Sunday, 1 September 2013

What's it all about, Alfie...?

Have you ever wondered why you bother? How often have you seen science mangled and screamed at your screen? This is my version of screaming at my screen. I've been prompted to start this blog by the latest Intelligent Design debacle involving none other than Jonathan McLatchie and his two execrable articles which deal with the GULOP gene in humans and his musings on the ability of RNA editing to resurrect pseudogene transcripts.

What has appalled me the most is the sheer incompetence and dishonesty demonstrated by his feeble retraction of his original erroneous article. Instead of accepting that he messed up and didn't have a clue what he was writing about, he chose instead to blame the ENSEMBL database, claiming it was inaccurate. That it is in fact accurate is blindingly obvious to anyone with even a basic ability to use it. Still, any port in a storm, as they say.

The really sad thing about this whole fiasco is that the Discovery Institute tweeted his original article as "new evidence". Even a cursory glance by a moderately competent molecular biologist would have exposed the fundamental flaws so why didn't the Discovery Institute notice this? You can supply your own answer as you see fit.

To make matters worse, the Centre for Intelligent Design UK Facebook page has now started removing any comments which draw attention to this false accusation against the ENSEMBL database, while still linking to the feeble retraction containing the accusation. They are also blocking those critical of either the articles or the subsequent cover up attempts. All of this could have been avoided if, in response to criticism of the original article, Mr McLatchie had said "Yup, I got it wrong. I retract the article. Sorry folks." Instead his squirming attempts at face-saving have done him and his ID masters no favours whatsoever.


  1. The really annoying part is that they are told about these problems but ignore until backed into a corner. Actual scientists comment in areas of their specialism, but are met with complaints that they don't take the IDists seriously. And the reason is ... they (the IDists) are not serious scientists. Real scientists work for decades, publishing their research in peer reviewed journals, speaking at scientific conferences, usually for little monetary reward - IDists try to take shortcuts and want a reputation for which they haven't worked.

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  3. Edited:

    You've just pointed out the difference between real scientists and those who speak about science. As the saying goes:

    “Science: If you don’t make mistakes, you’re doing it wrong. If you don’t correct those mistakes, you’re doing it really wrong. If you can’t accept that you’re mistaken, you’re not doing it at all.”

  4. Good luck with your new blog.

  5. I respect Fiona as a very hard working scientist and it's good to point out mistakes whenever they are made on all sides (not just one). Creationists have admitted mistakes when they made them and so have some Darwinians.

    But when Darwinians makes mistakes and admit it, other Darwinians often laud them for the their integrity. When creationists do the same thing, they are ridiculed as idiots and demeaned in every possible way by most Darwinians (with a very few exceptions). This is a very unfortunate double standard. Jonathan is a very has written an admission that he was mistaken on the above...but of course still gets inhumanely ridiculed just for making a mistakes, which happens to ALL scientists.

    Jonathan McLatchie holds an honors degree in Forensic Biology and is currently working on a Masters degree in Evolutionary Biology. He has solid scientific training, but not a Ph.D. yet. He had some serious science questions to ask of P.Z. Meyers, but about all he got was hedging, non answers and he and other IDers were falsely smeared and misrepresented (see:

    But, Jonathan Mclatchie has written a admission of error/retraction of his article on the GULOP gene, like other objective creationists and Darwinians have done when they've made mistakes. Jonathan wrote:
    For the record, I always respond to criticisms of my work (as anyone who follows my writing should know). If I have made a mistake (as is the case here), I am happy to concede the correction. I read all critiques of my work that come to my attention. I am more interested in getting at the truth than I am in winning an argument. It's certainly not a habitual practice on my end to make mistakes like this... I'm usually more thorough

    Laurence A. Moran wrote:So, what's your current position on whether the human GULOP pseudogene could produce a functional enzyme during early development? Do you agree that it's impossible?

    Jonathan Mclatchie wrote:
    Yes, I think it is extremely unlikely.
    And yes, I will be posting something to that effect.

    Jonathan Mclatchie wrote:
    I find it rather interesting, incidentally, that PZ Myers ignores what I write 99% of the time and virtually the only time he decides to engage with something I wrote is when I actually made a legitimate mistake.

    I had done extensive reading on RNA editing (which I still think could have important significance regarding unitary pseudogenes -- to be covered in a forthcoming article) but I hadn't been thorough enough with my reading regarding GULO. In any case, I am glad for the opportunity to be able to learn from this mistake...

    1. Typo above. Should be "Jonathan has written an admission..."

  6. Darwinians have a VERY large number of major mistakes still being printed in modern biology textbooks that everyone knows are wrong. Stephen Gould even lamented that there are many mistakes in Darwinian textbooks being taught as fact. Very unfortunate.

    Here are scans of modern biology textbooks promoting Haeckel's fraudulent embryo drawings STILL, and they have been known to be frauds for many decades.

    Dr. Prothero has some personal experience with promoting "fakery": he has reprinted Haeckel's embryo drawings in his textbooks for the express purpose of promoting evolution -- the very same drawings that have been called "fakes" and "fraudulent" by leading evolutionary scientists.

    At that time, I referred to one example from a textbook published in 1994 by Prothero and Robert H. Dott, which I used for an evolution course during my freshman year in college. Since this past January, I've discovered more examples of Prothero's textbooks that use Haeckel's drawings. Recently I had occasion to look through Prothero's 1998 textbook Bringing Fossils to Life, which I used later in my undergraduate and graduate studies of paleontology. Here is Haeckel's embryo drawings in Prothero's 1998 textbook, p. 18:

    ...there are textbooks still more recent than Prothero's that reprint Haeckel's embryo drawings -- for example, 2010 and 2011 texts by Sylvia Mader - See more at:

  7. Just a small suggestion for all. If you use different standards to judge people with views you like and those you don't like, you aren't really doing anything objective or rational at all. That's just not a way to find truth. Using double standards can literally "prove" Pinocchio real and "prove" Lincoln fictional. Literally. Using double standards, has never and will never be a way to find truth and be fair to all views. There are people in every view who have made mistakes. Some are more objective like Jonathan and admit them. Some are less so and never admit them until they die.

    Unfortunately Max Planck was right that sometimes:
    "A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it."

    “Nothing is easier than self-deceit. For what each man wishes, that he also believes to be true.” DEMOSTHENES

    That's true for every single person on the planet. But, those who are objective will use the same standards for all views. And a really good way to check and see if a person has this objectivity is simple. Can they recognize that views they don't agree with have evidence, using the normal objective methods of science. If they can, it's a lot more likely that they are reasoning objectively (since many if not most major controversies in science, history and other areas have legitimate evidence on both sides). The issue of course is which theory has the MOST and BEST evidence. There people can differ with integrity. But, if a person denies that rival views have evidence, that's a red flag that they are not willing to reason objectively.

  8. Bryan, It would very helpful to remain on topic, and I will try to do this here. This blog is specifically dealing with Jonathan's GULO hypothesis and whether he has admitted to be in error, where it really counts; and that is in association to the origianl publication of his "hypothesis" in the Evolution and Views website. While he has admitted that he was in error in the comments sections of various Facebook threads and blogs (as you have pointed out), this is what he wrote for the Evolution and Views website linked to the original article:

    "In 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."

    Now Bryan, when you read this "retraction" would you say that he is admitting that he was in error, or would you say that he is saying that the Ensembl Genome Database is in error? What is your opinion? Now the problem is that people reading the original article will believe that it was not him that was in error, but the Ensembl Genome Database that was in error. Would you say that this amounts to admitting his own error to the readership of the original article? If not, would you consider this an honest or dishonest move? I would be very happy to hear your objective reply. Thanks.

    1. If you read what he writes, he is saying that there are errors in Ensembl that caused his mistakes. Are you going to argue that Ensembl is infallible?

      Jonathan clearly admits errors on blogs and here says, "While my original hypothesis is probably incorrect with respect to this particular pseudogene...". I would prefer that he word the admission of wrong more strongly...but he seems to be hoping that more research will possibly vindicate his hypothesis at some point, which is not totally unreasonable. But, he should have apologized more strongly for this error I think. This does NOT justify his error at all, and it's good it was found and corrected, but countless Darwinians have not owned up to their numerous mistakes and are still using serious scientific errors that have been known to be errors for many decades:
      Here are scans of modern biology textbooks including Haeckel's frauds:

      Texas Reviewers Reject Accurate Evolution Curriculum Because It "Contradicts Biology Textbooks"...

      More examples:

      This is only one of MANY known false concepts in science that have been used in textbooks in very recent times and many continue to be used wrongly and it's known, Enrique.

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  10. Perhaps it might be important to mention that the Ensembl Genome Database is NOT in error. The clear problem was with Jonathan's ability to use and interpret the Ensembl database. The databse correctly assigns the hypothetical exons in the GULO pseudogene, and furthermore, it shows that the upstream exons and promoter required to make a functional protein are lacking in the GULO pseudogene. It also clearly shows that there is no evidence that this pseudogene is transcribed. All the data was there for Jonathan to see and ponder from the start. Had he known how to use and interpret the database correctly, he would have been able to see from the outset that his "hypothesis" of gene editing, as a mechanism for recovering function for the GULO pseudogene, was a non-starter. I and others were pleased when he appeared to admit his error (which was pointed out by others, rather than he recognizing it on his own), but then we were very disappointed that, when he came short of admitting his error publicly on the Evolution and Views website, alongside the original article. As you can see above, he blamed the Ensembl database rather than himself. I admit that I was totally speechless when I saw that....

    1. Well, I am not an expert in Ensembl, but you're quite likely right that he made a mistake in using/interpreting the database. That would seem to be confirmed by Moran on the sandwalk blog agreeing that Jonathan Wells wrote about it correctly in "The Myth of JunkDNA" (that's a book which you really should get by the way..very well done and I learned a lot from it although it's fairly technical in parts.). And again I wish his retraction on EV site was more like the ones he wrote on the blogs.

      I have no problem admitting that creationists make mistakes at times. They do. And this big to-do with Darwinians making this big to do about an innocent mistake, when they sweep thousands of similar and worse mistakes of their own under the rug all the time, is a bit comical to be frank.

      Nobody has ever claimed that creationists are infallible (except some very misguided atheists and Darwinians). They do make mistakes at times, and it's not a crime. It happens to all scientists, including Darwinians, since to err is human.

      But, are you willing to recognize these and many other far more egregious mistakes (since they're by someone with a Ph.D., a long time professor, an author and someone responsible to convey correct knowledge to the public):

      I listened to Dawkins and heard him say while reading his book on youtube that there are only 6 Christian who have won Nobel prizes.

      This is outrageously false. See:

      Here's another case of just rivers of lies by Dawkins on so many topics (even other atheists are embarrassed by his really bad ethics and absurdly irrational and untrue representations of Christianity in so many areas):

      Richard Dawkins Lies About William Lane Craig AND Christianity again:

    2. These are not just innocent lies, they are are extremely unethical lies that have robbed many, many people of many benefits in life. How? They caused people to reject following the habits of religion. And these habits of religion directly bring many benefits to life in many areas, not to mention the reality of eternal life.

      This site lists numerous benefits from Christianity/religion that people often lose when they follow atheism. There are ~150 references, many peer reviewed and secular.

      I have many more besides these on my sites such as this one (which shows that morality is vastly improved by Christianity and most human rights were pioneered by Christianity among many other advances Christianity gave to modern and esp. western civilization. And a lot of human rights progress was directly grounded in the concept of creation (Read the beginning of the Declaration of Independence which grounded equality in Creation by God to name just one famous example):

      Then there's the millions of lives that have been saved an 1.3 billion rescued from dire poverty in just the last 25 years in the Jubilee2000/ONE campaign that I have been personally involved in for quite a few years.

      This is one of many disastrous effects that atheism has on millions of people's lives. It robs them of much quality and quantity of life and much contribution to the lives of others, which God designed people to enjoy by following his wisdom.

      Paul wrote this in 1 Timothy 4:8:
      “Physical training is good, but training for godliness is much better, promising benefits in this life and in the life to come.”

      The historical and scientific evidence certainly shows that this has been fulfilled overwhelmingly in the areas of human rights and morality in history. And Christianity/creationism has MUCH more that it can contribute to the future, IF it is not censored and banned by atheism/Darwinism and objective science is allowed to function normally instead of the a priori fallacy of methodological naturalism. God always has many more things for us to learn and will throughout eternity as well.

  11. Bryan, once again you seem to have great difficulty staying on topic. This is not about Jonathan making a mistake (or anyone else for that matter). As you rightly point out, anyone can make mistakes. It is about properly and publicly admitting that one has made an error, particularly where it most counts. Jonathan demonstrably fell short of this, by suggesting that it was not him who was in error, but the database that he was using to back up his hypothesis that was in error. Fiona's blog highlights this, and also highlights the fact that the error was not identified by the Discovery Institute, but rather by other scientists. What does this say about the nature and strength of the peer review process within the DI? Also, what does this say about the personal integrity of Jonathan, who admits his error to those who have pointed out his error, but will not go as far as admitting his error to the very readership who, once again demonstrably, are unable to judge the quality of his work independently? These are the questions and points that Fiona is trying to highlight here. It would be very useful to limit the responses to these questions and points, rather than going off on tangents.

  12. Bryan, among other things you should read these threads, in this order: