He was one of the greatest Culture Warriors of our time – a towering intellect who possessed that rare combination of professional credentials and an indefatigable combative spirit. Having grown up in communist Russia and being an outspoken critic of Marxism (he was actually punished in Soviet gulags for his political views), Perakh might have used his considerable writing skills to become the next Alexandr Solzhenitzyn, arguing forcefully and eloquently against the abuses of Stalinism which took the lives of tens of millions. But he knew that there was an even more insidious and treacherous enemy that must be defeated: Intelligent Design.

As Mark wrote in 2006:

"it is ID advocates whose behavior is reminiscent of the oppressive Soviet regime."

Perakh was well aware of the fact that Intelligent Design advocates were eager to become like the Soviet and Nazi regimes which had murdered over 50,000,000 people, so he put all of his energies into defeating them at every turn.

"The ID advocates have no Gestapo or KGB at their disposal, so they can't muzzle their opponents as the Nazis and the Soviet communists did. However, as becomes clear from their publications (see, for example Johnson's Darwin on Trial), putting their opponents on trial (whose outcome — a verdict of guilty – would be easily predictable) is the ID advocates' sweetest dream."

Perakh was quick to note the similarities between ID proponents and totalitarian governments.

"it is the ID advocates who behave in a way similar to the Soviet communists and the Nazis, the two groups sent to the ash heap of history."

Having been a scientist in the Soviet system, Perakh was well aware of the horrific abuses of the notorious Trofim Lysenko, the Soviet scientist who infamously killed or imprisoned anyone who would dare disagree with him. He remembers vividly Lysenko's "bony, sharp-nosed peasant face." Mark became outraged when some Intelligent Design advocates began acting just like Trofim Lysenko! He decided to boldly speak the truth even though their wrath was certain to fall on him:

"My experience shows clearly that behavior and methods of dispute of the ID advocates are much closer to the behavior of Lysenkoists, Soviet authorities, or Nazis, than is the behavior of their opponents."

Key to identifying the Nazi-like tendencies of ID proponents, Perakh said, is their tendency to praise one another without ceasing – something which critics of Intelligent Design have never been known to do.

"The German nation was officially proclaimed to be the most authentic incarnation of these mythical Aryans, and everything German was acclaimed in superlative terms very much like the ID advocates incessantly praise themselves and their colleagues. Their opponents never do so."

This led to Perakh's book "Unintelligent Design" – a direct refutation of William Dembski's book "Intelligent Design" along with many other leading Intelligent Design proponents. It is speculated but not known whether Dembski made an attempt to jail or kill Perakh at that time.

In 1941 Mark Perakh fought against the Nazis for his Motherland and later was part of the Russian occupying force in Germany. Being fluent in German, Mark was able to read much of the Nazi propaganda that was left behind and noticed the precise similarities between ID proponent Jonathan Wells' propaganda and the anti-Jewish propaganda of Joseph Goebbels which led to the extermination of 6 million Jews.

"When Wells writes that after meeting [Anti-IDists Kenneth] Miller and [Lawrence] Krauss he needs to take shower, it is an equivalent of those Nazi and Soviet cartoons except that this time the picture is in words rather than in graphics."

Perakh was well known for being civil yet firm in his discourse. As he wrote:

"I admit that calling a person an ignoramus is not very polite, and I do not enjoy at all the situations in which I have reason to resort to such epithets…it is always hard to argue with ignoramuses"

-Signature of an Ignoramus, by Mark Perakh

But in a war like the Culture War it is sometimes necessary to fight with every weapon at your disposal.

As a working scientist who published over 300 papers, and as an eyewitness to the tragedy of Lysenkoism, Parakh was in a unique position to offer a scathing critique of the corruption within the scientific establishment. In an era defined by rampant scientific fraud, over $100,000,000 per year wasted on misconduct, and over 50% of research findings turning out to be false, Mark decided to confront one of the world's greatest threats to science: The Bible Code. His in-depth, exhaustive investigation into The Bible Code resulted in an exposé of bible numerology that was completely devastating to the Intelligent Design claim that there are lots of secret hidden messages in the bible.

“Finally, I came to the conclusion that 'The Bible Code' is a fiction. There is no code.”

The Culture War owes a debt of gratitude to this great warrior. Telic Thoughts would like to express our condolences to his friends and family. He will certainly be missed.

Teleology means that in addition to physical law of the familiar kind, there are other laws of nature "biased toward the marvelous."

-Thomas Nagel

I find Nagel's primary appeal to be his patent honesty. For all his inability to see divine purpose he still recognizes the need for a purposeful view of nature.

Strangely, he seems oblivious to the fact that biology research has already headed down the teleological road.

Interview with George Church in Der Spiegel.

"Yes, biology is complicated, but it's actually simpler than most other technologies we are dealing with. The reason is that we have received a great gift that biology has given to us. We can just take a little bit of DNA and stick it into a human stem cell, and all the rest of it is self-assembled. It just happens. It's as if a master engineer parked a spacecraft in our back yard with not so many manuals, but lots of goodies in it that are kind of self-explanatory. You pick up something and you pretty much know what it does after a little study."

Complicated in design, yet simple to use. A hallmark of great design.

Just like a master engineer from outer space…lol!

Plus 85 abstentions. This took place at Cambridge with the votes coming from Cambridge students, who I imagine don't exactly comprise a population of devoted Christian belief. What's really interesting is that the topic was whether religion had a place in the 21st century – and defending "religion" strikes me as dicier than defending, say, the reasonableness of believing in God's existence, at least from a popular standpoint. As the 'nones' in the US show, plenty of people believe in God while apparently having a damn low view of religion.

More than that… c'mon. Dawkins and company got rolled by a group led up by Rowan Williams of all people? This wasn't exactly a presentation of the heavy guns of Christian thought, philosophy or apologetics.

Biologist and atheist activist Jerry Coyne's reaction to the awesome complexity of the signaling mechanism was to proclaim:

"The amazing complexity of the G-protein coupled cascade – which no designer would ever build – shows the truth of Jacob’s aphorism that evolution doesn’t design, it ‘tinkers’."

I agree that evolution has tinkered with GPCRs over the years, but I'd like to know why Coyne thinks that no designer would ever build a GPCR given it's incredible effectiveness, utility, modularity, ubiquity, and flexibility. I'd also like to know if Coyne is aware that GPCRs have existed since the very beginnings of multicellularity.

Seems to me to be an extremely ingenious design strategy to include GPCRs in the first unicellular organisms – that is, if a designer wanted to insure the appearance of multicellularity, plants, animals, bodies, noses, eyes, hearts, and minds.

And a whopping 73% of atheists do not believe in God.

How long have I been telling you these are not rational people we are dealing with?

http://religions.pewforum.org/

I have enjoyed the conversations in this site. One issue that is central in the conversation between theists (of all stripes) and atheists (of any stripe) is the question of warranted belief. W.K. Clifford stressed an argument that’s popularly practiced among non-theists when discussing with theists, "It is wrong always, everywhere, and for anyone, to believe anything on insufficient evidence." Sounds very sane. And atheists, naturalists and reductive materialists use this often to butcher poor theists who cannot “prove” their faith.

But as Os Guinness said, “For no human being lives outside the reality common to us all. Whatever people may say the world is or who they are, it is what it is and they are who they are. Again, no argument is unarguable, but there are thoughts that can be thought but not lived. When all is said and done, reality always has the last word. The truth will always out. Standing up to falsehood, lies and crazy ideas is never an easy task, but it is far easier than the hardest task of all, becoming people of truth ourselves.” (Time for Truth [2000])

In actual experiential reality Clifford’s thesis falls in the category of “thoughts that can be thought but not lived.”

With the author’s permission (and also of Telic Thoughts) I am posting this brief but critically relevant (recently edited) piece, “The Pragmatic and the Evidential: Is It Ever Rational to Believe Beyond the Evidence?” by philosopher Bill Vallicella from his blog.

Thoughts?

The Pragmatic and the Evidential: Is It Ever Rational to Believe Beyond the Evidence?

Is it ever rational to believe something for which one has insufficient evidence? If it is never rational to believe something for which one has insufficient evidence, then presumably it is also never rational to act upon such a belief. For example, if it irrational to believe in God and post-mortem survival, then presumably it is also irrational to act upon those beliefs, by entering a monastery, say. Or is it?

W. K. Clifford is famous for his evidentialist thesis that "It is wrong always, everywhere, and for anyone, to believe anything on insufficient evidence." On this way of thinking, someone who fails to apportion belief to evidence violates the ethics of belief, and thereby does something morally wrong. This has been called ethical evidentialism since that claim is that it is morally impermissible to believe on insufficient evidence. Sufficient evidence is where there is preponderance of evidence. On ethical evidentialism, then, it is morally permissible for a person to believe that p if and only p is more likely than not on the evidence the person has.

A cognitive evidentialist, by contrast, maintains that one is merely unreasonable to believe beyond a preponderance of evidence. One then flouts a norm of rationality rather than a norm of morality.

Jeffrey Jordan, who has done good work on this topic, makes a further distinction between absolute and defeasible evidentialism. The absolute evidentialist holds that the evidentialist imperative applies to every proposition, while the defeasible evidentialist allows exceptions. Although Clifford had religious beliefs in his sights, his thesis, by its very wording, applies to every sort of belief, including political beliefs and the belief expressed in the Clifford sentence quoted above! I take this as a refutation of Clifford's evidentialist stringency. For if one makes no exceptions concerning the application of the evidentialist imperative, then it applies also to "It is wrong always, everywhere, and for anyone, to believe anything on insufficient evidence." And then the embarrassing question arises as to what evidence once could have for the draconian Cliffordian stricture which is not only a morally normative claim but is also crammed with universal quantifiers.

If I took Clifford seriously I would have to give up most of my beliefs about politics, health, nutrition, economics, history and plenty of other things. For example, I believe it is a wise course to restrict my eating of eggs to three per week due to their high cholesterol content. And that's what I do. Do I have sufficent evidence for this belief? Not at all. I certainly don't have evidence that entails the belief in question. What evidence I have makes it somewhat probable. But more probable than not? Not clear! But to be on the safe side I restrict my intake of high-cholesterol foods. What I give up, namely, the pleasures of bacon and eggs for breakfast every morning, etc. is paltry in comparison to the possible pay-off, namely living and blogging to a ripe old age. Surely there is nothing immoral or irrational in my behavior even though I am flouting Clifford's rule. And similarly in hundreds of cases.

The Desert Rat

Consider now the case of a man dying of thirst in a desert. He comes upon two water sources. He knows (never mind how) that one is potable while the other is poisonous. But he does not know which is which, and he has no way of finding out. Should the man suspend belief, even unto death, since he has insufficient evidence for deciding between the two water sources? Let us suppose that our man is a philosopher and thus committed to a life of the highest rationality.

Absolute evidentialism implies that the desert wanderer should suspend judgment and withhold assent: he may neither believe nor disbelieve of either source that it is potable or poisonous on pain of either irrationality or an offence against the ethics of belief.

On one way of looking at the matter, suspension of belief — and doing nothing in consequence — would clearly be the height of irrationality in a case like this. The desert wanderer must simply drink from one of the sources and hope for the best. Clearly, by drinking from one (but not both) of the sources, his chances of survival are one half, while his chances of survival from drinking from neither are precisely zero. By simply opting for one, he maximizes his chances of reality-contact, and thereby his chances of survival. Surely a man who wants to live is irrational if he fails to perform a simple action that will give him a 50-50 chance of living when the alternative is certain death.

He may be epistemically irrational, but he is prudentially rational. And in a case like this prudential rationality trumps the other kind.

Cases like this are clear counterexamples to evidentialist theories of rationality according to which rationality requires always apportioning belief to evidence and never believing on insufficient evidence. In the above case the evidence is the same for either belief and yet it would be irrational to suspend belief. Therefore, rationality for an embodied human agent (as opposed to rationality for a disembodied transcendental spectator) cannot require the apportioning of belief to evidence in all cases, as Clifford demands. There are situations in which one must decide what to believe on grounds other than the evidential. Will I believe that source A is potable? Or will I believe that source B is potable? In Jamesian terms the option is live, forced, and momentous. (It is not like the question whether the number of ultimate particles in the universe is odd or even, which is neither live, forced, nor momentous.) An adequate theory of rationality, it would seem, must allow for believing beyond the evidence. It must return the verdict that in some cases, to refuse to believe beyond the evidence is positively irrational.

But then absolute evidentialism is untenable and we must retreat to defeasible evidentialism.

The New Neighbors

Let us consider another such case. What evidence do I have that my new neighbors are decent people? Since they have just moved in, my evidence base is exiguous indeed and far from sufficient to establish that they are decent people. (Assume that some precisifying definition of 'decent' is on the table.) Should I suspend judgment and behave in a cold, skeptical, stand-offish way toward them? ("Prove that you are not a scumbag, and then I'll talk to you.") Should I demand of them 'credentials' and letters of recommendation before having anything to do with them? Either of these approaches would be irrational. A rational being wants good relations with those with whom he must live in close proximity. Wanting good relations, he must choose means that are conducive to that end. Knowing something about human nature, he knows that 'giving the benefit of the doubt' is the wise course when it comes to establishing relations with other people. If you begin by impugning the integrity of the other guy, he won't like you. One must assume the best about others at the outset and adjust downwards only later and on the basis of evidence to the contrary. But note that my initial belief that my neighbors are decent people — a belief that I must have if I am to act neighborly toward them — is not warranted by anything that could be called sufficient evidence. Holding that belief, I believe way beyond the evidence. And yet that is the rational course.

So again we see that in some cases, to refuse to believe beyond the evidence is positively irrational. A theory of rationality adequate for the kind of beings we are cannot require that belief be always and everywhere apportioned to evidence.

In the cases just mentioned, one is waranted in believing beyond the evidence, but there are also cases in which one is warranted in believing against the evidence. In most cases, if the available evidence supports that p, then one ought to believe that p. But consider Jeff Jordan's case of

The Alpine Hiker

An avalanche has him stranded on a mountainside facing a chasm. He cannot return the way he came, but if he stays where he is he dies of exposure. His only hope is to jump the chasm. The preponderance of evidence is that this is impossible: he has no epistemic reason to think that he can make the jump. But our hiker knows that what one can do is in part determined by what one believes one can do, that "exertion generally follows belief," as Jordan puts it. If the hiker can bring himself to believe that he can make the jump, then he increases his chances of making it. "The point of the Alpine hiker case is that pragmatic belief-formation is sometimes both morally and intellectually permissible."

We should therefore reject absolute evidentialism, both ethical and cognitive. We should admit that there are cases in which epistemic considerations are reasonably defeated by prudential considerations.

And now we come to the Big Questions. Should I believe that I am libertarianly free? That it matters how I live? That something is at stake in life? That I will in some way or other be held accountable after death for what I do and leave undone here below? That God exists? That I am more than a transient bag of chemical reactions? That a Higher Life is possible?

Not only do I not have evidence that entails answers to any of these questions, I probably do not have evidence that makes a given answer more probable than not. Let us assume that it is not more probable than not that God exists and that I (in consequence) have a higher destiny in communion with God.

But here's the thing. I have to believe that I have a higher destiny if I am to act so as to attain it. It is like the situation with the new neighbors. I have to believe that they are decent people if I am to act in such a way as to establish good relations with them. Believing the best of them, even on little or no evidence, is pragmatically useful and prudentially rational. I have to believe beyond the evidence. Similarly in the Alpine Hiker case. He has to believe that he can make the jump if he is to have any chance of making it. So even though it is epistemically irrational for him to believe he can make it on the basis of the available evidence, it is prudentially rational for him to bring himself to believe. You could say that the leap of faith raises the probability of the leap of chasm.

And what if he is wrong? Then he dies. But if he sits down in the snow in despair he also dies, and more slowly. By believing beyond the evidence he lives better his last moments than he would have by giving up.

Here we have a pragmatic argument that is not truth-sensitive: it doesn't matter whether he will fail or succeed in the jump. Either way, he lives better here and now if he believes he can cross the chasm to safety. And this, even though the belief is not supported by the evidence.

It is the same with God and the soul. The pragmatic argument in favor of them is truth-insensitive: whether or not it is a good argument is independent of whether or not God and the soul are real. For suppose I'm wrong. I live my life under the aegis of God, freedom, and immortality, but then one day I die and become nothing. I was just a bag of chemicals after all. It was all just a big joke. Electrochemistry played me for a fool. So what? What did I lose by being a believer? Nothing of any value. Indeed, I have gained value since studies show that believers tend to be happier people. But if I am right, then I have done what is necessary to enter into my higher destiny. Either way I am better off than without the belief in God and the soul. If I am not better off in this life and the next, then I am better off in this life alone.

I am either right or wrong about God and the soul. If I am right, and I live my beliefs, then then I have lived in a way that not only makes me happier here and now, but also fits me for my higher destiny. If I am wrong, then I am simply happier here and now.

So how can I lose? Even if they are illusions, believing in God and the soul incurs no costs and disbelieving brings no benefits.

As always, the work of the Lenski lab is solid and interesting, but is spun like a top to make it appear to support Darwinian evolution more than it does. As the authors acknowledge, this is certainly not the first time a lab has evolved a virus to grow on a different strain of host. In a recent review (Behe 2010) ( http://tinyurl.com/25c422s ) there is a section entitled “Evolution Experiments with Viruses: Adapting to a New Host” discussing just that topic. In general, viruses have been shown to be able to adapt to bind to related host cells which have similar surface features. In almost all cases the virus uses the same binding protein, and the same (mutated) binding site to attach to the new host cell. This seems to also be the case with Lenski’s new work. As stated above, the first several mutations apparently strengthen the ability of the J protein to bind to the original site, LamB, while the fourth mutation allows it to bind to OmpF. As the authors state, however, the mutated viral J protein can still bind to the original protein, LamB, which strongly suggests the same binding site (that is, the same location on the J protein) is being used. It turns out that both LamB and OmpF have similar three-dimensional structures, so that strengthening the binding to one fortuitously led to binding to the other. In my review (Behe 2010) I discussed why this should be considered a “modification of function” event rather than a gain-of-function one. The bottom line is that the results are interesting and well done, but not particularly novel, nor particularly significant.

To me, the much more significant results of the new paper, although briefly mentioned, were not stressed as they deserved to be. The virus was not the only microbe evolving in the lab. The E. coli also underwent several mutations. Unlike for lambda, these were not modification-of-function mutations — they were complete loss-of-function mutations. The mechanism the bacterium used to turn off LamB in 99% of cells to resist initial lambda infection was to mutate to destroy its own gene locus called malT, which is normally useful to the cell. After acquiring the fourth mutation the virus could potentially invade and kill all cells. However, E. coli itself then mutated to prevent this, too. It mutated by destroying some genes involved in importing the sugar mannose into the bacterium. It turns out that this “mannose permease” is used by the virus to enter the interior of the cell. In its absence, infection cannot proceed.

So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.

Literature Cited

Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and “The First Rule of Adaptive Evolution”. Quarterly Review of Biology 85: 1-27.

Meyer, J. R., D. T. Dobias, J. S. Weitz, J. E. Barrick, R. T. Quick et al. 2012 Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335: 428-432.

It seems to me that Richard Lenski, who knows how to get the most publicity out of exceedingly modest laboratory results, has taught his student well. In fact, the results can be regarded as the loss of two pre-existing abilities: 1) the loss of the ability to separate from the mother cell during cell division; and 2) the loss of control of apoptosis. The authors did not analyze the genetic changes that occurred in the cells, but I strongly suspect that if and when they do, they’ll discover that functioning genes or regulatory regions were broken or degraded. This would be just one more example of evolution by loss of pre-existing systems, at which we already knew that Darwinian processes excel. The apparently insurmountable problem for Darwinism is to build new systems.

Literature Cited

Ratcliff, W. C., R. F. Denison, M. Borrello, and M. Travisano, 2012 Experimental evolution of multicellularity. Proc. Natl. Acad. Sci. USA doi/10.1073/pnas.1115323109

I have written appreciatively about both Lenski and Thornton before, whose work indicates clear limits to Darwinian evolution (although they themselves operate within a Darwinian framework). Thornton’s latest work is beginning to show a convergence with Lenski’s that greatly boosts our confidence that they both are on the right track. In a recent review (Behe, 2010) I pointed out that all characterized advantageous mutations that Richard Lenski has observed in his twenty-year experiment have turned out to be degradative ones — ones in which a gene or genetic control structure was either destroyed or rendered less effective. (Random mutation is superb at degrading genetic material, which sometimes is helpful to an organism.) In his latest work Thornton, too, shows evolution of a system by degradation, although he speculates that the changes were neutral rather than advantageous.

In Finnegan et al (2012), “Evolution of increased complexity in a molecular machine”, Thornton and colleagues study a ring of six proteins in a molecular machine (that also has many other parts) called a V-ATPase, which can pump protons (acid) across a membrane. The machine exists in all eukaryotes. In most eukaryotic species, however, the hexameric ring consists of five copies of one protein (let’s call it protein 1) and one copy of another, related protein (call it protein 2). In fungi, however, the ring consists of four copies of protein 1, one copy of protein 2, and one copy of protein 3. Protein 3 is very similar in sequence to protein 1, so Finnegan et al (2012) propose that proteins 1 & 3 are related by duplication of an ancestral gene and subsequent modification of the two, originally-identical duplicated genes.

How did protein 3 insinuate itself into the ring? The original protein 1, present in five copies in most organisms, already had the ability to bind to itself, plus an ability to bind to one side of protein 2, plus a separate ability to bind to the opposite side of protein 2 (see Finnegan et al’s Figure 3). Thornton’s results are consistent with the idea that, by happenstance, the gene for protein 1 duplicated and spread in the population. (These events apparently were neutral, the authors think, not affecting the organism’s fitness.) Eventually one of the duplicates acquired a degradative mutation, losing the ability to bind one side of protein 2. This was not a problem because the second copy of the protein 1 gene was intact, and could bind both sides of protein 2, so a complete ring could still be formed. This also spread by neutral processes. As luck might have it, the second gene copy subsequently acquired its own degradative mutation, so that it could no longer bind the other side of protein 2. Again it’s no problem, however, because the first mutant copy of protein 1 could bind to the first side of protein 2, bind a few more copies of itself, then bind a copy of protein 3, which still had the ability to bind the other side of protein 2. So a closed, six-member ring could still be formed. This apparently also spread by neutral processes until it took over the entire kingdom of fungi.

The work of Finnegan et al (2012) strikes me as quite thorough and elegant. I have no reason to doubt that events could have unfolded that way. However, the implications of the work for unguided evolution appear very different to me then they’ve been spun in media reports. ( http://tinyurl.com/7lawgpl ) The most glaringly obvious point is that, like the results of Lenski’s work, this is evolution by degradation. All of the functional parts of the system were already in place before random mutation began to degrade them. Thus it is of no help to Darwinists, who require a mechanism that will construct new, functional systems. What’s more, unlike Lenski’s results, the mutated system of Thornton and colleagues is not even advantageous; it is neutral, according to the authors. Perhaps sensing the disappointment for Darwinism in the results, the title of the paper and news reports emphasize that the “complexity” of the system has increased. But increased complexity by itself is no help to life — rather, life requires functional complexity. One can say, if one wishes, that a congenitally blind man  teaming up with a congenitally legless man to safely move around the environment is an increase in “complexity” over a sighted, ambulatory person. But it certainly is no improvement, nor does it give the slightest clue how vision and locomotion arose.

Finnegan et al’s (2012) work intersects with several other concepts. First, their work is a perfect example of  Michael Lynch’s idea of “subfunctionalization”, where a gene with several functions duplicates, and each duplicate loses a separate function of the original. (Force et al, 1999) Again, however, the question of how the multiple functions arose in the first place is begged. Second, it intersects somewhat with the recent paper by Austin Hughes (2011) in which he proposes a non-selective mechanism of evolution abbreviated “PRM” (plasticity-relaxation-mutation), where a “plastic” organism able to survive in many environments settles down in one and loses by degradative mutation and drift the primordial plasticity. But again, where did those primordial functions come from? It seems like some notable workers are converging on the idea that the information for life was all present at the beginning, and life diversifies by losing pieces of that information. That concept is quite compatible with intelligent design. Not so much with Darwinism.

Finally, Thornton and colleagues latest work points to strong limits on the sort of neutral evolution that their own work envisions. The steps needed for the scenario proposed by  Finnegan et al (2012) are few and simple: 1) a gene duplication; 2) a point mutation; 3) a second point mutation. No event is deleterious. Each event spreads in the population by neutral drift. Notice that the two point mutations do not have to happen together. They are independent, and can happen in either order. Nonetheless, this scenario is apparently exceedingly rare. It seems to have happened a total of one (that is, 1) time in the billion years since the divergence of fungi from other eukaryotes. It happened only once in the fungi, and a total of zero times in the other eukaryotic branches of life. If the scenario were in fact as easy to achieve in nature as it is to describe in writing, we should expect it to have happened many times independently in fungi and also to have happened in all other branches of eukaryotes.

It didn’t. Thus it seems a good conclusion that such neutral scenarios are much rarer than some workers have proposed (Gray et al, 2010; Lukes et al, 2011), and that more complex neutral scenarios are unlikely to happen in the history of life.

Literature Cited

Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and “The First Rule of Adaptive Evolution”. Quarterly Review of Biology 85: 1-27.

Finnigan, G. C., V. Hanson-Smith, T. H. Stevens, and J. W. Thornton, 2012 Evolution of increased complexity in a molecular machine. Nature doi: 10.1038/nature10724.

Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan et al. 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.

Gray, M. W., J. Lukes, J. M. Archibald, P. J. Keeling, and W. F. Doolittle, 2010 Irremediable complexity? Science 330: 920-921.

Hughes, A. L., 2011 Evolution of adaptive phenotypic traits without positive Darwinian selection. Heredity (Edinb.) doi: 10.1038/hdy.2011.97.

Lukes, J., J. M. Archibald, P. J. Keeling, W. F. Doolittle, and M. W. Gray, 2011 How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63: 528-537.

In my comments on this interesting work ( http://tinyurl.com/3cjm4gr ), I noted that there is nothing time-asymmetric about random mutation/natural selection, so that the problem they saw in reversing the steroid hormone receptor evolution did not have to be in the past — it could just as easily have been in the future. The reason is that natural selection hones a protein to its present job, with regard to neither future use nor past function. Thus, based on Thornton’s work, one would not in general expect a protein that had been selected for one function to be easily modified by RM/NS to another function. I have decided to call this the Time-Symmetric Dollo’s Law, or “TSDL”.

But if there is such a thing as a TSDL, did the forward evolution of the steroid-hormone protein-receptor manage to avoid it? That question had not yet been addressed. Was the protein lucky this time, and encountered no obstacles to its evolution from the ancestral state to the modern state? If so, then maybe TSDL is occasionally an obstacle, but not so often as to rule out modest Darwinian evolution of proteins (as I had thought before reading Thornton’s earlier work).

Well, thanks to the Thornton group’s new work ( http://tinyurl.com/3dsorzm ), we can now see that there are indeed obstacles to the forward evolution of the ancestral protein. The group was interested in which of the many sequence changes between the ancestral and derived-modern protein were important to its change in activity, which consisted mostly of a considerable weakening of the protein’s ability to bind its steroid ligands. They narrowed the candidates down to two amino acid positions, residues 43 and 116. Each of the changes at those sites decreased binding by over a hundred-fold. However, when the researchers combined both mutations into a single protein, as occurs in the modern protein, binding was not only decreased — it was for all intents and purposes abolished. Upon further research the group showed that a third mutation, at position 71, was necessary to ameliorate the effects of the combination of the other two mutations, bringing them back to hundreds-fold loss of function rather than essentially-complete loss of function.

Carroll et al (2011) conjecture that the mutation at position 71 occurred before the other two mutations, but that it had no effect on the activity of the ancestral protein. So let us count the ways, then, in which “fortune” favored the evolution of the modern protein. First, an ancestral gene duplicated, which would usually be considered a neutral event. Thus it would not have the assistance of natural selection to help it spread in the population. Next, it avoided hundreds of possible mutations which would have rendered the duplicated gene inactive. Third, it acquired a neutral mutation at position 71. Thus, again, this mutation would have to spread by drift, without the aid of natural selection. Once more, the still-neutral gene manages to avoid all of the possible mutations that would have inactivated it. Next, it acquires the correct mutation (either at position 43 or 116) which finally differentiates it from its parent gene — by reducing its activity a hundred-fold! Finally, somehow the wimpy, mutated gene (putatively) confers upon the lucky organism some likely-quite-weak selective advantage.

The need for passage through multiple neutral steps plus the avoidance of multiple likely-deleterious steps to produce a protein that has lost 99% of its activity is not a ringing example of the power of Darwinian processes. Rather, as mentioned above, it shows the strength of TSDL. Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection.

Dollo’s law holds going forward as well as backward. We can state the experimentally based law simply: “Any evolutionary pathway from one functional state to another is unlikely to be traversed by random mutation and natural selection. The more the functional states differ, the much-less likely that a traversable pathway exists.”

1. Carroll, S. M., E. A. Ortlund, and J. W. Thornton, 2011 Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. PloS. Genet. 7: e1002117.

2. Bridgham, J. T., E. A. Ortlund, and J. W. Thornton, 2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461: 515-519.

The gist of the paper is this. The authors think that over evolutionary time, neutral processes would tend to “complexify” the cell. They call that theoretical process “constructive neutral evolution” (CNE). In an amusing analogy they liken cells in this respect to human institutions:

Organisms, like human institutions, will become ever more ”bureaucratic,” in the sense of needlessly onerous and complex, if we see complexity as related to the number of necessarily interacting parts required to perform a function, as did Darwin. Once established, such complexity can be maintained by negative selection: the point of CNE is that complexity was not created by positive selection. (1)

In brief, the idea is that neutral interactions evolve serendipitously in the cell, spread in a population by drift, get folded into a system, and then can’t be removed because their tentacles are too interconnected. It would be kind of like trying to circumvent the associate director of licensing delays in the Department of Motor Vehicles — can’t be done.

The possible problem the authors are trying to address is that they think many systems in the cell are needlessly complex. For example, the spliceosome, which “splices” some RNAs (cuts a piece out of the middle of a longer RNA and stitches the remaining pieces together), is a huge conglomerate containing “five small RNAs (snRNAs) and >300 proteins, which must be assembled de novo and then disassembled at each of the many introns interrupting the typical nascent mRNA.” (1) What’s more, some RNAs don’t need the spliceosome — they can splice themselves, without any assistance from proteins. So why use such an ungainly assemblage if a simpler system would do?

The authors think the evolution of such a complex is well beyond the powers of positive natural selection: “Even Darwin might be reluctant to advance a claim that eukaryotic spliceosomal introns remove themselves more efficiently or accurately from mRNAs than did their self-splicing group II antecedents, or that they achieved this by ‘numerous, successive, slight modifications’ each driven by selection to this end.” (1)

Well, I can certainly agree with them about the unlikelihood of Darwinian processes putting together something as complex as the spliceosome. However, leaving aside the few RNAs involved in the splicesome, I think their hypothesis of CNE as the cause for the interaction of hundreds of proteins — or even a handful — is quite implausible. (An essay skeptical of large claims for CNE, written from a Darwinian-selectionist viewpoint, has appeared recently (3) along with a response from the authors (4)).

The authors rationale for how a protein drifts into becoming part of a larger complex is illustrated by Figure 1 of their recent paper (similar to the single figure in their Science essay). A hypothetical “Protein A” is imagined to be working just fine on its own, when hypothetical “Protein B” serendipitously mutates to bind to it. This interaction, postulate the authors, is neutral, neither helping nor harming the ability of Protein A to do its job. Over the generations Protein A eventually suffers a mutation which would have decreased or eliminated its activity. However, because of the fact that Protein B is bound to it, the mutation does not harm the activity of Protein A. This is still envisioned to be a neutral interaction by the authors, and organisms containing the Protein A-Protein B complex drift to fixation in the population. Then other mutations come along, co-adapting the structures of Protein A and Protein B to each other. At this point the AB complex is necessary for the activity of Protein A. Repeat this process several hundred more times with other proteins, and you’ve built up a protein aggregate with complexity of the order of the spliceosome.

Is this a reasonable hypothesis? I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. The mutation rates of various organisms — viral, prokaryotic, eukaryotic — are known to sufficient accuracy (5) that estimates of how frequently the envisioned mutations arrive could have been provided. The neutral theory of evolution is also well-developed (6), which would allow the authors to calculate how long it would take for the postulated neutral mutations to spread in a population. Yet no numbers — not even back-of-the-envelope calculations — are provided. Previous results by other workers (7-9) have shown that the development of serendipitous specific binding sites between proteins would be expected to be quite rare, and to involve multiple mutations. Kimura (6) showed that fixation of a mutation by neutral drift would be expected to take a looong time. Neither of these previous results bodes well for the authors’ hypothesis.

The second thing to notice about the paper is that there is no experimental support for its hypothesis. As the authors point out:

Development of in vitro experimental systems with which to test CNE will be an important step forward in distinguishing complex biology that arose due to adaptation versus nonadaptive complexity, as part of a larger view to understand the interplay between neutral and adaptive evolution, such as the intriguing long-term evolution experiments of Lenski and coworkers. (1)

Yet no such experimental evolutionary results have been reported to my knowledge, either by Lenski or by other workers (10).

Besides the lack of support from calculations or experiments, the authors discuss no possible obstacles to the scheme. I certainly understand that workers want to accentuate the positive when putting a new model forward, but potential pitfalls should be pointed out, so that other researchers have a clearer idea of the promise of the model before they invest time in researching it.

The first possible pitfall comes at the first step of the model, where a second protein is postulated to bind in a neutral fashion to a working protein. How likely is that step to be neutral? At the very least, we now have two proteins, A & B, that now have a large part of their surfaces obstructed that weren’t before. Will this interfere with their activities? It seems there is a good chance. Second, simply by Le Chatelier’s principle the binding of the two proteins must affect the free energies of their folded states. What’s more, the flexibility of both proteins must be affected. Will these individual effects serendipitously cancel out so that the overall effect will be neutral? It seems like an awful lot to ask for without evidence.

In the next step of the model Protein A is supposed to suffer a mutation that would have caused it to lose activity, but, luckily, when it is bound to Protein B it is stabilized enough so that activity is retained. What fraction of possible mutations to Protein A would fall in that range? It seems like a very specialized subfraction. Looking at the flip side, what fraction of mutations to Protein A and/or Protein B which otherwise would not have caused A to lose activity will now do so because of its binding to Protein B?

The last step of the model is the “co-adaptation” of the two proteins, where other, complementary mutations occur in both proteins. Yet this implies that the protein complex must suffer deleterious mutations at least every other step, provoking the “co-adaptive” mutation to fix in the population. Wouldn’t these deleterious mutations be very unlikely to spread in the population?

Finally, multiply these problems all by a hundred to get a spliceosome. Or, rather, raise these problems to the hundredth power. But, then, why stop at a hundred? As the authors note approvingly:

Indeed, because CNE is a ratchet-like process that does not require positive selection, it will inevitably occur in self-replicating, error prone systems exhibiting sufficient diversity, unless some factor prevents it. (1)

Why shouldn’t the process continue, folding in more and more proteins, until the cell congeals? I suppose the authors would reply, “some factor prevents it”. But might not that factor kick in at the first or second step? The authors give us no reason to think it wouldn’t.

The CNE model (at least on the scale envisioned by the authors) faces other problems as well (for example, it would be a whole lot easier to develop binding sites for metal ions or metabolites that are present in the cell at much higher concentrations than most proteins), but I think this is enough to show it may not be as promising as the article would have one believe.

Besides the model itself, it is interesting to look at a professed aspect of the motivation of the authors in proposing it. It may not have escaped your notice, dear reader, that “irremediable complexity” sort of sounds like “irreducible complexity”. In fact, the authors put the model forward as their contribution to the good fight against “antievolutionists”:

… continued failure to consider CNE alternatives impoverishes evolutionary discourse and, by oversimplification, actually makes us more vulnerable to critiques by antievolutionists, who like to see such complexity as ”irreducible.” (1)

So there you have it. The authors don’t think Darwin can explain such complexity as is found in the proteasome, and they apparently rule out intelligent design. (By the way, when will these folks ever grasp the fact that intelligent design is not “antievolution”?) “Irremediable complexity” seems to be all that’s left, no matter how unsupported and problematic it may be.

Although the authors seem not to notice, their entire model is built on a classic argument from ignorance, beginning with the definition of irremediable complexity:

”irremediable complexity”: the seemingly gratuitous, indeed bewildering, complexity that typifies many cellular subsystems and molecular machines, particularly in eukaryotes. (1)

“Seemingly gratuitous”. In other words, the authors don’t know of a function for the complexity of some eukaryotic subsystems; therefore, they don’t have functions. Well the history of arguments asserting that something or other in biology is functionless is pretty grim. More, the history of assertions that even “simple” things (like, say, DNA, pre-1930) in the cell either don’t have a function or are just supporting structures is abysmal. Overwhelmingly, progress in biology has consisted of finding new and ever-more-sophisticated properties of systems that had been thought simple. If apparently simple systems are much more complex than they initially seemed, I would bet heavily against the hypothesis that apparently complex systems are much simpler than they appear.

References

1.  Lukes, J., J. M. Archibald, P. J. Keeling, W. F. Doolittle, and M. W. Gray, 2011 How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63: 528-537.

2.  Gray, M. W., J. Lukes, J. M. Archibald, P. J. Keeling, and W. F. Doolittle, 2010 Cell biology. Irremediable complexity? Science 330: 920-921.

3.  Speijer, D., 2011 Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity. Bioessays 33: 344-349.

4.  Doolittle, W. F., J. Lukes, J. M. Archibald, P. J. Keeling, and M. W. Gray, 2011 Comment on “Does constructive neutral evolution play an important role in the origin of cellular complexity?” Bioessays 33: 427-429.

5.  Drake, J. W., B. Charlesworth, D. Charlesworth, and J. F. Crow, 1998 Rates of spontaneous mutation. Genetics 148: 1667-1686.

6.  Kimura M., 1983 The neutral theory of molecular evolution. Cambridge University Press, Cambridge.

7.  Nissim, A., H. R. Hoogenboom, I. M. Tomlinson, G. Flynn, C. Midgley, D. Lane, and G. Winter, 1994 Antibody fragments from a ’single pot’ phage display library as immunochemical reagents. EMBO Journal 13: 692-698.

8.  Griffiths, A. D., S. C. Williams, O. Hartley, I. M. Tomlinson, P. Waterhouse, W. L. Crosby, R. E. Kontermann, P. T. Jones, N. M. Low, T. J. Allison, and G. Winter, 1994 Isolation of high affinity human antibodies directly from large synthetic repertoires. EMBO Journal 13: 3245-3260.

9.  Smith, G. P., S. U. Patel, J. D. Windass, J. M. Thornton, G. Winter, and A. D. Griffiths, 1998 Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. Journal of Molecular Biology 277: 317-332.

10.  Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and “The First Rule of Adaptive Evolution”. Quarterly Review of Biology 85: 1-27.

The term “evolvability” has been used widely and rather loosely in the literature for the past few decades. It usually means something like the following: a species possesses some biological feature which lends itself to evolving more easily than other species that don’t possess the feature, so that the lucky species will tend to adapt and survive better than its rivals over time. The kind of feature that is most often invoked in this context is “modularity.” That word itself is often used in a vague manner. As I wrote in The Edge of Evolution, “Roughly, a module is a more-or-less self-contained biological feature that can be plugged into a variety of contexts without losing its distinctive properties. A biological module can range from something very small (such as a fragment of a protein), to an entire protein chain (such as one of the subunits of hemoglobin), to a set of genes (such as Hox genes), to a cell, to an organ (such as the eyes or limbs of Drosophila).” (3)

Well, Lenski and co-workers don’t use “evolvability” in that sense. They use the term in a much broader sense: “Evolutionary potential, or evolvability, can be operationally defined as the expected degree to which a lineage beginning from a particular genotype will increase in fitness after evolving for a certain time in a particular environment.” (1) To put it another way, in their usage “evolvability” means how much an organism will increase in fitness over a defined time starting from genotype A versus starting from genotype B, no matter whether genotypes A and B have any particular identifiable feature such as modularity or not.

Lenski’s group published a very interesting paper last year showing that the more defective a starting mutant was in a particular gene (rpoB, which encodes a subunit of RNA polymerase), the more “evolvable” it was. (2) That is, more-crippled cells could gain more in fitness than less-crippled cells. But none of the evolved crippled cells gained enough fitness to match the uncrippled parent strain. Thus it seemed that more-crippled cells could gain more fitness simply because they started from further back than less-crippled ones. Compensatory mutations would pop up somewhere in the genome until the evolving cell was near to its progenitor’s starting point. This matches the results of some viral evolution studies where some defective viruses could accumulate compensatory mutations until they were similar in fitness to the starting strain, whether they began with one-tenth or one-ten-billionth of the original fitness. (4)

In a paper published a few weeks ago the Michigan State group took a somewhat different experimental tack. (1) They isolated a number of cells from relatively early in their long-term evolution experiment. (Every 500^th generation during the 50,000-generation experiment Lenski’s group would freeze away the portion of the culture which was left over after they used a part of it to seed a flask to continue the growth. Thus they have a very complete evolutionary record of the whole lineage, and can go back and conduct experiments on any part of it whenever they wish. Neat!) They saw that different mutations had cropped up in different early cells. Interestingly, the mutations which gave the greatest advantage early on had become extinct after another 1,000 generations. So Lenski’s group decided to investigate why the early very-beneficial mutations were nonetheless not as “evolvable” (because they were eventually outcompeted by other lineages) as cells with early less-beneficial mutations.

The workers examined the system thoroughly, performing many careful experiments and controls. (I encourage everyone to read the whole paper.) The bottom line, however, is that they found that changing one particular amino acid residue in one particular protein (called a “topoisomerase”, which helps control the “twistiness” of DNA in the cell), instead of a different amino acid residue in the same protein, interfered with the ability of a subsequent mutation in a gene (called spoT) for a second protein to help the bacterium increase in fitness. In other words, getting the “wrong” mutation in topoisomerase — even though that mutation by itself did help the bacterium — prevented a mutation in spoT from helping. Getting the “right” mutation in topoisomerase allowed a mutation in spoT to substantially increase the fitness of the bacterium.

The authors briefly discuss the results (the paper was published in Science, which doesn’t allow much room for discussion) in terms of “evolvability”, understood in their own sense. (1) They point out that the strain with the right topoisomerase mutation was more “evolvable” than the one with the wrong topoisomerase mutation, because it outcompeted the other strain. That is plainly correct, but does not say anything about “evolvability” in the more common and potentially-much-more-important sense of an organism possessing modular features that help it evolve new systems. “Evolvability” in the more common sense has not been tested experimentally in a Lenski-like fashion.

In my own view, the most interesting aspect of the recent Lenski paper is its highlighting of the pitfalls that Darwinian evolution must dance around, even as it is making an organism somewhat more fit. (1) If the “wrong” advantageous mutation in topoisomerase had become fixed in the population (by perhaps being slightly more advantageous or more common), then the “better” selective pathway would have been shut off completely. And since this phenomenon occurred in the first instance where anyone had looked for it, it is likely to be commonplace. That should not be surprising to anyone who thinks about the topic dispassionately. As the authors note, “Similar cases are expected in any population of asexual organisms that evolve on a rugged fitness landscape with substantial epistasis, as long as the population is large enough that multiple beneficial mutations accumulate in contending lineages before any one mutation can sweep to fixation.” If the population is not large enough, or other factors interfere, then the population will be stuck on a small peak of the rugged landscape.

This fits well with recent work by Lenski’s and others’ laboratories, showing that most beneficial mutations actually break or degrade genes (4), and also with work by Thornton’s group showing that random mutation and natural selection likely could not transform a steroid hormone receptor back into its homologous ancestor, even though both have very similar structures and functions, because the tortuous evolutionary pathway would be nearly impossible to traverse. (5, 6) The more that is learned about Darwin’s mechanism at the molecular level, the more ineffectual it is seen to be.

1. Woods, R. J., J. E. Barrick, T. F. Cooper, U. Shrestha, M. R. Kauth, and R. E. Lenski.  2011 Second-order selection for evolvability in a large Escherichia coli population. Science 331: 1433-1436.

2. Barrick, J. E., M. R. Kauth, C. C. Strelioff, and R. E. Lenski, 2010 Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Molecular Biology and Evolution 27: 1338-1347.

3. Behe M. J., 2007 The Edge of Evolution: the search for the limits of Darwinism. Free Press, New York.

4. Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and “The First Rule of Adaptive Evolution”. Quarterly Review of Biology 85: 1-27.

5. Bridgham, J. T., E. A. Ortlund, and J. W. Thornton, 2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461: 515-519.

6. See my comments on Thornton’s work at the middle of http://behe.uncommon descent.com/page/2/ and the bottom of http://behe.uncommondescent.com/.

Try as one might to keep Darwinists focused on the data, some can’t help reverting to their favorite trope: questioning Darwinism simply must be based on religion. Unfortunately Professor Coyne succumbs to this. Introducing his blog post he writes:

What role does the appearance of new genes, versus simple changes in old ones, play in evolution? There are two reasons why this question has recently become important…. The first involves a scientific controversy…. The second controversy is religious. Some advocates of intelligent design (ID)—most notably Michael Behe in a recent paper—have implied not only that evolved new genes or new genetic “elements” (e.g., regulatory sequences) aren’t important in evolution, but that they play almost no role at all, especially compared to mutations that simply inactivate genes or make small changes, like single nucleotide substitutions, in existing genes. This is based on the religiously-motivated “theory” of ID, which maintains that new genetic information cannot arise by natural selection, but must installed [sic] in our genome by a magic poof from Jebus. [sic]

Anyone who reads the paper, however, knows my conclusions were based on the reviewed experiments of many labs over decades. Even Coyne knows this. In the very next sentence he writes, schizophrenically, “I’ve criticized Behe’s conclusions, which are based on laboratory studies of bacteria and viruses that virtually eliminated the possibility of seeing new genes arise, but I don’t want to reiterate my arguments here.” Yet if my conclusions are based on “laboratory studies”, then they ain’t “religious”, even if Coyne disagrees with them.

Professor Coyne is so upset, he imagines things that aren’t in the paper. (They are “implied”, you see.) So although I haven’t actually written it, supposedly I have “implied not only that evolved new genes or new genetic ‘elements’ … aren’t important in evolution, but that they play almost no role at all….” [Coyne’s emphasis]

“Play almost no role at all”? When I first read these “implied” words that Coyne wants to put in my mouth, I thought the argumentative move rang a bell. Sure enough, check out the Dilbert comic strip from November 1, 2001 (http://tinyurl.com/6y6upgc), where Dilbert complains that a co-worker “changed what I said into a bizarre absolute.” If one person says that an event is “very unlikely”, and an interlocutor rephrases that into “so, you say it’s logically impossible and would never happen even in an infinite multiverse”, well then, the second fellow is setting up a straw man.

Contrast Coyne’s imagined “implications” with what I actually wrote in the review. Considering possible objections to my conclusions I noted that:

A third objection could be that the time and population scales of even the most ambitious laboratory evolution experiments are dwarfed when compared to those of nature. It is certainly true that, over the long course of history, many critical gain-of-FCT events occurred. However, that does not lessen our understanding, based upon work by many laboratories over the course of decades, of how evolution works in the short term, or of how the incessant background of loss-of-FCT mutations may influence adaptation.

Although I think that statement is clear enough in the context of the paper, let me say it differently in case some folks are confused. Loss of function mutations occur relatively rapidly, and LOF mutations can be adaptive. Gain of function mutations can be adaptive, too, but their rate of occurrence (including the rate of gene duplication-plus-divergence that Coyne is discussing) is much less. Thus whenever a new selective pressure pops up, LOF adaptive mutations (if such there be in the particular circumstance) can appear most swiftly, and will likely dominate short-term adaptation. So when a GOF mutation eventually appears, it will likely be against the altered genetic background of the selective pressure ameliorated by the adaptive LOF mutation(s). In order to understand how evolution works in the long term, we must take that into consideration.

Professor Coyne notes that the new genes studied by Professor Long “arise quickly, at least on an evolutionary timescale”. [my emphasis] But adaptive LOF mutations arise quickly even on a laboratory timescale. For example, as I note in my QRB review, in one experiment (http://tinyurl.com/4zyxt66) adaptive mutations in E. coli cultures due to loss of function mutations in the rpoS gene “occurred, and indeed spread at rapid rates within a few generations of establishing glucose-limited chemostats”. A few generations for E. coli can be on the order of hours. The gene duplications studied by Professor Long occur on the order of millions of years. Admittedly the situation in nature is more complex than in the laboratory. Nonetheless, whatever selective pressures the gene duplications encounter when they eventually show up will already have been substantially altered by adaptive LOF mutations. That’s a very important point for evolutionary biologists to keep in mind.

I have never stated, nor do I think, that gene duplication and diversification cannot happen by Darwinian mechanisms, or that “they play almost no role at all” in the unfolding of life. (As a matter of fact, I discussed several examples of that in my 2007 book The Edge of Evolution. (http://tinyurl.com/4nqxhvr)) That would be silly — why would anyone with knowledge of basic biochemical mechanisms deny that, say, the two gamma-globin coding regions on human chromosome 11 resulted from the duplication of a single gamma-globin gene and then the alteration of a single codon? What I don’t think can happen is that duplication/ divergence by Darwinian mechanisms can build new, complex interactive molecular machines or pathways. Assuming (since he is in fact critiquing them) Professor Coyne has been attentive to my arguments, one background assumption that he may have left unexpressed is that he thinks the newer duplicated genes discovered by Professor Long’s excellent work represent such complex entities, or parts of them.

There is no reason to think so. A gene can duplicate and diversify without building a new machine or network, or even changing function much. The above example of the two gamma-globin genes shows that duplication does not necessarily result in change in function. The examples of delta- and epsilon-globin, which, like gamma-globin, presumably also resulted from the duplication of an ancestral beta-like globin gene, show that sequence can diversify further, but function remain very similar. Even myoglobin, which shares rather little sequence homology with the other globins, has not diverged much in biochemical function.

In his recent work Professor Long discovered that many of the new genes were essential for the viability of the organism — without the gene product, the fruitflies would die before maturity. Perhaps Professor Coyne thinks that that means the genes necessarily are parts of complex systems, or at least do something fundamentally new. Again, however, there is no reason to think so. The notion of “essential” genes is at best ambiguous. We know of examples of proteins that surely appear necessary, but whose genes are dispensable. The classic example is myoglobin (http://tinyurl.com/4ogmd98). It is also easy to conceive of a simple route to an “essential” duplicate gene that does little new. Suppose, for example, that some gene was duplicated. Although the duplication caused the organism to express more of the protein than was optimum, subsequent mutations in the promoter or protein sequence of one or both of the copies decreased the total activity of the protein to pre-duplication levels. Now, however, if one of the copies is deleted, there is not enough residual protein activity for the organism to survive. The new copy is now “essential”, although it does nothing that the original did not do.

To sum up, the important point of “Experimental Evolution, Loss-of-Function Mutations, and ‘The First Rule of Adaptive Evolution’” (http://tinyurl.com/25c422s) is not that anything in particular in evolution is absolutely ruled out. Rather, the point is that short term adaptation tends to be dominated by LOF mutations. And, tinkerer that it is, Darwinian evolution always works in the short term.

Here’s an analogy that some people might find amusing and helpful. Think of GOF mutations (such as the gene duplication/divergence that Professor Coyne discusses) as the “snail mail” of evolution. And think of LOF mutations as the email, texting, and phone calls of evolution. In a busy world, by the time a real letter shows up at someone’s or some business’s door, a lot of communication concerning the subject of the slow letter would already have happened by faster means, and the more important the topic, the more fast-communication there likely would have been. That speedy communication can quite easily change the context of the letter, and either render it moot or at least less important. It is certainly possible that on occasion the slow letter will arrive with its impact unaffected by other messages, but it would be foolish to ignore the effect of the fast channels of communication.

Prof. Bull states that bacteriophage T7 (which he used in his studies) avoids taking up DNA from its host, E. coli, so it really isn’t an example of a system where novel DNA was available to the phage, despite his initial hopes that it would be. (In the paper describing the work he and his co-authors wrote, “At the outset, our expectation from work in other viral systems was that the loss of ligase activity would … require the [T7] genome to acquire new sequences through recombination or gene duplication.”) But, he writes in his new post, “what we failed to point out in our paper, and is fatal to MB’s criticism, is the fact that T7 degrades E. coli DNA, so even if the phage did incorporate an E. coli gene, it might well destroy itself in the next infection.” This reasoning strikes me as overlooking an obvious problem, and overlooking an obvious solution to the problem.

First, the problem. If T7, and presumably other bacteriophages, find it advantageous to have a mechanism that excludes host DNA from being incorporated into the phage genome, doesn’t this drastically cut down the opportunity for the very mixing of cross-species DNA that Coyne and Bull tout as the Darwinian solution to the problem of developing complex new functions? I suppose they could respond that, well, maybe the phages can’t exclude other, non-host DNA, so that’s where novel DNA would come from. But it seems host DNA would be by far the DNA the phages contacted the most. But if that is essentially excluded as a source, then the sorts of compensatory mutations that Professor Bull observed in his experiments are still by far the most likely ones to occur in nature. (And the grant application is saved!) It’s a matter of rate. The adaptive mutations that come along first will be selected first, and clearly point mutations and deletions come along very rapidly in phage populations.

Next, the solution. If a phage has a mechanism that is preventing it from taking up DNA that could be advantageous to it (such as the gene for a DNA ligase in the case of the experiment of Rokyta et al 2002 (http://tinyurl.com/3adlq6c)) then all it has to do is break that mechanism and the opportunity for acquiring DNA is now opened to it. After all, breaking things is what random mutation does best, and, as I reviewed, many of the reported adaptive mutations in lab evolution experiments resulted from broken genes. Broken genes can also be neutral mutations. In the majority of the cultures of E. coli that Richard Lenski has grown for 50,000 generations, “mutator” strains took over. A mutator strain is one which has lost at least part of its ability to repair its DNA. If E. coli can toss out part of its repair ability with impunity, why couldn’t T7 lose its inability to take up some helpful host DNA?

Professor Bull suggests (http://tinyurl.com/2cyetm7) that lab evolution experiments which use whole cells and viruses aren’t needed to show the power of Darwinian processes because that is apparent in experiments using “directed” evolution. I strongly disagree with his assessment. In directed evolution workers use an experimental set-up so that a single, particular gene or protein must mutate to be adaptive. “Directed” evolution is a much, much more artificial system than ones that use whole cells and/or viruses, as he did. In response to some selective pressure, a cell has potentially very many more ways to adapt to deal with it than does a single protein — a cell has thousands of genes and thousands of regulatory elements that can potentially help the cell adapt by gain- or loss-of-function, or tweaking of pre-existing function. On the other hand, directed evolution artificially constrains the system to mutate the component that the experimenter chooses. It seems a bit inconsistent to me for someone to claim that single species of cells (and/or viruses) are insufficiently complex to produce gain-of-function mutations by Darwinian processes, but that artificially constraining mutation/selection to single genes or proteins shows it clearly. Seems to me this is exactly backwards.

In his post (http://tinyurl.com/2cyetm7) Professor Bull describes an experiment (http://tinyurl.com/38qhow9) he did with coworkers which, they hoped, would mimic the process of gene duplication and divergence. They placed two copies of the same gene, each on its own kind of plasmid, into the same cell. The gene produced a protein that could disable one kind of antibiotic very well, and disable a second kind of antibiotic rather poorly. In the presence of both antibiotics, they expected one of the copies of the gene to stay about the same, degrading the first antibiotic. They expected the second copy of the gene to accumulate point mutations which would help it become more efficient at degrading the second kind of antibiotic (from other publications such mutants were already known to exist.) The system, however, had its own ideas. Bull says that contrary to expectations, one of the genes was deleted and the other gene accumulated point mutations so that it did a decent job degrading both antibiotics.

Professor Bull writes (http://tinyurl.com/2cyetm7) that, “This study merely illustrates that the conditions favoring the maintenance of two copies undergoing evolutionary divergence are delicate.” Skeptic that I am, instead of “delicate”, I would say it illustrates that the conditions are “rare”. That is, it demonstrates very nicely that having two copies of a gene under what seem to be ideal conditions for adaptive divergence is not enough. (A similar result using a different system was recently obtained by Gauger et al 2010 (http://tinyurl.com/2uc6d8g).) Other factors enter into the result as well. Since we don’t know exactly what those other factors are, or how rare they make successful duplication/divergence events, we should not automatically assume that the occurrence of duplicated and diverged genes in nature happened by unguided, Darwinian processes.

First, the nice thing. About half-way through his comments Professor Coyne writes:

My overall conclusion: Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes (note that at least one of these—Rich Lenski’s study— extends over several decades).

Thanks. Much appreciated.

Next, he turns to damage control. Directly after the mild compliment, Coyne registers his main complaint about the paper: the conclusions supposedly can only be applied to laboratory evolution experiments, and say little about (Darwinian) evolution in nature. “But his conclusions may be misleading when you extend them to bacterial or viral evolution in nature, and are certainly misleading if you extend them to eukaryotes (organisms with complex cells), for several reasons”. Below I deal with Coyne’s three reasons in turn.

Professor Coyne’s first objection is:

1. In virtually none of the experiments summarized by Behe was there the possibility of adapting the way that many bacteria and viruses actually adapt in nature: by the uptake of DNA from other microbes. Lenski’s studies of E. coli, for instance, and Bull’s work on phage evolution, deliberately preclude the presence of other species that could serve as vectors of DNA, and thus of new FCTs.

Coyne is simply wrong here, at least about phages (bacterial viruses). Viruses grow in other organisms — the cells they infect. Thus pretty much by definition they are in contact with other microbes for much of their life cycle, and it is thought that sometimes viruses acquire genes from their host cells. In fact, in one report by Bull’s group (http://tinyurl.com/3adlq6c) I reviewed, in which the gene for bacteriophage T7 ligase was intentionally removed at the start of an experiment, the investigators reported they initially expected the missing gene to be replaced.

At the outset, our expectation from work in other viral systems was that the loss of ligase activity would remain so deleterious to T7 that recovery to high fitness would require the genome to acquire new sequences through recombination or gene duplication and to replace ligase function by divergence of those sequences.

Unexpectedly, however, “This hope was not realized, and compensatory evolution occurred through point mutations and a deletion.” Thus it seems that Professor Coyne’s expectations about what is required for a gain-of-FCT event are not universally shared among scientists.

Coyne is of course correct that in experiments in which just one species of bacteria is present, the cells cannot acquire DNA from other species of bacteria. Yet those who conducted such experiments often had expectations for evolution much different from him. In the 1970’s and 1980’s many workers thought that gene duplication or recruitment plus divergence would allow bacteria to diversify the foodstuffs they could metabolize. Out of many such experiments, only one seemed to work by gain-of-FCT. Professor Coyne’s dismissal of such experiments is pure hindsight.

Professor Coyne doesn’t mention that in the review I argue that results from nature are consonant with conclusions drawn from lab experiments. I wrote:

One objection might be that the above examples are artificial. They concern laboratory evolution…. Nonetheless, results arguably similar to those that have been seen in laboratory evolution studies to date have also been seen in nature, such as the loss of many genes by Yersinia pestis (after, of course, the acquisition of new genetic material in the form of several plasmids), and the loss-of-FCT mutations that have spread in human populations in response to selective pressure from malaria. A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Coyne’s second objection is the following:

2. In relatively short-term lab experiments there has simply not been enough time to observe the accumulation of complex FCTs, which take time to build or acquire from a rare horizontal transmission event.

I addressed that very point in my review:

Furthermore, although complex gain-of-FCT mutations likely would occur only on long time-scales unavailable to laboratory studies, simple gain-of-FCT mutations need not take nearly as long. As seen in Table 1, a gain-of-FCT mutation in sickle hemoglobin is triggered by a simple point mutation, which helps code for a new protein binding site. It has been estimated that new transcription-factor binding sites in higher eukaryotes can be formed relatively quickly by single point mutations in DNA sequences that are already near matches (Stone and Wray 2001). In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand- to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of-FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

Yes, complex gain-of-FCT events would not be expected to occur, but simple GOF’s would. Yet they didn’t show up.

Professor Coyne then proceeds to put words in my mouth:

What [Be]he’s saying is this: “Yes, gain of FCTs could, and likely is, more important in nature than seen in these short-term experiments. But my conclusions are limited to these types of short-term lab studies.”

No, that is not what I was saying at all. I was saying that, no matter what causes gain-of-FCT events to sporadically arise in nature (and I of course think the more complex ones likely resulted from deliberate intelligent design http://tinyurl.com/32n64xl), short-term Darwinian evolution will be dominated by loss-of-FCT, which is itself an important, basic fact about the tempo of evolution.

Above I quoted Coyne talking about “complex FCTs, which take time to build or acquire from a rare horizontal transmission event”. Yet cells aren’t going to sit around twiddling their thumbs until that rare event shows up. Any mutation which confers an advantage at any time will be selected, and the large majority of those in the short term will be LOF. Ironically, Coyne seems to underestimate the power of natural selection, which “is daily and hourly scrutinising, throughout the world, every variation, even the slightest….” A process which scrutinizes life “daily and hourly”, as Darwin wrote, isn’t going to wait around for some rare event.

Professor Coyne’s third objection is:

3. Finally, Behe does not mention—and I think he should have—the extensive and very strong evidence for adaptation via gain-of-FCT mutations in eukaryotes.

As I show in Table 1 of the review, we have wonderful evidence of what Darwinian evolution has done to a multicellular eukaryotic species — Homo sapiens — in response to strong selective pressure from malaria over the past ten thousand years. A handful of mutations have been selected. The mutations are classified as: one GOF (the sickle mutation); two modification of functions; and five LOFs. That’s pretty much the proportion of what one sees in bacteria and larger viruses, so there is no reason to think that short-term evolution in eukaryotes has a substantially different spectrum of adaptive mutations than for prokaryotes.

Coyne wants to focus on long-term evolution:

While [eukaryotes] may occasionally acquire genes or genetic elements by horizontal transfer, we know that they acquire new genes by the mechanism of gene duplication and divergence: new genes arise by duplication of old ones, and then the functions of these once-identical genes diverge as they acquire new mutations. … Think of all the genes that have arisen in eukaryotes in this way and gained novel function: classic examples include genes of the immune system, Hox gene families, olfactory genes, and the globin genes.

Unfortunately, Professor Coyne isn’t making a critical distinction here. While we may know (or at least have very good evidence that is consonant with the idea) that new genes have arisen by duplication and divergence of old ones in eukaryotes, we do not know that happens by a Darwinian mechanism of random mutation and natural selection. And if some duplicate genes do arise and diversify by Darwinian processes, we do not know that explains all or even most of them. After all, while the long-term processes that Professor Coyne envisions are taking their sweet time to come together, the fast and dirty short-term adaptive processes will dominate. That’s what we know from the great efforts put into experimental evolutionary studies by many investigators over decades.

And as I point out in the QRB paper, all of this can be neatly summarized by The First Rule of Adaptive Evolution: Break or blunt any functional coded element whose loss would yield a net fitness gain.

For most of history such a question could not be investigated, but with the tools that have become available to molecular biology in the past few decades, a good start can be made on addressing it. The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. (I make a number of distinctions defining gain-, loss- and modification of function mutations, so for the complete story please read the paper.) Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.

Although the data reviewed are mostly from laboratory experiments, there are good reasons to think that the same situation would hold for Darwinian evolution in nature, too, as I discuss in the paper. From the data I propose a rule of thumb that could help guide researchers in their expectations of what they will find much of the time in studies of evolutionary adaptation. I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.