tag:blogger.com,1999:blog-37148773.post424250599181859541..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different RatesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger40125tag:blogger.com,1999:blog-37148773.post-9504838266980823222013-10-02T19:08:05.481-04:002013-10-02T19:08:05.481-04:00Oh and just to add, the subject in question was th...Oh and just to add, the subject in question was the organisation of bacterial flagellar genes and operons.Fiona Robertsonhttps://www.blogger.com/profile/09224992345898432113noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63205647503888246422013-10-02T19:07:13.213-04:002013-10-02T19:07:13.213-04:00I got blocked by him for daring to tag Vince Mulho...I got blocked by him for daring to tag Vince Mulholland. Vince spent 20-odd years working on bacterial flagellar genes. Prior to becoming a molecular biologist I was a microbiologist. It seems that Jonathan just doesn't want comments from anyone who may bring down his house of cards. Expect Vince to be blocked pretty soon.Fiona Robertsonhttps://www.blogger.com/profile/09224992345898432113noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46897060717020665012013-10-02T18:56:32.506-04:002013-10-02T18:56:32.506-04:00Well, it's hardly surprising, But Mclatchie...Well, it's hardly surprising, But Mclatchie's at it again. I have been blocked again, as has Fiona. His <a href="https://www.facebook.com/groups/151405404861/files/" rel="nofollow">thread of shame count rises</a>. <br />Expect a dire article on operons to appear in ENV soon. Vincent Mulholland has already destroyed it, but will that stop him?Billyhttps://www.blogger.com/profile/16602020760483338822noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16690686693178650782013-09-25T11:25:21.340-04:002013-09-25T11:25:21.340-04:00Yeah, it's not the first time he's been ca...Yeah, it's not the first time he's been caught quote mining, and it wont be the last. I particularly love the one that he copied directly from Harun Yahya mentioned <a href="http://scienceblogs.com/pharyngula/2011/06/17/jonathan-maclatchie-collides-w/" rel="nofollow">here</a>.Billyhttps://www.blogger.com/profile/16602020760483338822noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60082298555441410472013-09-25T07:49:09.832-04:002013-09-25T07:49:09.832-04:00Of course. A preprint vesion can be found HEREOf course. A preprint vesion can be found <b><a href="https://files.nyu.edu/jj1006/public/papers/gc_distribution.pdf" rel="nofollow">HERE</a></b>Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32711876127388601442013-09-25T07:25:50.292-04:002013-09-25T07:25:50.292-04:00There's one other minor detail, as well. I do...There's one other minor detail, as well. I don't have access to the full paper, but it seems from the abstract they hypothesize a mechanism by which the code could have arisen thru <i>evolutionary</i> processes.<br /><br />If so, that paper does not exactly support McLatchie's hypothesis of "goddidit".Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62370774487367793052013-09-25T06:23:30.787-04:002013-09-25T06:23:30.787-04:00Mclatchie is quote mining. He leaves out the part ...Mclatchie is quote mining. He leaves out the part that says the code is suboptimal:<br /><br />http://rsif.royalsocietypublishing.org/content/10/88/20130614<br /><br />"Biochemists have long wondered: If immutability and universality were early properties (i.e. the genetic code was a “frozen accident” [3]), then how could natural selection encourage error-minimization? If selection for an error minimizing genetic code predated immutability and universality, then why is the standard code less than optimal?"<br /><br />The authors further clarify:<br /><br />"Numerous hypotheses have been proposed to reconcile this apparent paradox [3][4][5][6]. <br />It has been hypothesized that neutral evolution, for instance through proto-tRNA duplication (also termed “expansion”), could account for the code’s near optimality (though not necessarily its universality) without the need for selection [6][7]. Other models have suggested that the code’s progression might be explained entirely by selection for the best combination of genetic code and genome in a greedy fashion; however, these models are prone to premature freezing, particularly if the genome evolves rapidly [5][8]. Here we introduce an evolutionary model based on information-asymmetric games, which allow for a rich combination of both neutral evolution and selection, leading in combination to the suboptimal yet stable genetic code described above."<br /><br />Additionally, Mclatchie is trying to state that substitution by similar amino acids is not a problem:<br /><br />"I stand by what I said. Phenylalanine, like leucine, is both hydrophobic and non-polar, which means that it can often substitute for leucine without affecting protein structure and function. You can also change the C in the 5' position to an A or a G, which alters the codon to specify isoleucine and valine respectively, which also have physical and chemical properties similar to leucine."<br /><br />But such substitutions can change protein function/activity as these papers show:<br /><br />http://www.nrcresearchpress.com/doi/abs/10.1139/g02-080?journalCode=gen#.UkK214bI1VQ<br />http://www.ncbi.nlm.nih.gov/pmc/articles/PMC51992/<br />http://jvi.asm.org/content/74/2/892.abstract<br />http://www.ncbi.nlm.nih.gov/pubmed/11389142<br />http://www.malariajournal.com/content/5/1/56<br />http://www.ncbi.nlm.nih.gov/pubmed/7538206<br />http://www.ncbi.nlm.nih.gov/pubmed/8916927<br /> <br />Thus, Mclatchie's claim that the code is exquisitely fine tuned (see: http://www.evolutionnews.org/2011/11/the_finely_tuned_genetic_code052611.html) is unfounded to say the least.Anonymoushttps://www.blogger.com/profile/04852803503240037336noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38029855647719308292013-09-24T11:08:40.883-04:002013-09-24T11:08:40.883-04:00Why did I bother Reading MacLatchie's link? Le...Why did I bother Reading MacLatchie's link? Let me quote the bit after his chrry pick "Biochemists have long wondered: if immutability<br />and universality were early properties (i.e. the genetic code was a ‘frozen accident’<br />[3]), then how could natural selection encourage error minimization?<br />If selection for an error-minimizing genetic code predated immutability and<br />universality, <b>then why is the standard code less than optimal?</b>"<br /><br />This is a side issue to him trying to re-write what was said, but it's fun to point out that a quote mine does not support what he says it does - even if it is not what he is being taken to task over.<br /><br />Also notice the word's I've made bold in MacLachie's quote:<br /><br />"The genetic code, the mapping of nucleic acid codons to amino acids via a set of tRNA and aminoacylation machinery, is near-universal and <b>near-</b>immutable. In addition, the code is also <b>near</b>-optimal in terms of error minimization, i.e. tRNAs recognizing similar codons may be mistaken for each other during translation, yet these mistakes <b>often</b> have no negative impact on translation because similar codons map to identical amino acids or ones with similar physiochemical properties."<br /><br />Of course, whe have already shown there are lots of exceptions to this, and substituting with similar aminoacids can severely affect function.<br /><br />He is also citing folk citing other work and not the evidence itself - effectively quotemining an argument from authority out or context.<br /><br />Anyway, let's not let him off the hook for his other crimesBillyhttps://www.blogger.com/profile/16602020760483338822noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-39011017836568305192013-09-24T10:41:47.107-04:002013-09-24T10:41:47.107-04:00Absolutely lutesuite.
It's a turn of phrase th...Absolutely lutesuite.<br />It's a turn of phrase that he'll understand to mean pretty much as you described :-)<br />Billyhttps://www.blogger.com/profile/16602020760483338822noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-83057768599401003612013-09-24T10:36:01.933-04:002013-09-24T10:36:01.933-04:00@ Billy
1: the database says there is no supporti...@ Billy<br /><br /><i>1: the database says there is no supporting evidence. It really does, and Fiona has clearly pointed this out to you. Who do you think you are convincing here?</i><br /><br />If I may, since we're hardly likely to get an honest answer from Habitual Liar for Jesus Jonathan McLatchie: He's not trying to convince anyone here. He just has to convince his fellow sycophantic IDiots at ENV (where no comments are allowed), few if any of whom will be privy to the present discussion. And what he is trying to convince them of is that his embarassing gaffe was not the result of his own laziness in failing to confirm whether GULOP was even transcribed, or his own incompetence in not knowing how to use the database that could have provided him with that information. Rather, he wants to create the impression that his error was not his fault, but that of the database which he claims is misleading and inaccurate. IOW, he want them to continue to believe he is an honest and competent scientist, and not an ignorant, incompetent, Habitual Liar for Jesus. <br /><br />Close to the mark, McLatchie?Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24823622772137501462013-09-24T09:52:34.756-04:002013-09-24T09:52:34.756-04:00@lutesuite
So you're back, McLatchie, to make...@lutesuite<br /><i><br />So you're back, McLatchie, to make more comments after what you yet again promised would be your "last comment."</i><br /><br />"Just the place for a Snark!" the Bellman cried,<br />As he landed his crew with care;<br />Supporting each man on the top of the tide<br />By a finger entwined in his hair.<br />"Just the place for a Snark! I have said it twice:<br />That alone should encourage the crew.<br />Just the place for a Snark! I have said it thrice:<br />What I tell you three times is true."steve oberskihttps://www.blogger.com/profile/14067724166134333068noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19021929319316624492013-09-24T09:29:54.363-04:002013-09-24T09:29:54.363-04:00"I lost interest in this discussion long ago....<i>"I lost interest in this discussion long ago. It has no relevance to any argument I currently defend"</i><br /><br />A couple of points here:<br /><br />1: the database says there is <b>no</b> supporting evidence. It really does, and Fiona has clearly pointed this out to you. Who do you think you are convincing here?<br /><br />2: The issue is now that you are lying about my understanding of the database!<br /><br />I can only echo Diogenes with resp[ect to what you actually said in your own quote. You are being dishonest again, and I am happy to have this exposed in as many places as possible<br />Billyhttps://www.blogger.com/profile/16602020760483338822noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62433545635390699262013-09-24T09:17:15.760-04:002013-09-24T09:17:15.760-04:00BTW, McLatchie, when you come back you really need...BTW, McLatchie, when you come back you really need to address this:<br /><br /><i>Billy wrote:<br /><br />Folk may be interested in this. McLatchie is now going about saying I didn't know how to use the database. This guy is far along the path to the darkside</i><br /><br />Do you have any explanation for this blatant lie you are spreading regarding someone who actually educated <i>you</i> on how to use the database?Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17916221795632363382013-09-24T07:10:34.465-04:002013-09-24T07:10:34.465-04:00So you're back, McLatchie, to make more commen...So you're back, McLatchie, to make more comments after what you yet again promised would be your "last comment." Is it possible for you to even open your mouth without a stream of lies spewing out? Not to say we don't like having you around, of course.<br /><br />Let me attempt to explain this to you in a childishly simple manner, so maybe you have at least a chance of understanding. I assume you know what "books" are, correct? And that some of these bigger books, generally long ones with big complicated words, have what are called "indexes." You are familiar with that as well, right?<br /><br />Well, now, let suppose you read the "index" of one of these "books" and find an entry that reads:<br /><br /><i>Loch Ness Monster, 123</i><br /><br />Now, suppose there is someone who understands how the "index" of a "book" is supposed to be used. She goes to p.123 and finds the following passage: "There is no evidence that the Loch Ness Monster exists."<br /><br />However, let's imagine another person who does <i>not</i> know how "books" and "indexes" are supposed to be used, because he is an ignorant, incompetent, idiot. He just sees the entry listing "Loch Ness Monster" then goes on the internet to say that the Loch Ness Monster exists, because this book says it does.<br /><br />Now, is this person's claim correct? <i>Does</i> the book say that? And suppose other people on the internet then pointed out his error and, rather than acknowledging his error, he deleted their comments and went on to say the book was to blame for his error because it was "misleading." Would he be speaking truthfully? Would be be correct? Or would he just be further confirming that he is either ignorant, incompetent or a liar, if not some combination of all three?<br /><br />Now, if you do not understand how this applies to your actions here, I'm happy to explain that for you, as well. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40665205818684086782013-09-24T07:01:48.603-04:002013-09-24T07:01:48.603-04:00What IS surprising is that a passage like this dem...<i>What IS surprising is that a passage like this demonstrates that the book was not reviewed by anyone who is knowledgeable about the field.</i><br /><br />How could they have gotten anyone truly knowledgeable who (1) would want to review the book in order to help prepare it for publication, and (2) would have left enough of the text post-review to publish?judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65056400031097917372013-09-24T06:02:23.727-04:002013-09-24T06:02:23.727-04:00McLatchie: "I lost interest in this discussio...McLatchie: <i>"I lost interest in this discussion long ago. It has no relevance to any argument I currently defend."</i><br /><br />We don't care what YOU are interested in! <br /><br />You banned four people from your website, and insulted them and personally attacked them! You don't care about that-- so what? Why should we care about what you care about?<br /><br />The ENSEMBL database entry said "Transcript not found" and you blamed it for your error. <br /><br />Everybody makes mistakes, but if you try to shift the responsibility off on others, and then <b>ban and insult and personally attack and misrepresent the people who taught you how to read the database,</b> it's not the error that bugs us. It's the dishonesty.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31777069534682543552013-09-24T05:59:29.781-04:002013-09-24T05:59:29.781-04:00NO McLatchie, NO. That is not what you wrote. Not ...<b>NO McLatchie, NO. That is not what you wrote.</b> Not ONE of the papers you cited in any way demonstrates the idiotic point you made!<br /><br />I asked you to copy and paste your actual words here, and defend them-- or take them back. You wouldn't-- you pussied out. You won't even copy your own words!<br /><br />So I have to.<br /><br />McLatchie wrote: <i>""Indeed, the genetic code found in nature is exquisitely tuned to protect the cell from the detrimental effects of substitution mutations. The system is so brilliantly set up that <b>codons differing by only a single base either specify the same amino acid, or an amino acid that is a member of a related chemical group."</b></i><br /><br />That sir, is a stupid thing to say.<br /><br />You have attempted to neuralyze us, Casey Luskin-style, and make us believe you said something else altogether-- that the genetic code was optimized.<br /><br />If you had said the genetic code was optimized, there would have been no controversy. But<br /><br /><b>NO. That is not what you wrote. Do not try to trick us into re-writing our memories-- it's insulting to our intelligence.</b><br />Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-598030457899260912013-09-24T05:30:24.595-04:002013-09-24T05:30:24.595-04:00>>>"Folk may also be interested in k...>>>"Folk may also be interested in knowing that he is repeating his claim that it's all the fault of the Ensembl database for being inaccurate/misleading in saying that GULOP has a transcript. This was thoroughly hashed out in a previous blog's comments section and it beggars belief that he is STILL making this claim."<<<<br /><br />I lost interest in this discussion long ago. It has no relevance to any argument I currently defend.<br /><br />Ensembl states clearly with respect to GULOP in humans, "This gene has 1 transcript (splice variant)." This, however, is not confirmed. At best, it is rather misleading.<br /><br />I'm not really interested in having this discussion anymore frankly. It's such a trivial matter with no relevance to any of the questions I'm interested in.Jonathan McLatchiehttps://www.blogger.com/profile/17106574852680885766noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32368201696452659652013-09-24T05:24:39.862-04:002013-09-24T05:24:39.862-04:00>>>"In short, even with a certain le...>>>"In short, even with a certain level of redundancy, any claim that the genetic code is "exquisitely tuned" to protect from detrimental effects does not stand up to an even casual analysis of the facts."<<<<br /><br />Is that why a paper just came out attempting to explain this feature of the genetic code? http://rsif.royalsocietypublishing.org/content/10/88/20130614<br /><br />From the paper,<br /><br />"The genetic code, the mapping of nucleic acid codons to amino acids via a set of tRNA and aminoacylation machinery, is near-universal and near-immutable. In addition, the code is also near-optimal in terms of error minimization, i.e. tRNAs recognizing similar codons may be mistaken for each other during translation, yet these mistakes often have no negative impact on translation because similar codons map to identical amino acids or ones with similar physiochemical properties."<br /><br />I also cited two papers above that make the very same point. How about another one? http://genome.cshlp.org/content/17/4/401.full<br /><br />"Other striking properties of the code that seem far from random were revealed. Woese observed that similar codons are assigned to amino acids with similar chemical properties, most notably, similar polar requirement (Woese 1965b; Woese et al. 1966a). He proposed that the code is optimized for minimizing the impact of mistranslation errors. These errors occur when a codon is translated via a tRNA with a near cognate anticodon. The finding that the genetic code is optimized with respect to minimizing the impact of translational misread errors was statistically quantified by Haig and Hurst (1991) and further strengthened by taking into account biased mistranslation and mutation (Freeland and Hurst 1998)."Jonathan McLatchiehttps://www.blogger.com/profile/17106574852680885766noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53569332577579528262013-09-23T02:46:21.128-04:002013-09-23T02:46:21.128-04:00Or that locusts use four legs for walking.
http:/...Or that locusts use four legs for walking.<br /><br />http://jeb.biologists.org/content/58/1/45.full.pdfPiotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55253811032075610392013-09-22T23:23:48.868-04:002013-09-22T23:23:48.868-04:00Well, robert? Let's see the scientific, biolog...Well, robert? Let's see the scientific, biological evidence! You do have and can show the evidence, right? I'd hate to think that you believe in all of that fairy tale stuff on a "hunch". The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17266053166858561032013-09-22T23:02:37.053-04:002013-09-22T23:02:37.053-04:00byers said:
"I don't mean a good hunch b...byers said:<br /><br />"I don't mean a good hunch but SCIENTIFIC evidence worthy to persuade creationists who are told SCIENCE is being done about evolutionary conclusions.??"<br /><br />That the scientific evidence doesn't persuade you and other creationists just shows that creationists choose to believe fairy tales over reality. Your willful ignorance and distortions regarding scientific methods and evidence is certainly worthy to persuade rational people that you are just plain nuts. <br /><br />You constantly assert that scientists do not use scientific methods and evidence, and especially <b>biological</b> methods and evidence, to study biological evolution. You're wrong. WAY wrong. Many thousands of previous and ongoing scientific studies show just how wrong you are. <br /><br />Since scientific, biological methods and evidence matters so much to you, robert, let's see your <b>scientific, biological methods and evidence</b> that supports or better yet verifies anything in the bible. For instance, let's see your scientific, biological methods and evidence that supports or better yet verifies that goats and sheep produce striped and/or spotted offspring by mating while looking at striped sticks. <br />The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23981428079234082522013-09-22T20:41:37.830-04:002013-09-22T20:41:37.830-04:00Folk may also be interested in knowing that he is ...Folk may also be interested in knowing that he is repeating his claim that it's all the fault of the Ensembl database for being inaccurate/misleading in saying that GULOP has a transcript. This was thoroughly hashed out in a previous blog's comments section and it beggars belief that he is STILL making this claim.Fiona Robertsonhttps://www.blogger.com/profile/09224992345898432113noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-967629149208507772013-09-22T20:25:52.188-04:002013-09-22T20:25:52.188-04:00Folk may be interested in this. McLatchie is now ...Folk may be interested in <a href="https://www.facebook.com/groups/151405404861/permalink/10151712109794862/" rel="nofollow"> this</a>. McLatchie is now going about saying I didn't know how to use the database. This guy is far along the path to the darkside Billyhttps://www.blogger.com/profile/16602020760483338822noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62109259765947772472013-09-22T15:21:36.035-04:002013-09-22T15:21:36.035-04:00http://www.sciencemag.org/content/341/6152/1344.1....http://www.sciencemag.org/content/341/6152/1344.1.full<br />Review in Science . Seems FREE!heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.com