tag:blogger.com,1999:blog-37148773.post2138589758808770788..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: How many proteins do humans make?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger22125tag:blogger.com,1999:blog-37148773.post-59739838503885255402015-11-21T23:41:55.983-05:002015-11-21T23:41:55.983-05:00I'm not sure this post addresses the original ...I'm not sure this post addresses the original question, which was, "How many proteins do humans make?" There are 17-18K protein coding genes. If one assumes one gene, one protein, then I guess it implies there are 17-18K proteins. But given alternative splicing, post-translational modifications, etc., there can be many proteins associated with a given protein-coding gene. In fact, some genes seem to encode 1000s of different proteins. So if there are 17-18K protein coding genes, humans make many more than this. This so far doesn't directly answer the question either but does set a lower limit. So the question stands: How many proteins do humans make? Would be curious to hear your thoughts.Anonymoushttps://www.blogger.com/profile/03261072963598618555noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7777777592894022822015-11-13T16:31:20.935-05:002015-11-13T16:31:20.935-05:00Some other interesting news:
TSRI and St. Jude Sci...Some other interesting news:<br />TSRI and St. Jude Scientists Help Launch Human Dark Proteome Initiative<br />https://darkproteome.wordpress.com/about/the-dark-proteome-animated/ <br />http://www.scripps.edu/newsandviews/i_20151116/dark_proteome.html <br />I am not sure yet what methods are they gonna use to estimate which proteins are disordered. Fernando Alemán Guillénhttps://www.blogger.com/profile/04642772262088212671noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32024811412412971012015-11-11T14:28:47.106-05:002015-11-11T14:28:47.106-05:00Thanks for the links Jim. It's good for me to ...Thanks for the links Jim. It's good for me to stay current in what is available for data.<br /><br />What I could not find though is the spatial and behavioral information needed to begin to model human cell nuclei. Behavioral information includes TF to TF interactions, as in a thread I linked to. Spatial information would show the 3D arrangement of normal uncoiled chromosomes, the "territories".<br /><br />Please let me know of any information you know of that gets into the functional details needed to model at least a portion of a nucleus. With the way information is now scattered around what is needed might already exist at a place that does not get as much news coverage. Gary Gaulinhttps://www.blogger.com/profile/10925297296758439900noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88053249458271383122015-11-10T09:55:00.461-05:002015-11-10T09:55:00.461-05:00Beau - Google "bikeshedding."Beau - Google "bikeshedding."judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53940938157264590142015-11-10T07:21:14.262-05:002015-11-10T07:21:14.262-05:00Beau:
Why aren't the scientists that read yo...Beau: <br /><br /><i>Why aren't the scientists that read your blog actually interested in the actual science? To be fair you do have a few posts that aren't science or ID that are treated the same. Why does ID drive such interest?</i><br /><br />Just as any fool can be an ID proponent, any fool can point out their errors. Peer-reviewed science is naturally less likely to attract comment, even from those in the field. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84797524921338171742015-11-10T02:24:26.402-05:002015-11-10T02:24:26.402-05:00Two or them have PubMed Central versions available...Two or them have PubMed Central versions available for free; <br /><br />Proteomics. Tissue-based map of the human proteome<br />http://www.ncbi.nlm.nih.gov/pubmed/25613900<br /><br />Analyzing the First Drafts of the Human Proteome<br />http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334283/The Other Jimhttps://www.blogger.com/profile/17570666738076378921noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2849592168547540322015-11-09T22:10:05.613-05:002015-11-09T22:10:05.613-05:00Larry, this is what I and others need to know more...Larry, this is what I and others need to know more about but it's stuck behind a paywall and the article sure does not explain much: <br /><br />Complex grammar of the genomic language<br /><a href="http://www.kurzweilai.net/forums/topic/complex-grammar-of-the-genomic-language" rel="nofollow">http://www.kurzweilai.net/forums/topic/complex-grammar-of-the-genomic-language</a><br /><br />Gary Gaulinhttps://www.blogger.com/profile/10925297296758439900noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63787505979206460282015-11-09T20:36:47.055-05:002015-11-09T20:36:47.055-05:00Commenters often feel they have less to add to the...<i>Commenters often feel they have less to add to the science posts, and commenters to these are usually those with special expertise in just that field; thus the commenter pool is reduced.</i><br /><br />Yes. I read the science-oriented posts just as much as the ones about superstitious beliefs like religion and creationism. But on the former I just shut up an listen to the experts. There's not much for me to add.<br /><br />On another board I frequent, I've noticed that many of the most protracted discussions tend to involve one or two recalcitrant denialists and the attempts of others to educate them. I recall one thread that went on for about 130 pages over 8 months in which a Muslim who, based on his reading of the Quran, was convinced that the earth did not revolve or rotate resisted all efforts to explain why this was false. They dynamic is of informed people trying their best to cure someone of his ignorance, when that person is highly invested in remaining ignorant. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24999830511603825092015-11-09T19:25:10.714-05:002015-11-09T19:25:10.714-05:00Oh, I didn't notice the 2,400 hundred error i...Oh, I didn't notice the 2,400 hundred error in the post. Yes, I presume the number should be simply 2,400. However, as the post relates some investigators claim that a larger fraction of the 20,000 or so protein coding genes could be considered "housekeeping" (i.e. essential for the basic functions of the cell) but all of this is based on expression patterns rather than detailed knowledge of function, I think.<br /><br />Yes, I believe the average bacterial gene is about 1000 bp long. The average eukaryotic gene (in terms of amino acid coding regions, i.e, exons) is only slightly larger but with non-coding introns included the gene may be many 10s of thousands of bp long.SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38385385891020981742015-11-09T19:01:59.014-05:002015-11-09T19:01:59.014-05:00Thanks SRM, I certainly need to learn the basics. ...Thanks SRM, I certainly need to learn the basics. A quick google search showed that genes are (or can be?) thousands of bp's long.<br /><br />So I take it "2,400 hundred genes are "housekeeping" genes" should be corrected to "2,400 genes are "housekeeping" genes"?Dazzhttps://www.blogger.com/profile/07619622297229101066noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33538600213174297962015-11-09T18:50:19.021-05:002015-11-09T18:50:19.021-05:00No, your math and figuring is all wrong. First, if...No, your math and figuring is all wrong. First, if 10% of the 3000 million nucleotide genome is devoted to genes, that is 300 mllion nucleotides - but each nucleotide is not a gene. Second, if the total number of genes is 20,000-25,000 or so, then the fraction that would be "housekeeping genes" would be a much smaller number.. quite possibly in the order of 2,000 to 3,000 or so.SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70144020935749212652015-11-09T18:36:22.464-05:002015-11-09T18:36:22.464-05:00Larry or others: regarding the finding that 144 ou...Larry or others: regarding the finding that 144 out of 15,000 pseudogenes produce products, it is a small percentage (0.01%). The number of products that will be functional (for the reason you gave in post) will be low. Are their any reliable estimates/speculations on the fraction that could be functional in some way? SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41829300487033593162015-11-09T18:31:46.177-05:002015-11-09T18:31:46.177-05:00Oh, 20000 is the number of protein coding genes, i...Oh, 20000 is the number of <i>protein</i> coding genes, if the genome is 3000M bases long and about a 10% are genes, that's 300M genes, so 240K would be entirely plausible for housekeeping genes I guess? Dazzhttps://www.blogger.com/profile/07619622297229101066noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52833992400057522042015-11-09T18:24:23.209-05:002015-11-09T18:24:23.209-05:00I'm trying to make sense out of this amazing p...I'm trying to make sense out of this amazing post with my ultra limited knowledge, but there's a couple of things I'm not sure about<br /><br /><i>About <b>2,400 hundred</b> genes are "housekeeping" genes</i><br /><br />Is that 2400 or 240000 please? If there are 20000 genes I guess it's the former right?<br /><br /><i>It reminds us that cells can produce junk proteins as well as <b>junk DNA</b></i><br /><br />Would that be junk RNA?Dazzhttps://www.blogger.com/profile/07619622297229101066noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4315568520210155202015-11-09T17:52:18.118-05:002015-11-09T17:52:18.118-05:00Beau,
ID is an important topic. The majority of p...Beau,<br /><br />ID is an important topic. The majority of people in this world are predisposed toward “wanting to believe” quite unsupported things. But it is becoming increasingly difficult to maintain belief in typical religious doctrines and dogma in the face of increasing scientific understanding of the nature of things. So, along comes ID which claims a scientific basis for god. <br /><br />Note that ID, even if true, would have no bearing on matters such as the existence of heaven and hell, or a lord that loves us and is in control, or the wishful thinking that death is not the end, or the efficacy of prayer, etc. But that doesn’t matter to someone who is predisposed to wanting to believe these things.<br /> <br />ID arose for political reasons, but for the average person it merely has the potential to justify believing in things that are hoped for, but for which there is no evidence. Many of us on this site are not so much opposed to religious practise in its most benign forms, but rather the irrationality that attends religious belief of all sorts. Sam Harris once wrote (paraphrasing here): if you examine the origins of every human atrocity you will find each and every time that the promoters and perpetrators of that atrocity were motivated by the belief in absurd, untrue things. Irrationality is the problem and falsely claiming there is a scientific justification for any irrational belief system only helps to maintain a human population that is dangerously credulous.<br />SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2475606562770818832015-11-09T17:07:37.237-05:002015-11-09T17:07:37.237-05:00At least two reasons, I think.
1) Comments are of...At least two reasons, I think.<br /><br />1) Comments are often in response to cdesign proponentsists' comments, and IDiots are less likely to enter into pure science posts.<br /><br />2) Commenters often feel they have less to add to the science posts, and commenters to these are usually those with special expertise in just that field; thus the commenter pool is reduced.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31655339308930111952015-11-09T16:55:53.874-05:002015-11-09T16:55:53.874-05:00Beau Stoddard asks:
In all seriousness why is the...Beau Stoddard asks:<br /><br /><i>In all seriousness why is the ID conversation so much more attractive to your readers? In October over %75 of the comments on your posts were made on ID related articles. Why aren't the scientists that read your blog actually interested in the actual science? To be fair you do have a few posts that aren't science or ID that are treated the same. Why does ID drive such interest?</i><br /><br />I think the interest is sociological.Alan Foxhttps://www.blogger.com/profile/16470368958109056177noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27087392047128030642015-11-09T16:55:33.608-05:002015-11-09T16:55:33.608-05:00Beau,
When Larry switches back to science, Barry ...Beau,<br /><br />When Larry switches back to science, Barry think he's won:<br /><br /><i>After two failed posts, Larry has put up a post on a completely unrelated topic, apparently giving up on even a pretense of backing up his claim. I expect to see him post an apology for his smear against me that, when challenged, he was unable to support (as soon as pigs fly).</i><br /><br />Personally, I much prefer science to ID. ID is OK for occasional entertainment, but too much concentrated idiocy in a short span of time has a nauseating effect on me.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-92220831277577296232015-11-09T16:49:36.286-05:002015-11-09T16:49:36.286-05:00In all seriousness why is the ID conversation so m...In all seriousness why is the ID conversation so much more attractive to your readers? In October over %75 of the comments on your posts were made on ID related articles. Why aren't the scientists that read your blog actually interested in the actual science? To be fair you do have a few posts that aren't science or ID that are treated the same. Why does ID drive such interest? Beau Stoddardhttps://www.blogger.com/profile/03617924374387662273noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-436591133683657972015-11-09T16:02:43.318-05:002015-11-09T16:02:43.318-05:00How 'bout I add some pointless name calling an...How 'bout I add some pointless name calling and specious arguments to the comments? Would that work?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33729893021205006022015-11-09T15:35:00.743-05:002015-11-09T15:35:00.743-05:00This type of good factual summary of recent papers...This type of good factual summary of recent papers of interest is very much appreciated, though due to lack of pointless name calling and specious argument it is very unlikely to attract as many comments as some of your other posts.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68558117856570401662015-11-09T15:34:00.196-05:002015-11-09T15:34:00.196-05:00You forgot to tell us how this confirms Intelligen...You forgot to tell us how this confirms Intelligent Design? :-)Ted Herrlichhttps://www.blogger.com/profile/03194189686075222808noreply@blogger.com