tag:blogger.com,1999:blog-37148773.post6515053809163943407..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The Top Ten Problems with DarwinismLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger94125tag:blogger.com,1999:blog-37148773.post-49118694710963399622012-07-20T08:58:20.359-04:002012-07-20T08:58:20.359-04:00Atheistoclast, see this paper.
Ventura M, et al...Atheistoclast, see this paper. <br /><br />Ventura M, et al. 2012. The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome research 22:1036-4rich lawlerhttp://www.propithecus-verreauxi.comnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11947376345275900072012-07-19T09:46:05.996-04:002012-07-19T09:46:05.996-04:00jim
"So in fact the evidence that reductioni...jim<br /><br />"So in fact the evidence that reductionism can work". Indeed, it works that way. Right. Thanks to Turing. I think that's the point Anderson (and other 'anti-reductionists' like e.g. R. Laughlin in physics, or Goldenfeld and Woese (2011) in biology) are trying to make: how do you get up from these circuits all the way to Turing. Or, how do you get (back again) from molecule to man? That's not a moot question as the people I mentioned, have shown.<br /><br />Anderson doesn't mention computers. He's talking solid state and body physics as an example, arguing that 'psychology is not applied biology, nor is biology applied chemistry'. <br /><br />I was not saying that reductionism doesn't work, or that it's not powerful.harry pinxterennoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79365269287744282982012-07-19T09:18:02.111-04:002012-07-19T09:18:02.111-04:00I think that J. Haldane knew what he was talking a...I think that J. Haldane knew what he was talking about, and especially what he was trying to say.harry pinxterennoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11102926398281868942012-07-18T09:06:32.588-04:002012-07-18T09:06:32.588-04:00Yet we know, thanks to Turing, that all the comple...Yet we know, thanks to Turing, that all the complex instructions which allow our computers to send information back and forth over the internet (and allow Siri to answer the question, "Is it raining?") can be reduced to a bunch of nested NAND circuits. So in fact the evidence that reductionism can work, from that one example, is quite powerful, it seems to me. (Haldane of course did not know this; I'm not sure about your Anderson - computers were not as amazing in 1972.) Bear in mind that we have not yet been able to build a super computer with the equivalent of 100 billion synapses.<br /><br />In any case, the logic of Haldane's case still escapes me. One of his premises seems to be that mechanical, reductionist processes are capable of, or even prone to, error. I would agree with that. But the world is full of false beliefs (possibly including all of us, at one time or another) - so no inconsistency with observation there. That's why we need the scientific method, to keep us honest.JimVhttps://www.blogger.com/profile/10198704789965278981noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1878670246784673582012-07-18T08:35:57.968-04:002012-07-18T08:35:57.968-04:00Actually the IDs are just echoing-- somewhat confu...Actually the IDs are just echoing-- somewhat confusingly-- what one reads in the scientific literature. Ernst Mayr famously predicted that the search for parallel genes and mutations underlying parallel changes would prove futile. Mayr's prediction follows from Fisher's rationalization of Darwin's pre-genetic concept of "natural selection" (which is the heart and soul of the Modern Synthesis) to the effect that smooth change happens at the phenotypic level because, at the genotypic level, there are infinitely many loci with variation affecting the trait, each one infinitesimal and additive. In this model, as in Darwin's original view, individual variations are like grains of sand-- each one is distinctive, for sure, but its uniqueness hardly matters because it is a tiny component of the whole sand-castle built by natural selection. <br /><br />Thus, to Darwin and his 20th-century followers, the notion that similar phenotypic changes (i.e,. parallel or convergent changes) must reflect identical mutations is silly, like imagining that two similar sand-castles must have grains of sand that are identical. This is the logical basis of Mayr's theoretical prediction. <br /><br />Mayr's prediction is famously wrong and is cited ad nauseam in the evo-devo literature. One also frequently finds statements revealing that the world's foremost experts on genotypic adaptation (e.g., Orr) understand that the emerging view of genetic adaptation is not the view advocated by 20th-century Darwinists. <br /><br />So, to summarize, the issue that is problematic for Darwinism, neo-Darwinism, and modern neo-Darwinism (the Modern Synthesis) is the discovery of frequent parallel genotypic evolution. This is not a contradiction of evolution, nor of population genetics, nor of the principle of differential reproduction-- it is a contradiction of the infinitesimalist theory advocated by Darwin, Fisher, Mayr, etc.Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84432874819352573142012-07-17T18:07:10.089-04:002012-07-17T18:07:10.089-04:00This isn't evolutionary biology, it's ideo...This isn't evolutionary biology, it's ideological babble. If atheists didn't endlessly assert that it was the nail in the coffin of God it would have probably never have developed into the disaster it's become for science.The Thought Criminalhttps://www.blogger.com/profile/01381376556757084468noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88110515658701348182012-07-17T17:28:53.122-04:002012-07-17T17:28:53.122-04:00I assume you hold to the Big Bang theory, right? T...<i>I assume you hold to the Big Bang theory, right? Then answer me this, a question of the same validity: What set it off?</i><br /><br />The most likely hypothesis is that a transient discontinuity in the quantum vacuum resulted in the creation of the matter in the universe. Because of CP violation, more particles then anti-particles were created so that the annihilation of particle/anti-particle pairs did not result in a return to the quantum vacuum, i.e. a residue of particles remained.SLCnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4053863251572577302012-07-17T15:23:40.735-04:002012-07-17T15:23:40.735-04:00What set it off?
I'm not a physicist, so do ...<i>What set it off? </i><br /><br />I'm not a physicist, so do not know what theories are held in highest esteem at the moment, but there are serious attempts to get at that. The problem, as with pre-LUCA evolution, is a lack of data...Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16299857168817837332012-07-17T15:16:35.669-04:002012-07-17T15:16:35.669-04:00I have repeatedly raised the issue of protein moti...<i>I have repeatedly raised the issue of protein motifs because, if the Darwinists actually provided a testable and plausible explanation for their origination, their ideology would become greatly more convincing and appealing to me.</i><br /><br />I seriously doubt that. But the fundamental requirement for making a protein 'motif' is the same as that for making any peptide chain - peptidyl transferase activity. Since you can't make protein catalysts without peptidyl transferase, early peptidyl transferase must have been a non-protein activity. It still is - things would get pretty messy if a protein tried to make protein. <br /><br />What's the shortest possible functional peptide chain?<br /><br />You can make some of the simpler motifs with just a handful of residues, or even a repeated unit such as polyglycine. You can combine different motifs in modular fashion to form higher-order structures. <br /><br />If every motif were dozens of residues in length, unrelated to all others and destroyed by the smallest substitution then yeah, maybe there would be an evolutionary puzzle. But that's not how it is.Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68251479141136836152012-07-17T14:56:49.281-04:002012-07-17T14:56:49.281-04:00"Who designed the designer" is a questio..."Who designed the designer" is a question that make an assumption, to wit that my 'design inference' premise is based on a preconceived notion, ergo a religious view. Both you, Dawkins and David Hume are asking an unanswerable question.<br /><br />I assume you hold to the Big Bang theory, right? Then answer me this, a question of the same validity: What set it off? Effects are often observed w/o a delineation of causality. <br /><br />ID does NOT postulate 'a designer', and in particular, a supreme god. Just because some of its adherents hold religious views that do, the 'Supreme God' premise is NOT a premise within ID, a further reason to discredit your (and Hume's) question.<br /><br />Design, where inferred, is just that, i.e. evidence that more than unguided natural causation can account for specific components within phylogenetic progressions (complexity, co-dependent systems, and novelty). ID makes no attempt to explain causalities from an <b>identity</b> standpoint.Lee Bowmanhttps://www.blogger.com/profile/11032697992689736055noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45182465559828608922012-07-17T13:12:17.299-04:002012-07-17T13:12:17.299-04:00There is no "body plan" contained in the...<i>There is no "body plan" contained in the genome. None of the biological structures and systems in your own body are represented somehow in DNA.</i><br /><br />Yeah, that would explain how my children resemble, respectively, a chive, a turtle and an amorphous blob. None of their form can be ascribed to anything inherited from my wife or me. Oh, hang on ...Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65010318164311507032012-07-17T12:19:01.610-04:002012-07-17T12:19:01.610-04:00Why insetad did evolution continue, to produce com...<i>Why insetad did evolution continue, to produce complex prokaryotes processing more than 10,000 genes, and more strikingly, eukaryotes, with their huge, elaboratedly regulated genomes: multiple tissue types; and even ability to develop mathematical theories of evolution?". Eugene Koonin. The Logic of Chance, 2012, 250.</i><br /><br />The answer to the question can be found on the next two pages in Koonin's book. Basically, it's the concept of non-adaptive genome evolution. Koonin argues that increases in complexity were actually neutral or maladaptive mutations that could not be overcome.<br /><br />In other words, complex prokaryotes, and even more complex eukaryotes, are an accident of evolution.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44151049211021730472012-07-17T12:03:04.392-04:002012-07-17T12:03:04.392-04:00This comment has been removed by the author.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71754383217097725352012-07-17T11:58:46.602-04:002012-07-17T11:58:46.602-04:00Do you really think that people in 1927 did not kn...Do you really think that people in 1927 did not know that the brain was composed of atoms?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45762989970160224022012-07-17T09:39:14.457-04:002012-07-17T09:39:14.457-04:00@ Lee Bowman,
Your flavor of ID is different tha...@ Lee Bowman, <br /><br />Your flavor of ID is different than the one offered by Luskin and Denny does differ in how awesome the designer is. But we were debating Luskin and Denny's version (the Christian God) who seems, by description, to not be one to make such bad design. <br /><br />Regarding yours, I ask again, who designed the designer? The introduction of a designer of any type just delays this same problem by one step. The religious invoke a super-being beyond the laws of space and time. How did your designer come to be?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36911351211089212882012-07-17T09:04:30.366-04:002012-07-17T09:04:30.366-04:00I'd like to know how JF thinks the chromosomal...I'd like to know how JF thinks the chromosomal fusion (of 2a and 2b) could have spread through the population when it effectively serves as a reproductive barrier. The guy with the fused chromosomes would likely not have been able to mate with anyone other than those with a similar condition. It is one reason why humans and chimps cannot interbreed successfully (not that I would want them to).Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12979541909861979722012-07-17T09:00:16.864-04:002012-07-17T09:00:16.864-04:00Apologies: I reacted to your comment without readi...Apologies: I reacted to your comment without reading a little further down to see whether you had already corrected it. Oops.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85792020709517824342012-07-17T08:59:30.423-04:002012-07-17T08:59:30.423-04:00I have repeatedly raised the issue of protein moti...I have repeatedly raised the issue of protein motifs because, if the Darwinists actually provided a testable and plausible explanation for their origination, their ideology would become greatly more convincing and appealing to me. But all they do is just invoke natural selection like it were some magic wand.<br /><br />There is no "body plan" contained in the genome. None of the biological structures and systems in your own body are represented somehow in DNA. Sure, protein production is absolutely necessary for morphogenesis to occur, but it doesn't explain why cells coalesce to form particular shapes of biological function.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14505592663070289122012-07-17T05:29:02.357-04:002012-07-17T05:29:02.357-04:00heleen
" its last sentence was known to be f...heleen<br /><br />" its last sentence was known to be false in 1927.<br />And hence I have no reason for supposing my brain to be composed of atoms<br />Clear error."<br /><br />could you, please, elaborate on this a bit? I am puzzled.harry pinxterennoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53879015817977343422012-07-17T05:25:37.064-04:002012-07-17T05:25:37.064-04:00Jim
I think the problem Haldane is trying to make...Jim<br /><br />I think the problem Haldane is trying to make is reductionism. 'All the arrows of explanation are pointing downwards', but still it is difficult to get upwards again, from the particles and forces back to the mind: reduction is easier than reconstruction (Anderson, more is different, 1972). That's the point I think. It's easier to test your beliefs about turbines, or computers for that matter, than ideas about the mind.harry pinxterennoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18868036715370991912012-07-16T22:15:26.666-04:002012-07-16T22:15:26.666-04:00The "Intelligent design" notion (I will ...The "Intelligent design" notion (I will not call it a theory) posits the existance of an intelligent designer, based on the intelligence they imagine behind the order in the physical world. <br /><br />I ask them: <br /><br />Does a TV have an intelligent design? They answer yes. <br /><br />In fact it doesn't. There are thousands of individual innovations, patents, and improvements behind a common contemporary TV. Not one designer, but thousands. <br /><br />Each such innovation provides a metaphor for the many individual adaptations that have rendered today's species. <br /><br />Just as market and technical pressures and the imperative to survive force certain design changes (improve or fail), others provide an advantage over competing species (improve and succeed) or models of televisions.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65493749415077061212012-07-16T21:05:29.085-04:002012-07-16T21:05:29.085-04:00Continuing with my post to Luskin's "junk...Continuing with my post to Luskin's "junk DNA" claim in the list of Top 10 problems with evolution [part 4]<br /><br />Casey, please answer the following questions:<br /><br />1. What fraction of all nucleotides in the human genome are now experimentally known to be functional—not just transcribed—but biochemically constrained as to sequence?<br /><br />2. Under ID theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from ID?<br /><br />3. Under evolutionary theory, what fraction of all nucleotides in the human genome would you predict to be biochemically constrained—and how do you compute that fraction from evolution?<br /><br />4. The science community may never forgive you for making up that story about how molecular biologists believe that ‘non-coding DNA = non-functional DNA.’ Casey, how do you sleep at night?Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7968022160892977042012-07-16T21:04:52.218-04:002012-07-16T21:04:52.218-04:00Continuing with my post to Luskin's "junk...Continuing with my post to Luskin's "junk DNA" claim in the list of Top 10 problems with evolution [part 3]:<br /><br /><b>Category #3 is for ID proponents to make quantitative statements that are simply false.</b> For example, in the OP above, Mr. Luskin linked to <a href="http://www.evolutionnews.org/2010/03/does_darrel_falks_junk_dna_arg033141.html" rel="nofollow">this ENV posting</a> which supposedly has evidence about false predictions of “Neo-Darwinism.” <br /><br />Here we find a rare quantitative (but obviously false) statement:<br /><br /><i> “But the [tiling array] study goes further, indicating for the first time that the vast majority of the 3 billion 'letters' of the human genetic code are busily toiling at an array of previously invisible tasks.”</i><br /><br />(Uh, for the first, and last, time.) At least that’s quantitative, but what’s wrong with it? It’s from a 2007 newspaper article, not a scientific publication, five years out of date and not correct when it was published. The claims that most of the genome is functional are all based on experiments using tiling arrays that allegedly showed almost all the genome was transcribed into RNA, though most of it at an extremely low level.<br /><br />However, the idea that ‘transcribed’ means ‘functional’ is a big assumption (the article uses the phrase “toiling away”), and at any rate, more recent research contradicts the 2007 claim. In 2010 research using a more accurate method, RNA-seq, showed that the tiling array data was unreliable and overestimated transcription, possibly due to cross-hybridization (in addition the RNA transcription apparatus is not perfectly specific and may make mistakes on rare occasions, still detectable by tiling arrays.) What’s worse, much of the transcribed regions are not evolutionarily conserved and/or are repetitive. Very hard to believe all that could be functional.<br /><br />See: van Bakel, H., Nislow, C., Blencowe, B. and Hughes, T. (2010) Most "Dark Matter" Transcripts Are Associated With Known Genes. PLoS Biology 8: e1000371 [doi:10.1371/journal.pbio.1000371]<br /><br />Larry Moran predicted results like this before the van Bakel study was published. <b>No ID proponent predicted this. Another falsified prediction of ID. </b><br /><br />So what fraction of nucleotides in the human genome are known to be functional?<br />Larry Moran summarizes <a href="http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html" rel="nofollow"> what we really know about junk DNA</a>. As of May, 2011, we know at least 8.7% of the human genome is essential or functional. As for junk, it is between 65 to 91.3%.<br /><br />The ID proponents mostly avoid Moran's arguments, and cannot contradict him. Here is <a href="http://www.evolutionnews.org/2011/12/larry_moran_def054371.html" rel="nofollow">an ID proponent at ENV trying but failing to refute Moran's points.</a> Read that post carefully-- the poster, Jonathan M, cannot factually state that most of the genome has been experimentally shown to be functional.<br /><br />Genes make up about 2% of the human genome. Currently we believe regulatory elements are smaller than genes. But let’s we go hog-wild, and let’s imagine that regulatory elements were 10 times larger than genes. Even in Casey’s dreams, well over 70% of the genome is still junk.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60304665739244566592012-07-16T21:01:04.327-04:002012-07-16T21:01:04.327-04:00Continuing with my post to Luskin's "junk...Continuing with my post to Luskin's "junk DNA" claim in the list of Top 10 problems with evolution [part 2]:<br /><br />These innuenodoes and false statements from ID proponents fall into three categories.<br /><br /><b>Category #1: I’ll call “vaguediction.”</b> This includes the use of weasel words to give a false impression of how much DNA is known to be functional—for instance, “much.”<br />Jonathan Wells: “The arguments by Dawkins, [Ken] Miller, Shermer, [Sean] Collins, [etc.] rest on the premise that most non-coding DNA is junk, without any significant biological function. [But] Much of the DNA they claim to be "junk" actually performs important functions in living cells.” [Well, The Myth of Junk DNA, p. 27. Note the first part of this sentence dishonestly portrays molecular biologists as believing ‘non-coding DNA = non-functional DNA.’]<br /><br />William Dembski: “If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.”—[First Things, 86, 21-27]<br /><br />What does “much” mean in the sentences above (note Mr. Luskin has made “much” statements many times)? “Much” is deliberately vague in order to be non-falsifiable.<br /><br />By “much” do they mean ten million nucleotides? Ten million might impress non-scientists, but it’s 0.3% of the genome. Does it mean 90% of the nucleotides in the genome? If that’s what they mean, it’s a factually false claim. This vague terminology--“much”-- impresses non-scientists, but scientists find it infuriating. Does “much” refer to an absolute count of nucleotides (in millions) or a relative fraction of the genome? Thousands? Millions? Billions? What the heck does it <i>mean? </i><br /><br />If these “much” statements of ID proponents have a definite meaning, they are factually false. If they have no definite meaning, they are not predictions and simply misleading.<br />Mr. Luskin: Do not say “much” ever again. Tell your readers: what fraction of nucleotides in human DNA will be functional, meaning biochemically constrained as to sequence?<br /><br /><b>Category #2 is to claim that entire classes of junk DNA are all functional, every last nucleotide of every last one, if an example can be found in which a small fraction of an instance of that type of junk DNA is functional.</b><br /><br />Casey Luskin: “Darwinists have commonly made this mistake with many types of "junk" DNA, now known to have function.”<br />This is false: in fact there are no types of junk DNA now known to have a function; if by “have a function” we mean that most or all of their nucleotides are biochemically constrained. <br /><br />Here is an example of the trick they pull. There are about 20,000 pseudogenes in the human genome, and a typical pseudogene may be 1,000 nucleotides. If 10 of those nucleotides (0.1% of one pseudogene out of 20,000) have been co-opted as, say, a regulatory element, then ID proponents like Jonathan Wells and Luskin assert that that whole pseudogene is now functional (because 0.1% of its nucleotides are constrained) and by extension, that that “type” of junk DNA is now proven to be “functional”, implying that all 20,000 pseudogenes are functional.<br /><br />In this way, ID proponents like Jonathan Wells and Luskin mislead their readers into thinking that 20-30 million nucleotides are now “functional”, because of the discovery of a few dozen functional nucleotides.<br /><br />They then repeat the trick for other classes of junk DNA, like defective transposons, Alus, etc. Presto! The whole genome is functional!Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81345880797644777282012-07-16T19:12:49.175-04:002012-07-16T19:12:49.175-04:001. Natural selection is a conserving force in Natu...<i>1. Natural selection is a conserving force in Nature. It tends to reduce variation rather than promote it. It is anti-evolutionary.</i><br /><br />Both Natural Selection and Drift tend to reduce variation rather than promote it. But you should, by now in your tireless Internet career, have come across these other evolutionary forces Mutation and Recombination. The variational and fixational forces TOGETHER form evolution. There isn't an 'evolutionary bit' and an 'anti-evolutionary bit'. <br /><br />When you introduce variation (by mutation or producing new combinations), Selection/Drift tends to eliminate it again. This does NOT mean that a population must therefore remain static - far from it. Can you really not see why? You appear to say that selection must always eliminate the most recent variant. How does it know which one that is?<br /><br /><i>2. As Luskin says, natural selection acting on random mutations does not adequately explain the origination of the important protein motifs [...]</i><br /><br />There are gaps in our knowledge? The hell you say! The jig's up, evolution is dead, long live the detailed explanation of the origin of these 'protein motifs' provided by good old ID. Feel free to fill us in on what that is. <br /><br /><i>3. An even bigger problem is that genomes don't seem to contain any morphological information [...]</i><br /><br />Development is not genetically controlled? Haha! Something non-heritable is at work, you think? A protein, perhaps? Produced by ... oh, never mind.Allan Millernoreply@blogger.com