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Sunday, August 04, 2013

Dear Denyse, Stop Digging

You're not going to believe what Denyse O'Leary just posted on Uncommon Descent: Junk DNA: Just because information is never used, doesn’t mean it is junk.
Further to Cornelius Hunter’s “Evolutionist: We do not promote any ‘spiritual ideologies,’” (in which he recounts that recent findings about RNA structure conservation suggest that even more of the mammalian genome is functional than supposed, hence there is less “junk DNA”:

I’ve never clearly understood Darwin’s fans attachment to junk DNA. It makes a good “anti-God” statement, as long as you are certain that the stuff is not and never could be any use. But that is precisely what is now widely contested. And it was a trap they need not have fallen into.

But a simple illustration will show that even if most of the information in DNA were never used, it would still be valuable. Let us say I have a directory of members of a club I belong to. I never use most of the phone numbers. Many numbers may never be used by anyone.

Does lack of use make that proportion of the directory junk?


  1. Denyse O'Leary: the gift that keeps on giving? ;)

  2. Larry. What it means that it does not look like it is all junk. It may not be junk because of its properties; we don't know yet. You may be wrong for once. I'm sure you been wrong at least once? So, what if you are wrong? I don't think it's a sin...Is it? Even if you are right, which is often the case, what is going to change? Tell me, what!!!

    1. If I may answer:

      On the personal level, nothing is going to change. On the scientific level, though, a lot of what we know and understand about biology will have to change. But the problem is that we haven't been shown any cogent argument for the claim of pervasive functionality in the genome. And until you do provide one, the null hypothesis of non-functionality still holds.

    2. There's plenty of solid evidence that most of our genome is junk. It's not a question of not knowling and it's not just a null hypothesis.

  3. Larry,

    Do you have access to the study that Dr. Cornelius Hunter cited in his original post? If you could comment on the results of the study and its scope, I'd very much appreciate it. The press release, unfortunately as usual, conflated the notion of non-coding DNA with junk DNA -- with the usual line about "far from being junk", etc.

    1. see How Not to Do Science

      The Mattick lab scanned the human genome using a program that they think will detect secondary structure. They found that 86% of the genome showed no evidence of RNA products with secondary structure. According to their conclusions, their data suggests that "a large proportion of the mammalian genome is functional."

      The main technical problem with their study is that they don't have a control. We need to know what they would find if they analyzed random sequence DNA.

    2. If it's originating from lost casual inadvertant retroreplication (since a lot of junk DNA originates that way), we would expect it to have signs of secondary structure. It still doesn't mean it would be functional though, and not be the junk it is. Why did they jump so quickly to the conclusion that it would?

    3. Larry,

      The article clearly states that, there is an increasing evidence that so called junk DNA has regulatory functions necessary in proper cell development. This means that removing those parst of DNA can lead to improper cell development and therefor to many serious diseases, like cancer. That's hardly junk, if it means life or death.

      "How 'Junk DNA' Can Control Cell Development

      Researchers from the Gene and Stem Cell Therapy Program at Sydney's Centenary Institute have confirmed that, far from being "junk," the 97 per cent of human DNA that does not encode instructions for making proteins can play a significant role in controlling cell development.

      And in doing so, the researchers have unravelled a previously unknown mechanism for regulating the activity of genes, increasing our understanding of the way cells develop and opening the way to new possibilities for therapy.
      Using the latest gene sequencing techniques and sophisticated computer analysis, a research group led by Professor John Rasko AO and including Centenary's Head of Bioinformatics, Dr William Ritchie, has shown how particular white blood cells use non-coding DNA to regulate the activity of a group of genes that determines their shape and function. The work is published today in the scientific journal Cell.

      "This discovery, involving what was previously referred to as "junk," opens up a new level of gene expression control that could also play a role in the development of many other tissue types," Rasko says. "Our observations were quite surprising and they open entirely new avenues for potential treatments in diverse diseases including cancers and leukemias."
      The researchers reached their conclusions through studying introns -- non-coding sequences which are located inside genes.
      As part of the normal process of generating proteins from DNA, the code for constructing a particular protein is printed off as a strip of genetic material known as messenger RNA (mRNA). It is this strip of mRNA which carries the instructions for making the protein from the gene in the nucleus to the protein factories or ribosomes in the body of the cell.
      But these mRNA strips need to be processed before they can be used as protein blueprints. Typically, any non-coding introns must be cut out to produce the final sequence for a functional protein. Many of the introns also include a short sequence -- known as the stop codon -- which, if left in, stops protein construction altogether. Retention of the intron can also stimulate a cellular mechanism which breaks up the mRNA containing it.
      Dr Ritchie was able to develop a computer program to sort out mRNA strips retaining introns from those which did not. Using this technique the lead molecular biologist of the team, Dr Justin Wong, found that mRNA strips from many dozens of genes involved in white blood cell function were prone to intron retention and consequent break down. This was related to the levels of the enzymes needed to chop out the intron. Unless the intron is excised, functional protein products are never produced from these genes. Dr Jeff Holst in the team went a step further to show how this mechanism works in living bone marrow.
      So the researchers propose intron retention as an efficient means of controlling the activity of many genes. "In fact, it takes less energy to break up strips of mRNA, than to control gene activity in other ways," says Rasko. "This may well be a previously-overlooked general mechanism for gene regulation with implications for disease causation and possible therapies in the future."

    4. The authors write: "This was related to the levels of the enzymes needed to chop out the intron."

      And thus it seems not related to the sequence of the introns-- esp. since said introns, with exons attached, are sent to the NMD to get chewed to bits. Not dependent on sequence of the vast majority of the intron bps.

      Junk DNA is defined as DNA that cannot suffer a deleterious mutation. Can the introns here? If no, they're junk. At best, some of it is needed as a spacer, sequence independent.

    5. P.S. doesn't pass the onion test.

    6. @LpuiseG

      The article clearly states that, there is an increasing evidence that so called junk DNA has regulatory functions necessary in proper cell development.

      We've known about regulatory sequences for about 50 years. Nothing new there.

      We've known about alternative splicing for 40 years. Nothing new there either. All that stuff is in the standard introductory textbooks of biochemistry and molecular biology.

      Researchers from the Gene and Stem Cell Therapy Program at Sydney's Centenary Institute have confirmed that, far from being "junk," the 97 per cent of human DNA that does not encode instructions for making proteins can play a significant role in controlling cell development.

      No knowledgeable scientist ever claimed that all noncoding DNA was junk. We have always known about other functions of the genome. That's why we say that "only" 90% of our genome is junk.

      Even if we generously assume that every single intron had previously unknown RNA binding sites it wouldn't amount to more than 0.05% of the genome.

      This press release is a farce. The University of Sydney and the authors of the paper should be embarrassed. They should publish a correction.

    7. Press release: 'far from being "junk,"'

      Whenever I hear this, I know the next bit will be bullshit, and they don't disappoint:

      "the 97 per cent of human DNA that does not encode instructions for making proteins can play a significant role in controlling cell development."

      What does "can" mean in the above sentence? "Can" in the sense that Little Johnny "can" build a faster-than-light starship? If they mean "can" in the sense of "anything can happen," then we knew this already. It is not news.

      If they mean "can" in the sense of "happening right now to somebody somewhere", then it's just lying.

      They want the muggles to interpret this as "can" meaning #2, and they want the scientists to interpret this as "can" meaning #1. Thus they can deny they were lying outright. It's the age of Birney-style equivocation: every press release has two meanings, one for muggles, another for scientists. Lie to them thar muggles!

  4. I recall that before 1969 (and I was already a faculty member by then) geneticists and evolutionary biologists knew there was too much DNA, but generally were hesitant to believe that much of it was junk. Contrary to the repeated claims that evolutionary biologists wanted and needed for most DNA to be junk, they had to persuaded that this was possible.

    It was after the discovery of transposons families, LINEs SINEs, triplet repeats, etc. that evolutionary biologists and geneticists understood that the processes generating junk DNA were frequent enough, and the rate of removal slow enough, that we do expect lots of junk DNA. That being true, similarity of parts of junk DNA between species is powerful evidence that they have recent common ancestry.

    And of course any "good design" argument is powerfully countered by all the junk. Creationists and "ID theorists" are completely inconsistent about this -- they argue that we can't assume that a Designer will want to make good design ... but then they completely lose it at the thought that lots of the DNA is junk. They both and do and don't want to make Good Design arguments. They can't make up their mind about it.

    So junk DNA provides powerful arguments for evolutionary biologists, but they were somewhat resistant initially to accepting it.

    This history gets rewritten every time creationists and "ID theorists" open their mouth.

    1. I'd just like to add my share here that whether or not a strand of DNA has a function or not really misses the point. It's not just the fact that we have junk DNA that makes a compelling case against design, but it's rather more of what that junk DNA is that makes it such a compelling argument for common ancestry. (Well, aside from the fact you'd have to be a complete troll to be infinitely powerful and still give us a bunch of crap in our genome.)

      Sure, we have things like pseudo genes that have taken on functions, some arguably very helpful and important. But don't the IDiots ever stop to think as to why a designer would use something that painfully resembles that of a broken vestigial gene as a first option for anything? And why does he always use pseudogenes that are homologous to the genes of the predicted ancestors of that said organism? No matter what angle you look at it, our genomes seem to have been designed by someone who quickly cobbled us up together in a hurry to beat rush hour traffic and the end of the day. But hey, at least it's STILL design, right?

  5. Denyse O'Leary wrote:

    Does lack of use make that proportion of the directory junk?

    If the phone directories are re-typed year after year, and there are typing errors, and no one proofreads that part of the directory, then ultimately, YES.

    (And, as many people have noted, the same problem -- mutation -- works against any imagined "front-loading" in which information is supposed to persist undegraded from the origin of life, or from the Cambrian, or whatever).

    1. NO GO JOE! If the junk's function is improved by being variable then the answer is NO. The intracellular "antibody RNA" hypothesis has been around since the 1990s and its predictions were happily met by the discovery of pervasive transcription. Put another way, typing errors in the variable part of your banks of immunoglobulin V-region genes would make your antibody repertoire different from that of Mum and Dad. So a pathogen would have a problem trying to anticipate the repertoire of its next host.

    2. Junk DNA is defined as DNA which cannot suffer a deleterious mutation relative to fitness of the host. The hypothesis you describe is not supported by evidence, but at any rate if it were true, such DNA would fit the definition of junk. It cannot suffer a deleterious mutation.

      At any rate, your hypothesis can't pass the onion test.

      Back in 1980 the authors of the junk DNA hypothesis knew that much junk DNA must be transcribed. How many times do we have to repeat that?

    3. I suppose Donald's hypothesis would be the case where the books do not contain phone numbers, but are tables of random numbers. Those do not become invalid as the result of typos.

  6. But Denyse O'Leary has urged that we throw out the science of genetics anyway-- the whole science is "discredited" by the fact that human women are not sexually attracted to chimps. Really.

    If genetics disproves intelligent design, then she says, keep ID and throw out genetics-- all of it.

    O'Leary wrote: "“Yesterday, another hack writer caught up with me, for an interview, and wanted to know: so why do you fight Darwinism … ?

    Yuh, I know. Why bother fighting the huge Darwinist tax burden. Of course, Darwinism is false, but so? People’s careers are wrecked if they oppose it.

    Among other things, her editor had demanded that I account for the fact that humans share 98% of our DNA with chimps.

    ...If both [man and chimp] are more than 30 years old, and are normal specimens, how many people will believe that they are 98% identical?

    What woman, otherwise consigned to being a spinster, would marry the chimp if she didn’t get the man? After all, the chimp is supposedly 98% of a man.

    Actually, the chimp isn’t a man at all... Every woman in the world knows this.

    None are the least bit interested in the chimp – unless entertaining children by a visit to the zoo.

    So, my question is, what is this 98% similarity thing based on, other than to discredit genetics?”

    [Just a hack writer". By Denyse O'Leary. Uncommon Descent. 31 March 2010.]

    She is one of the shining intellects of ID. May her "Darwinist tax burden" be heavy.

    1. Out of topic:

      Dear Diogenes: are you going to explain me why you accused me in a previous recent thread of being Vashti or will you keep ignoring it and pretend it didn't happen? Accusations directed at people posting in a blog that are unfundamented are bad enough, but even worse when you are called to attention and then you ignore it. It's not nice, Diogenes.

    2. I said exactly what my evidence was for believing you're Vashti/Witton: because Vashti/Witton herself said Pedro was one of her many sock puppets. She copped to several others, including two named "Diogenes". You know that already, I told you already, so you're playing dumb, which makes you dishonest.

      If you don't like being called Vashti, take it up with Vashti, not me.

      You're indubitably a troll trying to pick fights and push the discussion away from science. I'd rather discuss Mattick's paper. You don't want to and you won't let us talk about science, either.

      Like Vashti, rjop, misc, and several others, you have a Diogenes obsession, even to the point of identity theft. People like you want people to live in fear.

    3. "ou know that already, I told you already, so you're playing dumb, which makes you dishonest."

      You're way out of line, Diogenes. I have nothing watsoever to do with Vashti, if you cared only to look at my post history in this blog. But of course, you didn't bother checking. It's just easier to talk shit.

      "If you don't like being called Vashti, take it up with Vashti, not me."

      I don't care a fuck what Vashti thinks or says. Where are talking about your (mis)behaviour regarding myself here at this blog. You should know better than talking shit without any real evidence. Quite ironic, seeing how we spend most of our time debunking nonsensical "evidence" from IDiots.

      "You're indubitably a troll trying to pick fights and push the discussion away from science. I'd rather discuss Mattick's paper. You don't want to and you won't let us talk about science, either."

      Again, take a look at my post history in this blog for the last year or so. You're way out of line here and making unfounded accusations. I expected a lot more dignity from you than this.

      "Like Vashti, rjop, misc, and several others, you have a Diogenes obsession, even to the point of identity theft. People like you want people to live in fear."

      Diogenes obssession? Give me a break. The only reason why I bothered calling your attention to this was that you are a regular contributor to this blog and I had some respect for you, as well as thinking that by now you had realized your mistake. I guess you didn't, and without even bothering to check my contribution to discussions in this blog you took some carp Vashti said at face value. You're behaving as dishonestly as the rest of the IDiots, Diogenes. That's quite sad. From now on I'll just ignore you. Let others look at my entire post history if they care to see who I am, since you clearly just prefer to talk shit.

    4. And by the way, I appologise to professor Moran for this Out of Topic discussion, but being accused of being a Creotard without any evidence (quite the opposite) by someone who I thought was a sensible contributor to this blog was not nice.

      Again my appologies.

    5. I'll second that. Diogenes, Vashti never said he/she/it had a sockpuppet called "Pedro Pereira". It was your (over)interpretation of one of Vashti's posts, so it's obviously you, not Vashti, who owes Pedro a big apology. I pointed out your mistake the very first time you made it.

    6. Pedro, I apologize. I was tricked by Vashti. I'm sorry if I seem a little paranoid. Let's try starting over.

    7. @Piotr:

      a thousand thanks for clearing this mess up. I use my real name in this blog and, as you can imagine, Diogenes accusations could be quite damaging.


      please do make a BIG FUCKING EFFORT next time to actually check people's post history before posting unverified crap like you did about me. As I said, some of us use our real names. And you didn't seem a "bit paranoid"; you behaved like a total prick.

      With that said, apologies accepted.

    8. Diophsyco, Was reading this blog entry and noticed my handle mentioned. I have not corresponded with you since last year, and Pedro's assertion of "a total prick" says it all, Shapiro seems to also agree >

    9. @ Pedro, In addition to my link on Shapiro, "Upright BiPed" who commented on Shapiro's above linked article, invited Diogenes to debate here (starting @ 496>

      After making a complete ass of himself, also apologized. Seems Diogenes has a real problem not isolated only with your circumstances.

    10. What Misc wrote is untrue; she only read part of that thread. In fact at UD, I crushed UB's absurd "semiotic argument" in subsequent comments, which Misc apparently did not read. This is not the first time Misc has gravely misrepresented what happened on that thread. I crushed UB's argument, although it took me several comments, because at first I misunderstood some of its details.

      No one at Uncommon Descent addressed my refutation; none of them acknowledged that symmetry breaking even exists in physics. They don't know any real math, but the worst part is that they're not honest enough to admit their lack of education, so they bluff and bluff and bluff.

      At one point EARLY in the argument I apologized to UB for being insulting, not for making math errors-- because I didn't make any. Misc apparently never read past that comment, so she didn't see me crush UB's argument into dust, while the UDites had no response, no rebuttal, except to dribble on themselves.

      UDites don't know any math, they use cultic bafflegab, so they'll never have any refutation.

      Misc has before misrepresented what happened on that thread.

      But it does teach me a lesson: I should never apologize to donkey-sucking assholes out of a desire to be nice. You can't be nice to cosmic assholes, so don't even try.

    11. @ Misc, re the UD thread: It was very nice of Diogenes to apologise to Upright BiPed in Post #549, but the discussion continued for a few hundred more posts, and neither before nor after the apology can I see anything that could be honestly construed as Diogenes making an ass of himself. Quite the contrary: he talked sense all the time and it wasn't his fault if most of the discussants did not even try to understand the points he was making.

    12. Thanks to Piotr for wading through that long thread. The apology that Misc refers to is #549.

      My most detailed refutation of UB's argument is TWO HUNDRED COMMENTS AFTER THAT, comment #749 here. Note that after I wrote that, the UDites did not understand or address what I wrote.

    13. Yes they did address what you wrote. UB @ 813 and Joe did a great job calling out your misrepresentation on Myers. After you start up @ 749 you then bail again, claiming someone is "following you" and didn't continue. Perhaps it was your shadow 'following you'.

      But hey, if you and your fan club desire to think UB didn't understand nor respond and you're not rude and obnoxious, so be it. Perhaps it was just the UDites where 'scared to death' of you, as you claimed Shapiro was last year.

    14. ... your misrepresentation on Myers...

      As in "PZ Myers"? He and Meyer are different people. Very, very different.

      BTW, can't you see you are practising pure ad hominem right now? It's a rude and obnoxious thing to do.

    15. Misc, you're lying. I proved Joe "Security Clearance" Gallien was lying about what Meyer (not Myers) wrote. Joe simply denied and denied. To deny facts after I proved them is not calling me out on my "representation." It only shows that Security Clearance has mental problems. He's the Black Knight in Monty Python.

      Since you, Misc, present yourself as understanding the biochemistry, why don't you copy and paste the comment-- ANY comment-- where Security Clearance showed me misrepresenting Meyer.

      I dare you. I double dog dare you. Prove it. Prove it.

      As for UB in comment 813, he did not even get within a million miles of refuting my argument-- indeed he gave no sign of even UNDERSTANDING my argument. He never said the word "symmetry breaking" and never mentioned the papers I cited from Yarus et al. and gave no indication he had read or understood even their abstracts, or even their TITLES!

      Instead, UB merely INSINUATED that he had already answered just one of the questions I'd asked about his "semiotic argument"-- "How many parts are there in your semiotic system?" I asked this question over and over and over, and UB never did answer-- he just INSINUATED he had already answered, but he never actually answered. He insinuated the answer was two or three, but if you can't give a straight answer to the simplest question I can ask, the the hell with you.

      I tried to formulate UB's notion of "arbitrary" in the language of linear algebra, so I asked him if he understood linear algebra. Simple goddamn question. He never answered.

      That's not a refutation. It's being a weasel.

    16. Misc writes: you then bail again, claiming someone is "following you" and didn't continue. Perhaps it was your shadow 'following you'.

      Oh no, I bailed from that thread, after hundreds of comments, because YOU were the one following me.

      It didn't help that UB cannot give a straight answer to any question, no matter how simple.

    17. Diophsyco,

      I am the one who invited you back to finish the debate with UB after you bailed, and if you recall, we were both conversing on Encode, both on Shapiro's blog and this blog. Perhaps you should do something about your delusions of grandeu.

    18. This comment has been removed by the author.

    19. @ Gasiorowski

      Missed your comment earlier, you say:

      "BTW, can't you see you are practising pure ad hominem right now? It's a rude and obnoxious thing to do"

      Nope not ad hominem, an observed fact, backed by many besides myself. The guy is a delusional lunatic and the fact you want to ignore this and jump in to defend, gives the appearance you're in the same camp. I also find it amusing, Diogenes claims he left the debate at UD a second time after 'hundreds of comments' because in his delusional mind he perceived I was 'following' him, yet has no problem addressing me and UB's argument here, why doesn't he go back to OP and finish what he stared, last comment was 7/2013.

      In addition, I was the one who challenged him to go back and finish after he bailed the first time, in which he did, then bails again because he perceives I am following him. LOL..

      Also, why don't you ask your little friend where the blog is he promised on how Shapiro is 'scared to death' of him. I would suggest instead of his assertion Upright Biped is a "weasel", its the other way around and find it pathetic he apolozises for flaming UB and then turns around and does it again behind his back.

    20. Nope not ad hominem, an observed fact, backed by many besides myself.

      Check up the meaning of "ad hominem" in a dictionary. You are repeatedly attacking Diogenes's personal character, manners, and what not, instead of addressing the substance of his arguments (and there's tons of substance in what he wrote on that thread). Ad hominem may consist of "observed facts", but who cares if those facts are irrelevant?

    21. @ Piotr,

      That was fast. Why should I address Dio's arguments when he can continue himself with the OP? He states UB did not address his arguments, answer his questions etc etc. and then uses the excuse he bailed the second time, because of his perception I was 'following him'. If this was an issue, why is he responding to me here. Better yet, why don't you address UB's thesis yourself at UD and let him answer. The comments are still open...

    22. "Check up the meaning of "ad hominem" in a dictionary" You may also want to address this to Diogenes..

    23. @Misc

      Diopsych's delusions are getting worst. After Piotr has proven to him that Vashti never claimed that Pedro was her puppet, he still blamed her for triggering him into his delusion. Diopsych has serious issues, which has been proven here, at UD and Shapiro's blog. When most of human genome turns out to be functional, he will be suicidal.

  7. @ Misc

    Diogenes didn't make a fool of himself; the IDiots did (as usual).

    1. Well, you can't go wrong with this kind of argument.

    2. It's not an argument, it's a statement; the discussion is available at the respective site for everyone to read and the outcome should be pretty clear, assuming you have at least two working neurons.

  8. @Misc

    I'm not sure if you are aware of this that Diopsych claimed here, that he had been banned at UD.

    BTW: Both Piotr and Pedro are not scientist, so don't expect them to make an argument.

    1. Louise,

      As a scientist myself, if I were to chose between science as presented by Piotr or Pedro, compared to that presented by the most knowledgeable of the UD crowd, I would go for Pedro and Piotr. They might not be scientists, but they really try and understand what they are talking about. UD is all about obfuscation.

    2. ""Both Piotr and Pedro are not scientist""

      This is the way IDiots work; make statements for which you have no evidence and ask people to accept them at face value.

      Can you show your evidence that I'm not a scientist?

  9. Better yet, why don't you address UB's thesis yourself at UD and let him answer.

    First, Diogenes did a very good job there, so what else could I contribute? True, UB did not admit defeat, which doesn't matter: anyone who can muster enough patience may examine their exchange and form an opinion. I suppose Diogenes wrote for the sake of any interested external visitors, not for the regular UD claque.

    Secondly, I rarely if ever post on creationist blogs. I prefer let them stew in their own juice. I visit other people's blogs to learn something, not to engage in pointless debates just for the hell of it. If creationists, ID fans or any other pseudoscience mongers appear on the blogs I do read, I may argue with them briefly, but I wouldn't like it to develop into an addiction.

    BTW: Both Piotr and Pedro are not scientist...

    @LouiseG: I am not a biologist or a biochemist, so of course I can't offer an expert opinion on biological evolution. However, we linguists have out own arguments and I know how to make a valid one. I have had some science training as well. In the case at hand, I know enough about biology and maths to follow Diogenes's argumentation. All I found in UB responses was terminological word games -- hardly the kind of thing to encourage sensible discussion. If you feel like discussing evolution here, or linguistics at my blog, go ahead, make my day. But don't ask me to go to places I don't like.

    1. I just noticed that Piotr and Pedro are the same name in two different languages. I think.

    2. They are, but before anyone asks, we are different people.

    3. ""They are, but before anyone asks, we are different people.""

      I can confirm that. :)

    4. "Have they ever been seen together ?"


    5. First of all, linguistics is a science IMHO, and constructs phylogenetic trees which have some similarities to phylogenetic trees in biology, an analogy noticed by Darwin.

      Actually Piotr frequently makes interesting points about biology-- e.g. he recently cited the Doolittle 2012 paper on fibrinogen in a sea squirt species, which I didn't know about.

      More importantly, Piotr has never pretended to vast knowledge of fields in which he knows little. This is in direct contrast to ID creationists, who blather on pretending to be world-class experts in fields about which they know little or nothing, claiming to know more about science than the world's scientists, and using scientific jargon the meaning of which they don't understand.

      And I mean, specifically, philosophers William Dembski and Stephen Meyer, ex-embryologist Jonathan Wells, and lawyer Casey Luskin. None of them except Dembski know any information theory, but they pretend they do, and they make a hash of it. None of them know much paleontology or genetics, and their errors and blunders are bang-your-head-on-the-curb stupid. Even Wells makes terrible blunders in genetics. Anybody remember his claim that centrioles were tiny turbines? No? That's because it was disproven, easily.

    6. To be fair, "scientist" sometimes show a similar kind of hubris when they scout out into areas they know too little about:


    7. Sure, sometimes, but it's contrary to the spirit of science.

      Feynman wrote a charming story about how he tried to be a molecular biologist during the early days of mol. bio, he was all excited about DNA. And he started from scratch at the bench, and he told the truth about how he made rank amateur mistakes and totally screwed up the experiment. Very blunt honesty.

  10. @LouiseG he had been banned at UD

    Just another way of saying that Diogenes employs evidence based rational enquiry.


  11. >"@LouiseG he had been banned at UD

    Just another way of saying that Diogenes employs evidence based rational enquiry."<

    Except the problem is he left the debate because he perceived I was 'following' him, (as stated above by him) not because of being banned. He(Dio)also claimed he was banned from Shapiro's blog, in which Shapiro explicitly stated he was not. Perhaps the ban cry is a cop out, verses "Diogenes employs evidence based rational enquiry"

  12. I never said I ditched UB's thread at UD because I had been banned. I was banned from UD some time after that, I don't remember how long after.

    I was never given any reason for being banned, and my accounts did not disappear. Rather, all of my comments at UD disappear and never post. Which I conclude is banning.

    I suspect that I was banned from UD because of things I wrote HERE, at Sandwalk. I can't prove that. But at that point in time I was commenting at Sandwalk a lot, and then suddenly I couldn't comment at UD any more. I can't prove it, but it's my best hypothesis.

    About 3 months ago a creationist I didn't know showed up at Sandwalk, posing as a "neutral" concern troll. I forget his name. He claimed that he had knowledge that I had been banned from UD because I'd used dirty words there. I asked him: how could he know that? Did he know the mods at UD? Was he himself a mod at UD? He never answered, he disappeared from Sandwalk never to return.

    At any rate, his story is impossible: I never used foul language at UD, or any conservative Christian website, although the creationists at UD routinely directed foul language and insults at me. I never used foul language at any conservative Christian website or FB page, but almost all of them ban me. (Except Cornelius Hunter.)

    Every evolutionist who comments at UD knows the rules of UD. There is one standard for ID proponents and a different one for evolutionists. IDers: you can use dirty words, foul language, abuse, insults, ad hominems directed at evolutionists and you will NEVER be banned. Joe "security clearance" Gallien and Mung will never be banned for that. Evolutionists: use clean language, stick to the evidence, and they'll ban you BECAUSE you stuck to the evidence.

    1. For an excellent example of that, consider the very comment [#813] that Misc herself cites as an allegedly substantive rebuttal of my argument:

      Misc: "Yes they did address what you wrote. UB @ 813"

      O RLY? Let's look at UB's comment 813.

      UB @813: 'Now I can ask myself “why must I describe the translation of nucleic triplets into amino acids if the very men who elucidated the system ...(and who won Nobel prizes...) did not do so?”'

      Actually that's exactly what they DID do, and WHY they won the Nobel prizes, but anyway, continue genius:

      UB @813: 'It’s because your entire counter-argument is deliberate, wholesale obfuscation (i.e. bullshit)...' [UB's Comment #813 at UD]

      Note UB can and does say "bullshit" and will never get banned. I never used language like that at UD, but my banning is falsely claimed as being due to me allegedly talking like an ID proponent.

      Here are more typical comments from that thread. Mung does not address my argument; like UB, he just calls it bullshit:

      Mung wrote: "b.s. + bluster = diogenes"
      [Mung, comment #757 at UD]

      That's the whole comment. Mung expresses it as an equation because he was mocking me for trying to use mathematics.

      The use of foul language, "bullshit" and "bs", receives approval from UDites as long as it comes from ID proponents, who can barely spell, and who HATE and ridicule mathematics:

      Wateron1 wrote: "[Chuckle] Mungs analogy of bs + bolster [sic] = Diogenes seems to sum it up quite well" [Wateron1, comment #797 at UD]

      Later on, Mung develops his most intellectual refutation:

      Mung wrote: "what a maroon"
      [Mung, comment #793 at UD]

      That's his whole comment. He repeatedly ridiculed me for attempting to use mathematics.

      As for Joe "Security Clearance" Gallien, he was his usual self. I proved that he had misrepresented Stephen Meyer's false claims about biochemistry on page 303 of Signature in the Cell, in an attempt to protect Meyer. His response was deny, deny, deny. This is the kind of thing Security Clearance writes over and over and over, everywhere:

      Joe "Security Clearance" Gallien: "Face it diogenes, you are a demented lowlife liar- that is an observation, not an insult" [Joe Gallien, comment #782 at UD]

      It's "not an insult" because it's coming from an ID proponent. For IDers, ad hominem attacks are facts, and facts are ad hominem attacks.

      Then after UD bans an evolutionist, the UDites make up fake stories about how he was banned for being "uncivil"! That's the REASON why UD exists.

      UD exists for this purpose: to lure in evolutionists, who think they'll FINALLY get a chance to refute ID arguments in the faces of the IDers-- but the real purpose of UD is to ban evolutionists, and then make up fake stories about how they were banned for being "uncivil"!

    2. Diogenes, don't you realise that multiplying a v****r by a m****x is an extreme form of obfuscation? UB had no idea what the heck it was supposed to mean, but he couldn't say so in front of his fans without the risk of losing face, hence the desperate argument that the men [and women -- PG] who had "cracked the code" did not explicitly employ linear algebra in their publications. I suppose you eventually got banned for dropping profanities like "null hypothesis" and "symmetry breaking" (in addition to those asterixed out above).

  13. And yet again Diogenes has no problem addressing me here, yet used the excuse he bailed because of his perception I was following him at the OP. Perhaps his excuse for bailing was indeed a cop out as was his claim of being banned on Shapiro's blog when he was not. It is very easy to refute someone's argument when they are not here to respond themselves.

    "the real purpose of UD is to ban evolutionists"
    If this were the case Nick Matzke, Liddle and Moran himself along with others who are still there, would have been banned long ago, so your assertion is false.

    1. Liddle was banned from UD at least twice. From time to time they un-ban her so they can insult her some more and then ban her again.

      I've never seen Moran comment at UD. Larry, did you ever comment at UD?

      I often read UDites call for the banning of Matzke. But he's a special case. They keep him around so that ethically challenged accountant Barry Arrington can write OPs just to accuse scientist Nick Matzke of "jackbooted thuggery" and "incipient fascism." (Arrington hates incipient fascism-- he prefers the non-incipient kind. That's why he works for Michele Bachmann.)

  14. Your link page does not exist. If they insult and ban Liddle so much, why is she back there now? I saw Moran comment last year when encode came out, but perhaps he will answer for himself. And it doesn't matter what you read on Matzke, he is still there and has never been banned. You can spin and divert it any way you like, but again your assertion is false, get over it.

    Also, isn't it ironic you don't think I am 'following' you now, yet did at UD, so much so you used it as an excuse to bail out. Of course you repeatedly ignore this contradiction.

    1. You don't know how to repair a broken link? Let me lend you a hand:

  15. @ Piotr,

    Again, if she is banned and insulted so much why keep going back as she is now.

    1. No idea. Perhaps she suffers from SIWOTI syndrome. I am a mild case of it myself, which is why I normally stay away from creationist blogs. I'd waste too much time there. I accept the sad fact that some people will resist all efforts to educate them.

    2. Misc has abandoned her claim that Joe "Security Clearance" Gallien caught me lying.

      Misc: "Joe [Security Clearance] did a great job calling out your misrepresentation on Myers"

      So I asked for evidence:

      Me: "Since you, Misc, present yourself as understanding the biochemistry, why don't you copy and paste the comment-- ANY comment-- where Security Clearance showed me misrepresenting Meyer.

      I dare you. I double dog dare you. Prove it."

      Misc never responded.

      So let's talk about the biochemistry, which Misc portrays herself as understanding. Let's first recall what Stephen Meyer wrote, which I cited over and over at UD:

      Meyer wrote: "This obviously poses a couple of difficulties. First, it creates a dilemma for scenarios that envision proteins and nucleic acids arising out of a prebiotic soup rich in amino acids. Either the prebiotic environment contained amino acids, which would have prevented sugars (and thus DNA and RNA) from forming, or the prebiotic soup contained no amino acids, making protein synthesis impossible…

      The RNA-world hypothesis faces an even more acute, but related, obstacle—a kind of catch-22. The presence of the nitrogen-rich chemicals necessary for the production of nucleotide bases prevents the production of ribose sugars. Yet both ribose and the nucleotide bases are needed to build RNA."
      [Stephen Meyer, Signature in the Cell, p. 303]

      Meyer wrote: "Before the first RNA molecule could have come together, smaller constituent molecules needed to arise on the primitive earth. These include a sugar known as ribose, phosphate molecules, and the four RNA nucleotide bases (adenine, cytosine, guanine, and uracil)." [Stephen Meyer, Signature in the Cell, p. 301]

      Misc, are the sentences in bold true or false?

      I asked many people at UD, and no one dared answer.

    3. Misc, are the sentences in bold true or false?

      Since Misc is not likely to respond, may I help her? Some simpler intermediates are certainly needed, but not necessarily those that we regard as "building blocks" or "constituent molecules" (free ribose and free nucleobases). So neither assertion is correct.

    4. Note the date: Powner et al. was published in 2009, before Meyer's Signature in the Cell hit the bookshelves.

      "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions." Matthew W. Powner, Béatrice Gerland & John D. Sutherland. Nature 459, 239-242 (14 May 2009) | doi:10.1038/nature08013.

      Abstract. At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis1, 2, 3 this polymer was RNA, but attempts to provide experimental support for this have failed4, 5. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA6, 7, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively8, 9, and the addition of nucleobases to ribose is inefficient in the case of purines10 and does not occur at all in the case of the canonical pyrimidines11. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis—cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate—are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer.

      I would use the following analogy: Stephen Meyer (and fellow ID creationist author of "Of Pandas and People", Dean Kenyon, whom Meyer copies) says that the only possible way to form a bicycle is by starting with the half a bicycle frame with a front wheel attached, and half a bicycle frame with a real wheel attached, then welding them together. This the ONLY way to make nucleotides, says Meyer and Kenyon.

      In fact, Powner et. al. showed that natural processes can make the bicycle frame, then add a front wheel, then add a rear wheel. In short, the confident assertions of Meyer and Dean Kenyon were wrong.

      This was a simple argument I advanced at Uuncommon Descent, and the UDites continued to insist that Meyer, who just copied Dean Kenyon, was right. They could not admit he was wrong. They just engaged in sophistry and goalpost shifting, the worst being Misc's hero, her intellectual giant, Joe Security Clearance Gallien.

  16. Diophyco,

    Thanks for further demonstrating you lied when you claimed you left Upright Biped's OP because you thought I was following you. You now try and start your nonsense here, with the very person you claimed caused you to leave. Joe, UB and Stephen addressed the issue quite thoroughly, any reasonable and fair minded person can see that, but then again, I am not addressing one.

    1. Misc, all that "StephenB" did to refute Digenes was quote a fragment his own response to Darren Falk's review of Signature. The response is almost touching in its helplessness and artless naïveté. The main point seems to be that Meyer's biochemical argument can't be refuted experimentally by smart people working in a lab, because whatever they do requires intelligence and careful planning, and so it counts as Intelligent Design. What Joe said was even sillier, if possible (details on demand), and UB did not really address this particular issue.

    2. StephenB used standard Intelligent Design "logic": If evolution is not seen in a lab, evolution is disproven, because “real science” means you must reproduce it in a lab experiment. If evolution is seen in a lab, that also disproves evolution, because lab experiments are intelligently designed.

      StephenB just applies the standard ID logic to synthesis of organic chemicals. Creationist just redefine what "natural process" means.

      The creationist argument, up to about, say, late 1960's, was:

      "If something happens reproducibly in the lab, that proves it is a NATURAL process. Evolution of new complexity CANNOT be seen in lab experiments, therefore evolution is disproven."

      But starting from the 1970's onward, creationists started pooping their pants as scientists produced example after example of evolution of new complexity. The creationist argument then became:

      "If something happens reproducibly in the lab, that proves it is an INTELLIGENTLY DESIGNED process. Evolution of new complexity CAN be seen in lab experiments, therefore evolution is disproven."

      By the way, Powner et al. 2009 found that chemical reaction by blindly mixing the chemicals every which way, until they found a reaction that produced pyrimidines. Some intelligent design!

    3. Here's more news from the Sutherland lab:

  17. @ Piotr,

    Then post your views at the OP. You claim you don't post on 'creationist' website, yet have no problem addressing it here where you have no counter argument from the people you are addressing. Don't you think this is a bit cowardice, or are you going to claim I am following you also as a cop out.

    1. It isn't cowardice; it's a matter of taste. I love Professor Moran's blog, but I do not love the other one (yes, it is creationist, or at least cdesign proponentsist). Both are open to the public, so anyone who cares may read my posts here. I am not interested in debating things with the ID crowd. They live in a parallel universe and have their own alien "science" and "logic" quite different from those I know and respect.

  18. Another "Beneficial Jumping Gene Discovered"

    Less and less junk in the junkyard :)

    1. Quest,

      That one jump was beneficial does not mean that every transposon insertion is beneficial. It does not mean, either, that transposons are there to help. Either the news reporter, or the authors, are full of shit when they over-concluded from a result everyone expects. Nice discovery: some transposon jump resulted in an adaptation. But that's it.

      That insertions could be beneficial at times has always being acknowledged. It's exactly like mutations. Some mutations are detrimental, some mutations are neutral, some are beneficial. All with a whole spectrum of possibilities in between. The same is true for transpositions and other phenomena.

      By the way, active transposons are not considered junk. They are considered selfish DNA.