tag:blogger.com,1999:blog-37148773.post4869916273334001680..comments2024-03-19T09:50:39.449-04:00Comments on <center>Sandwalk</center>: Elizabeth Pennisi writes about Richard Lenski's long-term evolution experimentLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger37125tag:blogger.com,1999:blog-37148773.post-79038189318433639072013-12-04T12:30:28.174-05:002013-12-04T12:30:28.174-05:00Robert, you're the one who tries to change a t...Robert, you're the one who tries to change a thread every time you post a comment in one. All you do is deny anything that pertains to actual science and you push your YEC religious beliefs. You obviously think that your assertions and questions are legitimate and sciency but it's abundantly clear that you just won't accept anything that challenges or refutes christian YEC fairy tales. <br /><br />One of the points of mine that you are ignorantly dismissing is that no matter how much you try to to assert that evolution is "Just leaps and great stasis" or that "there is no evidence any evolution is going on" or that "constantly evolving is practically, i say practically, non existent" or that "there has been LITTLE or no evolution in great time periods" (make up your mind), the universe, the Earth, and life on Earth are OLD. Very, very OLD. Billions of years OLD. <br /><br />The other point is that none of your inconsistent or erroneous assertions about evolution and science provide any supportive, scientific evidence for your religious beliefs. <br /><br />By the way, how can there be "great time periods" if the whole universe is only 6,000 years old? <br />The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81061168215461253302013-12-04T10:51:43.491-05:002013-12-04T10:51:43.491-05:00And if anyone wants to read an article that (judgi...And if anyone wants to read an article that (judging from the abstract) is going to present what I would call the conventional view linking stasis to stabilizing selection, see: <br /><br />Estes, S. and S.J. Arnold, Resolving the paradox of stasis: models with stabilizing selection explain evolutionary divergence on all timescales. The American Naturalist, 2007. 169(2): p. 227-44.<br /><br />Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61845479590171298102013-12-04T07:49:10.662-05:002013-12-04T07:49:10.662-05:00Oh, and by the way, I stand corrected-- I mis-spok...Oh, and by the way, I stand corrected-- I mis-spoke when I said "classical dynamics". This is the point in chemicalscum's first paragraph-- the calculations in GAMESS are based on molecular orbital theory, which is based on quantum mechanics. So, this is not "classical dynamics", although in practice this kind of calculation does not allow quantum uncertainty to percolate up and result in indeterminate folding outcomes (if I understand correctly, this is the point in chemicalscum's second paragraph). Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33818909365261871882013-12-04T07:43:25.061-05:002013-12-04T07:43:25.061-05:00chemicalscum, thanks for writing this. You seem ...chemicalscum, thanks for writing this. You seem to know more about this issue than I do, though I'm quite skeptical of the claim in the arXiv paper that you cite. My experience is that I have seen many naive claims from biologists who don't know about physical biochemistry, physicists who don't know about the biology of mutation, and philosophers who don't know about either one, and I've discussed some of the issues with a colleague who is a quantum chemist (first author of http://www.annualreviews.org/doi/abs/10.1146/annurev.pc.35.100184.002041?journalCode=physchem, now retired). I'm currently writing a paper on mutation and randomness and I want to be sure to get this part right. Can you contact me to discuss this offline? I'm easy to find. Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46410032328557020502013-12-03T21:15:51.683-05:002013-12-03T21:15:51.683-05:00The difference was important relative to the discu...The difference was important relative to the discussion. Your changing the thread here.<br />Its a good point for creationism about claims that creatures lived soooo long but look so alike to modern relatives YET are said to have been evolving ever since the old fossil was found.<br />Very unlikely for a system saying evolution is constantly going on in all creatures.<br />The living fossil thing says otherwise at the least.<br />In fact there is no evidence any evolution going on. Just evidence for diversity within types. Anyways only the geology is "evidence" for evolutionary change. The biology of data points is silent.Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-83167902373725962472013-12-03T20:52:52.733-05:002013-12-03T20:52:52.733-05:00The copy of GAMESS (General Atomic and Molecular S...The copy of GAMESS (General Atomic and Molecular Structure System) that I have on the hard drive of this computer has routines for doing QM/MM calculations and using FMO (Fragment Molecular Orbital Theory) that enables calculations on very large systems. These routines can be used as part of protein folding studies. <br /><br />However this is not important. Like the ab initio, semi-empirical and DFT QM calculations I perform as a pharmaceutical chemist on much smaller systems, the calculations use the time independent form of the Schrödinger equation and treat the wavefunction of the molecule as a standing wave. In determining a molecular structure the QM programs seek out thermodynamic minima just the same a molecular mechanics (MM) ones do. This is static not dynamic and therefore is not relevant to evolutionary processes as here the wavefunction does not evolve.<br /><br />What is interesting are quantum processes where forking into different states is possible, such as the Schrödinger cat thought experiment. Here we have the (sorry about the bad spacing) density matrix in Dirac notation:<br /><br />|cat alive> |cat alive + cat dead><br />|cat alive - cat dead> |cat dead> <br /><br />Decoherence (interaction with the environment) destroys the off-diagonal elements of the matrix) leaving behind the trace, here two vectors in Hilbert space: |cat alive> and |cat dead> which continue to evolve independently and in parallel. <br /><br />This can simply be changed for a specific mutation in DNA that is caused by a QM event to this density matrix:<br /><br />|no mutation> |no mutation + mutation><br />|no mutation - mutation> |mutation> <br /><br />Again were are left with two vectors which continue to evolve independently and in parallel in Hilbert space. That is there are two different genomes evolving independently and in parallel in Hilbert space.<br /><br />The Löwdin mechanism proposed for some DNA mutations uses quantum tunnelling and thus is definitely a quantum stochastic process. <br /><br />I would draw attention to Andy Albrecht's arXiv paper I reference above where he argues "using simple models that all successful practical uses of probabilities originate in quantum fluctuations in the microscopic physical world around us, often propagated to macroscopic scales". In the above analyses the quantum event is clearly propagated to the macroscopic scale.<br /><br />Arlis you are right about the not. I didn't really think about the not vaguely remembering lots of deterministic looking equations when I tried to do a bit of self study of population genetics. Then it is dealing with probabilities and as argued above all probabilities ultimately derive from the quantum level. Dealing with populations is a bit like statistical thermodynamics, at root there is quantum indeterminacy at the atomic and molecular level which even Boltzmann didn't know about but for large ensembles there is FAPP determinism. Its when you deal with interesting complex individual things like cats and an individual DNA molecules that "worlds" or "histories" (use your favourite terminology here) split and evolve on separate parallel pathways.<br /><br />There is no classical world as quantum indeterminacy is continually welling up to the macroscopic level. This is why we live in a stochastic quasi-classical world.<br />chemicalscumhttps://www.blogger.com/profile/00456611765432242326noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61263636531066270572013-12-03T16:30:46.644-05:002013-12-03T16:30:46.644-05:00There are many alternatives to the Darwin-Fisher e...There are many alternatives to the Darwin-Fisher extreme view in which everything varies and selection keeps the population close to the current optimum. <br /><br />Wright's alternative doesn't really challenge this presumption, but emphasizes the importance of interactions, such that there are better optima that are not locally accessible via continuous upward (in terms of fitness) shifts. An interconnected set of demes that are individually subject to drift can overcome this challenge via the shifting balance mechanism (in theory). This is sort of like turning up the heat in simulated annealing. <br /><br />There is a structuralist alternative (invoked for over a century) that focuses on the idea that the organism is not infinitely malleable. Only certain types of changes are genetically-developmentally possible. When these "constraints" are limits on the variation that the system is capable of generating (i.e., system A can't generate a variant B), then it is clearly an alternative to the standard view. When "constraints" are understood as effects of selection (we can't get from A to B to C because B has a lower fitness), then this is less of a departure. Often it's hard to tell. But the structuralist would argue that stasis is often due to "constraints". When constraints are due to selection this is only slightly different from the Darwin-Fisher view, except that structuralists tend to rejection the assumption of natura non facit saltum. <br /><br />IMHO, this ambiguity is a reason that "constraints" has faded away as an alternative paradigm. If the currently accepted paradigm is P, then it's pretty hard to sell I-just-can't-decide-between-P-or-Q as a revolutionary alternative. <br /><br />There may be other views of stasis but nothing occurs to me at the moment. Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75329215969033150902013-12-03T12:50:30.763-05:002013-12-03T12:50:30.763-05:00Thanks Arlin, got it. Just for clarity, would you...Thanks Arlin, got it. Just for clarity, would you care to provide a summary of a non-ultra-adaptationist alternative?judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30801784209723763602013-12-03T10:52:07.539-05:002013-12-03T10:52:07.539-05:00I don't think you are missing anything. It...I don't think you are missing anything. It's just that your scenario conflicts implicitly with the premise that selection is powerful. If selection is ultra-powerful, then there can't be any neutral variation. <br /><br />The way that neo-Darwinians have negotiated this implicit conflict is to suppose that there are important features directly impacted by selection, and non-important ones that are hidden. The old neo-Darwinian rules still apply to everything important, but they don't apply at the "molecular level". <br /><br />This resolves the seeming conflict in which "living fossils" (horseshoe crab, coelocanth, platypus, snapping turtle, crocodile, chambered nautilus, etc) are morphologically stable for 10s or 100s of MY, yet still change at the molecular level. <br /><br />However, we still have to explain stasis in the "important" morphological features of all those "living fossils", and the neo-Darwinian explanation is, as always, selection. If important things change, it's selection. If they don't change, that's due to selection as well. Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1343540756121225182013-12-03T10:14:09.681-05:002013-12-03T10:14:09.681-05:00I found this quote from a paper by Lenski et al. i...I found this quote from a paper by Lenski et al. in a <a href="http://www.slideshare.net/dangraur1953/the-imperfection-of-evolution-and-the-evolution-of-imperfection" rel="nofollow">presentation</a> that Graur put up a couple of days ago, and it might be relevant to the first point you raised, Larry: <br /><br />"<i>The evolution of a phenotype is contingent on the particular history of a population. Historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.</i>"<br /><br /><a href="http://www.pnas.org/content/105/23/7899.abstract" rel="nofollow">Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli</a><br /><br />unhttps://www.blogger.com/profile/02527051725365759129noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40520423895226368432013-12-03T09:25:28.243-05:002013-12-03T09:25:28.243-05:00Byers said:
"Yet if morphology is so similar...Byers said:<br /><br />"Yet if morphology is so similar , after so long, then it suggests that constantly evolving is practically, i say practically, non existent."<br /><br />What difference does it make whether evolution occurs "constantly" or not when it comes to supporting your religious fairy tales? Even if ALL evolution were to take a million year break now and then that wouldn't add one bit of evidence to support your ridiculous YEC beliefs. <br /><br />Whether evolution occurs "constantly" or in spurts or a mixture of the two, there's NO way, other than by deluding yourself, that the evidence of the multi-billion year history of the Earth and the evolution of its life forms can be crammed into a 6,000 year time span. <br />The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53239379745305244282013-12-03T01:21:40.485-05:002013-12-03T01:21:40.485-05:00Aaargh, I left the "u" out of "favo...Aaargh, I left the "u" out of "favourite"! Living in the USA is really screwing up my English :-(Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63101997234899493012013-12-03T01:16:31.707-05:002013-12-03T01:16:31.707-05:00Actually, the beat poet seems to have stumbled on ...Actually, the beat poet seems to have stumbled on something useful upthread. I think I'm going to adopt "ordinary attrition in nature with new mutations helping out" as my new favorite definition of evolution.<br /><br />Q: How are new species created?<br />A: Ordinary attrition in nature with new mutations helping out.<br /><br />What could be more apt than that?<br />Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40371304351079852542013-12-03T01:01:01.040-05:002013-12-03T01:01:01.040-05:00Ludicrous that Lenski still has to compete in the ...Ludicrous that Lenski still has to compete in the regular NSF pool to keep this going. Perhaps the most remarkable aspect of the experiment is that it didn't get randomly defunded by a grant panel somewhere along the way.Konradhttps://www.blogger.com/profile/06867375994008638278noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66516843304544847462013-12-02T22:08:44.109-05:002013-12-02T22:08:44.109-05:00It is a creationist point about how some creatures...It is a creationist point about how some creatures have not changed in looks for claimed ages in millions. Quite a lot of millions of years.<br />I have heard the present denial there are "living fossils" a word coined be evolutionists previously.<br />Yet if morphology is so similar , after so long, then it suggests that constantly evolving is practically, i say practically, non existent. Looking for differences is looking too hard. People have more differences then many creatures noted by posters here and many more mere millions of years old. Horses for example are said to look exactly, almost, like they did 20 million years ago in the miocene. etc.<br />in fact our own body parts could be said to be living fossils. Our eyes, hearing, immune system , liver, etc are identical to claimed relatives which must mean from that common descent there has been LITTLE or no evolution in great time periods.<br />I think evolution should cling to PE and not constantly evolving concepts. Just leaps and great stasis. <br />Robert Byershttps://www.blogger.com/profile/05631863870635096770noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-50694726883982714942013-12-02T21:21:31.727-05:002013-12-02T21:21:31.727-05:00Larry said something that I think relates to what ...Larry said something that I think relates to what I said about scale/degree:<br /><br />"The are a few examlpes of species where that evolution didn't result in big changes in gross morphology but even there you can measure changes if you look closely enough."<br /><br />Yes, even in cases where changes aren't easily noticeable, if a close enough look is taken and enough time is allowed, changes will be apparent and measurable, and I would think that this applies to life forms and everything else in the universe. The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18944572633636010382013-12-02T21:08:52.737-05:002013-12-02T21:08:52.737-05:00The idea of an unchanging environment (in the wild...The idea of an unchanging environment (in the wild) seems counter-reality to me. Something that should be considered when talking about unchanging environments or stoppage of evolution is scale or degree. On what time scale (or other scale) is an environment unchanging and on what time scale can or does evolution stop?<br /><br />As anthrosciguy said:<br /><br />"All climatic variation, all other species, including microorganisms, everything must stop for there to be an unchanging environment."<br /><br />Even if that could happen, for how long could it last? A nanosecond, a minute, an hour? <br /> The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33854334731665907992013-12-02T12:57:10.106-05:002013-12-02T12:57:10.106-05:00In a nutshell, the neo-Darwinian view is that ever...<i>In a nutshell, the neo-Darwinian view is that everything varies, and selection is powerful. The only way these 2 things can be true in the case of stasis is if the species is at an optimum.</i><br /><br />As a layperson I'm probably missing something relatively elementary here, but what if the vast majority or even all of the variation is with respect to alleles that are neutral wrt selection? (Say for example that any variation of non-neutral alleles is very tightly constrained.)judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72612201919133688102013-12-02T12:51:46.749-05:002013-12-02T12:51:46.749-05:00There are a few examlpes of species where that evo...<i>There are a few examlpes of species where that evolution didn't result in big changes in gross morphology</i><br /><br />That is what I meant by "some species relatively closely resemble their ancestors."judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86583392130916717922013-12-02T11:50:10.139-05:002013-12-02T11:50:10.139-05:00Creating a "living fossil" category isn&...Creating a "living fossil" category isn't the issue. The classical neo-Darwinian view of the Modern Synthesis is that species generally are close to an adaptive optimum. If the environment shifts, they quickly adapt via available variation. If a species is not exhibiting changes, this would mean that the environment is not changing. <br /><br />There has long been another line of argument that species may become burdened with a tangle of "constraints" that prevents effective change. <br /><br />I think it is fair to say that there has been a widespread belief in stasis as an evolutionary pattern (I'm not sure if this is what Pennisi is saying). It hardly matters to the paleontological pattern of stasis that some molecules are changing invisibly! One still has to explain the pattern of stasis in those features for which there is stasis! In a nutshell, the neo-Darwinian view is that everything varies, and selection is powerful. The only way these 2 things can be true in the case of stasis is if the species is at an optimum. Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89762072568676798792013-12-02T11:34:06.412-05:002013-12-02T11:34:06.412-05:00No, no, this is not correct. It's easy to be ...No, no, this is not correct. It's easy to be misled because quite a lot of nonsense has been written on this topic by biologists and philosophers who apparently have not discussed the issue with their local quantum chemist. Just because something happens at the molecular level does not mean it is "microscopic" in terms of quantum indeterminacy. This is a common misconception, e.g., it's in Monod's _Chance and Necessity_. Most of biochemistry is "macroscopic" relative to quantum effects. <br /><br />For instance, when computational chemists model the folding of a protein they use classical dynamics with force-fields-- think of taking a physical model of a molecule made out of springs and magnets and so on, and throwing this physical model in a clothes dryer for a few hours to see how it folds. That is the kind of process that they are modeling, which includes no quantum magic. <br /><br />*Some* things that happen at the molecular level are subject to quantum indeterminacy. For instance, some enzymes appear to make use of quantum tunneling in their active sites. Anything involving electromagnetic radiation of course is subject to indeterminacy. But not all mutations involve radiation, and even the ones that involve radiation only involve it in an early step, i.e., a UVB or X-ray photon causes (indeterministically) the formation of a reactive species such as peroxide, which then diffuses (quasi-deterministically) and causes damage, which is repaired (quasi-deterministically) by enzymes, which is where the mutation comes in. Of course the causal chain leading to the mutation is indeterminate if any event in the chain is indeterminate. <br /><br />chemicalscum, I think you left out "not" in the sentence "whether a specific mutation in a specific genome is fixed in a specific population size is effectively deterministic." The chance of fixation for a new mutation is 1/N for a neutral mutation (haploid case) and ~2s for a beneficial mutation. <br /><br />Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27345015287176772462013-12-02T09:16:51.716-05:002013-12-02T09:16:51.716-05:00""""So yes, I do have an objec...""""So yes, I do have an objection.""""<br /><br />Fine by me, I'm a microbial ecologist, so I don't care about those pesky anatomical details anyway ;p Your should email Graur, then. He's honestly interested in other's opinions on the subject for his book. And I will buy the book, so the more discussion of opinions the better.<br /><br /><br /><br /><br />""""Horseshoe crabs are a bit different. There are only a few species, and to my eye they do all look quite similar to each other and their fossil relatives. The differences are there, but they're subtle. Not so for the others.""""<br /><br /><br /><br />So there's "living fossils" after all? ;)<br /><br />Kidding asside, Graur does say in another post that:<br /><br />"""On the other hand, living fossils do exist. For a species to be considered a living fossil, it must possess a great number of plesiomorphies (i.e., ancestral traits), and these ancestral traits must be shown to be of great antiquity. How many plesiomorphies and what constitutes “great antiquity” should be specified in each case under study. Opinions may vary on these two issues, and some researchers, like Mark Robinson-Rechavi, may find the term objectionable a priori as it tends to color subsequent inferences. Nonetheless, it is possible to define objectively a taxon as a living fossil."""<br /><br />So it seems that there is some significant arbitraritry to what should constitute enough differences for something to be called a living fossil or not.<br /><br />Anyway, keep the discussion going, I'm interested.<br />Pedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69102710171662176732013-12-02T08:50:01.899-05:002013-12-02T08:50:01.899-05:00I would point out that all of Graur's "li...I would point out that all of Graur's "living fossils" (except the horseshoe crabs) are diverse clades within which there is considerable extant morphological disparity. To claim that they haven't changed in two or three hundred million years is to ignore both extant and fossil disparity. It's like saying that mammals are living fossils because <i>Morganucodon</i> has all the features of extant mammals.<br /><br />So yes, I do have an objection.<br /><br />Horseshoe crabs are a bit different. There are only a few species, and to my eye they do all look quite similar to each other and their fossil relatives. The differences are there, but they're subtle. Not so for the others.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58779176031254976892013-12-02T08:37:10.826-05:002013-12-02T08:37:10.826-05:00Copying errors occur at the molecular level and ar...Copying errors occur at the molecular level and are quantum stochastic processes. Andy Albrecht argues that all probabilistic processes are fundamentally quantum mechanical, http://arxiv.org/abs/1212.0953. On this basis one needs to understand the implications of this for all stochastic processes in understanding evolution both at the molecular level and for macroevolution. The quasi-classical world is fundamentaly quantum mechanical and this has ontological implications.chemicalscumhttps://www.blogger.com/profile/00456611765432242326noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30852936995305079632013-12-02T08:18:47.308-05:002013-12-02T08:18:47.308-05:00""" How is that even remotely possi...""" How is that even remotely possible."""<br /><br />You should tell that to the hyppies and some people at Greenpeace.Pedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.com