Glen, thank you; these are excellent, The "GASP phenotype” is indeed exactly the keyword I was responding to and, characteristically, couldn’t remember the name of.
Whether any of these speakers was the one I heard at my own first exposure, I can’t recall. But I haven’t read any of the papers below (and only “have" Lennon/Shoemaker but have not read it yet either), so they actually need to go onto my reading list. Thank you for all of them. This is general stuff I should know. Result is that I can’t, yet, pick a best exemplar. But some form of contact-tracing, either forward or backward, from these, will surely lead to it. Just off a breathless few weeks, and sweeping my head back into at least something like a pile, so I will be slow. But these kinds of topics are where I want to be, so I will eventually follow them up. Many thanks, Eric > On Apr 30, 2026, at 2:38, glen <[email protected]> wrote: > > OK. I've done a little homework on what I'm calling your 3rd example of out > of equilibrium (OOE) patterns not well-classed as "evolution through > selection" (EtS). I watched and transcribed the Lennon talk, which was very > cool, particularly the sheer number of nearly inert spores in terms of > biomass and the energy required to produce an endospore in atp units. I can > use ffmpeg to extract the slides ... maybe later. Anyway, good stuff. Thanks. > > But in trying to hammer out what you're gesturing at, I went a couple of > rounds with Claude and Asta and landed on a 5 point ball of leads, hoping > that listing those 5 will trigger your memory or cajole you into winnowing it > down to 1 thing I can do more homework on. Here's the ball. Obviously, it's > not the Lennon-Shoemaker cite, since you gave that one to me. But it's > included for completeness. > > • Steven Finkel (USC): GASP/long-term stationary phase > > Finkel SE. "Long-term survival during stationary phase: evolution and the > GASP phenotype." *Nature Reviews Microbiology* 4(2):113–120, 2006. > doi:10.1038/nrmicro1340. PMID 16415927. > > • Zambrano & Kolter (Harvard): the GASP founding observation > > Zambrano MM, Siegele DA, Almirón M, Tormo A, Kolter R. "Microbial > competition: *Escherichia coli* mutants that take over stationary phase > cultures." *Science* 259(5102):1757–1760, 1993. doi:10.1126/science.7681219. > PMID 7681219. > > • Richard Lenski (Michigan State): LTEE > > Lenski RE. "Experimental evolution and the dynamics of adaptation and genome > evolution in microbial populations." *ISME Journal* 11(10):2181–2194, 2017. > doi:10.1038/ismej.2017.69. > > • Jay Lennon/William Shoemaker (Indiana → UCLA): extreme energy limitation > > Shoemaker WR, Jones SE, Muscarella ME, Behringer MG, Lehmkuhl BK, Lennon JT. > "Microbial population dynamics and evolutionary outcomes under extreme energy > limitation." *PNAS* 118(33):e2101691118, 2021. doi:10.1073/pnas.2101691118. > > • Cho / Palsson collaboration (KAIST + UCSD): adaptive laboratory evolution > of genome-reduced E. coli > > Choe D, Lee JH, Yoo M, Hwang S, Sung BH, Cho S, Palsson B, Kim SC, Cho B-K. > "Adaptive laboratory evolution of a genome-reduced Escherichia coli." > Nature Communications 10:935, 2019. doi:10.1038/s41467-019-08888-6. PMID > 30804335. > > As always, I don't intend to abuse your generosity. Feel free to ignore me. > The LTEE experiment is popular in the culture wars ... so I'm already > interested in that. >8^D > > On 4/12/26 6:29 PM, Santafe wrote: >> Sorry to drop; I also wanted to do a little looking for materials. >>> On Apr 11, 2026, at 0:43, glen <[email protected]> wrote: >>> >>> Very cool. Thanks for continuing this. I have 2 requests if you can answer >>> off the top of your head: >>> >>> 1. One or two good citations for the 2 classes of the out of equilibrium >>> patterns. I'm at a loss for an example pattern Lachman might include, but >>> you exclude. >> I can give you an idea how widely Michael wants to scope. But for the >> example I will mention, I can’t find any publication where he built this >> out, or even a podcast where he discusses it. Probably because it would be >> hard to find buyers. So these are just things he used as examples in >> working conversations (maybe even 6 or 7 years ago now? I’m not sure). >> Michael wanted to treat rocks rolling down hills at different rates as an >> equally good exemplar of selection. Take lifecycles and everything >> biological out of the picture entirely. This isn’t a terrible math-analogy >> for how mortality selection works, if we think of death as regression toward >> the equilibrium of a Gibbs chemical ensemble. (In other ways, that’s a >> terrible mangling of categories, but for the tiny bit of math that is left >> in this case, it works out the same way.) Michael’s limiting case, though, >> lacks any amplification step or anything like a lifecycle. So there can’t >> really be anything like fecundity selection, and there isn’t persistent >> non-equilibrium patterning. (One could go into the direction of erosion, >> and look for some kind of amplification, to produce a limited analogue to >> fecundity selection. But that is still only surfing the shoulder of a >> transient, so it isn’t a good model for true patterned persistent states in >> other ways.) >> As the other side, where there is differential amplification and >> attenuation, but in highly structured systems, a standard layout would be >> the one I always trot out by Michael Lynch, as a summary of the >> population-geneticsts’ abstraction: >> The frailty of adaptive hypotheses for the origins of organismal complexity >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.pnas.org%2fdoi%2f10.1073%2fpnas.0702207104&c=E,1,SEjdrDlaAVhgUCPw7DKwNWkTbJRuVRmuKU4pz59OSSsk3_oonUxuzIzs7V2wDBN4qLgnwCnjQV6Op4Y-Z3mavjH3OF1_Fbm2cbKxP8R7Bw,,&typo=1> >> https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fpnas.org&c=E,1,fjZ5phIk_IrqTJGgv17ah39fa1-Ybejc6F_QhQVELMjREITJqaRVltecU_KzmQNIvrsSIAcGY1q7dp2R_fdUqS3uql3-f5xv6rgEYMxEQw,,&typo=1 >> >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.pnas.org%2fdoi%2f10.1073%2fpnas.0702207104&c=E,1,A9SMkKPecJ36LM_L4GLTmNu9FKwPliysE1va4tRSMpZ63D7ZQROFmWAszZ-QamU0ioDtjn0xf2IdFbi8Cj5fab6CKVz_i8tBZwYh9GpUDUuaMOrssZ6tsA,,&typo=1> >> pnas.2007.104.issue-suppl_1.cover.gif >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.pnas.org%2fdoi%2f10.1073%2fpnas.0702207104&c=E,1,8A3gGNbv4ff1vr1N_zdD5r2m_RZucfXVWtzd0QbWE8csag7BBprLvlC3jZGtCxxCYW0CO5laRAWFJjoDDEqXF0M2RN6M29dkLt0_lKiiVdo5HoP4&typo=1> >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.pnas.org%2fdoi%2f10.1073%2fpnas.0702207104&c=E,1,zmgrLWHdvFbTlB2_-zN6U2-CqHTEDi4Rekb64e7Ha1no2l4gB316DPwrSlx939HUWtWcSzBSG2jaUxSXt_yTnNjlTPaqLeJDIWPVXtqHMfWpwiRj1io,&typo=1> >> Now, I generally put Lynch up as a foil, because he lays out a set of >> systems, arguing that they are all-and-everything you need, to belittle and >> attack those who try to put up further “evolutionary syntheses” or their >> equivalent. However, the formalisms that Lynch is actually offering only >> apply properly to the abstractions of the replicating genes of Williams and >> Dawkins. Then, without happening to comment on the fact that he is changing >> the subject, he goes on to shout “of course selection takes place at the >> level of genotypes” etc. Yet, where there is relational information that >> _makes_ genotypes genotypes, he has said nothing about the system of >> accounting that characterizes how such information is retained and >> propagated, in his earlier “all-and-everything”. And of course, it was the >> wish to deal with all that relational information (and other kinds, like >> symbiotic dependencies in communities) that motivated a lot of the extended >> syntheses that he mocks and criticizes. I do often find that his technical >> criticisms of the extended syntheses are appropriate, because many of them >> don’t seem anchored in really well-formed principles. But to criticize the >> argument that something is needed seems misguided to me. I can imagine >> things that go along the lines of conceptual clarity of the way Fisher >> worked, but that pick up the many interesting questions that were not in >> play in Fisher’s day. >> I don’t know the literature on pan-genomes well, so much of what I have of >> them is from meetings. I did want to mention Jay Lennon, from this meeting >> here: >> Microbial communities: Energetics and dynamics across space and time >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.nitmb.org%2fmicrobial-communities-workshop&c=E,1,R0Hz8SnR_Mao_B5uQ0AYJDDjNOoxBf1r9BR8Hs7yLsCtJKpl2zTtZiJWUwqhnEpyoZCubPD-Ths6yvXZOjUA-DYFnV3I6o90dqWLBplSlFWruIwmNIs-8A,,&typo=1> >> https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fnitmb.org&c=E,1,kn14GLBYf1We6T1emayQCuNYP0P9KCHKIndQDxF1WMlk8inTtcUgFnMcRugCqDk1RD_1cwYEK_bCiZxlRH_OEP-DciQ_P5b_C4lPMNdCObvuD7KZzx1rNf4,&typo=1 >> >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.nitmb.org%2fmicrobial-communities-workshop&c=E,1,whd93G0RgFxHPoK7SA-OiA3LlTimIIJhzZoJwkukPGJS9zJUknTL4rSeRViFmsZ5cmctvHESEqw4NIdDQr0avqLR3uz3SDD7fjWt6e1-OSpd90YN_RAcxyPX&typo=1> >> 95c3c6_6fcd4e52c85c426b8bc99314e9f0a8c4~mv2.png >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.nitmb.org%2fmicrobial-communities-workshop&c=E,1,B6y6NRbbdeITAJeAUZMQch1oEFB8hvGznBYPalQCF0fkdieTPUy80uhpekRXc7IZBBpwUcR8xYTGsOVd14nP7p2PG77t4kpDWXk7eU2Go6NtonAHFxk,&typo=1> >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.nitmb.org%2fmicrobial-communities-workshop&c=E,1,O2X0qJti2YiblXCFQAyGH70Sj_9jW8M9N9ov1EGIf0U_s1p1sIFM2irYtlyFbLizwVHglJXMQ2-qZDKuLf4or7aeDgoP3TBvkibcGemdgrLdYQ,,&typo=1> >> as someone interesting, whom I heard recently enough that I can remember the >> source. I don’t have a paper that seems to exactly cover the scope of his >> talk, which had lots of inter-related things and off-hand comments that >> reflect the breadth of intuitive appreciation that a worker often has of an >> area, beyond what ever makes it into papers. But, from the angle of >> sporulation, he does give some discussion of how dormant phases can be >> reservoirs of genetic capabilities, which can be actively and selectively >> re-activated, here: >> pmc-card-share.jpg >> Evolution with a seed bank: The population genetic consequences of microbial >> dormancy >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fpmc.ncbi.nlm.nih.gov%2farticles%2fPMC5748526%2f&c=E,1,hs8f9lgC-1OWO_1bMh5HblhkDobURbVgkAswA_GPVjzhPoExCJVXk1g86Odt55S_l61RofvaOaAcu_EIfx3mTogZ7fjh9vCThjUxzLHWXduIkwyj5FM,&typo=1> >> https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fnlm.nih.gov&c=E,1,h0fFWEpmjS7zQ2j1Zp0_WQFl1U953WMReiF6eaM0kvEeKzBDMdP5U43frE1khuFtAZPtzUdBRhQbgZ4PFQ7IP3IZmqCdlcJuU82BL7goNQ5b4V7XIPVm52Po_iEt&typo=1 >> >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fpmc.ncbi.nlm.nih.gov%2farticles%2fPMC5748526%2f&c=E,1,D_d3wMDx5uEwQvw3lH4hHYNT_euFKRYu6TeVTfhm0VdRPgXg_6k8B8Db5TXii9aE3N88JsZG6_qiY4ZUXgShUkU0FT-Zri3daGV7y7Lc_627IiL8NOs_4GJr-w-q&typo=1> >> <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fpmc.ncbi.nlm.nih.gov%2farticles%2fPMC5748526%2f&c=E,1,lAscp8Q6fxK2TjRnjRJIKXnaGw7JqyN0u9-wPU4qaWI2Ls40q7S5YkZ6e0knPyW0rdx5dMXa7YweRerDckHwsrm7mpFaPVIvYwf-uh0Rq_5St3u2VPwZ1uQT1MIa&typo=1> >> Somebody else, who does very-long-term starvation phenotypes on E. coli, and >> shows that the whole genome and cell form undergo radical metamorphoses, was >> the first person who really got my attention on the dynamic and intentional >> characteristics of pan-genomes. But I don’t remember who it was. (Oddly, I >> have some synesthetic image of the room I was sitting in watching, but I >> couldn’t tell you what meeting or what year it was in.) He is somebody >> well-known for this. >>> 2. I'm assuming you and Lachman's ability to grok and play along with each >>> others' preferences is *because* you work in the same physical location and >>> can talk informally back and forth. Is that true? Or do you think you could >>> come to the same facile donning-doffing of each perspective if you *only* >>> communicated by electronic means ... or through publication letters and >>> such? >> It’s a good question. Probably equal amounts of both. >> My impulse — being someone given to abstraction — is to suggest that the >> main driver is temperament. Neither Michael nor I is out to capture or >> defend territory. We also share taking no enjoyment in “conversations” that >> go in circles forever because the interlocutors talk past each other and >> misunderstand each other’s claims. Michael is, in general, a much more >> easy-going and tolerant person than I am, so he doesn’t tend to the >> immediate impatience and annoyance with such conversations that I have. But >> he never drifts into that direction, so there is never needless upstream >> swimming to do. He is also very clear with his categories. Since we both >> enjoy and are looking for questions that are actually about something, then, >> it is almost-always pretty systematic to see where a misunderstanding has >> happened, and figure out how to unravel it to get to a meaningful question >> we can try to puzzle out. >> But equally much, being in a room has mattered. For a long time now, it has >> been several years at a time between my path-crossings with Michael. >> However, it does turn out to be invaluable that I can trudge a half-hour >> across town in the snow, to sit for an afternoon in a room with him, to try >> to hash through something. The counterexample that shows this is probably >> essential is that he makes certain statements to the effect that Hector >> Zenil’s information-theoretic criticisms of Walker and Cronin’s Assembly >> Theory are “wrong”. While there is a lot of Zenil’s screed in his blog >> posts that is unhelpul — but which reviewers and editors were largely able >> to get him to cut out when he got a few papers on this published — there is >> a core of his assertion, that the Assembly Index is a certain version of a >> compression index, that seems correct to me. I am sure that Michael speaks >> in good faith, and also that he knows what he is talking about. And I am a >> semi-tourist in these algorithmic information things, not an essential >> worker. But for all that, I don’t understand just what Michael is claiming >> in detail, and probably won’t until I have a couple hours with him for which >> that is the main topic to sort out. I have felt the lack of that as a kind >> of exposure, because I worry where I am missing something. >> It’s all interesting, >> Eric > > > -- > ¡sıɹƎ ןıɐH ⊥ ɐןןǝdoɹ ǝ uǝןƃ > ὅτε oi μὲν ἄλλοι κύνες τοὺς ἐχϑροὺς δάκνουσιν, ἐγὰ δὲ τοὺς φίλους, ἵνα σώσω. >
WEBVTT 00:00.000 --> 00:07.000 Good afternoon, everyone. I can start off by challenging some assumptions, I guess, 00:07.000 --> 00:15.000 about the physiology of microbial systems and start with the proposition that most organisms, 00:15.000 --> 00:21.000 microbes included, but also plants and animals, live in environments that are typically not 00:21.000 --> 00:27.000 suitable for growth and reproduction, at least not maximal growth and reproduction. And as 00:27.000 --> 00:31.000 a result of that, those populations are at risk for extinction. But a lot of different 00:31.000 --> 00:38.000 strategies have evolved among diverse organisms, including their ability to alter their behaviors. 00:38.000 --> 00:43.000 Some organisms will disperse into new environments and take on the risk of encountering some 00:43.000 --> 00:48.000 new set of environmental conditions that might be better. Or some organisms may choose to 00:48.000 --> 00:54.000 just stay put and evolve locally through a process of natural selection and local adaptations 00:54.000 --> 01:00.000 to those model conditions. Another option, however, that I'm going to talk about today 01:00.000 --> 01:07.000 is that organisms can disperse in time. So many organisms have all the capacity to engage 01:07.000 --> 01:13.000 in dormancy, which we're going to define as the ability for an individual to enter a reversible 01:13.000 --> 01:20.000 state of reduced metabolic activity. And that's a pretty loose definition, but when we do 01:20.000 --> 01:27.000 that, there are many different types of plants and animals, bacteria, fungi, insects, rotifers, 01:27.000 --> 01:33.000 protists, amphibians, birds, all different types of organisms have this ability to engage 01:33.000 --> 01:38.000 in this process of dormancy. And so that's an example of convergent evolution, because 01:38.000 --> 01:43.000 the way in which those processes have evolved has arisen independently. There's no shared 01:43.000 --> 01:49.000 origin in their ability to achieve this process. So it kind of suggests that there's a solution 01:49.000 --> 01:56.000 to some kind of common problem that isn't encountered. And I guess I want to say by 01:56.000 --> 02:02.000 showing these different examples, also highlight the mechanisms by which organisms can. For 02:02.000 --> 02:07.000 some, it's a very passive process where an individual can just kind of passively fall 02:07.000 --> 02:14.000 into a state of inactivity. But in many instances, there's really complex underlying mechanisms 02:14.000 --> 02:20.000 that control the ability of an organism to engage in this life history process. Different 02:20.000 --> 02:25.000 pathways, different developmental pathways, different genetic regulatory mechanisms, often 02:25.000 --> 02:31.000 leading to vastly different changes in organismal morphology as it goes from a state of being 02:31.000 --> 02:38.000 an actively growing organism to one that's metabolically connected. 02:38.000 --> 02:43.000 So despite all those fascinating details, I'd like to argue that there maybe are just 02:43.000 --> 02:48.000 some three essential criteria that need to be met in order for an individual, regardless 02:48.000 --> 02:53.000 of what taxonomic group you're thinking about, to engage in this process. The first thing 02:53.000 --> 02:59.000 is that an individual needs to be able to occupy at least one of two different states. 02:59.000 --> 03:04.000 In the most simplest version of dormancy, you could have an on versus off metabolic 03:04.000 --> 03:09.000 state. Criterion two is that individual then needs to be able to move or transition between 03:09.000 --> 03:14.000 those two states. And that can happen in different ways. So we heard a little bit about this 03:14.000 --> 03:19.000 idea of stochastic switching so that environments may be so unpredictable that individuals would 03:19.000 --> 03:23.000 randomly move between an active and inactive state. But in many cases, they're tracking 03:23.000 --> 03:28.000 environmental cues and that's what's regulating the transitions between those two metabolic 03:28.000 --> 03:33.000 states. So it could be temperature, it could be a depletion of resources, the accumulation 03:33.000 --> 03:37.000 of waste products in the environment, all those occurring perhaps at the local patch 03:37.000 --> 03:43.000 scale, or individuals can be queuing in on broader geographic cues like changes in photo 03:43.000 --> 03:49.000 periods from here. The third criteria that must be met is that there's no benefit to 03:49.000 --> 03:53.000 be dormant because you're not reproducing. And that's ultimately what's important and 03:53.000 --> 03:59.000 selected for by natural selection. But you can enjoy protection against the environmental 03:59.000 --> 04:03.000 conditions that would otherwise increase your mortality. So there has to be some protection 04:03.000 --> 04:12.000 that's afforded to individuals that are not engaging in metabolism and replication. So 04:12.000 --> 04:19.000 those are the central criteria for being a dormant order and engaging in this process. 04:19.000 --> 04:24.000 So we've been thinking about these processes and how they influence microbial communities 04:24.000 --> 04:27.000 for quite a while now. I think we've been able to demonstrate that it's important for 04:27.000 --> 04:32.000 the maintenance of the diversity of complex microbial communities, and in some case helps 04:32.000 --> 04:37.000 us understand and predict the functioning of an ecosystem. And the figure I'm showing 04:37.000 --> 04:42.000 here right now is just looking at the accumulation of metabolically inactive individuals into 04:42.000 --> 04:49.000 all microorganisms. And so what you can see is that they're accumulating collectively 04:49.000 --> 04:54.000 the abundance and biomass of these different individuals in different ecosystems in a variable 04:54.000 --> 05:00.000 way. In some cases, in soil, which we care about in terms of thinking about the sequestration 05:00.000 --> 05:05.000 of carbon from the atmosphere, nutrient cycling for crop and food production, upwards of 90% 05:05.000 --> 05:10.000 or more of those microbial cells are in a state of metabolic inactivity. And so these 05:10.000 --> 05:15.000 observations that we made a long time ago, just by combing information from the literature, 05:15.000 --> 05:19.000 motivated us to be thinking about developing experimental systems that we can bring into 05:19.000 --> 05:25.000 the lab to generate and test theory regarding the evolutionary properties of microbial life. 05:25.000 --> 05:36.000 Yeah, so in this case, this is all based on single cell data where you could look at, 05:36.000 --> 05:42.000 for example, the recovery of ribosomes from cells or the ability of certain metabolic 05:42.000 --> 05:46.000 dyes that will fluoresce in a certain way if there's an active electron transport chain. 05:46.000 --> 05:51.000 And we're looking at, we're classifying those either after or in the next. 06:01.000 --> 06:05.000 Yeah, that's a good question. So the residence time of the ecosystem is really important. 06:05.000 --> 06:09.000 If you're not replicating, if you think about a chemostat and you put a bunch of cells in 06:09.000 --> 06:13.000 there and they go dormant, then they're just essentially inert particles that we would 06:14.000 --> 06:19.000 So it must mean that the human gut or the animal gut is kind of deviating in some way 06:19.000 --> 06:25.000 from first order expectations of something like a chemostat. There are lots of folds 06:25.000 --> 06:31.000 and villi and things and pockets and ducts that can trap microbiota from the gut and 06:31.000 --> 06:33.000 probably reduce residence time. 06:38.000 --> 06:40.000 Yeah, those are all surface water samples. 06:43.000 --> 06:51.000 So I'm just curious that the idea of this kind of binary decision between either being 06:51.000 --> 06:57.000 growing or not growing, I guess in principle some forms of, that's a wooden performance 06:57.000 --> 07:03.000 you could just be up on an end of a continuous gradient. Like, so I invest more in RPOS, 07:03.000 --> 07:09.000 but that slows my growth. I'm just wondering, like, how many of these cells that are active 07:09.000 --> 07:15.000 are at a lower activity level than they could in principle accidentally achieve in those conditions? 07:16.000 --> 07:20.000 Yeah, I think the idea that there could be some kind of binomial distribution of metabolic 07:20.000 --> 07:25.000 activity in a microbial community is something that we've recently kind of dismissed and 07:25.000 --> 07:30.000 or ruled out. It seems like there is more of a continuous distribution such that there 07:30.000 --> 07:35.000 is a small proportion of cells that are carrying out most of the activity and there's these 07:35.000 --> 07:41.000 long term distributions of metabolic and kinetics. But it's not two distinct distributions. 07:45.000 --> 07:52.000 So yeah, so we wanted to develop an experimental system that we could work with in the laboratory 07:52.000 --> 07:58.000 and address some questions. And for a long time I avoided the temptation and suggestions 07:58.000 --> 08:03.000 that we should be working with SCORE coming back to this. Mostly because I think there 08:03.000 --> 08:09.000 are organisms that don't do sporulation. I was initially a little bit reluctant to accept 08:09.000 --> 08:14.000 that this was the model. But then I realized that there were a lot of features to study 08:14.000 --> 08:20.000 SCORE forming bacteria regarding their genetics, their ability to be visualized, experimental 08:20.000 --> 08:26.000 trafficability in general. And so this is a really ancient form of a dormancy. It's 08:26.000 --> 08:31.000 only found within one phylum of bacteria. For those of you who are not microbial biologists 08:31.000 --> 08:36.000 or not familiar with the tecton and phylogeny, there's hundreds of different phylum. We 08:36.000 --> 08:42.000 are one phylum, a chordata, a little chord, basically every other organism that walks 08:42.000 --> 08:48.000 on the lens or tube. So there's only one phylum of bacteria in the tree of life, called the 08:48.000 --> 08:53.000 bacillota from accutes. And even within that lineage, not all organisms do that. But the 08:53.000 --> 09:00.000 ancestor that is at the root of that tree was a SCORE forming, had the SCORE forming 09:00.000 --> 09:05.000 capacity. And that dates back to about 3 billion years. So this is a really ancient trait. 09:05.000 --> 09:11.000 It's also very complex. There are upwards of 500 genes that are required and they're 09:11.000 --> 09:15.000 upregulated when a cell goes from growing under good condition, where an individual 09:15.000 --> 09:21.000 can divide once every 20 minutes, to entering into this pathway where you upregulate tons 09:21.000 --> 09:28.000 of genes to make SCORE. It's also very timely, time consuming. So again, 20 minutes. To carry 09:28.000 --> 09:35.000 out the whole process to create a mature SCORE takes about 8 hours. But when you're done, 09:35.000 --> 09:43.000 you have a structure that is extremely hardy. It's almost energetically inert. You can expose 09:43.000 --> 09:47.000 it to any kind of environmental condition you can think of and the cells usually survive. 09:47.000 --> 09:52.000 People put them on the outside of the International Space Station in the vacuum of space and they 09:52.000 --> 09:58.000 seem to survive those conditions just now. And as a result of that, they have a pretty 09:58.000 --> 10:02.000 wide geographic distribution. You can find endoscores virtually everywhere. They're littered 10:02.000 --> 10:07.000 across soils, they're found in our guts, they're found in the oceans, where it's been conservatively 10:07.000 --> 10:11.000 estimated that there are somewhere on the order of 10 to the power of 28 endoscores. 10:11.000 --> 10:17.000 And so if we use numbers that people have, thinking about global patterns of diversity 10:17.000 --> 10:23.000 and abundance, there's about 10 to the 30 cells, 10 to the 29 to 30 microbial cells 10:23.000 --> 10:28.000 from the planet. So just with this one group of organisms, we can conservatively conclude 10:28.000 --> 10:34.000 that about 10% of the global microbial biosphere is in a seed bank or is in some state of the 10:34.000 --> 10:45.000 environment. So I think this all kind of sets up a bit of an energetic paradox or a 10:45.000 --> 10:51.000 conundrum, at least for me, because these spores and the production of this pathway, 10:51.000 --> 10:56.000 which is time consuming and energy consuming, only happens when there's vanishingly small 10:56.000 --> 11:01.000 quantities of energy in the surrounding environment. So why would you go through this whole process 11:01.000 --> 11:07.000 of going through this elaborate process of up-regulating all these genes and making proteins 11:07.000 --> 11:13.000 to create this protein-rich complex structure when there's no energy around in the environment? 11:13.000 --> 11:19.000 And so this kind of just sort of begs the question in an unknown, which is what is the 11:19.000 --> 11:26.000 energetic cost of making an endoscore? And the approach to do this is what we thought 11:26.000 --> 11:30.000 about for a while. You could imagine that there are microcell limits in me and other 11:30.000 --> 11:35.000 types of approaches where you can carefully measure the amount of energy flux in a cell, 11:35.000 --> 11:41.000 and people have tried that without much success. We adopted another strategy that was developed 11:41.000 --> 11:47.000 by a colleague of mine, Mike Lynch, about 10 years ago, where he took a bottom-up approach. 11:47.000 --> 11:54.000 And initially it was used to quantify the cost of making a gene in units of ATP, which 11:54.000 --> 12:00.000 is a universal currency of life. Since then, that process has been extended to quantify 12:00.000 --> 12:05.000 the energy involved in making new membranes. It's been used to quantify the energetic 12:05.000 --> 12:10.000 cost of making entire viruses. And it's been recently used to estimate the cost of producing 12:10.000 --> 12:17.000 and making an entire multicellular metadome, all by based on the assumptions of the cost 12:17.000 --> 12:22.000 of making a nucleotide or a ribonucleotide, and then translating that information into 12:22.000 --> 12:26.000 protein. Those are the three dominant costs. There's other things that are going on that 12:26.000 --> 12:32.000 we can account for, but those are the three major sources of energy consumption in ATP 12:32.000 --> 12:39.000 for biosynthesis. So this work is all being conducted by a former postdoc of mine, John 12:39.000 --> 12:49.000 Impelli, a former Ph.D. student at Washington University. 12:49.000 --> 12:56.000 So we use this approach. Basically, it's just a detailed countdown. It's not really all 12:56.000 --> 13:01.000 that exciting. You know which genes in a genome are associated with the process of making 13:01.000 --> 13:06.000 a score, and you count those up. You know which ones are being transcribed by mining 13:06.000 --> 13:11.000 and existing transcriptome datasets that are being done at precise time resolutions. And 13:11.000 --> 13:15.000 there are databases where people have measured protein expression under those same conditions 13:15.000 --> 13:22.000 under these characteristic stages of development. And so the first thing that's interesting 13:22.000 --> 13:26.000 that the cell needs to do when it engages in the process of correlation is it makes 13:26.000 --> 13:33.000 a copy of its genome. So there's now two copies. And shortly thereafter, you get the formation 13:33.000 --> 13:45.000 of a septum. To the left of that, you have a larger mother cell, and to the right of 13:45.000 --> 13:49.000 that, you have the developing core cell. There's going to be one copy of the genome on the 13:49.000 --> 13:53.000 left side, and there's going to be another copy of the genome on the right side. After 13:53.000 --> 13:58.000 that, it's been set up. Now you have differential gene expression occurring on both sides of 13:58.000 --> 14:03.000 that barrier, and there is some exchange that's going on between the two of them. Eventually, 14:03.000 --> 14:07.000 there's a score that starts to develop. It engulfs the mother, and you result in the 14:07.000 --> 14:14.000 end with a free-standing mature endosport. This whole investment is extremely front-loaded 14:14.000 --> 14:19.000 based on the data that we've estimated. So in the first two hours of this eight-hour 14:19.000 --> 14:25.000 process, 85% of the ATP investment occurs. And it's sort of coincidental or not that 14:25.000 --> 14:30.000 this happens right before this dashed vertical line, which is the point of commitment or 14:30.000 --> 14:35.000 no return. Once you get beyond that point, the cell can no longer change its mind and 14:35.000 --> 14:40.000 go back to being a vegetative cell. So there's a decision that needs to be made with consequences 14:40.000 --> 14:45.000 for the recuperation of allocated energy, whether it's opportunity costs where energy 14:45.000 --> 14:50.000 and ATP can be used for other processes that might be generating energy and involved in 14:50.000 --> 14:54.000 other processes beyond dormancy. 14:54.000 --> 14:55.000 Yeah. 14:55.000 --> 15:02.000 How big is the exchange rate investment compared with the COVID-19 sales for experiential 15:02.000 --> 15:03.000 environment sales? 15:03.000 --> 15:07.000 So that's a great question. And if I can just pause for one second, I'll get to that because 15:07.000 --> 15:12.000 I have the same exact... What's the exchange rate or currency? I don't know how to interpret 15:12.000 --> 15:17.000 the nine ATPs compared to other cellular processes. So I'm going to have a figure where I go through 15:17.000 --> 15:22.000 and show that. 15:22.000 --> 15:31.000 Should we think of this as having accepted the ordinary life cycle reproductive system 15:31.000 --> 15:37.000 or is it something completely independent that is going to parallel in place? 15:37.000 --> 15:46.000 They're distinct. Yeah. There's a decision that's made and once they undergo that process, 15:46.000 --> 15:51.000 cells are no longer going under any kind of vegetative growth. So there's two distinct 15:51.000 --> 15:55.000 choices and bifurcations in there. 15:55.000 --> 16:02.000 Even the chromosome copy, is that using standard machinery and then stream some other choices 16:02.000 --> 16:03.000 maybe? 16:03.000 --> 16:06.000 Yeah. And it happens very early on. And so even if the cell were to proceed with vegetative 16:06.000 --> 16:11.000 growth, we'd still need to make a copy of its genome. But early on in the stages of 16:11.000 --> 16:16.000 spore relation, we need to have a second copy made and then there's chromosomal segregation 16:16.000 --> 16:26.000 into the development of the score. 16:26.000 --> 16:30.000 So translation costs dominate this. So genome replication that we're talking about right 16:30.000 --> 16:37.000 now is important, but it's not the predominant cost. Making proteins is the biggest thing. 16:38.000 --> 16:43.000 Thinking about this subcellular allocation strategy, there's analogies to thinking about 16:43.000 --> 16:47.000 embryogenesis and the way in which maternal investments in their offspring and we see 16:47.000 --> 16:51.000 parallels to that here. The mother cell is accounting for a disproportionate cost of 16:51.000 --> 16:58.000 the spore development. She's paying 90% of the total process of making a spore is occurring 16:58.000 --> 17:09.000 in that left-hand side of the middle cell. 17:09.000 --> 17:13.000 So what I showed you in the last process, early on there was a diagram showing the transition 17:13.000 --> 17:19.000 into dormancy and out of dormancy. So this is the cost of initiating dormancy. What I 17:19.000 --> 17:27.000 want to say is that if you stay as a dormant spore for 100,000 years, which one of my undergraduates 17:27.000 --> 17:33.000 now is resurrecting cells from ancient Vietnamese settlements and it seems to be pretty easy 17:33.000 --> 17:39.000 to do, if they stay in that state eternally, then there's no distinction between that being 17:39.000 --> 17:45.000 a potentially viable cell and a dead cell. In order for this to be an evolutionarily 17:45.000 --> 17:50.000 advantageous strategy, the spore needs to germinate, it needs to wake up, it needs to 17:50.000 --> 17:55.000 outgrow, and it needs to divide. And if that doesn't happen, then all of the investments 17:55.000 --> 18:00.000 of ATP up to that point are for naught. So what we wanted to do was come up with a full 18:00.000 --> 18:05.000 cost accounting of this entire life cycle, so we're also quantifying the costs associated 18:05.000 --> 18:11.000 with revival. And this happens over a much shorter time scale, so our intuition, naively, 18:11.000 --> 18:15.000 was that this should be a less costly process. In fact, what we found is that revival is 18:15.000 --> 18:23.000 more expensive than the initiation of formation. And that's probably due, again in retrospect, 18:23.000 --> 18:30.000 again to proteins, right? So transcripts of proteins are about 100 to 1,000 fold more 18:30.000 --> 18:37.000 abundant inside a cell than they are in transcripts. And this spore needs to, as it's outgrowing, 18:37.000 --> 18:43.000 needs to produce a vast repertoire of proteins that are needed for vegetative growth. And 18:43.000 --> 18:48.000 so there's a complete proteome turnover, and that seems to be why we're seeing a large 18:48.000 --> 18:54.000 decline associated with spore revival in general. And so how do they do this? It's 18:54.000 --> 18:59.000 not relying on the storage of internal ATP reserves, but these ATP surveys are certain 18:59.000 --> 19:05.000 of that. In the literature, we've done some careful investigation, and there's at most 19:05.000 --> 19:12.000 a couple hundred ATP molecules inside of an under-spore. So that must be enough to reboot 19:12.000 --> 19:17.000 a spore, but it's definitely not enough to meet a great shortfall by at least six orders 19:17.000 --> 19:24.000 of magnitude, and what's required for that under-spore to rebar. Which means, I think, 19:24.000 --> 19:29.000 that germinating an under-spore has to make the timing really important, because as soon 19:29.000 --> 19:34.000 as it germinates, it needs to get its hands on a sufficient supply of exogenous resources 19:34.000 --> 19:39.000 from outside the cell to meet a solid germination. Again, otherwise, the spore, the whole spore 19:39.000 --> 19:42.000 cycle will come to a close. 19:42.000 --> 19:48.000 So do you have any direct understanding of the degradation of proteins, the degradation 19:48.000 --> 19:54.000 flux of these things? There's this proposal of that. Sometimes it costs four ATP per amino 19:54.000 --> 19:57.000 acid to do preparation, but sometimes you can actually get energy from that process. 19:57.000 --> 20:03.000 Yeah, and I think there is some internal recycling. So we have kind of worked through this, and 20:03.000 --> 20:07.000 there's a manuscript that we can develop, and there are some calculations that might 20:07.000 --> 20:11.000 diminish some of that cost, and there's some internal recycling during the hydrolysis process 20:11.000 --> 20:19.000 associated with germination. But I don't have those numbers. 20:19.000 --> 20:27.000 Okay, so getting back to this question of how do we compare a process or a relative 20:27.000 --> 20:35.000 option, these costs, to other things that a bacillus cell might do. And so we carried 20:35.000 --> 20:39.000 out the same process, not just with sporulation and germination, but a whole bunch of other 20:39.000 --> 20:44.000 things that this cell does using data that we can get our hands on. And from that, we 20:44.000 --> 20:48.000 found that sporulation is probably one of the more expensive things that a cell can 20:48.000 --> 20:54.000 do. It makes up about 10 percent of the total budget of the cell. And there are a bunch 20:54.000 --> 20:59.000 of alternate strategies that these cells would prefer to engage in when confronted with stress 20:59.000 --> 21:05.000 that they do before they will produce an endosporin. So some of them, when stressed, will start 21:05.000 --> 21:12.000 to collectively engage in biofilm formation. They engage in things like cannibalism. They 21:12.000 --> 21:19.000 start expressing competence. They allow them to acquire genes from their environment, which 21:19.000 --> 21:23.000 perhaps could influence their fitness. There are a bunch of alternate strategies. All of 21:23.000 --> 21:28.000 those are much less expensive than making an endosporin. 21:28.000 --> 21:34.000 So at the end, there's a question about the break-even point here. And so let's imagine 21:34.000 --> 21:41.000 that you can reduce maintenance energy requirements by 100,000. So that's a cost that you have 21:41.000 --> 21:45.000 to pay continuously, but that might still be advantageous compared to the one-time big 21:45.000 --> 21:52.000 investment of making a score. And so the characteristic time or frequency at which fluctuations must 21:52.000 --> 21:57.000 occur between good and bad environments in order for sporulation to be optimal for this 21:57.000 --> 22:03.000 to be the favored, persistent strategy is about 30 days. So once the environment goes 22:03.000 --> 22:09.000 beyond being inhospitable for growth and reproduction, once you get to that 30-day 22:09.000 --> 22:14.000 point, now sporulation starts being a beneficial process. 22:14.000 --> 22:18.000 I see that we're standing here, so I'm going to just wrap up. We thought a little bit about 22:18.000 --> 22:22.000 how this could limit something called sporulation efficiency. If you put cells in a given environment 22:22.000 --> 22:27.000 that's not suitable for growth and reproduction, which fraction of those cells will be able 22:27.000 --> 22:33.000 to be producing endospores, we see in the literature it ranges from 0 to 100 percent 22:33.000 --> 22:38.000 and with a mean of about 30. This has commonly been in bulk as a form of bet hedging that 22:38.000 --> 22:43.000 not all individuals need to do this process to ensure the persistence of this sporulation. 22:43.000 --> 22:48.000 We don't acknowledge to us that actually it seems that there's constraints and energy 22:48.000 --> 22:53.000 limitation at the population scale that prevents cells from being able to form endospores. 22:53.000 --> 22:57.000 And the last thing I wanted to talk about, and I won't go into a ton of detail here, 22:57.000 --> 23:01.000 is the evolutionary implications for cost and the maintenance of this trait over long 23:01.000 --> 23:05.000 periods of time. I mentioned it was first evolved three billion years ago. This trait 23:05.000 --> 23:12.000 has been lost repeatedly over geologic time scales. And in addition, if you passage these 23:12.000 --> 23:16.000 cells in the laboratory, if I put them in a cleanest cell, if I put them in batch culture 23:16.000 --> 23:20.000 and I passage them under good conditions, in a matter of weeks, months, we see a three 23:20.000 --> 23:25.000 billion year old trait. You go, why is that? Because five to ten percent of the entire 23:25.000 --> 23:30.000 genome is devoted to sporulation. And when that's under relaxed selection, it's a large 23:30.000 --> 23:35.000 target for mutation to accumulate. Essential genes that once perturbed, you've lost that 23:35.000 --> 23:42.000 trait in perpetuity. So this is the use it or lose it idea that under relaxed selection, 23:42.000 --> 23:48.000 not knowing anything about energetics, we see the loss of this trait over geologic time 23:48.000 --> 23:53.000 scales. We did some work with mutation accumulation experiments, which allowed us to look at deletions, 23:53.000 --> 23:59.000 so large traits of DNA that can be lost. And this would be an energy-saving mechanism that 23:59.000 --> 24:04.000 is consistent with adaptive streamlining, so why genomes get small. So if evolution 24:04.000 --> 24:09.000 can see those nucleotides that are being paved through the process of genome duplication, 24:09.000 --> 24:13.000 selection can actually move them in a way that saves energy for the cell, becomes the 24:13.000 --> 24:20.000 consequence of losing this trait. And so I think some of these things could be important 24:20.000 --> 24:24.000 for thinking about community dynamics, which has been a theme of what we've been talking 24:24.000 --> 24:29.000 about. Some of the work that we're doing is trying to think about how spores can provide 24:29.000 --> 24:32.000 defense against phages, and that seems to be something that we're going to hear about 24:32.000 --> 24:38.000 tomorrow. They can't attach to the receptors, because there aren't any receptors on these 24:38.000 --> 24:44.000 spores. And so there is a physical defense that is important for phage attack, and subsequent 24:44.000 --> 24:51.000 rates of coevolution and diversification. So thinking about this as a mechanism of abiotic 24:51.000 --> 24:55.000 tolerance, there's implications for thinking about the diversity of biological systems. 24:55.000 --> 24:57.000 Okay, thank you. 24:57.000 --> 25:05.000 I have time for a few questions. 25:05.000 --> 25:30.000 Great talk. I was wondering about the 180Ps that you mentioned. Do you think they are 25:30.000 --> 25:34.000 not getting hydrolyzed, or are they getting constantly generated? In other words, is it 25:34.000 --> 25:40.000 a non-occurring, stationary-stating thing, or is it a turnover of ATP in the spore? 25:40.000 --> 25:45.000 From people I talk to, and people who study ribosomes and other cellular processes, it's 25:45.000 --> 25:51.000 a very hard thing to study and to measure. My expectation is that of any form of dormancy 25:51.000 --> 25:57.000 that I'm aware of, spore is the least amount of biological activity in a turnover. So perhaps 25:57.000 --> 26:01.000 there's actually consumption of ATP over time, but I don't think there's any generation of 26:01.000 --> 26:05.000 new ATP in the endosporus. 26:05.000 --> 26:27.000 Could you contrast the state of being dormant versus being an endosporus and develop the 26:27.000 --> 26:31.000 frequency at which one finds these two states in nature? 26:31.000 --> 26:36.000 I'm very careful in how I define dormancy, and I keep it super generic, because there's 26:36.000 --> 26:41.000 a lot of language to describe different ways in which organisms achieve the same thing. 26:41.000 --> 26:45.000 I think those differences are interesting and important. I would definitely say that 26:45.000 --> 26:50.000 endosporus is a classic example of dormancy. I'm not sure there being any other organism 26:50.000 --> 26:58.000 that would be more metabolically inactive than an endosporus. I'm not sure if that's 26:58.000 --> 27:02.000 your question, but... 27:02.000 --> 27:07.000 My question is, I just think that you refer to all the time that this is dormant. It's 27:07.000 --> 27:09.000 a wider classification. 27:09.000 --> 27:10.000 Wider? 27:10.000 --> 27:14.000 That's my guess. I don't know yet. Endosporus is dormant. 27:14.000 --> 27:15.000 For sure. 27:15.000 --> 27:22.000 Okay. I just don't know. 27:22.000 --> 27:24.000 It only occurs in one phylum. 27:25.000 --> 27:31.000 This particular flavor of dormancy only occurs in a subset of bacteria that fall within one 27:31.000 --> 27:32.000 phylum? 27:32.000 --> 27:36.000 Yes, it must be. Other phylum must have it. 27:36.000 --> 27:42.000 They do a different one, right? Maybe not to the same degree. Again, this is an example 27:42.000 --> 27:47.000 of a really complex form of dormancy. They're exceptionally long-lived compared to other 27:48.000 --> 27:55.000 One last question from Alfred. 27:55.000 --> 28:04.000 Yeah, very nice analysis. I really like this. Ten percent of the total energy budget for 28:04.000 --> 28:12.000 stolomation is not that bad. From your curve, it looks like the biggest energy expense is 28:12.000 --> 28:22.000 for the checkpoint. How much energy, in terms of metabolizing per unit time, or how much 28:22.000 --> 28:30.000 metabolism would need to go on to cover the last hum? And also, obviously, the cells cannot 28:30.000 --> 28:39.000 predict the environment and whether the snacks will be. Are there any ideas of what the selection 28:39.000 --> 28:44.000 is behind that, or is it simply those that can't make it, you don't have a file in this 28:44.000 --> 28:45.000 environment? 28:45.000 --> 28:51.000 I mean, some element of this is work hypotheses necessarily going in about the checkpoints, 28:51.000 --> 28:55.000 but we knew that those checkpoints existed, and it just so happens that a lot of the energy 28:55.000 --> 29:01.000 was expanded prior to that. If conditions change in that two-hour window before commitment, 29:01.000 --> 29:05.000 then the cell has an opportunity to reuse the energy that's been collected for other 29:05.000 --> 29:09.000 purposes. Once you get past that, that's the point of no return, and there's no way 29:09.000 --> 29:15.000 to recoup that energy unless you go all the way through the process of making a mature 29:15.000 --> 29:22.000 stool and then successfully germinate and outgrow. So, I'm not sure what happened after 29:22.000 --> 29:26.000 the checkpoint, but it looks like there's not as much in terms of energy as premature. 29:26.000 --> 29:31.000 It's just really 85 percent of it is in that first two hours leading up to the formation 29:31.000 --> 29:33.000 of the cell. 29:33.000 --> 29:40.000 And how much longer could the cell live with this 85 percent in terms of maintenance energy? 29:40.000 --> 29:42.000 I mean, how much mileage does it require? 29:42.000 --> 29:44.000 What could you do with that 85 percent? 29:44.000 --> 29:45.000 Right. 29:45.000 --> 29:50.000 Yeah, yeah. Let's probably go back to that table where I showed a comparative cost, and 29:50.000 --> 29:56.000 maybe you could make a bioform, or maybe you could express some compositions, or make 29:56.000 --> 30:02.000 up 75 percent in maintenance metabolism for that period of time. You could put in those 30:03.000 --> 30:04.000 Thank you. 30:04.000 --> 30:05.000 Somebody's over making bricks.
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