review of YEC 'science' paper

[SLP]

PART 1

I wrote this some time ago but never got around to posting it...

Here is a treatment of the ICR article “New Research Undermines Key Argument for Human Evolution” by Jeffrey Tomkins, Ph.D. YECs make much of Tomkins’ credentials (argument from authority) , but even with his credentials, his scientific output is pretty sparse – 15 publications in 19 years (I have a mere 9 publications, but then, they all came out in a 4 year period and I have only engaged in summer research projects with undergrads since then). He has since ran off from academia, and now works for ICR, churning out poorly supported knee-jerk diatribes attempting to rebut real research that does not jive with his bible-based ‘reality.’ Odd how so many legitimate scientists abandon science and reason when they decide to become full-time bible propagandists.

Anyway, I will take a look at Tomkins’ article point by point. I am including large-scale quoting from the article to avoid the usual accusations; I am omitting only passages that are irrelevant to the points being discussed.
On to YEC diatribe 1:

One of the leading arguments for human evolution from a shared common ancestor with apes is the “chromosome 2 fusion model.”

Hyperbole/misrepresentation in the very first sentence. The chromosome fusion model is an EXPLANATION as to why humans and the other apes have different karyotypes. It is not a ‘leading argument’ for shared ancestry.

New research is now seriously undermining the validity of the fusion model and human evolution in general. This author and Professor Dr. Jerry Bergman of Northwest State College, Ohio,

I am unsure why this embellishment continues to be made. In an email exchange Jerry and I had several years ago, he provided the following signature:

Jerry Bergman, Ph.D.
Department of Biology and Chemistry
Northwest State College
22600 State Route 34
Archbold, Ohio 43502
The only college in Archbold, Ohio, with the name “Northwest State College” in its name is Northwest State Community College, where Bergman is indeed listed as a faculty member. While this has noting specifically to do with their argument, it does call into question Bergman’s integrity – and integrity has been argued by a CARM creationist as being very important in deciding whether or not to trust a person’s argument.*
Anyway…

1. The purported fusion site on human chromosome 2 is actually located in a different position on chromosome 2 than predicted by the fusion model. The hypothetical fusion site is also in an area with suppressed recombination (meaning that the fusion sequence should be very pristine) and should exhibit very little degeneracy, compared to standard telomere sequence. Telomere sequences in humans normally consist of thousands of repeats of the standard 6-base sequence “TTAGGG.” We found that the hypothetical fusion region is completely degenerate and vaguely represents anything close to intact and fused telomeres.

Comment on this after my comment below.

An earlier 2002 research report by molecular evolutionists also made note of this extreme sequence degeneracy and the obvious discrepancies it presented for the evolutionary model.3

The ‘3’ refers to this paper:
3.Fan, Y. et al. 2002. Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes. Genome Research. 12 (11): 1651-1662.
It is available as a full free-text article. I urge any and all interested folks to read the paper in question and draw your own conclusions as to whether or not Bergman and Tomkins are accurately reporting the paper’s reported findings.
For a taste, I present the first part of the paper’s “Molecular Characteristics of the Fusion” section:

When observed at the sequence level, the ancestral chromosomes appear to have undergone a straightforward fusion. The sequence of RP11–395L14, like the cosmid partially sequenced by Ijdo et al. (1991), shows two head-to-head arrays of degenerate telomere repeats at the 2q fusion site, with no other sequence between the arrays. This observation indicated that the two ancestral chromosomes had joined end-to-end within the terminal telomeric repeats, with subsequent inactivation of one of the two centromeres. Kasai et al. (2000) showed using FISH that the chromosomes underwent no gross alteration in structure: The relative order of 38 cosmids derived from 2q12–2q14 was the same on human chromosome 2 and the short arms of chimpanzee chromosomes 12 and 13. Although the sequence is not yet available from the terminal regions of chimpanzee chromosomes 12p and 13p with which to compare to human 2q13–2q14.1, the human sequence is very similar to two extant human subtelomeres (9pter and 22qter) (Fig.3, Table 1). Very little, if any, distal material is unaccounted for in the two comparisons.​

So, what about this ‘extreme degeneracy’ and ‘discrepancy’ stuff? In classic YEC style, they report the supposed problem, but ignore plausible explanations:

&#8221; If the fusion occurred within the telomeric repeat arrays less than &#8764;6 Mya, why are the arrays at the fusion site so degenerate? The arrays are 14% diverged from canonical telomere repeats (not shown), whereas noncoding sequence has diverged <1.5% in the &#8764;6 Mya since chimpanzee and humans diverged (Chen and Li 2001) (Fig. 5). There are three possible explanations: (1) Given the many instances of degenerate
telomeric arrays within the subtelomeric regions of human chromosomes (Riethman et al. 2001), the chromosomes joined at interstitial arrays near, but not actually at, their
ends. In this case, material from the very ends of the fusion partners would have been discarded. (2) The arrays were originally true terminal arrays that degenerated rapidly after the fusion. This high rate of change is plausible, given the remarkably high allelic variation observed at the fusion site. The arrays in the BAC and the sequence obtained by Ijdo et al. (1991) differ by 12%, which is high even if some differences are ascribed to experimental error. (3) Some array degeneracy could be a consequence of sequencing errors. We have not been able to PCR successfully across the fusion site, which would be required to assess the contribution of sequencing errors to this measure of fusion-site sequence polymorphism. However, explanation 2is supported by the high variability
among allelic copies of other interstitial telomeric repeats and associated regions sequenced by Mondello et al. (2000) (AF236886 and AF236885). Considering the high mutability of interstitial telomere repeat arrays, the fusion partners could have joined either within terminal or subterminal arrays to form chromosome 2.&#8221;​

Huh&#8230;
In reference to their point 1 &#8211; the Abstract of that same paper:

Human chromosome 2 was formed by the head-to-head fusion of two ancestral chromosomes that remained separate in other primates. Sequences that once resided near the ends of the ancestral chromosomes are now interstitially located in 2q13&#8211;2q14.1. Portions of these sequences had duplicated to other locations prior to the
fusion. Here we present analyses of the genomic structure and evolutionary history of >600 kb surrounding the fusion site and closely related sequences on other human chromosomes. Sequence blocks that closely flank the inverted arrays of degenerate telomere repeats marking the fusion site are duplicated at many, primarily
subtelomeric, locations. In addition, large portions of a 168-kb centromere-proximal block are duplicated at 9pter, 9p11.2, and 9q13, with 98%&#8211;99% average sequence identity. A 67-kb block on the distal side of the fusion site is highly homologous to sequences at 22qter. A third &#8764;100-kb segment is 96% identical to a region in
2q11.2. By integrating data on the extent and similarity of these paralogous blocks, including the presence of phylogenetically informative repetitive elements, with observations of their chromosomal distribution in nonhuman primates, we infer the order of the duplications that led to their current arrangement. Several of these duplicated blocks may be associated with breakpoints of inversions that occurred during primate evolution and of recurrent chromosome rearrangements in humans.​

2. At the purported fusion site, there is a very small number of intact telomere sequences and very few of them are in tandem or in the proper reading frame.

As telomeres are not transcribed or translated, I have to wonder why the authors mention reading frame at all&#8230;

The small number of randomly interspersed telomere sequences, both forward (&#8220;TTAGGG&#8221 and reverse (&#8220;CCCTAA&#8221, that populate both sides of the purported fusion site are not indicative of what should be found if an end-to-end chromosomal fusion actually took place.

Then one has to wonder why Bergman and Tomkins cited a paper that states, quite clearly, the very opposite of that. Allow me to reiterate:

&#8221; When observed at the sequence level, the ancestral chromosomes appear to have undergone a straightforward fusion.&#8221;​

3. The 798-base core sequence surrounding the fusion site is not unique to the purported fusion site, but found throughout the human genome with similar sequences (80 percent or greater identity) located on nearly every chromosome. This indicates that the fusion site is some type of commonly occurring fragment of DNA in the human genome.

And the problem is&#8230;.?
They don&#8217;t really say&#8230;
None of this is evident or even mentioned in the 2002 paper they site. Perhaps it is their &#8220;original&#8221; research? If so, it is at odds with the 2002 paper they do cite.

4. No positionally corresponding regions of sequence similarity in the chimpanzee genome for the purported human fusion site were found. The 798-base core fusion-site sequence did not align (match) to any corresponding regions in the chimp genome. In fact, the sequence was considerably less common and more dissimilar in chimpanzees.

I suppose this is in reference to their &#8216;research&#8217;. If so, I have to question its veracity. I am in the process of reviewing one of Tomkins other papers, and he likes to play games with BLASTN to get what he wants. Of interest, Todd Wood recently published a paper using a BLASTN search and concluded that human and chimp genomes are ~98% identical. Tomkins did not like that, and in his paper he also used BLASTN to conclude that they are really only about 80% identical. How could two analyses using the same search tool come up with such different results? Well, Tomkins rigged his analyses: he ran three different searches, but only wanted returns if there were 5, 10, or 15 nucleotide blocks that were 100% identical.
So say you look at 10 15-mer blocks of sequence. 9 of them are 100% identical. In 1 of them, there is a 14 out of 15 nucleotide match. But if you were searching for 100% identity in 15-mer blocks, your &#8216;result&#8217; would show a 90% identity, rather than a 99.3% identity. IOW, Tomkins set the parameters of his BLASTN searches to return lower-than-actual percent identity, then boasted about how much lower HIS figures were than Wood&#8217;s&#8230; I suspect that they&#8217;ve done something similar here.

5. Queries against the chimpanzee genome with fragments of human DNA sequence (alphoid sequences) found at the purported cryptic centromere site on human chromosome 2 did not produce any significant hits using two different DNA matching algorithms (BLAT and BLASTN).

See above.

6. The purported cryptic centromere on human chromosome 2, like the fusion site, is in a very different location to that predicted by a fusion event.

Again, allow me to quote the paper that THEY cited:

&#8221; When observed at the sequence level, the ancestral chromosomes appear to have undergone a straightforward fusion.&#8221;​

7. The DNA alphoid sequences at the putative cryptic centromere site are very diverse and form three separate sub-groups. They also do not closely match known functional human centromeric alphoid elements. Alphoid sequences are commonly found throughout the human genome, and some types of alphoid sequences are not associated with centromeres. This strongly diminishes their probability of being part of an ancient de-activated (cryptic) centromere.

Hmmmm&#8230; So, are these folks of the same group of &#8216;scientists&#8217; as John Woodmorappe, who claims that ALL transposons are functional? L1 elements are also found throughout the genome. Some of them are associated with chromosome breakpoints (facilitating rearrangements), others are found nowhere near such places and fully intact. Reading the Fan et al. paper that THEY cite, I see no mention of alphoid sequences. Must be that those authors didn&#8217;t think much of them.

This human chromosome 2 research will be described in more detail in an upcoming Journal of Creation issue. Despite evolutionists&#8217; insistence that the chromosome 2 fusion model supports a human-chimp common ancestor, the so-called supporting data are not present.

According to the paper Bergman and Tomkins cited twice, the &#8216;so-called&#8217; supporting data is not only present, but trivially obvious. Of course, one has to wonder why, if their evidence is so rock-solid, it is being published in a magazine whose authors have to run a gauntlet manned by editors that ascribe to a statement of Faith?

Journal of Creation is dedicated to upholding the authority of the 66 books of the Bible, especially in the area of origins. All our editors adhere to the Creation Ministries International (CMI) Statement of Faith and most papers will be designed to support this.​

 

[SLP]

PART 2

All evidence points to man and ape as unique and separate creations.

Classic non sequitur.

References
1. Yunis, J. J. and O. Prakash. 1982. The Origin of Man: A Chromosomal Pictorial Legacy. Science. 215 (4539): 1525-1530.
2. Tomkins, J. 2011. New Human-Chimp Chromosome 2 Data Challenge Common Ancestry Claims. Acts & Facts. 40 (5): 6.
3. Fan, Y. et al. 2002. Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes. Genome Research. 12 (11): 1651-1662.
* Dr. Tomkins is a Research Associate and received his Ph.D. in Genetics from Clemson University.​

3 whole references!

What they did not cite:


Origin of human chromosome 2: An ancestraltelomere-telomere fusion. 1991.

"We have identified two allelic genomic cosmids from human chromosome 2, c8.1 and c29B, each containing two inverted arrays of the vertebrate telomeric repeat in a head-to-head arrangement, 5'(TTAGGG),,- (CCCTAA),,3'. Sequences fln g this telomeric repeat are characteristic of present-day human pretelomeres. BAL-31 nuclease experiments with yeast artificial chromosome clones of human telomeres and fluorescence in situ hybridization reveal that sequences flanking these inverted repeats hybridize
both to band 2q13 and to different, but overlapping, subsets of human chromosome ends. We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomeretelomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.​

Comparative FISH mapping of the ancestral fusion point of human chromosome 2.2000

Abstract

It is known that human chromosome 2 originated from the fusion of two ancestral primate chromosomes. This has been confirmed by chromosome banding and fluorescence in-situ hybridization (FISH) with human chromosome-2-specific DNA libraries. In this study, the order of 38 cosmid clones derived from the human chromosome region 2q12-q14 was exactly determined by high-resolution FISH in human chromosome 2 and its homologous chromosomes in chimpanzees (Pan trogrodydes, 2n=48) and cynomolgus monkeys (Macacafascicularis, 2n = 42). This region includes the telomere-to-telomere fusion point of two ancestral ape-type chromosomes. As a result of comparative mapping, human chromosome region 2q12-q14 was found to correspond to the short arms of chimpanzee chromosomes 12 and 13 and cynomolgus monkey chromosomes 9 and 15. It is noted that no difference was detected in the relative order of the cosmid clones between human and chimpanzee chromosomes. This suggests that two ancestral ape-type chromosomes fused tandemly at telomeres to form human chromosome 2, and the genomic organization of this region is thought to be considerably conserved. In the cynomolgus monkey, however, the order of clones in each homologue was inverted. In addition to cosmid mapping, two chromosome-2-specific yeast artificial chromosome (YAC) clones containing the fusion point were identified by FISH."​

Human intrachromosomal telomeric-like repeats: sequence organization and mechanisms of origin. 2001

"The intrachromosomal location of (T2AG3)n telomeric sequences has been reported in several species. It was proposed that interstitial telomeres (ITs) originated through telomeric fusion of ancestral chromosomes. However, the data so far obtained derive mainly from cytogenetic observations. Cloning and database searching of human IT sequences allowed us to identify three classes: (i) short ITs, composed of few, essentially exact T2AG3 units; (ii) subtelomeric ITs, composed of larger arrays (several hundred base pairs) including many degenerate units within subtelomeric domains; (iii) fusion ITs, in which two extended stretches of telomeric repeats are oriented head-to-head. The number of short ITs is over 50 and subtelomeric ITs are probably present at all chromosomal ends. Surprisingly, the telomeric sequence in 2q13 remains the only fusion IT so far characterized, and evidence presented here suggests that another member of this class may be present in 1q41. Different molecular mechanisms generated the three classes. In particular, several short ITs interrupt precisely repetitive elements or are flanked by direct repeats of 10-41 bp, and are conserved in gorilla and chimpanzee. These features strongly suggest that telomeric repeats were inserted at intrachromosomal sites through the repair of double-strand breaks that occurred in the germline during evolution."​

&#8216;Nuff said.

 

[sfs]

I suppose this is in reference to their ‘research’. If so, I have to question its veracity. I am in the process of reviewing one of Tomkins other papers, and he likes to play games with BLASTN to get what he wants. Of interest, Todd Wood recently published a paper using a BLASTN search and concluded that human and chimp genomes are ~98% identical. Tomkins did not like that, and in his paper he also used BLASTN to conclude that they are really only about 80% identical. How could two analyses using the same search tool come up with such different results? Well, Tomkins rigged his analyses: he ran three different searches, but only wanted returns if there were 5, 10, or 15 nucleotide blocks that were 100% identical.
So say you look at 10 15-mer blocks of sequence. 9 of them are 100% identical. In 1 of them, there is a 14 out of 15 nucleotide match. But if you were searching for 100% identity in 15-mer blocks, your ‘result’ would show a 90% identity, rather than a 99.3% identity. IOW, Tomkins set the parameters of his BLASTN searches to return lower-than-actual percent identity, then boasted about how much lower HIS figures were than Wood’s… I suspect that they’ve done something similar here.
See above.

It's possible that Tomkins was also bitten by a buggy version of BLAST when he did his analysis. See here and here.

 

[Aggie]

Note that their article says, "This human chromosome 2 research will be described in more detail in an upcoming Journal of Creation issue." I'm pretty sure these are the two papers they were referring to:

http://creation.com/images/pdfs/tj/j25_2/j25_2_106-110.pdf
http://creation.com/images/pdfs/tj/j25_2/j25_2_111-117.pdf

What these papers claim to show is that the structure of human chromosome 2 is different from what it would be if our ancestors' chromsomes 2p and 2q had fused together in a simple manner. What makes this interesting is that around six months later, Ventura et al. reached the same conclusion in a Genome Research paper. Carl Zimmer summarized the paper's conclusions here. These results show is that our what had been our current model of the chromosome 2 fusion was in fact incorrect.

If you look closely at the data in the Tomkins and Bergman papers, they're discussing some of the same problems with the current model that Ventura et al. discussed about six months later. Even though Tomkins and Bergman were wrong that the genetic data is incompatible with shared ancestry between humans and apes, they were right that it showed the current model was inaccurate, and they presented data showing this about six months before mainstream scientists demonstrated the same thing.

I've come across a few examples of things like this while researching creationist arguments for the evolution book I'm working on. Creation science has become a lot more sophisticated over the past decade or so, and even though their conclusions still are usually wrong, you can't always assume that their data itself is invalid.

 

[SLP]

It's possible that Tomkins was also bitten by a buggy version of BLAST when he did his analysis. See here and here.

In fact, sfs - Tomkins had a script written specifically to return only ungapped matches*. That is, IMO< he purposefully rigged his analysis to get results that would indicate a lower than usual % identity (this is detailed in one of his later papers).

AFAIAC - he lied for Jesus.


*see: https://answersingenesis.org/answer...analysis-of-chimpanzee-and-human-chromosomes/

"BLASTN algorithm parameters for the main study were as follows: -word_size 11, -evalue 10, -max_target_seqs 1, -dust no, -soft_masking false, -ungapped. "

 

[SLP]

Note that their article says, "This human chromosome 2 research will be described in more detail in an upcoming Journal of Creation issue." I'm pretty sure these are the two papers they were referring to:

http://creation.com/images/pdfs/tj/j25_2/j25_2_106-110.pdf
http://creation.com/images/pdfs/tj/j25_2/j25_2_111-117.pdf

What these papers claim to show is that the structure of human chromosome 2 is different from what it would be if our ancestors' chromsomes 2p and 2q had fused together in a simple manner. What makes this interesting is that around six months later, Ventura et al. reached the same conclusion in a Genome Research paper. Carl Zimmer summarized the paper's conclusions here. These results show is that our what had been our current model of the chromosome 2 fusion was in fact incorrect.

If you look closely at the data in the Tomkins and Bergman papers, they're discussing some of the same problems with the current model that Ventura et al. discussed about six months later. Even though Tomkins and Bergman were wrong that the genetic data is incompatible with shared ancestry between humans and apes, they were right that it showed the current model was inaccurate, and they presented data showing this about six months before mainstream scientists demonstrated the same thing.

I've come across a few examples of things like this while researching creationist arguments for the evolution book I'm working on. Creation science has become a lot more sophisticated over the past decade or so, and even though their conclusions still are usually wrong, you can't always assume that their data itself is invalid.

Good points. But I am far more concerned with their apparent willingness to rig data analyses only to boast about how robust their 'science' is.

 

[sfs]

In fact, sfs - Tomkins had a script written specifically to return only ungapped matches*. That is, IMO< he purposefully rigged his analysis to get results that would indicate a lower than usual % identity (this is detailed in one of his later papers).

AFAIAC - he lied for Jesus.


*see: https://answersingenesis.org/answer...analysis-of-chimpanzee-and-human-chromosomes/

"BLASTN algorithm parameters for the main study were as follows: -word_size 11, -evalue 10, -max_target_seqs 1, -dust no, -soft_masking false, -ungapped. "

Yes, I know. My point was that the version of BLAST that was publicly available around the time when Tomkins did his study (or at least the study I'd heard about) had a bug that made ungapped searches look even worse than they should. In the two posts I linked to, I did a similar analysis of my own, and found that non-buggy but ungapped searches did indeed do worse than gapped searches, but not anywhere near as bad as Tomkins reported, while buggy searches did very badly indeed.

 

[SLP]

Yes, I know. My point was that the version of BLAST that was publicly available around the time when Tomkins did his study (or at least the study I'd heard about) had a bug that made ungapped searches look even worse than they should. In the two posts I linked to, I did a similar analysis of my own, and found that non-buggy but ungapped searches did indeed do worse than gapped searches, but not anywhere near as bad as Tomkins reported, while buggy searches did very badly indeed.

Hoisted by his own petard, as it were..

 

[Aggie]

Yes, I know. My point was that the version of BLAST that was publicly available around the time when Tomkins did his study (or at least the study I'd heard about) had a bug that made ungapped searches look even worse than they should. In the two posts I linked to, I did a similar analysis of my own, and found that non-buggy but ungapped searches did indeed do worse than gapped searches, but not anywhere near as bad as Tomkins reported, while buggy searches did very badly indeed.

Can anyone provide some further documentation about this bug? I'd like to be able to explain how this study obtained a similarity of 70%, but it would be best to have an explanation I can cite that's more authoritative than a forum post.

 

[sfs]

Can anyone provide some further documentation about this bug? I'd like to be able to explain how this study obtained a similarity of 70%, but it would be best to have an explanation I can cite that's more authoritative than a forum post.

Aggie -- I saw your message, but I'm scrambling to finish some work right now. I can send you the email from NCBI, and point you to what might be the bug fix in a later version. PM me again if you haven't heard from me in a week.

 

[whois]

Good points. But I am far more concerned with their apparent willingness to rig data analyses only to boast about how robust their 'science' is.

to imply "creation scientists" only do this is simply wrong.
journals.plos.org/plosone/article?id=10.1371/journal.pone.0005738

on an unrelated note:
Biology Direct | Full text | On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence

 

[SLP]

Can anyone provide some further documentation about this bug? I'd like to be able to explain how this study obtained a similarity of 70%, but it would be best to have an explanation I can cite that's more authoritative than a forum post.

sfs seems to know about the bug - for my part, the fact that Tomkins had a script written for his BLASTN searches that would only return matches with no gaps seems pretty clear to me that he had rigged his search for the purpose of getting lover-percent results. Todd Wood (a YEC) did a search without such a limitation and got the standard 90+% range.

 

[SLP]

to imply "creation scientists" only do this is simply wrong.
journals.plos.org/plosone/article?id=10.1371/journal.pone.0005738

I don't recall making any such implication.

I do recall finding Tomkins' insistence that he "stands by his conclusions" to be standard YEC practice, even when confronted with the fact that their cat is out of the bag.

on an unrelated note:
Biology Direct | Full text | On universal common ancestry, sequence similarity, and phylogenetic structure: The sins of P-values and the virtues of Bayesian evidence

Yes, totally unrelated.

Was that on your hard drive too?

 

[whois]

I don't recall making any such implication.

the link was posted for clarification.

I do recall finding Tomkins' insistence that he "stands by his conclusions" to be standard YEC practice, even when confronted with the fact that their cat is out of the bag.

well, now the "cat is out of the bag" for both sides.

Yes, totally unrelated.

but relevant to the discussion.

Was that on your hard drive too?

yes, the entire text, all 25 pages, can be posted at your insistence.

 

[PsychoSarah]

PART 2



Classic non sequitur.

References
1. Yunis, J. J. and O. Prakash. 1982. The Origin of Man: A Chromosomal Pictorial Legacy. Science. 215 (4539): 1525-1530.
2. Tomkins, J. 2011. New Human-Chimp Chromosome 2 Data Challenge Common Ancestry Claims. Acts & Facts. 40 (5): 6.
3. Fan, Y. et al. 2002. Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes. Genome Research. 12 (11): 1651-1662.
* Dr. Tomkins is a Research Associate and received his Ph.D. in Genetics from Clemson University.​

3 whole references!

And one is very old, about 30 years old, and the other seems to be a citation of themselves. So, 1 reference with even a chance of really being valid.

 

[Aggie]

sfs seems to know about the bug - for my part, the fact that Tomkins had a script written for his BLASTN searches that would only return matches with no gaps seems pretty clear to me that he had rigged his search for the purpose of getting lover-percent results. Todd Wood (a YEC) did a search without such a limitation and got the standard 90+% range.

Most of the other creationist analyses that were limited to "ungapped" results produced a similarity in the 80-90% range. What I'm looking for is an explanation for why this particular one was so much lower. The 70% paper is important to address because at this point it's probably the best-known creationist paper comparing chimpanzee and human DNA. Google scholar shows it's been cited 32 times, which is above-average for a paper that's only two years old.

 

[SLP]

Most of the other creationist analyses that were limited to "ungapped" results produced a similarity in the 80-90% range. What I'm looking for is an explanation for why this particular one was so much lower. The 70% paper is important to address because at this point it's probably the best-known creationist paper comparing chimpanzee and human DNA. Google scholar shows it's been cited 32 times, which is above-average for a paper that's only two years old.

It seems most of the citations are Tomkins himself and other creationists.

 

[Loudmouth]

In fact, sfs - Tomkins had a script written specifically to return only ungapped matches*. That is, IMO< he purposefully rigged his analysis to get results that would indicate a lower than usual % identity (this is detailed in one of his later papers).

AFAIAC - he lied for Jesus.


*see: https://answersingenesis.org/answer...analysis-of-chimpanzee-and-human-chromosomes/

"BLASTN algorithm parameters for the main study were as follows: -word_size 11, -evalue 10, -max_target_seqs 1, -dust no, -soft_masking false, -ungapped. "

Since he described his methodology, the figures he gave are not dishonest in and of themselves. It only became dishonest when he used his ungapped alignments to cast doubt on the gapped alignments. If you use two different methodologies for aligning sequence, it is not a big surprise that you get two different numbers.

My memory may be failing me, but I thought I remembered Tomkins or someone else using the same ungapped analysis for comparing human genomes to each other. As expected, the result was lower sequence homology than what was reported for a gapped analysis of human genomes.

In the end, what really matters is the results you get when comparing multiple species using the same methodology. I doubt Tomkins would want to report that his methodology shows more differences between chimps and gorillas than chimps and humans.

 

[Aggie]

My memory may be failing me, but I thought I remembered Tomkins or someone else using the same ungapped analysis for comparing human genomes to each other. As expected, the result was lower sequence homology than what was reported for a gapped analysis of human genomes.

Can you find a source for that? I'd find it very useful to know where this was mentioned.

 

[Loudmouth]

Can you find a source for that? I'd find it very useful to know where this was mentioned.

Did a bit of digging and found it.

Over at Uncommon Descent, &#8220;niwrad&#8221; is back with more calculations showing that conventional figures for comparing sequences of genomes are all wrong. Last time &#8220;niwrad&#8221; showed that humans and chimp genomes match only about 62% of the time. The usual figure given is 98.77%. Niwrad did this by taking 30-base chunks of one genome, finding the best match in the other genome, and then asking what fraction of the time there was a perfect match of all 30 bases. That&#8217;s where the 62% figure comes from. I immediately pointed out here at PT that this was expected and did not represent some insightful new way of calculating these figures.

Now Niwrad has turned to comparing two human genomes. The figure for 30-base perfect matches is about 96%. The conventional figure is about 99.9%. Let&#8217;s see what is expected. If a single base position has a 0.999 probability of matching, two bases have a 0.999x0.999 probability, three bases a 0.999x0.999x0.999 probability. 30 bases then have a probability that is 0.999 raised to the 30th power. Which turns out to be (ta-da!) 0.97. Not a bad fit.

99.9% Wrong - The Panda's Thumb​

If we were to use creationist math, we could use this creationist study showing that two unrelated humans share 96% DNA while humans and chimps share 98% of their DNA. Chimps are more closely related to humans that we are to each other!!!!!!1111!!1!

Here is the link at Uncommon Descent:
http://www.uncommondescent.com/intelligent-design/a-statistical-comparison-of-two-human-genomes/