Tuesday, December 22, 2015

Waiting for multiple mutations: Michael Lynch v. Michael Behe

Casey Luskin is trying to help out a university student by describing some important ID contributions to science [No ID Research? Let's Help Out This Iowa State Student].

One of those contributions is a paper by Michael Behe and David Snoke published eleven years ago in Protein Science (Behe and Snoke, 2004). I described the result in a previous post: Waiting for multiple mutations: Intelligent Design Creationism v. population genetics.

If Behe & Snoke are correct then modern evolutionary theory cannot explain the formation of new functions that require multiple mutations.

Cassey Luskin is aware of the fact that this result has not been widely accepted. He mentions one specific criticism:
In 2008, Behe and Snoke's would-be critics tried to refute them in the journal Genetics, but found that to obtain only two specific mutations via Darwinian evolution "for humans with a much smaller effective population size, this type of change would take > 100 million years." The critics admitted this was "very unlikely to occur on a reasonable timescale."
He's referring to a paper by Durrett and Schmidt (2008). Those authors examined the situation where one transcription factor binding site was disrupted by mutation and another one nearby is created by mutation. The event requires two prespecified coordinated mutations.

Durrett and Schmidt show that in Drosophila such event can occur on a timescale of about 4,300 years. In humans with an effective population size of 10,000 the event would take about 160 million years. The authors point out that such and event—two prespecified mutations—is very unlikely. They also point out that their estimates are 5 million times more likely that those given by Michael Behe in The Edge of Evolution.

This study is not very relevant to the evolution of new functions as described in Behe and Snoke (2004).

Casey Luskin ignored the more relevant criticism of Michael Lynch (Lynch, 2005). Lynch's paper was published in the same journal as the Behe & Snoke paper and it's a direct attack on that paper.

Lynch wrote the editors when the Behe & Snoke paper appeared asking if they would be receptive to a rebuttal in the form of a new research paper. The editors agreed, subject to peer review [see Editorial and position papers].

Lynch begins with:
In a recent paper in this journal, Behe and Snoke (2004) questioned whether the evolution of protein functions dependent on multiple amino acid residues can be explained in terms of Darwinian processes. Although an alternative mechanism for protein evolution was not provided, the authors are leading proponents of the idea that some sort of external force, unknown to today's scientists, is necessary to explain the complexities of the natural world (Behe 1996; Snoke 2003). The following is a formal evaluation of their assertion that point-mutation processes are incapable of promoting the evolution of complex adaptations associated with protein sequences. It will be shown that the contrarian interpretations of Behe and Snoke are entirely an artifact of incorrect biological assumptions and unjustified mathematical oversimplification.
He continues by pointing out that, contrary to their claims, Behe & Snoke were not modeling "Darwinian processes" because they were examining intermediates that were neutral with respect to selection and created a nonfunctional product. (The initial "compatible" mutations inactivated one copy of a duplicated gene pair.) Lynch concludes that, "... there is no logical basis to the authors' claim that observations from a non-Darwinian model provide a test of the feasibility of Darwinian processes."

This is standard criticism of ID proponents. It will be familiar to most Sandwalk readers. It proves that even when Intelligent Design Creationists should know better—like publishing a paper about population genetics—they still get confused by their own rhetoric.

Lynch's model differs from the Behe & Snoke model in several ways. He does not assume, for example, that a gene duplication event is required before mutations can accumulate. That's because Lynch does not assume that the initial compatible mutations are deleterious. He assumes that the mutations leading to amino acid substitutions are neutral.

This gives rise to seven different alleles and allele combinations that form the initial features of his model. He also assumes that there can be more than one way to change the function via a combination of such different mutations.

The vertical lines in the figure indicate "compatible" mutations that, in combination, will change the function. As we see in allele #2, some of them can occur before the gene duplication because they are not disruptive. This is different than the Behe & Snoke assumption.

Lynch retains several other assumptions in the Behe & Snoke paper:
To simplify the presentation as much as possible, the focus here is on a nonrecombining haploid genome (as assumed by Behe and Snoke), with the origin of a new adaptive function involving a two-residue interaction, for example, the disulfide bond between two cysteines. As in Behe and Snoke (2004), this adaptation is assumed to be acquired at the expense of an essential function of the ancestral protein, so that the new function can only be permanently established via gene duplication, with one of the copies maintaining the original function. The Behe-Snoke assumption that a selective advantage only results after both participating residues are in place is also adhered to.
Lynch quotes several papers to justify his assumption that the initial mutations are neutral, not disruptive. He concludes, correctly, that "... most proteins in all organisms harbor tens to hundreds of amino acid sites available for evolutionary modification prior to gene duplication."

A new variable, n is introduced. This is the number of codons that can potentially mutate to produce a new function. In Behe & Snoke this number was 1. If three mutations were required then there were only three possible codons that could mutate. In the Lynch model this number could be 10 or even 50.

Here's how Michael Lynch describes the process:
Successful establishment of the new function (neofunctionalization of one of the copies) requires the founding pair of linked gene duplicates to (1) initially attain a high frequency; (2) acquire the mutations essential to the expression of the new function (allelic types 6 or 7) while en route or subsequent to fixation; and (3) be preserved by positive selection subsequent to the origin of the new function. All three processes occur in parallel with a background production of null alleles. The two central issues to be resolved are then: (1) How frequently will a duplication event lead to neofunctionalization; and (2) How long will this take? Answers to these questions can be acquired by recursively following the population through the sequential steps of mutation, selection, and random sampling.
The model includes parameters for the gene duplication event as well as the standard variables such as mutation rate and population size. The mutation rate for amino acid substitution is 10-8, the same as in Behe & Snoke. The mutation rate for production of a null allele (deleterious mutation rate) is 10-6 per gene per generation.

Simulations were run using the requirement that two mutations are required for neofunctionalization (formation of a new gene). As you might expect, the probability is very sensitive to the total number of codons that can potentially be mutated. If there are 50 such sites (n=50), then fixation is almost assured for a population size of 10,000 individuals. If there are only two such sites, then you need a population size of 100 million to reach a reasonable probability of success.

Combining equations leads to simulations that estimate the time to neofunctionalization in generations.

Behe & Snoke claimed that with two mutations you need a population size of 1012 in order to fix the new allele in one million generations. The Lynch simulation shows that the new allele can be fixed in one million generations with population size of only 106 provided there are 50 potential mutable sites (n=50). That's a difference of six orders of magnitude.

Even with n=2 (as in Behe & Snoke) a population of one million could lead to fixation in 108 generations in the Lynch simulation whereas it would take 100 times as long according to Behe & Snoke. Recall that most of these simulations apply to single-cell, haploid organisms such as bacteria. In those populations the generation times can be measured in days. There might be 100 generations per year so 108 generations could be only one million years—a short time in the history of life.

There are three important differences between the two approaches. First, as already noted, Lynch assumes that the initial mutations are neutral. Second, Lynch assumes that there are multiple pathways to the formation of a new functional protein.

The third difference is more subtle. Behe & Snoke failed to take into account the fact that a linked pair of functional genes has a selective advantage because it now takes two null mutations to silence both copies. This effect doesn't make much difference in small population but in large populations it makes fixation of the new allele more probable.

According to Lynch, there are several reasons for thinking that his estimates of time to fixation are too high. You should read the paper to see what they are. (They're a little too complicated for the average Sandwalk reader, e.g. me.)

The bottom line is:
In summary, the conclusions derived from the current study are based on a model that is quite restrictive with respect to the requirements for the establishment of new protein functions, and this very likely has led to order-of-magnitude underestimates of the rate of origin of new gene functions following duplication. Yet, the probabilities of neofunctionalization reported here are already much greater than those suggested by Behe and Snoke. Thus, it is clear that conventional population-genetic principles embedded within a Darwinian framework of descent with modification are fully adequate to explain the origin of complex protein functions.
Casey Luskin may be unaware of this criticism but Michael Behe was not.

Behe and Snoke were invited to comment on the Lynch paper when it was published and they did (Behe and Snoke, 2005). They quibble about some of the wording in Lynch's article but the important part of their letter is:
Our paper (Behe and Snoke 2004) contains one simple result. When reasonable parameters are used with our model to estimate actual time scales or population sizes for the evolution of multi-residue (MR) protein features, they are unrealistically large. This implies that the model we chose, which is restricted to point mutations and assumes intermediate states to be deleterious, isn't a plausible evolutionary pathway. One must therefore look about for a new model. We did not rule out such a possibility; in our original article, we explicitly stated, “we should look to more complicated pathways, perhaps involving insertion, deletion, recombination, selection of intermediate states, or other mechanisms, to account for most MR protein features.”

In his Editorial (this issue), Professor Hermodson reports that comments sent to him assume a consensus, “Thus, intermediate states must also be assumed to be selected.” Some significant previous work does not make this assumption (Kimura 1985; Ohta 1989), but our paper supports such a consensus. This is a strong requirement—that not only the end products, but steps along the way to a multi-residue function, must be either selected or at least neutral. Michael Lynch makes a similar assumption. Our model posited necessary intermediate mutations to be deleterious in the unduplicated gene; Lynch's model assumes them to be neutral: “all 20 amino acids are equally substitutable in the intermediate neutral state” (Lynch 2005, this issue). All of his objections to our work stem from this difference.
In other words, Behe and Snoke deliberately choose a model that leads to unrealistic results but they are perfectly willing to accept other valid evolutionary models that seem much more reasonable.

Recall that Casey Luskin touts this paper as one of the few results from ID proponents that produce a genuine "scientific discovery." He notes that there was criticism but fails to mention the Lynch paper or the concession published by Behe and Snoke.

Isn't that strange?


Behe, M.J., and Snoke, D.W. (2004) Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein science, 13:2651-2664. [doi: 10.1110/ps.04802904]

Behe, M. and Snoke, D.W. (2005) A response to Michael Lynch. Protein Science 14:2226-2227. [doi: 10.1110/ps.051674105]

Durrett, R., and Schmidt, D. (2008) Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. Genetics, 180:1501-1509. [doi: 10.1534/genetics.107.082610]

Lynch, M. (2005) Simple evolutionary pathways to complex proteins. Protein science, 14(9), 2217-2225. [doi: 10.1110/ps.041171805]

217 comments :

  1. About the "two prespecified coordinated mutations" that require 160My in the human lineage, is that for one in particular or if there were, say 10 of them, then there would be one every 16My? Is there evidence of any of these having happened in apes?.

    ReplyDelete
    Replies
    1. 160 million years ago, there weren't any apes. That was about the time of divergence between placentals and marsupials.

      Of course, if one wanted to actually research this question, then one could go exploring the entire human genome and compare with the entire chimpanzee genome. All of those differences happened within 13 million years (http://www.sciencemag.org/content/344/6189/1272.full.pdf). And then one would know.

      Delete
    2. Ogre, I realize it would be very unlikely to see that kind of one-in-160My type of thing in the ape lineage, it just wasn't clear to me (not being a biologist) if that event is a particular, specific simultaneous mutation or it refers to "any" event that requires two coordinated mutations. If one particular type of event happens every 160My on average, but there are many potential events of that type, then it wouldn't be surprising to find one a lot more often than every 160My. Hope that makes sense

      Delete
    3. Not particularly. Behe, if I understand correctly, was speaking of a particular event. Not any possible event. Which is a key difference.

      One experiment showed that 4 mutational families occurred in a particular ribozyme. The final result was a 94 fold increase in function. Those mutations (I think the total was 12 or 14 point mutations) occurred during the 72 hours the experiment ran.

      Again, if you actually compare the human to chimpanzee genomes, you will probably find tens of thousands of mutations. Changing everything from brain formation to hirsuteness. The genomes are published, you just have to look for them.

      Delete
  2. Behe says: "Our model posited necessary intermediate mutations to be deleterious in the unduplicated gene; Lynch's model assumes them to be neutral: “all 20 amino acids are equally substitutable in the intermediate neutral state” (Lynch 2005, this issue). All of his objections to our work stem from this difference."

    Obviously untrue, that was not the only difference between Behe and Snoke, and Lynch. Lynch explained clearly the several ways that Behe's model used unrealistical assumptions and parameters in order to vastly overestimate the time needed to evolve an MR feature.

    ReplyDelete
  3. I'm sure Behe will come over to this blog to defend his refuted work.

    Oh wait...

    ReplyDelete
  4. It's nice that Lynch doesn't require that the specific amino acids that evolve be prespecified, but he's still assuming that the gene that evolves is prespecified. There are ~25,000 genes just in the human line, and some of them are bound to evolve. Then whatever gene evolves, both Lynch and Behe make the mistake, after the fact, of assuming that the gene destined to evolve was specified at the start.

    ReplyDelete
  5. This comment has been removed by the author.

    ReplyDelete
  6. This comment has been removed by the author.

    ReplyDelete
  7. Larry,

    All of it is BS and you know it. Just because something is "possible" it doesn't mean it happened. People like Behe are just trying to prove that the Darwinian model of evolution is irrational; in other words the possibilities are minuscule and yet Lynch and you explore it as if it was a well knownscientific fact. It's nonsense. Well, at least I know why you chose to believe.

    ReplyDelete
    Replies
    1. Thanks for the reminder, Eric, of why Casey Luskin, Michael Behe et al keep publishing their nonsense. Anyone with a reasonable amount of intelligence and an open mind will be able to read the above article and realize that Behe has openly admitted, in a scientific journal, that the entire basis of his life's work has been refuted. How can he do such a thing, and yet continue that work? Because he knows his audience is not made up of reasonably intelligent, open minded people. It is, instead, made up of faith-addled imbeciles like yourself, Eric, who cannot even comprehend Behe's admission, and will keep on happily lapping up whatever bilge Behe and the rest of his crew of IDiots keep spewing out. While you all keep writing generous cheques to the Discovery Institute for the privilege, of course. You're being played for a sucker, and you don't even seem to mind.

      Delete
    2. "People like Behe are just trying to prove that the Darwinian model of evolution is irrational;"

      Silly me. And I thought that he was trying to prove ID. I must have missed the memo.

      Delete
    3. Eric says: People like Behe are just trying to prove that the Darwinian model of evolution is irrational;

      I have in the past said roughly the same thing. In context of the model and theory I have what Mike Behe said is true. Without the ability to self-learn (intelligence) a genetic system would not be able to do the otherwise impossible. I cannot disagree with him or others who showed the math and logic for unintelligent systems.

      The problem is that over a decade later the Discovery Institute has rehashed the same-old arguments so many times they have become annoying to have to read through even more times. Instead of developing theory that shows why what Mike said is true he was more or less left stranded.

      Delete
    4. Of course. Gary Gaulin, just like Eric, is unable to comprehend Behe's admission of failure, and his concession that neutral theory make it highly probable that "irreducibly complex" sets of adaptive mutations will arise thru observed evolutionary processes alone. Here,Gary, let me again quote Behe's admission of defeat for your benefit (with my added emphasis):

      This is a strong requirement—that not only the end products, but steps along the way to a multi-residue function, must be either selected or at least neutral.

      Game. Set. Match.

      Delete
    5. Gary Gaulin,

      You are so right about your hints. I personally think that ID at the Discovery is a bit divided and they can't get their story straight.

      I'm not blaming Mike Behe for this but I think his views have been "recently" influenced by more than science. I hope I'm wrong about it because I adore Mike Behe for what he stands for and how he handles himself.

      Delete
    6. Eric: People like Behe are just trying to prove that the Darwinian model of evolution is irrational

      Really?

      We subscribe neither to triumphant views in some circles that our paper disproved Darwinism, nor to overwrought ones that it supports some grand anti-science conspiracy.

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253464/#behe-and-snoke-2004

      Delete
    7. I hope I'm wrong about it because I adore Mike Behe for what he stands for and how he handles himself.

      You "adore" him because he stands for dishonesty and because he handles himself by lying and treating his acolytes like dupes?

      Delete
    8. Eric, from my experience the Discovery Institute has always been divided. If this information from the NCSE is true then they are soon to become a more openly religious organization:

      http://ncse.com/blog/2015/12/marriage-made-heaven-0016830

      As far as science is concerned there is nothing wrong with taking a scientific theory religiously. But not being able to get their story straight makes it clear no coherent scientific "theory of intelligent design" is to be found there. Without a computer model or at least useful description of one to experiment towards all they have are religious arguments that are unconstitutional to teach as science in the US public schools. The arguments against another theory does not make a positive case for ID theory, which leaves them open to another legal case like Dover that they will lose. This does not scientifically help Mike either.

      Delete
    9. Oh, Gary. Your naivete is almost cute. Or is that actually your disingenuousness?

      The DI's religious motivation has been obvious to all but the deliberately misinformed

      Delete
    10. Dazz,

      You are too incompetent to question people like me and more so Behe. Many people who disagree with Behe still consider him to be a true scientist for a very simple reason; unlike most on this blog he is an experimental scientist. Can you tell the difference between the two say Dawkins vs Behe?

      Delete
    11. Gary Gaulin,

      I have to agree with you on many issues, but if I were Behe, and he is definetally a very, very intelligent guy, I don't believe he would insist on teaching "the burning bush thing" as a scientific theory. I'm pretty sure about it. Mike Behe is trying to explain to the world of the open minded people, that science is definetally pointing toward what he known loooooong time ago.

      Delete
    12. You're such an idiot Eric. Behe himself explicitly contradicts your claim that he was trying to disprove "darwinism". Of course he fails to prove anything at all, but that's a different matter. I wasn't questioning Behe's work in my previous post, the pros have taken him to task already. You poor sycophant can't even figure out what your idols actually say

      Delete
    13. Would you like to test your faith Dazz. I can do it but I you need to commit to it. I will question 5 of your fundamental beliefs. If you provide experimental evidence for only 1 out of 5 in question, I will let you go. Are you ready for such a challenge?

      Delete
    14. Five of my "fundamental beliefs"? LMFAO. Here's the run of the mill creatard pretending the questionnaire he found at IamAProudCreatard.god represents anyone. Oh boy what a laugh

      Delete
    15. I'm still curious as to what those "fundamental beliefs" are, and why would anybody have "faith" in them. Why do creationists imagine that we think exactly like them?

      Delete
    16. What are those five beliefs Eric? I'm still curious.

      Delete
    17. "Well, at least I know why you chose to believe."

      Right, he wants to keep sinning and not go to hell. It's what we all want. You caught us.

      You people all have about a half-dozen lines among you, and you think saying them over and over somehow makes them true.

      Pathetic.

      Delete
  8. How do the assumptions and numbers in the Lynch paper compare to the data from the LTEE?

    ReplyDelete
  9. Could someone give me a link to an explanation of how larger population sizes generate faster fixations? That is counterintuitive to me.

    ReplyDelete
    Replies
    1. Here's some links, I haven't read all these. But the first PDF has citations from Lynch and Felsenstein.
      https://homepage.univie.ac.at/Reinhard.Buerger/04WhitlockBuerger.pdf

      Lecture notes
      http://www.nyu.edu/projects/fitch/courses/evolution/html/genetic_drift.html

      Delete
    2. I feel like I'm missing something. IIn that pdf he staates

      "Also, the smaller the population size (N), the faster the decline in heterozygosity."
      also
      "the time it takes a particular mutant to achieve fixation from the time it arises is dependent on population size (this time is 4Ne generations"

      So, that argues it takes longer (proportional to pop size, not inversely proportional) to fix a random mutant, in contrast to the chart above with the diagonal lines. I'd really appreciate it if someone could educate me on this little point.

      Delete
    3. Mutations do take longer to fix in large populations (in 2N haploid generations), but specific mutations are also more likely to appear in the population (probability uN per generation, or waiting time 1/uN). In the drosophila/human case, the time to wait for a specific mutation to appear somewhere in the population is much longer than its fixation time after it appears, so the fixation time can be ignored.

      As far as I have understood, that is what is going on in this example at least. The Durett paper has a sentence stating it explicitly.

      Delete
    4. The time to fixation isn't as relevant as the probability of fixation. In the haploid population mutations occur with rate µ, which means that the expected number of mutations is µN. A neutral mutation has a probability of fixation of 1/N, so the rate of fixation is µN*1/N=µ. If s>0 then the probability of fixation decreases as N increases, but this decrease is slower than linear and thus the overall rate of substitution goes up. If s<0 then the decrease is faster than linear and thus the rate goes down as population size increases.

      Delete
    5. And just to be clear, the results Larry quotes from the Durett paper assume the final genotype has a fixation probability of 1 (s >> 0). So the picture you should have is of a long wait until the mutant appears, after which it very quickly fixes.

      (The Durett paper is more complicated since they consider "stochastic tunneling" through an intermediate neutral genotype)

      Delete
    6. I'm not trying to be dense, but I clicked on Hindersin and Traulsen (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233741/ )and that paper shows increasing fixation times using the 'Moran' method (figure 9). That paper was 1962, so I'm not sure if related.

      Delete
    7. Let's try an analogy. Let's say you have a pipe and water flows through it. Then you can look at the rate at which water comes out at then end (liters per unit time). The inverse of this gives you the time it takes for a liter of water to come out. Now you could also take a liter of fluid (using some tracer for instance) and see how long it takes for that volume to pass through the pipe. Now the first one may mot depend on the length of the pipe, but the second one definitely does.
      Moving back to population genetics you can ask: given a population (in which mutations happen in every generation) how long will it take for a particular substitution to happen? This is analogous to the question about the time it takes for a liter to flow out of the pipe. On the other hand you can ask for a substitution that has happened: How far back did the mutation occur? And that's analogous to our second pipe question.
      The rate at which a substitution with s>0 occurs goes up as Ne increases. The time to fixation goes up as well.
      The rate at which a substitution with s=0 occurs stays the same no matter what Ne is. The time to fixation goes up.
      The rate at which a substitution with s<0 occurs decreases with larger Ne. The time to fixation goes up.

      Delete
    8. You're confusing "fixation time" and "waiting time". They're different. The waiting time is the time to wait until a particular mutant appears in the population. The fixation time is the time it takes to fix, *after* it first appears.

      *fixation time* increases with N. However, this blog post and the papers it cites are about the *waiting time*, which decreases with N. They ignore the fixation time because it's relatively short and the fixation probability is high.

      Delete
    9. In the Lynch paper the waiting time used is the time for a mutation to arise and rise to a frequency at which it has a 99% chance of fixation. It's not the time until the first time the mutation occurs (which is far shorter).
      Durrett and Schmitt estimate waiting times for the second mutation to occur, which in their model either happens after the first one has been fixed, before the first one has been fixed or a mixture of the two.

      Delete
    10. Oh my comment was mean for Eric, I agree with your comments Simon.

      Although, maybe with one difference. I think even in the Lynch paper the waiting time (which he calls "arrival time") is much longer than the fixation time, except maybe for very large populations. (See "Time to neofunctionalization"). The figure Larry pasted shows only the waiting/arrival time for first appearance a gene duplicate which will neofunctionalize and fix, and does not include the fixation time. It shows 1/Ndp, with d= duplication probability per individual, p=fixation probability.

      At least as far as I understood....

      Delete
    11. Yes. But the key here is that it includes the probability of fixation, which turns it from the waiting time for the first mutation to the waiting time for the first mutation that eventually fixes. This time goes down as N increases only if s>0, while it goes up if s<0 (and does not change in the neutral case). That's how selection enters Lynchs model (and I think it's very useful to think of selection primarily as something that modifies substitution rates).

      Delete
    12. In what percentage of a population does a particular mutation have to occur for that particular mutation to be labeled as 'fixed'?

      Or is 'fixation' of a particular mutation measured/determined in some other way?

      And I have another question: Would you guys and gals describe extant humans as one population, or multiple populations? If multiple, how many, and where/how do you draw the lines between them?

      Delete
    13. Reality often doesn't meet our human need to use words that label neat, either/or categories.

      Humans represent one metapopulation with many geographically (and occasionally culturally) separated populations where breeding occur mainly within the local population but sometimes occurs among separated populations. Before long distance transport was common, the populations were more distinct than they are now.

      If you start labeling the populations, you start with bigger groups and quickly notice two problems. The bigger groups don't have neat edges. Also, each bigger group is a metapopulation in itself, consisting of smaller populations that breed mainly within themselves, and these smaller groups usually have smaller subpopulations.

      Reality is messy.

      Delete
    14. "In what percentage of a population does a particular mutation have to occur for that particular mutation to be labeled as 'fixed'?"

      Ideally, 'fixed' means that the allele occurs in 100%. Reality is messy, though. Practically, no mutation ever stays at a 100% frequency in a big population because new mutations occur and purging even harmful rare recessive alleles takes a LONG time. Therefore, practical definitions for particular studies include 99%, 99.5%, 95%, and "It's the only allele I saw in my sample of 20 individuals."

      Delete
    15. @simon,

      Ah yes you're right, the waiting time to the first mutant *destined to fix* doesn't always decrease with N, as you described.

      Delete
    16. It seems the key is that fixation time and arrival time are inversely related to population size, which caused my confusion. Also, that fixation time is small relative to arrival time. Thanks for helping me understand.

      Delete
    17. Ugh. I mean to say, fixation and arrival time have differently signed derivatives with respect to population size.

      Delete
  10. Behe writes:

    In his Editorial (this issue), Professor Hermodson reports that comments sent to him assume a consensus, “Thus, intermediate states must also be assumed to be selected.”

    If you actually read the editorial, linked below, you will that at no point does Hermodson say this is a "consensus". He is merely paraphrasing a remark made by one or more (anonymous) commentators.

    http://onlinelibrary.wiley.com/doi/10.1110/ps.051654305/full

    Creationist lies! News at 11!

    ReplyDelete
    Replies
    1. Even if that was the consensus of expert opinion, it doesn't really help Behe. It seems his only response to Lynch is to claim that most biologists reject the idea of adaptations occurring thru neutral evolution. Whether or not that's the case, it certainly is true that most biologists reject Intelligent Design as nothing more than religious apologetics poorly disguised as science. So just where does that get Behe?

      In effect, Lynch and Behe are in agreement in saying that adaptive traits do not arise thru a series of incremental steps, each of which is subject to positive selection. Lynch, however, goes further and suggest a mechanism by which they actually can arise. And while Behe accepts that this mechanism is plausible, he nonetheless rejects it. He offers no alternative explanation in this article, but from his other writings we know that his preferred explanation is that adaptations are created thru the magical intervention of a supernatural being, who he believes to be his Lord and Saviour, Jesus Christ.

      Only of those explanations, Lynch's or Behe's, belongs in a scientific journal.

      Delete
  11. Can we please show a scholarly concern for being correct, and stop referring to Mendelian population genetics as "Darwinian processes" or "the Darwinian model"?

    This has NOTHING precisely to do with Charles Darwin and his completely antiquated ideas about evolution. Darwin rejected discrete inheritance, and rejected the importance of individual mutations in evolution. The Mendelian concept of selection (the increase of one type at the expense of another) was popularized in the early 20th century by Johannsen, Bateson, de Vries, Morgan, et al., and is not compatible with Darwin's thinking. In Darwin's world, you could not assign a selection coefficient to anything, because hereditary substances shifted during an organism's lifetime (in response to conditions) and then blended in reproduction, i.e., they acted like fluids.

    ReplyDelete
    Replies
    1. In Darwin's world, you could not assign a selection coefficient to anything, because hereditary substances shifted during an organism's lifetime (in response to conditions) and then blended in reproduction

      Lamarckism?

      Delete
  12. Arlin said:

    "Can we please show a scholarly concern for being correct, and stop referring to Mendelian population genetics as "Darwinian processes" or "the Darwinian model"?"

    I strongly agree with you, and I'll add that it really irritates me when scientists (and IDiots) use terms like 'Darwinian', 'neo-Darwinian', 'Darwinism', 'neo-Darwinism', or anything else with Darwin's name in it when they're talking about something that Darwin did not know about, think of, propose, publish, etc.

    And now maybe you'll understand what I said about the word 'theory'. Call it my "scholarly concern". :)

    ReplyDelete
  13. Unrelated,

    How do the atheists spend this special time of the year? Do they "Christmas" a lot?
    I'm pretty sure they do because this is the only time when they can celebrate something they rejected a long time ago but they agree with anyways.

    ReplyDelete
    Replies
    1. Hey Eric,

      I celebrate the feast of the Saturnalia and the birthday of Mithra by draping holly across my door way which the Druids held offered protection against evil spirits, installing a fir tree in my living room which was introduced to Canada in the winter of 1781 and is said to scare away the devil, depending a parasitic plant called mistletoe from door frames due to it's erotic properties and it's ability to kill Norse gods and exchange gifts with friends and relatives which is lifted directly from the practice of gift giving in the Roman celebration of Saturnalia.

      So what pagan rituals have you co-opted for this time of year Eric ?

      Delete
    2. Well at least Steve is in the Christmas spirit. It sounds like they went all out this year. Maybe next year they will even perform the newest ritual called "Christmas lights".

      Delete
    3. LMFAO. Another theoloon that's not aware Christ couldn't have been born in Dec 25th and he's actually celebrating pagan festivities. Happy birthday Sol Invictus!

      Delete
    4. Christ couldn't have been born in Dec 25th

      Ya, so? From my experience only someone like you even cares, Grinch.

      Delete
    5. Oberski,

      How on earth did you figure out that I was celebrating X-mas? Are you wearing the tight baseball cap or are you hearing voices again? Please educate me how you have done it again.

      Are you and Dazz related? Perhaps, because he sure thought I was the X-mas guy. Down in Spain they are not really all that well, so I'm going to let it go.

      Delete
    6. I'm doing perfectly fine "down here" in Spain Eric. I got a proper education here, unlike you... apparently. You certainly seem to be totally clueless about what you're actually celebrating. But then again, you're most likely a home-schooled moron. So yeah.

      Delete
    7. Hey Eric,

      I'm beginning to suspect that your question was not asked in good faith and a spirit of honest inquiry.

      How are we supposed to establish a relationship based on trust if the only thing you ever do is prevaricate ?

      Delete
    8. I'm doing perfectly fine "down here" in Spain Eric. I got a proper education here, unlike you... apparently.

      I could've been worst for you Dazz. You could've gotten the proper and unbiased knowledge. I hope you known that there is a huge difference between the two?

      You certainly seem to be totally clueless about what you're actually celebrating.

      Well, I definitely don't celebrate the greedy, corporate explored "Christmas" that has nothing to do with Christianity. It is funny, buy at the company where I work, there were only 3 people who identified themselves as those not celebrating Christmas. Besides myself, there was a 7th Day Adventist lady and a JW. The JW was the only one who refused to go to the free, company paid buffet lunch.

      But then again, you're most likely a home-schooled moron. So yeah

      Actually, you are quite right here. I was home-schooled since I was about 10, because my parents moved a lot. Since my mom was a collage professor and my dad was a physicist who worked for the same company that had like over 100 locations around the world.

      Delete
    9. Oberski,

      I looked at my post again, and I've just realized that I may have not worded it right. I think it was in good faith though but it didn't come across as such. Sorry

      Delete
    10. Well, I took biology classes in public school and also religion, which was mandatory at the time. I also had to go through catechesis in preparation for my 1st communion, soon before I decided I'd had enough of that crap. So biased? sure buddy. OTOH you were home-scooled and you claim it was because your parents moved a lot... let me guess, they never found the time to teach you any proper biology and creation myths permeated everything else, like most home-school programs do... but of course my education was biased and yours wasn't. Riiiiiight. LOL

      Delete
    11. Dazz,

      I think I went through the same thing. Well more or less. I love biology and I believe, so do you. I'm just wondering if you are ready to pass the real biology test. Are you sure you are not bias when it comes to the real biology ?

      Delete
    12. Go ahead Eric. Post whatever straw-man misrepresentation of us you have found at some creationist site.

      Delete
    13. Dazz,

      What part of Spain do you live in? I've visited some regions of your country. It is quite beautiful. I love, for the most part, your culture and your hospitality. I'm afraid things have deteriorated ever since I've visited your country the last time.

      Delete
    14. Dazz,

      I gotta tell you, no man passes my tests. You wouldn't be the only one. So, just keep pressing on the "proper education" you got. But, it ain't good enough to challenge moi, tronco.

      Delete
    15. Wow, you come across as a flat out psychopathic stalker dude. I sort of feel for you. Must be the spirit of Sol Invictus

      Delete
    16. Dazz exclaims: Wow, you come across as a flat out psychopathic stalker dude.

      Honestly, in my opinion your belief that someone asking you "What part of Spain do you live in?" is coming across as a psychopathic stalker makes you come across as suffering from paranoia. Needing to keep your identity hidden from others may be contributing to the problem.

      Delete
    17. Dazz: But then again, you're most likely a home-schooled moron. So yeah

      Eric: Actually, you are quite right here.


      Just quoted for posterity. I thought we'd never get a single honest word our of Eric, but he surprised me.

      Delete
    18. Dazz,

      You seem like a nice guy with the most proper education that one can get. I assume that the proper education must've convinced you that the complexity of life is a product of random processes that didn't require ID. Right?

      Please tell us all, which experimental evidence and in what text books you found the most convincing when it comes to:

      1. The origin of information required for life to exist
      2. The origin of the first self-replicating molecule
      3. The origin of the first cell
      4. The origin of eukaryotic cell via symbiosis
      5. The origin of the random mechanism that makes life appear designed.
      I must warn you Dazz beforehand, that I will definitely have A LOT of follow up challenges should you respond to one or more of my should we say, inquires.
      If I'm a home-schooled moron as latesuite suggests, you, and latesuite should have NO PROBLEM PROVIDING EXPERIMENTAL EVIDENCE FOR YOOOOOOOOUR ALL BELIEFS. Because I'm telling you right now, if you have one of it, I'm will restrain myself from drinking Tempranillo 1987
      My favorite vintage.

      Delete
    19. 1. The origin of information required for life to exist

      Information? FOX News, of course

      2. The origin of the first self-replicating molecule

      New Jersey

      3. The origin of the first cell

      These where farted into existence by some interdimensional squirrels

      4. The origin of eukaryotic cell via symbiosis

      Interdimensional squirrels from New Jersey

      5. The origin of the random mechanism that makes life appear designed.

      The origin of the appearance of design is most likely attributable to your abusing of that tempranillo

      How did I do?

      Delete
    20. Now please answer this question for me:

      1. The origin of the Halley Comet
      2. The origin of the rings of Saturn
      3. The origin of Asteroid Belt
      4. The origin of all the moons of Jupiter
      5. The origin of all the sand grains of Jersey Shore

      I hope you can provide solid evidence for those or I'll have to assume that we must reject the theory of Gravity

      Delete
    21. I knew what your "stand' was before I've tested it.

      Well, it seems that your choice and your "proper education" lead you to this point. What else can I do?

      Why are you angry? Just because you can't get a job?

      Delete
    22. Eric sez:

      If I'm a home-schooled moron as latesuite suggests....

      I suggested no such thing. Dazz hypothesized this is what you most likely were, and you were kind enough to confirm this.

      (And, BTW, it's lutesuite.)

      Delete
    23. Eric,

      I assume that the proper education must've convinced you that the complexity of life is a product of random processes that didn't require ID. Right?

      Wrong Eric. I don't know about Dazz, but I'm not convinced of that, and the proper education system gave me ways to try and figure out some answers, but it did not give me all the answers. Not everything is well known to science. What makes you think that we were taught that there was answers for everything? I certainly wasn't taught that.

      In any event, let's see if you can learn. I'm convinced that the complexity of life is the result of several factors, not just "random processes." That doesn't mean that I think that ID was involved. Natural processes are not all "random processes." For example, gravitation is not a random process, crystallization is not a random process. Thus, I do not see why we should be restricted to random processes and random processes alone to explain the origin of life's complexity. Did you understand this?

      Now, to ponder if life's complexity is the result of, or needed, "ID," would be absurd because such a thing as an "intelligent designer," would mean life. and If there's life already, then ID would not explain anything. It would merely be a claim that life has always been there and being complex enough to be intelligent. Therefore there would be no origin for life's complexity to talk about.

      (I'm still curious as to what those five basic beliefs are supposed to be and why should Dazz hold them.)

      Delete
    24. 1. The origin of information required for life to exist
      2. The origin of the first self-replicating molecule
      3. The origin of the first cell
      4. The origin of eukaryotic cell via symbiosis
      5. The origin of the random mechanism that makes life appear designed.


      We'll definitely get right on this as soon as you can give us the logical scientific reason why the universe should be unable to bring forth so much as an amoeba, but an all-knowing all-powerful Creator is no problem.

      Delete
    25. Oh, and by the way - I'm not a scientist, but I'm aware of some information responsive to your questions. They're just not that difficult, conceptually.

      1. Normal physics and chemistry. All the components of life were made in the Big Bang and exploding stars (physics), and they then combined in normal ways (chemistry). Simple stuff.

      2. Normal chemistry. Even just the energy available when the Solar System was forming (as billions of other planetary systems formed in each of billions of galaxies) was enough to act on the available chemicals to create amino acids in the leftover bits that fall to Earth all the time as meteorites. So "organic" chemistry is an extension of regular old physical chemistry that goes on all the time in the universe around us. Here on Earth, there was energy from the sun, volcanism, and lightning, and plenty of chemistry going on in the air, land and eventually liquid water. If amino acids can be commonly made in the unfriendly radiation and vacuum of space, then under the much more amenable conditions on Earth, do you really think it was just a bridge too far to combine a few amino acids into proteins, or to make self-replicating molecules? Of course we'll never be able to draw an arrow to a spot on the early Earth and say "first self-replicating molecule here," but there is no great difficulty in getting self-replicating molecules from the normal everyday chemistry that was going on everywhere around the early Earth.

      3. Lots of lively discussion about possibilities here. You should read the scientific literature (which is ongoing, with plenty of good articles published every year) sometime. The important thing to note is that none of it requires unknown forces beyond the normal everyday chemistry and biology we know of. I mean it's a marvelous thing, but the problem is not that no one can think of how it could be done, but rather than *many* people have competing logical, scientific ideas about how this could have happened using normal everyday principles of chemistry and biology.

      4. There are a number of ideas about candidate ancestors, being narrowed down by good work on the part of people like Eugene Koonin.

      5. The "mechanism that makes life appear designed," or at least the mechanism most responsible, would be natural selection, which is not random. So your question is incorrectly phrased.

      Delete
    26. "1. The origin of information required for life to exist
      2. The origin of the first self-replicating molecule
      3. The origin of the first cell
      4. The origin of eukaryotic cell via symbiosis
      5. The origin of the random mechanism that makes life appear designed."

      Eric, are you claiming that 'origin' and 'design' are the same thing? When you say the words origin and design (and "ID"), don't you mean creation, and don't you mean (and believe in) creation as described in the bible? If that is what you mean and believe in, why don't you be honest and say so?

      ID pushers (i.e. dishonest creationists) often claim that information is not material (matter), and that information existed before matter, and that without information nothing else would exist and function. Is that what you believe? If so, where, when, and how did information come into existence? Where, when, and how did matter come into existence? Where, when, and how was/is information installed in matter? Was/is information installed in all matter or just some matter? If just some matter, which matter? If you believe that information and matter were/are created by a so-called 'god', which of the thousands of so-called 'gods' that people have conjured up?

      Delete
    27. Scientists haven't even one clue how matter can self organize and become living. This fundamental issue clearly reaches beyond human intelligence and materialism.

      Since this is the case, how could everything else that is based on this simple truth can be explained by random processes; materialistic, baseless assumptions? It's a cliche.

      Delete
    28. This fundamental issue clearly reaches beyond human intelligence

      Everything reaches beyond creationist "intelligence". You can now go shove your god-of-the-gaps up where the sun don't shine. Thank you

      Delete
    29. "Now please answer this question for me:

      1. The origin of the Halley Comet
      2. The origin of the rings of Saturn
      3. The origin of Asteroid Belt
      4. The origin of all the moons of Jupiter
      5. The origin of all the sand grains of Jersey Shore

      I hope you can provide solid evidence for those or I'll have to assume that we must reject the theory of Gravity"

      Dazz, let me give you a word of advise to a kid that just finished schooling and thinks he/she can take on the world;
      The host of this blog professor Larry Moran has been fighting the main stream education system that he must be familiar with and then we have the opposite side. And they are tough man, because few of them, like Behe, Axe, A. Gauger-my favorite scientists because she is a much smarter woman than me.

      Delete
    30. Scientists have plenty of clues about abiogenesis.

      The fact and theory of evolution are not based on abiogenesis. Many people believe that God made it all including simple life, then let evolution take over. The ToE is perfectly consistent with that scenario.

      Delete
    31. Eric, I'm an atheist who doesn't celebrate anything at Christmas. Because I don't celebrate Christmas, I'm always the one tapped by the charity I volunteer with (which delivers free meals to needy people with HIV/AIDS and their families) to deliver toys to the families with children who are in our program. After I was done with that, I came home and listened to Powder Her Face by Thomas Adès and read a book on philosophy. So how does that fit with your preconception that all atheists are just tacit Christians (and does this apply equally to atheists in Asia and Africa, or are you one of those people who think that no place exists in the world except where you happen to live)?

      Delete
    32. A. Gauger-my favorite scientists because she is a much smarter woman than me.

      That may be true, but she isn't actually intelligent or knowledgeable. We've had fun kicking around Gauger's many flashes of dullness here at Sandwalk before.

      Delete
    33. Many people believe that God made it all including simple life, then let evolution take over.

      I believe that we were created by the (has many names) still all around us right now force(s) powering the behavior of matter.

      The belief that whatever created us "then let evolution take over" makes no scientific sense at all. It sounds more like an academic way of accepting a Santa Claus God that only visits on special occasions then sneaks away before we see them.

      Delete
    34. Scientists haven't even one clue how matter can self organize and become living.

      This may be a comforting thought to you, but it's quite wrong. Matter "self organizes" every day (gravity, crystallization, normal chemistry...). Regarding "becomes living," see my responses 1-3 to Eric. There's nothing extraordinary required for life to begin beyond the normal physics and chemistry we already know. Yes, life is awesome. Doesn't mean the possibilities for the way(s) it began are beyond comprehension.

      Delete
    35. @ Gary Gaulin,

      Santa Claus is all around us right now, too: "He sees you when you're sleeping, he knows when you're awake. He knows if you've been bad or good."

      So, sorry, your attempt to distance yourself from the ridiculous beliefs of the IDiots fails. You're one of them, whether you like it or not.

      Delete
    36. Anything is possible, doable and most of all can be denied by the followers of "Darwin of the Gaps".

      It is easier to simply say; "I won't agree, believe any scientific evidence unless it supports my predetermined views". Darwinists' devotion is absolute and it is pointless to argue with them or try to present scientific evidence against their blindness.

      Delete
    37. The use of the word "Darwinists" by creationists always shows that they don't have a clue about modern evolutionary theory.

      Delete
    38. R.E. Myers, what color is the sky on the planet where you live? Here on Earth, evolution is science and has been for over 150 years.

      If you're such a stickler for science, please point to a single thing about life on Earth, species, and their origins that contradicts known physics, chemistry or biology.

      Delete
    39. Eric, I'm an atheist who doesn't celebrate anything at Christmas. Because I don't celebrate Christmas, I'm always the one tapped by the charity I volunteer with (which delivers free meals to needy people with HIV/AIDS and their families) to deliver toys to the families with children who are in our program. After I was done with that, I came home and listened to Powder Her Face by Thomas Adès and read a book on philosophy. So how does that fit with your preconception that all atheists are just tacit Christians (and does this apply equally to atheists in Asia and Africa, or are you one of those people who think that no place exists in the world except where you happen to live)?

      This is ALL admirable. You may be one of the very few atheists I have come across that literally doesn't celebrate Christmas. I know for a fact that many atheists who publicly admit that they hate anything that has anything to do with religion or God (Christmas doesn't have anything to do with God), and yet, during Christmas season, they dress as Satan Claus, decorate a Christmas tree and even sing Christmas Carols. To me personally, it doesn't make any sense. If you are an atheist, where is your integrity? Maybe you can explain it to me because I can't comprehend this kind or sort of betrayal. I believe it is a betrayal and many, many atheists are closet-celebrators, which actually makes me mad.

      Delete
    40. Nullifidian,

      Just curious; How often do you serve at the soup kitchen?

      Delete
    41. many, many atheists are closet-celebrators

      Grew up Jewish, atheist now, so never celebrated Christmas.

      Are you a Christian? Because if you are, your love for your fellows is distinctly lacking. Having grown up Jewish, I know what it is to not be getting gifts, putting up and decorating the Christmas tree, sitting down to dinner with a passel of relatives, and all the other things that are not only in every TV advertisement but are the topics of most TV shows for a month or two, in every store, in every town square, all over the radio.... Think about what it is to be a parent and try to tell your 4 year old it's OK that everyone in the world it seems is getting presents and putting up a bunch of pretty decorations but her. Think about how it would be to be "different," the "outsider," when the social relationships between your child and all the other kids are just starting to develop.

      Think you'd be strong enough to go through with that? Would it be better or worse, do you think, to let your child feel part of what everyone else is doing, regardless of what your religious or non-religious feelings are?

      My parents had very definite ideas about that, and as I said, I never celebrated Christmas growing up and still don't today. On the other hand, my wife is Catholic, and though not very observant, she's always loved Christmas and wanted it to be the type of family time that she grew up with. I try to make sure she gets that. Do you think it's wrong to show my love for my wife in that way? Should I insist that we have no tree, no decorations, no family dinner, no presents? (We don't have young children. My wife's son is in his 40s. I give gifts to him and my wife and accept gifts from them.) What do you think, Eric? Got a simple answer?

      (By the way, my wife and I volunteer each year on Christmas Eve serving Christmas dinner to about 5000 local people who can't afford their own. I help wrap Christmas presents, do Christmas decorations, and assist with preparing and serving Christmas dinner. Does this make me a bad atheist?)

      Delete
    42. Eric says,

      To me personally, it doesn't make any sense. If you are an atheist, where is your integrity?

      We've already established that there are a ton of things that don't make sense to you and we've already established that "integrity" isn't a word that applies to you.

      But, out of curiosity, do you celebrate the pagan holiday on the evening of October 31st?

      How about the Roman Catholic feast of Saint Valentine? Do you celebrate that? Are you a Roman Catholic?

      Delete
    43. Eric, there have been celebrations around the time of the winter solstice since long before Christianity. Many of the trappings of Christmas as celebrated here come from pre-Christian celebrations co-opted to integrate Christianity into previously non-Christian societies. Even the choice to celebrate Jesus' birth at this season co-opted Roman Saturnalia.

      So, yes, I celebrate Christmas. I'm not celebrating Christ but am stuck with the terminology. I celebrate light in a season of darkness. I celebrate love of family and giving of gifts. And I do it with a Christmas (i.e., seasonal) tree covered with ornaments taking the form of diverse plants and animals.

      Delete
    44. Professor Moran,

      I don't celebrate any of the pagan holidays including 31st and others you've mentioned. Now, what are you going to do about it? You have nowhere to sting me, do you? Well, maybe one.

      Delete
    45. What's a Christian in your view? Someone who says I'm a Christian or someone who does what Christianity actually requires?

      Delete
    46. Eric, Christmas is a pagan festivity. Deal with it. If you're going to be a festivity fundie, go and find out what date Jeebus was born and celebrate it on your own as the lunatic you are

      Delete
    47. judmarc,
      My mom grew up in a very, very poor village somewhere in Poland that could have belonged to the Soviet Union at the time of the II World War. Besides the quite funny stories she conveyed to me from that time, she told me a story of a Jewish family that resided in her village. When the Germans came in for their last battle, their desperation must have been really bad as they had tried to recruit anyone but a Jew. At night a well known Jew neighbor came in and had a long conversation with my grandfather. After that he left, apparently a few days later, his Jewish family and him were taken away and nobody has heard about them the until the late 1980-or early 1990. My grandfather was 93 years old and in pretty good shape. Apparently, one car showed up, a Mercedes that had no brand name marks on it and few people in yarmulkes came out. My grandfather handed them in what they came for, and they left. My grandfather apparently never looked at the stash box that was left with him, so will will never know what what the content of that box was.

      Delete
    48. Eric -

      My stories about Polish/Russian ancestors are a little less amusing.

      My maternal great-grandmother and great-great-grandmother starved to death in Grodzisk (part of the Warsaw ghetto) shortly before most of the remaining residents were wiped out in the Nazi response to the Warsaw ghetto uprising.

      My paternal grandfather came from Palangen, a Jewish area of Riga, Latvia, which was part of Russia during World War II. When the Nazis invaded, they, with Latvian assistance, lined up and shot the vast majority of the Jewish residents (over 26,000 people).

      Sorry, I don't have any heartwarming stories of family members of mine stopping by in Mercedes a half century after the war to pick up their property saved intact for them by kindly Christians. If you watch the movie "Shoah" (a ten hour documentary), you will see interviews with Polish women whose reaction to the extermination of their Jewish neighbors was that there were empty homes they were happy to move into, and no more competition from Jewish women for Polish men.

      I do know of a family member who received help, but this was from "bad," "immoral" Christians. Friends in the Corsican Mafia arranged for my great-uncle, who'd moved from Grodzisk to Marseille, to be in a brothel with a prostitute when the Nazis came through searching for Jews, after which they smuggled him out of the country. So my great-uncle owed the last several decades of his life to criminals and prostitutes.

      Delete
    49. My mom grew up in a very, very poor village somewhere in Poland that could have belonged to the Soviet Union at the time of the II World War.

      Eric, you must know a helluva lot about your mom's old country, its geography and history.

      Delete
    50. Eric, I’m not sure if you are aware but birthday celebrations are also deeply rooted in pagan traditions and have been absorbed by Christendom as were other celebrations mentioned by bwilson295.

      I also wonder: Are you are aware of the one particular celebration that Jesus did ask his followers to celebrate or commemorate? It is the memorial of his-Jesus death.

      Luke 22:19
      “Also, he (Jesus) took a loaf, gave thanks, broke it, and gave it to them, saying: “This means my body, which is to be given in your behalf. Keep doing this in remembrance of me.”

      The followers of Jesus and first Christians were observing Jesus’ command as indicated in 1 Cor 11:20 and historians.

      “When you come together in one place, it is not really to eat the Lord’s Evening Meal”

      Delete
    51. Still, I liked the part about the Mercedes that "had no brand name marks on it". Probably so you wouldn't recognize it as a Mercedes.

      Delete
    52. Judmarc and Eric, Those are really interesting stories.

      When I was growing up, I got interested in stories like that by an old Jewish neighbor who survived the Warsaw ghetto and a concentration camp. He told me that he lost his faith in God and that Jews were God's chosen nation, when he saw all the suffering they have gone through during the war.

      As a young boy, I spent many hours researching the subject of "human suffering" and tried to convince the neighbor that human suffering, including the Jews, wasn't God's fault. Initially, he wasn't willing to accept any arguments. But, as the time went by, we became pretty good friends and his attitude gradually began to change.

      Although the neighbor never actually said so, I believe he accepted it that humans were and are responsible for the majority of the suffering in the world.

      Delete
    53. Eric, You misspelled Satan Claus instead of Santa Claus unless it was deliberate.

      Delete
    54. Still, I liked the part about the Mercedes that "had no brand name marks on it". Probably so you wouldn't recognize it as a Mercedes.

      So they wouldn't remember they were driving a German-made car? A great many camp survivors and other Jewish folks I knew when I was younger would not have bought anything made in Germany.

      Delete
    55. I know for a fact that many atheists who publicly admit that they hate anything that has anything to do with religion or God....

      You have misunderstood atheists. Frankly, I don't "hate anything to do with religion or God", nor do any of the atheists I've met. I listen to sacred music at times if I feel like it. Bach's b minor Mass remains a staunch favorite, as does Brahms' non-liturgical but still Bible-based Deutsches Requiem, Verdi's Requiem, and I also like modern works you may not have heard of like Olivier Messiaen's Vingt Regards, Kaija Saariaho's La Passione de Simone (a mashup of Simone Weil's writings with the Stations of the Cross), etc. Sometimes in listening to music, classical music especially, I will visit churches that are putting on concerts. That doesn't make me a closet Christian any more than going to synagogues that put on concerts makes me a closet Jew.

      Here's something that you will have to understand if you're to understand atheists at all: while your life may revolve around your religion, that doesn't mean that our lives revolve around your religion. I don't refrain from celebrating Christmas because it's associated with Christianity, but simply because I don't feel like it. I don't like Christmas jingles, I don't like the mad rush of shopping between Thanksgiving and Christmas, and my tastes are simple and my wants few and inexpensive, so if there's something I want I just go ahead and buy it. I give gifts around Christmas to friends and family and their children (I have none myself, and that's a major reason why I don't feel obliged to celebrate Christmas), but tell those who want to return the gesture to just give to charities or advocacy groups that I support.

      (Christmas doesn't have anything to do with God)

      So then why is it a "betrayal" of atheism to celebrate it if it has nothing to do with God? In fact, this is the one point where you're right. Christmas has become a secular, cultural celebration that can be observed by pretty much anyone, and that includes atheists.

      If you are an atheist, where is your integrity? Maybe you can explain it to me because I can't comprehend this kind or sort of betrayal.

      But what could be more indicative of one's atheism than a refusal to credit Christmas with any religious importance whatsoever? Recoiling from everything with a hint of Christianity in it is to give too much credit to Christianity. Where does it end? Should I stop reading anything that was ever written from a Christian background, even if the work itself treats the faith with a certain amount of irreverence? Then I'd lose out on some of my favorite comic works, like Erasmus' The Praise of Folly, Rabelais' Gargantua and Pantagruel, Boccaccio's Decameron, Hašek's The Good Soldier Švejk, Barth's The Sot-Weed Factor, etc. I read Margery Kempe's religious autobiography (in the original Middle English, even!) and thoroughly enjoyed it. But I also enjoyed works like Naguib Mahfouz's Akhenaten and the Völsunga Saga. I was raised outside the faith—outside all faiths—so I don't regard any specific one as more deserving of being taken more seriously than any other.

      Just curious; How often do you serve at the soup kitchen?

      It's not a soup kitchen, although cooking does enter into it. This charity creates and delivers meals cooked to serve the specific nutritional needs of people living with HIV/AIDS. I don't volunteer in the kitchen, but on the delivery side, and I do it twice a week at least. My regular route is on Tuesday and I'm also a standby driver, and there hasn't been one week I've not been called on to help out at least once.

      Delete
    56. So they wouldn't remember they were driving a German-made car? A great many camp survivors and other Jewish folks I knew when I was younger would not have bought anything made in Germany.

      This is a very good point judmarc. I've never thought of it this way but it makes sense.

      Another one I've just remembered that my former boss and big creationist told me once under the influence that when he pre-ordered his car, he made some special requests, such as the license plate holes not to be made in the bumper and all the AMG logos not to be installed, so that his partners wouldn't accuse his of stealing money from the company or something like that craziness.

      I gather that if there is a will (usually money) then there is a way.

      Delete
    57. Newbie,

      I did know about the birthday thingy, then I forgot, but I don't think it is as clear as you people try to present it to be. I think that you guys focus so much on death, that nobody wants to listen to you anymore because it is too negative a message or whatever IMO.

      Delete
    58. Nullifidian,

      You sound like a remarkable man and an unusual man. I mean it. I already know there are major differences in our views but I don't seem to care. I've read your last post several times and I have to take a break before I can respond to it. That is if I can respond to it. If you don't hear from me for a few days, you will probably know what happened.

      Delete
    59. Eric,

      I really don't see why. The only thing at all unusual about my background is that I'm an American who was raised without religion, but that wouldn't be unusual if I were in Europe, and if the trends hold for the U.S. it won't be that unusual here for very much longer. Even though not all of the "nones" call themselves atheists, they're not likely to be religiously observant or force their beliefs, if any, on their children. That was how I was raised. My mother lived and died without my knowing what she believed. I think my father believes in God, but only vaguely, like some background belief that he picked up in childhood but doesn't really care about. When my mother was alive, my parents celebrated Christmas—even putting out a Nativity set that had been handed down to my mother—but neither my father nor I have any use for it any longer. Even when I was a kid, I found the whole "What do you want for Christmas?" thing incredibly difficult to answer, since the honest answer of "nothing" clearly wasn't what was expected.

      Delete
    60. Jon Fleming,

      Just because YOU or a very few scientists in the field of the origin of life claim that they have clues and the reality of it, are very, very different things.

      There is absolutely not one piece of scientific evidence-meaning experimental, that the simplest of the cells could have originated by ANY OF THE RANDOM PROCESSES INCLUDING MODERN OR OTHER DARWINIAN. If you have proof, give it to me now. I bet you $10.000, you don't

      Delete
    61. There are experimental observations showing that simple organic molecules can form from collections of elements, under conditions that do occur in nature. Appropriate simple organic molecules can attach to make longer organic molecules, too. Hydrocarbons can form and when in water they can form bubbles -- functionally, simple cell membranes. Such bubbles can concentrate other organic chemicals within them. One of the longer molecules that can form from inorganic precursors is RNA. These are all clues and all observed in experiments.

      Experiments starting with random RNA molecules have shown that selection can lead to the formation of RNA molecules that are better at making copies of themselves than the first RNA molecules were. Another clue.

      I don't know if the work on evolution of using proton gradients to make ATP is theoretical at this point or if it includes experimental work. It's another clue, though probably not a firm one yet.

      Do we know how the first cells originated? No. Do we have clues? Yes, definitely. Is it likely that you, Eric, will understand that these things are clues to the origin of cells? I would bet not, though I'd like to think I was wrong about that.

      Delete
    62. It's interesting...the Christmas festivities of my atheist friends are virtually indistinguishable from those of my Christian friends (I'm an agnostic myself). Trees, lights, gift-giving, celebrations with family, etc...they do it all. About the only thing they don't do is go to church on Christmas eve.

      Even if you're not down with the whole Son-of-God thing, just about everybody loves baby Jesus, and they get into the spirit of the season just like the true believers. I think that's awesome.

      Delete
    63. Even if you're not down with the whole Son-of-God thing, just about everybody loves baby Jesus, and they get into the spirit of the season just like the true believers.

      Just shakin' my head here....

      Delete
    64. Eric, looks like you owe bwilson295 10 grand.

      Delete
    65. In some regions of Spain, these figures called "caganers" are typical in nativities

      Pics of Caganers

      Just to get in the spirit

      Delete
    66. This is a very good point judmarc. I've never thought of it this way but it makes sense.
      * * *
      I gather that if there is a will (usually money) then there is a way.


      I think you kinda missed the point, Eric. What Joe and I noticed is that of course the Jewish folks in the story had money, which is the point of mentioning they drove a Mercedes, which is somehow recognized even with no brand markings(?). The point of what I mentioned was to note it is somewhat unlikely people who'd been in the circumstances related in the story would have bought a German-made car of any brand.

      But as you say, where there's money there's a way, and we know Jews have money.

      Delete
    67. Hey Curt,

      I guess Herod just loved him some baby jebus and was just getting into the spirit of the thing when he "ordered the execution of all young male children in the vicinity of Bethlehem, so as to avoid the loss of his throne to a newborn King of the Jews whose birth had been announced to him by the Magi."

      Delete
    68. Eric--
      The Reason for the Season is the tilt of the Earth's axis relative to the plane of its orbit around the sun. People of any religion, or none, have as much right as you do to celebrate the winter solstice (or summer solstice, depending on hemisphere) in any way they choose. Insisting that the tilt of the earth belongs to your, personal, sect of the Abrahamic religion, and that the rest of us are impinging on your, personal, rights is very unlikely to convince anyone of your moral superiority.

      Delete
    69. Well, OK. Let's play!

      I didn't really start ITthis way, but others contributed now more, so I feel like I should pick up the leftovers and continue.

      1. If scientists were to create life, they need to know what life is and is not. So, we are stuck right at the beginning- the definition of life.

      How can scientists look for life on other planets or try to create life in the lab if what they've found or created may or may not be alive, depending on the definition of life of course.

      How can we even start breaking this issue down?

      Delete
    70. Exactly, Eric. Now are you starting to understand why one of the standard creationist arguments ("If evolution is true, why haven't scientists been able to create life in a lab?") is abject nonsense?

      Delete
    71. Well, there is more problems there (origins). Most people would agree that prokaryotic cells are alive but to get to a living cell from lifeless matter, KAZAM is required and science doesn't have it, although the worthless claims were and will be made. Because they need to be made to satisfy the faithful.

      Delete
    72. lutesuite,

      You are either too stupid or too bias for me to talk to you and waste my time.

      Here is an example as to why: If intelligent scientists were unable to create life, how would this make random, unintelligent evolution, not requiring ID true, IF ONE DAY, intelligent scientists do create life?

      Give me your full explanation on this, because this is going to make my day today. Give me ALL YOU GOT!

      Delete
    73. Eric, so if I understand your arguements, if scientists can't make living cells from non-living components, there's no evidence life can arise naturally. But if scientists some day can make living cells from non-living components, that's evidence that life can't arise naturally? Heads I win, tails you loose?

      This is not an argument worth having.

      Delete
    74. So, Eric, it seems your answer to my question is: "No, I still don't understand." Would a hint help?

      Delete
    75. Let's do some fact-checking that even modern evolutionary biologist would like not to talk about, second to endosymbiosis:

      DNA is essential for single protein to form
      DNA cannot form without protein
      Protein cannot form with no ribosome
      Protein cannot form with no RNA
      Protein cannot form without ATP
      Protein cannot form without the mitochondria and so on and so forth.

      There is tons of more of that but I don't want anyone to read this long list and get distracted from what follows.

      The logical conclusion is that the living cell is an interdependent/interconnected system that has to function simultaneously and one part will not function without the other.

      Well, maybe in the delusion-ruled world of Darwin followers but nowhere else in real, experimental scientific world.

      Delete
    76. R.E. Meyers, what you are stating is true for modern eukaryotic cells, but not for all chemistry.

      Proteins can form from RNA without DNA.
      DNA cannot form without protein, but RNA can.
      Proteins can form without ribosomes.
      Proteins, or at least short polypeptides, can form without RNA.
      Proteins can form without ATP.
      Proteins can form without mitochondria, and do in all bacteria.

      Try again after learning some organic chemistry.

      Delete
    77. "Proteins can...Try again after learning some organic chemistry"

      Organic chemistry is not about purpose and function. Proteins are.

      Delete
    78. bwilson295,

      This is your time to shine! Don't you leave us wanting more! Let's see the scientific/experimental evidence you obviously have for your claims.

      Delete
    79. There is a great deal of scientific/experimental evidence for each of the statements I made about protein chemistry. You can look it up as easily as I can.

      Organic chemistry is (in part) about proteins.

      Delete
    80. This is your time to shine! Don't you leave us wanting more! Let's see the scientific/experimental evidence you obviously have for your claims.

      Why exactly should he waste his time duplicating information you could find at your local public or university library if you were at all interested in actually learning something about these points? (Regarding which he is quite correct - you know amino acids, the building blocks of proteins, have been found in meteorites, right? So, far from being next to impossible, forming the building blocks of life is chemistry so ordinary it can and does quite commonly occur in the incredibly harsh conditions of outer space.)

      Delete
  14. Larry, there was no concession from Behe. He referred to his model as reasonable.

    Of course he would use this model first.

    Lynch uses the illogical assumption that the mutations are neutral. Yet, we cannot assume logically that mutations in early organisms were neutral for the very reason that according to the non-teleological step-wise change narrative, early organisms were simple and did not have all the systems in place that modern organisms use to manage mutations, whether deleterous, neutral or beneficial.

    We can only logically assume that mutations to early organisms would be more harmful.

    So Behe's assumption of deleterous mutations is the correct assumption to make.

    Lynch is simply wrong-headed in his attempted rebuttal.

    ReplyDelete
    Replies
    1. What are you talking about? Lynch was addressing humans. What do "early organisms" have to do with any of that?

      Delete
    2. did not have all the systems in place that modern organisms use to manage mutations

      OK, just think for a minute. If there's a mutation, then "the systems in place that modern organisms use to manage" have *failed*.

      Duh.

      Delete
    3. I wonder exactly what "systems in place that modern organisms use to manage mutations" Steve has in mind. Perhaps he could list some examples. What deleterious effect would result from a neutral mutation (e.g. a point mutation in a sequence of junk DNA that serves no function and which may not even be transcribed) without these "systems" in place to protect the organism?

      Delete
    4. Larry, there was no concession from Behe. He referred to his model as reasonable.

      If there are many "reasonable" models that can explain the origin of new genes by purely mechanistic means (evolution) then what was the point of his paper?

      Why did Behe and Snoke conclude in their abstract that production of a novel protein feature requiring two or more amino acid residues would require population sizes of at least 10^9?

      Would you make a statement like that if you already knew that there were other reasonable models that could explain the novel features using much smaller population sizes?

      Delete
    5. Of course you would, if you thought that publishing such an article would induce gullible cretins like Steve to keep money flowing into the coffers of an "Institute" to which you belonged.

      The more serious question, to my mind, is why the peer review process failed in this instance. Someone familiar with Michael Lynch's work, if not Michael Lynch himself, could have reviewed the article before publication to save the journal the embarrassment of having published such a shoddy piece of work. No?

      Delete
    6. Larry Moran,

      The point is not how many reasonable models are out there. rather, is Behe's model more reasonable than Lynch's?

      Behe's model is the more parsimonous.

      That is IMO where evolutionary models always go wrong. They inherently have to assume a slew of conditions to tie it all together.

      Lynch's model is no exception.

      Delete
    7. Behe's model is the more parsimonous.

      That is IMO where evolutionary models always go wrong. They inherently have to assume a slew of conditions to tie it all together.


      Behe's model is more parsimonious in the same sense as atomic theory is more parsimonious without quarks: Behe's theory is an oversimplification that excludes factual knowledge, such as the fact that we are aware of systems meeting his definition of "irreducible complexity" that have evolved, or that genetic drift is an operative factor in evolution.

      The "slew of conditions" you mention are not assumed, they're known and confirmed through research and experiment. Behe must deliberately ignore them to put forward his theory.

      Delete
    8. Behe's model is the more parsimonous.

      Really? Behe's model assumes that there exists some mysterious, as yet undetected, force that ensures that only highly deleterious mutations occur, even though it has been demonstrated that by far the majority of mutations are neutral or only slightly deleterious. And then Behe proposes the existence of yet another mysterious, as yet undetected, force (named "Jesus") that is able to overcome this first force (the one Behe just invented out of his own imagination) in order to allow novel adaptive traits to evolve.

      I don't think you understand the meaning of the word "parsimonious."

      Delete
    9. Besides, Occam's Razor applies to models with the same explanatory power. Behe's model was deliberately picked so that it wouldn't work, so it fails to explain anything at all. He might as well model it with no mutations whatsoever. Wouldn't that be more parsimonious?

      Delete
    10. This ID "researchers" have the best job ever. Imagine you are asked to model something at work and you present this thing to your client: "Here's my model but it doesn't work, someone else figure out another solution". Well, Behe actually gets paid for that

      Delete
    11. Another way of looking at it, Steve: If we stick with your particular understanding of the concept of "parsimony", the most parsimonious model is one in which every single intermediate mutation is adaptive. This would eliminate any need for the intervention of Behe's "designer" to ensure that all the mutations occur simultaneously. Can you explain why Behe does not suggest such a model, Steve?

      Delete
    12. This ID "researchers" have the best job ever.

      Only if they don't believe they possess immortal souls that will one day be called to account for their rampant dishonesty. It's strange that almost all of them believe that, yet they continue to lie.

      Delete
    13. IDiot-creationists and many other religious people lie because they believe that lies are justified in their crusade to shove their religious dogma into every aspect of everyone's life. To them, lies are a means of promoting the ultimate TRUTH. One of the main things that attracts people to christianity and similar religions is that it feeds their narcissistic personality. What better way to feel special/exceptional than believing and claiming that they are 'specially created in the image of god', the 'pinnacle of god's creation', and that they have 'a personal relationship with god', the 'creator of the universe'? And the jesus fairy tale gives them the belief that they have a 'personal savior' who will protect them from suffering unimaginable pain for eternity in a lake of fire. All they have to do is accept that imaginary character as their 'savior' and ask for forgiveness from that imaginary character no matter what they otherwise do (murder, lies, coercion, rape, abuse, etc.) and they will be forgiven and go to heaven where everything will be wonderful, or so the story goes. I'm sure that many of them also really enjoy picturing anyone who doesn't agree with them burning in hell forever.

      Delete
  15. Replies
    1. Feliz navidad to you too!

      (It means "merry Christmas")

      Delete
    2. (It means "merry Christmas")

      Keine Scheisse! (It means "no sh*t.")

      But happy holidays to you too.

      Delete
  16. sez eric, on Sunday, December 27, 2015 5:50:00 PM:

    "Please tell us all, which experimental evidence and in what text books you found the most convincing when it comes to:

    1. The origin of information required for life to exist
    2. The origin of the first self-replicating molecule
    3. The origin of the first cell
    4. The origin of eukaryotic cell via symbiosis
    5. The origin of the random mechanism that makes life appear designed. "
    This is, of course, the bog-standard Creationist tactic of Shifting The Burden Of Proof, which can be summarized as I don't gotta provide evidence for nothin' I say—but you gotta provide evidence for everything YOU say!!!

    Well, fine. For the sake of argument, I will accept the proposition that mainstream science doesn't actually have any "experimental evidence" for the mainstream scientific explanations of any of those five points eric raised. That means the tentative explanation(s) provided by mainstream science are completely off the table; it doesn't mean I am thereby obliged to accept any particular alternative to the tentative explanation(s) provided by mainstream science.

    And, in particular, it doesn't mean I am obliged to accept that a vaguely-defined 'Intelligent Designer' of unspecified powers was involved anywhere along the way.

    So: What do you propose as explanations for the five points you raised, eric? Do you propose that an 'Intelligent Designer' was involved in some way or other?

    ReplyDelete
  17. The rest of Behe's response to Lynch that Professor Moran neglected to include in his quotation:

    "1.Experimental studies contradict Lynch's assumption of complete neutrality as a rule; the majority of amino acid substitutions decrease protein function.
    2.Lynch's and our models are not mutually exclusive. Some evolutionary pathways might involve both deleterious and neutral mutations.
    3.Lynch writes in the section “The Model” that we “imply that all amino acid changes lead to nonfunctionalization.” We imply no such thing. Although we assumed that intermediate mutations required for a new feature decreased function, we wrote, “it can be calculated that on average a given position will tolerate about six amino acid residues and still maintain function.” Our estimation of ρ explicitly takes into account the tolerance of sites for substitution.
    4.In “The Model,” Lynch writes, “As in Behe and Snoke (2004), this adaptation is assumed to be acquired at the expense of an essential function of the ancestral protein….” We made no such assumption. In our model, the final mutation might restore and enhance the original function.
    5.In the Discussion, Lynch writes, “It is difficult to pinpoint the source of the difference between the results of Behe and Snoke and those contained herein….” The differences are largely due to opposing starting presumptions about whether mutations are deleterious.
    6.In the Discussion, Lynch writes, “Behe and Snoke assume that the forward and backward point-mutation rates (per amino acid residue) are equal.” We do not. The mutation rate we use is the nucleotide point-mutation rate.
    7.In the Discussion, Lynch writes that we assume mutations have “lethal pleiotropic effects.” We did not assume mutations to be either lethal or pleiotropic. We only assumed that they are “strongly selected against.”
    8.In the Discussion, Lynch writes, “If the intermediate steps … are entirely neutral after gene duplication, as Behe and Snoke assume, then there is no compelling reason that ‘one-off’ (type-2) alleles should be absent from the population prior to duplication.” The reason for no “one-off” alleles before duplication in our model is that intermediate mutations are assumed to be deleterious in a singlecopy gene.
    9.In the Discussion, Lynch writes, “Behe and Snoke failed to realize that a completely linked pair of duplicate genes has a mutational advantage equal to the mutation rate to null alleles….” Such an effect does not hold for a model like ours in which intermediate mutations are postulated to be deleterious.
    10.A recent report (Gao and Innan 2004) presents evidence that the gene duplication rate is lower by several orders of magnitude than that assumed both by Lynch and by us based on the work of Lynch and Conery (2000). If so, then both his and our calculations for the population sizes needed to fix a mutation in a duplicated gene are substantial underestimates."

    ReplyDelete
    Replies
    1. Blah, blah, blah. Michael Behe is a wordy little bugger, isn't he?

      None of those points even remotely address the fatal flaw in Behe's argument: He bases his calculations on the assumption that all intermediate mutations must be deleterious. The only basis for that assumption is that it is what is needed for Behe to make his theological argument. The empirical evidence flatly contradicts that assumption, as Lynch has demonstrated.

      To the readers of the journal this will, of course, be blatantly apparent. But he's not writing for those people. He's writing for the benefit of his creotard minions like Eric and Bilbo, who are easily bamboozled by big, fancy words they don't even comprehend. In that way, the donations keep flooding into the DI's coffers.

      Delete
    2. Bilbo -

      If you look carefully at 3, 4, 7, 8 and 9, problems with Behe's reply become very apparent.

      It's evident from these responses that his model assumes up to six negative mutations (selected against), followed by a final mutation that "might restore and enhance the original function."

      - First, there's no empirical evidence to support the notion that such a scenario is the only means for an organism to evolve, and much empirical evidence that contradicts it and supports a model with neutral intermediates.

      - Second, it's evident that Behe has stacked the deck by requiring strongly deleterious mutations and then assessed the chances that a single lucky mutation following up to six negative ones will not just allow some function, but will restore and enhance the specific original function we had at the start. There is absolutely no empirical evidence to restrict mutations in this way, or to restrict evolution only to the lucky re-acquisition of original function rather than acquisition of new function. This is like assessing the chances that you will make par on a golf hole by requiring that you hit up to six shots away from the hole first and then figuring the probability you'll hit your next shot right in the hole. , which Dr. Behe is happy with, but don't at all reflect reality.

      Delete
    3. "Creotard"? Ah yes, calling one's opponents names. No doubt a trait you have picked up from Professor Moran. Speaking of Moran, I am curious if he has any response to the rest of Behe's reply to Lynch.

      Delete
    4. Typical creotard evasion from Bilbo. Once Behe has admitted he was wrong, it doesn't matter what else he might have written, since the only purpose that serves is to bamboozle his creotard minions into overlooking his admission of defeat.

      Delete
    5. Bilbo asks,

      Speaking of Moran, I am curious if he has any response to the rest of Behe's reply to Lynch.

      No. I said, "They quibble about some of the wording in Lynch's article ..."

      I don't have anything more to add.

      Bilbo, if you think any of their response is important then feel free to post your opinion, with an explanation of why you think I should have discussed it.

      Delete
    6. Professor Moran, why not begin with what Behe says in his first point:

      "Experimental studies contradict Lynch's assumption of complete neutrality as a rule; the majority of amino acid substitutions decrease protein function."

      Delete
    7. Lynch provided several references to support his position. Behe provided no citations to the "experimental studies" which he alleges contradict Lynch's position. I guess we just have to take it on faith that they exist.

      Delete
    8. Lutesuite, would you at least agree with me that Behe's first point is more than just quibbling about some of the wording in Lynch's article?

      Delete
    9. Bilbo, like everyone else, you were born with some 100 unique mutations. If Behe was right and neutrality wasn't the rule, you wouldn't be alive to cheerlead for your favourite IDiot apologist Mr. Mousetrap

      Delete
    10. Dazz, so you, also, would agree with me that Behe's first point is more than just quibbling about some of the wording in Lynch's article?

      Delete
    11. You're right. Behe's first point (as numbered by you) isn't just quibbling. It's wrong. Behe is wrong. Most mutations are neutral.

      Delete
    12. I would agree that you're just quibbling about the wording in one of Larry's points, Bilbo.

      Delete
    13. Meanwhile, Professor Moran, how is Behe's first point mere quibbling about the wording of Lynch's article?

      Delete
    14. Lynch provided specific references to studies providing estimates of the frequency with which neutral mutations arise, and based is calculations on this data.

      Behe's response is to simply try to handwave this away by saying that "experimental studies" confirm Behe's model, but doesn't provide any citations to these alleged studies.

      What more do you need explained, Bilbo?

      Delete
  18. Not directly related to the topic of this thread, but the Discovery Institute has announced that Casey Luskin is leaving them to pursue unspecified further studies:

    https://sensuouscurmudgeon.wordpress.com/2015/12/31/casey-luskin-leaves-the-discovery-institute/

    What is it that people say about rats and sinking ships...?

    ReplyDelete
    Replies
    1. Dembski gone, Luskin gone, and Gauger is... er... fresh blood, right?

      Delete
    2. I wonder if this means "Green Screen" Gauger has left her former position at the Biologic Institute (which, of course, is a totally, completely different thing from the Discovery Institute, innit?), or if she'll now be doing both jobs?

      Delete
    3. What will you guys talk about if Discovery Institute dies? God forbid something happens to Barry......the silence would be deafening.

      Delete
    4. If the DI did not exist, it would be necessary to invent it.

      Delete
    5. If the DI did not exist, it would be necessary to invent it.

      So true.

      Delete
    6. And, once again, Beau Stoddard displays his hypocrisy. Suppose, just for the sake of argument, that some scientist (it wouldn't be an ID proponent, of course) were to discover evidence that definitively falsified the theory of evolution. The DI would no longer have to post articles attempting to attack evolutionary theory and would have a clear field to present their positive evidence in favour of ID. Except - oops! - despite almost two decades of effort, they haven't so much as a scrap. The ID blogs would have to close down.

      BTW, Beau, did you notice that one of the DI's leading "thinkers" recently posted a lengthy (and hilariously wrongheaded) screed attacking one of our members here, Mikkel "Rumraket" Rasmussen? So does the DI now owe him royalties, you think?

      http://www.donotlink.com/framed?826457

      Delete
    7. Proverbs 13:3

      “He that keepeth his mouth keepeth his life: but he that openeth wide his lips shall have destruction.”

      Delete
    8. So Steve, we should expect no more posts from you?

      (Far more likely is that you'll find a Bible verse to the exact opposite effect supporting your continued posting. Being able to find support for either of two completely contradictory positions is what helps make the Bible so useful, don't you think?

      Delete
  19. There idea of fortuitous mutations resulting in complex bio-features will always be a problem. Systems like biosonar aren't stand-alone. Starting from scratch, it would require the development of perhaps dozens of subsystems, brain reception, transduction and translation being several. Arriving at form, function and integration by way of random DNA replication errors is an idea you really have to like to believe.

    ReplyDelete
    Replies
    1. So the fact that it has actually been observed to have occurred under controlled, laboratory conditions. That doesn't mean anything to you, I suppose?

      Delete
    2. I would suppose you are talking about Lenski's bacteria or something similar. Those don't extrapolate into the simultaneous development of complex and complimentary components and subsystems. So no, those don't mean anything to me.

      Delete
    3. is an idea you really have to like to believe

      I love the smell of inferiority complex in the morning

      Delete
    4. Those don't extrapolate into the simultaneous development of complex and complimentary components and subsystems. So no, those don't mean anything to me.

      And since no one who actually understands biology believes the components of such systems developed simultaneously, your objection means nothing to anyone save your fellow creotards. Even Behe has given up talking about "irreducible complexity", since that only led him to be publicly humiliated at the Dover trial.

      Delete
    5. "no one who actually understands biology believes the components of such systems developed simultaneously"

      Then they have to believe they served in some other capacity and were altered and integrated by more DNA replication errors, which is even more absurd. You can discover the problems yourself by attempting to outline how something like biosonar could have developed.

      Delete
    6. Txpiper:
      " how something like biosonar could have developed. "

      Ah, after attempts at invoking IC of the flagellum, immune system, blood clotting and the eye have all failed utterly, we now turn the scope to biosonar? Why not the appendix? Or the hooves of a horse? Or hair growth?
      Or is biosonar another example of 'it looks to be complex (to me), thus it must be complex, aka goddidit?'

      Delete
    7. Unfortunately for Ed, he's living in lala land to think evolutionary biologists have succeeded in rebutting ID claims.

      For starters, the supposed precursor to the bacterial flagellum has been shown to more likely be a derivitive of the flagellum.

      Second, the blood clotting system of lampreys is not evidence that the human blood clotting system is not IC.

      Third, the bad eye design meme has been done to death. We all now know the ingenuity of reverse wiring. Ask a photographer how bad the design is.

      'nuff said.

      But hey Ed, if you've got something more that educated guesses, let's hear it.

      Delete
    8. txpiper,

      you will never get past the evolutionary magic wand of emergence.

      At a certain point (that can never be pinned down), the inevitable happened.

      Oh, what a wonderfullllllll woooooorrrrrrrld.

      Delete
    9. For starters, the supposed precursor to the bacterial flagellum has been shown to more likely be a derivitive of the flagellum

      More like a cousin I believe, but riddle me this Steve, if the T3SS is a "derivative" of an IC system (bacteria flagellum) that's missing parts, what does IC predict would happen to the T3SS?

      Delete
    10. You can discover the problems yourself by attempting to outline how something like biosonar could have developed.

      I don't have to. Richard Dawkins has already done so in The Blind Watchmaker. That's a thing known as a "book." You should try reading one some time.

      BTW, are you really under the impression that all of the components of the bats' sonar system are completely absent in other mammals? Things like ears, and a brain? Perhaps that's the case with you. It would certainly explain why you write such inanities.

      Delete
    11. Biosonar? You're taking biosonar as an example of a system that is too complex to evolve??? Even you, assuming you can hear at all, have some limited ability to determine whether things are closer or further away by sounds. Organisms like bats, dolphins, and certain swifts have modified the basic tetrapod ability to hear and to interpret sounds in ways that give them wonderful sonar. This can result from gradual small genetic changes in the pre-existing conditions. This is SO not a problem for the evolution theory.

      Delete
    12. Hi bwilson
      "This is SO not a problem for the evolution theory"

      Using Michael Lynch's model for time and resources required for evolutionary change can you reconcile this development?

      Delete
    13. I am not nearly as good as Michael Lynch at the math behind evolution, so no. I am pretty good at noticing that the changes from ordinary hearing to biosonar involve hearing becoming more acute and analysis of hearing becoming quicker. These are qualitative changes in existing traits, somewhat like the changes humans have brought about in dogs in a relatively short period of time, and the environment could bring about in flying mammals, birds, or aquatic animals more slowly. Biosonar is not an "irreducible complexity" argument at all.

      Delete
    14. "I am pretty good at noticing that the changes from ordinary hearing to biosonar involve hearing becoming more acute and analysis of hearing becoming quicker."

      Can you come up with a mutational pathway? Then we could plug it into Lynch's model.

      Delete
    15. Can you come up with a mutational pathway?

      Sure, as soon as you come up with the step by step method the Intelligent Designer used (consistent with the fossil record of course).

      Delete
    16. I have a better suggestion: Why doesn't Behe, or some other IDiot, detail every single possible mutational pathwau, and then demonstrate why every single step of every single one of these pathways is so deleterious it leads to the immediate death of the organism. A lot of work, sure, but at the end one would have scientifically proven the existence of God - Oops! Sorry - of the "intelligent designer." Surely that would be worth the effort, no?

      Delete
    17. lutesuite,

      Dawkins’ algorithm is too crude to use as an analytical tool.
      -
      “are you really under the impression that all of the components of the bats' sonar system are completely absent in other mammals?”

      Of course not. But echolocation is just one example of feature that would require a very complicated series of specific DNA replication errors to generate novel components. That should stand to reason since it is rare. That sequence and those errors are what you should focus on.

      If you use whales, there an generally accepted time frame for the errors to produce the specialties. Does that help you in developing an outline for how it all happened?

      ===

      bwilson295,

      “This is SO not a problem for the evolution theory.”

      Nothing ever is. There is a canned answer for everything. But for anyone thinking beyond a very protected and crafted narrative, there are all kinds of horrible problems. Would you like to address one? Tell me how the replication enzyme suite evolved.

      Delete
    18. You don't get it, do you txpiper? Irreducible complexity could have been a problem for evolution. If the multiple mutations needed really did have to happen simultaneously, and if the feature wouldn't be useful until all the mutations happened, evolution theory would have been in trouble. Scientists had to think, observe, and calculate carefully to figure out how apparently "irreducibly complex" features could evolve. It turns out such features can evolve, but that wasn't clear at first.

      Biosonar involves changes increasing, elaborating, intensifying traits shared by by all mammals (that can hear at all). Evolution of that sort is well understood.

      Delete
    19. But echolocation is just one example of feature that would require a very complicated series of specific DNA replication errors to generate novel components.

      And if none of the combinations of mutations that would possibly lead to it had occurred, echolocation would not arisen. Sure. So what exactly is the problem?

      Delete
    20. Tell me how the replication enzyme suite evolved.

      Ooh, ooh, I've even got a better one: How do you get a new species without at least two members of opposite genders evolving simultaneously?

      These logic puzzles appear to pose real problems if you don't understand evolution.

      Delete
    21. Yes, and more on IC systems, take the blood clotting system for instance. If it can't be gradually formed, how come every baby grows theirs progressively from a zygote to a full blown system? Does god need to keep nudging embryo's systems so they can develop?

      Delete
    22. "And if none of the combinations of mutations that would possibly lead to it had occurred, echolocation would not arisen. Sure. So what exactly is the problem?"

      That's an interesting rationale you have going there lutesuite. Popular, too. But it would be a nice touch if someone actually analyzed mutations in the context of a big developmental picture.

      I can appreciate, to some degree, why nobody does. It doesn't take long to figure out that it would be a nightmare, perhaps impossible to even conceive, much less comprehend. But inasmuch as DNA replication errors are supposed to have resulted in billions of sublime features, you'd think biologists would be interested in some kind of proof rather than just believing in things they don't understand.

      Delete