Saturday, 22 November 2014

Evolving Cooperation - But For Who Or What?

Bacteroides fragilis
Look after your gut bacteria; it might be your allotted purpose in life - if you subscribe to the evidence-free religious notion that you must be here for a purpose.

A couple of scientific papers in the last couple weeks have caught my attention because they demonstrate how Richard Dawkins' 'Selfish Gene' metaphor for how Darwinian evolution actually works gives, contrary to what a superficial reading of the term might suggest to those who don't understand evolution, cooperation rather than conflict.

We humans, as with all other multicellular species, are not just cooperative alliances of 'human' genes; not just cooperative alliances of prokaryotic cells and not even just cooperative alliances of eukaryotic cells making us, in reality, organised bacterial colonies. In fact, we are cooperative co-evolved and co-dependent alliances of human cells carrying 'human' genes, bacteria carrying bacterial genes and even viruses carrying viral genes.

These recent papers come on top of another paper which I blogged about earlier, showing how the human microbiome diverged from that of the other great apes as we diverged from them and raising the possibility that it might not always have been human genes which drove human evolution. Both of them add to this picture and show how evolution of complex organisms is really the evolution of alliances. Alliances of replicators such as genes, whether they occupy the same cell nucleus, the cells of different organisms, a small strand of viral RNA, or even in sentient species, cultural memes, are at the very centre of evolution.

The first paper, published in Nature by a team from New York University School of Medicine, New York, USA, showed how a virus can take on the function of beneficial bacteria in the gut if bacterial numbers fall too low. It has long been recognised that bacteria have an essential function in the gut both ensuring general health and stimulating the immune system. Now this team has shown that a murine norovirus can perform the same function in the gut of mice.

Abstract.
Intestinal microbial communities have profound effects on host physiology. Whereas the symbiotic contribution of commensal bacteria is well established, the role of eukaryotic viruses that are present in the gastrointestinal tract under homeostatic conditions is undefined. Here we demonstrate that a common enteric RNA virus can replace the beneficial function of commensal bacteria in the intestine. Murine norovirus (MNV) infection of germ-free or antibiotic-treated mice restored intestinal morphology and lymphocyte function without inducing overt inflammation and disease. The presence of MNV also suppressed an expansion of group 2 innate lymphoid cells observed in the absence of bacteria, and induced transcriptional changes in the intestine associated with immune development and type I interferon (IFN) signalling. Consistent with this observation, the IFN-α receptor was essential for the ability of MNV to compensate for bacterial depletion. Importantly, MNV infection offset the deleterious effect of treatment with antibiotics in models of intestinal injury and pathogenic bacterial infection. These data indicate that eukaryotic viruses have the capacity to support intestinal homeostasis and shape mucosal immunity, similarly to commensal bacteria.


It's not hard to imagine how this system could have evolved, given the mutual interest in maintaining a healthy micro-environment in the gut and given the susceptibility of the microbiome to sudden collapses in populations of the different organisms involved. Natural selection has ensured that a belt and braces approach has come to predominate because that produces more descendants in the long run and, given that the population of viruses is not affected by the same environmental factors that affect the population of bacteria, having the eggs in two baskets (to mix the metaphor) has an obvious advantage over having them all in one.

And so evolution in the murine norovirus, in the context of the mouse gut, has been beneficial to both the mouse and the virus, as well as the bacteria who get a surviving host gut to repopulate.

The gut-brain connection (via Grenham et al.), 2011
The second paper, regretably sitting behind a paywall but discussed in this blog by Rachel Zamzow, presented to a symposium of the Society for Neuroscience in Washington, DC, USA on 19 November, 2014 argued that our gut microbiome can influence our mental health and personality, and vice versa, and suggested a mechanism for doing so.

For example, mice displaying some of the symptoms normally associated with autism had a lower than normal population of the common gut bacterium Bacteroides fragilis. They also had raised blood levels of a bacterial metabolite, 4-ethylphenylsulphate (4EPS). Feeding these mice with B. fragilis reversed their symptoms while injecting normal mice with 4EPS gave them symptoms of autism. The mechanism for this is not yet known but it seems likely that B. fragilis in the gut reduces either the production or the absorption of 4EPS.

Note: this has only been demonstrated in mice with autism-like symptoms. This may not have any application to autism in humans, for which both the cause and mechanism may be different to those symptoms in mice.

So again we see our teeming gut microbiome, of which there are a hundred bacteria for every one of 'our' cells, may be influencing even our 'self' as expressed by our personality and behaviour. Although there is a great deal of woo in the marketing of preparations of 'friendly bacteria' as cures for all manner of things, there may well be a sound scientific basis for the idea that a healthy microbiome is at least an important part of having a healthy mind and body.

Biologically, what are we looking at here, in addition to the fundamental idea that evolution is the evolution of alliances of genes, and that it's not so important that these genes are in what science defines as a 'species' as that they are in alliance? It matters not one jot to the mechanism of neo-Darwinian, 'selfish gene' evolution where the genes reside.

Now, what if we put aside our tendency to see evolution in terms of the organism which is most obvious to us - human, mouse, mammal, reptile, fish, etc - and see this in whole alliance terms, including the microbiome? (Hopefully, regular readers of my blogs have already put aside any tendency to think of evolution as having a purpose, let alone being for evolving humans).

For every one of your human cells in your body, you have one hundred bacteria in your gut! In terms of the total evolving alliance - the organism that you see as you in a mirror and which all your friends and relatives think of as you; the organism currently reading this blog - it is only 1% Homo sapiens. Is it reasonable to suppose that this 1% is what evolution of humans has been all about? Even if we ignore this population ratio and look just at the number of genes involved in this alliance, the same principle holds. You, in your totality, are much more bacteria, virus (and other protozoans) than you are human.

Is it possible that bacteria are still in charge (metaphorically) of evolution and that the entire evolution of the protostomes and deuterostomes (animals with a gut with two openings) was driven by the fact that bacteria produce more descendants when secure inside a tube which supplies them with nutrients? Are we simply mechanisms for replicating our gut so our bacteria can replicate in safety in a self-repairing, self replicating fermentation vat made of human cells?

Any creationist prepared to either refute this interpretation of biology or explain how humans being designed to make it safe for bacteria to live in a hostile Universe fits in with a notions which says the Universe is 'fine-tuned' for human life because that's what some notional magic man in the sky made it all for? Why couldn't this magic designer have intended to make countless trillions of bacteria, especially since they outnumber humans by several orders of magnitude? An objective observer - the metaphorical alien spaceman - might well take a look at us and conclude that we're designed for producing bacteria, and who could dispute it? (Although any intelligent beings capable of travelling to Earth would be intelligent enough to know that there is no plan in evolution, so nothing was designed for anything).

Fortunately, science doesn't need to solve these sorts of conundrums because it doesn't need to force-fit observed reality into an evidence-free notion just to protect some sacred conclusion made up by primitive people who knew no better. I wonder if religious people ever wish they could be that honest and objective about the world.


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