Determining similarity statistics between the human and chimp genome

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,

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.

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.

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.”

Only if you fix the typo in the first sentence.

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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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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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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Exactly what I was trying to call out! Frankly they’ve got it backwards: I don’t know how they think there could be any wisdom or deeper meaning to be found if they’re limiting themselves to a strict historical-scientific interpretation. Myths are where you find all the important stuff.

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Frank

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.

James: 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.

Frank: Okay, I see. You justify your excoriating attacks which you admit to as hostile, absolutely scathing and falsehoods i.e. deceit, deception and dishonesty on Tomkins, a fellow Christian and scientist a Ph.D geneticist, on the grounds of “irregularities” (my description not yours) in computer programming using BlastN and other software packages, right?

This is the core of your argument (and that of other critics of Tomkins) right? Have I understood you correctly?

I think I have understood you and others in this “tolerant” “respectful of others” forum very clearly in that you, a software developer – you haven’t mentioned if you have any qualifications in genetics or microbiology or biochemistry etc – have accepted the findings of Glenn Williamson as written in stone.

Here is an extract from:

www.uncommondescent.com › Intelligent Design
Human and chimp DNA: They really are about 98% similar
October 22, 2015 Posted by vjtorley under Intelligent Design
260 Comments

“A few days ago, scientist and young-earth creationist Dr. Jay Wile wrote a post on his Proslogion blog, in which he reported that Dr. Jeff Tomkins had abandoned his claim that human and chimpanzee DNA are only about 70% similar, in favor of a revised figure of 88%. But even that figure is too low, according to the man who spotted the original flaw in Dr. Tomkins’s work.

Dr. Wile reports:

More than two years ago, Dr. Jeffrey P. Tomkins, a former director of the Clemson University Genomics Institute, performed a detailed, chromosome-by-chromosome comparison of human and chimpanzee DNA using a widely-recognized computer program known as BLAST. His analysis indicated that, on average, human and chimpanzee DNA are only about 70% similar. This is far, far, below the 95-99% numbers that are commonly cited by evolutionists, so once I read the study, I wrote a summary of it. Well, Dr. Tomkins has done a new study, and it invalidates the one he did two years ago.

The new study was done because last year, a computer programmer of financial trading algorithms (Glenn Williamson) discovered a bug in the BLAST algorithm that Tomkins used. This bug caused the program to ignore certain matches that should have been identified, which led to an artificially low similarity between the two genomes.

Here is what Glenn Williamson has to say about himself:

“Yeah – 36 year old, stay-at-home father of four – including triplets, ha!

I DON’T HAVE ANY FORMAL QUALIFICATIONS IN GENETICS, OR ANYTHING BIOLOGICAL for that matter. I have a bachelors degree in computing science (i.e. programming) from the University of Technology in Sydney. Started my career as a programmer, but transitioned into derivatives trading, which is a lot more fun… [my added emphasis]

And for what it’s worth, I believe that my paper is more of a computing science paper than a genetics paper. It’s more my area of expertise than Jeff Tomkins’ area.

In this paper I carefully reproduce a subset of Dr Tomkins’ results, and show clearly and unambiguously that Dr Tomkins has fallen victim to a serious bug in the software used to obtain his results. It is this bug that causes Dr Tomkins to report the erroneous figure of 70% similarity. After correcting for both the effects of this bug and some non-trivial errors in Dr Tomkins’ methodology, I report an overall similarity of 96.90% with a standard error of ±0.21%. This figure includes indels, and the result is largely in line with the secular scientific consensus.”

Frank: The article does go on to report that YEC Dr. Wile is most cautious about accepting this more recent research by Tomkins and Williamson again argues agains the findings and the revised figure of 88%.

However, there is marked difference between the comments of Williamson and your excoriating assaults on the character of Tomkins based on the findings of a derivatives trader with no qualifications in genetics or any other biological area.

James: 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.

Frank: This is a strawman and a gross distortion of the YEC (and ID position) and I will be charitable in saying that you can only have accepted this version third-hand and not actually personally researched the matter.

The YEC organisations and individuals I know do not see acceptance of an old earth and theistic evolution as a salvation issue and that Genesis MUST be accepted in order to be saved. If you have come to believe differently to that which I have just said you are very much mistaken.

As a software developer I think I would be correct in saying that you must have an IQ somewhat higher than the average and that being the case it greatly surprises me that a man of your intelligence could actually believe that YEC’s promote and insist that being a saved Christian depends on accepting the literal account of Genesis.

Having said that I am in agreement with YEC’s who say that what is important is the issue of Authority. Do Christians accept the Authority of Scripture which is God’s revealed word to Man or do we accept the authority of science – which is fallen men discovering knowledge which is (using hyperbole) one day considered to be accurate and true until tomorrow when something else is discovered that replaces yesterday’s truth and so on and so on.

That subject is for another thread I suppose and will not labour the point at present.

I will however repeat what I posted previously to Steve Schaffner it was, I think, if Adam was not a real literal historical figure there was no sin and no Fall and there was no need for Jesus Christ to undergo torture and crucifixion – it was all for nothing.

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.

James: 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.

Frank: On this particular issue of 88%, given that Tomkins, published a new report in which he abandons his 70% figure, as far as I’m concerned the jury is still out.

IF it turns out that the figure is, say, 95% similarity that still equates to some 150 Million DIFFERENCES (I’m not shouting merely emphasising).

Furthermore, Darwinian evolutionary naturalism contain a huge number of holes: where are the fact and evidence that life originated in “a warm little pond” or “hydrothermal vents”? Where did the specified information - recognised by Bruce Alberts see my post in this connection – as indispensible to life come from? From where did an organism “acquire” new increased additional information of the type necessary for the organism to evolve into a higher organism? Bruce Alberts et al admits he doesn’t know.

Those are only few but very wide and bottomless holes in Darwinism.

Where in your picture of life as a theistic evolutionist does God play a role? I do trust you will not be as facetious as beaglelady who evidently is stumped for a coherent explanation.

A final point. Before you next resort to excoriating hostile scathing attacks on IDers and YEC’s whom you think bring the Gospel into dispute I will kindly suggest that you may just want to consider if the attitudes and behaviours which you exhibit are beyond reproach.

May I suggest that you check out my posts to James and Steve Schaffner in which I discuss on most relevant matter in this connection - as I really don’t want to keep repeating myself.

Thank you.

If you have arthritis in your fingers why do you write such LONG posts?

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For the simple reason that it would serve no benefit. He’s made his claims public, so they need to be addressed in public. Besides, others have more expertise in the subject than I have and would be in a better position to do so.

No, you have not understood me correctly.

Frank, we are not hostile to young earth creationism specifically. We are hostile to bad science in general. I’ve pointed out the reason why to you twice and I will say it a third time: if you get science wrong, you can kill people. For that reason, we simply can not accept any portrayal of science, for any reason, that involves demonstrable falsehood, woolly thinking, or resistance to correction.

Tomkins’s claims could have been excused as mere “irregularities”—to use your description—if he had retracted them after the error had been pointed out, as is standard practice in science. It is the fact that they are still being promoted, and that no attempt has been made to address the issue, that is unacceptable.

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  1. How about a “real literal historical figure” who just isn’t the ancestor of all humanity? Can that be?
  2. No sin. If Adam’s story is in any way quibbled with, then sin just never existed!
  3. No Fall! Do you mind if I ask where in the Bible it talks specifically about a “Fall?” Is that a real literal Bible concept, or is it a human interpretation or doctrine?
  4. So the only possible reason for Jesus to be crucified was because thousands of years earlier, a couple people ate some fruit? Seriously? That’s what your takeaway is?

I can’t make you consider anything, of course. Nevertheless, I gently suggest that you may benefit from re-evaluating some of your underlying assumptions. The search for Truth is something to take extremely seriously.

I just wanted to clarify something that seems to be unclear here. It is well within the forum dialogue guidelines to criticize and vehemently disagree with ideas in published work. That is how academia works and it is not a personal attack. It is also acceptable to argue that a public figure’s credentials are inadequate to back up their claims of expertise. We expect people to treat the people they are in conversation with here on this forum with a certain level of civility and grace. That means not attributing nefarious motivations to others and not refereeing the legitimacy of someone else’s faith or integrity. It does not mean everyone has to treat all idea’s as equally valid.

@Frank I understand why you may feel defensive as someone defending a minority position on this forum. But please try not to read extra tone into other’s arguments.

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There’s a very good article that’s well worth a read here by a bloke called Paul Graham, entitled “How to Disagree.” He outlines a hierarchy of disagreement levels:

  • DH0: Name-calling (“evolutionist”, “compromiser” etc)
  • DH1: Ad hominem (e.g. questioning someone’s faith)
  • DH2: Responding to tone (“your remarks are excoriating”)
  • DH3: Contradiction
  • DH4: Counterargument
  • DH5: Refutation
  • DH6: Refuting the central point

@Frank, it might be a good idea for you to read this article before you respond any further. Please try to focus on the substance of what we’re saying rather than the style.

Frank:

if Adam was not a real literal historical figure there was no sin and no Fall and there was no need for Jesus Christ to undergo torture and crucifixion – it was all for nothing.

Lynne: How about a “real literal historical figure” who just isn’t the ancestor of all humanity? Can that be?

Frank: IF the sinless perfect (to begin with) Adam wasn’t the ancestor of all humanity then you can’t “be of Adam” and if you are not of Adam then neither can you be of Jesus Christ and in that case you cannot be saved.

As I get chastised by others for either writing post which are too lengthy or not providing references and or links I can’t post in entirety that which I would like to and instead kindly refer you to 1Corinthians Chapter 15 and with special emphasis on verses 45 - 49

 Lynne: No sin. If Adam's story is in any way quibbled with, then sin just never      existed!

Frank: My beliefs are informed by the knowledge that ALL Scripture is God breathed and is the inerrant and infallible ( I’m talking here about the original “autographs”)word of the Most High as His revelation to Man.

It seems that you do not share this view.

“Therefore just as sin entered the world through one man, and sin and death through sin……” Romans 5ff

Here Paul, who wrote that all scripture is inspired of God i.e. God breathed i.e. originating with God and not that of his own originality is talking about the literal historical person of Adam who was created in the manner described in Genesis.

Do you think that the same God who created the vast Universe is incapable of creating a tiny human in such a manner? If that’s your view do please tell how you can believe – if indeed you do believe – that God could bring a man back from the dead?

Lynne: No Fall! Do you mind if I ask where in the Bible it talks specifically about a “Fall?” Is that a real literal Bible concept, or is it a human interpretation or doctrine?

Frank: The Bible doesn’t specifically mention the term “Trinity”, does it? But you believe in the Trinity, do you?

It’s about discernment. Given that Adam was created sinless and perfect when he disobeyed and in effect told his Maker to “get lost” he Fell from that position.

If you don’t accept the Fall – and it appears by your use of exclamation mark and rather high-minded tone that you don’t – is this just your “human interpretation” which you esteem higher than God’s revelation?

Lynne: So the only possible reason for Jesus to be crucified was because thousands of years earlier, a couple people ate some fruit? Seriously? That’s what your takeaway is?

Frank: What you evidently fail to take on board – probably due to not actually giving this vital issue any real serious consideration – is that the eating of the fruit was a deliberate wilful act of disobedience and a denouncing of God, as the Maker, as the Sovereign who had the legitimate right to put in place certain requirements of His human family.

Do you have children? Do you just allow them to do whatsoever they want to irrespective of the consequences to others and themselves?

Adam wanted to be his own “god” deciding for himself what is right and wrong – if anything. Don’t you see the consequences of his action today?

God hates Sin. And that’s why he had to deal with sin – by coming in the flesh as Jesus Christ to negate its power and to save his human family.

Lynne: I can’t make you consider anything, of course. Nevertheless, I gently suggest that you may benefit from re-evaluating some of your underlying assumptions. The search for Truth is something to take extremely seriously.

Frank: Speaking as a former atheist I do take this matter most seriously to the extent that I rigorously investigated Darwinism to find out that it does not stand up to scrutiny. And then with the same rigour I investigated the claims for the veracity of the Bible which entailed carrying out research into many areas including that of textual criticism – and am indebted to Prof David C. Parker a world recognized expert in this field who freely gave of his time and advice – and had the wisdom to not try to influence me but allowed me to draw my own conclusions.

I am of the view, based on certain hard facts and evidence, that the Bible is reliable trustworthy and is indeed God- breathed.

You fail to see the irony in your comments?

When you read excoriating attacks on the character of jeff Tomkins in which he is accused of deliberately configuring a software programme to get the desired results and when others admit to being “scathing” “aggressive” and “hostile” those behaviours are acceptbale and my pointing out thos behaviours are uncharitable to say the least this isn’t acceptable?

When persons in this forum say that Jeff Tomkins is guilty of silly and sloppy science those ARE personal attacks. Do you really truthfully not recognize this to be the case?

What makes you think I feel defensive? You are reading into my posts something that is not the case and is only your imagination.

You talk about civility but there are certain persons in this forum who are just about as uncivil and hostile as one get in such forums.

I always thought that as Christians we need be on duty so to speak 24/7 and putting forward the defence that one is entitled to “vehemently” disagree is one thing but it’s quite another to condone slanders against the character of a fellow Christian, Jeff Tomkins.

If my comments are too much for you, a Moderator, to take then you can of course have me removed from the forum - and that will be a great victory for oh so tolerant theistic evolutionist Christians.

In light of the abuse which is freely hurled at Tomkins by Christians - I have the hide of a rhino and have immunity to attacks on me personally - may consider if I even want to be part of this particular intolerant “tolerant” society.

James, I think I will not take advice on how to conduct myself from anyone who makes such excoriating and slanderous attacks on anyone and especially when they are directed at a fellow Christian.

You may just want to read Paul’s words to the Corinthians.

Hi Frank,
Thanks for interacting here on the Forum. There are not many people with young-earth/anti-evolution views around here and I appreciate the input. I’m sorry that you haven’t experienced a very welcoming atmosphere here. I haven’t read the whole discussion, but it doesn’t come across as peaceful dialogue. I haven’t seen anyone here questioning your motives or faith, but if that has been the case I apologize.

Talking about “young earth scientists” is a different story. People are entitled to hold those who claim expertise in a particular topic to much higher standards than just the average Christian lay person when it comes to scientific reporting.

Just a tip. You can easily quote parts of people’s posts (including your own previous posts) by selecting those parts with your mouse and clicking the Quote-button that pops up.

Cheers,
Casper

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