Denis Noble has a new review out, in Experimental Physiology called Physiology is rocking the foundations of evolutionary biology. Unfortunately the article itself is behind a paywall, but here is the abstract:
The ‘Modern Synthesis’ (Neo-Darwinism) is a mid-20th century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection. Any role of physiological function in influencing genetic inheritance was excluded. The organism became a mere carrier of the real objects of selection, its genes. We now know that genetic change is far from random and often not gradual. Molecular genetics and genome sequencing have deconstructed this unnecessarily restrictive view of evolution in a way that reintroduces physiological function and interactions with the environment as factors influencing the speed and nature of inherited change. Acquired characteristics can be inherited, and in a few but growing number of cases that inheritance has now been shown to be robust for many generations. The 21st century can look forward to a new synthesis that will reintegrate physiology with evolutionary biology.
It’s a nice synthesis of the views he expresses in his book, The Music of Life, which I mentioned a previous post, Reductionism Redux , but he also lays out very clearly the ways in which four assumptions that have underlain much thinking in evolutionary biology since the “modern synthesis” (not so modern now), need to be revisited.
Ironically, Noble says:
In some respects, my article returns to a more nuanced, less dogmatic view of evolutionary theory (see also Müller, 2007; Mesoudi et al. 2013), which is much more in keeping with the spirit of Darwin’s own ideas than is the Neo-Darwinist view.
The four assumptions are these:
1. Genetic changes are random with respect to function. Noble argues that McClintock’s view of the genome as an “organ of the cell” is a more productive way of looking at DNA – as something that itself changes, as Shapiro is notable for claiming, in response to physiological demands.
DNA is not merely a one-dimensional sequence. It is a highly complex physiological system that is regulated by the cells, tissues and organs of the body.
2. Genetic change is gradual. Noble cites McClintock again, and also Margulis, to make the point that:
Mobile transposable elements that have been involved in evolution come in more forms than only retrotransposons and DNA transposons. They include the movement and/or fusion of whole genomes between species.
and that symbiogenesis, by which means, fairly radical genetic and phenotypic changes can come about in a single step, needs to be considered, as well as the fact that inheritance is not solely longitidinal:
One of the major developments of Darwin’s concept of a ‘tree of life’ is that the analogy should be more that of a ‘network of life’ (Doolittle, 1999; Woese & Goldenfeld, 2009).
3. That the unit of selection is the gene. It seems to me that this is a misreading – the unit of selection is, and has always been, the phenotype, in the sense that it is the phenotype that has to survive in the world. But it is true that with sexually-reproducing species, the gene can also be conceived of as the unit, and perhaps it is true that natural selection has been perceived as being too “gene-centred”, as with Dawkins’ conceptualisation of “The Selfish Gene”.
4.That acquired characterstics cannot be inherited. Epigenetics suggest that they can.
Noble suggests the following “Integrative Synthesis”.
| Before: Modern Synthesis | Now: towards an Integrative Synthesis |
|---|---|
| Gene-centred view of natural selection | Selection is multilevel |
| Impossibility of inheritance of acquired characteristics | Acquired characters can be inherited |
| Distinction between replicator (genes) and vehicle (phenotype) | The genome is an ‘organ of the cell’, not its dictator. Control is distributed |
| The central dogma of molecular biology | Genomes are not isolated from organism and environment |
I don’t think this renders previous models “wrong”, but I do agree that a model such as this could be useful. As a systems-level neuroscientist I tend to have sympathy with systems-level approaches. I think the chief adavantage is that it allows us to think in terms of evolution as a nested system – cells within organisms within ecosystems within the biosphere itself, where developmental processes at one level can be seen as evolutionary at the next. Indeed, I’ve argued for ages that the brain itself works as a kind of GA, in which fruitful processes are propagated, and less fruitful inhibited.
But I see that both Sal Cordova and Cornelius Hunter have already flagged up this paper as another nail in the coffin for evilution.
*sigh*
KF has a post at UD with a video and with what seems to be a working link to the article.
Ah cool. I didn’t need to use my Special Powers after all 🙂
Sal seems not to have noticed that it’s a review paper, just that it’s “peer-reviewed”. Honestly, sometimes ID proponents seem to think that non-IDists don’t read their own literature! Or do this work in the first place, come to that. I think Shapiro over-eggs his case sometimes, but it really is time ID opponents stopped jumping to the conclusion that because evolutionary biologists criticise previous elements of evolutionary theory, that Darwinism Is Dead! Evolutionary biologists have a far better record of finding problems in evolutionary biology than IDists have – and refining the model in the light of those problems, deriving new hypotheses from the new model, and testing them.
Hooboy, I’m feeling a bit cross this morning. It’s probably the sight of UD posters finally but somewhat ungraciously (apart from Dr Torley) twigging that Dembski’s CSI can’t be calculated. Though they (again apart from Dr Torley) still don’t seem to have seen the ele(P(T|H)ant
(I’m going to keep recycling that one for a bit).
My quick glance (as a non-biologist) persuaded me that there is probably little there that is new, and nothing to concern evolutionists.
For myself, I’m not a Darwinist. That is to say, I think neo-Darwinism oversimplifies things a tad. However, I agree with you that Shapiro overplays his disagreements with Darwinism.
ID people seem to have trouble with this. Because I am an evolutionist, they insist on seeing me as a Darwinist. And they see any small criticism of the neo-Darwinian account as counting against evolution and for ID.
Certainly nothing to “concern” evolutionists, even if “evolutionists” were to have some kind of vested interest in being “right”, which we don’t.
I find his approach exciting, if polemic (which he readily admits). As I said, I like systems, and I think evolutionary processes are really interesting as systems. I could even find myself arguing that, if Shapiro and Noble are right, there is a kind of minimalist counterpart to what we would call “intention” in an intelligent system, not surprisingly, as I think that intentional intelligence both develops (from non-intentional beginnings at conceptions) and evolves (over generations). Shapiro’s fundamental point, I think, is that evolvability itself evolves – populations whose members have characteristics that tend toward making the population more robust will tend to have longer lineages.
Perhaps the biosphere itself will evolve to ask itself how it evolved! After all, one component of it already does….
Neil Rickert,
That’s because they’ve never accepted that science advances through serial self–criticism. See KF’s oft-used snark about the “holy lab-coat”
ID isn’t very good at self-criticism, mostly because it has assumed its conclusion. I think it will likely fall apart completely if the only methods with the potential of independently supporting that conclusion – empirical and practical methods of detecting design, like calculations of CSI and its bastard offspring – are shown unequivocally to be useless.
Then it becomes apologetics
When people raise the issue of gene interaction and large mutations (and more generally of interaction of genotypes with environments) they often overlook several points:
1. Even if lots of genes interact, when one allele occurs by mutation in a population that is otherwise homogeneous, we analyze its fate by considering just the genotypes at that locus. (Of course populations with homogeneous genetic backgrounds are rare).
2. A mutation of large effect is a single copy. To take over the population it needs to spread and change in gene frequency. And that can be a gradual process.
3. Saying many genes have interactions with others does not mean that two randomly chosen loci in your genome will interact strongly. Most people have close relatives but that does not mean that two random people passing on the street are typically close relatives.
I would also add that epigenetic changes are very interesting. But for the mechanisms we know, they also have a very high rate of reversion. They cannot explain phenotypic differences of species separated by many generations — unless they are stabilized by subsequent genetic changes.
UDers have trouble understanding that Shapiro is not refuting Darwin, but emphasizing the importance of large scale mutations.
So how is evolvability any more difficult to evolve than eyes or brains?
Has anyone written a GA that evolves types of mutations?
You could have stopped that sentence at “understanding.”
I’d like to hear about any work like this as well. I’m playing around with using circular genomes to allow for indels and dups as well as point mutations, but haven’t had as much time to spend on it as I’d like.
I had a go. It was a recombination system (sexual reproduction) and number of cut points was one of the parameters that could evolve. It was a sentence-evolving algorithm, and I think it optimised the size of the chunks that got moved around. (It wasn’t a pre-set sentence, like weasel, the fitness function had a few parameters including pronouncability, Englishness and word type order (articles before nouns or adjectives, verbs non-adjacent. I’ll try and dig it out). There was no penalty for lack of semantic sense, but it did converge on stuff that looked like some kind of mad pidgin.
Seems to me all of this addresses HOW evolution works, not WHETHER it works. Clearly, very complex and interdependent processes are involved. But I thought the ID position was that evolution simply does not happen, and instead life was all Designed. As many have pointed out, when Einstein visualized gravity very differently from Newton, apples didn’t stop dropping from trees. Gravity remained as real as evolution.
So why would ID proponents find anything to celebrate in this material? Even if it’s all true, it simply makes evolutionary theory stronger and more complete. It certainly doesn’t reject evolution in favor of poof.
Well, there is no simple ID position. Even Creationists are more unified on evolution, as they seem to have figured out that the need “microevolution” (pretty substantial “micro” evolution at that) to get all known fauna from the animals on the Ark.
IDists range from those who don’t think evolution works at all (not even micro, from what I can make out) to those who accept it does but has “Limits”, to those who accept design-assisted common descent, to those who favour frequent Designer intervention, to those who favour Designer intervention at a few key nodes.
In contrast, what we have here is a rather nice piece of polemic making the case for a systems-based rather than a gene-based approach to evolutionary mechanisms.
What Noble is doing is saying that the assumptions of the neo-Darwinian view aren’t inviolate. I’d say they are still broadly true, myself, though, but I wouldn’t be at all surprised to find that evolutionary mechanisms have themselves optimised. Indeed, it’s hard to see how they wouldn’t.
One interesting argument I read about epigenetics was that it actually increased the random variance at phenotypic level i.e. loosened the coupling of genotype with phenotype, and thus blunted natural selection, keeping the gene pool rich and the population more robust to environmental change.
And thus selected for at population level. I thought that was rather cool. Can’t remember where I read it though.
Well, if people find it useful … still, as I’ve said before, I don’t find much to enthuse me. Physiology? I would say that this kind of metazoan-centricity is rife. Mostly among metazoans. 😉
I think it needs care in just what is meant by a ‘gene’ (and ‘selection’). The units are not ‘the things that makes eyes blue/brown’ or ‘the things that make peas wrinkly/smooth’. The genes of Dawkins (who is merely broadcasting Hamilton, Maynard Smith and Williams for wider consumption) are the evolutionary subunits revealed by repeat rounds of recombination. Where there is no recombination (see: most of the biosphere most of the time, LGT notwithstanding), the whole organism is the evolutionary allele. Perhaps counter-intuitively, physiology is not of prime evolutionary importance. Noble’s observation that multiple physiological genes interact in a phenotype is no different from that fact that multiple sites interact in a protein. The contribution of each acid cannot be separated, but the underlying DNA is still tested iteratively by survival of bearers, and variations can have a differential effect upon that DNA segment’s survival as a (fuzzy-boundaried) piece. There is simply no difference between a ‘particulate’ phenotype – wrinkliness in peas, say – and a composite one, in terms of the effect of selection and passage down the generations.
I’m very dubious about this. see here for a contrariwise view. People have combed paramecium’s hair the wrong way and had this pass down a few generations … but this is in great contrast to the idea that a somatic issue in a multicellular organism can reach into the germline and cause changes to the DNA, that then go on and are inherited for an evolutionarily significant number of generations. How? How does such a signal/response evolve (responding specifically to your parents‘ environment is unlikely to be strongly adaptive in most circumstances); what mechanism does it use to change gene regulation or to change it back? Of course, one can point to a phenomenon without knowing the mechanism, but I’m not sure we’re even at that stage.
Control ultimately arises from a stretch of DNA. There is some ‘inter-generational’ reach – the proteins acting on a particular DNA molecule may not have been synthesised by it, but by its pre-replication parent – but ultimately, the phenotype is the result of genotype. The multicellular soma that preoccupies us most is a reproductive dead end. Each cell happens to contain the same genome, and differential control according to where in the body it is, but these genes have no evolutionary future. Only their cousins in the germline do.
Blergh! The Central Dogma as defined by Crick is that sequential information can pass in only one direction between nucleic acid and protein. Reverse transcription (RNA -> DNA) was a bit of a surprise, but Crick’s dogma would be violated only by reverse translation. This has nothing to do with the fact that the genome is the target of some – or many – gene products.
I think you are forgetting that the ID program survives and replicates via obfuscation.
The damage done by people like Shapiro is not done by being wrong, but by being quote-mineable. In Shapiro’s case, it often seems to be deliberate.
Yeah. I do think Shapiro’s far too up himself.
But I did like his book. Trouble is, everyone wants to be in on a Paradigm Shift.
Paradigm is shifting all the time, sometimes it lurches a bit further than usual. But what Paradigms don’t tend to do is backtrack.
I’ve always said (seriously – I remember saying this to my mother when I was about 8 or 9) that evolution itself must be evolvable – that optimal rates and variance-producing mechanisms will tend to be selected at population level (I didn’t put it quite like that, but I got the gist), and, more recently, that in many coherent ways, evolutionary processes are intelligent processes. To that extent I’m an IDer – I’ve always had some sympathy for the idea that CSI (in its simplest form, without the eleP(T|H)ant) was a perfectly good idea for detecting things that had come about by “intelligence” as originally defined by Dembski: something with “the power and capacity to choose between options”. Evolution is a perfect example of that – it’s why Darwin used the term “natural” selection.
And some of us have also been saying for years, that Dawkins’ insistence that mutations are “random” and natural selection is “non-random” is highly misleading. Both are highly stochastic factors, but both have a non-uniform probability distribution that is really quite peaky. The interesting question is not whether either is, or is not “random” but whether they are orthogonal (except in the trivial sense that in a well-adapted population, most novel variants will be disadvantageous, while in a poorly-adapted population far more variants will be advantageous).
We have tended to assume “yes”. But perhaps not, always. I’m not entirely convinced, but it would be interesting if the answer was no, as Noble suggests. It adds yet another dimension along which things can evolve, as well as another level of selection (population rather than organism).
Cool. ID is true, as I’ve always said. Now let’s figure just how I it is, and how it figures stuff out.
KF is very excited about this!
Do come and discuss it here, KF! Seriously, you’d be very welcome.
But I’m very amused by the sudden enthusiasm.
Specfically, I posted, at UD:
Petrushka – I presume that was a reply to someone else? It is hilarious how a paper that purports to revise evolutionary theory is seized upon uncritically by ID – the authors are invariably prophets without honour, for whom Kuhn will out. Shapiro is the totem for that. Get 10 comments into any evolutionary blog post, and someone pops up saying “examine the work of James Shapiro. The way he is treated by the evolutionary establishment is just shameful”. And if the work appears to undermine any viewpoint held by Richard Dawkins*** – well, fill yer boots!
***On random, he’s wrong. On the rest, I think frequently misunderstood – including by Noble. He seems clear enough to me, but maybe I’ve got it backwards too.
Am I to believe that the UD crowd would accept “Darwinian” evolution if it weren’t for random mutations?
Well, my hunch is that the word “random” is what freaks people out, because it has so many definitions, and those definitions leak from one claim to another, and so the whole Darwinian project sounds as though life is “meaningless” (one usage of “random”). Whereas a materialist “law” sounds, if not benign, at least non-chaotic and comprehensible.
I think that’s why Darwin gets such stick, whereas Newton, or even Einstein, don’t trouble anyone.
My hunch is that if someone could show that evolution doesn’t depend on stochastic factors, but is the near inevitable corollary of early earth chemistry, no-one would have a problem with it, theologically or philosphically. We would just wonder at the magnificence of natural law, and, if theologically inclined, the genius of the God who dreamed it up.
I find the static view of existence favored by theists (and implicit in an omniscient god) to be the epitome of meaningless. In the eyes of the creator everything that will happen has already happened. Someone mentioned a 4D universe in which time can be vies as a static property like length and width. That’s what’s implied by omniscience.
An evolutionary world, on the other hand, has an indeterminate future and the chemistry of that world has unpredictable and unanticipated emergent properties. Such a chemistry and such a world is self-creating. It has freedom, and when sentient creatures evolve, they have the freedom to play the future game. to make things that have never existed and which cannot be anticipated.
Now that’s an existence having the potential for meaning.
The banishment of ‘randomness’ would appear to close the door on free will. Surely they aren’t closet hardline determinists?
Lizzie,
I think it’s important to be clear about the nature of distinctions between levels as well as concepts that might simplistically be thought to be inherited between them. The linkage unit is a vital piece of information – the team for whose benefit any adaptation might be said to arise. And this does not have a uniform dynamic across the levels.
The Mk l genome is a circle of DNA, covalently linked. Because that DNA can replicate, and that replication is exponential, it can fill an environment. New segments of DNA that join the circle make it better or worse at its ‘job’ in the environment, but in vertical inheritance, there isn’t a meaningful level below the genome in the evolutionary sense. Nor is there a meaningful level above. You get some ‘group’ effects – eg quorum sensing – but no such genome is going to sacrifice itself for a relative – even a sister, with the identical genome. Replicate yourself, or help your sister to replicate – what’s the difference? You are the same. There is little drive to higher-level interactions; prokaryotes are glorified molecules, serially crystallising the raw materials of the environment.
But things change with symbiosis (and I think sex is best considered as a kind of symbiosis). First you have endosymbionts, where there is a mix of common purpose and subterfuge, because the relationship is asymmetric. Broader asymmetries arise when haploid genomes start cohabiting in diploid germlines and somas, and these interact with the endosymbiont asymmetries – ‘foreign’ mitochondria attack each other, because it is in their interests to do so, which (among other factors) leads to cytoplasmic asymmetry between gametes, which leads to selection for mitochondria to render males sterile … and of course, eukaryotic recombination unchains the Selfish Gene.
At a group level, altruism can arise – but only through a gene-level dynamic, which itself is only generally available in a recombinant sexual population. The ‘good of the species’ does not work, despite E O Wilson’s recent attempt to revive it. One of the most important, but overlooked, ‘groups’ of all, the diploid soma, is only held together through the common future that it gives genes through the nurturing of the haploid pairing. This cannot happen in prokaryotes, but diploid genes have no way out other than through the haploid (well, they could try cancer …).
So while there are levels – the gene, the haploid, the diploid cell, the organism, the group – the dynamics do not transfer readily between them, largely because of differences in the dynamic of the linkage units. Dawkins is only giving voice to the work of Hamilton, Maynard Smith, Hamilton, Trivers and others. These were genuine advances in fundamental understanding, and I think Noble’s is a comparatively impoverished view, a backward step disguised as an advance.
No I don’t think that’s the idea. It comes back to “Chance, Necessity, and Design” as three separate causal agents. Dembski and Hunter roll up everything non-design into “Chance”, and Hunter essentially calls that “random”. Dembski, being a mathematician, is careful not to do so.
Eric and William regard “will” as an uncaused cause (like God), except that for Eric, will is “caused” ultimately by God. Not sure where William stands on that. That is fairly standard theology – that God’s gift to humanity is freedom, so our freedom is caused by God. It’s from Aquinas.
I think the whole notion makes category errors, as I’ve said before. I don’t think “chance” is a different kind of “cause” from necessity- it’s just an unmodelled oor unpredicted cause. If we improve our models we can often reduce the error term. It’s the catch all terms for the causes we don’t know. And “Design” is, in my view, a way of locating the proximal cause for an effect in a voltional agent, such as ourselves. Hence the arguments as to whether beavers design, or birds, or honeybees, “design” which seems to hinge on whether they are “free” to design otherwise. That’s why I tend to view “free will” as free in the sense that “degrees of freedom” represent what is “free”. And “will” as in volition, as in the degree to which we are able to form goals in advance and adjust our actions so as to maximise the probability of the desired outcome.
But if you regard Chance, Necessity and Design as being mutually exclusive categories of causes (as ID ists tend to do, but I do not), and you roll Necessity up into Chance) then non-design becomes “purposelessness”. And that is what I think they find terrifying.
Similarly chance-free necessity, but as we know (or think we know) that the universe is not deterministic, determinism is not a serious threat.
I think that’s why they tend to like QM. It wraps together Chance and Necessity, as “materialist” causes, but also provides provides a scientific precedent for causeless causes, and thus justification for considering will a causeless cause.
They are not alone. Lots of people (including me, once) think that QM is the saviour of free will. Hence Conway and Kochen’s Free Will Theorem. Ken Miller (no IDist!) also takes the same view.
Dennett persuaded me that not only does this make no sense, but that any version of Free Will that means what we actually want it to mean (that we can make informed, rather than “random” decisions) is as compatible with a Deterministic as with a QM universe. So I guess that makes me a “compatibilist” 🙂
Well, to be clearer, if evolutionary changes are not the result of ‘random’ (allowing it to be a binary characteristic for argument’s sake), then things like mate choice and all its antecedent causes would appear to need to be determined (since these have a massive and chaotic impact upon the genetic combinations that arise and persist). Perhaps we are exceptions – all our choices are free; all choices in as many antecedent species as one’s biblical literalism might allow were not.
Although of course an alternaitive is the kind of thing Conway Morris espouses – that all roads lead to Rome. We have a completely free choice in which one we take!
Just noted that my ‘contrariwise’ link on epigenetics does not work. What is it with me and links? try again
The multi-generational retention of epigenetic markers (histone modification; methylation state) has (AFAIK) yet to be demonstrated at the molecular level.
eta:OK, I’m feeling lucky, here’s the longer piece originally linked
You seem to be forgetting that TOE is a problem for Biblical literalists. Showing that evolution is an inevitable consequence of chemistry, or thermodynamics, would have very little impact on widespread acceptance of TOE. There would still be a conflict with a literalist reading of the Bible.
Also, lots of people have a problem with SR and/or GR. The cranks claiming to refute Einstein are legion. Conservapedia has a big problem with Relativity. One reason some people can’t accept GR and SR are that they are counter-intuitive. Surely God would make the world so it makes everyday sense to those made in his image? That is, ‘surely the mind of God is not alien.’
To be fair to Dembski, he did disown the Explanatory Filter a few years ago, for similar reasons:
(Damn, Google took me to UD. Eris truly is the goddess of the ‘net.)
Apparently the intelligent design creationists at UD refused to accept the memo.