tag:blogger.com,1999:blog-37148773.post5205368757291827633..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Do the IDiots Understand Evolution?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger54125tag:blogger.com,1999:blog-37148773.post-32229591984737974682012-07-01T00:08:43.557-04:002012-07-01T00:08:43.557-04:00Atheistoclast,
It is incredibly stupid to suggest...Atheistoclast,<br /><br />It is incredibly stupid to suggest someone to read that shit for definitions and understanding of information when there's this:<br /><br />http://www.ccrnp.ncifcrf.gov/~toms/<br /><br />Which by the way has there an article showing how easily and readily new regulatory sequences can evolve. (Nobody said that duplications explained every case of increased information you ass-hole.)<br /><br />So, obviously you did not read any literature, but whatever lead to your conclusions. Gene duplication is not the whole story, but it does increase information readily. If you gather the strength to read and understand Schneider's articles you might figure out how wrong you are. Maybe you need to go beyond definitions and into the equations. Maybe you need to go into the connection between energy and information. Maybe there is a lot you have no idea about.<br /><br />1. Copies are certainly more information. "GO TO BED GO TO BED GO TO BED " has more information than GO TO BED. The former required more energy to be written, but I do not need to explain that. Try to describe them and make those descriptions into bits and you will see that you need more bits to describe the first than the second. So, that soon you have been proven both wrong and ignorant about information.<br /><br />2. That changes can scramble existing information does not mean that changes are not new information. Try and describe both, the original and the changed copy into bits ... ups!<br /><br />3. Nope, they change activities in important ways. If a bacterium is able to not just resist, but eat antibiotics with a mutated gene, then that's new activities and new information. WIll you claim that because you despise the ability to eat lactose as "just another sugar" then lactase is not important information for survival when lactose is what's available? Are you that much of an ass-hole? (Oh. My bad. Sure you are that kind of an ass-hole.)<br /><br />4. Whether your examples are among the most cited or not is inconsequential, your abstract does not read as "thoroughly" debunking and refuting anything. It reads as not finding spectacular changes but finding new information nonetheless. Whether your examples are the most cited or not does not mean that you did not distort anything. With the careless way you distorted here the conclusions of an article you wrote yourself, why should I trust that you did not distort other articles you cited therein? <br /><br />5. Besides experimental evolution, I have already listed a couple well-known examples that you missed that show spectacular new stuff from duplications, which you conveniently ignored. Seems like your claims are the ones that have been thoroughly debunked and refuted.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79351238032748352042012-06-29T06:10:48.478-04:002012-06-29T06:10:48.478-04:00I have cited two papers that show that the majorit...<i> I have cited two papers that show that the majority of mutations are slightly deleterious where the phenotypic effect is detectable. </i><br /><br />The idea that something being "detectable" could have that kind of effect is pretty interesting. What in nature is doing the "detecting" in this case? Does the act of "detection" not really refer to scientists who, by detecting an effect transform that into a "phenotypic" trait? I wonder, before the evolution of eyesight, were traits that become "phenotypic" with that sense of a truly different kind before that was possible and what that means for this distinction. <br /><br />That's a matter of curiosity, only. It doesn't imply anything about the reality of evolution, which is a fact, it might, though, imply a lot about the scientific study of it.The Thought Criminalhttps://www.blogger.com/profile/01381376556757084468noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51121442378353091822012-06-28T13:52:26.604-04:002012-06-28T13:52:26.604-04:00No, I am not quote-mining. I have cited two papers...No, I am not quote-mining. I have cited two papers that show that the majority of mutations are slightly deleterious where the phenotypic effect is detectable. As for "silent mutations" you should know that years ago it was shown that many "synonymous mutations" believed to be innocuous can adversely affect mRNA stability.<br /><br />http://www.brighthub.com/science/genetics/articles/39340.aspx<br /><br />Here is another paper that finds that most amino acid substitutions in gene products are "strongly deleterious".<br /><br />http://homepages.ed.ac.uk/eang33/publications/eyrewalkeretal20022.pdf<br /><br />Enjoy.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18102458252245496322012-06-28T11:14:55.852-04:002012-06-28T11:14:55.852-04:00So it doesn't bother you at all that your cita...So it doesn't bother you at all that your citations don't support your point? You're just quotemining. And your new reference is talking about, and assaying, only those mutations with a detectable phenotypic effect. It isn't screening for silent mutations at all, which is where we would expect the bulk of neutral mutations to be. Have you no shame? No, don't answer that.john harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20934706366223166852012-06-28T10:05:29.480-04:002012-06-28T10:05:29.480-04:00Like I say, hardly any mutations are expected to i...Like I say, hardly any mutations are expected to incur a selection coefficient of exactly s=0.0 (i.e. be completely neutral). The vast majority of mutations are therefore predicted and observed to be slightly deleterious. This applies to both coding DNA and ncDNA. Here is a paper on mutations in the nematode that confirms this:<br /><br />http://www.indiana.edu/~lynchlab/PDF/Lynch138.pdf<br /><br /><i>In accordance with evidence that the <b>vast majority of mutations are deleterious</b>....</i><br /><br />There is no escaping this unquestionable fact.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79145284593347018522012-06-28T08:47:29.939-04:002012-06-28T08:47:29.939-04:00Wrong. That method doesn't even consider neutr...Wrong. That method doesn't even consider neutral mutations. And in fact, "The overall mutation rate in this mutator strain is expected to be 0.18 per genome per generation (based on the mutation rate for wild-type E. coli (Drake et al. 1998) and on the measured mutator strength), which is 36 times higher than the Ud estimated in our experiments. This implies that the majority of mutations are effectively neutral in our experiments or that we do not have the power to measure many of them, which is in full agreement with previous indications from other organisms that the distribution of sd is very leptokurtic."<br /><br />Further, I bet anonymous was thinking about eukaryotes, which have large amounts of junk DNA.john harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67560800486453998522012-06-28T08:11:28.950-04:002012-06-28T08:11:28.950-04:00I notice that you fail to provide any citation to ...I notice that you fail to provide any citation to support your assertion. You are wrong. The vast majority of mutations are slightly deleterious with respect to reproductive fitness. Hardly any have a selection coefficient of s=0.0.<br /><br />http://rstb.royalsocietypublishing.org/content/365/1544/1177.full<br /><br /><i>As predicted, most of our lines decreased in fitness, supporting the notion that the vast majority of mutations are deleterious</i>Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42648443901843990342012-06-28T07:09:12.103-04:002012-06-28T07:09:12.103-04:00See, one of the problems that science has is that ...See, one of the problems that science has is that people don't distinguish between what is a legitimate scientific idea and what is a legitimate idea OUTSIDE of science.<br /><br />Intelligent design as a philosophical or religious idea is legitimate, it's not legitimate within science because of technical requirements. You could say the same thing about materialism and any other philosphical, religious, political, ideas that are far more likely to be successfully and illegitimately asserted as science. Which is the entire basis of the atheist fad of the past decade and much of the junk that was once current as science and now can only be held to have been mistaken as being "science". Scientific racism, sexism, eugenics, etc. are all examples of that. When I look at who wants to bring some of them back today, I'm struck at how many of those within science are materialists who want to plug their ideological ideas into science. Many within cog-sci, and the various parts of the so-called sciences that have successfully invaded the real science of evolution. All to no to little objection among the materialists.The Thought Criminalhttps://www.blogger.com/profile/01381376556757084468noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6508247712626270972012-06-27T11:32:31.980-04:002012-06-27T11:32:31.980-04:00A-clast:
"Yes, John, the vast majority of mut...A-clast:<br />"Yes, John, the vast majority of mutations involve a loss of function. Often it is very slight, but can be very large."<br /><br /><br />Actually, the vast majority of mutations are neutral or nearly so.<br />I would also add that beneficial mutations can also produce effects that are "very slight, but can be very large."Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48288488374164751502012-06-27T11:30:37.889-04:002012-06-27T11:30:37.889-04:00Why does the DI need so many lawyers?Why does the DI need so many lawyers?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91722993040717819572012-06-27T09:43:30.366-04:002012-06-27T09:43:30.366-04:00Oh, I know perfectly well that "Intelligent D...Oh, I know perfectly well that "Intelligent Design" doesn't say anything at all, so that it is compatible with anything, including evolution. ID, in all of its vacuity, does get a bit tedious.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71963020050786109022012-06-27T08:17:55.059-04:002012-06-27T08:17:55.059-04:00You can't compare a qualitative feature saying...You can't compare a qualitative feature saying it has increased or decreased over time: it would be meaningless.<br />On the other hand, you can easily define a quantitative measure of information contained in the genome (it requires just a conversion from the base 4 to the base 2). Unfortunately, the quantitative measure of information thus defined does not support your claims. Too bad for your claims (you may still cherrypick the other possibility, namely "too bad for the qualitative measure of information", in order to "save" your claims from being duly rejected).M. Dionisnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52928848407740139122012-06-27T07:22:48.400-04:002012-06-27T07:22:48.400-04:00That is because information is fundamentally quali...That is because information is fundamentally <i>qualitative</i> in nature. However, some aspects of biochemical information may be quantitative - such as the catalytic properties and reaction rates of enzymes.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11154684938016269542012-06-27T07:01:47.051-04:002012-06-27T07:01:47.051-04:00By the way, lest there be any confusion, I am not ...By the way, lest there be any confusion, I am not arguing for a view of evolution as tending toward ever <i>more</i> complex forms over time. Both gains and losses of form and function occur over time via evolution and the processes that affect it, like contingency.<br /><br />The only overall tendency in all of this is one Stephen Jay Gould described in his book <i>Full House</i>. Since anything more simple than the simplest forms of life is not life, the "tree" of life is more like a bush growing against a wall. It can branch in the direction of equal or more complexity, but not of less or else it isn't life any more. Thus by far the greatest result of evolution is life of complexity equal to, not greater than, the ancestral forms. There are occasional outbreaks of greater complexity, like onions, salamanders, and to a lesser extent (at least based on genome size), us.Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24896222604110813402012-06-27T02:26:02.089-04:002012-06-27T02:26:02.089-04:00Well, if one would admit that the ultimate result ...Well, if one would admit that the ultimate result of the evolutionary process is Atheistoclast himself, his considerations would be actually consistent with his display on here: he shows a blatant lack of information and a clear inability to step towards higher & more complex levels of understanding. <br /><br />More seriously, it is obvious that when he writes "GO TO BED GO TO BED GO TO BED contains no more information than GO TO BED" he completely forgets about counting: even without getting into deeper computations it is easy to note that the string "GO TO BED" contains a certain message encoded in words with meaning, while the string "GO TO BED GO TO BED GO TO BED" contains the same message <b>plus</b> the supplementary information that it is repeated three times, which constitutes of course new information. Moreover, if instead of English words we think about initially perfect duplication of a gene, the mutations will affect differently the two copies (unless some very unlikely scenario happens and they both follow the same more or less random process) and they will tend to accumulate more and more information (of the kind "the n-th nucleotide is no longer an A but a C in the copied gene") over the time. Ultimately, after a long evolutionary time, the two genes could code for radically different proteins having also unrelated functions, that is the information increase would correspond to new different "meanings".M. Dionisnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75780597125695147132012-06-26T21:24:49.374-04:002012-06-26T21:24:49.374-04:00As Atheistoclast points out, only reduction in inf...As Atheistoclast points out, only reduction in information is possible, so only simplification of the originally created "kinds" can occur, resulting in the toverwhelming tendency toward ever simpler forms through time we clearly see in the fossil recor - oh, wait....Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87624466115770250102012-06-26T20:45:19.018-04:002012-06-26T20:45:19.018-04:00Please don't say "yes" and follow it...Please don't say "yes" and follow it with something quite different from what I said. That's cheesy.<br /><br />How about this one:<br /><br />1. Molecular evolution is reversible.<br />2. Mutations can lose information.<br />3. Therefore, the reverse mutation can gain information.john harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33078556340172226272012-06-26T20:42:59.330-04:002012-06-26T20:42:59.330-04:00Your definition is too vague to be useful. Another...Your definition is too vague to be useful. Another failing is that it isn't at all quantitative. If you can't quantify information, how do you know whether it's increased? And you've already claimed that both gains and losses of specificity are reductions in information.john harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55141985783872045902012-06-26T19:47:59.210-04:002012-06-26T19:47:59.210-04:00Negative entropy,
1. No a copy is not new informa...<b>Negative entropy</b>,<br /><br />1. No a copy is not new information: GO TO BED GO TO BED GO TO BED contains no more information than GO TO BED. <br /><br />2.Changes often scramble existing information.<br /><br />3. No, they show slight modifications to pre-existing activities.<br /><br />4. The examples provided are some of the most cited.<br /><br />5. Nope, I surveyed most of the literature. Most scientists would agree with me that gene duplication does not explain the origins of the really important molecular features, notably protein motifs and regulatory sequences.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17744858881453160692012-06-26T19:43:42.443-04:002012-06-26T19:43:42.443-04:00John, "Information" in the context of mo...John, "Information" in the context of molecular biology refers to the instructions encoded in DNA that confer biochemical function. Shannon defined information as the "reduction of uncertainty". Biological information is precisely that - it reduces uncertainty by providing specificity. I suggest you read this paper:<br /><br />http://octavia.zoology.washington.edu/publications/GodfreySmith11.pdfAtheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34147335687924341172012-06-26T19:35:27.501-04:002012-06-26T19:35:27.501-04:00Yes, John, the vast majority of mutations involve ...Yes, John, the vast majority of mutations involve a loss of function. Often it is very slight, but can be very large.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14899071146684866072012-06-26T19:34:30.294-04:002012-06-26T19:34:30.294-04:00especially so with the advocates of "Intellig...<i> especially so with the advocates of "Intelligent Design", is that they don't give a description of what their alternative is to evolutionary biology. </i> Anonymous. <br /><br />Now, here is an example of someone not understanding that you can believe that evolution, as it happened, in every detail is an intelligent design. <br /><br />A very large percentage, I'd guess most, of the people who accept evolution believe something like that, though they might also realize that their belief isn't a part of science, proper. <br /><br />It would be really helpful if scientists were more specific about what is said about science that is science, proper, and science, not exactly. It might help the laity from being confused.The Thought Criminalhttps://www.blogger.com/profile/01381376556757084468noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76281387749857333552012-06-26T17:01:46.099-04:002012-06-26T17:01:46.099-04:00So a less permeable membrane is a loss of function...So a less permeable membrane is a loss of function, and a more permeable membrane is a loss of function too. Why not just admit that every conceivable change is a loss of function?john harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86955144571412492662012-06-26T17:01:44.608-04:002012-06-26T17:01:44.608-04:00There are no limits to certain infinite series, su...There are no limits to certain infinite series, such as 1 + 1 + 1 + .... Mutations keep adding up indefinitely like this. Populations which does not become extinct, keep evolving indefinitely.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67073730047097648852012-06-26T17:00:01.652-04:002012-06-26T17:00:01.652-04:00Atheistoclast: Still don't know what "inf...Atheistoclast: Still don't know what "information" means. Lacking a definition, your comments only confuse the question. You clearly aren't using Shannon information. But what are you using?John Harshmannoreply@blogger.com