The Talk.Origins Archive Post of the Month: August 2008

Subject:    | News: 10 Questions, and Answers, About Evolution.
Date:       | 25 Aug 2008
Message-ID: | ywFsk.18915$cW3.9861@nlpi064.nbdc.sbc.com

John Harshman wrote:
I'm going to piggyback my own answers to some of these questions onto the NCSE answers, because I like mine. Of course I'm a lot more long-winded than they were. I wrote these for a project of the SSE (Society for the Study of Evolution) that was never published. They used to have diagrams attached, but I've rewritten around them.

From the Times article:
>>> "Ten questions to ask your biology teacher about evolution," a
>>> document by Jonathan Wells, a senior fellow at the Discovery
>>> Institute, a Seattle-based group that advocates intelligent design,
>>> aims to highlight the weaknesses in evolutionary theory. Here are his
>>> questions, along with responses compiled by the National Center for
>>> Science Education. More questions can be found on Dr. Wells's site,
>>> http://www.iconsofevolution.com/ More information about biological
>>> evolution can be found at http://nationalacademies.org/evolution/.
[snip]

Jonathan Wells asks:
>> 2. Darwin's tree of life. 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?

The NCSE answered:
> A. Fish, amphibians, reptiles, birds, and mammals all are
> post-Cambrian. We would recognize very few of the Cambrian organisms
> as "modern"; they're in fact at the roots of the tree of life, showing
> the earliest appearances of some key features of groups of animals –
> but not all features and not all groups. Researchers are linking these
> Cambrian groups using not only fossils but also data from
> developmental biology.

John Harshman answers:
There are a great many premises hidden in this question. Wells claims that

Let's use the scientific method to test Wells' hypothesis (cover-up) against an alternative hypothesis (limited space). The biggest event in the history of life since the explosion is undoubtedly the end-Permian (or Permo-Triassic) mass extinction, in which up to 90% of all animal species on earth died, but nobody suggests this extinction is a problem for evolution. Let's compare how many textbooks cover the Cambrian explosion vs. how many cover the end-Permian extinction. The prediction of the cover-up theory is that more texts would mention the end-Permian than the Cambrian explosion; the prediction of the limited space theory is that the same number or fewer will mention the end-Permian. Result? Of 18 texts examined (including Wells' ten), 16 mention the Cambrian explosion, while only 10 mention the end-Permian extinction. Of those that mention both events, all but one give more coverage – an average of three times more – to the Cambrian explosion than to the end-Permian extinction. (What does your textbook do?) So both Well's claim that textbooks don't mention the explosion and his implication that there is a coverup are refuted. Of course, Wells doesn't really mean that textbooks fail to discuss the Cambrian explosion. He means they don't consider it to be evidence against evolution, and he thinks they should. His reasons, however, don't hold up under examination.

It's important to note that our knowledge of the Cambrian explosion, and of still earlier life, is fragmentary. Most types of animals are rarely preserved as fossils, so we are limited for much of our information to a few deposits with exceptional preservation, like the famous Chengjiang and Burgess faunas. No deposits like these are known from the crucial period preceding the explosion. And even when we have exceptional fossils, the information we can get from them is limited. Fossils don't come with labels saying "I'm the common ancestor of mollusks and brachiopods", or even "I'm an arthropod". Much information available from study of living animals is missing from even the best fossil. Finally, remember that when we say a phylum "appears" in the Cambrian explosion, we mean that no earlier fossils that we are sure belong to that phylum are known yet. Just a few years ago, there were no known Cambrian vertebrates, but vertebrates have recently been added to the list of groups that originated in the explosion. But maybe that's just because we haven't found the still earlier vertebrate yet, or, worse, have failed to recognize it because the fossil is poorly preserved.

Do all major animal groups appear in the Cambrian explosion? No. By "major group" Wells means a phylum (plural: phyla). The Cambrian explosion, which may be as short as 5 million years in duration, saw the first unambiguous appearance of most of the major groups of marine invertebrates with calcified shells, and thus excellent fossil records, as well as several groups of soft-bodied animals: eight phyla in all, out of a total of nearly thirty. A few phyla appear before the explosion; in fact, depending on the debated interpretation of some fragmentary fossils, the number appearing in the explosion may be from one more to three less than eight. Eight more phyla first appear in the fossil record after the explosion, from the middle Cambrian to the Cenozoic, and nine in fact have no fossil records at all. (The last is almost certainly due to lack of preservation rather than a recent origin, because there are a very few ancient fossils of some such groups. For example, the earliest clearly identifiable nematode roundworm is Cretaceous in age; there are claimed earlier examples as early as the Mississippian, but they are all controversial, and nematode fossils of any age are extremely rare.) And note that Wells is entirely ignoring, for no good reason, all plants, fungi, and protists.

Were these first appearances "fully formed"? It's hard to say what Wells means by that. What would a "partially formed" animal look like? Cambrian animals certainly are not identical with modern ones. They possess some but not all the features that characterize the modern phyla to which they are related. For example, some Cambrian arthropods, such as Anomalocaris and Opabinia, seem to lack jointed legs except for a single pair near the mouth; the rest of the body had lobes, somewhat like the modern Onychophora, which are arthropod relatives but not arthropods. Cambrian relatives of Onychophora are common, but unlike their modern relatives they lived in the ocean and lacked important organs of the modern animals. There are still other Cambrian fossils that do resemble the possible ancestral forms of two or more phyla. Shelled and scaled animals called halkieriids, for example, have characteristics of both mollusks and brachiopods. There were vertebrates in the Cambrian, but they were more primitive than any living vertebrate, resembling most closely modern Amphioxus, a non-vertebrate chordate. There were no bony fish, no sharks, no amphibians, reptiles, or mammals. In fact, there was no life on land at all.

Wells also plays fast and loose with definitions. The Cambrian explosion is not synonymous with the entire Cambrian period. Even though Wells gives a length for the explosion of 5-10 million years, he also considers groups to have originated in the explosion if they appeared at any time during the Cambrian, a period of over 50 million years. He also counts groups that first appeared in the fossil record "shortly before" the Cambrian, and this is sometimes as much as 30 million years before the beginning of the Cambrian (or more than 40 million years before the beginning of the explosion). Thus the Cambrian explosion by his flexible definition can be as short (when he wants to emphasize its abruptness) as 5 million years or as long (when he wants to emphasize its magnitude) as 80 million years, and these different definitions are never distinguished, leaving the impression that everything that happened during the longer, 80-million year period can be condensed into the shorter, 5-million year period. No wonder he talks about an explosion!

It's not a matter of contention whether the Cambrian explosion happened. The question is what it was. Did new body plans appear suddenly (if 10 million years can be called sudden)? Or did they just become visible by becoming large and/or gaining hard skeletons? The fossil record is unclear, but there are clues. The Cambrian explosion (defined by the first appearance of trilobites) was preceded by the Tommotian stage of the Cambrian, whose fauna consists of a variety of small, enigmatic shells. Some may have been small mollusks. The Tommotian was preceded by the Late Precambrian, home of the Ediacaran fauna. Some of these may have been relatives of modern phyla – it's hard to tell because they weren't preserved in sufficient detail. It's certain that at least some fairly advanced animals were around, because burrows and tracks made by unknown but necessarily advanced animals became common in the late Precambrian.

Science works by comparing alternative explanations for data, provisionally accepting the alternative that best fits the data. Wells, however, presents no theory to explain the data. Were animal phyla created out of nothing during the Cambrian explosion? If so, does that mean that all modern species within those phyla are each descended from a single phylum ancestor? If that's not his theory, his question wouldn't make sense even if his premises were true. The earliest known vertebrates appear at the end of the explosion. They were "fully formed", meaning that we can tell they were vertebrates. But none of the modern vertebrate classes, let alone orders, families, genera, or species, are known from the Cambrian. Is Wells suggesting the modern vertebrates are all descended from a primitive vertebrate of the Cambrian? Or does he think they were all created, separately, later? But the latter theory would make the Cambrian explosion problematic from his perspective also. What does Wells think?

Literature Budd, G. E., and S. Jensen. 2000. A critical reappraisal of the fossil record of the bilaterian phyla. Biol. Rev. 75:253-295.

Valentine, J. W., D. Jablonski, and D. H. Erwin. 1999. Fossils, molecules and embryos: New perspectives on the Cambrian explosion. Development 126:851-859.

Jonathan Wells asks:
>> 3. Homology. Why do textbooks define homology as similarity due to
>> common ancestry, then claim that it is evidence or common ancestry – a
>> circular argument masquerading as scientific evidence?

The NCSE answered:
> A: The same anatomical structure (such as a leg or an antenna) in two
> species may be similar because it was inherited from a common ancestor
> (homology) or because of similar adaptive pressure (convergence) .
> Homology of structures across species is not assumed, but tested by
> the repeated comparison of numerous features that do or do not sort
> into successive clusters. Homology is used to test hypotheses of
> degrees of relatedness. Homology is not "evidence" for common
> ancestry: common ancestry is inferred based on many sources of
> information, and reinforced by the patterns of similarity and
> dissimilarity of anatomical structures.

John Harshman answers:
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.

Homologies can be tested to some degree by predicting that the characters will be similar in ways we haven't yet checked. For example, if we propose that similar-looking bones in two animals are homologous, we might predict that they would arise from similar precursors in the embryo, have similar spatial relationships to other bones in the organism, and have their development influenced by similar genes. And this is commonly the case.

But the main way of testing candidate homologies is by congruence with other proposed homologies. By congruence we mean that the two characters can plausibly belong to the same history. If the history of life looks like a tree, with species related by branching from common ancestors, then all true homologies should fit that tree; that is, each homology should arise once and only once on the tree. If a large number of functionally and genetically independent candidate homologies fit the same evolutionary tree, we can infer both that the candidates really are homologies and that the tree reflects a real evolutionary history.

And in fact that's what we commonly find. Mammals, for example, are inferred to descend from a common ancestor because they all have hair, mammary glands, and other more obscure characteristics like seven neckbones ^[1] and three earbones. All these characteristics go together: mammals have all of them and no other animals have any of them. Further, other characters support consistent groupings within mammals, and groupings within those groupings. Within most of life, groups are organized in a very special way called a hierarchy. In a hierarchy, every group is related to every other group in one of two ways: either one group entirely contained within the other, or they share no members at all. No two groups can partially overlap.

What we see if we try to organize species using candidate homologies is that groups organized according to different characters fit together into the same nested hierarchy. Why should characters all go together in this consistent way? Evolutionary biology explains these characters as homologies, all evolved on a single tree of descent.

Wells gives no alternative explanation for such patterns, and indeed they are hard to explain in any other way than as reflections of an evolutionary history. Wells has it all wrong. Homology isn't a circular argument, it's a branching tree of evidence. [snip]

Jonathan Wells asks:
>> 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?

The NCSE answered:
> A: The notion of a "missing link" is an out-of-date misconception
> about how evolution works. Archaeopteryx (and other feathered fossils)
> shows how a branch of reptiles gradually acquired both the unique
> anatomy and flying adaptations found in all modern birds. It is a
> transitional fossil. These fossils are not direct ancestors of modern
> birds but relatives, and, as everyone knows, your uncle can be younger
> than you!

John Harshman answers:
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 nine 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. Consider human relationships. 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 that question is silly. (OK, some creationists do make that argument; but other creationists realize that they shouldn't.) 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.

Are evolutionists covering up the evidence for sudden creation?

Post of the Month: August 2008