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.

How likely are we to find direct ancestors of living species in the fossil record? That depends on the quality of the fossil record. If we have found most of the extinct species that ever lived, our chances are good; on the other hand, if our knowledge is spotty, our chances are bad. We can judge the quality of the dinosaur fossil record based on the species we have found so far. Half of all known dinosaur genera are known only from a single specimen, which suggests that there are many more genera for which not even that single specimen has yet been found. Moreover, many of the genera with multiple specimens are known only from a single time and place. We have seven specimens of Archaeopteryx, all from a single limestone quarry in Germany. Archaeopteryx is the only known Jurassic bird. How likely is it that the single Jurassic bird we happen to have found is the ancestor of all subsequent birds? Given the small sample we have, we are unlikely to have found the ancestors for most dinosaur groups, including birds. Fortunately, we often can find fossils that are not too far removed in time and appearance from those ancestors. Archaeopteryx is one such fossil. It probably isn’t the ancestor of birds. (Distinguishing actual ancestors from cousins of the ancestors is itself an unsolved problem.) But it does represent a key transitional stage between theropod dinosaurs and modern birds. It has some features of theropods, some of birds, and others that are in between. Wells offers no explanation for the transitional nature of Archaeopteryx. We have other fossils for both more primitive and more advanced transitional stages. Some of the more primitive transitional stages — Velociraptor, for example — lived later than Archaeopteryx. Such are the vagaries of preservation. Nobody claims that ancestors appeared after their descendants, only that we have sampled a big family of cousins and siblings at random points through time, some of whom (like Velociraptor) resemble their common ancestor more closely than others (like Archaeopteryx).

A comparison may be helpful in understanding this point. On the top of the figure above is a tree showing human relationships. Dots at some points in time represent species we know about. We have a number of fossil apes, most over 10 million years in age. We also have a number of fossil hominids, of which Australopithecus afarensis, represented by “Lucy”, is perhaps the most famous and has often been mentioned as a possible human ancestor. While it’s not clear whether A. afarensis is or isn’t a direct human ancestor, it’s definitely not too far from that line. The next closest human relatives are the chimpanzees. Chimpanzees have no known fossil record. Someone might try to cast doubt on this human phylogeny by claiming that modern humans are probably not descended from Lucy, and her supposed ancestors (meaning chimpanzees) do not appear until millions of years later. Of course, there are other, earlier fossil apes, but they are much farther from humans than are chimpanzees. Nobody actually makes this argument, probably because we easily recognize it as ridiculous, equivalent to the question, “If humans are descended from apes, why are there still apes?” You don’t even have to accept human evolution to realize that question is silly. But Wells’ question about Archaeopteryx is exactly the same. We’re not sure if Archaeopteryx is a direct ancestor of modern birds, but it’s not far from that line. The theropod dinosaurs that Wells calls Archaeopteryx’s “supposed ancestors”, like Velociraptor, are merely the closest known relatives of Archaeopteryx, and stand in the same relationship to it that chimpanzees do to Lucy: later in time yet more primitive. And of course there are plenty of earlier, even more primitive theropod relatives. We know that the fossil record is incomplete, and it’s incomplete for both birds/dinosaurs and humans/apes. The fit between the actual fossil record and our natural expectations that primitive characters will appear earlier than advanced characters is surprisingly good, but it’s not perfect; as in these two cases, some fossils we would like to see have not been found. But enough have been found to give us a clear picture, at least in outline, of both human and bird evolution. “Lucy” and Archaeopteryx don’t have to be directly ancestral to make important contributions to those pictures.

Evo-Info review: Do not buy the book until…

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

… the authors establish that their mathematical analysis of search applies to models of evolution.

I have all sorts of fancy stuff to say about the new book by Marks, Dembski, and Ewert. But I wonder whether I should say anything fancy at all. There is a ginormous flaw in evolutionary informatics, quite easy to see when it’s pointed out to you. The authors develop mathematical analysis of apples, and then apply it to oranges. You need not know what apples and oranges are to see that the authors have got some explaining to do. When applying the analysis to an orange, they must identify their assumptions about apples, and show that the assumptions hold also for the orange. Otherwise the results are meaningless.

The authors have proved that there is “conservation of information” in search for a solution to a problem. I have simplified, generalized, and trivialized their results. I have also explained that their measure of “information” is actually a measure of performance. But I see now that the technical points really do not matter. What matters is that the authors have never identified, let alone justified, the assumptions of the math in their studies of evolutionary models.a They have measured “information” in models, and made a big deal of it because “information” is conserved in search for a solution to a problem. What does search for a solution to a problem have to do with modeling of evolution? Search me. In the absence of a demonstration that their “conservation of information” math applies to a model of evolution, their measurement of “information” means nothing. It especially does not mean that the evolutionary process in the model is intelligently designed by the modeler.1

Continue reading

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.

Continue reading

Can prairie dogs talk?

Ferris Jabr has recently written a highly illuminating article for The New York Times Magazine titled, Can Prairie Dogs Talk? (May 12, 2017), on the pioneering work of Dr. Con Slobodchikoff, an emeritus professor of biology at Norther Arizona University. Professor Slobodchikoff has been analyzing the sounds of prairie dogs for more than 30 years, and he thinks that they possess a form of genuine language. Specifically, he claims that when they give alarm calls for different kinds of predators, they identify not only the type of predator, but also its size, shape, color and speed. In other words, their messages do not consist merely of nouns; instead, they are more akin to descriptive phrases. In a follow-up interview with Professor Marc Bekoff (Psychology Today, May 14, 2017), Slobodchikoff argues that since the rate at which the alarm calls are produced tends to correlate with the speed of travel of the approaching predator (hawks, for example, elicit only a single bark because they are so swift), prairie dog talk also contains something analogous to a verb in human language. Most surprising of all, prairie dogs are capable of coming up with new alarm calls for abstract objects which they have never seen before, such as an oval, a triangle, a circle, and a square. And if that were not enough, it turns out that prairie dog calls, like human language, are composed of phonemes. Indeed, Slobodchikoff even declares that prairie dogs have the most complex language of any non-human animal.

Professor Slobodchikoff contends that it is only pure prejudice on the part of “human exceptionalists” (many of whom are linguists and philosophers) that prevents scientists from describing prairie dog calls as true language, rather than mere “communication.” In addition, many people’s thinking is still influenced by Aristotle’s Scala Naturae, which ranks humans at the top, followed by “higher” mammals such as apes and then “lower” mammals such as mice (and of course, prairie dogs), with birds, reptiles, amphibians and fish lower down in the pecking order, and with insects, worms and one-celled animals at the very bottom. Such a view, argues Slobodchikoff, is speciesist and profoundly primatocentric. It is time for scientists to cast aside their prejudices and recognize that humans are not the only animals that can talk.

Is Slobodchikoff right? In today’s post, I’d like to explain why I’m inclined to be skeptical of the claim that prairie dogs are capable of anything like language.

Continue reading

What is Death

In reading through a number of the threads, I’ve been struck by apparent conceptual acceptance most folk have with the term “death”, taking for granted (it appears) that everyone else reading the term understands it pretty much exactly as the poster intended. However, it also appears to me that there are a few different underlying understandings of the meaning of that term.

I for one am not and never have been all that comfortable conceptually with the term. I find the term to be sort of a contrast place holder for “that which is no longer alive”, but vaguely defined. And from there different folk attach all sorts of esoteric or assumed baggage that I don’t fully grasp or understand. For example, some folk apparently think of “death” as a thing – an actual object independent of (though clearly tied to) living things. I don’t understand that concept. Then there are some folk who think of “death” as something like a transition or perhaps threshold (portal…door…take your metaphorical pick) that living things “pass through” when they “lose life”. Uhh…oookay… And then there are some folk who think of death as something like a state of existence – like sleep I guess only…uhh…deeper…maybe? I do not understand any of those concepts of death.

To me, “living” is a term I use to denote a functioning autonomous system that seeks out resources for the perpetuation of the system’s operation and/or reproduction, and that expels byproducts derived from the system function and resource use. As such, fire to me is very much a living thing. And while in a metaphorical sense I might say that a fire has “died” after it’s gone out, I simply mean that the conditions for that combustion system no longer exist. Similarly, to me, bodies no longer living have simply reached a state where the conditions for the physiological system no longer exist. Systems, by their very nature of resource use and environmental stress, wear. As such, they eventually get to a point they stop functioning. Seems odd to call that “death” to me.


Evo-Info sidebar: Conservation of performance in search

Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.

Denyse O’Leary, an advocacy journalist employed by one of the principals of the Center for Evolutionary Informatics, reports that I have essentially retracted the first of my papers on the “no free lunch” theorems for search (1996). What I actually have done in my online copy of the paper, marked “emended and amplified,” is to correct an expository error that Dembski and Marks elevated to “English’s Principle of Conservation of Information” in the first of their publications, “Conservation of Information in Search: Measuring the Cost of Success.” Marks, Dembski, and Ewert have responded, in their new book, by deleting me from the history of “no free lunch.” And the consequence is rather amusing. For now, when explaining conservation of information in terms of no free lunch, they refer over and over to performance.1 It doesn’t take a computer scientist, or even a rocket scientist, to see that they are describing conservation of performance, and calling it conservation of information.

The mathematical results of my paper are correct, though poorly argued. In fact, the theorem I provide is more general than the main theorem of Wolpert and Macready, which was published the following year.2 If you’re going to refer to one of the two theorems as the No Free Lunch Theorem, then it really should be mine. Where I go awry is in the exposition of my results. I mistake a lemma as indicating that conservation of performance in search is due ultimately to conservation of information in search.
Continue reading

In Defense of Republican Atheism

In a recent comment, Vincent writes that

However, I would argue that if we believe in human freedom, then that freedom has to include the freedom to bind oneself to a particular vision of humans’ ultimate good – whether it be one that includes God as its core or one which excludes God as a hindrance to unfettered liberty.

I’m very interested in theories of freedom and this idea of atheism as somehow involving “unfettered liberty.”

Continue reading