Friday, November 01, 2013

A "Perfect Painting" Proves that Beneficial Mutations Are Impossible and Neutral Mutations Are Impossible

There are times when the stupidity of creationists just makes you gasp. This is one of those times. The creationist is Denyse O'Leary, who holds some kind of record for stupidity.

In this case she can be partially excused since she seems to be quoting someone named Laszlo Bencze. You can read the whole thing at: Is there no such thing as a neutral mutation? Art explains why there probably isn’t.

Denyse quotes Laszlo Bencze (I think) talking about a painting by French artist Jean-Auguste-Dominique Ingres (1780-1867).
Here is a famous and gorgeous painting by Ingres which I just saw in person at the Frick Museum in New York.

Let’s imagine we can improve it by adding a dot of paint 1mm in diameter to it. In evolutionary terms we will give it a “point mutation,” the smallest possible change. If we add this dot randomly, the odds are pretty high it will damage the painting by creating an obvious, intrusive speck. So let’s give evolution every advantage. Let’s make the process far more likely to succeed by having the great contemporary painter, David Hockney, add the speck wherever he thinks it will “do the most good.”

Now I happen to know that Hockney is a great admirer of Ingres and would be shocked and dismayed at any such request. But if a cruel tyrant under pain of death forced him to do it, Hockney would understand that there is no place he could possibly place a dot of paint that would improve the painting. Like a living thing, the painting is so well crafted that anything he might add to it could only be neutral at best. So Hockney would strive to place the most neutral dot he could by choosing a pigment that matched some dark portion of the painting and hope to hide his speck there.

But would such a speck be truly neutral? No matter how well it matched the color, wouldn’t it be visible as a raised dot under the right lighting conditions? And wouldn’t that actually damage the painting even if ever so slightly? And this is precisely Sanford’s point. In the world of biology it is impossible to create a neutral mutation. The change may be extremely slight, even invisible, yet always a degradation no matter how small.
When you think about it, it's really very sad this this is the best the Intelligent Design Creationists can offer. They are so ignorant that you can almost feel sorry for them.


164 comments:

  1. This is what happens when creative thinking is based upon a foundation of complete ignorance. It is perfect for the target audience: people who also know nothing about biology.

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  2. Science by idiotic analogy.

    Why haven't scientists hit upon such a great strategy before?*

    Glen Davidson

    *Yes, I know, it's not really new, but thinking people just see it as a pathetic mistake.

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    Replies
    1. How do they know the genome is an Ingres and not a Jackson Pollock? :)

      Delete
    2. Why haven't scientists hit upon such a great strategy before?*

      Yes, I wonder why? It would be much easier than all those tiresome observations and experiments.

      Delete

  3. That they would think the art world could be a model for biological evolution is just stunning. Consider how the art world works: Take an advertisement poster thats barely worth the paper its printed on. Now have Andy Warhol come along and put a dot on it. Now is worth $450,000.00

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  4. Not sure which way this cuts, but Ingres's painting is famous in another way -- the young woman is anatomically impossible. Her right arm apparently emerges from near the right side of her belly.

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    Replies
    1. And Ingres's Grande Odalisque has a few lumbar vartebrae too many (3-5 -- opinions vary).

      Delete
    2. Maybe her mother was frightened by a swan while her daughter was in utero.

      Dave Bailey

      Delete
    3. Joe, how does the population genetics explain the evolution of mouse eye and the night vision involving nuclear genome? I'm curios to hear your opinion because even creationist consider you as the best population geneticist in the world. So, you gotta know somethin about that....

      Delete
    4. Mouse eyes evolved from the eyes of their rodent ancestors, which are pretty darn similar, Night vision of who? Mice? Again, lots of other rodents have vision well adapted to night.

      So the first thing I can say is ... these sound like silly sound-bite questions.

      Delete
    5. Does this sound like sound like silly sound-bite questions to you now?

      Sounds like the ramblings of a drunken imbecile to me.

      Delete
    6. Does this sound like sound like silly sound-bite questions to you now?
      Yes.

      Delete
    7. That's funny. "Quest" asked silly sound-bite questions. I called them that. Then "John Witton" got mad, expressed vaguely similar questions (confusing inheritance with evolution and confusing his grandfather with a mouse).

      Could it be that Quest and Witton are [gasp] the same person?

      Delete
    8. Come on Joe! Show us the best of population genetics. Or how genders evolved at the same time.

      John, this is an old, old error of thought that you raise.

      Maybe the easiest way to begin thinking about this issue correctly is to think about languages. Did two people suddenly have to start speaking French for the French language to evolve from Latin and Frankish? No, there were many changes over historical time that eventually changed the older languages into the modern one, with no necessity for two people, or even one individual, to suddenly start speaking a different tongue than everyone around him or her.

      Same way with the spread of genetic changes through a population. No necessity ever for two individuals at once, or even one individual, to be so full of mutations that they or it couldn't interbreed with the rest. But over time, many changes accumulated, until eventually there were many genetic differences between the ancestral population and the new one, so that if you brought back a member of the ancestral population it would no longer be able to interbreed with the members of the new one.

      Delete
    9. One has to be quick to catch The Witton in action. A mere shadow of his passing remains. Quest, of course - someone entirely different, heh heh ...

      Delete
    10. So John Witton is Quest? That is interesting. Here is a quote where Witton makes fun of Quest (himself?):


      "John WittonSaturday, October 26, 2013 1:28:00 PM
      Qest,

      You forgot to ask your favorite part, if "stupidity can be synthesized without a brain".

      In this case you are proving me and everybody in the biz wrong thanks to Mikkel Rumraket Rasmussen, latesuite and others soon to join in buhahahahahaa

      You are gettin old you dumb ass buahahahaha"

      Delete
    11. That's what happens to so-called scientists who have nooooo arguments...They come up with another way of discouraging someone who asks difficult questions...Well... what can I do???

      The night vision in mice is a perfect example....It is obvious that Joe, world leading population geneticist, had known all along that rodents use most of the nuclear genome for night vision; their genome is turned into a very sophisticated optical device.... And yet, he had claimed not only on this blog many times that most of mammals', like rodents, genomes is junk...Why would he do that?

      Then he accused me of being Witton and Witton being me....

      Well, What's next Joe? Who else has been asking difficult questions here? Oh....Louise...Isn't he/she Witton? How about AndyW? Doesn't he sound a bit like ...hmmmmm...Who got banned not that long ago? What was his name? Dominick....

      What a pity....World's leading scientists can't deal with an uneducated, stupid and mentally ill creationists with their only and the best weapon-science....Bravo Joe and the rest!!!

      BTW: Louise,

      You were right... The origins of life blog was the the tipping point....They are trying to get back at us for it...Now, they have one more reason to do so---humble mouse night vision....

      Delete
    12. Witton can't even spell my name properly you morons..

      Delete
    13. You sound bitter, whoever you are. Mice use most of the nuclear genome for night vision? All other cells must maintain it so that eyes can be improved by it? What of non-nocturnal animals, or plants for that matter? Why do they have junk? Is it a different explanation in every organism?

      It is not necessarily the case that the junk is there because it aids night vision. An alternative explanation is that ancestors of mice had junk for other reasons, which has come to fulfil an optical function in those specific tissues in those specific organisms.

      Delete
    14. It is also worth considering the possibility that the organisms might see better yet if they could dispense with the junk altogether, but this is not a simple task. The 'normal' arrangement of hetero- and euchromatin is preserved throughout the rest of the mouse, and across multicellular and unicellular eukaryotes, suggesting that it is advantageous in most cells. But the inverted arrangement in nocturnal organism rod cells may be a question of making the best of a constraint - the least-bad arrangement of a junky genome for nocturnal vision. Given that you have to make eyes out of cells and all that they contain, inverting the arrangement has the minimal negative impact on light gathering caused by excess DNA. I'd be interested to know if the correlation holds equally in bats, which have less junk anyway (as do birds, which have not evolved the rod-cell rearrangement).

      Delete
    15. Quest, I will accept your declaration that you aren't Witton. I asked whether it could be, since he answered on your behalf. I'm sure everyone is relieved.

      So ... mice use most of their nuclear genome for night vision? Reference, please. And what about their relatives. Is it only mice? Seeing well at night is important to lots of small nocturnal mammals.

      Delete
    16. Joe - this is perhaps Quest's source. http://www.sciencedaily.com/releases/2009/04/090416125159.htm The 'normal' arrangement of the genome re: distributions of hetero- and euchromatin is inverted in the rod cells of several nocturnal mammals. A casual reader might see that as a function for junk.

      Delete
    17. If you clean out your garden shed and make a bonfire of the junk, it acquires a function by being co-opted as fuel ;)

      Delete
    18. Allan: Thanks. Reading that ScienceDaily report I see that it is about the distribution of heterochromatin versus coding sequences physically in the cell nucleus. Heterochromatin, as you note, is DNA with highly repeated sequences, usually argued to be "junk DNA", Nothing in the report suggests that the sequences of heterochromatin are constrained by natural selection (or even that the sequences of euchromatin are so constrained, for that matter). So there's nothing there that validates Quest's statements, which remain silly sound bites. In this case perhaps based on a misreading of the Science Daily report. I suppose that is an excuse.

      Delete
    19. Even a 'bulk function' explanation needs further support. Redistributing one's genome optimally for optical cells does not make a 'function' out of the bulk of that genome. It exists, and has to be arranged somehow! One would need to compare the optical properties of small-genome nuclei, for starters. They may (for all we know) be superior to either arrangement.

      Delete
    20. Joe,

      Here is the link to the original article in pdf:

      http://ac.els-cdn.com/S0092867409001378/1-s2.0-S0092867409001378-main.pdf?_tid=0a728180-4566-11e3-b0b4-00000aacb360&acdnat=1383579211_244d8a5f21e1ffa68368118780e8274f

      Also, a link to the summary:

      http://www.cell.com/abstract/S0092-8674(09)00137-8

      I'm not sure if full text in pdf is going to open for everyone though, as I have subscriptions to pretty much everything in full text that opens up automatically...



      Delete
    21. Another link to full-text:

      http://www.sciencedirect.com/science/article/pii/S0092867409001378

      Delete
    22. Or you could just point them directly to where you got this nonsense from. It's an article by no less than Richard Sternberg, committing the major fallacies that have been thoroughly debunked here on this blog (i.e. non-coding DNA is equivalent to Junk DNA). For those interested:

      Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye

      Delete
    23. The paper is in Pubmed central,

      "Nuclei with the inverted pattern also have a smaller size than nuclei with the conventional pattern (Figure 5F). This correlation did not depend on genome size (Figure S7), which is rather constant in mammals (Gregory et al., 2007)."

      I think that basically kills any supposed association to junk DNA.

      Delete
    24. I'm not sure what TheOtherJim is saying. Anyway, the full link provided by Quest says what I had inferred from the ScienceDaily article, It talks about how the heterochromatin is arranged in nuclei, not about any assertion that the base sequence of the heterochromatin is constrained substantially.

      So no argument there that heterochromatin is constrained in sequence, that it cannot be mostly "junk:".

      Thanks, ShadiZI, for the Sternberg link. I suspect Quest got this there.

      Delete
    25. I'm not sure what TheOtherJim is saying.

      Quest et all are arguing that this paper demonstrates the reason for the excess, non-functional DNA (aka junk DNA) in the genome of mice is there to support night vision. The only mention of anything relating to DNA content is in the quotes I provided above No junk correlations (or even the mentioning of it) at all in the paper. This connection is purely being made up by the creationists.

      Delete
    26. edit,

      "Quest et all" to "Quest et al."

      Delete
    27. I don't know much about junk dna. I don't care about it too much either. However, If Quest and Sternberg claim that mice have no junk DNA, because their entire nuclear genome is used to capture photons, why would the study published by Cell even mention junk dna? Were you looking for the actual statement "no junk dna"?

      Delete
    28. LouiseG, the study did not claim that the particular sequences in the heterochromatin were constrained by the need to use them to capture light. Thus they could change wildly. That constraint was what was not found in the Cell study and that was needed for Sternberg and Quest to be right. It was not just an absence of mention of "junk DNA". Besides, if their study had ruled out that most of the genome was junk DNA, the authors would almost certainly have mentioned that. Sequences that are not conserved by natural selection are effectively junk.

      Delete
    29. I have said it before and I will say it again: I don't know much about junk DNA. I don't see it to be a problem for both evolution and creationism. I'm however surprised after reading on the subject a bit, that few scientist on blogs like this seem to disagree with the findings of ENCODE about junk DNA in comparison to many scientific magazines that seem to support more and more the ENCODE.

      I have found a video that may interest you and others which seem to show Sternberg's refutation of endogenous retrovirus and junk DNA.

      http://www.metacafe.com/watch/4094119/refutation_of_endogenous_retrovirus_richard_sternberg_phd/

      I don't know if it is Sternberg speaking and how valuable it is though.

      Delete
    30. Nobody commented on the video? Is it bad or too good? :) Just asking

      Delete
    31. That's Richard Sternberg speaking. Everything he says in that talk has been refuted numerous times on this blog and on many other blogs ... not to mention the scientific literature. The irony is that he recommends entering "junk DNA" into a PubMed search engine to prove that scientists are finding lots of function in the genome. But you'll also find several important papers by prominent scientists showing the exact opposite.

      Delete
    32. Thanks Larry. Was there a particular theme (s) on this blog that talked about those issue Sternberg has been talking about? Links would be much appreciated.I just wanna learn more about the issues.

      Delete
    33. LouiseG says,

      I just wanna learn more about the issues.

      No, you don't, otherwise you would never have posted a link to a talk by a well-known intelligent design creationist.

      But, on the off chance that I'm wrong, read my posts at Genomes & Junk DNA especially the ones on The Myth of Junk DNA.

      When you're done with that, you should read these papers ...

      Eddy, S. R. (2012). The C-value paradox, junk DNA and ENCODE. Current Biology 22, R898. [PDF]

      Niu, D.-K. & Jiang, L. (2012). Can ENCODE tell us how much junk DNA we carry in our genome? Biochemical and biophysical research communications 430, 1340-1343. [doi: 10.1016/j.bbrc.2012.12.074]

      Doolittle, W. F. (2013). Is junk DNA bunk? A critique of ENCODE. Proceedings of the National Academy of Sciences 110, 5294-5300.
      [doi: 10.1073/pnas.1221376110]

      Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A. & Elhaik, E. (2013). On the immortality of television sets:“function” in the human genome according to the evolution-free gospel of ENCODE. Genome biology and evolution 5, 578-590. [10.1093/gbe/evt028]

      After you've done your homework, I expect you will never again have to ask a naive question about junk DNA or pretend you don't understand the issue. Good luck.

      Delete
    34. Nobody commented on the video?

      Yje only think that can be added to Larry's exhaustive reply is that the whole thing is hardly a video at all. It's one long still shot -- an illustration taken from someone else and slightly reedited (see here, Fig. 10.5). What's the matter with those added "X-ray breaks", anyway?

      Delete
    35. The only thing... (that's what comes of typing in the dark).

      Delete
    36. Larry, Now you got me really interested in the subject, so I began to read your blog on the issue on junk DNA. Guess what? For an unknown reason, you seem to have forgotten to give me a link to this discussion here:

      http://sandwalk.blogspot.ca/2013/07/how-not-to-do-science.html

      I guess Mart was not a good blogger?

      I would like to make an observation Larry about you comments about mine:

      "LouiseG says,

      I just wanna learn more about the issues.

      No, you don't, otherwise you would never have posted a link to a talk by a well-known intelligent design creationist."

      This was a genuine statement on my part, which I had stated on this blog many times: "I don't know much about junk DNA" and its true that I said I didn't care about it in the CONTEXT of not being a problem for both creationism and evolution. You obviously took it in a wrong way and I think I know why.

      Now, I gather that it would be next to impossible to step on you toe by disagreeing with you on a subject-especially junk DNA-and finish the course you are teaching. Some of your students apparently read your blog, so I can see their heads nodding in agreement with me. I don't know why you are like that especially when it comes to junk DNA, but I guess your professional reputation is running on it. Or maybe your father never hugged you and now you call everyone who disagrees with you and idiot.

      I don't know, if you remember that but you yourself have said it on this blog that you wouldn't have a problem, if 100% of our genome would turn out to be functional, do you? Since puffer fish and other organisms don't have any junk DNA, isn't it likely that our genome will also turn out to be fully functional? Our brain has been called the most complex thing in the universe and no human on earth really knows how it functions. Is it possible that human beings who have such a complex brain would also have a very complex genome which functions are beyond what scientists can test and understand for now?


      Delete
    37. Wow!!! Larry!!!

      Thank you very much for the link that totally opened my eyes!!! I thought it was going to take me year or more to figure it out and here it is in the first paragraph of the paper you provided me the link to. It is nicely laid out:

      "The C-value paradox is related to another puzzling observation, called “mutational load”: the human genome seems too large, given the observed human mutation rate. If the entire human genome were functional (in the sense of being under selective pressure), we would have too many deleterious mutations per generation. By 1970, rough calculations had suggested to several authors that maybe only 1-20% of the human genome could be genic, with the rest evolving neutrally or nearly so."

      So, simply put, human genome (without junk DNA) is just too large in comparison to the observed human mutation rate. So without junk DNA we would have too many deleterious mutations per generation and kaputt.

      So, simply put, neo-Darwinian evolution needs junk DNA or it is kaputt.

      So, here is where the bodies are buried lol.

      Well Larry, at least you can't blame this on creationists. You gave me the link yourself, intentionally or not. lol

      Delete
    38. So, simply put, neo-Darwinian evolution needs junk DNA or it is kaputt.

      You misunderstand the C-value paradox (like everything else). There are genomes with far less junk than we have, and there are genomes with hardly any junk at all. It just so happens that the human genome is way too big to be one of them. If it were lightweight, mutational load would be less of a problem.

      I will spare you comments on your use of "neo-Darwinian". Every creationist is incorrigible in this respect, so why bother.

      Delete
    39. So, simply put, neo-Darwinian evolution needs junk DNA or it is kaputt.
      No, stupid. Physiology needs junk-DNA. As in, if we had so many deleterious mutations, we simply couldn't be alive. This in itself is evidence that the majority of the genome is junk.

      Evolution could be false and the above statement would still be true. You really are completely clueless.

      Delete
    40. Louise wants us to believe Larry has given her evidence with which she can disprove... evolution, that is, if there's no Junk DNA, there's no evolution:

      So without junk DNA we would have too many deleterious mutations per generation and kaputt.

      So, simply put, neo-Darwinian evolution needs junk DNA or it is kaputt [sic].


      No Louise, You do not understand the magnitude of the mutational load problem. All biology needs junk DNA or it is kaput. Even creationist biology, yes even Intelligent Design, needs junk DNA or it is kaput-- but the authorities of ID are not smart enough to figure that out!

      CREATIONISTS and Intelligent Design proponents themselves have stated clearly that every and all mutations are CATASTROPHIC. Remember that? "Catastrophic."

      Every human baby born has somewhere between 100 to 200 more mutations than its parents (depending on how you count)-- and twice that number relative to its grandparents-- and thrice that relative to its great-grandparents-- etc.

      Young Earth Creationist Kent Hovind: “A change of only three [DNA] nucleotides is fatal to an animal. There is no possibility of [genetic] change.” [Ken Hovind, Source: http://media.drdino.com/sem/audio/mp3/books2.mp3 @ 82:10, March 2003, cited at http://kent-hovind.com/quotes/sciencei.htm]

      Got that? Kent Hovind says only three mutations will kill an animal.

      If creationism is correct, every baby has 100 to 200 new CATASTROPHES its parents didn't have-- and twice that number of CATASTROPHES relative to its grandparents-- and thrice that relative to its great-grandparents-- etc. Enough to kill every baby on Earth a hundred times over.

      Pro-ID Philosopher William Dembski: “[T]here is now mounting evidence of biological systems for which any slight modification does not merely destroy the system’s existing function but also destroys the possibility of any function of the system whatsoever.” [Dembski, The Design Revolution, p. 113]

      Pro-ID lawyer Phillip Johnson: “Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations…make birth defects” ["Berkeley's Radical: An Interview with Phillip E. Johnson", November 2000.]

      Pro-ID lawyer Edward Sisson: “[T]he theory of unintelligent evolution, which depends entirely on the supposed occurrence in history of trillions of DNA mutations that beneficially affect body shape, has not identified any such mutations” -- [Edward Sisson, “Darwin or Lose”, Touchstone, v. 17, issue 6, July/Aug. 2004]

      Uncommon Descent: “As far as I know, the current consensus of population geneticists is that mutations do indeed have disastrously bad fitness.” [Eric Holloway. Uncommon Descent. August 28, 2011.]

      Young Earth Creationist Henry Morris: “Inheritable and novel changes (mutations) which take place in organisms today have always been observed to be harmful.” [Henry Morris, The Remarkable Birth of Planet Earth, p.vii]

      Young Earth Creationist Duane Gish: “the mutations we see occurring spontaneously in nature or that can be induced in the laboratory always prove to be harmful.” [Gish, Evolution? The Fossils Say No, p. 47]

      Duane Gish: “all mutations are bad” [Gish, Dinosaurs by Design (1992), p.83]

      Duane Gish: “Remember, all the changes were just mistakes, they were genetic errors, mutations, almost everything which is bad… they're all bad” [Keith Saladin-Duan Gish Debate II, 1988]

      Delete
    41. Continuing with IDiots saying that all mutations are always catastrophic:

      Creationist Don Boys: “Not only are mutations always harmful, but they produce changes in present characters, never producing new characters. Mutations are the catalyst for defects, deformity, disease, and death; yet evolutionists scream that they are the explanation for all the varieties we see… [T]he results of all mutations: disorder, defects, disease, deformity, and death.” -- ["Almost a Thousand Major Scientists Dissent from Darwin!", Don Boys. Canada Free Press. May 2, 2010.]

      Muslim Creationist Harun Yahya: “[N]ot one single useful mutation has ever been observed… The slightest alteration in [genetic] information only leads to harm.

      The Muslim creationist sex-cult of Harun Yahya says all mutations cause only harm: “Mutations… like all accidents, they cause harm and destruction. The changes effected by mutations can only be like those experienced by people at Hiroshima, Nagasaki, Chernobyl … freaks of nature… because all efficient(?) observable mutations cause only harm to living things.”

      So there are only two possibilities:

      1. Most human DNA (~90%) is junk DNA-- which is defined as sequence which cannot suffer a deleterious mutation; or

      2. Humans have no Junk-- but then creationists have been lying to us about any, all and every mutation being "catastrophic."

      So which is it, Louise?

      Delete
    42. LuoiseG says,

      Now, I gather that it would be next to impossible to step on you toe by disagreeing with you on a subject-especially junk DNA-and finish the course you are teaching. Some of your students apparently read your blog, so I can see their heads nodding in agreement with me. I don't know why you are like that especially when it comes to junk DNA, but I guess your professional reputation is running on it. Or maybe your father never hugged you and now you call everyone who disagrees with you and idiot.

      My father died in a plane crash when I was four months old so, yes, he didn't hug me very much.

      I don't put up with people insulting me personally or referring to my family. This is your first warning. If you continue you will be banned.

      Delete
    43. LouiseG says,

      Wow!!! Larry!!!

      Thank you very much for the link that totally opened my eyes!!! I thought it was going to take me year or more to figure it out and here it is in the first paragraph of the paper you provided me the link to. It is nicely laid out:


      I can see that you're not really interested in learning because your mind is already made up.

      I'm sorry I bothered. I just wanted to give you the benefit of the doubt even though I was almost certain that you were lying.

      Delete
    44. Larry wrote: "My father died in a plane crash when I was four months old so, yes, he didn't hug me very much."

      I didn't know that but I suspected it. I'm sorry. I didn't mean to offend you. This definitely explains a lot of things. Please except my apologies.

      Delete
    45. I didn't know that but I suspected it. I'm sorry. I didn't mean to offend you. This definitely explains a lot of things.

      As far as I'm concerned that's strike two. It is extremely offensive. One more time and you are banned forever.

      Delete
    46. LouiseG,

      You need to educate yourself asap...

      "Why Evolutionists Need Junk DNA - December 2009
      Excerpt: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function, but it is something that is required by evolutionary theory. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane's work. Without junk DNA, evolutionary theory cannot currently explain how everything works mathematically. Think about it; in the evolutionary model there have only been 3-6 million years since humans and chimps diverged. With average human generation times of 20-30 years, this gives them only 100,000 to 300,000 generations to fix the millions of mutations that separate humans and chimps. This includes at least 35 million single letter differences, over 90 million base pairs of non-shared DNA, nearly 700 extra genes in humans (about 6% not shared with chimpanzees), and tens of thousands of chromosomal rearrangements. Also, the chimp genome is about 13% larger than that of humans, but mostly due to the heterochromatin that caps the chromosome telomeres. All this has to happen in a very short amount of evolutionary time. They don't have enough time, even after discounting the functionality of over 95% of the genome--but their position becomes grave if junk DNA turns out to be functional. Every new function found for junk DNA makes the evolutionists' case that much more difficult.
      Robert W. Carter"

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    47. LouiseG,

      Haldane's Dilemma

      Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift - creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors - it surely would have killed us. Since Haldane's dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation - but has obtained identical results.
      John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 159-160

      Kimura's Quandary
      Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most 'evolution' must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom's (neo-Darwinism's) very validity.
      John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 161 - 162

      A graph featuring 'Kimura's Distribution' being ‘properly used’ is shown in the following video:

      Evolution Vs Genetic Entropy - Andy McIntosh - video
      http://www.metacafe.com/watch/4028086

      At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno's work in the late 1950’s, 60’s through the early 70’s

      Delete
    48. Watch this video as well. It gives you an idea what a mind boggling complexity is found in a cell and what scientists had to do just to follow few pathways of what is going on in there... They used 128 computers simultaneously...

      http://www.metacafe.com/w/8905583

      Enjoy!

      Delete
    49. Larry wrote,

      "That's Richard Sternberg speaking. Everything he says in that talk has been refuted numerous times on this blog and on many other blogs ... not to mention the scientific literature."

      LouiseG, Don't buy it! They also say they refuted the origins of life arguments you also presented. They have to say it. They are defending not only an ideology but also their livelihood. Evolution "science" is like any other business. You have to protect it or you are out on the street. Do you think they don't know what would happen, if one day governments decided not to fund this "science"...

      Delete
    50. So, Quest, in that screed you quote from Robert W. Carter (whoever he is), how is Junk DNA supposed to solve the "problem" he imagines exists? Whether or not a sequence is functional, if it varies between two organisms then that still represents a change that had to occur since the common ancestor they both share. Whether the sequence is a coding gene or non-functional junk makes no difference.

      Thanks for again demonstrating that the problem that creationists suffer is no so much the result of ignorance. It is that they simply do not know how to think.

      Read this previous post from Larry to understand why the "problem" Carter describes is not actually a problem:

      http://sandwalk.blogspot.ca/2012/01/whats-difference-between-human-and.html

      Delete
    51. LouiseG doesn't need lessons from you on how to misunderstand science, Quest. She's already as expert at that as you are.

      What she seems to need are lessons in common courtesy and simple human decency.

      Delete
    52. lutesuite,

      Did you really expect Larry to write that there is a problem in any pieces of ET? Well, he had a couple of slips here and there but you closed you eyed and hoped for the the best, right?

      Larry may not know that, but I respect him for one quality: when he sees something to be terribly wrong he may more a less admit it under certain circumstances. I had been reading Larry's blog starting in 2007 and he had a lot of slips.... Good ones....He is not stupid... that's all I can say and possibly not get in trouble as LouiseG did....

      Delete
    53. lutesuite,

      You are probably familiar with at least the basics of quantum mechanics; i.e. quantum entanglement and the theory of general relativity? Right?

      Delete
    54. LousieG is apparently only 24 years old and a very good prospect to became a psychologist/psychiatrist/scientist.... I also hear that she is more than just a woman... She is a superwoman... unless....

      Delete
    55. @ Quest. That is one part. You seem to be ignoring the part about much of the eukaryotic genome being observably the result of old, broken genetic parasites.

      Seems like you failed to understand this hint.

      Next reading assignment - why does random-integration BAC trans-genesis work so well in mice, but not in organisms with smaller genomes? If all was functional, inserting a huge piece of DNA in the middle should have a disruptive effect.

      And why does most of like (prokaryotes) seem to not have any junk DNA?

      Delete
    56. Hi, Quest!

      I couldn't help noticing that you addressed a couple posts to me just above. That would usually indicate that you were responding to what I had written. However, your messages had no conceivable logical connection to my post, or to anything else for that matter. Perhaps you were thinking of something else?

      My post did have a question. Perhaps you could try answering it. To remind you:

      (I)n that screed you quote from Robert W. Carter (whoever he is), how is Junk DNA supposed to solve the "problem" he imagines exists?.

      You might also indicate what errors you found in that link from Larry that I posted, where he demonstrates that the available time is easily adequate to allow the genetic differences between humans and chimps to have arisen thru drift alone.

      Delete
    57. lutesuite,

      You wrote: "You might also indicate what errors you found in that link from Larry that I posted, where he demonstrates that the available time is easily adequate to allow the genetic differences between humans and chimps to have arisen thru drift alone."

      If we aske Jerry Coyne, he would say natural selection did it. I have had this conversation with Larry few months ago...

      Since then new research has come out:

      Primate Transcript and Protein Expression Levels Evolve under Compensatory Selection Pressures
      ABSTRACT
      Changes in gene regulation have likely played an important role in the evolution of primates. Differences in mRNA expression levels across primates have often been documented, however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines (LCLs) and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.

      http://www.sciencemag.org/content/early/2013/10/16/science.1242379


      Gene Regulation Differences Between Humans, Chimpanzees Very Complex

      "Some of these patterns of mRNA regulation have previously been thought of as evidence of natural selection for important genes in humans, but this can no longer be assumed," Gilad said.
      The study raises questions over why mRNA expression levels differ between species if they do not necessarily cause protein differences. Although further study is needed, Gilad believes this study suggests that protein expression levels evolve under greater evolutionary constraint than mRNA levels, via a yet-uncharacterized compensation or buffering mechanism.
      For now, research that uses mRNA expression levels as a measure of the functional importance of a gene requires reassessment, and not just in studies on evolution."

      http://www.sciencedaily.com/releases/2013/10/131017144632.htm

      Delete
    58. lutesuite,

      Another article that "totally agrees" with you and Larry as well as with all the believers of junk DNA fiasco like Dan Growler lol

      'Junk DNA' Defines Differences Between Humans and Chimps

      Oct. 25, 2011 — For years, scientists believed the vast phenotypic differences between humans and chimpanzees would be easily explained -- the two species must have significantly different genetic makeups. However, when their genomes were later sequenced, researchers were surprised to learn that the DNA sequences of human and chimpanzee genes are nearly identical. What then is responsible for the many morphological and behavioral differences between the two species?

      Researchers at the Georgia Institute of Technology have now determined that the insertion and deletion of large pieces of DNA near genes are highly variable between humans and chimpanzees and may account for major differences between the two species.

      The research team lead by Georgia Tech Professor of Biology John McDonald has verified that while the DNA sequence of genes between humans and chimpanzees is nearly identical, there are large genomic "gaps" in areas adjacent to genes that can affect the extent to which genes are "turned on" and "turned off." The research shows that these genomic "gaps" between the two species are predominantly due to the insertion or deletion (INDEL) of viral-like sequences called retrotransposons that are known to comprise about half of the genomes of both species. The findings are reported in the most recent issue of the online, open-access journal Mobile DNA.

      "These genetic gaps have primarily been caused by the activity of retroviral-like transposable element sequences," said McDonald. "Transposable elements were once considered 'junk DNA' with little or no function. Now it appears that they may be one of the major reasons why we are so different from chimpanzees."

      McDonald's research team, composed of graduate students Nalini Polavarapu, Gaurav Arora and Vinay Mittal, examined the genomic gaps in both species and determined that they are significantly correlated with differences in gene expression reported previously by researchers at the Max Plank Institute for Evolutionary Anthropology in Germany.

      "Our findings are generally consistent with the notion that the morphological and behavioral differences between humans and chimpanzees are predominately due to differences in the regulation of genes rather than to differences in the sequence of the genes themselves," said McDonald.

      The current analysis of the genetic differences between humans and chimpanzees was motivated by the group's previously published findings (2009) that the higher propensity for cancer in humans vs. chimpanzees may have been a by-product of selection for increased brain size in humans.

      http://www.sciencedaily.com/releases/2011/10/111025122615.htm

      LouiseG,

      Watch this one carefully.

      Science Daily and the scientists from whatever institute are going to be either wrong or called creationists....lol

      Delete
    59. Y'see, Quest, it works like this: If you write a post that is an attempt to answer one of my questions, it's very helpful if it has something at least vaguely to do with my question. I mean, actually answering the question would be great, but baby steps first.

      Maybe you can explain why you think those papers present even the slighest problem for evolutionary theory in general, or the existence of Junk DNA in particular. Oh, dear. I just asked another question that is destined to be ignorerd.

      Delete
  5. She doesn't know art, either. No artist that I've ever known or heard of ever considers any of their work to be perfect. It's always in a state of "have to let it go at that".

    ReplyDelete
  6. If you're going to make arguments by analogies, it usually helps if the two phenomena are actually analogous.

    *galactic facepalm*

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    Replies
    1. Like the one below, which I think is one of your better ones?

      "Any particular tornado at any given moment is a unique event that will never be repeated in the lifetime of the universe and it's really simple to see why this is. No two areas are exactly alike, the winds blowing across them will therefore never be exactly alike, the debris they pick up will never be exactly alike, and so on and so forth. There will always be minor differences.

      And yet tornadoes happen frequently, and it's just physics.

      Why should DNA be any different? We've already established that improbability is not a barrier to the creative power of physics."

      Delete
    2. You never had even a cursory interaction with statistical mechanics did you?

      Delete
    3. So you think you can make macroscopic predictions from the microscopic properties of a tornado? I think were you need to start is to try to grasp the difference between complexity and specific complexity.

      Delete
    4. So you think you can make macroscopic predictions from the microscopic properties of a tornado?

      Yes. Welcome to the world of weather modelling and prediction.

      As the resolution of the modelling grid and the associated observational data (wind velocity, humidity, temperature etc.) increases, the more accurate the model becomes, limited by the chaotic nature of the model itself and space and time constraints of the modelling and observation hardware.

      Current models use the physics of fluid dynamics and attempt to solve the system numerically using partial differential equations as an analytic solution is not possible.

      I would think that with sufficient historical data it would be possible to deduce the underlying physical system using a neural network.

      For example, with time series data of sufficient resolution and duration one should be able to accurately model a tornado without making any assumptions about the underlying physical model, namely one could deduce the macroscopic properties from the microscopic data.

      And this is not what I think is possible, this is what is actually being done.

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    5. So you think you can make macroscopic predictions from the microscopic properties of a tornado?
      Sure, but that's not my point. My point is that any particular microstate of a tornado is incredibly improbable, and even further, of all the possible microstates a system can take, the subset of them that correspond to "tornadoes" are an infinitesimal fraction. Yet tornadoes are routinely made and sustained by the laws of physics. So I was right, mere improbability is no barrier to the creative powers of physics.

      Why do you think DNA would be any different from any other historically and physically contingent, improbable matter microstate?

      Delete
    6. Steve, how does what you write even remotely have anything to do with statistical mechanics that Rumraket was proposing for analyzing tornados?

      Rumraket, your argument is like saying that flipping a coin a hundred times and getting any string of "heads and tails" is as likely/unlikely as to do it over again and repeat the exact same string.

      Delete
    7. Rumraket, a tornado does not need to be very specific to be functional. You say yourself that no two tornados are alike and clearly they do not need to be. Genes that code for protein on the other hand need to be specific. You cannot shuffle around the base pairs any given way and still get a functional protein fold. You could say that a tornado is complex, but it's not specified complexity as in the case of the gene.
      Furthermore, the physics of tornados is well known and generally understood while very few would claim that the arrangement of the DNA nucleotides follow any physical law.

      Delete
    8. Rumraket, your argument is like saying that flipping a coin a hundred times and getting any string of "heads and tails" is as likely/unlikely as to do it over again and repeat the exact same string.
      How?

      Rumraket, a tornado does not need to be very specific to be functional.
      Sure it does. Just as specific as DNA. How many possible, different functional DNA strings can you think of? We have people coming to this blog to tell us that some DNA can have function independent of sequence, as in it's mere presence. That's what many IDcreationists argue when they claim the many known junk regions are functional.

      You cannot shuffle around the base pairs any given way and still get a functional protein fold.
      Now we're talking proteins suddenly? Regardless, functional proteins have indeed been found in randomly shuffled pools. The Szostak lab and others have proved as much in the late nineties and early 2000's.
      Take a look here and scroll down to the time period I mentioned.

      You could say that a tornado is complex, but it's not specified complexity as in the case of the gene.
      Sure it is. It is only an unfathomably miniscule subset of all possible matter microstates that make functional tornadoes.
      It is both specified(only a specific small subset of all microstates correspond to "tornado"), functional(can pick things up and transport them great distances, dissipates atmospheric heat) AND complex(many interacting parts that correspond to a pattern).

      Delete
    9. Rumraket, I give up, it is obvious that no communication is taking place.

      Delete
    10. I answered all your claims and questions, do what you feel you must.

      Delete
    11. Rumraket, a tornado does not need to be very specific to be functional.

      I think that one could come up with some pretty specific criteria for a tornado to be said to exist, or, alternatively, for how it arises. I'm not saying that it is "specified complexity," actually, as I agree that it does not fit the term, I'm just saying that "specified complexity" can be viewed as a special (in our eyes, anyway) case of "natural phenomena," and that we shouldn't give the IDiots any chance to claim that "specified complexity" is some absolute category.

      You say yourself that no two tornados are alike and clearly they do not need to be. Genes that code for protein on the other hand need to be specific.

      True, and that is important, but it seems likely that they're far more specific now than they were, and that probably there was a time when genes coded something sort of "intermediate" between today's fairly rigid amino acid sequences and the quite a lot more free forms of weather phenomena.

      You cannot shuffle around the base pairs any given way and still get a functional protein fold. You could say that a tornado is complex, but it's not specified complexity as in the case of the gene.

      No, it's just that "specified complexity" needn't be considered to be categorically different from other phenomena (not that you do, the IDiots do), reproducing genes (or at least the information in them) exist far longer than do transient phenomena, so become far more specific.

      Furthermore, the physics of tornados is well known and generally understood while very few would claim that the arrangement of the DNA nucleotides follow any physical law.

      This is the major reason why I'm responding at all, because the physics of DNA chemistry and the physics of evolutionary change are in fact fairly well understood. I know what you're saying, it's just that it's important that it's still just physics (tornados and DNA both have contingent factors), even though we have gotten to something we may call "specified complexity" that doesn't exist as we mean that term on Mars, save in the machines we sent there. It's a special case (in our eyes, at least) of physics, but we have to keep bringing up the fact that it's still just physics in the end.

      "Specified complexity" is only known to result from evolutionary processes and intelligent processes, it's just that evolution manages to preserve information, yet allows it to change, for billions of years. Specification = preservation, that's about it for evolution. Maybe not so much with intelligence (preservation of knowledge is important for complex thought, however), but biologic intelligence is a product of evolution, not, as some IDiots claim, vice versa. Systems developed that preserved functional information, and that's all that it really took for "specified complexity" to exist, evolve, and eventually produce intelligence.

      So it's different from a tornado, all right, but it's just different because functional information was conserved, if not too rigidly, by cells. Any system that conserved and reproduced information like life would, which is why I'd rather bring up (non-strict, non-IDiot, of course) conservation of information in these discussions. Specification suggests a specifier, and only in the broad sense (which includes genomes) is this a reality in evolution. Conserved but evolving information is all that "specified complexity" is on earth up to, roughly, the Cambrian, and it is like a tornado in terms of contingency plus "laws" interacting, while being unlike a tornado in terms of preservation of information of what worked in the past. Imperfect conservation of information makes a huge difference, but it's still just contingency plus law in either case, as we'd expect in nature.

      Glen Davidson

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    12. try to grasp the difference between complexity and specific complexity.

      It's so cute when creationists who have no understanding of terms like "complexity" and "information" bandy them around as if they understood them.

      Delete
    13. Andy Wilberforce I give up,

      This is, I suspect, like pretty much every other assertion you've made on this blog, a lie.

      Delete
    14. So, big Jeff, why don't you take a shot at "debunking the pseudoscience and pseudomathematics" of what I wrote above and explain just why Rumraket is right in his claims?

      Delete
    15. Because I did so myself, and your response was to "give up" with some lame excuse following it.

      Delete
    16. Andy, this video explains the concept you are failing to understand:

      http://www.youtube.com/watch?v=SxxolSyWd6Y

      Of course, this will make no difference to you. "Understanding" is the last thing a creationist wants to achieve. A creationist just wants to believe, and understanding is antithetical to his beliefs. But just watch the video, anyway, 'kay?

      Delete
    17. The funny thing about tornadoes is that they're thermodynamic phenomena that emerge when hot and cold air meet and form a temperature and pressure gradient.

      Ironically, the origin of life is suspected not to be too different from thermodynamic perspectives. Where there's a natural gradient, the 2nd law of thermodynamics can give rise to complex phenomena. That's why things like hydrothermal vents feature so often in origin of life scenarios.

      Delete
    18. "Specified complexity" would be better called "conserved information,"--nothing to do with IDiots' conservation of information, of course. Conserved information of what has worked in the past is what makes the difference between tornadoes and life, both of which incorporate contingency and the regularities of physics.

      Glen Davidson

      PS, this is mostly a test to see what happens, since a much longer comment of mine posted, then disappeared. Not that I don't endorse what's written, it's just that it's short because I want to know if I can comment. If not, I'll just go.

      Delete
    19. Rumraket has now outdone himself by saying: "Where there's a natural gradient, the 2nd law of thermodynamics can give rise to complex phenomena." That statement is wrong at so many levels that I hardly know where to begin. The second law of thermodynamics states that the entropy of an isolated system never decreases, because isolated systems spontaneously evolve toward thermodynamic equilibrium—the state of maximum entropy. This often expressed as that the natural flow goes from order to disorder. What I guess that you are trying to say is that if you have a decrease of entropy outside a hydrothermal vent, such as the spontaneous creation of life, then that decrease of entropy is offset by the increase of entropy at the source of the hydrothermal vent, i.e. you include the vent in your system. That is like saying that we would not be surprised if tornados would run "backwards", i.e. creating order instead of disorder. Because the Earth is an open system, tornados derive their energy from the sun, and while turning rubble into houses and cars represents a decrease in entropy, the increase in entropy outside the Earth (in the sun) far exceeds this decrease.

      Delete
    20. Lutesuite, I guess you did not notice that the link you posted supports my claim an debunks Rumraket's. Creating a none specific tornado vs a gene corresponding to a functional protein fold is indeed very different. You could compare it to flipping a coin and getting any string of "heads and tails" vs. to do it over again and repeat the exact same string. This is exactly what I have tried to explain to him over and over.

      Delete
    21. I guess I must mention that in other places the video is horribly wrong such as when it claims that evolution had 60 my to turn an Artiodactyla into a Cetacea. Whales is said to be specifically related to the hippopotamus. However, the anthracothere ancestors of hippos do not appear in the fossil record until millions of years after Pakicetus, the first known whale ancestor.

      Delete
    22. Rumraket has now outdone himself by saying: "Where there's a natural gradient, the 2nd law of thermodynamics can give rise to complex phenomena." That statement is wrong at so many levels that I hardly know where to begin.
      No it isn't. It's a demonstrable fact. There has to be a difference in temperature or concentration where one dissipates into the other. That's where you'll find things happening, where complex phenomena emerge. The subject is called non-equilibrium thermodynamics for the same reason, we're talking about a system that's not in equilibrium, where a great difference in pressure or temperature (or the concentration of ions) allows useful work to be done, exactly because heat is dissipating into the cold. That's where you'll find winds moving fast, this is where nature does "work". This dissipation towards equilibrium is the increase in entropy of the system.

      Btw, nice to see you copy-pasting the first sentence of the wikipedia article on the 2nd law of thermodynamics at me without referencing it. That's simply hilarious.

      What I guess that you are trying to say is that if you have a decrease of entropy outside a hydrothermal vent, such as the spontaneous creation of life, then that decrease of entropy is offset by the increase of entropy at the source of the hydrothermal vent, i.e. you include the vent in your system.
      No that's not correct. The heat and ions dissipate out from the vent into the surroundings, slowly tending towards equilibrium. The total average entropy of the system always increases, not just "at the source of the hydrothermal vent". The vent is simply the local path through which heat and dissolved minerals and metals from the interior of the planet can seep out into the surrounding cooler ocean.

      This natural gradient of heat and ions is doing work at the conversion and dissipation of useful energy. It is here it's hypothesized you could find something like life emerging, like the tornado where hot air meets cooler air. Because it is here that nature, just like designers, can do useful work. At a natural gradient where one feeds into the other.

      That is like saying that we would not be surprised if tornados would run "backwards", i.e. creating order instead of disorder.
      Now you're confusing the tornado itself with the effect it has on it's surroundings. The tornado here is analogous to the organisms, the complex emergent phenomena is the tornado, but that tornado is sustained at the conversion of useful energy into less usable forms. The heat of the warm air is dissipating into the surroundings, the tornado is creating a mess. Of course, the same is true for organisms, including human beings. It doesn't matter how much order you think you make, you have to expend energy to do it, which means that "order-creation" of yours still happens at the expense of useful energy. The total entropy of the system, no matter how neatly you stack and organize and design things around you, still increases. You still have to eat stuff, you will convert that energy, you will radiate heat into the surroundings. The harder you work at it, the faster the rate of increase of entropy.

      Delete
    23. Lutesuite, I guess you did not notice that the link you posted supports my claim an debunks Rumraket's. Creating a none specific tornado vs a gene corresponding to a functional protein fold is indeed very different.
      Not really, no. Why are you ignoring the references I gave you? Go to the publications from the Szostak Lab from the nineties, they found so many functional polymers, whether RNA, DNA or proteins, in randomized libraries(as in, the actual sequence was just randomly put together), they found functional polymers already in their first attempts. Both structural and enzymatic functions.

      Selection of Functional RNA and DNA Molecules from Randomized Sequences

      Structurally complex and highly active RNA ligases derived from random RNA sequences

      Isolation of a new ribozymes from a large pool of random sequences

      You'll like this one:
      Chance and Necessity in the Selection of Nucleic Acid Catalysts.

      Functional proteins from a random-sequence library.

      These are from the Szostak lab alone and there are many more. And it's not the only lab to have done similar work. This creationist strawman you've been sold, that functional polymers are small miracles in themselves, is simply a big fat lie. Obervational reality refutes it, you need only open your eyes.

      Delete
    24. Andy Wilberforca: Whales is said to be specifically related to the hippopotamus. However, the anthracothere ancestors of hippos do not appear in the fossil record until millions of years after Pakicetus, the first known whale ancestor.

      So what? If the Whippomorpha hypothesis is correct, then hippos and whales are more closely related to each other than either is to any other extant group of artiodactyls. It doesn't make either of them the ancestor of the other. There's little doubt that the common ancestor of anthracotheres and whales was superficially more similar to an anthracothere than a whale, but that's because anthracotheres are more conservative, not because they are ancestral to whales. The exact relationships among the obscure extinct groups of Eocene artiodactyls (possible whippomorphs or their close cousins) remain to be sorted out. The fossil record of the early whale lineages is pretty good today (though it was non-existent before the 1980s!), but several other groups related to them are still poorly known.

      Delete
    25. Andy, what do you call an animal whose ankle bones have a double-spooled trochlea?

      What are the ankle bones of whales like?

      Have a look at Rodhocetus before you answer.

      Game, set, and match. You will never win with by arguing about whales. When will you learn...

      Delete
    26. Piotr, you say: "So what? If the Whippomorpha hypothesis is correct, then hippos and whales are more closely related to each other than either is to any other extant group of artiodactyls. It doesn't make either of them the ancestor of the other." I have never claimed any such thing. What I wrote was "However, the anthracothere ancestors of hippos do not appear in the fossil record until millions of years after Pakicetus, the first known whale ancestor." You see? Proto-hippo vs proto-whale. Don't you find it at least a little disturbing that even if you try to stretch it, there is very limited time for very major changes to take place? Or do you just see it as a proof of the "creative powers" of evolution is even stronger than expected? The latter is to me a sign of "blind faith".

      Delete
    27. Diogenes, we have had this debate before, remember? Nobody claims that whales are Artiodactyla. What some do claim is that whales and the even-toed both belong to Cetartiodactyla. But no, whales do not have a double-spooled trochlea, nor are they "even toed".

      Delete
    28. 'Nobody claims that whales are Artiodactyla. What some do claim is that whales and the even-toed both belong to Cetartiodactyla. But no, whales do not have a double-spooled trochlea, nor are they "even toed".'

      Wrong again. The "Cetartiodactyla" includes both whales and what is now a paraphyletic assemblage of terrestrial forms called "artiodactyls". But whales are firmly within this grouping, not the sister taxon, so they are indeed "artiodactyls" in the phylogenetic sense. All scientists now actually would claim this. Whales are artiodactyls like humans are primates, even if we don't own up to being monkeys or apes.

      As Diogenes noted, artiodactyls are defined by the double-trochlea astragalus. Many early artiodactyls are not "even-toed", but more derived ones become so when they lose toes and changed their foot posture. Oh, and I have held the original double-trochleared astragalus of Pakicetus in my own hands in Phil Gingerich's office.

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    29. " Oh, and I have held the original double-trochleared astragalus of Pakicetus in my own hands in Phil Gingerich's office." Is he sure that it's from the same animal this time? We all remember the debacle when he had to retract his claim that Rodhocetus had a fluke and flippers...

      Delete
    30. Christine, I know I shouldn't resort to quoting Wikipedia, but it seems more people than me exclude whales from Artiodactyla..."Artiodactyla comes from (Greek: ἄρτιος (ártios), "even", and δάκτυλος (dáktylos), "finger/toe"), so the name "even-toed" is a translation of the description.[1] This group includes pigs, peccaries, hippopotamuses, camels, llamas, chevrotains (mouse deer), deer, giraffes, pronghorn, antelopes, sheep, goats, and cattle. The group excludes whales (Cetacea) even though DNA sequence data indicate that they share a common ancestor, making the group paraphyletic. The phylogenetically accurate group is Cetartiodactyla (from Cetacea + Artiodactyla).[2]"

      Delete
    31. Andy, you lost this point, you were proven wrong by Christine, who is a comparative anatomist, so you're dead in the water. But you change the subject to new lies.

      Rodhocetus had four toes on its hind limbs, and it had hooves, and like Pakicetus, it had a double trochlear astragalus.

      But argue some more, Andy, Christine is a professional in this field. Tell us more about Gingerich.

      Delete
    32. Diogenes, a few years ago a wolf like animal was the undisputed whale ancestor, today it's some even-toed Artiodactyla. If we give it a few more years it will be something else. Phil Gingerich will keep changing his story and will always be right. I will stick to my story, being fully aware that for now it's not the majority view.

      Delete
    33. Don't you find it at least a little disturbing that even if you try to stretch it, there is very limited time for very major changes to take place?

      What has that to do with the fact that known anthracothere fossils are younger than known cetacean ones?

      What time span would you regard as "not very limited"? Judging from the fossil record, it took the proto-whales some 6 million years (about a million generation) to become fully aquatic (under powerful selective pressures), and some 20 million years to evolve into modern-looking whales. I don't find it very disturbing.

      Delete
    34. I will stick to my story, being fully aware that for now it's not the majority view.

      What's your story, pray, sir?

      Delete
    35. Christine, I know I shouldn't resort to quoting Wikipedia, but it seems more people than me exclude whales from Artiodactyla..."Artiodactyla comes from (Greek: ἄρτιος (ártios), "even", and δάκτυλος (dáktylos), "finger/toe"), so the name "even-toed" is a translation of the description.

      Andy, the membership of a taxon in a clade is not established by analysing the etymology of the name of the clade. Names are only labels. We are not perissodactyls despite the fact that we have five digits per limb and so meet the Greek "description". Some of the living perissodactyls, by the way, are partly "even-toed" (tapirs have for toes on their forefeet); quite a few carnivores are vegetarian; and there are marsupials without a pouch.

      Delete
    36. Piotr, you wrote "What time span would you regard as "not very limited"? Judging from the fossil record, it took the proto-whales some 6 million years (about a million generation) to become fully aquatic" Could you tell me which proto-whale that you start with and which one you consider to be fully aquatic to make up the 6 my?

      Delete
    37. Piotr, again your missing the point, Wikipedia writes explicitly that whales are not included in Artiodactyla.

      Delete
    38. Thanks for confirming my prediction in such spectacular fashion, Andy, which, to refresh your memory, was:

      Of course, this will make no difference to you. "Understanding" is the last thing a creationist wants to achieve. A creationist just wants to believe, and understanding is antithetical to his beliefs.

      As we watch yet more facts and evidence fly over your head, we are left to ask one question: Is that because your head is just too low, or is it because you are desperately ducking in order to avoid being struck by the evidence that will leave your belief system a crumbled pile of rubble?

      Delete
    39. Wikipedia is a great source, Andy. Almost like the Bible. If Cetacea originated within Artiodactyla, then either Artiodactyla is a paraphyletic group (and therefore not a valid clade) or it includes Cetacea. If you don't like the idea that cetaceans are placed under the "even-toed" label, you can rename the larger clade as Cetartiodactyla (which I personally find too long, too clumsy and too misleading to be very useful), but then you have to abandon Artiodactyla altogether. The other option is to retain the traditional name and come to terms with the fact that cetaceans are artiodactyls too, just like all birds ARE members of the clade Dinosauria.

      Delete
    40. Andy Wilberforce spews ignorantly:

      Piotr, again your missing the point, Wikipedia writes explicitly that whales are not included in Artiodactyla.

      Right, Andy. Piotr is the one missing the point. LOL!

      Tell me, Andy: How to do you think the fact that whales are more closely related to hippos than to cows affect the estimate of the time required for whales to evolve from their common ancestor with cows?

      Delete
    41. Typo warning.
      I wrote: tapirs have for toes on their forefeet

      Four toes, of course.

      Delete
    42. So Piotr, are you going to tell me how you came to the 6 my for whales to evolve?

      Delete
    43. That's roughly the distance in time between the oldest known seashore proto-whales (Himalayacetus, probably an ambulocetid) and the putative basilosaurid from Antarctica whose disvcovery was announced in 2011. Both are known from teeth and mandibular fragments only, and I'm not sure how reliable the dates are. I haven't seen any publications confirming or rejecting the sensationally early dating and basilosaurid affinities of the Antarctic jaw fragment. If you disqualify uncertain and fragmentary evidence and consider only more complete fossils, the distance gets much longer, of course. And anyway, fossils give you only a lower limit on the age of any group. If Himalayacetus is indeed an ambulocetid, the MRCA of ambulocetids and pakicetids must be still older.

      Delete
    44. Himalayacetus was described as a pakicetid because the dentary has a small mandibular canal and a dentition similar to Pakicetus. That is a wolf-sized animal was a meat eater that sometimes, it is speculated, ate fish. Thewissen et al. 2001 concluded that "pakicetids were terrestrial mammals, no more amphibious than a tapir." According to them, none of the aquatic adaptations found in the oldest obligate aquatic cetaceans, basilosaurids and dorundontids, are present in pakicetids. The tympanic bulla in pakicetid ears is similar to those in all cetaceans, with a relatively thin lateral wall and thickened medial part known as the involucrum. However, in contrast to later cetaceans, the tympanic bone makes contact with the periotic bone which is firmly attached to the skull leaving no space for isolating air sinuses, effectively preventing directional hearing in water.
      To me it seems there is still a lot of evolution needed before we are getting close to a proto-whale...

      Delete
    45. To me it seems there is still a lot of evolution needed before we are getting close to a proto-whale...

      There are enough "transitional" taxa illustrating the stages of the process.

      Delete
    46. Piotr writes: "There are enough "transitional" taxa illustrating the stages of the process."
      Next after Pacicetus, the land dwelling wolf sized animal, comes Ambulocetus natans, it was probably amphibious, and resembled the crocodile in its physical appearance.

      Do you know what connects Ambulocetus to Pacicetus? -Assertion.

      Delete
    47. Andy,

      Would you like to explain the alternative hypothesis to which you would like to compare the standard theory of whale evolution? Science require comparisons of alternatives against the data. The usual story fits pretty well; yours, in order to be preferable, must fit better.

      Delete
    48. To me it seems there is still a lot of evolution needed before we are getting close to a proto-whale...
      Oh look, it's the gaps-in-the-fossil-record-argument. Does it even get any more creationist than this?
      This picture shows the moment when the builders of the bridge over Sydney harbour gave up their project because it had become obvious the ends would never join up.

      Delete
    49. Do you know what connects Ambulocetus to Pacicetus? -Assertion.

      Above, you reject the connection by making an assertion.

      First you have terrestrial animals living close to rivers, capable of wading, diving, and occasionally catching fish, then semiaquatic ones specialised in catching fish on the sea coast, then excellent swimmers similar to seals in their life styles, spending less and less time on beaches, then fully aquatic marine animals. Lots of parallel adaptations, visible in the fossil material accompany these shifts. Darren Naish lays it out nicely for lay folks here with suggestion for further reading:

      http://darrennaish.files.wordpress.com/2013/01/naish-2004-geology-today-archaeocetes.pdf

      But if you prefer to ignore the evidence (paleontological as well as genetic) for whale origins and relationships, go ahead. I don't care what you believe in.

      Delete
    50. Andy invokes Gish's Law: each transitional fossil creates two gaps, one before it and one after it.

      "There are no transitional fossils leading to Z!"

      "Here's one: M."

      "There are no transitional fossils leading to M! No transition between M and Z!"

      "G and S."

      "There are no transitional fossils leading to G! No transitions between G and M, none between M and S, none between S and Z!"

      "D, J, P, V, W..."

      "GOD DID IT GOD DID GOD DID IT!!"

      Delete
    51. Andy says: "Do you know what connects Ambulocetus to Pacicetus? -Assertion."

      Drat! Paleontologists should have invented a system for measuring the characters of fossils, entering them into a computer in the form of a matrix, constructing a phylogenetic tree with numerical methods, then testing said tree by various statistics e.g. scrambling the data randomly and seeing if an equally robust tree can be constructed.

      Nah-- paleontologists would never think of that. Good thing we've got creationists to teach church audiences what really goes on in the science labs they will never enter: "ASSERTION! ASSERTION!"

      Delete
    52. Hey Andy,

      Polar bears have been found swimming 200 miles from shore. How many mutations did it take to adapt a brown bear to a semi-aquatic lifestyle?

      How many years after Noah's Flood did it take for brown bears to evolve into semi-aquatic polar bears? Did I say evolve? You may substitute "adapt" if it protects your feelings.

      By looking at a polar bear skeleton, could you tell it could swim 200 miles offshore in the open ocean?

      Next: answer the same questions as above for: sea snakes, anacondas, the S. American bush dog, the marine iguana, and those swimming monkeys from "Planet Earth."

      Delete
    53. Diogenes writes: "Andy invokes Gish's Law: each transitional fossil creates two gaps, one before it and one after it."
      I have claimed no such thing, my question was simply why connect them in the first place. Isn't it less contrived that the one that looks like a wolf is related to wolfs and the one that looks like a crocodile is related to crocodiles? If you are going to connect them I would like a little more than the ear bones from fragmented skulls to be somewhat, possibly, vaguely similar

      Delete
    54. Diogenes writes: "Polar bears have been found swimming 200 miles from shore. How many mutations did it take to adapt a brown bear to a semi-aquatic lifestyle?"

      Darwin wrote: "In North America the black bear was seen by Hearne swimming for hours with widely open mouth, thus catching, like a whale, insects in the water. Even in so extreme a case as this, if the supply of insects were constant, and if better adapted competitors did not already exist in the country, I can see no difficulty in a race of bears being rendered, by natural selection, more aquatic in their structure and habits, with larger and larger mouths, till a creature was produced as monstrous as a whale.

      I have a problem imagining a bear (or a proto-wolf, or a proto-hippo) turning in to a whale, since the claims are not supported by evidence showing how it would have happened. I cannot say, however, that I find it hard to believe that polar bears and black bears, or what have you, all share a common ancestor.

      Delete
    55. Diogenes writes: "How many years after Noah's Flood did it take for brown bears to evolve into semi-aquatic polar bears? Did I say evolve? You may substitute "adapt" if it protects"

      I have been very clear on that I'm not a YEC, furthermore I do not have a problem with adaptation.

      Delete
    56. Isn't it less contrived that the one that looks like a wolf is related to wolfs and the one that looks like a crocodile is related to crocodiles?

      Are you saying this seriously?

      Delete
    57. If you are going to connect them I would like a little more than the ear bones from fragmented skulls to be somewhat, possibly, vaguely similar

      Thank you for this. You have absolutely zero goddamn clue how much work is put into comparative anatomy or even how it's done.

      Quick hint: It's not "it sorta looks like this".

      Delete
    58. "Isn't it less contrived that the one that looks like a wolf is related to wolfs and the one that looks like a crocodile is related to crocodiles? "

      Well, Andy, you've shown that you know absolutely nothing about how anatomical features relate to vertebrate classification. Why should anyone take any opinion you express seriously?

      Here's a question for you. Whales live in the water -- so why aren't they fish?

      Delete
    59. Maybe Andy thinks they are fish. Actually, as a creationist who denies common descent, he can classify organisms any way he likes. There is no objective and non-arbitrary means of grouping them, as there is in phylogenetic classification. So there's nothing stopping him from classifying all things that swim in the water and have fins as members of the "fishy kind". See, creationism is so much easier than actual science. That's one of its allures.

      Delete
    60. Christine, so let me know what else connects Ambulocetus to Pacicetus besides the ear bones from fragmented skulls being somewhat, possibly, vaguely similar. How about the double-trochleared astragalus from the Pacicetus that we have already established that whales do not have. Does Ambulocetus have that? Did you btw know that Phil Gingerich discarded Ambulocetus from being on the evolutionary line of whales because of the position of the eyes?

      Delete
    61. "Christine, so let me know what else connects Ambulocetus to Pacicetus besides the ear bones from fragmented skulls being somewhat, possibly, vaguely similar."

      The known complete skulls of Pakicetus and Ambulocetus show a unique morphology of the petrosal bone housing the inner ear, otherwise seen only in cetaceans among living and extinct animals, and the middle ear bones are also similar in being heavily ossified, all features related to the demands of underwater hearing (but different from the way that the ear region is modified in seals and sea cows). This is not quite the same as "vaguely similar ear bones", which you would know if you had read any of the science about this.

      Meanwhile, Ambulocetus is considered to be more closely related to modern whales than is Pakicetus because it has the anatomy of the lower jaw indicative of the beginnings of the type of fat pad in a groove along the jaw that whales use to receive sound underwater.

      "How about the double-trochleared astragalus from the Pacicetus that we have already established that whales do not have."

      The astragalus does not, of course, link Pakicetus to recent whales. It does, however, link the entire cetacean lineage (including Pakicetus) with artiodactyls. Did you understand the original issue here? I think not.

      The astragalus is not preserved in Ambulocetus. However another bone in the ankle, the ectocuneiform, shows strong resemblances to that of terrestrial artiodactyls

      "Did you btw know that Phil Gingerich discarded Ambulocetus from being on the evolutionary line of whales because of the position of the eyes?"

      Nobody would imagine that Ambulocetus was on the direct line to modern whales --- it's far too specialized in its own right. However, it is a basal cetacean. Blue whales are not ancestral to dolphins, yet both are cetaceans. Can you see the analogy here?

      Delete
    62. [Andy:]How about the double-trochleared astragalus from the Pacicetus that we have already established that whales do not have.

      [Christine Marie:] The astragalus does not, of course, link Pakicetus to recent whales. It does, however, link the entire cetacean lineage (including Pakicetus) with artiodactyls. Did you understand the original issue here? I think not.

      Perhaps Andy would be interested to know that Pakicetus is not the only early whale with a double-pulley astragalus. Actually, all protocetids whose astragali are preserved (Rodhocetus, Articetus, Maiacetus) have it, while the fully marine basilosaurids show a transitional anatomy of the astragalus, largely fused with other bones, but with part of its ancestral structure still recognisable. One can predict (or bet $$ agains doughnuts) that if the complete astragalus of Ambulocetus (or any other ambulocetid) is ever found, it will be of the same shape. The fact that we haven't got one is just an accidental attestation gap.

      Delete
    63. Thanks Piotr

      Who says that evolutionary science can't make predictions!

      Delete
    64. Andy, it's obvious that you really don't like the ToE and that you want to find and establish a controlling position in nature for your chosen designer-god. You say a lot about what you think hasn't been found and established by scientific methodology but I haven't seen you explaining the wheres, whens, and hows of what you believe your chosen designer-god has done and/or is doing to make nature the way it was and is. Will you please do so, and in doing so will you be sure to include your thoughts/beliefs about the following: common descent, micro-evolution, macro-evolution, kinds/baramins, front loading, extinction, transitional organisms, aging, disease, races, genetic disabilities and disfigurements, mutations, pathogens, venoms, parasites/parasitoids, meteorite/comet/asteroid impacts, ice ages, plate tectonics and orogenies, and the origin and evolution of humans, including relationships between humans, other primates, and other organisms?

      And I have another question for you and any other 'intelligent designer' pusher:

      IF there actually were some sort of a so-called 'intelligent designer', either just way back in the past or continuing to this day and beyond, exactly how would that support anything in your or anyone else's religious beliefs?

      Delete

    65. I wrote: "Did you btw know that Phil Gingerich discarded Ambulocetus from being on the evolutionary line of whales because of the position of the eyes?"

      Christine responded: "Nobody would imagine that Ambulocetus was on the direct line to modern whales --- it's far too specialized in its own right. However, it is a basal cetacean."

      Isn't precisely the problem with comparative morphology? There never seem to be any fossils found that are at the nodes of the phylogenic trees, or as I put it "on the evolutionary line" between extinct and extant species. The fossils always represent sub-groups at the branches. What this means in plain language is that if Christine can find any anatomical feature that is similar, then there is an evolutionary connection. Dissimilarities can on the other hand be explained away by that trait being lost in that sub-group or that the sub-group has developed a trait due to as Christine puts it being "specialized in its own right".

      To make morphological classification even further flexible terms like "convergent evolution" are introduced to explain away similar appearance in taxa that are deemed to be unrelated because they do not fit the intended pattern.

      Clearly this provides a toolbox to explain anything and hence nothing is explained.

      Delete
    66. Christine writes: "The known complete skulls of Pakicetus and Ambulocetus show a unique morphology of the petrosal bone housing the inner ear, otherwise seen only in cetaceans among living and extinct animals, and the middle ear bones are also similar in being heavily ossified, all features related to the demands of underwater hearing (but different from the way that the ear region is modified in seals and sea cows). This is not quite the same as "vaguely similar ear bones", which you would know if you had read any of the science about this."

      I recommend everyone to see for themselves the sound transmission mechanism for whales an land mammals and whales on:

      http://140.220.1.9/DEPTS/ANAT/Thewissen/pdf/2004NummelaEAlNature.pdf

      In figure 2, on the first page, you can easily see that sound transmission mechanism for Pacicetus is very similar to that of land mammals, only the medial synostosis between periotic and tympanic bone is missing. In Cetaceans and Pacicetus this synostosis is absent and is homologous to a gap between these bones. This gap, as strange as it sounds, is the basis for connecting Cetacea and Artiodactyla.

      Delete
    67. This gap, as strange as it sounds, is the basis for connecting Cetacea and Artiodactyla.

      Really? No other morphological data whatsoever? No genetic evidence, including convergent trees using sequences which are very unlikely to have anything to do with building the phenotype - SINEs etc?

      Delete
    68. Isn't precisely the problem with comparative morphology? There never seem to be any fossils found that are at the nodes of the phylogenic trees

      This is actually a convention. It is regarded as highly unlikely that one has an actual ancestor fossil on one's bench, or even a representative of an actual ancestor species, so bets are hedged by placing them on side branches, not at the node. 'Transitional' does not mean what you think it ought to mean.

      Delete
    69. Andy,

      If I find the tombs of people who lived by places where my ancestors lived, say, 600 years ago, that does not mean that I have found the tombs of my ancestors. It's simple logic. A few of the tombs might be, but, without further information I could not know. What if my ancestors were not buried there for example? So, the rests in the tombs would most probably be "branches," rather than "nodes" in my lineage.

      Delete
    70. "Isn't precisely the problem with comparative morphology? There never seem to be any fossils found that are at the nodes of the phylogenic trees, or as I put it "on the evolutionary line" between extinct and extant species. "

      Due to your lack of familiarity with the actual science, you're confusing the practice of phylogenetics, whereby cladograms show the sequence of acquistion of shared derived characters, with the notion of actual ancestor/descendent relationships. That is, you are conflating process and protocol with actual information. Cladograms show no "ancestors" at the base of the branches. One could do a molecular phylogeny of modern dog breeds that would show the same pattern. Does that mean that there were no actual ancestors for the dog breeds seen today?

      "What this means in plain language is that if Christine can find any anatomical feature that is similar, then there is an evolutionary connection. Dissimilarities can on the other hand be explained away by that trait being lost in that sub-group or that the sub-group has developed a trait due to as Christine puts it being "specialized in its own right"."

      Again, an argument from ignorance. There are alogrithmic programs that can sort out these differences. But one can also do so using common sense. The differences that are there are unique ones to the group, while they share common characters with the main lineage. So, again, there are similarities that link dolphins and blue whales as both being cetaceans --- the differences are irrelevant at this level, but do show that they belong to different cetacean suborders.

      If morphological techniques were indeed so shady, then the discovery of molecular data and molecular phylogenies would have disproved the relationships proposed by the morphologists (one might even say that they would have "blown them out of the water"). However, as the molecular phylogenies are in broad agreement with the morphological ones for extant animals, our confidence in using them for extinct animals is increased.

      But, let me ask you a question, Andy. If all of these 60+ species of semi-aquatic whale-like animals in the Eocene, with increasing similarity to modern whales through time, are NOT whales --- then what are they? Just God's continual attempts at trying to produce something vaguely like a whale?

      Within phylogenies, those are best illustrated by paraphyletic stem groups --- in the case of the cetaceans particularly by the paraphyletic nature of the "Protocetidae" that range between the specialized early archeocete "offshoots", such as the Ambulocetidae and the Remingtoncetidae, and the more derived Basilosauridae that are basal to the divergence of the extant cetaceans. Within the protocetids we can see the gradual loss of the connection between the hind limb and the vertebral column, and movement of the nostrils more dorsally on the skull.

      Delete
    71. "In figure 2, on the first page, you can easily see that sound transmission mechanism for Pacicetus is very similar to that of land mammals, only the medial synostosis between periotic and tympanic bone is missing. In Cetaceans and Pacicetus this synostosis is absent and is homologous to a gap between these bones. "

      Bingo --- a transitional form!

      Delete
    72. I wrote: "This gap, as strange as it sounds, is the basis for connecting Cetacea and Artiodactyla."

      Christina answered: "Bingo --- a transitional form!"

      I'm glad that we finally agree on the facts. Even if we disagree on the interpretation. I'm more like: "Really, is that it? That's not even a significant part of the whales echolocation system!"
      Christine, is this not just an Artiodactyla "specialized in its own right" instead of the missing link connecting whales to hippos?

      I wrote: "What this means in plain language is that if Christine can find any anatomical feature that is similar, then there is an evolutionary connection. Dissimilarities can on the other hand be explained away by that trait being lost in that sub-group or that the sub-group has developed a trait due to as Christine puts it being "specialized in its own right".
      To make morphological classification even further flexible terms like "convergent evolution" are introduced to explain away similar appearance in taxa that are deemed to be unrelated because they do not fit the intended pattern.
      Clearly this provides a toolbox to explain anything and hence nothing is explained."

      Christine answered: "Again, an argument from ignorance. There are alogrithmic programs that can sort out these differences. But one can also do so using common sense."

      Really!? Is that the best of science? No set criteria to accept or refute instead algorithmic programs and common sense!? I must admit that I'm a tad flabbergasted.

      Delete
    73. Andy, I'm sorry for your predicament, but what "rules" would you like to have? Reconstructing the structure of family relationships is like detective work based on all sorts of relevant evidence. You can apply "common sense" to generate relationship hypotheses, but common sense does not give you any confidence metrics, so algorithmic methods have to be used to search for the best phylogenies and evaluate the statistical support for them. They are always hypothetical and may be revised -- like everything else in science. The best one we have at present places Cetacea squarely inside Artiodactyla, with raoellids as their sister group, and both of them close to the anthracothere/hippo clade. Of course there are rival hypotheses, the most serious of them regarding Cetacea as the sister group of traditional Artiodactyla. You can test other groupings too: Cetacea with bats, Cetacea with rodents, odontocetes with aardvarks but mysticetes with xenarthrans -- none of them is a priori impossible; they just happen to be ruled out by the evidence.

      If your real quibble is that biologists assume in advance that all mammals are ultimately related, and that creationist hypotheses are not even considered, please tell us something about those hypotheses -- how you arrive at them, how they can be tested, and how they explain the empirical data. Please lay out your model and your hypotheses if you wish to be taken seriously. Don't hypocritically complain that scientific knowledge has too slim a basis, in your strictly private opinion, when your alternative view (to the extent that we can guess what it is) is based on bugger-all.

      Delete
    74. PS Note that the correct spelling is Pakicetus, from "Pakistan", not from "Pacific" (or whatever you associate it with). You misspell it every time you mention the poor critter.

      Delete
    75. No set criteria to accept or refute instead algorithmic programs and common sense!? I must admit that I'm a tad flabbergasted.

      Meh. What's particularly cool about molecular phylogeny is that it enables one to set aside a great deal of subjectivity and pass the data through algorithmic processes that one can test and tune with artificial data - test its accuracy on computer-generated (but 'real') trees, then set it loose on real-world data. Congruence is never exact - there are many well-worked-out reasons why we should not expect the methods to reveal The One True Tree - HGT, excision, finite character states, homoplasy - but there is every reason to agree that they are absolutely in the right ballpark when it comes to the 'higher' taxonomic levels - such as the Cetartiodactyla.

      Among the most convincing to my mind is the transposon data. This needs far less fancy footwork with algorithms, because of the the simplicity of the character states. One can look at transposons and look for the sequences flanking the insertion site in animals that lack the transposon itself. Lack of the transposon is far more likely due to descent from an ancestor that also lacks the insertion than to subsequent excision. Stack a number of such sites and one builds up a clear picture that is very hard to explain by any hypothesis other than that whales are more closely related to artiodactyls than anything else. This binary data can be refined by tracking changes in the flanking sequences and the SINEs themselves. It does not rule out Design, but if Design, the designer kicked off with a land-dwelling proto-Artiodactyl. Or made Artiodactyls from a sea-going mammal, but common sense (and the data) would seem to rule that one out.

      Delete
    76. Allen wrote: "One can look at transposons and look for the sequences flanking the insertion site in animals that lack the transposon itself. Lack of the transposon is far more likely due to descent from an ancestor that also lacks the insertion than to subsequent excision. Stack a number of such sites and one builds up a clear picture that is very hard to explain by any hypothesis other than that whales are more closely related to artiodactyls than anything else. This binary data can be refined by tracking changes in the flanking sequences and the SINEs themselves."

      Allen, do you know if such a study is done to compare Artiodactyla and Cetacea?

      Delete
    77. Sure - try this: http://mbe.oxfordjournals.org/content/16/8/1046.long

      Delete
    78. 'Christine, is this not just an Artiodactyla "specialized in its own right" instead of the missing link connecting whales to hippos?

      I wrote: "What this means in plain language is that if Christine can find any anatomical feature that is similar, then there is an evolutionary connection. '

      Aha, "any anatomical feature". No wonder you think that pakicetids should be classified with wolves and ambulocetids with crocodiles. No, it's the presence of a unique, shared derived feature (usually more than one), seen in no other animal outside of the particular group.

      "To make morphological classification even further flexible terms like "convergent evolution" are introduced to explain away similar appearance in taxa that are deemed to be unrelated because they do not fit the intended pattern."

      Find me the definitive non-cetacean that has that ear character and you might have a point. As it is you're guessing from a "knowledge base" of wondering why scientists don't fess up and stick Ambulocetus in with the alligators.

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    79. Christine wrote: "Find me the definitive non-cetacean that has that ear character and you might have a point."

      I say: Give me one objective criteria why this is not a case of convergent evolution...

      I think it's all too subjective for me, so I'm shifting focus to molecular phylogeny for now. Still thanks for the discussion and I'm sure we will get the chance to "fight" about something else in the future :-)

      Delete
    80. See also this total evidence analysis (Spaulding, O'Leary & Gatesy 2009), which tests phylogenetic hypotheses against both morphological and molecular data.

      Delete
    81. "I say: Give me one objective criteria why this is not a case of convergent evolution..."

      Easy. Because it is unknown in any other kind of animal. And it's specific and complex, --- convergent features tend to be more generalized adaptive ones, like the long, crocodile-like body of Ambulocetus common to many semiaquatic vertebrates.

      But, like I said --- you find the same specific ear anatomy elsewhere and you might have a case for convergence. The difference is that you have not looked, and others have.

      "I think it's all too subjective for me,"

      Nah, the ear region anatomy is extremely specific and objective. I think it's just to difficult for you to understand. One does need training in anatomy to understand the science (like any other science). BTW, the molecular phylogeny won't help your case here, either.

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    82. "I think it's all too subjective for me, so I'm shifting focus to molecular phylogeny for now. "

      PS. Of course morphology is still essential if we want to place fossils in phylogenies, and use fossil evidence to understand how, when, and where evolution happened. It's convenient that the molecular phylogenies, for the most part, reflect those originally created by morphology --- that means that the consilience adds to the power of the phylogeny, and also that we we can be confident in using morphology to assign fossils within the phylogenies.

      BTW --- re the previous comment I made about "common sense". As someone who both teaches and writes for a non-specialist audience, I consider that trying to present things in a "common sense" way is invaluable. But did you intend to imply that real, objective science should *not* reflect common sense?

      Delete
    83. I said: "Give me one objective criteria why this is not a case of convergent evolution..."

      Christine wrote: "Easy. Because it is unknown in any other kind of animal."

      Hmm, did you not earlier say that Pakicetus was a Cetacea BECAUSE of the gap (caused by the medial synostosis between periotic and tympanic bone missing)? That sounds like circular reasoning to me.

      Christine wrote: "And it's specific and complex, --- convergent features tend to be more generalized adaptive ones, like the long, crocodile-like body of Ambulocetus common to many semiaquatic vertebrates."

      What about the mole-like forelegs of the mole cricket? Are they generalized or as specific and complex as the gap?

      Christine wrote: "I think it's just to difficult for you to understand."

      I don't know why you keep coming back to this being "difficult". Nobody else seem to have any problem. Piotr hasn't even studied science and he's not complaining. Let's face it, this isn't exactly rocket science.

      Christine wrote: "It's convenient that the molecular phylogenies, for the most part, reflect those originally created by morphology"

      That is the main reason why I don't take it at face value. It's just a little too convenient. This discussion hasn't really helped building my confidence in morphology and paleontology as objective sciences.

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    84. What about the mole-like forelegs of the mole cricket? Are they generalized or as specific and complex as the gap?

      They are similar the way the slowworm is similar to the earthworm (they are both "worms", aren't they?), or Ambulocetus to an alligator. Their forelegs are obviously adapted to digging, so they display the expected superficial overall similarity due to convergence. Their detailed morphology reveals no similarity at all, nor does anything elese in the anatomy of the mole and the mole cricket.

      Let's face it, this isn't exactly rocket science.

      As opposed to Intelligent Design and/or Creation Science? Let's see how they deal with the same data.

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    85. That is the main reason why I don't take it at face value. It's just a little too convenient.

      That's a curious attitude. Morphology was the only tool available at one time, and has, with relatively few exceptions, been confirmed by the molecular data. This means that the morphological analysis was right. It bolsters the validity of the method. How convenient! Of course it's not right in every case, but that's no reason to doubt it in all.

      I'm shifting focus to molecular phylogeny for now

      To try and find a reason it's wrong? ;)

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    86. Me: the morphological analysis was right ...

      although of course in the instance under discussion, the morphological data alone placed Cetacea as a sister group to Artiodactyla. Molecular data places them slap bang inside. So 'right-ish', in this instance. Either way, what's the deal? It's a process of refinement as more data is unearthed. None of it supports the notion that whale evolution can't have happened.

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    87. I wrote: "I'm shifting focus to molecular phylogeny for now"

      Allan responded: "To try and find a reason it's wrong? ;)"

      Well, what can I say. I'm a skeptic...

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    88. "Hmm, did you not earlier say that Pakicetus was a Cetacea BECAUSE of the gap "

      No, those were your words.

      "What about the mole-like forelegs of the mole cricket? Are they generalized or as specific and complex as the gap?"

      They would certainly be a good shared derived character for other types of crickets. For an actual mole, with an internal skeleton rather than exoskeleton, not so much.

      "I don't know why you keep coming back to this being "difficult". Nobody else seem to have any problem."

      Yes, nobody else seems to have this problem. Only you. It's not rocket science, but somehow it still defeats you.

      "That is the main reason why I don't take it at face value. It's just a little too convenient. "

      Consilience in science works. Just too convenient? ----- don't believe the evidence, stick to being an uneducated rebel. At least that way you have an identity, right? Otherwise you're just another uneducated creationist.

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    89. "Well, what can I say. I'm a skeptic..."

      Yeah, you're a real man ---- takes a lot more than piles of evidence to convince you. Stick to your guns Andy, it's all you have in the face of science.

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    90. I'm a skeptic...

      Don't flatter yourself. A sceptic is someone who refused to accept ideas unsupported by empirical evidence. Any respectable research worker is a sceptic. A person who refuses to accept the validity of an empirically verifiable hypothesis just because he doesn't care for science in general is not a sceptic but a denialist.

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  7. This was not intended to prove a point (although Denyse O'Leary might actually think that it does, based on my experience with her writing). This is intended to be an analogy to make an emotional point that is far more compelling to people who want to agree with it already. And, as Susannah mentions, besides not being good math or science, it's horrible art. But that fits their ideas about a lot of things, such as there is a "correct" person God intends you to marry. There was a "perfect" way for that to be painted, and it happened. Of course, the Bible might have some other ideas about such a suggestion of perfection in a human act! Don't distract Denyse, though, she's on a roll!

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  8. In Solzhenitsyn's "The First Circle", an artist is asked when he considers a painting to be finished. He replies that his paintings are never finished, but he stops working on them when he notices that his changes are making them worse instead of better.

    Which of course I regard as another small piece of evidence for my hypothesis that every complex, functional creation is made by a process of evolution.

    Speaking of which, one good place for IDists to study design (so that they know something of what they are talking about) might be "The Mythical Man-Month" by Frederick P. Brooks, Jr., which describes better and worse ways of designing computer systems, such as the IBM/360 system, for which he was the project manager. Especially the 1995 edition which evolved from the original 1975 edition, with four new chapters and some changes in recommendations based on further experience.

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  9. I would like to ask her, if every organism is unimprovable of its kind, why aren't all members of a species identical?

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    1. That's simple. Their ancestors were created perfect, but after the Fall mutations started gnawing at their DNA, so today they are somewhat sub-optimal. She doesn't say that mutations are impossible, but only that they are always deleterious.

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    2. is it possible that cdesign proponentsists have just reached some greater sub-optimal state faster than the rest of us?
      Mock the idea if you will, but it means one day we will all degeneratively evolve into creationists and believe in god and lo and behold, gods plan will be complete. Our god truly is an awesome god.

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  10. If we're doing the analogy, surely we've got one - a painter is asked to copy the whole painting. It can not be an exact copy. If a third painter is asked to make a copy from the copy they might copy one of the differences. And so on. Without anything checking the differences, we can imagine that the hundredth copy would have significant differences from the original.

    As for tiny copying errors ... well, here's one the American right might appreciate: the comma in the Second Amendment.

    http://www.businessinsider.com/the-comma-in-the-second-amendment-2013-8

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