Thursday, August 29, 2013

What Happens When a Creationist Argument Is Refuted?

A few days ago, Jonathan McLatchie published an article on evolution News & Views (sic) where he claimed that humans embryos synthesize the enzyme that makes vitamin C [A Simple Proposed Model For Function of the Human Vitamin C GULO Pseudogene]. This is important for creationists because the gene for that enzyme is a classic pseudogene—a formerly active gene that has lost it's function.

Intelligent Design Creationists don't like pseudogenes because they are junk and their intelligent designer would not fill up the human genome with junk. Hence, pseudogenes must have some function that has yet to be discovered.

Unfortunately for Jonathan McLatchie, his argument was ridiculous. He proposed that RNA editing could resurrect the GULOP pseudogene during embryogenesis. What he failed to notice was that the pseudogene is not transcribed and, furthermore, it is missing seven exons. It's very difficult for RNA editing to recreate seven exons in a nonexistent transcript [see How IDiots Would Activate the GULOP Pseudogene].

To his credit, McLatchie realized that he was wrong and he posted an update that linked to a revised post. Let's look at this mea culpa to see how creationists respond to criticism [Unitary Pseudogenes and RNA Editing].
n a previous article, I argued that pseudogenes could be rendered functional by post-transcriptional RNA editing. I used the specific example of the vitamin C GULO gene and suggested the possibility that the human GULO pseudogene may be functional in utero but subsequently turned off. Such a hypothesis requires that GULO produce an mRNA transcript. I had consulted the Ensembl Genome Database regarding the GULO pseudogene in humans, and that database reported that it produces a transcript but no known protein product.

Upon further investigation, however, I've discovered that the Ensembl database appears to be inaccurate on that point, and it's not confirmed that the GULO pseudogene produces a transcript (indeed, clicking on "Supporting evidence," one finds that there is "No Transcript supporting evidence for this transcript"). Part of the reason for this is that the GULO pseudogene lacks a canonical promoter. However, that doesn't necessarily mean this pseudogene produces no RNA transcript. Many metazoan loci possess non-canonical promoters that, moreover, can be millions of base pairs upstream of annotated exons (e.g., see Manak et al., 2006). A further complication with the proposed hypothesis is that some exons are absent from the GULO pseudogene, and it's not entirely clear to me how they could be created by RNA editing. While my original hypothesis is probably incorrect with respect to this particular pseudogene, it remains possible that the human GULO pseudogene yields RNAs that perform some other function in the cell.
That's not bad as far as confessions go but it does raise some questions. If Jonathan McLatchie really was interested in pseudogenes then why didn't he do the appropriate research BEFORE publishing his original post? He might have found my original 2007 post on the subject, complete with references to the scientific literature [Human GULOP Pseudogene] or he could have found the scientific papers directly by searching PubMed.

Maybe he doesn't trust scientists? In that case, he could have read the Appendix to Jonathan Wells' book The Myth of Junk DAN. The papers giving the correct structure of the pseduogenes are all referenced in that creationist book.

The important point here is that the GULOP pseudogene really is a pseudogene and no amount of special pleading is going to resurrect it. It's very unlikely that human embryos can synthesize the enzyme L-glucono-γ-lactone oxidase in spite of the "evidence" that McLatchie presented in his original post. (He doesn't mention that in his mea culpa post.)

That means that creationist really do have to come to grips with the idea that our genome contains dead, inactive, genes that used to be functional in our ancestors. And the fact that our closest relatives, the chimpanzees, contain a similar GULOP pseudogene cries out for an explanation. So far, Intelligent Design Creationism, has not produced an explanation. It made a prediction: namely that pseudogenes are actually functional, but that prediction has not borne fruit.

So, in the face of an argument that has been soundly refuted, what is an IDiot supposed to do? Here's how Jonathan McLatchie responds ....
Moreover, there's a much more important point to take note of, which I hope is not lost in this discussion -- namely that my original hypothesis could be more generally applicable. What I proposed might be happening in the GULO pseudogene could very well be happening in other unitary pseudogenes. Unitary pseudogenes are genes that have been disabled by mutations such as frame shift mutations, deletions, or point mutations resulting in premature stop codons.
Yes, it's a remote possibility that a gene could become a pseudogene by acquiring mutations that affect the coding region but not transcription. As long as the pseudogene is transcribed and no coding region is deleted, it is possible that a specific RNA editing system could evolve that would make the gene capable of producing a functional protein.

Of course if there was strong selective pressure to reactivate the gene there are probably easier ways to accomplish that goal. Furthermore, it probably wouldn't have been inactivated in the first place.

This is a classic example of special pleading. There's no scientific reason whatsoever to imagine that pseudogenes could be reactivated by RNA editing. It's all speculation motivated by a desire to avoid the obvious conclusion: pseudogenes are dead gene.

McLatchie failed utterly to give us a plausible example when he discussed the GULOP pseudogene and his hand-waving references to RNA editing are useless unless he can point to another specific example. But that's what counts as legitimate argument on the creationist blogs. All they need to do is raise doubts about evolution and it doesn't really matter if their arguments make sense. McLatchie's error was to pick a specific example that could be easily refuted. Most creationists don't make that mistake. I think Jonathan McLatchie has learned the lesson. We probably won't see much science from him in the future.


[Photo Credit: The photo is from the Apologetics 315 website. Follow the link to hear the interview with McLatchie.]

187 comments:

  1. McLatchie deserves credit for his partial retraction. It seems to me that what he misses, and what many IDers miss, is that because evolution is science all the evidence for it is mutually supporting. When ID has to give up one of its claims, many other fall like a row of dominoes.
    Theres absolutely no evidence for it, but perhaps there are pseudogenes edited into function. That will still leave many more, including GULOP that aren't. Each one of these is very complelling evidence for common descent with modification - something McLatchie "doubts". Will he now admit common descent? This also suggests a radical change in ecology and diet in some primate ancestors. More problems for ID.
    McLatchie offers a ray of hope by suggesting GULOP may have taken on a new function. It clearly cant bind FAD anymore ( that domain is gone) and cant perform VC synthesis. So it must have evolved a radically new function. I think Axe and Meyer would be distressed to hear this suggestion. It pretty much demolishes everything they've claimed about the difficulty of proteins evolving new functions.

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    1. McLatchie offers a ray of hope by suggesting GULOP may have taken on a new function. It clearly cant bind FAD anymore ( that domain is gone) and cant perform VC synthesis. So it must have evolved a radically new function. I think Axe and Meyer would be distressed to hear this suggestion. It pretty much demolishes everything they've claimed about the difficulty of proteins evolving new functions.

      LOL! Nice catch.

      Delete
    2. Thank you McLatchie for once again confirming evolution. *facepalm*

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    3. The problem with this whole issue is that, as you allude to, there are always OTHER pseudogenes that MIGHT do what JM desires them to, so he wasn't totally wrong and ID is still true because one day they might find one pseudogene that was 'resurrected.'

      Rational folks know that that is not how reality operates, but then...

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    4. The hypothesis was never intended to be a positive argument for ID. Nor does the truth of ID rest in any way on it being correct. And it's not merely hypothetical in any case -- there *are* examples of genes that require RNA editing in order for them to be translated into a functioning protein. I gave the example of cytochrome c oxidase III from Trypanosoma brucei. In that case, a whopping 58% of the gene has to be written post-transcription (the editosome is directed by guide RNAs to insert and remove uridines at specific locations). Without this extensive editing, the gene is broken (being completely scrambled). In a sense, therefore, it is a pseudogene. There are plenty of other examples too -- see my article for a few of them.

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    5. Yet, it was tweeted as evidence

      T brucei is not Homo sapiens, and as has been pointed out, this form of editing is very different to that which would be needed for your poorly conceived hypothesis.
      Again, you have no evidence of such a process in humans, so, it is wishful thinking.

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    6. BTW, ever heard of guide RNA JM? Another testable pre-requisite you overlooked!

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    7. I discussed guide RNA in my article and mentioned it above. This condescending attitude ("ever heard of...?") is part of the reason I don't like to engage with you. I even note in my second article that "This form of editing involving uridine insertion and deletion is restricted almost entirely to the mitochondrial RNAs of single-celled eukaryotes. Likewise, cytidine insertion has so far only been found in the mitochondrial RNAs of slime molds (e.g., Physarum polycephalum)." But there are other forms of editing found in higher metazoans, as I also discuss (e.g. C to U editing; A to I editing), which involve deaminase enzymes. There are also other mechanisms besides RNA editing of inducing ribosomal frameshifts, and it is quite possible that there are even RNA editing mechanisms yet to be discovered.

      In any case, why are human pseudogenes the only ones that are of interest to you?

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    8. You fail to get the point I am making - you could have searched for them!!!

      FYI - you're the one that wrote an article on human pseudogenes, proposing an undescribed mechanism to save your hypothesis.

      Do you expect respect when you lie and censor?
      You have outstanding questions about your integrity and the truth of the database in your second article

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    9. I also want to know why you claimed I said something that I didn't, and Vincent is waiting for answers too

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    10. What did I falsely claim that you said?

      I don't know of any evidence for RNA editing by editosome & guide RNAs in humans. My point, however, was that this kind of process is known to occur, and I suggested that something similar might be going on in humans. My examples were not limited to this type of editing found in Trypanosomes in any case. RNA editing is also known to be able to expunge premature stop codons (e.g. U to C editing has been documented in plant mitochondria and chloroplasts -- albeit to a lesser extent than C to U).

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    11. For starters you said I said you were out of your depth -you even put it in quotes!

      You still have learned nothing. You need an extensive editing system. There is none known, but there were thing you could do to back up that hypothesis, if it were true. This however is somewhat pointless, as there is no known transcript. Any idea how bad that is? You propose an unknown mechanism for a transcript that all other lines of evidence says is not and should not be there.
      I think evolution is safe with dishonest incompetents like you around.
      Care to confess the database was not wrong, that you had to be prompted, and that you had to be corrected yet?

      Delete
  2. McLatchie only searched the Ensembl database after he was given a hard time about providing no supporting evidence, or even suggested how he would investigate his claims.
    He later came back after some prompting and claimed he found a transcript. It was only after this, that he was informed that he hadn't actually checked the supporting evidence, which said there was no RNA found. So he is misleading folk and not admitting to his incompetence.

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    1. Billy,

      Can you please upload the screenshots from the thread on Facebook onto imgur.com or any other image hosting service? Thanks!

      Delete
    2. Hi ShadiZI,
      This any use? http://www.facebook.com/groups/151405404861/files/

      Delete
    3. After asking for thoughts from the Glasgow Skeptics community Jonathan McLatchie then decided to block member from the community who disagreed with his position. I understand ENV does not allow the public to comments on their forum but this behaviour of blocking member who are actually qualified and have a Phd in Microbiology from Jonathan McLatchie is disgraceful.

      He then went about deleting the thread but luckily a copy of it was made.

      You can find out more information by going to the Glasgow Skeptics site on Facebook where they have saved all this information.

      ************************************************************
      Glasgow Skeptics http://www.facebook.com/groups/151405404861
      ************************************************************

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    4. For the record, the reason I blocked certain people on facebook was the personal attacks and the constant tagging. It had already been established I made a mistake loooong before anyone got blocked. I wasn't hiding anything. In fact, I noted the error on my part at ENV.

      Delete
    5. For the record, folk can now see for themselves!
      Folk can also see you reacting to a question asking if you thought a paper was fine and calling it a snide comment.

      Delete
    6. jonathan, I read your new article at ENV and I didn't see where you "noted" your error(s) and I didn't see a retraction and apology for misleading people. All I saw was a bunch of weasel wording intended to save your face, evade your responsibility, avoid evidence, move the goal posts, and shift the blame. That's mighty christian of you.

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    7. So are you denying that you deleted the thread, Jonathan?

      Delete
    8. Jonathan,

      I'd also be interested in your response to the point raised in the first comment by lantog, that your claim that proteins can evolve new functions thru RNA editing directly contradicts the claim by fellow ID proponents Axe and Meyer that this is impossible.

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    9. This is what Jonathan said on another thread.

      The name of the thread at Glasgow Skeptics is;

      It appears that in attempt to hide is incompetence, Johnathan McLatchie has deleted his GULOP post. That's not very honest now, is it?

      Jonathan McLatchie states, "Jonathan McLatchie What does it matter? It had been established a while back that I made a mistake; and I drafted a blog post accordingly. I deleted the thread because the thread descended into personal attacks."

      However the thread over at Glasgow Skeptics shows no such thing.

      https://www.facebook.com/groups/151405404861/10151664876239862/

      Jonathan McLatchie Repeatedly calling me "incompetent" or "out of my depth" and such like. When I ask for comments, I expect them to be constructive.

      Fiona Robertson Jonathan McLatchie, everyone started out rather polite to you, but your total intransigence in the face of experienced people explaining why you were wrong is enough to test anyone's patience. You need to wind your neck in and stop writing articles on subjects you don't understand. Get into the lab, do the work, take advice from other post grads, post docs and academics. Test your ideas by asking others to review them critically. The best critic is always one who doesn't share your viewpoint. They will find the flaws in your work. When you can satisfy your critics, you know you have a good idea.

      At this point Peter Milligan asks why he has been blocked by Jonathan. A look back over the thread which Jonathan deleted shows these comments for Peter;

      Peter Milligan It would be interesting to know just how much internal peer review goes on inside ID. My suspicion is not a great deal.

      A valid point there by Peter. If this paper by Jonathan was peer-reviewed then it would not have been published.

      Jonathan Mclatchie continues, "I prefer to write detailed responses in a blog post rather than in a facebook thread. I also don't like to engage with people who aren't being respectful (like the snarky and condescending attitude." exhibited by some here).

      Let’s deal with the Peter Milligan blocking first. Can you confirm Jonathan what snarky and condescending remarks Peter gave?

      Jonathan, I hope you can give sufficient answers to this first query, from how I am viewing this is look like you have just blocked people who disagreed with you and that is disgraceful.

      Delete
    10. Just so you know: this post is nearly unreadable. It's difficult to determine who is saying what, or when one person's comment leaves off and another's begins. If you're going to post things like this you will need to edit them to provide clues, at the very least.

      Delete
    11. Ooh, I've never heard that one before.

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    12. You shouldn't have. I just made it up :)

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    13. I just read the saved thread at Glasgow Skeptic on Facebook (the one that maclatchie deleted). I'm not surprised at all that he deleted it because it made him look like the IDiot he is, and deleting embarrassing refutations is what IDiots often do.

      jonathan, one of the the things you complained about in that thread is the questioning of your competence as a biologist. I'm curious, what exactly is your competence as a biologist? What have you accomplished as an allegedly competent biologist? What discoveries have you made and what hypotheses have you posited that are testable and likely to be productive? What papers have you written and gotten published in legitimate, peer reviewed journals?

      If you have a specialty, what is it? What field work have you done, if any? Which other biologists have you worked with, and on what projects/research? What were the results of the projects/research and were the results published in a legitimate, peer reviewed journal? How many years of competent biology experience do you have? Have you presented any of your hypotheses, research, or papers at any scientific conferences? What do you hope or plan to be doing 10, or 20 years from now?

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    14. Is there any way to view that saved thread without needing a facebook account ?

      Delete
    15. Steve and anyone else who's interested, you can download the saved thread from mediafire: Click here.

      I included both files (one is by Billy and the other is by Fiona). Billy's file includes most of the conversation from the very beginning. Fiona's file isn't as complete.

      Delete
    16. Thanks ShadiZ1, very illuminating thread.

      it is hard to decisively demonstrate that a gene
      never produces a transcript


      That seems to be a handy, dandy, good for any occasion creotard argument.

      I also don't like to engage with people who aren't being respectful

      And another all purpose creotard argument.

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    17. "it is hard to decisively demonstrate that a gene
      never produces a transcript"


      That's precisely why the burden of decisive demonstration is on those who claim that it produces a transcript.

      Delete
    18. It's clear from the flow of the discussion that Jonathan never checked the Ensemble database before being challenged to show that a transcript is being produced. Therefore, to blame the database for his mistake and shoddy reasoning is quite dishonest. If he really consulted the database beforehand, he'd point to it without the need for the empty talk about the transcript being produced by accident or the impossibility of showing that "a gene never produces a transcript".

      And by the way, as Fiona Robertson and Vincent Mulholland have pointed out, the Ensemble database is NOT "inaccurate" or "mistaken". Jonathan is the one who doesn't know how to use it properly. If the database says that there's no evidence for a transcript, and you were misled by the fact that the database automatically creates hypothetical transcripts based on nucleotide sequence, then you are the one to blame for not learning how to use it.

      No wonder that he deleted the original thread on Facebook.

      Delete
    19. Maclatchie's behavior in that thread shows clearly that Maclatchie is unprofessional and unethical and does not have the integrity that all PhD's should be required to have. Vincent Mulholland did Maclatchie a big fat favor by showing him how to interpret ENSEMBL entries, and Maclatchie responds by blocking him and calling him "obnoxious" and not "constructive".

      What a horrible little creationist. By "constructive" criticism he must mean the grovelling of sycophantic non scientists like at UD. If Maclatchie goes for a Ph.D. he will find his thesis committee is not "constructive" in the way creationists demand, but he will find himself unable to block them, delete their comments and censor them as creationists do to their critics on the internet.

      Science progresses precisely because it does not tolerate "constructive criticism" as creationists like Maclatchie define it. Scientists have a moral responsibility to treat dishonest pseudoscientists with disrespect.

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    20. The centre 4 intelligent Design have now removed comments criticising the "retraction". I am now no longer able to comment.
      I have posted a screen shot of the censored comments on the Glasgow Skeptics page for those interested

      Delete
    21. Well, the saga rumbles on. I posted a comment on the Centre for Intelligent Design UK Facebook page where they had linked to McLatchie's revised atricle on ENV. I asked if he was willing to acknowledge that ENSEMBL was not inaccurate as he claimed. I have now been blocked from commenting on said page.

      McLatchie and the intelligent design crowd are not interested in science, but in propaganda. They are feeding their followers misinformation and silencing any attempt to expose this misinformation for what it is.

      This latest debacle with McLatchie's two articles demonstrates why ID is not considered science. They have no interest in actually engaging the scientific community in any sort of dialogue. Morally and intellectually bankrupt!

      Delete
    22. Isn't Jonathan McLatchie also the administrator on the Centre for Intelligent Design UK Facebook page so he has actually just linked onto ENV to promote his own material?

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    23. I compiled Billy's screenshot with mine in this new image: ID hypocrisy.

      It's indeed hilarious that he deleted your comments while at the same time holding the banner of "free speech".

      Delete
    24. A question earlier asked Jonathan what was his competency for being a biologist. Other then the posts at ENV, all I have found is when he edited CreationWiki, The Encyclopaedia of Creation Science page on cell biology. Jonathan states;

      "21st century technology reveals that although the tiniest bacterial cells are incredibly small, weighing less than 10-12 grams"

      http://www.creationwiki.org/index.php?title=Cell_biology&diff=prev&oldid=113582

      Delete
    25. Such things happen when one copies and pastes but forgets to think. They got it right eventually:

      http://creationwiki.org/Cell_biology

      ... weighing less than 10ˉ¹² grams (or 1 picogram)...

      Delete
    26. In an answer to your question, Dimemire, you should see C0nc0rdance rebuttal to Jonathan's claims about the irreducible complexity of the bacterial chemotaxis system:

      ID Creationism and Bacterial Chemotaxis

      A Response to Jonathan M on Bacterial Chemotaxis

      Delete
    27. "Maclatchie's behavior in that thread shows clearly that Maclatchie is unprofessional and unethical and does not have the integrity that all PhD's should be required"
      Well, what does professional mean? Agreeing with you at best?

      Delete
    28. That's an interesting video ShadiZ1, I have missed that one on Youtube. I was wondering if you have caught this car-crash of a programme with 'Doctor' McLatchie?

      http://www.youtube.com/watch?v=ekY71uVXECs

      Delete
    29. In the deleted thread, mclatchie said:

      "Transcription can even happen by accident sometimes --RNA polymerase binds to non-promoter binding sites."

      Did he actually say "by accident"?

      jonathan, do you believe that some things are designed/guided/caused/created by yhwh and that some things happen "by accident"? When you say "by accident", do you mean that it's 'natural' and that yhwh has nothing to do with it?

      In your opinion, as an allegedly competent biologist, what tests could be performed to determine what is designed/guided/caused/created by yhwh and what happens "by accident"? Will you please name 4 or 5 other things (regarding biology) that do or could happen "by accident", and the reasons that you think so?


      Delete
    30. And how often is "sometimes"? Perhaps (perish the thought!) often enough for "unintelligent chance-based mechanisms" to affect the course of evolution?

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    31. And Maclatchie has called this not just "intelligent design", but BRILLIANT design. Is "happens by accident" a defining feature of BRILLIANT design?

      Delete
    32. ShadiZ1, I love your graphic on ID hypocrisy.

      Why do the loudest yelps for free speech come from intolerant censors?

      Delete
    33. Just for the record, I have nothing to do with CreationWiki. From what I've seen of it, I don't consider it a credible site.

      Regarding chemotaxis, the intent of my article from back in 2011 hadn't really been to provide a detailed defense of irreducible complexity with respect to chemotaxis. I am very familiar with bacterial flagella -- it's one of my specializations and I'm quite acquainted with both flagellar assembly and chemotaxis. I am well aware of the diversity in mechanisms among bacterial taxa for both these systems.

      I could get into a detailed discussion on whether chemotaxis is irreducibly complex (but have no intent to get into a debate here). That would be a subject for another blog post. It wasn't really the intent of my 2011 article, however.

      Delete
    34. I should also note that I never claimed that the GULO transcript is produced "by accident". That would be a preposterous claim. I was only noting that it is hard to show that a gene *never* produces a transcript. Indeed, as I noted, many loci have non-canonical promoters that are not as easily detectable. Moreover, sometimes promoters can exist at loci far away from the actual gene, and may transcribe stretches of a chromosome for many many kilobases, and may not immediately be recognized as connected to the gene.

      Delete
    35. Jonathan is trying to change the subject and distract our attention away from his censorship and intolerant crushing of criticism among all those who pointed out, rather gently, his continuing serious scientific errors at his FaceBook page and at the Centre for ID UK, where he banned almost all his critics.

      MacLatchie banned all his critics for pointing out his several serious errors, and for teaching him how to interpret molecular biology databases correctly instead of incorrectly. Maclatchie deleted all their comments totting up his errors, then he added insult to injury by insulting them when they could not respond.

      Vincent Mulholland was nice enough to try to teach MacLatchie how to interpret ENSEMBL entries, which MacLatchie got wrong. So Jonathan banned him, deleted his comments, and called him "condescending and obnoxious" and not "constructive" after Mulholland had been banned and could not respond.

      In fact, MacLatchie has continued to misrepresent the contents of the ENSEMBLE database, calling it "INACCURATE" when it was not, after MacLatchie had banned Mulholland-- an error on MacLatchie's part which Mulholland's expertise could have saved him from, had MacLatchie not BANNED him and other critics.

      Fiona Robertson: Jonathan McLatchie, have you blocked Vincent Mulholland?

      Jonathan McLatchie: Yes. He was being obnoxious

      ...

      Jonathan McLatchie: It wasn't the fact that I was criticized that drove me to block him.... he was being condescending and obnoxious. Criticism should be constructive.

      Now we know that's not true, nor would be relevant if it were true. I have read the Facebook thread with their comments (PDF); none were abusive, but many complained about ID's thought police policy of not permitting comments (a censorship policy ironically affirmed by Jonathan when he BANNED them!); and others pointed out, that his hypothesis was supported by no data; a few complained he had described his hypothesis as non-falsifiable; etc. These ARE constructive criticisms.

      According to the Glasgow Skeptics thread, MacLatchie banned Billy Sands, Fiona Robertson, Vincent Mulholland, and Peter Milligan.

      For ID proponents, ad hominem attacks are "facts", and facts are "condescending and obnoxious."

      Delete
    36. I don't think there's anything unethical or unprofessional about what I did. It had already been established that I was mistaken on this point. It was a simple error I shouldn't have made, and I learned from it to check things more thoroughly. Everyone makes mistakes at some stage, particularly as grad students. :)

      I don't think what I did can be construed as an attempt to cover anything up. I even posted about the error at ENV and linked to it in the original article. I won't tolerate the way I was being spoken to, however, hence why I decided to be done with the conversation.

      Delete
    37. Jonathan McLatchie, you have learned NOTHING from this fiasco as can be seen from your comments here. Here is one of your c omments from the thread that you deleted

      ""Transcription can even happen by accident sometimes --RNA polymerase binds to non-promoter binding sites."

      And here is what you claimed on this blog this afternoon

      "I should also note that I never claimed that the GULO transcript is produced "by accident". That would be a preposterous claim. "

      Now, would you care to explain yourself. You did c laim that transcripts are sometimes produced by accident. You see, I was bright enough to grab a copy of that thread before you deleted it and let Glasgow Skeptics I had it in case they needed it. So anyone can actually go and read said thread and see where you DID say that.

      You are lying through your teeth now. You see nothing unprofessional and unethical about rewriting the history of this debacle, you see nothing unprofessional or unethical about denying things you actually said and you see nothing unprofessional or unethical about accusing Vince Mulholland of being obnoxious when he was actually trying to help you.

      As for posting about your error at ENV, no, you didn't, you posted that the ENSEMBL database was in error and had misled you. Again an untruth to cover up your incompetence.

      Your reputation is in tatters after this mess. You have tried to cover up your incompetence, your petulance and your arrogant dismissal of those who tried to advise you. So from now on, stick with the DI - they didn't c riticise your erroneous original article, they tweeted it as being "new evidence" for pseudogene function. For all I know they still think that, despite you now realising that your article was so much marsh gas.

      Delete
    38. He's a very naughty little creationist!
      Don't change the subject!

      Delete
    39. Here is yet another falsehood from MacLatchie: "I don't think there's anything unethical or unprofessional about what I did. It had already been established that I was mistaken on this point."

      WRONG. MacLatchie did not begin asserting (falsely) that ENSEMBL was inaccurate until AFTER he banned two of his critics. Here's a snippet from the thread; let's start from MacLatchie banning people:

      Jonathan McLatchie: ...both Vincent [Mulholland] and Billy [Sands] were explicitly attacking my competence as a biologist -- e.g. saying that I was "out of my depth" (I forget who precisely said that)... I found this rather insulting.

      ...

      Jonathan McLatchie: I got my information on GULO being transcribed from http://www.ensembl.org/index.html. But this database it seems to me is mistaken.

      Fiona Robertson: If you had clicked on the "Evidence" you would have got a message "No evidence". It's a hypothetical based on the nucleotide sequence. These are the little details that Vincent Mulholland was pointing out to you, but you were having none of it. The database isn't mistaken, you just don't know how to use it properly.

      AFTER MacLatchie banned his critics, and until the present moment, he has never admitted he was wrong to claim ENSEMBL was inaccurate.

      Delete
    40. I will return to this statement of MacLatchie's:

      "...both Vincent [Mulholland] and Billy [Sands] were explicitly attacking my competence as a biologist -- e.g. saying that I was "out of my depth" (I forget who precisely said that)... I found this rather insulting."

      What do you think getting a Ph.D. IS, anyway? If you go to get your Ph.D., grad school is just a bunch of old guys telling you you don't have experience in this, and you don't have knowledge of that. That's what grad. school is FOR.

      You have made your supposed expertise an argument in favor of your scientific assertions-- why then are we forbidden to question or challenge your supposed expertise, when it is presented by you as evidence that your scientific claims are trustworthy?

      You pose in your profile picture in graduation garb and you put science images on your facebook page. If you have made your expertise into a central pillar of your anti-evolution claims, why are we not allowed to question your expertise-- especially when you present us with substantial evidence to the contrary?

      What next, Jonathan? Upon boarding an airplane, will you push your way into the cockpit in a pilot's uniform, and announce you have a grondbreaking hypothesis about what the red lever does? And if the captain should point to your lack of experience, will you grandly announce that "Explicitly attacking my competence as a pilot is INSULTING", and then put duct tape over the captain's mouth to silence his insolence?

      Delete
    41. both Vincent [Mulholland] and Billy [Sands] were explicitly attacking my competence as a biologist -- e.g. saying that I was "out of my depth"

      Funnily enough, it was actually Mark Gordon who said that. The fact he puts it in quotes means he is claiming we said something we didn't. So, we couldn't have been banned for saying that.....

      Delete
    42. I mean blocked and deleted, on banned

      Delete
    43. Spot on, Billy. I noticed that as well. Vince Mulholland said nothing about JM being out of his depth. Seems reading for comprehension isn't one of JM's strong points.

      Delete
    44. Jonathan,

      Let's have a moment of truth here. Did you check the Ensemble database before you wrote the article and had it published on ENV? I'm not arguing with you because you made a mistake, everyone does, and I agree with that. (In fact I expressed my respect for you when you admitted your mistake and was willing to publish a retraction). I'm frustrated with you because you were not completely truthful in the way you presented your the position in the new article. The Ensemble database is NOT inaccurate, and it's NOT mistaken.

      And let's be honest here, you never checked the database before being challenged to show that a transcript is being produced. Therefore, to claim that the database was the source of your error, and to claim that you yourself detected that error "upon further investigation", is intentionally misleading. When pressed by Vincent to show that a transcript is being produced, instead of resorting to the database (which is the course of action I expect from someone who did the homework beforehand), you claimed the following:

      "[I]t is hard to decisively demonstrate that a gene never produces a transcript..."

      And to that, Vincent answered as follows:
      "[I]t is NOT hard to demonstrate a transcript - it's a routine. Look at RNA sequencing via next gen sequencing. Millions of transcripts identified per experiment."

      And your answer to that was:
      "Correct. But it is hard to demonstrate that a transcript is NEVER produced."

      And right after that comment, you stated the following:
      "Transcription can even happen by accident sometimes -- RNA polymerase binds to non-promoter binding sites."

      Yes, you were not talking specifically about the GULO pseudogene, but that was the context of the discussion. You were relying on the fact that even if the pseudogene lacks a promoter, it could still be transcribed. You stated that it's at least a possibility.

      You didn't point the Glasgow Skeptics to the Ensemble database except after the passing of more than 30 minutes on your initial discussion with Vincent about the possibility of transcription, saying that:

      "Apparently GULO in humans does produce a transcript."

      Now, let me ask you again Jonathan, and I hope that you answer me honestly and truthfully, did you check the Ensemble database before publishing your article on ENV? Was the database the source of your error? Or did you turn to the database after being pressed in the discussion?

      All your actions (your words and the flow of the discussion) point me to the latter conclusion. But I could be mistaken. In either case, YOU didn't discover that the database was inaccurate "upon further investigation". Vincent and others have pointed it out to you that you were not using the database properly. And if the database was the source of your error, then you're the one to blame -- not the supposed inaccuracy of the database.

      Delete
    45. This will likely be my final contribution to this thread. Yes, I take full reponsibility for having made an error: I should have been more thorough. The lack of a canonical promoter isn't absolutely damning to the hypothesis I put forward. But I find it very difficult to see how those exons that are missing from human GULOP could be recreated by RNA editing -- unless there is some RNA editing mechanism that we just aren't aware of yet (which is conceivable I suppose, but I wouldn't want to hang an argument on that remote possibility). That for me is the real cruncher. I had been aware of the missing exons when I did my reading on GULOP a couple years back (when I had also checked ENSEMBL for whether GULO produced a transcript, incidentally), but it had slipped my mind when I formulated this hypothesis a number of weeks ago. I should have been more thorough and normally I would be. It was an off-day -- mistakes like this are not the norm for me, and everyone makes blunders like this at some stage. As far as I am concerned, I made a mistake; I corrected it and revised the argument; that's the end of the matter.

      Delete
    46. Hi Jonathan

      As a Christian myself, but not a biologist or even involved in the sciences (apart from teaching 5 Grade, as I'm a school teacher), I would like you to please consider that you continue to engage the forum here. You see, this thread is unlikely to be deleted ever, and they've really called you out on hypocrisy and dishonesty, while their humour and sarcasm stings somewhat these issues are of far more importance than RNA editing mechanisms don't you think?

      Please don't back out. We're reading out here. So far, as a Christian, the evolutionists read as a more noble species judging from this conversation (notwithstanding all the bad taste as in "IDiots" etc.)

      Be strong! Christ was crucified (literally not in an online forum) so that we don't have to be ashamed ever!

      And besides which, science is really cool, it deals with truths.....................

      Delete
    47. What an appalling post by JM - he does not even touch on the integrity issues.
      Here's another reason why it is unacceptable to publish such nonsense at env, where no comments are allowed : The nonsense you write is used in their propaganda. I honestly don't know what purpose you think it serves to have such nonsense used for such purposes. If you are going to preach against real science, without allowing response, having "an off day" is even worse.
      However, it wasn't an off day - you have been called out on your incompetence many times, and you have not retracted. Remember this howler?

      Delete
    48. Oh yeah, that's right, you can't see that link because you censored your critics. Never mind, everyone else can see it though :-)

      Delete
    49. "truth seeker": I think any fair minded individual can see that I did nothing that was unethical. I corrected the mistake, and that's that. But I will not engage with people who are going to continuously attack me personally in the way that Billy et al are doing.

      Delete
    50. You then ignore the obvious misconduct that is evident and presented.
      You have no integrity!

      Delete
    51. And there is the lie of a personal attack, repeated yet again. Please show the evidence that I was obnoxious and/or insulting. Transcripts are available if you've forgotten the words used.

      Delete
    52. Diogenes writes, "If you have made your expertise into a central pillar of your anti-evolution claims..."

      I have never done this -- my arguments stand or fall on their own merit. My own scientific credentials are irrelevant. Plenty of biologists higher credentialed than I disagree with me on various things. But I consider their ideas on the basis of the arguments and evidence presented, not the letters after their name.

      Delete
    53. Still waiting for any kind of justification, Jonathan, that I was obnoxious. Please support with quotes.

      Delete
    54. mclatchie said:

      "I think any fair minded individual can see that I did nothing that was unethical. I corrected the mistake, and that's that. But I will not engage with people who are going to continuously attack me personally in the way that Billy et al are doing."

      jonathan, here's some constructive criticism for you:

      You might as well get used to personal attacks, because you are personally unethical. If you want respect you're going to have to show respect for people who are smarter and more educated than you, are much more honest than you and are sick and tired of being talked to as though they're gullible dummies.

      If you want respect, you should also stop thinking that deleting, blocking, or banning people who question you or point out your errors, agenda, and lack of ethics is a good idea.

      If you want a career in science you're going to have to get rid of your religious programming or learn to thoroughly compartmentalize it. Trying to force-fit reality to your fairy tale religious beliefs will get you nowhere in science.

      So far the only thing you're qualifying yourself for is a lame career as a mouthpiece for dishonest organizations like the DI, ICR, AIG, etc. Is that what you really want to do with your life?

      Delete
    55. "truth seeker": I think any fair minded individual can see that I did nothing that was unethical. I corrected the mistake, and that's that.

      You continue to lie thru your teeth. What you did was not merely "correcting the mistake". You said the error was in the ENSEMBL data base and implied that you were the one who discovered this error. Not the truth, which is that there was no error in the database, and the error was yours in not understanding how the database worked.

      An ethical scientist would have acknowledged that he had made an error, and thanked the people who had pointed out the error to him. A liar would do what you have done, which is to blame the error on the database, neglect to mention that others had to point your error out to you, and delete the evidence that this had occurred.

      So are you an ethical scientist? Or a liar?

      Delete
    56. So are you an ethical scientist? Or a liar?

      These questions are not diagnostic. Either way, the answer would be "yes" to the former, and "no" to the latter. ;)

      Delete
    57. Jonathan, I understand that you feel victimized. However, the transcript is public, as is this thread, and it's not just about "you" and "them".

      Actually, I sense more than a fair dose of patience from your detractors. Apart from anything else, you still have a chance to humble yourself and do the right thing.

      Again, honesty and ethical conduct are of more importance ultimately than this or that hypothesis. Running away from this situation would be a very cowardly thing to do. Understandably you are feeling defensive, but there is no shame in apologizing and making up with the evolutionists... when you have shown so conclusively to be wrong.

      I'm sorry, but I have to disagree with your assessment of the ethics of your actions, and I think to go further and assume that "any fair-minded individual" would come to the same conclusion as you have is completely wrong. It would probably be a good idea to expose this whole fiasco to someone you will listen to.

      Delete
    58. @ Truth Seeker, would you consider it honest to pretend to be someone / something that you are not in a debate? Does it fall within what you deem to be ethical conduct? No special reason for this question, I'm just curious...

      Delete
    59. @ Andy

      I would agree with you (if this is what you are trying to say) that pretending to be something you are not in a debate is dishonest, perhaps more accurately it amounts to a misrepresentation of ones true intentions.



      Delete
    60. Ok, so now when we have established that common ground, is it anything you want to get off your chest concerning your alleged background as a Christian 5th grade teacher?

      Delete
    61. @ Andy - there is more to me than this, but I am a Christian, and I am teaching 5th Grade. Do you doubt this? That interests me.

      Delete
    62. Ok, so as a Litmus test, what would you say is the core message of Christianity and Jesu advise/commandment for his disciples?

      Delete
    63. @ Andy - love one another as I have loved you

      Delete
    64. So knowing that, why don't you go after the "school yard bullies" instead of Jonathan?

      Delete
    65. @ Andy - my appeal to Jonathan to be sincere, was "speaking the truth in love". Our righteousness must surpass that of the scribes and pharisees... Jonathan would lose nothing by a humble, truthful apology and recantation.

      Delete
    66. What we see here is not a debate, it's bullying. Jonathan has admitted that he made a mistake, but his opponents wants to make the most of this (obviousy) rare opportunity. You pulled him back into the debate under false pretenses only to then leave him to the lions.

      Delete
    67. Andy Wilberforce said:

      "You pulled him back into the debate under false pretenses only to then leave him to the lions."

      What false pretenses? If anything, it's mclatchie who is acting under false pretenses.

      And equating the people who have pointed out mclatchie's 'errors' to "lions", as though mclatchie is a captive, helpless, innocent victim being viciously and fatally mauled in an arena filled with jeering, blood thirsty barbarians, is ridiculous.

      You're just pushing the same old, lame old 'everyone is picking on me' victim mentality that so many christians have and portray with the expectation of getting preferential 'kid gloves' treatment.

      Believe it or not, being a christian does not entitle mclatchie or anyone else to 'kid gloves' treatment in science or on websites devoted to promoting science and reality. If he's looking for or expecting automatic agreement and adulation he should forget about science and get a gig as a church preacher.

      truth seeker is actually showing some integrity, which I've found to be extremely rare in christians. You and mclatchie should follow his/her example.

      Delete
    68. What we see here is not a debate, it's bullying. Jonathan has admitted that he made a mistake, but his opponents wants to make the most of this (obviousy) rare opportunity.

      Well, I will admit it is a rare opportunity when a creationist will actually participate in a forum where opposing views can be expressed without being censored. But you continue to propagate the lie that McLatchie has admitted his mistake. He continues to prevaricate on his error, deny its true nature and blame it on others (the ENSEMBL database).

      You pulled him back into the debate under false pretenses only to then leave him to the lions.

      "Lions"? If by some miracle he actually manages to get into a PhD program and produces work as shoddy as his article here, the response he gets at his thesis defense will make this look like a walk in the park. And he won't be able to hide from it by deleting their comments. So he'd better get used to it.

      Delete
    69. @ Andy - there is more to me than this, but I am a Christian, and I am teaching 5th Grade. Do you doubt this? That interests me.

      Yes, that interests me, too. Here is Andy, defending a baldfaced liar without a shred of integrity (McLatchie), and them making this unfounded accusation against someone who has behaved with nothing honesty in this discussion. What's with that, Andy?

      Delete
    70. Andy, I don't believe for a second you actually care what is going on here. I think you just want to scream persecution. Why is it so hard for you to accept that a Christian is asking questions of JM?
      In addition to his plentiful mistakes (they are not rare at all) there is the issue of him lying. Perhaps truth is not that important to you, so maybe you don't get that!

      Delete
    71. @lutesuite, name calling and unsubstantiated accusations are rare in thesis reviews, so I think he will do just fine. I admit that my choice of words was poor. Wolfs is a more adequate description than lions of course.

      Delete
    72. What unsubstantiated accusation, Andy? Please list them and explain why they are unsubstantiated. What exactly were the things Jonathan didn't do but was accused of having done? And what "names" do you mean? "A liar"? He wasn't called that until he started lying to cover up his blunders. Let's imagine that a PhD candidate responds to the reviewers of his thesis by twisting the facts so as to make their criticism appear pointless, or by calling valid criticism obnoxious. I have witnessed many PhD defences but not a single one in which such tactics were successful.

      As for animal allegory, methinks Jonathan is like a weasel.

      Delete
    73. PS Wolfs? Adequate or otherwise, it's incorrect.

      Delete
    74. Piotr, English obviously isn't my first language. Wrong use of idiom and terrible spelling...I admit, I made a mistake. The question can we leave it at that or will you keep bitching about it for the next 2 weeks?

      Delete
    75. I mentioned in once in a postscript and actually left it at that. Are you already feeling harrassed by hungry wolves?

      I'd be more interested in your response to the main post above, not to the trifling grammatical correction. What unsubstantiated accusations have been rolled out against poor Jonathan? What undeserved names has he been called?

      Delete
    76. Wilberforce: English isn't Piotr's first language either, but the content of your point is incorrect-- forget the spelling.

      It takes a lot of chutzpah for you to accuse the people banned by McLatchie of being "bullies" when HE banned THEM and deleted the comments in which they corrected his many errors. Now you call McLatchie's ban-victims "wolfs" and "lions!" What hypocrisy!

      McLatchie banned four people and deleted their comments, which pointed out his errors. After they had been banned, McLatchie attacked them personally calling them "condescending and obnoxious" and saying that, when they corrected his errors, they were not "constructive."

      McLatchie attributed to the people he had banned, statements that they did not make (and were not ad hominem attacks anyway.)

      These were false statements and personal attacks, issued by McLatchie toward people who could not respond because he had banned them.

      And you call the people he attacked "Lions" and "Wolfs" and "Bullies"!? Wow.

      By contrast, on this thread, McLatchie has NOT been banned and is free to respond. We tot up a list of McLatchie's numerous mistakes and errors and false claims (MOST of which he has NOT corrected, despite Wilberforce's false claims that McLatchie corrected his errors) and we tot up a list of the questions directed at McLatchie which he dodged completely, despite their relevance.

      McLatchie has not been banned by us. He just wants to dodge the questions, while falsely claiming he has corrected his mistakes. He has NOT.

      I repeat: you are not telling the truth when you claim that McLatchie has corrected his errors. False-- he made more than a half dozen false statements and has corrected 1 or 2. We made a list of them above, which you ignore at your peril.

      Whited sepulchres of hypocrisy.

      Delete
    77. It doesn't take much chutzpah to write here anonymously, not for me and nor for you. Of course I know English isn't Piotr's first language, we have had exchanges before. His command of the English language is admirable, and he's also doing a good job at trying to grasp the subjects discussed here even though he has no background in science...as for your accusations against Jonathan I must admit I haven't read his blog, but judging only from the writings here I think there may be some truth to the "condescending and obnoxious" statement.

      Delete
    78. Andy Wilberforce, I suggest you scroll up the comments and find the link to the original FB thread, the one that JM deleted. That's where he began ignoring what he was told by scientists far more experienced and better qualified than him, that's where he began c omplaining about obnoxious and condescending behavious and that's where he blocked certain other posters so that he couldn't see their comments and they couldn't see his. Coinc identally those people were sc ientists trying to explain to him why his original article was so much marsh gas. Even after discovering they were correct, he has continued to accuse them of being obnoxious and condescending.

      You need to read that original thread before jumping to unwarranted conclusions.

      Delete
    79. You need to read that original thread before jumping to unwarranted conclusions.

      But if creationists didn't jump to unwarranted conclusions, they wouldn't be creationists, would they?

      Delete
    80. @Fiona, my smart phone didn't let me download the file. I will try to remember to look at it when I get to a computer. My main point though, is that the way some people express themselves here is just appalling. I guess we all have that in common the we are interested in life sciences, I cannot understand why it must be so difficult to discuss different views in a sensible and factual way. I stay on this blog because I find many of the posts interesting, but for most parts I stay away from the discussions, it's just not worth it.

      Delete
    81. Well, once you've read the threads in question, you may understand why this discussion has the tone it does. It's absolute frustration on the parto sc ientists that first JM refused correction, then he realised he had messed up yet left the original article in place for 4 days and when he finally came up with his "retraction", he blamed the Ensembl database even though it was Ensembl that had been used to show him there was no transcript. Now, if he's been told that Ensembl says there is no transcript and he can go check that for himself (I even provided screenshots to prove it), why would he subsequently write an article blaming Ensembl for leading him astray when he knew that it was the Ensembl database which put the kybosh on his original, erroneous musings? THAT is what people are annoyed about. He has not and will not accept that HE made a mistake. He's blaming everyone and everything. Heck, he even admitted he wrote the original article without taking into account that the first six exons of the gene are missing and there is no promoter. Given that hios original article was full of holes you could drive a truck through, the responses he gotwere very polite. His response? To accuse those disagreeing with his article of being obnoxious and insulting and blocking them. He even blocked Vince, the one who tried to help him and who first asked if he'd bothered to check Ensembl for a transcript. He hadn't. Now, how could Ensembl have led him astray in his originalarticle if he hadn't even used it? When he finally did, he claimed there was a transcript and it was Vince and others who had to show him that Ensembl stated categorically that there was NO evidence of a transcript according to Ensembl. It was only AFTER all of this that JM wrote his "retraction" and in it blamed the Ensembl database. Now, how would you react?

      The bottm line is that he made an honest, but really stupid bunch of errors in his original article. The dishonesty appeared in his so-called retraction.

      Delete
    82. Fiona, thanks for filling me in. I have now read the Facebook thread and the comments does not cross the line for what I consider obnoxious and maybe some of the condescending remarks were warranted...but still, cut the kid some slack. He made a mistake and he knows it. I think we've all been there. Some more often than others.

      Delete
    83. Nobody has a problem with him making a mistake - we all make them. Where the line was crossed was in the "retraction" where he claimed it was the Ensembl database that was inaccurate and that's what caused him to make the mistake he did. That is patently false when you look at the timeline. The database is NOT inaccurate and he already knew that BEFORE he wrote his "retraction".

      Delete
    84. @Andy Wilberforce

      If I understand you correctly, it's not that it is being pointed out that Jonathan Mclatchie is a lying, dishonest sack of shit, it how it's being pointed out that you take issue with.

      In fact it seems that you are now in agreement that Jonathan Mclatchie is a lying, dishonest sack of shit.

      Delete

  3. I believe Larry mentioned here, when he was tearing the ENCODE consortium a new one, that many of the 'transcripts' covering 80% of the genome were exceedingly rare - perhaps one transcript every few days. McLatchie could have appealed to this and claimed that although the databases say its not transcribed thats because they werent doing the extremely sensitive tests in fetal brain during the correct time window

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    1. The problem is that he was claiming there was a transcript in the database, when there actually was further info that he did not check

      Delete
    2. The issue of transcription is peripheral, anyway. Even if the pseudogene was transcribed, he still needs to demonstrate a mechanism by which RNA editing could conjure up entire deleted exons, as well as the promoter and regulatory sequences, out of thin air. As Larry points out, McLatchie makes no mention of this more profound problem with his "hypothesis", and leaves his gullible readers with the impression that his error was just a minor oversight, rather than that his claim is hogwash top to bottom.

      Delete
    3. It's peripheral to the article, which has much wrong with it, but it questions his integrity in his response

      Edited to include:
      The database was not inaccurate. He just didn't know how to use it.

      Delete
    4. "McLatchie makes no mention of this more profound problem with his "hypothesis", and leaves his gullible readers with the impression that his error was just a minor oversight, rather than that his claim is hogwash top to bottom."

      Actually, I did mention it (did you read the article, or just take Larry's word for it?). Second, my hypothesis is not "hogwash top to bottom." The material on RNA editing was accurate, and -- as I mention in the original article and elaborate on in the second one -- likely more generally applicable.

      Delete
    5. Actually, I did mention it (did you read the article, or just take Larry's word for it?).

      Yes, I now see that you did mention it. Just a brief mention, easily missed (as I did), but it is mentioned.

      Second, my hypothesis is not "hogwash top to bottom." The material on RNA editing was accurate, and -- as I mention in the original article and elaborate on in the second one -- likely more generally applicable.

      You're acting like you've discovered RNA editing yourself. Your material on that was "accurate". Well, congratulations. You finally managed to recount some science without mangling it beyond recognition.

      Your hypothesis, need I remind you, was that RNA editing could cause the human GULO pseudogene to become functional in the prenatal period. That claim is hogwash, as you've admitted yourself. Or are you now backtracking from that?

      Delete
  4. "Upon further investigation, however, I've discovered ..."

    Classic weasel words. It's amazing to me what advice these good people with their dedication to Jesus and personal relationships with him get in their daily spiritual inboxes: cover it up; move the priest to another parish; stonewall; don't allow comments on your websites; and never take full responsibility for errors or credit the opposition for pointing them out.

    I'm not saying the last one is easy, but without a god whispering to me I've managed to do it a few times, just on the the basis of my reason and mirror neurons telling me it was the right thing to do.

    One of the clearest missing pieces of evidence for the Christian god is the behavior of many Christians, Monday through Saturday.

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  5. It somehow slipped Jonathan's mind to thank Larry and other people who helped him to understand his mistake. He gives himself all credit for "discovering" the relevant facts "upon further investigation", but it's no big feat to discover something that has been pointed out to you.

    ReplyDelete
  6. McClatchie wrote Moreover, there's a much more important point to take note of, which I hope is not lost in this discussion -- namely that my original hypothesis could be more generally applicable.

    That's another classic creationist move: 'So, the flagellum isn't irreducibly complex? OK, well then, look at the immune system! It is!' It's a slow motion Gish Gallop.

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    Replies
    1. I have an alchemical hypothesis: if I piss on phosphorus, it will be transmuted into gold. Let's see...

      [Five minutes later] Mmm, no, it doesn't seem to work with phosphorus. But my original hypothesis could be more generally applicable. There are many other stuffs I could piss on to see if they turn into gold.

      Delete
    2. Piotr, on a search for the philosopher's kidney stone? ;-)

      Delete
    3. Very funny, Piotr, but your analogy misses the crucial point that Maclatchie's rewritten version of history is totally self-flattering: Maclatchie portrays himself as SMARTER than the curators of ENSEMBL! He's smarter than them, see-- the ENSEMBL curators made a mistake, and Maclatchie says that he, through his diligent investigation, caught THEIR error! Bwa ha ha.

      Not only did Maclatchie not make any mistake, but he portrays himself as SMARTER than the ENSEMBL curators-- now THAT's what I call ID attitude, baby!

      A better analogy would be the following: would-be alchemist Johannes Maclatchicus announces that his Lord don't make no junk, therefore ANY element will transmute to gold if you piss on it. His logic is that it's already been PROVEN that sodium transmutes into gold if you piss on it; so by generalization and wishful thinking, this must be true of all elements.

      Critics on the interparchment then inform him if you piss on sodium, it will explode but not transmute into gold.

      Johannes replies that he has consulted the Corpus Hermeticum, and it says that sodium transmutes into gold if you piss on it.

      Critics on the interparchment then point out that the Corpus Hermeticum in fact says no such thing.

      Maclatchicus then bravely announces that the Corpus Hermeticum has a grave error which he, Maclatchicus, has caught: shockingly, it says that sodium WON'T explode if you piss on it-- everyone knows sodium explodes if you piss on it, and Maclatchicus, through his brilliant diligent investigation, has caught their error.

      However, Maclatchicus insists his original hypothesis is still viable, that ALL elements will transmute into gold if you piss on them. He hypothesizes that sodium is prevented from turning into gold by an invisible sylph, nymph, salamander or other elemental being. Thus it is still possible that sodium MIGHT turn into gold if you piss on it-- after all, no one can disprove the existence of an invisible elemental being.

      Since this is POSSIBLY true of sodium, then it is DEFINITELY true of all other elements! He has thus proven that his Lord don't create no junk.

      Delete
    4. I don't think this is an illegitimate approach at all. I hadn't chosen the best example for the point I was making. But RNA editing I think has potentially broader applicability to pseudogenes generally. I'm not claiming that all pseudogenes undergo editing in this manner -- But I think it is quite plausible that a significant number do. Cytochrome c oxidase III in Trypanosoma brucei, for instance, is in a sense a pseudogene. It doesn't work unless it undergoes extensive editing. Larry wanted specific examples -- so there's one.

      By the way, Larry was also incorrect in his comment that I didn't mention in my latest post that the original hypothesis is very likely incorrect. In fact, I did. GULOP is missing several exons, and it is very unlikely that it could all be written by RNA editing -- unless of course there's some mechanism that has yet to be discovered.

      Delete
    5. Johannes Maclatchicus: Have you admitted yet that you were wrong when you claimed the ENSEMBL database was inaccurate? Do you think we'll let you drop that one?

      "I hadn't chosen the best example for the point I was making"

      I suspect you did, and that all the other examples are worse!

      If you had a PI, he would ask you: what's your negative control?

      Simple experiment: take a gene, mutate it, insert a few stop codons and indels. Does it keep getting transcribed, translated, and forms a folding protein? There's your negative control, Maclatchicus.

      Delete
    6. FYI, Trypanosome editing is not like the proposed editing in your "masterpiece". It uses an actual transcript for a start, but there are more differences. More incompetence? No need to thank me.
      Do you not think you would be better off actually doing things properly?

      Delete
    7. Now MacLatchie is not merely hypothesizing an invisible transcript of GULO with an invisible function, but also an invisible RNA editing mechanism that fixes indels and stop codons, and that, although invisible, is CONSERVED between humans and protozoans-- all to prop up the idea of an invisible designer.

      If this invisible RNA editing mechanism were conserved between protozoans and humans, wouldn't it be much easier to find, instead of being supported by no evidence?

      Delete
  7. I think that we should view Jonathan's original post as a failed attempt in a still larger context: Creationists are trying to hit back at the argument from plagiarized errors that Edward Max and others have advanced in favor of the theory of common descent. They know very well what the implications of a functionless human GULO pseudogene are. Even their hero Michael Behe cites this particular example as one of the main reasons why he accepts the theory of common descent:

    "For example, both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C. ... It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans. ... Despite some remaining puzzles, there’s no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.” (Emphasis added)

    ~ Michael Behe, The Edge of Evolution, pp 71–2.

    However, as Casey Luskin and others have tried to argue, if the human GULO pseudogene turns out to be functional, then the argument from plagiarized errors would fail. Because now you could argue that the "Designer" provided humans and the other apes with this piece of DNA to perform a common function.

    If we look at the larger context, we'll see that functionless pseudogenes aren't the only problem that ID Creationists are trying to tackle. They have tried to argue against ERVs in the past, and every once in a while we see a post on ENV proclaiming the discovery of a functional ERV.

    Of course, all of this discussion means nothing to Jonathan. He's willing to believe that RNA editing could resurrect 7 exons intact as they were, he's willing believe in an assumed promoter millions of base pairs upstream, and he's willing to believe that a higher concentration of vitamin C in embryos couldn't come from any other source except the baby's own cells. But he cannot possibly believe that he descended from an ape, that's too much for him.

    Thanks Jonathan for the half-baked retraction. You'd make a good politician.

    ReplyDelete
    Replies
    1. Another point for the record... I am inclined to accept common ancestry, so it is hardly "too much for [me]" to "believe that [I] descended from an ape." At the very least, I consider it to be quite a defensable position. That doesn't mean I don't think there's no evidence on the other side of the scale. On the balance of evidence, however, I'm currently inclined to think common ancestry makes sense of a lot of evidence that is otherwise surprising given the alternative hypothesis.

      You mention specifically ERVs. This strikes me as quite a compelling argument for common ancestry. Things one needs to explain include: (a) The shared orientations of orthologous ERVs; (b) the nested hierarchical distribution of ERVs within primate genomes (it is the distribution of similarities and differences which is the important thing to consider); and (c) The striking correlation between the distribution of ERV placement and the distribution of point mutations in env, gag, and pol genes. The general reliability (albeit with exceptions due to gene conversion) of LTR-LTR divergence as a predictor of time since integration is also, in my judgment, a compelling argument.

      Function of ERVs are irrelevant to the argument for common ancestry. First, target-site duplication is the hallmark of insertion by integrase, and we can use this to infer that these elements are indeed inserts, irrespective of whether they are functional. Second, I don't know of a single case where an entire ERV is known to be functional. In all cases that I know of (and I have a whole database of examples), it is particular ERV components (e.g. LTRs frequently serve as promoters or enhancers) that are functional, not the full sequence.

      Delete
    2. Maclatchicus says, re common descent of humans and chimps: "That doesn't mean I don't think there's no evidence on the other side of the scale."

      OK. List three lines of evidence AGAINST common descent of humans and chimps.

      Delete
    3. MacLatchicus, the fellows at the Ministry of Magic repeatedly assert that the case for common descent is destroyed if any snippet of DNA has function. You seem to dispute this where ERV's are concerned. Why have you never criticized them, particularly Casey Luskin, on this point when they are so obviously wrong?

      Delete
    4. I think the evidence for primate common ancestry is quite strong. But I think the evidence becomes more ambiguous when you extrapolate to universal common ancestry. Maybe I'll write a blog post fully fleshing out my views on this.

      Delete
    5. Ignoring various points, you refuse to take up a challenge about primate common ancestry and decide to blog about a different topic. Of course, no one will be allowed to criticise this at the source.
      Perhaps if lots of folk that are better placed than you, say you committed an act of intellectual suicide by censoring critics, you should listen.
      Loving the fact that no one at the DI spotted your errors. Says a lot, don't you think?

      Delete
    6. MacLatchie: "I think the evidence for primate common ancestry is quite strong"

      That is certainly NOT what Casey Luskin, Axe and Gauger wrote in Science and Human Origins! Indeed, one of Casey's key arguments in "SHO" was that if any snippet of non-coding DNA (which Luskin falsely says scientists equated to "junk DNA") turns out to have function, that demolishes the case for common ancestry of humans and chimps.

      The title of that chapter was "The Science of Adam and Eve." Yah, nothing religious about that.

      When Paul McBride wrote a negative review of "SHO", focusing on debunking Luskin's genetic arguments, the Ministry of Magic (that you work for) dropped a shit brick and sent their aurors and dementors after McBride. How DARE anyone criticize lawyer Luskin! This is forbidden! Off to Azkaban with the young Kiwi!

      But now... NOW you say that if bits of ERV's are functional (e.g. their promoters), it doesn't destroy the case for common descent from chimps.

      Oh NOW you say that! Well! Why didn't you stand up for McBride when the Ministry of Magic (that you work for) sent their dementors after him? (Yes I mean Klinghoffer)

      Delete
    7. For comparison with what MacLatchie wrote above, here's Casey Luskin on the very same topic:

      "If we find the same ERVs in the same genetic loci in different species of primates, [Douglas] Theobald concludes they document common ancestry. But what if ERVs do perform important genetic functions? Even theistic evolutionist Francis Collins acknowledges that genetic similarity "alone does not, of course, prove a common ancestor" because a designer could have "used successful design principles over and over again." (The Language of God, pg. 134.) The force of Theobald's argument thus depends upon the premise that ERVs are selfish genetic "junk" that do not necessarily perform any useful function for their host." [Casey Luskin, Aug. 21, 2008]

      Jonathan, you completely contradicted Casey Luskin. Who is right-- you or him?

      Delete
    8. Newsflash: Proponents of ID are allowed to have differences in opinion.

      Delete
    9. Straw Man Attack! We have no doubt that proponents of ID are permitted to have differences of opinion.

      The questions are:

      1. Whether these contradictions, which go unaddressed, demonstrate that IDers are not honest when they claim to be interested in science research-- because research involves resolving contradictions via experimentation; and

      2. Whether IDers treat the VERY SAME ARGUMENTS totally differently depending on whether they come from designated "Darwinists" or from an IDers.

      This was the point of my previous post, which I need to repost, I guess:

      When Paul McBride wrote a negative review of "SHO", focusing on debunking Luskin's genetic arguments, the Ministry of Magic (that you work for) dropped a shit brick and sent their aurors and dementors after McBride. How DARE anyone criticize lawyer Luskin! This is forbidden! Off to Azkaban with the young Kiwi!

      But now... NOW you say that if bits of ERV's are functional (e.g. their promoters), it doesn't destroy the case for common descent from chimps.

      Oh NOW you say that! Well! Why didn't you stand up for McBride when the Ministry of Magic (that you work for) sent their dementors after him? (Yes I mean Klinghoffer)

      Delete
    10. Hi Jonathan Mclatchie,
      I'm probably the only uneducated moron on this forum, except for Gasarsracy, Poter but I had a chance to humiliate the famous Hollywood star NickM. How? It is very simple.
      Here it goes:

      "NickM, Let's talk the origins. Would you like to do it here or via email? If you are not sure, here is my fist question:
      1. Can proteins self-assemble in the the pi-soup? (no cell membrane)
      The reason why I ask is that proteins tend to "avoid" the connection" or an "attraction". So, what makes them so "loving" in a cell?
      2. It is not may question but my brother has been asking me this question for months. Since I have no answer, I thought I would ask you, since you are such a smart guy; you and Larry that is.

      "Enzymes are needed to produce ATP. However, energy from ATP is needed to produce enzymes. However, DNA is required to make enzymes, but enzymes are required to make DNA.
      However, proteins can be made only by a cell, but a cell can be made only with specific proteins. So, how is this ALL possible in view of evolutionary prospective?"

      Obviously, there have been attempts from the experts to convince me, that science "does not know" everything and IT IS WORKING ON IT, but the reality of this challenge must have even discouraged NickM. I have some money to take this issue further; a lot further but for some reason nobody wants to hear it. They want the money but not the content.

      Delete
    11. Newsflash for you, Jonathan: It's very interesting that while you were so eager to trumpet how your stillborn "hypothesis" contradicted "Darwinism", you made no mention of how it contradicted the claims of your fellow ID proponents. I wonder why that was?

      Delete
    12. Jonathan,

      I specifically stated that I was looking at the larger context of what type of arguments ID Creationists are trying to conjure in order to challenge the theory of common descent. You may think that ERVs are a strong evidence of common ancestry, but that's in no way representative of the majority position among the people who hold your views (or views similar to yours). And these people are the same type of people who got excited about your last article. They know very well what the theological and philosophical implications of common descent are, as I'm sure you yourself understand them.

      In fact, I wasn't judging you based solely on the majority view of your peers. You yourself, my friend Jonathan, have argued for the existence of of a literal Adam and Eve, and a literal flood (that at least wiped all humans except a few individuals), just a year and a half ago, as evidenced by the following article:

      Did They Really Exist? A Biblical and Scientific Defence of Adam and Eve

      In that article, while in the process of justifying Cain's incestuous marriage, you stated:

      "Adam and Eve were probably created genetically pure. It is, therefore, likely that the genetic defects resulting from marriage between siblings would not present an issue for the first couple of dozen generations."

      Now, you have to excuse our presumptuous interpretation of your words, but what do you exactly mean by the words "created genetically pure"? If you believe that all modern humans descended from a literal Adam and Eve, and at the same time believe in common descent, then you have to assume a severe bottleneck (something equivalent to the Founder's Effect). This will necessarily mean that the genetic variability in the said population will be severely reduced.

      Unless you have your own version of common descent, where at each turn or speciation event the Designer takes two individuals and magically makes them "genetically pure" (a view that isn't very much different from the "special creation with common design" view), and unless you have retracted and corrected that article somewhere else, I cannot see, in all seriousness, that you accept the theory of common descent that I have studied in school.

      You may have changed your position about this particular issue since then. But I haven't seen anything to that effect, as of yet. If you indeed expressed a different opinion more recently, please do direct me and my fellow sandwalkers to the new corrected article.

      Thanks!

      Delete
    13. @ShadiZ1

      (Quoting McLatchie)

      "Adam and Eve were probably created genetically pure. It is, therefore, likely that the genetic defects resulting from marriage between siblings would not present an issue for the first couple of dozen generations."

      I posited something similar the other day - although I presented it as a parody for possible creationist evasions of the implications of Original Incest.

      In the same vein, I presume God must've reset (defragmented - re-fragmented?) Noah's family's DNA post-flood so the ensuring and very necessary incest wasn't too much of a problem when they began the arduous task of filling the planet with 7 billion people in just under four millennia.

      Delete
    14. Hank, as you know, Noah's grandkids married their first cousins, righteous Lot impregnated both his daughters, and righteous Abraham married his half-sister. So incest does not become immoral until relatively late, and Christian morality is based on moral relativism.

      Delete
    15. ShadiZ1, fascinating link. MacLatchie's version of ID, like most defintions of ID pre-2004, is based on a religious belief in the inerrancy of a literal interpretation of the Christian Bible.

      As Casey Luskin always says, there's nothing religious about ID, except for God, Jesus, Adam and Eve, Noah's global flood, Jonah in the belly of the whale, Balaam and his talking donkey, and everything else in the Bible.

      Delete
    16. Diogenes, you wanted to know what the "evidence on the other side of the scale" was. You have it: Genesis 26-27, inerrant, therefore irrefutable.

      Delete
    17. NickMistake still has no answer for this issue. He never will but he and other so-called scientists and believers think the above issue is going to go away. Not so. My buddy is writing a book that will make these morons clowns. Larry is going to lead the field and now we know who geneoshit is lol

      Delete
  8. Larry, what happens to an evolutionist who gets refuted? Let'say on this blog? Should he/she be allowed to comment, especially on this world's best EID blog?? Or should she/he be banned?

    ReplyDelete
    Replies
    1. Quest, when it happens, you'll find out along with everyone else.

      Delete
    2. Quest, John Mattick is exactly such an evolutionist. Larry has several posts on him and his mistakes.

      Delete
    3. "Larry, what happens to an evolutionist who gets refuted?"

      It happens all the time, e.g. when you submit a paper and it doesn't pass peer review due to shoddy logic, mistakes, unwarranted conclusions, unjustifiable assumptions, whatever.

      Delete
    4. Larry also has plenty of posts where he disagrees with Richard Dawkins on evolution. How does that factor in to your feigned ignorance, Quest?

      Delete
    5. Applying what you are suggesting would mean that Larry would have to ban himself ten times over you moron!!! Just look at your last thread with J. Coyne. Larry is the host and he can do whatever he wants. If you don't like, too bad. Move on to another blog.

      PS. I have asked you several times to insert a ling to the Venter discussion. Why do you keep ignoring me? Are you f...ing blind?

      Delete
    6. That was my point. If Larry has stuck to the rules he would have had to shoot himself in the leg or head or...who knows?

      Delete
  9. As a scholar in another field, perhaps a bit closer to Larry's age than Jonathan's, reading this thread but not the other one, what strikes me is the lack of charity Jonathan's critics show, and frankly in some cases a certain amount of small-mindedness.

    Jonathan is a young scientist who deigns to challenge reigning orthodoxy. He's wading into the fray outnumbered 20 to 1, including against far more eminent and experienced scientists.

    It's never easy to admit errors in public. No doubt he has a lot to learn. People learn more by degrees than in sudden leaps, most of the time. (Darwin would have understood.) I'd frankly have more respect, especially you, Larry, if you'd cut the young man a wee bit of slack, and acted a wee bit less like witch-hunters throwing kindling around the burning flames of a sentenced defendant. And maybe showed more interest in the bigger issues, and less in building a "case" against the sacrificial lamb.

    ReplyDelete
    Replies
    1. Well here's the thing, you can't actually read that original thread anymore, because poor persecuted, young "scientist", "challenge the orthodoxy" Jonathan went and deleted it.

      And as the author of "True Son of Heaven: How Jesus Fulfills the Chinese Culture" I suspect that you are not quite the disinterested and dispassionate observer that you pretend to be, are you ?

      In general, respect is earned, not bestowed, and in the case of Jonathan Mclatchie, he has built up quite the deficit.

      Delete
    2. @David B
      I read the Glasgow Skeptic thread, prior to it being deleted - but it is preserved so you will still be able to access it (from what you write I suspect you have not yet done so).
      Ugly. Very ugly. As in: straight to the firing-squad without appeal kind of ugly. Thing is, Jonathan has more cause to repent these sins than he does the _other_ (Oops! who put that banana skin there, wrapped around that bright, yellow banana) purely scientific ones .. Scots' tact at its very finest ..

      Delete
    3. @David B. Marshall

      So you agree that Jonathan has made errors here to which he has not admitted. Good. Maybe you could spell those out for him. We don't seem to be getting thru to him, and perhaps he'll listen to a fellow Christian.

      Maybe you could also spell out the "bigger issues" you believe are being missed here. Larry and others have discussed the many errors and flaws in Jonathan's argument in great detail and specificity. So I'm not sure what you think has been overlooked.

      I also don't know how old Jonathan is, but most elementary school students of my acquaintance have figured out what it means to lie, and how to apologize when found out. So I don't think his youth excuses his behaviour.

      Delete
    4. @David B.

      My reading of the thread, as a Christian, is that the evolutionists have been rather charitable. Even their teasing of "Jonathan the alchemist", whilst silly, was not malicious, in my reading. Of course I could be missing something, as Jonathan himself seems very sensitive to what he perceives to be a patronizing and insulting attitude from some of this colleagues.

      But Jonathan has chosen this field and will no doubt face worse than this if he persists with his unorthodox views. So I still say he shouldn't run away from this - it was his statement that he was no longer going to comment that elicited my response.

      While "he that fights and runs away, lives to fight another day" may have been the case in earlier times, with the internet this debacle is permanently visible for all to see (unless you take it upon yourself to delete entire threads, and even in such cases there are screen shots that may have been saved, as happened here).

      Delete
    5. "truth seeker": So there's no ambiguity, please list those items on which you think I have erred. I will then respond on whether I agree or not. Then I really am leaving this thread.

      Delete
    6. As far as I'm concerned, giving a creationist like McLatchie so much as the time of day is already being charitable. In a just world, creationists would be treated with as much respect and courtesy as Holocaust deniers, w/ whom they share so much in common.

      His views are not merely "unorthodox". They are wrong. Period. Full stop.

      Delete
    7. David Marshall,
      Integrity and impartiality are central to scientific pursuit. Do you think he can be trusted not to make data up in future, or to not cover up data that contradicts his hypothesis?
      Do you think liars should be left off the hook?
      Why do you think we decided it would be a good idea to keep a permanent record of JM's thread? Could there perhaps have been previous lies from him?

      Delete
    8. So there's no ambiguity, please list those items on which you think I have erred.

      Well, to begin with, when one has outright lied, it is an error to say you have merely "erred".

      Delete
    9. Still no evidence of my being insulting and obnoxious - start there.

      Delete
    10. And these baseless personal attacks are precisely why I deleted the thread in the first place.

      Delete
    11. Classic JM - get you to do all the work for him.
      Jonathan, the accusations are all over this thread - why not be diligent and find them?

      Delete
    12. Baseless?
      Pointing out your incompetence was hardly baseless. Come on, where did Vincent personally attack you?

      Delete
    13. There you go again - WHAT ATTACKS?

      Delete
    14. His reluctance to comment is consistent with the hypothesis that he doesn't have a leg to stand on :-)

      Delete
    15. I reject your claim that I "outright lied".

      Delete
    16. You lied about my attacks and insults. Start there.

      Delete
    17. Outright lies - you claimed the Ensembl database was in error AFTER it had been demonstrated to you that there was no transcript. Your "retraction" gives the impression that the Ensembl database claims that a transcript is produced. You wrote your retraction after you knew that Ensembl doesn't make that claim.

      You have also claimed that Vince Mulholland said you were out of your depth and that was what you found obnoxious. In actual fact it was SOMEONE ELSE ENTIRELY who said you were out of your depth. You have been corrected on this at least 3 times, yet you persist in repeating your erroneous accusation against him.

      Is that the behaviour of an honest, ethical person? You slander Vince rather than admit you were wrong to accuse him in the first place. Let's face it, Jonathan, the people you blocked were scientists, molecular biologists, who knew just how wrong you were.

      Delete
    18. Okay, this is my final contribution to this thread. But let me just set the record straight.

      Yes, I'm aware it wasn't Vince who made that comment -- I think I said in the original thread that I couldn't recall precisely who had said that. In any case, it was part of what led to me eventually deciding to close it down.

      The Ensembl database DOES give the impression that a transcript is produced. I should have been more thorough in double-checking, but that's the impression given. In any case, as noted above, I actually had checked Ensembl when I did my original reading up on GULOP. But I do not wish to participate here any further.

      Delete
    19. Right, so you blocked me for personal attacks I didn't make?

      Delete
    20. Then how come nobody else got that impression from the Ensembl database? You know, the molecular biologists who know how to use it. Face it, the database specifically states that there is NO EVIDENCE OF A TRANSCRIPT. How you can get the impression that the database says there is a transcript is beyond me. The bottom line is that YOU didn't know how to use it and you are still trying to wriggle off the hook by saying it "gives the impression" that a transcript is produced. NO IT BLOODY DOESN'T!!!

      Now, if you are aware that Vince didn't make that comment, why the heck are you repeating your accusation that he was obnoxious? Initially you claimed it was that comment by him that caused you to block him for being obnoxious. Now you admit he never made the comment, yet you have repeated your accusation against him. If truth be told, you have demonstrated why someone would say you were out of your depth...because you were.

      Delete
    21. And there you have it, clear for all to see - JM had it pointed out to him that he goofed up before that second blog post, but he wont admit it

      Delete
    22. I apologize for calling McLatchie "a horrible little creationist", which was over the top.

      However, the fact remains that McLatchie is the aggressor, not the victim here-- because he blocked at least 4 people on the FB thread, deleted their comments, and deleted the evidence that he, McLatchie, had made the errors.

      McLatchie added insult to injury by insulting his critics after he had banned them and could no longer respond-- critics who had done him a big fat favor and helped him out by teaching him to interpret ENSEMBL correctly. He called them "condescending and obnoxious" and other things, and attributed to them statements they did not make.

      Then he compounded it by falsely stating that the ENSEMBL database was in error, when in fact it wasn't, McLatchie made the error. This error of his has been pointed out to him literally dozens of times, on FB and here on Sandwalk and who knows where else, and he refuses to acknowledge this, while simultanously claiming he responds to ALL criticisms on his blog. He does not.

      These ironies are insufferable:

      At the thread that McLatchie deleted, thus concealing evidence of his mistakes, he wrote, "I've always responded to criticisms to my blog posts." NO HE DID NOT AND DOES NOT. He never acknowledged that ENSEMBL was accurate and he was wrong. Previously, MacLatchie never admitted he was wrong about the genetic code (mutations of one nucleotide don't change physicochemical character of amino acids, said McLatchie.) This was such a rank amateur error (where did he get it from? Answers in Genesis?) that it was immediately and easily pointed out; he responded with nothing, except the excuse "I will perhaps comment further tomorrow"; THAT WAS TWO AND A HALF MONTHS AGO.

      And when on rare occasions he does "respond", he only knocks down straw-man arguments published at ENV blog which tolerates no comments.

      Then the ID proponents flip the frame and accuse US of suppressing free speech!-- Indeed, in the very thread on the topic of GULO at Centre for ID (UK), directly below that thread is yet another pretentious "Promote Free Speech on Evolution" post-- this coming from the ANTI-DARWINIST THOUGHT POLICE who ban and block all critics, delete their carefully referenced comments, and tolerate no comments at their blog!

      Why do we hear the loudest "yelps" for free speech from the intolerant Anti-Darwinist Thought Police?

      Delete
    23. I don't understand, how come saying that someone was out of their depth is an insult? If the claim is inaccurate, then it's inaccurate, but far from an insult. If it's accurate, then it's accurate, but far, again, from an insult.

      If that's what it takes to insult creationists then they are really out of their depth.

      The Whole Truth asked:
      So far the only thing you're qualifying yourself for is a lame career as a mouthpiece for dishonest organizations like the DI, ICR, AIG, etc. Is that what you really want to do with your life?

      Of course McLatchie really wants that. He's getting a degree just to be able to claim having a "scientific background."

      Delete
    24. Above I re-iterated some questions that McLatchie had dodged, but there are some others he dodged, which I wish to raise again:

      McLatchie, on the common descent of humans and apes: "That doesn't mean I don't think there's no evidence on the other side of the scale."

      Me: OK. List three lines of evidence AGAINST common descent of humans and chimps.

      Response from McLatchie: silence.

      The only response I got was from ShadiZ1, who posted this link to "Did They Really Exist? A Biblical and Scientific Defence of Adam and Eve" in which McLatchie clearly bases his version of Intelligent Design on Biblical literalism, with the evidence for Adam and Eve being that the Bible says so-- nothing religious 'bout that.

      But McLatchie also said there's positive evidence for common descent. Thus, I will again repeat the question that McLatchie did not answer:

      When Paul McBride wrote a negative review of Casey Luskin's Science and Human Origins, which says basically that there's no evidence for the common descent of humans and chimps, and when McBride debunked Luskin's genetic arguments, the Ministry of Magic (that you work for) dropped a shit brick and sent their aurors and dementors after McBride. How DARE anyone criticize lawyer Luskin! This is forbidden! Off to Azkaban with the young Kiwi!

      But now... NOW you say that if bits of ERV's are functional (e.g. their promoters), it doesn't destroy the case for common descent from chimps.

      Oh NOW you say that! Well! Why didn't you stand up for McBride when the Ministry of Magic (that you work for) sent their dementors after him? (Yes I mean Klinghoffer)

      Delete
    25. Are there any other questions you can think of, that have been posed to McLatchie, and which he dodged? Let's compile a list. (See the comments immediately above this one).

      Delete
    26. Are there any other questions you can think of, that have been posed to McLatchie, and which he dodged?

      How Vincent was "obnoxious" to him.

      Various questions remain about the Andersson paper he originally cited to support his agenda (sorry, "hypothesis") - missing controls, no stats, the fact there was vitamin C in the diet and used it to claim folk with no vitamin C do not get scurvy.

      Delete
    27. Any takers on how soon McLatchie will be back after making his latest "final" comment on the manner?

      Delete
  10. Yeah, the evidence is pretty clear you did lie, and everyone can see it.
    You are just digging a bigger hole for yourself. This issue will now follow you around. You will be known as the creationist who was caught lying and still denied it. Good luck trying to have a future in science!

    ReplyDelete
    Replies
    1. You will be known as the creationist who was caught lying and still denied it.

      Actually, the competition for that title is pretty extensive....

      Delete
    2. A school boy error, and I thank you for correcting me :-)

      Delete
  11. I've just browsed from this blog over to a website called evolution news and views and found that Jonathan has not removed the post about the pseudogene. http://www.evolutionnews.org/2013/08/a_simple_propos075721.html
    Why would he leave work on the internet that has been so thoroughly discredited? I mean, leaving this up there seems worse than deleting the facebook thread,as people are going to read it and believe that it has scientific value.
    I also realize now I've been a little naive about the turf war going on between these opposing websites.... hmmmmm.... I understand better why it seems so hard for Jonathan to face his critics.

    ReplyDelete
  12. "Why would he leave work on the internet that has been so thoroughly discredited?"

    Because he has no scruples and neither does anyone else at ENV. The least mclatchie should do is post a firm but humble, no nonsense retraction and apology on the SAME pages at ENV as the original article and his subsequent article, and he should do the same at the Glasgow Skeptics site and here, with specific apologies to the people he falsely accused and blocked.

    "...I understand better why it seems so hard for Jonathan to face his critics."

    He wouldn't have to be so afraid of facing his critics if he were open and honest about his non-scientific, creationist agenda (and everything else), and if he would educate himself and actually do something in the scientific field of biology before arrogantly trying to pass himself as a 'competent biologist'.

    ReplyDelete
  13. From what I can gather, it takes humility to devote oneself to a significant, isolated problem and do the work required to investigate it scientifically.

    I think the "evolutionists" have a major competitive advantage over the "creationists" in terms of doing the science in the sense that they seem more humble in dealing with the data, not seeking to know or explain it all but with an incremental approach to developing knowledge about life on earth (past and present).

    That is probably why the evolutionists have built up such a large consensus in the scientific community, and I agree: the only way I can see for the creationists to make inroads is to do the science (and not the sort that always grabs the headlines).

    While another part of this blog is discussing irony, I am pondering an irony of my own - why atheistic evolutionist scientist seem for the most part more modest than their God-fearing creationist counterparts.

    In saying this I must qualify: I have a friend, with whom I've unfortunately lost contact in recent years, who is a prominent evolutionary biologist and a dynamic Christian. He is a specialist in the evolution of snakes, and a more humble person I have yet to meet.

    ReplyDelete
  14. The above comment was mine, but I had not signed in.

    I still hope Jonathan swallows his pride comes back as I would like to engage him further if he is willing.

    ReplyDelete
    Replies
    1. I would suggest taking it up with him on the centre 4 intelligent design facebook page. However, you will end up blocked and your comments will be deleted

      Delete
    2. I looked and found two separate Intelligent Design facebook pages in direct competition with each other but with the same photos being posted and in some cases the same people posting stuff - bizarre!

      The one threatens to remove all creationist comments and the other rails against pseudoscientific imbeciles. These two groups have exactly the same name. So I'm pretty confused - where do I find Jonathan?

      Delete
    3. This is the page you want. I suggest posting in the unitary pseudogene thread. That's the one we were all banned from.

      Delete
    4. @ Billy

      Thanks for pointing me in the right direction. I discovered quite a few other facebook groups while pottering around. I'll continue the conversation with Jonathan over yonder.

      Delete
    5. At least you will until that crusader for truth and defender of free speech bans you.

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    6. As of about 7 hours ago, McLatchie is STILL claiming on Centre for Intelligent Design UK that the Ensembl database is inaccurate. He doesn't accept that it was his own incompetent use of it that caused him to misinterpret it. On this blog alone, I've lost count of the number of times that it has been demonstrated beyond all doubt that Ensembl is NOT inaccurate, yet McLatchie is still parroting this. This can only be intentional, given all the preceding comments and means that he is, once again, intentionally lying through his teeth.

      Not only that, but he is making accusations against people he has blocked and booted from C4ID, me for one. I got booted for asking if he would retract his claim that Ensembl was inaccurate, yet he is claiming that I've been insulting him. I have no way to see his posts, someone I know has copied them for me, and I have no way to respond to yet more of his scurrilous and dishonest accusations.

      As far as I'm concerned, McLatchie has committed professional suicide before he's even begun his PhD. Dishonesty has no place in science and he has demonstrated he wouldn't know honesty if it bit him in the balls.

      His difficulty is that he no longer has to admit to an honest error. He now has to admit to intentionally misleading the readers at C4ID as well as defaming other scientists.

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    7. Yes, here is the recent Facebook post from Jonathan, in response to a post I made (under my real name, Faizal Ali):

      Faizal, Ensembl is a well-known database and of course I was familiar with it. And yes, that was indeed my source on the transcription of GULOP. The database does state that GULOP produces a transcript but lists no supporting evidence. That's not really the main problem with the argument advanced in the previous article in any case. I really don't appreciate you insinuating that I'm a liar. If you have a problem with the argument advanced in the article above, then please share it. Personal attacks will get us nowhere.

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    8. It will be interesting to see how your latest comment goes down. Might be worth taking a screen shot :-)

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    9. This comment has been removed by the author.

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    10. You are demonstrating once again precisely why I don't like to engage with you. But just to set the record straight...

      "This gene has 1 transcript (splice variant)" (Ensembl on GULOP).

      Can we move on to discussing arguments that I actually presently defend now?

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    11. @ Jonathan Mclatchie

      You are demonstrating once again precisely why I don't like to engage with you. But just to set the record straight...

      "This gene has 1 transcript (splice variant)" (Ensembl on GULOP).


      Yes, well, it's understandable that an uneducated layperson might be confused by that. As an uneducated layperson, myself, when it comes to molecular biology, I might also have misunderstood that. However, thanks to people like Billy and Fiona, I now understand that it is not enough to simply look for a transcript being listed, but one has to click on the "supporting evidence" tab to determine whether the sequence is actually transcribed. For the I-don't-know-how-manyth time, the ENSEMBL database does not say the pseudogene is transcribed. That is what you thought it said, because you are incompetent and ignorant regarding its correct usage.

      Can we move on to discussing arguments that I actually presently defend now?

      You mean the argument that pseudogenes might be resurrected into functional genes by RNA editing? What's to discuss? First, present some evidence that this actually occurs, and that it's not just some Biblically-induced fantasy of your faith-addled brain. Then maybe we can "discuss".

      Oh, BTW:

      Jonathan Mclatchice wrote on September 7, 2013, 3:48 PM

      "Okay, this is my final contribution to this thread."



      Who had 9 days, 15 hours, and 18 minutes in the "Jonathan McLatchie Shaker's Law" pool? Step up and collect your winnings.

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  15. "other scientists", Fiona? You're being way too generous to mclatchie. He's far from being a scientist. :)

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