Sep 06 2007

Why ID Should Not be Taught in Science Class

I am glad that my post from Tuesday has sparked so much debate and discussion and that many of my readers have so capably dealt with the pseudoscientific claims put before them. John, who is bravely if not adequately holding up his end, has raised many invalid points – too many to deal with. To further the discussion I will pick out one comment in which John clipped an article from prominent ID’er Jonathan Wells from the Discovery Institute. The article is hopelessly flawed in every argument it attempts to make, and all of his points have been thoroughly refuted. I will choose a few to demonstrate the level of intellectual dishonesty vs scientific incompetence with which we are dealing.

Wells writes:

“Similarly, the only scientific way to demonstrate that similarities in living things are due to common ancestry would be to identify the natural mechanism that produced them. According to Darwin’s theory, that mechanism is natural selection.”

This is one of the main thrusts of the article – that all the evidence for evolution rests on proving natural selection as the mechanism. This is a common ploy of deniers – try to boil down a complex set of independent lines of evidence and arguments to a single claim, and then attack that claim. Unfortunately for Wells, this strategy is false and therefore forces him to make unsound arguments.

It is simply not true that “the only scientific way” to prove homology, meaning common descent, is to prove natural selection as the mechanism for evolution. Either Wells does not understand this undergraduate level, basic concept in evolutionary theory or he doesn’t care. Homology refers to morphological features in different species that are similar because they derived from a common ancestor. Features that look similar because they serve a similar function, yet evolved independently, are called analogous. How do scientists tell the difference? Homologous features share details of structures that are not necessary for function. Analogous structures are superficially similar but vary in the tiny details.

So, for example, giraffes and people both have seven cervical vertebrae, despite the huge disparity in the length of their necks. All vertebrate eyes share in common structural details that indicate that the common ancestor of vertebrates had already evolved eyes and all vertebrates derived their eyes from this common ancestor. Therefore vertebrate eyes retain certain similarities despite adaptation to a variety of environments.

Creationists argue that similarities in design can simply reflect their creation by the same designer. But this is an unfalsifiable notion – because the designer could design anything, without limitation. This answer does not lead to any predictions that can be tested.

Evolution, by contrast, makes very specific predictions – that we will encounter a pattern of homologous morphology among species that falls into an evolutionary pattern. So, we will not see structures that share many precise details that are not relevant to function in different species that do not share an ancestor with that structure. In other words – no bird wings on horses. A designer could have plopped bird wings onto a mammal (not just any wings, like a bat’s, but wings similar to avian wings in many details), but not common descent through evolution.

Yet, we never see anything like this. This represents countless opportunities to falsify evolution, yet no such thing as ever been observed. The best that creationists can come up with to counter this fact is the ridiculous notion that the designer simply chose to design life in this pattern – in other words (although they never admit this is what they are saying) the designer designed life to look as if it had evolved.

It is also very telling that Wells completely ignores the most compelling line of evidence for common descent – the genetic evidence. He does this by focusing on Darwin’s writings, ignoring the century and a half of advances since Darwin and perpetuating this creationist myth that modern evolutionary theory is equivalent to “Darwinism.” Rubbish. But more importantly for Wells he skirted a line of evidence that proves beyond any reasonable doubt that all life on earth derives from common descent.

To be fair, some ID’ers do not deny this. They think that life did evolve over time and that all life does share common descent – but that random natural selection could not have produced this. The hand of the designer pushed the process along at every step to a desired and designed outcome.

But back to the genetic evidence.

Genetics has offered biologists the ability to look at homology with much greater objectivity and mathematical rigor. Here is an excellent summary. But let me give my own quick summary of one line of genetic evidence. DNA, the molecule that contains the genetic code of life, is a long string (actually two complementary long strings wound in a double helix) of four base pairs – making a four letter genetic code – (G C U A for RNA, G C T A for DNA). Every “word” in the genetic code is three letters long (a trinucleotide), and most three letter words code for one particular amino acid. So there are 4^3 combinations, or 64 different three letter words in DNA’s code. The proteins out of which organisms are built are made of up 20 different amino acids. So for each amino acid there are 2-4 different three letter combinations that will code for them, with a couple left over that do not code for an amino acid but rather are stop codons – they tell the machinery where to stop stringing along a particular section.

Without getting into more detail than is necessary, this redundancy in the genetic code provides the perfect opportunity to test evolution’s predictions about homology. For example, UUA and UUG both code for the amino acid leucine. Therefore there is no (zero, zip, nada) functional difference between UUA and UUG – they both have the EXACT same result, the placement of a leucine at that particular place in the amino acid sequence of a protein. Therefore if the same gene in two different species have a UUA in the same position instead of a UUG, there can be no possible functional reason for this. The only possibilities are therefore chance or homology (common descent).

Now, of course, one UUA in common is a 50% probability, so chance is a viable hypothesis. But genes are made of thousands of the three letter codes. This enables us to compare the genetic sequence of genes between different species and calculate the probability of the degree of similarity being observed. To use a simple hypothetical example, if a gene coded for a protein 30 amino acids long, and each amino acid had two three letter codes for them, the number of possible gene sequences that would code for that exact protein is 2^30 or 1,073,741,824. For many real genes the number of permutations is far higher – for cytochrome C, for example, there are 10^46 possible gene variations.

If a gene is homologous between two species that means they have a common ancestor from whom each species derived the same gene. This does not mean the gene should be identical, because there is a spontaneous mutation rate. Over evolutionary time homologous genes should drift apart. The further in the past the common gene is (meaning the more distantly related the two species) the greater the number of random mutations that separate the homologous genes.

Therefore evolutionary theory makes very specific predictions about what we should see when we look at genes in different species – we should see a pattern of homology with more closely related species having more similar DNA sequences in their genes. This is exactly what we find – no matter what genes we look at and in which species the evolutionary pattern exquisitely holds up. Chance is ruled out by the astronomical odds of such matches occurring at random.

What prediction does ID make about what we should observe when we look at DNA homology? None. Because ID is not science. ID’ers will not put there nickel down and say that their theory predicts a specific observation. If, however, intelligent design proponents were willing to do the thing they are unwilling to do – make logical assumptions about what a top-down designed system might look like – we can derive some probable predictions. For example, once the designer came up with an intelligent design for cytochrome C why not just use the same template over and over. Therefore we might predict that one possible pattern suggestive of design is that gene sequences would match perfectly (or nearly perfectly to account for very recent mutations) across all species with no pattern of branching relatedness.

Alternatively, just to spice things up, a designer might have given each species its own personal version of cytochrome C – each version unique and again with no pattern of relatedness. Or perhaps the pattern of variation could have had some deeper purpose – to convey some mystical meaning or perhaps just for aesthetics.

Given all the possible patterns that a designer could have designed would we expect that the designer would have chosen the one pattern that is predicted by evolutionary theory? Such a notion is absurd on its face, but even worse, once again renders ID unfalsifiable, for it says that the designer designed the world to look as if it had evolved, therefore there is no observation we can make that would distinguish an evolved world from such a designed world.

Creationists must either ignore the implications of the genetic evidence, lie about it or commit some horrendous error in logic, or they must admit that the world looks evolved to the eye of science. Even if they do not believe metaphysically that the world did in fact evolve naturally, they have to admit it looks like it did, and that is all science can really say.

To complete this line of argument, there is redundancy in the amino acid sequence in proteins just as there is in the base pair sequence of DNA, and there are other features of DNA, like transposons, that vary without selective pressure. Each line of genetic evidence produces the same pattern of evolutionary relationships – of a branching pattern of common descent.

This genetic argument is an ineluctable chain of logic and evidence. No creationist has raised any legitimate counter argument or weakness with this evidence. Like Wells, most just try to avoid it, or they boldly lie about it. But the evidence is there for anyone to see.

On the Evolution News and Views blog – a propaganda blog for ID proponents at the Discovery Institute – Casey Luskin lays out a standard creationist response to the molecular evidence. He writes:

So they predicted that similarities in predicted trees between organismal taxonomy and DNA sequences would be the ultimate “proof” of macroevolution. Has history borne out their hypothesis? Let’s consider what more recent authorities have said since we unlocked the sequences of the genetic code:

“As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology” (Patterson et al., “Congruence between Molecular and Morphological Phylogenies”, Annual Review of Ecology and Systematics, vol 24, pg. 179)

“New genome sequences are mystifying evolutionary biologists .. . on one front the study of evolution-the information pouring out in the genome sequences has so far proved more confusing than enlightening. Indeed, it threatens to overturn what researchers though they already knew about how microbes evolved and gave rise to higher organisms”
(Science V. 280, May 1, 1998 pg. 672)

“Molecular systematics has not yet produced phylogenetic tress of broad phylum relationships more robust than those based on morphology”
(Turbeville, J. M., Schulz, J. R., and R.A. Raff (1994) Deuterostome phylogeny and the sister group of the chordates: Evidence from molecules and morphology. Mol. Biol. Evol. 11:648-655. )

“That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.”
(Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” Journal of Molecular Evolution 44 (Supplement 1, 1997): S117-S120)

“the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.”
(De Jong, W. W. Molecules remodel the mammalian tree. Tree Vol 13, No 7, pg. 270-274 (July 7, 1998))

“When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species’ morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. (“Bones, Molecules or Both” by Trisha Gura in Nature vol 406, 230 – 233 (2000).)

“[O]ur ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years”
“Despite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.”
(Wills, M. A., “The tree of life and the rock of ages: are we getting better at estimating phylogeny” in BioEssays 24:203-207 (2002) reporting on the findings of Benton, M. J., “Finding the tree of life: mapping phylogenetic trees to the fossil record through the 20th century” in Proc. R. Soc. Lond. B. 268:2123-2130 (2001).)

Clearly there are large discrepancies between molecular data and morphological data, and between various molecule-based trees. These discrepancies contradict the expectation that Pauling and Zuckerkandl said would provide “best available single proof of the reality of macro-evolution.”

Luskin pulls two classic creationist (actually denialist) tricks here. He takes quotes out of context to make it seem as if scientists are saying something they are not. He then puts the statements into a false context, by confusing different levels of scientific argumentation. Specifically, he confuses evidence and arguments for common descent with evidence for the details (and I mean details, not the big picture) of the phylogenetic tree.

It is true that the pattern of relatedness scientists infer from morphological and fossil evidence does not match exactly with what we infer from genetic evidence. This is because patterns of relatedness and morphology and the inferences we make from them are very complex. Is an orangutan more closely related to a gorilla or a chimpanzee? It’s not obvious from how they look, and even detailed anatomical analysis my not produce a clear answer.

Luskin is pulling quotes from scientists discussing the finer details of evolutionary relationships – at the limits of our ability to make clear distinctions. He then falsely pretends as if this calls into question the broader brushstrokes of the phylogenetic tree. In other words, while there may be room for debate about the exact relationship among the great apes (I am not saying there is, this is just hypothetical to illustrate the point), it is clear from all lines of evidence that the apes are all more closely related to each other than any of them are to rodents, and that all mammals are more closely related to each other than any of them are to reptiles.

Here is an example of a paper exploring the phylogeny of one kind of insects, and using DNA evidence to clarify ambiguities in the morphological lines of evidence. It’s a bit technical, but it gives you an idea of how these lines of evidence are used (working out the fine details of phylogeny) and you can see how such detailed discussion can be taken out of context by unscrupulous ID proponents.

Since I mentioned apes, here is another one on apes. The authors write:

“Evidence from DNA sequences on the phylogenetic systematics of primates is congruent with the evidence from morphology in grouping Cercopithecoidea (Old World monkeys) and Hominoidea (apes and humans) into Catarrhini,…”

Huh! DNA evidence congruent with morphology. You will notice I also provide a link so that you can easily read the entire paper if you wish to see if I am fairly representing the quote.

Despite the false impression Luskin created by selecting these quotes out of context, the molecular phylogenetic tree and the morphological tree are in broad agreement. When you get down to a fine enough level of detail, however, we have discovered more chaos than was previously thought. This is likely due to the fact, as has been independently discovered over recent years, there is more interbreeding (and therefore exchange of genetic material) between different species after they apparently separated than was previously thought. Even the concept of species is now known to be much more fuzzy at the edges than was previously thought.

And, to be crystal clear, none of this changes the even bigger fact that morphology and molecular genetics occur in a phylogenetic pattern (even if the overlap is imperfect). According to ID they should not fall into any such pattern at all. Luskin completely dodges this critical point.

So let me answer the question in the title of this blog entry. ID should not be taught as science because it is not science. It fails to meet the minimum criteria for science – it does not make testable claims. The proponents of ID do not have any legitimate criticisms of evolution or how it is taught. They try to hide behind calls for openness and fairness, but in reality what is keeping them out of academia and science classrooms is appropriate standards of quality, not protectionism. The arguments put forward by ID proponents are intellectually vacuous – except perhaps as object lessons in pseudoscience and logical fallacies.

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