tag:blogger.com,1999:blog-37148773.post5906184370410706113..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The Central Dogma StrawmanLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger76125tag:blogger.com,1999:blog-37148773.post-20731046422509433692011-06-15T15:10:56.219-04:002011-06-15T15:10:56.219-04:00@Louis,
I don't understand why you think that...@Louis,<br /><br />I don't understand why you think that nucleic acid binding proteins or nucleases are violations of the correct Central Dogma of Molecular Biology.<br /><br />Why is that any different than, say, DNA polymerase, that was known when Crick first formulated the Central Dogma? When we talk about "information" we are not talking about enzymatic activity.<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40921042025601996572011-06-15T14:52:47.878-04:002011-06-15T14:52:47.878-04:00I keep hearing about "splicing regulatory net...I keep hearing about "splicing regulatory networks" from fellow grad students studying splicing, and I believe that the existence of specific splicing factor isoforms regulating specific splicing/editing events has been found and published. This demonstrates the flow of information from nucleic acid to protein, and back to nucleic acid. Thus I think this directly (as opposed to indirect arguments where evolution requires protein function to alter nucleic acid sequences) contradicts the "correct" statement of the central dogma, that information placed proteins cannot return to nucleic acids. Just my two cents.Louisnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18452543242871695802011-06-09T23:57:00.733-04:002011-06-09T23:57:00.733-04:00@ Jud
I'm trying to stay away from the comment...@ Jud<br />I'm trying to stay away from the comments in the Nature Hype Machine articles. The paper itself is everything that I think is wrong in all this next-gen, high throughput data analysis. "My method is perfect, so all things I see are real biological events". <br /><br />I think your "more than a little" is quite an understatement. <br /><br />/TheOtherJimAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31639256905724486282011-06-09T13:24:48.789-04:002011-06-09T13:24:48.789-04:00The other Jim writes:
Isn't 15 single base ev...The other Jim writes:<br /><br /><i>Isn't 15 single base events in hundreds of complete human genomes is a bit of a stretch to call "widespread"?</i><br /><br />As I commented above, "there is more than a little dispute about whether they [the 'hitherto unknown RNA editing mechanisms'] even exist."Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24657761751742043462011-06-09T09:33:04.490-04:002011-06-09T09:33:04.490-04:00My apologies for interrupting this lovely "de...My apologies for interrupting this lovely "debate" and trying to discuss the science. <br /><br />Has anyone actually read the referred to Li et al. paper (doi 10.1126/science.1207018)? <br /><br />Doesn't it seem like they are reporting 15 interesting events where the RNA and protein don't match the DNA. But the rest looks suspiciously like RNA polymerase errors, compounded by RT-PCR errors, compounded with short-read sequence and bioinformatic errors? And finally followed up with the human inability to tell what "random" actually looks like? To call these events true RNA editing occurrences is a bit premature, isn't it? <br /><br />Isn't 15 single base events in hundreds of complete human genomes is a bit of a stretch to call "widespread"?<br /><br />/TheOtherJim<br />(Having a problem with my Account...sorry for the Anonymous post).Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86176492649973819012011-06-07T14:08:45.775-04:002011-06-07T14:08:45.775-04:00Is everyone going to continue to pretend?
The cal...Is everyone going to continue to pretend? <br />The calculation is misconceived because it divides RNA by DNA and then claims the result is a percentage of the genome. <br />That is a misconception. <br />People can try excuse after excuse if you wish. <br /><br />By the way this misconception applies to other percentages Moran has calculated.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10363545569956556242011-06-07T13:28:20.980-04:002011-06-07T13:28:20.980-04:00I wrote of Dr. Moran's ballpark calculation:
...I wrote of Dr. Moran's ballpark calculation:<br /><br /><i>No, it's not misconceived.</i><br /><br />Anonymous responded:<br /><br /><i>Jud recognizes that the calculation is misconceived and not simply an arithmetic error.</i><br /><br />OK, that certainly clears up a lot. Whenever you read something, you think it says the precise opposite of the actual meaning.Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15775369784129616432011-06-07T10:31:52.734-04:002011-06-07T10:31:52.734-04:00To clarify a sentence from my last comment:
whate...To clarify a sentence from my last comment:<br /><br /><i>whatever the variation in the </i>[DNA-to-RNA]<i> ratio, </i><b>the resulting difference in the amount of DNA that would be used to make the guide RNAs is</b><i> so small - some fraction of .13% - as to be utterly insignificant.</i>Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57860971499916810472011-06-07T10:05:33.009-04:002011-06-07T10:05:33.009-04:00Jud recognizes that the calculation is misconceive...Jud recognizes that the calculation is <i>misconceived</i> and not simply an arithmetic error. That is good. <br />Does everyone see that now? <br /><br />But go ahead and pretend you saw that from the beginning. (If so, why did nobody admit it then).<br />What a laugh you folks are. <br /><br />And nobody has yet acknowledged that a prof specializing in this field should not misconceive such a calculation in the fist place. <br /><br />And by the way this misconception applies to other percentages Moran has calculated. Will anyone admit that?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44008384231489484912011-06-06T22:15:00.917-04:002011-06-06T22:15:00.917-04:00Anonymous writes:
The point I am making about Mor...Anonymous writes:<br /><br /><i>The point I am making about Moran's calculation of the .13% is that it is misconceived.</i><br /><br />Oh, you had a point (you thought)?<br /><br />No, it's not misconceived. It's a ballpark estimate, with overly generous allowances for most of the factors, showing that within any conceivable magnitude of variation, the DNA that would ostensibly make all these guide RNAs doesn't amount to a pimple on the butt of the total genome.<br /><br />As you yourself quoted and bolded repeatedly, these are "hitherto unknown mechanisms;" and there is more than a little dispute about whether they even exist. Then you quibble about the amount of DNA it takes to make 4.1 million nucleotides of RNA. The reasons the rest of us aren't bothering are (1) it was a proof-of-concept ballpark calculation; (2) because of #1, it's impossible to be certain exactly what the DNA-to-RNA ratio would be; and (3) whatever the variation in the ratio, it's so small - some fraction of .13% - as to be utterly insignificant.<br /><br />That much was obvious to the rest of us from the beginning. Your obsessive concentration on this insignificant item can only be attributed to insincerity - you knew it made no material difference, but you decided to try to make a big deal of it anyway - or such complete lack of understanding as I've never seen in the comments on this blog before.Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53069390795375455882011-06-06T19:52:38.667-04:002011-06-06T19:52:38.667-04:00Anonymous had time to respond to a later comment, ...Anonymous had time to respond to a later comment, but not my earlier question:<br /><br />"Please do clue us in regarding what linguistic or scientific usage equates 'required to produce' with 'spliced out.'"<br /><br />We're waiting....Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24756492711546118652011-06-06T19:39:14.764-04:002011-06-06T19:39:14.764-04:00The point I am making about Moran's calculatio...The point I am making about Moran's calculation of the .13% is that it is <i>misconceived.</i><br />That might be okay in a high school student but not so good in a prof who specializes in exactly this subject. <br /><br />But no doubt there will excuses. There always are.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60958032506058386122011-06-06T19:17:41.052-04:002011-06-06T19:17:41.052-04:00@Anon
One, gRNA doesn't have introns you dolt ...@Anon<br />One, gRNA doesn't have introns you dolt there average length is only 20bp long. Two, what the hell was the point of all this? The 0.13 estimate was already extremely generous and even if we assume the amount of gRNA is double, triple or quadruple that it has no significant effect on the estimates of junk DNA within the human genome. It's like you've come dead last in a marathon and are squabbling with the officials about whether you finished at time fifteen hours and ten minutes or fifteen hours and nine minutes.Boojumnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35232744609991319072011-06-06T19:06:57.995-04:002011-06-06T19:06:57.995-04:00Anonymous (aka Anus., the IDiot),
Take into consi...Anonymous (aka Anus., the IDiot),<br /><br /><i>Take into consideration that the DNA contains introns which are spliced out.</i><br /><br />No IDiot, the DNA "introns" are not spliced out. The introns in RNA are. (Since you like playing games with semantics you got what you deserve.)<br /><br /><i>So the DNA required would be just under double, it would seem.</i><br /><br />It does not matter that the DNA for 4,100,000 nucleotide RNA is "double." The 0.13% is calculated for the length of DNA you imbecile, not counting but one strand.<br /><br />So, that RNA is one strand and DNA is two is not an issue. Your lack of intelligence for anything but rhetorical stupidity is.<br /><br />I can't believe how much of an imbecile can a creationist be.<br /><br />Can we all ignore this utter imbecile now? Can we ban the imbecile or do we need any more examples of the levels of stupidity attainable through creationism? I am truly just asking. If this display of imbecility is fun for you to witness, or tolerable, then I said nothing.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54597064913879795542011-06-06T14:51:17.946-04:002011-06-06T14:51:17.946-04:00http://en.wikipedia.org/wiki/Intron
"An intro...http://en.wikipedia.org/wiki/Intron<br />"An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene.[1][2] The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts."Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29088161013634394622011-06-06T13:39:41.790-04:002011-06-06T13:39:41.790-04:00@ Anonymous Monday, June 06, 2011 11:52:00 AM
If ...@ Anonymous Monday, June 06, 2011 11:52:00 AM<br /><br />If I were a pedantic ass like other Anonymous posters, I would point out that DNA does not have introns... RNA does... ;-)<br /><br />Honestly, this is the depth of your contribution to the discussion.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27747983354745292802011-06-06T13:21:00.266-04:002011-06-06T13:21:00.266-04:00I would look to you to tell us how much DNA is req...<i>I would look to you to tell us how much DNA is required to produce 4,100,000 bp of guide RNA.</i><br /><br /><i>Take into consideration that the DNA contains introns which are spliced out.</i><br /><br /><i>So the DNA required would be just under double, it would seem.</i><br /><br /><br />Please do clue us in regarding what linguistic or scientific usage equates "required to produce" with "spliced out."Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33604745838321215032011-06-06T11:52:36.550-04:002011-06-06T11:52:36.550-04:00Moran this is not an ID issue. It is an evolution ...Moran this is not an ID issue. It is an evolution issue. <br /><br />I would look to you to tell us how much DNA is required to produce 4,100,000 bp of guide RNA.<br /><br />Take into consideration that the DNA contains introns which are spliced out. <br />So the DNA required would be just under double, it would seem.<br />On this specific question you really can contribute.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73415018511311855092011-06-06T10:45:46.549-04:002011-06-06T10:45:46.549-04:00anonymous says,
We still have not calculated the ...anonymous says,<br /><br /><i>We still have not calculated the correct value. It is of course not .13%.</i><br /><br />Please don't keep us in suspense any longer.<br /><br />What value does Intelligent Design Creationism predict?<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28772484053640405622011-06-05T22:27:30.160-04:002011-06-05T22:27:30.160-04:00Now that people's thinking has been corrected ...Now that people's thinking has been corrected about this calculation*, we can look at the question concerning introns that is posted here:<br />http://sandwalk.blogspot.com/2011/05/whats-in-your-genome.html?showComment=1307215457419#comment-c7407141412117820523<br /><br />* We still have not calculated the correct value. It is of course not .13%.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74766094982483352742011-06-05T19:03:35.926-04:002011-06-05T19:03:35.926-04:00Anonymous writes:
For this to be a valid calculat...Anonymous writes:<br /><br /><i>For this to be a valid calculation of genome percentage, the units must be both DNA units.</i><br /><br />No! You don't say! What are "both DNA units"?<br /><br />Oh, you mean they must both be DNA units.<br /><br />Glad I could help you with your English grammar skills in return for you showing me how to do math!Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45907979708289089962011-06-05T17:45:30.193-04:002011-06-05T17:45:30.193-04:00Dr. Moran writes:
There are several possible scen...Dr. Moran writes:<br /><br /><i>There are several possible scenarios that would require more DNA (e.g. promoters, secondary structure, multiple copies of guide RNA genes) but none of them makes much of a difference.</i><br /><br />Thanks for the correction.Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54928892014511457902011-06-05T17:35:06.112-04:002011-06-05T17:35:06.112-04:00Moran posted:
"There are 20,500 protein-encod...Moran posted:<br />"There are 20,500 protein-encoding genes in our genome. That means a (generous) total of 20,500 X 200 = 4,100,000 bp of guide RNA. The DNA for all these guide RNAs would make up 0.13% of the genome."<br /><br />The .13% was calculated by dividing 4,100,000 bp of guide <b>RNA</b> by 3,200,000,000 bp of <b>DNA. </b><br />Note the RNA in the numerator and the DNA in the denominator. <br /><br />For this to be a valid calculation <b>of genome percentage,</b> the units must be both <b>DNA </b>units. <br /><br />So the first question is how much DNA bp are required to produce 4,100,000 bp of guide RNA? <br />Then divide that number by 3,200,000,000. <br /><br />That is how to calculate a valid percentage of genome. <br /><br />Is there someone here who did not realize this or is everybody just pretending? <br />And spare us the excuses. <br /><br />If you are going to calculate to two decimal places at least know what you are doing.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44547003223308527572011-06-05T16:56:05.898-04:002011-06-05T16:56:05.898-04:00anonymous says,
So you are saying that 4,100,000 ...anonymous says,<br /><br /><i>So you are saying that 4,100,000 nucleotides of guide RNA is produced from 4,100,000 nucleotides of DNA?<br />Is that it?</i><br /><br />Do you have a specific question?<br /><br />I could guess at what your problem is but it would be far more helpful if you would just tell me. <br /><br />There are several possible scenarios that would require more DNA (e.g. promoters, secondary structure, multiple copies of guide RNA genes) but none of them makes much of a difference.<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72111875177258124712011-06-05T16:28:48.440-04:002011-06-05T16:28:48.440-04:00Anonymous wrote:
Boojum, I wasn't asking you....Anonymous wrote:<br /><br /><i>Boojum, I wasn't asking you. I was asking Moran.</i><br /><br />Anonymous later wrote:<br /><br /><i>Anyone can answer this question.</i><br /><br />So you're now in charge of who gets to respond to comments on Dr. Moran's blog?<br /><br />Must you practice to be this obnoxious or does it come naturally?<br /><br />Now, since you're allowing us all to answer, let me take a shot at what I think the answer is, and someone will tell me if I'm wrong.<br /><br />A one-to-one correspondence is the <i>highest</i> DNA-to-RNA ratio possible, and thus 4.1 million base pairs of DNA (.13% of the genome) is the <i>most</i> additional DNA that would not be considered junk. RNA editing or any other mechanism that changes the guide RNA nucleotides from what's in the DNA template would reduce the amount of DNA that winds up being reflected in the structure of the guide RNAs. So as he did all through his calculation, Dr. Moran erred on the side of additional functional DNA.Judnoreply@blogger.com