Thursday, 24 May 2012

Dolphins and Porpoises and...Bats? Oh My! Evolution's Convergence Problem

This article was originally published on Evolution News & Views.

I have recently been reading George McGhee's Convergent Evolution: Limited Forms Most Beautiful. McGhee's book is a gripping read, and it favorably cites the work of both Michael Denton and Douglas Axe, ID-friendly scientists well known to readers of ENV. The book documents a multitude of cases of convergent evolution (homoplasy), the phenomenon of repeated evolution. When similarity is thought to have arisen by means of common ancestry, the features in question are said to be "homologous." When similarity is thought to have arisen by means other than common ancestry, the features are said to be "analogous."

Convergent Evolution.jpgThose who subscribe to universal common ancestry interpret biological similarity of sequence, structure and anatomy as resulting from descent with modification from a common ancestral source. ID proponents who question common ancestry typically interpret biological similarity as resulting from a common blueprint. Is there a way to evaluate which of these two competing hypotheses better fits the evidence?

If you take such similarity as pointing to common descent, then you would expect to see it exhibiting a nested hierarchical distribution, the more seamless the better. In other words, the patterns of distribution of this similarity ought to mutually corroborate a single family tree. Sure, there might be occasional deviations from that tree, the results of phenomena such as incomplete lineage sorting. One would not expect to see the pervasive occurrence of a high degree of similarity -- what would normally be regarded as "homology" -- that decidedly cannot be accounted for within the framework of common descent. Yet that is in fact what we do observe.


Perhaps the most impressive examples of convergent evolution are those that occur at the molecular level -- that of amino acid or even nucleotide sequences. Assessing the pervasiveness of convergence at the nucleotide sequence level is difficult, however, owing to a current lack of available data. Indeed, Castoe et al. (2010) point out that "complete vertebrate nuclear genomes still number in the tens, not hundreds."

Even so, the little data that we do have yield startling results. One example of such convergence, documented by Zhang (2006), is the case of the pancreatic RNase in the African colobine monkeys and Asian colobine monkeys (thought to have diverged some 13 million years ago). Three identical nucleotide substitutions occurred in the DNA coding for these enzymes in the two lineages. This resulted in a lowering of the pH of the enzyme's maximum ribonucleolytic activity from 7.4 to 6.3, allowing the enzyme to work in more acidic conditions than normal, making it perfectly suited for the small intestine.

Cuevas et al. (2002) have furthermore documented, in retroviruses, the occurrence of molecular convergences in 12 variable sites in independent lineages. Some of these convergent mutations even took place in intergenic regions (changes in which are normally thought to be selectively neutral) and also in synonymous sites. The authors note that this is fairly widely observed among HIV-1 virus clones in humans and in SHIV strains isolated from macaques, monkeys and humans.

Mitochondrial DNA data has revealed even more astonishing results. Castoe et al. (2009, 2010), for example, report the occurrence of 44 parallel amino acid substitutions in all 13 mitochondrially encoded oxidative phosphorylation metabolic proteins in the distantly related snakes and agamid lizards. Their 2009 paper notes:
"These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution."
Stern and Orgogozo (2009) examine 350 different mutations responsible for phenotypic variation and conclude that "more than half of these represent cases of parallel genetic evolution." Moreover,
"Gene function explains part but not all of the observed pattern of parallel genetic evolution. In several cases, parallelism has been observed even though mutations in a large number of genes can produce similar phenotypic changes. For example, although more than 80 genes regulate flowering time, changes in only a subset of these genes have produced evolutionary changes in flowering time. Hundreds of genes regulate the pattern of fine epidermal projections, called trichomes, on Drosophila melanogaster larvae. But only one gene, called shavenbaby, has evolved to alter larval trichome patterns between Drosophila species, and this gene has accumulated multiple evolutionarily relevant mutations." [internal citations omitted]
It is suggested that "hotspot genes" such as shavenbaby exist because,
"In the entire regulatory network governing development of the Drosophila embryo, only shavenbaby, with its specialized function to rally the entire module of trichome morphogenesis, can accumulate mutations that alter trichome patterns without disrupting other developmental processes."
Protein amino acid sequences also exhibit pervasive convergence. One of my favorite examples is the convergent evolution of the motor protein Prestin in echolocating bats and cetaceans. Take a look at the following figure, excerpted from Liu et al. (2010). prestin.jpg
The paper reports that echolocating dolphins "group with echolocating bats in a phylogenetic tree of Prestin." Jones (2010) states that,
"...dolphins and porpoises share at least 14 derived amino acid sites in prestin with echolocating bats, including 10 shared with the highly specialized CF bats. Consequently, dolphins and porpoises form a sister group to CF bats in a phylogenetic analysis of prestin sequences (Figure 1). This finding is arguably one of the best examples of convergent molecular evolution discovered to date, and is exceptional because it is likely to be adaptive, driven by positive selection."
Another example is reported by Robson et al. (2000), who document that 28 of the amino acids in the oothecin protein of the cockroach are in exactly the same order as those in the lampry lamprin protein. The authors state that "sequence similarities between lamprin and oothecin, which share a 28/30 amino acid sequence identity, may represent one of the best examples of primary sequence convergence so far identified."

Furthermore, Lawn et al. (1997) report on the "convergent evolution of apolipoprotein(a) in primates and hedgehog." Apolipoprotein(a), or apo(a), a low-density lipoprotein (LDL) that is a risk factor for human atherosclerosis, is found in Old World primates (Catarrhini), and has also been identified in European hedgehogs. Remarkably, the protein functions identically in both organisms. The paper reports,
"By apparent remodeling of a plasminogen-like gene, hedgehog and human ancestors independently evolved an apo(a) protein with multiple kringle domains that covalently links to apoB-containing lipoproteins, binds fibrin, lacks proteolytic activity, and competitively inhibits plasminogen activation."
An additional example is the "sequence convergence in the peptide-binding region of primate and rodent MHC Class Ib molecules" (Yeager et al., 1997) and the "independent origin of Prosimian, Platyrrhine, and Catarrhine Mhc-DRB genes" (Kriener et al., 2000). Moreover, Jost et al. (2008) report on "4 taxonomically diverse species of pufferfishes (Tetraodontidae)" which "each evolved resistance to the guanidinium toxins tetrodotoxin (TTX) and saxitoxin (STX) via parallel amino acid replacements across all 8 sodium channels present in teleost fish genomes."

Even highly sophisticated molecular mechanisms have often evolved multiple times independently. One especially remarkable case of this is the convergent evolution of very similar DNA biosynthesis mechanisms in the archaea and the eubacteria (Leipe et al., 1999). Complex camera eyes have also arisen independently in multiple ineages, having evolved in chordates and molluscs, as well as alciopid annelid worms (Wald and Raypart, 1977) and two different groups of spiders (Laughlin, 1980; Williams and McIntyre, 1980).
Finally, one of the most astonishing cases of convergent evolution is discussed by Lukes et al. (2009). This paper concerns the evolution of two major distantly related phyla of flagellate protozoa, namely, the dinoflagellates and euglenozoa. These two groups are taxonomically so far apart that they are even members of different kingdoms (chromalveolates and excavates respectively). What is remarkable about these groups is that their evolutionary trajectories -- indeed the evolution of "fundamental structures and processes" -- have substantially deviated, in numerous respects, from other eukaryotes.

But here's the point: Despite being very distantly related, these two lineages have deviated from the eukaryotic norm, in many cases, in much the same fashion. Indeed, there is a treasure trove of independently acquired features and characteristics. The paper (whose contents are helpfully summarized in this lecture) discusses numerous instances of convergent evolution pertinent to cellular organization, the nucleus, the plastid and the mitochondrion.

Convergent evolution is everywhere in biology. Many more examples could be given: The cases described above barely scratch the tip of the iceberg.

In his book Convergent Evolution: Limited Forms Most Beautiful, George McGhee reflects,
"But what about the numerous cases in nature whether the morphological data and the nuclear data clash? In those cases, it is generally assumed that similarities in morphological traits have arisen by convergent evolution and are not synapomorphies, because the nuclear genome data can be trusted to be almost free from molecular convergences. What if this is not true?"
In other words, extensive convergent evolution at the DNA level is considered to be so improbable under standard evolutionary assumptions that the nuclear data is preferred over morphological data in those many cases where conflict exists. In light of the numerous instances of demonstrable molecular convergence, however, the validity of this assumption -- perhaps even some of the key tenets of the modern evolutionary paradigm -- may need to be revisited. The widespread nature of homoplasy at both the molecular and morphological level substantially undercuts the frequent argument for common descent based on the nested hierarchical distribution of shared traits among organisms.

For further material on homoplasy and convergent evolution, in addition to George McGhee's book mentioned above, I refer readers to Simon Conway Morris's Life's Solution: Inevitable Humans in a Lonely Universe (you can also find Conway Morris's website on the topic here); as well as Fazale Rana's contribution (chapter 21) to The Nature of Nature. No doubt the more genomes that are sequenced the more the pervasive nature of homoplasy will come to be appreciated.

11 comments:

  1. Ok this is where you go wrong. . .

    "Is there a way to evaluate which of these two competing hypotheses better fits the evidence?"

    That is in paragraph two - you have made this error several times before and always seem to ignore my comments - or you post where comments are not allowed or are censored for pseudo-moralistic/fascist reasons.

    The second of the two hypothesis i.e. "it was designed!" can fit any evidence at all, ever.

    Therefore it isn't science. It is too vague. It doesn't teach us anything or move us any further forward. It can't be tested. Not without giving your designer some actual characteristics that allow such testing and this you steadfastly refuse to do i.e. the designer is not evil and therefore won't designer a flagellum to power diseases or to design malaria itself to cause suffering on purpose (as claimed by Behe)

    Common ancestry can be falsified.

    Without addressing this point the rest of your article is just meaningless verbiage.

    Please respond this time. . .

    Your past behaviour brings shame on christians but here is a chance to rectify that somewhat.

    Regards,

    Psi

    ReplyDelete
  2. LOL

    Read any Augustine yet Psi?

    Who appointed you the watchdog for Christian shame? lol

    As a self professed Atheist you have no intellectual foundation upon which to rest the existence of an objective right and wrong. Making the idea of shame a meaningless concept.

    You atheists are soooo lame.

    ReplyDelete
  3. Very polite.

    Both legs working well. Check.

    Intellectual foundation for morales in good working order thanks. Check.

    Are you curious as to what it is?

    Here you go;

    http://cogitatute.blogspot.co.uk/2008/06/being-good-without-god.html

    Happy to get feedback - but please drop the insults - that is not very Christian either.

    I have as much right to my opinion as you do to yours - at least I know that mine is an opinion and I have thought about it.

    AND yes here is Augustine and this is exactly the quote I had in mind;

    Usually, even a non-Christian knows something about the earth, the heavens, and the other elements of the world, about the motion and orbit of the stars and even their size and relative positions, about the predictable eclipses of the sun and moon, the cycles of the years and the seasons, about the kinds of animals, shrubs, stones, and so forth, and this knowledge he holds to as being certain from reason and experience. Now, it is a disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. The shame is not so much that an ignorant individual is derided, but that people outside the household of faith think our sacred writers held such opinions, and, to the great loss of those for whose salvation we toil, the writers of our Scripture are criticized and rejected as unlearned men. If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods on facts which they themselves have learnt from experience and the light of reason? Reckless and incompetent expounders of Holy Scripture bring untold trouble and sorrow on their wiser brethren when they are caught in one of their mischievous false opinions and are taken to task by those who are not bound by the authority of our sacred books. For then, to defend their utterly foolish and obviously untrue statements, they will try to call upon Holy Scripture for proof and even recite from memory many passages which they think support their position, although they understand neither what they say nor the things about which they make assertion [quoting 1 Tim 1:7].


    Psi

    ReplyDelete
  4. Sorry but those links do not even come close to answering my question.

    You can differentiate between good and evil, right and wrong, good for you. Never doubted it for a second. That's not the problem an atheistic world view faces.

    An evolutionary explanation as to why we've come to differentiate right from wrong is not an intellectual foundation for believing that right and wrong do in fact objectively exist.

    Upon what intellectual foundation do you rest a belief in the objective existence of right and wrong?

    ReplyDelete
  5. So you go from this:

    As a self professed Atheist you have no intellectual foundation upon which to rest the existence of an objective right and wrong.

    To this:

    You can differentiate between good and evil, right and wrong, good for you. Never doubted it for a second. That's not the problem an atheistic world view faces.

    Back to this:

    Upon what intellectual foundation do you rest a belief in the objective existence of right and wrong?

    Sigh.

    In the piece I linked to I told you that

    1) by thinking about it carefully,
    2) talking to other people and
    3) by living in and contributing to a democracy and
    4) always being prepared to go back to point 1) and think again in case I got it wrong,

    I work out my moral framework.

    This is my foundation.

    You seem happy to accept it works.

    You just don't want to define it as a foundation.

    Tough.

    You'll need to engage with the topic and not just argue about your own self appointed definitions.

    Care to actually engage with that argument? Or are you just going to claim it doesn't count because it doesn't feature your god? You do realise that this doesn't address my points don't you?

    Your own behaviour towards me has been insulting, rude and prejudiced. Any idea just ironic it is that you are telling me I have no moral foundations?

    e.g. People taking their faith as a moral foundation both supported and opposed slavery, it took quite a while to drop from 100% support to about 50% support - the very few secularists who dared to declare their non-faith at the time where much more likely to be against it. Where were your foundations then? Was that just random chance or does this mean that thinking about the issues make it more likely to get the right answer? I think it did. If you don't then explain why.

    You also ignore all the points I make in my piece pointing out what appear to be significant holes in your own claimed "foundations". Again no response at all.

    I will be happy to discuss these issues, that's partly why I am here, so why don't you?

    In the mean time I note you don't mention Augustine again - whoops. Did you not know he said that? What do you think of it? Is that not a clear indication that JM should be ashamed of his antics bringing scorn on christianity by his pseudo-scientific posturing?

    I'm happy to engage with the points made.

    - - -

    In the meantime, and back on topic, can anyone address the problems with JM's post that I point out in the first comment (preferably without throwing prejudice and insults around)?

    Thanks,

    Psi

    ReplyDelete
  6. Let me see if I can't do the Christian thing here.

    You appear to me to be confused.

    The problem:

    You have given an epistemologic answer to an ontological question.

    This makes your answer a non sequitur.

    Understand?

    I am not saying that you as an atheist can not use logic and reason to deduce right from wrong.

    I am saying that as an atheist you have no rational foundation for a belief that right and wrong exist.

    If you can satisfactorily answer the question you'll become the most famous atheist philosopher of our age. And I'll bet with only a cursory knowledge of philosophy. Imagine that lol.

    ReplyDelete
  7. Let's see - muddled communication followed by arrogance and condescension - not still not much Christian spirit there then.

    If that's what you wanted why didn't you ask for it more clearly?

    Brace yourself.

    I don't see a need for an ontological explanation because my steps 1 to 4 work therefore I am happy to take them as my foundation.

    Just as I would be happy to state that I don't know why we have a universe or exactly how it all came about, and that I can't logically prove an ontological foundation for logic. It all seems to work and I am happy to work on that basis. I don't see the need to invent other steps for no reason just to fill in some gaps.

    Are you going to critique them or address any of the other points raised or address the questions I raised about the actual post

    You really are being unnecessarily unpleasant. Are you someone trying to make christians look bad?

    Psi

    ReplyDelete
  8. The one demonstrating arrogance and hubris is you my fine feathered friend. Give up the "your giving Christians a bad name" BS for someone who cares what some arrogant nobody like you thinks. That isn't me.


    So the great philosopher Psi doesn't see a need to explain the existence of right and wrong. So you do what it is you accuse Christians of doing. Believing something without a sound rational. That's irrational. You are treading on ground that is well gone over by philosophers throughout the ages but a nit wit like you doesn't seem to think it's a problem. Well then fine. But you're going to have to stop accusing Christians of doing what it is you have done. Believing in things without a solid rational foundation for those beliefs.

    We're done.

    I'm bored of you now.

    ReplyDelete
  9. Thanks for that Cam,

    Manners maketh the man, but apparently not the Cam.

    People can read for themselves that it was your own declarations about my position that lead to my offering my own actual views. I even asked for feedback from you and tried to engage in a dialog.

    I am still more than happy to do that with others here.

    Regards,

    Feathered, BS, arrogant nobody, great philosopher, irrational, nit wit Psi

    - - -

    In the meantime I wonder if JM will finally address my points about his post?

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