From: everything-list@googlegroups.com [mailto:everything-list@googlegroups.com] Sent: Sunday, April 05, 2015 7:58 PM To: everything-list@googlegroups.com Subject: Re: DNA Wormholes can cause cancer (what!?) Chris, Hi. It is kind of an interesting job in that I can keep up with the latest stuff and I do find the idea of organizing scientific information very interesting. But, it can be a little boring sometimes, too. But, I guess most people would say that about their jobs, though. Epigenetics is pretty neat. When the histones are methylated/demethylated and acetylated/deacetylated by various enzymes, this can cause the DNA wrapped around them to become less or more compact, which affects how the genes in that area are expressed. You're sure right about their finding more levels of operation than ever before. Since they developed what they call "next generation sequencing" about 2005 or so, they've been able to find out a lot more levels in all areas. One thing that's kind of neat is that the supposedly junk DNA between genes can encode small RNAs that regulate the expression of the genes. These "microRNAs" are really a hot area of research now. Another big breakthrough was the combination of various techniques to make very large scale analysis of proteins (proteomics) possible. So, they're combining gene expression, protein studies, epigenetics, etc. to see how it all fits together in the body. They call that systems biology, and it's bringing more progress. But, there are so many interacting molecules inside a single cel, they've got a long way to go. Life seems to use whatever pathways (and combinations of pathways) it can leverage in order to transmit – over many layered systems of encoding (even within DNA itself) – the complex and dynamically responsive best response. I suspect the multi-layered dimension of heredity provides it with greater meta-stability than a system, exclusively reposited (comp term for the act of being stored within a repository) within a single mechanism. Have you heard about the computer model they ran in which they used the pretty well known well sampled current diversity of life on the planet in combination with the also pretty well known rates of mutation for life on earth and using these rates (and admittedly extrapolating backward in time based on the application of these rates of mutation) they ran the model backwards to discover the singularity… the moment of genesis so to speak of life. The answer they got was entirely unexpected. Based on all the parameters for their model, which were well checked – e.g. current planetary genetic diversity, recursively getting applied to a rewinding function based on known rates of mutation. – the genesis of earth life, according to this model is some eight billion years ago – that being four billion years before our star first formed in its birth cloud. Raises some interesting speculation as to the origins of life. Maybe life really is seeded everywhere in those great stellar nurseries and every newborn star (+whirling accretion disk that is not swept away by the energetic wave front powered by the star as it lights up) is seeded with icy cometary spores, bearing microbial life Often people think of microbes as miniscule blobs, which of course they also are, but the levels and depth of levels of complexity operating within, even a single microbe are stunning and hard to grasp and understand all together. I really like the systems approach that the wave front of research seems to be focusing on. Reductivism is fine, and has yielded impressive results in some areas, but somethings are best understood from the dynamic whole-systems viewpoint. Even just a single organelle in a cell is amazing molecular machinery… take a ribosome for example… or the complex lipid interface of the cell wall. The level of nanoscale sophistication in a single microbe is impressive. By far most evolution happened before multicellular creatures evolved. All multicellular life is the result of a symbiosis of earlier life forms (some like the mitochondria seeming like symbionts that took up cellular residence, a long time ago, preserving their own DNA). But even just a single ribosome is a molecular factory of incredible complexity, where the protein folding magic goes on. A ribosome is around 40% RNA by weight and has all kinds of different RNA variants doing many different things, interacting with animo acids, assembling proteins, QA-ing them and destroying faulty product… a very sophisticated muli-step process. It would not surprise me in the least if they discover that ribosomes themselves have some kind of run-time RNA based OS – a kind of frontline processing unit right there in the protein assembly plant. Cells also have very fine scale highly branched networks within their own cellular inner-verse; these function like super-highway networks, leading to arterial roads and then smaller feeder roads. Cells could not function if they functioned based on simple diffusion; stuff is being moved around inside a cell all the time along these internal networks. When viewed like this cells can be seen as being like huge metropolitan regions… within just a single cell there are so many layers upon layers of inter-acting dynamic networked systems, with feedback channels operating everywhere – from the DNA to the assembly that goes on within the nucleus of the messenger RNA, continuing inside the ribosomes, that also seem to have certain feedback systems going on at that molecular scope. The foundation of all multi-cellular life is this amazingly sophisticated building block; in the hypothesis of pangenesis within interstellar gas cloud stellar nurseries, comets play a central role. It is assumed that these vast regions contain countless slowly circulating chunks of primordial ices and all the cooked up complex organics that have been stewed of the billions of years. All star systems, including our own sun, periodically traverse through these clouds, as they bob up and down on their slow dance around the milky way. As a star traverse a massive stellar nursery its accompanying outer shell of comets becomes gravitationally disturbed knocking some of them onto a trajectory that produces a comet impact event on a life bearing planet. If the comet is big enough quite a bit of material will be ejected with some of that material escaping from the star system to seed the cloud. Prevailing opinion is that microbial life could survive, in a dormant state for quite some time in the deep freeze matrix of some car or house sized chunk of rock it had been in that was blasted out from its home planet. The wandering piece of rock could find a new home on a baby planet circling a newborn star…. Maybe our star was such a star, seeded with life at birth… or perhaps later on one of its many passages through these giant interstellar nurseries. The emergence of intelligence and especially self-aware intelligence, that comprehends it is acting in a world with other actors, and can see itself, as other actors see it (e.g. as we do through the conjurers trick of sympathetic neurons) this area as well is also one where reductivism kind of misses the picture precisely because of its highly focused perspective. Getting kind of late on the west coast… sorry for all the rambling on about the pangenesis hypothesis, which I view as being plausible. Yeah Monday hehe, oh well. Cheers, Chris I'll check out the link you provided on bacterial heredity right after this post. These microbiome (microbes in intestinal tract, mouth, skin, etc.) studies are pretty neat, too. One neat thing the next-gen. sequencing has allowed is that they can now get a big glob of all different kinds of microbes from a site (intestine, environment), sequence it all and map the resulting reads to known genomes to find out what microbes are present at that site. Sorry to write so much. Biochemistry is one area I know a little about (real little!) as opposed to metaphysics. I wish tomorrow weren't Monday. Have a good week! Roger On Sunday, April 5, 2015 at 1:11:14 PM UTC-4, cdemorsella wrote: From: everyth...@googlegroups.com <javascript:> [mailto:everyth...@googlegroups.com <javascript:> ] Chris, Roger – what an interesting job, if you like reading this kind of stuff that is J I knew about DNA being wound around a supporting matrix – e.g. the histones – but I never knew that this non-DNA structural protein had any interactions with the DNA Wrapped around it) that could control expressing sections of encoding DNA. Of course this implies that the histone does more than just provide a structural matrix for the DNA to become tightly packed in, and that was news to me. I have been following epigenetic stuff for a while, especially well documented for the methylation pathway, but this appears to be yet a separate pathway for genomic expression and hereditary transmission of information. The story of heredity is getting more and more interesting. For example, check out the link to the story below; life (and living systems) seem like they have more levels of operation than previously believed. Mothers can pass traits to offspring through bacteria's DNA, mouse study shows <http://www.sciencedaily.com/releases/2015/02/150216125425.htm> http://www.sciencedaily.com/releases/2015/02/150216125425.htm Cheers, Chris Hi. It's good that they have new studies confirming this stuff, but the looping of DNA into 3D structures inside the nucleus has been known for awhile. I think they're even starting to map these interactions just like the human genome project. One of the methods they use is to crosslink the DNA in the nucleus so that the shape it's currently in is saved, and then sequence the crosslinked areas to identify the crosslinked segments of DNA. But, I admit calling this a wormhole is kind of just good marketing. I guess the everything list is kind of like a wormhole that brings together distant people so they can talk about "everything"! :-) Also, on the epigenetic inheritance thing via histones, it's also good that new studies are proving this stuff, but epigenetic changes (changes in gene expression caused by things other than changes to the DNA sequence) that can be inherited have also been known for 10 years or so. So far, what they know are that these changes are caused by adding or removing methyl groups to the DNA bases or methyl and acetyl groups to the histones. That affects how the genes are expressed. These changes can be affected by the environment and your own activities (like exercise). So, your descendants may thank you for exercising and eating right! The only reason I know some stuff about this is that I have kind of a weird job where I read biochem. articles all day and put the new stuff into a database. See you! Roger On Saturday, April 4, 2015 at 3:08:19 PM UTC-4, cdemorsella wrote: -----Original Message----- From: everyth...@googlegroups.com [mailto:everyth...@googlegroups.com] On Behalf Of Russell Standish Sent: Thursday, February 26, 2015 1:44 PM To: 'Chris de Morsella' via Everything List Subject: Re: DNA Wormholes can cause cancer (what!?) Of course, this is what Australia's John Mattick has been saying for decades (I heard him talk on this nearly 15 years ago, for instance, and he'd been railing at the establishment sometime before that). >> But "wormholes"? Really? Someone in marketing has been given far too liberal >> a rein. They're always on the hunt for that catchy title aren't they; I find them amusing :) Still, in seriousness, it's an interesting idea: that previously overlooked, non-local effects, naturally operating within an organisms DNA may be playing a more fundamental role in life than previously believed (or even considered to be occurring at all) Chris Cheers On Thu, Feb 26, 2015 at 05:26:16PM +0000, 'Chris de Morsella' via Everything List wrote: > [Have been very busy on a new software project and have not had time > to follow and participate on this list... such an active list :). ] > Came across this article and found it interesting also from an > information science point of view -- taking the perspective of DNA > being a fairly dynamic information repository. It seems like the > butterfly effect is operating in DNA... a small difference one place > can result in effects being triggered in very distant DNA locations... > or as the researchers said... kind of like a wormhole.-Chris > > Cancer risk linked to DNA ‘wormholes’ > > February 25, 2015 > Single-letter genetic variations within parts of the genome once dismissed as > “junk DNA” can increase cancer risk through remote effects on far-off genes, > new research by scientists at The Institute of Cancer Research, London > shows.The researchers found that DNA sequences within “gene deserts” — so > called because they are completely devoid of genes — can regulate gene > activity elsewhere by forming DNA loops across relatively large distances.The > study helps solve a mystery about how genetic variations in parts of the > genome that don’t appear to be doing very much can increase cancer risk.Their > study, published in Nature Communications, also has implications for the > study of other complex genetic diseases.The researchers developed a technique > called Capture Hi-C to investigate long-range physical interactions between > stretches of DNA – allowing them to look at how specific areas of chromosomes > interact physically in more detail.The researchers assessed 14 regions of DNA > that contain single-letter variations previously linked to bowel cancer risk. > They detected significant long-range interactions for all 14 regions, > confirming their role in gene regulation.“Our new technique shows that > genetic variations are able to increase cancer risk through long-range > looping interactions with cancer-causing genes elsewhere in the genome,” > study leader Professor Richard Houlston, Professor of Molecular and > Population Genetics at The Institute of Cancer Research, London said.“It is > sometimes described as analogous to a wormhole, where distortions in space > and time could in theory bring together distant parts of the universe.”The > research was funded by the EU, Cancer Research UK, Leukaemia & Lymphoma > Research, and The Institute of Cancer Research (ICR). > > -- > You received this message because you are subscribed to the Google Groups > "Everything List" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to everything-li...@googlegroups.com. > To post to this group, send email to everyth...@googlegroups.com. > Visit this group at http://groups.google.com/group/everything-list. > For more options, visit https://groups.google.com/d/optout. -- ---------------------------------------------------------------------------- Prof Russell Standish Phone 0425 253119 (mobile) Principal, High Performance Coders Visiting Professor of Mathematics hpc...@hpcoders.com.au University of New South Wales http://www.hpcoders.com.au Latest project: The Amoeba's Secret (http://www.hpcoders.com.au/AmoebasSecret.html) ---------------------------------------------------------------------------- -- You received this message because you are subscribed to the Google Groups "Everything List" group. To unsubscribe from this group and stop receiving emails from it, send an email to everything-li...@googlegroups.com. To post to this group, send email to everyth...@googlegroups.com. Visit this group at http://groups.google.com/group/everything-list. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "Everything List" group. To unsubscribe from this group and stop receiving emails from it, send an email to everything-li...@googlegroups.com <javascript:> . To post to this group, send email to everyth...@googlegroups.com <javascript:> . Visit this group at http://groups.google.com/group/everything-list. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "Everything List" group. To unsubscribe from this group and stop receiving emails from it, send an email to everything-list+unsubscr...@googlegroups.com. 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RE: DNA Wormholes can cause cancer (what!?)
'Chris de Morsella' via Everything List Sun, 05 Apr 2015 23:22:24 -0700
- RE: DNA Wormholes can cause cancer... 'Chris de Morsella' via Everything List
- Re: DNA Wormholes can cause c... Russell Standish
- Re: DNA Wormholes can cau... LizR
- RE: DNA Wormholes can cau... 'Chris de Morsella' via Everything List
- Re: DNA Wormholes can... 'Roger' via Everything List
- RE: DNA Wormholes... 'Chris de Morsella' via Everything List
- Re: DNA Worm... 'Roger' via Everything List
