Thursday, February 19, 2015

The top ten problems with evolution according to Intelligent Design Creationists

Most of Intelligent Design Creationism consists of whining about evolution. Their main goal seems to be to discredit scientists and evolution in order to lay the ground work for a new approach to science, one that demonstrates the existence of an intelligent designer.

Most of their criticisms of evolution are ridiculous but a few of them require a response. So far, after more than 25 years of whining, the creationists have utterly failed to make a convincing case against evolution.

Are they still trying? You bet. Casey Luskin has done us the favor of listing "The Top Ten Scientific Problems with Biological and Chemical Evolution" in a series of blog posts on Evolution News & Views (sic).

Here they are for your amusement.
  1. No Viable Mechanism to Generate a Primordial Soup. I think he's right about this one. But then, I don't think a primordial soup plays a role in the origin of life.
  2. Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code. This has nothing to do with the origin of the genetic code. It's an argument against "RNA world." Casey Luskin is correct. We don't know how the first information-containing molecules arose and how they came to be self-replicating.
  3. Step-by-Step Random Mutations Cannot Generate the Genetic Information Needed for Irreducible Complexity. Luskin is dead wrong about this one.
  4. Natural Selection Struggles to Fix Advantageous Traits in Populations. Casey Luskin doesn't understand modern evolutionary theory, and it shows.
  5. Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution. Casey Luskin doesn't understand modern evolutionary theory, and he doesn't understand the scientific literature. What else is new?
  6. Molecular Biology Has Failed to Yield a Grand "Tree of Life". Modern scientific discoveries have revealed that there may not be a universal tree of life common to all genes. Casey Luskin accepts the evidence but rejects the idea that scientific explanations can change when new data comes in.
  7. Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry. This is nonsense compounded by wishful thinking.
  8. Differences Between Vertebrate Embryos Contradict the Predictions of Common Ancestry. Dead wrong.
  9. Neo-Darwinism Struggles to Explain the Biogeographical Distribution of Many Specie. What?
  10. Neo-Darwinism's Long History of Inaccurate Predictions about Junk Organs and Junk DNA. You'll have to read that post yourself to see how many different ways Casey Luskin can go wrong and the very few ways he can go right.

169 comments :

  1. Casey, IIRC, has a geology degree. He was probably taught (as I was) that tectonic activity was the cause for things like flightless birds being in Australia, Africa, and South America. That's a problem because those birds didn't exist at the time of the big break up.

    Casey hasn't kept up in the literature though. Geologists and other scientists have pretty much abandoned that line of thinking for the rafting hypothesis, which has significant support from experiment, observation, and timing of fossils.

    ReplyDelete
    Replies
    1. Rafting? Doubtful. Flight, more likely. They weren't always flightless, you know. How can the timing of fossils support rafting, which could have happened at any time?

      Delete
    2. "Casey, IIRC, has a geology degree.

      Master's in Earth Science. In his published work he calls it geology.

      Delete
    3. "Casey, IIRC, has a geology degree.

      Master's in Earth Science. In his published work he calls it geology.

      Delete
    4. Sorry, I was ambiguous, there's lots of methods by which trans ocean movement could occur. Rafting, flight, island hopping (think as the Atlantic expanded), etc.

      If the fossils of such creatures are not present before the breakup, but they are after the breakup, then tectonic activity isn't the cause of the organisms being on both continents. Some other factor occurred... again, I used rafting as an example, but any method would account for it.

      Delete
    5. Ah, what you mean is that the timing of fossils largely precludes vicariance as an explanation for trans-oceanic distributions. And thus we must seek other explanations. Casey doesn't like rafting or, presumably, flight (and he was talking about monkeys anyway; no flying monkeys outside of Oz). Oddly enough, he never says what he does like.

      Delete
    6. heh, it's actually monkeys that put me on to this. I reviewed a book called The Monkey's Voyage by Alan de Queiroz. I all set to trash it, but he did what the ID people I'm used to don't. He provided a ton of evidence and a well written explanation. It's a good book, entertaining and well written. (My review: http://www.skepticink.com/smilodonsretreat/2014/01/27/the-monkeys-voyage-book-review/)

      Delete
    7. If I recall, it isn't just monkeys that appear at about that time. It's also caviomorph rodents. Something else too?

      Delete
  2. I only read #4, as one dose of Luskin's weasily writing is all I can stomach in one sitting. It is interesting that he is now widely quoting Mike Lynch. A few years back when I had a short run of trying to discuss this stuff at Uncommon Descent, "read some Lynch" was a refrain that I often wrote in response to the frequent claims about what NS can and cannot achieve. Well, it looks like some of them have finally read some Lynch, and have found a way to misinterpret and distort his message.

    ReplyDelete
    Replies
    1. It's ironic isn't it?

      The IDiots used to rant and rave about the limits of natural selection and how it couldn't explain lots of things. We used to tell them repeatedly that there's more to evolution than natural selection and urge them to catch up on modern evolutionary theory.

      Now that some of them have finally learned about random genetic drift they completely ignore all the strawman arguments against evolution that they were promoting just a few years ago. Even worse, most of them still use those arguments.

      Delete
    2. Indeed. I saw Stephen C. Meyer speak in New Zealand at the start of this week. He literally reduced evolutionary theory to being random mutation and natural selection. It is astonishing that someone with a PhD in the philosophy and history of science can suggest that there isn't a modern version of evolutionary theory that incorporates mutation, selection, and drift, and the entailing complexities of nearly neutral population dynamics.

      Delete
    3. Yes I've seen the Lynch paper quoted quite a lot by various ID proponents recently on discussion forums. They like to quote the part where Lynch show the "average waiting time for two mutations" in a population of some size, is about 216 million years or thereabouts. Then they say "but humans and chimps differ by millions of mutations" therefore not enough time for life to evolve QED.

      They don't understand what Lynch is calculating there, they think he's calculating the average time to establishment of just any two mutations, instead of what he's actually calculating: the average waiting time for the establishment of two particular mutations.

      When this is pointed out to them, they either:
      1) Outright deny there's a difference, or
      2) Ignore it and keep citing the Lynch paper as if it falsifies evolution.

      How do you argue with such people? What is more interesting is also how they got this misconception in the first place? I've seen this particular misconception about Lynch's work now several time parroted, so I gather they all get this shit from the same source who's either dishonest or laboring under the same misapprehension.

      Anyone run into any of the higher-ups in the ID movement(Behe, Meyer, Luskin?) actually cite Lynch as if it was in their favor? I'd be interested to see how this crap originates.

      Delete
    4. Incidentally, I think the estimate of 216 MY comes from Durrett and Schmidt (2008). Curiously, IDCs rarely cite Lynch's 2005 paper that eviscerates the argument from Behe and Snokes about protein evolution and waiting times. For example, Ann Gauger is quoted in Luskin's #4 as saying that Lynch "offers no explanation of how non-adaptive forces can produce the functional genomic and organismal complexity we observe in modern species". It's a farce.

      Delete
    5. They don't understand what Lynch is calculating there, they think he's calculating the average time to establishment of just any two mutations, instead of what he's actually calculating: the average waiting time for the establishment of two particular mutations.

      Yes. The difference is analogous to that between the odds of you winning the lottery, and of the lottery being won by someone, anyone.

      Delete
    6. Incidentally, I think the estimate of 216 MY comes from Durrett and Schmidt (2008).

      Yes:

      http://people.mbi.ohio-state.edu/dschmidt/genetics.pdf

      The hilarious thing is that much of the article is devoted to debunking some of the claims made by Michael Behe, naming him specifically.

      Delete
    7. Ahh okay, I misrembered the author. But this is what gets me, how is it possible to so massively misconstrue what that paper says that you end up thinking it's arguing in favor of ID and against evolution?

      How steeped in apologetics and religious propaganda are the morons who frequent Uncommon Descent and other Discovery Institute related websites when they end up getting these impressions? It's simply amazing to me.

      Delete
    8. And, remember, it's not just the stupid creationists who are not scientists making this error. It is also being made by Behe, himself, who is one of the smarter creationists and is an actual scientist. That's when one starts to suspect that it is not just incompetence involved here, but outright dishonesty.

      Delete
    9. Paul McBride said:

      "Indeed. I saw Stephen C. Meyer speak in New Zealand at the start of this week. He literally reduced evolutionary theory to being random mutation and natural selection. It is astonishing that someone with a PhD in the philosophy and history of science can suggest that there isn't a modern version of evolutionary theory that incorporates mutation, selection, and drift, and the entailing complexities of nearly neutral population dynamics."

      Creatiionists, whether of the IDiot variety or otherwise, have been attacking "Darwinism" and Darwin himself for a very long time and they are obviously determined to stay in that rut, no matter what is actually involved in modern evolutionary theory. And they are determined to make it personal by focusing on Darwin. To them, he's the 'authority' figure that they must destroy. He's the Satan to their 'God', the demon to their 'angels', and the anti-christ. The obsessive hatred they have for Darwin is way out of control, to put it mildly.

      Delete
    10. Paul: "IDCs rarely cite Lynch's 2005 paper that eviscerates the argument from Behe and Snokes about protein evolution and waiting times"

      Do you have a reference for that?

      Delete
    11. That's when one starts to suspect that it is not just incompetence involved here, but outright dishonesty

      If one remembers that ID is not a scientific endeavour but rather a political one, dishonesty becomes less difficult to fathom.

      Its no different than the less sophisticated strategies of creationists past (and present). Claim that a scientific principle (eg the 2nd law of thermo) disproves evolution. In a debate they might even acknowledge that they are wrong about that, but then in the very next speaking engagement repeat the falsehood to a new scientifically-iliterate audience.

      This isn't actually about proving science right or wrong, but mostly about maintaining an otherwise unwarranted faith in god in as wide a population as possible, and consequently as much a theocratic power structure in society as possible. I think.

      Delete
    12. Paul: "IDCs rarely cite Lynch's 2005 paper that eviscerates the argument from Behe and Snokes about protein evolution and waiting times"

      Presumably this one:

      Lynch, Michael (September 2005). "Simple evolutionary pathways to complex proteins". Protein Science. 14 (9): 2217–2225. doi:10.1110/ps.041171805. ISSN 0961-8368. PMC 2253472. PMID 16131652.

      Behe’s rebuttal to Lynch's rebuttal:

      Behe, Michael J.; Snoke, David W. (September 2005). "A response to Michael Lynch". Protein Science (Hoboken, NJ: Wiley-Blackwell) 14 (9): 2226–2227. doi:10.1110/ps.051674105. ISSN 0961-8368. PMC 2253464.

      Delete
    13. The whole truth: "Creatiionists, whether of the IDiot variety or otherwise, have been attacking "Darwinism" and Darwin himself for a very long time and they are obviously determined to stay in that rut, no matter what is actually involved in modern evolutionary theory. And they are determined to make it personal by focusing on Darwin. To them, he's the 'authority' figure that they must destroy. He's the Satan to their 'God', the demon to their 'angels', and the anti-christ. The obsessive hatred they have for Darwin is way out of control, to put it mildly."

      Very true. Meyer spent quite a bit of his "Darwin's Doubt" presentation talking about how confounded Darwin was about the Cambrian explosion, rather than focusing on modern scientific explanations of diversification. Even though I was expecting him to do this, I was *still* surprised at how unsophisticated it all was. He never even mentioned fundamental things like Hox genes. Instead, he just focussed on how phyla "suddenly" appeared, and how this can't be explained by genetics because of various computer programming analogies. It was embarrassing/nauseating.

      Delete
  3. 2. "Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code." Larry, you're wrong to say that Luskin is correct on this point. You say, to paraphrase, we can't explain it now (which itself is a questionable, though not unreasonable, claim), but that is not what Luskin nor any IDiot says.

    IDcreationists do not say, "We can't explain it now, therefore God." Rather, they claim there is some kind of alleged law of probability, like Specified Complexity or Ooga Booga Information, which proves that no possible future experiment could ever explain the origin of the genetic code. That is not at all like claiming we don't have enough knowledge. They say they know for certain that no natural process, which might be detailed later, could make the genetic code, because it is "semiotic" and it's exactly like Shakespearean sonnets, and only intelligent beings (= humans OR spooks) can make sonnets. Since a human wasn't there to do it, they have proved, and know for certain, that a spook did it. This is a positive claim to absolute certainty.

    I think you make a mistake in conceding too much to the hoaxers who brought us "Specified Complexity" and the "Semiotic Argument." This IDiots say that you DNA code is "digital" even though there are no digits in it, and that it's language-based though it has no grammar like any human language! Come on, we can't grant them such hoaxes.

    ReplyDelete
    Replies
    1. Not to mention that chemistry is not a computer, and copy errors in chemistry do not behave like errors in computer code.

      Delete
    2. Diogenes,

      Unlike you, I actually read what Casey Luskin wrote in his blog post. I pretty much agree with his conclusion that we can't explain how to get from primitive catalysts to DNA encoded proteins.

      I'm not sure that we will ever have a completely satisfactory explanation but that doesn't bother me and it doesn't mean that god did it.

      I think you make a mistake in conceding too much to the hoaxers ...

      I think you make a mistake by not taking some of their arguments seriously and by not admitting that there are lots of things we don't know at the present time.

      Delete
    3. " I pretty much agree with his conclusion that we can't explain how to get from primitive catalysts to DNA encoded proteins."

      I think we can, I have seen such explanations, it's just that we can't have any great confidence that they're correct. The problem isn't a lack of possible explanations, the problem is time has reversed so much data we can't ever be sure.

      I guess it comes down to what it means to for an explanation to be "completely satisfactory". If it means we should be able to reconstruct past events with great certainty from present data, then I agree we will never know. But that doesn't mean we cannot alight on, or already have, in principle explanations for the origin of an RNA-peptide world that evolves coded protein synthesis.

      With regards to what Diogenes is saying I agree, and I think you're making a mistake Larry. Diogenes is responding to the fact that Luskin is relying partly on heavily criticized bullshit probability calculations and apologetics principles invented by Theology-statistician William Dembski, such as his "upper probability bounds for the cosmos" and "no free lunch theorems". We should't just blindly accept arguments based on these bogus concepts. There might be(and are) legitimate problems with various RNA-world scenarios and self-replicators-first, but those arguments should stand on their own terms, not be propped up further by apologetics lies and fantasy statistics like the shit one finds in Dembski's work.

      Separate the wheat from the chaff so to speak.

      Delete
    4. I said,

      I pretty much agree with his conclusion that we can't explain how to get from primitive catalysts to DNA encoded proteins.

      Mikkel Rumraket Rasmussen says,

      I think we can, I have seen such explanations, it's just that we can't have any great confidence that they're correct.

      Do you really think there's a big difference between those statements?

      There might be(and are) legitimate problems with various RNA-world scenarios and self-replicators-first, but those arguments should stand on their own terms, ...

      I agree and that's exactly how I treated them. You and Diogenes, on the other hand, are muddying the waters by dragging in other arguments and criticizing Luskin's motives. Why not just admit, as I did, that there are legitimate problems?

      Separate the wheat from the chaff so to speak.

      I'm trying to do that. We don't know how life originated. That's a fact. Now let's deal with the argument that our lack of knowledge means that god did it.

      Delete
    5. "Do you really think there's a big difference between those statements?"

      Uhm, well yes that's why I responded the way I did. But now it seems like we essentially agree anyway, so okay. There was miscommunication.

      With respect to your latter point, I don't see any one here refusing to admit we don't know how life originated, but Luskin isn't just making an argument from ignorance.
      He's making an argument based partly on ignorance, but also partly on a bogus principle that if it was correct, would make it impossible for the emergence of life and the genetic code.

      So we can do both, we can point out the argument from ignorance, admit to the ignorance part and show it doesn't rationally lead to god anyway, and then we can refute the bogus principle too.

      It is not enough to just point out there's an argument from ignorance in there, when there's an actual false positive claim also.

      Delete
    6. Larry, I did not criticize Luskin's motives. I object to his invocations of Ooga Booga information theory.

      Larry in the OP: "Casey Luskin is correct. We don't know how the first information-containing molecules arose and how they came to be self-replicating."

      The word "information" occurs 14 times in Luskin's essay for problem 2. Let's look at a few uses:

      Luskin: "Third, the RNA world hypothesis does not explain the origin of genetic information."

      What would self-replicating RNA molecules do, except accumulate information?

      "But there is a much deeper problem with theories of chemical evolution, as well as biological evolution. This pertains not just to the ability to process genetic information via a genetic code, but the origin of that information itself."

      Uh huh. The usual Dembskian Ooga Booga Information (OBI) theory, or to ape Rumraket, Statistical Theology. I have zero tolerance for OBI.

      Delete
    7. Larry Moran: «I'm not sure that we will ever have a completely satisfactory explanation but that doesn't bother me and it doesn't mean that god did it.»

      Correct. And claiming otherwise would constitute an argument from ignorance, not to mention that what we in fact know about this points (at least) to the possibility that life originated naturally - much was accomplished in laboratory experiments simulating natural conditions and - it's like having a puzzle where pieces are missing, but we can give possible accounts that fit (some better than others) the rest of the puzzle, but without reaching any complete solution.

      Delete
    8. It gives the impression that the complete (and right) solution is nearby.

      Delete
    9. Larry says:

      "I'm not sure that we will ever have a completely satisfactory explanation but that doesn't bother me and it doesn't mean that god did it."

      I think you should be careful with this view. You have to remember the IMMENSE amount of time that humans have to solve this problem, given that nothing gets in the way our existence. Research into this still uninvented area of science will definitely be highly slow, and it'll probably only significantly speed up once we start exploring other solar systems and try to find chemical processes on distant planets that are similar to life or perhaps have already given rise to life. Is possible that we'll never have a completely satisfactory answer? I'ts really hard to say. But given that we have all the time in the universe to speculate and test theories, develop new methods and ways to extract information and analyse the limited data that we have better and better, I think that it's inevitable that we'll come up with a satisfactory answer.

      Delete
    10. Do 'unguided chemical processes' need to explain the origin of the genetic code? It's not far from saying 'unguided chemical processes cannot explain the origin of the liver'. If one determines that the origin of the code is an Origin-of-Life problem, one does so without a particularly firm base. Issues with RNA world notwithstanding.

      Delete
    11. I agree, we don’t know how life originated. Some of the earliest, most interesting steps are nearly entirely a mystery (as you mentioned, the origin of the first informational replicators is a big one). This often gets obscured by silly press releases claiming the new theory/molecule/reaction has “solved” the origin of life (see the recent stuff about Jeremy England work - interesting, but way exaggerated in the press). We should be upfront and clear about this uncertainty, it doesn’t help science education to argue for certainty when there isn’t any. HOWEVER, it’s also inaccurate to suggest that the history of life before the common ancestor is some complete, inscrutable mystery, and for all we know life with a modern translation system just popped into existence billions of years ago.

      Luskin is arguing (basically in the same form Meyer argued in SitC) that the RNA world doesn’t offer any insight into how the genetic code evolved. I’d say most scientists familiar with the data would disagree, even most metabolism-first folks who disagree with RNA-first theories. The evidence suggests the existence of RNA-based ancestors to modern life, most notably because the modern translation system does seem to have evolved from something simpler, and the most fundamental components of translation are RNA-, not protein-, based. We also know from in vitro evolution experiments that ribozymes can catalyze the basic reactions you’d need for a replicating, metabolizing, even crudely protein-translating cell. Luskin and Meyer ignore, misrepresent, or otherwise make a hash of this evidence. That a great deal about early life history remains unclear and that even more is unknown about what preceded it, doesn’t change that fact.

      Delete
    12. Larry, although the origin of life problem is unsolved, I think you're wrong in conceding that point to Casey Luskin. The reason is that, despite swearing his criticisms are entirely scientific, he doesn't carry out an unbiased discussion of the available data, as any honest science advocate must do. He cherry-picks only the data that suits his weird stories and deliberately distorts them, while leaving out the rest.

      Contrary to what Luskin is telling us, our knowledge on the origin of life subject is constantly increasing. Anyone interested should see these lectures by Jack Szostak:

      https://www.youtube.com/watch?v=PqPGOhXoprU
      https://www.youtube.com/watch?v=CJ5jh33OiOA
      https://www.youtube.com/watch?v=jfq5-i8xoIU

      Delete
    13. I don't find Szostak's scenarios particularly plausible. The lab is doing good work on the many physical mechanisms and interactions between lipid membranes and various genetic polymers, but I just don't see it tied to any plausible geochemical circumstances for the origin of life. It kinda lacks that bottom-up approach that starts with a natural environment and then tries to extract what happened, instead of making up a scenario and then imagining a natural environment that "fits it".

      I think this scenario by Nick Lane is significantly more plausible: Energy at the origin of life -- Nick Lane -- How Life on Earth Began event

      The audio quality gets much better about 4 minutes into the video, so it's definitely worth watching.

      Delete
    14. John

      Just to add on to what you were saying, I agree very strongly with you that at one time in life's history RNA was highly common, much much more than it is today. After all, why else would modern day translation systems use so much RNA? However, here's a study that seems to imply that the origin of the genetic code was much more complicated than what the usual RNA world theorist would tell you.

      http://r.search.yahoo.com/_ylt=A0LEVvXjyedUJH8AcGknnIlQ;_ylu=X3oDMTEzM2pkdDNiBHNlYwNzcgRwb3MDMQRjb2xvA2JmMQR2dGlkA1lIUzAwMl8x/RV=2/RE=1424505444/RO=10/RU=http%3a%2f%2fwww.ncbi.nlm.nih.gov%2fpmc%2farticles%2fPMC3299690%2f/RK=0/RS=j4oxVwnVk5hExwJ3Hed3vIbaB.4-

      www.rdmag.com/news/.../study-ribosome...rna-world-hypothesis

      Assuming there`s nothing insufficient about the studies methods, what their results came out as was that the r-RNA and the the ribosomal proteins co evolved with each other while the ribosome grew in complexity over time. What the exiting part of the result says is that the peptidyl transferase center, which is directly responsible for peptide bond formation, actually evolved AFTER the two subunits appeared, not the other way around, as was previously assumed. What this implies is that before the ribosome with it`s current function evolved, proteins were already in use in the cell.

      One way to interpret this is that proteins were being synthesized enzymatically; without a code but perhaps just ribozymes putting amino acids together. The problem with this is that it doesn`t explain the coded proteins that were in the sub units BEFORE the PTC appeared. What this implies, that there actually was coded proteins before the ribosome became functional, which means there must of been a coding system before the ribosome that we aren`t aware of. Ford Doolitle comments on this.

      "'This is a very engaging and provocative article by one of the most innovative and productive researchers in the field of protein evolution," said University of California at San Diego research professor Russell Doolittle, who was not involved in the study. Doolittle remains puzzled, however, by "the notion that some early proteins were made before the evolution of the ribosome as a protein-manufacturing system." He wondered how—if proteins were more ancient than the ribosomal machinery that today produces most of them—"the amino acid sequences of those early proteins were 'remembered' and incorporated into the new system.'"

      Please feel free to correct me on any of my points.

      Delete
    15. K mooney,

      I'm not sure which 'usual RNA world theorists' you had in mind, but the Harish & Caetano-Anolles paper is fairly well known (not least because Creationists trumpet it, not realising that it relies on phylogenetic methods whose validity they elsewhere argue against!). Discussed here

      Delete
  4. Re #2, a friend has an open access journal publication that makes interesting reading. "RNA Catalysis, Thermodynamics, and the Origin of Life," at http://www.mdpi.com/2075-1729/4/2/131/htm .

    ReplyDelete
  5. I notice that one thing Casey never does, at least in any of the posts I've sampled, is present his alternative hypothesis. I suppose he's an old-earth creationist, and I suppose he thinks that there are "kinds" at some unspecified level, possibly species. But he appears to have forgotten to say.

    ReplyDelete
    Replies
    1. "I notice that one thing Casey never does, at least in any of the posts I've sampled, is present his alternative hypothesis."

      He invokes rule 3 by Judge Jones: negative attacks on evolution aren't proof that goddidit.

      He has read Coyne's book though and realizes the damage for example geographical distribution of seemingly similar species can do on ID, so he turns the evidence 180 degrees around.

      Delete
    2. He doesn't mention an alternative because to humans, it couldn't be anything other than magic, an unsatisfying conclusion. No known or proposed mechanisms, no mechanism even knowable in principle.

      One gets the sense that even religious people, if they think about things too deeply, begin to sense the emptiness of their convictions. But still their faith is too important to abandon. It's no coincidence that the central tenet of most every religion is: Don't question, just obey. Questioning is a perilous path that can lead to dangerous notions.

      Delete
  6. What does the origin of life have to do with whether evolution can explain the diversification of life?

    "Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code."
    What the hell does this even mean? What's an "unguided" chemical process and why would the genetic code have to arise by such a thing? Plenty of theories for the origin of the code (and by that I mean the translation system), while relying on some kind of RNA-protein world to exist, are not intrinsically dependent on there being an actual self-replicator, or that RNA was the first stage of life.

    ReplyDelete
    Replies
    1. Ahh, I guess I should read his title, he also mentions chemical evolution which I take to mean the origin of life.

      It seems most of the efforts of IDcreationists against a natural origin of life are concentrated against RNA-first type theories, probably because they're the most well-known.

      Delete
    2. Mikkel: What the hell does this even mean? What's an "unguided" chemical process and why would the genetic code have to arise by such a thing?

      Ah, but you haven't studied Complex Specified Information Theory. According to Dembski's Law ot the Conservation of Information, CSI cannot be produced by any unguided natural process. The genetic code is an example of CSI, therefore it can't have a natural origin. As simple as that.

      Delete
    3. It is definitely shown that Complex Specified Information cannot be produced by any natural evolutionary process. How is this shown? Simply by defining CSI as not being present if a natural evolutionary process can produce the pattern. Dembski has clarified his notion to make clear that this is the way it is defined.

      So the argument now goes, after the clarification:

      1. We want to show that no natural evolutionary process can produce the adaptation.
      2. We show, by some means or other, that natural evolutionary processes cannot have produced the adaptation (how? we'll tell you later.)
      3. The adaptation is thus shown to be extemely improbable under natural evolutionary processes. It therefore has CSI.
      4. Thus the presence of CSI proves that natural evolutionary processes cannot have produced the adaptation.

      Thus the genetic code cannot have been produced by natural evolutionary processes. To show that all we have to do is show that it has CSI. And to show that all we have to do is first to show that it cannot have been produced by natural evolutionary processes.

      Isn't CSI helpful?

      Delete
    4. O/T: Piotr, as you have been spending some time at UD, you may enjoy an argument about quantum mechanics... and the Magic Quantum Shroud of Turin again! It was 10 of them against me, so they were outnumbered.

      Delete
    5. The magic Quantum shroud of Turin. I have never laughed so hard in my life. This is supreme-woo at a scale I have yet to fully understand. It's like very fucking idiotic deepity was forced into that single idea.

      Holy fucking shit that is some knee-deep brainshite on that site, fuck me.

      Delete
    6. I've been following it. It's been fun. But I see BA77 is now trying a new manoeuvre, probably anticipating how little impact Barrie Schwortz's Youtube testimonials are likely to have. You and your maths, Diogenes! Do you think you can impress BA77 with maths? Human maths is inevitably incomplete (Gödel), perhaps as a result of Original Sin, and only God can make it complete. And since Lie groups and differentiable manifolds have the power to interact with elementary particles and accelerating forces (no, it isn't Sokal, it's Berlinski, speaking in earnest!), we know how God manipulates things at the quantum level without getting his fingers entangled: he constructs a Lie group and pushes particles about with it.

      Delete
    7. Diogenes, that is a hilarious thread! I can only imagine that Banhammer Arrington will need to step in soon to restore order.

      Delete
    8. Piotr: "Human maths is inevitably incomplete (Gödel), perhaps as a result of Original Sin, and only God can make it complete. And since Lie groups and differentiable manifolds have the power to interact with elementary particles and accelerating forces (no, it isn't Sokal, it's Berlinski, speaking in earnest!), we know how God manipulates things at the quantum level without getting his fingers entangled: he constructs a Lie group and pushes particles about with it."

      Stop, Piotr, you've giving me flashbacks. The tented fingers...

      Delete
    9. How is this shown? Simply by defining CSI as not being present if a natural evolutionary process can produce the pattern.

      Heh, yep, I'd noticed that a few years ago, after the Original Complex Specified Information didn't do the trick, Dembski needed the New Improved Version that wins by definition.

      Delete
    10. Take cover, Diogenes. Wallstreeter43 is in full Gish Gallop mode, spewing a flood of logorrhea.

      Delete
    11. One of the funniest things in that thread is gordo's usual act of sanctimonious desperation that he always trots out because he and his IDiotic ilk are getting their asses kicked on the relevant, scientific topic:

      "On matters of morality, I suggest your problem lies at a deeper level. Lab coat clad evolutionary materialism has in it no IS capable of grounding OUGHT with all sorts of things stemming from it. Including, as Plato warned, the highest right is might (including might at manipulation). So, when preening yourself on currently popular agenda points consider where having no rights safe from ruthless power agendas and their publicists ends up. Including, when you play with big matches on fundamental human identity, familial and socio-cultural stability concerns. (You would be well advised to ponder the doctrine of unintended consequences and some linked hard-bought history, in that context.)"

      Delete
    12. That was sanctimonious desperation? I took it for incoherence. "Playing with big matches on...socio-cultural stability concerns"? "[H]ard-bought history"?

      Delete
    13. "I took it for incoherence."

      Well, it's that too. :)

      Incoherent sanctimonious desperation pretty much describes everything that gordo spews.

      Delete
    14. Just started reading through the UD thread. Best line so far:

      Funny– why is it you always accuse us of religion, but we never, never accuse you of science?

      Delete
  7. Larry can you see if you can stop the bottom half of the left side bar jiggling up and down? I'm using Chrome.

    ReplyDelete
    Replies
    1. I've complained about this several times, and have reported it to Chrome.

      Delete
    2. Just to add: the jiggling up and down starts at the f"Quotations" section (the first one). It also sends the cpu on my laptop into a frenzy of activity.

      If I use the Chrome developer tools to delete the div showing "Followers" (the one just above the first set of quotations) the problem goes away.

      Delete
    3. That jiggling is aggravating. I'm also using Chrome, although I don't know if that matters.

      Delete
    4. I'm using SRWare Iron, which is Chromium-based but apparently jiggle-proof.

      Delete
    5. I removed the slideshow and the "Followers" widget. Does that help?

      Delete
    6. I don't see a problem when I use Chrome under Windows 8.

      Delete
    7. Larry, I don't see any jiggling now! Yeehaa!

      There's something else though. On the left where it says Subscribe To Sandwalk in bold, capital letters, the word Sandwalk juts out into the text of of your posts. Maybe you could put the word Sandwalk under the words Subscribe to instead of next to them?

      Delete
    8. Just so you know, I'm using Windows 7, and I just checked the version of Chrome. It's Version 40.0.2214.111 m

      Delete
    9. The jiggling only seemed to happen on XP. Not on Windows 7. It's gone now.

      Delete
    10. Doesn't happen with Firefox for MAC.

      Delete
  8. the Magic Quantum Shroud of Turin

    I appreciated their citation to that well known academic journal The Discovery Channel.

    ReplyDelete
    Replies
    1. All sindonologists agree the shroud is authentic, just like all UFOlogists agree UFO abductions happen.

      Delete
    2. I won't believe it till I see it on The History Channel. Preferrably as part of an hour long show involving a team of genuine real scientists who investigate the mystery.

      Delete
  9. I just read a press release by the group Dorothee Kern from the Brandeis University about reconstructing of a billion year old (common ancestor) kinase. They were interested in the mechanism behind drug resistance to a specific drug, Glivec, when comparing leukemia and f.e. lung cancer.

    I can't find the original paper right now.

    But from what I understand, they reconstructed a common ancestor kinase using modern day knowledge of evolution, and with it they were able to find out the mechanism how and why the drug does work effectively on leukemia, but not lung cancer.

    I'd be interested in how the DI can explain this, perhaps a prof. in the biochemistry did come up with a DESIGN, where DI and BI failed?

    (The press release of the university (Jurassic park under the microscope) fits under the bad press release topic though)

    ReplyDelete
    Replies
    1. Hmm. Douglas Theobald. Name sounds familiar. Oh yes, the guy who wrote the 2010 paper on "A formal test of universal common ancestry", who has wriiten posts at Panda's Thumb, and who is the author of the talk.origins page on "29+ Evidences for Macroevolution". That Theobald. Must be biased in favor of evolution.

      Delete
    2. So it's not just ... like ... y'know ... flipping a coin 500 times then? As you patrol the beaches of Functional Island? Shocked.

      Delete
    3. It's also weird how, if evolution didn't actually happen, his "evolution bias" actually helps him elucidate how the drug works. :P

      Delete
    4. LoL! The argument pertains to UNGUIDED evolution. Mere evolution isn't being debated.

      Delete
    5. So you are happy with universal common descent?

      Delete
    6. When it can be tested, scientifically, I will be. Right now there aren't any known evolutionary processes that can get beyond populations of prokaryotes given starting populations of prokaryotes. So that would be a huge problem for UCD.

      Delete
    7. RE Theobald- The "Arrival of the Fittest" says evolution is too messy to produce e nested hierarchy and Theobald uses a nested hierarchy as evidence for UCD.

      Whoops...

      Delete
    8. Can anyone who has read the book "Arrival of the Fittest" tell me what Joe is talking about?

      Delete
    9. Joe, please, can you cite the passage where Andreas Wagner makes such a claim?

      Delete
    10. I have Arrival of the Fittest and have read it. Joe G is simply lying. Not misreading or misinterpreting. Just flat out lying.

      Delete
    11. When it can be tested, scientifically, I will be. Right now there aren't any known evolutionary processes that can [...]

      Whoah, Neddy. The evidence for common descent is independent of any proposed mechanism of change.

      Delete
    12. The phrase "nested hierarchy" does not appear in Wagner's book. But this does:

      "We do know, however, that we all come from a single common ancestor. This is not the same as saying that life originated only once. Given the powers of self-organization, I would not be surprised if life arose many times, in hydrothermal vents, in warm ponds, or who knows where else. Among a multitude of faint lights that flickered on and off throughout the earliest history of the planet, some held steady, while others shone more and more brightly. But only one of them became bright enough to spawn all of today’s life. This is not a matter of opinion.

      Wagner, Andreas (2014-10-02). Arrival of the Fittest: Solving Evolution's Greatest Puzzle (Kindle Locations 1021-1025). Penguin Publishing Group. Kindle Edition. "

      Delete
    13. Quest: I still offer $100.000 to anyone who is able to reassemble a cell that its membrane has been broken and all its contents leaked out into primordial soup or any other soup...

      I'm sorry, Quest, your brain can't be repaired -- not even for $100,000. You'll have to live with that soup.

      Delete
    14. I've done it Quest. I will send you the intact bacterial cells on a plate as proof. No other evidence can be provided because I used a supernatural miracle, and miracles do not consist of mechanisms that can be demonstrated. Send me my money.

      Delete
    15. "mere" evolution, joey?

      You crack me up.

      Hmm, what's next, "mere" star formation vs.guided star formation, "mere" radioactive decay vs. guided radioactive decay, "mere" Stonehenge builders vs. guided by ancient aliens Stonehenge builders, and "mere" ghosts vs. guided ghosts?

      Define "mere" evolution and explain how you determine the difference between "mere" evolution and guided evolution.

      P.S. Is there a difference between "mere" design-creation and special design-creation? If so, how can you tell?

      Delete
    16. It is unbelievable... but has to be true...

      That's exactly right. Send me my money.

      Delete
  10. Unguided evolution can't even muster testable hypotheses. It cannot be modeled. There aren't any experiments that support it.

    If it could do any of things you would have a case against Luskin, but it can't so you lose.

    ReplyDelete
    Replies
    1. You're an idiot Joe,

      Unguided evolution can't even muster testable hypotheses.

      Can, has, and continues to have. There's a few journals that present articles after articles with testable, and therefore tested, hypotheses based on evolutionary theory.

      It cannot be modeled.

      I have told you, and others have told you: read about population genetics idiot. It's all about mathematical models. Not only that, those journals I was talking about, they present models after models showing how some process and other processes can influence evolutionary trajectories, etc. You seem to be pretty stupid coming with your inexcusable ignorance in this time and day, when a few searches would have proven you so wrong as to shatter your fantasies about gods.

      There aren't any experiments that support it.

      Again, you're an idiot. There's experiments after experiments after experiments. From evolution of RNA and protein activities, to evolution of model organisms, in the lab, to the examination of fossils, and other lines of evidence, like DNA sequences, insertion elements, and a long etc.

      If it could do any of things you would have a case against Luskin, but it can't so you lose.

      Since it obviously can, seems like you lose. Pathetically.

      Go get a proper education you imbecile.

      Delete
  11. Is genetic drift a proposed designer mimic? No. That is why it can be ignored because it doesn't do anything. ONLY natural selection has been posited as a mechanism for producing the observed design in living organisms.

    Why is Moran such a moron that he cannot grasp that simple fact?

    ReplyDelete
    Replies
    1. It's what makes folks like Behe incorrect. They see mutation A that needs to become C, but step A->B is disadvantageous. They never account for neutral mutation A->X, where X can become C without going through disadvantageous step B.

      Why are you such a moron you cannot grasp that simple fact?

      Delete
    2. LoL! We don't make that claim and if all you have is sheer dumb luck then just say it!

      Drift is not a designer mimic. It does nothing.

      Delete
    3. You're just not getting it, Joe - right there in that Lenski experiment you refer to yourself.... One of these days it might penetrate - kinda like a flash on the road to Damascus.

      Delete
    4. I wonder... do you think that there could MULTIPLE mechanisms that result in change over time?

      I also wonder... do you think that science can never change, once someone says something?

      Are you an authoritarian?

      Delete
    5. Quest hasn't read the book. His post will be deleted, and it is not worth responding to.

      Delete
    6. joey drooled:

      "Drift is not a designer mimic."

      A designer mimic, joey? Can you show where evolutionary scientists claim that drift mimics a designer? Do you believe that drift should mimic a designer? Describe the designer that drift doesn't mimic.

      Delete
    7. TWT, most reasonable people would agree that there is at least an appearance of design in biology.
      I do agree with you that it doesn't make mathematical sense that drift would lead to that.
      Natural selection is another candidate in the materialistic world view. It is the only natural process that could lead to adaptation. It should therefore be able to at least refine traits.
      Ideally random drift and natural selection should combine to amplify their separate effects, but it seems more logical that they would instead counter act each other.
      I do agree that evolution can achieve something, but to me it's an open question what it's reach is and in general I'm skeptical of its ability to explain the appearance of design in complex systems.

      Delete
    8. "I do agree with you that it doesn't make mathematical sense that drift would lead to that."

      Show your math then.

      "Natural selection is another candidate in the materialistic world view. It is the only natural process that could lead to adaptation."

      Prove it.

      Delete
    9. Andy, you're being short-sighted.

      If you picture fitness mathematically as a landscape, with various hills, peaks, valleys, plateaus, flat areas, etc.:

      If all you've got is positive selection for increased fitness/adaptation, and you're on a small local hill, you're stuck - you can only move up.

      On the other hand, drift allows you to move sideways or slightly downward to get off the local hill and eventually onto another, higher, peak of fitness/adaptation (i.e., something that appears "better designed").

      So that's the way it makes mathematical sense that drift and selection working together allow more of an appearance of design than positive selection working alone.

      Delete
    10. Rumraket, which other natural process can lead to adaptation?

      Delete
    11. Judmarc, that's pretty much how I picture it, only it seems to me that the random drift will interfere with the "climbing" of natural selection, i.e. the processes will counteract each other.

      Delete
    12. "Rumraket, which other natural process can lead to adaptation?"

      You're the one who said there is no other one. Prove it or retract the claim as the blind assertion it is.

      "I do agree with you that it doesn't make mathematical sense that drift would lead to that."

      Show your math then.

      "Natural selection is another candidate in the materialistic world view. It is the only natural process that could lead to adaptation."

      Prove it.

      Delete
    13. Rumraket, let's just say that it's the only natural process known to me, and apparently to you, that leads to adaptation. I'm open for suggestions for other possible candidates.

      Delete
    14. "Judmarc, that's pretty much how I picture it, only it seems to me that the random drift will interfere with the "climbing" of natural selection, i.e. the processes will counteract each other."

      Then it is clear that you do not actually understand what genetic drift is, and you also have this typical "all or nothing" misconception. It is not that they will counteract each other, it's that they can counteract each other. And even then, in the circumstances where they do work against each other, there will invariably always be a loser.

      While an advantageous allele arises in the population it will have a low frequency when it first arrives due to mutation, and this is where drift has the strongest effect, when alleles are at a low frequency. That doesn't mean it WILL delete the advantageous allele, only that it is under this condition that there is the biggest chance that it does.

      It is not all-or-nothing, black/white where drift always "destroys" the effect of selection, or the other way around. Evolution is a stochastic process, there are no guarantees, there are only different probabilities. Some times they are high, some times they are low, but high is not a guarantee of success, and low is not a guarantee of failure and vice versa.

      I know IDcreationist heads explode when they try to comprehend how a "random" process could ever "work" at achieving or building anything functional/useful/adaptive, but that's because they have had their heads filled with religious propaganda about some kind of "uselessness" about randomness. "It's random so it can't ever work" - that's actually wrong!. It is a lie that religious propagandists have been working hard to construct.

      Delete
    15. "Rumraket, let's just say that it's the only natural process known to me, and apparently to you, that leads to adaptation."

      So you admit that it was an assertion based on nothing more than your own ignorance. Okay, thank you Andy that took some courage.

      You're wrong by the way, I know of two other natural processes that lead to adaptation: Mutation+Genetic drift,- and intelligent design by natural designers.

      I wouldn't even claim that these are the only possible ones, but those are the ones I know about in addition to natural selection. Unlike you, I wouldn't go so far as to claim there couldn't possibly be any more just because I don't know of any them. So I'm open to suggestions too.

      "TWT, most reasonable people would agree that there is at least an appearance of design in biology.
      I do agree with you that it doesn't make mathematical sense that drift would lead to that."


      So, show your math then Andy.

      Delete
    16. Rumraket wrote: "Then it is clear that you do not actually understand what genetic drift is, and you also have this typical "all or nothing" misconception. It is not that they will counteract each other, it's that they can counteract each other. And even then, in the circumstances where they do work against each other, there will invariably always be a loser."

      So your saying that they are equally strong processes and that it's a toss-up which wins? Mathematically I then don't have any other way to describe the combined effect than a random walk and we can forget about adaptation as long as we do not stumble on traits with strong positive selection. If we look at e.g. proteins the question then becomes how common functional combinations of amino acids are compared to all the possible combinations. Based on the work that Douglas Axe has done it seems that they are not very common.

      Delete
    17. "So your saying that they are equally strong processes and that it's a toss-up which wins?"

      No, my post was longer than what you quoted. You know you can actually look up the equations for drift and selection under population sizes right?

      "If we look at e.g. proteins the question then becomes how common functional combinations of amino acids are compared to all the possible combinations. Based on the work that Douglas Axe has done it seems that they are not very common."

      Douglas Axe failed in his attempt to design a specific protein, by taking mutations from another protein and inserting into it, and from this you want to conclude functional combinations of amino acids are rare?

      It's funny because the Szostak lab did a much better experiment, they tested actually random sequences of amino acids approximately 80 residues long for a single function only (bind to ATP) and found that about 1 in 10^11 completely random amino acid sequences of 80 residues in length could bind ATP.

      And that was a test for a single function. How many millions of possible functions exist in living organisms?

      Delete
    18. Rumraket, I thought you commonly defined potential function in a protein when you have a 3-d fold, not when amino acid activation occur, i.e. the attachment of an amino acid to its Transfer RNA (tRNA).

      Delete
    19. "Rumraket, I thought you commonly defined potential function in a protein when you have a 3-d fold, not when amino acid activation occur, i.e. the attachment of an amino acid to its Transfer RNA (tRNA)."

      Then you are mistaken in both cases. There are unfolded proteins within the ribosome without which the ribosome would stop functioning if they are removed. So protein function is not intrinsically dependent on folding, and I have no idea why you bring up tRNA, it does not relate to anything I said.

      You know ATP is a monomer of DNA right? Adenosine-triphosphate. An important biochemical function in cells is for various proteins to be able to bind ATP. One of these is that the ATP synthase, when running in reverse, actually binds ATP and uses the energy it pump protons back out through the cell membrane.

      So ATP binding is a biologically extremely important and useful function without which living cells as we know them would stop working. The Szostak lab made, to see how rare "function" was in phenotypical space of proteins, random proteins that were about 80 amino acids in length. Billions and billions of them, random in sequence, no particular order of amino acids.

      Random sequence proteins, 80 amino acids in length. Only tested against a single function. They could have tested their starting pool against millions of additional functions, massively increasing the amount of potentially functional proteins in sequence space.

      What they also found is that the proteins that could bind ATP that they found, were not related to any biological protein in structure or sequence. So since we already know ATP binding exists in nature, it turns out that there is even more function in sequence space than the function discovered and used in life.

      (They also later did more experiments with these newly discovered, novel functional proteins, found simply by making random sequences, and found out that they could further enhance them with in vitro selection to strongly discriminate between ATP, ADP and AMP). So there was an additional function closeby in sequence space, the ability to discriminate between two three very similar substrates).

      Delete
    20. Quest brayed,

      "Give me one reason why I should even read the book...? Only one... and I will do it..."

      A good reason, Quest, would be if you cared about understanding what you so adamantly oppose. After all, if you were a reasoning person, you would want to know what you're opposing. Otherwise you're opposing out of mere ignorance. However, you're not a reasoning person.

      I also doubt that you would understand anything in the book. You're too much of an imbecile, besides having a very closed mind, both of which would interfere with your understanding. So, don't read it. It would be useless.

      Delete
    21. Andy Wilberforce said:

      "TWT, most reasonable people would agree that there is at least an appearance of design in biology."

      Well, Andy, that's a very vague statement, and while some parts of "biology" have what humans would call a design or pattern, that doesn't necessarily mean that those things were intelligently (intentionally/purposefully) designed, and it really doesn't necessarily mean that they were intelligently designed-created by a supernatural, so-called 'God', and it really, really doesn't necessarily mean that they were intelligently designed-created by your chosen, so-called 'God'.

      In your opinion, is there anything in the universe that was/is not designed-created by your chosen, so-called 'God'?

      Consider this: Scat (animal poop) is 'biological' and it occurs in a huge variety of appearances (colors, shapes, sizes, visible contents, patterns, or 'designs'). The animal that excreted some scat can often be identified by the appearance of its scat, Tests beyond what is visible can also be used but let's focus on visible 'appearance'). Do you believe that scat was/is intelligently (intentionally/purposefully) designed and do you believe that it was/is intentionally designed-created by your chosen, so-called 'God'?

      "I do agree with you that it doesn't make mathematical sense that drift would lead to that."

      I don't understand why you said that since I didn't say anything about what would or wouldn't make mathematical sense in regard to drift. I just asked joey some questions about his statement.

      "Natural selection is another candidate in the materialistic world view."

      You obviously expect the same thing as joey expects, and that is for 'materialists' to demonstrate (or prove) that natural selection and/or other natural processes/events can and do mimic a designer, and especially your chosen, so-called designer-creator-god, but there's no need to demonstrate (or prove) that. It is not necessary for 'materialists' or anyone else to demonstrate (or prove) to your satisfaction or to the satisfaction of any other religious person that natural processes/events can and do 'mimic' your or their chosen, so-called 'God'. Religious people are the ones making all kinds of extraordinary claims with nothing but 'faith' in antiquated, ridiculous, horrible, impossible fairy tales to rely on.

      As far as I'm concerned, I don't care much whether something is labeled as 'material' or not. I'm much more concerned with whether it exists or not, and I'm open to accepting anything that actually exists, which does not include any of the thousands of so-called 'Gods' that people have imagined, believed in, and promoted. Some of the stories that people have come up with about some so-called 'Gods' are interesting and/or entertaining, while others are just despicable, and they're all fiction.

      See part two.

      Delete
    22. Part two.

      "It is the only natural process that could lead to adaptation."

      Others have responded to you about that and what I'd say is this: Natural selection is one of the processes/events that can and/or does 'affect' or 'result in' adaptation. I'm not sure that I'm comfortable with "lead to". The relative effects/results or 'importance' of natural selection and other evolutionary processes and events are debated by some scientists and as more is learned more agreement about the particulars will likely be reached. The exact particulars of evolution are not easy to figure out, especially when considering the entire history and diversity of biological entities and all of the non-biological processes/events that affect evolution. Current evidence and knowledge should be more than enough to convince people that evolution has occurred, does occur, and will continue to occur via natural processes/events.

      "It should therefore be able to at least refine traits."

      In a way, natural selection does "refine" traits in the sense that filters can be said to "refine" what passes through them. In my opinion though, there's more to natural selection than the 'refinement' of traits. For example, natural selection can be the cause, or part of the cause, of extirpation or extinction, which I wouldn't describe as a 'refinement' of the traits of the biological entities that are wiped out.

      "Ideally random drift and natural selection should combine to amplify their separate effects, but it seems more logical that they would instead counter act each other."

      I'll leave that one to others who are more knowledgeable about the particular relative processes/events/effects/results of drift and selection.

      "I do agree that evolution can achieve something, but to me it's an open question what it's reach is and in general I'm skeptical of its ability to explain the appearance of design in complex systems."

      I can't appropriately respond to that because I don't know what you mean by your vague use of the words "evolution", "design", and "complex". Do you subscribe to the '500 bits of CSI' claims of ID pushers? Do you believe that 'the designer' (creator-god) designs (creates) some things but not other or all things?

      Delete
    23. The thing is: for what I've read, until now (that we know of), there's nothing in the biological world which cannot be explained by known natural processes - biologists have investigated and even, in some cases, reconstructed, the evolution of proteins, including the evolution of the bacterial flagellar proteins (which involves gene duplication and co-option), the proteins involved in the blood clotting and krebs cycle (the ones that were singled out by intelligent design creationists as being the product of intelligent design). Until now, creationists couldn't demonstrate that any of that is designed - by the contrary, real researchers found that there's nothing there that cannot be achieved by evolutionary mechanisms. Real scientists will continue to investigate the evolution of complex systems, and they'll let everyone (including creationists) know if there's something that seems not to fit in with what can be produced by known (natural) mechanisms.

      Delete
    24. Rumraket wrote: "Then it is clear that you do not actually understand what genetic drift is, and you also have this typical "all or nothing" misconception. It is not that they will counteract each other, it's that they can counteract each other. And even then, in the circumstances where they do work against each other, there will invariably always be a loser."

      So your saying that they are equally strong processes and that it's a toss-up which wins? Mathematically I then don't have any other way to describe the combined effect than a random walk and we can forget about adaptation


      Mikkel clearly says adaptation and drift don't have to be in opposition, after which you, Andy, conclude from this clear statement the very same thing you said before that Mikkel was correcting, that they must always be in opposition, and therefore we can't have adaptation.

      I can't think of a better demonstration that you're hanging onto this willful misunderstanding as if - actually, because - your belief in the impossibility of evolution depends on it.

      Delete
    25. Creationists: stop saying that we cannot "prove" that natural mechanisms can produce what we observe and that god did it, etc. - I repeat until now, as far as we know, there's nothing that clearly isn't likely to have been accomplished by natural process, and in some cases evolution has been reconstructed, based on the available evidence. Scientists can (and are) investigating this. And yes, "naturalistic" evolution can be modeled (study a little bit of population genetics, please).

      Delete
    26. Rumraket, it takes too much time to muddle through all the crap you spread around you and correct all your misstatements, but here is a part of the summary from one of your references. It hardly supports that high levels of of functional proteins will come out from random chains of amino acid residues as you claim.
      "Summary...We have previously isolated a family of nonbiological ATP binding proteins from an unconstrained random sequence library. One of these proteins was further optimized for high-affinity binding to ATP...Starting from a pool of protein variants, we evolved a population of proteins capable of binding ATP in 3 M guanidine hydrochloride. One protein was chosen for further characterization. Circular dichroism, tryptophan fluorescence, and 1H-15N correlation NMR studies show that this protein has a unique folded structure."

      Delete
    27. It hardly supports that high levels of of functional proteins will come out from random chains of amino acid residues as you claim.

      Err, no he didn't.

      Delete
    28. You are right Judmarc, Rumraket is actually underpinning Douglas Axe's claim that functional proteins are very rare. I guess I was reading his reply a bit rash.

      Delete
    29. Hm… So… protein function is rare, hein creationists? And, more importantly, is it isolated? can’t tell, isn’t it, creationists? Or will you just make it up as usual?

      Delete
    30. MA32 wrote: "Hm… So… protein function is rare, hein creationists? And, more importantly, is it isolated?"
      Well I would say that for the studied function it was both rare and isolated. Total of 60 functional proteins found belonging to four families out of 6,000,000,000,000 proteins studied.

      Delete
    31. Yes, but only a single function was looked for in the initial population: Bind ATP. Who knows what else was in that initial pool of random proteins? How many possible enzymes were in there, how many possibly structural proteins etc etc.? Only a single function was tested for, and was found already in the beginning pool.

      So what we can definitely say is that there are even more than what was found, but they only bothered looking for a single one.

      In contrast, the work of Douglas Axe estimates the number of functional proteins in sequence space to be about 1 in 10^77'th power.Which means he's off by at least a trillion trillion trillion trillion trillion times.

      One cannot be that wrong by accident.

      Delete
    32. «Only a single function was tested for, and was found already in the beginning pool. So what we can definitely say is that there are even more than what was found, but they only bothered looking for a single one...In contrast, the work of Douglas Axe estimates the number of functional proteins in sequence space to be about 1 in 10^77'th power.Which means he's off by at least a trillion trillion trillion trillion trillion times.» - Exactly. Compare that number with Axe's. Besides... The poor enzyme that Axe used was already crippled - it probably made it more difficult.

      Delete
    33. Andy, the creationist said: «Well I would say that for the studied function it was both rare and isolated.» Isolated? How so?

      Delete
    34. I don't think (although I didn't read the all paper) anyone ever investigated if it was isolated

      Delete
    35. Rumraket, I don't remember his exact claim, but if he meant for a specific function, then he may still be right. The end product here was one stable functional protein fold from a selection of 8.3x10E105 possibilities. There is no way to tell from the report how well they covered the whole search sequence though.

      Delete
    36. «Rumraket, I don't remember his exact claim, but if he meant for a specific function, then he may still be right.» - What about the fact that he crippled the poor enzyme?

      Delete
    37. MA32, I'm talking about the study Szostak Lab's did. I don't remember any details from Axe's study.

      Delete
    38. From a Panda's thumb post:
      «There is, however, a fly in the ointment. (Actually, there are many.) Recall that Axe did not work with the native TEM-1 penicillinase, but rather with a variant that had a lower activity. The assay system made this necessary. (Scoring bacteria on antibiotic-containing media isn’t particularly discriminating, and it’s hard to tell is, say, if a wild-type detoxifying enzyme has lost 90% of its activity.) In other words, Axe decided to select a particular part of the “hill” such as that shaded in black in the following illustration (Figure 2):..»

      (http://www.pandasthumb.org/archives/2007/01/92-second-st-fa.html)

      So... Axe probably cheated.

      Delete
    39. Andy:
      Ok, my bad. But it's relevant what I said. Axe cheated.

      Delete
    40. MA32, my main point here is that we are talking big numbers...Did you know that Penrose estimates the number of baryons in the observable universe to be of the order of 10E80? That is about the same as the possible combinations of proteins 60 residues long.

      Delete
    41. "Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77."

      Axe simply CANNOT conclude this from the work he did, the number is so grossly exaggarated it boggles belief.

      First of all, Axe simply mutates the protein he has until the function it originally had stops working.

      That means a single function is being tested, the function the protein already has. Axe doesn't attempt to find out whether his protein, when mutated, can do other functions. He also absurdly and grossly overestimates the rarity of the function he tests for, because the spread of mutations he tests cover an unimaginably small fraction of the sequence space of his chosen protein length (150 residues), and gives bogus arguments for why his chosen search-space is capable reflecting the functioanality of the rest.

      In short: Axe does everything in his power not to produce a remotely accurate estimate of the rarity of function in protein sequence space.

      This pretension you're keeping up about this is laughable, there is no debate here.

      Notice what the Szostak lab did, first they found a function in a pool of random proteins. Then when they found one (bind ATP), they tested whether there was another useful function nearby in sequence space (discriminate between ATP, ADP and AMP) and found that there was. The protein they initially found was able to bind ATP, and they could even modify it further to be able discriminate between highly similar substrates while retaining the original function.

      It's true what MissAtheist32 says, Axe cheated. Deliberately, it's what he's being paid to do, and you don't have the desire or state of mind to investigate the merits of the work he did. Does it in point of fact accurately reflect protein sequence space? No it doesn't and we have shown this many times. Notice how the Panda's Thumb article demonstrated this all the way back in 2007. Axe's been wrong for over a decade and this fact has yet to find it's way into the ID community, there's an absurd willingness to believe there.

      Do yourself a favor and take on a coat of some healthy skepticism, not just towards evolution, but towards those that propagandize against it too. You're not doing yourself any favors by just regurgitating the claims of Discovery Institute shills.

      Delete
    42. My point here is that Axe's "big numbers" are wrong and you don't know if protein function in general is rare (some results point to the hypothesis that it is way less rare than creationists say it is)

      Delete
    43. I am now going to post this paper everytime someone talks about how great ID is... http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118093

      ID is little more than a conspiracy theory. That's all. A minuscule group of people who think that they, above everyone else, has The Trooth.

      They use 8th grade algebra and common sense (the same common sense that told us that the Earth was flat and the sun orbited Earth) to reject hundreds of thousands of pieces of evidence collected over more than a hundred years which in dozens of fields of study, which all point to the same thing.

      Life evolves. There are not limits except contingency. And that's the end of it.

      Delete
    44. «some results point to the hypothesis that it is way less rare than creationists say it is» - Andy could say: «There are stil big numbers»
      (Not so) big numbers, yes… or not (for function in general).

      Delete
    45. By the way, creationists love big numbers... And they'd love if those numbers really proved them right. Well, I'm still not impressed by their "big numbers".

      Delete
    46. Rumraket, Szostak Lab's started with a database search. That's how you have to do it to find the functional sequences of amino acid residue combinations among all the possible because there just isn't enough matter or time to actually test all for functions. So how do you propose that it happened at the origin of life? Did nature just stumble on the functional forms with just the right combination of traits by shear luck?

      Delete
    47. Andy, in nature, these sequences just existed and reacted with what was around.

      «Did nature just stumble on the functional forms with just the right combination of traits by shear luck?» - You could say the same about many other things in nature (for instance, did the tornado just stumbled on that BMW with that combination of traits to hit that house over there? No! It was gawd who made it happen!) - But we observe those things happening naturally and we know that it doesn't need god to happen. It's just how things work in nature - by "luck".

      Delete
    48. "Rumraket, Szostak Lab's started with a database search."

      Straight up false Andy. Where are you even getting this nonsense? They started by generating random sequences. There was no "database search". All they did was make sure that their sequences were actually 80 amino acids in length, instead of being shorter or longer(by avoiding stop codons and frameshift mutations). Nothing was done to search any database to find existing or functional proteins.

      From the paper: "Because protein sequences with speci®c functions are expected to be quite rare in protein sequence space, we prepared a DNA library of 4 x 10^14 independently generated random sequences. This DNA library was specifically constructed to avoid stop codons and frameshift mutations4, and was designed for use in mRNA display selections. This DNA library was then used to generate 6 x10^12 purified non-redundant random proteins that were used as the input into the first selection step. These proteins contain a contiguous stretch of random amino acids 80 residues in length, long enough to form known protein domains. Unlike other libraries that have been used in protein selections, this random region is not part of a larger structure that would otherwise tend to constrain or bias the conformation of the resulting proteins. This library randomly samples the whole of sequence space, rather than the vicinity of a known protein. The random region of each library member is flanked by short invariant sequences encoding affnity tags for purification (Fig. 1)."

      So Andy, if you really have the correct position on this, why are you forced to make shit up to defend it?

      Delete
    49. "So how do you propose that it happened at the origin of life?"

      Why are you blathering about he origin of life? We are discussing whether evolution can find functional proteins in sequence space. It clearly can.

      Delete
    50. Even if we were to discuss the origin of life, certain potentially functional sequences just existed and reacted with what was at hand. Why do we need to invoke a god?

      Delete
    51. It occurs to me that Andy might have misinterpreted the word "library".

      Delete
    52. @Andy, I must re-iterate Rumraket's comment until you grasp the size of Doug Axe's error:

      Rumraket: In contrast, the work of Douglas Axe estimates the number of functional proteins in sequence space to be about 1 in 10^77'th power.Which means he's off by at least a trillion trillion trillion trillion trillion times. One cannot be that wrong by accident.

      To which Andy replies: my main point here is that we are talking big numbers

      One wonders why big numbers don't matter when they measure how large your errors are. Axe's errors are almost as large as his big numbers. Most of his big number is due to error.

      I call this "the Fallacy that Fallaces don't matter."

      Creationist: I computed a probability of evolution happening. It's 1 over a big number.

      Scientist: You made an error of astronomical size.

      Creationist: But it's a big number.

      Scientist: It's only a big number because you made an error of astronomical size.

      Creationist: But it's a big number.

      Repeat ad infinitem.

      MissAtheist32 replies: "Well, I'm still not impressed by their "big numbers".

      Andy, I have a word of advice. You keep saying "It's big, it's really big!" but when a lady says, "I'm not impressed by it" you should drop the subject.

      Delete
    53. Diogenes, not quite correct. My response to Rumraket was:
      "Rumraket, I don't remember his exact claim, but if he meant for a specific function, then he may still be right. The end product here was one stable functional protein fold from a selection of 8.3x10E105 possibilities. There is no way to tell from the report how well they covered the whole search sequence though."
      But ok, let's call it close enough by your standards. Your, let's call it "flexibility", with facts may also help explain your experience with the ladies that you shared.

      Delete
  12. Intelligent Design is not anti-evolution. Not even YECs argue against evolution.

    What is Intelligent Design and What is it Challenging?- a short video featuring Stephen C. Meyer on Intelligent Design.

    ReplyDelete
    Replies
    1. "Intelligent Design is not anti-evolution. Not even YECs argue against evolution."

      Joe we can disagree on a whole host of things, but this one is straight up silly. I have had arguments with YEC's who denied clear and obvious cases of bacteria evolving resistance to antibiotics because they totally and utterly denied ANY creative power of evolution, no matter how small. They rejected anything about evolution, not just macroevolution or common descent, but also microevolution of all kinds. They claimed that any kind of adaptive change was "pre-programmed" or "front-loaded".

      Delete
    2. ... and you can't prove it wasn't, so win win win!

      Delete
  13. As Dembski/ Wells said Intelligent design only has an issue with materialistic evolution- the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms. (Also known as the blind watchmaker thesis)

    Intelligent Design is OK with all individuals in a population generally having the same number and types of genes and that those genes give rise to an array of traits and characteristics that characterize that population. It is OK with mutations that may result in two or more slightly different molecular forms of a gene- alleles- that influence a trait in different ways and that individuals of a population vary in the details of a trait when they inherit different combinations of alleles. ID is OK with any allele that may become more or less common in the population relative to other kinds at a gene locus, or it may disappear. And ID is OK with allele frequencies changing as a result of mutation, gene flow, genetic drift, natural and artificial selection, that mutation alone produces new alleles and gene flow, genetic drift, natural and artificial selection shuffle existing alleles into, through, or out of populations. IOW ID is OK with biological evolution. As Dr Behe et al., make very clear, it just argues about the mechanisms- basically design/ telic vs spontaneous/ stochastic.

    Now we are left with the only way Intelligent Design can be considered anti-evolution is if and only if the only definition of evolution matches the definition provided for materialistic evolution. However I cannot find any source that states that is the case.

    So the bottom line is Intelligent Design says “evolved, sure”. The questions are “evolved from what?” and “how did it evolve?”.

    ReplyDelete
    Replies
    1. Joe, can you wxplain why we detect transition bias for relatively closely related species when using comparative genetics, and why the signal for this pattern becomes weaker the greater the distance of the relationships in time, if these mutational patterns weren't the product of basic biochemical processes but instead due to design by an intelligent agent?

      Can you find somewhere in the ID litterature where such an explanation (to account for this pattern with a design-hypothesis) is even attempted?

      Delete
    2. Hey Joe,

      Can you explain how IDiots explain the designer ?

      Delete
    3. Joe states: "So the bottom line is Intelligent Design says “evolved, sure”. The questions are “evolved from what?” and “how did it evolve?”.

      The design inference starts and ends with the idea that because we only know of information being generated by a mind, therefore a mind must have generated biological information.

      Steven C. Meyer has stated that ID does not have and in fact does not need a mechanism--there is no ID contribution to the 'how'. ID only has the design inference.

      Delete
    4. YEC-IDiot joey said:

      "IOW ID is OK with biological evolution."

      And:

      "As Dr Behe et al., make very clear, it just argues about the mechanisms- basically design/ telic vs spontaneous/ stochastic."

      joey, your statements above are lies of course but first, as you've been told MANY times, it doesn't matter if you and your fellow IDCs are "OK with biological evolution" or not because biological evolution has occurred, does occur, and will continue to occur whether you or anyone else is "OK with" it or not. As you have been told MANY times, evolution, and evolutionary theory, are NOT the same thing. In other words, and to put it very simply so that even you may eventually get it and be honest about it, the scientific study and description of biological evolution (evolutionary theory) is not the same thing as the processes/events ("mechanisms") or the results/extent of biological evolution.

      With that in mind: When it comes to evolutionary theory (or being "OK with biological evolution") you IDiots make up or adopt ridiculous fairy tales about the ancestry and diversity of life forms/biological entities (evolution) and you distort and lie about the scientific description of biological evolution (evolutionary theory) to suit your asinine, dishonest, non-scientific/pseudo scientific creationist beliefs and claims. You deliberately try to create confusion and fake 'controversies' and you pretend that you and your creationist ilk accept that evolution occurs and that it occurs as described by evolutionary theory except for the "mechanisms".

      Biological evolution as described by evolutionary theory is not what you and your fellow IDCs are "OK with". You cannot distort, ignore, exclude, and/or argue against virtually every part of evolutionary theory and especially major parts (such as evidence and descriptions of common descent, speciation, convergence, etc.) and then claim that you accept evolutionary theory except for the described or proposed "mechanisms". Common descent, for example, is not described or proposed as a 'mechanism' by evolutionary theory. Common descent, as described by evolutionary theory, is an observation, or a 'conclusion', based on tested evidence. No matter how much you don't want to be descended from a long line of what you arrogantly see as 'lower life forms', and no matter how much you don't want to be related to all other life forms on Earth, you are descended from a long line of what you arrogantly see as 'lower life forms', and you are related to all other life forms on Earth. If you were actually "OK with biological evolution" (as you put it) you wouldn't have any problem with being descended from previous life forms and related to all life forms/biological entities. The truth is that you only accept and believe in "Special Creation" and minor (micro) variation within 'kinds'.

      See part two.

      Delete
    5. Part two.

      If your statements that I quoted above were true you IDiot-creationists would only argue against the proposition of a non-teleological 'origin' of biological evolution, but that's not what you do. Oh sure, you argue against the proposition of a non-teleological (non- your chosen, so-called 'God') origin of biological evolution (and everything else) but you IDiots go way beyond that by arguing against the obvious results/extent of biological evolution (including the relatedness of all life forms) and you do so in ways that put ridiculous limits on the results/extent and the "mechanisms" of biological evolution (and everything else).

      You assert that a designer-creator (i.e. your chosen, so-called 'God') designed and created the entire universe which means that you believe in a designer-creator that is powerful and knowledgeable to an unlimited 'extent', yet you put limits on your chosen, allegedly unlimited, so-called 'God' and you even claim that your chosen, allegedly unlimited, so-called 'God' did not and does not design-create diseases and deformities. I'd ask you why you impose such limits but I already know why. You and other creobots put very particular limits on your chosen, allegedly unlimited, so-called 'God' because you believe that 'He' designed and created everything only in ways that fit your particular, narcissistic attitudes, and the main reason that you put limits on the results/extent (and even on the "mechanisms") of biological evolution (and therefor on your chosen, so-called 'God') is because you believe (or desperately want to believe) that you are 'specially created in God's image'. I'm sure that in your narcissistic, delusional mind you believe that that is not putting limits on your chosen, allegedly unlimited, so-called 'God', but it is.

      Because you believe (or desperately want to believe) that you are really, really special you try to convince yourself (and others) that your chosen, allegedly unlimited, so-called 'God' did a really, really special thing by creating humans (a man first of course) separately from all other life forms and that biological evolution (including common descent) as described by evolutionary theory cannot be correct. It just can't be correct, can it, joey, because then you wouldn't be 'specially created in God's image', would you? It just can't be true that you're descended from icky 'lower life forms' and that you're related to any or all icky 'lower life forms', and one of the ways that you try to convince yourself (and others) of that is by putting ridiculous limits on biological evolution even though you claim that you and the other IDCs are "OK with biological evolution" as long as evolutionary theory posits that it was/is designed-created by your chosen, allegedly unlimited, so-called designer-creator-god. Of course you also push your "guided" assertion so you must believe that 'God' sometimes or constantly guides evolution but you also push your "front-loaded" assertion and claim that evolution (your very distorted version of it) occurs only as it was originally programmed to do, and you assert all kinds of other contradictory crap.

      See part three.

      Delete
    6. Part three.

      Tell me joey, if there is such a thing as a designer-creator that is powerful and knowledgeable enough to design-create the entire universe, why couldn't or wouldn't it have designed-created biological evolution so that everything is related and so as to eventually produce humans (including you) from previous life forms? If there is such a designer-creator, who are you to put limits on how or why it could or would go about designing-creating biological evolution, including the biological evolution of humans from previous life forms and the relatedness of humans to all other life forms/biological entities? And why couldn't or wouldn't it have designed-created diseases and deformities? Yeah, I know, the koran and bible say blah blah blah blah blah God-did-it and joey is really, really special and God is omnibenevolent blah blah blah blah blah and you desperately want to believe that your chosen, so-called 'God' is the one and only designer-creator-god and that 'He' couldn't and wouldn't design-create diseases and deformities and that you're specially created in 'His' image because you're enormously insecure and fearful, which you try to cover by being a narcissistic, belligerent jerk, but where is your evidence based, rational, sane argument that supports your beliefs, attitude, and assertions, including the limits you put on your chosen, allegedly unlimited, so-called 'God'?

      joey, you blatantly lie, make things up, deny reality, avoid questions, contradict your own assertions, accuse your opponents who aren't at all afraid of you of being cowards, threaten opponents that you would run from if you were ever face to face with them, spew tons of unwarranted insults, behave as a childish, incorrigible brat, and are obviously intent on arrogantly arguing from just about any foolish 'position' that is against what actually occurs in biological evolution and the rest of nature. You've tried pretty much every stupid, dishonest assertion and accusation there is in your belligerent attempts to destroy science and push your muslim-christian-YEC-IDiot-ghosts-ancient-aliens-wacko beliefs, and to call your attempts a failure would be putting it extremely mildly. You're wasting your miserable existence. Get some competent counseling and get a life.

      Delete
    7. The design inference starts and ends with the idea that because we only know of information being generated by a mind

      Which is of course false by every scientific definition of the word "information."

      Delete
    8. judmarc: "Which is of course false by every scientific definition of the word "information."

      Absolutely. So that leaves ID without a rationale for its inference, as well as without a mechanism. Compelling stuff.

      Delete
  14. oooooh.....sophisticated theology...got it.

    ReplyDelete
  15. Apologies for the threadjack, but I need a biochemist consult and I'm confident that there are some here.

    I'm reading this paper: http://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Keefe_Szostak_Nature_01.pdf

    I'm trying to understand the use of "immobilized ATP, washed and eluted with free ATP" in this context.

    Does it just mean that the ATP bonded to the protein and was subsequently released from the protein? I know i"m missing something here. Any help is appreciated. 

    ReplyDelete
    Replies
    1. What it relates to is how they manage to control the binding properties of the protein between individual selection rounds so they can subsequently amplifiy the attached mRNA of the corresponding protein(so they can mutate it further between rounds of selection).

      They have this column with tiny beads covered with ATP, they then put their random proteins (with a piece of mRNA that codes for the corresponding protein, attached) into the column, then wash the column with a solution that removes all the proteins that don't bind ATP. So now their column only have the proteins left that bind ATP, sitting there attached to the ATP on the beads.

      That's the initial round of "selection".

      Then they need to get their protein out again(in order to generate new mutants of them, using them as a template), so they alter the properties of the solution (probably with some ammunium salt or other solution that changes pH or ionic strength in the column) such that the ATP sitting on the beads release so they can get their protein out again by washing it with an ATP solution.

      They then use the mRNA attached to their successfully ATP binding proteins to generate mutated clones of, then repeat the process with a new column filled with beads covered with ATP.

      The methods are not well described in the paper, so the exact solutions they use to get their ATP and proteins out of the columns are not described, only that this is what they do. I guess you will have to look into the supplementary materials addition to the paper to get more details.

      Delete
    2. I'd have to look at the SI to be sure, but I believe they aren't releasing the ATP from the beads, they're just adding a large excess of free ATP in solution. Every aptamer has a rate of releasing and rebinding ATP, when the free ATP is present, aptamers binding surface-bound ATP will slowly exchange to binding free solution ATP, thus releasing themselves from the beads. This basically works as a second selective step, since aptamers that have bound to the beads but not specifically via binding to the ATP molecule on the beads will not remain stuck to the beads after elution.

      Delete
    3. OK, that helps a bunch. Thank you!

      Delete
    4. Yeah David is right, the paper mentions agarose-ATP gel beads so that settles it.

      Delete
  16. Oh, this is rich. Denyse O'Leary just quoted Luskin's list on Uncommon Descent. I was startled to read one of the knowledgeable biologists who was quoted as arguing that mutations could only be deleterious. Pierre-Paul Grassé. Luskin apparently wrote:

    "Similarly, past president of the French Academy of Sciences, Pierre-Paul Grasse, contended that “[m]utations have a very limited ‘constructive capacity’” because “[n]o matter how numerous they may be, mutations do not produce any kind of evolution.”

    Grassé -- don't I remember his name in some unfavorable context? Well, let's look at Wikipedia. Oh yes:

    "Grassé was a supporter of the French tradition of Lamarckism. He occupied the Chair of Evolutionary Biology of the Faculty of Paris, of which the two previous occupiers, Alfred Giard (1846–1908) and Maurice Caullery (1868–1958), were both also supporters of Lamarckism. Only after Grassé's retirement did the chair become occupied by a partisan of Darwinism, Charles Bocquet (1918–1977).

    Grassé died 30 years ago after having embarrassed French biologists for decades. He was holding out for Lamarckism even as Jacob and Monod did their Nobel-Prize-winning work on operons, even as Gustave Malécot pioneered modern theoretical population genetics, even as French virologists did pioneering sequencing of the HIV virus. Even as the well-known Montpellier evolution group started to gain attention. Even as Piotr Slonimski in Gif-sur-Yvette started to gather together European scientists who went on to make yeast the first sequenced eukaryote. Even as Emile Zuckerkandl returned to a job in Montepellier after his pioneering work on molecular evolution with Linus Pauling.

    Obviously none of them held a candle to Grassé, at least in Luskin's eyes.

    He was probably a pretty good termite biologist, though.

    Wow, Luskin is really up-to-date!

    ReplyDelete