Minor quibble: If the similarity is 95%, then we differ by 150 million base pairs, not 150 million differences. It’s actually about 40 million differences, since many of the differences involve more than one base pair.
To answer your question, though: No, it’s really not. You and I differ by 10 or 15 million base pairs, and all humans are pretty similar to each other.
I’m unlikely to do more than skim it. Two comments:
I see reference to end-trimming poor quality bases, but nothing about masking poor quality bases within the read. I also see nothing about applying any version of Neighborhood Base Quality filtering. That’s done because even if the raw phred score says a base call is good, it has a good chance of being bad if it’s surrounded by low quality calls. The chimp genome paper supplemental information gives details about how NQS was applied to the chimp reads.
It seems to me there’s an easy way to look for human contamination, and that’s to examine the sequence for chromosome 21, which was sequenced using bacterial artificial chromosomes, rather than by shotgunning. (Note: I don’t know whether it was chromosome 21 by the old or the new numbering scheme.) Since the two datasets were produced by very different approaches, there would be no reason to expect contamination to be the same. Is measured human-chimpanzee divergence the same on that chromosome as in the rest of the genome?
More importantly, even if contamination were present and to the same degree, it should be very easy to spot with BAC sequencing. In that sequencing approach, a segment of chromosome ~200,000 base pairs long is all amplified as a unit and then sequenced. So if human DNA is being sequenced, a ~200 kb segment of the chromosome will all be human. Just chop the finished sequence up into 10 kb windows, calculate divergence from human in each window and histogram the results. Any human contamination will cause a clear second peak in the distribution.
Well done post. Unfortunately, “evidential immunity” is a recurring theme among those who show up here to dispute with actual scientists. But I’m not sure that believers like Frank are your target audience. Don’t let his hard-headedness kill the idea entirely, although it’s probably wise to hit the “pause” button and rethink the project before investing all that time and effort into it.
Open data can open minds, right? 
How on earth could you possibly think that Jeff Tomkins who posts his articles on various sites has “a reason to hide from scientific colleagues”? Huh?
I seem to recall suggesting that those who found fault with his work ought to contact him directly -but it seems no-one has done so.
I found his email address with ease, contacted him with specific criticisms of his work, he responded graciously and wasn’t in the least thrown by criticism and put me in the picture, and provided the link to his latest findings which and which deals with software programming issues.
Interestingly, no-one has responded to my observation that even IF the chimp - human similarity is as high as 95% this equates to approximately 150 Million real differences.
Speaking as a former atheist who moved from a belief in evolutionary naturalism to an understanding it i.e. Darwinism doesn’t stand up to scrutiny, to agnostic, to belief in an Intelligent Creator, to belief in the God of the Bible YHWH aka Jesus Christ, but an Old Earther, to a YEC, I have come to realize that one needs to be totally and utterly ruthlessly honest with oneself when it comes to challenging/interrogating our assumptions/conceptions/worldview - and many people don’t want to go through the process for a number of reasons.
Anyway, I’ll let you have the last word as I have a number of projects on the go and sorry to say that I think we are not going to see eye to eye on this.
www.genomenewsnetwork.org/resources/whats_a_genome/Chp4_1.shtml
Scientists estimate that the genomes of non-related people—any two people plucked at random off the street—differ at about 1 in every 1,200 to 1,500 DNA bases, or “letters.” Whether that’s a little or a lot of variation depends on your perspective. There are more than three million differences between your genome and anyone else’s.
Would you rather have 3 million dollars or 150 million?
Good question. I could probably handle 3 million OK, and no major upsets, but 150 million would have the potential to ruin my life and the lives of my family, judging by lottery winners. On the other hand…
The suggestion that I long-ago made was that you privately provide Dr. Swamidass with the email address. It seemed self-evident that there was no reason for you not to do this, but I made the point explicit in my rhetorical remark about Tomkins’ having no reason to object to it, either. So, to make it clearer, let me rephrase it: Tomkins should have no reason to object to you providing his email address privately to a scientific colleague, unless Tomkins has a reason to hide from them. Since it is obvious that Tomkins isn’t hiding, pass along the email to Dr. Swamidass! You could have easily done so already, rather than complaining that no one has contacted Tomkins directly. Is this what an alternate reality feels like?
“To what can I compare this generation? They are like children sitting in the marketplaces and calling out to others:
‘We played the pipe for you,
and you did not dance;
we sang a dirge,
and you did not mourn.’
Why does everyone want to make their own spiritual journey normative for all of God’s people?
The page you cite was last updated in 2003. With a tiny amount of effort, one could discover that the 1000 Genomes project reported on human genetic variation just a little more than a year ago. I believe the publication of these findings was very broadly publicized, such that no one with a beginner’s understanding of the literature would be unaware of their existence. Here is the relevant paragraph from the open access paper at Nature:
We find that a typical genome differs from the reference human genome at 4.1 million to 5.0 million sites (Fig. 1b and Table 1). Although >99.9% of variants consist of SNPs and short indels, structural variants affect more bases: the typical genome contains an estimated 2,100 to 2,500 structural variants (~1,000 large deletions, ~160 copy-number variants, ~915 Alu insertions, ~128 L1 insertions, ~51 SVA insertions, ~4 NUMTs, and ~10 inversions), affecting ~20 million bases of sequence.
Three million isn’t even close.
Let’s try harder to cite relevant scientific data.
Someone check my math here. If I read Tomkins correctly, the (hypothetically) less contaminated set of reads gives 85% human/chimp identity while the full set gives 90% identity. If we assume that the human contamination is 100% identical to the human reference, then two-thirds of the reads are of the less-contaminated type and one-third consists of nothing but human reads: 0.67 * 0.85 + .33 = 0.90. So if his numbers and explanation are correct, one-third of the chimpanzee reads are actually human. That strikes me as a trifle implausible.
That’s a pretty concise paragraph … I can see now that the only reason I’ve resisted this view up to now is that it was easier to dispute a Creationists who thought there was only Adam’s family in the beginning !
As Mr. Rogers always said:
“You are special in approximately 20 million ways.”
Frank: Many thanks for your considered response which, as you say, took some time to write up.
I should like to address your latter points first to clear up a misunderstanding you have.
You said that I had said I had no interest in running the code should you make it available to me. I haven’t checked the forum post for verification but I’m fairly sure I would not and did not actually say that at all. I think what I said is that my programming is limited to C++ and that this particular area is out of my level of experience.
You’ll see therefore that the two statements are entirely different.
You fear that I will accuse you of attacking him (Jeff Tomkins) and that “people like me are evidence immune.” Hmmm.
On this first point I can allay your fears as having read your comments it’s clear to me that unlike certain others in this forum who indulged in the logical fallacy of an ad hominem attack you have critiqued in some detail his methodology and findings and not the man.
As to your latter point your comments reveal a certain default attitude that some persons have towards Biblical creationists whether they are Old earthers but more especially to YEC’s.
I do have to say that whilst it is water off a duck’s back to me personally and especially so when attacks are made by atheists it does cause me some concern when negative comments are made by fellow Christians as I find such comments say more about them than me. Do you appreciate the point I’m making?
To get things into perspective on this issue of “immunity to evidence” you may want to reconsider your attitude when you learn that I’m a former atheist who moved to agnostic to believer in an Intelligent Force/Creator of the fine-tuned for life Universe to a believer in the God of the Bible (firstly as an Old earther to a YEC) to a born-again believer in Jesus Christ.
Therefore, to say that “people like me are immune to evidence” is stating it baldly – quite wrong.
As to your analysis and critique of Tomkins research you will appreciate that as I haven’t engaged in “hands-on” research as have you and Jeff that I do not have the experience and depth of knowledge to drill down into the step-by-step details and I freely openly and transparently admit to this deficiency.
I would like to swiftly add that I am completely fascinated by this area of research and am reading copiously on the subject and with a focus on the programming technology used. On that latter point I’ve read a number of articles and one thing that stands out clearly is that advances in that area are making rapid progress and that great care must be taken to not set up parameters to achieve the desired results to accord with one’s starting assumptions – and this cuts both ways, or to be more accurate, as many ways as people have different assumptions ranging from atheism, theistic evolution, to Intelligent Design, and Creation science. And yes I realise that the latter term may just possibly not compute with you and some others.
Thank you for your time and consideration.
Yes, which is why peer review and verification of results by other scientists, who may have opposite assumptions, is so important. The “atheist scientist” has his work checked by the Christian scientist (not the Mary Baker Eddy type), and the Christian scientist has his work checked by the atheist. Oh, and in between, atheists are checking up on other atheists, and Christians are checking up on other Christians. That is how false assumptions and errors are discovered. That is how science works. Even a layman like me can understand that. This whole idea of science’s inherent bias against God just strikes me as another manifestation of conspiracy-theory thinking.
You are welcome. I’m glad you can see the effort there. And I appreciate your largely defferential response.
That is a great story and I am glad you found Jesus, the One who is greater than anything we find in science. Peace.
Your story, though, I read as evidence that a loving God has searched for and called you to Himself. It is not your “responsiveness to evidence” that brought you to Him, but Jesus work in you through the cross. I thank Him for that good work, and as it is for all of us, coming to him does not automatically make us clear thinkers in all areas of life. That is not how following HIm works. So, as is true for all our journeys, I give credit to Him and not to us.
You do not need to know how to program to run the code. I’m happy to show you how. This is so easy to do, that a high schooler can do it. Do you have interest? Would this change your mind if you could see for yourself the data?
That is exactly right. That is why scientific controls are necessary. Scientific control - Wikipedia
It does not take technical or programming expertise to understand that this analysis needs to add positive controls: human reads to human genome comparison, and chimp reads to chimp genome comparison. Both these control" experiments should produce very high similarity (because they are positive controls) if his methodology is good. However, because he is using a poor analysis, the will not come out correct.
And if you take me up on the offer, I’ll show you how to run this analysis with controls too. You can see for yourself his mistake.
I am concerned about some being evidence immune and anticipate being accused of attacking Jeff. You seem puzzled by this, and think this is a general bias I have against YECs.
I wrote…
Then…
So thank you for not accusing me of excoriating attacks on Jeff this time, but I think you are missing something here.
We need to remember the history here. I fear you will accuse me of ad hominems this because you did this to me already earlier this thread (see next quote). It has nothing to do with you being a YEC, but my prior experience with you on this thread.
If you go back and read the thread, I did not attack Tomkins at all, but carefully explained why the ~88% figure you quoted was wrong.
With that experience, I do wonder about similar non-sequitors in the future. This wondering does not expose a general attitude about YEC, but a specific experience I have had with you.
That is not what I said. Rather…
Notice the “if”. I am still curious how you go from here. Will you choose to be immune to the evidence or will you enter in?
So this is really in your hands. Right now you are being presented with evidence that counters your presuppositions. There are multiple genuine experts (myself, @glipsnort, and @DennisVenema) who are also Christians willing to answer the questions. Will you be immune to the evidence?
This case should be particularly easy too, because…
So, in this really simple and easy case, can you change your mind? Can you come to a different view of the world based on well reasoned explanations and clear data?
If not, I will continue to wonder if you are evidence immune. And I see no point in explaining how (for example) 150 million base differences are understood by evolutionists and why we find no difficulty here. If we can’t come to agreement about the most obvious facts, what point is their in going back and for about that?
Any how, I sincerely hope you can change your mind and prove my fears are misplaced. I encourage you to do so.
I had it in mind to make a lengthy response addressing each of the points raised but for a reason which will become crystal clear have decided against it and will cut to the chase.
Let’s for the sake of the argument say that the chimp human difference is only, say, 2% or even 1%.
So what?
That factor is not hard facts and evidence for a common ancestor which is an assumption which goes back to the time of Darwin who, as you know, was ignorant of the specified information content and the nanomachines in the cell of even the least complex organism.
The notion of a common designer who front loaded the cell with specified information and nanomachines is at least as viable as the notion of a common ancestor.
The “only” 2% or 1% difference is ENORMOUS.
When and if a chimp can write algorithms, compose the music for an opera, sing Nessum Dorma, produce a Space Shuttle or type the 23rd Psalm or even one line from a play by William Shakespeare then I’ll give credence to the notion of a common ancestor.
But until such time I’ll continue to believe that chimps and humans are different “kinds” (baramin) of creatures.
So, the bottom line is this. I’m pretty sure that as a theistic evolutionist you’re not going to embrace the Genesis account of creation. You will understand that I am not going to reject the authority of the infallible Scriptures (I’m talking about the original “autographs”) in favour of science which in reality is knowledge arrived at by fallen men and which changes when new “truths” replace that which was previously held to be “true.”
I entirely embrace the Genesis account of creation, and hold it as a trustworthy account of our origins.
I believe that Jesus physically rose from the dead, and because of this I believe that the Bible is the infallible and authoritative Word of God and all Scripture is useful for teaching and instructing.
Believing all this myself, of course I have no intention of dissuading you from agreeing with me here. Please do not turn from trusting Scripture because of this conversation. Rather, I call you to trust it more, but trust your personal interpretation less. Maybe there is a way to understand it better.
I am not willing to proceed on this point if all you can do is concede “for the sake of argument” an obvious and clear point of evidence.
You are entirely right that this fact alone does not mean evolution is true or YEC is false, which is why it is so strange that there is so much resistance to recognizing the reality of this detail of God’s world. Given that this is not even a definitive fact, why is it so hard for you to change your position?
Yes and no.
Turns out this is 1/10th the differences between mice and rats, and many YECs think mice and rats share a common ancestor (because they are the same “kind”). So this is really a very tiny difference. From a genetic point of view, we look like we are the same baramin, there is no way around this without doing backflips to discard clear evidence.
On the other hand, there is no way we would mistake a human genome for a chimp genome, because the difference is very clear too. So in this is a substantial difference too. And these differences are consequential and important.
And your observations of the differences are correct too, and many scientists agree with you. You can read my thoughts about this here: More Than Just Apes. But the logical jump to rejecting common ancestry for this reason is a non-sequitur.
The real question is whether or not evolution is expected to produce this amount of difference between two genomes in 6 to 10 millions years. Turns out that the answer, using simple to understand formulas, is that this is exactly how much we expect genomes to be different when they diverge this recently. The mathematics of this come out of something called “neutral theory” and are directly verifiable with several experiments.
That is as much detail as I can into this with you though. Until we are operating from similar facts, there is no reason to get into the details of this.
I should also offer I am open to that possibility, though I have yet to see clear evidence that God did it this way. Just we can’t find the evidence, however, does not mean it did not happened this way.
As Denise has mentioned, chimps are our closest living relatives but there were many intermediate forms between the common ancestor of humans and chimps. Why are you not considering these intermediate forms? Didn’t it take a long time (about 200,000 years) for humans to compose the music for an opera, sing Nessum Dorma, and produce a space shuttle? During that time, the human genome hasn’t changed much. In addition, many of us have 1 to 2% Neanderthal DNA mixed into our genome. Neanderthals are genetically more similar to Homo Sapiens than Chimps are. Let’s says that Neanderthals didn’t go extinct, do you think Neanderthals could have composed an opera at some point in the last 600,000 years? How about the Denosivans? Do you think if they survived to this day, they would have discovered the natural laws of science such as quantum mechanics, general relativity, and the genetic code?
My point is that it was humans who discovered the laws of nature over thousands of years. If Neanderthals lived to present times, they too would have discovered the exact same laws of nature that we discovered. But I am sure that Neanderthals would not have came up with the same story of creation as written in the bible. To me, this says the biblical story of creation can’t be deemed more credible than what we know is true about the nature of the universe.
“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6
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