Tuesday, March 10, 2015

A physicist tries to understand junk DNA

Rob Sheldon has a PhD. in physics and a M.A. in religion.1 With two strikes against him already, he attempts to understand biology by discussing evolution, junk DNA, and the Onion Test [Physicist suggests: “Onion test” for junk DNA is challenge to Darwinism, not ID]. As you might imagine, posting on Uncommon Descent in support of Intelligent Design Creationism leads directly to strike three.

The Onion Test was created by Ryan Gregory in 2007 [The Onion Test] and published in the scientific literature by Palazzo and Gregory in 2014. It goes like this. Take your favorite hypothesis suggesting that most of the DNA in the human genome is functional and use it to explain why the onion, Allium cepa, needs a genome that is five times larger than the human genome. Then explain why closely related species of onion need twenty times more DNA than humans.

Rob Sheldon has an intriguing answer that can only be created by someone with a lot of biases and very little knowledge of biology. He claims that the human genome is chock full of information and it is packaged and condensed in a way that is the best possible code. Humans have the machinery to decode this sophisticated packaging algorithm but other species are more primitive so they have much less efficient compression algorithms. Here's how he describes it ...

There may be some very good reasons for onions to have large genomes....

The DNA is software. The proteins are the video feed. The nucleus is the CPU. Humans have highly complex coding/decoding machinery in the nucleus. When mathematical analysis is performed on human DNA, it is found to have a fractal information dimension greater than 3 (papers available upon request)–indicating that at least 3 different codes are simultaneously present. This is a number bigger than chimpanzees, whose DNA is not so compressed, and if I recall correctly, come in around 2.5 or so in fractal dimensions. The paper did not analyze onions, but I think it is safe bet that the fractal dimension is < 2.0. What does this changing dimension mean for DNA size? Well the information in DNA is proportional to the volume of phase space, so if humans have dimension 3.0, then the volume ~ (3.2GBytes)^3 ==> 27 GBytes. This dwarfs the 15GBytes of the onion, but then I don’t know the fractal dimensionality of onions.

Now admittedly, the papers don’t do the entire genome, they look at little subsets, so I may be generalizing too much to say that I know the dimension of information packing. But if the genome had junk DNA in it, it would drive the number lower, not higher, because junk DNA is uncorrelated to everything else.

This is categorically what is NOT found, and so even without the ENCODE results, it is manifestly obvious that human DNA is not mostly junk.
I think that's his main argument—something to do with fractal dimensionality.

But, not content with that, he enters another dimension ....
But if DNA is compressed and packed so efficiently in humans, why is it not packed that way in onions?

One paper that was published 3 years ago or so, suggested that embryonic development from ovum to embryo was driven by a clock. As the transcriptase zipped along the DNA, proteins were made successively by the cell, and the ordering and timing of the proteins were such as to drive the embryogenesis and development. In other words, the spatial location of the DNA was converted into temporal development of the organism. Then if an organism needed to prolong a stage of embryogenesis, the most direct way would involve adding more DNA. No extra machinery is needed, no added complications and regulators, just another 1GByte of DNA to transcribe and the necessary 30 minutes will be added to the development.
Most undergraduates could destroy this argument in a few seconds so I'll leave it to them in the comments.2 It's a classic example of why a physicist should not try to understand biology without consulting a basic introductory textbook.

There's more ...
Crude, but why do that at such a high cost to the genome of every cell?

Well, perhaps there is a plant virus that hijacks the "clock" to crank out tumors. This onion solution would then be impervious to such a virus. It might even give it an "evolutionary advantage".

Then the "Onion Test" is not a Darwinian challenge to ID, but an ID challenge to Darwinian imagination. Why don’t they take their own medicine: if the junk isn’t functional why doesn’t it get selected out?
We are gradually making some progress in educating Intelligent Design Creationists but it is a slow and painful process. Some of them actually begin to understand modern evolutionary theory and population genetics and there's a brief glimmer of hope, from time to time, suggesting that they know the difference between Darwinism and modern evolutionary theory. Some of them even admit that natural selection isn't all there is to evolution.

All this learning seems to disappear in the junk DNA debate. They still insist that advocates of natural selection (Darwinists) are the ones who invented the idea of junk DNA. That's just dead wrong but we may never be able to convince the IDiots.


1. Google "Sheldon physics" and look at the images. It gets you lots and lots of cool photos that I would love to incorporate into my blog.

2. Hint: how many regulatory genes would have to be regulated in this manner by inserting extra long introns and how much DNA would have to be added to delay production of the first transcript by 30 minutes?

Palazzo, A. and Gregory T.R. (2014) The Case for Junk DNA. PLoS Genetics (published May 8, 2014) [doi: 10.1371/journal.pgen.1004351]

217 comments :

  1. Present depends on contingent past,
    Balanced multiplication can long last.
    ‘Twill topple not our onion,
    If satisfies new equilibrium.
    And better still, satisfies more,
    Than that which existed long before.

    No one-fits-all,
    No excess fattegy,
    But what recalls,
    Evolution’s strategy!

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  2. Hey, at the very worst you can get a homework exercise out of it. That's what I did with the bogus "there is no more information in two copies of Shakespeare's Hamlet than in a single copy" claim for my 4th year course on formal languages. Nearly every student can prove that is wrong.

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  3. The only DNA information I know about is the codon-specifies-amino acid kind. Is the fractal dimension supposed to mean there's something else going on as well? (My vote is on: it's an irrelevant number).

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    1. Sheldon on 'information':

      http://link.springer.com/chapter/10.1007/978-94-007-2941-4_21

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    2. From Sheldon's cv:

      Experience in Higher Education

      2006-present Covenant Christian Academy, Academic Team Coach 2012-2013 Covenant Christian Academy, High School Astronomy


      From the Covenant Christian Academy Statement of Faith:

      STATEMENT OF FAITH

      Every family joining with CCA becomes part of an extended family. School requirements are that the parents of our families be born again believers in the Lord Jesus Christ who agree with this Statement of Faith. This statement is by no means complete, and it is not offered as a final doctrinal statement. CCA families come from diverse denominational backgrounds. However, the statement represents a core of central beliefs that are considered essential for effective bonding and fellowship among families. Our Statement of Faith is as follows:

      We Believe:

      The Bible is the only inspired and infallible written Word of God and constitutes complete and final revelation and is the final authority for faith and life. The Bible, in its original autograph of Old and New Testaments, is without error in whole and in part; including theological concepts as well as geological and historical details.

      That one God has existed from all eternity in three persons: God the Father, God the Son, and God the Holy Spirit. Jesus Christ was God come in the flesh being fully God and fully man, being born of a virgin and found without sin.

      All men are in violation of God's righteous requirements and His holy character both by nature and act; and are therefore under His wrath and condemnation. The central purpose of the first coming of Jesus Christ was to pay the penalty for man's sin through His substitutionary death on the cross, the accomplishment of which was attested to by His subsequent visible, bodily resurrection.

      Salvation is offered to everyone as a gift, free to the sinner. This gift must be responded to in individual faith, not trusting in any personal works whatsoever, but relying wholly on the sacrificial work and death of Jesus Christ and His atoning blood.

      ------------------------------------------

      For more about the "Academy" go here:

      http://www.ccahuntsville.org/1801.html

      The statement of faith is in the policy manual.

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    3. THAT's what he calls "experience in higher education"?

      Dummy Sheldon probably believes in Flintstones creationism. Vegetarian tyrannosaurs eating watermelons etc.

      Uncommon Descent, and the Intelligent Design "movement" in general, is a pathetic simulacrum of science constructed from credential inflation and bottom-of-the-barrel scraping. Scrape, scrape.

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  4. Fractal dimension? FRACTAL DIMENSION? What the fuck is this lunatic gurgling about?

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    1. More than 10 years ago Ramon Roldan already published on the fractal dimension of DNA. It might be a code to build 3D organisms, a socalled bauplan.

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    2. Yeah you like that word a lot. Enough with the "might be's", why aren't the discovery institute's laboratory actively trying to find out what it is?

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  5. Mik...n, "Fractal dimension? FRACTAL DIMENSION? What the **** is this lunatic gurgling about?
    I don't exactly understand Fractal dimension, but google seems to. It certainly is a phenomenon. Over at ID, there seems to be an opinion from Zachriel that the fractal dimension of human DNA is 0.8 -- quite different from the 3.0 Rob Sheldon sites. However, the concept of Fractal dimension is a valid concept, and it appears that it relates to biological DNA.

    Before you call somebody a lunatic it might dawn on you that they actually know something that you don't. You might just want to pass the concept by google before spouting your ignorance.

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    1. Before you call somebody a lunatic it might dawn on you that they actually know something that you don't.

      I agree. I took that into consideration.

      Rob Sheldon is a lunatic.

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    2. I wasn't able through a google search to find anything about the "fractal dimensionality" of DNA that made any sense to me.

      The closest I could find was something about chromatin packaging, but what the hell this has to do with junk DNA is anyone's guess. What is particularly absurd to me is the claim that there would be significant differences in how chimpanzees and humans pack their DNA.

      This nutjob religious physicist doesn't know any more about DNA than I do, in fact I suspect it's the other way around.

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    3. This is exactly demonstrating your lack of knowledge on biology, gene expression and regulation in particular.

      Packaging of DNA is extremely important for expression and regulation of the information present in the sequences. Packeging follows rules and legeslation and is clearly demonstrating design (in decay).

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    4. Peer you IDiot, Rumraket did not say packaging was irrelevant. He said it had nothing to do with junk DNA, and indeed no experimental test nor hypothetical model has shown why the 90% junk is needed to pack the chromatin in a functionally significant way. He also said it's absurd to think there are significant differences in packaging between humans and chimps. You did not address Rumraket's arguments.

      Moreoever, your claim that packaging of chromatin "follows rules and legislation" is pure speculation backed up by no experimental work.

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    5. The use of the word "legeslation" (sic) is indicative of the trouble IDiots have in discerning the difference between man made laws (prescriptive) and natural laws (descriptive).

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    6. It's a strange choice of words, but I suspect Peer is not a native English speaker, so I won't pick on him over vocabulary.

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    7. Many leaves exhibit a fractal pattern. Obviously, the Yahweh designed it thus. You see, all one has to do is find a way to describe a phenomenon using mathematics, and VOILA! Design.

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    8. Diogenees: "Moreoever, your claim that packaging of chromatin "follows rules and legislation" is pure speculation backed up by no experimental work."

      This is what I mean by devoid of any knowledge on biology: The packaging follows rules, for instance the AA/TT/TA rule.

      A fractal pattern is what indeed might be expected from programs that constructed as repetitive loops.

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  6. His most recent publication has an ominous title: ""Comets and entropy hydrodynamics: How does evolution violate the 2nd law?". Unfortunately I get a 404 when I try to access it, so I don't know what answer he gives to his question.

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    1. The abstract can be found here. But I wouldn't pay 18 bucks to read about magnetised comets driving evolution by carefully controlling the flow of entropy.

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    2. I've found it: link

      Wow, the authors explain the origin of life. Why didn't it occur to anyone to ask a physicist earlier?

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    3. Heh. One of the editors of the journal is Chandra Wickramasinghe.

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    4. I think physicists have solved the origin of life problem several times already. Unfortunately, their solutions don't agree.

      I've developed a unified field theory while I was waiting for my car to be fixed. Should I tell the physicists or blog about it?

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    5. I've developed a unified field theory while I was waiting for my car to be fixed. Should I tell the physicists or blog about it?

      And you have a wonderful proof, but the margins of this page are too small to contain it? (See http://primes.utm.edu/glossary/xpage/fermatslasttheorem.html )

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    6. The classic in this genre:
      http://arxiv.org/abs/adap-org/9910002
      A simple model of the evolution of simple models of evolution

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    7. Thanks for that. I read it expecting the worst, but no, it's deliberately funny and right on the mark. I will assign it as reading to any physicists I encounter who are proposing to revolutionize the study of evolution.

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    8. In addition to physicists who are proposing the first-ever quantitative treatment of evolution, there are biologists who need a measure of diversity (say, of the species encountered on an island), computed from the fractions of individuals from each species. They find the formula
      (minus) Sum p log2(p) useable for that. They could just as well have tried 1/(Sum p^2) but they chose this one, with the base-2 logarithms.

      Then they go around proudly proclaiming that they have "used information theory".

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    9. Well, it's usually referred to as the Shannon-Index. Then again, one could use the Simpson index instead, or the analogue defined in Gunkel and Wappler (2015) where appropriate. And for richness of course there's a non-parametric test...

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    10. Cosma Shalizi is brilliant, and well worth reading on a number of subjects. Among other things he has published on a web an English version of Mettrie's L'Homme Machine, in which the dirty bits are left in French. I was surprised that he had done that, as I thought he had done the translation himself, but he told me that he doesn't know French and was just reproducing an out-of-copyright translation done a century ago.

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    11. Cosma Shalizi is brilliant

      I love reading his stuff. Have you seen his essay(s) on IQ tests, (beginning with) "g, A Statistical Artifact"?

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  7. By 'fractal dimension' he could be referring to the fact that chromatin is packaged in the nucleus as a 'fractal globule' This maximizes packaging efficiency while at the same time making chromatin accessible to proteins and allowing different domains to be brought together in 3 dimensions for expression. I really doubt there is any difference in this regard between humans and chimps.
    He could also be referring to the fractal dimension of the genetic regulatory networks. You could only determine this in well studies genomes. I expect there would be a difference between humans and yeast but again I doubt you'd see any difference between humans and chimps.

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    1. If it were only for packinging purposes, you might be right. It is however for expression purposes and here differences between man and ape may indicate a different bauplan.

      It is known that man and chimp differ wrt the non-coding unique part of their genomes, about 15%.

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    2. Peer, it is well known that you are an IDiot. Man and chimp non-coding DNA do not differ by 15%. Which Young Earth creationist did you copy that from-- Jeffrey Tompkins, I bet? Or Jerry Bergman?

      Refernce to creationist literature, please, for your 15%. All creationist calculations of human-chimp genetic difference are marred by FRAUD or incompetence, except Todd C. Wood's.

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    3. Any 2 humans differ in the coding as well as their coding DNA. It is likely that any 2 humans also differ in the number of copies they have of some genes. Creationists would do themselves a favor by applying their latest 'humans and chimps cannot be related' proofs to either different populations of humans or to species that they allow to be micro-evolved from a single "kind." Weird that they never do that.

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    4. make that coding as well as non-coding

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  8. I suspect that the fractal business comes from the teamwork of Sanford, ReMine (engineer YEC), and fake PhD Fernandez. They use the word 'code' in such a way as to render it meaningless. Just as meaningless as getting information on DNA from a creationist with a physics degree.

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    1. No, it was coined over a decade ago and proposed then as a sort of bauplan, but was completely ignored by...yeap, the science stoppers (aka Darwimps).

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    2. 'Science stoppers'? "Darwimps"? You're an idiot.

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    3. It's funny how the "Darwimps" are the ones doing all the actual science, while all the creotards are standing on thesidelines yelling "you're doing it wrong".

      What experiments in genome functionality has an IDcreationist lab done? That's right. None. Zero. Not a single fucking one.

      The grand total of creationist labwork on "junk DNA" is nonexistant, instead we get charlatans seeking to baffle the gullible with fanciful technobabble and bible-numerology compiled on their expensive macintosh computers.

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    4. It is not about the data generated by a truck load of taxpayer's money, it ist the silly 19th century conclusions drawn from the data: selection.

      Selection has merely become synonymous with god, omnipotent and all-present. Presented as fact, the19th century naturalistic philosophy is now the religion for atheists, the only people stubbornly defending it.

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    5. You draw conclusion from data by doing experiments. So there's all this DNA and you say we don't know what it's doing, but you're sure it does something important. Okay, sounds like a fine hypothesis. Go test it. Why isn't the IDiot institute trying to find out?

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  9. Somebody named Zachriel posted this:

    Garte, Fractal properties of the human genome, Journal of Theoretical Biology 2004: “Human chromosomes exhibited a fractal dimension (D) of about 0.8, while values for a bacteria, yeast, worm and plant were higher.”

    This suggests that the fractal dimension correlates with the proportion of coding DNA, since this proportion is higher in those smaller-genomed species. (Presumably worm=C. elegans and plant=Arabidopsis.)

    But the Sheldon guys says humans are 3.0, and chimps are less, and other things are even less. So who knows what he's using. And his numbers are allegedly based on "little subsets", so who knows if they are representative at all. Par for the course for ID...

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    1. 2004....every paper before the NGS era can be dismissed as outdated.

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    2. Peer, you keep posting and you keep talking as if you know something. But Zachriel presented a reference, while you blather idiotically yet present no references to your alleged super science.

      Because it doesn't exist.

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    3. What I'd really like to know is why genomic data that wasn't sequenced using NGS can be dismissed. NGS techniques do not generally produce higher quality genomes, quite the opposite. They just produce them much faster and at a far lower cost, which makes it worth it. NNGS is shaping up to be even faster and cheaper, but right now the quality isn't up to speed AFAIK.

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    4. "2004....every paper before the NGS era can be dismissed as outdated."

      You have absolutely zero clue what you're talking about.

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  10. It sounds like his idea is that this number would be more like that larger number if you multiplied this number. Reminds me of those articles trying to make you feel sorry for rich people by claiming that a very large salary is not much money after you've spent it. Absolutely true. And absolute nonsense.

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  11. What I would like to know is what kind of a cheap trick could they do that they've got different "fractals" from human and chimp DNA.

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  12. Ye gods, that is painful to read if you know the least bit about DNA.

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  13. I'm not sure how fractal dimensionality is calculated, but there may be a hint in this sentence: "But if the genome had junk DNA in it, it would drive the number lower, not higher, because junk DNA is uncorrelated to everything else." They appear, then, to measure correlation (of sequence?) across the genome. And hey, I know a lot of sequences that are correlated across the genome: Alu insertions, for instance. And since humans have a bit more Alu than chimps, maybe that translates into a higher fractal dimension. I suppose that proves they aren't junk.

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    1. I've looked through some papers and in general the fractal dimension is calculated in this way:
      First a Chaos game representation of the sequence is generated. This is done by setting points for all nucleotides (WLOG: A (0,0),G(0,1),C(1,0), T(1,1) and then starting with n_0=(0.5,0.5) to initialize the process, n_N=0.5n_(N-1)+0.5Base(N), where Base(N) is the point corresponding to the Nth base.
      What this does is that it gives you points in an area between the 4 points picked for the bases and if you divide this up into 4 equal sectors, then all the points in one sector correspond to a particular base. If you divide it into 16 equal sectors then these correspond to 2 base long sequences. 64 sectors - 3 base sequences, etc.
      Now you count how many of these sectors contain at least one point for various steps. The fractal dimension is given as D(n)=log_2(Boxes needed for n BPs)-log_2(Boxes needed for n-1 BPs)
      You can also take multiple steps and adjust accordingly. It has to be noted that D(n) generally is a function of n - you don't get a constant value (the boring limit are of course 1 for small n and 0 for large n, but in between you get values between 0 and 1 and that can be interesting). And yes, any repeated sequence of a particular length will tend to reduce D around that length.

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    2. Uhm, the boring limit for small n should of course be 2 and intermediate values fall between 0 and 2.

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    3. That's really interesting. Except not at all. So you can play math games when you assign arbitrary values to individual bases and then jumble it around with chaos games. Whoa, stop the press, what has this to do with DNA functionality? What does it have to do with anything? I wonder if Sheldon can tell us.

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    4. I don't think it allows you to make any statement about functionality. But it's a method to visualize patterns - repeated phrases show up as clusters of points and the longer the phrases are the tighter the clusters are. So if you print out the CGR you can get an idea of what repeats you have. Also transforming sequences into floating point numbers is useful if you want to use everything CPUs can offer. I think there are quite a few bioinformatic problems you could speed up this way (then again, I would like to stick to integers and CUDAfy things if possible).

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    5. For what it's worth Robert Sheldon has posted a comment on that UD article saying that he was on track to be medical doctor in college before he went into physics. He further said:

      "I even stained the chromosomes and prepared a microscope slide full of onion root-tip cells, which means I actually studied onion genetics too."

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    6. Oh Jibbers Crabst. My wife and I just prepared microscope slides full of onion and garlic cells, and displayed the microscope images on our big screen TV... to entertain a visiting 12 year old.

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    7. P.S. He was smarter than Rob Sheldon.

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    8. Oh no doubt Rob Sheldon is clueless on the issue of junk DNA!

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    9. I once made slides of mouse liver - Hey! I'm a mammalian hepatologist!
      I had a telescope when I was a kid - I'm an astronomer!
      I drive a car - I'm a Formula 1 racer!

      Oh to be among the creationists, where embellished educations and relevance is only the beginning.

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    10. It's no joke N., the Reverend David Rives, whose 90-second videos are often featured at WorldNetDaily and who runs a "Creation Institute" out of a double wide somewhere in rural Tennessee hilariously and pathetically visible in Google Street View, often poses next to an amateur telescope. The IDiots think he is an astronomer.

      (The Reverend has no scientific background, nor even a degree in divinity.)

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  14. I am pretty dense when it comes to science. I enjoy reading the back and forth in these blogs. For someone like myself it is confusing when you pull the scientific discipline card. Last week I read your Carl Zimmerb post, celebrity picture and all, he was bathed in glory. As a casual observer I wonder why does the English major trump the physics major? Obviously one is right the other it's wrong or maybe they are both wrong? It just seems weird to bring their discipline into question only when they disagree with your stance.

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    1. Carl Zimmer knows something about evolutionary biology. I have no idea what his college major was, and anyway it's irrelevant.

      On the other hand, Rob Sheldon clearly knows very little about evolutionary biology, and moreover he's part of a grand tradition of physicists who know very little about evolutionary biology but nevertheless consider themselves qualified to revolutionize the field. Larry is reacting to this history as much as to Sheldon himself.

      So it isn't just a matter of who agrees with Larry.

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    2. You're getting it backwards, Beau.

      It starts from the clear demonstration that Sheldon doesn't have the first clue about even some very basic concepts of the subject about which he writes. From that, the knowledge that he is a physicist raises the question of why anyone would even consider his uninformed opinion worth publicizing in the first place.

      Whereas, when a biochemist such as Michael Behe displays the same degree of ignorance, different questions arise, mainly involving whether a trained biochemist could really be this ignorant, or if he is just putting on an act.

      In any event, your question might be better directed at the creationists of the Discovery Institute, who go to great lengths to make sure we are aware that Rob Sheldon is a physicist which, while true, is of no bearing here. In the current context, he's just guy with strong opinions regarding a topic of which he is wholly ignorant. it doesn't matter of he's a physicist or a garbage collector.

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    3. Beau, I think some of your confusion would be cleared up if you go back and re-read the two original pieces. Carl Zimmer was performing his role as a science journalist - presenting a balanced and detailed view of the two sides of the junk DNA debate. This effort was certainly helped by his having broad knowledge of evolution (he is the co-author of a texbook on evolution).

      Rob Sheldon, on the other hand, has not attempted to present a balanced view. He hasn't even attempted to understand the topic he is critiquing. For example, if you read this blog a lot, you would know immediately what is wrong with this statement from Sheldon: "Why don’t they take their own medicine: if the junk isn’t functional why doesn’t it get selected out?"

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    4. I completely agree with Stoddard. This is not a discussion on science, but on atheistism vs theism.

      Carl Zimmer is not a biologist, not a geneticist and not an evolution biologosts. Het is but a journalist, who is parading the consensus (but wrong) views of a handful of Big-mouth Darwimps. His copied ideas about endogenization of viruses and a genome ful of virus remnants are completely wrong. It is the other way around: exogenization of recombinde ERVs.

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    5. Peer Terborg says,

      He is but a journalist, who is parading the consensus (but wrong) views of a handful of Big-mouth Darwimps.

      Just out of curiosity, when other journalists and press releases proclaim that there's no such thing as junk DNA do you criticize them as well? Have you posted comments on the IDiot websites whenever they highlight the writings of those journalists?

      Inquiring minds want to know.

      I'd hate to think you were a hypocrite.

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    6. Peer: "His copied ideas about endogenization of viruses and a genome ful of virus remnants are completely wrong. It is the other way around: exogenization of recombinde ERVs. "

      So your God front-loaded the information to make the AIDS virus into human DNA?

      So our junk DNA isn't junk, it has a function, and it's function is to evolve HIV vurus, the flu epidemic of 1918 and kill tens of millions of people?

      That's some brilliant front-loading. And by brilliant I mean psychopathic.

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    7. Well Dio - I have long believed that creationists simply do not think through their knee-jerk reactions and anti-evolution assertions. Thanks for providing me with another clear-cut example of this. Of course, peer does seem to make it easy...

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    8. Diogenes, we've been having this debate over here

      It seems to be a popular creationist tactic these days to claim that we were created with our ERVs and that all viruses come from these.

      Here are some things that creationists have no answer for when they employ this tactic:

      - If we always had ERVs, then why are almost all of our ERVs flanked with identical LTRs which are only produced in the reverse transcription process from RNA -> DNA?

      - Why are almost all of our ERVs and Solo LTRs flanked by TSRs which are a clear sign of integration?

      - If we were created with our ERVs then why are so many of them overlapping?

      - Why do they all have genes for ENV which is essential for viruses but not so much for ERVs?

      - Why do the older ERVs that we share with most other primate species have the most mutated LTRs?

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    9. There's another level to that argument, in favor of common descent and against design. Substitution biases. Assuming ERV's originated as germline infections that subsequently became inactivated and diverged through accumulating mutations, we would expect to find that the distributions of mutations in them roughly follow the same distributions we get from transition bias and so on.
      This is a very clear prediction from biochemistry, which if confirmed, strongly implies the mutations that happened in them were due to well-known stochastic biochemical processes taking place over millions of years and not due to some kind of deliberate design.

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    10. To elaborate a little, it is not just that we find increasing accumulation of mutations in increasingly older and inactivated ERV's. If the ERV's are inactive the mutations should be neutral, and if they're neutral they should follow the well-known distribution expected from transition bias.

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    11. I recommend you all read the reddit thread that Ace linked to, in which he discusses ERVs as evidence for common descent-- he's very knowledgeable on the subject, and rebuts creo arguments with the quickest and most definitive counter evidence. He is arguing (remotely) with IDcreationist (YEC?) JoeCoder, a computer programmer, who has encyclopedic knowledge of creationist arguments and evasions and who goes through every one of them; Ace then knocks down every creationist evasion of the evidence.

      I'm sorry I haven't had time to jump into that, but Ace can take care of himself.

      I would like to see what Ace has to say about Rumraket's point re transition bias in accumulated mutations in ERVs.

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    12. How many dead ends in your beliefs would it take for you to reconsider your position? 10? 20? More? I do take bets. Wanna try me? It may do you some good. If... you want it.

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    13. @Motörheadsong

      Let me do your questions. They are easy to address. First of all, you need to know that the genetic elements known as ERVs have been frontloaded as VIGEs (=variation-inducing genetic elements). LINEs also qualify as VIGEs (but are not related to ERVs).

      - If we always had ERVs, then why are almost all of our ERVs flanked with identical LTRs which are only produced in the reverse transcription process from RNA -> DNA?

      The original frontloaded ERVs can still be traced back in the genomes. They propogated through a copy-paste mechanism, leaving behind a copy, so that acquired variation is also preserved and can be inherited. Novel variation is generated through novel integrations and will also become inheritable. The process is trictly controlled by the genome itself involving hundreds of proteins and RNA (including piwis).

      - Why are almost all of our ERVs and Solo LTRs flanked by TSRs which are a clear sign of integration?

      Because they are variation-inducing genetic elements that instantly generate novel genotypes for adaption and speciation purposes. What you call evolution is the result of a frontloaded genetic mechanism: VIGEs

      - If we were created with our ERVs then why are so many of them overlapping?

      We are not created with every VIGE in its current position. Instead we are created with a variation-inducning genetic system that allows for raüid adaptation, variation, speciation.

      - Why do they all have genes for ENV which is essential for viruses but not so much for ERVs?

      They don't have all ENV genes. They are characterized by gag and pol genes and the envelope genes are picked up from the genome. HIV picked up a part of the IL8 gene (which is used to bind to CCR5 to enter immune cells), Influenza viruses picked up the neuramidase gene as an envelope gene, etc. You can simple infer what part of the genome has been added to a VIGE to become an active retrovirus. In other words, the RNA viruses have their origin in the genome and stem from VIGEs. Screening the human genome I found several socalled ERVs that are on their way to become a full blown virus. The HERW, for one, is such a previrus.

      - Why do the older ERVs that we share with most other primate species have the most mutated LTRs?

      These might be the originally frontloaded VIGEs and be subject to a non-random mutational mechanism, although it my also be due to an analysis-bias.

      Delete
    14. Furthermore, ENV genes code for a protective capsid that keeps the VIGE RNA molecule from sticking around and prevents random integration (which is integration-enzyme specific).

      As said, belief Darwinism is simply a consequence of ignorance of biology.

      Delete
    15. In biologal systems, everything is regulated and controlled, the induction of variation included. Derailed control is always for the worse of the system. Derailed control networks = disease, cancer. Derailed VIGEs = retroviruses.

      Why is the ERV = VIGE = true?

      Think LINEs...then you know.

      Delete
    16. @maninthebarrel

      Ace may be your man of knowledge on ERVs, it is my special topic of biological research. I am studying this type of genetic elements, which are particualrly good at generating variation. So, your argument from authority does notz work out, since I am the authority myself. I have formulated a novel theory on VIGEs myself, including a theory to account for the origin of viruses, and I know what they mean for the genome.

      Do not hesitate to ask any questions if you are stuck in my train of thoughts.

      Delete
    17. Peer, if front-loading was done by 'God', then how could anything be "Derailed"? Are Satan and demons doing the derailing? If so, can't 'God' stop them? Are Satan and demons more powerful than 'God'? Is 'God' a wimp?

      Delete
    18. Oh Peer,

      You are so modest and coy.

      Instead of providing these tantalizing tidbits copy and pasted into Larry Moran's blog what say you provide links to the (presumably) "Peer" reviewed journals that you have published in.

      No need to hide your light under a bushel anymore, who knows, perhaps Diogenes will finally find his honest man in you.

      Delete
    19. Is this a peer-reviewed blog? I did not know.

      I simpyl addressed some easy to answer questions on ERVs.

      This is common knowledge. At least it should be.



      Delete
  15. The "calculation" (3.2GBytes)^3 ==> 27 GBytes has incoherent units. The RHS should be 27 (GBytes)^3. Leaving aside the question of what it means to cube a GByte, one cannot compare 27 (GBytes)^3 to "the 15GBytes of the onion" since one number has units (GBytes)^3 while the other has units of GBytes. Assuming we can ignore the different units and assuming that the fractal dimension of the onion genome is 2, then the comparison would be27 (GBytes)^3 to (15GBytes)^2 = 225 GBytes)^2. 225 beats 27 which would imply that the onion genome is bigger.

    Another obvious problem is that the comparison is not scale invariant. If we measure the genomes in MBytes then we get (3,200 MB)^3 vs (15,000 MB)^2 or 32.768 x 10^9 vs 225 x 10^6, so now the human genome is bigger. Different conclusions follow from different choice of units.

    Perhaps Rob Sheldon understands what he is talking about, but that is hard to believe when he expresses himself so badly, making childish blunders with basic concepts.

    As a physicist myself I apologize for my field, noting only that most of us are not like that. From anecdotal evidence mathematicians are worst: e.g. Granville Seward (Ph.D. Perdue) who says that entropy disproves evolution and the ineffable William Dembski (Ph.D. U. of Chicago)

    ReplyDelete
    Replies
    1. Also note, human genome is 3.2 billion base pairs, not gigabytes. Since a base pair is 2 bits (4 possible pairs), and a byte is 8 bits, he's off by a factor of 4.

      Delete
    2. Unitary analysis is one of the first things physicists are taught. It is a simple "double check" on the validity of any equation, just to make sure you didn't screw it up. If a physicist can't do that, his education was woefully deficient.

      Rob Sheldon screwed up his units and that proves his physics education was woefully deficient. Somewhere, a thesis committee went horribly awry. His thesis committee is ultimately responsible for giving a Ph.D. to this IDiot. They should be held accountable, and Sheldon's Ph.D. should be revoked. Does anybody know in which benighted department he got his degree?

      Sheldon is ignorant of the most basic physics. He thinks evolution violates the second law of thermodynamics. That is pure creationism not physics. I can't believe this IDjit got a Ph.D. in physics. It embarrasses us all. For the sake of physics, his Ph.D. should be revoked.

      Delete
    3. Ted - do not despair. We still have the engineering field from which, it seems, a disproportionate number of such folk arise.

      Delete
  16. Here's the "details", in a comment from Sheldon on the same UD blogpost:

    ============
    33
    Robert Sheldon
    March 10, 2015 at 4:54 pm

    I knew if I mentioned papers available I’d get a request. Here’s one of Todd Holden’s more recent papers from the arXiv server: http://arxiv.org/abs/1404.2540/

    I realized in reading it that I misspoke in the blog post above. The Shannon entropy was 3.80, but the fractal dimension was 1.98, at least, for the Y-chromosome of humans.

    The paper gives references as to how these numbers are derived, but not much help explaining what they mean. It is my interpretation that fractal dimension relates to the number of simultaneous codes present. Once again, read the literature if you need to know more about them.

    Nevertheless, and pertinent to my argument above, the paper shows that “false” genes were easily distinguished by their improper dimensions. Something about these 2 dimensions of human genes sets them apart from other species.

    As to whether a physicist can ever study biology, I will confess that I was on track to be a biology major and medical doctor in college. I even stained the chromosomes and prepared a microscope slide full of onion root-tip cells, which means I actually studied onion genetics too. But I’m afraid those slides are not available upon request.
    ============

    So: even Sheldon has nothing but the vaguest possible idea of how fractal dimension is calculated or how it relates to what he believes (that the human genome has the most complex "codes")

    ReplyDelete
    Replies
    1. From a quick read through, it appears they restricted analysis to exons. So hard to fathom relevance to junk DNA at all.

      Delete
    2. I wouldn't even call it a vague idea. The paper he cites here uses something called the Higuchi fractal method, which I haven't seen used when I went looking for papers on the fractal dimension of genomes, because it's rarely used. To make things worse, the paper he cites uses this method to check gene predictions. The gene prediction pipeline used generated 426 candidates, of which their method rejected 43. And to quote from the paper Sheldon uses to argue that there is no junk:
      "Of these 43 sequences, the National Center for Biotechnology Information (NCBI) gene database lists 6 as withdrawn, 1 as not in the current assembly, 9 as lncRNA (long non-gene coding RNA), and 27 as pseudogenes. None of these are listed in the NCBI database as known gene-coding sequences"

      In other words: The paper can be summarized as "new method detects junk, that in widely used pipelines is not detected".

      I'm also astounded to find him talking of the fractal dimension and the Shannon entropy. The Shannon entropy here is the di-nucleotide Shannon entropy (which ranges from 0 to a maximum of 4). Other approaches might use single nucleotide SE, or triplets (0-2 and 0-6 respectively). The same issue appears for the dimension, not just because the CGR approach I discussed above is more common (and yields different results), but also because the Higuchi method requires normalization and the few papers I have found that use it take different approaches making it impossible to compare values across studies.

      It is his interpretation that "fractal dimension relates to the number of codes" is patently BS. His notion that "something about these 2 dimensions of human genes sets them apart from other species" is as well - some of the papers that exist using Higuchi compare genes for different species, and Holden et al 2013 for instance compare mouse and human genes, finding 6 of 8 mouse genes with higher dimension than humans and 2 higher for humans. From the same paper a human chimp comparison that included two variants of the human sequence, the dimension of the chimp lay between the two.

      Describing what Sheldon has as the vaguest possible idea gives him too much credit. he has no clue whatsoever.

      Delete
    3. That's where his MA in religion takes over. His phd in physics means he presumably knows how to do math, so throw in a fancy-sounding term like "fractal dimensionality" or "shannon entropy", maybe if you're not exaclt sure this will sufficiently baffle your gullible audience you can spice it up with some "complex specified information" and all you need is religion to reach the conclusion that it means there's no junkDNA.

      The worst part is that Sheldon seems to only be a beginner at the "fancy technobabble" game. YEC veterinarian David L Abel has mastered the art.

      Behold The Cybernetic Cut. Or how about The role of complexity at the edge of chaos. I can't even process the abstract on that one there's so much babbling technical jargon and fancy buzz terms stuffed into every sentence.

      The man has more than 20 "papers" full of shit like this. They're not even read by anyone, they're just mindlessly linked by creationists who see the title, perhaps read three sentences from the abstract and then faint from the Jesusgasm it gives them to read all that fancy technobabble from a guy who believes in The Truth(tm).

      Delete
    4. I realized in reading it that I misspoke in the blog post above. The Shannon entropy was 3.80, but the fractal dimension was 1.98, at least, for the Y-chromosome of humans.

      The paper gives references as to how these numbers are derived, but not much help explaining what they mean. It is my interpretation that fractal dimension relates to the number of simultaneous codes present.


      Correct me if I'm wrong, but doesn't this amount to a wholesale retraction of his claim? Should we expect UD to publish a followup post documenting this retraction?

      Delete
    5. What you should do, math and calculus and philosopy guys, is go back to the lab, construct yourself a --what you believe is-- junk DNA free organism and study its properties, characteristics, and abilities (to adapt and evolve).

      Pretty sure you will run into some amazing surprises.

      Delete
    6. Biology commited suicide when it adopted a creed.

      Delete
    7. Peer Terborg, There's no point in replying to you, and yet it's hard to resist when a refutation is so easy to find that even you should have noticed it before you wrote.

      1. A few organisms nearly lacking junk DNA exist naturally, e.g. many bladderworts (small carnivorous plants such as Utricularia gibba), and they seem to be evolving as well as everything else.

      2. Biologists have gone to the lab and constructed mice that lack many of the DNA sequences thought to be junk. The mice did just fine.

      Delete
    8. Peer you IDiot, you IDiots cited a pompous know-nothing Rob Sheldon who wrote streams of arglebargle that he himself didn't understand. Then you all call him "physicist" in hopes of invoking argument from authority. We pointed out that the authorities you cite are idiots and demonstrable know-nothings. When you try to cite authorities, you cannot distinguish smart from moronic, but anti-evolutionists are forced to cite the moronic. You anti-evolutionists must scrape the bottom of the barrel and Sheldon is that bottom. Scrape, scrape.

      Now you seek to change the subject to evade your collective exposure as pompous morons.

      So your tell us what experiments WE should do, do you, pompous moron who thinks Rob Sheldon is a great intellectual?

      As for your proposed experiment, we have already pointed out to you that the bladderwort Utricularia has almost no junk DNA. Its evolution has been studied in the literature. We did ours. Now you IDiots do your own experiment.

      The Discovery Institute receives $5 million a year, year after year, from Christofascist billionaires. They have spent $0 looking for functions in non-coding DNA. How about if you piss off to the Discovery Institute website and tell THEM to spend a few millions on your experiment?

      Delete
    9. wilson,

      "Many knockout experiments don't actually reveal the function of the knocked-out gene. In yeast, for example, there's a study that 80 percent of knockouts don't have an obvious phenotypic effect until you stress the organism."

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060581/

      Delete
    10. The 80% frequency of silent genes applies to more than just mice: it also works in yeast, for example. It's easy enough to understand in terms of metabolic control analysis, but unfortunately Larry isn't convinced by that. (It's also unfortunate that your link leads to a paper by Denis Noble, who, we may recall, doesn't command universal respect in this group). My sources for yeast are Raamsdonk et al. (2001) Nat. Biotechnol. 19, 45-50, and (being immodest for a moment) Cornish-Bowden and Cárdenas (2001) Nature 409, 571-572.

      Delete
    11. To this list of organisms without much junk DNA, add fugu.

      Delete
    12. For fugu, do we know what fraction of its DNA is non-coding? With Uticularia, we know the fraction is very small.

      Delete
    13. Whoa, Diogenes, did you just use "non-coding" as a synonym for "junk"?

      Delete
    14. Further to Athel Cornish-Bowden's point about metabolic control theory, there was once an editorial in Cell by Daniel Lewin, then the editor of that journal and the author of the many editions of the textbook of that name. He noted that many of the loci in a mouse could be deleted individually, with the mouse looking perfectly normal. How, he asked, could we then explain the persistence of these loci in the genome?

      When I heard of that it was facepalm time. Apparently he thought that fitness came in two values, 0 and 1, with nothing in between.

      Delete
    15. "I even stained the chromosomes and prepared a microscope slide full of onion root-tip cells, which means I actually studied onion genetics too. "

      So an exercise that I made in middle school biology makes somebody an onion geneticist? Holy crap.

      Delete
    16. Peer said,

      "Biology commited suicide when it adopted a creed."

      Peer means something on the lines of "I commit to the belief that everything was Front-Loaded into the human genome by The Intelligent Designer[TM]."

      Delete
    17. John asks: "Whoa, Diogenes, did you just use "non-coding" as a synonym for "junk"?"

      NEVER. I assume junk is a subset of non-coding, so the fraction of ncDNA gives me an upper limit on the fraction of junk. With Utricularia, it's very small.

      Delete
    18. The Discovery Institute receives $5 million ...

      5 million is nothing. The ENCODE received at least 500 million and all the get in return is Darwinian deniers....

      Darwinian religion needs a predominantly uselss genome.

      Keep science free from religion.

      Delete
    19. @Bwilson295,

      can you provide refernces for your claims:

      1. A few organisms nearly lacking junk DNA exist naturally, e.g. many bladderworts (small carnivorous plants such as Utricularia gibba), and they seem to be evolving as well as everything else.

      Maybe they lost it? Did you check for that?

      2. Biologists have gone to the lab and constructed mice that lack many of the DNA sequences thought to be junk. The mice did just fine.

      No, you mix this up with the observation of conserved junk DNA that could be removed from the mouse genome without any measurable consequences. This is not a problem for ID. It poses a huge threat to selectionism, however, and the long ages (how do you prseserve conserved regions without selection...)

      I have the advanatge of real knowledge on biology over your parotting the bigmouths.

      Delete
    20. You were indeed parotting the wiki-bigmouths. A quick search reveals that the evolution of bladderworts is non-observed, but assumed from DNA sequences.

      Do some homework yourself, please.

      Delete
    21. Peer, have you observed your chosen, so-called 'God' doing any front-loading?

      Delete
  17. Larry, this could be of direct interest to you:

    http://www.nature.com/news/dna-mutation-clock-proves-tough-to-set-1.17079

    I'm keen to know your opinion on the matter.

    ReplyDelete
  18. Dont ask Moran, ask me:

    The discrepancies exist because they are comparing apples and oranges, intra and interspecies and pretening they are all one. Further, mutations are not just a stochastic phenomenon; there are cold spots, hot spots and extreme hot spots. The whole idea of a constantly ticking cklock is an ideé fixe, devoid of biological reality.

    ReplyDelete
    Replies
    1. We know that mutation rate varies through the genome, Peer. That's basic kindergarten stuff. How does it answer the onion test?

      Within the genus Allium, there are variations in genome sizes that are 10 times larger than the whole human genome. Whyzat?

      Delete
    2. "Within the genus Allium, there are variations in genome sizes that are 10 times larger than the whole human genome. Whyzat?"

      Because some species of onion are more "frontloaded" than others.

      See? Easy. All a creationist needs to do is repeat "frontload" many many many times until it becomes their default answer. This works much better when the creationist repeating the word is very stupid.

      Delete
    3. Frontloading is a particularly entertaining concept when combined with Young Earth Creationism.

      - Every kind of living thing was created in a week, including humans.

      - All these genes need to be frontloaded in preparation for - what, exactly, now that the creation of life has been complete for 6,000 years?

      Delete
    4. It's even funnier under an old earth. All sorts of genetic information is built into the ancestor. Everything needed to build whales, sparrows, and tuna fish is there in the chordate ancestor. Then somehow it doesn't degrade by mutation. Or rather, in each lineage the part needed for its descendants does not degrade. The part needed to make tuna fish can degrade once we've gotten past the split that separates the teleosts from the lungfish, and we're in the latter lineage. But the part needed for whales does not degrade until after a later split.

      The mechanism for storing all this information and preventing it from degrading? ... (crickets) ...

      Delete
    5. Behe hypothesized that the information for all IC systems in all of biology would have been present in the first living cell. So it would have more DNA than Courtney Love's underpants.

      (That joke was funnier in the 90's.)

      Delete
    6. Joe Felsenstein, the part needed to make tuna fish cannot degrade until we have chickens to make the eggs for mayonnaise!

      Delete
    7. Your comments simply show that 1) you do not understand how genomes evolve, 2) the creationst paradign.

      Why would it all be frontloaded and prespecified? It is very simple for poepl who are able and willing to hear.

      What has been frontloaded is 1) the tools and bauplan for ur-organisms ("kinds") and 2) a mechanism that is continously inducing variation for adaptive and speciation puposes. The latter generates a load of noise, including accumulated duplications.

      What you must do is an experiment in the lab, an make organisms lacking such accumulated sequences and perform phenotypic studies and asssess whether such organisms are still able to bring forth variation, are able to adapt and evolve.

      I bet they won't.





      Delete
    8. "Behe hypothesized that the information for all IC systems in all of biology would have been present in the first living cell. So it would have more DNA than Courtney Love's underpants."

      This is indeed what evo-minded scientists have proposed for LUCA, same info present in many different forms (which creates a redundancy-stability problem).

      Every bit of real observational and experimental bioscience points in the direction of frontloading of several kinds, which an intrinsic ability to evolve/adapt. This is the best explanation for what we observe.

      Delete
    9. Peer:
      "What you must do is an experiment in the lab,"
      Since you're the one trying to give evidence of frontloading, the logical path would be for you to send in a grant proposal to NWO (Dutch Science grant organization), get funding and setup this experiment.
      Good luck!

      Delete
    10. "This is indeed what evo-minded scientists have proposed for LUCA, same info present in many different forms (which creates a redundancy-stability problem). "

      LOL. No it is not. Once again you have no clue what you're talking about Peer.

      Delete
    11. What has been frontloaded is 1) the tools and bauplan for ur-organisms ("kinds") and 2) a mechanism that is continously inducing variation for adaptive and speciation puposes.

      Humans, the pinnacle of creation, were already there, beginning in the first week. So please tell me why it's necessary to have a "bauplan for ur-organisms" if the denouement of it all has already occurred?

      Delete
    12. @ Ed, the burden of evidence is still on the side of the Darwinians who must still show that minor changes to genetic programs are the source of the same genetic programs. You know, extraordinary claims require extraordinary evidence. The Darwinian claim is rather extraordinary.

      Delete
    13. @Mikkel,

      Pharyngula is not a OOL researcher. You know that. It is not even acceptable as a reference. Please show some science.

      Delete
    14. It was an actual paper he referenced you numbnut.

      Delete
    15. Peer said:

      "Every bit of real observational and experimental bioscience points in the direction of frontloading of several kinds, which an intrinsic ability to evolve/adapt."

      Peer, how would you explain extirpations and extinctions?

      Delete
    16. which an intrinsic ability to evolve/adapt

      Yes, all of Creation needs to evolve/adapt, since it began in perfection in the Garden of Eden, and so needed to evolve to something bett...oh, wait....

      Delete
  19. "YEC veterinarian David L Abel" --> Do we actually know this? Last time I checked -- many years ago -- I found nothing about David Abel's background. Cheers! Nick

    ReplyDelete
    Replies
    1. He sometimes places DVM after his name, so he does appear to be a(n ex-)vet:
      LINK

      Delete
    2. Sure, but he DOES run a whole ID Institute out of his basement, and since it is just down the road from the Goddard Space Center, it MUST be cutting edge ID stuff that goes on there. And his online CV is totally impressive - sure he lists the same papers over and over under different headings, and sure he includes hallway chats as publications, but he's a rock star!

      Delete
    3. Our YEC doggie doctor's "Origin of Life Foundation Incorporated" can be easily seen in Google Earth: it is an ordinary home with a one car garage in a residential neighborhood. I must say his lawn appears well tended.

      Piotr's link to the tax documents gives the assets of the Foundation Incorporated as "$0 to 9,999", so clearly he has no lab equipment with which to investigate the origin of life problem. Thinks deep thoughts though.

      I believe his "Origin of Life Foundation Incorporated" was once called something even more important sounding, like "Biosemiotic Informatics Foundation incorporated." It was arglebargle but it impressed the IDiots. Does anyone recall the exact name?

      Delete
    4. Why is it no evolutionist ever does this? Let's all name our homes Foundations Incorporated. Let's have a contest to see who can come up with the most pompous, important sounding name.

      I'll start.

      Hmm. All I can come up with is Goddamn Giant Lawn That Needs Mowing Institute. Accurate, but somehow not pompous enough.

      Delete
    5. What's even more striking is the respectful way these guys' credentials are treated by Denyse O'Leary at UD. "Physicist" Rob Sheldon, "Physicist" David Tyler (an expert in textile production these days). "Philosopher" Lazslo Bence (change "philoso" to "photogra"). "Mathematician" David Berlinski.

      Then contrast that to her descriptions of actual working scientists. "Tenured bores", "Darwin lobbyists". People who publish in the deeply-corrupt peer-review system. People who are only where they are because all the insightful and talented people, who are creationists, have been "expelled".

      Delete
    6. O'Leary gave a puff piece interview to Muslim creationist Adnan Oktar, aka Harun Yahya, and treated him like a major intellectual, and tossed him softball questions designed to elicit answers supporting the DI's party line. Oktar is the guru of a religious sex cult in Turkey, a high school dropout, druggie, who copied all his anti-evolution "facts" from American Christian creationists. He also brainwashes, rapes and physically beats his female cult members according to his ex-cult members, uses the Turkish court system to censor and shut down all of Blogspot because of a few pro-evolution blogs, and files hundreds of SLAPP lawsuits against critics Scientology-style. He is also an antisemitic Holocaust denier who blames Darwin for the Holocaust he said never happened, and says Islamic terrorists are all really atheist Darwinists. His book "The Atlas of Creation" was infamous for disproving evolution by comparing photos of fossils of insects against "living insects", the latter being photos of fishing lures made from foam and thread.

      O'Leary sometimes cites racist wackjobs and makes racist comments herself. When you're an anti-evolutionist, you can't afford to be choosy. Scrape the bottom of that barrel. Scrape, scrape.

      O'Leary, in her puff piece interview, treated Oktar as a great intellectual, making no mention of the rapes, brainwashing, antisemitism, Holocaust denial, fishing lures etc.

      At least he wasn't a "tenured bore." Now that would really enrage O'Leary. Rape, OK. Racism, OK. Holocaust denial, meh. But TENURE...! Now that's out of line, mister!

      Delete
  20. The title is very wrong. The "physicist" is not trying to understand anything, let alone DNA. He's selling snake oil to some creationists.

    ReplyDelete
  21. But why the junk/neutral DNA was not lost if there is no selective pressure to keep it there? Just curious.

    ReplyDelete
  22. Professor Felsenstein, please explain the above academic question.

    ReplyDelete
    Replies
    1. That's the common-sense question that many biologists initially asked. Won't natural selection eliminate all the junk DNA?

      But what they did not realize was that
      1. There are a number of processes continually adding junk DNA to the genome, and ...
      2. The selective advantage from eliminating modest-sized pieces of junk DNA is extremely small.

      To show the latter, consider a large stretch of junk DNA, say 1 million bases long. If all of it were neatly deleted, there might be a noticeable selective advantage. Let's say 1%. Then if a deletion of modest size, say 100 bases, came along, what would be its fitness advantage? Naïvely, 0.01 x (100/1000000) = 0.000001. That might not be effective in moderate-sized populations.

      To the amount of explain junk DNA, one must make a quantitative account of all of these processes, those adding junk and those removing it, and take population size into account. The amount of junk in the genome should be a balance between all these processes. For a much more realistic and careful account, let me point you to Michael Lynch's excellent book The Origins of Genome Architecture which makes basically this kind of argument.

      Delete
    2. Thank you very much for the reply. Both notions may be good reasons but are not without some serious weaknesses, seems to me at least. 1. this notion of adding junk DNA in the past, any evidence to it besides speculation no matter how seemingly reasonable it might be? Is it testable? 2. junk or neutral DNA is supposed to be free from natural selection. Its deletion or insertion should hence be stochastic without preference either way. Thus, a genome should not increase by much from its initial size of relatively much less junk. For a genome to grow to be extremely large like the onion's, obviously the adding process grossly overwhelmed the deletion process, which has to be extremely odd for a random process with equal probability of adding and deleting, isn't it?

      Delete
    3. Besides, adding junk to any system of order (hope we agree that onions do have some degree of order) is to create disorder or entropy, which could only be expected to be deleterious and hence negatively selected.

      Delete
    4. 1. this notion of adding junk DNA in the past, any evidence to it besides speculation no matter how seemingly reasonable it might be? Is it testable?

      Of course it's testable. You can map sequences onto phylogenetic trees and use that to detect indels.

      For a genome to grow to be extremely large like the onion's, obviously the adding process grossly overwhelmed the deletion process, which has to be extremely odd for a random process with equal probability of adding and deleting, isn't it?

      Why do you assume that all random processes must be symmetrical? There are a number of mechanisms that can add or remove DNA from the genome, and there's no reason to expect all those various processes to exactly balance out. There may in fact be a fairly strong bias in favor of either insertion or deletion in any given group. And this too can be tested.

      Delete
    5. Gnomon: "Besides, adding junk to any system of order (hope we agree that onions do have some degree of order) is to create disorder or entropy, which could only be expected to be deleterious. and hence negatively selected."

      Where did you learn about thermodynamics? I hope you didn't learn about it from a creationist source that equates low entropy with "stuff convenient for me" and high entropy with "stuff inconvenient for me."

      No, there are chemical equations and rules for computing intrinsic entropy and you have to follow the rules. I have never seen any creationists do a real thermodynamic analysis of any biological system, computing the intrinsic entropies of input chemicals, heat radiated to the environment, etc. Creationists just pull assertions out of their ass. If something is convenient for them, they say, "low entropy", and if it's inconvenient for them, they say, "high entropy." That's not even remotely physics.

      You also say "disorder or entropy, which could only be expected to be deleterious".

      Entropy isn't really disorder, except in analogies that we teach in the class called derisively "Physics for Blondes". The pop science media uses a lot of analogies and they're not science.

      No matter; on what basis can you say increases in entropy must be deleterious? Did you do a thermodynamic calculation? I suspect not.

      And even if they were deleterioius, Prof. Felsenstein has already pointed out that slightly deleterious mutations may NOT be selected out, depending on population size, with low population sizes increasing the likelihood of accumulating junk DNA.

      Let's test if you know what "entropy" means.

      If a piece of metal, let's say a car, rusts, is that an increase or decrease in entropy? How do you know? Show all work.

      If your sofa grows mold, is that an increase or decrease in entropy? How do you know?

      The popular analogies equate "low entropy" with "stuff convenient for me", but that's not science. Science requires math. From which sources have you learned your genetics and thermodynamics? Seriously, you can tell us where you got this stuff.

      Delete
    6. LOL, we are just going through the same ritual at UD:

      Entropy according to Niwrad

      They do feel strongly about the Second Law: for the first time I infuriated Kairosfocus so much that he issued a "warning" and complained about my manners (I committed first-degree blasphemy by speaking irreverently of FSCO/I). But they'll never grasp thermodynamics beyond the slogan: "Things naturally get messy, but it takes intelligence to create order."

      Delete
    7. Joe Felsenstein: ”But what they did not realize was that: 1. There are a number of processes continually adding junk DNA to the genome, and ... 2. The selective advantage from eliminating modest-sized pieces of junk DNA is extremely small.”

      The notion that ‘junk DNA’ (jDNA) has been evolutionary maintained simply because of a mutational imbalance, favoring amplification of jDNA versus deletion, has been around for quite some time. For example, a quarter century ago (that sounds more impressive than ‘25 years ago’, doesn't it?), I used it as a null hypothesis in my brief paper (http://twl.sh/1c3IM9x) on the potential biological function for jDNA:

      “It is not known if secondary DNA (that is ‘junk DNA’) has accumulated simply because its rate of deletion has been lower than that of origin, or because individuals possessing secondary DNA have a selective advantage.

      And here comes a critical question that apparently nobody wants to address here at Sandwalk:

      Can genomic DNA that exists simply because of a mutational imbalance (that is, no selection) have a biological function or not?

      Delete
    8. Disclaimer: This is to let you know that I’m writing a paper specifically addressing this question, and that: You have the right to remain silent. Anything you say can and will be used against your pet hypothesis and in favor of my hypothesis; in the latter case, without necessarily giving you credit, as apparently is within the acceptable standard of conduct in our scientific culture.

      Signed, Miranda

      Delete
    9. Piotr,

      I was reading that UD link. My brain melted.

      How you can discuss anything with the insufferably sanctimonious KF is beyond me.

      I may jump in if I find the time. Niwrad is an idiot.

      Delete
    10. Cubist, Saturday, March 14, 2015 3:11:00 PM:

      “sez claudia bandea: "Can genomic DNA that exists simply because of a mutational imbalance (that is, no selection) have a biological function or not?"
      I have a counter-question, for you, CB: Is it possible for DNA that does have a "biological function", to not be under selection? I ask because your question only makes sense if "bio-functional DNA that's not under selection" is a real thing—if there is, in fact, no such thing as not-under-selection DNA which possesses some sort of biological function, your question is based on a false premise.”


      Well Cubist, you have heard of ‘first come, first served’; that applies also to questions. We all can reply to a question with another one, in order to avoid an answer.

      Don’t take me wrong, your counter-question is ingenious, but you need to respond first. Possibly, if you respond, you might not even feel it is necessary to ask your question, or you might decide just to ask me for an answer to my own question.

      In any case, why don’t we wait and give some other people the chance to answer this relatively straightforward question, as the readers of Sandwalk are among the most knowledgeable people in the field of genome biology and genome functionality.

      Delete
    11. How about genetic load? Can anybody remember Dan Graur and his famous proclamation about how everyone of us including Larry & Joe F should have 7 x '10^45 children if ENCODE is right.

      Joe is an expert in PG so maybe he should speak first.
      Can anyone still stand by this proclamation?
      http://sandwalk.blogspot.ca/2015/01/a-lesson-on-genetic-load.html

      Delete
    12. Oh, BTW: Dan has kindly removed his post. It was a total embarrassment.

      I don't think he is going to admit he was wrong..

      Delete
    13. Oh yeah? Provide the link straight to the post rather than to introduction.
      Let's see

      Delete
    14. Looks like the link in Dan's post is broken. But his post is still there, so it's kinda idiotic to conclude he's "removed his post". Actually not just kinda, it is fully and utterly idiotic.

      Delete
    15. This is the message I get when I try to access the file:

      "The file you're looking for has been moved or deleted."

      So, if you have some psychic powers and know something we don't, let us know.

      Delete
    16. LOL, we are just going through the same ritual at UD:

      Piotr, I learned two things from that UD thread:

      Firstly, IDers seem to have developed an alternative 2nd LOT wherein the concept of entropy is considered an obfuscation. This is actually an important scientific development because their law does not suffer from the inherent defect in the original 2nd LOT, namely, that it permits things like life and evolution.

      Secondly, since it was mentioned in every reply to your comments, I learned that you are an exceedingly ill-mannered individual. If you would only stop being correct, they might learn to like you more.

      Delete
    17. They have now posted a whole new OP with my name in the headline. I must say I have asked for it. I don't think they will ever forgive me for calling "FSCO/I" (or is it "FCSI/O"? I have to look the abbreviation up every time I mention it) technobabble.

      Delete
    18. Piotr, I've seen several IDiots, including gordo (kairosfocus), write it both ways. If you want to irritate gordo, write it backward, especially if you're responding to niwrad at the time.

      Delete
  23. sez claudia bandea: "Can genomic DNA that exists simply because of a mutational imbalance (that is, no selection) have a biological function or not?"
    I have a counter-question, for you, CB: Is it possible for DNA that does have a "biological function", to not be under selection? I ask because your question only makes sense if "bio-functional DNA that's not under selection" is a real thing—if there is, in fact, no such thing as not-under-selection DNA which possesses some sort of biological function, your question is based on a false premise.

    ReplyDelete
    Replies
    1. All depends on what "function" means. What does Claudiu mean by it? A phenotypic effect isn't necessarily a function, if that's what he means. But of course he doesn't. His "function" is as a buffer against the deleterious effects of retroposons and other insertions. Now it's possible that species that just happen to have a lot of junk DNA will have a selective advantage vs. species with less junk but the same amount of insertion activity. That however would be species selection, not individual selection, and that seems not to be what he's going for.

      Delete
    2. Cubist, see my reply to your comment, above.

      John,you are right, I’m not implying some confusing, multilevel definitions for ‘biological function’ or ‘selection’; just straightforward meanings that we all are familiar with.

      Delete
    3. Claudiu,

      That isn't what I said at all. I don't know what you mean by "function", and I don't know whether you're proposing species selection; that's just the only selection that I can see would be conceivable here.

      Delete
    4. This is what you wrote: “A phenotypic effect isn't necessarily a function, if that's what he means. But of course he doesn't. His "function" is as a buffer against the deleterious effects of retroposons and other insertions.”

      My answer was that you were right when you said that “His "function" is as a buffer against the deleterious effects of retroposons and other insertions”, not some kind of “phenotypic effect”.

      Delete
    5. You still need to give a definition of function and consider what sort of selection might apply.

      Delete
    6. John,

      The hypothesis promoted by you, Laurence Moran, Joe Felsenstein and others is that ‘junk DNA’ has accumulated because of a mutational imbalance, as we discussed above, not because of selection.

      Let’s consider that this hypothesis is correct. My question to you, Joe Felsenstein, Laurence Moran and other proponents of ‘junk DNA’ is: Can this jDNA have a biological function or not?

      You wrote that in order to answer this question, you need to know what I mean by ‘biological function’ and elaborated that: “A phenotypic effect isn't necessarily a function, if that's what he means. But of course he doesn't. His "function" is as a buffer against the deleterious effects of retroposons and other insertions.

      Yes, that is one potential biological function for ‘junk DNA.’ Now, do you or anybody else feel confident enough to answer the question without beating around the bushes?

      Delete
    7. Claudiu Bandea,

      One of Larry's and the gang other favorites is the genetic load argument.

      Are you familiar with that?

      "Genetic Load
      Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk."


      Five Things You Should Know if You Want to Participate in the Junk DNA Debate

      Also by Dan Graur:

      If @ENCODE_NIH is right, each of us should have 7 x 1045 children.

      It looks like Graur has removed the post ever since some have pointed it out to him that his calculations were way off.

      Delete
    8. Claudiu asks a stupid question

      My question to you, Joe Felsenstein, Laurence Moran and other proponents of ‘junk DNA’ is: Can this jDNA have a biological function or not?

      No. If it had a function it wouldn't be junk.

      Delete
    9. Larry,

      Apparently, you don’t understand the question, but I’m not surprised, as you have a history of not understanding what you read. Here is what your friend T. Ryan Gregory wrote about that: “Sorry, Larry -- you know I appreciate your blog posts, but it's clear that you didn't understand the paper(s) you criticize” ( http://sandwalk.blogspot.com/2014/07/the-function-wars-part-ii.html)

      If the people here at Sandwalk, who are bashing the ENCODE leaders, are not willing to address inconvenient questions, why in the world would you expect them to answer your critique?

      Delete
    10. So, Claudiu, what does "function" mean?

      Delete
    11. @Claudiu Bandea

      I answered your question and you resonded with an insult.

      Why?

      Delete
    12. “Sorry, Larry -- you know I appreciate your blog posts, but it's clear that you didn't understand the paper(s) you criticize”

      Claudiu, as you're saying that, you should specify what Larry didn't understand. Or are you just trolling?

      Delete
    13. John : “So, Claudiu, what does "function" mean?”

      As I already responded to Cubist (please see above), we all can reply to a question with another one in order to avoid an answer.

      However, because you brought up my hypothesis about the putative biological function of the so called ‘junk DNA’ (jDNA) as a protective mechanism against deleterious insertion mutagenesis by endogenous and exogenous insertional elements, let me ask you the question as it applies to this specific biological function in humans, in which jDNA occupies more than 90% of the genome. Let’s assume that this jDNA has accumulated in the human genome because of a mutational imbalance between the rate of its origin and that of its deletion.

      Can this jDNA provide a protective mechanism against deleterious insertional mutagenesis by endogenous and exogenous insertional elements or not?

      Delete
    14. Laurence A. Moran: ”I answered your question and you “resonded with an insult”. Why?”

      I did not intend to “resonded with an insult.” Based on your answer, I don’t think that you understood the question or the context in which it was asked. This is not the first time it happened, and I’m not the only one stating it: that’s why I quoted your good friend T. Ryan Gregory.

      Delete
    15. @Claudiu Bandea

      The question you meant to ask is whether a certain fraction of DNA could have a function or not.

      But you didn't ask that question. Instead, you asked whether junk DNA (jDNA) could have a function. I answered that question.

      I don't think I'm the one who is guilty of not understanding the question. Apparently you didn't understand your own question.

      BTW, Ryan Gregory now understands what I was asking him last summer. I asked him whether active transposons count as junk DNA or not. He was wrong when he said that I didn't understand his paper. He didn't understand the question. (He still hasn't answered the question.)

      Delete
  24. John Harshman,
    I am an experimental geneticist with a side interest on theory. Your test is a good try but not very convincing. let's say if onion separated from its closest sister species for 20 million years (which could be anywhere from 10 to 100 myr depending on which mutation rate you use, haha very uncertain science), and you see that onion today has 1 GB more bp than its sister. Your so called test would say, a haa, here is the evidence for added junk. But wait. 1. junk or not is uncertain. 2. it is not clear if the 1GB was added when or by how many times of repeated addition. But the hypothesis to test is that there are repeated number of additions over time. So the real test is to look for a 10 myr old fossil onion and examine how big is its genome. Now if you say that is not possible. then too bad, your speculation is just so and not hard science. Better think of something better to do the test. And keep in mind that if an idea is universal and not just ad hoc, there should be many ways to test it.

    ReplyDelete
    Replies
    1. You may be an experimental geneticist, but you sure aren't an evolutionary biologist. The way to find out about repeated additions is to find a tree with a lot of species whose divergences are closely spaced, not highly divergent sister species.

      And the best way to find out if a sequence is junk is also to look at the tree to see if it's conserved over evolutionary time.

      You actually can, in principle, get an estimate of genome size from fossils too, as long as you can see the sizes of the leaf stomata.

      Delete
    2. But to find a lot of species with closely spaced divergence may not be so easy. Otherwise you probably have already figured out how the onion genome evolved.

      Non conservation is absolutely not the equivalent of junk. This is the biggest misunderstanding in the field right now. Non conserved just means fast changing. and what does fast changing do? to adapt to quick changing environments. how HIV could escape the cocktail? how flu virus could erupt every few years? all because of their non conserved parts in their genome. In contrast, a conserved sequnce means slow changing, which is useless for adaptation. They could die out before a useful mutation appears.

      Delete
    3. How do you know nobody has figured out how the onion genome evolved? There are plenty of species of onions.

      There is such a thing as a rate of neutral evolution. Anything evolving at that rate is very likely to be evolving neutrally. Much slower is conservation. Much faster is positive selection. Of course the neutral rate in viruses is very fast; even so the rate of positive selection in viruses is faster, and the rate under stabilizing selection is slower. At any rate, it's surprising that you don't know that conservation is in fact evidence of selection: adaptation, not "useless for adaptation".

      I don't think you have any understanding of evolution.

      Delete
  25. John Harshamn and Prof. Felsenstein,

    Simple questions for you two professionals.
    1. Is a universal molecular clock still valid and how many experts consider it valid?

    If it is not valid which was the impression I got last time I checked, would not the neutral theory fall apart automatically, since Kimura and Ohta say: “Probably the strongest evidence for the theory is the remarkable uniformity for each protein molecule in the rate of mutant substitutions in the course of evolution.”

    Kimura M, Ohta T (1971) Protein polymorphism as a phase of molecular evolution. Nature 229: 467-479.

    3. If the neutral theory is invalid, would not the idea of junk DNA falls apart also automatically?

    4. the onion test is suppose to argue that because onion has so much junk, human must do too. It implies the onion genome is not just a simple ad hoc exception. And yet, ironically, your speculation of more addition over deletion is certainly ad hoc just for the onion. In most cases, addition and deletion cancel out each other and we see much smaller genomes. So the fact that humans have no junk has nothing to do with the special ad hoc case of onions having lots of junk. The onion test has no real meaning besides onion itself if its big genome is indeed explained by your ad hoc proposal of more addition over deletion.

    ReplyDelete
    Replies
    1. 1. No. Nobody that I know of. And no, neutral theory doesn't fall apart because there is no universal molecular clock.

      3. No. You aren't making any sense.

      4. No, that's not what the onion test means. The rest is word salad. I'm finding it very difficult to believe that you have any degree in biology. What's your real name?

      Delete
    2. Actually, I would expect additions to the genome to out number deletions in most species. There are some "accidental" changes that might add or delete DNA and might cancel out, but both transposons and viruses add DNA. In general, organisms don't have a good mechanism for removing the transposon or virus DNA. Most can compete just fine when they have a tiny bit more DNA than other individuals around them. So lineages probably do tend to gain DNA with time.

      Not to mention the matter of the residual increase in total DNA content that remains after after polyploidy even if it is followed by diploidization.

      Obviously, genomes can also shrink (e.g. Utricularia and Fugu), but the shrinking is odd and more in need of explanation than the increase of genome size.

      So anyway, a tendency toward increasing genome size isn't an ad hoc explanation for anything. Which is irrelevant anyway, Gnomon, since you have missed the point of the onion test.

      Delete
    3. John,

      My name is Shi Huang. feel free to check out my credentials http://www.sklmg.edu.cn/articles_98.shtml?l=en-us

      Delete
  26. There is no such a verified thing known today as a neutral mutation rate. They are all ASSUMED to be neutral rate. While the assumption of neutrality has often passed tests by sequence-alignment based informatics approaches, such methods usually have their own set of assumptions, including assuming certain DNAs to be neutral such as synonymous (syn) sites and transposon-element derived sequences, and are therefore not truly conclusive tests free of neutral or uncertain assumptions.

    ReplyDelete
    Replies
    1. John,
      So you said no to universal molecular clock. Very well. I agree too. But here is a challenge to you. How do you explain the following data (merely one example of a universal phenomenon) that yeast is approximately equidistant to worm and human in the proteins listed below (nearly all proteins do):

      H4 histone: yeast-worm identity 91%, yeast-human identity 92%
      H3 histone: yeast-worm identity 89%, yeast-human identity 90%
      Ubiquitin: yeast-worm identity 88%, yeast-human identity 89%

      Are these not plain evidence of a universal molecular clock that all species have similar mutation rates, be it yeast or human. At least Zuchkendle/Pauline and Kimura all thought so. Why today no one agreed with them? or is it because the clock idea is just an ad hoc tautology without any other independent evidence other than the result it is trying to explain?

      Such a universal clock hypothesis directly inspired Kimura to propose the neutral theory. It follows of course that if the clock is invalid, the neutral theory is largely dead (true only in very small scale for perhaps very small part of genome). After all, Kimura said that the clock is the strongest evidence for his theory. Without the clock, what other evidence is left?


      Data from Copley et al. 1999, Current Opinion in Structural Biology, 9:408

      Delete
    2. I actually published a dozen peer reviewed papers on the topic since 2008, although most of my 70 papers are on cancer genetics and epigenetics. In case you are clueless regarding the above challenge, feel free to go to my website and download my papers there.

      http://www.sklmg.edu.cn/articles_98.shtml?l=en-us

      Hu, T., Long , M., Yuan D., Zhu Z., Huang, Y., and Huang, S. (2013) The genetic equidistance result: misreading by the molecular clock and neutral theory and reinterpretation nearly half of a century later. Sci China Life Sci, 56:254-261.

      Huang, S. (2010) The overlap feature of the genetic equidistance result, a fundamental biological phenomenon overlooked for nearly half of a century. Biological Theory, 5: 40-52.

      Delete
    3. It's no good looking at histones and ubiquitin under a critique of neutral theory. They aren't assumed by anyone to evolve neutrally, as witness the high degree of sequence conservation.

      Delete
    4. I wasn't aware that we were in the presence of the very scientist who propounded the First Axiom of Biology. From Dr.Huang's 2010 paper:

      The equivalent of this fundamental axiom in the field of biology is the First Axiom of Biology stating that genetic diversity is inversely related to epigenetic complexity (Huang 2008b, 2009a). Genetic diversity is here defined as percent position difference in aligned sequence in a homologous protein or DNA.

      I am surprised that biology managed to go on for hundreds of years without a First Axiom.

      Delete
    5. Allan,

      The equidistance result has nothing to do with how conserved a protein is. It is also found in the protein that directly led to the molecular clock. From wikipedia:
      The genetic equidistance phenomenon was first noted in 1963 by Emanuel Margoliash, who wrote: "It appears that the number of residue differences between cytochrome C of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged. If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds. Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish. Similarly, all vertebrate cytochrome c should be equally different from the yeast protein."[2] For example, the difference between the cytochrome C of a carp and a frog, turtle, chicken, rabbit, and horse is a very constant 13% to 14%. Similarly, the difference between the cytochrome C of a bacterium and yeast, wheat, moth, tuna, pigeon, and horse ranges from 64% to 69%. Together with the work of Emile Zuckerkandl and Linus Pauling, the genetic equidistance result directly led to the formal postulation of the molecular clock hypothesis in the early 1960s.

      Delete
    6. Ha ha, well, without a First Axiom, molecular evolutionary biology has managed to produce a lot of senseless or counter intuitive results, much to the dismay of biologists before the molecular clock era, including grouping chimpanzees with human rather with other great apes of the pongid clade, the out of africa model replacing the multiregional, etc etc. Worst of all, the very result explained by the now defunct molecular clock has remained unsolved until half a century later. As a consequence, the field treats (mistakenly) nearly every genetic distance or diversity as still increasing with time, without a consideration of when or whether a maximum limit should be reached. The fact is, which had been easily verified, that the vast majority of genetic distance/diversity observed today is at a optimum balance and no longer correlates with time.

      All hard sciences like physics are based on intuitions/axioms. Why should biology be any exception? Stamp collection has been going on for long enough in biology and today is the era of unification with common sense ideas.

      Delete
    7. The equidistance result has nothing to do with how conserved a protein is. It is also found in the protein that directly led to the molecular clock.

      Which is also highly conserved. Still, you appear to be arguing that conserved proteins have sequence similarity consistent with clade divergence times, so neutral theory is wrong.

      Delete
    8. regardless of conservation, you still need to explain such facts. The molecular clock is not a real explanation but mine is. It is even worse for Kimura to propose the neutral idea to explain such a fake clock. He was misled.

      Delete
    9. So there are clearly problems with the state of peer review in some Chinese journals, and it's possible to get a degree in medical genetics without learning anything about evolution.

      How can there be a universal molecular clock when the proteins you reference have evolved at different rates from each other? And who thinks protein evolution is neutral? And whatever does protein evolution have to do with junk DNA?

      And wait, you think chimps and humans are not closest relatives? On the basis of what?

      Delete
    10. I'm not understanding the First Axiom very well. How can a characteristic of a single species be inversely related to a pairwise comparison between species?

      Delete
    11. "The molecular clock is not a real explanation but mine is."

      Explanation for what?

      Delete
  27. ‘intuition is the source of scientific knowledge.’
    — Aristotle
    ‘The only really valuable thing is intuition.’
    — Albert Einstein
    ‘I believe in intuition and inspiration; at times I feel certain I am right while not knowing the reason.’
    — Albert Einstein
    ‘The intuitive mind is a sacred gift and the rational mind is a faithful servant. We have created a society that honours the servant and has forgotten the gift.’
    — Albert Einstein
    ‘The intellect has little to do on the road to discovery. There comes a leap in consciousness, call it intuition or what you will, and the solution comes to you and you don’t know how or why.’
    — Albert Einstein
    ‘I have had my results for a long time, but I do not yet know how I am to arrive at them.’
    — Carl Friedrich Gauss
    ‘Instinct leads, logic does but follow.’
    — William James
    ‘Intuition does not denote something contrary to reason, but something outside the province of reason.’
    —Carl Gustav Jung
    ‘The disclosure of a new fact, the leap forward, the conquest over yesterday’s ignorance, is an act not of reason but ofimagination, of intuition.’
    — Charles Nicolle
    ‘Knowledge has three degrees—opinion, science, illumination. The means or instrument of the first is sense; of the second, dialectic; of the third, intuition.’
    — Plotinus
    ‘It is through science that we prove, but through intuition that we discover.’
    — Henri Poincaré

    ReplyDelete
    Replies
    1. Is all that intended to imply that you're Einstein and you don't have to show any evidence for your claims?

      Delete
    2. Gnomon,

      Thanks for these revealing quotes
      .
      You might be interested in taking a look at this paper by Matthew Hahn: “Toward a selection theory of molecular evolution” ( http://www.ncbi.nlm.nih.gov/pubmed/18302709).

      In regard to Neutral Theory, indeed, it is becoming increasingly *neutral* in directing the thinking on evolution.

      Delete
    3. Most people intuitively fail the monty-hall problem.

      Intuition is good as a general guide, but it is not some infallible tool of enlightenment. Our intuitions can and do fail us, particularly when it comes to extremely long or short term (microseconds or millions of years), or microscopic and astronomical scales. Generally our intuitions fail us for things far outside our experience, which is normally things of the very small (microscopic, atomic, quantum level), very fast (special relativity) or very large (astronomic, general relativity) or very old.

      That's where we have to do science and use math and empirical evidence instead of just ballparking it on a gutfeeling.

      Delete