What’s wrong with this paper?

Taking a new tack with the common descent/common design theme, I’d like to sneak up on it. As Sal Cordova likes to do, I offer a hypothesis for critique. Here’s an old phyogenetic analysis of mine. Does it show common descent? If not, what’s wrong with it?

Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003;  52:386-402.

This one is about crocodiles. Are crocodiles all the same kind? How do you know? If they aren’t how many kinds are there within the group and how do you know? If they are, are they a whole kind or just part of a larger kind? And if the latter, what is the larger kind?

That Dead Horse Just Won’t Stay Down

This isn’t one of the 10 unanswerable questions, but it’s still from Jonathan Wells’ book Icons of Evolution, p. 51. Wells is attempting to cast doubt on the efficacy of molecular systematics, by pointing out how silly some of the results are:

Even when different molecules can be combined to give a single tree, the result is often bizarre: A 1996 study using 88 protein sequences grouped rabbits with primates instead of rodents; a 1998 analysis of 13 genes in 19 animal species placed sea urchins among the chordates; and another 1998 study based on 12 proteins put cows closer to whales than to horses.

Of course the last example is the funniest, given the wealth of molecular and fossil data showing that cows and whales are indeed related. Continue reading

Jonathan Wells and Homology

This is the third and last of my answers to Jonathan Wells’ 10 unanswerable questions for evolutionists.

Question 3: Homology.

Wells: Why do textbooks define homology as similarity due to common ancestry, then claim that it is evidence for common ancestry — a circular argument masquerading as scientific evidence?

This question stems from confusion on Wells’ part between how something is defined and how it is recognized, which are two quite different things. Homology is indeed defined as similarity due to common ancestry. But we don’t just label any similarity a homology and call it evidence for common ancestry. That would indeed be circular. What we really do is quite different. Similarity between the characteristics of two organisms is an observation. If the similarity is sufficiently detailed (“both are big” or “both are green” won’t do) we consider it a candidate for homology.

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Jonathan Wells and Archaeopteryx

Since I’ve been asked, I’m posting another of my answers to the 10 unanswerable questions for evolutionists in Jonathan Wells’ book Icons of Evolution.

Question 5: Archaeopteryx.

Why do textbooks portray this fossil as the missing link between dinosaurs and modern birds — even though modern birds are probably not descended from it, and its supposed ancestors do not appear until millions of years after it?

What does Archaeopteryx have to be to qualify as a “link” (not a missing link, because it isn’t missing)? Wells apparently (he never really says) requires an insensible gradation of ancestors and descendants leading from an unquestioned dinosaur to an unquestioned bird, with Archaeopteryx in the middle. While that would be nice, it’s hardly necessary — and considering the quality of the fossil record, that’s lucky.

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Jonathan Wells and the Cambrian explosion

In honor of Jonathan Wells’ new book, which I haven’t yet seen, I’m recycling from his first book Icons of Evolution, in which he poses 10 unanswerable questions for evolutionists. Here’s my answer to question #2: Darwin’s tree of life.

Wells: Why don’t textbooks discuss the “Cambrian explosion,” in which all major animal groups appear together in the fossil record fully formed instead of branching from a common ancestor — thus contradicting the evolutionary tree of life?

There are a great many premises hidden in this question. Wells claims that 1) textbooks don’t discuss the Cambrian explosion, 2) all major animal groups appeared during the explosion, 3) the groups were “fully formed” when they appeared, and 4) that this all somehow falsifies the idea of common descent. As we will see, none of these premises is true, so the question is pointless. It’s would be surprising if textbooks didn’t discuss the Cambrian explosion, since it’s a major event in the history of life. And in fact they do. Of ten textbooks examined by Wells, he claims that eight don’t even mention the explosion.. In fact all but one does mention it, and four of those give it more than a hundred words. Still, a hundred words isn’t much to deal with such a major event; Wells’ implication is that coverage of the explosion is being deliberately suppressed. Then again, textbooks have limited space to deal with all of the complex field of biology; an alternative explanation is that these books just have limited coverage of the history of life and of evolution in general.

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Baraminology of the Flood

Baraminology and the Flood

Presented for your amusement as a relief from all the very deep philosophy: a fine example of the cargo cult science of young-earth creationist baraminology. That label “cargo cult science” refers to attempts to ape the surface features of science, perhaps in hopes of gaining a similar degree of prestige. Think of Ann Gauger in a white lab coat, standing in front of a green screen.

Our example today comes from Kurt Wise, perhaps the most famous of the scientifically trained creationists — Harvard degree in paleontology with no less an advisor than S. J. Gould. Specifically, this publication:

Wise, Kurt P. 2009. Mammal kinds: How many were on the ark? Pages 129-161 in T. C. Wood and P. A. Garner (eds.), Genesis kinds: Creationism and the origin of species, Issues in creation #5. Wipf & Stock, Eugene, OR.

As we shall see, one of the attributes of cargo cult science is the very careful handling of assumptions; their implications must be considered only in so far as they contribute to the desired conclusion, and any inconvenient consequences must be ignored. Wise actually does better than most, and is willing to let the data take him farther than most, but not so far as to endanger his beliefs.

The central task of baraminology, and the one that has most interested me, is the attempt to identify the created kinds. Wise proposes a novel method for this using the fossil record. But first, some assumptions, which must be granted for the sake of argument.

We must first suppose the literal truth of the entire Genesis story, including a strict timeline. Life, including all the kinds, was created over a week about 6000 years ago. These various kinds contained the potential to develop — one should not say “evolve: — into a great many species very quickly, which they proceeded to do. Around 1500 years later, there was a great Flood that covered the world, killing all terrestrial animals (at least) other than those preserved by Noah on the Ark. And Noah carried a few individuals of one species of each created kind; thus each kind suffered a severe bottleneck in the Flood: not only was each species reduced to a few individuals, but each kind was reduced to a single species.

Directly after the flood, the kinds re-diversified into new species (or quickly went extinct, in many cases). Traditionally in baraminology, the kind has been roughly identified with the family, thus the cat kind is considered to include lions, cheetahs, domestic cats, etc., 30+ living species and a fair number of extinct ones, all from an original pair of cats on the Ark. (Wise is willing to go much further than that, as we will see.)

There are also a number of assumptions about the stratigraphic record. The record can be divided in two: Deposits of the Flood, including the entire Paleozoic and Mesozoic and unspecified portions of the Precambrian, and deposits of the post-Flood, the Cenozoic. The K-T boundary represents the end of the Flood. Within these strictures, Wise accepts the worldwide correlation and sequence of rocks. It just all happened a lot faster than mainstream geologists think. And here’s the timeline, a combination of Wise and other papers in the same volume. Deposition gradually decreases in rate as time goes by, slowing to roughly modern rates around 650 years after the Flood, and the entire Tertiary is compressed into that time.

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Wise’s final assumption is that the fossil record is very close to complete, at least at the level of mammal kinds.

And here we arrive at a test for kind status. As soon as a kind gets off the Ark and has had time to increase to a reasonable level of population, it should be represented in the fossil record. Wise figures that 30 years or so should be enough time, so that every kind should be represented in the fossil record by the end of the Lower Eocene. Taking a standard classification of mammals, he assigns kind status as the lowest taxonomic level having any representative by the end of the Lower Eocene.

This results in some interesting developments. The approximate level of the kind is not the traditional family but superfamily and suborder. For example, Wise considers Feliformia and Caniformia to be single kinds. The former includes cats, mongooses, civets, and hyenas, while the latter includes dogs, bears, weasels, raccoons, and, most interestingly, seals. By similar reasoning, he also supposes that whales are descended from terrestrial mammals aboard the Ark. This is much more evolution — sorry, diversification — than most creationists are willing to swallow. Wise, to his credit, doesn’t shy away from that.

Now, there is one group excluded from this method. Can you guess which one? Yes, it’s humans. Wise supposes that, given their long post-flood life spans, no human died until long after the Lower Eocene, and thus there could be no human fossils.

The fact remains that, given his assumptions and specifically excluding hominids, his method for determining kinds is perfectly valid. The assumptions are correctly followed where they lead. So where does this become cargo cult science? It’s in the failure to consider other implications of the scenario.

Wise completely ignores the Flood sediments. Under his assumption, every mammal kind (including humans, incidentally, which had a large pre-Flood population) should be represented in the Paleozoic and/or Mesozoic record. But this would imply that there are at most three or four kinds of placental mammals. And that’s being generous; many paleontologists think that no Mesozoic fossils represent placental mammals, which would make them at best a single kind.

Here’s another corollary that Wise does not consider: any species that appears both before and after the K-T boundary must be a separate kind from any other. While this applies to very few mammals, it would be useful for other taxa.

Speaking of other taxa, it’s clear that most kinds — tyrannosaurs, gorgonopsians, stegocephalians, palaeodictyopterans, and so on — became extinct too soon after the Flood to leave any fossil record at all. It isn’t clear why YHWH felt it necessary to put them all on the Ark, only to abandon them immediately after, but I suppose He moves in mysterious ways, etc.

We will not even think about plants, aquatic animals, forams, and such. They aren’t important, and Wise’s line of reasoning depends entirely on the Ark.

One final tidbit: if we accept the K-T boundary as the end of the Flood, and accept further that the Ark grounded on Mt. Ararat (which most creationists do), we have a conundrum, as Mt. Ararat is a Pleistocene volcano, which formed, by the chronology above, several hundred years after the Flood ended.

“Kinds”

Time for a discussion of “kinds”, i.e. “created kinds”, known to some as baramins. More specifically, holobaramins, an originally created (no ancestors, that is) population and all its descendants. But from now on I’ll just call them kinds, as long as we can agree on the intended meaning. There can be no kinds within kinds. Each one is a separate tree in a creationist’s phylogenetic orchard.

I don’t mean to go on long. This is really intended as a place for creationists to attempt to answer important questions of baraminology. Can a kind encompass more than one species? How can you know whether two species belong to the same or different kinds? Would we expect to see something obvious to differentiate them?

I’ve seen several criteria proposed, some of which work in only one direction. If two species hybridize, it’s claimed, they must be the same kind; but if they don’t, that doesn’t mean they’re different kinds. If a transition between two species is not “mechanically feasible”, they must be different kinds; but if it is, that doesn’t mean they’re the same kind. Other criteria I’ve seen are “discontinuity”, whatever that is, intuitive recognition (seriously, that’s an actual claim), and of course biblical exegesis. Can we agree to leave out the last?

Finally, can some creationist use those criteria, or any other, to designate at least a few entities that he is sure are kinds? Then we’ll have something concrete to argue about.

Phylogenetics. Huh! What is it good for? Absolutely nothing.

I do think this site needs a thread to discuss phylogenetics and whatever the creationist alternative might be. Let’s start with this quote from Sal Cordova:

stcordova: Insisting on the truth of naturalism in the disguise of evolutionary theory could impede scientific progress in the medical sciences if the whims of some evolutionary biologists like Dan Graur are realized. The National Science Foundation (NSF) has invested 170 million dollars in unresolvable evolutionary phylogenies of little or no utility to medical science.ii To date, no therapies based on the 170 million dollar phylogeny project have come to market. By way of contrast, with the help of research like ENCODE, epigenetic therapies are already being delivered to patients with more such therapies in the pipeline. Therefore, a gambler’s epistemology that seeks to maximize reward in the face of uncertainty would seem a superior approach versus blind insistence on impractical naturalism.

This short paragraph raises a number of questions, a few of which seem like topics for discussion.

1. Assuming for the sake of argument that investing in phylogenetics doesn’t help medical science, why should we ignore other benefits? Is basic knowledge useless unless it contributes directly to human health? Should NSF be concerned only with medical sciences, and if so, shouldn’t it be folded into NIH?

2. Phylogenetics actually does have practical applications, even in medical research. Feel free to discuss that. Me, I’m into knowledge, regardless.

3. What is “unresolvable” intended to mean here? NSF grants, the AToL program in particular, have produced great amounts of phylogenetic resolution. My project, Early Bird, for example. Is it all somehow bogus? How much phylogeny is there, anyway, and how would a creationist tell where it begins and ends?

4. And a minor point: Where does this figure of $170 million come from? Is it the total amount awarded by the NSF Assembling the Tree of Life program from beginning to end? Or does it also count various other programs that have funded systematics research? I find it hard to pull any aggregate info from the NSF web site.