Luskin: Comparing human DNA to chimp DNA

The Pixie

Well-known member
Casey Luskin at the Discovery Institute has made a post on this issue. He introduces it:

For years we’ve been told that human and chimp DNA is some 99 percent identical. The genetic similarity statistic is then used to make an argument for human-ape common ancestry, and human-ape common ancestry is then employed in service of the larger philosophical point that humans are just modified apes, and nothing special.

I think most people would say we are special. In fact, many people would say we are so great that we do not deserve to be tortured in hell for eternity, but besides that, Luskin sums it up.

But then he goes on:

In 2007, not long after the chimp genome was first sequenced, the journal Science published an article, “Relative Differences: The Myth of 1%,” which called the idea that humans are only 1 percent genetically different from chimps a “myth” and a “truism [that] should be retired.” It observed that the genetic differences between humans and chimps amount to “35 million base-pair changes, 5 million indels [sequences of multiple nucleotide bases] in each species, and 689 extra genes in humans.” The article further reported that if we consider the number of copies of genes in the human and chimp genomes, “human and chimpanzee gene copy numbers differ by a whopping 6.4%.”

The problem is that there are different ways to measure these things; if you want to emphasise the similarity you choose one, and if you want to emphasise the difference you choose the other. So where does that leave us?

The important point is that chimp DNA is closer to human DNA than it is to gorilla DNA. And all three are closer to each other than they are to orangutans. And all the great apes are more similar to each other than they are to monkeys.

While the genetic difference between individual humans today is minuscule – about 0.1%, on average – study of the same aspects of the chimpanzee genome indicates a difference of about 1.2%. The bonobo (Pan paniscus), which is the close cousin of chimpanzees (Pan troglodytes), differs from humans to the same degree. The DNA difference with gorillas, another of the African apes, is about 1.6%. Most importantly, chimpanzees, bonobos, and humans all show this same amount of difference from gorillas. A difference of 3.1% distinguishes us and the African apes from the Asian great ape, the orangutan. How do the monkeys stack up? All of the great apes and humans differ from rhesus monkeys, for example, by about 7% in their DNA.

How does Luskin address that?

Well, of course he does not. He knows creationism cannot explain it, so he quietly sweeps in under the rug. It is, of course, pseudo-science, not real science, so ignoring evidence you do not like is standard procedure.
 

rossum

Well-known member
A simple explanation of how differences between two genomes can have different values. Short answer, it depends on how you measure the difference.

Take genome X: AAAAAAAAAA and genome Y: AAAAAAAAAT

If we directly compare the whole genomes then there is 0% match because the two genomes do not match.

Now split each genome into two pieces:

X: AAAAA AAAAA​
Y: AAAAA AAAAT​

Comparing those pieces gives a 50% match. The first halves match, the second halves do not.

Next split each genome into five pieces:

X: AA AA AA AA AA​
Y: AA AA AA AA AT​

Comparing those pieces gives an 80% match. The first four fifths match, the last fifths do not.

Now split each genome into ten pieces:

X: A A A A A A A A A A​
Y: A A A A A A A A A T​

Comparing those pieces gives a 90% match. The first nine tenths match, only the tenth tenths do not.

The measured difference between genome X and genome Y depends on the technique used to measure the difference.
 

Gus Bovona

Well-known member
A simple explanation of how differences between two genomes can have different values. Short answer, it depends on how you measure the difference.

Take genome X: AAAAAAAAAA and genome Y: AAAAAAAAAT

If we directly compare the whole genomes then there is 0% match because the two genomes do not match.

Now split each genome into two pieces:

X: AAAAA AAAAA​
Y: AAAAA AAAAT​

Comparing those pieces gives a 50% match. The first halves match, the second halves do not.

Next split each genome into five pieces:

X: AA AA AA AA AA​
Y: AA AA AA AA AT​

Comparing those pieces gives an 80% match. The first four fifths match, the last fifths do not.

Now split each genome into ten pieces:

X: A A A A A A A A A A​
Y: A A A A A A A A A T​

Comparing those pieces gives a 90% match. The first nine tenths match, only the tenth tenths do not.

The measured difference between genome X and genome Y depends on the technique used to measure the difference.
Do you know what the method or approach is that produces the 99% figure? I have occasion to quote this figure regularly, and it would be better if I could give some context to it.
 

The Pixie

Well-known member
What did your leader Chuck say about DNA?
Just as much as Jesus.
How many proteins are found in humans that are never found in animals?
Sweep it under the rug? Word games?
How does that compare between species?

Cytochrome C is a short protein at about 100 amino acids, and relatively slow to change. It is interesting to look at the differences between different species. Turns out they are exactly what you expect with evolution. Closer related species have more similar amino acid sequences.

See here for more.

So yes, if you are talking about specific amino acid sequences, only about 20% are identical to chimps. But that would seem to be a general pattern, and the figure is even smaller when comparing chimps to gorilla. If you are talking about proteins with the same name, that is, you consider Cytochrome C to be a single protein with a somewhat variable sequence, then I am not sure there are any differences.

When the protein-encoding genes of the human are compared with the protein-encoding genes of the chimpanzee, they are about 99 percent the same. Moreover, the one percent that are distinctive aren't obviously interesting, being involved with such traits as sperm surface proteins and immune responses.

So your claim is an interesting sound bite, but actually does not help creationism at all. Which sums up ID really.
 

rossum

Well-known member
If you are talking about proteins with the same name, that is, you consider Cytochrome C to be a single protein with a somewhat variable sequence, then I am not sure there are any differences.
Chimp and human cytochrome Cs have identical amino acid sequences. There is a single different amino acid in the Rhesus monkey sequence. Other species differ in more amino acids:

Code:
Hum:          mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgiiw gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne
Chm:          mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgiiw gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne
Rhe:          mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgitw gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne
Mou:          mgdvekgkki fvqkcaqcht vekggkhktg pnlhglfgrk tgqaagfsyt danknkgitw gedtlmeyle npkkyipgtk mifagikkkg eradliaylk katne
Frg:          mgdvekgkki fvqkcaqcht cekggkhkvg pnlygligrk tgqaagfsyt danknkgitw gedtlmeyle npkkyipgtk mifagikkkg erqdliaylk sacsk
Fly:     mgvp agdvekgkkl fvqrcaqcht veaggkhkvg pnlhgligrk tgqaagfayt dankakgitw nedtlfeyle npkkyipgtk mifaglkkpn ergdliaylk satk
Sun: masfaeap agdpttgaki fktkcaqcht vekgaghkqg pnlnglfgrq sgttagysys aanknmaviw eentlydyll npkkyipgtk mvfpglkkpq eradliaylk tsta

Hum - human, Chm - Chimpanzee, Rhe - Rhesus monkey, Mou - mouse, Frg - bullfrog, Fly - fruit fly, Sun - sunflower.
 

CrowCross

Super Member
Articles about what we have learned.

Since evolutionists speculate that humans and chimps shared a common ancestor about three to six million years ago, their theory requires a human-chimp DNA similarity of 98 to 99%. The first time they constructed a chimp genome and compared it to humans, they claimed 98.5% DNA similarity based on cherry-picked regions that were highly similar to human. However, an extensive DNA comparison study I published in 2016 revealed two major flaws in their construction of the chimp genome.1

First, many chimp DNA data sets were likely contaminated with human DNA, especially those produced in the first half of the chimpanzee genome project from 2002 to 2005. Second, the chimpanzee genome was deliberately constructed to be more human-like than it really is.2 Scientists assembled the small snippets of chimp DNA onto the human genome, using it as a scaffold or reference. It’s much like putting together a jigsaw puzzle by looking at the picture on the box as a guide. Since many chimpanzee data sets likely suffered from human DNA contamination, the level of humanness was amplified. I studied the 2005–2010 data sets that showed less human DNA data contamination and found they were only 85% similar to human at best.1 Article.


A review of the common claim that the human and chimpanzee (chimp) genomes are nearly identical was found to be highly questionable solely by an analysis of the methodology and data outlined in an assortment of key research publications. Reported high DNA sequence similarity estimates are primarily based on prescreened biological samples and/or data. Data too dissimilar to be conveniently aligned was typically omitted, masked and/or not reported. Furthermore, gap data from final alignments was also often discarded, further inflating final similarity estimates. It is these highly selective data-omission processes, driven by Darwinian dogma, that produce the commonly touted 98% similarity figure for human–chimp DNA comparisons. Based on the analysis of data provided in various publications, including the often cited 2005 chimpanzee genome report, it is safe to conclude that human–chimp genome similarity is not more than ~87% identical, and possibly not higher than 81%. These revised estimates are based on relevant data omitted from the final similarity estimates typically presented. article.

Often scientific reports or mainstream media claim 99% identical comparisons between human and chimp genomes. The number has been dropping in some circles recently, but is still on the order of 95+%. There is inherent bias in these calculations because significant lengths of DNA that are quite different between the two species are omitted from the results. A very simplified comparison would be comparing blue jeans (pardon the pun) with cut-off jeans. The fact that the legs are missing on one is discounted and only the upper portion is compared, with particular emphasis on the comparison of the rivets, buttons, pockets, topstitching, and zipper, but not much comparison on the brand, color, or the quality of the fabric. In a similar way, gaps or missing portions (like the missing legs on the cut-off jeans) and regulatory portions (like the fabric) from one are typically ignored, and only gene-rich segments of DNA are analyzed (like pockets, buttons, and rivets). Taking all those things into account, in 2012 creationist scientists Drs. Tomkins and Bergman came up with an overall similarity of around 81%—quite a difference!1 Other researchers have come up with even lower percent similarity, averaging around 70%. In 2013, Tomkins tested alignment of each chimpanzee chromosome against its human counterpart and only found an overall genome similarity of about 70%, which was published in Answers Research Journal. Article
 

Gus Bovona

Well-known member
Articles about what we have learned.

Since evolutionists speculate that humans and chimps shared a common ancestor about three to six million years ago, their theory requires a human-chimp DNA similarity of 98 to 99%.
Where are the calculations that *require* a 98-99% DNA similarity after 3-6 million years?
 

The Pixie

Well-known member
Articles about what we have learned.
...
What you are missing there is a comparison between chimp and gorilla DNA.

If, using the same methofology, chimp DNA is only 70% similar to gorilla DNA then that confirms chimps are closer to humans than gorillas. You do not have that data, one way or the other, so your data fails to address the OP. All you have done is shown how either side can cherry pick, which I said in the OP already: "The problem is that there are different ways to measure these things; if you want to emphasise the similarity you choose one, and if you want to emphasise the difference you choose the other. "
 

Gus Bovona

Well-known member
I believe the argument can now say....using your ages, there wasn't enough time for those mutations to occur and produce all of those differences.

I believe Haldane presented quite a dilemma.....and now that dilemma has gotten notably harder for the evos to explain.
Do you know where the calculations are that require a 98-99% difference in 3-6 millions years? Whether those calculations are wrong or not (whether Haldane's dilemma is apt or not) isn't the point to the question I asked you.
 

evoguy313

Active member
Casey Luskin at the Discovery Institute has made a post on this issue. He introduces it:

For years we’ve been told that human and chimp DNA is some 99 percent identical. The genetic similarity statistic is then used to make an argument for human-ape common ancestry, and human-ape common ancestry is then employed in service of the larger philosophical point that humans are just modified apes, and nothing special.

I think most people would say we are special. In fact, many people would say we are so great that we do not deserve to be tortured in hell for eternity, but besides that, Luskin sums it up.

But then he goes on:

In 2007, not long after the chimp genome was first sequenced, the journal Science published an article, “Relative Differences: The Myth of 1%,” which called the idea that humans are only 1 percent genetically different from chimps a “myth” and a “truism [that] should be retired.” It observed that the genetic differences between humans and chimps amount to “35 million base-pair changes, 5 million indels [sequences of multiple nucleotide bases] in each species, and 689 extra genes in humans.” The article further reported that if we consider the number of copies of genes in the human and chimp genomes, “human and chimpanzee gene copy numbers differ by a whopping 6.4%.”

The problem is that there are different ways to measure these things; if you want to emphasise the similarity you choose one, and if you want to emphasise the difference you choose the other. So where does that leave us?

The important point is that chimp DNA is closer to human DNA than it is to gorilla DNA. And all three are closer to each other than they are to orangutans. And all the great apes are more similar to each other than they are to monkeys.

While the genetic difference between individual humans today is minuscule – about 0.1%, on average – study of the same aspects of the chimpanzee genome indicates a difference of about 1.2%. The bonobo (Pan paniscus), which is the close cousin of chimpanzees (Pan troglodytes), differs from humans to the same degree. The DNA difference with gorillas, another of the African apes, is about 1.6%. Most importantly, chimpanzees, bonobos, and humans all show this same amount of difference from gorillas. A difference of 3.1% distinguishes us and the African apes from the Asian great ape, the orangutan. How do the monkeys stack up? All of the great apes and humans differ from rhesus monkeys, for example, by about 7% in their DNA.

How does Luskin address that?

Well, of course he does not. He knows creationism cannot explain it, so he quietly sweeps in under the rug. It is, of course, pseudo-science, not real science, so ignoring evidence you do not like is standard procedure.
When Tomkins first published a paper on how he had amazingly proven that chimps and humans are really only about 70% similar (using a buggy version of Blastn and using a script to rig the result sin his favor) I emailed him via CMI and asked if he would be publishing a paper using the same techniques and parameters to assess the % similarities of pairs of taxa that YECs believe to share a common 'Kind' ancestor. He was too cowardly to reply directly, but I received his response via CMI weeks later - he did not address my question at all, he just wrote that he "stands by" his paper and threw in some usual insults.
Luskin is a clown. They all are.
 

evoguy313

Active member
Do you know what the method or approach is that produces the 99% figure? I have occasion to quote this figure regularly, and it would be better if I could give some context to it.
Having published a paper that indicated as much many years ago, there are several techniques which have produced such figures. It is right that it depends on what you are comparing and how you are doing the comparison.

The original 99-ish% figure (re: DNA) came from a technique called DNA hybridization. I do not know the specifics of the technique, just the "gist" of it, but the original papers were published by Sibley and Ahlquist*. This is where labeled DNA (labeled using radioactive nucleotides back then) segments of DNA from the taxa being compared are heated until the strands separate, then allowed to cool slowly until they reanneal. The temperature at which this occurs can be used to calculate the extent of the similarity (again, I do not know how exactly, but this is the gist of it). There are limitations to this technique (such as it only uses single copy DNA, so things like copy number variation will not be detected), but the results were generally in line with previous analyses using amino acid sequence data and immune analyses.

Later, when DNA sequencing became cheaper and more reliable, direct site-by-site comparisons of DNA could be made (we're talking late 19809s, early 1990s) . Sequencing was still not easy, so comparisons were typically done on a few kilobases of DNA. However, that limitation was dealt with by comparing DNA from many different parts of the genome - a quasi-random sampling. All such analyses came up with % identities well into the nineties, this included genes, noncoding regions, etc.

Of course, % similarities only tell part of the story. When sequencing and sequence analysis became feasible, the focus shifted to patterns of unique shared mutations, not solely overall similarity. Because it is the patterns of shared similarity that can allow for resolution of questions of ancestor-descendant relationships (heredity and all that). When I did such work, % similarity was a 'byproduct' of the actual focus of our work. We did not set out to determine that the % similarity was - we assumes that it would be pretty similar based on previous analyses. We focused on the patterns of mutation. And regardless of what regions or how large the regions examined were, the results were all pretty much the same.

Luskin and Tomkins and all these people are just desperate.


*The Sibley/Ahlquist saga is an interesting one. In one of their papers (the fist one, I think), they forgot to mention that they had made some sort of adjustment to their calculations. It was a relatively minor thing, IMO, but one of their main rivals - John Marks - discovered this when he tried to replicate their work, and he (and a few others) made a huge stink about it, accusing them of fraud and such. Marks was mad because they had scooped him - he was working on something similar using chromosome banding patterns. Others replicated their work and found that the calculation issue did not affect the actual results, just the specific numbers used - if I remember correctly, it amounted to 1/10 of a percentage point difference, something like that. Other did similar work, with 'better' calculations, so it really didn't matter much.
 

evoguy313

Active member
Chimp and human cytochrome Cs have identical amino acid sequences. There is a single different amino acid in the Rhesus monkey sequence. Other species differ in more amino acids:

Code:
Hum:          mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgiiw gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne
Chm:          mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgiiw gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne
Rhe:          mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgitw gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne
Mou:          mgdvekgkki fvqkcaqcht vekggkhktg pnlhglfgrk tgqaagfsyt danknkgitw gedtlmeyle npkkyipgtk mifagikkkg eradliaylk katne
Frg:          mgdvekgkki fvqkcaqcht cekggkhkvg pnlygligrk tgqaagfsyt danknkgitw gedtlmeyle npkkyipgtk mifagikkkg erqdliaylk sacsk
Fly:     mgvp agdvekgkkl fvqrcaqcht veaggkhkvg pnlhgligrk tgqaagfayt dankakgitw nedtlfeyle npkkyipgtk mifaglkkpn ergdliaylk satk
Sun: masfaeap agdpttgaki fktkcaqcht vekgaghkqg pnlnglfgrq sgttagysys aanknmaviw eentlydyll npkkyipgtk mvfpglkkpq eradliaylk tsta

Hum - human, Chm - Chimpanzee, Rhe - Rhesus monkey, Mou - mouse, Frg - bullfrog, Fly - fruit fly, Sun - sunflower.
Golly... Almost like a pattern that matched hypotheses of phylogeny...:unsure:
 

evoguy313

Active member
Since evolutionists speculate that humans and chimps shared a common ancestor about three to six million years ago, their theory requires a human-chimp DNA similarity of 98 to 99%.
Since that part is 100% false, the rest is irrelevant.
Just the usual - what shall we call it? Creo-babble?
At least you didn't plagiarize, so that is a start.
 

evoguy313

Active member
I believe the argument can now say....using your ages, there wasn't enough time for those mutations to occur and produce all of those differences.

I believe Haldane presented quite a dilemma.....and now that dilemma has gotten notably harder for the evos to explain.
Explain it all to us, genius.

I'm betting you can't - not without more plagiarizing.
But why reinvent the wheel? I wrote this elsewhere:


In 1957, JBS Haldane calculated, under a certain set of assumptions, the rate at which a new beneficial mutation can reach fixations in a population. That rate was about 1 every 300 generations. Haldane felt that this was problematic, for reasons I will not get into here.

I bring this up because this was unfortunately referred to as "Haldane's dilemma", and was pounced upon in the 1990s by creationist electrical engineer Walter ReMine in a book that he wrote. He used Haldane's model to conclude that at most, 1667 beneficial mutations could have been fixed in the lineage leading to humans since the split with the lineage leading to chimps. He extrapolated that 1667 fixed beneficial mutations was just not enough to account for human evolution from a common ancestor with chimps (despite never even suggesting which new traits were needed that the common ancestor did not have). He never actually explained why this was a problem, except with the standard 'argument via awe and big numbers' (which consisted entirely of rhetorical questions, like even if there 500,000 such mutations, would even that be enough to get a "sapien from a simian?" Yes, that was supposed to be an argument).

Well, this "dilemma" came up recently in a thread discussing a paper from creationist John Sanford et al's relatively recent paper in which these creationists declare that there is just not enough time for evolution to have occurred (providing that evolution occurs via a series of pre-specified mutations occurring one at a time and one after another in regulatory sequence...), and I was reminded of the habit creationists have of providing quotes from people only as it suits them.

ReMine, for example, relied heavily on geneticist Warren Ewens as his primary resource for his pro-Haldane dilemma argument. He provided many quotes from Ewens in which it seemed that he agreed that Haldane's model was indeed a 'problem' for evolution as it limited the number of beneficial mutations that could become fixed over time.

And yes, Ewens did believe that Haldane's model, as calculated by Haldane, was a problem.

But more importantly, Ewens did not think Haldane's model was accurate, and thus there is no "dilemma" - but Remine just, I guess, forgot to mention that.

Here is Ewens, in an interview in 2004:


A second form of the load concept was introduced by the British biologist-mathematician Haldane who claimed, in 1957, that substitutions in a Darwinian evolutionary process could not proceed at more than a certain comparatively slow rate, because if they were to proceed at a faster rate, there would be an excessive “substitutional load.” Since Haldane was so famous, that concept attracted a lot of attention. In particular, Crow and Kimura made various substitutional load calculations around 1960, that is at about that time that I was becoming interested in genetics.
Perhaps the only disagreement I ever had with Crow concerned the substitutional load, because I never thought that the calculations concerning this load, which he and others carried out, were appropriate. From the very start, my own calculations suggested to me that Haldane’s arguments were misguided and indeed erroneous, and that there is no practical upper limit to the rate at which substitutions can occur under Darwinian natural selection.

And further:

AP: Can I follow that up? Can you, in layman’s terms, explain why you think that there is no upper limit in the way that Haldane suggested?


WE: I can, but it becomes rather mathematical. Let me approach it this way. Suppose that you consider one gene locus only, at which a superior allele is replacing an inferior allele through natural selection. In broad terms, what this requires is that individuals carrying the superior allele have on average somewhat more offspring than the mean number of offspring per parent, otherwise the frequency of the superior allele would not increase. This introduces a concept of a “one-locus substitutional load,” and a formal numerical value for this load is fairly easily calculated. However, the crux of the problem arises when one considers the many, perhaps hundreds or even thousands, substitution processes that are being carried out at any one time. In his mathematical treatment of this “multi-locus” situation, Kimura, for example, in effect simply multiplied the loads at the various individual substituting loci to arrive at an overall total load. The load so calculated was enormous. This uses a reductionist approach to the load question, and to me, this reductionist approach is not the right way of doing things. Further, the multiplicative assumption is, to me, unjustified. It is the selectively favored individuals, carrying a variety of different genes at different loci, who are reproducing and being required to contribute more offspring than the average. If you consider load arguments from that individual-based, non-reductionist basis, the mathematical edifice which Kimura built up just evaporates, and in my view the very severe load calculations which he obtained by his approach became irrelevant and misleading. The individual-based calculations that I made indicated to me that there is no unbearable substitutional load.


ReMine's book came out in 1993. I find it hard to believe that Ewens did not already have these same opinions and had not already published the relevant papers well before then (most of his relevant papers on this issue came out in the 1970s). Not hard to believe that he told this all to ReMine and ReMine, being a creationist with souls to save and profits from a book to earn*, just ignored it all because it did not help his cause.



*Another of ReMine's (and other creationists') tactics is to artificially inflate the relevance and impact of their books to not only boost their sales, but to boost their credibility (for the cause, after all). ReMine did this by sending copies, unsolicited, to public and college libraries, or sending boxes of the book to fans and having them 'donate' the book to the same. Thus, he could then boast that his book is on the shelves of major universities at the like. I have seen 2 copies of ReMine's book at 2 of the universities that I have been associated with - both were "gifts" (i.e., the university did not actually purchase them).
 
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