Uncommon Descent Serving The Intelligent Design Community

Human and chimp DNA: They really are about 98% similar

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

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

Dr. Wile reports:

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

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

Here is what Glenn Williamson has to say about himself:

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

I don’t have any formal qualifications in genetics, or anything biological for that matter. I have a bachelors degree in computing science (i.e. programming) from the University of Technology in Sydney. Started my career as a programmer, but transitioned into derivatives trading, which is a lot more fun…

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

Glenn Williamson’s detailed takedown of Dr. Tomkins’s 70% similarity figure can be accessed here. Dr. Tomkins claims he submitted his paper to the creationist publication, Answers Research Journal, but it was never published. Here’s an excerpt from the paper (emphasis mine – VJT):

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

What happened next? Dr. Wile takes up the story:

As a result, Dr. Tomkins redid his study, using the one version of BLAST that did not contain the bug. His results are shown above… The overall similarity between the human and chimpanzee genomes was 88%.

In an update at the top of his post, Dr. Wile now admits to having cold feet, even about the revised 88% figure:

Based on comments below by Glenn (who is mentioned in the article) and Aceofspades25, there are questions regarding the analysis used in Dr. Tomkins’s study, upon which this article is based. Until Dr. Tomkins addresses these questions, it is best to be skeptical of his 88% similarity figure.

So what was wrong with Dr. Tomkins’s new study? I’ll let Glenn Williamson explain (emphasis mine – VJT):

October 16, 2015 4:22 pm

As I’ve said many times, if there is a single base pair indel in the middle of a 300bp sequence, Tomkins will say this is a 50% match.

Tomkins is most certainly aware of this, yet he chose to publish it. I think that says pretty much everything.

Another commenter named Aceofspades25 has this to add (emphases mine – VJT):

October 16, 2015 2:13 pm

The other obvious thing that Thompkins hasn’t dealt with in his BLASTN analysis, I talk about here.

There are a few cases where no match will be found because this entire sequence appears de-novo in Chimpanzees as the result of a single mutation (e.g. a novel transposable element – see here) or because humans have had a large deletion which other primates don’t. Deletions like this also likely occurred in a single mutation – see here

Thompkins (sic) would count both of these as being a 0% match (or 600 effective mutations if the sequences he was searching for were 300bp each). In reality, these probably represent just 2 mutations.

I’ll let Glenn Williamson have the final word (emphases mine – VJT):

Thanks Ace, for letting me know about this post. I reiterate here a few things about my (unpublished!) paper, and about Tomkins’ new paper.

The first thing is that he uses the “ungapped” parameter in his BLAST comparisons. As I’ve written in a few other places now, using this parameter, and calculating results in the way that Tomkins does is entirely disingenuous. If you are comparing two 300bp sequences, and one of those sequences has a single indel smack bang in the middle, Tomkins counts this as the sequences being only 50% identical.

I’ve told him at least twice that he cannot use ungapped and then calculate the result in this way. He can do one of two things:

1. Use ungapped, which ignores indels and therefore he can only report the substitution rate. (emphasis mine – VJT)If he did this, he would get a result of around 98.8%.

2. Allow gaps, and – this is what he fails to mention in his paper – get a result of around 96.9%. And this is using a very conservative method of calculation as well, since it counts a 50bp indel as having the same weight as 50 individual mutations. If you counted a 50bp indel as a single event (which it probably was), then the overall result would be pushed up towards 98%, which is the figure usually thrown around anyway.

In a comment dated 14 August 2015 (at 03:44) on an article titled, Chimp and Human DNA vs “Sophisticated Nonsense”! on a blog called Marmotism, Glenn Williamson adds:

I’ve actually written a paper on Tomkins’ 70% result, and have _ATTEMPTED_ to get it published in Answers Research Journal. Obviously they are not having a bar of it – Tomkins is the sole peer-reviewer, and he is currently refusing to provide any critique of my work – he has been silent for 8 months, while the ball is in his court ..

See the paper here:

https://www.dropbox.com/sh/dm2lgg0l93sjayv/AAATnWSJdER53EYEYZvcgiwma?dl=0

It’s the two PDFs ..

Dr. Tomkins’s latest article in Answers Research Journal (October 7, 2015) acknowledges Williamson’s work in a single sentence:

As of 2013, the issue of overall genome similarity between chimpanzee and humans seemed to be about 70% based on five different reports, three of which were based on actual data analyses. However, in 2014 , a computer programmer of financial trading algorithms discovered an apparent bug in the BLASTN algorithm and notified this author of the situation (Glenn Williamson, Tibra Capital, personal communication).

So, a submitted article only counts as a “personal communication”? Perhaps Dr. Tomkins needs to be a little more up-front about giving credit where credit is due, and acknowledging his mistakes. At any rate, the ball is definitely in his court, and his latest 88% similarity figure warrants skepticism. I have to say that Dr. Tomkins’s methodology sounds rather suspicious to me.

What do readers think?

Comments
This would be surprising, as “junk dna” should drift at a rate of about 1% per million years (if I recall correctly).
You do not. Junk DNA would drift at the individual mutation rate ~ 2e-8mu/site/generation. In 15 year generations that's' (2e-8 mut/site) / 15 years ) * 6 million years = 0.008 mutations per site per branch Two branches makes 1.6% divergence which is about what we actually see. That's a very back-of-the-envelope sort of calculation, but shows we are in about the right place. (you might be thinking of the so called "2% rule" for mitochondrial DNA, which has a much higher mutation rate)wd400
October 22, 2015
October
10
Oct
22
22
2015
03:55 PM
3
03
55
PM
PDT
Zachriel:
Andre: How did 60 000 000 Base pair differences become fixed in only a short 6 000 000 years of unguided evolution from out last common ancestor? The average human has 175 mutations or so, most of them neutral. The rate of fixation of neutral mutations is the same as the rate of introduction of neutral mutations, so 175 mutations will become fixed per generation. Six million years is about 300,000 generations, which leads to the fixation of about 50 million mutations. Give or take.
50 billion mutations would make no difference let alone 50 million. The search space is not 60 million but 4 ^ 60 million. Stop lying, Zachriel.Mapou
October 22, 2015
October
10
Oct
22
22
2015
03:53 PM
3
03
53
PM
PDT
"Both combined." Is that so? Who exactly are you trying to kid? I or yourself?Vy
October 22, 2015
October
10
Oct
22
22
2015
03:53 PM
3
03
53
PM
PDT
In supplement to post 13, to further falsify the erroneous Darwinian belief that mutations to DNA will generate new body plans, according to the following experiments, the ‘form’ of a body plan is not reducible to any conceivable mechanism of molecular reductionism, i.e. reductive materialism, as is falsely presupposed in neo-Darwinian evolution:
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012 Excerpt: The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. http://www.netfuture.org/2012/May1012_184.html#2 What Do Organisms Mean? Stephen L. Talbott – Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,, http://www.thenewatlantis.com/publications/what-do-organisms-mean “Last year I had a fair chunk of my nose removed in skin cancer surgery (Mohs). The surgeon took flesh from a nearby area to fill in the large hole he’d made. The pictures of it were scary. But in the healing process the replanted cells somehow ‘knew’ how to take a different shape appropriate for the new location so that the nose now looks remarkably natural. The doctor said he could take only half the credit because the cells somehow know how to change form for a different location (though they presumably still follow the same DNA code) . — I’m getting the feeling that we’ve been nearly as reductionist in the 20-21st century as Darwin and his peers were when they viewed cells as little blobs of jelly.” leodp – UD blogger https://uncommondescent.com/evolution/whats-this-about-the-strange-inevitability-of-evolution/#comment-563451 Epigenetics and neuroplasticity: The case of the rewired ferrets – April 3, 2014 Excerpt: Like inventive electricians rewiring a house, scientists at the Massachusetts Institute of Technology have reconfigured newborn ferret brains so that the animals’ eyes are hooked up to brain regions where hearing normally develops. The surprising result is that the ferrets develop fully functioning visual pathways in the auditory portions of their brains. In other words, they see the world with brain tissue that was only thought capable of hearing sounds. – per UD If DNA really rules (morphology), why did THIS happen? – April 2014 Excerpt: Researchers implanted human embryonic neuronal cells into a mouse embryo. Mouse and human neurons have distinct morphologies (shapes). Because the human neurons feature human DNA, they should be easy to identify. Which raises a question: Would the human neurons implanted in developing mouse brain have a mouse or a human morphology? Well, the answer is, the human neurons had a mouse morphology. They could be distinguished from the mouse ones only by their human genetic markers. If DNA really ruled, we would expect a human morphology.” – per UD DNA doesn’t even tell teeth what they should look like – April 3, 2014 Excerpt: A friend writes to mention a mouse experiment where developing tooth buds were moved so that the incisors and the molars were switched. The tooth buds became the tooth appropriate to the switched location, not the original one, in direct contrast to what we would expect from a gene’centric view. – per UD
I would also like to further highlight that emphasizing protein coding regions of the genome (2%), to the exclusion of almost all the rest of the 'species specicific' regulatory regions of the genome, as Darwinists currently do, is to miss a huge elephant in the living room. Talbott, in his unique style, puts the 'elephant in the living room' situation like this:
HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling... and so on without end. Yet the coherence of the whole is maintained. The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way: "The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)",,, And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,, http://www.netfuture.org/2012/May1012_184.html#2
bornagain
October 22, 2015
October
10
Oct
22
22
2015
03:43 PM
3
03
43
PM
PDT
The rate of fixation of neutral mutations is the same as the rate of introduction of neutral mutations,
That is the untested claim, anyway.Virgil Cain
October 22, 2015
October
10
Oct
22
22
2015
03:23 PM
3
03
23
PM
PDT
"Er, ~98% of what? The ~2% protein-coding regions or the ~98% non-protein-coding regions? :/" "Both combined." This would be surprising, as "junk dna" should drift at a rate of about 1% per million years (if I recall correctly). Human and chimp have been separated for abt 6 million, so between the two should account for 12 million years drift. This should add to about 12% drift in "junk".bFast
October 22, 2015
October
10
Oct
22
22
2015
03:19 PM
3
03
19
PM
PDT
Andre: How did 60 000 000 Base pair differences become fixed in only a short 6 000 000 years of unguided evolution from out last common ancestor? The average human has 175 mutations or so, most of them neutral. The rate of fixation of neutral mutations is the same as the rate of introduction of neutral mutations, so 175 mutations will become fixed per generation. Six million years is about 300,000 generations, which leads to the fixation of about 50 million mutations. Give or take. - edit mathsZachriel
October 22, 2015
October
10
Oct
22
22
2015
03:09 PM
3
03
09
PM
PDT
As somewhat hinted at in post 10, it is the regions of DNA that do not code for proteins, i.e. the regulatory regions in DNA, that most dramatically separate us from other species.
An Interview with Stephen C. Meyer TT: Is the idea of an original human couple (Adam and Eve) in conflict with science? Does DNA tell us anything about the existence of Adam and Eve? SM: Readers have probably heard that the 98 percent similarity of human DNA to chimp DNA establishes that humans and chimps had a common ancestor. Recent studies show that number dropping significantly. More important, it turns out that previous measures of human and chimp genetic similarity were based upon an analysis of only 2 to 3 percent of the genome, the small portion that codes for proteins. This limited comparison was justified based upon the assumption that the rest of the genome was non-functional “junk.” Since the publication of the results of something called the “Encode Project,” however, it has become clear that the noncoding regions of the genome perform many important functions and that, overall, the non-coding regions of the genome function much like an operating system in a computer by regulating the timing and expression of the information stored in the “data files” or coding regions of the genome. Significantly, it has become increasingly clear that the non-coding regions, the crucial operating systems in effect, of the chimp and human genomes are species specific. That is, they are strikingly different in the two species. Yet, if alleged genetic similarity suggests common ancestry, then, by the same logic, this new evidence of significant genetic disparity suggests independent separate origins. For this reason, I see nothing from a genetic point of view that challenges the idea that humans originated independently from primates, http://www.ligonier.org/learn/articles/scripture-and-science-in-conflict/ Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F MicroRNA Study: “We Liberated Ourselves” From the Evolution Requirement - And Had Great Success - Cornelius Hunter - March 2, 2015 Excerpt: The new study found that imposing the common descent pattern, where microRNAs must be conserved across species, is hampering the search:,,, "In our effort to further characterize the human miRNA repertoire, we liberated ourselves from the conservation requirement: not surprisingly then, 56.7% of our newly discovered miRNAs are human-specific whereas 94.4% are primate- specific. Considering that many miRNA studies to date have focused on seeking and analyzing conserved miRNAs, it is not surprising that, of the human miRNAs in miRBase, we found a larger fraction to be conserved in rodents and invertebrates. These findings strongly suggest the possibility of a wide-ranging species-specific miRNA-ome that has yet to be characterized." http://darwins-god.blogspot.com/2015/03/microrna-study-we-liberated-ourselves.html Expanding ENCODE - Aug. 2014 Latest Encyclopedia of DNA Elements data enable researchers to compare genome regulation across species Excerpt: Ho and his coauthors also found key differences in the structure of heterochromatin between species.,,, ,,,these data show that “heterochromatin is not the same thing in different organisms, not only in terms of distribution but also in terms of composition.” http://www.the-scientist.com/?articles.view/articleNo/40891/title/Expanding-ENCODE/
Dr. Sternberg gives a very informative talk on 'species specific' regulatory regions in the following podcast
Richard Sternberg PhD – podcast – On Human Origins: Is Our Genome Full of Junk DNA? Part 2. (Major differences found in higher level chromosome spatial organization, and regulatory regions, between species) http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-2/
Moreover, mutating these significantly different, i.e. 'species specific', regulatory regions between species is found to be, unlike mutating an amino acid in the protein coding regions, 'always catastrophically bad'. i.e. mutating 'species specific' regulatory regions of DNA is far more unforgiving than merely mutating the protein coding regions of DNA:
A Listener's Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin - December 4, 2013 Excerpt: "There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way." - Eric Davidson - developmental biologist http://www.evolutionnews.org/2013/12/a_listeners_gui079811.html
Thus, where Darwinists most need plasticity in the genome to be viable as a theory, (i.e. developmental Gene Regulatory Networks), is the place where mutations are found to be 'always catastrophically bad'. Yet, it is exactly in this area of the genome (i.e. regulatory networks) where substantial, ‘orders of magnitude’, differences are found between even supposedly closely related species. Needless to say, this is the exact opposite finding for what Darwinism would have predicted for what should have been found in the genome. If Darwinism were a normal science, instead of being basically the unfalsifiable 'blind faith' religion of atheists, this finding, by itself, should have been more than enough to falsify neo-Darwinian claims. Another erroneous evolutionary assumption that is overlooked is that Darwinists assume that mutations to DNA will produce fundamentally new body plans. They simply have no empirical basis whatsoever for assuming that changes to DNA will generate new body plans.
Response to John Wise - October 2010 Excerpt: A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html
As Dr. Stephen Meyer puts the situation, you can mutate DNA until the cows come home and it doesn't matter because you are not going to generate new body plans:
‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009) (52:57 minute mark) https://youtu.be/7yqqlZ29gcU?t=3177 "These different sources of epigenetic information in embryonic cells pose an enormous challenge to the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops—for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand." Stephen Meyer - Darwin's Doubt (p. 281)
bornagain
October 22, 2015
October
10
Oct
22
22
2015
03:07 PM
3
03
07
PM
PDT
Both combined.wd400
October 22, 2015
October
10
Oct
22
22
2015
03:01 PM
3
03
01
PM
PDT
Er, ~98% of what? The ~2% protein-coding regions or the ~98% non-protein-coding regions? :/Vy
October 22, 2015
October
10
Oct
22
22
2015
02:45 PM
2
02
45
PM
PDT
wd400, I recall the discounting of the dissimilar regions as being merely 'junk', as you are currently doing, as the disingenuous method by which ENCODE skeptics, (i.e. Darwinians), denied the widespread functionality of the genome that ENCODE had found.
DNA mostly 'junk?' Only 8.2 percent of human DNA is 'functional', study finds - July 24, 2014 Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution -- a clear indication that this DNA matters, it has some important function that needs to be retained. http://www.sciencedaily.com/releases/2014/07/140724141608.htm
So according to these Darwinian critics of the ENCODE study, which found widespread functionality for 'junk' DNA by direct experimental research, actual functionality does not determine if a sequence is functional, only 'conservation of sequence' determines what is functional? So basically, only if Darwinian evolution is assumed as true from the outset will Darwinists be willing to accept that a given sequence of 'junk' DNA may be functional? That is called 'assuming your conclusion into your premise' and is an absolutely horrible way to practice science! Moreover, these following researchers noted that assuming most of the genome is junk, as Darwinists disingenuously insist on doing so as to protect their dogma of common descent, is a science stopper as far as bio-medical research is concerned:
Junk or functional DNA? ENCODE and the function controversy Pierre-Luc Germain, Emanuele Ratti, Federico Boem - 21 Mar 2014 Abstract: In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. http://link.springer.com/article/10.1007%2Fs10539-014-9441-3
Further notes:
Do Scientists Accept the Results of the ENCODE Project? September 12, 2013 - By Dr. Fazale Rana Excerpt: In a recent article, Mattick and his coauthor, Marcel Dinger, argue, like me, that the criticisms of ENCODE are unwarranted technically and are motivated by non-scientific considerations. One of the chief criticisms leveled at ENCODE relates to its use of a causal definition of function to determine functionality within the human genome. That is, a sequence element in the genome possesses function if it performs an observationally or experimentally identified role. ENCODE skeptics argue that this definition is faulty; instead, the project should have relied on sequence conservation (the so-called selected effect definition) as a way to measure function. According to the selected effect definition, sequences in genomes can be deemed functional only if they evolved under evolutionary processes to perform a particular function.,, Hence, functional sequences are those under the effects of selection. And based on a selected effect definition of function, only 10 percent (not 80) of the human genome could be considered functional. Mattick and Dinger decry the weakness of the selected effect definition.,,, (So do I) http://www.reasons.org/articles/do-scientists-accept-the-results-of-the-encode-project The ENCODE Embroilment, - part 3 Excerpt: Only if we assume that strictly unguided evolutionary mechanisms produced our genome can we infer that such a small fraction of our genome is functional. Under this logic, when evolutionists cite the preponderance of junk DNA as evidence for evolution, they engage in circular reasoning. Junk proponents seem blind to these flaws. A co-author of the 8.2-percent paper boasted, "our approach is largely free from assumptions or hypotheses."8 Apparently he was forgetting about assumptions and hypotheses like evolution. Even worse, ENCODE critic Dan Graur called it "'idiotic' to suggest that a part of the genome could be functional if it didn't respond to pressure from natural selection."9 He further charges that "what ENCODE researchers did not take into account . . . is that everything is shaped by evolution."10 In Graur's Darwinian world, the possibility that some important functional genetic element arose from a cause other than natural selection is simply inconceivable.... In any case, ENCODE provides a nice empirical test of the evolutionary assumption that only conserved DNA can be functional: It finds evidence of mass functionality in "non-conserved" (i.e., unique) DNA sequences. As one lead ENCODE researcher explains: "Most elements defined by biochemical signatures lacked strong evolutionary conservation."12 Other ENCODE defenders argue that the research shows that "absence of conservation cannot be interpreted as evidence for the lack of function."13 - They conclude that ENCODE's empirical evidence for functionality is the ultimate test: "differential expression (including extensive alternative splicing) of RNAs is a far more accurate guide to the functional content of the human genome than logically circular assessments of sequence conservation."21 Bottom line: good evidence trumps bad theory.,,, A Great Divorce Critics like Dan Graur charge that ENCODE is guilty of "divorcing genomic analysis from its evolutionary context"22—and that's exactly right. ENCODE's empirically based finding that the vast majority of our genome is functional has withstood theoretical, evolution-based objections from critics. Maybe a divorce from evolutionary thinking is exactly what we need to liberate biology from bad evolutionary assumptions and explain what's happening inside our cells.,,, http://www.salvomag.com/new/articles/salvo33/the-encode-embroilment-part-III.php
bornagain
October 22, 2015
October
10
Oct
22
22
2015
02:07 PM
2
02
07
PM
PDT
Am I the only one who thinks it's utterly useless to try and compare genomes between species as long as we're not even close to a complete understanding of how it all works? If it's anything like software very similar sections could have vastly different effect but vastly differing sections could have a similar effect. Likewise, equal sections used in a different context could also have vastly different effects. SebestyenSebestyen
October 22, 2015
October
10
Oct
22
22
2015
02:06 PM
2
02
06
PM
PDT
We share 25% of our DNA with dogs. Not sure about cats. DNA is an awesome design tool. Now will someone please scratch my belly.ppolish
October 22, 2015
October
10
Oct
22
22
2015
02:05 PM
2
02
05
PM
PDT
Documented Anomaly in Recent Versions of the BLASTN Algorithm and a Complete Reanalysis of Chimpanzee and Human Genome-Wide DNA Similarity Using Nucmer and LASTZ by Jeffrey P. Tomkins on October 7, 2015 Excerpt Summary: Thus, 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. https://answersingenesis.org/genetics/dna-similarities/blastn-algorithm-anomaly/
bornagain
October 22, 2015
October
10
Oct
22
22
2015
01:38 PM
1
01
38
PM
PDT
News, What if the genome is mostly junk? Andre, Genetic drift, mostly.wd400
October 22, 2015
October
10
Oct
22
22
2015
01:21 PM
1
01
21
PM
PDT
The whole case still doesn't make any sense unless the genome accounts for far less than we used to think about what makes a life form. Of course there is increasing evidence that that is true.News
October 22, 2015
October
10
Oct
22
22
2015
01:02 PM
1
01
02
PM
PDT
This has been known for … some time
Not sure how the following supports one side of the debate or the other, but it's very recent Salk scientists discover protein factories hidden in human jumping genes http://www.eurekalert.org/pub_releases/2015-10/si-ssd101915.phpawstar
October 22, 2015
October
10
Oct
22
22
2015
12:56 PM
12
12
56
PM
PDT
So even if there is an actual 2% difference it's still a whopping 60 000 000 Base pair difference. How did 60 000 000 Base pair differences become fixed in only a short 6 000 000 years of unguided evolution from out last common ancestor? Over to the unguided experts......Andre
October 22, 2015
October
10
Oct
22
22
2015
12:55 PM
12
12
55
PM
PDT
This has been known for ... some time Edit: perhaps I should say this was pointed out quite some time ago, didn't seem to change anyone's mind.wd400
October 22, 2015
October
10
Oct
22
22
2015
12:32 PM
12
12
32
PM
PDT
Perhaps the problem is we don't know how, exactly, to compare the two genomes. Take the 1 base pair deletion mentioned above. If that is a sentence and the word "no" was deleted or inserted it would change the entire meaning of the sentence. The sentences could be 98% identical and mean opposite things.Virgil Cain
October 22, 2015
October
10
Oct
22
22
2015
12:25 PM
12
12
25
PM
PDT
1 7 8 9

Leave a Reply