A Possible Paradigm Shift in Evolutionary Biology? Thank the Microbes

Full disclosure: This post is from the “I wish I had paid better attention in high school science rather than play Rock’em Sock’em Robots with the lab frogs, which is why I work in the humanities” department, but a friend of mine in the sciences passed this on to me a couple of days ago, and even *I* saw how interesting and important this might be.

Apparently there is ferment in the life sciences as there is in Christian theology. A recent paper in the Proceedings of the National Academy of Sciences (PNAS) sums up what is going on from the biology side, and general gist of the study is that it draws a hugely more complicated picture of the interconnectedness of life.

The emerging wealth of data on bacteria-animal (and bacteria-plant) associations is profound in its implications. We are not just us, we are inextricably linked to other living things as well –way beyond the standard ecological argument. Our associations with bacteria, at least, means we are necessarily united with our symbionts.

Here are two teaser quotes from the paper:

Furthermore, recent studies link the gut microbiota to brain physiology and animal behavior. For instance, germ-free mice have defects in brain regions that control anxiety, and feeding probiotic bacteria to normal mice re- duces depression-like behaviors. The finding that TLRs, which transduce bacterial signals to host cells, are present on enteric neurons reveals one mechanism by which microbiota can communicate with the central nervous system through the brain–gut axis. Thus, maintaining homeostasis with the normal microbiota is essential to a healthy nervous system. (PE: I was informed that TLR refers to receptors on some of our cells that recognize structurally conserved molecules derived from microbes.)

……new data are demanding a reexamination of the very concepts of what constitutes a genome, a population, an environment, and an organism.

Here is a blog post, Whose Planet is it Anyway?, that rehearses the implications of the study.

For readers of this blog, here is one implication: Christians who have not yet come to grips with evolutionary biology may soon be hit by a revised, and theologically more challenging, new synthesis.

This new synthesis will not replace what we already know about evolution, but it will show there is much more to the complexity of life than we had known before. I can imagine this would inspire theological discussions on the nature of humanity that would be several giant steps beyond where things are today.

Oh how I wish I had paid attention in high school.

best book on evolution and faith I've read in years (or, constructing a cathedral in your mind)
Adam’s Fall and Early Christian Notions of Sin
What I think about NOMA (not the ex-Red Sox shortstop but the evolution thing)
creating Adam, again and again
  • Evidence2Hope

    Got to love the inter-connectivity of life :)

  • Matt Tebbe

    Pete – Similar connections (re: brain and gut, as it pertains to mood, depression, anxiety) can be found in this Radiolab podcast, for ‘readers’ who would prefer to listen to similarly incredible scientific findings: http://www.radiolab.org/2012/apr/02/

    Most neuroscience phd’s at Cambridge today study…not brains…but digestive tracts. We’re only just beginning to understand this connection.

    • http://www.tiffanyjane.tumblr.com Tiffany Taylor

      I remember when I first listened to this being blown away. It’s like we are more than just a single person, but entire ecosystems within ecosystems. I am not me without the bacteria in my gut helping me be me. Truly no man is an island..

    • Susan Gerard

      Matt, I appreciate the immense popularity of Radiolab (my adult, science-minded children listen to it). But their science is ***terrible***. It’s greatly anecdotal. But popular. Not to diminish the glory of interconnectedness.

      • Matt Tebbe

        Hey Susan – Yep. I can appreciate that. In this case the science isn’t ‘theirs’; they interview a neuroscientist and summarize a few studies. Just had the same themes and connections that Pete mentioned. But your caution is a good one: the entertainment industry doesn’t have the same rigor or standards as a scientist, institution, journal, etc. Peace.

  • Chris

    So I wrote this sentence: “While fascinating, I think most of the question of our humanity lies in the philosophy of mind.” Then I realized, “Oh wait, it just said that gut bacteria influence our thoughts…” Then I thought, “This will be fun!”

    Then I thought, “I’m hungry.” Damn gut influencing my thoughts!

    • peteenns

      Didn’t Paul say, “Their stomach is their God”? I am waiting for someone to argue that Paul anticipated all of this.

  • candeux

    And here I thought that it was anxiety that was upsetting my stomach…looks like it might be the other way around!

  • Jack

    What exactly is this supposed to prove?

  • david carlson

    Not sure how this proves either side

  • http://www.waivingentropy.com/ Daniel Bastian

    Excellent post, Pete. Though it is a bit of an excursus from your usual, I wouldn’t mind seeing more of this variety in the future.

    We are indeed deeply interconnected and inseparable from the rest of biology. There is precious little, in fact, that separates us genomically from other animals, plants, fungi and protists. The latest research even indicates that our earliest ancestors were RNA viruses, which today comprise a whopping 8% of the human genome. Further, research into what has been dubbed the ‘microbiome’ has revealed that as many as 1^15 microbes are, right now, foraging and scuttling about inside each and every one of us. It could in fact be said that biology is 99% “micro”. Their influence on the planet and on us is just beginning to be unearthed.

    The results are in: We are intertwined with an imponderably vast chain of life reaching back to unicellular organisms and and to the interstellar maelstroms out of which they arose. To get a bird’s eye view of this interconnectedness, see the following graphic:


    This is exhilarating, breathtaking even. And it’s far moreso than the prosaic, simplistic ideas guarded so diligently by Christian fundamentalists.

    - Daniel

    • Susan Gerard


      You are misrepresenting the role of viruses in evolution. There is no RNA in our genome, only DNA. What you are referring to is a class of retroviruses called Bornaviruses. Humans have nucleoproteins that resemble theirs, thought to have entered primate genomes about 40 million years ago through “endogenization”. They are mostly multireplicated (repeated sequences) “degraded” genes – non-functional, nonsense sequences if you will. The fact that these are degraded sequences, which self-replicate over long evolutionary periods and that some other mammalian species have only been carrying these fragments for 10 million years suggests infection, not evolution. If you need citations, let me know, I’d be happy to provide.

      Please know that we are absolutely *not* descended from retroviruses.

      • http://www.waivingentropy.com/ Daniel Bastian

        Thanks for the clarification, Susan! I am basing my comment somewhat on the following study:

        “Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.”


        Perhaps I misread the conclusions of the study? Could you clarify for me? Thanks!

        - Daniel

        • http://timebottle.weebly.com/ Beau Quilter

          Hi Daniel and Susan

          To clarify, there are origin of life hypotheses that consider a form of RNA as a possible forerunner to DNA; but this research is not related to the study of retrovirus sequences that may have found there way into our genome. The latter is not evidence for the former, because, as Susan stated, if we have retrovirus sequences in our genome, they are late additions in our biological history, not remnants of our origins.

          • Susan Gerard

            thank you, beau. Well stated.

        • Susan Gerard


          This article is solely about the evolution of viruses. The model they’re using is the model of cellular evolution. They’re comparing the two models. If you re-read the article from this perspective, I think you’ll see this. The simplest model for cellular evolution is that cells arose from a primordial soup of inorganic elements. The authors are suggesting that viruses, which are simpler, arose before cells did, not that cells descended from viruses.

          I feel compelled to point out that this is purely theoretical. The work of the earliest proponent of the primordial soup model could not be replicated by independent researchers, nor could his work be replicated when observed by others. Just need to say this.

          • ridahoan

            Good clarification. I think the idea that viruses predated cells outlandish. What we currently see is a continuum of ‘semi-autonomous mobile elements’ from transposons to viruses, some more autonomous than others, but all fundamentally dependent on a host cell for replication. I never understood the argument that viruses could predate metabolic life. What do you think? Is there something new?

          • Susan Gerard

            The only thing that’s new to me is that retroviruses left a fossil record. But that doesn’t place it in the timeline.

            I find it a hard theory to think seriously about, for that would mean viruses (obligate intracellular parasites, as you pointed out) *anticipated* cell formation. To think they somehow evolved and then were waiting (for how long, and under what environmental conditions?) to pounce on the first cells seems very strange at best, even given that retroviruses often do not kill their host cells and that the bornavirus does not need a specific cell membrane receptor cite (as do most all other viruses, including most retroviruses). Wouldn’t that suggest that bornaviruses would have entered our genomes much earlier than about 40 million years ago?

  • Susan Gerard

    I have to admit that I’m struggling a bit with your post. The interconnectivity of life, esp. between bacteria and animals, is not new, esp. in veterinary and human medicine. Horizontal gene transfer and inter-kingdom signalling were published in 2008. The timeline of eukariotic evolution is still extremely speculative,
    and no one yet knows how multicellular organisms evolved, but the latter
    will be known long before the former. So, I guess I’m saying, ok, how does this relate in a new way to evolution? The surprise to me is not co-evolution, but that 37% of human genes (not our genome) have homologs in bacteria and 28% “originated” in unicellular eukaryotes.

    That’s saying more definitively, “we all descended from single-celled organisms”, instead of “we descended from apes”, which is both more palatable to people who hate apes and more supportive of evolution in general. Am I missing something? I’m really not trying to be foolish – I just am.

    • ridahoan

      Hmm. Good points, but maybe you ask too much of the popular press. HGT among prokaryotes, well, that’s been well studied since the 1980′s, especially since the mid-1990s. And Agrobacterium’s genetic control of plants — well, Monsanto’s been making hay out of that for about 20 years now.

      It’s my experience that the press picks up on some paper written with a slightly sensational angle, eg a Nature paper ;-) , and we get another news cycle of ‘new science.’ But hey, at least its science in the press. There must be some feedback into science again.

      Personally I trace the less ‘Darwinian’ slant (though probably not fair to Darwin, how about ‘neo Darwinian’) through the late great Lynn Margulis, champion of the endosymbiotic origins of eukaryotes, and cooperation vs competition in general as an important contributor to evolution, as I’m sure you know, starting in the late ’60s. And she was reviving some crazy Russian work, among others, from the turn of the previous century.

      Few truly new ideas under the sun, it would seem.

  • rvs

    I read a book last year that intrigued me. Darwin’s pharmacy: sex, plants, and the evolution of the noösphere, by Richard Doyle. –A guy who is finding his way back to spirituality, after a journey through the underworld of grim naturalism. Christian metaphysics? No, not exactly, but didn’t C.S. Lewis involve himself in a kind of reluctant incrementalism before arriving at theism? I would file Doyle’s argument under “speculative philosophy,” which perhaps is sort of like speculative fiction. Caveat: I did not do well in science class, and I am sure that I do not understand the science of the post above, but I do see how it might be used to tell dramatic stories.

  • Tony Springer

    In the early 70s, I did pay attention in science class, but we did not have much of this genetics stuff. Thankfully, my son recently finished high school biology and I learned more about it by helping him study for the class. Genetics was a huge part. Interesting thoughts from your post

  • Hallvard N. Jørgensen

    Thanks for this interesting post! I would also really endorse Conor Cunningham’s “Darwin’s pious idea”, where he sums up much evidence from cutting-edge research that has huge implications for the relationship between biology and theology. Briefly, the general point is that the neo-darwinian synthesis (evolution=mutations+natural selection) really just gives a part of the picture, and that lots of other mechanisms are at play. Incidentally, it is this – now “old hat” – picture of biology that has informed, and provided a sort of metaphysical foundation, for much of the new atheism.

    Most of the new evidence comes from evolutionary development and molecular biology. Cunningham believes that the new picture in biology actually speaks against reductionist materialism (i. e. the idea that “everything is matter”, and that all things in the sciences in principle could be reduced to the motions of matter.) Again: A wonderful book, deeply relevant to theology.

    • http://timebottle.weebly.com/ Beau Quilter

      There is a problem with Cunningham’s proposal that new atheism is led by “old hat” biology, unfamiliar with the latest in cutting-edge biological research. Some of the “new atheists” are evolutionary biologists at the top of their field. They are far better informed about the latest in “cutting-edge research” than Cunningham, who is a professor of philosophy with no background in biological research.

      • Hallvard N. Jørgensen

        Well – I’m not sure whether you’ve read the book. Cunningham basically quotes rather liberally a whole lot of top scientists – Oxford, Harvard, Princeton etc. It is *they* that are saying that notions of “selfish genes”, of “panselectionism” etc. are no longer tenable in the light of recent developments in biology (if they ever were). It’s just a fact that the neo-Darwinian synthesis is in a process of either being much transformed, or else disbanded altogether.

        • http://timebottle.weebly.com/ Beau Quilter

          So these Oxford, Harvard, and Princeton professors are saying that New Atheism is led by scientists with old biological models? Are they saying that they are against reductionist materialism? Or is Cunningham simply using their research on new biological mechanisms to draw his own conclusions?

          • Hallvard N. Jørgensen

            Well, that’s a good question. It is a fact that much of new atheism builds a worldview/metaphysics on certain interpretations of science, cf. Dennett’s “universal acid” or Dawkins’ “Selfish Genes.” So if Dawkins’ view of the functions of the DNA are revised, so must the metaphysics that is built on it (i. e. “we are survival machines for DNA, that is the fundamental reason for our existence etc.”) The same goes for the mechanisms of evolutionary development; if it is true that “natural selection of the fittest” does not by far account for all kinds of development, then views of human nature and psychology that are built on this idea, must also be revised. So Cunningham does quote a whole lot of recent research that both implicitly and explicitly criticises selfish genes and panselectionism.

            The question of reductionism and materialism is admittedly more tricky. It has to do with whether the new developments in biology favor a “top down” approach to biological organisms rather than a “bottom up”, as strict reductive materialists would say (i. e. everything is in principle to be explained by motions of matter at the deepest level). I suspend judgment here; I do not have the competence to assess Cunninghams reflections here; they build much on the notion of “self-organizing principles” in the realm of nature. But the conclusions and inferences about reduction are rather controversial, I guess (reduction is, of course, a hotly debated topic within philosophy of science).

            I should mention that he also has a brilliant and thorough chapter on exactly materialism and physicalism later on in the book, there drawing much on modern physics, but also on what kind of metaphysical implications that must be drawn from any strict reductive/restrictive materialist (i. e. no objects, no morals, no you and me, no meaning, no teleology etc.)

            Well, again; if you are interested in these matters, I encourage you to take a look at the book.

          • River Lizard

            Actually until you are honest with yourself regarding Atheism and Evolution, how can anyone take you seriously.
            Atheism is only 1 thing….disbelief in the claims of gods. That’s it.
            You don’t know what you’re talking about, please educate yourself.

  • http://jesuswithoutbaggage.wordpress.com/ jesuswithoutbaggage


  • Bev Mitchell

    Thanks for this Pete.

    Theology and biology are the two formal sciences that study life. They do it from very different perspectives and use very different tools, however both are needed to understand life at its fullest. Just thinking out loud and at great risk, would it not make sense to suggest that seminaries, divinity schools, and yea even Bible colleges ask students to arrive with or to take two credits of university biology?

    On another note, did you notice the large number of women among the 26 authors of the PNAS paper? This large contribution from women is now typical in the life sciences. Of course, it is growing in theology, but probably a full generation behind. I’m a guy, BTW, and a biologist who watched the amazing growth of women in biology for over 40 years. First undergrad, then grad (most of my grad students were women), then large numbers of hires at the assistant/associate professor levels until today we see scholarly leadership in biology almost equally shared among women and men.

    And finally, in the book recommendation department (with thanks for those already made) those with a bit of biology under their belt will find this one very interesting. It’s much in the same vein as the PNAS paper but with much broader coverage.

    “Ecological Developmental Biology: Integrating Epigenetics, Medicine and Evolution” by Scott F. Gilbert and David Epel

  • C. Trace

    Life is miraculous. Atheists, materialists, evolutionists have been around since before our Savior’s Incarnation. This current era we are in is an era of extreme ignorance of the history of science. Atheists and logical positivists have captured the universities and the media. If Isaac Newton were alive today he’d be mocked as an occultist. Each new discovery in, for instance, micro biology that so makes a mockery of evolutionary dogma is stated dogmatically to further evolutionary claims, and if you don’t believe it you are a flat earther.

  • http://www.infidels.org/library/modern/ed_babinski/babinski-bio.html EdwardTBabinski

    Not great news for “Bible believers.” The research only demonstrates that humanity is that much more firmly rooted in the biological world. Species can evolve in groups. Parasites as well as benign bacteria and beneficial bacteria evolved along with the species carrying them.

  • Eric (Sargon?) Kunkel

    You were always a fine Lab partner.

    All this symbiosis must have something to do with Monism and some kind of Panentheism. All that seems scary at first.

    But it can bring you back full circle to an ontological triune God.

    Tell them “I am sent me”… “The Alpha and Omega”.

    God is not not understandable; or “Our God is too small.” He is both transcendent and immanent within Creation, IMHO. That remains a paradox, but we can work on that, the paradox versus antinomy thing.

    And so He remains a God worthy of worship. Not like one of those “deities” guarding the gates of the Mesopotamian cities.