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My private revenge on the creationists

Who is wise? He who learns from everyone. So said Rabbi Simeon ben Zoma, some 1800 years ago. My private revenge on the creationists is to learn from them what they cannot or will not learn for themselves.

A friend of mine regularly forwards me stuff from a Discovery Institute publication calling itself Evolution News and Views (ENV), although it seems to be devoted to the systematic denigration of each new piece of evidence that enhances our understanding of evolution. Indeed the pretence that the Intelligent Design (ID) movement is anything more than elaborate cover for old-fashioned Separate Creationism is one that grows flimsier with every new issue.

I used to delete these unread, but lately a couple of headlines have caught my eye, and convinced me to start following ben Zoma’s advice. The first of these was back in July, when ENV went, as I wrote, “barking mad” about the fact that Australopithecus sediba seems to have eaten tree bark. This, they claimed, showed that it could not be one of our ancestors, but is an example of a separate Intelligent Design, and should be “relegated to the side of the ledger that’s filled with ape-like non-ancestors.” Leaving aside the question of whether Au. sediba’s high-fibre diet really does help us decide whether we should consider it a grandparent or great-aunt, notice how the very evidence that ENV refers to in support of ID is actually part of one of the most powerful arguments against it. Sediba joins the 20 or so different species intermediate between non-human apes and humans, and its description shows it to have many human-like features. I have no difficulty in acknowledging that ENV is perfectly entitled to consider this creature to be more like a chimp than a human, just as, I expect, they would regard Homo ergaster as more human than chimp, but the implication is the very opposite of what ENV is suggesting. If self-styled Homo sapiens is the product of a separate act of design, then Au. sediba is the product of another. Twenty or so separate designs in the Pliocene, all but one of them now extinct; this doesn’t seem very intelligent.

Now they’ve done it again, taking a paper reporting results that only makes sense in the light of evolution, and, more specifically, of common descent, and managing by a piece of blinkered quote-mining to draw the exact contrary conclusion. The paper in question  (PLoS ONE 7(7): e40861. doi:10.1371/journal.pone.0040861) critically examines the use of what are called microsatellites in the working out of family relationships between species. Microsatellites are very short pieces of DNA, replicated several times over in the DNA of eukaryotes (that means organisms where the cell possesses a separate nucleus, i.e. all organisms more complex than bacteria). They are more vulnerable to change than the rest of the DNA, and as a result are very useful in following recent changes. To quote the first paragraph of the paper,

 As widely used molecular markers, microsatellites have their strength in their high variability [1]. The relative power of the microsatellites over Single Nucleotide Polymorphisms (SNPs) due to the high variability of microsatellites is 4–12 fold for population genetic structure [2][3], 5–12 fold for association or linkage disequilibrium studies [4] and 10 fold for sibling reconstruction [5].

(SNPs are “single nucleotide polymorphisms”, i.e. the replacement of one of the four “letters”, A, G, C, T, by another.) So we know that microsatellites change faster over time. We also know that it is difficult to sort out family relationships over very long times using conventional DNA techniques, for complex statistical reasons that are well understood.

It therefore makes sense to look very critically at attempts to use microsatellites to sort out relationships between species well separated in time. And here is what they found, quoting from the abstract to the paper:

 It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

(A clade is just any group that includes all the descendants of a particular ancestor. Thus birds are a clade, but dinosaurs are not unless we are willing to call birds dinosaurs. Fish are not a clade, since the split between fish and land vertebrates is more recent than the split between bony fish and sharks, and apes are only a clade if, as I think we should, we include humans among the apes.) Now let’s see what ENV makes of this paper. They quote the abstract, adding their own emphasis, thus:

 It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

And what do they infer?

 There are two ways to interpret this anomaly. One is that microsatellites mutate too fast to maintain the phylogenetic signal. (This is known as a “post hoc rationalization.”) The other is that Darwin was wrong. Data do not show a phylogenetic pattern; they show common design with some variation.

What they infer is the exact opposite of what the paper shows. Firstly, there is no issue of “post-hoc rationalisation”, because the rapid rate of change of microsatellite DNA was already known (I left in the references in my quotation from the paper, just to make this clear). Secondly, and most importantly for our argument, ENV’s own selection from the abstract provides powerful support, if such were needed, for the well established phylogeny. Let’s take their quotation again, and just make a slight change in where we place the emphasis:

 It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

So the data confirm the existence of clades, and match up with the ideas we had formed earlier about how they are related. The “clades more recent than 200 Mya” include flowering plants, birds, mammals, amphibians, bony fishes, and squamata (roughly speaking, lizards and snakes), and microsatellite coverage (the ratio of the number of microsatellites to total amount of DNA) is well correlated within each of these clades, but not between them. Crudely, microsatellite coverage shows that men are more closely related to monkeys than to molluscs, but cannot distinguish the difference between men and molluscs from the difference between men (or molluscs) and mushrooms, because that difference is beyond the range of the technique.

ENV, of course, has its own suggested explanation for this fact:

Design researchers, by contrast, might be surprised at the variations, but not worried. They had no need to predict a phylogenetic pattern. ID advocates could accept quite a bit of variation by epigenetic coding algorithms that respond to environmental cues.

We can now set up a direct competition between the evolutionary and the Intelligent Design explanations, using data in the body of the paper (which I rather suspect that the ENV team haven’t actually read). We do this by comparing a recent clade that provides and inhabits highly variable environments, with an ancient clade that shows much less variation. For example, mammals and gastropods (slugs and snails). If microsatellite cover reflects recent ancestry, mammals should be similar to each other while gastropods (which have been around far longer) should not. If microsatellite cover reflects “environmental cues”, whether the reference is to the internal or external environment of the organism, then mammals should be diverse while gastropods are similar. And the answer is clear. Using the microsatellite cover test, mammals show up as similar, while gastropods don’t.

So yet again, we have an important and interesting paper that strongly confirms, and adds further detail to, the established scientific account, being presented by the self-styled “Intelligent Design community” as evidence against the very things that it establishes.

This post is also available on the BCSE website.

Discovery Institute barking mad over Australopithecus sediba’s diet

This post originally appeared on The 21st Floor

I don’t normally bother with the Creationist newssheet, Evolution News and Views, but the recent article there by David Klinghoffergoes beyond what I am willing to suffer in silence. Klinghoffer himself, of course, is a senior fellow of the Discovery Institute, and the author of How Would God Vote? Why the Bible Commands You to Be a Conservative. I do not know his academic credentials – I seem to remember that he is a lawyer, but neither his biography on the Discovery Institute website, nor his Wikipedia entry (which follows that biography rather closely), give any details, and I hope that some readers can tell us more about this.

I also think it worth noting that Klinghoffer’s article has nothing to do with Intelligent Design, misguided though that may be. Like so much Discovery Institute material, it is an attack on the well-established facts of common ancestry. In other words, what is being advocated is, in the strictest and narrowest sense of the word, creationism. And not even creationism as a philosophical or religious position, but as an interpretation of the facts of biology, in a manner that has been intellectually unsustainable since around 1830.

Anyway, to business: in my own recent posting here I describe why, when announcing their finding in 2010, the discoverers of Au. sediba chose, on reflection, to include it in the genus Australopithecus rather than in the genus Homo. That 2010 account does, however, give a long list of ways in which Au. sediba is closer than Australopithecus to modern humans, and the title I chose for my piece (An Almost Human Tragedy) reflects this. I also described the most recent, rather surprising, finding; that the diet of Au. sediba ignored available grasses, in favour of woodland products such as tree bark.

Now here is what Klinghoffer has to say about this same finding:

Another Human “Ancestor” Bites the Dust Bark

…Sure enough, the cooling trend [concerning the importance of Au. sediba] is now plainly in evidence, with Nature reporting that the creatures had a very notable characteristic in common with chimps, not humans, that had not previously been recognized: their diet, highlighted by tree bark and wood. This was found thanks to an analysis of tooth enamel and dental tartar and microwear. The NY Times lets its readers down softly:

“Dr. Berger was an author of the new journal report. Few other paleoanthropologists agree with Dr. Berger’s contention that the new species is the most plausible known ancestor of archaic and modern humans. [Emphasis added by Klinghoffer]. Dr. [Amanda G.] Henry’s group said that studies of additional fossils from the Malapa caves “will provide a better understanding of the dietary ecology of Au. sediba.””

Actually, the New York Times account amplifies an earlier one, which said

The discoverer of the fossils, Lee Berger of theUniversityofWitwatersrandinJohannesburg, says the new species, known as Australopithecus sediba, is the most plausible known ancestor of archaic and modern humans. Several other paleoanthropologists, while disagreeing with that interpretation, say the fossils are of great importance anyway, because they elucidate the mix-and-match process by which human evolution was shaped.

And the original paper in Science actually said, in the Abstract,

Combined craniodental and postcranial evidence demonstrates that this new species shares more derived features with early Homo than any other australopith species and thus might help reveal the ancestor of that genus

…and, in the body of the paper (p 203, column 3),

We can conclude that combined craniodental and postcranial evidence demonstrates that this new species shares more derived features with early Homo than does any other known australopith species, and thus represents a candidate ancestor for the genus, or a sister group to a close ancestor that persisted for some time after the first appearance of Homo [my added emphasis].

The situation is exactly as I described it, with no great claim to originality, in my earlier account here:

The problem is no longer one of finding a missing link, but one of tracing an individual branch (the one that led to us) through a densely forking bush. It is always notoriously difficult to distinguish closely related species, because of individual differences. Even when we can, we have no way of being sure which extinct species lie on our direct ancestral line; it is difficult to tell the difference between our great-grandfather and our great-great-uncle, or between one great-great-uncle and another.

In short, then, on the basis of newspaper accounts and apparently without having read the original literature, Klinghoffer gleefully demotes Au. sediba from a position that most workers in the field had never even claimed for it, in the belief that the evolutionary account is thereby in some way undermined. Actually, the boot is on the other foot; the loser is the religious doctrine of separate creation. For if the 20 or so known distinct australopithecine and other early hominin species are not related by common descent, and were therefore doomed to extinction without progeny, why were they ever created in the first place?

A (near) human tragedy, and a visit to the dentist; a new hominin find, and what it signifies

Some time a little less than 2 million years ago, an adult female of the family of apelike creatures to which humans are related by descent was walking through the woodland of southern Africa with her younger companion (child? brother?) when the soft soil gave way beneath their feet. They were plunged down a sinkhole almost 100 feet deep into an underground cavern, and killed (let us hope) instantly. Fragments of their skeletons were first discovered in 2008 and described in the scientific literature in 2010. Burial in the cavern had protected their bodies from predators, and the continuing infall of rubbish into the sinkhole meant that some fragments were unusually well-preserved. It was even possible to examine the teeth in enough detail to study these animals’ (people’s?) diet. Being distinct from but clearly related to Australopithecus Africanus, their species has been given the name Australopithecus sediba. This follows the admirable new fashion of incorporating words from local languages into the names of fossil species; sediba is a seSotho word meaning “fountain”.

Malapa Cave, scene of these events, is one of a group of caves in South Africa that now form the South African Cradle of Humankind World Heritage Site. The surrounding rock is dolomite, laid down in the late Archaean (a little over 2.5 billion years ago), and fractured much more recently by tectonic forces. Water flowing through these fractures has hollowed out a series of caves, while surface run-off seeping from above has given rise to sinkholes, such as the one involved in this tragedy. Animals including carnivores are often drawn to such sinkholes, attracted by the smell of water or of decaying flesh, with deadly results. Debris falling into the sinkhole forms a cone, burying their remains. Water running through the cave deposits layers of flowstone, calcium carbonate containing traces of uranium, and uranium-lead dating of these layers enable us to bracket the age of the sediments lying in between them. Additional dating information comes from palaeomagnetism (the Earth’s magnetic field changed direction several times during the period of interest, affecting the magnetisation of sediments). Further confirmation comes from other associated fossil remains; the cave also contains bones of horses, which did not arrive in this part of the world until 2.6 million years ago, and of the sabretoothed cat Megantereon, which became extinct roughly one million years later.

Au. sediba is distinct from Au. Africanus in many ways, so much so that the discoverers think it worthwhile to discuss whether it should actually be included in the genus Homo. On the whole, they think not, because the cranial capacity of around 420 cm3 is in the range associated with australopithecines, or even chimpanzees, rather than the more than 600 cm3 for all species classified as Homo. Moreover, Au. sediba has long arms, and ape-like shoulder bones, suggesting that it was partly arboreal. Nonetheless, the shape of the skull, the relatively small size of the back teeth, and the shape of the pelvis and hip region are decidedly more human than those found in Au Africanus.

The biggest surprise about Au. sediba is its diet. Thanks to the beautifully preserved back teeth of the juvenile, we can learn about this in three distinct ways. Firstly, and most obviously, there is the roughness and degree of wear and tear on the tooth surfaces. Secondly, there is the isotopic composition of carbon in the teeth. This requires a little explanation. We are talking about the stable isotopes of carbon, the exact amount of carbon-13 compared with carbon-12; the radioactive carbon-14 that must have originally been present has long since decayed to completely undetectable levels. One of the near-truths that I used to tell my classes when I was a chemistry teacher, was that different isotopes of the same element have identical chemical properties. This is not exactly so. As a result of what is called zero point vibrational energy, which is itself a consequence of quantum mechanical uncertainty, there is a small but definite tendency for the heavier isotope to concentrate in environments where the carbon atom is more tightly bound, and to react more slowly because reaction almost always involves loosening of bonds. For this reason, plants contain measurably lower concentrations of carbon-13 than the carbon dioxide they use in photosynthesis.

Not all plants are created equal. They can be divided into C3 and C4 types, depending on the pathway by which they fix carbon dioxide. The older C3 pathway involves conversion of carbon dioxide and the five-carbon sugar ribulose into two molecules of the three-carbon molecule glyceric acid (I have missed out some phosphate groups for simplicity). The C4 pathway involves an additional step, and, as the name implies, gives rise to 4-carbon products. C4 material is less depleted in carbon-13 than that formed by the C3 pathway. The C4 pathway is more advantageous than the much older C3 pathway under conditions of drought, or relatively low carbon dioxide abundance, and seems to have arisen independently 40 different times in the past 30 million years or so.

Finally, we can examine the actual dental tartar of these specimens. This contains phytoliths (Greek; phyton, plant; lithos, stone), fragments of non-crystalline silica formed within plants from silica dissolved in groundwater, and different plants give rise to differently shaped phytoliths.

The results were surprising. We know that C4 grasses abounded in the neighbourhood, from the presence of grazers such as the horse, and Megalotragus, a bovid related to the hartebeest, whose skeletons unsurprisingly give the carbon-13 abundances characteristic of animals living on such grasses. However, Au. sediba showed the highest degree of depletion of carbon-13 in any fossil related to humans, indicating something close to a pure C3 diet. The worn surfaces of the teeth (and remember that these teeth were small, compared with Au. Africanus) showed that their owner had been chewing on hard materials. Finally, the phytoliths recovered show that the diet included fruit, bark, and sedges. The importance of fruit and bark is consistent with tree climbing ability, but so far we have no idea why Au. sediba, or at least these two particular individuals, avoided the abundant C4 grasses.

Darwin, famously, lamented the inadequacy of the fossil record in his time, in words that continue to be quoted by Creationists, as if nothing had been discovered in the meantime.

Alfred Russel Wallace,Darwin’s friend and co-discoverer of the principle of Natural Selection, believed human intelligence to be the product of special intervention or purpose. When he wrote, there was a clear gap between humans and apes, the “missing link” of popular imagination.

It was in 1925, Raymond Dart, professor at the University of the Witwatersrand, described the skull of what would become known as the “Taung child“, found in what is now Botswana, the first virtually complete cranium of animal clearly intermediate between apes and humans, which he called Australopithecus Africanus

 Since that time, excavations worldwide, but especially in South Africa and in the Horn of Africa, have vastly extended the range of known pre-human species. The problem is no longer one of finding a missing link, but one of tracing an individual branch (the one that led to us) through a densely forking bush. It is always notoriously difficult to distinguish closely related species, because of individual differences. Even when we can, we have no way of being sure which extinct species lie on our direct ancestral line; it is difficult to tell the difference between our great-grandfather and our great-great-uncle, or between one great-great-uncle and another. Nonetheless, the 2007 Yale University Press compendium, The Last Human, lists some 20 different species somewhere on or near the line of descent from non-human ape to human. The fact that neither Australopithecus sediba, nor Denisovans, are among them, is proof of how fast our knowledge is still developing, and, by inference, how much still remains to be discovered.

References: Discovery of Au. sediba and description of cave setting, Science 328, 195 and 205, 2010; diet, Nature doi:10.1038/nature11185, published online 27 June 2012. Discovery of Au. Africanus, Nature 115, 195, 1925.

This post first appeared on 21st Floor, at http://www.thetwentyfirstfloor.com/?p=4272

 

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