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Wednesday, December 10, 2014


a week ago, i reported that I was reading THE ARRIVAL OF THE FITTEST, by andreas wagner, a fascinating book about evolutionary biology recommended by my big sister barbara.  in my slow, steady way i have now finished the book, and in this relatively brief post i am going to try to say just enough to persuade you to read it.

even though the book is intended as a popularization, it is quite demanding for someone [like me] who is not already fully conversant with microbiology and evolutionary genetics.  Let me try to state the central idea as simply and clearly as i can.

organisms evolve by changes in their genotypes -- which is to say, changes of a single gene at a time[there are other changes, but i am desperately trying toi keep this simple].  these in turn alter what the organism can do.  can it metabolize sucrose?  or fructose? or ethanol? or acetate?  All of this shapes the way that genes are 'expressed,' which means which of them are turned on to produce proteins, which block the expression of other genes, in what environment, in what sequence, and so forth.  these changes in the genotype produce changes in the organism's phenotype -- how it is shaped, what it can do as an organism, what parts it has and what they can do.  natural selection, or selection of the fittest, now determines which of these changes survive and flourish, and which result in the death of the organism and hence do not get passed on.  if a change to the genotype of a simple bacterium like e. coli enables the individual bacterium with the change to metabolize fructose, and if that bacterium happens to be in a fructose rich environment [like a bit of rotting pear], then it will survive and reproduce, passing on the changed genotype to its descendants.  by this process, one gene at a time, primordial slime evolves into rick santorum [not such a reach, as it happens.]

my sister, who vetted this for obvious mistakes, made the following comment:  "You employ a usage that is essentially universal, among experts as well as science writers, namely imputing agency to genes. I am not suggesting you change this. I just thought you should be aware of it. A "gene," that is to say the DNA in the genome, doesn't DO anything. It is just a code that specifies the order of amino acids in a protein (or alternatively, the order of nucleotides in an RNA molecule. Many of the regulatory molecules are RNA, not protein). Almost all the time, using this shorthand is perfectly reasonable, but it lies at the heart of the newspaper language that talks about genes for homosexuality, or aggression, or infidelity or whatever anyone likes. There are no such things!!! Even the gene for cystic fibrosis doesn't do anything. It codes for a protein that is essential for a specific process (I think it is uptake of mucus in the lung or something like that) and when the protein is made incorrectly the process doesn't work, and symptoms ensue. But it is WAY too awkward to say things like that all the time, so everyone talks about the gene for cystic fibrosis."

continuing with my exposition, 
there is a problem, a very big problem, one that, i confess, i had never thought about until reading wagner's book.  the development of a more fitting phenotypic change, one that will make the organism better able to survive and reproduce, will typically involve a series of changes to the genotype.  a number of molecules may have to be altered or swapped or dropped out of the genotype to get from the old phenotype to the better adapted new one.  and in nature, there is of course no intelligence guiding this process, no purpose, no pre-identified goal [now i shall develop an eye because with an eye i can avoid predators more successfully].  it might, let us say, require six changes to the genotype to produce what turns out to be a better adapted phenotype.  but the changes to the genotype are utterly random.  some result from copying errors when the dna replicates itself.  some result from gamma rays [or something] hitting a strand of dna and knocking out a gene.  some result from one organism actually inserting some new genetic material into another organism's dna [this apparently happens quite a lot to microbes and other tiny critters;  not so much to elephants.]

since all this is unplanned and not guided by any telos, we can compare it, as wagner brilliantly does, to a random walk through a digital library of all the logically possible genotypes.  we, looking at the process in retrospect, may say that the organism was 'seeking' the new genotype that will result in a phenotype better fitted to survive, but of course it was not. 

now comes the kicker.  suppose the genome of an e. coli strain enables it to metabolize sucrose.  if it drops on a piece of rotting pear, rich in fructose, it might do much better if it were to randomly go through the six changes needed to enable it to morph into a strain of e.coli that can metabolize fructose.  but if the first of those changes, happening randomly, makes it unfit anymore to metabolize sucrose, then it will die out before it can go through enough random changes to reach the better adapted ability to metabolize fructose.  and this problem, quite obviously, is not peculiar to e.coli and sucrose, but arises in the case of every single evolutionary change to the genome of any organism.

well, you might say, given millions of critters and billions of year, one of them will hit on the right combination by chance, survive, flourish, and pass it on.  alas, not so simple.  wagner does some elementary but startling calculations that show that the number of genomes is vastly greater than the number of hydrogen atoms in the universe!  There has barely been enough time since the earth was formed for primordial slime to evolve into slightly less primordial slime, let alone into rick santorum.

UNLESS one at a time changes to an organism's genome are not by and large fatal, but permit the organism to continue to function in the old way.  if, as wagner puts it, the organism is robust, if it can survive and function despite a number of genomic changes, then perhaps it can, by a random 'walk,' make its way to the new genome that translates into a phenotype better fitted to survive.

combining some very elegant computer simulations and calculations with the vast amount of laboratory experimental work that has been done on many different species by tens of thousands of research scientists, wagner has been able to ascertain that there is an astonishing degree of robustness in the organisms studied.  what is more [this involves more technical detail than i am capable of summarizing easily], the 'neighborhoods' into which an organism will wander randomly by genomic change, one gene at a time, are sufficiently diverse genomically that the probability is not bad of an organism stumbling, as it were, on a promising new genome.

well, i am sure you can see that like wile e. coyote, i am now way over the edge of the cliff with nothing underneath me, so before i fall down splat on the ground, to be crushed by an ACME safe landing on top of me, i will quit.

if you want a charming, fascinating, important read, try THE ARRIVAL OF THE FITTEST by andreas wagner.




David Auerbach said...

I've just started reading it and it is indeed a marvel of expository writing; the mathematics is as crucial as the biology. What your summary of genetics leaves out about genotypes is that, although many genes do indeed code for amino acids that make up proteins that's not the whole picture. When the encoding for protein picture first emerged there was a puzzle: the genome would have to be very big to encode, sequentially, all the relevant proteins. And, it turned out, it wasn't that big. This was in the early 70s, I think. Since I was programming computers back then, it occurred to think about it as programing problem, which it turned out to be. That is, some genes are dedicated to controlling other genes, while others serve as punctuation marks, so that the same sequences can be used again and again, in different orders to make the proteins. Much more efficient. So the genome is really a computer program rather than a straight encoding of proteins.

Robert Paul Wolff said...

Very nice. Thank you for the addition and clarification.

J.R. said...

"'[A] usage that is essentially universal, among experts as well as science writers'... since all this is unplanned and not guided by any telos"

I am often struck by the fact that no matter how much we know better, when it comes to biology people, even experts, cannot stop talking about the "function" of organs, the "desires" of genes and other such teleological language.

This is quite unlike physics, where no-one is even tempted to talk about what an electron "wants."

I am fumbling towards a vaguely Kantian point that I cannot quite complete about self-consciously fictional but seemingly indispensable notions. There is, no doubt, a huge literature on this that I have not read (and probably will not) but if my comment inspires a riff by my host on regulative ideas and biology I would be pleased.

(Incidentally Blogger Captchas all seem to involve transcribing house numbers from photographs now. I suspect Google has figured out how to extract some surplus value from even idle blog commenting now.)

Robert Paul Wolff said...

JR, the notion is certainly Kantian, as is clear from his category of Ideas of Reason, and also the curious notion of subjectively universal judgments of taste in the Third Critique. I once remarked to my sister that when I am playing spider solitaire, I sometimes think that at the end of a winning game I ought to complete the spades before the hearts because the spades have been very patient. My sister said, '
that is just how biologists think.'

J.R. said...

I have never dipped into the Third Critique. (To my greater shame, I have not even read the Second.)But perhaps I should now.

Robert Paul Wolff said...

you can take a pass on the second critique but you must read the groundwork of the metaphysicsa of morals.

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