Friday, July 26, 2013

On Beating Dead Horses

I've mentioned this before but it bears repeating. One of my Ph.D. students (Sharon Shtang) wrote her thesis on sequence comparisons and phylogenetic trees. She found a quotation from Emil Zuckerkandl and Linus Pauling in their 1965 review. They were commenting on using amino acid sequences to prove evolution. This seemed at the time to be an example of overkill since evolution was then, and is now, a fact. They said ...
Some beating of dead horses may be ethical, where here and there they display unexpected twitches that look like life.
I was reminded of this while reading Salvador Corova's latest post on Uncommon Descent because he refers to beating dead horses [If not Rupe and Sanford’s presentation (8/6/13), would you believe Wiki? In this case, yes]. I'm not going to make any comments. Read it and weep for the IDiots.
Theme

Mutation
Evolutionists reluctantly admit most evolution is free of selection and therefore non-Darwinian (neutral evolution). When pressed, they’ll say neutral drift is real, but they don’t like it when the dots are connected in a way that demonstrates neutral evolution refutes Darwinism, that there is a contradiction between Dawkins’ vision and neutral evolution! The way Darwinists deal with this violation of the law of non-contradiction is to pretend no contradiction exists. They’ll obfuscate and fog the issue with myriad technical terms and irrelevancies so that the illusion of non-contradiction is protected from public view. Confusion and the illusion of some higher knowledge are their friends, clarity and education of the public are their enemies.

If Dawkins had been faithful to the facts, he wouldn’t have even written The Blind Watchmaker because population genetics precludes his vision of evolution from being reality in anything but his silly Weasel simulations.

There is a simple formula from Wiki that says the rate of new mutations is the rate at which new mutations become features of every member of the population (a process called fixation).

http://en.wikipedia.org/wiki/Fixation_(population_genetics)


The population size is N and the Greek symbol μ (mu) is the mutation rate.

It stands to reason a slightly deleterious mutation is almost neutral, hence, approximately speaking the rate that slightly deleterious mutations become part of every member of the population is on the same order of the slightly deleterious mutation rate. That means if every human is getting 100 dysfunctional mutation per generation, about 100 dysfunctional mutations are getting irreversibly infused into humans every generation (a ratchet so to speak).

But as bad as that is, it’s actually worse in reality. Remember broken bacterial parts in anti-biotic resistance, or blindness in cave fish, or sickle cell anemia? Those are “beneficial” (in the Darwinian sense) mutations, but destructive in the functional sense. So it is actually generous the creationists are modeling the dysfunctional mutations as slightly deleterious (whereas a fair argument might actually model some of the dysfunctional mutations as “beneficial”). So the creationists are cutting Darwinists a lot of slack, and yet, even then the dysfunctional mutations will get fixed (become members of all individuals) in a population! Not to mention, lots of bad may get purged from a population only to get replaced with new generations of bad....

But obvious math is something Darwinism hates dealing with! The above equation should be painful evidence against evolution being some process of increasing complexity from a primordial virus to incredible minds like Newton or Einstein. Darwinist won’t come to terms with it, they won’t come to terms with even a computer simulation based on population genetic models. Oh well! But anyway, Christopher Rupe and John Sanford will be presenting the results of a computer simulation that illustrates the above equation. It’s sort of like beating a dead horse or beating living puppies. It’s not very sporting, but Darwinists keep propping up that dead horse for creationists to keep beating.


Zuckerkandl, E. and Pauling, L. (1965) in EVOLVING GENES AND PROTEINS, V. Bryson and H.J. Vogel eds. Academic Press, New York NY USA

90 comments :

  1. So Sal Cordova admits that Intelligent Design is creationism:

    It’s not very sporting, but Darwinists keep propping up that dead horse for creationists to keep beating.

    Thanks for the clarity Sal-- Casey Luskin stopped calling ID "creationism" about 2004, but Sal is less cunning.

    ReplyDelete
    Replies
    1. How petty. Lets get honest, you are a creationist. That is, you believe that the internet was created by intelligent designers. The product of intelligent design, whether human or otherwise, is realistically called creation, is it not?

      That said, the young earth creationist community, of which most IDers are not, takes a fundamentally different approach to science than the ID community does. They begin with a "divine" text. They conclude that this text is on at least equal footing with scientific data. They come up with conclusions that are very difficult to support logically.

      The ID community, for the most part, does not hold a "divine" text as one of its scientific textbooks. The ID community, for the most part, accepts scientific data using the same methods of analysis that you do. Using that same data, we come to different conclusions that you do, mostly because we do not reject the "intelligent designer (unknown to science)" hypothesis a priori.

      Delete
  2. Remind me who this idiotic IDiot is, again.

    ReplyDelete
  3. As for the usual bull about how "blind cavefish" are analogous to evolving anti-biotic resistance, we know that antibiotic resistance, and many other OBSERVED examples of evolution, are beneficial, adaptive, often involve gains in complexity and gains in "information" by any real scientific definition of "information."

    Scott Buchanan neatly summarizes experimental estimates of rates of beneficial mutations including antibiotic resistance, which according to creationists, should all be zero. News flash Sal: they're not. One study found that among mutations that confer increased fitness in the presence of antibiotics, 2.6% of the antibiotic-resistant bacteria ALSO had increased fitness in the original environment WITHOUT the antibiotic present. That's death to creationism. Buh bye.

    ReplyDelete
  4. Sal begins with ...

    Evolutionists reluctantly admit most evolution is free of selection and therefore non-Darwinian ...

    I've been trying to teach this to the IDiots for over twenty years. Yet they still insist on referring to evolution as "Darwinism" and they continue to ignore random genetic drift in their attacks on evolution. About 99% of all IDiots have no idea what Sal is talking about. (Sal Cordova doesn't know either.)

    What Sal is saying is that practically all of the mutations being fixed in humans are either neutral or slightly deleterious. That has implications. It strongly suggests that most of our genome is junk.

    Not only that, it raises questions about design. Doesn't it?

    I wonder if Sal Cordova and Casey Luskin have ever talked about this? I wonder if he's told Michael Behe and Jonathan Wells about his "new" discovery?

    ReplyDelete
    Replies
    1. Not only that, it raises questions about design. Doesn't it?

      It doesn't. Everybody knows that genetic deterioration in populations is a consequence of the Fall. Before that, there were no mutations. Since we're all headed for genetic disaster soon, that proves the time since the Fall is only 6000 years.

      Delete
    2. Let's be clear. What John Harsman says is in fact what they think. It might be a joke to us, but that IS how they reason this.

      Delete
  5. Beating a dead Darwin.

    That's the best they can do.

    Glen Davidson

    ReplyDelete
  6. The Zuckerkandl and Pauling paper is awesome and still deserves to be widely read - it's from the period when sequences were scarce (that is, amino acid sequences were scarce; DNA sequences were non-existent), so scientists had to put actual thought into their papers instead of just data. Also, those guys knew how to write.

    ReplyDelete
  7. Not that long ago Jerry Coyne has desperately tried to convince me and others, that macroevolution can be observed just like sunset. He pointed to dog breeders doing it everyday, who breed dogs with short legs and longer hair, and something else. Is this the best example of macro that an authority of evolution can present? How about you Larry? If evolution is true, there should be thousands, if not hundreds of thousand of examples of macro-evolution right now. Where are they? I believe in micro but macro is a bit science-fiction to me. I'm sure I will be overwhelmed with proof today.

    ReplyDelete
    Replies
    1. Does it have to happen in front of your face, or are you allowed to infer it from data? Makes a big difference. Also, you will need to tell us what you are willing to accept as macroevolution. Jerry obviously meant to refer to large changes in morphology, which dog breeds fit well. In nature, this sort of thing seldom happens fast enough to sit around watching, which is why happening in front of your face is a problem.

      Now, if inference will work, please consider the phylogenetic tree of any random group of organisms and notice that the species in that group are quite different from each other, yet descend from a common ancestor. Looks like macroevolution to me. Or are you a creationist who refuses to believe in common descent?

      Delete
    2. Larry doesn't define macroevolution as a process, but rather it's a field of study that examines the large scale evolutionary patterns that we see in the fossil record and the biogeography of living organisms. There are certainly more to macroevolution than the simple microevolutionary changes, but any macroevolutionary theory should be consistent with microevolution, just like astronomy or cosmology is consistent with physics.

      He has a nice article about the subject here:
      http://bioinfo.med.utoronto.ca/Evolution_by_Accident/Macroevolution.html

      Delete
    3. So you say you believe in micro, but not macro, eh? Where does one end and the other begin in your mind?

      Delete
    4. Beware creationists in "I accept evolution, but need to see proof of X" clothing.

      Delete
  8. Larry,

    I would like to let you know, that I was at a party where a lot of creationist came by-(I'm not sure if all people who believe in creation are creationist? Does anybody know that? Please let me know if you do)

    Anyhow, quite a few creationists spoke very highly of you and your blog. That is why I have ended up joining the discussion. So, I'm not really sure if calling all of creationist IDiots is correct since quite a few of them follow your blog and speak very highly of it and you. Also, I was pretty surprised to learn that few of them believe in evolution (micro) though Behe was the STAR there. He also spoke about you with dignity and respect, which I was surpised about because I had known how much you hate him, creationist like him and people in general who don't agree with you.

    ReplyDelete
    Replies
    1. Not all creationists are IDiots. That's a term reserved for fans of intelligent design, which is a subset (mostly for tactical reasons) of creationists. Larry doesn't hate Behe, though he certainly has contempt for his ideas. Contempt and hate are different, as are people and ideas.

      Why were you surprised to learn that few creationists believe in evolution?

      Delete
    2. John,
      As far as I know, contempt and hate are closely related aren't they? What puzzles me is how you are able to sense what kind of feelings Larry has toward Behe? Are you that close?

      Delete
    3. I can read. You can learn a lot by reading.

      Delete
    4. Well, I guess you might be right. You have probably read Larry's blog for few years. After a while, one can sense what he is all about. I will give you the benefit of the doubt in this case.

      Delete
    5. So why were you surprised to learn that few creationists believe in evolution?

      Delete
  9. Carl Zimmer wrote a nice piece two weeks ago over at Scientific American describing how the latest research shows that neutral evolution can indeed result in a net increase in complexity over time.

    The Surprising Origins of Evolutionary Complexity
    http://www.scientificamerican.com/article.cfm?id=the-surprising-origins-of-evolutionary-complexity

    ReplyDelete
    Replies
    1. I have a problem with the idea. Part of it is the notion of "complexity" which is poorly defined. I prefer to think in terms of information, in that a genome contains information about the environment in which it reproduces. Taken that way, the alleged "complexity" of the fruit flies in the study can only become information when they are exposed to the selecting power of the environment: i.e. natural selection. Without selection the changes they are reporting are just so much random static--the same random static you might see in the wild just before natural selection eliminates it.

      Delete
  10. The fun thing about Sal's post is the massive internal contradictions. Darwinism is wrong because most of the genome evolves neutrally! But wait, saying this is basically another way of saying that most of the genome is junk or at least junky, which is something Sal doesn't believe.

    Another one -- 6 million years from the human-chimp ancestor to humans is only enough time for thousands of positively selected mutations. But, says Sal, there must have been millions of positively selected mutations. But, the only way you can get a count of millions of differences between humans and chimps is to include all of the neutral substitutions, which he just sold us were neutral and not selected, which is how they disproved Darwinism.

    It's like the different pieces of his brain aren't connected to each other, they are only separately connected to his mouth/typing fingers.

    Also, who calls Wikipedia just "Wiki"?

    ReplyDelete
    Replies
    1. Better, I think, is his central claim that all those beneficial but nevertheless bad in some way mutations will become fixed and thus beneficial mutations cause dysfunction, which is bad even though it's good.

      Delete
    2. Good point. Simpler version: deleterious mutations are easy to fix and are leading to the rapid genetic decay of the human species in mere thousands of years, but beneficial mutations are hard to fix and you could only get a few in millions of years. Therefore EvolutionIsWrongDogmaticDarwinistCensorshipThey'llBeUpAgainstTheWallSoonWhenTheRevolutionComes.

      Delete
    3. No, it's worse than that. He's claiming that most beneficial mutations are also bad for you -- they are the result of deterioration of the genome and so must be deleterious in some unclear way.

      Delete
  11. NickM,

    I assume you are Nick Matzke?

    ReplyDelete
  12. If you are, I like your views, to a degree obviously. You are a very smart guy. Very smart. You must be very happy.

    ReplyDelete
    Replies
    1. Find me a tenure-track job, then we'll talk about happy. :-) PS: Gotta go I should be dissertating.

      Delete
    2. Or wait, I may be happy, I guess Quest is not. In reply to me, I think, on the "Every non-lethal genome position is variable in the human population" thread:

      ================
      QuestThursday, July 25, 2013 7:21:00 PM

      Berlinski spanked your a.s big time, so if I were you, I would take some math courses this summer or I would go to the atheistic confession. I'm afraid however, that people like you lie to themselves so much, they can no longer distinguish what it is; what is the truth and a lie.
      ================

      What is your beef with evolution, then? If you can explain why evolutionary biologists think Berlinski is a silly person because of his node-rotation mistake, you might be worth talking to.

      Delete
    3. NickM,
      Berlinski's node-rotation mistake? How is that going to change anything? Do you really think that creationist/evolutionist shallow polemics are going to end there? Forgive me, but I had thought you were smarter than that.

      Additionally, I can't hire you Nick. You are not only way to smart but you wouldn't last few months doing the boring stuff probably for over $100 grand a year. You need the controversy because it keeps you alive; it keeps you going.

      I personally think that you have two choices: remain who you are or become a politician.

      If you choose the first option, just pray that evolution issue remains an issue for years to come. Can you imagine what would happen if evolution was either proved or disproved? Do you know how many evolutionists and creationist for that matter would lose their jobs?

      Would the Discovery Institute need to exist one way or the other?

      What do you think Nick?

      Delete
    4. "Berlinski's node-rotation mistake? How is that going to change anything?"

      Well, Mr-no-polemics-except-when-I-use-them, it would change an informed person's opinion of who is spanking who.

      "Can you imagine what would happen if evolution was either proved or disproved?"

      Why, yes, I can, since evolution already has been proved, in various commonsense meanings of the word "proved". If you disagree, little passive-aggressive snipes about my personality will establish absolutely nothing. Your only hope is you wrestle with the data and propose a better explanation of the data. You can start with Doug Theobald's 29+ Evidences for Common Ancestry FAQ, here: http://www.talkorigins.org/faqs/comdesc/

      "Do you know how many evolutionists and creationist for that matter would lose their jobs?"

      No evolutionists would lose their jobs, since there is a ton to study even though evolution is already proven. Geologists still have jobs even though it's proven that the Earth is old, etc.

      Re: creationist jobs, there are probably a few hundred, tops, in the whole country anyway. They don't do anything useful or scientific right now, so it wouldn't effect things much if they disappeared.

      "Would the Discovery Institute need to exist one way or the other?"

      It doesn't "need" to exist, right now! So what's your point?

      The people who need it to exist are basically, to a first approximation, conservative evangelicals who think evolution contradicts their theological views and especially their doctrine of Biblical inerrancy. They have weak faith, and so are insecure about simply asserting up front that they are choosing to ignore the evidence in favor of their particular sectarian beliefs, and instead do an elaborate pseudoscientific show and dance to try and reassure themselves that the evidence is on the side of creationism (mostly old-earth creationism, in this case, but with some young-earth creationism mixed in).

      Delete
    5. Well, good for you Nick, You are so predictable. I love it.

      Here is test # 1 for you

      http://www.youtube.com/watch?v=IQWsdZxRFWY

      I'm sure you can lie your brains out to deal with this one ;) I know you can and will ;)

      Delete
    6. Quest seems to be a rather mercurial troll. I don't think he's ever going to respond to anything.

      Delete
    7. Quest,

      You don't need a PhD in biochemistry to answer that old creationist line. Does Wells really think that any modern scientist in his right mind has ever suggested that a complex mammalian cell would evolve or self-assemble from "a few amino acids dissolved in the ocean"? And does he really think that a test tube successfully models all the physical and environmental forces that were present in the early oceans? And by all means, what does this have to do with evolution anyway?

      In just this thread, you complained about Larry being too judgmental and uncivil in his writings about creationists. Yet, the video you presented is just a prime example of everything that is wrong with the creationist movement: Misrepresenting other people's views, complete disregard for the evidence, and complete disrespect for the countless hours that real scientists spend in tackling real scientific questions.

      Maybe you should invest your time watching a real seminar about the latest research in Abiogenesis (and NOT evolutionary theory), instead of watching an 82 seconds video three times a day and thinking to yourself that you have the answers to everything there's to know.

      Here's an almost 3 hours seminar by Prof. Jack Szostak, from Harvard University, exploring the latest developments in his research on the origins of life:

      Jack Szostak (Harvard/HHMI) Part 1: The Origin of Cellular Life on Earth
      http://www.youtube.com/watch?v=PqPGOhXoprU

      Jack Szostak (Harvard/HHMI) Part 2: Protocell Membranes
      http://www.youtube.com/watch?v=CJ5jh33OiOA

      Jack Szostak (Harvard/HHMI) Part 3: Non-enzymatic Copying of Nucleic Acid Templates
      http://www.youtube.com/watch?v=jfq5-i8xoIU

      Enjoy!

      Delete
    8. ==============
      QuestFriday, July 26, 2013 10:13:00 PM
      Well, good for you Nick, You are so predictable. I love it.

      Here is test # 1 for you

      http://www.youtube.com/watch?v=IQWsdZxRFWY

      I'm sure you can lie your brains out to deal with this one ;) I know you can and will ;)
      ==============

      Hmm, it's called "Disproving Atheists in 82 seconds!" I'm not an atheist, so who cares? We were talking about population genetics or, on the previous thread, the Cambrian. Can't stay on topic, going in my ignore list.



      "John Harshman Friday, July 26, 2013 11:14:00 PM

      Quest seems to be a rather mercurial troll. I don't think he's ever going to respond to anything."

      Yeah I think you're right, he hasn't given a straight answer to anything yet, I'm done with him.


      Shadi -- I recall you saying you wanted to contact me, do so at your leisure, email is matzkeATberkeley.edu

      Delete
    9. Well, good for you Nick, You are so predictable. I love it.
      - he says, without predicting anything, but links a skullvoided youtube video instead.

      *facepalm*

      Delete
    10. ShadiZ1,

      Thanks for the links to Jack's videos!

      Delete
    11. Hi Nick, I'm really disappointed with your links to mr. Shitstuck ideas of the orgin of life. I have a hard time believing that you believe this shit. I mean thought you were a scientists not a fairy-tail enthusiast. If you are, you'd better find some evidence or I will do some very nasty stuff to your beliefs. Nick, fix this shit quickly and don't embarrass yourself. I can help you but I can also be mean.

      Delete
    12. OMG! as Larry would say. Do you really believe Shitstock's stuff? Please tell me that you have brains. I can't wait....

      Delete
  13. The term "IDiot" is reserved for the fraudsters pushing the Intelligent Design brand. It's just a marketing tool for a product that doesn't sell as well as it used to. It has nothing to do with science and a lot to do with creating fear, uncertainty and doubt.

    What I find particularly irksome is that they persist in demonstrating that they do not know what they are talking about. They have been doing it so long that I have long since given up believing that they are sincere, and I suspect everyone else here has as well. This is probably why they are held in such contempt, which is all the consideration the professionally oblivious deserve.

    ReplyDelete
    Replies
    1. I meant to say "professionally obtuse." I should really preview more.

      Delete
  14. I noticed this in the quoted abstract (?): "This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage." Considering that there are only around 18 million nucleotide substitutions, total, in the human lineage, how did the authors come up with that number of selective substitutions?

    ReplyDelete
    Replies
    1. The genome is 100% functional, didn't you hear?

      Delete
    2. ...and it's all evolving neutrally too. But God resolves all contradictions.

      Delete
    3. Guys, John, you already resolved the contradiction earlier. Creationists reject all "our facts" about genomes and evolution. To them, it looks like WE are the ones who believe in a position that contains internal contradictions.

      The creationists insist that the contradictions are actually there, and that this disproves our "belief", but the only reason we still believe is because, you know, our "atheistic delusional leaning and fear of comming to terms with reponsibility to god" etc. etc.

      When you simply point out that what Sal says is self-contradictory, all you get is his agreement. He thinks this is a problem for US, because we're the ones who's supposed to be believing this self-contradictory stuff.

      Delete
    4. NickM says: “The genome is 100% functional, didn't you hear?”

      Nick,

      Even our host Larry is adapting to the idea that, in addition to their informational roles, the genomic DNA sequences can play non-informational roles, although he pretends that the current prevalent hypotheses on non-functional roles for the so called ‘junk DNA’ (jDNA), the nucleoskeletal and nucleotypic hypotheses on the biological roles of jDNA promoted by Thomas Cavalier-Smith and by Ryan Gregory (who apparently is Larry’s friend), which have been discussed in dozen of scientific publications, don’t exist.

      However, when it comes to my model on the biological function of jDNA (http://comments.sciencemag.org/content/10.1126/science.337.6099.1159), he completely denies it despite overwhelming supporting evidence.

      Delete
    5. Where's all this overwhelming supporting evidence?

      Delete
    6. The rationale for the model is presented in the original paper (1) and the series of comments posted in Science (http://comments.sciencemag.org/content/10.1126/science.337.6099.1159).

      Regarding the evidence, let’s consider the humans, in which non-informational DNA sequences, usually referred to as junk DNA (jDNA), occupy well over 90% of the genome. This jDNA provides significant protection against deleterious insertional mutagenesis by endogenous and exogenous inserting elements, particularly against insertional oncogenic transformation.

      Indeed, given the enormous number of somatic cells and their high turnover rate during reproductive span, the number of insertion events that could lead to neoplastic transformations in the absence of protective mechanisms could be evolutionarily drowning. A dramatic example of the tremendous selection pressure imposed by cancer-inducing insertion mutagenesis in humans is provided by the highly promising biomedical field of gene therapy using viral vectors, a field that has been devastated by high prevalence of cancer in treated patients (2).

      1. Bandea CI. A protective function for noncoding, or secondary DNA. Med Hypotheses 1990 Jan;31(1):33-4.
      2. Baum C. Insertional mutagenesis in gene therapy and stem cell biology. Curr Opin Hematol 2007 Jul;14(4):337-42.

      Delete
    7. Hi Claudiu,

      Please google "Onion Test" and give us your answer. Thanks, Nick

      Delete
    8. "When you simply point out that what Sal says is self-contradictory, all you get is his agreement. He thinks this is a problem for US, because we're the ones who's supposed to be believing this self-contradictory stuff."

      Well, if he could get it into his head that we think basically a few percent of the genome is under selection, and most of that is stabilizing, and that the selected differences between humans and chimps are just a subset of that, and all the other millions of genomic differences between humans and chimps are mostly neutral, then there would be something to talk about. But since Sal just randomly rounds up or down as convenient to produce his "contradictions" there's little for us to do but point and laugh.

      Delete
    9. Nick,

      I don’t know if you are aware but the person who introduced the ‘onion test’ as a powerful metaphor for the C-value enigma is Ryan Gregory, who throughout his scientific career has promoted the nucleotypic hypothesis on the evolution of gnome size. Ryan is one of the top scholars in this field, so it would make sense for everyone engaging in scientific discussions on the subject to study his work and ideas. Here are some of Ryan’s statements:

      “Although some researchers continue to characterize much variation in genome size as a mere by-product of an intragenomic selfish DNA "free-for-all" there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates” (Gregory TR, Hebert PD. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res; 9(4):317-24).

      “These are the “nucleoskeletal” and “nucleotypic” theories which, though differing substantially in their specifics, both describe genome size variation as the outcome of selection via the intermediate of cell size” (Gregory TR. 2004. Insertion-deletion biases and the evolution of genome size. Gene, 324:15-34).

      I don’t know exactly how Ryan reconciles his nucleotypic hypothesis with the onion test, but the model I'm proposing on the evolution of genome size, c-value enigma, and the biological role of the so called ‘junk DNA’ (jDNA) passes the test.

      The quantity of jDNA in various species depends primarily on the insertional activity of viral and transposable inserting elements. This insertional activity can vary greatly not only between distantly related species, but also between closely related species, such as various onion species. Therefore, based on this activity, even highly related species can accumulate various amounts of jDNA sequences within a relatively short period of evolution.

      The model I’m proposing is a classic example of ‘fighting fire with fire’. Similar to the amount of viral DNA sequences co-opted by some of bacterial and archaeal species in their adaptive CRISPR/Cas antiviral defense mechanism, which depends on the viral activity, the amount of jDNA sequences (and the level of protection) is associated with the level of insertion activity.

      However, the quantity of jDNA also depends on the differential constrains (e.g. energetic costs) on genome size in various species (e.g. humans vs. hummingbirds). Nevertheless, in related species, such as onions, these constrains tend to be similar, so the difference in genome size is based primarily on the rate of insertional activity.

      In summary, as an adaptive defense mechanism against insertional mutagenesis, the amount of protective DNA (jDNA) varies from one species to another based on the insertional activity of viral and transposable elements and on the evolutionary constraints on genome size.

      Delete
    10. Nick,

      You will notice that in all that verbiage, Claudiu never answered you. He has consistently avoided addressing the onion test, so that's probably all you'll ever get out of him. And he never seems to notice that he's proposing the cause and the explanation as the same phenomenon with no way to distinguish them. That's been mentioned to him many times too.

      Delete
    11. John,

      I think Nick is capable to judge for himself the merit of my model or that of my explanations, without your preemptive and, in my opinion, biased ‘advise’.

      You might not understand my perspective or that of other people, such as that of Gregory (nucleotypic hypothesis) and Cavalier-Smith (nucleoskeletal hypothesis). As a matter of fact, I don’t think that you have commented on any of these two hypotheses, which have been developed and discussed in dozens of scientific papers and books.

      Also, I don’t think you have answered the straightforward question that I asked you and other readers here at Sandwalk:

      Does the so called jDNA, which in humans is estimated to comprise more than 90% of the genome, provide protection against insertional mutagenesis (particularly in the somatic cells), by endogenous and exogenous viral elements, which can cause deleterious mutations or can lead to oncogenic transformations?

      Delete
    12. Claude,

      I'm not sure if I accurately understood your point. But it seems to me that your idea is quite similar to the mutation protection hypothesis that Ryan Gregory has already addressed on his blog. He says that the idea has been around for some time, but there's no data to support it. And although he didn't totally dismiss the idea, he remarked that the proponents of such hypotheses tend to ignore counter-examples.

      You can read his blog post here:

      Does junk DNA protect against mutation?
      http://www.genomicron.evolverzone.com/2009/12/does-junk-dna-protect-against-mutation/

      Also, how does your hypothesis explain the relatively small percentage of jDNA seen in the bladderwort's genome? Especially considering the fact that these plants occupy diverse habitats, from Canada to Australia.

      Nick,

      I just sent you an e-mail right now. Make sure it didn't get caught by the spam filter. Thanks!

      Delete
    13. Claude

      If you are right about "the so called jDNA, which in humans is estimated to comprise more than 90% of the genome, provide protection against insertional mutagenesis (particularly in the somatic cells), by endogenous and exogenous viral elements, which can cause deleterious mutations or can lead to oncogenic transformations?"

      What does this mean for evolution? I'm a layman on this subject, so please, bare with me.

      Delete
    14. I would like to think that everyone seriously interested in the evolution of genome size and the C-value enigma has studied Ryan’s work, including his blog Genomicron. Too bad that the leaders of the ENCODE project did not study Ryan’s work on the principles of genome evolution and the historical developments concerning the c-value paradox and the concept of ‘junk DNA’.

      In regard to his post “Does junk DNA protect against mutation?” (http://www.genomicron.evolverzone.com/2009/12/does-junk-dna-protect-against-mutation/), I would highly recommend it.

      Briefly, Ryan starts his historical review on this matter by mentioning a paper published in 1971 in Science by Yunis and Yasmineh (http://www.ncbi.nlm.nih.gov/pubmed/4943851). As emphasized by Ryan, the authors focused primarily on the potential structural roles for heterochromatin:

      “With the assumption that a portion that comprises some 10 percent of the genomes in higher organisms cannot be without a raison d'être, an extensive review led us to conclude that a certain amount of constitutive heterochromatin is essential in multicellular organisms at two levels of organization, chromosomal and nuclear. At the chromosomal level, constitutive heterochromatin is present around vital areas within the chromosomes. Around the centromeres, for example, heterochromatin is believed to confer protection and strength to the centromeric chromatin.” (emphasis added).

      Then, Ryan outlines the ‘bodyguard hypothesis’ proposed by Hsu in 1975 (A possible function of constitutive heterochromatin: the bodyguard hypothesis. Genetics 79 (Suppl. 2): 137-150), who wrote:

      “The hypothesis proposed here is a simple-minded one: constitutive heterochromatin is used by the cell as a bodyguard to protect the vital euchromatin by forming a layer of dispensable shield on the outer surface of the nucleus. Mutagens, clastogens [inducing chromosome breakage] or even viruses attacking the nucleus must first make contact with the constitutive heterochromatin which absorbs the assault, thus sparing the euchromatic genes from damage, unless the detrimental agents are overpowering.”

      I don’t think that these scientists advanced the model I proposed, but even if they did, what’s relevant here is whether the model is correct or not. If it is correct, then we resolve the c-value enigma and have a better understanding of genome evolution.

      Delete
  15. Why does this blog attract so many ignorant creationist trolls?

    (Also, "from Wiki"? Is that how Wikipedia is called in American English or something? And if yes, how does one differentiate it from the hundreds of other wikis that exist?)

    ReplyDelete
    Replies
    1. how does one differentiate it from the hundreds of other wikis that exist?

      God tells us so.

      Delete
    2. No, Americans do not call Wikipedia "wiki." Wiki is still a generic term for the editing system. As well as being the Hawaiian word for fast.

      Delete
  16. Sal on UD in comments: "slightly deleterious means approximately not being subject to selection". And vice versa? I'm reminded of the UK education minister who wants all schools to be above average.

    ReplyDelete
  17. Larry,

    You are an imbecile. Only natural selection is sed to be a designer mimic. Drift does nothing. That is the point.

    ReplyDelete
    Replies
    1. Actually, design is a natural selection mimic.

      Drift does nothing? It is one of several factors that increases the variation in a population. It helps ensure that populations cannot stand still, however much you'd like them to. It ... meanwhile, what did the designer do, Joe? Be specific.

      Delete
  18. Can Larry or any evoTARD produce testable hypotheses wrt unguided evolution actually constructing something like a multi-protein configuration? The safe money is on the "no they cannot" side.

    ReplyDelete
    Replies
    1. Joe's stock comment makes its 17,561th appearance. What in heck is a multi-protein configuration? Does boiling an egg count?

      Delete
    2. Yeah sure. If multi-protein configuration evolved, we should be able to find similar structures in related organisms, and we should be able to construct phylogenies from increasingly dissimilar sequences in related organisms.

      Turns out we can. QED.

      Delete
    3. I think Joe's position would be that if we can't show the 'unguided' processes in action, they must have been guided.

      Delete
    4. In which case, if Joe can't show the "guided" piece of the process, we are only justified in inferring evolution operates the way we observe it in nature in the here and now: Unguided.

      I'll be happy to be told someone has observed the hand of god guiding evolution, followed by a way to independently confirm that observation.

      Delete
    5. True enough. I'm not saying his case has any merit! But this is his stock MO. I'm surprised he hasn't stuck around - not like him to post 'n' run.

      Delete
    6. Joe "security clearance" Gallien asks

      "Can Larry or any evoTARD produce testable hypotheses wrt unguided evolution actually constructing something like a multi-protein configuration?"

      "Something like" is the usual vague terminology employed by IDiots, it allows them deniability, but at any rate, Joe Thornton's lab has published many papers on ancestral sequence reconstruction/resurrection (ASR).

      Having answered that, it's now our turn to ask Security Clearance:

      Can Joe "National Security" Gallien or any creationist produce testable hypotheses wrt invisible spooks actually constructing something like a multi-protein configuration? Or a single protein? Or one change in one nucleotide from any genome of any species ever?

      Delete
    7. "That doesn't count the experiments I conduct in my basement. Some labs would be jealous of the equipment I house & use there.

      For example I now know that ticks are more attracted to watermelon rinds then they are to orange peels or orange slices. I also know that dragonflies play.
      "

      HAHAHAHAHAHAHAHHAhahahaha ...

      *deep inhale*

      HAHAHAHAHAHHAHAHAHAHAHAHAHAHAHAHahahahahaha...

      *gurgle, snort, gasp*

      Teeeeheeeheeehehehehehihihihihihihihihihh....

      Delete
    8. Joe G: "BTW without free oxygen how did the nucleotides- you know the building blocks of DNA & RNA- come to be?

      (only the purine adenine is without O)
      "

      HAHAHAHAHAHAAAHAHAHHAHAHAHAHAHAHAHAHAHA...

      *heave, become teary"

      HAAARHAAARHAAARHARHARHAHARHARHAHAHAHAHAHAHAHAahahahahaahaha

      Delete
  19. There is a simple formula from Wiki ...

    That "formula" is more than simple. it's meaningless. It just multiplies mu by 2N and divides by 2N, and you get mu. Duh!

    ReplyDelete
    Replies
    1. I'll let Kimura know you don't like him.

      Delete
    2. Love this passage by Zuckerkandl:
      "As one continues to be faced with the task of sorting out the curses and the blessings of faith, “intelligent design” plays the role of offensive little swarms of insects that more and more fill the air and must be taken care of by spraying biological knowledge before they multiply explosively and threaten civilized life — or its possibility; only its possibility: one must indeed recognize that nobody quite has civilization — apparently because the Great Designer has failed to design humans that, en masse, would do better than produce it in tainted varieties. That is no excuse for losing the measure of civilization we have.” (Zuckerkandl,Gene, 2006, 285,p. 15)

      Delete
  20. Liar, liar pants on fire!!! Who is telling the truth about chimp and human ancestry?

    I don't know who to believe anymore, shoot


    http://www.youtube.com/watch?v=x-RWG6lawaM

    ReplyDelete
    Replies
    1. The comments on that nonsensical video totally eviscerate it. The claim that the structures identified as telomeres aren't really telomeres is total nonsense. The amount of DNA gone missing at the fusion points is miniscule.

      Delete
    2. LouiseG, are you JoeG's mother? If you are, can you hear him screaming in your basement?

      Delete
  21. BTW:

    John Mattick just published this:

    http://www.thehugojournal.com/content/pdf/1877-6566-7-2.pdf

    Abstract
    Recently articles have been published disputing the main finding of the ENCODE project that the majority of the human genome exhibits biochemical indices of function, based primarily on low sequence conservation and the existence of larger genomes in some ostensibly simpler organisms (the C-value enigma), indicating the likely presence of significant amounts of junk. Here we challenge these arguments, showing that conservation is a relative measure based on circular assumptions of the non-functionality of transposon-derived sequences and uncertain comparison sets, and that regulatory sequence evolution is subject to different and much more plastic structure-function constraints than protein-coding sequences, as well as positive selection for adaptive radiation. We also show that polyploidy accounts for the higher than expected genome sizes in some eukaryotes, compounded by variable levels of repetitive sequences of unknown significance. We argue that the extent of precise dynamic and differential cell- and tissue-specific transcription and splicing observed from the majority of the human genome is a more reliable indicator of genetic function than conservation, although the unexpectedly large amount of regulatory RNA presents a conceptual challenge to the traditional protein-centric view of human genetic programming. Finally, we suggest that resistance to these findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design.

    ReplyDelete
    Replies
    1. I just wonder how Dan is going to respond to this.

      Delete
    2. Who cares about Dan Grauer? :-)

      Wait 'till you see what I have to say. That paper by Mattick is very revealing. He's defending Intelligent Design Creationism!

      Delete
    3. He didn't defend it outright. But he did no say anything bad about it. And that's bad enough...

      Delete
    4. Basically, he is accusing people of clinging onto junk DNA despite all the supposed evidence to the contrary due to ideological commitment to atheism.

      But of course, one can flip that argument and start wondering what his motivation for attacking junk DNA despite all the evidence (I have never seen him say anything about population genetics) is..

      Delete
    5. His attacks on the onion test and lack of conservation are seriously lame. I'm more interested in his main defense of tissue-specific expression. First, is it true? Second, would we expect this from random sequences? They would, after all, include random promotor sequences that would act to increase or decrease expression of downstream sequences in ways depending on the regulatory molecules expressed in that tissue.

      Delete
    6. One may wonder if any of the 32 references that remain after Mattick's and Dinger's 26 papers are substracted are really supportive of Mattick's views. Graur et al., Doolittle, Niu and Jiang as well as van Bakel er al. surely don't. Collins? Dawkins? Unlikely. However, Behe likely and Wells surely will.
      BTW, the piece of HUGO council member and HUGO Chen award winner 2012 Jon Mattick appeared in The HUGO Journal.

      Delete
    7. I find it strange that he cited Behe on this particular issue. Did Behe explicitly speak about jDNA before? The letter that he cited was way back from 2003. In his book, the Edge of Evolution (2007), Behe seemed to be content with the idea that there seems to be non-functional sequences in the human genome. Though I have to admit, you can interpret his words as though he was advocating the mutation protection hypothesis.

      This is what he had to say:

      "If DNA were exactly like a blueprint, with no wasted space, and every line and curve representing a point of building, then this mutation rate would be fatal. After all, one critical mistake is all it takes to kill (or cause the building to collapse). But in fact, DNA isn't exactly like a blueprint. Only a fraction of its sections are directly involved in creating proteins and building life. Most of it seems to be excess DNA, where mutations can occur harmlessly."

      ~ Michael Behe, The Edge of Evolution, P. 66

      Delete
    8. Mattick actually wrote THAT in the abstract?

      "we suggest that resistance to these findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design."

      I've never read any sentence like that in any of the hundreds of scientific papers I've read.

      Mattick, like the IDers, sets himself up as a psychonanalyst. They're not competing with Darwin-- they're competing with Freud to make a great psychoanalytic theory.

      C. S. Lewis called this the fallacy of bulverism-- I need no evidence against your claims, because I can make claims about your bad motivations.

      That doesn't belong in a science paper, and it makes Mattick look batshit insane.

      Delete
  22. On beating dead horses... Many years ago, Sal Cordova wrote a post on a cre/ev discussion forum in which he claimed, in all seriousness, to have disproved the utility of using DNA in phylogenetic analyses. His paradigm crushing method? He used a couple of 8-'base' sequences, proposed that each generation one 'base' mutated' and VOILA! After only 8 generations, Sal's 8-'base' sequence was totally different, thus, you cannot rely on DNA analyses in phylogenetic analyses.


    And he meant it...

    There really is no arguing with people that think that way.

    ReplyDelete
  23. Dr. Moran, "Evolutionists reluctantly admit most evolution is free of selection and therefore non-Darwinian..."

    Dr. Moran, this is a greased pig, an attempt to call the ID community wrong for using the term Darwinian. Neutral drift remains to be random mutations filtered by selection. The fact that selection gave these mutations neither the benefit of promotion nor the challenge of rejection is irrelevant. Selection still determined what class these mutations fall into, in this case the "who cares" class.

    The term darwinian, as use by the ID community to describe the current dominant paradigm is still very valid.

    ReplyDelete