Barry Arrington Part II: questions from Phinehas

A very nice post by Barry at UD struck me as worth reposting here (as I can’t post there), inspired by Neil Rickert:

Phinehas asks Neil Rickert a fascinating question about the supposed direction of evolution.  Neil says he will address it in a separate thread, and I started this one for that purpose.  The rest of the post is Phenehas’ question to Neil:

@Neil I also appreciate the professional tone. I am a skeptic regarding what evolution can actually accomplish. In keeping with your demonstrated patience, I’d be grateful if you would give serious consideration to something that keeps tripping me up. I’ve often thought of natural selection as the heuristic to random mutations’ exhaustive search.

A path-finding algorithm can be aided in finding a path from point A to point B by using distance to B as a heuristic to narrow the search space. Without a heuristic, you are left to blind chance. It is said that evolution has no purpose or goal, so there is no point B. It is also claimed that evolution isn’t simply the result of blind chance, so a heuristic would seem to be required. Somehow, natural selection is supposed to address both of these concerns. Nature selects for fitness, we are told, so somehow we have a heuristic even without a point B.

But what is fitness? How does it work as a heuristic? How is it defined? Evidently, it is all about reproductive success. But how does one measure reproductive success? This is where things get fuzzy for me. Surely evolution is a story about the rise of more and more complex organisms. Isn’t this how the tree of life is laid out? Surely it is the complexity of highly developed organisms that evolution seeks to explain. Surely Mt. Improbable has man near its peak and bacteria near its base. But by what metric is man more successful at reproducing than bacteria? If I am a sponge somewhere between the two extremes, how is a step toward bacteria any less of a point B for me than a step toward man? Why should the fitness heuristic prefer a step upward in complexity toward man in any way whatsoever over a step downward in complexity toward bacteria?

It seems that, under the more obvious metrics for calculating reproductive success, bacteria are hard to beat. Even more, a rise in complexity, if anything, would appear to lead to less reproductive success and not more. So how can natural selection be any sort of heuristic for helping us climb Mt Improbable’s complexity when every simpler organism at the base of the mountain is at least as fit in passing on its genes as the more complex organisms near it’s peak? And without this heuristic, how are we not back to a blind, exhaustive search?

 

Excellent questions.

273 Replies to “Barry Arrington Part II: questions from Phinehas”

  1. Neil Rickert
    Ignored
    says:

    Phenotype exists ‘for’ genotype continuation, not the other way around.

    I tend to think of it in terms of metabolism continuation. So I think of genetics as an implementation detail, and of genotype and phenotype as artifacts of that implementation.

  2. Lizzie
    Ignored
    says:

    Well, I don’t think Noble is saying that Dawkins is wrong or right. In fact, in his book and in his lecture, he deliberately rewrites a key passage from Dawkins, turning it upside down – and makes the point that both are ways of looking at the same phenomenon, even though one is the mirror of the other.

    But he finds his approach more useful, and so do I. It’s for the same reason that I think the word “reductionist” is problematic, and implies that the “reductionist” in question thinks that low-level analysis trumps any higher one. It’s also why I get a bit irritated when people accuse me of equating “mind” with “brain”, or even assuming I am saying that brains have minds. Brains don’t have minds, people do.

  3. Allan Miller
    Ignored
    says:

    It really depends what you’re trying to understand. If it’s evolution, then I don’t think the organism perspective has much explanatory power – though it should never be a strict either/or in any case. “Gene Thinking” does not mean never using a holistic approach, but provides a useful corrective to certain mechanistically dubious flights of fancy.

    As I’ve said elsewhere, ‘organisms’ are mostly just shells made of diploid cells. If you’re trying to understand how they work, regarding the various stretches of DNA that make them as ‘entities with a perspective’ does not help much in understanding them. But if you’re trying to understand the dynamic of the evolutionary process, the thing that survives and evolves – the genotype – is the material with the capacity to pull levers. Organisms are just the medium through which those levers are pulled. It is not strictly ‘reductionist’ in the sense that it claims one can, say, understand the eye thoroughly gene by gene, but simply that genomes themselves are ‘reduced’ by iterative meiosis into separate, quasi-independent evolutionary units, which fact introduces a particular dynamic to subgenome interactions. Their contribution to each organism is not separable, but they have individual selective advantage (positive, neutral or negative) regardless, in the complex context provided by the action of the rest of the series of genomes in which they find themselves.

  4. Allan Miller
    Ignored
    says:

    Mmmmm … I think the publishers might have taken some persuading on that one! “The focus group are saying ‘What the f***’s an allele'”?

    But anyway, competition is not always between alleles at a locus. I think he does make it pretty clear what he means by ‘gene’, and discusses the merits of not calling it “the Selfish stretch of DNA”. His gene is the same as Williams’s evolutionary allele, a segment that ‘recombines with appreciable frequency’, though ‘reasonable’ is not particularly rigorous. It is not a segment producing a particular peptide or a binary phenotypic character, which are other potential sources of confusion.

  5. Mike Elzinga
    Ignored
    says:

    Who needs genes?

    Here is an analogy that involves only collections of a single element.

    Carbon has many allotropes; but as the old song goes, “Diamonds are a Girl’s Best Friend.”

  6. petrushka
    Ignored
    says:

    Allan Miller,

    I’m afraid I don’t know enough to argue this constructively. I was just taken by the thought that genes have to cooperate at some level. But variants can compete. I’ll have to go back to the book.

  7. Allan Miller
    Ignored
    says:

    Absolutely they have to cooperate. It’s a bit like the ‘no true altruist’ ethical conundrum – co-operation in a team is the means by which most genes further their ‘selfish’ end: to become replicated. Dawkins has said that he could have called it “The Co-operative Gene” without changing a word. But the underlying nature of DNA, its inherent tendency to increase on its own account, is important.

    Traditional biology focussed on the organism, and DNA was just one of the things the organism used in its ‘struggle’. I recall in a lecture on DNA being told that someone had just written a book saying that chickens were just DNA’s means of making more DNA, with a wry smile, but this apparently trivial inversion actually turned biology ‘the right way round’ for me.

    It’s all about linkage. The simplest chromosome is a complete loop, which contains within it various segments with various properties – a bit here makes a DNA polymerase, a bit there a protein that allows a DNA polymerase (and itself) to be expressed as protein, a bit there a tRNA or bit of a ribosome. None of these works independently of any other in this [IC!] system.

    If one of these elements became ‘rogue’ – increased its copy number, say – it would damage the fortunes of the entire collection, ultimately to its own detriment, so selection favours actions that benefit the collection. The whole genome is an evolutionary allele, and competes with other evolutionary alleles to which it is not linked.

    With a sexual species, the situation is more complex and subtle. Crossovers appear in meiosis between diploid chromosomes and the entire upstream/downstream linkage is swapped. This happens iteratively, and so over the generations, subgenome fragments acquire a kind of independence, down to the geneticist’s unit: the ‘classical’ allele. They must co-operate with all the genes they are linked to in a life, and with their near neighbours over a few generations, but the potential for genetic conflict arises because linkage is not indefinite. Chromosomes or genes can disable their opposite numbers, or, where two genomes exist in the one body (eg viviparous species, or eukaryote cells), genes in the mother have different ‘interests’ from those of genes in her children (even though she herself was once a child).

    And there can be conflicts of interest between genders – most genes spend half their time in one gender and half in the other, and so you get the curious setup where genes expressed to aid females in the ‘battle of the sexes’ are present, but quiescent, in their male partner/opponents, and vice versa.

  8. Robin Robin
    Ignored
    says:

    No, and that’s the whole point. Similarly, I don’t see the humans as having any “incredible fortune” when it comes to environment/molecules/laws/constants/etc. That’s just looking at water from the perspective of a pothole. We are the product of the environment/molecules/constants/universe and whatnot – thus it makes sense we fit neatly into them. I just don’t get the magic thinking some adopt to rationalize it as some big deal.

  9. llanitedave llanitedave
    Ignored
    says:

    Allan Miller,

    I’ve watched Noble expound his ideas in a video, and have skimmed a paper in J Physiol. I think he actually misunderstands Dawkins. He is interested in complex phenotype, and finds the ‘selfish’ metaphor to be of no use in that, and nor is it intended to be. The ‘selfish gene’ is essentially a linkage unit, a fuzzy-boundaried haplotype of ‘reasonable’ persistence, but organisms are an undivided whole. DNA’s inherent ‘selfishness’ – tendency to increase by hook or by crook – is largely silenced in favour of collective co-operation (though cancer bucks this tendency).

    It is an evolutionary issue, not one intended to deal with phenotypic complexity. From an evolutionary perspective, the organism is a black box, into which go genes and out of which come copies of those genes. A succession of these ‘black boxes’ live their lives and selection delivers verdicts upon the many genes that occupy the genetic loci, integrating the complexities into their net effects on offspring production in a succession of lives.

    Genes are entirely favoured to behave in a co-ordinated, ‘unselfish’ manner in an organism, because their futures are linked. On the scramble for the gamete lifeboats, or spilling out into the wider population of loci, genes are instead favoured to beat each other up – but the ‘competition’ is mainly between alleles of a locus, less readily between different genes in the same linked team. You need them; you don’t need your allele, and indeed it is in the way.

    A gene’s options are limited. Mostly, the best a gene can hope for is to enhance offspring production over invisible allelic rivals. But there are certain mechanisms that can be employed to more directly influence matters. One such is direct attack on the allele in meiosis, to enhance segregation over the Mendelian 50%. Mechanisms are limited, though, and the allele soon starts to encounter copies of itself and gains nothing by beating up such copies – the mechanism is self-limiting. Another is in competitions between internally-borne offspring and the mother, but this cannot impact more than a subset of genes.

    Although Dawkins is most known for his catchy title, his book is actually as much about the opposite – given the thesis (a reasonable one) that DNA sequences in a finite world compete for their share of ‘resources’ (instances of a locus), just as ecologically-overlapping organisms do, how are co-ordination and co-operation sustained?

    It’s been years since I read it, but the above was pretty much my take as well. It’s an interesting and useful perspective, it’s not to be taken as a fixed ideology.

  10. petrushka
    Ignored
    says:

    Many issues in biology can be seen as chicken and egg problems. From my limited understanding of things the answer is always both.

  11. damitall2
    Ignored
    says:

    llanitedave,

    I think a number of people misunderstand Dawkins, for a variety of reasons. Speaking as an educated (I hope!) virtual layman in such things, Dawkins’ books have taught me a great deal, and guided me to more; but I’ve never felt tempted to think he was providing anything that could be called an ideology. Maybe he’s not always right or bang up to date, but books intended to make complex science more accessible usually have some faults. IMHO, he’s done more than most in improving the public perception and knowledge of a subject which becomes rapidly more complex the further one delves into it.
    I have on occasion felt he’s taken some rather unjustified stick from scientists.

  12. Allan Miller
    Ignored
    says:

    I have on occasion felt he’s taken some rather unjustified stick from scientists.

    I’d agree on that – he makes millions from science while others plug away for slim research grants … he’s seen by the public as a foremost evolutionary biologist when his original contributions to the field have been minor … these in themselves would not explain why he gets the stick, but I think it may be a factor.

    He certainly rekindled my own interest in evolutionary biology, having only covered it tangentially at university. I don’t think he’s an oracle, but he writes well and clearly – making it the more mystifying how often he’s (in my view) misunderstood, by some equally bright people. Several light bulbs have popped on in my head due to reading him.

  13. petrushka
    Ignored
    says:

    He makes some money because he is entertaining,and that’s a rare commodity in science writing. BF Skinner had a best seller. Stephen Gould a series of best sellers. Feinman. Sagan. And of course Asimov, Fred Hoyle, Hawkins and Clarke. I suppose I’ve left out a bunch.

    Anyone who writes for a general audience will use metaphors and analogies to convey complex ideas, and all such figures of speech will distort the science somewhat.

  14. DNA_Jock
    Ignored
    says:

    damitall2:

    I have on occasion felt he’s taken some rather unjustified stick from scientists.

    Well, he is something of a polarizing character.
    I think many scientists are peeved that he is viewed as a foremost authority on evolution, or the inventor of the Selfish Gene concept, when he’s just a writer. A very good writer. There’s a silly jealousy because successful writers get paid more than scientists. Furthermore, IMHO he’s done more to educate the public than anyone else, which is very laudable.
    So I agree he’s taken some unjustified stick.

    On the other hand, in the political battle over education, I worry that CRD (and PZM) are the best weapons the sectarians will ever have: poster children for the “evolutionism=atheist proselytizing” meme.
    Personally, I found the scientific mistakes in “The Selfish Gene” very annoying. Happily, he fixed the egregious ones in “The Extended Phenotype”, so I got over it. But I’m not a fan.
    So I reckon some of the stick he’s taken from scientists has been justified stick. As to the relative proportions, YMMV.

  15. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    This is simply too rich to overlook. Over on UD (here) “niwrad” is trumpeting the great achievement of “Joe” in refuting evolutionary biology. It seems that Joe (JoeG) has noticed that bacteria can reproduce much faster than eukaryotes, so in evolving eukaryotes evolution decreased their fitness:

    [JoeG]: Kind of makes you wonder why eukaryotes even got started. And it seems to go against natural selection. The less fit appear to be doing very, very well.

    and “niwrad” drives the point home:

    Bravo Joe. If bacteria are the “pinnacle of fitness” you ask “why eukaryotes even got started”? In prokaryotes natural selection worked to increase fitness. In eukaryotes natural selection worked to decrease fitness. Evolution does X and NOT X in the same time.

    Discovered the n-th contradiction of Darwinism. I am going to insert it in my collection. Thanks Joe.

    For the record, this supports my argument about the weakness of the concept of fitness …

    A commenter in that thread (“goodusername” in comment 6) made the point that what was fit in one environment wasn’t fit in another, and the eukaryotes and prokaryotes are in different environments. But they are so busy applauding JoeG over there that they have not realized that they simply misunderstand that one organism will displace another if it has higher fitness and is in perfect competition with the other.

    Of course this has already been addressed over here, earlier in this thread. A bit over a week ago I mentioned that

    Success of different populations are measured in success at survival and reproduction. But the successful growth of moss on rocks on a mountain does not mean that sea anemones in the ocean are outcompeted. It’s called ecology — for growth of one population to decrease the success of another they have to be in strong competition (we even call it “perfect competition”). And fundamentally, that’s why there are still monkeys.

    Not a mysterious point — see there is thing called ecology, and organisms don’t all compete perfectly with each other. But the cheering section at UD doesn’t get it.

  16. Lizzie
    Ignored
    says:

    Well, ID proponents would do their cause a favour if they actually didn’t make so many basic mistakes about what they are trying to refute.

  17. Neil Rickert
    Ignored
    says:

    Over on UD “niwrad” is trumpeting the great achievement of “Joe” in refuting evolutionary biology.

    I saw that thread this morning. It was worth a laugh.

    It did occur to me that they chose a poor title. They called it “Joe scores”. However, the title should obviously be “If humans evolved from apes, why are there still bacteria?”

    That post is a great demonstration that they don’t know what they are talking about.

  18. Mike Elzinga
    Ignored
    says:

    It’s another clear example of the fact that ID/creationists don’t even know the material taught in high school. In fact, they still bollix up middle school science.

    Joe G’s knowledge of middle school science is marginal at best; but now it appears that niwrad has just demonstrated that he is incapable of assessing science concepts at the high school and middle school levels.

  19. Allan Miller
    Ignored
    says:

    This is simply too rich to overlook.

    Joe [G] scores – deep in the back of his own net, with an assist from Niwrad!

    there is thing called ecology, and organisms don’t all compete perfectly with each other.

    Though in principle, even with a competition between identically fit close competitors, one will displace the other – exactly the same rationale as genetic drift of neutral traits.

    Hmmm. A prokaryote that can only absorb nutrients through its single, energetic membrane, and a eukaryote that can munch its way through many prokaryotes, and cast their dissolved bodies to its menagerie of ravening mitochondria. Which is fitter? Only one way to find out – FIIIIIIGHT!

  20. Allan Miller
    Ignored
    says:

    Joe has respotted the ball, and proceeded to stick it in his own net once more.

    we cannot test the endosymbiotic hypothesis.

    Nonsense. Genetic continuity with separate free-living prokaryotes? Check. Specifically, alpha-proteobacteria. Hypothesis tested. Passed. Genome-architecture continuity with prokaryotes? Check. Many more tests possible and done. Hypothesis tested. Supported. Not proven, but tested, and passed.

    All we can do is say “Hey those organelles “look like” they could have been bacteria”, and that ain’t scientific.

    That may be all you could do, but analysis goes a little – a lot – deeper than that. But wait … when people say biology “looks like” exquisite engineering … ? Scientific, or not? When ID comes up with tests of equivalent rigour, then it would be scientific, but so far, nada. He shoots, he scores! Pssst – wrong end, Joe.

  21. cubist
    Ignored
    says:

    DNA_Jock:
    On the other hand, in the political battle over education, I worry that CRD (and PZM) are the best weapons the sectarians will ever have: poster children for the “evolutionism=atheist proselytizing” meme.

    Disagreement. It is demonstrably true that Creationists have always made noise about “evolution = atheism”; to cite just one prominent example, the 1961-vintage Creationist tract THE GENESIS FLOOD is all about how evolution is bad ‘coz it stops people from Coming To Jesus. Likewise, it is demonstrably true that despite such very real counterexamples as Theodosius Dobzhansky (Russian Orthodox), Bob Bakker (Pentecostal—and a P’cost. preacher, to boot!), and Francis “Language of God” Collins, Creationists have never discernably hesitated to disgorge yet another instance of their “evolutionism=atheism” meme. Why, then, do you blame atheists for that meme? Why do you not blame the friggin’ Creationists for being world-class False Witnesses?

  22. DNA_Jock
    Ignored
    says:

    cubist: Disagreement. It is demonstrably true that Creationists have always made noise about “evolution = atheism”; to cite just one prominent example, the 1961-vintage Creationist tract THE GENESIS FLOOD is all about how evolution is bad ‘coz it stops people from Coming To Jesus. Likewise, it is demonstrably true that despite such very real counterexamples as Theodosius Dobzhansky (Russian Orthodox), Bob Bakker (Pentecostal—and a P’cost. preacher, to boot!), and Francis “Language of God” Collins, Creationists have never discernably hesitated to disgorge yet another instance of their “evolutionism=atheism” meme.

    No. No disagreement here. I would add Ken Miller to your excellent list.

    Why, then, do you blame atheists for that meme?

    What leads you to conclude that I blame “atheists”?

    Why do you not blame the friggin’ Creationists for being world-class False Witnesses?

    Well, I do blame creationists for their dishonesty.
    You seem to have skipped over the words “political”, “education” and “proselytizing” in my comment.
    To clarify, I don’t blame anyone but creationists for the “evolution=atheism” meme, but I do blame arrogant, dickish atheists with megaphones for facilitating the “evolutionism=atheist proselytizing” meme.

  23. damitall2
    Ignored
    says:

    DNA_Jock,

    I can agree with most of what you say. But not that CRD and PZM are necessarily the “best weapons”

    Doing honest science and presenting it honestly; having honest and open-minded discussions – these are the best “weapons”

    It’s my view (but open to correction by evidence) that the “public faces” of ID and Creationism are far, far more dishonest and closed-minded about science than any “public” atheist scientist. The whole wretched edifice at UD is testament to that.

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