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    • I love learning about human evolution and couldn't believe there were not yet any conversations about it on Cake.co. There are so many current and interesting scientific questions about this going on right now. Here's a primer video on the topic:

    • Thanks for posting this. As far as I can tell a better understanding of the principles of cause along with the implications involved in terms of how it shapes development in biological systems over time can unlock the ability to steer it intentionally the same way that understanding material sciences can help us build effective bridges for instance.

      One of the critical things I think the conventional wisdom of modern evolutionary biology misses is due to a categorical errors combined with a tendency toward linear reductionist thinking. This severely limits what can be rendered through the theoretical lenses we apply to evolution as a process. As a consequence we cannot see the systemic nature of complex adaptive systems as they are, an integrated set of inseparable interdependent nested processes, rather than a single cause linear developmental line.

      As far as I can tell, some of these folks are the vanguard for understanding evolution more clearly.

      Guenther Witzany who approaches the topic through a lens where biology is governed by
      sign-mediated interactions within and between cells, tissues, organs, and organisms in all domains of life. In other words, if I understand him correctly, it is in essence linguistic at all levels and all creatures relate to all other creatures across domains of life. Here is a list of his publications.

      http://www.biocommunication.at/modules/publications/index.php?id=1:1

      Another person with keen insight on the systemic nature of evolution is Maximo Sandin. Because his, and some of these other people's discoveries put pressure on the conventional paradigm, their work does not come without its critics, but I think they have something valuable to say. Maximo's work is stellar, particularly these two papers of his:

      https://aimingfurtherstrikingbetter.wordpress.com/2012/03/01/more-biology-synthetic-theory-crisis-and-revolution-by-maximo-sandin/

      https://aimingfurtherstrikingbetter.wordpress.com/2011/12/21/biology-an-old-perspective-by-maximo-sandin/

      A third person to look at is Seth Bordenstein, he and his wife, along with their team, specialize in how the microbiome is involved in the processes of speciation among other things. Their work on the hologenomic (microbial/host relational effects) on speciation are gaining quite a bit of traction in the evolutionary biology world, for good reason from my perspective.

      http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2000225


      Lastly, Luis P Villareal has a focus on the viral aspects involved in evolution. He illustrates the tapestry of biology as a body of life, where relationships form and persist based on their ability to contribute nourishing and or defensive value to the coherency of the entire community of relationships as a whole over time. Here is his paper on the connection between the placenta and a persistent (non-lytic) virus.

      (I have a copy of this paper if you would like to read it.)

      He also has many other papers and books that are fantastic reads. This is a good start I think. I would love to hear your feedback on all of it. My guess is a whole new exciting world is about to open up. Here's a few references from Luis:

      “Force for ancient and recent life: viral and stem-loop RNA consortia promote life” Villarreal LP, Ann N Y; Acad Sci. 2014 Nov 6. doi: 10.1111/nyas.12565. [Epub ahead of print] PMID: 25376951

      “Rethinking quasispecies theory: From fittest type to cooperative consortia”
      Villarreal LP, Witzany G.; World J Biol Chem. 2013 Nov 26;4(4):79-90. doi: 10.4331/wjbc.v4.i4.79. Review. PMID: 24340131

      “Phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis”;Hamacher K, Greiner T, Ogata H, Van Etten JL, Gebhardt M, Villarreal LP, Cosentino C, Moroni A, Thiel G.;PLoS One. 2012;7(6):e38826. doi: 10.1371/journal.pone.0038826. Epub 2012 Jun 7. PMID: 22685610

      “Viral ancestors of antiviral systems” Villarreal LP.; Viruses. 2011 Oct;3(10):1933-58. doi: 10.3390/v3101933. Epub 2011 Oct 20. Review. PMID: 22069523

      “The source of self: genetic parasites and the origin of adaptive immunity” Villarreal LP., Ann N Y; Acad Sci. 2009 Oct;1178:194-232. doi: 10.1111/j.1749-6632.2009.05020.x. PMID: 19845639

      “Viruses are essential agents within the roots and stem of the tree of life” Villarreal LP, Witzany G.;J Theor Biol. 2010 Feb 21;262(4):698-710. doi: 10.1016/j.jtbi.2009.10.014. Epub 2009; Oct 13. PMID: 19833132

      I hope this sparks some discussion!

    • I'll have to break my reply up into sections. At first I believe you're referring indirectly to convergence. I'd also add that our 2D pictures of the evolution of humans (and any organism for that matter) is reducing or impeding our (lay people) ability to fully understand the complexity of an organisms evolutionary development and history. The comparison of the evolutionary tree being more like a coral is more apt to get us there but 3D modeling will help us even further. More fossils will be needed to be sure but until we get there we have to stop thinking linearly as you've stated.

    • So much to think and talk about but even more to learn. I thought that my biggest shortcoming of evolutionary understanding was to get a better grasp of epigenetics and now you throw all this other stuff my way.

      First off I'll say that I first started as a selfish gene guy and thought that evolution at the level of the organism or species was rubbish. My current view is that gene based evolution is mostly correct but far too simple and that evolution also (at least part of the time) acts on the level of the organism, species, relational community possibly even some abiotic factors outside the organism itself. The complexity is such that it can never be 100% solved or so I'm thinking. 98% of the complexity may be fleshed out but the number of factors is just too great to fully get it. I laugh when people see some new modification to evolutionary theory and then use some small addition to claim that evolution is failing. As you know that's certainly not the case.

      Is there any one book (accessible by me) that explains a lot of these new understandings and speculations? I'm guessing it's too new.

      Keep the ideas coming :) Oh so much to read and so little time.

    • I have attempted to craft an easier to understand synthesis of the thematic properties of the relationship economy we see in biology. This first link is a effort to form a theoretical lens that wound bring the clarity what makes the relational aspect of the biological economy work the way it does. This lens transcends our categories like species and treats collections of relationships that operate on what a community of relationships model. My hope is this kind of model can help us understand that when we become nourishing and or antagonistic agents in the overall biological economy, that this will translate into what we experience as health (sustainability, stability etc.) or disease (disrupted systems and instability. ( in other words triggering immune responses from systems which we have a parasitic and or predatory relationship with, or failing to contend properly with toxic agents)

      I called the lens "ectosymbiotic theory". I did this in honor of Lynn Margulis, Dorian Sagan and others who first popularized endosymbiotic theory, which descrives the merging of organisms as a community under a single membrane, and their later attempt to expand on that idea with Gaia theory. I think this kind of systemic thinking offers us a more useful rendering to negotiate, or at least understand the consequences of our behaviors with our eyes open than the linear tree-like bifurcated model that "starts with genes and goes linearly outward from there model currently in use. I liken the current model with attempting to define which contributes more to the area of a square, length or width. It's a malformed lens that produces clear information, but that does not make it correct.

      This next link is a later refinement of something I am working on right now which attempts to differentiate the axiomatic themes in relational systems from the variations on the theme. The idea being we often get lost in the weeds, misidentifying symptoms as cause and so on because we do not have an appropriate model to differentiate theme from variation. I call the lens "coherence theory". This is a theoretical lens that attempts to bring the characteristics of all distinct entities in nature into focus, although this link concentrates on the biological aspect again.

      https://thewisdomoflife.wordpress.com/2018/09/14/the-relationship-engine-that-defines-biology/

      You might also enjoy the article linked in this short introduction. I think it illustrates well the sacrificial compromises you have been intuiting about the "decisions" nature makes:

      https://thewisdomoflife.wordpress.com/2018/10/12/the-behavioral-theme-of-biology-is-nourishment-and-defense/

    • I do think the discipline of evolutionary science in general has been stagnated and confused because of an unfortunate and irrelevant false dichotomy battle between Christian apologists (of either the young Earth creation or intelligent design variety) and evolutionary science. This is on top of the fact that all sciences have a social aspect that can have a stagnating effect, where defending existing ideas because of their role in things like status, funding and the like has an effect on a particular discipline. Most people already established in the conventions of thought within a discipline spend their time propagating and defending what has already been established, not exploring new territory. It has been my experience that most sit firmly in the seat of scientific progress, sword of convention in hand, facing backwards, ever ready to defend what was.

      One book you might start with to expand your horizons is "The Music of Life" by Denis Noble. It is about epigenetics, not all the new concepts, but it is a great start as far as I can tell. Here is a video overview by him which may satisfy the depth you are looking for.

      https://www.youtube.com/watch?v=ug2ESBHalm4

    • Hmm a few things to consider there. First I'll start by saying the Gaia hypothesis is dead - not that it can't be useful as a muse to think about the relationships between and among various biotic things on earth and their complex relationship. I think that some of what you're trying to communicate sounds a bit like it's overly biased towards a human view of things. I definitely agree with you about the problematic nature of a linear view common in science but I find your writing a bit obfuscatious and it can be a challenge to figure out exactly what you're getting at. It almost sounds like you're a postmodernist (definitely not like Faucault thank goodness). I aknowledge I am no expert in this area but I really like many of your ideas but I find them obscured at times by superfluous language. I'm sure with a bit more reading I'll start to get better at following your ideas. Keep them coming because they're engaging!

      I'll give your article a reading and get back to you. The first paragrah is very clear and well written! I'll be back...I'm finding the article easy to follow compared to what you typed on Cake - that makes sense as you'd have taken the time to edit it :)

      I'm seeing a problem whereby we couldn't identify what is important. What level of community if you will is the one we are trying to keep alive? Many things are both good and bad depending on whose perspective we are taking. Whose - can mean what level of relationship are we considering. Is it Gaia? Organisms on one continent? Organisms in one area? Can there actually be any other level that is meaningful other than the whole planet? If not then we have a problem with the thematic approach. I'll have to read further... Unified purpose of maximal carrying capacity of the land... Hmmm, this is problematic. Yes parts of the system can be imagined as part of a yet greater system/organism and so on ad infinitum. This could be stretched to a cosmic level even a multi-universe level. It seems doing this or thinking this way is almost artificially giving meaning to a system or complex relationship that has no purpose and just is because. Because of physical laws. Because of 'rules' or limits of life and because evolution is what it is and acts how it does.

      To say ectosymbiotic organisms (ESO) are mainly composed of mutualistic and commensalistic relationships really ignores the necessity or reality of the vicious world nature is. I'm of course applying your ESO at a larger community level here which is where it breaks down. I would however agree with you in that we too often use the skin or other membrane to demarcate our organisms without giving credit to the things that are outside the membrane yet may make a significant contribution to that organisms surival. The ESO would be a more useful idea if it was given various names to identify different levels or sizes within a great whole. I can expand on this idea later if you're wondering what I mean. Your idea of functional lines is problematic because it's not easily identifiable and in my mind arbitrary (though much of what we do and categorize is). When I read your ideas I can't help but think of the philosophical speculation about our planet being like the community of organisms within a single drop of pond water. You talk about ESO containing a single body of life but again it's not identifiable. There are no boundaries and although that's part of your point, I see this as a problem. You can't have it both ways.

      You talk about the benefits of using ESO framework but I don't see a problem or shortfall with our current way of talking about things except that I agree with you that we sometimes don't pay enough attention to 'outside' factors. Certainly our attempts to use control species to 'fix' invasive species 'problems' has had an impact on the thinking of biological ecologists. We are more aware of unintended consequences because the system of interdependencies is in some cases extremely complex and relies on both biotic and abiotic factors. I think we can deal with these challenges without the need for a new framework. I also think we are becoming more aware of the dependencies that humans for example have on microorganisms inside and outside of our own skin. Recognizing these important relationships doesn't require a new ESO language.

      You said "It may also be that a singular self-correcting ectosymbiotic body exists and parasitic and predatory mechanisms within it are methodologies for self-correction." You'd be guilty of creating a just-so story if you applied this anywhere. Virtually anything that was 'bad' could be called good so long as you were flexible on the level of ESO you were talking about. There is no purpose to life except that which we give it. Organisms exist because they could make copies of themselves. To be sure they're interdependent on other organisms and abiotic factors but it's not all for the common good if you will. The logical conclusion to the ESO idea is pretty much Gaia. Well actually even further and saying Gaia is likely a tiny piece of a great ESO that's we are not yet aware of. Not to say that panspermia can't be real or that what has happened elsewhere doesn't have an effect on here and vice versa but it's not one ESO. Gaia is dead. Recognizing various complexities we may not have been aware of before - or that we downplayed in importance - is good, and for that I give you credit. However at this point I am not sold on the value of taking on the ESO thematic lense.

      Primary producers - whether photosynthetic or chemosysthetic are not the lungs of the earth organism. I just finished the article and read Carol Wuenschell's response. I think she has succinctly said what I think is true.

    • Viral affects on evolution are certainly important but they are generally not the main driver of all evolution. I therefore put them into the regular new biology synthesis. I see no challenge to evolution and in fact want to point out that we regularly acknowledge the role viruses have had in our own evolution. I recall recently reading about schizophrenia and some viruses inside human DNA that could be expressed and lead to disease. Viruses can and have fit into our own DNA as well as other creatures. This is not something that has shaken the foundations of evolutionary theory but rather been incorporated as a small part of the larger puzzle.

    • Joe Carter

      I will attempt to digest what you have said and consider the value of attempting to clarify or not. I recognize I am trying to push past existing conventions and that comes with more than a slight risk to both opportunity and of error. I really could be missing some things.

      At first glance I see strawman arguments against things I did not intend to say, and other statements I would agree with that you present as if they refute the idea I am getting at, rather than clarify as a natural extension of what I am attempting to say.

      I would agree that communication can be a barrier. Anyone with a conventional view of biology would see what I say and dismiss it with a clear conscience. People who report what others have discovered tend to act as the immune system of every discipline, defending it from disruption. As a consequence new perspectives are frequently rejected. So entrenched is our penchant for confirmation bias, and all the attending stagnation that comes with it, we held on to humors for 1500 years even though Galen used some pretty fair scientific method for his day that, if it has continued would have made medical science advance much quicker. Instead, we simply bought what he said at face value and kept the lens there. This does not imply I am right by any stretch, but it does mean that if I am, it would not be easily recognized through the many presuppositional conventions that have accumulated in the discipline of understanding the biological economy.

      If you want to understand some positive extensions of conventional thought and not wade too far into into the deep end and choppy waters (where admittedly I may be drowning in speculation) I would suggest Denis Nobel's "The Music of life". Another interesting guy in my view is E.O Wilson if you are not already familiar with him. I think he is on to something with the way he applies eusociality to hymenoptera, isoptera and humans.

      Thanks for the feedback. I appreciate it and again, I am exploring far more than attempting to make statements of fact. Ultimately we are all better off with a more refined understanding of nature to navigate more effectively with intention.

    • Joe Carter

      Viruses can and have fit into our own DNA as well as other creatures. This is not something that has shaken the foundations of evolutionary theory but rather been incorporated as a small part of the larger puzzle.

      I completely agree. If we define evolution by natural selection as the process by which organisms change over time as a result of changes in heritable physical or behavioral traits, then as far as I know there is solid evidence to consider this a useful lens to understand biological development over time. I am pretty sure any legitimate scientific wrangling is not about whether this is true, but about how it happens.

      My guess is that things like the central dogma of molecular biology" (admittedly a poor choice of words on Francis Crick's part) that describes the flow of genetic information in cells from DNA to messenger RNA to protein has played an out sized influential role in the thinking in both biology in general and evolution more specifically. Early discoveries tend to have a primacy effect, much like G.I. Joe has more shelf life than the latest action figure which is crafted and soon forgotten. Another example in biology is because we discovered harmful bacteria and harmful viruses first, that also colored our thinking. The point is it can take a while to develop clarity out of the distorting effects of the out sized influence of the happenstantial sequence of discovery. I think all disciplines are subject to this primacy effect because of the way our perception is wired.

      With the recent recognition of the powerful role of the microbiome and so on in our development and equilibrium we are beginning to see the extended relationship field on which we depend for an optimal experience of life. I do not know if viral influence are the main driver of evolution, but I would agree they appear to be a significant one. Since 5 to 8% of the human genome appears directly connected to information left there by Human endogenous retroviruses (HERV's) and since the presence of Transposable Elements (TEs) is 44% of the human genome, and if this portion is (as suspected in some circles) the result of remnants of former non-lytic (persistent) viral contact, then I would say this, coupled with the voluminous evidence built around how bacterial fungal and archeal organisms influence, physiology, behaviors, and by extension, our evolutionary track, then using a relational model (rather than a more of less linear genetic organism based one) suggests that nature values whatever relationships (DNA, RNA Protein, other creature's behavior such as nitrogen fixers for instance and so on) that lend themselves to the perception and response traits that are able to nourish and defend the coherence of that extended set of relationships that transcends organism and is threaded throughout portions of the ecosystem. As I understand it, we would not be placental mammals without the contributory actions of a certain virus.

      For this, and other reasons, I see this relational lens I propose as a useful tool to render a clearer image of what goes on in complex dynamic adaptive systems like biology. My thought is that with a clearer understanding, we can more effectively navigate and cultivate our experience of life, and improve our chances for growing toward our potential more effectively with intentional behaviors.

      I would also say that as a metazoic creature, dependent on specific replication of cells within certain ranges that contextually service the integrity of the larger system in which they exist, that certain aspects of viral behavior such as a form of quorum sensing to trigger collective behaviors, meaning the ability to go dormant or active depending on environmental signals, that this activity could be what was at least in part co-opted to service our multicellularity.

      Again I am so pleased to share understanding here. Please do not hesitate to throw as much "wet blanket" information on what I say. I am not positive either as I can only share a perspective based on limited information and my own limited capacity to synthesize.

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332834/

      P.S. on postmodernism and obfuscatory language that is getting at a hidden agenda: I will plea guilty to using non-fiction hyperbole as a communication style that some can find difficult to navigate, but there is no hidden agenda I am aware of. My about page states my agenda as clearly and transparently as I know how. It is based on trying to cultivate the kind of world I would like to live in, where we have each other's backs to leverage our opportunity. My about page says:

      "...I do my best to explore biology specifically and natural sciences in general to understand not only the process, but the underlying themes communicated through these natural systems, and to synthesize this information into a pragmatic lens to better understand what is within our range of possibilities to cultivate on a number of fronts such as medicine and psychology as well as on an individual and community level.

      The premise of this exploration is that nature is more than a process, nature is a language that communicates our opportunity and the dangers we must avoid to cultivate that opportunity. – For instance; biological process communicate the following: When collections of entities (such as molecules, organelles, organs, species etc.) assemble in coherent relationship with each other, they do so by way of offering nourishing value in the context of the nourishment and or defense of that shared community of relationships, that the whole becomes greater than the sum of its parts. This “community principle” is the source of all coherent structures in nature and offers clues to our opportunities for sustainable wealth and a path to realize our full potential, which itself is a function of community."

      I may be wrong, but I am not big on left column dog whistle type conversations. As far as I can tell, I am more a victim of having to deal with a Gordian knot of a topic, coupled with wanting to communicate a 3 dimensional idea while having access to a 2 dimensional aperture through which to do it.

    • You stated that: "This does not imply I am right by any stretch, but it does mean that if I am, it would not be easily recognized through the many presuppositional conventions that have accumulated in the discipline of understanding the biological economy." My response is that while sometimes new 'truths' or helpful ways of thinking about things may sometimes be hard to recognize, generally speaking if something is clearly stated, and better explains things or helps us understand it more clearly, then it would be fairly easily recognized and appreciated. In this case I do not see the benefit of taking on the ESO framework as useful. I'd also add that making a case for why paradigm shifts are often impeded by the entrenched establishment and it's bulwarks really doesn't support your case or certainly an extremely weak case. Essentially any crackpot can (and most do) make this same case. I'm not suggesting you are a crank or crackpot but this is what they do. I'd say focus directly on why it's more valuable to use ESO than the current framework and terminology. Thus far I am not convinced.

    • In response to the first part of your reply up to the ncbi link: While early findings/discoveries can certainly lead to a situation where we give a disproportionate weight to certain things, I think our ongoing modifications of the current synthesis does a reasonably good job of explaining how evolution works. I think most researchers in the field have a solid grasp of the various effects on human evolution that go well beyond just the simple random mutation of genes that create variety for nature to act upon. The lay common understanding (or lack of it) of evolution is abhorent (especially in the USA) and over simplifies how it works and I see a need to increase the general populations understanding of things. In this better understanding we could or should include the various contributors (such as viruses) to the shaping of species. The lay population however is so backwards and ignorant on the topic however that this may simply serve as a way to further distance them from reality. So we are then left to focus on the scientific community where again I think the current jargon is largely sufficient to explain the complex relationship among and within species and individual organisms.

      I'm not saying that energy shouldn't be spent helping to promote this deeper complexity of the relationships within organisms and species but I don't see ESO as the answer. Maybe we could pick up a useful word or two from it, but not the wholesale framework.

    • In response to the first part of your reply up to the ncbi link: While early findings/discoveries can certainly lead to a situation we give a disproportionate weight to certain things, I think our ongoing modifications of the current synthesis does a reasonably good job of explaining how evolution works. I think most researchers in the field have a solid grasp of the various effects on human evolution that go well beyond just the simple random mutation of genes that create variety for nature to act upon. The lay common understanding (or lack of it) of evolution is abhorent (especially in the USA) and over simplifies how it works and I see a need to increase the general populations understanding of things. In this better understanding we could or should include the various contributors (such as viruses) to the shaping of species. The lay population however is so backwards and ignorant on the topic however that this may simply serve as a way to further confuse and distance them from reality. So we are then left to focus on the scientific community where again I think the current jargon is largely sufficient to explain the complex relationship among and within species and individual organisms.

      I'm not saying that energy shouldn't be spent helping to promote this deeper complexity of the relationships within organisms and species but I don't see ESO as the answer. Maybe we could pick up a useful word or two from it, but not the wholesale framework.

      Response to the part AFTER the link:

      I found the article to be more clearly written than the Cake commentary and so it should be since it was edited and got more of your time to develop your ideas. Still, I think it could be a bit more clear - and whose writing couldn't be improved to be more clear?? Certainly mine could be.

      I think your idea of ESO could be more appropriately used - not to understand nature - but to understand a human goal going forward into the future and out into the universe. Maybe make a list of terms used in current evolutionary theory that do NOT adequately explain the facts. Use that list to restart your quest for a clearer explanation of how things work and interact.

      In my mind a good thinker/writer should be able to convey a deep understanding of how things work without using almost ANY jargon at all (if writing for a lay audience or trying to prove they understand something). Certainly it'd have to be more wordy but this should be possible. As a science teacher of grades 5-9 I am continually forced to try to explain complex things in simple language. Einstein is sometimes credited with saying "genius is the ability to explain complex things in simple language". Whether or not he said it, it's spot on. While jargon often effectively conveys larger ideas in fewer words, there is always a point where it starts to impede with understanding rather than further it. ESO framework is as much obfuscatious jargon as it is a poor representation of how the biological world and biology actually work. I would say the later is the more important concern here. It simply isn't helping further our understanding of the way things are. It's unnecessary and while sometimes a new view or lense of things can toss off the old stale and outdated ideas, in this case I feel the current language is working better than the proposed new one.

    You've been invited!