Quasispecies: Trapped in Sequence Space

Edward C. Holmes and Andre´s Moya make some interesting comments in "Is the Quasispecies Concept Relevant to RNA Viruses?" JOURNAL OF VIROLOGY, Vol. 76, No. 1, Jan. 2002, p. 460–462:

Unlimited Variation: The Dark Energy of Biology

 

Alfred Russel Wallace, the co-discoverer of natural selection, wrote in 1858 that his theory could be summarized as “indefinite departure from the original type.” “Indefinite departure” is in fact the central claim of the theory of evolution by natural selection. But it still hasn’t been observed. Richard Dawkins, Jerry Coyne and others keep trying to bully us into accepting that it is a “fact.” OK. Maybe it is. So give us the evidence. We have to read their books carefully to realize how meager it is. They still haven’t shown us that extrapolation.

Back in 2013 Tom Bethell wrote an interesting piece about the "central claim" of modern evolutionary theory.  As with many interesting articles of this nature, my attention was drawn to it by a caustic review by a renowned ID-hater, in this case the inimitable Jeffrey Shallit. 

Shallit pedantically quibbles about Bethell's criticism of Charles Darwin.  Darwin stated that there was no reason to suppose any limit to variations of forms, e.g. no reason a fish couldn't become an elephant through a long enough series of minuscule changes, which casts natural selection as Dr. Moreau's scalpel working at a geological pace. This has enormous relevance to the extrapolative nature of evolutionary theory, for it is the justification for what Wallace called (as Bethell points out) "indefinite departure from the original type." By "indefinite" Wallace meant that for practical purposes it can be considered infinite, the limits being so indefinitely far out as to not rule out any connection between the varied forms we see and the simplest cell.

It is this sense of extrapolation that is central to evolutionary theory, more so than either common descent or natural selection. 

In a particularly Dawkins-esque stroke, Shallit pounds the pulpit:

What we do see is evolution taking place today, and we have the fossil record that shows the changes in the past. You have to be particularly dense or dishonest to deny this.

In other words, we already know that any limits to variation don't matter to macroevolutionary theory, because macroevolution must have occurred.  We have these here fossils, and we know Mr. Darwin's speculations about them must be true because we observe limited variation now.  Accept the extrapolation or be denounced as a "denier"! Shallit and his audience stand ready to punish the deniers by pointing and laughing while simultaneous shaking their fists in furious rage. 

Shallit invokes speciation.  I'm not certain if everyone would agree on his instances of speciation (none of which he offers--it is left as an exercise to the reader), but perhaps he would be surprised to know that even most "Young Earth" creationists believe in some limited form of speciation.  In spite of considering himself an expert on pseudo-science, he doesn't even understand the nature of his favorite "pseudoscientific" bugbear, Young Earth Creationism.  He might also be unaware that even though undirected speciation may be necessary for macroevolution, it is not sufficient to explain macroevolution.  In fact, Cornelius Hunter, who is not a Young Earth creationist, does not deny ultra-fast adaptation or an old age of fossils.  Shallit seems to consider him a run-of-the-mill creationist.  It seems that Shallit does not recognize any significant differences among those he considers "creationists" (which for him includes ID advocates).    

All of this is probably lost on evolutionary materialists who depend on a quasi-Newtonian metaphor in which evolution is moving with a sort of inertia.  This is why Jerry Coyne can liken macroevolution to a train in motion (though it is also an artificially powered and directed machine) and Shallit can compare it to cosmological materials flying apart.  (Although, the hypothetical drive powering the quasi-infinite variation of evolution is, in epistemological status, somewhat reminiscent of poorly understood "dark energy.")  

As natural as a train in motion...  Give this choo-choo
enough time and it just might reach the Galapagos Islands. 

The Engineer and the Chalk

In Charles M. Vest's speech at MIT in 1999 attributes the parable of The Engineer and the Chalk (or The Handyman's Invoice) to electrical engineering expert Charles P. Steinmetz:

LEADERSHIP IN A TECHNOLOGICAL AGE

I want to tell you a story about an incident in the career of Charles Proteus Steinmetz, the great electrical engineer.
In the early years of this century, Steinmetz was brought to General Electric's facilities in Schenectady, New York. GE had encountered a performance problem with one of their huge electrical generators and had been absolutely unable to correct it. Steinmetz, a genius in his understanding of electromagnetic phenomena, was brought in as a consultant -- not a very common occurrence in those days, as it would be now.
Steinmetz also found the problem difficult to diagnose, but for some days he closeted himself with the generator, its engineering drawings, paper and pencil. At the end of this period, he emerged, confident that he knew how to correct the problem.
After he departed, GE's engineers found a large "X" marked with chalk on the side of the generator casing. There also was a note instructing them to cut the casing open at that location and remove so many turns of wire from the stator. The generator would then function properly.
And indeed it did.
Steinmetz was asked what his fee would be. Having no idea in the world what was appropriate, he replied with the absolutely unheard of answer that his fee was $1000.
Stunned, the GE bureaucracy then required him to submit a formally itemized invoice.
They soon received it. It included two items:
1. Marking chalk "X" on side of generator: $1.
2. Knowing where to mark chalk "X": $999.
Thus Steinmetz left his mark in more ways than one in early 20th century technology and business. You will do the same in the early 21st century.
Because you too will know where to put the "X."
But Steinmetz lived in the age of iron machines. Your careers will play out in the age of knowledge and information.
Fifteen years ago, shortly before his untimely death, the author Italo Calivino wrote Six Memos for the Next Millennium. In his memo entitled "Lightness," he put it simply:
"I look to science to nourish my visions in which all heaviness disappears. Today, every branch of science seems intent on demonstrating that the world is supported by the most minute entities...
The iron machines still exist, but they obey the orders of weightless bits."
The iron machines obey the bits.

PZ Myers: The Biology Does Work

Evolution 2.0

Perry Marshall is raising some eyebrows and saying some interesting things about his Evolution 2.0.   I mostly like what he has to say, although I don't think he is giving proper credit to what Intelligent Design is or where some of his arguments come from.  He presents 'Evolution 2.0' as a kind of bridge between evolutionary thinking and design intuitions (what started as 'Mere Creation') and this is essentially what Intelligent Design already is.  Marshall does seem to bring a lot of the collective arguments of Bill Dembski, Steve Meyer, and Mike Behe framed succinctly within the past 30 years of genetic discoveries.

However, the confusion is in no small part because of the willful conflation of ID with creationism by ID's critics.  'ID Creationism' is a worthless term that is nothing more than a dishonest advertising campaign co-developed by Barbara Forrest and the NCSE.  Its effect has been to shut down discussion before it happens, and I believe that was precisely the intention.  This ploy was opportunistic ideological propaganda "in a cheap tuxedo."  If this lame political stunt now ends up causing people to pick up a book like Marshall's, so be it.  In the end inquiring minds will probably find that Evolution 2.0 is simply the more evolution-friendly version of ID.  

An interesting exchange between Perry Marshall and PZ Myers appears online and I was struck by various attempts by Myers to dismiss an engineering perspective of biology.  This one stood out in particular:

Over and over again what you do is you tell me ‘well from my perspective as an electrical engineer this doesn’t work, it can’t work’ and I’m telling you yeah but biology does work, so maybe your perspective is wrong.

What does Myers mean by "biology does work"?  In context, he seems to be saying that even though perspectives from engineering and computer science cast doubt on the very idea of a coding system arising through natural, random processes, it does indeed work so phooey on perspectives outside the fiefdom of biology.  Does he mean that the science of biology gives us useful technology (e.g. penicillin) and therefore we shouldn't question that life had a spontaneous origin?  Or is he dogmatically asserting that in modern biology it is a matter of unquestioned orthodoxy that natural processes are sufficient to produce whatever exists?  Fossils therefore abiogenesis?

Marshall challenges (with a 3 million dollar prize) the realm of biology to generate a coding system through an undirected chaotic process, and Myers states that this challenge is a sham because he should be able to present the already naturally occurring genetic code as evidence that this can happen and thus get the prize.  He doesn't need to question his assumption that abiogenesis happened because "biology does work"!  It is obvious that he, like so many others in evolutionary biology, are completely unaware of just how much intellectual laziness is represented here. 

He then goes on to ironically accuse Marshall of assuming what he intends to prove.  While Marshall is simply using the same abductive argument championed by Stephen Meyer, PZ Myers is unaware that museums full of fossils do not demonstrate that our DNA has a perfectly coherent natural explanation.  He fervently believes no one should actually have to do the work of demonstrating the random genesis of a code to get that 3 million dollar prize.  Darwin's "one long argument" showed the world that science had no need for God, and since there is no God we know that amazing codes like DNA have a perfectly natural explanation, even if we don't know what that could be (RNA, crystals, abiogenetic molecules du jour). 

I wish that Myers had promoted Tom Schneider's work as proof of a randomly generated code.  Then there might be some interesting back-and-forth about what a coding system is vs. a lock-and-key system.  While I suspect that there are flaws in the applicability of Schneider's model to actual site recognition, the bigger flaw is in its applicability to the sorts of biological "innovation" that Wagner and others have tried to characterize. 

Myers also criticized Marshall for what he considers an 'appeal to authority'.  Now you have to keep in mind that to Myers a 'creationist' isn't necessarily someone who believes that the world was created in 6 days, a 'creationist' is anyone that thinks that there are evidential reasons for thinking that life is the result of a conscious, creative act.  This is never more evident than in Myers' insinuation that Perry Marshall is a creationist.  As a rabid anticreationist, Myers will not only belittle 'creationists' for citing other 'creationists', but will get much more upset if they cite a figure that has some weight and is not already discredited as being skeptical of neo-Darwinism.  When 'creationists' do this, it must be characterized as an 'appeal to authority'. 

But if you read carefully, you'll see that Myers doesn't think it's wrong to appeal to authority; he faults Marshall for not appealing to the correct authorities. 

Myers and likeminded crusaders against anti-science tend to dismiss the engineering/software analogy.  Dawkins and others embrace the analogy because they don't see the problem.  Regardless of the definitions, orthodox evolutionary biology has the unique problem of trying to explain how engineering happens without an engineer, how a coding system develops without a coder, how purposeful machines arise in entropy-ridden purposelessness.  The Myers approach is to claim that the analogies from digital engineering don't apply to the digital wetware in our bodies.  It is too different they claim because it is (a) complicated, (b) replicated, (c) fault-tolerant, and (d) so darn wet.  All that math and computer science that is applicable to artificial digital systems is therefore not applicable to biological wetware (except when it seems to confirm an evolutionary point of view, of course).  Biological matter is too different in its complicated, self-reproducing electrochemical wetness to be beholden to information principles.
Engineering analogies must not be applicable because fossils and stuff show that the "biology does work", and after all, there are random errors that follow known distributions.  Therefore we can safely conclude that all the non-randomness is due to the accidents of genome arrangement.  After all, hundreds of thousands of biologists show up for work each day, and do science, and get their findings published.  There's no need to demonstrate how such elaborate order arises from disorder, because evolutionary biologists already know that it did.  All this "brute force molecular biology" really has no place weighing in on the matter.  Myers can join Jerry Coyne here in lamenting how molecular biology is not bolstering evolutionary theory--the weed of secular creationism seems to be sprouting up in molecular biology.  Seems like we will have to extend the Salem Hypothesis to include molecular biologists. 

Pay no attention to any ramifications of Craig Venter's work.  Why?  'Cause biology does work already!  It works!  We're not going to give up a hundred years' worth of conjectures and plausibility stories for some preposterous "brute force molecular biology" experiments!  The biology has worked just fine without them.

PSA from Dr. Pangloss

For example epigenetics ...

Evolution -- the theory so malleable that every failure is really just a success in disguise. 

James Shapiro & Why Evolutionary Theory Is Getting Unrecognizable

Recently I got to see a debate between Michael Ruse and Cornelius Hunter.  For the most part, Hunter argued that the facts of biology, mostly citing recent research, discredit an evolutionary explanation based on Darwin's original theory, esp. any theory dependent on common descent or positive selection.  For the most part, Ruse discussed what was historically so convincing to Charles Darwin.  This latter scheme, though it did not in any way rebut Hunter's points, seems to fit the mainstream approach. 

A similar pattern ensued in a debate a few years about ID with Michael Shermer and Donald Prothero on one side, and Stephen Meyer and Rick Sternberg on the other.  If memory serves, Shermer and Prothero mostly summarized the century-old argument for common descent for the audience, while Meyer and Sternberg attacked natural selection as a sufficient explanation.  (Reminder: ID in no way require common descent to be false, though it is quite at home in the anomalies in phylogenetics.)

With more recent mosaics (e.g. Tiktaalik and Pakicetus and other "missing links") in tetrapod evolution, the "overwhelming evidence" for "evolution as fact" seem to be an abductive inference based on fossil geology, comparative anatomy, and embryological similarity.  And now, as then in Darwin's day, a historical evolutionary process (whatever the mechanism) is compared to what a typically atheist/deist biologist presumes an anthropomorphized cosmic designer would or wouldn't have done.  This is the "one long argument" of Mr. Darwin and these theological arguments haunt science textbooks to this day. 

In an era of evolutionary thought where Darwin's Tree of Life is being discussed as an outdated concept and natural selection as maybe not being a central explanatory mechanism for macro evolution, it begs the question what biologists (or anybody) mean when they assert that "Evolution is a fact." "Evolution" may be the most overloaded term in all of science.  It refers to a historical "fact" and a "theory" of causation and a trivial phenomenon (microevolution) and a research program and a narrative (and a religion according to Michael Ruse).

James Shapiro, a fairly mainstream microbiologist and evolutionary biologist has written a book Evolution: A View from the 21st Century that challenges a lot of the assumptions of the mainstream Evolutionary Synthesis.  He differentiates between several key aspects of evolution.

General discussions of evolution, especially in the context of the “Intelligent Design” controversy, suffer from an unfortunate conflation in the minds of the lay public (and also of scientists) of three distinct questions:
• [1] The origin of life
• [2] The evidentiary basis for an evolutionary process
• [3] The nature of evolutionary change
[emphasis mine]

When you think about, the 3rd item is all over the place right now.  There is no consensus on whether natural selection is a sufficient explanation for what Darwin used it to explain--the origin of all species--and that is an understatement.  The 1st item is in a similar state of disarray in terms of a coherent theory, but this is less surprising and more widely understood--and the chief reason why many theorists separate it from the Evolutionary Synthesis.  Now, the 2nd item is something that many, though not all, ID theorists either agree with or at least grant for argument's sake. Many ID theorists do dispute whether the evidentiary basis for common descent is as strong and coherent as neo-Darwinists and evolutionary materialists aver, but ID is generally not in conflict with an "evolutionary process" of some kind.

The one issue that has effectively been settled in a convincing way is the evidence for a process of evolutionary change over the past three billion years. The reason the answer to this question is so solid is that every new technological development in biological investigation—from the earliest days of paleontology through light microscopy and cytogenetics up to our current molecular sequence methodologies—has told the same story: living organisms, past and present, are related to each other, share evolutionary inventions, and have changed dramatically over the history of the Earth.* [emphasis added] 

How much an ID theorist agrees with a common "story" depends on what he means by "related to", "share", and "history."  Even a Young Earth Creationist might agree with these articles as stated, though Shapiro probably means "history" as the mainstream interpretation of the "fossil record" rather than simply as time.  But the majority of ID theorists, including Steve Meyer, Michael Behe, William Dembski, and even Jonathan Wells, seem to adopt or use the mainstream view of fossil dating. 

The central point of departure for Intelligent Design is whether there is a significant component of intelligence that is required for a complete explanation for the biological world.  But there is a real and general way in which both ID theorists and creationists see organisms as related to each other and sharing innovations in a non-Darwinian sense, an innovative relationship between living things that has unfolded in a dramatically changing diversity over Earth's history (whether a long history or short).  

And the question remains whether even the evidence for an evolutionary process, intelligent or not, is quite so strong without a prior conviction that all natural phenomenon have a strictly natural cause (where "natural" essentially means "material" or "physical").  As evolutionist par excellence Richard Lewontin said:

Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science [defending science against "attackers"?] in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to [seek only material causes  in science]. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.

And that, Charlie Brown, is the meaning of Slippery Slope. Somehow, this "Divine Foot in the door" didn't stop scientists like Isaac Newton, nor the many "creationist" scientists that preceded both Darwin and widespread Deism, from real, ground-breaking science. Somehow, in the absence of an "absolute" materialism, both common sense and the belief in a universe made comprehensible by a rational Designer made them expect an orderly world where miracle was exceptional but not excluded.

Non-Haeckelian Development

Some fun weirdness in the tangled “tree of life.”  Donald Williamson, a marine biologist who wondered why very different larval forms pop up willy-nilly in very different species, has a bold hypothesis.  Although his explanation is very heterodox (though it received serious support from Lynn Margulis) and is yet to be supported by any molecular data, what is much more fascinating is the extent of the problem his theory aims to solve, including the following oddities:

1. Very similar larval forms appear in phyla with dissimilar adult body plans.
2. Wholly different larval forms appear in the same phylum
3. Some echinoderms are develop as protostomes, some as deuterostomes. 
4. Some mollusks, annelids, sipunculids, and even some deuterostomes have rotifer-like trochophore larvae.

These larval variations not only challenge the Haeckelian expectations of neo-Darwinism, but they potentially put the whole protostome/ deuterostome division in question.  Here’s Williamson’s attempt to fit these larval epicycles into a Darwinistic history:

   … Brittle stars and sea urchins are very different as adults but share the unique pluteus form of larva. Why would similar larvae produce dissimilar adults [in different phyla]? Larval transfer proposes that the basic pluteus larva evolved only once, in a sea urchin, and was retained in this sea urchin’s descendants.  An ancestor of most existing brittle stars then acquired a pluteus larva by hybridizing with a sea urchin. 

    One member of this group, Kirk’s brittle star, develops directly from the fertilized egg, with no trace of a bilateral larva, and its blastopore becomes a mouth. It is, therefore, a protostome.  All echinoderm larvae are in a different developmental class, the deuterostomes, in which the mouth is a new opening; several echinoderms that have lost their larvae develop as deuterostomes. If Kirk’s brittle star lost its larva, it must have also adopted a fundamentally different pattern of cell division in the embryo. We believe, however, that Kirk’s brittle star has no larva because none of its ancestors hybridized with a sea urchin. The heart urchin Abatus cordatus and the three known species of sea daisies also have no larvae and develop as protostomes.  We suggest that this is the ancestral method of echinoderm development, and the pattern called deuterostomy came with the transferred larvae. 

  Two sea urchins, Lytechinus variegatus and Lytechinus verruculatus, are of the same genus, but the similar adults each develop from very different pluteus larvae. Such cases are difficult to explain if larvae and their corresponding adults evolved from one common ancestor.

 

It’s pretty curious stuff.