Science is a human endeavor with all the messiness that such endeavors entail. From ego battles to funding concerns, there is much that doesn’t look very much like science. But somewhere in between there is, at least sometimes, a search for truth. Hypotheses and models may be rough and approximate, but most scientists think of their work as driven by how the world really works.
Law is a very different endeavor. One of the basic tenets law students learn is to apply the law. That is not always as obvious as it may seem. Both the law and the evidence may be complicated, and the application may violate your knowledge or even common sense. So be it, that is how our legal system works.
In fact judge Jones did not research evolution or Intelligent Design for the Kitzmiller case. The law is applied to the evidence, and the evidence is provided in the court case itself. Jones understood the law and its application, but the evidence would be given to him. As Jones recalls:
The very first witness for the plaintiffs was Ken Miller. He is very invested in this issue. He writes a textbook that is used substantially in high school biology classes throughout the country. And I think it's fair to say that the plaintiffs knew what they had in terms of their judge. They knew that I was not a scientist, but hopefully that I had a reasonably good head on my shoulders, that they were going to need to take me to school. So their first witness did just that.
Yes Miller did take Jones to school. Jones was heavily influenced by Miller’s testimony which contained several compelling evidences for the fact of evolution. Unfortunately those evidences were not true.
Before the trial Miller and the ACLU lawyers had carefully designed Miller’s testimony to persuade the Dover court lay audience that Darwin’s idea was scientific and absolutely undeniable—a no-brainer.
But to do so they would need to twist the truth. Ever so slightly they manipulated the scientific evidence. And in science, subtle adjustments can make all the difference. Here are some of the lies that Miller fed to Jones.
Lie #1 A pseudogene has no function and is broken
Miller’s first powerful evidence for evolution came from pseudogenes, DNA sequences that are similar to genes but have important differences. Miller’s example was the beta globin pseudogene which he described as non-functional and broken:
2 If you could advance the slide, please.
3 I've zeroed in on the six copies of the beta-globin
4 gene sequence. Each of these copies is a set of
5 instructions for how you build this polypeptide. Five
6 of them work, but one of them doesn't. It's given the
7 Greek letters psi, beta, and then the number one. And
8 the psi-beta-1 sequence isn't a gene. It doesn't
9 work. It's a pseudogene, and a pseudogene is
10 recognized as a gene because it's so similar to the
11 other five in its DNA sequence, but it has some
12 mistakes. It's broken, and it has a series of
13 molecular errors that render the gene non-functional. 
The lie here is not in the word “broken” but in the word “is.” It is reasonable to think that the beta globin pseudogene is broken, but we don’t know this for certain. I suspect it is, but we can’t say with certainty that it is broken. In fact we still have much to learn about the biomolecular world.
Whether the pseudogene is simply broken or has some subtle, perhaps rarely used, function is difficult to say. My guess is the former, but to be sure the history of evolutionary thought is full of such claims gone wrong. From the appendix to the thyroid gland, evolutionists have been quick to claim non function for structures that years later are found to do various jobs. And this holds even for some pseudogenes.
And while a consistent function has not been found for pseudogenes in general, it is difficult to be sure that the beta globin pseudogene, for example, is non-functional and broken, as Miller unequivocally informed the court. The distinction may seem to be minor, but it was crucial to Miller’s case.
Lie #2 Pseudogene DNA sequences have “errors” or “mistakes”
While informing the court that the beta globin pseudogene is broken, Miller also explained that its DNA sequence has “errors” or “mistakes.”
14 Now, I'd like to show you exactly what those
15 molecular errors are in the next slide. This is a
16 blow-up of the pseudogene. These are the portions
17 that actually do the coding, if it was coded in red
18 here. And you'll notice that there are six distinct
19 mistakes in this gene.
20 Now, I don't know if I really want to try
21 the patience of the Court in terms of going into the
22 details of molecular biology, but in a very simple
23 way, the altered initiator means that the signal that
24 exists at the front of the gene that says "copy me" is
25 missing. And therefore RNA preliminaries, the
1 molecule that copies genes, can't bind, and it never
2 gets expressed.
3 But even if it did get expressed, it has
4 five other errors that would keep this, the RNA copy
5 of this gene, from being translated. It's missing the
6 start signal. It's got stop codons that would cause
7 the synthetic apparatus to grind to a halt. It's just
8 a mess. [79-80]
Just as we are not certain that the pseudogene has no function and is broken, likewise we are not certain that its DNA sequence contains “errors” or “mistakes,” caused by mutations. That certainly could be the case, but it may not be.
As we will see shortly, Miller will use this claim as circumstantial evidence for evolution. What Miller did not inform the court of is that globin genes (from which the pseudogene is supposed to derive) have about 140 amino acid residues, and since there are 20 different amino acids this means there are 20^140 sequences for evolution to choose from in creating a globin gene. This number, 20^140, is astronomically huge. It is equivalent to a 1 with more than 180 zeros after it.
And of all those different sequences, only a tiny fraction result in a functioning globin protein, meaning that it is highly unlikely evolution could have luckily hit upon the globin design in the first place. This is to say nothing of how the molecular machinery to construct the protein, and make use of it once constructed, could have already been in place.
Furthermore, there are a great many proteins that are far bigger, and so even less likely to have evolved, than the globin protein. Evolutionists have little more than just-so stories to explain how such genes arose, but judge Jones’ new biology degree did not include such conundrums.
Lie #3 There is no reason for broken genes aside from common descent
Miller next move was to evolution’s venerable “shared-error” argument that has swayed so many. If these DNA errors or mistakes are found to be repeated in different species, then those species must have evolved via a common ancestor.
9 Now, the reason that this is important in
10 evolution is actually very simple, and that is, these
11 errors appear in a gene, they have no functional
12 purpose. And you might ask yourself, what would I do,
13 what would you do if we were to find another organism
14 that didn't just have similar genes but also had a
15 pseudogene in the same spot and had the same set of
17 There's no reason why evolution would
18 produce a duplicate set of mistakes in two copies of
19 things. It must mean that these two organisms are
20 descended with modification from another organism that
21 had the same set of mistakes.
22 And if you go on to the next slide, what I'd
23 like to show you are three organisms, the gorilla, the
24 chimpanzee, and the human being that share the exact
25 same set of molecular mistakes.
1 Now, why is this significant? One of the
2 core principles of evolution is common descent. One
3 could always argue that because the three species that
4 I've depicted on this slide are all African species,
5 that's where they all come from, they're all primates
6 and they all probably started out living in similar
7 environments, that the functional parts of this gene
8 locus, they might work the same. But you cannot argue
9 that the mistakes should match.
10 And the fact that all three of these species
11 have matching mistakes leads us to just one
12 conclusion, and that's the same conclusion that
13 Charles Darwin predicted almost a century and a half
14 ago, and that is that these three species share a
15 common ancestor. Matching mistakes are evidence of
16 common ancestry. [80-81]
But as any expert witness would know, this is not true. Assuming that the beta globin pseudogene is indeed broken, and that the DNA sequence “errors” are indeed errors, there is no reason to conclude they must have arisen via a common ancestor. Even evolutionists agree with this obvious fact.
Shared errors can arise from the independent occurrence of like mutations. Indeed, from viruses and bacteria to primates, like mutations that must have occurred independently (even if evolution is true) have been repeatedly observed. Similarly, mutational “hotspots” are common and, of relevance here, have been observed in pseudogenes.
In fact, comparison of pseudogenes in different species have forced evolutionists to conclude that like mutations must occur independently. Urate oxidase pseudogenes are just one such example, and it simply is false that such similarities can only be explained by common descent.
Lie #4 This is objective science
Even if there were no examples of independent, shared mutations such as in the urate oxidase pseudogenes, Miller’s argument is not objective science as he presents it to be. Miller gave testimony about how science works, but here uses the shared-error argument which is a metaphysical argument that goes back centuries.
Miller informed the court that these shared errors “must mean that these two organisms are descended with modification from another organism” and “the fact that all three of these species have matching mistakes leads us to just one conclusion, … that is that these three species share a common ancestor.”
But how does Miller know that common descent is the only possible explanation? As I have discussed before, this is one of the many entry points of evolutionary metaphysics into science. Evolutionists consistently make this claim that only their theory can explain what we find in biology, and such a claim requires knowledge unavailable to science.
The short explanation is that this shared-error argument is a form of an IF-AND-ONLY-IF statement, which is non scientific. The long explanation is that the non scientific element arises from Enlightenment theology, supplied by Lutherans and Roman Catholics on the continent and Anglicans in England in the 17th and 18th centuries. It entered into science mainly via evolutionary thought. Darwin repeatedly used the argument and it is now rampant in the evolutionary apologetics literature. As Stephen Jay Gould explained:
Odd arrangements and funny solutions are the proof of evolution--paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.
Elliot Sober, a philosopher who analyzes evolutionary arguments in great detail has explained how the argument works in terms of likelihood ratios. Sober refers to the argument as Darwin's Principle. As he explains,
Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.
Miller’s “broken” pseudogenes with their DNA “errors” were the perfect example of such useless similarities. And why are useless or deleterious similarities so helpful? It is not because they raise the probability of common ancestry, but rather because they lower the probability of separate ancestry. In other words, the reason common descent is a no-brainer is that the alternative, separate creation or design, is extremely unlikely.
From before Darwin to Miller this argument has been a crucial weapon in evolution’s apologetic arsenal. Miller began using this non scientific argument against Intelligent Design when the new movement first began. He was well practiced by the time the Kitzmiller opportunity arose, and the small-town Lutheran lawyer from Pennsylvania coal country didn’t stand a chance. Did judge Jones “get it right” as he so confidently asserts? Yes, he correctly applied the law, but he applied it to a set of lies.