Saturday, January 23, 2016

Richard Dawkins makes a mistake when describing why gene trees are evidence of evolution

Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."

There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.

As for the history of life, we are still working out the details but the broad outlines are firmly established. The best evidence that evolution accounts for this history comes from molecular data that involve the comparison of DNA sequences from different species. I would then go on to describe a generic comparison of genes from different species pointing out that they generate a tree that looks very much like a tree of common descent. This is incredibly strong support for the trees that previously were independently constructed by comparing morphology and embryology before DNA sequencing became common.

I would mention that it's the agreement of these twin nested hierarchies from independent data that overwhelmingly convince us that species evolved from a common ancestor. I would be sure to mention that the genetic data is based on random changes so not all trees will agree in detail all the time but when you put together the data from over one hundred robust trees the conclusions are irrefutable.

Here's how Richard Dawkins answered the question ...


This seems like a pretty good answer until you realize who you are dealing with. The creationist crowd isn't interested in the big picture view of evolution and they're not interested in making allowances for trivial errors. They are more interested in nitpicking about details and showing that evolutionary biologists are wrong about evolution.

In that case, Dawkins played right into their hands. A video appeared just a year later and it pretty much refuted what Dawkins had said about the specific example he choose (FOXP2). This video was brought to my attention through today's post by kairosfocus on Uncommon Descent: BA77 and a vid on FOXP “1/2/3” molecular trees vs Dawkins’ claim of “You get the same family tree”.


The information in the video is essentially correct even though we can all agree that there are better ways of constructing phylogenetic trees. The FOXP2 example was a bad one for many reasons and using it undermines the correct point that Dawkins was making about the molecular evidence for common descent, and evolution as the mechanism.

This is why you have to be careful when dealing with creationists. The original answer by Richard Dawkins was posted over five years ago but the creationists are not going to let you forget it.


143 comments :

  1. It's pretty clear that Dawkins would have been talking the transcribed gene or the exons. I imagine that which ever idiot made this video knew this But he chose to misrepresent him - lying for Jesus of you will.

    I don't know whether Dawkins' numbers are right or wrong - I'm interested in looking into it now but in any case Dawkins argument is flawed. The best evidence is not the total number of similarities between closely related species but rather the nested genetic mutations shared by members of a clade.

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  2. “The creationist crowd isn't interested in the big picture view of evolution and they're not interested in making allowances for trivial errors. They are more interested in nitpicking about details and showing that evolutionary biologists are wrong about evolution.”

    I don’t think this is an accurate appraisal. It isn’t lack of interest in the big picture. It is that it is inappropriate to paint a big picture until the details make sense. It is one thing to say that mutations and natural selection working in tandem can result in biodiversity. It is another thing entirely to describe how in hell DNA replication errors could result in butterfly metamorphosis.

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    Replies
    1. Dawkins here is specifically making a case for common descent (not so much for evolution itself). Do you accept or reject the overwhelming evidence for common descent?

      Delete
    2. It depends on the depth of the claim. I don't buy sappy ideas like Pakicetus evolving into whales. On the other hand, I can easily accept that polar and brown bears are related since they can interbreed.

      Delete
    3. It's fairly easy to demonstrate that cetaceans share common ancestry with other ungulates.

      But I guess the theologically important question is whether you accept that humans and other primates share common ancestry.

      Delete
    4. "I don't buy sappy ideas like Pakicetus evolving into whales."

      Pakicetus *is* a whale, albeit outside of the extant crown group.

      Delete
    5. I don't buy sappy ideas like Pakicetus evolving into whales.

      Yes, and you believe the Noahic flood accounts for geology, too, if I remember correctly.

      So yeah, no wonder people can't prove to you that evolution is real, if all we've got to go on is paleontology backed up by geology backed up by various methods of dating backed up by botany and nuclear physics and quantum theory proved by experiment to as many decimal places as anyone's ever been able to test it.

      Whereas, you got yer unassailable book. Ouch, game, set, match for you I'm afraid.

      Delete
    6. Aceofspades,

      "It's fairly easy to demonstrate that cetaceans share common ancestry with other ungulates."

      The time available for the supposed evolution of the favorite ungulate candidate to the first fully aquatic whale is down to about 4 million years, if I recall correctly. How many beneficial mutations would you suppose were involved in the transition?

      ===

      judmarc,

      “no wonder people can't prove to you that evolution is real”

      My objections are very basic.

      Delete
    7. txpiper,

      That's quite a weird claim for several reasons.

      1. When I check about whale evolution, the times could be between 10 million and 40 million, depending on what we call "fully aquatic" and "favourite ungulate."

      2. I hope that you did not mean a living ungulate when you said "favourite ungulate" because then you have quite a misunderstanding.

      3. However long it took, the fact is that there's fossils of previously living forms that show unambiguous characteristics between one form and the other. Each showing a few steps further into the aquatic form. As if that wasn't enough, there's also lots of data on embryo development, gene divergences, and insertion elements showing the story of the common ancestry between whales and terrestrial mammals. So, whether it happened in just 5 million or in 55 or 60 million, the fact is, it happened. We are left with no other question but "how."

      4. You might hold the illusion that if the question is "how" there's room for your imaginary friend. However, no matter how deep or far our ignorance about how many mutations were required, your fantasies remain fantasies.

      Your objections are not very basic. They're pathetic attempts at defending your religious fantasies.

      Delete
    8. photosynthesis,

      "Your objections are not very basic.”

      Yes, they really are. Do you want to pursue this?

      Find the oldest known Pakicetus fossil (that does seem to be the favorite) and start from there. It wouldn’t be fair to use the youngest, since some of them might have not have been bright enough to hang around the water’s edge and get caught up in the selection pressure of wanting to eat seafood.

      Next, find the earliest reported definite fully marine animal. I’ll help you out if you have any trouble.

      That will give us some dates to work with, and then we can look at the mutations issue.

      Delete
    9. txpiper,

      What part of "however long it took ... the fact is that it happened" did you not understand?

      After you get that point, we can look at the issue that your fantasies remain fantasies regardless on whether we know, or not, what thunder is, or how volcanoes form.

      (I knew you would insist on the time and ignore the rest.)

      Delete
    10. photosynthesis,

      I expected as much. You are frightened. Good show.

      Delete
    11. "Next, find the earliest reported definite fully marine animal. I’ll help you out if you have any trouble. "

      Help us out, txpiper. What is your hypothesis on how whales came to be, and what is your evidence for it?

      Delete
    12. @txpiper

      A paper was published back in 1997 detailing 9 independent SINE insertions events that link whales to ruminants and hippopotamuses but exclude camels and pigs (identical complex elements that would have had to randomly find their way into identical locations if they weren't inherited by common descent).

      http://www.nature.com/nature/journal/v388/n6643/full/388666a0.html

      Not only that, but they clearly form a nested hierarchy that looks like this:

      http://imgur.com/iM0s5Us

      Then another paper was published 2 years later that found 10 independent SINE and LINE insertion events common to various whales and hippopotamuses.

      http://m.pnas.org/content/96/18/10261.full

      This really is a slum dunk for cetacean common ancestry. It's time to move on and pick some other obscure thing to argue about.

      Delete
    13. txpiper,

      Frightened of what? Do you really think that anything in my life depends on whether whales are closer relatives to ungulates than to, say, fish?

      It's you who refuses to read what I'm saying. It would seem that it's you who's frightened.

      Delete
    14. Aceofspades,

      “This really is a slum dunk for cetacean common ancestry. It's time to move on and pick some other obscure thing to argue about.”

      I don’t think we’re ready yet. The common ancestry will hippos might look good (or perhaps not) in terms of SINE/LINE insertions, but maybe not so good in a broader view:

      “However, the earliest known anthracotheres appear in the fossil record in the middle Eocene, well after the archaeocetes had taken up totally aquatic lifestyles. Although phylogenetic analyses of molecular data on extant animals strongly support the notion that hippopotamids are the closest relatives of cetaceans (whales, dolphins and porpoises), the two groups are unlikely to be closely related when extant and extinct artiodactyls are analyzed. Cetaceans originated about 50 million years ago in south Asia, whereas the family Hippopotamidae is only 15 million years old, and the first hippopotamids are only 6 million years old.”
      https://en.wikipedia.org/wiki/Anthracotheriidae

      You can probably see the problem. They might be referring to this relatively recent discovery:

      “…the fossilized archaeocete jawbone found in February dates back 49 million years. In evolutionary terms, that's not far off from the fossils of even older proto-whales from 53 million years ago that have been found in South Asia and other warmer latitudes.
      Those earlier proto-whales were amphibians, able to live on land as well as sea. This jawbone, in contrast, belongs to the Basilosauridae group of fully aquatic whales…”
      http://en.mercopress.com/2011/10/12/argentine-swedish-team-discovers-49-million-years-fossil-of-fully-aquatic-whale-in-antarctica

      You can scroll down to the chart showing most of the supposed whale antecedents here; https://en.wikipedia.org/wiki/Archaeoceti
      Some of them don’t appear until after the one in Antarctica, and the earliest only precede it by about six million years, and continue for some time afterwards.

      You can read all kinds of stuff about all this, but nothing really leaves you with a slam-dunk. Actually, it makes you wonder if they know what they are talking about at all. I’d like to move on, and argue about mutations, but we need to have some sort of time interval in mind to do that.

      Delete
    15. You can probably see the problem.

      LOL! Yes, I can see the problem. You've got a pile of fetid excrement where your brain should be.

      Explain to us all what you perceive to be the "problem" here. It's always amusing to watch creationists blather on and on like they think they're speaking intelligently, when all they're really doing is the equivalent of soiling their bed sheets.

      Delete
    16. "Let's test yours."

      Now who's frightened?

      Delete
    17. > You can probably see the problem. They might be referring to this relatively recent discovery:

      No... it's not at all clear what the problem is. This doesn't contradict at all the notion that the hippopotamids are the closest LIVING relatives of cetaceans.

      So please explain how you think this contradicts the clear genetic evidence?

      Delete
    18. Ace,

      I thought it was pretty straight forward:

      "Although phylogenetic analyses of molecular data on extant animals strongly support the notion that hippopotamids are the closest relatives of cetaceans (whales, dolphins and porpoises), the two groups are unlikely to be closely related when extant and extinct artiodactyls are analyzed. Cetaceans originated about 50 million years ago in south Asia, whereas the family Hippopotamidae is only 15 million years old, and the first hippopotamids are only 6 million years old"

      Their is an apparent conflict between the phylogenetic analysis, and the fossil dates. That's why they brought it up in the article.

      Delete
    19. It is straightforward, txpiper.

      That's why it's so amusing that you don't get it.

      Delete
    20. txpiper - The quote in the Wikipedia article comes from reference '13' which is this paper The authors of that paper (and hence your quote) have Pakicetus in Cetacea, and Cetacea in Artiodactyla. As you quote them with presumed approval, do you agree with them on the common descent issue? They are hardly likely to be contradicting themselves; I think you may have misread the significance of the taxonomic discussion you quoted.

      On the mutation issue, how long should it have taken, if 4 million years (or 10) was insufficient?

      Delete
    21. Aceofspades,

      I just wonder how large we should make that word so that, maybe, txpiper will be able to take notice of it and stops just copy/pasting without any thinking. I'll give it a try:

      ----------
      txpiper,

      No... it's not at all clear what the problem is. This doesn't contradict at all the notion that the hippopotamids are the closest LIVING relatives of cetaceans.
      -----------

      Maybe we need to put those words alone in there and maybe:

      closest LIVING relatives of cetaceans.

      So txpiper, what about you think this time instead of just pasting the same stuff yet again? We understand them. Do you?

      Delete
    22. @photosynthesis

      I think he might actually believe that whales descend from hippos. If that's the case, we're going to have to go right back to 8th grade biology to explain this to him.

      @txpiper..

      I'll give you a clue.. Just because hippopotamidae are the closest EXTANT family to cetaceans, that doesn't mean they are closely related. The wiki here is telling you that hippopotamidae are a fairly new family but there is still a rich history of artiodactyls that precede them.

      Delete
    23. Allan Miller,

      “As you quote them with presumed approval, do you agree with them on the common descent issue?”

      No.
      -
      “I think you may have misread the significance of the taxonomic discussion you quoted.”

      I don’t think so. The quote reads slightly differently in the paper you linked to:

      “In spite of [phylogenetic analyses of molecular data], it is unlikely that the two groups are closely related when extant and extinct artiodactyls are analysed, for the simple reason that cetaceans originated about 50 million years (Myr) ago in south Asia, whereas the family Hippopotamidae is only 15 Myr old, and the first hippopotamids to be recorded in Asia are only 6 Myr old.”

      The point is made in the phrases “in spite of” and “for the simple reason”. I didn’t see anything indicating that this issue was resolved.

      As a reference, this article was was published along with the paper.
      http://www.theguardian.com/science/2007/dec/19/whale.deer?gusrc=rss&feed=networkfront
      -
      “On the mutation issue, how long should it have taken, if 4 million years (or 10) was insufficient?”

      There are lots of factors to consider. To answer that, some kind of basis is necessary. I think Lenski’s bacteria acquired a modest adaptation after some 31,000 generations. Would you use that, or something else?

      Delete
    24. You are such a buffoon, txpiper.

      Suppose there is some person living in Mongolia with whom you share a most recent ancestor from 2000 years ago. Would it be incorrect to call him your "distant relative"? And would the fact that there are thousands of people to whom you are more closely related but who are now dead change the fact that you share a common ancestor with your Mongolian cousin (many time removed)? I guess you think it would, if you insist on following the line of "reasoning" you are pursuing here.

      Keep it up, txpiper. You're providing a splendid example of what passes for "thinking" among creationists.

      Delete
    25. That's good input. But make it 5000 years, and call it recorded history. The next step would be to pick a reasonable number of years to represent a generation. If you use 20, it would mean 250 generations elapsed with only superficial changes occurring.

      Delete
    26. To everyone trying to deal rationally with txpiper, you most likely have figured this out by now, but txpiper is just trolling. (S)he won't answer any of your questions, (s)he won't deal truthfully, and (s)he won't lay out in specific terms what Her/his position is on any issue relating to the evolution of cetaceans.

      Delete
    27. No, Chris. I am only pointing out that there is some timeframe involved in whale evolution according to evolutionary researchers. I am fair and flexible in how long that is, and just as fair and flexible on all the other things that have to be considered. I will let you fill in the blanks with reasonable numbers. You need not waste keystrokes with warnings to other readers.

      What would you use for the number of generations before a significant evolutionary event occurred in whale evolution? If Lenski's experiment is inappropriate, then choose something else and explain why it is more reasonable.

      Delete
    28. Keep in mind that phylogenetic "trees" are actually bushes. After the last common ancestor of whales and hippopotamuses (hippopotami??) there were lots of branches, and one branch didn't necessarily die out when another started. Early, amphibious whales can even coexist with fully aquatic whales. (Obviously, the fully aquatic whales would have evolved from earlier amphibious whales that were common ancestors that also produced later amphibious whales.) Modern hippopotamus can evolve long after the last common ancestor of whales and hippopotamuses, from ancestors that one would never call a hippopotamus. On the other hand, maybe for all I know fully aquatic whales did evolve from amphibious ancestors in 10 million years. There are interesting things regarding whale and hippo evolution that we'd like to know more about, yes, but there's no evolution-denying contradiction here.

      And yes, Chris, I know you're right. But sometimes it's hard to resist responding to the trolls.

      Delete
    29. Txpiper wrote, "You need not waste keystrokes with warnings to other readers." Txpiper, if we have keystrokes to waste responding to you, we have keystrokes to waste warning other readers.

      Delete
    30. txpiper writes, "My objections are very basic."

      If "basic" means "unsophisticated stuff we'd expect from grade school kids," I fully agree.

      Say, here's something basic about whales and evolution: You want to tell us where the internal rear foot bones in whale skeletons came from if they didn't evolve from land animals?

      Or is this just more of your Deity's apparently antic sense of humor?

      Delete
    31. I think Lenski’s bacteria acquired a modest adaptation after some 31,000 generations. Would you use that, or something else?

      What? Why would you even consider comparing an asexual bacterium in a highly bottlenecked, environmentally constrained lab flask population with a multicellular sexual eukaryote in the wild?

      Bottom line is we don't have the genomes at either end of the Pakicetus-'true whale' transition, so we don't know how many mutations accumulated. Which means you don't know how many years would be an acceptable time for that accumulation.

      A converse problem which we could get a better handle on would be to determine the amount of mutation connecting two 'kinds' fresh off the Ark. If we can have that much mutation in 4,000 years, I'm sure we could get some whales in 4-10 million. Do you have a 'kind' we could compare, to get the basic annual rate?

      Delete
    32. @txpiper

      All “in spite of” means in this context is this: You might be tempted to think that because Hippos are the closest EXTANT relatives to whales, this implies that they are closely related, this is not the case. There is at least 50 million years of evolution separating modern hippos from modern whales and perhaps a lot more than this.

      Now onto your claim that fully aqautic cetaceans have only had 10MYR to evolve...

      Let's say the oldest pakicetus (an amphibious cetacean) we've ever found is 50 million years old and the earliest fully aqautic cetaceans we've found are 40 million years old. Does this imply that cetaceans have had only 10 million years to become fully aquatic? The answer here is not necessarily because it is highly unlikely that pakicetus is a direct ancestor of modern cetaceans. Very few fossils we find in the fossil record are going to be direct ancestors of anything alive today - the chances of this are extraordinarily unlikely. Instead, the chances are that pakicetus is going to be a close cousin species of somethging that was well on its way to becoming fully aquatic.

      It's quite possible that the pakicetus we find in the fossil record could have been heading on its own evolutionary pathway for 10 million years following the split that would ultimately lead to fully aquatic cetaceans - we don't know.

      I drew a diagram for you to illustrate my point.

      http://i.imgur.com/XWlNC6i.png

      Delete
    33. That's good input. But make it 5000 years, and call it recorded history. The next step would be to pick a reasonable number of years to represent a generation. If you use 20, it would mean 250 generations elapsed with only superficial changes occurring.

      And, of course, the point sails a mile over txpiper's pointy little head. Why am I not surprised?

      Shut up and pay attention, moron: Does the fact that you are only "distantly" related to your Mongolian cousin mean the two of you are not related at all? Or does the fact that thousands of individuals to whom you were more closely related are no longer alive?

      Just a simple answer. Yes or no.

      If you answered "Yes" to either, then you're even more hopeless than I feared. I'm going to give you the benefit of the doubt and presume you answered "No" to both.

      But, if that's the case, then why do you think the paragraph you quoted from Wikipedia means that hippos and whales are not related by common ancestry? The only difference between that and your relationship to your distant Mongolian cousin is that, in the latter, there are many people still alive to whom you are more closely related. But there is no reason that, millions of years from now, one of your descendants might not be the closest living relative of one of the descendants of your distant Mongolian cousin, even though they will be far more distantly related to each other (in terms of number of generations since the MRCA) than you are to your Mongolian cousin.

      Understand? I doubt it. But maybe you'll surprise me.

      Delete
    34. we can look at echolocation whale. this sonar system is like a submarine sonar and need a lot of parts at once to function. lets say that its need only 3 parts for a minimal function when the chance to get one functional part (new gene)is about on in a bilion mutation (10^9). then we will need about 10^27 mutations to evolve a whale sonar. and for this evolution we will need more then the age of the universe.

      Delete
    35. dcdcccc,

      Therefore the models you're using about what was needed in order to evolve the whale sonar are wrong.

      Did you get it? Scientists don't think: if I model this this way, the numbers won't match, therefore gods-did-it. Scientists think: this model fails so ridiculously badly that we must be missing something about how this thing happened/works/etc. They collect more and better data, they perform experiments (if possible and appropriate), and, if they solve some problem(s), they publish their solution(s).

      Delete
    36. The thing is, nearly all mammals have some minimal ability to echolocate, including humans. Not that we're good at it, but we can sometimes tell when we're getting near a wall just from the sound.

      Therefore, the basic parts needed to evolve a system of echolocation are already present in ancestors of whales and hippos. In whales those parts are incredibly enhanced. Eventually, some new parts evolve to give even better echolocation, but the process starts just by selecting extremes of what exists.

      Delete
    37. Allan Miller,

      “Why would you even consider comparing an asexual bacterium in a highly bottlenecked, environmentally constrained lab flask population with a multicellular sexual eukaryote in the wild?”

      First, I’d consider Lenski’s numbers because they are known. But the circumstances you mention were obliging to the experiment, so that could be a low number for the generations required to get results in the wild. I would think using sexual eukaryotes would be much larger.
      -
      “Bottom line is we don't have the genomes at either end of the Pakicetus-'true whale' transition, so we don't know how many mutations accumulated.”

      Well no. But we’re talking about a complete physiological renovation, so you probably can’t be wrong if you say that millions of unique beneficial mutations were involved.

      ===

      Aceofspades,

      “Let's say the oldest pakicetus (an amphibious cetacean) we've ever found is 50 million years old and the earliest fully aqautic cetaceans we've found are 40 million years old. Does this imply that cetaceans have had only 10 million years to become fully aquatic? The answer here is not necessarily because it is highly unlikely that pakicetus is a direct ancestor of modern cetaceans.”

      That’s all fine, but all the possible convolutes shouldn’t prevent you from finding a reasonable starting block, and a marine adapted finish line.

      The figures in this article are probably too tight for you:

      "Based on 53-million-year-old fossils of whale-like, semi-aquatic mammals, scientists had thought mammals gave rise to whales in a process that took 15 million years. The new find suggests it took just 4 million years."
      http://news.nationalgeographic.com/news/2011/11/111116-antarctica-whales-oldest-evolution-animals-science/

      It is believed that echolocation was up and running 35 or so million years ago. You could use that as a benchmark, and get back up to 15 million. Anything beyond that is probably too long.

      Delete
    38. txpiper,

      "First, I’d consider Lenski’s numbers because they are known. But the circumstances you mention were obliging to the experiment, so that could be a low number for the generations required to get results in the wild. I would think using sexual eukaryotes would be much larger."

      What conclusions are you drawing from the Lenski experiments, and how do they relate to your ideas on whale evolution?

      Delete
    39. txpiper, you haven't answered, so I'll ask my simple direct question again:

      You want to tell us where the internal rear foot bones in whale skeletons came from if they didn't evolve from land animals?

      Delete
    40. bwil and photo.

      humans can do it underwater. so it will not help in this case. even more- the melon organ is unique to the whale. and this indeed a complex system that need at least several new genes.

      Delete
    41. @txpiper

      You wrote: "Well no. But we’re talking about a complete physiological renovation, so you probably can’t be wrong if you say that millions of unique beneficial mutations were involved."

      Well this is where your ignorance shines through. It turns out that only a tiny number of mutations are required to radically after the body plan because bodies are constructed recursively.

      All it takes to lose your hind limbs or modify your forelimbs might be a single mutation. Incidentally, modern whales still haven't fully lost their hind limbs. They still begin to grow in whale embryos but then are stunted in later development.

      Looking at the National Geographic article you shared, I'm afraid that Thomas Mors appears to have made the same mistake that you did. He provides a guesstimate that whales took 4 million years to evolve based on other 53-million-year-old fossils of semi-aquatic mammals.

      He's assuming here that whales descend DIRECTLY from these semi-aquatic mammals. But there is no way he could know this for sure - it could be that the jaw bone he found and these semi-aquatic mammals are sister clades that diverged 10 million years previously.

      Now on to what they found:

      Here is an artists rendition of this animal which they displayed at their press conference. This rendition is based on a single jaw bone. When we compare this picture to Pakicetus, it doesn't seem all that hard to imagine now does it? No tail fluke. No flippers. Still has 4 limbs. Has a slightly more muscular tail. These are all possible features because all we know for sure was the shape of the snout.

      In that slide it says they lived from 55.8 to 48.6 MYA. In other words these could even have lived BEFORE 53-million-year-old fossils of semi-aquatic mammals - in that case, these could only have been a sister clade and we would have no idea when the common ancestor between these and the semi-aquatic mammals lived.

      Finally it doesn't appear as though the paper on this fossil was ever published so the dating of the fossil, the extrapolation as whether it was marine only and the conclusion that this particular cetacean took only 4 million years to adapt from an amphibious to an aquatic only environment has never been peer reviewed.

      Here is a google scholar search for the papers published by these two scientists

      So to summarise:

      You've been presented with overwhelming genetic evidence that hippos and cetaceans share a common ancestor and you've responded to this with a national geographic article in which a paleozoologist expresses his opinion that it took 4 million years to adapt to a marine only lifestyle - an opinion that was based on similar amphibious fossils laid down 4 million years earlier when it could well be the case that these similar amphibious fossils could be a sister clade that share ancestry with whales going back tens of millions of years - nobody knows.

      Add to this the fact that all the researchers had found was a jaw bone so we don't actually know whether it had a tail fluke and flippers - it might well have looked like this and then to top it all off this discovery wasn't even published in the scientific literature.

      Delete
    42. @dcsccc

      Which new genes are required for this echolocating organ? And how much time has there been available for this organ to evolve?

      Delete
    43. dcdcccc,

      What I'm trying to get across is that you're mistaking your model about how things should happen in evolution, for how things actually might happen in evolution. Scientists don't do that. We don't go, hey, that looks like a new organ, therefore it required new genes, and leave it there. We check if that's the case. We don't go, hey, new genes must have a probability of 1/10E9, we try and check which, if any, new genes, and where they might have come from.

      Also, beware of creationist style "probabilities." They assume models that have nothing to do with how things happen in nature. They're also after-the-fact probabilities. For example, if a person won the lottery, well, the fact is that the person won. Calculating the probabilities and then declaring that it is impossible for this person to have won the lottery is nonsensical. Sure, the probability was tiny, but it happened. In evolution is not even that simple. The issue is that you don't know how hard or how easy it is to evolve a melon. It could be that several different mutations could lead to Rome. It could be that the ones present were the only possible options. But we don't know either way. The reasonable approach is to try and figure it out. Getting stuck in a failed model (like yours) is not the best approach in science.

      So, again, the message is, science doesn't work that way. We investigate. We try and model based on the evidence, not based on uninformed, misinformed and/or deformed "intuitions."

      I hope that helps.

      Delete
    44. txpiper First, I’d consider Lenski’s numbers because they are known.

      That's like saying you'd take the weight of E Coli as the weight of Pakicetus because it is known.

      But the circumstances you mention were obliging to the experiment, so that could be a low number for the generations required to get results in the wild. I would think using sexual eukaryotes would be much larger.

      You'd think wrong. Totally different genomic and environmental circumstances. It would be foolish to equate two such different scenarios. Recombination has a massive effect. As does not pipetting off a fraction of the population every morning, and not growing it in a very restricted, monotonous environment to which the species was already adapted.

      We’re talking about a complete physiological renovation, so you probably can’t be wrong if you say that millions of unique beneficial mutations were involved.

      You can, you know.

      Delete
    45. "We’re talking about a complete physiological renovation, so you probably can’t be wrong if you say that millions of unique beneficial mutations were involved."

      And this is exactly txpiper's problem. She has to be right no matter what the evidence might indicate. I blame it on his fantasy-loaded worldview. This txpiper thinks that if she imagines it to be so, it is so. No amount of evidence matters, her model of what's required must be the only possible way. Forget evidence, forget science, txpiper's misinformed imagination should suffice.

      Delete
    46. ace. any genes that code for new structures with new function can consider as new genes. we can check this by a submarine sonar. can you as intelligent designer made a functional sonar by adding one part at time or even by changing one exist part? its impossible even to an intelligent designer to do so. so why do you think its possible by a natural process?

      photo- we can make calculations. e ven scientists do so all the time to check their models. the lottery example isnt good because there is nilions of peoples that sending tickets. so the probability to win is actually very large.

      take even 100 my to evolve an echolocation system. if if we talking about 10^27 mutations it will not make any different.

      Delete
    47. dcdcccc,

      You're again missing the point. Yes, scientists make calculations and models, but when the models and calculations fail, they go and check for what they might be missing. Do you get it now?

      Do you see the difference? You're stubbornly stuck with your model, and you will never change your mind about it no matter how much others here are explaining to you. This is why I tried a different approach. One explaining how we reason in science.

      It's always easy to model things in a way that they look impossible. It's harder to check for further and better data. To understand biological processes, to understand the difference between a human-made sonar and the systems in whales, to understand genetics and that several paths might lead to some kind of evolutionary outcome, long etc.

      But you won't consider that you might have the wrong model playing in your mind at all. Why not? Because you're not reasoning towards actual answers. You want the answer to be whatever it is that you want it to be. If reason interferes with your preferred conclusion, then you rather forget reason.

      Delete
    48. Chris B,

      “What conclusions are you drawing from the Lenski experiments, and how do they relate to your ideas on whale evolution?”

      One obvious conclusion is about the frequency of mutations. The adaptation itself is not particularly impressive in my view, and it took many thousands of generations acquire it, or reacquire it.

      ===

      judmarc,

      “You want to tell us where the internal rear foot bones in whale skeletons came from”

      Show me what you are talking about.

      ===

      Aceofspades,

      “It turns out that only a tiny number of mutations are required to radically after the body plan”

      As if relates to the mammals we are talking about, this is nonsense.
      -
      “All it takes to lose your hind limbs or modify your forelimbs might be a single mutation.”

      Such events, if they are actually single mutations, are in evidence. They are called abnormalities. A good example would be the victims of a mutagen called Thalidomide.
      -
      “Here is an artists rendition of this animal which they displayed at their press conference. This rendition is based on a single jaw bone. When we compare this picture to Pakicetus, it doesn't seem all that hard to imagine now does it? No tail fluke. No flippers. Still has 4 limbs. Has a slightly more muscular tail. These are all possible features because all we know for sure was the shape of the snout.”

      You should review this and see if you can detect what is wrong with your analysis.
      -
      Your questions to dcscccc:

      “Which new genes are required for this echolocating organ?”

      How many would be a better question. Sensory systems require lots of them. Humans have around 300 photoreceptor genes. Elephants have some 2000 olfactory genes. Hundreds of genes and gene combinations are involved in hearing.

      ===

      Allan Miller,

      “Totally different genomic and environmental circumstances. It would be foolish to equate two such different scenarios.”

      They don’t equate.
      -
      “Recombination has a massive effect.”

      Horsefeathers. There are seven billion humans, and countless billions of other sexually produced organisms living right now. They are all recombinants.

      Delete
    49. Chris B,

      “What conclusions are you drawing from the Lenski experiments, and how do they relate to your ideas on whale evolution?”

      One obvious conclusion is about the frequency of mutations. The adaptation itself is not particularly impressive in my view, and it took many thousands of generations acquire it, or reacquire it.

      ===

      judmarc,

      “You want to tell us where the internal rear foot bones in whale skeletons came from”

      Show me what you are talking about.

      ===

      Aceofspades,

      “It turns out that only a tiny number of mutations are required to radically after the body plan”

      As if relates to the mammals we are talking about, this is nonsense.
      -
      “All it takes to lose your hind limbs or modify your forelimbs might be a single mutation.”

      Such events, if they are actually single mutations, are in evidence. They are called abnormalities. A good example would be the victims of a mutagen called Thalidomide.
      -
      “Here is an artists rendition of this animal which they displayed at their press conference. This rendition is based on a single jaw bone. When we compare this picture to Pakicetus, it doesn't seem all that hard to imagine now does it? No tail fluke. No flippers. Still has 4 limbs. Has a slightly more muscular tail. These are all possible features because all we know for sure was the shape of the snout.”

      You should review this and see if you can detect what is wrong with your analysis.
      -
      Your questions to dcscccc:

      “Which new genes are required for this echolocating organ?”

      How many would be a better question. Sensory systems require lots of them. Humans have around 300 photoreceptor genes. Elephants have some 2000 olfactory genes. Hundreds of genes and gene combinations are involved in hearing.

      ===

      Allan Miller,

      “Totally different genomic and environmental circumstances. It would be foolish to equate two such different scenarios.”

      They don’t equate.
      -
      “Recombination has a massive effect.”

      Horsefeathers. There are seven billion humans, and countless billions of other sexually produced organisms living right now. They are all recombinants.

      Delete
    50. "One obvious conclusion is about the frequency of mutations. The adaptation itself is not particularly impressive in my view, and it took many thousands of generations acquire it, or reacquire it. "

      If you think this was the only mutation documented in those experiments, you have not absorbed the information in the peer reviewed publications resulting from the Lenski lab experiments.

      Delete
    51. txpiper,

      "judmarc,

      “You want to tell us where the internal rear foot bones in whale skeletons came from”

      Show me what you are talking about."

      judmarc is talking about this:

      https://commons.wikimedia.org/wiki/File:Sperm_whale_skeleton.png

      Where do you suppose those little degenerate hind limbs came from?

      Other interesting whale stuff to peruse at your leisure:

      http://www.smithsonianmag.com/videos/category/at-the-smithsonian/a-right-whale-skeleton-arrives-at-the-smiths/?no-ist

      http://galleries.neaq.org/2011/08/its-bird-its-plane-its-whale.html

      http://dolphinity.tripod.com/mysticetitekst.htm

      Delete
    52. photo- we have 2 options. so if the chance for one of them is very low- then the second one is the best explanation.

      Delete
    53. dcdcccc,

      The problem being that it's not just two "options," but plenty of options, and that your "second option" is nothing but an imaginary being.

      All of this time I have been trying to explain to you that there might be many ways in which things happen in nature, and in which things could happen in nature. Yet you didn't even get that single point. You would have to understand what's wrong with your model of nature, and then understand that there's many ways other than "many genes each with extremely very low probabilities for arising" in which a sonar system could have evolved in whales.

      There's only so many times I can repeat something, If you'd rather not understand, there's nothing else I can do. I cannot force you to understand, right? Have a nice life.

      Delete
    54. "If the chance for one of them is very low- then the second one is the best explanation."

      You are assuming that the probability of the second is not lower, and that you can calculate or estimate probabilities sufficiently accurately.

      After that you need to compare explanatory power and predictions.

      Delete
    55. Chris B,

      “If you think this was the only mutation documented in those experiments, you have not absorbed the information in the peer reviewed publications resulting from the Lenski lab experiments.”

      I understand that, but if I recall, the mutations resulted in a transporter protein. That is a rather modest acquisition after 31,000 generations.

      I think it is presumptuous to conclude that the small bones in the whales are foot bones.

      =====

      photosynthesis,

      “there's many ways other than "many genes each with extremely very low probabilities for arising" in which a sonar system could have evolved in whales”

      I don’t know how you could know that, but this article would seem to contradict that idea:

      “ "The results imply that there are very limited ways, if not only one way, for a mammal to hear high-frequency sounds," said Jianzhi Zhang of the University of Michigan, who led the other study. "The sequence convergence occurred because the amino acid changes in prestin that result in high-frequency selection and sensitivity were strongly favored in echolocating mammals and because there are [apparently] very limited ways in which prestin can acquire this ability." Prestin is found in outer hair cells that serve as an amplifier in the inner ear, refining the sensitivity and frequency selectivity of the mechanical vibrations of the cochlea, Zhang explained.”
      http://www.sciencedaily.com/releases/2010/01/100125123219.htm

      Delete
    56. Cutting to the chase on whale evolution, if you were to assume:

      -1 generation each year (unrealistic, but very generous)
      -15 million years (which is also generous)
      -15,000 generations per adaptation (which compared to Lenski’s E coli, is very generous)

      you would have 1000 adaptation increments to complete the transition from a wolf-sized animal to an actual whale.

      Any serious appraisal should conclude that this is totally unrealistic for a long list of reasons, starting with a suite of replication enzymes which were designed to specifically prevent mutations, the very thing that evolution depends on. The list of “living fossils” is still growing, thus proving that Gould and Eldredge were correct: stasis or extinction are the rules.

      Delete
    57. Dear 'God' believers, instead of going on and on about the alleged probability/improbability of things THAT HAVE ALREADY OCCURRED, and instead of asserting irrelevant, unfounded numbers (e.g. 15,000 generations per mutation), and instead of asserting unfounded stuff like "we have 2 options", "were designed to", etc., and instead of suggesting that your irrelevant, unfounded assertions amount to or warrant a "serious appraisal", and instead of basing virtually all of your assertions on what you think is wrong with evolutionary theory and other aspects of science that you don't like, why don't you present POSITIVE arguments for the existence of your chosen, so-called 'God' and the design-creation-guidance of the universe including life and its diversity (and don't leave out extirpations and extinctions) by your chosen, so-called 'God', with specific details and verifiable, supporting evidence? Some unique, specific predictions would be nice too.

      Delete
    58. txpiper said 15,000 generations per adaptation, not mutation. But that doesn't change the fact that the figure is pure fantasy, derived from his misunderstanding of Lenski's data. Potentially adaptive mutations are not going to declare their presence as readily in a population of bacteria who are being carefully fed and tended by a dedicated staff of researchers, just as such mutations in the wild will go undetected until the population is subjected to an environmental pressure, such as being subjected to antibiotics.

      Delete
    59. judmarc,

      @txpiper:

      You asked me to show you what I meant when I talked about the internal rear foot bones in whales. Chris B gave you the link to a picture first thing yesterday morning (https://upload.wikimedia.org/wikipedia/commons/4/43/Sperm_whale_skeleton.png), and no response from you. Here's a photo of the relevant portion of an actual whale skeleton showing just what I'm talking about: https://whyevolutionistrue.wordpress.com/2011/02/10/the-hind-legs-of-whales/dscn5720/

      There are those foot bones, inside the whale's body, connected to absolutely nothing. So, what, the Designer got sloppy, had some bone material left, didn't clean up after himself? And while He was at it, just for fun He made the skeletons of the animals between Pakicetus and modern whales with progressively more rudimentary rear foot and leg bones until they became the totally non-functional remnants you see in the photo. Oh, and He also remembered to change the genetics of those animals and all their offspring to the present day in just the way they would be if in fact Pakicetus, hippos, whales, etc., were related through a common ancestor. What a kidder that Designer is, changing bones, genes, geology, quantum field theory, and everything else in the Universe to be just the way it ought to be if evolution were true! Big cosmic joke, eh?

      Now regarding your math ("15,000 adaptations," etc.): The chance of winning the PowerBall lottery is nearly 300 million to 1. They draw that lottery twice a week. So that should mean a winner once every 3 million years. But there were 3 winners of a single PowerBall lottery just weeks ago, and there are more winners every few weeks.

      Big hint, txpiper: Tell me how it is there are lottery winners so often, and I'll show you exactly why your "evolution math" is complete trash. And then you can remember, every time you see someone has won the lottery, how wrong you were about evolution.

      Delete
    60. txpiper writes:

      I think it is presumptuous to conclude that the small bones in the whales are foot bones.

      It would be presumptuous if there were not so many intermediate skeletons showing, like frames in a time lapse movie, those bones progressively becoming smaller, more rudimentary, and internal. So rather than saying what you've literally written - that this is "presumptuous" - what you've actually declared, here in writing in front of everyone, is that "I, txpiper, am totally ignorant of the paleontology and genetics of the evolutionary story between Pakicetus and whales that I have been arguing about."

      Here's a link to one image from the Web showing some of the paleomorphology: http://www.nature.com/nature/journal/v413/n6853/images/413259aa.2.jpg

      There's plenty more, laying it out in all the detail anyone serious and honest could want. Are you serious and honest about learning, or are you intent on defending the impregnable fortress of your ignorance against all comers?

      Delete
    61. lutesuite said: "txpiper said 15,000 generations per adaptation, not mutation."

      Yes, I mistakenly typed mutation instead of adaptation. Thanks for the correction.

      Delete
    62. judmarc,

      look at this paper:

      http://www.sciencedaily.com/releases/2014/09/140908121536.htm

      this structure is actually important to the whale reproduction.

      Delete
    63. So? Why would a "designer" repurpose a pelvic bone as a reproductive organ?

      Delete
    64. this structure is actually important to the whale reproduction.

      And where did those bones come from? Did the Designer, with his antic sense of humor, decide to put them right where those foot and pelvic bones were already getting smaller and smaller so the comparative skeletons look like a time lapse photograph, in order to have them look just exactly like they evolved? And then to top off the joke, he wangled the genetics to tell exactly the same story?

      Or do you figure the more sensible explanation is that yes, the pelvic and rear limb bones evolved to become vestigial, and then as it must do since it doesn't have access to the services of a Designer, evolution worked with what it already had (internal bones that once served for locomotion but no longer), and these bones and the muscles around them became the object of selection for reproductive advantage? (If that's what in fact happened. The people who are saying this are also saying the appendix has an immune system function, so they seem predisposed to find function where others have seen none.)

      Delete
    65. dcsccc,

      Why would the designer give the whales degenerate pelvic bones that look just like evolutionary reduction produced them, in a fossil sequence from ancestors with hind limbs, when a single smooth bone or even partially calcified tendon would do?

      It's another evolutionary link to the Artiodactyla, many members of which also attach their penile muscles to the pelvic bones.

      And, of course, why would all the girl whales have these bones, too?

      Delete
    66. And, of course, why would all the girl whales have these bones, too?

      Why, the same reason the Designer gave guys nipples, of course.

      Delete
    67. judmarc,

      “There are those foot bones, inside the whale's body, connected to absolutely nothing.”

      Better stated, the bones, like your own hyoid bone*, are not connected to other bones. They are however, very functional.
      http://phenomena.nationalgeographic.com/2014/09/05/the-erotic-endurance-of-whale-hips/

      *http://www.livescience.com/7468-hyoid-bone-changed-history.html

      I think that the evolutionary short stories and language are responsible for perceptions about things like leftover whale feet. The tale about two reptile jawbones migrating to the middle ear and becoming two of the three tiny ossicles is a good example. If you hear things like that often enough, I guess they can seem real. But DNA replication failures cannot tinker with or co-opt things for alternate purposes.

      Delete
    68. hey to all. first- in rare cases shark also born with "legs":

      http://sarasotafins.weebly.com/shark-blog/how-sharks-show-err-love3

      so according to this we need to believe that sharks use to live on land.

      secondly- human embrio also have gills-like structures. but they never evolve to gill but something else. so if we see 2 similar stuctures in 2 animals it cant prove that they have the same function.

      third-it can be a vestigial flipper.

      the fact that this structure is functional can disprove any claim about a commondescent of whales with land mammales..

      Delete
    69. by "can disprove any claim about a commondescent of whales with land mammale"-

      i mean any evidence for commondescent in this specific example.

      Delete
    70. hey to all. first- in rare cases shark also born with "legs":

      You're link doesn't work.

      secondly- human embrio also have gills-like structures. but they never evolve to gill but something else.

      HA HA HA HA! Do you not understand the evolutionary significance of the similarities between organisms at early developmental stages.

      third-it can be a vestigial flipper

      AAH HA HA HA HA! Do you understand what "vestigial" means?

      Delete
    71. Remove the 3 from the end of dcscccc's link and it will work.

      Delete
    72. Ah, OK. So dsccc's "sharks with legs" don't have legs.

      AAH HA HA HA HA HA!

      Here's a question: Why don't we find sharks with vestigial legs, like we do with, say, snakes?

      I mean, that's an easy question for someone who understands evolution and knows that intelligent design is a crock of shit. But how to you explain this, dcsccc?

      Delete
    73. My link and dsccccc's one have the same picture, the woman holding up the male shark. With *ahum* 'legs'.

      Delete
  3. "This is why you have to be careful when dealing with creationists. The original answer by Richard Dawkins was posted over five years ago but the creationists are not going to let you forget it."

    Even if they have to lie about it. Gordon Mullings (adba KairosFocus and GEM of Tiki) stated in the post that BA77 just posted this, when in fact he posted it in April 2014. It would be very difficult for BA77 to post anything at UD as Barry has banned him.

    ReplyDelete
    Replies
    1. I missed him to (last post on 28th of december). How do you know he got banned? I posted twice on UD that I missed BA but nobody reacted.

      Delete
    2. BA77 is now back. I would guess BA77 needed a break to cool down from the stress of doing all that cut-and-paste.

      Delete
    3. Apparently BA77 is not back. They seem to be saying that BA77's "reappearance" is based on some old comment of BA77 reappearing in a way that, to me, passeth understanding.

      Delete
    4. Barry has stopped announcing when someone has been banned. But when someone asks if someone has been banned who hasn't been, Barry is very quick to announce that the person hasn't been banned.

      Delete
    5. Gordon (kairosfocus) Mullings responding to me at UD: " Mr Spearshake would do better to refrain from outing tactics and accusations."

      Gordon should realize that I reserve outing to people who resort to name calling and unfounded accusations against others. So far, you and Mapou are the only two. If you want to out me, go right ahead. My name is Kevin Middlebrook and I live in Canada.

      You use the word "accusation" as if it is a bad thing. It is only bad if it is untrue. Otherwise it is just a statement of fact.

      Delete
    6. Barry banned BA77? Wow... Almost like Stalin's order to assassinate Trotsky.

      Delete
    7. "Barry banned BA77? Wow... Almost like Stalin's order to assassinate Trotsky.

      I think a better analogy would be Henry the 8th's "Off with their heads".

      Delete
    8. The tale about two reptile jawbones migrating to the middle ear and becoming two of the three tiny ossicles is a good example. If you hear things like that often enough, I guess they can seem real. But DNA replication failures cannot tinker with or co-opt things for alternate purposes.

      The DNA and fossils tell exactly the same "tale." In other words, we have cross-confirmation of data from numerous actual observations and experiments. But observed reality confirmed by experiment "can't happen," why? 'Cause you say so? 'Cause your faulty math says so? (Oh whoops, someone else just won the lottery, guess your math is wrong again.)

      Delete
  4. Replies
    1. From where? As far as I'm aware he's never been a member here.

      Delete
  5. The unmitigated duplicity of the creationists is galling – raising the question whether they have any scruples at all by deliberately failing to heed the 8/9 Commandment

    https://en.wikipedia.org/wiki/Thou_shalt_not_bear_false_witness_against_thy_neighbour

    FOXP2 is one of several interesting genes that constitute an EXTRAORDINARY EXCEPTION to the rule when expecting the inexorable ticking of some presumed neutral molecular clock – to wit Human accelerated regions (aka HARs).

    https://en.wikipedia.org/wiki/Human_accelerated_regions
    http://www.ncbi.nlm.nih.gov/pubmed/12524352

    https://en.wikipedia.org/wiki/Human_accelerated_regions

    I had my own high school students investigate this very phenomenon with yet another HAR called HACSN1 which was only identified due to the unusual and unexpected exuberant increase in nucleotide differences between Chimpanzees and Humans as would be expected by unusually strong selection pressures operating on that small region of DNA.

    Here is the ENSI link to the activity I constructed 8 years ago before ENCODE was on the horizon and before I even knew of the “junk” DNA controversy.

    http://www.indiana.edu/~ensiweb/lessons/Hum-Chimp%20DNA.pdf

    Of course – this activity now requires revistation and reediting - now that I have been enlightened regarding the junk-DNA non-controversy.

    Of course – I still stand by my original contention that it still remains within the realm of possibility that the really interesting differences between humans and chimpanzees (i.e. HARs) are mostly a result of natural selection and not neutral or almost neutral theory… but that is another can of worms I would prefer to kick down the road of mixed metaphors.

    Best regards

    ReplyDelete
    Replies
    1. To Tom Mueller

      Thank you for bringing up Human Accelerated Regions

      http://darwins-god.blogspot.ca/2009/08/human-accelerated-regions-you-cannot.html

      I laugh out loud to witness the contortions of evolutionists like Laurence Moran who deny they are Darwinists because Evolution is driven by the random processes of Neutral Theory which is nothing more than Hardy Weinberg's Genetic Drift in small populations but still believe that HARs can be generated in large populations without SPECIAL CREATION!

      Of course humans are special and of course there is only ONE reason! GOD! Evolution's mathematics says so.

      Delete
    2. That blog post claims there are hundreds of HARs. Where are these hundreds of HARs?

      Remember that every time you lie for Jesus, an angel loses its wings!

      Delete
    3. Fact remains that Tom Mueller is wrong! Hundreds or dozens... HARs could not occur by evolution and HARs make humans special as in special creation

      It mathematically impossible by random mutation (even by intense "selection") to generate either that large a cluster of mutations in such a small region of DNA that makes just one HAR or that cluster of HARs that make humans special

      Delete
    4. What in your simple mind makes HARs impossible? I've looked into a few of them (they are extremely tiny regions) and I can't work out for the life of me why creationists get so excited by them.

      Delete
    5. Jesus B God,

      I doubt that Larry is performing any contortions. It seems more like Cornelius is performing contortions our of the wording chosen by those who were announcing the HARs thing. Like the good old nothing-but-rhetoric imbecile that Cornelius is.

      Anyway, you've got it quite wrong. Larry thinks that Neutral theory explains a lot more than natural selection. Not that natural selection doesn't happen.

      You seem to be unable to read and check for yourself, since the HARs were not described in the scientific publications as being "Hundreds or dozens." In any event the issue here is one where you look like an idiot, while we look at you astounded that someone could be so self-deceived. Suppose it was hundreds of dozens. OK then, what makes you think that the only natural way to get many positions with lots of mutations is point mutations? What makes you think that regions cannot recombine? What makes you think that regions cannot get duplicated? What makes you think that random mutations cannot be some more clustered than others? What makes you think that population bottlenecks won't have any effect in the proportion of mutations fixed?

      Long long etc.

      Anyway, in order to consider "SPECIAL CREATION!" there would have to be a creator to begin with. All we have seen on that regard is idiotic claims like yours, coming out more from your ignorance than anything else. They are but gods-of-the-gaps arguments. As useful as the belief that volcanoes are gods when people didn't know how volcanoes formed.

      Delete
    6. Evolution's mathematics says so.

      Except it doesn't. Evolutionary mathematics are the same as a lottery's. There was a 1 in 292 million chance of winning the billion dollar PowerBall lottery a couple of weeks ago. The drawing is held twice a week, so I guess that's once every 146 million weeks, or a little less than once in three million years. But 3 people won that same week! Now how did that happen, Jesus B. God, and since evolution operates on the same mathematics, what does it tell us about evolution?

      Delete
    7. To judmarc

      If three people in the same household with connections to the mafia won those three PowerBall tickets, suspicion would be justified that something else than random chance occurred.

      HARs represent clusters of many mutations concentrated in very small regions of DNA crucial to special differences between chimps and humans such that random chance could not explain their occurrence. That is how the computer program to find their occurrence was written.

      Delete
    8. The only argument that could convince me I am wrong would be a mathematical analysis of the probabilities.

      So far I have no answer but insults and angel wing jokes which only confirms I must be correct.

      Delete
    9. JBG: You're making two logical errors. First, you're assuming that if there is a cluster of differences between human and chimp in a small bit of DNA, those differences are all independent. They may not be and if they're not but you're "mathematical analysis" treats them as if there are, your results will be way off.

      Second, you're asking "What is the probability that these specific changes will happen?" when it is more appropriate to ask "What is the probability that something useful will happen?"

      As a bonus, you seem to have a double standard as you don't provide calculations and justify those calculations, and yet you call for other commenters to provide you a mathematical analysis of the probabilities.

      Delete
    10. To answer your question JBG, lets look at HAR1 which contains the greatest density of mutations found compared to all the other HARs.

      The region is 118bp in length and instead of the usual 2-3 differences that we would expect to find in a region this long, we find 18. Instead of the usual 98% similarity to Chimps, in this tiny segment it's closer to 83%

      Wow! That's an extra 15 whole mutations than we might not expect otherwise, how will we ever explain that?

      It turns out that every single one of these 15 mutations involve a flip from A/T (weak nucleotides) to C/G (strong nucleotides).

      A strong mutational bias like this is a clear indicator that something else is going on here. It turns out that that something else is called GC-biased gene conversion. This phenomena has been observed to occur preferentially in regions with high recombination rates.

      So in the case HAR1, it turns out that this is a mutational hotspot due to a high recombination rate in this area.

      Delete
    11. JBG said:

      "If three people in the same household with connections to the mafia won those three PowerBall tickets, suspicion would be justified that something else than random chance occurred."

      So you're saying that you're justifiably suspicious that HARs exist due to "random chance", therefor HARS must be due to your 3-in-1 "God" (yahoo-yeshoo-holy-spook) being connected to the mafia?

      You do realize, don't you, that "random chance" is not and never has been an honest way to describe evolutionary theory?

      Delete
    12. Let see if I understand your argument. There exist 49 HARs that are responsible for the remarkable difference between humans and chimpanzees.

      Each of these crucial regions are "mutational hotspots" that mutate 6 to 9 times faster than expected.

      Each of these 49 HARs are crucial in determining the difference between humans and chimpanzees.

      Would that not mean that whatever unlikely probability is calculated for the first HAR, that fractional value would need to be raised to the power 49?

      At what point would probabilities become so small that the possible explanation of Intelligent Design becomes a reasonable option?

      Delete
    13. The very name 'human accelerated region' contradicts the very idea that evolution has occurred.

      Some unusual improbability to the power 49 becomes so very improbable indeed, that others have suggested the comparison to "Darwinian epicycles" not much differently than Ptolemy.

      Delete
    14. JBG,

      The very name "human accelerated region" only illustrates that the authors made a poor choice of a name for their discovery. Nothing else. You do know that it's people who name their discoveries, right?

      Mutations can be found more concentrated in particular regions for obvious reasons. She of them have been explained to you quite clearly. You're just too stubborn to try and reason about it.

      Delete
  6. Dawkins is recognized as worlds' most famous atheist and the promoter of atheism based on his scientific conviction that evolution is a fact that "killed GOD".

    Within the last few weeks I have learned that Dawkins didn't know that:
    1. The genetic code is not uniform in all species
    2. The tree of life has been uprooted
    3. Now the gene trees folly

    I think the "new atheists" need a new leader. I propose Bill in the redneck baseball cap. I think he can do a much better job than Dawkins. At least he believes in something... that could be verified ... by...

    ReplyDelete
    Replies
    1. Eric,

      Really man, you come out as just a little idiot when you make comments like that. Dawkins doesn't think that evolution "killed GOD." He just doesn't believe that your god exists. Then, well, atheism doesn't depend on the words of the most famous or least famous of them all. You're trying to make of atheism something like your religion. But it's not. Atheism is not a philosophy or a religion. It's just a statement of something we don't believe: gods. Anything else is up to each of us.

      So, for example, I could not care less if Dawkins makes a mistake in choosing an example about evolution. The ridiculous nature of your beliefs stand just as ridiculous whether Dawkins knows his genes well or not. I don't need any leaders to notice that.

      Then, for another example, sometimes I disagree with Larry. Again, that doesn't make your beliefs any less ridiculous either.

      Are you learning something now? We're not like you. You believe in some sacred fantasy figure, we don't. Learn the difference or you will be thinking that you're making fun of us, when in reality you'll only be ridiculing yourself.

      Delete
    2. Hi Eric, you were gonna show all of us that slam dunk proof you had that Coyne was wrong?

      I figured maybe you wanted to clear up that little detail before you started in on Dawkins.

      Delete
    3. So, creationists were right all along about the gene trees you just couldn't swallow mentioning it...

      I guess professor Moran failed to mention that many "creationists" had challenged Dawkins' a totally uneducated claim many times. He didn't respond. He was too busy.

      This time though it was unavoidable for Larry...

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    4. The creationists here seem to have a hard time letting go of the idea that there must be some sort of infallible authority we must all abide by.

      Atheists don't have a pope, or universal atheistic teachings in some atheist holy book. Richard Dawkins is just another atheist, he's not somebody we all must listen to and agree with, and nothing any of us believes hinges on what Richard Dawkins gets right or wrong.

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  7. What exactly is ridiculous in believing in God?

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    1. Francesco, if you admit that you have no evidence for your preferred god, Quetzalcoatl or Thor or Mercury or the Great Spirit or whoever and that your faith is simply a choice, a preference, a prejudice then, at least, you are intellectually honest, but if you insist there is evidence or logic to support your choice, then you are reasonably the subject of spirited opposition, and ridicule from many quarters.

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    2. If you live in a bubble where everybody else believes in god, and you all have grown up believing there's lots of good evidence for god, then it's not really ridiculous for you.

      But to outsiders who aren't part of that bubble and do not have been indoctrinated in those beliefs, it looks just as ridiculous as belief in Santa Claus, the tooth fairy and so on.

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  8. Trees from different genes are not all exactly the same. There is noise owing to accidental convergence, reversals, and parallelism. But they do come out very similar, and when you look at many loci in eukaryotes the signal of an underlying evolutionary tree becomes overwhelming. See, for example, Doug Theobald's papers on formal tests of common ancestry (here, for example).

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    1. It's true even for prokaryotes with their "rampant HGT". Statistically speaking, lateral transfer is still much much more frequent than horizontal, so you should still be able to detect the preponderance of lateral stems over horizontal branches.
      And they do, see for example:
      Seeing the Tree of Life behind the phylogenetic forest.

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    2. I think you may mean horizontal versus vertical (or lateral versus vertical), as usually Horizontal Gene Transfer and Lateral Gene Transfer are just synonyms.

      I think it is vertical transmission that is much more frequent than horizontal transmission. Nevertheless if there is HGT for a typical gene only in one generation out of 1000, but the depth of the tree is hundreds of millions of years, most genes will have trees greatly different from the tree of descent of the cells.

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    3. Yes, I mixed up the words there. Almost all inheritance is vertical rather than horizontal.

      Delete
  9. Francesco asked: "What exactly is ridiculous in believing in God?"

    Which "God"?

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  10. IMO, simply answering the question as asked is a losing game. Whether deliberately or not, it asks you to give one small detail (no matter how important, how big, any one point in favor of evolution is a relatively small part of an enormous amount of evidence)and that one thing can then be (will be) treated as if it were the whole enchilada.

    The only good response, IMO, is to reply that the best single point is that there are thousands of lines of inquiry, making up many millions of bits of data, that all point to evolution being so, and virtually nothing legitimate saying the opposite.

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    1. anthrosciguy--

      So right. And not only are there thousands of unrelated pieces of evidence, but so many of them came, completely unforced, from people who weren't even interested in proving evolution. Physicists, astronomers, geologists-- even quarry workers and Christian monks-- discovered important data supporting the fact of evolution while they were going about their business doing apparently unrelated work.

      There is just no way that could have happened if evolution weren't real.

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  11. The regulars at Uncommon Descent are having an awful time trying to figure out why Dawkins' error does not invalidate common ancestry. Very strange, given how much time they spend discussing evolution, that they are not able to figure it out themselves. And their situation is not helped by Barry's habit of banning people who might be able to help them out. Here's how I have explained this topic before. Maybe someone might want to pass this on to them (I'm looking at you, Gary Gaulin.)

    Suppose we have sequenced the genome of you, your brother, and your cousin. It is entirely possible that there will be an allele that both you and your cousin share in common (inherited from one of your grandparents) that your brother did not inherit. In terms of this one gene, then, you would appear to be more closely related to your cousin than to your brother. However, if you were to take your entire genome into account, it would still show that you are more closely related to your brother. The one discordant locus does not invalidate the use of genomics to determine patterns of ancestry between organisms.

    Make sense?

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    1. What was Dawkins' mistake? As far as i can tell he never made one.

      He compared the gene FOXP2 between humans and chimpanzees and humans and mice. It wasn't clear whether he was including the introns or whether he was talking about just the exons. But if you consider just the exons, he was completely correct that humans are very similar to chimps, slightly more dissimilar to mice and slightly more dissimilar still to frogs. The response video was irrelevant because it just looked at the relative difference in gene sizes (introns and all) without even attempting to count up the actual number of differences and it ignored the fact that Dawkins was clearly not considering introns.

      Dawkins claimed there were about 9 differences between humans and chimps. I count 16.

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    2. Lutesuite looking at me: "The regulars at Uncommon Descent are having an awful time trying to figure out why Dawkins' error does not invalidate common ancestry. Very strange, given how much time they spend discussing evolution, that they are not able to figure it out themselves. And their situation is not helped by Barry's habit of banning people who might be able to help them out. Here's how I have explained this topic before. Maybe someone might want to pass this on to them (I'm looking at you, Gary Gaulin.)"

      How about something to (either way around) keep the Biologic Institute busy?

      http://www.uncommondescent.com/atheism/ba77-and-a-vid-on-foxp-123-molecular-trees-vs-dawkins-claim-of-you-get-the-same-family-tree/#comment-595861

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    3. @Aceofspades

      Lutesuite is referring to incomplete lineage sorting. This is indeed one of the issues of comparing single genes, and it will affect exons as well. Look it up if you don't know what it is.

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    4. Thanks Corneel... I know what it is. I was just pointing out that Dawkins didn't pick a bad example here.

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    5. Yes, I see now what you meant. Very well.

      Delete
  12. I often ask evolutionists what is their top three, or one, favorite evidence for evolution.
    Molecular evidence says Dawkins. Hmmm.
    he says the likeness of dna for different species proves a common origin for that species and by extrapolation common decent for biology etc.

    Yet creationism would predict this also. Like species WOULD have like dna.
    Then hr says morphology is a twin to the dna evidence for common descent.
    Creationism would predict this.
    If species look alike then a twin dna likeness would also be predicted.
    How else could it be?
    One should not think evidence for evolution comes from a comparative discipline. Other options are there for likeness in biology.
    Anyways its not biological scientific evidence.
    Its just connecting dots, like fossils, without evidence for process. Its just looking at results and not imagining other options or the option for other options.

    People look like apes and so one shoyld expect like dna.
    Yet like dna is not evidence for common descent.
    Thats just a line of reasoning.
    DNA likeness would also be that way because of morphology likeness.
    Yet a creator could make people to just have the best type of body on earth within the common boundaries of biology.
    Likeness is not evidence for process at all. Not at all.

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    1. "Creationism would predict this.
      If species look alike then a twin dna likeness would also be predicted.
      How else could it be?"

      Shame, then, Bob that DNA shows thylacines and wolves to have separated from each other at least 150 million years ago.

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  13. Robert Byers says: Yet like dna is not evidence for common descent.
    Thats just a line of reasoning.


    Lines of reasoning?
    'Reasoning' stems from 'reason' - the mental powers concerned with forming conclusions, judgments, or inferences With lack of sufficient mental powers, no reasonable lines of reason can be formed.

    Likeness of DNA indeed is evidence for relationship. DNA reveal child/parent relationships with near 100% certainty. You can't say the same for morphology.

    Your oft repeated claim that DNA likeness would also be that way because of morphology likeness is an absurd, nonsensical and brainless statement.

    But go ahead and explain: What causes morphological likeness? There's one thing about all your statements that stick out: They are baseless, disconnected from reality. They are emanations from a muddled creationist brain. You are prime evidence that creationism is c**pology.

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    1. Robert, do you know what creationism doesn't predict?

      I didn't predict that humans and chimpanzees should have the same fossils of genes that once worked in distant ancestors and that those gene fossils are broken in exactly the same way.

      It also doesn't predict that viruses would have left their mark on the chimpanzee genome in exactly the same way and in exactly the same places as the human genome.

      Face it, you have a failed hypothesis. All you have left now is motivated reasoning arising from the desperation to invent stories to explain away difficult truths.

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    2. Rolf.
      If you were the creator what would you do for basic creation of biology?
      Would you be forced to make biological entities with wildly different dna on all parts of the entity? or rather would you give all parts a NUMBER/Dna point and thus all biology would have like dna relative to parts used.!!
      Why not the latter?
      Your saying that if God did create man and ape separately THEN we should have great dna difference. I say it would be the same because we are so alike in our bodies. Yet created differently. Its a viable option if not a demanding if one already thinks there was a creator doing the work.
      Why is it lacking in base.?

      Its only a special case with parent/kid dNA.
      Indeed morphology of parent/kid is inferior to dna. why is that?
      Why if the dna is so alike why is the looks not so alike?
      It must be that both parents dna interferes with a exact copy. at least this. Yet the morphology is very close if not perfect.

      Its not two points, as Dawkins says, for dna and morphology that prove evolution.
      Its one point. And the point fits excellent with a creator.
      Its what I would do!

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    3. Ace
      These are points that I think can work. Why not that both bodies react to some threat the same way? Or why not the bodies never reacted but have some ability encoded in them to deal with problems?
      I know these things are brought up but other options can be imagined. Its too little details to say common descent is demonstrated.
      The likeness of our bodies seems to me it would bring likeness in these ways. I nknow your side says the dice is against it but it seems to smell it woiuld be this way.
      anyways comparitiveness of dna/morphology is the point i bring up.
      Creationism would predict likeness of dna etc .
      All this is about comparing things. Then process is presumed.
      Its not biological evidence for process but a inference of process.
      Inference is not evidence. The data doesn't insist on these evolution conclusions.
      In fact its very poor for evolutionism to say THIS is their evidence. Its just data being interpreted.
      Its not like in physics or chemistry. Hands on evidence.

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    4. ace said:

      "I didn't predict that humans and chimpanzees should have the same fossils of genes that once worked "-

      so evolution doesnt predict that 2 different species will get the same pseudogene with the same mutation convergently? if we will find such case the evolution is false?

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    5. so evolution doesnt predict that 2 different species will get the same pseudogene with the same mutation convergently? if we will find such case the evolution is false?

      No. A "failed hypothesis" is not the same as a falsified one. The point is that evolutionary theory was able to provide an explanatory framework by which these predictions could be made. Creationism is able to make no such predictions.

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    6. Also note, dcsccc quote mined ace and based his remark on a typo (I instead of it)

      "Robert, do you know what creationism doesn't predict?

      I didn't predict"
      It didn't predict that humans and chimpanzees should have the same fossils of genes that once worked in distant ancestors and that those gene fossils are broken in exactly the same way.

      Delete
  14. txpiper says,

    Cutting to the chase on whale evolution, if you were to assume:

    -1 generation each year (unrealistic, but very generous)
    -15 million years (which is also generous)
    -15,000 generations per adaptation (which compared to Lenski’s E coli, is very generous)

    you would have 1000 adaptation increments to complete the transition from a wolf-sized animal to an actual whale.


    Okay, let's run with those numbers.

    Let's assume that in each of those "adaptation increments" you fix 1000 new adaptations. We know from Lenski's work that multiple adaptations are constantly being fixed simultaneously in his cultures.

    That's 1000 × 1000 = one million adaptations. Is that enough for you?

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    1. Larry,

      “Let's assume that in each of those "adaptation increments" you fix 1000 new adaptations. We know from Lenski's work that multiple adaptations are constantly being fixed simultaneously in his cultures.

      That's 1000 × 1000 = one million adaptations. Is that enough for you?”

      I don’t think 1000 fixed adaptations would be realistic. I didn’t follow the reference, but this does not seem to support a number that large:

      “Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that within this time frame, only 10 to 20 beneficial mutations achieved fixation in each population, with fewer than 100 total point mutations (including neutral mutations) reaching fixation in each population.”
      https://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment

      In another paper, Lenski offered the following:

      “Given that the genomic mutation rate of E. coli is approximately 3x 10[-3] mutations per replication (Drake, 1991), one can infer that the proportion of mutations that are beneficial is roughly one in a million.”
      http://lenski.mmg.msu.edu/lenski/pdf/1998,%20Genetica,%20Gerrish%20&%20Lenski.pdf

      I think it should be emphasized that only one of original twelve populations isolated in Lenski’s experiment acquired the adaptation that made his work famous. That said, in all honesty, I don’t know how to manage a comparison between bacteria in a controlled experiment, and large animals in at large, wild populations. I would welcome your thoughts.

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    2. Did you not notice this, txpiper:

      Lenski has estimated that within this time frame, only 10 to 20 beneficial mutations achieved fixation in each population

      I know you're stupid. But I would expect even you to understand that 10-20 adaptations per population is more than 1 adaptation among all the popilations. I didn't think it was possible, but I'm disappointed in you.

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    3. I'm glad we cleared that up. In the future when you do your anti-evolution calculations try and remember that many alleles in a population are reaching fixation simultaneously not sequentially.

      I think it should be emphasized that only one of original twelve populations isolated in Lenski’s experiment acquired the adaptation that made his work famous.

      All twelve of the populations are constantly evolving and becoming more fit. Lenski has published dozens of papers and only a few of them deal with the culture that acquired the ability to use citrate.

      We have learned a ton of stuff from his experiment.

      Keep in mind that nearly neutral alleles are being fixed at a rate equal to the mutation rate. This is important because when you are looking at the evolution of new species (i.e. whale evolution) it's quite likely that many of the phenotypic changes are not adaptations.

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    4. lutesuite,

      Try again, and notice that the time frame for fixing the 10 to 20 mutations was 20,000 generations.


      Delete
    5. Larry,

      “In the future when you do your anti-evolution calculations try and remember that many alleles in a population are reaching fixation simultaneously not sequentially.”

      That should stand to reason. Novel features like echolocation would require complex, regulated muscle, skeletal and neural accommodations for the new components. In the context of random, extremely rare beneficial mutations, how would you account for all the control mechanisms?

      Delete
    6. we need to add the chance to get the correct functional amino acid sequence. a short protein need about 100 aa. the space is about 20^100. so what is the chance to evolve echolocation in this space?

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    7. Read what Larry wrote in the post just above yours, you morons.

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    8. we need to add the chance to get the correct functional amino acid sequence

      No. This is provably incorrect as a matter of mathematics. Look back through Larry's recent posts until you find the "Lottery Fallacy."

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  15. With many more genes sequences it has even become worse for Dawkins. Check this out:
    http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?db=core;g=ENSG00000128573;r=7:114086327-114693772



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