Determining similarity statistics between the human and chimp genome

Faith & Science Conversation
41

When you say that others have been commenting on Tomkins second article and then go on to say “all of Tomkins research and articles…” and “his analysis of genetic data is not to be trusted” you have disclosed an almost “blanket” attitude demonstrated by theistic evolutionists towards IDers and creationists.

It is my observation which applies in many different walks of life that when someone or a group have entrenched beliefs that their reaction is to instantly dismiss the views of an opposing person or group and that they find ways to “rationalize” their refusal to objectively give consideration to such opposing views.

I will suggest to you that it’s not, in any area of life when one puts forward a view, a case of “one thing wrong - therefore everything wrong” nor is it a case of “one thing right - therefore everything right.”

Quite clearly in this forum there are persons with a demonstrably, from their comments, an almost knee-jerk reaction to anything that Tomkins has to say and to IDers and creationists generally.

In my opinion that attitude is not conducive to good science.

Let us for arguments sake say that Tomkins research which produced a figure of 70% is flawed (and given the excoriating nature of attacks I am less inclined to accept the objections to his research) and that on that particular matter he got it wrong - does it mean he gets everything thereafter wrong?!

When Darwin suggested that the fossil record would produce evidence of slow step-by-step transitions and which has turned out NOT to be the case do you and others jump on this and say: well in that case he got everything wrong? I think you do not. But it appears that people in this forum do not extend to a fellow Christian the same benefit of the doubt as they do to a man who loat his faith and became an atheist or at best an agnostic.

42

Bald hearsay?

I think given your totally uncompromising attitude and refusal to accept certain evidence leads me to conclude that further discussion will not be meaningful as I have no wish to argue simply for the sake of arguing.

43

Thanks for your comment.

You will not, I think, disagree with me when I say that Ken Miller believes that the bottom to top model is the explanation for the diversity of life in which a self replicating molecule over eons evolved in a step by step process which included fish evolving into man ( or as PZ Myers put it: Sure. Man is just a fish).

In this transitionary model Miller will hold the view that apes evolved into man and so whilst Statham who made the comment you refer to may have been taking some “poetic licence” he was nonetheless reporting accurately the view of Miller. You do see that, do you not?

44

Frank,

The point that we have been making is that any meaningful DNA comparison MUST report that human DNA is 100% identical to itself. If it does not, it is a case of “garbage in, garbage out” and the comparison is meaningless at best.

This is programming 101. It’s a simple matter of supplying test cases with known expected results to check whether your analysis makes sense. As a C++ programmer, you should understand this. Do you, or do you not?

We could assume good faith on the part of Tomkins and AiG if he had published a retraction once this flaw in his work had been made known, as would be standard practice in real science. Or, at the very least, if the offending studies had been taken offline “pending further investigation.” However, the fact that Answers in Genesis continues to publicise these results without addressing the problem is simply not acceptable.

On the subject of contacting him directly, Tomkins’s claims have been made public and submitted for public scrutiny. It is only appropriate, therefore, that any response should also be public.

Could you cite your sources for this claim please—with clickable links, so that we can verify them?

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45

Saying that apes evolved into humans is a far cry from saying that a half-ape/half-human population evolved into humans. That isn’t poetic license. It’s just plain inaccurate. Like your spelling of “license.”

46

Hi Frank,

I went to John Mackay’s web page to see how these similarity measures were computed. Based on what we have already seen in this thread, I think you would agree it is important to double-check. Unfortunately, Mackay provides no citations or links.

Since you’re the person who introduced this line of thinking into the thread, would you be so kind as to provide a link to the original research paper that Mackay is citing?

Thanks!

47

It is my observation that “some” theistic evolutionists have feelings of antipathy for scientists who are creationists to the extent that they very speedily accept the findings of their fellow theistic evolutionists and instantly reject the research of creationists and IDers. Such prejudice is of no benefit to any of the parties involved.

Hi Frank,

James: Did you understand the nature of the criticisms of Tomkins’s papers? They were not “instantly rejected”; they were tested.

Frank: Whoa! Slow down James. You’ve jumped to a wrong conclusion. If you re-read my above comment you will see that I was taking about “SOME” i.e. not all theistic evolutionists.

People in this forum have been most explicit in where they are coming from – and I’m expressing my experiences and observations and making it clear, or at any rate hopefully making it clear, where I’m coming from.

James: As @Swamidass and others have pointed out, he configured the software in such a way that when human DNA is compared to itself, the result is far below 100%. Do you understand why this is a very serious error that no PhD geneticist—and certainly not one with clearly non-trivial computer programming skills—should make?

Will: Yes. And I think I caused some confusion here when I mentioned the figure of 85% similarity. I was talking about that figure as the similarity between chimps – humans and omitted to say there would be a DIFFERENCE of 15%.

So, that’s my fault and I apologise for the confusion.

This is off the top of my head now and I do believe I’ve read an article in which errors in a software programme produced – as you say in connection with the human genome only an 85% compatibility with itself which is of course absurd.

As I said previously and honestly I’m limited to C++ programming and don’t have your level of software knowledge. I may be wrong but it seems to me that any software involved in such projects could be “problematic” and that the findings may possibly be not altogether reliable in the same manner as 2 multiplied by 2 equals 4.

But as I’ve said elsewhere in this forum even IF the difference between chimp and human is only 5% that equates to a massive some 150 Million differences.

Now if you and others want to see that as evidence for a common ancestor that is a matter of your faith – personally I see no evidence for common ancestry and do see evidence for a common designer.

James: The fact of the matter is that YEC science is riddled with schoolboy errors such as this one. Errors that are purely technical and procedural in nature. Errors that should never have passed peer review, and that should have been retracted when pointed out. Yet Tomkins’s articles are still being promoted on the Answers in Genesis website. In fact I could give examples where objections to even more serious errors are rejected as “nitpicking” or “petty” and even denounced as “compromise” or “atheism.”

Frank: Yes, I keep hearing about objections to Creation and ID but I’ve yet to see those objections backed up by any real hard facts and evidence.

Even in the instance above if Tomkins findings of 70% are erroneous his error does not give evidence for evolutionary naturalism and dismissing 150 million differences without a sound explanation is, it has to be said, a position of faith in the bottom to top model.

Furthermore, if you are so adamant about your beliefs and do think that Tomkins is guilty of what would, if you are correct, amount to malpractice and given the seriousness of this issue – it’s a bit more important than the contents of a beefburger – I thought you, who are strongly expressing your opinions to me, would take this matter up with Tomkins himself.

That you do not do so is not impressive.

James: Given this complete absence of any kind of meaningful quality control, and a completely unjustifiable hostility towards correction, is it any wonder that many Christian evolutionary scientists are upset about YEC “science”?

Prejudice has absolutely nothing whatsoever to do with it.

Frank: Well, you’ve gone and said it again James to emphasize how strongly you feel – “hostile” – and yet you won’t challenge Tomkins head to head.

The nature of some of the comments in this forum – and from people who would describe themselves as Christians is somewhat worrying – do indeed demonstrate a certain level of prejudice.

All in all this very short visit to this forum has been most informative and further enlightening into the mind of theistic evolutionists.
f

48

That is so blatantly and obviously true that I don’t know what to say!

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49

Your continued attacks on my tone and character are off-topic, inappropriate and, dare I say it, discourteous and aggressive. Could we please confine ourselves to a discussion of the science?

Now, I note that you haven’t answered my question about Tomkins’ work. Do you understand why using an ungapped alignment is an incorrect way of assessing how similar two genomes are? Do you agree or not? There’s not a lot of point to moving on to other topics if we can’t settle this one.

Entering into a discussion on one topic does not imply willingness or ability to discuss all other possible related topics. I offered to discuss any topic of your choosing. Why not choose one and and start discussing it, instead of starting a discussion about not discussing the topics we’re not discussing?

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50

I think that if you visit the link I gave to his article gice certain references at the footer.

51

I was referring to all of his research/articles that had been cited in this thread on this forum. I did not intend to refer to everything he has ever written. Thank you for giving me the opportunity to clarify.

Tomkins wrote exactly 2 articles on human-chimp DNA similarity. Those are the only two I am speaking of. And those are the only two you have cited, as far as I can tell.

Anything he writes in the future, or anything else he wrote on different subjects in the past, will of course be analyzed on its own merits. I’m sure you will understand, however, that based on the way he has conducted himself already, I am not going to just accept whatever he says about DNA similarity without first examining it closely.

Best,

52

Blast is written in C++. The scripts Tomkins used to slice genomes and parse results would have been written in Perl, or at least that’s what I would do. In any case, no one is suggesting that we look at the source code for Blast, which is a very large program.

53

Go back and check it and you will see that I am right.

The ICR article has references but nothing of relevance to the similarity measure between chimpanzee GLO pseudogene and human GLO pseudogene.

The Mackay article makes bold claims about the similarity measure, but does not provide any documentation whatsoever.

Thanks,

54

Sorry about my typo - I have arthritis in my fingers and am blind in one eye with a cataract. I will try to do better in future.

I fail to see why you find this form of “poetic license” (oh by the way it is the correct English spelling of the word and as the English gave this langauge to the world I’m happy to use the spelling of my homeland) with this problematic because in the Darwinian model of life there would be step by step transitions - unless that is you are of the belief that apes chimps humans are not transitionally linked and are distinct separate kinds of creatures produced by an Intelligence?

Perhaps you will tell me please where in your view of life God is involved?

Thank you.

55

Why do you have to be so harsh on “mere myth?” After all, literal history is a mere string of facts. The instant you want to attach story or a message to your facts, you’ve begun to mythologize it. I would never expect pure literal history to teach me anything about what it means to be human or how we should live our lives. You NEED myth to operate on a grander scale for that. And yes, it invariably involves distorting mere history, because you have to pick and choose what to put in and what to leave out, and that means you are biasing your data for the sake of the story you want to tell, because the story is the important thing!

As a convenient example of this process, you are cherry-picking a few beliefs about Adam and hanging the validity of the entire Old and New Testaments on them. I believe if you look, you’ll find that there’s more to the story than that.

56

You need to be careful with the word “myth.” It’s like the word “hacker”—It has a technical meaning that is completely at odds with its popular meaning.

YECs adopt a very polarised approach to the Genesis account. They only recognise two options: a strict, blow-by-blow historical-scientific interpretation, or complete fiction that serves no purpose whatsoever. Furthermore, they teach that the integrity of the entire Bible stands or falls on our ability to accept the former, and they denounce anything in between as “compromise.”

57

Only if you fix the typo in the first sentence.

58

Frank, you need to realise something about us science/tech types. We tend to be absolutely scathing about anything where we see demonstrable falsehood, woolly thinking, or resistance to correction.

This is simply because we are all too aware that when science and technology are involved, getting things wrong can put people’s lives at risk.

When, as Christians, we see the YEC organisations not only promoting extreme sloppiness in science, but also insisting that the authority of the entire Bible depends on it and denouncing anyone who questions it as “compromisers” and “faithless so-called Christians” … I think you can see why we’re scathing. That kind of attitude brings the entire Gospel of Jesus Christ into disrepute.

What do you mean? The misconfigurations of BLAST, nucmer and LASTZ in a way that reports that human DNA is only 85% similar to itself, and the failure to correct or withdraw the resulting claims are evidence.

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59

That link no longer works but the article, which is by Tomkins, is still there.

Only if you use the same incorrect measure of identity that we’ve already discussed at length.

See above. (It’s also not clear why this is relevant.)

This, on the other hand, is a completely different analysis. Unfortunately, it too is incorrectly done. He constructs his trees based on simple genetic identity, rather than on any of the standard approaches that look for shared features. He also counts every base in an insertion or a deletion as additional difference. Thus, if orangutan differed from human by 20 single-base mutations, while chimpanzee differed from human by the deletion of a single 100 base-pair chunk, he would calculate the chimpanzee sequence to be five times as diverged from human as the orang sequence, even though it has experienced only 5% as many mutations.

There are lots of subtleties to phylogenetic analysis, and better and worse ways of doing it. Tomkins’ method isn’t one of them – it’s just wrong.

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60

In case it’s of interest, I BLASTed the entire GULO pseudogene in humans against chimpanzees and gorillas this morning. (Anyone can do it – just go here(*) and click on "BLAST this sequence(**).) In shared sequence, gorilla/human identity is 97.1% and chimpanzee/human identity is 97.9%, a bit less than the genome average. The chimpanzee sequence is missing one chunk of about 800 base-pairs in the middle.

(*) What, you don’t have the human GULO sequence bookmarked in your browser? For shame.
(**) Note: BLASTN will take a couple of hours. BLAT will be much faster, but give more fragmented results.

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