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Post-Modern Evolution

Razor's Edge
From time to time TOF has touched upon the peculiarities of the varioustheories of evolution: Lamarck, Blythe, Darwin/Wallace, Mendel, Kimura, Shapiro, et al.   Prior posts include:
And some of the topics that have bubbled up include
  • the persistence of teleology in evolutionary thought (apparently tworked off Fodor, who dissed natural selection precisely because it was inescapably teleological)
  • the importance of the environment, including the organism's own behavior at shaping evolution
  • that genetics and molecular biology may be more important than natural selection
James Shapiro

Some of these thoughts were initially triggered years ago by an essay for the educated lay public by James Shapiro that deconstructed both Michael Behe (the ID-guy) and Richard Dawkins (the science popularizer).  Both, he said, were dealing with obsolete metaphors of genetics.  This resulted in a correspondent immediately denouncing Shapiro as a shill for the Discovery Institute.  He wasn't and isn't,  but it is interesting to note that the first reaction of the Third Way-denialists was to make up something scurrilous about the guy.  Similar thing happened to Eldrege and Gould when they introduced punctuated equilibrium.  Students of the history of heresies will recognize the behavior instantly. 



( 9 comments — Leave a comment )
Jan. 8th, 2013 04:11 pm (UTC)
Here are some problems with your interpretation of Shapiro's talk:

(1) Shapiro initially sets up strawman arguments contradicted by his counterfactuals. As the first commentator points out, all of Shapiro's counterfactuals are widely accepted, and are, in fact, taught in freshman biology courses. None of the strawman arguments are. This might not have been how Shapiro was taught, but Shapiro is no spring chicken. The field has moved forward.

(2) Shapiro creates a false dichotomy between relatively large-scale (as opposed to the point mutation) genomic rearrangements and natural selection, however natural selection works independently of the source of novelty. The real issue at hand is the importance of point mutations versus these larger scale mutations. This is interesting in its own right, but not terribly controversial.

(3) Shapiro observes that stress causes a breakdown of molecular systems protecting the genome from instability (adaptive for a variety of reasons, ranging from protecting bacteria from UV to protecting humans from cancer). This is not terribly eye-popping, since many systems begin breaking down under duress. It would certainly speed evolution, but it hardly infers a process that works "as an arrow toward a target."

(4) Speaking of the teleology imputed by the susceptibility of various regions of the genome to modification (and setting aside the logistical problem of your "intercellular signals within the genome itself") one should keep in mind that a genome is not simply a long string of information. DNA is a chemical with a structure that has many idiosyncratic properties, including epigenetic modifications (nucleosomes and histone packaging, to name a few which particularly influence vulnerability to mutation). Anyone who has designed PCR primers can discuss the headaches sequence alone can cause.

(5) The issue of targeting is also complicated by evolutionary logic. A gene sequence (and by extension an entire genome) can be represented as a point on what Stuart Kauffman calls an "n-dimensional fitness landscape." Mutation (of all sorts) acts as a random walk on this topology. Combining this random walk with selection effectively results in an evolutionary hill-climbing algorithm optimizing for fitness. Given multiple trials with the same fitness criteria, shorter walks along the topology will be overrepresented in surviving genomes and will tend to cluster around the same local fitness maxima. In other words, given the same base population and pressure, you will tend to see similar sequences and resulting traits selected for repeatedly--this does not require a special mechanism.

(6) We only characterize and sequence the survivors. As a statistician, the implications, particularly potential for misreading teleology from the action of selection, should be obvious to you.
Jan. 8th, 2013 04:45 pm (UTC)
Mutation (of all sorts) acts as a random walk on this topology. Combining this random walk with selection effectively results in an evolutionary hill-climbing algorithm optimizing for fitness.

That is a wonderful example of teleology. ("Optimizing" is not required for "towardness," however.) Jerry Fodor's whole argument against natural selection stemmed from its essential teleology.

All species are survivors. Adaptation stories (ad-apt = "toward being apt at something") propose reasons post facto. The giraffe's long neck provides an advantage. How do we know? Because giraffes survive. Meanwhile, their short-necked cousins, cattle, have also survived, so the advantage must not have been all that crucial. In fact, the awkward stance puts the giraffe at a disadvantage vis-a-vis lionesses at watering holes.

"Optimizing" for fitness presumes some a priori notion of "fitness," and that stems in large part from what the critter is trying to do. For higher animals at least, intentions and purposes do come into play.

Headaches abound. Darwin's metaphysic was falsified at the time of writing, as he himself acknowledged in Origin. But he maintained his faith that he was right, and eventually the re-discovery of Mendel's genetics provided a solution to the headache: namely, the manner in which inheritance takes place.

I guess the attacks on Eldrege and Gould over punctuated equilibrium have been forgotten. They were predicated precisely on gradualism as a dogma. (This was dogma because catastrophism was associated with Biblical literalists; the same reason why Hoyle and others resisted the Big Bang theory in physics.) But Shapiro explains quite nicely why E&G's theory ought to be the norm. It also explains why species appear nearly fully formed in the fossil record in the blink of a geological eye and why arguments against evolution based on the low probabilities of accumulated chance mutations don't hold water.
Jan. 8th, 2013 05:57 pm (UTC)
"That is a wonderful example of teleology."

Not really. Understanding evolution by natural selection requires disentangling two separate processes. The first is the blind generation of novelty--the "random walk." This is not toward anything in particular (although, as Shapiro and most contemporary biologists observe, the jumps in sequence-space can be large relative to point mutations). The second process is selection, in which underperforming recombinants are outcompeted by their conspecifics. Selection occurs after the generation of novelty. Neither process operates toward an end--if anything, a species is a residue of evolution rather than its product. A priori notions of fitness are completely irrelevant.

Your story of giraffes and cattle misses an important point. A biologist would never compare the fitness of a giraffe versus that of a cow. To correct your example, one would compare the relative fitness of a longer-necked giraffe versus a shorter-necked giraffe (or a taller versus a shorter cow . . . more specifically, we would be comparing the fitness of particular traits, resulting from particular genes) within its own breeding population and in its own environment. From this comparison, we could generate testable hypotheses regarding the physics of cervical elongation, the advantage of a long neck in obtaining food versus its disadvantage in obtaining water, its effect on predation by lions, and so forth--in terms of successful gene transmission.
Jan. 8th, 2013 06:54 pm (UTC)
My apologies. I was placing myself mentally into the time of the common ancestor of cattle and giraffes. So there are not yet giraffes doing giraffy things. I was thinking of the origin of species, not the perfection of species.
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The statement
"Combining this random walk with selection effectively results in an evolutionary hill-climbing algorithm optimizing for fitness."
led me to mistakenly believe that the described mechanism led to the end of "optimizing for fitness." Perhaps it results only in random chaos and "fitness" is only defined retroactively. That is, once one has a definable giraffe one can see what the giraffe does and then define that as "fitness." But to do this the species must already have originated and the theory is intended to explain the origin of species.

When you say "This is not toward anything in particular," I am puzzled. Why should a generic cause lead to a specific result? Cause and effect should be proportional.
Evolution in its most generic sense is ordered toward the origin of species. (Someone should write a book about that.) This does not mean that a new species is always the result any more than the intention to hit a target always results in a bulls-eye. "Towardness" ≠ "success."
In the more restricted sense, natural selection (rather than evolution in general) is toward greater fitness in a niche (ad aptatus in Latin, "toward that which is more apt/fit"). But "fitness" is supple and may be increased by long necks, short necks, or a get-out-of-jail-free card. The means are not the "ends." The mechanism of "mutation"+"selection" is simply the means by which the end is attained. It does not mean that there is no end. Mutations may (or may not) be random; but evolution is not. The selection half of the mechanism assures this.
It is only in the particular context of a particular species in a particular niche attempting to make a particular living that one may postulate a particular end to evolution. But I would be rather cautious of just-so stories.

Jan. 8th, 2013 08:17 pm (UTC)
"What a giraffe does" does not define the fitness of the giraffe. The transmission of genes from that giraffe into future giraffes (or giraffe-descended creatures) defines fitness, in the biological sense.

What you describe as speciation requires the partition of a breeding population into two or more separate populations across which genes do not flow (in your example, each would consist of proto-cows). This partition can be spatial (a mountain range emerging, a river changing course, the split of a biome by an intruding biome, the migration of a subpopulation across vast distances, etc.), genetic (in plants, this is often the doubling of a genome, resulting in a filial generation that cannot backcross to its parents), or behavioral (there are genetically compatible songbirds for example, that will not mate because their mating songs are different; this is usually a byproduct of a population spread out over some distance). Often these populations will become visibly distinct from one another within a few generations due to a combination of the founder effect and genetic drift (the subpopulation's distribution of alleles rarely being identical to that of the parent population). Without this partitioning, your proto-cows, subjected to giraffe-selective-pressure or cow-selective-pressure, would all ultimately be giraffes or cows, and there would be no taxonomic split.

This is one of the reasons that the "problem" of biologists generating species in the laboratory is an empty question, something on the order of "are viruses alive?"

So, no, evolution "in its most generic sense" is not "ordered" toward the origin of species in-and-of-itself, but species are a byproduct of evolutionary processes.

Also, your lessons in etymology are not useful. We are hampered by a language that routinely humanizes (attributes agency) to nonhuman phenomena with existences independent of human experience, and biologists are well-known for repurposing words, generating neologisms (often Latinisms), and deploying metaphors that fall short of the phenomena under investigation ("natural genetic engineering" is a wonderful case-in-point). This can be a problem for laypeople. Don't assume that what once was "ad adaptis" in Latin still means "toward fitness" (with the teleological connotation) when a biologist uses it today. Language evolves, too, in a different sense.
Jan. 8th, 2013 11:55 pm (UTC)
Don't be too sure that because moderns have been taught to ignore telos that there is none. It is entirely possible to learn to follow a procedure without thinking of or even knowing what that procedure is supposed to accomplish. Can biologists explain everything they need to without reference to the regularities and lawlike tendencies of natural beings? In the old terminology, these were called "final causes" or "telos."

If biologists misuse "adaptation," it is simply because they have been trained to think that way. It is strange to think that one has somehow denied the end result by precisely describing the means by which it is reached.

If there were no natural telos there would be no regularities or lawlike tendencies in nature. That is, if nothing in A pointed toward B "always or for the most part" then A would not be a cause of B, but would sometimes result in C, D, or nothing at all.

The laws of evolution were invented specifically to explain the origin of species. If they are not ordered toward that end, then they explain nothing. They are simply instrumentally useful rules of thumb.
+ + +
"What a giraffe does" does not define the fitness of the giraffe. The transmission of genes from that giraffe into future giraffes (or giraffe-descended creatures) defines fitness, in the biological sense.

But of course as Darwin saw, the drive of an organism to go on living is one of the drivers of natural selection. The transmission of can only provide capabilities by producing this protein or that or unfolding into this organ or that. Suppose the genes code for the size and shape of the beak of a bird. A long thin beak enhances fitness only insofar as the bird is trying to suck nectar from deep flowers (or some such thing). If it is trying to crack nuts, the trait reduces fitness. So the word "fitness" is inherently teleological: one must be fit to something.

Now the rub is this: a nectar-sucking bird born with a mutant nut-cracking beak is as likely as not to turn to nut-cracking as a result of its efforts to survive. This is teleological at the level of the organism.

The intriguing thing is how throwing out the postulates needed for natural science quickly degenerates to such things as denying the usefulness of language or, in Hume's case, denying even efficient causation. In some cases, scientists with bad metaphysics even have denied that their own minds exist.
Jan. 9th, 2013 02:00 am (UTC)
We are not misusing the word 'adaptation.' Its technical definition within the field has been refined to fit its referent. Cannibalizing Latin for this purpose has been a productive endeavor for generations of scientists, and will be for the foreseeable future as our understanding of the physical universe outstrips the capacity of contemporary language to express that understanding efficiently. Your etymological disputation does not affect the referent--that is, the concept biologists are actually discussing.

Darwin's original purpose may have been to explain the origin of species, but what we have now is the evolving (as we learn more) paradigm by which the entirety of biology is understood. You might as well say that the purpose of hydrodynamics is the delivery of rivers into the sea as say that the purpose of evolution is the generation of species. No one denies that life falls out of evolutionary processes (interestingly, if you ask serious biologists what exactly a "species" is, you will get a variety of answers--I'd suggest you try this some time), but to say that this is a goal or purpose of evolution is unnecessarily limiting.

On your mutant-nutcracker-nectar-sucker being "as likely as not to turn to nut-cracking," I'm . . . well . . . intrigued. You are explicitly proposing that if some poor graduate student tempted by a dangled research stipend managed to sneak a proposal past IACUC to surgically remove the slender nectar-sipping beaks from a population of hummingbirds and replace the lost appendages with sturdy nut-cracking beaks, 50% of those birds would take up nut-cracking and ultimately successfully reproduce. That there is a testable prediction. Now you're cooking with science.

This highlights the problem with subordinating the natural sciences to philosophy. The physical sciences are explicitly evidence-based (social sciences have it a little tougher, but some of them get to tag along). When scientific inquiry returns a result unanticipated by theory, we might argue over it until the result has been reproduced, but--validated--it's incorporated into the literature and the theory is revised. This can take a few years, and science is very large; there is a lot of ground to cover. When a certain subset of philosophers less accustomed to evidence encounter an unexpected result, however, they pitch a fit. In one particular case that you bring up, the problem is not so much that the mind doesn't exist as that neuroscientists are busily demonstrating that the mind is not exactly what philosophers of yore had always assumed. This upsets the philosophical applecart, and is why neuroscience is causing such a raging schism among philosophers.
Jan. 9th, 2013 02:59 am (UTC)
Like mathematics, philosophy tends toward logical conclusions. Neither field is based on "evidence."

Your example of artificially replacing the beaks makes no sense, since the natural behavior of the bird is unlikely to be affected. It's not clear that the bird would even "sense" the artificial beak in any meaningful way. A better example would be the cannibalistic Mediterranean wall lizard whose descendants twenty years later on a second island to which they had been transplanted had become vegetarians and had developed a new organ. This was entirely natural. Introduced to a new environment, the lizards turned to a different way of making a living, and this in turn made certain mutations advantageous that had previously not been. (Vegetarianism on the original island had not been an option: it had been essentially devoid of vegetation. The lizards had survived by eating one another.

You are probably correct about the confusion among biologists over definitions of things like "species." Of course, when the very objects of study are ill-defined, the conclusions are likely to be a bit like a house built upon the sand. Darwin himself took a nominalist position, which really upset Mayr.

Neuroscientists cannot demonstrate anything regarding mind. At best, they can talk about the brain using the New Phrenology of fMRI bumps on the head. There is likely to be some correlations. Problem is, when they talk about will and self and the like, they are simply trying to do philosophical arguments while wearing a white lab coat.
Jan. 9th, 2013 01:23 pm (UTC)
Biology employs mathematics and logic, and adds evidence (just like physics and chemistry do). It's awesome. It is also extremely effective if one's goal is to understand the physical universe. If the case were otherwise, then biotech companies would be employing as many philosophers as they do biologists and chemists.

It's not clear that the bird would even "sense" the artificial beak in any meaningful way.

Birds are not that stupid. Anyway, this is why we include controls. A prerequisite of your experiment would be a second group in which the naturally occurring hummingbird beak is replaced with an artificial hummingbird beak. Alternatively, we could use what we know of beak development to adjust levels of BMP4 and associated bone morphogenetic proteins in the embryonic beak prominence in ovo via microinjection to sculpt our nut-cracking beaks. This technique could be successfully argued in your proposal to IACUC, assuming that you were able to support your contention that teleology predicts a 50% rate of opportunistic feeding consistent with the new beak shape.

Your Mediterranean wall lizards had survived by eating one another? I find this unlikely. There are many, many reasons (most of them thermodynamic) that no living organism subsists exclusively by cannibalism. This is an easier catch than notes (1) and (2) in my initial comment. You can do better. Recalling the article, the original diet was one of insects, and the intestinal modification described was less a "new organ" than an overdeveloped circular muscle in a tube composed more-or-less entirely of circular muscle. In many of your other posts, you argue snarkily against exaggerations made by science journalists in magazines written for popular consumption; I am not sure why you are so enamored of this particular one.

I think you are mistaken in your assertion of terminological "confusion" among biologists. Just because species can be a nebulous concept does not mean that it is a useless concept or one which cannot be studied. It's like trying to define in few words a human being: Two arms? Two legs? Walks upright? 99% genetic congruity to the average of what we point at and call "human being"? Participation in the breeding population? Uses language? Capability of breeding with known conspecifics? These alone are each useless criteria if your subject is crippled, confined to a wheelchair or not yet walking, a HeLa infection in the wrong petri dish, a lifelong celibate, a prairie dog or coma patient, or just plain sterile. What I mean when I say you will find multiple definitions of "species"--that biological definitions can be nebulous--is that there is a great deal more to it than the circular dictionary definition a layperson is inclined to leap at. Formal study would clarify this.

Finally, self-styled "neuroskeptics" are going to have to get used to fMRI. It is not going to go away. In your lifetime it will become less expensive, easier to use, and more common. New machines will have increasingly greater resolution, and researchers will have access to better analytical tools, more powerful computational resources, more extensive libraries of scans, and more detailed brain atlases. The comparison to phrenology is trite (I suppose it makes a catchy bumper sticker) and in my experience is usually followed up by gratuitous abuse of the dead salmon (however, when pressed, the garden variety neuroskeptic cannot describe the dead salmon trial, explain the purpose of the dead salmon trial, or highlight what the researchers involved purposely left out of the dead salmon trial in order to generate their intentionally ridiculous result).

Components of the brain will be broken down further by task. My personal baseless speculation is that when the dust settles, we will conclude that "mind" is a verb rather than a noun, but I'm open to evidence otherwise and my worldview will not be shaken if this speculation proves false.
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