ramos PhD Student Wetland Ecosystem Ecology Lab Arizona State University WEEL website: http://weel.asu.edu/http://weel.asu.edu/ -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Sarewitz on Systematic Error
On Tue, May 15, 2012 at 7:06 PM, malcolm McCallum malcolm.mccal...@herpconbio.org wrote: This entire commentary is actually a criticism of our lack of replication by multiple researchers. When a study comes out, it needs to be reinvestigated by others, not just accepted. Take a landmark paper, hand it to an MS student and have them redo the study and then add a follow up twist. This is simply not done enough today. I wonder if this is related to the apparent decline in the numbers of MS students, as opposed to PhD students, from whom more originality is expected. I was discouraged from pursuing an MS and ended up straight out of undergrad, like many grad students in my program. (We had more PhD students than MS students.) This worked out well for me, but I wonder about the larger consequences. -- - Jane Shevtsov, Ph.D. Mathematical Biology Curriculum Writer, UCLA co-founder, www.worldbeyondborders.org In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Ecology (the journal) stalled?
One way to get the serendipity of articles that catch your eye is to subscribe to email notifications or TOCs of journals in your field. Jane Shevtsov On Thu, Mar 15, 2012 at 2:35 PM, Ruhland, Christopher T christopher.ruhl...@mnsu.edu wrote: I certainly can see the need to keep paper journals, but the reality of the situation is that I spend more time reading PDFs of papers (or PDFs that I've printed) than I do actual *bound* journals. As a graduate student, I used to walk across campus and spend every Friday afternoon in the library reading the latest journals directly of the racks. Of course I was limited to the journals that my library happened to subscribe to, but at least I was keeping up with most of the newest findings in my field. As technology progressed, I then spent every Friday morning on the Web of Science looking up keywords and limiting my search to papers published within the past 14 days or so. The ability to find papers published in journals I didn't even know existed was very exciting. I'd then get a PDF of the paper, and I wouldn't even have to leave my lab. It's been a while since I was required to heaven forbid walk over to the library and pull a journal off the shelf. Technology sure is wonderful. That being said, I only read what my key-word searches bring me now a days, and I miss the articles that would catch my eye (even though they had nothing to do with my field). I sure do miss those Friday afternoons in the library somedays. Cheers Chris Christopher T. Ruhland, Ph.D. Professor of Biological Sciences Department of Biology TS 242 Trafton Sciences Center South Minnesota State University Mankato, MN 56001 -Original Message- From: Ecological Society of America: grants, jobs, news [mailto: ECOLOG-L@listserv.umd.edu] On Behalf Of David L. McNeely Sent: Thursday, March 15, 2012 4:07 PM To: ECOLOG-L@listserv.umd.edu Subject: Re: [ECOLOG-L] Ecology (the journal) stalled? Lonnie Aarssen aarss...@queensu.ca wrote: I wonder if Don Strong would explain to us why Ecology is still publishing on paper? No ecologist that I know reads paper journals anymore, and hasn't for years. I read paper journals, and I have for years. i hope to be able to continue to do so. And libraries everywhere are cancelling their paper subscriptions and supporting only electronic journal subscriptions. Libraries are doing everything they can to corral costs, mainly because of the political climate that is withdrawing funding from education and research support. The fact that they are cancelling paper journals has nothing to do with the desirability of keeping them. When we have only digital information, tell me how that information will be guaranteed into the future? One of the functions of libraries is curation of the knowledge we have accumulated. In the 60 year lifetime of digital information storage and retrieval the media of choice have changed more times than I care to try to count, from paper punched tapes and cards, to tape, and so on, with multiple ways of reading those media. Most of them can no longer be read. In the news this week we also learned that Encyclopedia Britannica has decided to publish its last print edition this year, with only online editions available in the future. Encyclopedia Britannica is not a journal. Is it not time for Ecology to do the same? No. The advantages seem obvious. If Ecology has a limited number of pages that the ESA can afford to publish, then why not simply break free from this limitation by publishing electronically only? The ecological community could then benefit from a greater number of high quality Ecology articles. and the disadvantages are also obvious. BTW, I have paper journals on my bookshelves that I have cherished for years. I hope to keep them until I pass them on to a library that is more understanding of its curatorial role than those you admire so. mcneely -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] ESA Position on Open Access
Here's a blog post that analyzes whether inter-library loan is an adequate solution. http://scientopia.org/blogs/christinaslisrant/2012/01/11/access-to-the-literature-does-interlibrary-loan-solve-our-problems/ Jane Shevtsov On Wed, Jan 11, 2012 at 12:11 PM, mcnee...@cox.net wrote: Jane Shevtsov jane@gmail.com wrote: On Wed, Jan 11, 2012 at 7:32 AM, David L. McNeely mcnee...@cox.net wrote: The money that ESA and other scholarly organizations charge for electronic copies of their reports goes to support the organization. The organization makes possible the publication and decimination of new knowledge. There are costs involved, whether or not you think that the only thing the organization has to pay is for the electrical power to zip electrons around. Yes, the incremental cost of pushing out another copy is small. But all the infrastructure of the organization is involved in getting there, and is at stake if we succomb to the idea that only the incremental cost should be paid by the user. Then what did ESA and other publishers do before widespread Internet use? Back then, people would go to the library and, if the library subscribed, photocopy the articles they needed. They paid the library for copies, but publishers saw none of that money. And if they just read the article without copying it, they paid nothing at all! So, just go to the library and photocopy the article, like in the old days 10 years ago. That is still an option. mcneely Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One -- David McNeely -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] ESA Position on Open Access
On Wed, Jan 11, 2012 at 7:32 AM, David L. McNeely mcnee...@cox.net wrote: The money that ESA and other scholarly organizations charge for electronic copies of their reports goes to support the organization. The organization makes possible the publication and decimination of new knowledge. There are costs involved, whether or not you think that the only thing the organization has to pay is for the electrical power to zip electrons around. Yes, the incremental cost of pushing out another copy is small. But all the infrastructure of the organization is involved in getting there, and is at stake if we succomb to the idea that only the incremental cost should be paid by the user. Then what did ESA and other publishers do before widespread Internet use? Back then, people would go to the library and, if the library subscribed, photocopy the articles they needed. They paid the library for copies, but publishers saw none of that money. And if they just read the article without copying it, they paid nothing at all! Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] ESA Position on Open Access
On Mon, Jan 9, 2012 at 6:00 PM, mcnee...@cox.net wrote: H. Jane, perhaps you might include sorts of institutions other than universities, such as government agencies, industrial organizations (why should Exon Mobil get a free ride?), NGOs? Sure. Maybe any entity that downloads more than X papers a month. The New York Times has this sort of system. They allow non-subscribers 20 free articles a month. A scientific publisher would have to set a lower threshold than that, but you get the idea. Also, the regulation that ESA's letter was written about includes an embargo period. Suppose a student or faculty member works at home at night, and makes the request from there? Free then, but if he makes the request from his office or a laboratory, he gets dinged? No, he doesn't get dinged if the university library has a subscription, which it normally would. Fact is, the publisher has to recoup costs and costs for a a scholarly organization include things other than publishing. When students first get into this game most are unaware that authors pay for preprints (including electronic preprints) and pay page charges for publication. That being the case, why shouldn't the publisher offset some costs by charging users for access? Again, libraries would pay for access, as would anyone else who wanted an article during its embargo period. BTW, the part of the letter arguing that an embargo period won't work for ecology journals because our research takes longer than many other kinds is flawed. Citation half-lives are the wrong measure, precisely because our research takes a long time. If I download a paper today, get excited by it, and decide to base a field project on it, I may not publish for several years. This makes the citation half-life much longer than the reading half-life or download half-life. ESA and most scholarly organizations that publish journals are truly nonprofit. Elsevier Press is another matter, and There oughta be a law ... . Which really stinks for me, as Ecological Modelling is a major journal in my area and is published by Elsevier. There definitely oughta be a law Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] ESA Position on Open Access
I just checked, and ESA charges nonsubscribers $20 for a single article published in the December 2011 issue of Ecology. How is that reasonable? And I'm no business maven, but isn't that far past the optimal price point in terms of revenue generation? I could see paying $2 or $3 for an article if I was an infrequent reader, but $20? There's a good blog post on what alternatives publishers might support at http://researchremix.wordpress.com/2012/01/07/what-should-the-publishers-lobby-for/ . Jane Shevtsov On Fri, Jan 6, 2012 at 9:08 PM, M.S. Patterson tertiarym...@gmail.comwrote: Here's an additional opinion on the matter, and it is rather less charitable: http://phylogenomics.blogspot.**com/2012/01/yhgtbfkm-** ecological-society-of-america.**html?utm_source=feedburner** utm_medium=twitterutm_**campaign=Feed%3A+**TheTreeOfLife+%28The+Tree+of+* *Life%29http://phylogenomics.blogspot.com/2012/01/yhgtbfkm-ecological-society-of-america.html?utm_source=feedburnerutm_medium=twitterutm_campaign=Feed%3A+TheTreeOfLife+%28The+Tree+of+Life%29 http://phylogenomics.**blogspot.com/2012/01/yhgtbfkm-** ecological-society-of-america.**html?utm_source=feedburner** utm_medium=twitterutm_**campaign=Feed%3A+**TheTreeOfLife+%28The+Tree+of+* *Life%29http://phylogenomics.blogspot.com/2012/01/yhgtbfkm-ecological-society-of-america.html?utm_source=feedburnerutm_medium=twitterutm_campaign=Feed%3A+TheTreeOfLife+%28The+Tree+of+Life%29 The fact that ESA forces authors to cede the copyright to their work is offensive, IMO, even if they 'grant' the author reprint or reproduction rights. It also means that ESA could choose to rewrite their rules such that authors could lose rights to reprint or reproduce their own work. Academic publishers should be granted first printing rights, with the option to acquire additional rights at a later date, as they desire. Nothing more. As it currently stands, ESA's policy is essentially treating research articles as work-made-for-hire, which is ludicrous, given that authors must pay page charges to print the work! In essence researchers are paying to have their work printed, while ceding all of their rights to the publisher in the process. Further, I don't think anyone is suggesting that ESA should be denied all subscription fees (or page fees), but simply that papers should become available publicly over time, and that any research funded by public monies should be available to the public sooner rather than later. Which is entirely reasonable, and more than likely beneficial to the public. -m On 1/5/2012 12:33 AM, Jane Shevtsov wrote: Fellow Ecologgers, Have people read ESA's response to a proposed requirement that the results of federally funded research be publicly available, possibly after an embargo period? It's available here. http://www.esa.org/pao/**policyStatements/Letters/** ESAResponsetoPublicAccessRFI20**11.pdfhttp://www.esa.org/pao/policyStatements/Letters/ESAResponsetoPublicAccessRFI2011.pdf I have to say I find this response somewhat disappointing. While some of the concerns raised in it are certainly valid, I believe it underestimates ecologists' desire to read an interesting new paper now rather than later. Also, kudos to ESA for allowing authors to freely post their papers online, something I relied on when I didn't have university journal access, but how is this financially different from open access? ESA's 2009 financial statement (the latest available online) may be of interest. http://www.esa.org/aboutesa/**docs/FS2009.pdfhttp://www.esa.org/aboutesa/docs/FS2009.pdf Thoughts? Jane Shevtsov -- Matt Patterson MSES/MPA 2012 Indiana University School of Public and Environmental Affairs Center for the study of Institutions, Population and Environmental Change (CIPEC) Room 226A | 408 N Indiana Ave | Bloomington, IN 47408-3799 Environmentally Scientific Emblogulations http://env-sci-blog.blogspot.** com http://env-sci-blog.blogspot.com -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] ESA Position on Open Access
Dear David, You make some very interesting points. On Mon, Jan 9, 2012 at 6:51 AM, mcnee...@cox.net wrote: Is it really so difficult to get a paper? I have never been unable to get a paper I wanted or needed, and I have never paid the high prices that publishers demand for instant access on the internet. Most of us live within 50 miles of a library. If the library does not subscribe to the journal in which the paper appears, interlibrary loan will get it for a reasonable cost. If you know that a paper is the one you need, that's a reasonable strategy. But if it's a case of this might be relevant, or it might not, you're not likely to go to the trouble. I was in that position some time ago when interning at Kennedy Space Center. NASA didn't subscribe to ecological journals, as most of its staff didn't need them -- but they were certainly relevant to groups working on bioregenerative life support or environmental impact analysis. The real problem is the demand for instant gratification that we have developed. It is that that we are being asked to pay for. When delivery is essentially free, why is a desire for instant gratification a problem? Should a paper cost $50? I really don't know what it costs the journal to produce the paper, what the demand is (well, for some papers the demand is virtually nothing), or what distribution costs. I do know that such services as BioOne have greatly improved the bottom lines of some scholarly organizations, which in the long run makes papers more available, not less. Having more papers in existence is not the same as improving the availability of each paper. I guess in this one instance I am suggesting that free market is not so bad. There's no free market here. A free market would exist if you could get the same paper from several different stores. From a reader's point of view, a publisher is a monopoly. It's a natural monopoly -- but natural monopolies must be regulated. If you really must have the paper the instant you locate it through the free search and free abstract mechanisms of the publishers, why then pay the asking price. Otherwise, use more traditional means of getting it. If publishers are getting the asking price, they will maintain it, or maybe ask a little more. If they are not getting it, they will back off. Now this is a fascinating point. How often do people actually pay the publisher's asking price? Like you say, a reader can go to a university library (public libraries rarely subscribe to technical journals), go to an author's web site, or email the author. Heck, if you access the Web without a university IP address, Google Scholar will automatically try to find free copies of papers you search for. So is the $20 per paper price really intended to make money directly, or to get people to do something else, like joining ESA and buying a journal subscription? Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] ESA Position on Open Access
To be fair, ESA's profit margin is much smaller than that of commercial publishers. But I wonder how much of that money comes from people paying outrageous sums for individual articles. Not much, I'll bet. There would seem to be a simple technical solution. Just as IP addresses are currently used to check whether someone is at a subscribing institution, they could be used to see whether an article request is coming from someone at a university. If yes, they'd only have access if their library subscribed (or if they had an individual subscription). Non-institutional users would get free access. Jane Shevtsov On Mon, Jan 9, 2012 at 2:39 PM, M.S. Patterson tertiarym...@gmail.comwrote: David, you're correct that many libraries have subscriptions to various journals, and are capable of getting an article via interlibrary loan. However, this is simply a case of passing the buck. Do you think publishers give free access to libraries and universities? They do not. The subscription fees that libraries pay are exceedingly steep, and as library budgets have been getting slashed, many have been cutting back substantially on their journal access, counting on others within the library system to maintain subscriptions. And, of course, every interlibrary loan request costs time, labor, and money to the communities involved. Surely it is more socially efficient to charge a few dollars for an article, and make it easily available to people, than it is to charge a large sum to a library, and then incur additional labor costs to shuttle a document around from place to place? The cost of distribution for the publishers is essentially nil, given that they already have invested in the sites in place to distribute their articles, whether they cost $50 or $2. Electrons are quite cheap. This is a simple case of an industry with substantial monopoly power engaging in rent seeking. A simple search on academic publisher profits would be extremely enlightening, I suspect. Here is a good place to start: http://www.economist.com/node/**18744177http://www.economist.com/node/18744177 -m On 1/9/2012 9:51 AM, David L. McNeely wrote: Jane Shevtsovjane@gmail.com wrote: I just checked, and ESA charges nonsubscribers $20 for a single article published in the December 2011 issue of Ecology. How is that reasonable? And I'm no business maven, but isn't that far past the optimal price point in terms of revenue generation? I could see paying $2 or $3 for an article if I was an infrequent reader, but $20? There's a good blog post on what alternatives publishers might support at http://researchremix.**wordpress.com/2012/01/07/what-** should-the-publishers-lobby-**for/http://researchremix.wordpress.com/2012/01/07/what-should-the-publishers-lobby-for/ . Is it really so difficult to get a paper? I have never been unable to get a paper I wanted or needed, and I have never paid the high prices that publishers demand for instant access on the internet. Most of us live within 50 miles of a library. If the library does not subscribe to the journal in which the paper appears, interlibrary loan will get it for a reasonable cost. The real problem is the demand for instant gratification that we have developed. It is that that we are being asked to pay for. Should a paper cost $50? I really don't know what it costs the journal to produce the paper, what the demand is (well, for some papers the demand is virtually nothing), or what distribution costs. I do know that such services as BioOne have greatly improved the bottom lines of some scholarly organizations, which in the long run makes papers more available, not less. I guess in this one instance I am suggesting that free market is not so bad. If you really must have the paper the instant you locate it through the free search and free abstract mechanisms of the publishers, why then pay the asking price. Otherwise, use more traditional means of getting it. If publishers are getting the asking price, they will maintain it, or maybe ask a little more. If they are not getting it, they will back off. If you are so far back in the sticks that you don't have ready access to a library, investigate a bit. I'll bet some library serves you if you find out how. If you are living in a cabin off the traveled roads and off the grid, then you don't have internet access either, so your complaints about no open access are moot. David McNeely Jane Shevtsov On Fri, Jan 6, 2012 at 9:08 PM, M.S. Pattersontertiarymatt@gmail.**comtertiarym...@gmail.com wrote: Here's an additional opinion on the matter, and it is rather less charitable: http://phylogenomics.blogspot.com/2012/01/yhgtbfkm-** ecological-society-of-america.html?utm_source=feedburner utm_medium=twitterutm_campaign=Feed%3A+ TheTreeOfLife+%28The+Tree+of+* *Life%29http://phylogenomics.**blogspot.com/2012/01/yhgtbfkm-** ecological
Re: [ECOLOG-L] ESA Position on Open Access
On Mon, Jan 9, 2012 at 1:31 PM, mcnee...@cox.net wrote: You can get the same paper from different sources. You can subscribe to the journal in print or online. You can go to a library that subscribes to the journal. You can request a reprint from the author (who may have had to pay for it himself). You can use online sources that may or may not have a cost associated, depending on the journal and the source. You can use interlibrary loan. There are multiple media through which a journal article may be obtained. These different media have different costs in coin and effort associated with them. And ironically, the source with the lowest cost charges the most! On a related but broader note, people might want to read John Perry Barlow's classic essay, Selling Wine Without Bottles: The Economy of Ideas on the Global Net. http://virtualschool.edu/mon/ElectronicFrontier/WineWithoutBottles.html So is the $20 per paper price really intended to make money directly, or to get people to do something else, like joining ESA and buying a journal subscription? Which is a pretty good idea. It supports ESA (or whatever organization publishes the journal, not all ecological work is published in ESA journals), and it gives one an opportunity to regularly review the spectrum of work being done in Ecology. Joining provides a great many benefits beyond the opportunity to subscribe to the journals, as well. One of those benefits is eventual life membership in emeritus status, which I have earned and take advantage of. Indeed, but I hope you're not saying that everyone who might read a few papers a year should necessarily join and subscribe. If they want to, great, but it shouldn't be a condition of access. Just to be clear, I've been an ESA member since 2005, when SEEDS awarded me a one-year membership along with a scholarship to attend the annual meeting. That felt pretty cool to an undergrad, and I've proudly maintained a membership ever since. This is the first time I'm considering not renewing, not because of ESA's own practices, but because of that letter, which supports not only society publishers but the worst actors in the industry. Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
[ECOLOG-L] ESA Position on Open Access
Fellow Ecologgers, Have people read ESA's response to a proposed requirement that the results of federally funded research be publicly available, possibly after an embargo period? It's available here. http://www.esa.org/pao/policyStatements/Letters/ESAResponsetoPublicAccessRFI2011.pdf I have to say I find this response somewhat disappointing. While some of the concerns raised in it are certainly valid, I believe it underestimates ecologists' desire to read an interesting new paper now rather than later. Also, kudos to ESA for allowing authors to freely post their papers online, something I relied on when I didn't have university journal access, but how is this financially different from open access? ESA's 2009 financial statement (the latest available online) may be of interest. http://www.esa.org/aboutesa/docs/FS2009.pdf Thoughts? Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] UC-Berkeley and other ‘public Iv ie s’ in fiscal peril
Nobody gets a full ride from the Feds. The maximum Pell Grant this year is $5530. Other federal aid is in the form of work-study or loans -- stuff that the student has to work for or pay off later. The state money is replaced by payments from the students and families (including work-study) or loans (also money from the students, just delayed). Jane Shevtsov On Wed, Dec 28, 2011 at 9:32 AM, malcolm McCallum malcolm.mccal...@herpconbio.org wrote: Its all pretty obvious. Federal government establishes federally funded financial aid to help those in need. State governments cut funding to universities, so universities are forced to raise tuition and get more of their finances from the federal financial aid programs. Lets say a ficticious state, say State A, funded its university system 50% so that 50% of all costs were paid by tuition (we will ignore donations). Every student who gets a full ride from feds has 50% of costs paid by state and 50% of costs paid by fed financial aid. However, if a state reduces its contribution to the costs of running that university to 25%, the cost of attendance rises as every school raises tuition. Then, more students in that state become eligible for financial aid because of the higher cost of attendance. Now, students on full rides get only 25% of their education costs from state, but 75% from the feds. Essentially, State A has shifted the burden of funding higher education to the feds while not losing any return on the total investment in higher education. Then the state can throw money elsewhere or issue tax breaks for companies to come into the state. I am pretty sure this conspiracy theory would work, and if it does, it is likely why we see escalating tuition. Its not the schools raising tuition, its the state governments lowering investment leading to higher tuition to cover costs which get more and more shifted to federal financial aid programs. Anyone who doesn't get financial aid just fronts the whole bill. As for the condition of buildings, its a long known fact that it is easier as a government entity to build a new building than it is to repair an old one because of the way funding mechanisms work in states. So, if you have a choice between building a new building and refurbishing an old one, as an institution you are more likely to approach building a new one even if the costs are way higher. No building will last forever, no matter how well you take care of it. If politicians really had our interest at heart, none of this would be happening. Instead, they are busy capitalizing on loopholes in insider trading law to make billions for their own pocketbooks. :) On Tue, Dec 27, 2011 at 6:29 PM, Paul Cherubini mona...@saber.net wrote: The University of California at Berkeley subsists now in perpetual austerity. Star faculty take mandatory furloughs. Classes grow perceptibly larger each year. Roofs leak; e-mail crashes. One employee mows the entire campus. Wastebaskets are emptied once a week. Some professors lack telephones. If all of the above is true, then can someone please explain why for 20+ years the annual increase in the cost of college tuition has far outpaced the consumer price index, heath care, energy costs, etc. http://www.nas.org/polArticles.cfm?doc_id=1450 http://tinyurl.com/6xq6hv Paul Cherubini El Dorado, Calif. -- Malcolm L. McCallum Department of Molecular Biology and Biochemistry School of Biological Sciences University of Missouri at Kansas City Managing Editor, Herpetological Conservation and Biology Peer pressure is designed to contain anyone with a sense of drive - Allan Nation 1880's: There's lots of good fish in the sea W.S. Gilbert 1990's: Many fish stocks depleted due to overfishing, habitat loss, and pollution. 2000: Marine reserves, ecosystem restoration, and pollution reduction MAY help restore populations. 2022: Soylent Green is People! The Seven Blunders of the World (Mohandas Gandhi) Wealth w/o work Pleasure w/o conscience Knowledge w/o character Commerce w/o morality Science w/o humanity Worship w/o sacrifice Politics w/o principle Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] Summary: Transformation of percent cover data for power analysis
The purpose of a power analysis to simulate data that you'll collect in the field. There's no such thing as negative cover, so if your simulation can produce those kinds of values, it's not really doing what you want. Have you considered tinkering with your simulation so it produces only sensible values? Then there will be no need for a transformation. Hope that helps! Jane Shevtsov On Wed, Nov 30, 2011 at 6:00 PM, Brian Mitchell brian.mitch...@uvm.eduwrote: Hello ecolog, Thanks to all of you who responded to my question about data transformations suitable for my power analysis of percent cover data (original post is repeated at the bottom of this summary). A number of people suggested the “standard” transformation for percent cover data, the arcsine square root transform. While this transformation would have bounded the data between zero and one, it has the undesirable side effect of being non-monotonic, which would have been an issue with my simulated data. Several people pointed me towards a recent paper, Warton and Hui 2011 (Ecology 92:3-10). These authors propose a modification to the logit transformation, specifically adding a small value to both the numerator and denominator of the logit function. This is the approach that I am now pursuing with my analysis. There is clearly a lot of debate back and forth about the merits of transforming data, and the difficulty of interpreting the output when transformations are used, and I appreciate the recommendations I have received about using data transformation sparingly. I tend to agree with these comments, but in this case I feel that having a simulation with realistic data and meaningful predictions outweighs the difficulties of back-transforming and interpreting the output. Thanks again for the helpful feedback to my query! Original post: I am working on a power analysis simulation for long-term forest monitoring data, with the goal of documenting our power to detect trends over time. The simulation is based on a repeated measures hierarchical model, where future data is simulated based on the initial data set and a bootstrap of pilot data differences between observation periods, multiplied by a range of effect sizes (50% decline to 50% increase). My question is about the appropriate transformation to use for percent cover data in this simulation. I don’t want to use raw percentages because the simulation will easily result in proportions less than zero or greater than one. Similarly, a log transform can easily result in back-transformed proportions greater than one. Most other transforms I’ve looked at would not prevent back-transformed data from exceeding one or the other boundaries. The exception is the logistic transform, which would indeed force all simulated data to be between zero and one when back-transformed. However, the logistic transform gives values of negative infinity for a percent cover of zero, and positive infinity for a percent cover of one. I was thinking that adding a tiny number to zeros and subtracting a tiny number from ones (e.g., 0.1) would solve the problem (roughly equivalent to a log of x+1 transform), but I have been unable to find reference to anyone using this approach for percent cover data. Does anyone have any thoughts about the validity of my proposed approach or of another approach that would help solve my problem? Brian Mitchell NPS Northeast Temperate Network Program Manager Adjunct Assistant Professor, University of Vermont brian_mitch...@nps.gov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] Summary of Ecology in AP responses
Just send them to college can only be done in cities that have colleges. Also, AP classes are slower-paced than college courses and taught in a more interactive manner. (AP Environmental Science, for example, is a year-long course but replaces a one-semester course.) I didn't take AP Bio but attended a biology magnet school that offered lots of science courses. 90% of my first-year biology at UCLA was review. If students who test out of intro courses are struggling, maybe it's because they missed a chance to learn to take college science courses, not because they missed content. Jane Shevtsov On Mon, Nov 21, 2011 at 1:12 PM, Joey Smokey northwestbird...@gmail.comwrote: Hi all, As a biology major recently graduated, as well as a science and math tutor, I have also seen the trouble of AP credits in science programs. Many of my peers who think they are ready for college-level science from AP classes seem to struggle the most. I also tend to be old-fashioned in thinking that AP coursework tends to be weak and any credit should be given to electives or non-major classes. Like somebody mentioned earlier, if students are ready for college, just send them to college. I think Head Start and Running Start programs are far more successful than AP and honors programs in high school. Joey Smokey WSU Vancouver On Mon, Nov 21, 2011 at 12:17 PM, Corbin, Jeffrey D. corb...@union.edu wrote: Hello Ecologgers - Thank you for your quick and numerous responses to my query about the treatment of ecology in AP classes. I received a wide range of responses and suggestions. Some summaries: Regarding the coverage of ecology in high school AP classes: - Based on the College Board's published coverage of biology material, ecology is 10% of the test. This is comparable to the percentage for cells, evolutionary biology, and heredity. (Structure and function of [organisms] gets a much larger 32%, but that also encompasses many topics) - The logical point was made that if a student received a 4 or 5, then the student must have retained enough of the ecology material. - Several current or former H.S. teachers emailed me to say that ecology is well-covered. - However, I also received far more comments from individuals who said that their own AP class barely, if at all, covered ecology. Anecdotal evidence yes, but it was a common comment Regarding the awarding of credit in college: - I agree with the comments of many that to award credit to biology majors for a high school class is to place a lot of faith in high school instruction without any oversight. - Many institutions offer no credit; many others offer non-major credit for a 4 or 5 on the AP. If nothing else, this informal survey did forestall a hasty decision on our part, and I think we are going to do a more complete survey of what is common for Colleges and Departments like ours. Thanks again for all of the generous responses. -Jeff *** Jeffrey D. Corbin Department of Biological Sciences Union College Schenectady, NY 12308 (518) 388-6097 *** -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org She has future plans and dreams at night. They tell her life is hard; she says 'That's all right'. --Faith Hill, Wild One
Re: [ECOLOG-L] a non Ivory Tower view of invasive species
What fraction of the weeds affecting agriculture are native? -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org All wars are civil wars, because all men are brothers... Each one owes infinitely more to the human race than to the particular country in which he was born. --Francois Fenelon, theologian and writer (1651-1715)
Re: [ECOLOG-L] Ethics of spousal hires (was Re: [ECOLOG-L] Job Announcement: US Forest Service Ecologist)
First of all, most spousal hires that I've seen get new, specially created positions. They're not outcompeting or displacing anyone. Second, you're assuming that the primary hire has a lab that their spouse can use. But what if the primary hire is a historian or mathematician and their spouse is an ecologist or, worse, a biochemist? Also, please stop invoking nepotism. That word refers to hiring relatives of a person *in power*. If a dean or department chair (or even an established faculty member) insisted that their spouse be hired when they were not the best person for the job, that would be nepotism. Being or hiring a package deal is not. Finally, I would propose that relaxing the emphasis on quantitative qualifications is probably a good thing. This emphasis leads to piecemeal, shallow work that churns out large numbers of papers and an emphasis on flashy, fashionable topics at the expense of others that often have more depth. Of course, this should be changed across the board, but hiring at least some people by a different pathway should be healthy for a university. Oh, and for the record, I am single. Jane Shevtsov On Sat, Aug 20, 2011 at 8:32 AM, Aaron T. Dossey bugoc...@gmail.com wrote: It's easy to rail against those who demand higher ethical standards when one benefits personally from lax ethical practices. Personal interests like but my wife/child/friend wants a job too! should not be a consideration of any hiring entity. Where does it end? Is it ok for a chair and group of faculty to decide only to hire members of their church or their own religion, or only hire other atheists? Is it ok for them to only hire their friends to the exclusion of all other applicants regardless of QUANTITATIVE qualification/skill/talent (which are frequently quantified for other purposes such as grants etc., so this well, everyone with a Ph.D. and the minimum credentials is basically equally qualified excuse often used is BS)? Maybe a department wishes to be all white, or all Chinese, or all Jewish? Kosher? I understand in England that there are even laws against nepotism even in the private sector? If so, they will probably over-take us in science soon if they haven't already. Spousal hiring is not benign, it is not a victimless crime. It is an unethical tragedy which is leading to many very good hard working scientists to leave the field and their dreams, some of us who have worked hard all our lives toward this goal of starting our own lab one day, and were the first in our families to even go to graduate school (and second to college at all). The American Dream has been dead in the private sector for many years, is it dead in Academia too? If you want to say well, what about the trailing spouse? what about their plight? - I will leave you with the following scenarios to consider: 1) The department decides not to hire the primary recruit and the spouse. What of the spouse? So now we have a home with one spouse bringing in a new faculty salary, both of them are likely covered under the one person's healthcare plans and other benefits. The unemployed spouse has access to their spouses lab, University resources (core facilities, library, etc.). They have a home and bills paid. With these resources, they can likely continue much or at least some of their research endeavors, continue to apply for positions at that or a nearby institution as they come up (if they deem it necessary, which it might not even be to continue their professional/research interests) and likely even write grants submitted through the department as PI on a guest appointment of some sort and possibly even leverage a position of their own with said grants. Hell, their spouse might even be able to hire them as a postech, adding an additional small salary to the home. What of the top candidates who were not the trialing spouse? Well, one of them will get the opportunity of a lifetime they have been dreaming of: a tenure track position and a lab of their own. Happy day! Rightly so, they've EARNED it! 2) The department decides to hire the primary recruit and the spouse. Yay, happy day for the cute couple. What of the spouse? Well, they've now got the holy grail of all science positions, a tenure track faculty position with a lab of their own, healthy startup package (around a million or more invested in the average hire including startup package, salary, benefits, etc.), the home how has TWO faculty salaries - and all is right with the world. HOWEVER: What of the candidates whose qualifications outweighed those of the spouse. who don't have a leading spouse of their own to leverage a position for them? Well, they're unemployed. No salary, no benefits, no way to pay their bills, etc. Not ONLY that: BUT they NOW also have no way to continue even the smallest shred of their research. They languish for a year or more longer, not being able to publish or apply
Re: [ECOLOG-L] Disseminating scientific thought to the general public: are scientists making science readily accessible?
On Sun, Apr 10, 2011 at 11:38 AM, Wayne Tyson landr...@cox.net wrote: I am not suggesting that there be a LAW that reporters clear their stories with the interviewee, but a CUSTOM. Getting at truth is the issue, reducing error. Once the cat is out of the bag, it is not a matter of suffering in silence or writing the editor and getting a correction buried in an obscure corner of some obscure page. The place to work on the issue is where it starts. Maybe those being interviewed should insist that the reporter explain back to the interviewee what she/he has just heard, like a pilot repeating a clearance to an air traffic controller. APPROVAL is NOT the point--getting it RIGHT is the avowed MUTUAL goal. So I don't disagree with Dave's point, but it's not my point. Wayne makes an excellent point. Dave, the reason it would be a bad idea to have a politician check a story before you publish it is that it would interfere with conveying the facts to the public. And the reason why it would be a bad idea NOT to have a scientist check a story before you publish it is that it would interfere with conveying the facts to the public. The same goal may be served by different actions in different circumstances. Jane Shevtsov - Original Message - From: David M. Lawrence d...@fuzzo.com To: ECOLOG-L@LISTSERV.UMD.EDU Sent: Sunday, April 10, 2011 4:22 AM Subject: Re: [ECOLOG-L] Disseminating scientific thought to the general public: are scientists making science readily accessible? Let's do a thought experiment here. Do we want journalists clear pieces with politicians, powerful political interests, and attorneys persons accused of serious crimes first? If not, why should journalists do the same with scientists? I personally know a handful of scientists whose word I would never take for granted -- and I damn sure wouldn't get their approval of a story I wrote involving them first. Many of us who specialize as science/environment reporters work very hard at getting facts correct and in making sure we get them correct by running quotes past sources. Many of my colleagues won't share an advance copy of a story with a source (for the implications above). I understand why -- it creates a huge ethical problem for journalists -- how can we fulfill our CONSTITUTIONALLY recognized (in the U.S., at least) role as an independent source of information when we submit our stories to our sources for approval? We cannot. I can assure you that you don't want to live in a society where such clearing is required. There is no shortage of evidence to support my statement. There is an unfortunate trend in the news business in which specialist reporters -- such as science and environment reporters -- are removed from their beats (because the news publication cannot or does not want to support such specialist beats) or are removed from their jobs altogether. The coverage gets picked up in a haphazard fashion with more generalist or less experienced people who often don't work as hard to understand the material or make sure they understand the material. Even when we are allowed to specialize, we are forced to achieve unrealistic productivity targets that may make it difficult to adequately examine our copy for things that need to be checked out with a source. And once we file, other people take our stories and edit them either to fit the space or time available, or to suit their own interests (there has been an interesting thread on a science journalism list recently where my colleagues discussed stories they've asked to have their name taken off of the byline). And Wayne, my sympathies to your wife. I see those documentaries where I would have been embarrassed to have been interviewed in. They'll ask a scientist about emerging diseases, then the scientist will find himself seeming to endorse an oncoming zombie apocalypse. Those programs are not journalism. They are entertainment, nothing more. I wish I could offer better advice on how to weed out requests to be interviewed for such programs. I don't know enough about how they approach sources to know what to say. Dave On 4/9/2011 7:34 PM, Wayne Tyson wrote: Of course, mistakes can happen. From my own experience, reporters can get it wrong--not because they intentionally do so, but because they were CERTAIN that they understood (and I must say that I have erred in presuming that they understood, too). This unfortunate phenomenon could be averted much of the time if the reporters/editors/producers would clear the piece with the originator of the information/testimony. ... -- -- David M. Lawrence | Home: (804) 559-9786 7471 Brook Way Court | Fax: (804) 559-9787 Mechanicsville, VA 23111 | Email: d...@fuzzo.com USA | http: http://fuzzo.com -- All drains
Re: [ECOLOG-L] Need textbook Suggestiond
Meadows' book is excellent -- by far the best I've read on intro-level systems thinking. Also, have you looked at G. Tyler Miller's Essentials of Ecology? I haven't read it, but Miller's environmental science textbooks are substantive and very engaging. Jane Shevtsov On Tue, Mar 8, 2011 at 6:44 AM, Doug Miller mil...@eesi.psu.edu wrote: Donella Meadows book Thinking in Systems: A Primer would appear to fit one of your needs. I was impressed with this book after a quick hands-on review at a local bookstore. I recall thinking it would make a nice intro to the subject... Doug Penn State University mil...@eesi.psu.edu On 3/8/11 12:06 AM, Rebecca Sherry wrote: I am developing a course in Ecological Literacy. At a minimum, I would like to use one book on systems thinking, and one general ecology text. I may use two books on systems thinking and also add a book on ecological resilience, and of course, individual papers and book chapters. I am having trouble finding an appropriate general ecology text. I need something with an emphasis on ecosystem science and climate interactions (don't need any autecology). Many of the students may not be science majors, so the typical ecosystem science textbook is not appropriate. But the students will have had some science and will be very into the subject and fairly knowledgeable on environmental issues, so a typical environmental science text for non-majors may not be right either. I need something in between. Finally, I don't want anything too big, heavy or expensive. Any suggestions? Thanks! Becky Sherry University of Oklahoma rshe...@ou.edu -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Hypothesis Testing in Ecology
Jeff's comments are good ones. I don't know why all the apostrophes came through as question marks, but maybe that's appropriate -- these are difficult issues and I, for one, have more questions than answers. On one hand, there are certainly examples that demonstrate that understanding is neither necessary nor sufficient for prediction. On the other hand, the two are certainly connected. It's been pointed out that causal knowledge, unlike statistical knowledge, enables us to predict how a system will behave under interventions. Maybe that helps -- I don't think you can understand a phenomenon without causal knowledge. Also, let's look at pedagogical questions. How do we ask students to demonstrate understanding of concepts? BTW, I want to clarify a remark I made earlier about chaos. While the long-term behavior of a system exhibiting chaotic behavior cannot be predicted in the sense that the time series can't be predicted, we CAN predict other aspects of its dynamics, such as the parameter values resulting in different modes of behavior. So maybe before we can productively discuss the relationship between prediction and understanding, we ought to clarify what we mean by prediction. How broadly or narrowly do we want to construe the term? Best, Jane On Thu, Mar 3, 2011 at 7:19 AM, Jeff Houlahan jeffh...@unb.ca wrote: In response to Jane?s comments ? I admit that understanding and prediction are not the same thing but they are much more closely related than most people appreciate, in my opinion. I would go so far as to say that prediction is a necessary if not sufficient condition of understanding. So while it is possible to predict without understanding (as in Jane?s Babylonian?s example ? although I knew nothing about the Babylonians and their ability to predict, I have no doubt that?s true) I think it is impossible to demonstrate understanding without prediction. In fact, I realized that I can?t come up with a definition of understanding that satisfies me without talking about prediction (none of the on-line definitions that I found worked very well for me). My definition of understanding would be ?The ability to make specific predictions based on a general description of how the world works.? Now, I guess it?s possible that somebody could understand how the world works but not be able to make any predictions but that means that they can?t demonstrate their understanding. In my opinion, understanding that can?t be demonstrated has little(no?) value because I can?t distinguish that person from all the people who claim they have understanding but have none. My above definition leaves room for ?thinking? you understand when you don?t, in situations where you make good predictions for the wrong reasons. But, even here prediction is critical because we will only detect our mistake when we try to make a new prediction and our ?understanding? leads us astray. That is, the only evidence of our mistake will be poor prediction. So, my original claim was not that understanding and prediction are the same thing but that understanding cannot be demonstrated without prediction. And predictions have to better than we would make by chance. And the only way to evaluate that is through some measure of probability/likelihood. Best. Jeff Houlahan PS I would be interested to hear any examples where understanding can be demonstrated without prediction. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Hypothesis Testing in Ecology
One more thing: what predictions can you make if you understand what caused the extinction of the (non-avian) dinosaurs? Jane On Thu, Mar 3, 2011 at 7:19 AM, Jeff Houlahan jeffh...@unb.ca wrote: In response to Jane?s comments ? I admit that understanding and prediction are not the same thing but they are much more closely related than most people appreciate, in my opinion. I would go so far as to say that prediction is a necessary if not sufficient condition of understanding. So while it is possible to predict without understanding (as in Jane?s Babylonian?s example ? although I knew nothing about the Babylonians and their ability to predict, I have no doubt that?s true) I think it is impossible to demonstrate understanding without prediction. In fact, I realized that I can?t come up with a definition of understanding that satisfies me without talking about prediction (none of the on-line definitions that I found worked very well for me). My definition of understanding would be ?The ability to make specific predictions based on a general description of how the world works.? Now, I guess it?s possible that somebody could understand how the world works but not be able to make any predictions but that means that they can?t demonstrate their understanding. In my opinion, understanding that can?t be demonstrated has little(no?) value because I can?t distinguish that person from all the people who claim they have understanding but have none. My above definition leaves room for ?thinking? you understand when you don?t, in situations where you make good predictions for the wrong reasons. But, even here prediction is critical because we will only detect our mistake when we try to make a new prediction and our ?understanding? leads us astray. That is, the only evidence of our mistake will be poor prediction. So, my original claim was not that understanding and prediction are the same thing but that understanding cannot be demonstrated without prediction. And predictions have to better than we would make by chance. And the only way to evaluate that is through some measure of probability/likelihood. Best. Jeff Houlahan PS I would be interested to hear any examples where understanding can be demonstrated without prediction. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Hypothesis Testing in Ecology
On Wed, Mar 2, 2011 at 5:41 AM, Manuel Spínola mspinol...@gmail.com wrote: I think there is a confusion about hypothesis testing that Jane was referring to in the original post. We are moving away from her questions. Well, I was asking about both types of hypothesis testing. They're different things but strongly reinforce each other. Best, Jane On 01/03/2011 10:50 a.m., Matt Chew wrote: Ecology without hypotheses has been dismissed (sometimes derided) as natural history, but even natural history requires one hypothesis. Reporting an observation requires0 confidence that an observation is meaningful, can be communicated, and can be interpreted. There are also tacit hypotheses inherent in scale, including the duration, extent and complexity of natural history observations. Hypothesis testing is a particularly relevant topic in US ecology at the moment because choices made in establishing the NEON program involve numerous hypotheses about ecosystem identity, composition, extent and location, the relevance of potential instrumentation and particular scales. However, the term 'hypothesis' is absent from NEON's website ( http://www.neoninc.org ). Explicit hypothesis testing done under NEON auspices will be subject to an array of tacit hypotheses, none of which have been articulated (or, it seems, even considered) by NEON's creators and promoters. Any supposedly non-hypothetical work conducted under NEON will face the same challenge. Matthew K Chew Assistant Research Professor Arizona State University School of Life Sciences ASU Center for Biology Society PO Box 873301 Tempe, AZ 85287-3301 USA Tel 480.965.8422 Fax 480.965.8330 mc...@asu.edu or anek...@gmail.com http://cbs.asu.edu/people/profiles/chew.php http://asu.academia.edu/MattChew -- *Manuel Spínola, Ph.D.* Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036 Personal website: Lobito de río https://sites.google.com/site/lobitoderio/ Institutional website: ICOMVIS http://www.icomvis.una.ac.cr/ -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Hypothesis Testing in Ecology
Hi Matt, Since this conversation has gotten off to a solid start (but where's Wirt Atmar? I expected to hear more from our resident ex-physicist), I can now reveal more of my thoughts. Specifically, you've come near a very important point. Even natural history requires what may be called hypotheses or assumptions, but these are even more crucial in hypothesis testing. We have to make all kinds of auxiliary hypotheses (things like I identified these plants correctly or these animals move randomly over the landscape) in the course of testing a focal hypothesis. If the prediction derived from this hypothesis fails to come about, we have to figure out which hypothesis to blame. And that's absolutely deadly for falsificationism. I recommend an excellent essay called The 'Corroboration' of Theories by the philosopher Hilary Putnam. (Don't worry about the fact that it's philosophy -- it's actually far more readable than the average ecology paper.) It's not available online, but I'll be happy to send a PDF to anyone who asks. Jane Shevtsov On Tue, Mar 1, 2011 at 8:50 AM, Matt Chew anek...@gmail.com wrote: Ecology without hypotheses has been dismissed (sometimes derided) as natural history, but even natural history requires one hypothesis. Reporting an observation requires 0 confidence that an observation is meaningful, can be communicated, and can be interpreted. There are also tacit hypotheses inherent in scale, including the duration, extent and complexity of natural history observations. Hypothesis testing is a particularly relevant topic in US ecology at the moment because choices made in establishing the NEON program involve numerous hypotheses about ecosystem identity, composition, extent and location, the relevance of potential instrumentation and particular scales. However, the term 'hypothesis' is absent from NEON's website ( http://www.neoninc.org ). Explicit hypothesis testing done under NEON auspices will be subject to an array of tacit hypotheses, none of which have been articulated (or, it seems, even considered) by NEON's creators and promoters. Any supposedly non-hypothetical work conducted under NEON will face the same challenge. Matthew K Chew Assistant Research Professor Arizona State University School of Life Sciences ASU Center for Biology Society PO Box 873301 Tempe, AZ 85287-3301 USA Tel 480.965.8422 Fax 480.965.8330 mc...@asu.edu or anek...@gmail.com http://cbs.asu.edu/people/profiles/chew.php http://asu.academia.edu/MattChew -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Hypothesis Testing in Ecology
Hi Jeff, Prediction and understanding are actually very different things and being good at one doesn't necessarily imply being good at the other. An example from the book _Foresight and Understanding_ by Stephen Toulmin: the Babylonians had no concept of the heliocentric solar system but they were quite good at predicting the movements of planets in the night sky. In fact, even after Newton, it took quite a while for astronomical tables based on a real understanding of the solar system to catch up to the accuracy of those made by the old method, which took no understanding at all. On the other hand, if a system exhibits chaotic behavior, long-term prediction is impossible -- but we can certainly understand the dynamics. Best, Jane Shevtsov On Tue, Mar 1, 2011 at 6:24 AM, Jeff Houlahan jeffh...@unb.ca wrote: Hi Chris and all, I actually think that it's a mistake to diminish the role of p-values. My opinion on this (stongly influenced by the writings of Rob Peters) is that there is only one way to demonstrate understanding and that is through prediction. And predictions only demonstrate understanding if you make better predictions than you would make strictly by chance. The only way to tell if you've done better than chance is through p-values. So, while there is a great deal more to science than p-values, the ultimate tests of whether science has led to increased understanding are p-values. Best. Jeff Houlahan Dept of Biology 100 Tucker Park Road UNB Saint John -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
[ECOLOG-L] Hypothesis Testing in Ecology
Fellow Ecologgers, Lately, I've been thinking a lot about the role of hypothesis testing (both the statistical and falsificationist varieties) in biology in general and ecology in particular. Before saying anything, I want to ask the forum a few questions. 1. What do you think of the current emphasis on hypothesis-driven research? Does it help you do better science? Is it crowding out other approaches? 2. Have you ever had a grant proposal or publication declined because of an absent or unclear hypothesis? 3. Have you ever recommended that someone else's grant proposal or publication be declined for that reason? Was it the main reason? I look forward to hearing what people have to say. Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
Re: [ECOLOG-L] Hypothesis Testing in Ecology
Dear Manuel, Thanks for your reply! I'll have to look up the books you recommended. On Mon, Feb 28, 2011 at 7:49 AM, Manuel Spínola mspinol...@gmail.com wrote: Is necessary to distinguish between statistical and scientific hypothesis. Statistical hypotheses is about patterns, scientific hypotheses are about process (they are based on why or how). My experience on this topic tells me that most ecologists do not know the difference between the 2 kind of hypothesis. I agree. The fact that the two are conflated so often is why I decided to ask about them together. Falsification is the contribution of Karl Popper to the Hypothetic-Deductive method. It has nothing to do with statistics or statistical hypothesis. The hypothetic-deductive method has been considered as the scientific method, however not many people know how it works. The hypothetic-deductive method is inductive and not deductive like the namesuggest. Now that's an interesting comment. Popper went out of his way to avoid induction. In fact, he actually claimed that it doesn't exist in science! Why do you say that the hypothetico-deductive method is actually inductive? Best, Jane On 27/02/2011 11:44 p.m., Jane Shevtsov wrote: Fellow Ecologgers, Lately, I've been thinking a lot about the role of hypothesis testing (both the statistical and falsificationist varieties) in biology in general and ecology in particular. Before saying anything, I want to ask the forum a few questions. 1. What do you think of the current emphasis on hypothesis-driven research? Does it help you do better science? Is it crowding out other approaches? 2. Have you ever had a grant proposal or publication declined because of an absent or unclear hypothesis? 3. Have you ever recommended that someone else's grant proposal or publication be declined for that reason? Was it the main reason? I look forward to hearing what people have to say. Jane Shevtsov -- Manuel Spínola, Ph.D. Instituto Internacional en Conservación y Manejo de Vida Silvestre Universidad Nacional Apartado 1350-3000 Heredia COSTA RICA mspin...@una.ac.cr mspinol...@gmail.com Teléfono: (506) 2277-3598 Fax: (506) 2237-7036 Personal website: Lobito de río Institutional website: ICOMVIS -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes In the long run, education intended to produce a molecular geneticist, a systems ecologist, or an immunologist is inferior, both for the individual and for society, than that intended to produce a broadly educated person who has also written a dissertation. --John Janovy, Jr., On Becoming a Biologist
[ECOLOG-L] Model Fitting and Data Quality
I have been following the AIC thread with some interest. While I'm a newcomer to the subject and don't know much about the ins and outs of model selection, it seems like data accuracy and precision should drive how much we penalize extra parameters. Kepler rejected circular planetary orbits and went with elliptical ones only because he believed Tycho Brahe's data was of such high quality that even a very small discrepancy between observation and prediction was worth taking seriously. Data that was not known to be as precise as Brahe's would not have convinced him to fit elliptical rather than circular orbits to the observations. I'd very much like to hear people's thoughts on this. Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Transformations for Normalized Data
Thanks, Gavin. I've already been told that normalizing the data is unnecessary and proceeded to not do so. The further analysis is a rather unusual one; the only ecologist I know of to have used it is Bill Shipley. My goal is to see how different species affect each other's abundances. Multiple regression isn't an option as I have more species than plots -- and besides, regression isn't really causal, especially when you can't single out independent variables. Instead, I'm going to use the causal discovery algorithms of Judea Pearl and Peter Spirtes. They don't require anything beyond correlation in terms of statistics but can find causal relationships from observational data if you assume that the underlying causal structure is acyclic. I found an R package, pcalg, that implements these algorithms, so hopefully I won't have to program them myself. I strongly encourage people to check out these methods. Shipley's website is a good place to start. Best, Jane On Mon, Nov 8, 2010 at 1:22 AM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Sat, 2010-10-30 at 13:04 -0700, Jane Shevtsov wrote: It's an intermediate step. I need to control for elevation before going on to further analysis. (My data comes from plots at varying elevations in the Smoky Mountains.) The ultimate goal is to find species' influences on each other's abundances, for which I'll probably use Pearl's Inferred Causation algorithm. (I was originally planning to just use multiple regression but have too many species and not enough data points for that.) Jane, Sorry to come to this late. Hope that makes it a little clearer. Not really. Surely this depends on what subsequent analysis you want to do. If it involves regression or ordination, you could just as well include altitude in your models and work from their, assessing improvements in fit over a null model that includes altitude. Abundance data are unlikely to be Gaussian - why force them to be so? The canonical transformation for such data is the log. A recent paper by Bob O'Hara and Johan Kotze [1] shows us that doing this is not a good idea. Instead use a statistical model that seems plausible; Poisson GLM or extensions to this if overdispersion and/or zero-augmentation is an issue, such as negative binomial models, zero-inflated or zero-altered models etc.. If you are fitting individual regressions to each species, why normalize them at all? Why don't you want residuals in the same units as the original data? If you are interested in the community/assemblage level then wouldn't an ordination-based approach be more useful? CCA/RDA/db-RDA are all just regression models after-all, and Thomas Yee's Canonical Gaussian Ordination (see his papers in Ecology and Ecological Monographs) is a formal representation of this. But allow you to work at the community level, include altitude as a nuisance variable etc. Perhaps if you explain what your further analyses are, you'd get more relevant replies HTH G [1] http://onlinelibrary.wiley.com/doi/10./j.2041-210X.2010.00021.x/abstract Best, Jane On Sat, Oct 30, 2010 at 5:32 AM, Bill Silvert cien...@silvert.org wrote: I'm not clear on whether this is a thread about ecology or statistics. Jane writes My goal is simply to do a regression which seems a strange kind of goal. If she wants to predict abundances or identify causative factors, that I understand, but what kind of goal is doing a regression? How do we even know that the regression she is looking for exists? Even obvious regressions can be misleading. I was once approached by a colleague who asked for my help finding the relationship between parental biomass and surviving offspring, but a quick look at the data showed that no relationship existed. So instead we set about looking for factors that determined the number of offspring and found a good correlation with environmental factors (Koslow, J. Anthony, Keith R. Thompson, and William Silvert. 1987. Recruitment to Northwest Atlantic Cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) Stocks: Influence of Stock Size and Environment. Can. J. Fish. Aquat. Sci. 44:26-39). We not only identified a predictive pattern, but we could conclude that even though the fish were extremely fecund, the number of survivors depended on an environmental bottleneck so that the number of eggs was not very important. William Silvert -Original Message- From: Jane Shevtsov Sent: Friday, October 29, 2010 12:31 AM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: Re: [ECOLOG-L] Transformations for Normalized Data Hi Mike, Dividing by the mean helps. Still, there are definitely too many zeros in my data, so what should I do with the distributions you mentioned? My goal is simply to do a regression. Thanks, Jane On Thu, Oct 28, 2010 at 8:11 PM, mdie...@life.illinois.edu wrote: 1) divide by the mean instead of the maximum 2) abundance
[ECOLOG-L] Looking for Article
Does anybody have a PDF of McArdle 1988 The structural relationship: regression in biology, published in the Canadian Journal of Zoology? My school doesn't have web access going back that far and it'll be a few days before I can get to the library. Thanks, Jane -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Transformations for Normalized Data
Yes, I should have said more about my goals. I'm not actually interested in the equation resulting from the regression. Rather, I need to control for the effects of elevation on the abundance of different taxa before going on to further analyses. Basically, I want residuals. Jane Shevtsov On Fri, Oct 29, 2010 at 9:17 AM, Quan Dong quan.d...@inbox.com wrote: The questions/hypotheses should dictate the selection of statistical approaches. Please note, when you transform the data, you interpretation also changes, and sometimes the interpretation is very complicated and weakens the conclusion. In your case, you did not provide the questions of interest. You might consider the models with assumptions of non-normal distributions, e.g., zero-inflated models, or quantile regression, (particularly if you are interested in quantification of the relationship between the abundance and habitat conditions). qd -Original Message- From: jane@gmail.com Sent: Thu, 28 Oct 2010 14:31:49 -0700 To: ecolog-l@listserv.umd.edu Subject: [ECOLOG-L] Transformations for Normalized Data I have abundance data for a number of different species that I need to use in a regression. Since the data encompasses a variety of taxa (from trees to soil mites) whose abundances are measured differently, I normalized it, dividing abundances of each species by the maximum abundance of that species. This, of course, produces numbers ranging from 0 to 1, with a 1 for every species. Now I'm trying to transform the data into something approaching normality. I've tried various combinations of arcsin, square root, fourth root, and log (after adding 1, as there are plenty of zeros in the data), but nothing seems to help much. The problem appears to be the presence of a 1 in every column. Any ideas for what might work? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight Share photos screenshots in seconds... TRY FREE IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if1 Works in all emails, instant messengers, blogs, forums and social networks. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Transformations for Normalized Data
It's an intermediate step. I need to control for elevation before going on to further analysis. (My data comes from plots at varying elevations in the Smoky Mountains.) The ultimate goal is to find species' influences on each other's abundances, for which I'll probably use Pearl's Inferred Causation algorithm. (I was originally planning to just use multiple regression but have too many species and not enough data points for that.) Hope that makes it a little clearer. Best, Jane On Sat, Oct 30, 2010 at 5:32 AM, Bill Silvert cien...@silvert.org wrote: I'm not clear on whether this is a thread about ecology or statistics. Jane writes My goal is simply to do a regression which seems a strange kind of goal. If she wants to predict abundances or identify causative factors, that I understand, but what kind of goal is doing a regression? How do we even know that the regression she is looking for exists? Even obvious regressions can be misleading. I was once approached by a colleague who asked for my help finding the relationship between parental biomass and surviving offspring, but a quick look at the data showed that no relationship existed. So instead we set about looking for factors that determined the number of offspring and found a good correlation with environmental factors (Koslow, J. Anthony, Keith R. Thompson, and William Silvert. 1987. Recruitment to Northwest Atlantic Cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) Stocks: Influence of Stock Size and Environment. Can. J. Fish. Aquat. Sci. 44:26-39). We not only identified a predictive pattern, but we could conclude that even though the fish were extremely fecund, the number of survivors depended on an environmental bottleneck so that the number of eggs was not very important. William Silvert -Original Message- From: Jane Shevtsov Sent: Friday, October 29, 2010 12:31 AM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: Re: [ECOLOG-L] Transformations for Normalized Data Hi Mike, Dividing by the mean helps. Still, there are definitely too many zeros in my data, so what should I do with the distributions you mentioned? My goal is simply to do a regression. Thanks, Jane On Thu, Oct 28, 2010 at 8:11 PM, mdie...@life.illinois.edu wrote: 1) divide by the mean instead of the maximum 2) abundance data is rarely normal even before normalization because A) abundance can never be negative and B) it usually has too many zeros because one is convolving two processes (probability of presence times abundance given presence). If your data shows (B) I recommend using a zero-inflated distribution while if it shows (A) I would recommend a distribution that is positive (e.g. lognormal or gamma). Because I usually work with count data I prefer the zero-inflated Poisson or zero-inflated Negative Binomial, but once you've normalized that's no longer an option. I'd probably try a zero-inflated lognormal or zero-inflated gamma, with the former being conceptually simpler because it doesn't require a link function. If neither (B) nor (A) is present in your data you're very luck and can stick to the normal (possibly with transformation). -- Mike I have abundance data for a number of different species that I need to use in a regression. Since the data encompasses a variety of taxa (from trees to soil mites) whose abundances are measured differently, I normalized it, dividing abundances of each species by the maximum abundance of that species. This, of course, produces numbers ranging from 0 to 1, with a 1 for every species. Now I'm trying to transform the data into something approaching normality. I've tried various combinations of arcsin, square root, fourth root, and log (after adding 1, as there are plenty of zeros in the data), but nothing seems to help much. The problem appears to be the presence of a 1 in every column. Any ideas for what might work? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Transformations for Normalized Data
Hi Mike, Dividing by the mean helps. Still, there are definitely too many zeros in my data, so what should I do with the distributions you mentioned? My goal is simply to do a regression. Thanks, Jane On Thu, Oct 28, 2010 at 8:11 PM, mdie...@life.illinois.edu wrote: 1) divide by the mean instead of the maximum 2) abundance data is rarely normal even before normalization because A) abundance can never be negative and B) it usually has too many zeros because one is convolving two processes (probability of presence times abundance given presence). If your data shows (B) I recommend using a zero-inflated distribution while if it shows (A) I would recommend a distribution that is positive (e.g. lognormal or gamma). Because I usually work with count data I prefer the zero-inflated Poisson or zero-inflated Negative Binomial, but once you've normalized that's no longer an option. I'd probably try a zero-inflated lognormal or zero-inflated gamma, with the former being conceptually simpler because it doesn't require a link function. If neither (B) nor (A) is present in your data you're very luck and can stick to the normal (possibly with transformation). -- Mike I have abundance data for a number of different species that I need to use in a regression. Since the data encompasses a variety of taxa (from trees to soil mites) whose abundances are measured differently, I normalized it, dividing abundances of each species by the maximum abundance of that species. This, of course, produces numbers ranging from 0 to 1, with a 1 for every species. Now I'm trying to transform the data into something approaching normality. I've tried various combinations of arcsin, square root, fourth root, and log (after adding 1, as there are plenty of zeros in the data), but nothing seems to help much. The problem appears to be the presence of a 1 in every column. Any ideas for what might work? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
[ECOLOG-L] Transformations for Normalized Data
I have abundance data for a number of different species that I need to use in a regression. Since the data encompasses a variety of taxa (from trees to soil mites) whose abundances are measured differently, I normalized it, dividing abundances of each species by the maximum abundance of that species. This, of course, produces numbers ranging from 0 to 1, with a 1 for every species. Now I'm trying to transform the data into something approaching normality. I've tried various combinations of arcsin, square root, fourth root, and log (after adding 1, as there are plenty of zeros in the data), but nothing seems to help much. The problem appears to be the presence of a 1 in every column. Any ideas for what might work? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Naturefaking in media
This all seems related to the question of whether drawings or photographs are best in field guides. Many (not all) modern guides use photos, but I find drawings more useful, as these are usually composites that capture the important characteristics of the species. The individual details in a photograph can be distracting. My two cents, Jane On Mon, Sep 27, 2010 at 6:17 AM, Cara Lin Bridgman cara@msa.hinet.net wrote: The most exciting thing Nick Upton, his photographer, and my husband saw when in the field was a muntjac deer running in terror from two yellow-throated martens. The deer was in such a panic that it ran within 2 meters of the film team. Did they catch any of this on film? No. Cameras have to be set up and in place and waiting. Scenes like martens hunting deer are once in a life-time. The cameras and the film crew were not ready for it. One reason for the scores of man vs nature type films is because the producing companies and the television channels are looking for things that will sell. Abn unfortunate thing about Typhoon Island (preview here: http://www.sciencevision.at/en.php/movie_taiwan) is that US distributors and TV channels were not interested in the film. As far as I know, it has never been shown in the USA. It has been shown throughout Europe and Taiwan. BBC only became interested in supporting the film after an Austrian company, Science Vision, put most of the funds. Film producers like Nick Upton work hard to accurately capture animal behaviors and habitats. This involves filming in the wild, filming on sets, some 'faking' with zoo animals, and very careful editing. After filming, however, the producer often must get into a huge fight with the funding companies to maintain details of behavior in the face of demands for more violence and disasters. In the case of Typhoon Island, these were typhoons and earthquakes. One of Nick's fights with Science Vision, however, boiled own to film quality vs story completeness. Nick had to insist on inclusion of biologically accurate sequences filmed using infra-red cameras, which produce grainy pictures. Science Vision wanted to replace these grainy scenes with aesthetically pleasing time-lapses of Taiwan's scenery filmed during the day at better resolution. Having training in science is important for helping a producer make a film scientifically accurate. Nick got his Ph.D. in Zoology at Cambridge. He asked Taiwan's scientists to review the script to ensure accuracy. It was this sort of attention for detail and cooperation with scientists that really impressed me. CL -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
[ECOLOG-L] Mushroom Spores in Lake Sediments
Does anyone know whether basidiomycete spores, particularly ones from ectomycorrhizal species, are ever found in lake sediment cores? If so, has any paleoecological work been done on them? Thanks, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] MEETINGS Organized or Unorganized? Re: [ECOLOG-L] alcohol consumption and citation counts
Such unconferences are pretty well established in the tech world, particularly among programmers working on open-source projects. See http://barcamp.org and the Wikipedia entry for unconference http://en.wikipedia.org/wiki/Unconference. Jane Shevtsov On Fri, Sep 17, 2010 at 6:06 PM, Wayne Tyson landr...@cox.net wrote: Ecolog: Methinks there might be even more elephants in the saloon--perhaps of many hues. It has been my observation in the past that I have learnt more in the hallways, WC's, and saloons than I have being driven nuts listening to 20-minute presentations (attention ethologists!), in darkened halls enduring the maddening, warp-speeding of laser traces across extensive, unreadable tables and under-wowed by power-pointless pontifications and dull-drumming, self-indulgent preening reading of newly-minted number-crunchers, ad nauseam. Yea, tho there be the occasional exception, I have long dreamt of unorganized groupings, pre-read pre-publication papers cussed and discussed with the authors in a more playfully serious atmosphere than the arbitrary, jammed, expensive meetings at resort destinations. I even participated in one experiment in unorganizing such a gathering; it was soon organized into a real organization, however. The only such unorganization I ever knew to last was The Friends of the Pleistocene, which still exists, I believe, in some form. Not a bad model, though, even though it would never pass PC muster these days . . . too much wild behavior back in the sixties and seventies. The trouble with unorganizations is that they don't pad résumés or bring in money for institutions, not to mention status. With or without booze, they seem to me to work better than organized meetings. WT PS: Seriously, folks, whatever it takes to puncture caution, lower guards, and stir up passions. I may yet collect the beer Silvert promised me a long time ago, but I'd rather he came to San Diego . . . I love Europe, but have come to hate airlines so much . . . - Original Message - From: David Inouye ino...@umd.edu To: ECOLOG-L@LISTSERV.UMD.EDU Sent: Friday, September 17, 2010 5:09 AM Subject: [ECOLOG-L] alcohol consumption and citation counts http://blogs.nature.com/news/thegreatbeyond/2010/09/make_mine_a_double.html Make mine a double - September 15, 2010 There have been http://www.nature.com/news/2010/100813/full/news.2010.406.htmlsome radical suggestions to increase citation counts of late but heavy drinking would probably rank at the bottom of most researchers' lists. Yet a new study has found that the world's most highly cited ecologists and environmental scientists typically consume more than double the amount imbibed by the general population. http://www.springerlink.com/content/j5205442788316v6/Published in the October issue of http://www.springerlink.com/content/j5205442788316v6/Scientometrics, John Parker, a post-doctoral sociologist at the National Center for Ecological Analysis and Synthesis at the University of California, Santa Barbara, and colleagues report the results of a survey of the drinking habits of 124 of the most highly cited researchers in ecology and environmental science: the vast majority men aged between 50 and 70 based in either North America or Western Europe. The results reveal that consumption for this group averages around 7 alcoholic beverages per week, about 2.5 drinks over the weekly consumption of the average American. Though a fifth of the group does not drink, more than half consume 10 or more alcoholic beverages a week, 20% consume 12 or more and 10% consumer 21 or more. The largest consumer downed 31 per week. The researchers are quick to point out the obvious - correlation does not equal causation. We are definitely not saying 'drink more to do better', Parker stresses. But he does believe that more and better information is needed to unravel the observed relationship and the non-scientific activities that affect scientific productivity. The results support the positive association between national per capita beer consumption and a country's citations per paper reported http://www.springerlink.com/content/lp34234k59473xkt/in a 2009 paper by Canadian ecologist Christopher Lortie, who collaborated with Parker on the current paper. But they stand in contrast to a http://onlinelibrary.wiley.com/doi/10./j.0030-1299.2008.16551.x/abstract2008 survey of Czech ecologists by Thomas Grim, also an ecologist. Grim, based at Palacky University in the Czech Republic, found the opposite: that increased levels of beer consumption were associated with lower numbers of citations. Because of well documented negative and causal effects of ethanol, independently of dose, on both mental performance and health, I find it unlikely that the Parker et al. finding reflects more than a spurious relationship, Grim told Nature News. Eminent Oxford ecologist Bob
Re: [ECOLOG-L] Making Species Co-Occurrence Matrix
Hi Gavin,
Thanks! For just getting the data into R, speed isn't an issue, but it
could be important for null model analysis. But is it possible to make
this function correspond to my version that changed any() to sum() in
order to make the co-occurrence matrix say how many times the species
co-occurred?
Thanks,
Jane
On Wed, Sep 1, 2010 at 4:49 AM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote:
Andy, Jane,
If speed is an issue or you are working with larger problems than the
example Andy used, then we can exploit other tools in R to get the same
answer as Andy's spp.cooc() function, but much more efficiently, using a
matrix multiplication:
Here's Andy's example and my version with some timings:
## Set a random seed
set.seed(123)
## dummy data
sppXsite - matrix(rpois(15,0.5),nrow=3)
colnames(sppXsite) - paste(spp,1:5,sep=)
rownames(sppXsite) - paste(site,1:3,sep=)
sppXsite # here's what it looks like
# now make a function to compute the co-occurrence matrix
spp.cooc - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*any(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
## And my version
spp.cooc2 - function(mat) {
ncol - NCOL(mat)
res - matrix(as.numeric((t(mat) %*% mat) 0), ncol = ncol)
rownames(res) - colnames(res) - colnames(mat)
return(res)
}
all.equal(spp.cooc(sppXsite), spp.cooc2(sppXsite)) ## TRUE!
## Timings
system.time(replicate(1000, spp.cooc(sppXsite)))
system.time(replicate(1000, spp.cooc2(sppXsite)))
system.time(replicate(1000, spp.cooc(sppXsite)))
user system elapsed
0.728 0.004 0.733
system.time(replicate(1000, spp.cooc2(sppXsite)))
user system elapsed
0.067 0.000 0.068
## larger problem
set.seed(123)
sites - 100
species - 50
sppXsite.big - matrix(rpois(sites * species, 0.5), nrow=sites)
colnames(sppXsite.big) - paste(spp, seq_len(species), sep=)
rownames(sppXsite.big) - paste(site, seq_len(sites), sep=)
## Timings
## Note the first line below takes ~40 seconds on my fast PC
system.time(replicate(1000, spp.cooc(sppXsite.big)))
system.time(replicate(1000, spp.cooc2(sppXsite.big)))
## Timings
system.time(replicate(1000, spp.cooc(sppXsite.big)))
user system elapsed
41.049 0.043 41.244
system.time(replicate(1000, spp.cooc2(sppXsite.big)))
user system elapsed
0.423 0.037 0.468
If speed or size of problem is not an issue then either works just well
enough.
I don't think we have anything like this in Vegan, but happy to be
corrected if we do. If we don't, I'll chat with Jari and see about
adding it to the package.
All the best,
G
On Fri, 2010-08-27 at 12:41 -0400, Andy Rominger wrote:
Hi Jane,
I think someone may have asked something similar on the r-sig-eco email list
(which is a good resource in general:
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology)
I think the answer may have been there there's a function in the vegan
package for R (http://cran.r-project.org/web/packages/vegan/index.html).
But it would be pretty simple to write something up in R. Here's one way of
doing it (if I'm correct in my interpretation of a co-occurrence matrix!).
The actual function (called `spp.cooc') is really only 2 lines long--the
code just looks longer from making up example data and adding in the
comments.
Hope this might do the trick for you! Note that in it's current form you
would have to give the function a matrix or data.frame of ONLY NUMBERS in
which species are columns and sites are rows. This could be changed by
manipulating the MARGIN argument of the apply command below, i.e., site.list
- apply(matrx,1,...)
Hope this helps--
Andy
# make some example data
sppXsite - matrix(rpois(15,0.5),nrow=3)
colnames(sppXsite) - paste(spp,1:5,sep=)
rownames(sppXsite) - paste(site,1:3,sep=)
sppXsite # here's what it looks like
# now make a function to compute the co-occurrence matrix
spp.cooc - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*any(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
# here's how it works
co.matrix - spp.cooc(sppXsite)
co.matrix
On Fri, Aug 27, 2010 at 12:46 AM, Jane Shevtsov jane@gmail.com wrote:
Is there a fast way to make a species co-occurrence matrix given a
site-species matrix or lists of species found at each site? I'm
looking for a spreadsheet or database
Re: [ECOLOG-L] Making Species Co-Occurrence Matrix
Thanks, Andy. I made a small modification to the code to make it give
the number of sites at which two species co-occur. (This just involves
changing any to sum.)
spp.cooc.count - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*sum(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
Jane
On Fri, Aug 27, 2010 at 9:41 AM, Andy Rominger ajromin...@gmail.com wrote:
Hi Jane,
I think someone may have asked something similar on the r-sig-eco email list
(which is a good resource in general:
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology)
I think the answer may have been there there's a function in the vegan
package for R (http://cran.r-project.org/web/packages/vegan/index.html).
But it would be pretty simple to write something up in R. Here's one way of
doing it (if I'm correct in my interpretation of a co-occurrence matrix!).
The actual function (called `spp.cooc') is really only 2 lines long--the
code just looks longer from making up example data and adding in the
comments.
Hope this might do the trick for you! Note that in it's current form you
would have to give the function a matrix or data.frame of ONLY NUMBERS in
which species are columns and sites are rows. This could be changed by
manipulating the MARGIN argument of the apply command below, i.e., site.list
- apply(matrx,1,...)
Hope this helps--
Andy
# make some example data
sppXsite - matrix(rpois(15,0.5),nrow=3)
colnames(sppXsite) - paste(spp,1:5,sep=)
rownames(sppXsite) - paste(site,1:3,sep=)
sppXsite # here's what it looks like
# now make a function to compute the co-occurrence matrix
spp.cooc - function(matrx) {
# first we make a list of all the sites where each spp is found
site.list - apply(matrx,2,function(x) which(x 0))
# then we see which spp are found at the same sites
sapply(site.list,function(x1)
{
sapply(site.list,function(x2) 1*any(x2 %in% x1))
})
# the result is returned in a symmetrical matrix of dimension
# equal to the number of spp
}
# here's how it works
co.matrix - spp.cooc(sppXsite)
co.matrix
On Fri, Aug 27, 2010 at 12:46 AM, Jane Shevtsov jane@gmail.com wrote:
Is there a fast way to make a species co-occurrence matrix given a
site-species matrix or lists of species found at each site? I'm
looking for a spreadsheet or database method (preferably OpenOffice)
or R function.
Thanks,
Jane
--
-
Jane Shevtsov
Ecology Ph.D. candidate, University of Georgia
co-founder, www.worldbeyondborders.org
Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes
The whole person must have both the humility to nurture the
Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream
of Spaceflight
--
-
Jane Shevtsov
Ecology Ph.D. candidate, University of Georgia
co-founder, www.worldbeyondborders.org
Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes
The whole person must have both the humility to nurture the
Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream
of Spaceflight
[ECOLOG-L] Making Species Co-Occurrence Matrix
Is there a fast way to make a species co-occurrence matrix given a site-species matrix or lists of species found at each site? I'm looking for a spreadsheet or database method (preferably OpenOffice) or R function. Thanks, Jane -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Good news from the Gulf? not so fast...
To expand on this point, if you were to drink methanol (wood alcohol), your body would metabolize it to formaldehyde and then formic acid. It's the formic acid that would blind or kill you. (This happened a lot during Prohibition.) Jane Shevtsov On Wed, Aug 11, 2010 at 12:22 PM, David M. Lawrence d...@fuzzo.com wrote: Metabolize is not the same as saying their bodies break down the chemicals with no negative effects. All is says is their bodies process the chemicals -- but the act of processing the chemicals or their breakdown products may very well have harmful effects either right away or at some point in the future. I would ask Peterson to explain precisely what he means here. Dave On 8/11/2010 1:02 PM, Wendee Holtcamp wrote: When I went on my Great Gulf Coast Road Trip recently, I visited with several biologists at the Gulf Coast Research Lab in Ocean Springs MS and one of them, Mark Peterson, told me that most fish actually metabolize oil (PAH). This abstract says These experiments confirm that the use of oil dispersants will increase the exposure of ovoviviparous fish to hydrocarbons in oil. Now I'm not a physiologist and so now that I've seen the abstract below, and started to think about it, I'm not quite sure whether that means that they break it down into less toxic substances and it does NOT really impact them negatively, or that their gut is now exposed to this PAH/oil and that could potentially be harmful? Maybe I need to read the paper... Does anyone know? I'll be writing about this soon so I'd love to talk to someone who knows a bit more about it (and yes I can follow up with Mark as well). I also met with Harriet Perry the lady who discovered that virtually ALL the blue crab larvae (zoea) she was collecting daily had a little droplet of oil under their carapace. They get it in there when they molt. So this raises the possibility of it getting into the food chain. So that makes me curious - if fish can metabolize PAH/oil in a way that does not harm them directly (as Mark suggested to me), what about invertebrates like shrimp, squid, crabs etc? Is there any evidence that they can metabolize PAH, and/or that there are any sublethal impacts people should be looking for? Best Wendee Blogs for Nature from the Bering Sea ~ http://tinyurl.com/2ctghbl ~~ Wendee Holtcamp, M.S. Wildlife Ecology ~ @bohemianone Freelance Writer * Photographer * Bohemian http://www.wendeeholtcamp.com http://bohemianadventures.blogspot.com ~~ 6-wk Online Writing Course Starts Sep 4 (signup by Aug 28) ~~ ~~~ I’m Animal Planet’s news blogger - http://blogs.discovery.com/animal_news -Original Message- From: Ecological Society of America: grants, jobs, news [mailto:ecolo...@listserv.umd.edu] On Behalf Of Geoffrey Patton Sent: Wednesday, August 11, 2010 11:12 AM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: [ECOLOG-L] Good news from the Gulf? In response to Bill's discussion points, I would like to suggest the following paper: Jee Hyun Jung, Un Hyuk Yim, Gi Myeong Han, Won Joon Shim Comparative Biochemistry and Physiology, Part C 150 (2009) 218–223 Biochemical changes in rockfish, Sebastes schlegeli, exposed to dispersed crude oil Abstract: This paper describes the response of the ovoviviparous rockfish, Sebastes schlegeli, to hydrocarbons in the water-accommodated fraction (WAF) of crude oil, in the presence or absence of oil dispersants. Concentrations of cytochrome P-450 1A (CYP1A) and levels of its catalytic activity ethoxyresorufin O-de-ethylase (EROD) in rockfish exposed to WAF at concentrations of 0.1% and 1% were significantly increased by the addition of a dispersant, Corexit 9500 after 48 h exposure. After 72 h exposure, the levels of CYP1A and EROD activity were significantly increased in 0.1% and 0.01% chemically enhanced WAF (CEWAF) (Corexit 9500 and Hiclean II dispersant). Bile samples from fish exposed toWAF alone had low concentrations of hydrocarbon metabolites, exemplified by 1-hydroxypyrene. After 72 h exposure, hydrocarbon metabolites in bile from fish exposed to WAF in the presence of either Corexit 9500 or Hiclean II were significantly higher compared with fish exposed to WAF alone or control fish. These experiments confirm that the use of oil dispersants will increase the exposure of ovoviviparous fish to hydrocarbons in oil. Cordially yours, Geoff Patton, Ph.D. 2208 Parker Ave., Wheaton, MD 20902 301.221.9536 --- On Wed, 8/11/10, William Silvertcien...@silvert.org wrote: From: William Silvertcien...@silvert.org Subject: Re: [ECOLOG-L] Good news from the Gulf? To: ECOLOG-L@LISTSERV.UMD.EDU Date: Wednesday, August 11, 2010, 4:58 AM I confess that I posted this in large part because I was curious to see the reactions. As expected, all replies (on- and off-list) were critical and skeptical
Re: [ECOLOG-L] An article to make you think why did I pick (insert your speciality) to spend my life studying.
equivalent of the blobfish, the African manatee. “The manatee was the least studied large mammal,” Ms. Trimble said. Speculating on a possible reason for the disparity, she said, “Most scientists are in it for the love of what they do, and a lot of them are interested in big, furry cute things.” Or little cute things. Humans and other mammals seem to have an innate baby schema, an attraction to infant cues like large, wide-set eyes, a button nose and a mouth set low in the face, and the universality of these cues explains why mother dogs have been known to nurse kittens, lionesses to take care of antelope kids. On a first pass, then, “ugliness would be the deviation from these qualities,” said David Perrett, an evolutionary psychologist at the University of St. Andrews in Scotland. Tiny, close-set eyes, prominent snout, no forehead to speak of: it sure sounds like a pig. A helpless baby grows into a healthy, fertile youth, which in humans is visually characterized by clarity of shape, sleekness of form and visibility of musculature, said Wendy Steiner of the University of Pennsylvania, who is author of “Venus in Exile” and “The Real, Real Thing,” to be published this fall. “An animal with saggy skin, whiskers and no neck will look like some old guy who’s lost it,” she joked. The more readily we can analogize between a particular animal body part and our own, the more likely we are to cry ugly. “We may not find an elephant’s trunk ugly because it’s so remote,” Dr. Dutton said. “But the proboscis on a proboscis monkey is close enough to our own that we apply human standards to it.” You can keep your rhinoplasty, though: the male monkey’s bulbous proboscis lends his mating vocalizations resonant oomph. People are also keenly, even obsessively vigilant for signs of ill health in others. “That means anything that looks seriously asymmetrical when it should be symmetrical, that looks rough and irregular when it should be smooth, that looks like there might be parasites on the skin or worms under the skin, jaundice or pallor,” Dr. Miller said. “Anything mottled is considered unattractive. Patchy hair is considered unattractive.” We distinguish between the signs of an acquired illness and those of an innate abnormality. Splotches, bumps and greasy verdigris skin mean “possibly infectious illness,” while asymmetry and exaggerated, stunted or incomplete features hint of a congenital problem. If we can’t help staring, well, life is nasty and brutish, but maybe a good gander at the troubles of others will keep it from being too short. “Deformities provide a lot of information about what can go wrong, and by contrast what good function is,” Dr. Miller said. “This is not just about physical deformities. People who seem crazy are also highly attention-grabbing.” And as long as we’ve been gawking and rubbernecking, we’ve felt guilty about the urge. In his book “The Art Instinct: Beauty, Pleasure, and Human Evolution,” Dr. Dutton recounts a passage from Plato in which a man passing by a pile of corpses at the feet of an executioner wants desperately to look, tries to resist and then finally relents, scolding his “evil” eyes to “Take your fill of the beautiful sight!” The appeal of ugly animals is that neither they nor their mothers will care if you stare, and if you own a pet that others find shocking or ugly, you probably won’t mind if others stare, too. Joan Miller, vice president of the Cat Fanciers’ Association Inc., said she found the hairless Sphynx cat, with its “huge ears” and only “a minor amount of wrinkling,” to be “absolutely marvelous looking” and “strong as an ox,” although she conceded it sometimes needed to wear a sweater. Classical beauty is easy, but a taste for the difficult, the unconventional, the ugly, has often been seen as a mark of sophistication, a passport into the rarefied world of the artistic vanguard. “Beauty can be present by its violation,” Dr. Steiner said, and the pinwheel appendages of the star- nosed mole are the rosy fingers of dawn. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] fixing peer review - elegant new proposal and petition - ideas
I am strongly in favor of #2 rather than #1. Full disclosure will tend to make reviewers nicer, but this is not always a good thing. I believe that complete anonymity is the way to go. Jane Shevtsov On Thu, Jul 22, 2010 at 10:05 AM, Aaron T. Dossey bugoc...@gmail.com wrote: These are some good ideas - we DEFINITELY need more INDEPENDENT research jobs in science - this is a HUGE problem. I would start there before deciding to reduce the number of PhD's earned. The problems science solves will not go away, in general, so we will always need more independent thinkers employed to solve them. A couple of ideas for peer review: 1) make the reviewers names available: ie: not anonymous. 2) make the author(s) names anonymous. Too many papers get published and grants get funded because of WHO is on the author/PI line rather than the content of those documents. Aaron T. Dossey, Ph.D. Biochemistry and Molecular Biology (Candan Soykan) wrote: I believe that the problem is much broader than individuals cheating the peer review system. Rather, why has the number of manuscripts increased so dramatically? Many bemoan the increasing quantity and decreasing quality of papers these days, and yet few are willing to discuss the root cause - competition for jobs/grants. So long as there are too many individuals vying for too few jobs/research dollars, the incentive will be to publish often, even if the quality of the work is low (i.e., satisfy the search committees and reviewers who value quantity over quality). There are several ways to address this issue (and I doubt that my list is exhaustive): 1) Increase the number of jobs/grants for ecologists; 2) Decrease the number of ecologist we train so as not to exceed the number of jobs/grants that are available; or 3) Change the way we evaluate candidates to better reflect the quality of the work they have done, rather then just reward output per se. In my opinion, option #1 is largely out of the hands of researchers; moreover, if the amount of funding did increase, there is always the risk that the number of ecologist we train would as well, leading to no net gain. I have seen certain individuals refrain from taking students, fulfilling the second option above, but getting a whole community of ecologists to do it seems problematic (who would decide how many students each researcher can train?). The third option seems the most realistic, but will require a shift in the way we evaluate research productivity. Moreover, it brings with it risks as well - counting pubs is, at the very least, objective, whereas who is to evaluate the quality of the work done by an applicant? I'd be interested to hear others' thoughts on this issue ... Candan Soykan csoy...@mail.sdsu.edu -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
[ECOLOG-L] Analyzing a Large Correlation Matrix
Dear list members, Stats books (and common sense) typically insist that you need to examine scatter plots of your data before computing a correlation coefficient. However, I have a species-plot matrix with 150 species, for which I plan to generate a correlation matrix as a start for further analysis. (I'm using the Spearman rank-order correlation to be on the safe side.) That works out to 11,175 pairwise scatter plots! What do you recommend I do in order to get a feel for the data and diagnose potential problems without looking at all of them? Thanks in advance, and I'll post a summary of responses. Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] evolution for non-scientists textbook
For many students, particularly nonmajors, the history of life is far more exciting than the details of how evolution works. Stanley's textbook _Earth Systems History_ is quite good, as is Dawkins _The Ancestor's Tale_ and Richard Fortey's book _Life_. (The latter is a bit dated, as it was published in 1992.) Actually, my favorite book on the subject is a children's book from the 1980s: _The Evolution Book_ by Sara Stein. You might want to keep a copy on hand for teaching ideas. Jane Shevtsov On Wed, May 12, 2010 at 9:08 AM, Madhusudan Katti mka...@csufresno.edu wrote: Just following up on my earlier suggestion, there is a positive review of The Tangled Bank in the recent American Biology Teacher: http://www.bioone.org/doi/abs/10.1525/abt.2010.72.3.13 “For students of evolution or scholars who want to know the specifics about particular evolutionary processes, this is an excellent read. The fact that it is understandable to beginners and fascinating to scientists makes this book truly unique and valuable.” I would also recommend Carl Zimmer's excellent blog The Loom (http://blogs.discovermagazine.com/loom) as a companion to any course on evolution. I like some of the other suggestions in this thread as well, especially Sean Carroll's book. Coyne is very good too, and Dawkins new book is probably dependable in getting the students' attention (I haven't read it). The Selfish Gene is too old to be used as a general text for a course on evolution. Moreover, with Coyne and Dawkins, I'd worry about alienating some of the religious-minded students. I would hesitate to use those in a non-majors class here in the central valley of California, for example. In fact, I suspect that Coyne's book may have played a role in pushing one of my own students (a grad student no less!) away from Biology because the evidence/arguments in that book were too strong for this religious student to handle. Of course that end result was good in some ways, but it depends on what your goals are with the class. Besides, your audience in Princeton (presuming it hasn't changed in the decade since I was there) will be rather different from what I face here in Fresno - so your mileage may vary! __ Madhusudan Katti Assistant Professor of Vertebrate Biology Department of Biology, M/S SB 73 California State University, Fresno Fresno, CA 93740-8034 +1.559.278.2460 mka...@csufresno.edu http://www.reconciliationecology.org/ __ -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] decline in education, comment on active learning
As a student, I also prefer traditional lectures. Powerpoint seems to interfere with the social aspect of lecturing, perhaps by forcing the lecturer to follow a pre-determined outline or by drawing the students' eyes toward the screen and away from the teacher. Dimming the lights doesn't help! Jane On Mon, Jan 25, 2010 at 1:51 PM, David L. McNeely mcnee...@cox.net wrote: Your post is interesting. It is the first time I have ever heard a student state a preference for more traditional lecturing over PowerPoint lectures. I happen to think you make a very important point. However, I have heard the complaint from students, regarding a colleague whom they chose to blame for their lack of success, that, He doesn't even use PowerPoint for lectures. He just uses overheads and the chalk board. Sometimes it looks like he is making things up as he goes, and he makes us tell him what we want to know. He needs to just tell us what we need to know. I was required to attend that colleague's lectures as part of a university peer evaluation program. He was doing a superb job of leading students to make points for themselves, and at one point even asked students to put diagrams on the board themselves, while he coached them through the exercise. This was in a freshman level honors section. But most of his time was spent in a chalk talk type lecture, fairly traditional with good content. Many of the students seemed very pleased with the process, and despite the complaints I heard (from multiple students), my colleague received decent student evaluation scores. That was several years ago, when PowerPoint was fast becoming a dominant approach to lecturing. Thanks for your post. David Mc On Mon, Jan 25, 2010 at 11:56 AM, Kevin Mueller wrote: Perhaps this is well tread ground, but I think there is an important element missing in the recent discussion regarding effective teaching styles, particular with respect to lectures. What is the impact of detailed PowerPoint presentations on student attendance, participation, and learning? My experience (mostly as a student, some as a teaching assistant) is that lectures can be very effective means to reach a majority of students in a classroom, regardless of size. However, when the lecture consists of detail laden PowerPoint slides, active thought by students is discouraged because more of the information is at hand at any given moment of the lecture and there is less incentive to anticipate where the lecturer is going or follow his/her thought process. Moreover, when the PowerPoint presentations are made available before, during, or after class, there is little incentive to go to class or to pay attention because the student perceives that they can get most of the information without attending class. This style of lecturing is inherently 'less active' than more traditional lecture styles with chalkboards or overheads and has become increasingly common. Thus, following the posts by Bill, Luke, Arathi and Jane, I think lectures can accommodate something that approaches active learning and teaching, but the means of transferring information is critical. Lectures such as those described by Bill and Luke may represent the best available compromise between two distinctly different learning and teaching styles (pure lecture vs. pure active learning). In the absence of having institutions that are dedicated to one or the other teaching style, which would give students the ability to choose which style suits them best, it seems most prudent to aim for middle of the road approaches such as that outlined by Luke. Kevin Mueller Penn State University Intercollege Graduate Program in Ecology kem...@psu.edu -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] decline in education, comment on active learning
One problem with many active learning methods is that they constrain when and how the student is to learn the material. In a traditional situation, I can attend lecture/lab, read the textbook, study with friends, study alone, decide our book sucks and use another one, look up material online, try problems, etc. It doesn't matter what methods I use or don't use. The only thing that matters is the result. In particular, I've had several math professors who graded homework to give students an incentive to do it, while also providing a way to get an A without turning in homework -- and gave fair warning that this was very unlikely to happen! On the other hand, active learning tends to be method-dependent. You're graded on the intermediate steps of learning, not just the outcome. If the methods a particular professor decides to use don't work well for me or if I already have a good grasp of the material, I still have to put in the time. Furthermore, if the professor decides that everybody needs to read the book before coming to class and gives a daily quiz to enforce the policy, the student has just lost some of the freedom to decide when to study. Maybe I find it helpful to have a lecture overview of the material before reading the more detailed book. Maybe I just have a big biochemistry exam and need to focus on that for a few days. Thus, many active learning methods have a paradoxical effect. By drawing attention to the process of learning as opposed to the outcome, they make the student more dependent on the professor for structuring their learning experience. Despite all of the above, I am not opposed to all active learning methods. In particular, I had a physiology professor in undergrad who would interrupt himself during lecture and start evaluating an idea he'd thought of or asking a question and trying to reason out the answer, thus modeling the process for us. This, plus the fact that he told the class on day one that he expected us to make mistakes and that these were just part of learning, really got people to ask questions and speak up in class -- and imposed no extra constraints. I myself, as a TA, have inflicted a journal assignment on ecosystem ecology students in which they were asked to wrestle with class material, ask questions and draw connections with their daily experiences or other classes. (This journal was only a small part of their grade and I gave substantive feedback, in the form of letters to each student.) And some things can only be learned through first-hand experience. I just wish the enthusiasm for active learning methods was tempered by an awareness of the constraints and dependence they can impose on students. Jane Shevtsov On Sat, Jan 23, 2010 at 1:28 AM, Sarah Berke skbe...@gmail.com wrote: Hi, I want to briefly respond to David Lawrence's comment from several days ago, about evaluation scores declining when he switched to active learning. This comment probably hit home for anyone who has tried active learning: I watched my evaluation scores decline when I switched to active learning. ...It was also unreasonable for me to expect them to ask questions relevant to the material we discussed in class. I had students complain they didn't learn anything from me For anyone who has ever been in this boat, you are not alone--this is a common phenomenon when introducing active learning methods to a student body that is accustomed to traditional lecture-based methods. Based on my own experiences, and those of various colleagues, I would guess that most instructors got similar comments when they first switched over from lecturing. I am fairly new to active learning myself, but I've talked with colleagues who have been doing it for years, and everyone says that it really does get better (particularly if many faculty in the department all start using it). I think comments like I didn't learn anything stem from problems with metacognition. How do you know when you've learned something? Memorizing 30 vocabulary words is a concrete achievement, you can point and say There, I learned these words. But interpreting data, or designing an experiment, or predicting the outcome of a perturbation to a system are all rather amorphous--there's no one thing to point to and say I've learned this. That can throw students for a loop. Furthermore, the level of energy and preparation required to participate in a learner-centered classroom can push students out of their comfort zones, particularly if they are accustomed to the ease of showing up and taking notes through a lecture. I am not trying to dismiss your student's comments, I'm just pointing out that some negative comments might have more to do with feeling uncomfortable in a new situation than with learning science per se. Happily, none of these issues are insurmountable. The trick is to help students be aware of their own progress, and to bring them on board with the goals of a learner
Re: [ECOLOG-L] now I've seen it all: IQ
On Thu, Jan 21, 2010 at 6:02 PM, Fann, Sarah Lynn slf5...@uncw.edu wrote: Jane and rest of the ECOLOG listserve, Let's think critcally about the assumption that it is easy for bright students who are poor to get funding for college. If that were true, wouldn't we expect a significant portion of American children to be born poor, get educated, and thus rise up through the socio-economic ranks? However, isn't it a known trend that children born poor tend to stay poor and not get an education? Doesn't this trend directly contradict the assumption that it is easy for bright, poor students to get full funding for college? No, it doesn't, and I didn't say it was easy, just that even a free ride was possible. (I graduated from UCLA without paying a dime.) When I said bright, I wasn't referring to inborn intelligence but to the result of education. And that's the kicker. If a poor student has a solid high school program and good SAT scores, financial considerations are unlikely to prevent them from attending college. But few get the kind of K-12 education that will enable this. In regards to the middle-class, I find it interesting that you dropped the bright adjective to describe these students. Because Luanne's hypothesis was that cost was preventing TOP poor students from attending college, thus lowering overall performance. Does that mean that we expect all students from the middle-class to attend college? If that's true, than I expect it would be harder, on average, for middle-class students to get scholarships compared to poor students because 1) they represent a broader range of capabilities, and only those considered best are normally eligible for scholarships, and 2) there is a larger number of middle class students competing, thus the probability of any one middle-class student getting a scholarship is less. Exactly. Plus, middle class students get less need-based aid. Finally, if only a few bright poor students are getting into college, yet a larger range of IQ's from other socio-economic classes are getting into school, than that would lend support to Luanne's hypothesis. The trends of America's poor certainly seems to lead to the conclusion that few poor students are given the oppurtunity to attend college. On the other hand, it is almost expected that every middle or upper class child should attend college. There's no question that cost is a barrier to higher education, but that's not the question that was being discussed. The question was, roughly, Assuming there has been a decline in the average performance of college students in recent decades, can this decline be explained by rising college costs that prevent poor students with high IQs from attending college?. Therefore, only the situation faced by top-performing low-income students is relevant. Best, Jane _ From: Ecological Society of America: grants, jobs, news [ecolo...@listserv.umd.edu] On Behalf Of Jane Shevtsov [jane@gmail.com] Sent: Thursday, January 21, 2010 10:47 AM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: Re: [ECOLOG-L] now I've seen it all: IQ I don't think this would be a very strong influence. Bright students with little money get financial aid, sometimes to the point of a free ride. It may be harder for middle-class students than for those who are poor, but still, schools compete to get the really good students. Jane On Tue, Jan 19, 2010 at 1:47 AM, Luanne Roth ro...@citytel.net wrote: I have been wondering if the increase in the unequal distribution of wealth and the increased costs of higher education might be causing a large shift towards college students who fall into the middle of the bell curve. I recall reading at least one study which showed no relationship between wealth and IQ. If we are eliminating many high IQ students by income constraints and the bell curve has very little area under it at the high IQ end Luanne At 12:18 PM 1/18/2010, you wrote: I watched my evaluation scores decline when I switched to active learning. I got tired of lecturing from powerpoints that the students could memorize, regurgitate on tests, and quickly forget. Somehow, it was unreasonable for me to expect the students to show up for the lectures prepared and willing to participate in class discussions. It was even more unreasonable for me to refuse to just tell us what we need to know, when they couldn't answer very simple questions that I'd toss out to stimulate discussion. It was also unreasonable for me to expect them to ask questions relevant to the material we discussed in class. I had students complain they didn't learn anything from me, but it seems to me that if they weren't asking questions -- either in class, on class discussion boards, or via e-mail -- they couldn't have been trying very hard. Maybe I am unreasonable... Dave On 1/18/2010 12:17 PM, James Crants wrote: On Sun, Jan 17, 2010
Re: [ECOLOG-L] Not now I've seen it all - says Orwell
I've always thought the main reason for avoiding I in scientific papers was to prevent self-aggrandizement. It's not about you -- it's about the research. We may be ok, but the passive voice serves a moral/social purpose in single-authored works. Jane On Mon, Jan 18, 2010 at 11:10 AM, David L. McNeely mcnee...@cox.net wrote: Bill, thank you. Not to hammer a dead horse, but I wrote my dissertation in the seventies. I was encouraged to use active voice and first person. The most recent edition of the CBE Style Manual that I actually own is the third edition (copyright 1972), though I have generally had access to more recent (and massive) versions over the years since. From my third edition (page 5): Write in the active voice unless you have a good reason for writing in the passive. The active is the natural voice, the one in which people commonly speak and write, and it is less likely than the passive to lead to ambiguity. There follows a series of explanations and examples detailing why first person is generally preferable to other persons, especially in describing methods where it provides clear explanation of who did what, rather than the ambiguity of the third person passive, where one might wonder who at all did the experiments described. Thanks, David On Sun, Jan 17, 2010 at 3:29 PM, William Silvert wrote: Several subscribers have disagreed with my statement about passive/active voice, and I stand corrected. Perhaps the case was best stated by someone who wrote me off-list to say I have noticed a change in the last 4 years...I was instructed by many to use the passive voice and to shy away from the active voice which very often required the use of first person pronouns. But in the last year, a growing trend has led away from the use of passives. Just today, when haphazardly choosing 3 abstracts from the most recent issue of Science, I found all to be written in the active voice and found the first person 'we' in two of them...I think 'modern scientific writing' may indeed be evolving again. I am pleased to be shown wrong and commend the scientific community for this stylistic improvement. Bill Silvert -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Not now I've seen it all - says Orwell
I wonder why the writers of the CBE Style Manual are opposed to using the passive voice. Is it the usual Strunk White stuff? It's interesting that they say 'I' may embarrass the writer, but not, 'I' may startle the reader. There's an excellent article on The Passive in Technical and Scientific Writing at http://www.jacweb.org/Archived_volumes/Text_articles/V2_Rodman.htm. You might also want to check out the Language Log piece, How long have we been avoiding the passive and why? http://itre.cis.upenn.edu/~myl/languagelog/archives/003380.html The essay in which Orwell recommends avoiding passives itself has 20% passives! Language Log, a blog run by linguists, is generally excellent on the topic of passives. See http://languagelog.ldc.upenn.edu/nll/?cat=54 (material posted since April 8, 2008) and http://tinyurl.com/yldaltf (prior to that). Jane On Mon, Jan 18, 2010 at 2:28 PM, mcnee...@cox.net wrote: Again quoting from the third edition (but the admonishment has persisted) of the CBE Style Manual (page 6): Avoid the 'passive of modesty,' a favorite device of writers who shun the first person singular. The authors devote a whole paragraph to explaining why. Further down in the paragraph they state: 'I' may embarrass the writer, but it is less likely to be ambiguous. Look up the instructions to authors for the journals published by ESA or any other scholarly organization in our field, or simply consult publications in those journals to satisfy yourself on this matter. David On Mon, Jan 18, 2010 at 1:12 PM, Jane Shevtsov wrote: I've always thought the main reason for avoiding I in scientific papers was to prevent self-aggrandizement. It's not about you -- it's about the research. We may be ok, but the passive voice serves a moral/social purpose in single-authored works. Jane On Mon, Jan 18, 2010 at 11:10 AM, David L. McNeely wrote: Bill, thank you. Not to hammer a dead horse, but I wrote my dissertation in the seventies. I was encouraged to use active voice and first person. The most recent edition of the CBE Style Manual that I actually own is the third edition (copyright 1972), though I have generally had access to more recent (and massive) versions over the years since. From my third edition (page 5): Write in the active voice unless you have a good reason for writing in the passive. The active is the natural voice, the one in which people commonly speak and write, and it is less likely than the passive to lead to ambiguity. There follows a series of explanations and examples detailing why first person is generally preferable to other persons, especially in describing methods where it provides clear explanation of who did what, rather than the ambiguity of the third person passive, where one might wonder who at all did the experiments described. Thanks, David On Sun, Jan 17, 2010 at 3:29 PM, William Silvert wrote: Several subscribers have disagreed with my statement about passive/active voice, and I stand corrected. Perhaps the case was best stated by someone who wrote me off-list to say I have noticed a change in the last 4 years...I was instructed by many to use the passive voice and to shy away from the active voice which very often required the use of first person pronouns. But in the last year, a growing trend has led away from the use of passives. Just today, when haphazardly choosing 3 abstracts from the most recent issue of Science, I found all to be written in the active voice and found the first person 'we' in two of them...I think 'modern scientific writing' may indeed be evolving again. I am pleased to be shown wrong and commend the scientific community for this stylistic improvement. Bill Silvert -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, Check out my blog, Perceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] now I've seen it all
On Sun, Jan 17, 2010 at 10:43 AM, Alyson Mack alym...@gmail.com wrote: the sad truth is, our children ARE becoming more stupid every year. The fact Do you have any evidence for this claim? IQ scores have been rising pretty steadily for a century. (Look up the Flynn effect http://en.wikipedia.org/wiki/Flynn_effect.) SAT scores are the highest they've been since the 1960s, although a somewhat larger percentage of high school students are taking the test. There are always fluctuations, but are there any measures of intelligence that have been showing a consistent decline? On a different note, who here has read _The Demon-Haunted World_ or _Why People Believe Weird Things_? They're both relevant to the larger discussion of critical thinking. Jane On Fri, Jan 15, 2010 at 5:11 PM, malcolm McCallum malcolm.mccal...@herpconbio.org wrote: At what point does the scientific community realize that the current surge in patent medicines and nonsense medical devices are seriously eroding the nation's confidence in science? This is not directly related to ecology, but ecology is science and if people misuse science to sell products that are medically irrelevant it certainly must affect all science. For example, if the average person sees a supposed physician on TV parading products that absorb fat out of your body or send magnetic impulses into your joints or provide the healing effects of light, he/she does not necessarily recognize the difference between commercial claims and scientific ones. Further, if that person is suckered in to buy this sucker bait, he/she is certain to find, once any placebo affect passes, that it is shear snake oil. Consequently, these folks see these advertisements with supposed nutritionists, phds, MDs, etc. and learn not to believe what they say. Along comes a scientist claiming extraordinary changes such as climate change, ozone layer issues, problems with pollution, and endangered species...on TV, even in commercials. Why should they believe them? It looks and smells just like that snake oil aunt Martha bought off TV that did nothing but moisten her skin. Does anyone else see that a deeper problem exists here? These products are much more harmful that simply misleading people, they are more than simply false advertising, they really should not be allowed to make the extraordinary claims that they do. Some of the products are harmless, some are dangerous simply in the fact that folks choose to depend on these prior to seeking real medical advice, but all have a serious potential to erode the general public's view of the scientific community. -- Malcolm L. McCallum Associate Professor of Biology Managing Editor, Herpetological Conservation and Biology Texas AM University-Texarkana Fall Teaching Schedule: Vertebrate Biology - TR 10-11:40; General Ecology - MW 1-2:40pm; Forensic Science - W 6-9:40pm Office Hourse- TBA 1880's: There's lots of good fish in the sea W.S. Gilbert 1990's: Many fish stocks depleted due to overfishing, habitat loss, and pollution. 2000: Marine reserves, ecosystem restoration, and pollution reduction MAY help restore populations. 2022: Soylent Green is People! Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] now I've seen it all
use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -- Malcolm L. McCallum Associate Professor of Biology Managing Editor, Herpetological Conservation and Biology Texas AM University-Texarkana Fall Teaching Schedule: Vertebrate Biology - TR 10-11:40; General Ecology - MW 1-2:40pm; Forensic Science - W 6-9:40pm Office Hourse- TBA 1880's: There's lots of good fish in the sea W.S. Gilbert 1990's: Many fish stocks depleted due to overfishing, habitat loss, and pollution. 2000: Marine reserves, ecosystem restoration, and pollution reduction MAY help restore populations. 2022: Soylent Green is People! Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] now I've seen it all
a word out, always cut it out. (iv) Never use the passive where you can use the active. (v) Never use a foreign phrase, a scientific word, or a jargon word if you can think of an everyday English equivalent. (vi) Break any of these rules sooner than say anything outright barbarous. Rules 2-5 lead to precisely the kind of oversimplification of language that you worry about. I do not know what should be done about it or even if it really is a problem. (The case can be made that your reading comprehension skills should match the material you are actually likely to encounter, not more challenging material that few people write any more.) Still, it would be interesting to find out what our colleagues in English departments think of the situation. Jane On Sat, Jan 16, 2010 at 9:12 PM, malcolm McCallum malcolm.mccal...@herpconbio.org wrote: Your point is well taken, except that they did not contain the same information. The modern book is a joke next to the old one. If you are not challenged to improve your reading comprehension, your reading comprehension will not improve. If you are not challenged to improve your vocabulary, your vocabulary will not improve. And, if you are reading watered down elementary-level material, you will have an elementary-level education. Unfortunately, the 8th graders in 1908 (or close to that) could easily read and absorb that book, and most of the undergraduates who come out of our current highschool systems likely could not. He has moved away, but if I can get some jpgs of the darn thing, I'll post them. On Sat, Jan 16, 2010 at 4:19 PM, Jane Shevtsov jane@gmail.com wrote: Let me play devil's advocate on this one. Is a more difficult-to-read textbook better than an easier one that conveys the same information? My impression is that writers like George Orwell and E.B. White were largely responsible for the increased streamlining of modern prose compared to that of 100 years ago. (I am not saying that streamlined prose is necessarily better -- IMHO, Strunk and White are responsible for a great deal of mediocre writing.) BTW, what fraction of children in Texas completed the eight grade in 1908? The state did not have a compulsory education law until 1915. Jane On Sat, Jan 16, 2010 at 12:46 PM, malcolm McCallum malcolm.mccal...@herpconbio.org wrote: Its actually much worse than that. A retired friend of mine brought me a book on Human Health. It was dated around 1908. The student who read this book would require a much higher reading comprehension, larger vocabulary, and greater dedication than a student using the health book widely used for principles of health in modern college classes. The book had depth, provided specifics and generalities, and it very aptly provided positive guidance on the overview of how to live a healthy life based on the dogma of the time. Now here is the punchline, that book was mandated by the stated board of education in Texas for 8th grade. I almost fell over. I have seen some graduate level textbooks that are not as good as that 8th grade text. I suspect that this is more widepread than we might want to believe. Malcolm On Sat, Jan 16, 2010 at 10:47 AM, Abraham de Alba A. aalb...@yahoo.com wrote: Yes Mal, it is depresing to see that critical thinking is very seldom applyed even in educated persons, I myself think that it is a primary fault of our educational system. It is not until you are in your masters or even PhD that your mentor appreciates your thinking capabilities and not your knowledge. What can we expect after 20 years of indoctrination in school ? and that´s for the ones that manage to go to school. Abraham de Alba Avila Terrestrial Plant Ecology INIFAP-Ags Ap. postal 20, Pabellón Arteaga, 20660 Aguascalientes, MEXICO SKYPE: adealba55 Tel: (465) 95-801-67, 801-86 ext. 126, FAX ext 102 alternate: dealba.abra...@inifap.gob.mx cel: 449-157-7070 From: malcolm McCallum malcolm.mccal...@herpconbio.org To: ecolo...@listserv.umd..edu Sent: Fri, January 15, 2010 7:11:47 PM Subject: [ECOLOG-L] now I've seen it all At what point does the scientific community realize that the current surge in patent medicines and nonsense medical devices are seriously eroding the nation's confidence in science? This is not directly related to ecology, but ecology is science and if people misuse science to sell products that are medically irrelevant it certainly must affect all science. For example, if the average person sees a supposed physician on TV parading products that absorb fat out of your body or send magnetic impulses into your joints or provide the healing effects of light, he/she does not necessarily recognize the difference between commercial claims and scientific ones. Further, if that person is suckered in to buy this sucker bait, he/she is certain to find, once any placebo affect passes, that it is shear snake
Re: [ECOLOG-L] Ecology as Science Status and Future
Can you elaborate? While there are certainly some examples of cases where evolution is important in ecology, it seems to me that if the creationists turned out to be right, most of ecology would remain the same. If I had to pick a short basis of ecology, it would consist of two facts. 1. Organisms are open systems. 2. If resources (per Item 1) were unlimited, populations would grow exponentially. Much of ecology follows from there. Add the existence of heritable traits, and so does natural selection. Jane Shevtsov On Sun, Dec 27, 2009 at 11:11 AM, malcolm McCallum malcolm.mccal...@herpconbio.org wrote: Evolution by Natural Selection. Its the basis of ecology. It always shocks me though when people try to separate it from ecology. On Sat, Dec 26, 2009 at 5:16 PM, Wayne Tyson landr...@cox.net wrote: Honorable Ecolog Forum: There's something about the imminent end of still another year that gets me to thinking about where things are, where they have been, and where they are going. It's a time for reflection that's as good as any, but a life well-lived is in a continuous state of reflection. Ecology seems to me to be a comprehensive way of looking at biology, an attempt to include everything and to see all the connections and relationships in time and space. That's a tall order, more than any one individual can hope to fully comprehend, or even see, hear, smell, or touch, much less interpret correctly such that we can reach conclusions that more closely match reality than fantasy. The more I know about where things are the minds of others, the better I am able to extend my own vision, and challenge it. While I don't want bias your answers, I will say that I am, for the moment, more interested in learning more about your INDIVIDUAL views (not those of other authorities, textbooks or websites) in the realm of scientific/disciplined study and thinking about the present state of ecology as an intellectual activity, and not so much interested, for the moment, in applied aspects of ecology. So I would be interested in as many thoughts as anyone cares to share about his or her OWN thoughts about the important questions in the scientific study of the ecological phenomenon, and, by reflection, critical views of the current status of ecology as a form of intellectual enquiry in its present state. I am particularly interested in any views about the fundamental principles of ecology that have stood the test of time and testing and retesting, that is theories that have been demonstrated to be valid in the real world. So the answers can be anything, such as theories that have not been fully tested. For now, I am not so much interested in political and policy issues, even though these are important. Thanks for sharing your thoughts. Peace, WT PS: I will be away from the computer for two or three weeks beginning sometime next week. Happy New Year! (And thank you all for your past generosity in sharing your insights; that has greatly helped me to sort out the wheat from the chaff.) http://www.euractiv.com/en/environment/analysis-top-100-ecological-questions-identified/article-156507 http://britishecologicalsociety.org/blog/blog/2009/04/28/100-questions-to-conserve-global-biodiversity/ -- Malcolm L. McCallum Associate Professor of Biology Managing Editor, Herpetological Conservation and Biology Texas AM University-Texarkana Fall Teaching Schedule: Vertebrate Biology - TR 10-11:40; General Ecology - MW 1-2:40pm; Forensic Science - W 6-9:40pm Office Hourse- TBA 1880's: There's lots of good fish in the sea W.S. Gilbert 1990's: Many fish stocks depleted due to overfishing, habitat loss, and pollution. 2000: Marine reserves, ecosystem restoration, and pollution reduction MAY help restore populations. 2022: Soylent Green is People! Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
[ECOLOG-L] Carbon Footprint of Flying
For most of us, flying is mass transit. However, as far as I know, the amount of carbon you are responsible for when you fly is almost always calculated as C/passenger rather than as marginal effect. Does anybody know what this marginal effect actually is? Also, considering the in-person global connectivity that long flights make possible, I think we should focus our decarbonization efforts on electricity production and local transportation -- applications where C emissions aren't necessary. Oh, and we should reconsider short flights, as these are the least efficient. (A large amount of the fuel burned by an airplane is used at takeoff.) Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] applying for PhD programs
Hi Andy, I second the recommendation of the Odum School. It's a great place to study and has a very active and friendly bunch of graduate students. In particular, look up Cathy Pringle, Alan Covich and Amy Rosemond. As an undergrad, I once heard one of my professors complain about students applying to him without having read any of his papers, so when I was applying to grad school, I looked up articles by the people I was emailing and worked that fact into the initial email. Asking a question or briefly connecting your interests to their work is good. Hope that helps! Jane Shevtsov Odum School of Ecology Ph.D. Candidate On Tue, Aug 18, 2009 at 12:09 PM, Christopher Blairblair@gmail.com wrote: Hi Andy, If your interests are in community/stream ecology I would definitely check-out the Odum School of Ecology at the University of Georgia. It is an excellent, but quite competitive program, but I think you would find what you're looking for. As far as an initial email goes, it is always a good idea to briefly discuss your research interests along with any relevant experience you may have. Remember that the more experience you can get the better. It is also important to be professional in any email you send to potential supervisors. Also try not to get discouraged if finding a program takes a year or two. Hope this helps a little? Chris On Tue, Aug 18, 2009 at 2:32 PM, Andrew Oguma ayog...@sbcglobal.net wrote: I recently earned a BA biology concentration in ecology, minor in chemistry from Western CT State University, graduating magna cum laude with some academic awards. I have also been invited to speak at the North American Lake Management Society International Symposium in Hartford, CT on October 30th about my undergraduate research project. Although my research project focussed on using herbivorous weevils to control Eurasian watermilfoil in Candlewood Lake, my interest in pursuing a PhD is in stream community/ecosystem ecology especially invertebrate communities. I am looking for suggestions on professors and schools that may be suited to my interests within the United States and preferably east of the Mississippi River. I am also looking for any suggestions on what to include in an initial e-mail and in general on how to put my best foot forward, so to speak. Finally, any suggestions from those who have been in my shoes are welcome. I intend to be accepted into a program for fall of 2010. Thankyou for your time. Please feel free to contact me personally. My name is Andy Oguma and my e-mail is as follows: ayog...@sbcglobal.net -- Christopher Blair, Ph.D. Candidate Department of Ecology and Evolutionary Biology University of Toronto and Department of Natural History Royal Ontario Museum 100 Queen's Park Toronto, ON M5S 2C6 Canada (416) 333-2236 (cell) (416) 586-8094 (office) http://individual.utoronto.ca/chrisblair/index.html -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
Re: [ECOLOG-L] Listserv posting and email subject line additions Ecolog
For what it's worth, I'm also in favor of not changing subject lines until the thread has diverged significantly from the topic described in the subject line. It makes life a lot easier for the Gmail users among us! Jane On Fri, Jul 31, 2009 at 4:32 PM, Wayne Tysonlandr...@cox.net wrote: Ecolog: I received the following message from a listserv subscriber who wishes to remain anonymous: I know people have asked before and you have dismissed it, but I find your changing of seemingly every subject line annoying and presumptuous. In this case, what was gained by changing the subject line? It made referencing back the original email more difficult. . . . and in later message: PS This is a personal message and I would appreciate it not being forwarded to the whole list. Thanks, [Name withheld at sender's request]] I understand the poster's annoyance; ironically, being able to consistently track archived subjects is exactly why I often add a subject lead-line to the original or preceding message. Please note that I do not delete the original subject line; it is always retained behind the added one. The change in question: CLIMATE Global warming and ESA meetings Re: [ECOLOG-L] 2010 ESA Annual Meeting: Call for Symposium and OOS Proposals This kind of addition both preserves the original or preceding subject line and adds a subject label or sequential descriptive string that is more related to the content, thus enabling, merely by clicking on Subject in the email program, all of the material related to CLIMATE, Global warming and ESA meetings. Otherwise, one would have to remember that the subject under discussion started with 2010. If the content had to do primarily with ESA meetings, I would have added (not changed) ESA to the subject line in front of 2010. I very much appreciate David's light hand on listserv administration, leaving, as he does, the decision about subject line discipline up to the subscriber making the post. I do not object to anyone adding a lead subject line to any of my posts that more accurately reflects the primary content of the current message, nor to I object to the central focus of the discussion changing and a subsequent posting adding a more appropriate lead, while retaining the subject line of the original post(s). I hope that this answers the query, and welcome any on-list discussion of this issue before the Forum as a matter of common interest. It is my policy not to respond directly to personal emails regarding matters of interest to all or a number of listserv subscribers. I do welcome and generally respond to off-list enquires that are not of interest to the list. (When I am away on trips I often miss emails or take some time to respond; I apologize in advance for any inconvenience, and ask that if I do not respond that the email be re-sent periodically if the matter is of great importance. For urgent matters or true emergencies, there are people on this list who have my phone number who might call to inform me accordingly. I do sometimes correspond with individuals as a result of their emails when the subject matter seems to be of limited interest or too controversial for on-list discussion to be productive.) WT PS: Please feel free to add to the subject line of this post to improve its descriptive value in terms of content. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes The whole person must have both the humility to nurture the Earth and the pride to go to Mars. --Wyn Wachhorst, The Dream of Spaceflight
[ECOLOG-L] ESA Student Section Poetry Contest Call for Judges
The ESA Student Section is organizing a poetry contest for students and we are searching for judges. There are only six entries and judging can be performed by email. You don't have to be an ESA member, but experience with literary writing or poetry is, of course, valuable. Please email me if you are interested Sincerely, Jane Shevtsov -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] stealing from websites
theft only when there is an actual loss involved - money, prestige, etc. Copying a CD or DVD instead of buying it is theft, but if a CD is not available for sale, why enforce the copyright? If a grad student uses your photo in a presentation and doesn't pay you for it, what have you lost (unless the student might really be willing and able to pay for it)? I should however add that there are a lot of photos relevant to ecology that really are commercial. Aside from those taken by professionals, which are often sold to publications like National Geographic, I have discovered that very few photos of gelatinous cnidarians are available for free. I recently searched the ASLO website for photos of ctenophores and siphonophores and found almost none. A colleague explained to me that most of the photos are taken commercially and are only for sale, which is perhaps not surprising given the work involved - also of course photos are often the primary data in studies of these animals. I respect the rights of those who expect to profit from their work and who lose out when their photos or other materials are copied or stolen. But if there is no real loss involved, I am not very sympathetic, and I also think that when a copy is properly acknowledged, they benefit even if they did not give prior authorisation. Bill Silvert - Original Message - From: Jane Shevtsov jane@gmail.com To: ECOLOG-L@LISTSERV.UMD.EDU Sent: Thursday, May 14, 2009 2:11 AM Subject: Re: [ECOLOG-L] stealing from websites Jim, Please note that what follows is meant mainly as a general discussion of intellectual property, not of your particular case. Why would you think that you can use my hard work without asking? For the same reason you can cite or quote a paper of mine without asking -- even if you're using it to make a case I strongly disagree with. (That case is not directly analogous, as you wouldn't be copying the entire paper, but then if I use a photo of yours in a presentation, it'll only be on screen for 30 seconds or so.) Moreover, you can make copies of my paper and give them to students or colleagues without my permission. They can read the paper or use it to line the birdcage. If I'm sending you, say, a prepublication copy as a favor, I can ask you not to redistribute it, but once it's published, it's out of my hands. I am honestly intrigued by how people come to think of copying as stealing. If I walk into your house and steal your TV, you no longer have a TV. If I use a photo from your website and credit you, what have you lost? Now, the situation is different if you are a professional photographer and rely on photography to make money. Then the problem becomes truly difficult -- and beyond the scope of ECOLOG! (But keep in mind that hardly anyone is going to pay for a photo for a presentation. If it's not free, I'm just not going to use it.) Don't worry -- I'm not actually going to use anything from your website. You can set whatever conditions you want and, morally and legally, I have to abide by them. But this line of discussion is closely related to that about access to the scientific literature. BTW, why do you set such restrictive conditions on who can use your photos? Best, Jane -- -- David M. Lawrence | Home: (804) 559-9786 7471 Brook Way Court | Fax: (804) 559-9787 Mechanicsville, VA 23111 | Email: d...@fuzzo.com USA | http: http://fuzzo.com -- We have met the enemy and he is us. -- Pogo No trespassing 4/17 of a haiku -- Richard Brautigan -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] Open Access and Intellectual Imperialism
The assumption here, of course, is that the person downloading something free would have paid for it if the free version was not available. In some cases, particularly with inexpensive items, this is actually true; much of the time, it's not. For example, if I'm looking for photos to illustrate a lecture, find yours and discover I have to pay for it, I'm moving on. (Does ANYBODY here pay for pictures they use in lectures?) We're certainly not going to resolve these issues here and now. However, simply realizing how complicated they are is huge progress. Jane Shevtsov On Fri, May 15, 2009 at 11:07 AM, David M. Lawrence d...@fuzzo.com wrote: It is apparently easy for scientists who don't derive a salary from sales of their creative works to dismiss the concerns of those who do derive their salary from such sales. If you make an unauthorized download of my work for free, the work may still be available on whatever Web site -- probably unauthorized itself -- for others to likewise download. What is missing is INCOME THAT I SHOULD HAVE RECEIVED from a legitimate sale of that item. That is still theft, no different from snatching cigars from a store, and no amount of rationalization will change that. If you want to give away your money, feel free to do so. But I demand you respect my right to decide when or when not to give away mine. Dave Alexey Voinov wrote: There is a huge difference between downloading an image or paper from a web site and stealing a box of cigars from a shop. 1. Cigars are in a shop and for sale. There is a price tag and a clear procedure for purchasing them. 2. More important, as Jane already noted: When you take that box of cigars from the shop, they are no longer there. You took them and they are gone for anybody else to use. With files it does not matter how many downloads occurred - the files are still there nice and intact for others to use. Information does not get destroyed when it's used. That's the beauty of information. -- -- David M. Lawrence | Home: (804) 559-9786 7471 Brook Way Court | Fax: (804) 559-9787 Mechanicsville, VA 23111 | Email: d...@fuzzo.com USA | http: http://fuzzo.com -- We have met the enemy and he is us. -- Pogo No trespassing 4/17 of a haiku -- Richard Brautigan -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] Copyrighted Image Use
Hi all, Not surprisingly, there are many different opinions as to how we're comfortable having people use our work. I'd encourage folks to explore Creative Commons. You check a few boxes and they'll give you a customized, readable copyright agreement. For example, my website World Beyond Borders uses an Attribution - Noncommercial - Share Alike Creative Commons license. Jane Shevtsov On Wed, May 13, 2009 at 8:12 PM, Thiago Silva thi...@uvic.ca wrote: Hi Tom, I work very hard at my photography as well, but being a fellow scientist I wouldn't mind usage with attribution as long as it is for educational purposes and not-for-profit. Of course, being asked prior to use would just make me much happier. However, as you can see, each photographer has it's own line drawn on the matter, so asking for permission is always the best alternative. Cheers, Thiago Sanna Freire Silva PhD Candidate - Department of Geography University of Victoria MSc. Remote Sensing BSc.(Hons) Biology htp://thiagosilva.wordpress.com SPECTRAL LAB - http://www.geog.uvic.ca/dept2/SPECT/index.html thi...@uvic.ca On 13-May-09, at 2:22 PM, Jim Boone wrote: Tom, I work very hard at my photography, and if you stole a photo from my website to use in your presentation, I'd be pissed. Cheers, Jim http://www.birdandhike.com -Original Message- From: Tom Mosca III t...@vims.edu To: ECOLOG-L@LISTSERV.UMD.EDU Sent: Wed, 13 May 2009 5:47 am Subject: Re: [ECOLOG-L] Open Access and Intellectual Imperialism Correction Hello Folks, What are your thoughts on using a copyrighted image in a presentation at a meeting? No copies are distributed, but merely displayed. Thanks, Tom -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] Open Access and Intellectual Imperialism Correction
Jim, How do you define stealing? Is it only if the photo is not attributed to you? If the photo is attributed but used without your explicit permission, would you call that stealing? I'm just interested in how different people think about these issues. Best, Jane Shevtsov On Wed, May 13, 2009 at 5:22 PM, Jim Boone jlbo...@aol.com wrote: Tom, I work very hard at my photography, and if you stole a photo from my website to use in your presentation, I'd be pissed. Cheers, Jim http://www.birdandhike.com -Original Message- From: Tom Mosca III t...@vims.edu To: ECOLOG-L@LISTSERV.UMD.EDU Sent: Wed, 13 May 2009 5:47 am Subject: Re: [ECOLOG-L] Open Access and Intellectual Imperialism Correction Hello Folks, What are your thoughts on using a copyrighted image in a presentation at a meeting? No copies are distributed, but merely displayed. Thanks, Tom -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] stealing from websites
Jim, Please note that what follows is meant mainly as a general discussion of intellectual property, not of your particular case. Why would you think that you can use my hard work without asking? For the same reason you can cite or quote a paper of mine without asking -- even if you're using it to make a case I strongly disagree with. (That case is not directly analogous, as you wouldn't be copying the entire paper, but then if I use a photo of yours in a presentation, it'll only be on screen for 30 seconds or so.) Moreover, you can make copies of my paper and give them to students or colleagues without my permission. They can read the paper or use it to line the birdcage. If I'm sending you, say, a prepublication copy as a favor, I can ask you not to redistribute it, but once it's published, it's out of my hands. I am honestly intrigued by how people come to think of copying as stealing. If I walk into your house and steal your TV, you no longer have a TV. If I use a photo from your website and credit you, what have you lost? Now, the situation is different if you are a professional photographer and rely on photography to make money. Then the problem becomes truly difficult -- and beyond the scope of ECOLOG! (But keep in mind that hardly anyone is going to pay for a photo for a presentation. If it's not free, I'm just not going to use it.) Don't worry -- I'm not actually going to use anything from your website. You can set whatever conditions you want and, morally and legally, I have to abide by them. But this line of discussion is closely related to that about access to the scientific literature. BTW, why do you set such restrictive conditions on who can use your photos? Best, Jane On Wed, May 13, 2009 at 8:35 PM, Jim Boone jlbo...@aol.com wrote: Jane, If the photo is attributed but used without your explicit permission, would you call that stealing? In general, yes; but of course, it depends. I have a conditions for use statement on my website that spells out how people can use my hard work. Turning the question back to you, why would you think that you can use my hard work without asking? Cheers, Jim http://www.birdandhike.com -Original Message- From: Jane Shevtsov jane@gmail.com To: Jim Boone jlbo...@aol.com Cc: ECOLOG-L@listserv.umd.edu Sent: Wed, 13 May 2009 3:06 pm Subject: Re: [ECOLOG-L] Open Access and Intellectual Imperialism Correction Jim, How do you define stealing? Is it only if the photo is not attributed to you? If the photo is attributed but used without your explicit permissi on, would you call that stealing? I'm just interested in how different people think about these issues. Best, Jane Shevtsov On Wed, May 13, 2009 at 5:22 PM, Jim Boone jlbo...@aol.com wrote: Tom, I work very hard at my photography, and if you stole a photo from my website to use in your presentation, I'd be pissed. Cheers, Jim http://www.birdandhike.com -Original Message- From: Tom Mosca III t...@vims.edu To: ECOLOG-L@LISTSERV.UMD.EDU Sent: Wed, 13 May 2009 5:47 am Subject: Re: [ECOLOG-L] Open Access and Intellectual Imperialism Correction Hello Folks, What are your thoughts on using a copyrighted image in a presentation at a meeting? No copies are distributed, but merely displayed. Thanks, Tom -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_ Dell Mini Netbooks: Great deals starting at $299 after instant savings! -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] Open Access and Intellectual Imperialism
The physical sciences seem to be halfway there with arXiv.org . Jane On Tue, May 12, 2009 at 3:22 PM, joseph gathman jpgath...@yahoo.com wrote: Jane wrote: The journal's contribution is coordinating peer review, formatting the paper and, most importantly, disseminating the paper. It seems we are approaching the time when journals become obsolete for these functions. We could do all this through the internet right now. Imagine just posting your paper here on ECOLOG-L, where anybody can review it and comment publicly. It would make for more dynamic review and discussion of research. So now it seems the main function of journals is to make the publication official so it will count toward retention and tenure and other professional tally counting. Joe Gathman Assistant Professor University of Wisconsin - River Falls It's called the American dream because you have to be asleep to believe it. -George Carlin Date: Mon, 11 May 2009 14:26:26 -0400 From: Jane Shevtsov jane@gmail.com Subject: Re: Open Access and Intellectual Imperialism Approval required Strictly speaking, you're correct. However, the purpose of copyright law is to reward people who do creative work. That would be us. The journal's contribution is coordinating peer review, formatting the paper and, most importantly, disseminating the paper. For this, they get paid by subscribers and sometimes page charges. That seems more than fair -- really, the for-profit journals should be paying us, the way magazines pay writers. -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] Open Access and Intellectual Imperialism Approval required
Strictly speaking, you're correct. However, the purpose of copyright law is to reward people who do creative work. That would be us. The journal's contribution is coordinating peer review, formatting the paper and, most importantly, disseminating the paper. For this, they get paid by subscribers and sometimes page charges. That seems more than fair -- really, the for-profit journals should be paying us, the way magazines pay writers. Allowing them to dictate what we can do with our work after publication seems rather excessive! As a practical matter, are there any cases of scientists being sued or prosecuted for posting their publications on their websites? Anyone interested in these issues should read Lawrence Lessig and John Perry Barlow, particularly the latter's essay The Economy of Ideas: Selling Wine Without Bottles on the Global Net. Jane Shevtsov On Mon, May 11, 2009 at 1:24 PM, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Sun, 2009-05-10 at 11:14 -0400, Alexey Voinov wrote: Instead of or in addition to boycotting and protesting, I think there is a much simpler and effective solution. Ask your kids. If they can share their music, why can't we share our papers? It's called peer-to-peer technology and requires just a little bit of good will from ourselves. All we need is to assemble our collections of pdf articles that I bet each and everyone of us has on our hard disks, and make them available for sharing. Students are already doing this. See this article: http://eaves.ca/2009/04/28/education-where-copyrighters-and-publishers-are-the-pirates/ Unfortunately these efforts seem to be sharing the fate of Napster, attacked by lawsuits. However this can and will still develop without any centralized services on a peer-to-peer basis as supported by bit-torrent and other software. So it's really up to us to make it happen. Only if you condone copyright theft. Invariably, journals do not grant you a non-exclusive right to do anything with your own publications that you might have in PDF format. Sometimes they allow you to post to a website your final version before journal formatting. Sometimes a journal may allow you to do this only after a certain period of time, or they may allow you to post their version of the manuscript on your (or your institutes's) website after a period of time (6-12months say). It all depends upon what rights you signed away when you completed your copyright transfer form. Reproducing or distributing any publications that are not your own, that are not covered by a licence that allows you to do this, provided to you by the publisher of said content, would also constitute copyright theft. Circumventing these restrictions, could, in some countries, be considered violation of copyright laws. Doing this with software in the US for example cold make you fall foul of the DMCA: http://en.wikipedia.org/wiki/DMCA Whilst I'm no fan of the current predominant publication model, nor many of the associated citation indices, rampant disregard for copyright law is *not* the way to solve these problems. You should exercise your right to do with your work (i.e. your final draft, not a journal compilation/formatting of your work) as you see fit, and publish it in journals that have more open policies regarding works published by them. Or try to retain some of the rights you wish for, for example by attaching a Creative Commons Scholars Copyright Addendum to the publisher's copyright transfer forms, in an attempt to negotiate retaining some rights: http://sciencecommons.org/projects/publishing/ So it's really up to us to make it happen. So, I agree with the sentiment, but not with the means by which you suggest we go about it. G -- Alexey Voinov _ !!! please note new e-mail address: aavoi...@gmail.com !!! _ Chesapeake Research Consortium Community Modeling Program Johns Hopkins University Dept. of Geography and Environm. Engineering 645 Contees Wharf Road, P.O. Box 28, Edgewater, MD 21037 TEL: 410 798-1283; 703 880-1178 WWW: http://www.likbez.com/AV Fellow, Gund Institute for Ecological Economics,University of Vermont President,Int.Envir.Modeling. and Software Soc.,http://www.iemss.org/ New book: Systems Science and Modeling for Ecological Economics http://books.elsevier.com/companions/9780123725837 -- Date: Sat, 9 May 2009 16:56:12 -0700 From: Wayne Tyson landr...@cox.net Subject: Re: Open Access and Intellectual Imperialism Approval required Re: [ECOLOG-L] Teaching Biostatistics !!! (Suggested replacement post) Ecolog: In my university I do not have access to literature sources like = Biological Abstracts for example to reach the authors and articles
Re: [ECOLOG-L] PEER TO PEER PDF SHARING
Peer-to-peer is great for sharing large files, like music or videos, but for most PDFs I think it has little advantage over simply putting the files on your website. Downloading peer-to-peer requires special software; downloading from a website does not. Also, search is easier if the paper is on the web. Jane Shevtsov On Mon, May 11, 2009 at 11:56 AM, Sarah Frias-Torres sfrias_tor...@hotmail.com wrote: Dear EcologsFollowing on Alexey Voinov's suggestion of sharing our pdf papers like kids today share music, but at the same time, avoiding any copyright mess (i.e. peer-review journals where you published your papers), I would like to remind all that copyright laws allow reproduction of copyrighted material (in paper or electronic form), when the purpose is TEACHING, SCHOLARSHIP or RESEARCH. As long as you indicate that this is the purpose for your pdf sharing, you are within what is allowed by copyright laws. For the benefit of the Ecolog community, below is a short copyright use text. If you choose to do peer-to-peer pdf sharing of your papers, attaching your pdfs to your web sites, or providing upon request, providing also this copyright text might be useful I'm no lawyer, just a research scientist trying to open up communication with other scientists and the general public also interested in science. ***COPYRIGHT WARNING Under the Copyright Law of the United States of America and Related Laws Contained in Title 17 of the United States Code, applicable also to non-U.S. copyrights based on the Berne Convention, of which the U.S.A. became a member on March 1, 1989: No part of any copyrighted material may be reproduced or transmitted in any form or in any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. However, Limitations on exclusive rights, as established by Section 107 (“fair use”) of the Law, indicate that: the fair use of a copyrighted work, including such use by reproduction in copies or phonorecords or by any other means specified by that section, for purposes such as criticism, comment, news reporting, teaching (including multiple copies for classroom use), scholarship, or research, is not an infringement of copyright. The electronic copies provided here are based on the “fair use” limitation of the U.S. Copyright Law, and we are not to be held responsible of those recipients who wrongly choose to use such materials for purposes other than the “fair use” as described above.*** Sarah Frias-Torres, Ph.D. Marine Conservation Biologist Ocean Research Conservation Association 1420 Seaway Drive, 2nd Floor Fort Pierce, Florida 34949 USA www.TEAMORCA.org Date: Sun, 10 May 2009 11:14:46 -0400 From: aavoi...@gmail.com Subject: [ECOLOG-L] Open Access and Intellectual Imperialism Approval required To: ECOLOG-L@LISTSERV.UMD.EDU Instead of or in addition to boycotting and protesting, I think there is a much simpler and effective solution. Ask your kids. If they can share their music, why can't we share our papers? It's called peer-to-peer technology and requires just a little bit of good will from ourselves. All we need is to assemble our collections of pdf articles that I bet each and everyone of us has on our hard disks, and make them available for sharing. Students are already doing this. See this article: http://eaves.ca/2009/04/28/education-where-copyrighters-and-publishers-are-the-pirates/ Unfortunately these efforts seem to be sharing the fate of Napster, attacked by lawsuits. However this can and will still develop without any centralized services on a peer-to-peer basis as supported by bit-torrent and other software. So it's really up to us to make it happen. -- Alexey Voinov _ !!! please note new e-mail address: aavoi...@gmail.com !!! _ Chesapeake Research Consortium Community Modeling Program Johns Hopkins University Dept. of Geography and Environm. Engineering 645 Contees Wharf Road, P.O. Box 28, Edgewater, MD 21037 TEL: 410 798-1283; 703 880-1178 WWW: http://www.likbez.com/AV Fellow, Gund Institute for Ecological Economics,University of Vermont President,Int.Envir.Modeling. and Software Soc.,http://www.iemss.org/ New book: Systems Science and Modeling for Ecological Economics http://books.elsevier.com/companions/9780123725837 -- Date: Sat, 9 May 2009 16:56:12 -0700 From: Wayne Tyson landr...@cox.net Subject: Re: Open Access and Intellectual Imperialism Approval required Re: [ECOLOG-L] Teaching Biostatistics !!! (Suggested replacement post) Ecolog: In my university I do not have access to literature sources like = Biological
Re: [ECOLOG-L] Open Access and Intellectual Imperialism Approval required Re: [ECOLOG-L] Teaching Biostatistics !!!
It is sometimes not practical to publish in open access journals, because of cost or other reasons. (I wish PLoS would say exactly under what circumstances they waive publication charges.) But most of us have web pages. Once you have a PDF of your article, put it on your web page! Thanks to Google, anybody will be able to find it. Jane Shevtsov On Sat, May 9, 2009 at 7:56 PM, Wayne Tyson landr...@cox.net wrote: (Suggested replacement post) Ecolog: In my university I do not have access to literature sources like Biological Abstracts for example to reach the authors and articles . . . This is an excellent example, unfortunately, of how pricing intellectual resources out of range for outsiders is a moral indictment of much of academia. This man--or any man or woman or child (especially) should never have to hit a university firewall, be required to pay tens of dollars ($30, $40, and more) to download a pdf file, ad nauseam. Think of the burdensome expense and effort required on the part of so many even to gain the privilege of Internet access in the first place! Those truly concerned about the future of the earth and its life, even civilization, should realize that the history of intellectual development is one of free exchange of ideas and information, not its conversion into profit centers. It is not the struggling who should pay the comfortable, it is the comfortable who benefit from free intellectual synergy that compounds like a breeder-reactor, who should pay forward and backwards to ensure rather than obstruct such exchange. At long last, hath academia no sense of decency? Are there no institutions out there sufficiently well endowed and clearly beneficiaries of the wealth of intellectual struggle handed down from people like Dr. Voltolini throughout history (and still do--Copernicus, Darwin . . .) who will turn this embarrassing state of arrogant possessiveness around? Can you imagine having to make this kind of request at every stage of your own process of intellectual enquiry? How is it possible that, this many years into one of the most transformational achievements of human society, that Dr. Voltolini should still be barred from journal access that costs zero to provide? Why not, at the individual level, that academics simply boycott journals which charge for access and publish in open access journals? While these may not be perfect at the moment, might not such a second-stage transformation accelerate their development and foster rather than retard intellectual synergy? WT PS: David has suggested that I explain how journals (e.g. those of the Ecological Society) are supposed to pay to publish papers if nobody has to pay to read them. This email is intended to illuminate the problem and hear from others before deigning to suggest how all of the complexities of this issue should be resolved. The first step, of course, is in recognizing the problem or refuting the assertion that there is a problem. I do not pretend, in as brief an email as possible and still state my position unequivocally, to cover every aspect of the subject. I do, however, know of institutions that have cancelled journal subscriptions. I believe that very large institutions (e.g. the University of California Library may have negotiated price reductions from some journals; I am not up-to-date on this case, but the UC Library did raise the issue quite vigorously a few years ago. I will offer the following observations, and invite correction if they are in error. I hope this helps 1. The major clay paper journals are VERY profitable. 2. Publishing in such journals is a political balancing act, not to mention that author charges are often involved. (I am not against reasonable author charges if they do not inhibit publication on the basis of merit and are collected on the basis of the ability to pay by, and the benefit to, sponsoring institutions.) 3. It is impossibly expensive for independent researchers or those whose affiliations do not subscribe to Internet journal service to scan great volumes of literature. Abstracts are wholly inadequate for literature review. 4. I recognize that publication costs must be met, but scientific/scholarly/intellectual publications should be financed by the nobility, not enrich them. Peer reviews should be the obligation of the reviewers to the discipline involved. 5. I suggested a boycott, but only intend that measure for those entities looking at pdf downloads (for example) as ways to embellish their bottom-lines, particularly when they gouge for them (charge out of proportion to their actual marginal cost). Since intellectual articles are in relatively scant demand, they are not likely to be priced according to pricing theory anyway, so the benefiting institutions should pay the actual costs--plus a margin for a cushion-endowment perhaps
Re: [ECOLOG-L] looking for a freshman seminar book
I just read Paul Colinvaux's _Amazon Expeditions_ and it's excellent. Jane Shevtsov On Fri, Apr 24, 2009 at 3:31 PM, Bomar, Charles bom...@uwstout.edu wrote: So we are looking for a good read for next falls honors colloquium-something that deals with the discovery process in science. May people on campus have suggested the double-helix which would be fine, but I was hoping for something more recent to engage students on more recent discoveries in science and technology . While I know there is no perfect read, your suggestions will be greatly appreciated Charles R. Bomar PhD Applied Science Program Director Executive Director, Orthopterists' Society Professor of Biology University of Wisconsin-Stout Menomonie, WI 54751 bom...@uwstout.edu mailto:bom...@uwstout.edu office 715-232-2562 fax 715-232-2192 -- - Jane Shevtsov Ecology Ph.D. candidate, University of Georgia co-founder, www.worldbeyondborders.org Check out my blog, http://perceivingwholes.blogspot.comPerceiving Wholes Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
[ECOLOG-L] Ph.D. With/Without Master's
I'm a Ph.D. candidate who entered the University of Georgia Odum School of Ecology (formerly the Institute of Ecology) without a Master's, as did a large number of my fellow students. Actually, I considered getting a Master's first, mainly as a way of working in a larger number of fields, but several professors who mentored me as an undergrad advised against it. One said, very simply, If you're sure you want to get a Ph.D., do it. If you're not sure, do a Master's. (Also, there's more money available to support Ph.D. students.) And I would pit the rigor of my research program, consisting of field work in gradient analysis and two theoretical/modeling studies of food webs, against anyone's. From my own experience and that of many of my friends, who went both routes, I can say that it's the most highly qualified undergraduates who are advised to go straight for a Ph.D. This is not to say that those who get a Master's first END UP less qualified -- they may have to do less coursework at the Ph.D. level, but in the end, we all have to do the same work. Of course, many Ph.D. students do a Master's first out of tradition, university requirement, uncertainty about their desired career path, or because they're switching fields. Hopefully, this will correct some misconceptions. Jane Shevtsov On Fri, Mar 13, 2009 at 1:45 PM, Pete Rissler peter_riss...@rissler.reno.nv.us wrote: What concerns me more then EdD vs PhD is getting a PhD without fist getting a Master's degree. Whenever I see an applicant with a PhD and no Master's, I view their PhD as either a glorified Master's or a watered down PhD. I know there are advantages for doing this for both the school and students but call me old school I think a PhD should be earned without any short cuts. Pete -Original Message- From: Ecological Society of America: grants, jobs, news [mailto:ecolo...@listserv.umd.edu] On Behalf Of Mitch Cruzan Sent: Friday, March 13, 2009 8:58 AM To: ECOLOG-L@LISTSERV.UMD.EDU Subject: Re: [ECOLOG-L] EdD vs PhD Whether it sits right with you or not, it is true. Not everybody has the same intellectual ability, the same as we are not all able to be Olympic athletes no matter how hard we work. Otherwise, universities would not require high scores on entrance exams for undergraduate study, and we would not require our applicants to our PhD programs to perform well on GREs. This is not elitism, it is just a consequence of genetic variation in human populations. -- - Jane Shevtsov Ecology Ph.D. student, University of Georgia co-founder, a href=http://www.worldbeyondborders.org;World Beyond Borders/a Check out my blog, a href=http://perceivingwholes.blogspot.com;Perceiving Wholes/a Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
Re: [ECOLOG-L] CLIMATE CHANGE Anthropogenic ignition? Re: [ECOLOG-L] Thank you for responding to the survey!
approach also strongly discriminates against those living in poorer, more rural areas, singling out the activities that support the economies in those areas as the major problem, as opposed to the much more destructive activities of people who live in urban areas, particularly modern urban areas. It's obvuiously more politically prudent to attack the weak. There is an issue with global warming, but it is relatively minor, as far as we know at this point in time, and it appears to be just another way of deflecting the real issue, habitat conversion. Allowing people in large modern cities to feel good about themselves re environmental issues while continuing on with the most destructive of lifestyles. I recall reading many months ago about Leonardo DeCaprio wanting to buy a tropical island and build an eco friendly resort being presented as evidence of some sort of environmentally responsible act. Ridiculous, of course, but one of the best examples of the sort or poor thinking that drives a lot of the pop culture based environmental movement. Rob Hamilton So easy it seemed once found, which yet unfound most would have thought impossible John Milton Robert G. Hamilton Department of Biological Sciences Mississippi College P.O. Box 4045 200 South Capitol Street Clinton, MS 39058 Phone: (601) 925-3872 FAX (601) 925-3978 No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.0.237 / Virus Database: 270.11.6/1981 - Release Date: 03/03/09 07:25:00 No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.0.237 / Virus Database: 270.11.7/1983 - Release Date: 03/04/09 07:41:00 -- - Jane Shevtsov Ecology Ph.D. student, University of Georgia co-founder, a href=http://www.worldbeyondborders.org;World Beyond Borders/a Check out my blog, a href=http://perceivingwholes.blogspot.com;Perceiving Wholes/a Political power comes out of the look in people's eyes. --Kim Stanley Robinson, _Blue Mars_
