tag:blogger.com,1999:blog-37148773.post7716824129040553422..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Branko Kozulic has questions about fixationLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger142125tag:blogger.com,1999:blog-37148773.post-59038568563061388232014-04-19T16:23:25.593-04:002014-04-19T16:23:25.593-04:00JoeG in a hilarious exchange with his arch enemy ...JoeG in a hilarious exchange with his arch enemy "Thorton". I'm sure the accusations made against him are totally without foundation.<br />http://tinyurl.com/lclqzck<br />aljones909https://www.blogger.com/profile/10277116174278206834noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82897835060509318152014-04-19T12:18:29.623-04:002014-04-19T12:18:29.623-04:00Joe Gallien repeatedly threatens scientists and/or...Joe Gallien repeatedly threatens scientists and/or atheists with violence and/or extermination, at the Intelligent Design website Uncommon Descent, where name-calling, insults and threats of violence or persecution are applauded-- as long as they're directed at scientists. UD treats Joe Gallien as their greatest intellectual. Here's his evidence against evolution:<br /><br />Joe Gallien: <i>"If this is true, that he [Mark Armitage] was fired for writing that paper and questioning evolutionism, then it is time for a <b>war- a bloody war</b> at that because this crap has to stop and obvioulsy <b>the only way to stop it is to rid the world of all the cry-baby loser materialists.</b>"</i><br />[<a href="http://www.uncommondescent.com/expelled/mark-armitage-possibily-the-latest-victim-of-darwinist-inquisition/#comment-466909" rel="nofollow">Joe G comments at UD</a>, August 6, 2013 at 7:15 am ]<br />Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35930889195399297172014-04-19T11:20:58.815-04:002014-04-19T11:20:58.815-04:00I see JoeG is a 'Field Service Engineer' a...I see JoeG is a 'Field Service Engineer' and fixes things "mechanical, electrical, electronic and personal". Washing machine repair man? Eminently qualified to contradict those who have actually been educated in biology.See rationalwiki for 'the salem hypotheses'. "engineers as a group have a noted tendency to pontificate on things well outside their area of expertise, to the point of actual fallacy. This phenomenon is so prevalent that users of talk.origins have come up with the Salem Hypothesis, which predicts that any creationist claiming scientific expertise or advanced degrees is likely to be an engineer."<br /><br />A sample of his blogging style:-<br />"Larry Moran- The Idiot Who Refuses to Get It"<br />"Kevin R, McCarthy- Still a Lying Little Bitch"<br />"A Dog is Still a Dog and Kevin McCarthy is Still a Moron"<br />aljones909https://www.blogger.com/profile/10277116174278206834noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67968364421797894532014-04-18T08:37:23.245-04:002014-04-18T08:37:23.245-04:00@John S. Wilkins:
Well, your post does provide amp...@John S. Wilkins:<br />Well, your post does provide ample reason to make the distinction between type and species.<br />Using potential gene flow as a definition is universal - you can easily apply this to bacteria (you've got different mechanisms of gene flow, but that's not something the definition can't handle). And it might turn out that some types consist of multiple species or that a species contains multiple types. In the extreme cases, most of non-multicellular life is one species, or conversely you get species consisting of a single individual. Neither of these is a problem for the concept.<br /><br />In the rest of your post you define something that definitely falls under the type label and is in fact close to the "cynical species concept": A species is whatever a competent taxonomist declares to be a species (in the common case of multiple opinions, pick a side). Types are useful, arguably even indispensable. But we do need a species concept to adequately adress questions about speciation and even to give a solid definition of macroevolution. You try to do these things with types and you end up with fuzzy nonsense.<br />A chemist picks up a bottle labeled "Water". The content has a density of 0.789 g/cm³ and it burns. The chemist should conclude that the bottle contains ethanol and was mislabeled. Instead he publishes a paper saying that water sometimes has the property of burning and can have lower densities. Spectral analysis also shows that water sometimes contains carbon. In short: There's something wrong with the usual concepts of water...<br />Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47747584665792527312014-04-18T08:24:25.724-04:002014-04-18T08:24:25.724-04:00The level of invective there (much of it reflectin...<i>The level of invective there (much of it reflecting hatred of gays and the tactic of baiting men by calling them women) has always been remarkable.</i><br /><br />I mentioned this regarding JoeG on another thread as well. As a generality, its perhaps not remarkable how often things like hostility toward science and emotional immaturity go together.SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70190148885844417412014-04-18T05:43:08.051-04:002014-04-18T05:43:08.051-04:00@John Wilkins,
Thanks, but now I'm even more ...@John Wilkins,<br /><br />Thanks, but now I'm even more confused. If I want to refer to the idealized definition of species as populations that cannot interbreed, as I wanted to do in this post, is there a term I can use? Apparently the old term "Biological Species Concept" has been modified. It's a shame that most internet sites are using it in the old way but I've seen lots of examples where bad definitions are widely used.<br /><br />I hope everyone reading this understands that I was not trying to pretend that real species were defined that way. I've written many posts about the problems of defining species and how scientists in different fields use different ways of defining a species.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35223348327526873382014-04-18T01:12:32.713-04:002014-04-18T01:12:32.713-04:00I take issue with the idea that the BSC isn't ...I take issue with the idea that the BSC isn't operational. At least, it can be. If there's any sympatry at all you can investigate gene flow, and this happens often enough. You can investigate selection against hybrids, and this too happens often enough. And if you know the nature of the isolating mechanism (which you frequently can in some taxa, e.g. birds) you can test whether that mechanism is operating in the present case, and this too happens often enough. John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14137153749796543722014-04-18T00:44:59.323-04:002014-04-18T00:44:59.323-04:00Some thoughts:
John is right about the BSC. Even ...Some thoughts:<br /><br />John is right about the BSC. Even in Coyne and Orr's recent Speciation book, they modify the Mayrian definition to include some introgression. Systematists have an operational concept of a "good species" which is a meld of morphological, genetic, reproductive and ecological conceptions, and these things (if they are things at all) are allowed to share genes via hybridisation. I was at a conference on hybridisation in primates, held in Göttingen a while back, and every specialist (in macaques, baboons, etc.) described repeated hybrids that were interfertile with one of the parental species.<br /><br />The BSC is not an operational definition, by the way. Almost no studies are done on introgressive breeding before identifying a species. This was an early critique of Mayr's definition by none other than Paul Ehrlich.<br /><br />As to "type concepts", I think this is an artificial distinction. I do think there are some "pure" notions of species (phylogenetic, genetic, ecological, etc.) and most "definitions" are a mix of criteria from these, but the notion that "species" applies solely to a class of multicellular sexual organisms is not now nor ever has been the standard rule. Instead, it is because people who describe species dealing with multicellular sexual organisms tend to overgeneralise from their own experience. Bacteriologists have troubles defining what counts as a species, to be sure, but nevertheless, they describe them. Likewise, some species (e.g., of lichens) are obligate or even facultative mutualisms between vastly different organisms.<br /><br />Finally I note that there is only one "concept": species. These are not concepts of species, but criteriological or theoretical *definitions* of species. A species has always been a sort of organism in which progeny resemble parents more than they resemble organisms from other sorts of organisms. All the rest is argument over preferred criteria for delimitation.John S. Wilkinshttps://www.blogger.com/profile/04417266986565803683noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71795079911447095362014-04-17T18:41:32.504-04:002014-04-17T18:41:32.504-04:00It seems like a bit of a hurdle. Have him learn to...It seems like a bit of a hurdle. Have him learn to read German, then track down Peils "Grundlagen der Biomathematik" which has been out of print for a while...<br /><br />@Piotr Gąsiorowski<br />I don't think it makes sense to think of it as an emergent property. A more apt relation migh tbe analogous to - say - differential equations. There are no "naked" differential equations in nature. A lot of natural processes can be described using differential equations, but if one was to say that differential equations were energy or matter one would be wrong. Information as a mathematical concept can be used to describe things in nature, but it isn't itself nature. Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63837230817183818752014-04-17T18:24:35.253-04:002014-04-17T18:24:35.253-04:00"I thought that systematicists used some of o..."I thought that systematicists used some of other 27(?) species concepts in their everyday work."<br /><br />Are all of them species concepts though? Arguably a lot of the "species concepts" are better refered to as type concepts. Generally we can take an approach that defines sets of organisms through some dynamical properties - in that case there is uncertaincy on which organisms belong to a particular set - or we can define a set of organisms through some diagnostic criteria - in which case there is uncertaincy about the dynamics.<br />Some authors would reserve the term species for the former and assign type to the latter and I agree with that position. The minimal position is that there should be separate terms.<br />Now type concepts are used, because they allow other people to identify what you are working on. If somebody works on E.coli, somebody else can figure out what that is. That doesn't imply that E.coli meets the criteria of a species concept. Generally a taxonomic paper will describe types and then present the hypothesis that these are also species. The former isn't testable - there's nothing that would falsify a type, but species status is. And hypotheses about the species status of some set of organisms generally are hypotheses about the species status of a particular type.<br /><br />The language convention has been somewhat popular in German literature and isn't really doing a lot of work in the english literature. But it is a useful convention and an awful lot of the discussions about species concepts get very clear once you adopt it.<br />Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77939288409179702772014-04-17T17:03:43.234-04:002014-04-17T17:03:43.234-04:00Well, joey g, are you going to respond to my point...Well, joey g, are you going to respond to my points and questions? How about Jem's request? Name some things (How about 5?) in nature that were/are not designed by the 'intelligent designer' (allah in your case) and how you know. I've asked you and other IDiots to do that many times and NONE of you ever do it. You all just ignore it and run away. <br /><br />Come on joey g, be a Real Man™ (LOL) and let's see what you've got. The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25786049035213821592014-04-17T10:31:26.672-04:002014-04-17T10:31:26.672-04:00Mayr didn't phrase it that way. He said "...Mayr didn't phrase it that way. He said "...interbreeding or potentially interbreeding populations...". That doesn't quite say that there must be zero introgression. And in fact Mayr at one point worked on ducks, and despite the fact that he was well aware of hybridization did not merge them all into a single species. Clearly even Mayr thought there was some give in the definition.<br /><br />So is it your fallback position that nobody actually uses the BSC? I would agree that nobody does if we accept your version as the real one. But most systematists at least claim to use the BSC, even though they allow for hybridization. Consider, for example, all the work on hybrid zones between species. Under your BSC, that was a nonsense sentence.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10204405857443538532014-04-17T10:25:44.861-04:002014-04-17T10:25:44.861-04:00Typo: "...Though Branko "Numerous Patent...Typo: "...Though Branko "Numerous Patents" Kozulić may refuse to accept it..."John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46109593114406066592014-04-17T08:57:15.579-04:002014-04-17T08:57:15.579-04:00That's a good point and unfortunately there...That's a good point and unfortunately there's quite a lot of ambiguity going around concerning the meaning of the word 'random'. If we go by Li and Graur's implied definition being 'evenly distributed across the total space of outcomes(with respect to fitness)', then mutations definitely aren't random, since they're mostly (nearly)neutral. A better word to use then would be 'stochastic', which basically means they must be analysed in terms of probability theory. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11138862958119495102014-04-17T08:34:45.052-04:002014-04-17T08:34:45.052-04:00@Simon Gunkel: Peil mainly discusses how populatio...@Simon Gunkel: <i>Peil mainly discusses how population genetics and statistical mechanics are related, mainly in that they are both stochastic theories and therefore can make use of the same mathematical tools in a lot of cases.</i><br /><br />So, unlike JoeG, Peil did not reject the relevance of population genetics to the study of evolution. Maybe JoeG would accept population genetics equations if they came from Peil.<br />Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16540712171581038062014-04-17T08:28:17.910-04:002014-04-17T08:28:17.910-04:00The level of invective there (much of it reflectin...The level of invective there (much of it reflecting hatred of gays and the tactic of baiting men by calling them women) has always been remarkable. JoeG is a Real Man™, obviously.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13136423612836443002014-04-17T06:52:03.272-04:002014-04-17T06:52:03.272-04:00if people want to really see what he is like see h...<i>if people want to really see what he is like see his own blog Intelligent Reasoning, easily found by searching on that phrase.</i><br /><br />Thanks, Joe F. Wowee. I see over in Joe G's alternate universe that Michael Behe is "correcting" Judge Jones (of the <i>Kitzmiller v. Dover</i> trial) with regard to evolution.<br /><br />Here in the real world, Behe's credibility was so thoroughly destroyed at that trial on cross-examination it's been suggested it should be used as a teaching example in law schools.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90433988867103240672014-04-17T06:39:13.807-04:002014-04-17T06:39:13.807-04:00and you think your ignorance means something- stra...<i>and you think your ignorance means something- strange</i><br /><br />Just when one thinks the irony can't get any richer, the fellow who's unaware of 170 years of science regarding "unguided evolution," and thus confidently proclaims there is none, says to someone <i>else</i> that they think their ignorance is meaningful.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40049379182726213362014-04-17T06:34:28.110-04:002014-04-17T06:34:28.110-04:00judmarc LoL! how does materialism explain rain and...<i>judmarc LoL! how does materialism explain rain and gravity?</i><br /><br />I have no idea at all what you're trying to ask here. I'm assuming you're aware of the science of how precipitation occurs, and general relativity (gravity).judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90468660170340809272014-04-17T06:19:00.170-04:002014-04-17T06:19:00.170-04:00Creationists who quote Peil somehow fail to reflec...Creationists who quote Peil somehow fail to reflect that, since information <i>requires</i> "matter" (mass/energy) as its vehicle, it must be an emergent property, <i>presupposing</i> the existence of mass/energy. It can't come from an immaterial god.Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86047245540166472882014-04-17T05:58:50.548-04:002014-04-17T05:58:50.548-04:00There's an eternal discrepancy between what &#...There's an eternal discrepancy between what 'random' means when biologists typically say it, and what mathematicians (including many population geneticists) mean. Li and Graur (somewhat surprisingly) seem to be treating 'nonrandom' as 'not equiprobable'. But that's still 'random', in a probabilistic sense, regardless of the importing of <i>yet another</i> definition, approximately according with 'unplanned, 'aimless'. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-48653054594534892762014-04-17T05:53:21.470-04:002014-04-17T05:53:21.470-04:00"Who, or what, is, or was, J Piel?"
Joe..."Who, or what, is, or was, J Piel?"<br /><br />Joe G *meant* 'Peil', but a random transcription error changed the function of his sentence. <br /><br /><br />Jemhttps://www.blogger.com/profile/10359685574788608040noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49158020281477099272014-04-17T05:49:31.740-04:002014-04-17T05:49:31.740-04:00"Ooh, show and tell, brilliant. Please show u..."Ooh, show and tell, brilliant. Please show us something in nature God didn't design, and explain how you know he didn't design it."<br /><br />Joe G. Still waiting. Or has a miracle happened, and you realized you couldn't open your mouth without sounding foolish? If so, now you've got proof of that concept, why not apply it more generally? Jemhttps://www.blogger.com/profile/10359685574788608040noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54218868025931353832014-04-17T05:39:18.597-04:002014-04-17T05:39:18.597-04:00Joe "Clueless about the subject he's atte...<b>Joe "Clueless about the subject he's attempting to criticize" G</b> fails as usual. Mutations are only said to be random with respect to their effect on fitness and even that statement is subject to some debate. <br /><br />"<i><b>Patterns of mutation</b><br />The direction of mutation is nonrandom. In particular, transitions were found<br />to occur more frequently than transversions. In animal nuclear DNA, transitions were found to account for about 60-70% of all mutations, whereas the proportion of transitions under random mutation is expected to be only 33%. Thus, in animal nuclear genomes, transitional mutations occur twice as frequently as transversions. In animal mitochondrial genomes, the ratio of transitions to transversions is about 15 to 20. Some nucleotides are more mutable than others. For example, in nuclear DNA of mammals, G and C tend to mutate more frequently than A and T.<br /><br /><b>Are mutations random?</b><br />Mutations are commonly said to occur "randomly." However, as we have<br />seen, mutations do not occur at random with respect to genomic location, nor do all types of mutations occur with equal frequency. So, what aspect of mutation is random? Mutations are claimed to be random in respect to their effect on the fitness of the organism carrying them (Chapter 2). That is, any given mutation is expected to occur with the same frequency under conditions in which this mutation confers an advantage on the organism carrying it, as under conditions in which this mutation confers no advantage or is deleterious. "It may seem a deplorable imperfection of nature," said Dobzhansky (1970), "that mutability is not restricted to changes that enhance the adeptness of their carriers." And indeed, the issue of whether mutations are random or not with respect to their effects on fitness is periodically debated in the literature, sometimes with fierce intensity (see, e.g., Hall 1990; Lenski and Mittler 1993; Rosenberg et al. 1994; and Sniegowski 1995).</i>"<br />Graur, D. and W-H. Li, 2000. Fundamentals of Molecular Evolution; <br />Second Edition. Link to a free<a href="http://www.ehu.es/biofisica/juanma/libros_no/Fundamentals+of+Molecular+Evolution.pdf" rel="nofollow">pdf version of the book</a>.Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47913549627443558492014-04-17T05:22:26.802-04:002014-04-17T05:22:26.802-04:00So ... the math that deals with the population-lev...So ... the math that deals with the population-level consequences of random birth and death is not "math that supports unguided evolution", and such a treatment is not a "model". Got it. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.com