tag:blogger.com,1999:blog-37148773.post516983361885669487..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Bacteria Genomes Are DegradingLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger44125tag:blogger.com,1999:blog-37148773.post-88989344187897901972007-11-27T11:38:00.000-05:002007-11-27T11:38:00.000-05:00Functional information can be defined as the infor...<I>Functional information can be defined as the information required to find any sequence that produces the given functional fold. As mutations, indels, etc. occur, sequence space is sampled, those areas that still enable the same fold/function can be preserved in the record of the genomes of life. If just one sequence will work, then the information required to find it is extremely high. However, if 10 sequences will work, then the functional information required to find a working sequence is reduced.</I><BR/><BR/>So, bar technical reasons, "functional information" is simply the likelihood for a "a working sequence"? Why not say so?<BR/><BR/>Oh, I forgot, creationists wants to infer "information" from agency instead of likelihood from process.Torbjörn Larssonhttps://www.blogger.com/profile/02022193326058378221noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89159899574228730512007-11-25T21:39:00.000-05:002007-11-25T21:39:00.000-05:00... and that it [the Bible] was written without er...<I>... and that it [the Bible] was written without error (inerrant) in the original manuscripts. It is the supreme and final authority in all matters on which it speaks."</I><BR/><BR/>Could someone remind me again how many books of the Bible are available <I>in the original manuscripts</I>? Thank you.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89766251696143032572007-11-24T16:38:00.000-05:002007-11-24T16:38:00.000-05:00And what about the fact that almost all proteins e...And what about the fact that almost all proteins evolve not from a random sequence but by exaptation from another protein with another function? That eliminates most of the need for "walking", doesn't it?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43366748376695190342007-11-24T12:26:00.000-05:002007-11-24T12:26:00.000-05:00Oops, sorry. I meant Kirk.Oops, sorry. I meant <I>Kirk</I>.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49245874350942684632007-11-24T12:25:00.000-05:002007-11-24T12:25:00.000-05:00Kurt writes: "My point was that there is evidence ...Kurt writes: "<I>My point was that there is evidence that the functional information in bacterial genomes is degrading.</I>"<BR/><BR/>Does Kurt mean net? Generically? Universally? Or sporadically? What's the context of that comment? The context certainly matters because the response is either "In some some lineages under a particular set of conditions? Well, duh." or "An irreversible trend seen across all bacteria? Stop the presses!"<BR/><BR/>And what of the opposite? Aren't there mechanisms that reverse the degradation and increase "information" (such as duplication and horizontal transfer)?<BR/><BR/>Why not mention some of Howard's other papers on the subject:<BR/><BR/>H. Ochman, J. G. Lawrence & E. A. Groisman, Nature 405, 299-304 (18 May 2000) "Lateral gene transfer and the nature of bacterial innovation"<BR/><BR/>J. G. Lawrence* and H. Ochman, PNAS Vol 95, Issue 16, 9413-9417(August 4, 1998) "Molecular archaeology of the <I>Escherichia coli</I> genome"<BR/><BR/>It seems our little friends, <I>E. coli</I> and <I>S. typhimurium</I> have been sampling <B>megabases</B> of newly acquired sequences since their split.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59390690770267379782007-11-24T05:47:00.000-05:002007-11-24T05:47:00.000-05:00The more one reads Mr. Durston, the more one gets ...The more one reads Mr. Durston, the more one gets just plain weirded out by his bizarre positions on certain topics.<BR/><BR/>Here's Kirk from an earlier comment on making assumptions:<BR/><BR/>"<I>2. I would appreciate it if individuals could abstain from speculating about what Kirk Durston believes and then posting their assumptions.</I>"<BR/><BR/>On the other hand, individuals would have no <I>need</I> to speculate about what Kirk believes if he just explained it clearly and concisely. Typically, the only time one needs to speculate is when the speaker/writer is maddeningly vague and evasive, as is Kirk when he continues:<BR/><BR/>"<I>For example, the post about how old Kirk Durston thinks the universe is. There are different exegetical views on Genesis 1 & 2, and I'm not about to bet the farm on any particular view, nor do I feel qualified or knowledgeable enough to do so. The NSS permits it's members to work through their own exegetical approach to the issue. I do want to note, however, that Genesis 1:1 states that 'in the beginning, God created the heavens (cosmos) and the earth and the earth was without form (presumably not yet accreted) and empty. There is no indication whatsoever when this occurred. Therefore, I think it is exceedingly risky for theologians to decide when this happened. As for me, if the origin of the cosmos was 15 billion years ago, so be it.</I>"<BR/><BR/>Um ... wha? So how old <I>does</I> Kirk think the universe is? Scientifically speaking, that is. And, keep in mind, this is an eminently fair question.<BR/><BR/>If proponents of ID want to be taken seriously, then they have an obligation to demonstrate that they understand and accept the basic findings of science. And one of those basic findings is that the universe appears to be around 15 billions years old.<BR/><BR/>But notice that Kirk doesn't explicitly take that position. Instead, he makes it clear that he's not taking any position whatever, and simply admitting that, if that's the value, he's good with that.<BR/><BR/>But that's an amazingly inadequate answer and, besides, one is probably not asking Kirk what he thinks the age is from a <I>religious</I> perspective. Instead, one might want to know how old Kirk thinks the universe is based on his understanding of the <I>scientific</I> evidence, and it's really not acceptable for him to just brush it off with, "Hey, if you want 15 billion, that's fine with me."<BR/><BR/>But it's <I>not</I> fine with us, Kirk, as it shows an amazing contempt for what the scientific evidence shows. So if someone gets the chance, they might want to put the question directly to Kirk, "Based purely on the scientific evidence, what is your opinion of the age of the universe?"<BR/><BR/>And if the answer is anything but a firm and unambiguous, "Oh, about 15 billion years," then we have real credibility problems here.CChttps://www.blogger.com/profile/11406057201126015750noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41586755186574806222007-11-23T22:36:00.000-05:002007-11-23T22:36:00.000-05:00I look at entire protein families (no phylogenetic...<I>I look at entire protein families (no phylogenetic restrictions). I tend to agree with Lee but I want to add a few things. First, I've looked at several universal proteins which, presumably, have been in place since the LUCA. Presumably, they've been around for a long time in all known life forms and have had plenty of time to sample their area of stable folding sequence space.</I><BR/><BR/>No, I didn't mean that you sample only a limited amount of organisms. I meant the relatedness of the protein family. It has its own phylogenetic contingency and constraints in its evolution, as pointed out above.<BR/><BR/><I>A fair amount of sampling seems to have gone on, inferring from our observations that, at many sites, all common 20 amino acids are observed to occur.</I><BR/><BR/>Stable folded proteins aren't that rare, then?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41996179757741996102007-11-23T15:01:00.000-05:002007-11-23T15:01:00.000-05:00Not to get off topic here, but I think this is at ...<I>Not to get off topic here, but I think this is at least somewhat relevant. You are the director of the New Scholars Society. http://www.newscholars.com/ The statement of faith of your society reads, in part:</I><BR/><BR/><I>"The sole basis of our beliefs is the Bible, God's infallible written Word, the 66 books of the Old and New Testaments. We believe that it was uniquely, verbally and fully inspired by the Holy Spirit, and that it was written without error (inerrant) in the original manuscripts. It is the supreme and final authority in all matters on which it speaks."</I><BR/><BR/>Who would ever think such a thing. There is no possible way to know that. Even if they pretend like they talk to voices in their heads (which they do), there is no way to know that their imaginary voice friends even know what they're talking about. That's just kooky.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55048740279290912982007-11-23T12:22:00.000-05:002007-11-23T12:22:00.000-05:00Kirk Durston says,Well Larry, since you are so int...Kirk Durston says,<BR/><BR/><I>Well Larry, since you are so interested in honesty, you did suggest 'millions' in my lecture, not thousands like you just claimed here.</I><BR/><BR/>I don't remember if I said millions or thousands. It doesn't matter. The point is whether you have any evidence for the total number of *possible* stable folded proteins as opposed to the total number of observed folds that have survived selection and drift.<BR/><BR/><I>Current research in classifying protein folds is not merely concerned with just known protein folds, contrary to what you just implied in your response.</I><BR/><BR/>Current research is focused almost exclusively on classifying known folds and in trying to discover whether they are evolutionarily related. There's some work on trying to identify the universe of all possible protein folds but not much compared to the work on existing folds. <BR/><BR/>I notice in your responses you refer frequently to <A HREF="http://pfam.sanger.ac.uk/" REL="nofollow">Pfam </A> for data in support of your case. That database only includes existing proteins, as you well know. <BR/><BR/>Finally, I am quite familiar with analyzing the amino acid sequences of proteins families. In a modern protein there are many restraints on those sequences that have nothing to do with the "fold" and everything to do with function. For example, some amino acid residues are invariant (or nearly so) because they make up part of the active site of the enzyme. Others are constrained because they serve as binding sites for other emzymes or ligands.<BR/><BR/>It is perfectly reasonable to imagine that these sites were more relaxed in the past when the protein was first evolving. Thus, the amount of sequence space taken up by existing proteins is considerably less that the amount taken up by that protein before it was selected for specific functions like binding allosteric effectors or other proteins.<BR/><BR/>How do you account for this in your analysis of existing gene families?<BR/><BR/>Kirk, I'm not pretending that I have the answer to the problem. What I object to is your conclusion. You've done a few calculations that make a prediction and your prediction is falsified by the data. Therefore, you conclude that proteins are intelligently designed. That's not science.<BR/><BR/>In another posting I'm going to think about how you would present this result in your thesis. I hope you'll respond.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16601561638078329912007-11-23T11:55:00.000-05:002007-11-23T11:55:00.000-05:00In terms of wandering around through sequence spac...In terms of wandering around through sequence space, I glanced at a paper quickly today. Haven't entirely got to grips with it yet (I'm a geologist so this is way out of my area of expertise), so I might be wrong. Anyway, what the authors did was:<BR/><BR/><I>To each of the 1000 arbitrarily chosen sequence segments the following simple procedure was first applied. The initial segment was consecutively compared with all 20 aa fragments of the proteomic database. After the first similar sequence fragment was encountered (60% identity), the same search with this new fragment was conducted and continued with each succeeding fragment. The process stops when no new fragments could be found. The sequence segments, similar to their immediate neighbors, make a “walk”, a pair-wise connected list of 20 aa long sequences. The same procedure was applied to 1000 fragments taken from shuffled sequences.</I><BR/><BR/>Resulting in the conclusion that:<BR/><BR/><I>The results of this work suggest simple procedures for exploring the space of natural protein sequence fragments. Contrary to random sequence space, the walks in natural space are significantly longer. This means, that the natural space, for the same number of sequence fragments, has substantially more connections between similar fragments</I><BR/><BR/>My tentative first reading is that these connections will facilitate movement around sequence space. Could be misreading it though.<BR/><BR/>Frenkel, Z.M. and Trifonov, E.N. (2007) Walking through protein sequence space. Journal of Theoretical Biology, 244, 77-80SteveFhttps://www.blogger.com/profile/06089429778294973157noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78241133345853647472007-11-23T11:48:00.000-05:002007-11-23T11:48:00.000-05:00Btw, Timothy links to New Scholars Society, which ...<I>Btw, Timothy links to New Scholars Society, which purports to be "... an affiliation of Canadian, christian university professors. Our motto is "Petere Veritas", which means, "pursue truth"."</I><BR/><BR/>That's some rich irony. I love how the ID folks are desperate for the trappings of legitimacy, if not the substance. Their "Latin" motto is not only grammatically incorrent -- "to pursue truth" should be "petere <B>veritatem</B>" -- but the primary meaning of the verb <B>petere</B> is usually a hostile sense. Their motto might as well mean "to attack the truth".Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-117655686305963792007-11-23T11:21:00.000-05:002007-11-23T11:21:00.000-05:00A couple quick comments and my apologies to all th...A couple quick comments and my apologies to all those who raised points that I won't have time to respond to. I can't even afford to take the time I have been taking to respond to these threads, and I'll likely have to bow out of this discussion after today .... but please at least see comment (1) below:<BR/><BR/>1. Please see my suggestion for a live event as proposed in my response to 'Kirk's argument for God' thread that Larry started.<BR/><BR/>2. I would appreciate it if individuals could abstain from speculating about what Kirk Durston believes and then posting their assumptions. For example, the post about how old Kirk Durston thinks the universe is. There are different exegetical views on Genesis 1 & 2, and I'm not about to bet the farm on any particular view, nor do I feel qualified or knowledgeable enough to do so. The NSS permits it's members to work through their own exegetical approach to the issue. I do want to note, however, that Genesis 1:1 states that 'in the beginning, God created the heavens (cosmos) and the earth and the earth was without form (presumably not yet accreted) and empty. There is no indication whatsoever when this occurred. Therefore, I think it is exceedingly risky for theologians to decide when this happened. As for me, if the origin of the cosmos was 15 billion years ago, so be it. <BR/><BR/>2. Re. Windy's and lee merrill's comments re. exploring sequence space: Windy, I look at entire protein families (no phylogenetic restrictions). I tend to agree with Lee but I want to add a few things. First, I've looked at several universal proteins which, presumably, have been in place since the LUCA. Presumably, they've been around for a long time in all known life forms and have had plenty of time to sample their area of stable folding sequence space. How can we test this? One way is to plot the functional information vs. sample size. Functional information can be defined as the information required to find any sequence that produces the given functional fold. As mutations, indels, etc. occur, sequence space is sampled, those areas that still enable the same fold/function can be preserved in the record of the genomes of life. If just one sequence will work, then the information required to find it is extremely high. However, if 10 sequences will work, then the functional information required to find a working sequence is reduced. For an average protein of 300 amino acids, there will not be time enough in the history of the universe to completely sample all of 300 amino acid sequence space. The question is, however, 'has there been an adequate sampling of sequence space to give us a decent idea as to its size?' A fair amount of sampling seems to have gone on, inferring from our observations that, at many sites, all common 20 amino acids are observed to occur. We can do better than this, however. What I did was to write an algorithm that computed functional information for various sample sizes and then I plotted the results. If there is an adequate sampling of sequence space, the curve should approach a horizontal asymptote after an adequate sample size has been reached. I found that one needed at least 500 sequences before the curve started to level out, although this is also dependent upon the size of the protein. For this reason, if PFAM cannot supply me with at least 500 sequences for a protein family, then I have not analyzed it. My preference is for at least 1,000 aligned sequences. Of course, PFAM is not error free either. It uses, among other things, a HMM for a significant part of its sorting. False positives will lower the horizontal asymptote. Also, assuming site independence will lower the asymptote as well. <B>bottom line:</B> according to this method, we have many protein families which appear to offer a good representative search of sequence space such that we can get a reasonable estimate of its size. By the way, my current phase of research involves locating pairwise and higher order relationships within a entire protein family structural domain. Initial results with ubiquitin suggest that this is a more effective way to expose the 'secrets' of the structure for a given domain. In other words, I may be able to estimate the size of a given fold-set area with far fewer samples than 1,000. This, by the way, is incidental to my research. My goal is to be able to computationally predict 3-D structure of domains that have not yet had their structure determined through experimental methods such as NMR or X-ray crystallography.<BR/><BR/>2. Re. Larry's suggestion of fibrils, bridges, etc.: within a given region of stable folding sequence space, fibrils and bridges seem to exist. Think of a sponge floating on an ocean of non-stable folding sequence space. One or two, or maybe even three entirely distinct folds may be encoded within this fold-set region. I would describe it as a fold family, the exact fold which will be determined by the meta-stable states permitted by that area of sequence space. I've seen a more detailed graphical illustration of Doug Axe's work, which portrays a fold-set region as a tight cluster of islands joined by short bridges or even not joined, but still very closely situated to the main island. Darwinian processes can readily take place in a fold-set 'island' or 'cluster' to fine tune a protein for the given organism. The problem as I see it is that these fold-set clusters or islands appear to be extremely rare in sequence space such that finding another fold-set island or cluster for an average structural domain will require a random walk search across non-stable-folding sequence space that will take more trials than what we have available in the entire mutational history of organic life (in general). I doubt that the islands are uniformly distributed in sequence space so it is possible that some are attainable within a reasonable search time and others are not.<BR/><BR/>2. re. anonymous's point that simple proteins are easier to obtain that those that are not: I certainly agree. In fact, the degree of simplicity can be estimated by computing the functional information required to find them and my own results support this. As a result, instead of concerning myself with entire proteins, I am beginning to focus on structural domains, which are the simplest, stand-alone component of a protein. My working hypothesis is, 'if the structural domains can be found within a reasonable search of sequence space, then the origin of entire proteins should be vastly simplified.' I've only begun the work in that area and have only looked in detail at ubiquitin so far. I'd like to look at 50 different structural domains over the next year and only then will I be in a position to start drawing some good inferences.<BR/><BR/>3.I really cannot afford to spend this kind of time, as much as I am enjoying civl discussion on these issues. I'll have to bow out today, but please see (1) for my proposal of a live seminar chaired by Larry, within which everyone's questions and objections could be raised and, hopefully, responded to.Kirk Durstonhttps://www.blogger.com/profile/00678032887521146961noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20989829621698388462007-11-23T10:16:00.000-05:002007-11-23T10:16:00.000-05:00> Windy: Looking within single protein families, y...> Windy: Looking within single protein families, you are looking at a phylogenetically biased, related sample! Therefore lots of the proteins will be similar because they inherited similar forms from ancestors, not necessarily because they have explored the entire available sequence space for that family!<BR/><BR/>Not to speak for Kirk, but if I'm understanding correctly, the point is not that the entire space has been explored, but that a sample was explored comparable to what other protein families explored.<BR/><BR/>The question then becomes whether this sample was representative, the general papers on this subject seem to indicate that they are, so then empirical results matching theoretical ones gives reason to accept the conclusion.lee_merrillhttps://www.blogger.com/profile/08757197085138422700noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33261905809883225262007-11-23T08:59:00.000-05:002007-11-23T08:59:00.000-05:00Reading and re-reading ‘The Hulk vs The Thing’ exc...Reading and re-reading ‘The Hulk vs The Thing’ exchange between Larry and Kirk and endeavoring to boil it down to something definite I conclude that my original query doesn’t have an unequivocal answer: Larry suggests that chains/filaments/fibrils may run through sequence space facilitating standard evolutionary mechanisms. Kirk suggests that this is an area of active research, although he feels that the direction this research is going in favors his views. (That is, he is extrapolating what he sees as a trend). <BR/><BR/>As a theist who favors evolution, (but I try not to be dogmatic), let me ask Kirk this theological question: there is a measure of uncertainty as to whether the set of stable/functional proteins are sufficiently connected to facilitate evolution, but how would Kirk react if it was discovered that sequence space was so resourced to favor evolution? What if God created a contingent world with the necessary features and potential to ‘seek and find’ the complex adaptive systems of life? Why is the absence of a sequence space connected with fibrils/chains/filaments so important to Kirk? In our state of knowledge a physical world resourced to evolve complex adaptive systems seems at least to have the status of mathematical possibility. If this possibility should eventually become unequivocal (some might regard the paleontological evidence in favour of evolution as unequivocal) would Kirk lose his killer evidence for a Creative deity? I assume Kirk thinks of complex configurations of life as necessarily ‘given’ just as the backdrop of some more basic physical regime is inevitably a ‘given’. ‘Givens’ raise philosophical questions about their ultimate origin. True, until some hard irreducible given is arrived at we can put off the challenging day when we have to face the intractable epistemological problems that the ultimate ontology presents. But as a theist who favors evolution let me express the opinion that it causes needless provocation to raise the epistemological barriers presented by ‘given’ contingences too early in our probings toward ultimate origins.Timothy V Reeveshttps://www.blogger.com/profile/03913020911593893925noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30176291167746318342007-11-23T06:01:00.000-05:002007-11-23T06:01:00.000-05:00I pointed out how you can find out for yourself ho...<I>I pointed out how you can find out for yourself how scarce stable folded proteins are. Simply download the entire aligned set of proteins for a family. Choose one that gives you at least 1,000 sequences. You can then go down each column in the aligned set and compute the frequency of occurrence of each amino acid at each site. I've written some software that will do just that. Once you've done that, you are now in a position to estimate the size of sequence space for that particular protein family and, from that, the probability that a sequence will fall into that region.</I><BR/><BR/>No, you are <I>not</I> in a position to estimate that from your phylogenetic exercise! You'd have been better off sticking with your "protein families are few and far between" argument. Looking within <I>single</I> protein families, you are looking at a phylogenetically biased, related sample! Therefore lots of the proteins will be similar because they inherited similar forms from ancestors, not necessarily because they have explored the entire available sequence space for that family!<BR/><BR/>This is kiddie phylogenetics - no offense, kiddie stuff has its place - but this is like estimating the probability of limb numbers changing through evolution by looking at the variation in limb number within mammals.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16117222985062872282007-11-23T01:37:00.000-05:002007-11-23T01:37:00.000-05:00Hes one of the supporters of one of my favorite id...<I>Hes one of the supporters of one of my favorite ideas.</I><BR/><BR/>Contrary to what my previous comment may suggest, as a naive layman I like this particular paper too. It builds a large speculative model perhaps without (yet) suggesting much of testable predictions, compared to say <A HREF="http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16505372" REL="nofollow">Forterre's more minimal "three viruses, three domains" hypothesis</A>. But I find it really stimulating, and I'm glad professionals reacts the same - perhaps something eventually comes out of this or similar suggestions.<BR/><BR/>And besides, anything that attempts to embed viruses and other non-cellular evolutionary biological replicators into the old domain description must be lauded, right? :-PTorbjörn Larssonhttps://www.blogger.com/profile/02022193326058378221noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21314424648016230912007-11-23T01:17:00.000-05:002007-11-23T01:17:00.000-05:00IANAB, but as there is so much independent evidenc...IANAB, but as there is so much independent evidence that supports evolution beyond reasonable doubt, it is IMHO to put the cart before the horse to ask if there is any difficulties for the process pathways. <BR/><BR/>The right question would be, how is any observed difficulties surmounted? And if there now is a reasonable effort to classify protein folding and stability, this look like an exciting area.<BR/><BR/>Btw, Timothy links to <A HREF="http://www.newscholars.com/" REL="nofollow"><I>New Scholars Society</I></A>, which purports to be "... an affiliation of Canadian, christian university professors. Our motto is "Petere Veritas", which means, "pursue truth"." But instead of pursuing facts and other truths by science it's library of "Available papers" is filled with apologetics (mostly by Durston), which as we all know for a fact at most can be assured to be valid logic (it fails though) but never truth as there is no evidence.<BR/><BR/>Durston says,<BR/><BR/><I>a Shakespearean phrase that goes something like, 'methinks the lady protests too loudly'.</I> <BR/><BR/>"<A HREF="http://www.enotes.com/shakespeare-quotes/lady-doth-protest-too-much-methinks" REL="nofollow">Hamlet: Madam, how like you this play? Queen: The lady doth protest too much, methinks. [Hamlet Act 3, scene 2, 222–230]</A>"<BR/><BR/>Which is an ironic way to start a rant.<BR/><BR/><I>Finding a novel fold in sequence space is a genuine problem that Koonin suggests can be surmounted if there are an infinite number of worlds (see Eugene Koonin, ‘The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life’, Biology Direct, 6/27/2007).</I><BR/><BR/>Koonin's cosmological thinking is IMO confused, in much the same way that creationists confuse a priori probabilities with a posteriori likelihoods. <BR/><BR/>The weak anthropic principle is used in cosmology to predict likely values (conditional on the weak anthropic principle). It is not preferred as an open unfalsifiable “just so” description for finetunings <B>or other low likelihood scenarios</B>.<BR/><BR/>I don't think it does anyone credit to refer to these speculative and from a physics view IMHO odd papers of Koonin. (Who seems to interchange a spat of solid papers by speculative ones, much as Max Tegmark in cosmology. And like Tegmark, maybe Koonin sometimes strike out.)<BR/><BR/><I>If we step out of the creative story telling world of the Darwinist</I><BR/><BR/>Either you haven't read Moran on evolution much, or you are in creationist mode.Torbjörn Larssonhttps://www.blogger.com/profile/02022193326058378221noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79986283718560236552007-11-23T00:36:00.000-05:002007-11-23T00:36:00.000-05:00Mr. Durston (Kirk, if I may), Not to get off topic...Mr. Durston (Kirk, if I may), <BR/><BR/>Not to get off topic here, but I think this is at least somewhat relevant. You are the director of the New Scholars Society. http://www.newscholars.com/ The statement of faith of your society reads, in part:<BR/><BR/>"The sole basis of our beliefs is the Bible, God's infallible written Word, the 66 books of the Old and New Testaments. We believe that it was uniquely, verbally and fully inspired by the Holy Spirit, and that it was written without error (inerrant) in the original manuscripts. It is the supreme and final authority in all matters on which it speaks."<BR/><BR/>I have heard you speak, and as best as I can summarize it (please correct me if I am mistaken), your exegetical understanding of the Bible, which you apparently believe to be inerrant and the supreme final authority, is that God created the universe and everything in it in 6 days about 6000 years ago. Furthermore, you believe that at least some science supports this claim. I’d like to know what science you think supports such a young age for the earth. Is the Mira, et al. paper part of this “supporting evidence”?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65054127004993966192007-11-22T23:11:00.000-05:002007-11-22T23:11:00.000-05:00Kirk:Personally, I would agree with you that stabl...Kirk:<BR/><BR/>Personally, I would agree with you that stable, and especially functional, regions of sequence space are fairly isolated. I've seen a lot of published and unpublished work to that effect.<BR/><BR/>However, your larger conclusion is entirely unfounded. If even true that the regions are highly quantized, it may simple be that they are so only from the perspective of current biochemistry and evolutionary fitness demands.<BR/><BR/>There is also much research showing simpler peptides have much more common stable folds. In a precursor to the modern cell, proteins with a reduced amino acid composition were very likely.<BR/><BR/>And further, the demands upon specificity and efficiency of these proteins were likely far less. It's even possible that initial production of protein was a non-functional by-product of the metabolic system.<BR/><BR/>In such cases, the distance between stable regions was far more accessible, and the modern, but inaccessible regions of stable sequence space were originally populated by "primitive" precursors.<BR/><BR/>So it's not that we once had a more "advanced" system that has since degraded, but that we had a more generic system that has since specialized. And that last sentence is not a terrible definition of evolutionary processes.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78452546440320205482007-11-22T22:54:00.000-05:002007-11-22T22:54:00.000-05:00There is a Shakespearean phrase that goes somethin...<I>There is a Shakespearean phrase that goes something like, 'methinks the lady protests too loudly'.</I><BR/><BR/>Thanks. That was a work of fiction, IIRC.<BR/><BR/><I>It is often the case that the person who is most free with their accusations is the one who is most guilty.</I><BR/><BR/>Thanks. Looks like another ID theory in the making. You guys should formalise that or something. <BR/><BR/>Watch out for the mean peer reviewers though. They might try to oust it or something. Then they will try to cover their tracks of course. Watch out for bigfoot though. Kudos.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58591748225582828652007-11-22T21:33:00.000-05:002007-11-22T21:33:00.000-05:00I am aware that various Darwinists are now tryng t...<I>I am aware that various Darwinists are now tryng to oust Koonin from the fold with the idea that 'real' scientists will not ask embarrassing questions about Darwinian theory...</I><BR/><B>**VOMIT**</B><BR/><BR/>Excuse me, do you even know who Koonin <I>is</I>, other than the fact he is the owner of a publication you want to *commandeer*? No one is trying to *oust* him from any *folds*. Hes one of the supporters of one of my <A HREF="http://www.biology-direct.com/content/1/1/29/abstract" REL="nofollow">favorite ideas</A>. My mentors have always encouraged thinking games, whether youre ultimately right or wrong-- Theyre fun, and you learn things (Im sure Koonin learned some things from his reviewers... thats why we have peer review).<BR/><BR/>The <I>problem</I> with professional scientists writing their thinking games for others to read NOW is you Creationists coming in and pubjacking and quote-mining like a bunch of jerks and ruining the fun for the rest of us.<BR/><BR/>I repeat, <B>**VOMIT**</B>ERVhttps://www.blogger.com/profile/02070086354372691880noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48897824120959222232007-11-22T21:09:00.000-05:002007-11-22T21:09:00.000-05:00Well Larry, since you are so interested in honesty...Well Larry, since you are so interested in honesty, you did suggest 'millions' in my lecture, not thousands like you just claimed here. Current research in classifying protein folds is not merely concerned with just known protein folds, contrary to what you just implied in your response. Rather, we are concerned with how many different folds are permitted by physics. The general consensus is that regions of sequence space that code for stable folded proteins are exceedingly rare. Your hopeful suggestion is that there are bridges or filaments that may help connect these exceedingly rare regions. That would be a massive stroke of luck indeed. Some work suggests that regions of fast folding sequence space are surrounded by slow-folding, low stability shells (see PNAS -- Nelson and Onuchic 95 (18): 10682). Quite apart from this, in my lecture I presented a method to test what you suggest, that consisted in mapping sequence space with the data from PFAM. In general, what I see from my own work is that the larger the protein, the more sparse stable, folding sequence space seems to be. It may be that two islands of fold/function sets are close together, but there is no reason at present to suspect that all protein folds necessary for biological life are fortuitously close together in sequence space.<BR/><BR/>I am aware that various Darwinists are now tryng to oust Koonin from the fold with the idea that 'real' scientists will not ask embarrassing questions about Darwinian theory, or point out problems that could potentially bring the entire 19th century theory crashing down around the ears of its devotees. Koonin isn't the only person pointing out the extremely low probabilities involved in 'finding' folding proteins. In my lecture, I pointed out how you can find out for yourself how scarce stable folded proteins are. Simply download the entire aligned set of proteins for a family. Choose one that gives you at least 1,000 sequences. You can then go down each column in the aligned set and compute the frequency of occurrence of each amino acid at each site. I've written some software that will do just that. Once you've done that, you are now in a position to estimate the size of sequence space for that particular protein family and, from that, the probability that a sequence will fall into that region. I've done that for 35 proteins. Bottom line: Koonin is pointing out a serious problem that Darwinists do not want to acknowledge and the problem is thinly veiled in the PFAM data base for the whole world to see. It's time for Darwinists to pull their head out of the sand and do the work. Ostracizing those people who are asking embarrassing questions is not good science. You need to do the work. If you think there are filaments joining different island fold sets, do the work. The computational capability and the data is already available. Do the work. Those that are, are starting to ask embarrassing questions that you probably do not want to hear. So just do the work yourself if that is what it takes.Kirk Durstonhttps://www.blogger.com/profile/00678032887521146961noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36796284024288861502007-11-22T20:54:00.000-05:002007-11-22T20:54:00.000-05:00hehehehe!PUBJACK!!!hehehehe!<BR/><BR/><B>PUBJACK!!!</B>ERVhttps://www.blogger.com/profile/02070086354372691880noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63245940956435424702007-11-22T20:32:00.000-05:002007-11-22T20:32:00.000-05:00Kirk Durston says,Finding a novel fold in sequence...Kirk Durston says,<BR/><BR/><I>Finding a novel fold in sequence space is a genuine problem that Koonin suggests can be surmounted if there are an infinite number of worlds (see Eugene Koonin, ‘The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life’, Biology Direct, 6/27/2007). I also pointed this out in my lecture.</I><BR/><BR/>I was amused that you quoted Koonin's work and even more amused that you specifically referred to the comments of his reviewers.<BR/><BR/>I'm sure others will not be surprised that Intelligent Design Creationists have homed in on Koonin's ideas like a moth to a flame.<BR/><BR/>As a student of this field you certainly must know that Koonin's ideas about evolution are far from mainstream. In fact, it seems likely that Koonin doesn't understand the basic principles of evolution [<A HREF="http://sandwalk.blogspot.com/2007/10/eugene-koonin-and-biological-big-bang.html" REL="nofollow">Eugene Koonin and the Biological Big Bang Model of Major Transitions in Evolution</A>]. <BR/><BR/>Many people predicted that the Intelligent Design Creationists would gleefully quote Koonin in support of the idea that evolution is in trouble. You guys are so predictable.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31946545670633181932007-11-22T20:16:00.000-05:002007-11-22T20:16:00.000-05:00Kirk Durston says,I've certainly have thought abou...Kirk Durston says,<BR/><BR/><I>I've certainly have thought about how many different protein folds there might be and have several papers on my hard drive that discuss it. It is an area of interest in my own research. I wasn't 'puzzled', but instead surprised that you would suggest there were 'millions' in light of the literature that is out there on this subject.</I><BR/><BR/>Just as I expected. You didn't understand the question.<BR/><BR/>I wasn't questioning how many different folds are known in biology. I was questioning your assumption that these are the only possible folds. I asked you whether there could be thousands of other peaks in the landscape that don't happen to be part of the sample that survived. <BR/><BR/>In other words, how do you know there aren't many connecting chains between each peak that's represented by a modern protein family?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.com