tag:blogger.com,1999:blog-37148773.post278214874379322002..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The proteome complexity mythLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger142125tag:blogger.com,1999:blog-37148773.post-83769045471278618202017-01-03T17:39:10.082-05:002017-01-03T17:39:10.082-05:00Well I don't know, but there is a considerable...Well I don't know, but there is a considerable amount of data that there are lot's of protoforms out there in biology. And it's been known for a long time that many of them have real biological functions (oxidation, phosphorylation, methylation, glycosylation just to name a few) <br /><br />and just because they are at low levels doesn't mean they are non functional. <br /><br />This is just one study of the phosphoproteome (there are many) which identified over 20K phosphorylated peptides and linked many of these low level modifications to biological activity<br /><br />http://stke.sciencemag.org/content/3/104/ra3.full<br /><br />Anonymoushttps://www.blogger.com/profile/08212045838700585784noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19419955948256074212017-01-03T15:54:47.394-05:002017-01-03T15:54:47.394-05:00Brett: "There are also new technologies comin...Brett: <i>"There are also new technologies coming on line that are identifying hundred of thousands of modified peptides from bottom up human proteomics experiments"</i><br /><br />Uh, identifying, OK. But are they assayed or something so the modification is known to have a functional purpose, as opposed to just assuming "it exists in multiple forms, so all differences between them exist for functional reasons"? Some, I presume, exist at low levels and could just be necessary side-effects of synthesis processes. Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48263432782234754442017-01-03T14:40:28.331-05:002017-01-03T14:40:28.331-05:00I'm not an expert on proteoforms by any means,...I'm not an expert on proteoforms by any means, but there does seem to be some really good evidence for some classes of proteins to have many many proteoforms. Histones in particular <br /><br />http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b01090<br />http://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.6b00694<br />http://www.sciencedirect.com/science/article/pii/S002196731630601X<br />http://repository.topdownproteomics.org/Proteoforms?query=Q7L7L0<br /><br />In addition there seems to be approximately 140K human PTM's cataloged in the nextprot database<br /><br />https://www.nextprot.org/about/human-proteome<br /><br />There are also new technologies coming on line that are identifying hundred of thousands of modified peptides from bottom up human proteomics experiments<br /><br />http://www.nature.com/nbt/journal/v33/n7/abs/nbt.3267.html<br /><br />From what data I have seen, we are just scratching the surface of what is out there. This is pretty clear to anyone who actually does these types of experiments in the labAnonymoushttps://www.blogger.com/profile/08212045838700585784noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67280483340467174462016-12-27T13:41:06.633-05:002016-12-27T13:41:06.633-05:00My random act of mischief:
The evident nested hie...My random act of mischief:<br /><br />The evident nested hierarchy of mutation events in the of the GULOP gene sequence can be best explained per phylogenetic tree positing humans & chimps with a very recent common ancestor; whereas Humans/Chimps have a more distant common ancestor with the outgroup Macaques; while Gorillas and other primates are related to Humans/Chimps in a most predictable fashion (according to expectations of current evolutionary “theory”)<br /><br />This provides an opportunity where we can pose and juxtapose:<br /><br />Pose: <a href="http://sandwalk.blogspot.ca/2007/02/human-gulop-pseugogene.html" rel="nofollow">Professor Larry Moran on the Human GULOP Pseudogene</a> <br /> <br />As opposed to Juxtapose:<a href="http://www.evolutionnews.org/2013/08/a_simple_propos075721.html" rel="nofollow"> a fast and easy ID synopsis of how an accumulation of mutations in the GLU/GLO/GULO/GULOP locus represents an exaptation made possible by differential mRNA editing</a> <br /><br />Two contrary questions may vex some present: <br /><br />1- Does the constellation of GULOP mutations indeed represent an adaptive exaptation? (Fast answer = <a href="https://www.ncbi.nlm.nih.gov/pubmed/7087819" rel="nofollow"> Yes! </a><br /><br />2- Does differential editing of GULOP mRNA in fact rescue endogenous production of Ascorbic acid in fetus’ brains and breast-fed infants? (Fast answer: No – but not to hear the ID protagonists tell it.)<br /><br />In any case, <a href="http://www.bbc.com/future/story/20161208-why-vitamin-supplements-could-kill-you" rel="nofollow"> the inactivation of the GULO gene may indeed have proven adaptive.</a> for more elaborate reasons (than suggested by E.G. Calabrese) as explained in this easy to read summary from the BBC.<br />anonymoushttps://www.blogger.com/profile/06178384393256601953noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51297935450652225902016-12-21T06:38:46.396-05:002016-12-21T06:38:46.396-05:00I was VERY patient, tolerating your behavior as mo...<i>I was VERY patient, tolerating your behavior as moderator</i><br /><br />Wait, you as a *guest* "tolerated" your *host's* behavior?judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31807912751670927392016-12-20T18:59:08.459-05:002016-12-20T18:59:08.459-05:00"WTF is second degree of speciation?"
..."WTF is second degree of speciation?" <br /><br />A misdemeanor? Jon Fleminghttps://www.blogger.com/profile/08191822787220580152noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52966824616417479752016-12-20T17:38:55.767-05:002016-12-20T17:38:55.767-05:00This is the way it always goes. The IDiots talk a...This is the way it always goes. The IDiots talk a great game about the new methods they've discovered to detect "design" (Complex specified information! No free lunch! Explanatory filter! Irreducible complexity!). But when challenged to actually demonstrate the utility of these methods in real world situations, they don't even try. Here are a couple prominent examples:<br /><br /><a href="https://pandasthumb.org/archives/2008/01/take-the-intell.html" rel="nofollow">Take the Intelligent Design Challenge!</a><br /><br /><a href="https://pandasthumb.org/archives/2008/02/the-intelligent-3.html" rel="nofollow">The Intelligent Design Challenge-Denouement</a><br /><br /><br /><a href="http://www.softwarematters.org/mathgrrl.html" rel="nofollow">My Life as Mathgrrl</a> Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41528752175201142382016-12-20T17:16:43.968-05:002016-12-20T17:16:43.968-05:00OG,
"Anyway, it was fun here. This was a gre...OG,<br /><br />"Anyway, it was fun here. This was a great venue to expose the bankrupcy and irrationality of naturalism. "<br /><br />Please don't play the martyr. No one is buying it. What you have exposed is your inability to answer questions about ID/creationism. I never did get an answer about how you scientifically determine how things are ID. There is nothing irrational about naturalism. What is irrational is believing a supernatural being intelligently designed the Universe, and expect people to agree with you without producing any evidence of how you know this.Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-257860852930070082016-12-20T17:01:18.702-05:002016-12-20T17:01:18.702-05:00Otangelo kvetches to the bitter end:
At the mean ...Otangelo kvetches to the bitter end:<br /><br /><i>At the mean time, you find it perfectly fine, when trolls and clowns make personal attacks.</i><br /><br />"Personal attacks"? Like calling people "trolls and clowns", for example?<br /><br />If that really is your last post, how fitting that it highlights yet again your breathtaking hypocrisy and lack of self awareness.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55204401479205478902016-12-20T16:58:17.987-05:002016-12-20T16:58:17.987-05:00Learn how to use quotation marks (or italics) to i...<i>Learn how to use quotation marks (or italics) to identify material you did not write. It's not that hard.</i><br /><br />I guess it <i>is</i> too hard, for some people. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19012342284397539532016-12-20T16:52:31.291-05:002016-12-20T16:52:31.291-05:00@Larry Moran
The post you deleted was perfectly c...@Larry Moran<br /><br />The post you deleted was perfectly clear. There was no justification to delete it. Neither the last other two. Your acusations were not justified either. I have no need to plagiarize. Neither here, nor at my forum, nor anywere else. I was VERY patient, tolerating your behavior as moderator, vandalizing and deleting my posts without real justification. <br /><br />At the mean time, you find it perfectly fine, when trolls and clowns make personal attacks.<br /><br />Anyway, it was fun here. This was a great venue to expose the bankrupcy and irrationality of naturalism. <br /><br /> Anonymoushttps://www.blogger.com/profile/05265343573323745994noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80945702169372012382016-12-20T14:39:48.607-05:002016-12-20T14:39:48.607-05:00I wonder what Otangelo thinks...
The answer to a...<i>I wonder what Otangelo thinks...</i> <br /><br />The answer to any question of that form is quite easy, and is in the negative.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25233034657849335882016-12-20T14:20:20.947-05:002016-12-20T14:20:20.947-05:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/05265343573323745994noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-50880384221783275812016-12-20T14:11:53.966-05:002016-12-20T14:11:53.966-05:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/05265343573323745994noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20344787258695345852016-12-20T14:03:01.380-05:002016-12-20T14:03:01.380-05:00@Otangelo Grasso
This is your last warning. Learn...@Otangelo Grasso<br /><br />This is your last warning. Learn how to use quotation marks (or italics) to identify material you did not write. It's not that hard. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58415238173498880102016-12-20T13:33:24.980-05:002016-12-20T13:33:24.980-05:00This comment has been removed by a blog administrator.Anonymoushttps://www.blogger.com/profile/05265343573323745994noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52829077725753274322016-12-20T13:14:39.496-05:002016-12-20T13:14:39.496-05:00I wonder what Otangelo thinks of that fact that on...I wonder what Otangelo thinks of that fact that one of his heroes, Micheal Behe, accepts common descent as obviously true.<br /><br />https://en.wikipedia.org/wiki/Michael_Behe#Darwin.27s_Black_BoxFaizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66878677829647710552016-12-20T12:55:24.398-05:002016-12-20T12:55:24.398-05:00OG wrote, "I do not stick neither to OEC nor ...OG wrote, "I do not stick neither to OEC nor YEC ( despite its my preference ) , since i do not understand all data available, specially in geology, to have a informed opinion."<br /><br />Odd. That's never stopped him before!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64687356130828131212016-12-20T12:46:38.014-05:002016-12-20T12:46:38.014-05:00What is disputed, is common ancestry, and macro-ev...<i>What is disputed, is common ancestry, and macro-evolution of first degree os speciation. Second degree of speciation is a observed fact. <br /><br />Neiter OEC, nor YEC agrees with these two points.</i><br /><br />Sorry Otangelo, you blew it again. OEC does admit to common ancestry, with just a bit of tweaking by the Deity every so often. <br /><br />James Shapiro does not profess "front loading" in the least. What he believes is that bacteria *themselves*, with no help from any deity, are capable of directing their mutations in ways favorable to their *evolutionary adaptation*. From everything you've ever said here, you don't agree with anything Shapiro thinks.<br /><br />It's just as I said previously: You've got a soup of half-baked, contradictory ideas swimming around your head about evolution with no rhyme or reason to it. You just know you don't like the idea of evolution, i.e., species arising without the necessity for a deity to oversee it all.<br /><br />That's fine, none of us cares if you want to be ignorant of the science. But you're not accomplishing anything at all by spewing this nonsense at an audience that includes scientists who do this stuff for a living, except reinforcing the idea that the sort of person who disbelieves evolution is someone ignorant of the science and not very capable of logical reasoning about it - someone very much like you, Otangelo.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21092833586128929422016-12-20T12:39:46.821-05:002016-12-20T12:39:46.821-05:00Otangelo,
"
We know from an extensive litera...Otangelo,<br /><br />"<br />We know from an extensive literature on insertional mutagenesis in nature and the laboratory that introduction of a transposable element into a particular location CONFERS NEW FUNCTIONAL PROPERTIES on that region of the genome (Shapiro, 1983; Craig et al., 2002; Deininger et al., 2003)."<br /><br />We also know that those same transposons insert elsewhere in the genome where they perform no function, or even have detrimental function. You can't focus on just the beneficial functions and pretend that the neutral and detrimental insertions don't happen.Erichttps://www.blogger.com/profile/09481645265615126897noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46815687485581322652016-12-20T10:44:06.368-05:002016-12-20T10:44:06.368-05:00Even when you think you've read it all, OG pul...Even when you think you've read it all, OG pulls even more new factoids out of his ... hat:<br />"What is disputed, is common ancestry, and macro-evolution of first degree os speciation. Second degree of speciation is a observed fact. "<br /><br />WTF is second degree of speciation?<br />Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20270684013449134942016-12-20T10:37:27.089-05:002016-12-20T10:37:27.089-05:00"But to get back to the point about what'..."But to get back to the point about what's comedic, it's that you strongly hold positions from YEC and OEC that are completely contradictory to each other,"<br /><br />But OG has a 'natural' defense against contradictions, he calls them 'personal opinion'. Thus parts of his holy book are personal opinion, other parts are things he abides by. <br />In the same way he reads his holy book, he reads science blurbs. One liners which fit his needs, he quotes mines and calls scientific evidence in favor of design. Even if in the same paper/ book/ blurb the author writes creation myths are myths indeed or somethings which contradicts OG's needs, OG invokes the personal opinion defense.<br /><br />It's like a lawyer claiming "evidence of the police which points to his client having murdered somebody" being mere "personal opinion".Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15188740321645846032016-12-20T10:25:53.712-05:002016-12-20T10:25:53.712-05:00Judmarc wrote:
"and it's fine with you t...Judmarc wrote:<br /><br />"and it's fine with you to hold on to this incoherent soup of ideas as long as they all try to dispute evolution. "<br /><br />As said previously, you need to define what you mean with evolution. What is disputed, is common ancestry, and macro-evolution of first degree os speciation. Second degree of speciation is a observed fact. <br /><br />Neiter OEC, nor YEC agrees with these two points. <br /><br />Maybe the common meaning of "front loading" is different than i used. I just meant what Shapiro says, namely that the hability of adaptation to the environment is a pre-programmed process.<br /><br />I do not stick neither to OEC nor YEC ( despite its my preference ) , since i do not understand all data available, specially in geology, to have a informed opinion. Anonymoushttps://www.blogger.com/profile/05265343573323745994noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6947224638703036742016-12-20T10:08:35.081-05:002016-12-20T10:08:35.081-05:00OG,
"Where is God When Bad Things Happen? Wh...OG,<br /><br />"Where is God When Bad Things Happen? Why Natural Evil Must Exist"<br /><br />But you reject naturalism as an explanation for the existence of the Universe and life here on Earth. You claim it was intelligently designed. So there is no 'natural' evil, there is only 'designed' evil.Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22369306047081048572016-12-20T10:04:47.081-05:002016-12-20T10:04:47.081-05:00OG,
"My special brand of theism and its book ...OG,<br />"My special brand of theism and its book says in the first versicle:<br /><br />In the beginning God created the heavens and the earth.<br /><br />that answers your first question."<br /><br />That's not science, that's religious belief.<br /><br />"and in regard of ID predictions, what about you google :<br /><br />Confirmation of intelligent design predictions."<br /><br />I'm sure if you resorted to your origins of life dodge and I responded with an invitation to google the current state of scientific knowledge on the subject for yourself, you would be perfectly satisfied with that answer, right?<br /><br />Do you really want to get into theodicy, because the implications of ID for the nature of the designer are both frightening and unavoidable.Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.com