Casey Luskin Takes on Homology

This is an excessively recursive post: my review of Casey Luskin's review (on the Evolution News & Views website) of Henry Gee's, Rory Howlett's and Philip Campbell's review (in Nature) of a scientific paper by Toshiyuki Matsuoka et al.  This is not "blogging on peer-reviewed research;" this is blogging on tendentious carping about a popularization of peer-reviewed research.

The paper describes Matsuoka's research into which parts of the skeleton originate from the neural crest cells formed in the outermost of the three layers (the ectoderm) of the developing embryo, and which parts originate from the mesoderm, the middle layer.  This, in turn, the Nature editors state, gives us insights into the evolution of the various parts of the skeletons of modern vertebrates.

Luskin makes two points.  The first is that Matsuoka's research doesn't depend on the assumption of common descent, and could be done simply on the basis of comparative anatomy.  I'm pretty sure this is true.  The second, which takes up most of his article, is that Matsuoka's research throws a monkey wrench into the whole idea that homology is a result of common ancestry (actually, it's not quite clear whether Luskin means to attack the whole idea of homology -- which was identified by creationist biologists before evolution was invoked to explain it -- or just "Darwinian" explanations of it).

Luskin notes that Matsuoka notes a bizarre feature of embryonic development across species: the development of muscles from particular groups of cells is far more consistent ("more conserved") than are the actual bony sites to which  they attach.  Matsuoka, rather than reject the idea that the detailed similarity in form, location, and embryology of the neck muscles are homologous, proposes a startling idea:

The rather counterintuitive "scaffold model" perceives muscle connectivities as the basic units (because they precisely correspond to cell populations) but considers the bones that everyone can see as mere epiphenomena and subjects of change.

Luskin mocks this as a "bizarre" conclusion, forced by Matsuoka's slavish adherence to the dogma of common ancestry.   But it's not entirely clear what is so "bizarre" about it.  Vertebrates, after all, don't literally inherit their bones, or muscles, or nerves, or other body parts; they inherit genes, which interact with cellular mechanisms to grow all these parts.  Genes are not literally blueprints; there is no gene for a scalpula located right next to the genes for the clavicle or cervical vertebrae.    Matsuoka is suggesting that rather than trigger bone development directly, genes trigger muscle development in such a way as to promote bone development, with some interspecific variation in exactly how they accomplish this.  Interestingly, David Klinghoffer has a post on EN&V today that makes just this point: the genome isn't literally a "code" or blueprint (how exactly this makes the case for intelligent design is not quite clear).  Luskin can't quite get his head around the point that just because bones are more likely to be preserved than muscles or genes, they don't have to be directly inherited rather than effects of things that are directly inherited (of course, as Upton Sinclair noted of some other people, his salary depends on not understanding certain things).

Luskin goes on to note some further oddities of the homologies in vertebrate skeletons, such as the apparent loss, on multiple occasions, of the cleithrum, the major shoulder bone of primitive tetrapods, in different tetrapod groups (frogs still retain it, though salamanders don't, and many ancient amniotes did, though no modern amniotes do):

You've got to love the last sentence, which is worth repeating: "We speculate that a common, as yet unknown, genomic cis-regulatory architecture governing neck ossifications in tetrapod ancestors might have predisposed different descending tetrapod lineages to similar parallel trends." This is almost starting to sound like teleological evolution--but of course that's not allowed in Darwinian thinking, so it's just by the luck of the draw that all of these taxa independently arrived at the same bone structure. 

Now, Stephen J. Gould used to argue against the instinctive resort to "adaptionist" explanations; not every feature of biology or evolution, he argued, was an adaption.  One alternative that he mentioned more than once was developmental constraints: species descended from a common ancestor inherited developmental pathways that made some possible evolutionary changes difficult or impossible, while making others very easy and likely to arise as a side effect of other changes, whether they were directly beneficial or not.   This is not "teleological" thinking, as though evolution meant to lose this bone in advanced tetrapods; this is a suggestion, very common in evolutionary thinking for a century or more, that some changes are easier and more likely than others, and thus are likely to occur independently in multiple lineages.

Luskin includes in the article a quote from the creationist textbook Explore Evolution:

In sharks, for example, the gut develops from cells in the roof of the embryonic cavity. In lampreys, the gut develops from cells on the floor of the cavity. And in frogs, the gut develops from cells from both the roof and the floor of the embryonic cavity. This discovery -- that homologous structures can be produced by different developmental pathways -- contradicts what we would expect to find if all vertebrates share a common ancestor. (Explore Evolution, p. 44)

The book is right: we would, as a first rough estimate, expect that homologous structures develop through homologous pathways.  On deeper reflection, though, it's not quite clear whether we ought to invariably expect that.  On the one hand, if genes and tissues can evolve, presumably developmental pathways can evolve also, and still remain homologous.  In principle, one might find that novel genes had taken over some part of a developmental pathway from the ancestral form, though given that the same genes are found in all cells of the embryo, this is hardly necessary; the phenomena cited by Explore Evolution could result  from changes in where various gene cascades were triggered, without much change at all in the genes that actually build the gut.

There's a point that keeps going through my mind as I read Luskin's articles on the Nature series on "Evolutionary Gems," and that is, how does this support design?  If he's denying that homologies exist, he's basically telling us to believe him and not our own (and several centuries' worth of comparative anatomists') lying eyes; if he's arguing that homologies represent "common design," then how is this helped by arguing that in fact the designs are not common at all?  The variations in detail of how vertebrate bodies are built with conservation of basic elements (across disparate body shapes and lifestyles) fits at least as well with our expectations of evolution as with intelligent design.  But then, we're not really entitled to have expectations of intelligent design; it's sole testable hypothesis is that somewhere, somehow, evolutionists have got some stuff wrong.  Unfortunately, that testable hypothesis doesn't really differentiate intelligent design from evolutionary theory, whose proponents have generally followed Charles Darwin in realizing that they don't understand everything.

Evolution News & Views on the Human Genome Project

The Discovery Institute's Evolution News & Views blog has posted an article (seriously, the author is given as "Evolution News & Views," so it's the intelligently designed product of another intelligently designed product, designed, in the opinion of its own designers, by intelligently designed products, so we're dealing with massively recurrent design here) on "The human genome project ten years later."  Research on the human genome has, as the blog sees it, has undermined "Darwinism" in a couple of different ways.

First, it notes, research has found that much so-called "junk DNA" is actually functional.  This is presumably relevant because, to ID proponents (or at least to their blogs), "junk" DNA is relevant as evidence for common ancestry and natural selection only because it's supposed to be useless.  But of course "junk" DNA, like other vestigial structures, is evidence because it is homologous to structures with entirely different functions from whatever function it might have.  It is an example of "parahomology," adaption of one structure to serve an entirely different use.  In principle, a pseudogene or endogenous retrovirus is evidence of the same kind as the homologies among a whale's flipper, a bat's wing, and a human arm and hand: even when they are all fully functional, their detailed similarities aren't required by their divergent functions, and are far easier to explain in terms of descent with modification from a common ancestor than in terms of separate origins (whether "common design" or some sort of separate evolution to fit their different niches).  Vestigial organs have from Darwin on been defined as lacking the most obvious or important function of their homologs, not as lacking all function, and there's no obvious reason this shouldn't apply to vestigial genetic elements.

On the other hand, large swaths of the genome in fact not only haven't been discovered to serve any function, but there is some evidence that they really don't have any function to discover; at least, they can be removed without any discernible effect.

Anyway, the blog's second, and main, argument, is that evolution (and the blog seems to mean common descent, not just naturalistic mechanisms to produce this effect, since it speaks of the inference of "evolutionary relatedness") is undermined because "scientists are coming to a sobering conclusion that perhaps their models and assumptions on the nature of disease may be mistaken."  Rather than most non-infectious diseases being, like sickle-cell anemia or cystic fibrosis, the results of single mutations to single genes, most, like breast cancer, are the result of subtle and hard-to-trace interactions among dozens or hundreds of genes. Given that the genome isn't literally a "blueprint," with one set of nucleotides corresponding to one particular trait, but that polygeny (multiple genes influencing a single trait) and pleiotropy (multiple traits affected by a single gene) have been necessary terms in genetics for decades, arguably this was more of a disappointment than an actual surprise to anyone: it makes finding cures for things more difficult but is pretty consistent with what has been known about genes since before the Human Genome Project was started.

The blog's opinion on this research concludes:

 Given the presupposition that a complex organism is engineered, then the parts themselves must be taken within the context of the whole. ... A reductionist, neo-Darwinian view of the human genome does not seem to have explanatory power regarding disease. This is a clear case where some scientists' dedication to the presupposition that similar DNA sequences means whole organism similarity, the same presupposition that many have used to argue for evolutionary relatedness among species and against man being anything more than another animal, has, 138 million dollars later, lead to more dead ends than cures.

 I find myself bemused.  From intelligently designed kitchenware that differs from other pots and pans because of single, "reductionist" features such as stickproof coating, to cars and computers chock-full of features and components that can be discussed and evaluated in isolation, "reductionism" seems an ubiquitous feature of human design.  It "does not seem" to me that one can simultaneously claim, as various human writers on Evolution News & Views have done, that "design" in nature is recognized by analogy to human design, and that "design" in nature can be recognized because it resists analysis in terms of modules, reductionism, and other methods used by human designers.

There is also an element of desperation in seizing on the discovery that trying to examine things as a collection of disparate components that produce no more than the sum of their parts doesn't always work.  I suspect, again, that actual scientists figured this out a long, long time ago ("make everything as simple as possible, but not simpler," as Einstein uncontroversially noted), but one has to look for simple patterns before one can make out the complicated ones.

And one must really wonder if the blog, or its human designers, assume that other animals really can be explained more reductively and simply than Homo sapiens.

Mutation Rates and the Age of the Human Race

Brian Thomas, a science writer for the ICR, has an article up titled "New Genome Projects Data Indicate a Young Human Race."  He refers to three recent studies (done for the "1000 Genomes Project") summarized in the journal Science which determined that each human born carries an average of sixty mutations, down from an earlier estimate of one hundred.  Thomas raises two separate questions regarding this finding.  On the one hand, does the new lower rate provide for enough changes to derive humans and other primates from a common ancestor over the last few dozen million years?  On the other, will not the accumulation of harmful mutations over time wipe out the human species, and does this not imply a maximum possible age for the human race?

Thomas used a program called Mendel's Accountant to model a human population over time, assuming sixty mutations per individual.  He notes the result:

Assuming a population size of 2,000 individuals, assuming that each mother has six children, and using the rate of 60 mutations per generation in the algorithms, the simulation shows the extinction of the human race after only 350 generations. This also assumes that natural selection would have been effective at removing the least fit from the population every generation.

This account does not mention the percentage of mutations which are beneficial, harmful, or neutral or near-neutral, which the program allows one to select, and whose values, one assumes, would have major import on the outcome of the experiment.  I also cannot help but note that Thomas, as a writer for the ICR, is supposed to assume that human populations started out much smaller than 2000 individuals, and have apparently ended up much larger.  But that aside, Thomas notes that evolutionists assume that the human species is far, far more than 350 generations old (it is unlikely that H. sapiens is less than 10,000 generations old, and of course we have pre-sapiens ancestors going back long, long before that), whereas creationists assume that the human species is only about 300 generations old (having gone through a really intense bottleneck around 4500 years ago, when our effective population was reduced to Ham, Shem, Japheth, and their three unnamed wives; I wonder if Thomas tried to model that particular feature).

Here is one thing that struck me: the human genome is about the same size as most other mammalian genomes, and there's no obvious reason to suppose that our mutation rate differs much.  If we can't survive for a thousand generations, much less ten thousand or ten million, then it's hard to see how rats could.  Rats rarely live more than a year in the wild, reach sexual maturity in under two months, and so can have several generations a year.  I think that what Brian Thomas' use of "the latest and most accurate research into human genetics" has proved that all rodent species (not to mention all domestic mammals and indeed most supposedly extant mammals) are extinct, which is a somewhat problematic outcome.   I cannot help but feel that further research into population genetics, or perhaps just into the assumptions programmed into Mendel's Accountant, are warranted.

Cornelius Hunter Attacks Darwinist Metaphysics

Cornelius Hunter has, these last few days, been much better about updating his blog than I have been.  To be sure, two of his recent articles have been little more than excuses to repeat his favorite complaint about "Darwinism" -- that it is supported primarily be metaphysical, even religious, arguments against intelligent design, and his favorite confusion, between "being an explanation" and "being logically possible".  For example, in one essay, he deals with the claim that "If species had been independently created, no explanation would have been possible of this [consistent nested hierarchy]" as a claim that an Intelligent Designer would definitely not have created species whose traits were arranged in a consistent nested hierarchy.

But that is not the claim being made.  The point is that descent with modification, at least as it typically works in eukaryotes, predicts that species will be arranged in a nested hierarchy; it explains why, e.g. we find species grouped in genera and families and orders, why animals that have one bone in the lower jaw and three in the inner ear also happen to have mammary glands and a left but not a right aortic arch.  Yes, a Creator could have made separate species that way, but creationism doesn't predict such a pattern (indeed, ID proponents seem quite careful to make sure that intelligent design doesn't predict any pattern, except perhaps that we will never be able to conclusively prove that any feature is functionless) or explain why it should exist.  Certainly designers in our own experience do not design in that way.  This is less a metaphysical argument than an epistemological one, a preference for inferring known causes from their known results than in inferring unknown causes on the grounds that we can't say that the results couldn't be produced by them.  Hunter complains that evolutionists, in citing evidence for evolution, "consistently turned to organic parts and geographic distributions that make the least sense."  But that is not quite true; the parts that literally make the least sense are the parts that ID proponents crow that "Darwinists" cannot explain, such as the many problems involved in abiogenesis, that provide gaps ID proponents can stuff a Designer into.  The parts cited by Darwin and later evolutionists are the parts that make perfect sense, given common descent from ancestors that had obvious reasons for such odd traits.

Hunter makes the point that Linnaeus certainly did not think that species falling into a nested hierarchy disproved special creation, and that Linnaeus was one of the greatest scientists of his day.  On the other hand, attempts to impose Linnaean classifications to things that clearly aren't the results of branching descent with modification (e.g. orders and genera and species of clouds,  or minerals) simply didn't work as well: one can arrange any suite of objects into a nested hierarchy, but getting a single, consistent hierarchy (rather than different ones depending on which traits one selected for comparison) proved impossible for such objects.  There was something special about life, and it was something shared with suites of things (e.g. languages within the Indo-European family, breeds of domestic animals, etc.) that were derived through branching descent with modification.

Darwin's argument, and Phillip Kitcher's argument, and many other arguments for common descent, is not that a good Creator would not have made bad designs, or that an Intelligent Designer would not have made a world laced with "natural evil," it is that common descent with opportunistic modification can explain these features rather than simply accept them as the ineffable whims of a Designer/Creator.  But to Cornelius Gordon, a preference for explaining data is a religious bias when it is even acknowledged; mostly, he treats all such arguments simply as strawman attacks on Intelligent Design.  Intelligent Design is simply the position that "somewhere, sometime, Somebody did something;" insisting that the Somebody was competent, or benevolent, or supernatural, is just imposing extraneous fillips on the basic ID model (though somehow, when ID proponents are not complaining about such misrepresentations of their model, they manage to imply that ID will manage to save human dignity, fight racism, and give purpose to our lives and hope in the face of death: ID has facultative details).

Now, Hunter's latest argument is a bit different.  It deals with a recent paper by Carl Woese et al. on the origin of the genetic code.  The paper is an attempt to explain the origin of a (more or less universal -- with slight variations) genetic code in light of Woese's ideas that the original life didn't have species, that it was a community of replicating entities that freely exchanged genetic material among themselves in a truly promiscuous fashion (even more so  than modern bacteria), and were especially subject to group rather than individual selection.   Hunter's complaint, basically, is that Woese doesn't explain in detail how the ability to exchange genes arose (that is, he deals with the origins of the modern genetic code rather than with earlier stages of abiogenesis) or exactly how it works (this is in stark contrast, of course, to the detailed explanations that ID theorists provide for the origin and implementation of intelligent design).   That gene exchange, at least in bacteria, is well-demonstrated and that there are at least well-evidenced theories of how it can happen even between eukaryotes (such as plants and animals) goes unmentioned.

I'm rather hesitant to comment on Woese's paper; I'm very far from an expert on biochemistry, genetics, or abiogenesis, and do not particularly trust my competence to exegete it.  On the other hand, I can't quite help but notice that Hunter's take-away message from Woese's article seems to be that the genetic code is just a "frozen accident," something Woese is rather explicitly arguing against (and which is dismissed in Nick Lane's widely acclaimed Life Ascending, which offers a quick sketch of an attempt to explain the genetic code in terms of the chemical properties of different nucleotides, a subject alluded to in Woese's paper as well).  I'm pretty sure that Woese doesn't solve the problem of abiogenesis.  I doubt he even definitively solves the problem of the origin of a (more or less) singular, optimized genetic code.  But he does make use of known processes to move a few steps closer to such an explanation.

Hunter gets a number of interesting comments in his blog.  One of his commentators, replying to a creationist's objection (implicit in Hunter's original critique) that Woese was either oblivious or hypocritical to use an intelligently designed computer program (that simulated gene exchange in his hypothetical early community of living protocells) to argue against the intelligent design of the genetic code, noted that programs used to model and predict the weather are also intelligently designed, but this doesn't argue that thunderstorms are designed (much less designed in the same way).  This is, I think, a splendid retort to a common creationist critique of genetic algorithms and biological simulations of many types.

AiG News to Note, November 6, 2010

Answers in Genesis' weekly roundup of science news seems a bit drab this week: creation is proved by the fact that fossils have not been found on Mars, that studies in fruit fly genetics study genetics rather than whatever AiG thinks of as information theory, that behaviorally modern humans were behaviorally modern, that a boa constrictor gives virgin birth to female offspring, and (coming round full circle) that there are plenty of planets in the universe that don't seem very hospitable to life.

The section on Martian life (or the lack thereof) is rather puzzling.  It notes a story on the National Geographic website about some scientists' best idea of where future Mars landers ought to look for signs of life or for fossils.  Alexis Palermo Rodriguez of the Planetary Science Institute in Arizona mentions various fractured basins on the planet where stable bodies of waters might have lasted for millions of centuries, and where their sediments are still likely to be accessible.  The article mentions a region in Mars' northern hemisphere named Gemini Scopuli, though it notes that a spot on NASA's list of possible future landing sites, Mawrth Vallis, also looks good.  Another scientist, Victor Baker of the University of Arizona, is quoted and comes across as cautious: he warns not to expect anything as complex as typical Cambrian fossils on Mars, though he thinks unicellular organisms are possible.

"Microorganism fossils on Mars is not too big a stretch of the imagination" is, of course, from AiG's standpoint, the credulity of "evolution-believing astrobiologists" who are convinced without evidence that life must exist on other planets (though nowhere in Baker's or Rodriguez's statements is any indication that life must exist on Mars).  AiG shows proper creationist caution: although they are convinced on theological grounds that intelligent life does not exist elsewhere in the universe, they concede that God might have created non-intelligent life on other planets.  But it is, of course, overconfident to expect to find evidence of such life.

The next section of "News to Note" covers research on fruit flies by scientists at the University of California, Irvine.  The researchers bred two populations of fruit flies, one artificially selected for long life (and slow growth and reproduction as side effects), the other bred to life fast, die young, and leave a lot of orphaned maggots.  They were trying to see which genes determined the difference between the populations, and discovered that rather than a few easily identified genes that accounted for most of the difference, found that scores or hundreds of different genes played a part even in these relatively simple differences.  From the UCI researchers' standpoint, they were settling (or at least providing some clues towards solving) a quarrel over population genetics that went back to Ronald Fisher and Sewell Wright (who favored the "lots of small changes" model) and J.B.S. Haldane (who favored the "few big changes" model).  From AiG's standpoint, they were failing to explain how "new information" (undefined, as usual) entered the genome through mutation, and illustration how evolution is impossible because genetics is really complex (that several generations of evolutionists had suspected that genetics was really complex and didn't see this as an impediment to large-scale common descent with modification does not trouble them, of course).

The next section explains how the evolutionary timeline has been confounded again, showing that evolution is wrong, that radiometric dating is worthless, and that cave men were descendants of Noah.  The confounding research was done by archaeologists at the University of Tolouse-Le Mirail in France, on artifacts dug up from 75,000-year-old deposits in a cave in South Africa.  They determined that these artifacts were made by pressure flaking, a technique for making stone tools not previously known to have been used before 20,000 years ago.

Now, it's worth noting that these were not "primitive" men.  Homo sapiens dates back to almost 200,000 years ago.  It's unlikely that the oldest H. sapiens fossils represent the earliest members of our species, since anatomically modern humans -- relatively gracile H. sapiens with chins -- are almost as old.  The makers of these stone tools were physically modern.  How behaviorally modern they were is an open question; the oldest cave paintings are perhaps 40,000 years old, and some paleoanthropologists think that language use is not much older, but again, fossils and artifacts can only show that something (e.g. art, or particular techniques for working stone) were known by such and such a date at latest, not that they could not have been known before then.  I'm unaware of any aspect of evolutionary theory that says that humans could not have invented language, art, abstract thought, and pressure flaking shortly after H. sapiens sapiens first appeared.  Answers in Genesis writers are either uninformed about the actual "evolutionary timeline" or else assume that their readers don't understand it and that the details don't matter as long as faith in Genesis is supported.

The next section is on a BBC news article that caught everyone's attention: a female boa constrictor, confirmed by her keepers to be a good girl and not at all slutty, has managed to give birth to a brood of baby boas without male help.  Given that parthenogenesis has been demonstrated before in other reptiles (famously, a Komodo dragon last year), this was not by itself a shock.  What was a shock was that the babies were all female: boa constrictors, like birds and Komodo dragons, use a WZ sex chromosome system (some other reptiles use other systems) rather than the XY system used by most mammals (and some other groups -- both systems appear to have evolved multiple times).  Since normally, in a WZ system, the W chromosome (like the Y chromosome in XY systems) is reduced and dedicated mainly to sex determination, it was assumed that WW individuals were inviable (just as there aren't humans who are YY).  All the viable babies produced by parthenogenesis of a species with WZ sex determination should be male, like the Komodo dragon babies.  But the snakes are apparently healthy WW females, which is knocking biology for a bit of a loop and giving researchers something to study.

AiG, rather astoundingly, does not declare that evolutionists being caught by surprise this way discredits evolutionary theory.  Rather, they are concerned that stories about parthenogenesis in various species will lead people to suppose that the virgin birth of Jesus may not have been a miracle (that it may not have happened at all is apparently too shocking for even an evolutionist to suggest).  They therefore end the section with a reminder that "parthenogenesis results in a near-clone of the parent -- and hence all offspring are female."  This would actually presumably be true if parthenogenesis ever occurred in a mammal, as the virgin Mary presumably was.  The authors don't seem to have quite grasped that if the virgin Mary had been a monitor lizard -- or a boa constrictor -- then it would have been quite astonishing if her child had not been a male (note to creationists: I am not in fact suggesting that Mary was a reptile).

The penultimate section of this weeks "News to Note" covers a computer model of planetary system formation that suggests that as star systems form, rocky planets several times the size of Earth and very close to their primaries (close enough to have 24-hour years) could be surprisingly common.  These planets are not expected to be very long-lived (or very habitable), but given that gas-giant-sized worlds that are very close to their primaries have been discovered, they seem plausible.  Nothing in the article in Science suggests that such "super-Earths" would be the only planets formed in their planetary systems, but Answers in Genesis notes that the existence (even the modeled existence) of numerous planets unsuitable for life in the galaxy shows just how special Earth is, and hence supports creationism (which implies that while the Earth was made to be inhabited, the rest of the hundred-billion or so galaxies and all their worlds were created just to mark seasons -- even the stars that can't be seen without massive telescopes).

This weeks summary of the news ends with a snarky mention that the Large Hadron Collider is getting ready to try to recreate conditions (in miniature) that last existed in the early stages of the Big Bang.  AiG does not seem quite clear on the difference between trying to recreate a very dense, hot state of matter and trying to prove the Big Bang, or trying to create a new universe.  They also allude to a Science Daily article on attempts to use insect fossils to estimate oxygen levels in the past, as evidence that the "pre-Flood world" had an atmosphere different from the post-Flood world we live in (which would help explain why so many of the "kinds" that God had ordered Noah to bring aboard the Ark had promptly gone extinct once they disembarked, making the whole exercise of trying to save them rather one in futility).

John G. West Discusses Racism, Eugenics, and "Darwinism"

In an earlier post I mentioned the debate scheduled at the Charles H. Wright Museum of African American History between Intelligent Design proponents and scientists who actually do science.  The debate has since been held, and John G. West, one of the participants from the Discovery Institute, has provided his own report.  West describes the proceedings as "serious, thoughtful, and civil."

West notes that he has never claimed that Darwin invented racism, or was the worst racist who ever lived, but that his theory contributed to racism by providing a scientific rationale for it:

Despite his personal opposition to slavery, Darwin clearly believed that natural selection working on different populations produced "higher" and "lower" races with different mental capacities. Hence, according to Darwinian theory, one should expect to find races with unequal capacities. This expectation of Darwinian theory helped fuel scientific racism for decades and provided a research agenda for a number of leading evolutionary biologists, most notably National Academy of Sciences' member Charles Davenport, one of the founding fathers of modern genetics.

Now, West's analysis misses a few points.  First, given that "Darwinian theory" is notable in part for replacing the Lamarckian evolutionary ladder with an evolutionary tree, why should we expect it to yield a prediction of "higher" and "lower" races?  Given that there are no universally fit traits, how would one decide which suite of traits was "higher" rather than merely "different," and fit for a different environment?  Second, how does one get the prediction that races should differ in mental capacities?  Certainly, as far as I can tell, they might, but why ought a "Darwinian" expect such a thing?

The answer, of course, is that evolutionary theory did not prohibit such differences in mental capacities, and Darwin's contemporaries examined race expecting to find racial differences in mental traits and prepared (by a history of colonialism and slavery that had preceded Darwin's birth, to say nothing of his theory) to evaluate them as "higher" or "lower."  They assumed that their own race was smarter than others (an idea that had originated as a justification for slavery) and set out to prove it, and to fit their findings, or supposed findings, into an evolutionary framework.

West goes on:

The Darwinian connection to the eugenics movement was even more direct. Darwin thought that human beings and their capacities only arose through a merciless process of natural selection that ruthlessly exterminated the weak and the inferior. But according to Darwin, civilized societies did their best to counteract natural selection and preserve those nature would have killed off. Darwin thought that this counteracting of natural selection had serious negative consequences for the future of the human race.

I assume by "more direct" he means "less direct."  And one might suppose that if a "merciless process of natural selection" exterminated the weak and inferior, then those "savage societies" that lacked the medical means to counteract this ruthless process would end up with superior races.  That would be on average, of course: an implication of evolutionary theory is that variation exists in all populations, than new variation arises all the time (even if Darwin himself had vague and inaccurate ideas of how this happened), and that there could be no trait, on which one could base a claim of racial superiority or inferiority, that would be present in all members of one race and no members of others.  But West's argument that "Darwinism" supported eugenics would not seem to comport all that well with his argument that it implied that less technologically advanced races were "inferior" in body and/or mind.

Now, it seems to me that Darwin was subtly wrong, on his own terms, in his worries about the effects of medicine and vaccination on the overall fitness of civilized society.  By his own theory, fitness is relative to a particular environment, not an absolute, and if the environment changes, then what is "fittest" must change with it.  Vaccination, charity, etc. alter the criteria for fitness rather than cause some objective decline in it.  Here Darwin's moral intuitions (that refusing aid to "the weak" went against "the noblest part of our natures") arguably served him better than his first deductions from his own theory.

Darwin wasn't always right.  And his contemporaries, of course, were aware of this and at times eager to remind him of it.  Early evolutionists challenged Darwin on the primacy of natural selection, on Darwin's view that only minute variations were relevant to selection (rather than large-scale "saltational" changes), on his view that humans had evolved in Africa rather than in Asia, etc.  "Darwin's theory" didn't simply emerge into an intellectual vacuum and sweep all before it on the force of his own scientific authority.  People had their own ideas about human biology and anthropology, and modified evolutionary theory to fit them as often as the reverse.  The illustration accompanying this article was produced in 1857, by an author who held (at the time) to multiple independent creations of human beings, and who argued that the gap between whites and blacks was on a par with the gap between black humans and chimpanzees.  People didn't deduce from evolutionary theory that human inequality existed; they already assumed such inequality and sought new justifications for it in new theories.

John D. Morris Reads the Fossil Record

There are a few articles in the current Acts & Facts to cover.  One, by John D. Morris (current president of the ICR and son of its founder -- and if Henry M. Morris was "the father of modern [young earth] creationism," does that make John D. the "brother of modern creationism?"), is basically an advertisement for Morris' and Frank Sherman's new book The Fossil Record.   He states that the book was written "with Christian students in non-science majors in mind," out of concern that such students would have their faith swayed by evolutionary interpretations of fossils in biology classes or the media.  One wonders if this is a tacit admission that many of their statements would not stand up to the knowledge a science major would acquire.

Obviously, a short article is not going to provide us with the full wealth of Morris and Shermer's opus.  But in the article, Morris offers a few comments that do not fill me with confidence in his insight into the fossil record.  He states, for example:

The Fossil Record doesn’t just show how a full understanding of the fossils contradicts evolution; it specifically supports creation and the Flood. It documents the sudden appearance of basic types, not a slow development of one type from some other type through transitional fossils. Fossils exhibit stasis, not the change that evolution requires. The animals represented in the fossil record typically died in catastrophic conditions of rapid water movement, not in uniform conditions. Fossilization occurred through rapid burial. The case is strong for the creation/Flood scenario. Only a willful commitment to naturalism would lead one to conclude evolution and uniformity instead.

Note that "stasis" is a property of well-represented fossil species.  A fossil species with many specimens will show variations between specimens (just as living species do).  Some of these variations will make individuals look a bit more like species that preceded it; others will make other individuals look a bit more like later species.  But the latter sort of variations do not become more common (or the former type less common) over the duration of the species in the fossil record; the species as a whole shows no "microevolution" before being replaced by another, similar but distinct species in the same genus.  But here is the relevant point: there are observed instances of speciation.  Furthermore, the ICR (like Answers in Genesis and most other young-earth creationists) admits -- indeed insists -- that one species can change into another.  "Stasis" as the term is used by paleontologists means that the fossil record has a paucity of evidence for the very level of evolutionary change that they insist has happened!  Species well-represented enough to to demonstrate stasis, meanwhile, often themselves form transitions between genera.

And what is one to make of the claim that fossilized animals died in "catastrophic ... not in uniform conditions?"  "Uniformitarianism" means that geological processes at work in the present were at work in the past; it does not mean that the past was an unbroken succession of mild spring days.  Floods and storms and tsunamis and earthquakes occur today; a "uniformitarian" would assume that they occurred in the past (indeed, since the worst flood, earthquake, meteorite impact, etc. of the last century was probably worse than the last flood, earthquake, or impact of the last year, a "uniformitarian" would hardly be shocked at the suggestion that the worst natural catastrophes of the last million centuries were probably worse than the worst such catastrophes known from recorded history).  A herd of Centrosaurus drowning in a flooded river in the late Cretaceous is just as "uniformitarian" as a herd of caribou doing so in the last century (and that one doesn't find the "ceratopsian kind" and the "deer kind" fossilized in the same watery catastrophes hardly seems like support for a single global flood depositing most of the fossil record).

Extraordinary Mosasaur Fossil Reveals Creationist Can't Read

Brian Thomas, a science writer at the Institute for Creation Research, has an article in the current issue of the ICR's Acts & Facts.  The actual title of the article is "Extraordinary Mosasaur Fossil Reveals Original Soft Tissue."  This title is not entirely accurate.  The fossil of Platecarpus tympaniticus has matter that is "interpreted as" (one wonders how an ICR science writer would have dealt with that phrase if it had concerned, say, the 75 million year age of the fossil) compacted remains of the retina: structures that have "a morphology that is comparable to "  that of retinal melanosomes in its eye sockets.  It has a reddish splotch that is interpreted as indicating the position of the heart and liver.  Thomas notes that:

Using state-of-the-art equipment, they identified “hemoglobin decomposition products.”¹ Hemoglobin is a major chemical constituent of blood. Anyone who has accidentally left meat out of the refrigerator overnight knows that it decomposes quickly. After death, hemoglobin proteins always fall apart, even when sterilized and with no water, spontaneously converting into smaller, simpler molecules.

The authors did not address the glaring question of why there was dried blood residue in a fossil dated as millions of years old. The reason is simple—they have no idea why!

But then, "hemoglobin decomposition products" are not the same thing as hemoglobin, much less the same thing as blood and actual tissue.  The fossil has chemical stains that probably indicate where blood-rich organs once were; it doesn't actually have those organs.  And while it's very rare for fossils to preserve outlines and stains indicating former soft tissue, it's hardly unheard of.  It seems rather more likely that they don't address this "glaring question" because they didn't consider it a glaring question at all: some fossils just have better soft tissue impressions than others.

Thomas introduces a quote from a different article about a different fossil -- Mary Schweitzer's stinky T. rex bones with their apparent blood vessels and reddish spots (but no actual surviving blood cells): “all of the chemistry, and all of the molecular breakdown experiments that [scientists have] done don’t allow for this" -- and concludes that this is another fossils that undermines the idea that fossils could be tens of millions rather than mere thousands of years old.  That all the physics and all the research done on decay rates doesn't allow radiometric dating to be off by about four orders of magnitude is not, of course, a point he brings up, nor does he dwell on the point that we have considerably less evidence for the mutability of radiometric decay rates than we do for the mutability of decay rates of organic compounds like hemoglobin or collagen.

Thomas closes by declaring that the fossil and its sediments are "powerful evidence" of Noah's Flood.  He doesn't dwell on the question of why, e.g. if all these different created kinds lived simultaneously, we don't find mosasaurs in the same strata as ichthyosaurs, on the one hand, or cetaceans, on the other.  Nor does he dwell on the rather puzzling question of why we don't find a lot of mosasaurs swimming off the coast today.  After all, the whole point Noah taking every kind of land animal aboard the Ark would seem to be that God did not wish any of His "created kinds" to go extinct in the flood.  Yet young-earth creationists seem to casually assume that He would not trouble to preserve dinosaurs, or cynodonts, or plesiosaurs, or the aforementioned mosasaurs, once they disembarked from the Ark or swam away from the rapidly rising mountains.  For a great many "kinds" and their constituent species, YECs have turned the Ark from a story about preservation to one about extinction.

Jason Lisle and Distant Starlight

The Skeptical Lutheran, or qpsk (I suspect that's not what his parents named him, but I'm not sure) has suggested that I examine and comment on a paper by Jason Lisle published in the Answers Research Journal of Answers in Genesis.  The paper is an attempt to solve one of the most vexing problems in young Earth creationism, the "distant starlight problem:" why, if light travels at one light year per year, and the universe is only about 6000 years old, can we see the Andromeda Galaxy, which is two million light years away, and even far more distant galaxies?

Lisle opens by noting that the distant starlight problem is, after all, very similar to the "horizon problem" in mainstream Big Bang theory: just as YECs don't quite have an explanation for why we can see distant galaxies, mainstream cosmologists don't quite have an explanation for why the cosmic microwave background is so uniform, when the universe is supposed to have been expanding faster than light so that distant regions could never have been in contact with each other.  He doesn't mention inflationary theory, though he does note elsewhere in his paper that "secular scientists" have auxiliary hypotheses that they can use to patch up the problems with their old-universe models.  More importantly, he doesn't note that the Big Bang theory isn't just some fad that caught on like bellbottoms; it explains the distribution of galactic redshifts, and predicts the cosmic microwave background whose uniformity is so puzzling.  I don't think you could really say that the "creation model" predicts the existence of galaxies most of which can't even be seen with the naked eye.

Lisle, like most modern YECs, dismisses without comment the possibility that the entire visible universe is within 6000 light years of us.  Since he gives no explanation, I can only speculate, but I suspect that he doesn't really want to argue that all those apparent galaxies (with their apparent Cepheid variables, supernovae, etc.) are really something else much closer (and if they're really what they appear to be, of course, they won't all fit within a few thousand light years of Earth).   There is one other point: if the stars were created "for times and seasons, days and years" (Genesis 1:14), it would seem fitting for those stars to be visible by the end of the creation week, when Adam and Eve first got to look at them.

He likewise dismisses the classic omphalist suggestion that light was created, already in transit, from those distant stars.  While Lisle agrees with other AiG writers that the term "appearance of age" is meaningless, and has no problem with the idea that various things from galaxies to Adam himself were created "mature," he is bothered by suggesting that God has created a false appearance of history, by, e.g. creating light from supernovae that never occurred.

At the same time, he rejects the possibility that the Earth and universe are really billions of years old and that this light has had time to reach us at 300,000 kilometers/second.  He does mention and courteously allows the possibility of Humphreys' hypothesis that time proceeds faster the  further one is from Earth (so that distant galaxies really are billions of years old), but notes that in that case, we'd expect distant starlight to be strongly blueshifted, not redshifted (unless the expansion of space were very fast indeed).  He also argues that distant galaxies are probably not very old anyway: he disputes mainstream cosmologists' suggestions for forming new stars (and hot, blue stars don't last billions of years) and for keeping the spiral pattern of galactic arms from winding up tight.

Rather, Lisle finds a possible solution in an odd fact of modern physics: it's apparently impossible to measure the speed of light going only one way: all methods for measuring it depend (explicitly or implicitly) on measuring the time it takes for light to make a round trip.  The usual assumption, of course, is that light travels at the same velocity in each direction, but it's conceivable that it travels faster in one direction and slower in another.  His suggestion is that lightspeed is near-infinite travelling to Earth from distant stars, and only about 150,000 km/sec. travelling away from Earth.   Thus, he argues, galaxies billions of light-years away were in fact created only about 6000 years ago, on day four of the creation week, and their light reached Earth only seconds or minutes later.

Technically, this is an "anisotropic synchrony convention" (ASC) for dealing with measurements of the speed of light, and is allowed under relativity theory (which traditionally has used Einstein's synchronization convention: that light has the same speed no matter which direction it's going); he's careful to note that he's not trying to come up with a radically new theory in physics.  Some of the weirder passages in Lisle's paper come from his attempts to argue that the ASC is used in the Bible and even in modern astronomy (e.g. supernovae are labeled by the year they're observed, not the year they're thought to have occurred in ... but then, this is a date for the observation, not a date for the actual explosion of the star).  The Bible, he notes, always treats light as though it moves instantly from source to observer.  Of course, over terrestrial distances, this is virtually  true.  It is not obvious at all that the Bible uses ASC rather than simply assuming that in  fact light just has infinite velocity and/or the universe is actually pretty small (e.g. those stars are fixed to the solid dome of the sky a few dozen miles over  toour heads).  Like Johnson and Humpreys, Lisle finds himself arguing that the Biblical text is really asserting something that its original readers (and indeed any reader prior to the 20th century) would never have suspected lay in the text.

The very aspect of measuring the speed of light that makes his model possible means that testing it needs to be indirect.  Lisle argues for it by suggesting that distant galaxies look as if in fact they haven't had much history: as noted, he brings up creationist arguments against forming new stars as old ones expand into red giants or go supernova, and against the possibility of natural processes maintaining spiral arms.  Despite his earlier suggestion that his model and and Humpreys' could be combined, his evidence for his model implies the falsity of Humphreys' varied cosmologies.   And of course one objection that "secular" cosmologists will have to his idea -- that it creates a favored frame of reference rather than treating all positions in the universe equally -- is a feature, not a bug, for a model designed to rescue the idea that the Earth and humanity are more or less the whole point of the universe.

One point in favor of old distant galaxies is rather quickly hand-waved away.  Quite a few distant galaxies look "old" in the sense of looking as if they have a past history.  It's one thing to be "mature" in having a panoply of stars and dust clouds and spiral arms (even if they won't last: it sometimes seems to me as if YEC vaguely denigrates the Creator, implying that He's churned out some cheap gimcrack of a universe that falls apart after a few thousand years of normal use); it seems rather another for galaxies to look, for all the world, as though they've just collided with one another (see the photo above) (note that given the size and speed of galaxies, a collision would take millions of years) or as though massive explosions have wracked their cores.  Lisle tries to argue that galaxies with massive flares of gas and dust were simply created "mature," but this is a sort of maturity analogous to trees created with ring patterns showing the effects of nonexistent droughts, fires, and lightning strikes in nonexistent centuries past, or of Adam being created with healed scars from nonexistent past injuries.  Whether or not distant galaxies look old, quite a few of them look very experienced.  It's very, very hard for YECs to avoid invoking, at some point, what looks very much like the omphalos "hypothesis" (except that, of course, by its very nature it's completely untestable).

There is one more point, brought up by Skeptical Lutheran himself and several other people more knowledgeable than myself about physics, who've examined Lisle's thesis: there are physical constants important in electronics that are dependent on light being a wave, and the performance of capicitors and magnets ought to vary as you change their position and orientation unless light waves move at the same speed in all directions.  I presume that Lisle, who seems rather bright, will eventually come up with an auxiliary hypothesis of his own to deal with this problem.  He doesn't, however, seem to have done so yet.