Determining similarity statistics between the human and chimp genome


(Frank Cross) #1

1.From where did you get the figure of 70%?
Recent research shows the difference to be ‘about’ 85% and this would equate to about 450 Million differences.

  1. From where did you get that quotation? Is it actually a quotation from a YEC book/article/scientist?
  2. Richard Dawkins, for example, had some serious back -pedalling and face saving to do on this issue because he was of the belief as were many mainstream scientists that DNA contained about 98% “junk.” I believe I’m corrrect in saying that Francis Collins of Biologos who was in charge of the Human Genome Project scotched that erroneous notion. And this is something that creation scientists had predicted years in advance and for a fact DNA is much more than just one dimensional linear digital code and has been discovered to contain gene switching mechanisms.controls.
  3. Yes, indeed and this is a circular argument oft times used by Darwinists who needs must subscribe to the notion of uniformitarianism and with it billions of years lest evolutionary naturalism fall flat.

A disturbing conversation with a YEC friend
(James McKay) #2

Didn’t the 85% figure came from a comparison algorithm that showed that human DNA is only 89% similar to itself?

The “fossils are used to date rocks and rocks are used to date fossils” argument is completely untrue. Rocks are dated first and foremost using radiometric dating. Which is far, far more reliable than YEC organisations make it out to be.


(Steve Schaffner) #3

I’ve seen it many times. Here is one place, for example.[quote=“Frank, post:12, topic:34955”]
Recent research shows the difference to be ‘about’ 85% and this would equate to about 450 Million differences.
[/quote]
No, recent research really doesn’t show that; this is one of those completely wrong claims that was being discussed. The best estimate of the differences between the genomes hasn’t changed since the chimpanzee genome paper: 1.2% or so different where they share common DNA, plus another 1.5% of unique DNA in each genome.

I’ve seen it many times in online discussions. Here is one place of many you can find it.

I’m not aware of any scientist who ever claimed that 98% of the genome was junk. (And I’m not interested in what Dawkins thought or thinks.) The original guess was that about 20% of the genome was likely to be functional. The current best estimate is something like 10% to 15% functional.[quote=“Frank, post:12, topic:34955”]
I believe I’m corrrect in saying that Francis Collins of Biologos who was in charge of the Human Genome Project scotched that erroneous notion.
[/quote]
Didn’t happen. The ENCODE project (which Francis wasn’t directly involved in, if I recall correctly – but my memory is fuzzy on this point) showed that 80% of the genome was biochemically active. The best estimate from that project was that ~11% actually affected the well-being of the organism, i.e. had a function.

I’m afraid this does indeed come under the heading of “not having a clue” responses. All absolute dates of rocks ultimately come from radiometric dating.


(Frank Cross) #4

There’s a lot of material to cover in one post and so if you have no objection perhaps we could deal with one subject at a time?

Here below is an extract from the article ypu cited about the 70% percent figure mentioned. I confess I hadn’t come across this particular article and thanks for drawing it to my attention:

"For the past several decades, the standard mantra has been that humans are 98 percent genetically identical to chimpanzees. However, this claim is based on cherry-picked data and does not take into account the vastly different regions of the two respective genomes.

Major research published over the past decade comparing human and chimpanzee DNA was recently reviewed and critiqued.1 In every single publication, researchers only reported on the highly similar DNA sequence data and discarded the rest—apparently because it was too dissimilar. In fact, when the DNA similarities from these studies were recalculated using the omitted data, markedly lower levels—between 81 and 86 percent similarity—were found. Even the well-known chimpanzee genome paper published by evolutionists in 2005 provides a genomic similarity of only about 80 percent when the discarded nonsimilar data are included and only 70 percent when the estimated size of the chimpanzee genome is incorporated.2,3

In 2011, I tested a wide variety of DNA alignment parameters for 40,000 segments of chimpanzee DNA that were already known to be similar to human. The parameters that gave the longest DNA alignment matches produced 86 percent similarity.3 Another interesting outcome from this study was that the 740-base-long chimp DNA sequences became too different to align after just a few hundred bases, on average."

Now, this article has been written by Jeff Tomkins a Phd geneticist who carried out hands-on research so please explain what issues you have with his findings.

Thanks


(Frank Cross) #5

I think one subject at a time is best due to time considerations and the amount of space taken up in lengthy posts, okay?

Perhaps on the topic of DNA and alleged “junk” you’ll see my post to glipsnort.

Thanks


(Benjamin Kirk) #6

[quote=“Frank, post:12, topic:34955”]
Richard Dawkins, for example, had some serious back -pedalling and face saving to do on this issue because he was of the belief as were many mainstream scientists that DNA contained about 98% “junk.”[/quote]
I believe you’re wrong about that.

[quote]I believe I’m corrrect in saying that Francis Collins of Biologos who was in charge of the Human Genome Project scotched that erroneous notion.
[/quote]I believe you’re wrong about that too.


(Steve Schaffner) #7

Hi Frank,

The problems with Tomkins’ study are described in detail in this article by Glenn Williamson. (I carried out a similar attempt to replicate Tomkins’ work myself, by the way, and I reported the BLAST bug that’s described there to NCBI; I’ve also discussed the issues with Williamson.) You can also read the backstory of Williamson’s attempts to correct the mistakes here. Short summary: Tomkins used standard genetic software, but happened to be using a version that had a serious bug in it. The way he was using the software, though, was also completely and inexcusably wrong, and guaranteed to underestimate the similarity between the genomes.

For the record, I am also a geneticist, and I was one of the authors of the paper that described the chimpanzee genome and compared it to human.


(Frank Cross) #8

Hi Steve,

I read the article by Glenn Williamson who discusses at some length the issue of software problems and in his conclusion he is somewhat more charitable than you who thinks Tomkins was “inexcusably wrong.” Hmm.

May I ask if you gave your feedback to Tomkins inviting as response? It would seem to me the right and proper thing to do, don’t you agree?

I carried out a Google search and came across an article by a writer at the DI, an organisation with which Biologos contributors seem to be at loggerheads, who although he disagrees with Tomkin’s findings of 70% does argue for a figure in the 80’s %.

Anyway, as this is getting a bit lenghty I’m not posting that article and instead below are extracts from another article which cites later work of Tomkins:

A Fresh Look at Human-Chimp DNA Similarity
by Frost Smith on December 30, 2015

BLASTN Away at Percent Similarity

BLASTN, an online program (an algorithm, actually) that many scientists use to compare the sequence of DNA bases comprising the genomes of organisms, occasionally gets updated as any software.

In 2014, a programmer reported a bug in BLASTN to Dr. Tomkins. At that point, Dr. Tomkins noticed that the most recent versions seemed to be omitting many results that weren’t at least 98% similar to the target human base sequences. Dr. Tomkins decided to investigate using six versions of this algorithm, including the recent versions in question. Additionally, he used two other common algorithms for DNA comparison, Nucmer and LASTZ.3

Both the earlier version of BLASTN and Nucmer returned an average of 88% identity overall between the human and chimp compared chromosomes. LASTZ returned a surprisingly lower average of only 73% matching. Dr. Tomkins suggested more research into the LASTZ program to investigate this.

Taking the more reliable results provided by the earlier BLASTN version corroborated by the whole chromosome alignments of Nucmer obtained in this study, it is likely that the 88% similarity number is considerably more accurate than other methods to date. Additionally, studies show that chimpanzees have a genome size about 8% larger than humans, so “the actual genome similarity with human, even using the high end estimate of 88% for just the alignable regions, is realistically only about 80% or less when the cytogenetic data is taken into account,” according to the latest Tomkins study.

Why Are Evolutionists’ Numbers So High?

Chimpanzee sequences were assembled using the human genome as a framework and the program’s parameters omitted non-alignable sequences.

The premier publication comparing the human and chimpanzee genome was from the Chimpanzee Genome Sequencing Consortium in 2005.4 But the methodology was biased: chimpanzee sequences were assembled using the human genome as a framework and the program’s parameters omitted non-alignable sequence. So if you assume humans and chimps are related, match up the DNA sequences based solely on evolutionary bias, match only the most similar regions, and ignore the rest (consider that humans have 23 chromosome pairs and chimps have 24 pairs), you’ll come up with some pretty high similarity, too! A 2012 Journal of Creation (JoC)5 paper sheds some light on some of these earlier studies, reporting bias beginning even in the selection of sequences to compare. One study even admitted to some “quality control,” where one-third of the chimp sequences were thrown out before the comparison because they didn’t have enough of a human match. In other early studies, unintentional human contamination aside, “human sequence contamination is . . . added to fill in putative missing chimp sequences.”6

Is the Test Tube 80% Full or 20% Empty?

Looking at Tomkins’ lower percentages may give some a sigh of relief, but the fact that we’re even 80% similar is disconcerting to many, or perhaps causes evolutionists to still assert common ancestry. But step outside either paradigm for a moment and consider how all plants and animals must function together, sharing organic material and using the same inorganic resources. Life simply wouldn’t work on this planet without some degree of sameness. The biologic functions that we all share involve the same mechanics: intake, metabolism, mobility, output, and so on. While there are numerous ways this is accomplished throughout the animal and plant kingdom, there are still these basic functions on even a cellular level, as well as a “macroorganism” and environmental level.

Looking at the numbers of actual bases puts the problem in even clearer light.
And consider what that 20% difference means. There are roughly 20,000 protein-coding genes in the human genome. That would be a difference of roughly 4,000 proteins. And given that we expect there to be some commonality in proteins, for example, digestive enzymes, that 80% should be looking a bit less impressive. And keep in mind that less than 5% of the human genome contains protein-coding sequences. Looking at the numbers of actual bases puts the problem in even clearer light. Conservatively, if the human genome is over 3,000,000,000 base pairs, and the difference is 20%, that is 600,000,000 base pair differences just between humans and chimps! That adds up to a lot of evolution when you consider all the organisms in the kingdoms of life—that couldn’t happen even in 6 billion years, especially considering the changes that are kept have to be viable, too!


(Frank Cross) #9

Hi Benjamin,

Here below are two article which you may want to consider in connection with your response to my earlier post:

Bonobos Join Chimps as Closest Human Relatives
By Ann GibbonsJun. 13, 2012 , 1:30 PM
Chimpanzees now have to share the distinction of being our closest living relative in the animal kingdom. An international team of researchers has sequenced the genome of the bonobo for the first time, confirming that it shares the same percentage of its DNA with us as chimps do. The team also found some small but tantalizing differences in the genomes of the three species—differences that may explain how bonobos and chimpanzees don’t look or act like us even though we share about 99% of our DNA.

“We’re so closely related genetically, yet our behavior is so different,” says team member and computational biologist Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “This will allow us to look for the genetic basis of what makes modern humans different from both bonobos and chimpanzees.”

Ever since researchers sequenced the chimp genome in 2005, they have known that humans share about 99% of our DNA with chimpanzees, making them our closest living relatives. But there are actually two species of apes that are this closely related to humans: bonobos (Pan paniscus) and the common chimpanzee (Pan troglodytes). This has prompted researchers to speculate whether the ancestor of humans, chimpanzees, and bonobos looked and acted more like a bonobo, a chimpanzee, or something else—and how all three species have evolved differently since the ancestor of humans split with the common ancestor of bonobos and chimps between 4 million and 7 million years ago in Africa.

This is delightful. In a BBC-sponsored debate with Richard Dawkins, Britain’s chief rabbi, Lord Jonathan Sacks, tweaked Dawkins with the ENCODE project results. He does it right out of the box, in the opening moments of the encounter, observing that whereas until recently 98 percent of the genome was "dismissed as junk DNA, " “actually that 98 percent that people thought was junk isn’t junk at all. It’s absolutely essential to the maintenance of life.”

Watch the video – Rabbi Sacks provides an important lesson not only in science and philosophy but in the human art of treating an opponent with unfailing grace, warmth, and a genuine friendliness that can’t be faked and that disarms even Richard Dawkins.

On the junk DNA point, though, Dawkins manages to squirm out and seems to turn it to his own advantage (at about 13:00). In his telling now, the discovery that junk DNA is not junk at all isn’t a blow to Darwinist predictions but – yes, you guessed right – exactly what a Darwinist would expect.

I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that’s awkward for Darwinism. Quite the contrary it’s exactly what a Darwinist would hope for, to find usefulness in the living world…

Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something. What it’s doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals – mice and men have the same number, roughly speaking, of protein-coding genes and that’s always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that’s calling them into action is the rest [of the genome] which had previously been written off as junk.

If I had been whispering at Rabbi Sacks’s elbow, I would have suggested he point out that Dawkins has changed his tune. Back in 2009, in The Greatest Show on Earth (pp. 332-333), he was presenting the supposed junkiness of the vast majority of the genome as an assured scientific reality and one that is, in the specific case of “pseudogenes,” “useful for. . . embarrassing creationists.”

It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene – a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something – unless he was deliberately setting out to fool us.

Dawkins goes on:

Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.

That was in 2009, just three years ago. Back then, the purported fact that 95 percent of the human genome “might as well not be there” was an embarrassment “for creationists,” whom in typical Darwinian fashion Dawkins conveniently conflates with intelligent-design advocates. Junk DNA is just what a Darwinist would expect, in other words.

Cut to 2012, and now the evident fact that “junk DNA” isn’t junk at all but is instead vital for life has become “exactly what a Darwinist would hope for,” namely, "to find usefulness in the living world."
That is, heads you lose, tails I win. A wonderful man like Rabbi Sacks would probably have to shed his courtliness for a moment to properly call out Dawkins on this blatant, unacknowledged and suspiciously convenient self-contradiction. Ah well, as we knew already, being a Darwinist means never having to say “I was wrong.”

On Junk DNA Claim, Francis Collins Walks It Back, Admitting "Hubris"
David Klinghoffer July 19, 2016 12:44 PM | Permalink

Count on Marvin Olasky at World Magazine not to miss something like this. InThe Language of God, theistic evolutionary icon Francis Collins used so-called Junk DNA as homerun evidence against intelligent design. He has since backed down on that, honorably, admitting “hubris” in the process. Olasky:

Collins claimed on page 136 that huge chunks of our genome are “littered” with ancient repetitive elements (AREs), so that “roughly 45 percent of the human genome [is] made up of such genetic flotsam and jetsam.” In his talk he claimed the existence of “junk DNA” was proof that man and mice had a common ancestor, because God would not have created man with useless genes.

Last year, though, speaking at the J.P. Morgan Healthcare Conference in San Francisco, Collins threw in the towel: “In terms of junk DNA, we don’t use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn’t functional. … Most of the genome that we used to think was there for spacer turns out to be doing stuff.”

Good for Collins – and maybe he’ll go on to deal with other times scientists feel sorry for God as they look at His purportedly poor design. For example, evolutionists use the retina of the eye as evidence against creation, because nerve endings are at the front rather than at the back, which at first glance seems better placement. Yet, as Lee Spetner explains in The Evolution Revolution(Judaica Press, 2014), physicists now see front placement as the best one for “ingeniously designed light collectors.”

The list of needed retractions should include what you probably learned in high school about apparently purposeless human vestigial organs. Robert Wiedersheim’s 1895 list of 86 has shrunk, as almost all of them have proved to have functions. For example, the most famous vestigial organ – the vermiform appendix – is a crucial storage place for benign bacteria that repopulate the gut when diarrhea strikes. The appendix can be a life-saver.

By “hubris” perhaps he means the overweening tendency to assume that scientific opinion as constituted at the moment has got everything all figured out. The repeated need to retract and walk back previous certainties should be a lesson to all, a warning that we can’t simply hand over our intellects to “science.”

In briefest form, that’s the message of Doug Axe’s book Undeniable. When it comes to big-ticket science questions like evolution, not only do you get to think for yourself. You have a positive obligation to do so.
I’m on Twitter. Follow me @d_klinghoffer.


(George Brooks) #10

@Frank

So you would reject common ancestry with chimpanzees? Am I understanding what you are saying correctly? If not, please let me know. But if you are rejecting common ancestry, that would mean you are rejecting this particular item of evidence as well?

You would think it is pure coincidence that Humans have one less chromosome than chimpanzees (23 instead of 24) and that - - amazingly enough - - one of the human chromosomes looks exactly like 2 chimpanzee chromosomes (Chimp chromosomes 2A & 2B) merged into a single body?


(Steve Schaffner) #11

What I wrote was my charitable description. I’ll be happy to retract the “inexcusably” adjective if you can provide an excuse. (I’m talking scientifically here – I make no judgments about the man’s character. It’s the work that’s bad.)

No, I don’t agree. Tomkins has the necessary information from Williamson’s piece, and yet his article is still online. What would be the point? I suppose I could ask him to apologize for impugning my colleague’s scientific competence and integrity with a fatally flawed piece of sciency-looking silliness, but somehow I don’t think that’s what you had in mind. I really don’t see the point of chasing down everyone who has said something wrong about human genetics somewhere on the web.

So if you if you stop suffering from a massive bug in the program you’re using to do a completely meaningless analysis, the completely meaningless analysis becomes less grossly wrong. That’s the only thing I can take away here. Did you understand why an ungapped comparison is simply wrong?

Look, if you have any actual scientific criticism to make of the human-chimpanzee comparison, offer it. Address the paper itself, not the misrepresentations by creationists.


(Steve Schaffner) #12

Fail city. That’s an adverb, not an adjective.


(Stephen Matheson) #13

An appallingly error.


(Frank Cross) #14

Yes George you understand me correctly in that I reject common ancestry and I do so for a great number of reasons.

Here below is a very short article - there are others which go into greater detail - in connection with this point you’ve raised:

Heads I win, tails you lose
The power of the paradigm
by Dominic Statham
Published: 11 November 2010 (GMT+10)

Kenneth Miller is Professor of Biology at Brown University, Rhode Island, and a prominent critic of creationism and the intelligent design movement. He has supported court actions against schools that seek to protect children from evolutionary indoctrination, even appearing as a witness for the plaintiffs,1 and regularly speaks in defence of the teaching of evolution as a scientifically proven fact. A Roman Catholic, he is a theistic evolutionist.

A few years ago, Miller gave a lecture at Case Western Reserve University entitled, “The Collapse of Intelligent Design. Will the next Monkey Trial be in Ohio?”2 In this, he freely lambasted all who would question the Darwinian paradigm. Most of the lecture was about politics, but some time was also given to scientific issues. Particularly, he made much of recent studies of human and chimp DNA and argued that this provided irrefutable evidence of evolution. As I listened to this, I became open-mouthed, almost in disbelief, at the incredibly unscientific nature of his claim. Two pairs of human chromosomes had been found to be fused, he said, providing clear evidence of our shared ancestry with apes.3

[Kenneth Miller] made much of recent studies of human and chimp DNA and argued that this provided irrefutable evidence of evolution.

Chromosomes are packages of DNA, wound around proteins called histones. Humans have 23 chromosome pairs, as we inherit 23 chromosomes from our father and 23 from our mother. Chimps inherit 24 chromosomes from each parent and have 24 chromosome pairs. Although far from being beyond doubt, a good case can be made that humans did, indeed, have 24 chromosome pairs originally, and that chromosome fusion has occurred, resulting in our now having only 23. For the sake of the argument, let us concede that this is true.4

According to Miller, there are only two possible explanations for this. The first is that we share a common ancestor with chimps and that, during the course of evolution, chromosome fusion has taken place. The second is that the creator/designer made humans with chromosomes which had the appearance of having been fused at some time in the past, when in fact this never happened. The second explanation, he argued, is ridiculous, thus showing the first to be correct.

For someone who prides himself as a scientist and critical thinker, Miller’s argument beggars belief. Even a child could see the fallacy of it. If, in Miller’s view, it is reasonable to believe that the chromosomes became fused in a small population of half-ape/half-humans a few million years ago, why is it not reasonable to believe that this occurred in a small population of actual humans a few thousand years ago? This could have happened very early on in human history, soon after Adam and Eve were expelled from the Garden of Eden, or in a small, isolated group from which Noah and his family were drawn prior to the Flood.

Professor Miller, of course, is a very capable and knowledgeable scientist. How, then, could he make such a basic error? The answer, surely, lies in the ‘Power of the paradigm.’ If it is accepted that ‘evolution is a fact’ then data will always be interpreted according to this belief—irrespective of whether there is a valid alternative interpretation. If humans had been found to have 24 chromosome pairs, this would have been understood as evidence for common ancestry with apes because apes also have 24. Since humans actually have 23, it is understood that this provides evidence that evolution resulted in ape chromosomes being fused. For the evolutionists, then, it’s ‘heads I win, tails you lose’.
Related Articles
• The chromosome 2 fusion model of human evolution—part 1: re-evaluating the evidence
• The chromosome 2 fusion model of human evolution—part 2: re-analysis of the genomic data
• Chimp genome sequence very different from man
• The strange case of the ‘Humanzee’
• The design of life: part 4—variation-inducing genetic elements and their function
• Chimps ‘natural killers’ after all
Further Reading
• The Great Dothan Debate
• The sticker didn’t stick (or did it?)
• Science Creation and Evolutionism
References

  1. Selman v. Cobb County, 2005 and Kitzmiller v. Dover Area School District, 2005. Return to text.
  2. This was given on 3 January 2006 and can be viewed at http://www.youtube.com/watch?v=JVRsWAjvQSg. Return to text.
  3. Ref. 2, beginning at 0:35:10. Return to text.
  4. Sodera, V., One small speck to man—the evolution myth, 2nd edn, ch. 12, Vij Sodera Productions, 2009. Return to text.

(Frank Cross) #15

Frank: I read the article by Glenn Williamson who discusses at some length the issue of software problems and in his conclusion he is somewhat more charitable than you who thinks Tomkins was “inexcusably wrong.” Hmm.

Steve: What I wrote was my charitable description. I’ll be happy to retract the “inexcusably” adjective if you can provide an excuse. (I’m talking scientifically here – I make no judgments about the man’s character. It’s the work that’s bad.)

Frank (now): I think I don’t actually need an “excuse” to ask you to retract your remark because I never asked you to do so in the first place.

I highlighted your term “inexcusable” because it seemed to me that as one Christian (I am assuming you identify as a Christian) talking about another, namely, Tomkins, that your comment was somewhat over the top.

In reading your response in its entirety I have to say that you demonstrate feelings that could accurately be described as somewhat more than simply assertive and could be construed as mildly aggressive.

May I ask if you gave your feedback to Tomkins inviting as response? It would seem to me the right and proper thing to do, don’t you agree?

Steve: No, I don’t agree. Tomkins has the necessary information from Williamson’s piece, and yet his article is still online. What would be the point? I suppose I could ask him to apologize for impugning my colleague’s scientific competence and integrity with a fatally flawed piece of sciency-looking silliness, but somehow I don’t think that’s what you had in mind. I really don’t see the point of chasing down everyone who has said something wrong about human genetics somewhere on the web.

Frank(now): As one Christian to another I thought you would have done so as a matter of courtesy. Evidently I was mistaken.

The point in contacting him directly, in my view, would have been as stated previously as a matter of courtesy and out of scientific curiosity.

Yes, your aggression is showing through much clearer but I do wonder if you recognize this to be the case.

Anyway, as this is getting a bit lenghty I’m not posting that article and instead below are extracts from another article which cites later work of Tomkins:

Steve: So if you if you stop suffering from a massive bug in the program you’re using to do a completely meaningless analysis, the completely meaningless analysis becomes less grossly wrong. That’s the only thing I can take away here. Did you understand why an ungapped comparison is simply wrong?

Look, if you have any actual scientific criticism to make of the human-chimpanzee comparison, offer it. Address the paper itself, not the misrepresentations by creationists.

Frank (now): You describe Tomkins work as “bad.”

You haven’t actually addressed the points raised in the article I subsequently posted and which does in fact present evidence which conflicts with your particular view of the human-chimpanzee issue.

If you had specific issues with the findings in that article I thought you may address those issues on a point-by-point basis instead of resorting to the dismissive hand-waving away of alleged “misrepresentations by creationists” which is really nothing less than an ad-hominem.
Would you be so kind as to answer a question, please?

But firstly I should like to preface my question with an observation. My observation is based on the assumption that you identify as a Christian and that you would describe yourself as a “theistic evolutionist.”

Science is not static; new discoveries are being made and previously held notions/beliefs/knowledge which at one time were held to be factually true are no longer held to be so and are replaced with new knowledge which is held to be factually true. And this includes in the area of Darwinian evolution.

So, my question, which is based on discussions with quite a number of theistic evolutionists, is this. Why are you and other theistic evolutionists ( I’m not, of course, asking you to speak for all theistic evolutionists and asking only in general terms) so antagonistic and in some instances outright hostile to Christians who believe in either Intelligent Design or Creation?


(James McKay) #16

Hi Frank,

You need to realise here that Tomkins has a PhD in genetics. He knows—or should reasonably be expected to know—what he is doing. Yet he configured his software in ways that were guaranteed to give demonstrably wrong results.

You could argue, of course, that his computing skills are considerably weaker than his genetics skills, but given that he’s programming in Perl (a language whose practitioners tend to be vastly better at programming than the script kiddies who cut and paste SQL injection vulnerabilities from Stack Overflow into their WordPress themes) that’s stretching it, to say the least.

Besides, even if his computing skills really were that weak, this kind of mistake should have been picked up in peer review.

You also need to realise that in many areas of science, engineering and technology, if you get things wrong, you can kill people. For example, what would happen if Tomkins’s error—or at least, his methodology—were influential in the design of some new kind of medical treatment that turned out to be harmful as a result?

So no, speaking as a Christian software developer, “inexcusable” is the correct word here. It’s evidence of a level of sloppiness that is simply not acceptable for anyone working in any area of science or technology.


(Frank Cross) #17

Hi James,

Yes, I realize that Tomkins has a Ph.D in genetics and that’s why I mentioned it in my first post on this topic.

I did post another article which provides information that he used other programmes in addition to the BlastN under discussion.

As a software developer James you’ll know much more than do I whose experience in programming is limited to C++. What I do know is that programmes can be written as you say: “in ways that were guaranteed to give demonstrably wrong results.”

You’ll realize of course that that cuts both ways.

However, I would be very reluctant to say without solid evidence that a scientist who is a Christian would deliberately stack the cards in his favour which in effect would be a fraud. I apply this standard to scientists whether they are IDer’s , creationists, or theistic evolutionists.

It seems to me with my limited programming know-how that projects such as those in which Jeff Tomkins and Steve Schaffner engage in which programmes seem to be a key factor open up the possibility of a number of researcher/operator errors/interpretations. But I do stress that my computing skills are limited and I very well may be one of those in this particular area “who doesn’t know what he’s talking about.”

Now, having said all that, you seem to be taking this beyond just mere researcher/operator error/interpretations in that you are accusing Tomkins that he “configured his software in ways that were guaranteed to give demonstrably wrong results.”

That is a very serious accusation to make. What evidence do you have that he “configured” his programme in such a way? IF your sole defence is that the answer the programme gave is a 70% percent figure I would have to say your defence is very weak indeed and that your accusation is unwarranted.

I asked Steve if he had contacted Jeff Tomkins in this connection and as you probably know he has not done so.

What about you? Have you or will you contact him to point out what in your opinion is a deliberately misleading article?

In common with Steve Schaffner you have made no comment about the subsequent article I posted.


(George Brooks) #18

@Frank

That was an awful lot of text for a position that cannot hold when related evidence is brought to bear. This is one of the amazing strengths of Evolutionary theory in general. It is so robust it survives analysis from dozens of different scientific perspectives!

In the case of the primates … you are propose the following:

“If, in Miller’s view, it is reasonable to believe that the chromosomes became fused in a small population of half-ape/half-humans a few million years ago, why is it not reasonable to believe that this occurred in a small population of actual humans a few thousand years ago? This could have happened very early on in human history, soon after Adam and Eve were expelled from the Garden of Eden, or in a small, isolated group from which Noah and his family were drawn prior to the Flood.”

This means, of course, that the fused chromosome event would have involved one of Noah’s few ancestors, right? If it had happened after Noah, there would be humans without the fused Chromosome, right?

So let’s hang onto this point and bring in the broken Vitamin C gene.

See how the coincidences start to become a little too much to swallow? And this is only the 2nd evidence. We haven’t even begun to discuss the aggregate genetic markers that show approximately when various changes happened, based on analyzing the genetics of all the surviving examples of primates!

But let’s wrap up the Vitamin C issue: Certainly you can’t argue that it is coincidence that Noah’s lineage just coincidentally suffered a corruption of the Vitamin C gene in exactly the same way that the Primates suffered the same corruption.

It seems God is pretty intent on trying to convince Evolution-deniers, that it looks like evolution! He gives primates the same chromosome count as pre-Fusion humans … and then creates all these primate kinds (and humans) with exactly the same broken Vitamin C gene.

But he breaks the Vitamin C gene in guinea pigs and fruit bats in 2 other ways.

I can only guess that the reason you oppose Common Ancestry is that you think it is unlikely that natural selection can work quickly enough to cause speciation. And yet, if all terrestrial life was destroyed in the Global Flood, then all the hundreds of thousands (nay, millions!) of terrestrial “species” and “kinds” that we find on Earth today had to be speciated from the surviving kinds released from the Ark!


(Steve Schaffner) #19

I didn’t suggest you had. My point was that my description is evidence-based, and I will change it if offered evidence.

I’m a scientist. Scientists typically react vigorously, even aggressively, to bad science. That doesn’t mean we don’t like the person responsible (although that happens too). It means we don’t tolerate crappy science out of politeness.

I don’t see what courtesy has to do with this issue. I’m responding publicly to a published, nominally scientific argument, just as Tomkins responded publicly to our published work on the chimpanzee genome. As for scientific curiosity – no. Just no. I’ve read Tomkins’ article, and there is nothing of scientific interest in it.

Pick a particular claim and we can discuss it in detail. I don’t have the time to undertake a response to the whole thing. We have a Zika paper to get this week.

I’m not hostile to Christians who are creationists. I was raised as a creationist, my mother was a creationist, many members of my church are creationists. I pray with them, worship with them and hang out with them. I am hostile toward bad arguments and falsehoods, especially when offered in the name of Christ. I am hostile toward professional creationists, because they produce and promote those bad arguments and falsehoods; based on decades of experience with the material they produce on science, it is routinely wrong, misleading and unscientific. I am hostile to attempts to stake the truth of the gospel to the rejection of science – I think it’s bad for the church, especially bad for our young people, bad for science and bad for society.


#20

Let’s leave tone trolling out of the discussion.