Thursday, May 26, 2011

Junk & Jonathan: Part 8—Chapter 5

This is part 8 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

Pseudogenes are the classic example of junk DNA and, as pointed out by many evolutionary biologists, they represent a difficult challenge for Intelligent Design Creationists. It's especially difficult to explain pseudogenes that are located in the same place in different species.

Chapter 5: Pseudogenes—Not so Pseudo After All

Chapter 5 is Pseudogenes—Not so Pseudo After All. This is the chapter where Jonathan Wells takes the standard creationist approach to the problem of pseudogenes—he denies that they exist!

Wells begins the chapter by reminding us that several evolutionary biologists have challenged the IDiots to come up with an explanation for pseudogenes, especially those that are found in closely related species. The usual suspects are quoted: Ken Miller, Douglas Futuyma, Jerry Coyne, Richard Dawkins, and John Avise. All of these challenges are based on solid evidence that most pseudogenes are actually pseudogenes (non-functional, degenerate copies of functional genes). But Wells says, "Yet there is growing evidence that many pseudogenes are not functionless, after all."

Types of Pseudogenes

There are three kinds of pseudogenes [Pseudogenes]. The first category contains genes that used to be functional in our ancestors but currently are non-functional. The best example is the human GULOP pseudogene that used to encode a key enzyme in the pathway for synthesis of vitamin C [Human GULOP Pseudogene]. This gene is active in most animals but it has become a pseudogene in primates and, independently, in a few other animals.


The second category includes genes that arise from a gene duplication event followed by inactivation of one of the copies. These pseudogenes tend to be located near their active siblings and they retain most of the features of the original gene except they can't produce an active product. Many of them are transcribed, especially if they have only recently become pseudogenes.

The third category is called "processed" pseudogenes. They arise when a mature mRNA molecule is copied into DNA by reverse transcriptase and the resulting DNA is integrated into the genome. Processed pseudogenes will usually not have any introns and when they integrate they will not be near a promoter. Many of them are truncated because the copying process was not complete. Processed pseudogenes were never able to produce their original functional product (protein or RNA) and they accumulate mutations at the rate expected from fixation of neutral alleles by random genetic drift.

The first two categories of pseudogene will also accumulate mutations once they become inactive. It's a characteristic of pseudogenes that the older they are the more mutations they have. Thus a pseudogene that is only found in chimpanzees and humans will have fewer mutations than one found in monkeys and apes and even fewer that one found in both rodents and primates.

The human genome contains about 20,000 pseudogenes, about the same as the number of genes. Many of these pseudogenes belong to the same family so not every gene has a corresponding pseudogene. About 6,000 of these pseudogenes arose from duplication events and 14,000 are processed. (The first category is rare.)

The pseudogenes in the "duplicated" category tend to be associated with large families of related genes. For example, in the human genome there are 414 pseudogenes in the olfactory receptor gene family [Olfactory Receptor Genes, The Evolution of Gene Families]. It's difficult to imagine how any substantial number of these genes could have a function.

As expected, the processed pseudogenes are scattered thoughout the genome because they insert at random. Roughly 2,000 of them are found in introns and this is further evidence that introns are mostly junk. Of course, if a processed pseudogene plunks down in an intron sequence it will be transcribed. Processed pseudogenes tend to come from functional genes that are abundantly expressed in the germ line. That's because the processed pseudogene has to be integrated into germ line DNA in order to be passed on to the progeny. Most of these genes are standard housekeeping genes. For example, there are 1300 pseudogenes derived from ribosomal protein genes.

Jonathan Wells describes the three categories but doesn't explain any of the other things I just mentioned.

Transcribed Pseudogenes

The first important section of his chapter is "Transcribed Pseudogenes." He quotes a number of papers showing that some pseudogenes are transcribed in humans, cows, and plants. In humans he claims that about one-fifth of pseudogenes are transcirbed at some time or another. This is probably an upper limit since most workers suggest that only 10% are transcribed.

I'm sure that some pseudogenes are transcibed. Many of the pseudogenes derived from gene duplication events will still be transcribed from active promoters even though they may not produce a functional product. Many of the processed pseudogenes will be transcribed because they are found within a gene (introns) or have fortuitously integrated near a promoter.

'Pseudogenes' That Encode Proteins

The key question is whether any pseudogenes produce a functional product and that's addressed in the next section: "'Pseudogenes' That Encode Proteins." Wells describes five studies where presumed pseudogenes were found to be genes after all (three in humans and two in fruit flies). Interesting but irrelevant. These genes are not junk. What about the other 20,000 real pseudogenes? Here's what Wells says at this point in the chapter ...
To be sure, only a relatively small proportion of known pseudogenes have been shown to encode proteins. But there is growing evidence that RNAs transcribed from pseudogenes perform essential functions in the cell
Here's where we get to the most important part of the chapter. It's in a section called "RNA Interference."

RNA Interference

RNA interference arises when one RNA molecule interferes with the expression of another. The easiest example to understand is when part of a gene is transcribed in the opposite direction producing what's called "antisense" RNA. This antisense RNA will hybridize to the functional mRNA and either block translation or induce degradation. In either case, less protein is made.

If a pseudogene is transcribed in the opposite direction then its antisense RNA could interfere with the expression of the normal gene. Wells gives us three examples of this phenomenon: one famous one from snails (1999), one from mouse oocytes (2008), and one from rice (2009). I don't know whether all these results have been confirmed but even if they have it doesn't amount to much. All kinds of strange things happen in biology and the fact that a few pseudogenes might have acquired a regulatory function isn't shocking. What about the other 20,000 pseudogenes?

Pseudogene Enhancement of Gene Expression

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Genomes
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Well, there's always the possibility that pseudogenes could enhance gene expression. The next section is "Pseudogene Enhancement of Gene Expression." Jonathan Wells begins this section with a description of the results on the mouse Mkrn-1-p1 pseudogene. The authors of this famous 2003 Nature paper claim that transcripts from the pseudogene protect the functional mRNA by shielding it from degradation. The title of their paper is "An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene" (Hirotsune et al., 2003).

Wells devotes three paragraphs to this important paper. There's only one slight problem. This work has been discredited in a 2006 PNAS paper with the title "The putatively functional Mkrn-1-p1 pseudogene is neither expressed nor imprinted nor does it regulate its source in trans." (Gray et., 2006) Oops!

Wells knows about this 2006 paper because he discusses it in Chapter 8 when he attacks the defenders of junk DNA. In chapter 5 he adds the following remark in parentheses, "Other biologists later challenged the Makorin-1 pseudogene results, which remain controversial." I think this is the only time when he mentions any legitimate scientific controversy.

There are three other examples of pseudogenes that might have an enhancement function: one from plants and two from humans. I don't know if these studies have been confirmed but even if they have they don't have much of an impact on the possible functions of the remaining 20,000 pseudogenes.

Sequence Conservation

The only significant evidence of widespread functionality of pseudogenes comes from two studies on sequence conservation. Wells covers this in a one-page section on "Sequence Conservation." The studies purport to show that pseudogene sequences are much more conserved than expected if they are really junk DNA. These studies have not been reproduced, as far as I know, and they fly in the face of much evidence to the contrary—evidence that Wells forgets to mention.

The first paper is a review by Balakirev and Ayala (2003). They review the possible functions of some pseudogenes in Drosophila and mammals. Some of them show evidence of sequence conservation. They conclude that most pseudogenes are probably functional. A study published that same year looked at all the known pseudogenes in the human genome and concluded that 95% of them evolved as though they had no function (i.e. they were not conserved) (Torrents et al., 2003)

The second paper that Wells mentions is Khachane and Harrison (2009). They identify 68 human pseudogenes whose sequences appear to be conserved in at least two other mammals. These are good candidates for functional genes.

The strange thing about this argument is that Wells doesn't believe in common descent so the evidence of sequence conservation really shouldn't have any meaning for him. Nevertheless, he says ...
How odd! As we saw in Chapter 2, Kenneth Miller, Richard Dawkins, Douglas Futuyma, Michael Shermer, Jerry Coyne and John Avise argue that pseudogenes confirm Darwinism because they are non-functional. But if we assume that Darwinism is true and then compare the DNA of unrelated organisms, sequence similarities imply that many of their pseudogenes are functional. So nonfunction supposedly implies Darwinism, but Darwinism plus sequence conservation implies function. When it comes to conserved pseudogenes, it seems, Darwinism saws off the very branch on which it sits.
For the record, if the majority of pseudogenes really are more conserved than expected from random mutations and fixation by random genetic drift then this would, indeed, be evidence that something is going on. Maybe they do have a function we don't know about. I don't think the evidence points in this direction at all—in fact much of the evidence contradicts it. Balakirov and Ayala (2003) are just speculating. I prefer the evidence of Torrents et al. (2003) suggesting that only a small number of potential pseudogenes have a function. This is consistent with the results of Khachane and Harrison (2009).

[If all 1,000 presumed pseudogenes turned out to be real genes then this moves about 0.06% of the genome from the junk category to the functional category. This isn't enough to save the IDiots.]

The Vitamin C Pseudogene

Finally, there's a section I haven't covered. It's titled "The Vitamin C Pseudogene." Wells has to address this particular pseudogene because it's the one that comes up most often when evolutionary biologists (e.g. Ken Miller and Jerry Coyne) criticize Intelligent Design Creationism. Here's what Wells says,
The evidence is not as straightforward as Miller and Coyne make it out to be, however, and their argument is ultimately circular. In any case, common ancestry and intelligent design are two different issues, and the vitamin C story would take us on a detour from the issue of junk DNA that's the focus of this book, so the details are omitted here and included in an appendix.
Which brings us to the Appendix: "The Vitamin C Pseudogene."

The main argument of scientists like Ken Miller and Jerry Coyne is not that the GULOP pseudogene exists. It's that the GULOP gene and its pseudogene are at the same location in the genomes of all mammals. In the primate lineage this gene is non-functional due to a number of mutations that make it impossible to produce a functional protein. Some of the same deactivating mutations are found in related species such as humans and chimpanzees. This suggests strongly that the non-functional pseudogene was inherited from a common ancestor. How do Intelligent Design Creationists deal with this evidence?

How does Wells respond?
... intelligent design and common ancestry are two different issues. Major ID proponents pointed this out before Miller wrote his book....Although some ID proponents (including me) question universal common ancestry on empirical grounds (as do some evolutionary biologists), intelligent design is not necessarily inconsistent with common ancestry.
I'm not sure what this means. Does it mean that people like Wells are completely bamboozled by this data since they can't refute either the evidence of common descent or the evidence of bad design? Other IDiots, like Michael Behe, only have to explain the bad design?

Jerry Coyne has published a similar argument but Wells attacks him on two fronts. First, he claims that human and chimpanzee Y chromosomes differ by 60 million nucleotide substitutions. If they really have a common ancestor then one would expect much greater sequence similarity. According to Wells, "If similarities in the vitamin C pseudogene are evidence for common ancestry, then differences in the Y chromosome are presumably evidence against it."

The Y chromosome paper is Hughes et al. (2010). Their results show that in orthologous regions of the Y chromosomes the human and chimp sequences are 98.3% identical. However, the chimp and human chromosomes differ in other regions because of large inserts and deletions. This is still evidence of common ancestry.

As usual, Wells is wanting to have his cake and eat it too.

The second attack is based on a number of quibbles. Coyne said that all primates need vitamin C in their diets but Wells points out that prosimians are primates and they can make vitamin C. Furthermore, according to Wells the requirement for vitamin C has only been established in nine species of monkeys. There are 251 other species and we don't know if they need vitamin C. Not only that, Coyne claimed that all primates have the same single nucleotide deletion in their GULOP pseudogene but Wells is quick to point out that only five primate sequences have been published.

Put that in your pipe and smoke it, Jerry Coyne! I assume that Wells is completely incapable of answering the challenge that's been issued and that's why he resorts to red herrings.

Continuing with this shotgun approach we quickly encounter several other arguments that are designed to distract from the main topic.
  • "Miller and Coyne rely on speculations about the motives of the designer or creator that have no legitimate place in natural science." (I hope you turned off your irony meter before reading that.)
  • Miller and Coyne have not provided any evidence to justify their claim that the GLO pseudogene is completely nonfunctional.
  • (Turn off your irony meter!) Their argument is circular. The similarities in sequence between chimp and human pseudogenes could be due to natural selection. "To break the circle, Miller and Coyne would either have to establish the recent ancestry of humans and chimps on other grounds (but why then bother invoking the vitamin C pseudogene at all?), or they would first have to establish that the vitamin C pseudogene has no function whatsoever (but this is impossible). So their argument not only fails to refute ID, but it also fails to establish that humans and chimps are descended from a common ancestor."
I feel a bit sorry for Ken Miller and Jerry Coyne. If this is the best the IDiots can do then why bother trying to argue with them in the first place?

Thus endeth Chapter 5.


Gray TA, Wilson A, Fortin PJ, Nicholls RD. (2006) The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc. Natl. Acad. Sci. USA 103:12039-12044. [PDF]

Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A., and Yoshiki, A. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423:91-6. [PDF]

Hughes, J.F., Skaletsky, H., Pyntikova, T., Graves, T.A., van Daalen, S.K., Minx, P.J., Fulton, R.S., McGrath, S.D., Locke, D.P., Friedman, C., Trask, B.J., Mardis, E.R., Warren, W.C., Repping, S., Rozen, S., Wilson, R.K., and Page, D.C. (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536-539. [Nature]

Khachane, A.N., and Harrison, P.M. (2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics 15:435-449. [PDF]

Torrents, D., Suyama, M., Zdobnov, E., and Bork, P.. (2003) A genome-wide survey of human pseudogenes. Genome Res. 13:2559-2567. [PDF]

416 comments:

  1. The authors of this famous 2003 Nature paper claim that transcripts from the pseudogene protect the functional mRNA by shielding it from degradation.

    A more contemporary take (citation below) on this concept is that pseudogene transcripts protect the functional mRNA by competing for miRNA interference.

    A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
    Nature 465, 1033–1038 (24 June 2010) doi:10.1038/nature09144

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  2. This is really astounding; I thought ID types were at least able to make some good arguments, even if ultimately wrong, at the molecular genetic level, but apparently not.

    Its actually so bad that I almost feel /embarrassed/ for Dr. Moran for responding to this stuff.

    If it weren't for the unfortunately large amount of support that these IDists have, it probably /would/ be embarrassing for people like Dr. Moran to bother refuting them and exposing what look basically like lies of omission!

    Also, I seem to recall that the big deal with ID was defining and actually measuring 'degree of purposeful design', but here they seem to have completely abandoned that! Instead they are citing /function/ as support for ID, neverminding that the /design/ of that function if horrible. If anything the pattern we're seeing here, with genes being duplicated, RNA being back-jacked randomly, even partially, into DNA, and then being transcribed from that, that seems like something Nature, not an Intelligent Agent, would create; they should probably be running away from this issue.
    It sounds like Wells is too enamored of his 'icono-clasm', he's decided that junk DNA is an Icon of evolution, and that therefore he just has to break it, and since his faith tells him that evolution is wrong anyway, then his iconoclasm MUST be fruitful.

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  3. Could the same single nucleotide deletion in their GULOP pseudogene be convergent evolution and not common ancestry?

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  4. Anonymous writes:

    Could the same single nucleotide deletion in their GULOP pseudogene be convergent evolution and not common ancestry?

    It might have a chance to be if broken vitamin C synthesis were strongly adaptive (it isn't), and evolution somehow decided to accomplish this in exactly the same way multiple times out of uncounted possibilities (not bloody likely), and there weren't excellent corroborating evidence of common ancestry from other genetic sources, paleontology, morphology, geography, etc. (there is).

    Or to state this more simply: If all the facts were the exact opposite of what they are, the answer might be yes.

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  5. Just something I thought I'd throw out there... since Old World "monkeys" are actually more closely related to us apes than they are to New World "monkeys", does the term "monkey" have any actual scientific validity at all? Isn't it really just an arbitrary label grouping animals that simply bear a resemblance? YouTube's Aron Ra is of the opinion that if it has any use, it has to include apes since one of the included groups is more closely related to them than to the other included group.

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  6. Jud I have a question:
    Concerning GULOP, does "evolution accomplish this in exactly the same way"?
    Is the nucleotide sequence exactly the same in all the creatures that have this characteristic?

    Anyone who wishes can answer this.

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  7. anonymous asks,

    Could the same single nucleotide deletion in their GULOP pseudogene be convergent evolution and not common ancestry?

    No.

    (See Jud's answer for more detail.)

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  8. Prof. Moran has written:
    The best example is the human GULOP pseudogene that used to encode a key enzyme in the pathway for synthesis of vitamin C [Human GULOP Pseudogene]. This gene is active in most animals but it has become a pseudogene in primates and, independently, in a few other animals.

    So we may presume that GULOP was once functional. Have you ever read some courses of "evolutionary biolology" or any book written by R.Dawkins? Then you must have noticed how important is any selective "advantage" however small it is and how quickly it tends to spread over population?

    I would say that having functional GULO would give any given organism a small "advantage" however small it can be. How is it possible that once functional GULO has been displaced by non-functional GULO seems to be in odds with all those speculation of effectiveness of "natural selection".

    How do Intelligent Design Creationists deal with this evidence?

    It seems to be evidence against natural selection imho. GULO obviously remains functional in many mammals and using professor's "irony meter" - in these cases obviously "natural selection" didn't sleep and has wiped out "deleterious mutation" in GULO in accordance with the wise law of "survival of the fittest".

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  9. Dr. Moran:
    "The best example is the human GULOP pseudogene that used to encode a key enzyme in the pathway for synthesis of vitamin C [Human GULOP Pseudogene]. This gene is active in most animals but it has become a pseudogene in primates and, independently, in a few other animals."

    Independently in humans for example.

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  10. VMatrin says,

    I would say that having functional GULO would give any given organism a small "advantage" however small it can be. How is it possible that once functional GULO has been displaced by non-functional GULO seems to be in odds with all those speculation of effectiveness of "natural selection".

    I agree, it conflicts with evolution by natural selection. But it's not in conflict with modern evolutionary theory.

    You do know about modern evolutionary theory, don't you?

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  11. From Dr. Moran:
    "You do know about modern evolutionary theory, don't you?"

    Dr. Moran, just can't seem to control himself. It is not enough for him to make a point. There always has to be some snarky, ridiculing part.
    It is really sad to see that over and over again.

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  12. Anonymous writes:

    Dr. Moran, just can't seem to control himself. It is not enough for him to make a point. There always has to be some snarky, ridiculing part.

    It is really sad to see that over and over again.

    Yes, please be more like that nice VMartin, who posts such polite, respectful things to Dr. Moran:

    Have you ever read some courses of "evolutionary biolology" [sic] or any book written by R.Dawkins?

    No patronization or sarcasm there, oh no.

    anonymous, this sort of one-sided tone trolling is the refuge of the intellectually bereft, so it's not a place you want to keep going.

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  13. Jud I have a question:

    Concerning GULOP, does "evolution accomplish this in exactly the same way"? Is the nucleotide sequence exactly the same in all the creatures that have this characteristic?

    Yes, exactly the same cytosine deletion is responsible for lack of function of this pseudogene in primates.

    But even there you're barking up the wrong tree. The sequences wouldn't have had to be identical (as they are), they'd just have to form what's called a "nested hierarchy." And the other thing to be aware of is that there are 3 enzymes involved in this vitamin synthesis, so if a designer had wanted to stop it, it would have been just as acceptable to make a critical change at any point along any of the coding genes for any of the 3 enzymes. That's a huge number of options, but instead we see the same one, indicating common descent.

    And that's just the pseudogenetic evidence. There's a huge amount of other pseudogenetic and genetic evidence, plus corroborating information from all the other scientific disciplines I mentioned in my prior answer to this question.

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  14. anonymous writes:

    "This gene is active in most animals but it has become a pseudogene in primates and, independently, in a few other animals."

    Independently in humans for example.

    Ah, the entertainment never stops. So let me get this straight:

    1. The Designer decided He didn't like Vitamin C synthesis in primates and various other mammals. What, He owns orange groves in Florida?

    2. Having thousands of ways to bung up the synthesis, He chose the very same one independently in each and every primate. So He wasn't content to do it once and let these animals evolve, carrying the mutation; instead, He made much more work for Himself by doing this mutating on a one-off basis multiple times. He'd fired His planning and efficiency expert, then?

    3. And we know this because you are either -

    a. So brilliant that you know the unknowable, unfathomable ways of the omniscient Designer; or

    b. You gotta hotline straight to Da Lord Hisself.

    I'm so very curious, is it a or b in your case?

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  15. Really, because it looks pretty funny to me.

    Sad would be getting all butt-hurt over it.

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  16. If this deletion has occurred independently in some animals why did people earlier say that it was not an example of convergent evolution?

    ReplyDelete
  17. Jud had earlier said:
    "It might have a chance to be if broken vitamin C synthesis were strongly adaptive (it isn't)"

    If it is not adaptive why would it have survived at all in any animal?

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  18. I came to your site to learn something. Within a few sentences you told me that I was an idiot so I went elsewhere.

    "Wells begins the chapter by reminding us that several evolutionary biologists have challenged the IDiots to..."

    If you want to teach you should treat your students, no matter how stupid, with dignity and respect otherwise they will leave.

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  19. anonymous asks:

    If it is not adaptive why would it have survived at all in any animal?

    Oh please do catch up to the evolutionary theory of 80-100 years ago when this question was answered. Your personal level of ignorance does not constitute a problem for evolutionary theory.

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  20. Anonymous writes:

    If this deletion has occurred independently in some animals

    The only one I've seen here who says it was independent is you. And you are wrong.

    why did people earlier say that it was not an example of convergent evolution?

    Because you are wrong about it occurring independently, and so for that reason as well as the many others mentioned to you multiple times now, it is quite obviously (to anyone who will open his/her eyes to see) not an example of convergence.

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  21. Dr. Moran posted:
    "This gene is active in most animals but it has become a pseudogene in primates and, independently, in a few other animals."

    Jud is really having troubles.

    ReplyDelete
  22. Jud had earlier said:
    "It might have a chance to be if broken vitamin C synthesis were strongly adaptive (it isn't)"

    If it is not adaptive why would it have survived at all in any animal?

    Jud does not seem able to answer this. Can anyone else?

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  23. Ron Van Wegen says,

    I came to your site to learn something.

    I doubt that very much.

    Within a few sentences you told me that I was an idiot so I went elsewhere.

    Too bad you're gone 'cause I'd really, really like to know what IDiot site you came from. I'm not aware of one that treats evolutionary biologists with dignity and respect.

    You must be very thin-skinned. If you had stayed you would have been criticized by your fellow IDiots. :-)

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  24. Prof.Moran:
    You do know about modern evolutionary theory, don't you?

    A little bit. Combination of natural selection, neutral drift, neutral draft accompanied by evolutionary games and frequency dependent selection plus evo-devo... Add to this kin selection and inclusive fitness and you get a conglomerate of ratione no one can ever check.

    In the case of Ascorbic Acid we know that not even birds, but also Prosimian can produce it in their livers. The deleterious mutation should have occured in our ancestor some 65 mil. years ago. Prosimian obviously have retained it. Is there such a diffrence in the diet?

    According to Irwin Stone "In the long period of human prehistory and history, scurvy has caused more deaths, created more human misery and has altered the course of history more than any other single cause."

    It is hard to believe that our putattive ancesstors didn't miss the gene for millions of years and that they have all the time enough Ascorbic Acid and we miss it only now (scurvy was described also by Hippocrates).

    One wonders if fruit eating birds do not have enough intake of AA while it seems their gene is functional. Why do they still produce AA?

    The most curious thing is that transition of land mammals into whales should have taken cca 10 mil. years. Yet 50 mil. years was not enough time to reestablish internal production of AA in primates.

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  25. Ron Van Wegen, I would not worry too much about Dr. Moran. He has his agenda to promote and is also filled with disdain that surfaces constantly as ridicule.

    ReplyDelete
  26. anonymous asks,

    If it is not adaptive why would it have survived at all in any animal?

    You've seen me state, on many occasions, that I am not a Darwinist. You've seen me criticize the IDiots repeatedly for using the term Darwinism and for not understanding evolution.

    The fact that you would even ask such a question tells me that you haven't been paying the least bit of attention. That's why I call you IDiots.

    ReplyDelete
  27. Jud had earlier said:
    "It might have a chance to be if broken vitamin C synthesis were strongly adaptive (it isn't)"

    If it is not adaptive why would it have survived at all in any animal?

    Jud and Dr. Moran do not seem able to answer this. Can anyone else?

    ReplyDelete
  28. Anon:"The most curious thing is that transition of land mammals into whales should have taken cca 10 mil. years. Yet 50 mil. years was not enough time to reestablish internal production of AA in primates."

    Its curious, definitely, but does the failure of evolution to produce an adaptation mean that evolution doesn't occcur? Clearly not.

    Anon:"Dr. Moran...is also filled with disdain that surfaces constantly as ridicule."
    Seems to me that he should ridicule the ridiculous.


    Anon:'If it is not adaptive why would it have survived at all in any animal?"

    So non-adaptive features contradict evolution. But, Intelligent Design means, well, good functional design. So non-adaptive features contradict evolution AND they really actually serve good function and this supports Intelligent Design.

    Derp.

    Side note:
    Really, is it SO HARD to use a name in these postings? Richard Dawkins seemed to be posting here for a while, is Phil Johnson, Behe, Wells, et al actually posting here, and are they such wimps that they won't even use their names? Is that what's going on? Because who /wouldn't/ use a name anyway? At least use a pseudonym consistently.

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  29. Schenck seems to be acknowledging that "non-adaptive features" like the GULOP gene "contradict evolution".
    Is there agreement on that point?

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  30. Anonymous: Schenck seems to be acknowledging that "non-adaptive features" like the GULOP gene "contradict evolution".
    Is there agreement on that point?


    Absolutely not. If there is consensus on anything it is that adaptation is not the sum total of evolution. On a genomic level, adaptation (i.e. positive selection) is unlikely to be even a quantitatively large part of evolution, certainly not in large, multicellular eukaryotes with (in relative terms) small populations.

    If it is not adaptive why would it have survived at all in any animal?

    If there was a high level of vitamin C, e.g. fruit, in the diet of the ancestral haplorhine species in which GULO became GULOP, then the synthesis of vitamin C is not beneficial and its loss via genetic drift becomes possible.

    Presumably such a loss could have held a slight fitness advantage at the time (i.e. cutting out an unnecessary biosynthesis pathway) but this is certainly not required to explain its loss.

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  31. VMartin:One wonders if fruit eating birds do not have enough intake of AA while it seems their gene is functional. Why do they still produce AA?

    Tully et al. (2000) state that some frugivorous birds have lost the VitC synthesis pathway (sorry I don't have a list, but I'm sure you could find out if you're interested). Amongst the passerine birds able to synthesise VitC, their rates of synthesis are 2-10x lower than in e.g. ducks, quails and chickens.

    Also, Cui et al (2011) discuss the progressive loss of VitC synthesis in bats, with reference to its independent loss in haplorrhine primates and guinea pigs.

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  32. PaulM posted:
    "Presumably such a loss could have held a slight fitness advantage at the time (i.e. cutting out an unnecessary biosynthesis pathway) but this is certainly not required to explain its loss."

    If this just-so story is not required, not sufficient, to explain its loss then there must be some other (or additional) reason for the continuing survival and flourishing of animals that have that lost that ability.
    The bottom line is that evolution theory still has a problem explaining how animals with a distinctly non-advantageous mutation flourished.

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  33. If the just-so story posted by PaulM is acceptable to evolutionists, then the same just-so story could be used by ID people to explain the intentional design of the GULOP feature.

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  34. PaulM:
    "Also, Cui et al (2011) discuss the progressive loss of VitC synthesis in bats, with reference to its independent loss in haplorrhine primates and guinea pigs."

    And the independent loss in humans as well.

    ReplyDelete
  35. Dr. Moran I am glad you have responded to the point I am making.
    Before we look at how ID would deal with this, we should spend time in thinking about how evolution theory deals with this.

    You have simply asserted that
    "This history is perfectly compatible with modern evolutionary theory."

    But you have given no explanation. You have not even given a just-so story. You simply assert it.
    Please give a scientific explanation about how animals with a distinctly non-advantageous mutation flourished.

    Anyone else can offer an explanation as well.

    ReplyDelete
  36. Anon:'seems to be acknowledging that "non-adaptive features" like the GULOP gene "contradict evolution"."
    Fascinating. I said nothing of the sort.

    "The bottom line is that evolution theory still has a problem explaining how animals with a distinctly non-advantageous mutation flourished."
    But it doesn't. There are plenty of adaptations that would be totally awesome in terms of fitness to have, but not having them hardly means evolution doesn't happen.
    And, again, IDists seem to be saying that non-adaptation, iow lack of function, refutes evolution, but at the same time that there really infact is a secret function, and that it was intelligently designed.
    Dumb.

    Moran: "I assume that Intelligent Design Creationism has a perfectly reasonable explanation of these facts since they have been well-known for deceades and the mark of a scientific theory is that it accounts for known facts. What is the explanation?"

    I think I hear the chirping of intelligently designed crickets.

    ReplyDelete
  37. Same question for Schenck:
    What reasonable explanation does evolution theory provide?
    Please give a scientific explanation about how animals with a distinctly non-advantageous mutation flourished.

    ReplyDelete
  38. Larry - I'd just like to point out that quote was from Anonymous, not from me!

    ReplyDelete
  39. anonymous says,

    If this just-so story is not required, not sufficient, to explain its loss then there must be some other (or additional) reason for the continuing survival and flourishing of animals that have that lost that ability.

    Let's assume, for the sake of argument, that the original mutations was slightly disadvantageous. Nevertheless, it became fixed in the population of the primate ancestors.

    All descendants will, of course, lack the ability to make vitamin C even though it may be beneficial to regain that ability. All descendants will carry the defective gene (pseudogene).

    This history is perfectly compatible with modern evolutionary theory.

    The question is, is it compatible with Intelligent Design Creationism? Inquiring minds want to know.

    Humans have lost the ability to make a dozen or so essential vitamins that other species can make routinely. (They are enzyme cofactors.) We are incapable of making a couple of essential fatty acids that we absolutely need. We can't make half the amino acids that we require for survival.

    These are incontroverible facts of biology. I assume that Intelligent Design Creationism has a perfectly reasonable explanation of these facts since they have been well-known for deceades and the mark of a scientific theory is that it accounts for known facts. What is the explanation?

    ReplyDelete
  40. PaulM says,

    Larry - I'd just like to point out that quote was from Anonymous, not from me!

    Thanks. I apologize.

    I corrected it.

    ReplyDelete
  41. Dr. Moran I am glad you have responded to the point I am making.
    Before we look at how ID would deal with this, we should spend time in thinking about how evolution theory deals with this.

    You have simply asserted that
    "This history is perfectly compatible with modern evolutionary theory."

    But you have given no explanation. You have not even given a just-so story. You simply assert it.
    Please give a scientific explanation about how animals with a distinctly non-advantageous mutation flourished.

    ReplyDelete
  42. anonymous asks,

    Please give a scientific explanation about how animals with a distinctly non-advantageous mutation flourished.

    Nearly Neutral Theory has been around for 28 years. It's covered in all the standard textbooks of evolution and population genetics.

    I'm not surprised that the average IDiot is ignorant of modern evolutionary theory. They're still stuck in the nineteenth century when it comes to their understanding of evolution. That's why they think "Darwinism" is the appropriate name for evolutionary theory.

    It's sad, really, but it's one more reason why I call them IDiots. They don't make even the slighest attempt to understand the theory they criticize. We know this because any textbook would have answered the questions they pose.

    ReplyDelete
  43. When Dr. Moran uses the phrase "modern evolutionary theory" we need to look again at his post entitled:
    Junk & Jonathan: Part 4—Chapter 1
    http://sandwalk.blogspot.com/2011/05/junk-jonathan-part-4-1.html

    Here his conception of "modern evolutionary theory" turns into its opposite with no concern that anyone will notice.

    It is humorous to see him talk in such a high handed manner now.

    And we still do not have an answer to the question:
    What reasonable explanation does evolution theory provide?
    Please give a scientific explanation about how animals with a distinctly non-advantageous mutation flourished.

    ReplyDelete
  44. Evolution theory cannot explain the GULOP feature. But it is even worse than that, because according to Dr. Moran GULOP is not unique:
    "Humans have lost the ability to make a dozen or so essential vitamins that other species can make routinely. (They are enzyme cofactors.) We are incapable of making a couple of essential fatty acids that we absolutely need. We can't make half the amino acids that we require for survival."

    ReplyDelete
  45. Anonymous,

    Here's an idea, find out a little about what evolutionary theory actually is before you start trowing around the bold text and the explanation marks.

    In this case its easy.

    1) It's not actually clear a broken GULO gene would be 'distinctly disadvantageous'. The most parsimonious explanation for the loss of GULO is that the mutation was first fixed in the ancestor of modern monkeys and tarsiers. Most monkeys eat fruit, and fruit-based diet provides enough vitC that losing a the ability to make your own would be no big deal

    2) Slightly deleterious genes get fixed all the time, especially in small populations. Selection can only favour a given gene against alternatives in the population. If the difference between two genes is only small, then, sometimes, the 'best' gene won't be the one that fixed. This is a very basic piece of evolutionary biology - it's fine to not understand something abut it's pretty stupid to rant and rave about a theory before you understand it

    ReplyDelete
  46. David Winter is giving it the old school try. Trying to defend the indefensible.
    Nobody can honestly say that they think that all those distinctly deleterious mutations could go to fixation. That is a ludicrous proposition.

    Please explain how that could happen.
    At least PaulM presented a just-so story.
    Nobody else here has even done that.

    ReplyDelete
  47. You know, I used to think calling people IDiots was unfair...

    ReplyDelete
  48. Anonymous,

    1. You are a complete IDiot. And proud of it.
    2. You are making those questions for rhetorics rather than for answers.
    3. You just want to label any answers as "just-co stories" or continue trying to make it all look contradictory.

    David Winter is giving it the old school try. Trying to defend the indefensible.

    I did not see David trying to defend IDiocy. You on the other hand ...

    Nobody can honestly say that they think that all those distinctly deleterious mutations could go to fixation. That is a ludicrous proposition.

    Who said those mutations were distinctively deleterious? Do you think that the great apes evolved in ships carrying no vitamin C sources?

    Please explain how that could happen.

    People have been trying to tell you that population genetics can explain this. Go read about it. Essentially, if a species evolves in a place where some ability is not needed, the probability for fixing a mutation where a gene product is not much needed increases. Much more if you get population bottlenecks. This is not a just-so story, some math would explain it to you if you cared to take the time to learn it (population genetics).

    At least PaulM presented a just-so story.
    Nobody else here has even done that.


    Well, would you expect lots of answers if all you want to do is label them or throw rhetoric without trying to pay the slightest attention? You are a complete IDiot. Most of us here know that rhetoric is all the IDiots have. Reason and study would be too much for you, wouldn't them? Tricks is all we get from you and then you act surprised that we call you by your proper names (IDiots, liars ...).

    ReplyDelete
  49. All you folks have is bluster and attempts at insults.
    I was expecting just-so stories but you do not even have that.
    Nobody can honestly say that they think that all those distinctly deleterious mutations could go to fixation. That is a ludicrous proposition.
    And we all know it. You are only fooling yourselves.

    ReplyDelete
  50. AND
    Evolution theory cannot explain the GULOP feature. But it is even worse than that, because according to Dr. Moran GULOP is not unique:
    "Humans have lost the ability to make a dozen or so essential vitamins that other species can make routinely. (They are enzyme cofactors.) We are incapable of making a couple of essential fatty acids that we absolutely need. We can't make half the amino acids that we require for survival."

    This is much more than GULOP.

    ReplyDelete
  51. "There are 251 other species and we don't know if they need vitamin C. "

    OK, so on one hand, Wells wants to claim that because a handful of pseudogenes are functional therefore all of them probably are, but on the other hand, he wants to reserve judgement on whether or not ALL monkeys need vitamin C BECAUSE vitamin C requirements have not yet been established in all monkeys...

    Sounds like typical IDCreationist double standards at work.

    AnonX

    ReplyDelete
  52. anonymous says,

    Evolution theory cannot explain the GULOP feature. But it is even worse than that, because according to Dr. Moran GULOP is not unique:
    "Humans have lost the ability to make a dozen or so essential vitamins that other species can make routinely. (They are enzyme cofactors.) We are incapable of making a couple of essential fatty acids that we absolutely need. We can't make half the amino acids that we require for survival."

    This is much more than GULOP.


    I was going to mention that humans have also lost the glyoxylate cycle but I'm not sure how much truth the IDiots can handle in one week.

    ReplyDelete
  53. The just-so story that is given concerning GULOP is that because the animals eat fruit they are not disadvantaged by the loss of the GULO.
    What explanation(s) can be given for the loss of these other vitamins and fatty acids etc?

    ReplyDelete
  54. Anonymous:

    "Nobody can honestly say that they think that all those distinctly deleterious mutations could go to fixation. That is a ludicrous proposition."

    Somehow, Anonymous must have missed all the comments noting that mutations in vitamin synthesis genes aren't deleterious if the vitamin is abundant in the diet. Nobody could honestly think that Anonymous would purposely mischaracterize what people say. That would be a lucidrous proposition.

    ReplyDelete
  55. qetzal, is your thinking concerning all these vitamins, fatty acids, etc that they are all "abundant in the diet" of these animals?
    Can you support that idea?
    Please do.

    ReplyDelete
  56. Anon writes: "Can you support that idea?"

    Ummm... How about: 'The animals aren't dead'

    ReplyDelete
  57. Anonymous the IDiot (aka Anus.) said...

    qetzal, is your thinking concerning all these vitamins, fatty acids, etc that they are all "abundant in the diet" of these animals?
    Can you support that idea?
    Please do.


    It would seem, Anus., that you are lacking some very basic logic there. Your "question" is like asking: "Can anybody support the idea that my ancestors survived to reproductive age?"

    So, tell me: do you see great apes, such as us, around or not? Thus, what would be your conclusion about whether those diets provide enough of those nutrients for these species to survive without those genes? Come on, should be a no brainer even if you are an IDiot. Of course, we know why you pretend to be that stupid. All you want is to create confusion. Answers don't matter to you. I am always amazed at how triumphant IDiots like yourself feel when we just look at you with a perplexed stare. It is a trick for you to claim that you "got us," since you know that your customers won't notice, or will pretend not to notice, that you displayed such an unsurmountable level of stupidity that we are left speechless. What matters is the rhetorical effect. Right Anus.?

    Do you really want the world to think that the "IDiot" title is that much well deserved?

    (I have a note here about what you next rhetorical trick will be. Will you disappoint?)

    ReplyDelete
  58. I am not sure if the people here don't get it or if they are pretending.

    And vulgar to boot.

    ReplyDelete
  59. Anonymous asks:

    What explanation(s) can be given for the loss of these other vitamins and fatty acids etc?

    The same as the explanation of the loss of functionality of the genes and regulatory sequences that promote the growth of leg and foot bones in whales. This results in back leg and foot bones in whales that don't grow enough to be visible outside the whale's body or have any function at all.

    Or are you going to regale us with the notion that we can't say definitively there is no function for the relatively tiny vestigial internal rear leg and foot bones in a whale skeleton?

    I'm sure they must have some design function, and not be leftovers from the whales' land-dwelling hippo-related ancestors, since we know macroevolution doesn't happen and thus common ancestry's a crock, right?

    ReplyDelete
  60. Anonymous,

    Your original claim was this:

    "Evolution theory cannot explain the GULOP feature. But it is even worse than that, because according to Dr. Moran GULOP is not unique...."

    This is proven false. Evolutionary theory can easily explain these features in the manner that I and others have repeatedly described to you.

    Before we let you shift the goalposts, do you at least agree that this is a *possible* evolutionary explanation for these features?

    ReplyDelete
  61. > Prof. Moran: All kinds of strange things happen in biology and the fact that a few pseudogenes might have acquired a regulatory function isn't shocking. What about the other 20,000 pseudogenes?

    The point here being that function in some pseudogenes increases the burden of proof on those who would claim that the remaining ones have no function.

    ReplyDelete
  62. lee_merrill writes:

    The point here being that function in some pseudogenes increases the burden of proof on those who would claim that the remaining ones have no function.

    "I have seen a black swan. This increases the burden of proof on those who contend that most remaining swans are not black."

    Sorry, elementary logic fail.

    ReplyDelete
  63. lee,

    The point here being that function in some pseudogenes increases the burden of proof on those who would claim that the remaining ones have no function.

    This is badly worded and contains a false dichotomy.

    1. The claim from junkers is not that "the remaining" ones have no function, but that only a few might.
    2. What increase in burden of proof? Do you know of any mechanisms that would give functions to all those 20,000 pseudogenes that you mentioned? (Do you now see the problem with those dichotomies?)
    3. In terms of science, we try not to talk in such absolutes ("the remaining" vs. "all 20,000 pseudogenes").
    4. So what burden of proof and who has it?

    Creationists (IDiots are but one subspecies of creationists) feel reinvigorated by that kind of rhetoric, and get all enthusiastic because of the finding of a function for 0.001% of a genome, and then make grandiose claims out of it and write stupid books about it. Scientists prefer science. Scientists rather wait and see, while sometimes making educated predictions.

    ReplyDelete
  64. > Jud: "I have seen a black swan. This increases the burden of proof on those who contend that most remaining swans are not black."

    > Sorry, elementary logic fail.

    Alas, verifying lack of function in X items is not however, analogous to counting up colors. Your analogy would then be flawed.

    ReplyDelete
  65. What lee_merrill has said is logical.
    Folks here just don't want to acknowledge it.

    ReplyDelete
  66. qetzal:
    "Before we let you shift the goalposts, do you at least agree that this is a *possible* evolutionary explanation for these features?"

    In what way am I shifting the goalposts?
    Or are you saying that, just because you like the sound of that phrase?

    ReplyDelete
  67. Moran:
    "All kinds of strange things happen in biology and the fact that a few pseudogenes might have acquired a regulatory function isn't shocking."

    This is the kind of absurd statement that evolutionists make all the time.
    Let's look at the phrase: "Pseudogenes acquiring a regulatory function".
    For evolutionists who have no experience with the development of complicated mechanisms this is the kind of simplistic idea they come up with. Pseuogenes just "acquire" the function - no problem. What a joke.
    I don't expect evolutionists to acknowledge this.

    ReplyDelete
  68. qetzal:
    "..do you at least agree that this is a *possible* evolutionary explanation for these features"?

    The "possible explanation" that has been given so far is a just-so story.
    Evolution theory is filled with these just-so stories.
    If you want to learn about just-so stories, see Moran's article on it.

    ReplyDelete
  69. Anonymous,

    I'm not asking whether you agree with that explanation. I'm just asking whether you agree that it's a theoretically possible explanation that's fully consistent with modern evolutionary theory.

    Not much point in discussing evidentiary support if you're unable/unwilling to acknowledge even the logical possibility.

    ReplyDelete
  70. For evolutionists who have no experience with the development of complicated mechanisms this is the kind of simplistic idea they come up with. Pseuogenes just "acquire" the function - no problem. What a joke.

    You really have no idea whatever what you're talking about, do you?

    "No experience with the development of complicated mechanisms," eh?

    I will personally pledge $100 to either a personal PayPal account or the cause of your preference (your choice) if you can correctly describe even one single valid molecular biological mechanism involved in genes becoming pseudogenes or vice versa of which Dr. Moran has no knowledge.

    ReplyDelete
  71. The issue is not whether I agree or disagree with the just-so story.
    It is still a just-so story. A story made up out of the blue, with no evidence to support it.

    But the bigger issue is whether you are saying that that kind of just-so story would explain all the losses that number well over a dozen according to Moran!

    Is there any limit to how far you want to stretch that type of just-so story.

    Why not just be honest and say that the facts contradict evolution theory?

    ReplyDelete
  72. Anon,

    Your refusal to answer a simple and direct question is noted, but not surprising. I infer that you are the type that cannot bear to admit being wrong about anything.

    The reason I can't honestly say that the facts contradict evolutionary theory is because they don't. I can't quite tell if you're consciously refusing to admit that, or if you simply lack the mental capacity to understand it. Either way, I think I've had enough here. Feel free to tell yourself you won, if that makes you feel better.

    ReplyDelete
  73. > Negative Entropy: What increase in burden of proof? Do you know of any mechanisms that would give functions to all those 20,000 pseudogenes that you mentioned? (Do you now see the problem with those dichotomies?)

    Well, yes, I was referring to Prof. Moran, I agree he may possibly be exceptional in using the broad "junk" brush.

    And the burden of proof does increase when function is found, this increase is not just proportionate to the amount of pseudogenes found to have function.

    I would hope for a healthy skepticism here, negatives such as "no possible function" being rather suspect in an area as volatile as biology has turned out to be.

    Nope, its not just little bags of protoplasm in each cell.

    Nope, you're not likely to get life from a primordial soup.

    Have we even gotten to the bottom of photosynthesis yet?

    ReplyDelete
  74. Evolutionists are very creative at distracting from any issue that they do not wish to acknowledge.
    I am very familiar with it.

    As I said:

    "But the bigger issue is whether you are saying that that kind of just-so story would explain all the losses that number well over a dozen according to Moran!
    Is there any limit to how far you want to stretch that type of just-so story."

    ReplyDelete
  75. "The issue is not whether I agree or disagree with the just-so story.
    It is still a just-so story. A story made up out of the blue, with no evidence to support it. "


    "Anonymous", you're not Rudyard Kipling, you're not Stephen J. Gould and unless I'm very much mistaken you're not Richard Lewontin. So maybe have a think before you bandy that term around again.

    A think, and a closer read of what you are purportedly criticising. Allow me to reiterate: Haplorrine diets typically contain a lot of fruit. Many fruits contain a lot of vitamin C. The loss of vitamin C synthesis under these conditions is consistent with evolutionary theory.

    Note the use of the word 'consistent'. Has the chain of events that caused the loss of vitamin C biosynthesis been demonstrated? No, nor has anyone here claimed it to be. In fact, above I distinctly remember pointing out that either drift or selection could be responsible. It is your claim that GULOP is somehow incompatible or inconsistent with evolutionary theory with which I have taken issue.

    ReplyDelete
  76. Lee,

    I think you missed the point. In any event, I don't see why should every pseudogene have a function, and I don't see why finding functions for some puts any burden of proof at all on junkers. None whatsoever.

    I would hope for a healthy skepticism here, negatives such as "no possible function" being rather suspect in an area as volatile as biology has turned out to be.

    I find it even more suspect to think that everything should have a function. Not only that, I would find such kind of "skepticism" far from healthy. I lean towards most of the genome being junk. If I see a broken gene, it is most probably junk. Thus, I can expect someone to find a function for a few of them, but man, would you expect every broken car to have some function because some broken buses are made into restaurants?

    Nope, its not just little bags of protoplasm in each cell.

    I never said the opposite.

    Nope, you're not likely to get life from a primordial soup.

    I dont know. Maybe yes, maybe not. But you're at least somewhat likely to get life out of something primordial. Otherwise we would not be here.

    Have we even gotten to the bottom of photosynthesis yet?

    Yes. But suppose we hadn't. What would that mean other than we still don't know? I'll make it easier for you to grasp. Once we did not know that thunder was a natural phenomenon. Did our ignorance make it truly the work of Thor, or was it a natural phenomenon before we learned about it being so? Apply this to knowing or not about photosynthesis. Not knowing would not make Hegemone or Demeter or any other gods real. Not even by a little tiny bit. Would it?

    ReplyDelete
  77. PaulM, you and the others here want me to evaluate your just-so story. Whatever I say will not change the fact that it is a just-so story.

    But even taking your just-so story seriously, are you proposing that that story has occurred in the over a dozen situations that Moran mentioned?

    How many times do you want to use that particular story?

    ReplyDelete
  78. Anonymous writes:

    It is still a just-so story. A story made up out of the blue, with no evidence to support it.

    I don't know where you think you're going with this, but it really isn't headed anywhere good for you.

    It's an observed fact that various mammals, including primates and thus humans, have lost the ability to synthesize Vitamin C. Since we're still here, the Vitamin C had to come from food sources. This is so whether it occurred via evolution or through the fiat of a designer.

    Lets' consider the design alternatives.

    "Front loading" is one hypothesis that's been floated by Intelligent Design supporters. So let's see, the designer made changes to primate genomes so people around the world could suffer from scurvy? Hmm, doesn't seem like a good idea, does it? So much for the concept of genetics being forward-looking.

    There are other Intelligent Design supporters who question common descent, so "front loading" is not available to them. For them, design decisions have to be made on an individual species basis. For them, a designer had to individually decide that gorillas, orangutans, chimps, and humans should lack the ability to synthesize Vitamin C. For the apes, this isn't a problem because there are dietary sources. For humans outside of the African savannahs where we evol- err, were originally designed, it's a big problem. Not terribly good, forward-looking design, is it - unless you think it was purposeful and G- err, the designer, had it in for British sailors.

    So it's either evolution or crappy design - which would you rather blame it on?

    ReplyDelete
  79. Here is what I posted:
    "PaulM, you and the others here want me to evaluate your just-so story. Whatever I say will not change the fact that it is a just-so story.

    But even taking your just-so story seriously, are you proposing that that story has occurred in the over a dozen situations that Moran mentioned?

    How many times do you want to use that particular story?"

    Do people think this subject will go away if they simply ignore it?

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

    ReplyDelete
  81. Anonymous:"But even taking your just-so story seriously, are you proposing that that story has occurred in the over a dozen situations that Moran mentioned?

    Great. So, did you actually read my post from start to end?

    Quite aside from your ignorant misuse of the term 'just-so' story, could you explain why it is implausible for genetic drift to act on 'more than a dozen' loci? Does it have an upper limit of 12?

    "How many times do you want to use that particular story?"

    I want to use it 30 more times and then I'll stop.

    But thank you, I must remember that response next time someone wants talk to me about jesus. I will ask them, "How many times do you want to use that particular story?"

    "Do people think this subject will go away if they simply ignore it?"

    Why would I want it to go away?

    ReplyDelete
  82. Okay, finally someone (in this case Paul) has actually acknowledged that evolution theory requires the just-so story for all these other vitamins, fatty acids etc.

    The story for Vitamin C is that there was ample fruit available, so it was not necessary or even advantageous to produce it endogenously.

    So for all these other vitamins, fatty acids etc the idea is that there was ample sources providing all of them?

    Do people really think that anyone will buy that idea?

    Why even pretend that will fly? It is absurd and we all know it.

    ReplyDelete
  83. "Okay, finally someone (in this case Paul) has actually acknowledged that evolution theory requires the just-so story for all these other vitamins, fatty acids etc."

    Sigh.

    As much as I enjoy having my every word distorted and misrepresented, I think I'm done with this thread.

    ReplyDelete
  84. Anus. The IDiot said,

    Why even pretend that will fly? It is absurd and we all know it.

    Of course it's absurd. Our diets providing what those pseudogenes don't produce? Nonsense!

    [We still have this little problem: if our genes don't produce such necessary nutrients/cofactors/whatever, and our diets don't contain them, why are we alive? But who cares, it is still absurd to suppose that our diets provide anything. Anus., The Utmost IDiot, has said so, and that makes it so!]

    ReplyDelete
  85. Anonymous writes:

    Okay, finally someone (in this case Paul) has actually acknowledged that evolution theory requires the just-so story for all these other vitamins, fatty acids etc.

    The story for Vitamin C is that there was ample fruit available, so it was not necessary or even advantageous to produce it endogenously.

    So for all these other vitamins, fatty acids etc the idea is that there was ample sources providing all of them?

    Do people really think that anyone will buy that idea?

    Why even pretend that will fly? It is absurd and we all know it.

    It is extremely difficult to believe that even you are that thick.

    Do animals need food? Yes. Why? Because they can't synthesize all the substances they require. What happens when you or any living thing gets no food? It dies. Are we and all the apes dead? No. Are we therefore getting all nutrients essential for life from dietary sources? Why yes, I suppose that is the inescapable conclusion, isn't it?

    Does hypothesizing a designer change any of this? Lets' see - we and the apes need food, aren't dead, and are therefore getting all the nutrients we need from diet, designer or no designer - so I guess having a designer doesn't change anything.

    Anything about the above that you care to argue with? You want to try to convince us that we don't need food, or that we're not alive?

    ReplyDelete
  86. Evolutionists are very creative at distracting from any issue that they do not wish to acknowledge.
    I am very familiar with it.

    As I said:

    "But the bigger issue is whether you are saying that that kind of just-so story would explain all the losses that number well over a dozen according to Moran!
    Is there any limit to how far you want to stretch that type of just-so story."

    ReplyDelete
  87. Anonymous writes:

    Evolutionists are very creative at distracting from any issue that they do not wish to acknowledge.

    Yes, let's not distract from the issue. The issue is that animals have lost abilities they once had, and you think saying the environment is relevant (allows the animals to live despite the lost abilities) is a problem for evolution.

    So I guess the fact that fish can breathe underwater but we can't is a problem for evolution?

    ReplyDelete
  88. Here is the total of what you folks have contributed:
    "If there was a high level of vitamin C, e.g. fruit, in the diet of the ancestral haplorhine species in which GULO became GULOP, then the synthesis of vitamin C is not beneficial and its loss via genetic drift becomes possible".

    This is your just-so story related to GULOP.
    Moran mentions the other vitamins, fatty acids etc for which there is a loss.

    Are people here thinking that the
    high level of FRUIT, in the diet of the ancestral haplorhine species satisfied the need for ALL these other vitamins etc. as well?

    This is a pretty simple question, but let's see how people avoid answering it.

    ReplyDelete
  89. It looks like people are avoiding answering it by ignoring it.
    Do people think this subject will go away if they simply ignore it?

    ReplyDelete
  90. Yes. It's a senseless, dishonest question, and those are always best ignored, as are the dishonest people that ask them.

    BTW, Have you stopped beating your wife?

    ReplyDelete
  91. Anonymous writes:

    Do people think this subject will go away if they simply ignore it?

    No, we know you're determined to keep asking as if there really were a valid subject.

    ReplyDelete
  92. Looks like ScienceAvenger wants to distract from the question I have posed.
    "Are people here thinking that the
    high level of FRUIT, in the diet of the ancestral haplorhine species satisfied the need for ALL these other vitamins etc. as well?"

    Is anyone willing to answer this question?

    ReplyDelete
  93. Anonymous, please tell us in detail how the Designer coped with the fact that we cannot efficiently digest grass like cows. I want to see what sort of just-so story you come up with about how we replace those vital nutrients.

    And you still haven't answered how the Designer managed to cope with the fact that we cannot breathe underwater like fish. Inquiring minds want the answer to that one also.

    Please do tell us how the Designer managed to make humans viable without these abilities, essential to maintaining life, that other animals possess.

    ReplyDelete
  94. From the panicky and vulgar posts from the folks here, I can see that they actually understand the problem they have, that I am pointing out.
    They have to make themselves believe (pretend they believe) that the food sources for ALL the vitamins, fatty acids etc were so abundant for ALL of them that the creatures could survive the loss of the endogenous production of All of those vitamins, fatty acids etc.
    Everyone knows that is absurd.

    No creatures ever experienced that abundance of All those food sources supplying ALL those essential vitamins, fatty acids etc.

    This is a scientific question and your attempt to personalize it does not change the facts

    But pretend you do not get it. That is up to you.

    ReplyDelete
  95. Anonymous writes:

    From the panicky and vulgar posts from the folks here....

    Vulgar? Is it because I mentioned cows?

    ...I can see that they actually understand the problem they have....

    The problem we have? If you think so, you don't understand the problem.

    It's a problem for everyone - how do living things survive despite lacking abilities that are vital to the viability of other living things?

    It's a problem for you as well, but you've completely refused to respond when the question's been asked repeatedly. So I'm politely inviting you once again: If you are so knowledgeable that you can characterize the obvious, logical answer you've received multiple times now as a "just-so story," what's the real answer?

    ReplyDelete
  96. Anonymous writes:

    No creatures ever experienced that abundance of All those food sources supplying ALL those essential vitamins, fatty acids etc.

    So we don't get the vitamins, fatty acids, etc., essential for life from our diets? Then how are we alive?

    Simple question: Where do we humans get the nutrients essential for our survival, if not from our diets? Please do favor us with your answer.

    ReplyDelete
  97. "No creatures ever experienced that abundance of All those food sources supplying ALL those essential vitamins, fatty acids etc."

    How do you suppose Anon. thinks those creatures survive right now, today? Does he think they buy supplements from their local GNCs?

    This guy is comedy gold!

    ReplyDelete
  98. Just a reminder of the just-so story given by PaulM:

    "If there was a high level of vitamin C, e.g. fruit, in the diet of the ancestral haplorhine species in which GULO became GULOP, then the synthesis of vitamin C is not beneficial and its loss via genetic drift becomes possible. "

    AND

    from qetzal:
    "mutations in vitamin synthesis genes aren't deleterious if the vitamin is abundant in the diet."

    Note the requirement that the food source must be "abundant".
    When were food sources "abundant" for providing ALL the vitamins, fatty acids etc.

    Will someone be honest and acknowledge the problem or will everyone just keep pretending not to get it?

    ReplyDelete
  99. The Anonymous logician asked, deeply:"When were food sources "abundant" for providing ALL the vitamins, fatty acids etc."

    Never, and certainly not now. There's good evidence for that. It's a massive problem, the importance of which could hardly be overstated.

    All species that ever lost biosynthetic pathways experienced extended illness before presumably going extinct. As predicted by population genetics and observed in situ, such deleterious loss-of-function mutations spread rapidly through populations. It is a notorious problem (e.g. Anonymous, 2011).

    As qetzal was forced to admit, dietary needs aren't and couldn't possibly be met by diet. It's not feasible for a diet to include so many naturally occurring compounds. It would be just too large a coincidence for the plants and/or animals in a diet to fortuitously contain those compounds. Frankly, it beggars belief. Hence, the extinction of those species that have lost biosynthetic pathways has occurred, most regrettably including our own species. Their status as extant species is nothing more than a lie, perpetrated by the evolutionists, who are also communists, which is a terribly dishonest thing to be.

    Unfortunately, the consequence for us all is that we must admit that life itself is not 'real', but rather more like a dream and we are the imagination of ourselves (Hicks, 1989).

    ReplyDelete
  100. Paul is good at sarcasm.
    When you don't have the facts on your side then sarcasm and ridicule is all you can try.

    I am familiar with evolutionists pretending.

    ReplyDelete
  101. Paul is so right!

    Plus, have you ever seen a cat breed with a dog and give birth to a dat?!! Of course not! And even if you had, it would immediately go extinct due to vitamin deficiency.

    And what holds up the sky?

    ReplyDelete
  102. The idea behind Paul's post is that evolution theory must be correct because we exist.
    But evolution theory cannot account for our existence. GULOP and the other losses contradict evolution theory.
    There is a flaw in people's thinking which is hard for them to see. The flaw is that our existence does not prove any particular explanation. The explanation must stand on it's own.

    Evolution theory based on mindless, random action is contradicted by GULOP and the other losses.

    Only an explanation which includes the intelligence of Nature and the intelligence of the cell can explain the evidence.

    ReplyDelete
  103. Anonymous said...
    GULOP and the other losses contradict evolution theory.

    I am unsure of what charactetures of the actual evolutionary theory you are referring to.

    Some papers that can show the adaptive value of gene loss. Not to say it must be adaptive. Just limiting the search.

    Human-specific;
    References 15-25, found here...
    http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040052

    Recurrent gene loss and change in vertebrates;
    http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0022890/pdf

    Bacterial;
    http://life.bio.sunysb.edu/dykhuizenlab/papers/tim99a.pdf

    A system somewhat analogous to the example you are blathering about is bacterial symbiont gene loss.
    First, host tissues provide a constant supply of many metabolic intermediates, eliminating the pressure to maintain many biosynthetic genes; all small genome pathogens and symbionts obtain some amino acids and cofactors from hosts. Second, even if living within a host does not affect the intensity of selection on a gene, it can amplify the corrosive forces of mutation and genetic drift, resulting in loss of beneficial but non-essential genes. This occurs because host-associated bacteria have small genetic population sizes relative to free-living relatives.
    http://www.sciencedirect.com/science/article/pii/S1369527403001073

    ReplyDelete
  104. "GULOP and the other losses contradict evolution theory."

    War is peace! Freedom is slavery! Ignorance is strength!

    Anon. is especially partial to that last one.

    ReplyDelete
  105. Paul posted:
    "The Anonymous logician asked, deeply:"When were food sources "abundant" for providing ALL the vitamins, fatty acids etc."
    Never, and certainly not now. There's good evidence for that. It's a massive problem, the importance of which could hardly be overstated."

    That part of Paul's post is correct.
    And that is indeed a "massive problem" for evolution theory.

    ReplyDelete
  106. Anonymous writes:

    Evolution theory based on mindless, random action is contradicted by GULOP and the other losses.

    Only an explanation which includes the intelligence of Nature and the intelligence of the cell can explain the evidence.

    Here are a few questions. Please provide a reasonable, logical answer to any one of them based on "the intelligence of Nature" or cellular intelligence.

    - How do "the intelligence of Nature" or cellular intelligence account for GULOP and the other losses?

    - If vitamin C is not available in the diet, how does cellular intelligence allow survival of creatures that lack the ability to synthesize vitamin C?

    - What in cellular intelligence accounts for diseases stemming from genetic mutations (e.g., cancer)? Are these cells stupid, or have they gone over to the Dark Side and become Al Qaeda "cells"?

    - Similar question with regard to the recent E. coli outbreak in Europe. What in cellular intelligence accounts for the mutation of bacteria that normally coexist peacefully with humans (in fact, are necessary to our healthy existence) into forms that sicken or kill us?

    - Again with respect to the E. coli outbreak, what in cellular intelligence accounts for the fact that some people die while others only become ill? Are their cells less intelligent?

    - Are introns or other "junk DNA" the fount of cellular intelligence? If so, why do onions and primitive species of worms need more cellular intelligence than we do, and where do we see indications of this superior intelligence manifested?

    - What in "the intelligence of Nature" or cellular intelligence accounts for men having nipples?

    ReplyDelete
  107. @Anon
    You do realize that primate diet has been previously studies and contains ample amounts of micronutrients....

    Your argument rests on the premise that native populations of primates are all nutrient deficient, but why then aren't wild primate populations dying of scurvy?

    Your failure to grasp this extreme simple point after it has been pointed out multiple times is incredible.

    Also as a note- people aren't slow to answer you because your questions are difficult but because they are mind blowingly stupid.

    ReplyDelete
  108. Moran posted:
    "Humans have lost the ability to make a dozen or so essential vitamins that other species can make routinely. (They are enzyme cofactors.) We are incapable of making a couple of essential fatty acids that we absolutely need. We can't make half the amino acids that we require for survival."
    AND
    "I was going to mention that humans have also lost the glyoxylate cycle".

    ReplyDelete
  109. Further to the 7 questions I asked Anonymous earlier, here's another I'd forgotten:

    - Why didn't "the intelligence of Nature" and/or cellular intelligence prevent GULOP and the loss of the glyoxylate cycle?

    ReplyDelete
  110. @Anon
    Ok lets me try to put this as simply as goddamn possible. Haplorrhini needs X to survive, Haplorrhini gets X from diet, do Haplorrhini need to be able to synthesis X to survive?

    NO!!! How is this not completely obvious. I need water to survive, I cannot synthesis sufficient amounts of water to keep myself alive, but this has never been an issue for me because I don't live in a bloody desert.

    The lose of these pathways were not deleterious in the environment ancient Haplorrhini lived in, if evolutionists were postulating this all happened onboard a 17th century sailing ship,then you would have a point but they arn't and you don't.

    ReplyDelete
  111. Boojum said to Anonymous:

    "Also as a note- people aren't slow to answer you because your questions are difficult but because they are mind blowingly stupid."

    Even his mind blowingly stupid questions have already been answered dozens of times. Yet he cotinues to insist that they haven't. That's the real reason people aren't bothering to answer him any more.

    ReplyDelete
  112. Boojum posted:
    "The lose of these pathways were not deleterious in the environment ancient Haplorrhini lived in,"

    Please give a reference or two to support that statement.
    When and where did the "ancient Haplorrhini" live?

    It would be particularly helpful if you could present evidence for the claim of abundance of the various food sources that supplied the range of vitamins, fatty acids and glyoxylate cycle that Moran mentioned.

    ReplyDelete
  113. Jud asked: "Why didn't "the intelligence of Nature" and/or cellular intelligence prevent GULOP and the loss of the glyoxylate cycle?"

    Um, because that didn't even happen, Jud. Evolution is a just-so story perpetuated by anarcho-communist atheists. You're not looking at it logically, so let me explain:

    God took away GULO, the glyoxylate cycle and other biosynthetic pathways to properly punish mankind for eating an apple.

    It is appropriate that especially poor people today suffer from malnutrition to pay for what they didn't personally do in the garden of eden. There's an important lesson for all of us in that.

    Now they - and we - know never to do it again, or even for the first time. Instead we learn to cower appropriately under the mercy of our ever-loving God. His apparent absence - puctuated by bouts of fruit-based traps and pestilence - is not for us to contemplate. Ours is the special unquestioning love of a cosmic Stockholm Syndrome.

    It's all very simple.

    The alternative is some sort of population genetics myth, propped up with all sorts of fancy statistics. And I really don't trust that sort of thing.

    ReplyDelete
  114. @Anon
    You mean like these...

    Milton K. Micronutrient intakes of wild primates: are humans different? Comp Biochem Physiol A Mol Integr Physiol. 2003 Sep;136(1):47-59.

    Smith T., Rose K. D., Gingerich P. D. 2006 Rapid Asia–Europe–North America geographic dispersal of earliest Eocene primate Teilhardina during the Paleocene–Eocene Thermal Maximum. Proc. Natl Acad. Sci. USA 103, 11 223–11 227.

    ReplyDelete
  115. Thanks, Paul. I doubt Anonymous' version would be as coherent. In fact I doubt Anonymous will have any explanation at all, since as I recall, previous calls for him to say anything at all in support of what he says is a vastly superior explanation have been met with deafening silence. Quite odd considering the huge volume of his recent output here. One would almost think his alternative theory doesn't really exist, eh?

    ReplyDelete
  116. I think we have missed something important.
    Moran posted:
    "Humans have lost the ability to make a dozen or so essential vitamins that other species can make routinely. (They are enzyme cofactors.) We are incapable of making a couple of essential fatty acids that we absolutely need. We can't make half the amino acids that we require for survival."
    AND
    "I was going to mention that humans have also lost the glyoxylate cycle".

    We are only talking about humans, not monkeys.
    Humans lack these vitamins, fatty acids etc.
    We are not talking about monkeys (aside from GULOP).
    We are talking about all the vitamins, fatty acids etc lost in humans that Moran listed.

    When did all that happen in humans?

    ReplyDelete
  117. Anonymous writes:

    When did all that happen in humans?

    When the "intelligence of nature" and cellular intelligence permitted it to, evidently. I'm sure you'll be able to tell us when and how that occurred.

    ReplyDelete
  118. Humans lack the ability to make the vitamins, fatty acids etc. that Moran mentioned

    I have asked people here to say WHEN that happened.
    We can then look into what food sources were available at that time (and their abundance or lack of abundance).

    That will give us an objective and scientific way to judge this topic.

    ReplyDelete
  119. @Anon
    I suspect you already know the answer yourself and your just trolling. As far as I'm aware all these pathways were lost prior to the divergence from chimps.

    All that your pedantry reveals is you have no substantial arguments to make.

    ReplyDelete
  120. Perhaps Dr. Moran can contribute.
    When did the losses occur?
    And was it before or after the claimed split from apes/monkeys?

    ReplyDelete
  121. Still no answer by Anonymous to even a single one of my questions.

    Yet he claims "an explanation which includes the intelligence of Nature and the intelligence of the cell can explain the evidence" - in fact that only such an explanation will suffice.

    I think his claim of an explanation is, in Shakespeare's words, "full of sound and fury, signifying nothing," i.e., I think he has never had such an explanation.

    So here's your big chance, Anonymous. Prove me wrong. Better yet, prove yourself right. Give us that explanation, the existence of which you so confidently and recently proclaimed, and show us all you have something more than empty bluster behind your words.

    ReplyDelete
  122. Jud, I have already said that talking to you is a waste of time.

    Perhaps Dr. Moran can contribute.
    When did the losses occur?
    And was it before or after the claimed split from apes/monkeys?

    ReplyDelete
  123. "I think we have missed something important.
    Moran posted:
    "Humans have lost the ability [...] We are only talking about humans, not monkeys."


    I think you missed something important. Referring specifically to the ability to synthesize the Vitamin C, this is obviously a feature shared by all Haplorrhini suborder of the Primates (including here the Tarsiers which stay with Anthropoidea, according also to Pollock and Mullin - "Vitamin C biosynthesis in prosimians: Evidence for the anthropoid affinity of Tarsius". American Journal of Physical Anthropology 73 (1): 65–70, 1987) and differentiates us from Strepsirrhini. Since on all branches of the clade the aforementioned ability has been lost, the decisive common mutation which turned off the functionality of the terminal enzyme has occured:
    1. after the branching between Strepsirrhini and Haplorrhini (~ 63 MYA BP)
    2. before the divergence of the Tarsiidae and Anthropoidea (~ 58 MYA BP)
    Dr. Moran used the word "Humans" because his argument was built on our own species (genus) and he's obviously right: we humans are Haplorrhini and consequently the mutation occurred on our own lineage. What Dr. Moran did not mention in the same phrase (but it was more than obvious from all other comments) is that at the moment of the mutation one could not speak yet about Humans but about "ancient Haplorrhini".

    If you are interested in refining the time-window for the mutation, you should give a look to a recent article coping specifically with that issue (M.Y. Lachapelle & G. Drouin - Inactivation dates of the human and guinea pig vitamin C genes, Genetica 139:199–207, 2011) from which I quote: "We used a method based on sequence comparisons of lineages with and without functional GLO genes to calculate inactivation dates of 61 and 14 MYA for the primate and guinea pig genes, respectively. These estimates are consistent with previous phylogeny-based estimates." Incidentally, you may notice that the authors also speak about "human" gene even if it referes to a larger group than humans.

    ReplyDelete
  124. "We can then look into what food sources were available at that time (and their abundance or lack of abundance)"

    As stated, the problem is ill-posed. You should keep in mind a basic common-sense tenet of biology of populations: if a population survives at the time T, their ancestors survived somehow at any time T' < T . That implies the biological needs of the ancestors have necessarily been met by then available supplies of food, water, atmosphere etc. at any moment in the past.

    We know that nowdays primates do have a more or less omnivourous diet in which fruits are an essential part, see for instance:

    "All primates eat a variety of different food items to obtain the carbohydrates, fats, and proteins they need. Energy and nutrient requirements vary with body size and metabolism, and, therefore, differ among individuals and species (Sussman, 1978). [...] most primates consume a variety of different food types, with the majority considered to be either insectivore-frugivores or frugivore-folivores because, while nearly all primates consume some fruit as their primary sources of energy, they differ in whether they rely on insects or leaves for their protein." (Strier - Primate Behavioral Ecology 4th ed., Pearson 2011)

    "There is a strong tendency toward omnivory in primates, and their tooth pattern, though heterodont, is generalized for the consumption of foods from many sources. Most species will favor some kinds of foods over others, but all will consume a variety of fruits, nuts, leaves, and other plants, in addition to some meat." (T. Holmes - Primates and Human Ancestors: the pliocene epoch, Chelsea House 2009)

    A shared feature of all members of a clade has a very high probability to characterize also their ancestors, so one can safely infer that ancient Haplorrhini were also regular fruit eaters. This view is supported by independent considerations:

    "The size and morphology of molar teeth from 38 species of omomyoid primates were compared to those of an extant database to investigate the dietary adaptations that may have characterized omomyoids. These comparisons indicate that the overwhelming majority of these early primates, especially the anaptomorphini and trogolemurini, were primarily frugivorous." (S. Strait - Dietary reconstruction of small-bodied omomyoid primates, Journal of Vertebrate Paleontology, 21(2):322-334. 2001)

    "The variety of dental pattern is great, however, so inference as to diet is at best a variety of fruit, flower, nectar, gum, and insect feeding, with no clear-cut emphasis in any reconstructed common ancestor. [...] Sussman (1995) and I are in broad agreement on the importance of frugivory early in primate evolution." (F. Szalay - Ancestral Locomotor Modes, Placental Mammals, and the Origin of Euprimates: Lessons from History, in Primate Origins: Adaptations and Evolution, Springer 2007)

    "In addition, primate gut morphology reflects adaptations for an omnivorous diet (Martin et al., 1985). Sussman (1991, 1999; Sussman and Raven, 1978), therefore, proposed that early primates had an omnivorous diet that included a significant part of plant material [...] the first primates would, therefore, have had to include a substantial amount of fruit in their diet." (A. Muller, C. Soligo, U. Thalmann - New Views on the Origin of Primate Social Organization, in Primate Origins: Adaptations and Evolution, Springer 2007)

    So the frugivority of the first Primates and Haplorrhini looks like a very safe assumption. Now, we recall that if the Primates are an extant order, the necessities of their ancestors (including regular fruit eating) have been met at any moment in the past. Consequently, wherever these ancestors were to be found, they necessarily were finding the needed fruits containing fair amounts of Vitamin C. You may bet on that as safe as on the existence of water or of atmospheric oxygen in their origin area.

    ReplyDelete
  125. Jud, I have already said that talking to you is a waste of time.

    O, Brave Sir Anonymous! All over the comments here, and not one single question have you dared answer having to do with this superior "explanation" you supposedly have for all the "problems" you cite with evolutionary theory.

    You have no explanation. The "problems" you cite are with your (lack of) understanding of evolutionary theory, not with the theory itself.

    So, a bravely claimed explanation that is never forthcoming. You, sir, are a fraud, and a loud one at that.

    Still a chance to make me eat these words, and more important, show you are something other than a fraud - just come forward with your promised explanation.

    ReplyDelete
  126. Hello M. Dionis.
    Thank you for all the references and the quotes from those references.
    Please note that I am talking about all the other losses beyond GULOP.

    Can you address the many non GULOP losses please?
    When did they occur? What was the food situation like at that time (or those times)?
    What creature are we actually talking about? What genus? What species?

    Together we may be able to analyze this to a conclusion.

    I am also hoping that Dr. Moran will contribute. Presumably he knows this topic well.

    ReplyDelete
  127. Anonymous writes:

    Can you address the many non GULOP losses please?

    When did they occur? What was the food situation like at that time (or those times)?

    What creature are we actually talking about? What genus? What species?

    Together we may be able to analyze this to a conclusion.

    "Together"? "We"?

    Does this mean we can anticipate your long-awaited explanation, showing how evolutionary theory is inadequate, and bringing into play "the intelligence of Nature and the intelligence of the cell"?

    O, do let it be so!

    ReplyDelete
  128. To get the discussion going let me ask the following:
    Did the non-Gulop losses occur during the time of Australopithecus?
    If not, during what period?

    ReplyDelete
  129. Jud asks of Anonymous:

    "Does this mean we can anticipate your long-awaited explanation, showing how evolutionary theory is inadequate...."

    But of course, Anon. has already shown that last part. As he's said repeatedly, he thinks it's absurd that the food sources for ALL the vitamins, fatty acids etc were so abundant for ALL of them that the creatures could survive the loss of the endogenous production of All of those vitamins, fatty acids etc.

    Clearly, evolutionary theory is inadequate for Anonymous. Whether the fault lies in evolutionary theory or in Anonymous is left for the reader to judge.

    ReplyDelete
  130. This topic is not a question of opinion. It is a question of fact. What are the facts?

    For example:
    To get the discussion going let me ask the following:
    Did the non-Gulop losses occur during the time of Australopithecus?
    If not, during what period?

    And I am still hoping that Dr. Moran will contribute as well.

    ReplyDelete
  131. qetzal writes:

    Clearly, evolutionary theory is inadequate for Anonymous.

    Yes, what I've been waiting for from Anonymous is the intelligence aspect.

    ReplyDelete
  132. @Anon
    Why don't you just look it up yourself? No one here seems to be particular keen to waste the rest of their day looking up data on every single dysfunctional synthesis pathway in the human body. If your too lazy for this option how about picking out ONE pathway to troll people about and you may actually irritate someone sufficiently to get a reply after a few days.

    ReplyDelete
  133. Hi Boojum.
    It is silly and rude to claim me of trolling when I have asked you and the others reasonable questions that you then evade.
    Can you answer the question I have been asking? For example did any of the losses that Moran listed occur in
    Australopithecus?

    ReplyDelete
  134. Dr. Moran can you answer my question? That would be very helpful.

    Can anyone answer my question?

    ReplyDelete
  135. @Anon
    There were many loses and occurring at many different times, I am not wasting the rest of the day looking every single one of them up. If you think that these loses are incompatible with evolution then demonstrate it yourself, we have already indulged you by answering your ridiculous questions for well over a hundred comments. Why is it in any way reasonable to expect others to do all the work for you?

    Your argument up to this point has been "I don't think this could happen" and when asked if you have any evidence to back this up you reply "find it for me".

    ReplyDelete
  136. Anonymous writes:

    when I have asked you and the others reasonable questions that you then evade.

    This blog has been full of people answering your repeated questions, only to receive the consistent reply from you that our answers are inadequate and don't measure up to your explanation. But when asked quite reasonably what that explanation is, you have consistently evaded giving it.

    ReplyDelete
  137. People here (including Moran) do not seem able to present any material about the timing of the losses that Moran listed.
    And yet you are all very sure that evolution theory can explain it.
    Even though nobody here has a clue about when those losses took place, what creature (species, genus) was involved and what the food sources were like at the time.

    Is there anyone honest enough to admit it?
    Or will people keep pretending and making excuses.

    ReplyDelete
  138. Anonymous writes:

    People here (including Moran) do not seem able to present any material about the timing of the losses that Moran listed. And yet you are all very sure that evolution theory can explain it.

    You seem unable to answer a single question about how "an explanation which includes the intelligence of Nature and the intelligence of the cell" can make up for what you claim are the inadequacies of evolutionary theory. Yet you have not withdrawn your positive claim that you have a superior explanation.

    Is there anyone honest enough to admit it?

    Are you honest enough to admit that the reason your explanation isn't forthcoming is because you have no such explanation?

    Even though nobody here has a clue about when those losses took place, what creature (species, genus) was involved and what the food sources were like at the time.

    You're ignoring multiple research articles cited in the responses to you that give answers to many of the questions you've asked. But in a time-honored tactic, once many of your questions are answered you simply ask more and more until people run out of time and patience to do your work for you, then claim "victory." It's such a hollow triumph, in reality a sad loss on your part. You are missing so much fascinating knowledge, the sort of thing that has drawn us to science.

    Or will people keep pretending and making excuses.

    Or will you keep pretending you have such an explanation, and making excuses for your entire failure, after over a hundred comments here, to present any reasoned argument laying it out?

    ReplyDelete
  139. By the way, speaking of the fascination of science, and of fruit diets, here's a very interesting article on reproductive isolation and incipient speciation in apple maggots:

    http://www.biomedcentral.com/1471-2164/10/633

    ReplyDelete
  140. This topic is not a question of opinion. It is a question of fact. What are the facts?

    For example:
    To get the discussion going let me ask the following:
    Did the non-Gulop losses occur during the time of Australopithecus?
    If not, during what period?

    And I am still hoping that Dr. Moran will contribute as well.

    Given that this is a blog about evolution, written by a university professor, it is odd that nobody (including that professor) can answer the simple question that I have posed.

    ReplyDelete
  141. Anonymous wrote:
    Can you address the many non GULOP losses please? [...] People here (including Moran) do not seem able to present any material about the timing of the losses that Moran listed.

    Do you really believe that not giving a quick answer to a rather long list of questions you rose indicates inability to answer?! You should consider that blog comments, while entertaining to some extent, are not rewarding in terms of scientific research and nobody gets paid for illuminating anonymous contributors on some issues of scarse interest with tons of information and references. Since this is a key limiting parameter, in order to save everybody's time I suggest you to focus on a few losses mentioned by Dr. Moran.

    Did the non-Gulop losses occur during the time of Australopithecus?

    Not necessarily. Actually, since the number of pseudogenes in the human genome ranges in the (tens of) thousands, a small fraction of the associated losses are statistically "recent"; for instance we humans... "have lost activity of the enzyme CMP-N-acetylneuraminic acid hydroxylase because of a 92-bp deletion in the corresponding CMAH gene. The normal mammalian enzyme converts the sialic acid derivative N-acetylneuraminic acid into N-glycolylneuraminic acid, which is generally found on the cell surface. The loss of enzyme activity in humans could have had far-reaching consequences, e.g., in the modulation of interactions of cells with pathogens that use sialic acid derivatives as receptors (Chou et al. 1998 [...])." (H. Winter et al. - Human type I hair keratin pseudogene ϕhHaA has functional orthologs in the chimpanzee and gorilla: evidence for recent inactivation of the human gene after the Pan-Homo divergence, Hum Genet (2001) 108:37–42; the authors study essentialy the keratin pseudogene inactivation which happened at most 240 KYA BP). For an overview of some recent losses see e.g. Wang X, Grus WE, Zhang J (2006) Gene losses during human origins. PLoS Biol 4(3):e52; most of them are marginal or have "good" implications: "The overwhelming overrepresentation of chemoreception and immunity functions among the human-specific pseudogenes indicates substantive changes in these two aspects of physiology during human evolution. The loss of chemoreception genes is broadly consistent with the common belief that humans have a reduced sense of smell [...] and may reflect significant changes in the way humans interact with each other and with the environment, human diet, and human behavior during the past few million years [...]. The losses of many immunity genes are consistent with and may in part account for the many differences between humans and their related primates in susceptibility to various pathogens such as HIV/simian immunodeficiency virus and Plasmodium falciparum (malaria)." Some adaptive gene losses are also taken into account, see also Zhu et al. (2007) Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol 3(12): e247.

    you are all very sure that evolution theory can explain it

    Of course. The standard interpretation is straightforward: either an otherwise deleterious inactivation is hidden by some redundance (as is the mechanism proposed by Koshizaka et al. 1988 for the GULOP pseudogene: the guinea pig/human ancestors had a diet naturally rich in ascorbic acid -> the loss of the enzyme did not constitute a disadvantage), or the loss causes an adaptive advantage (as for the CMP-N-acetylneuraminic acid hydroxylase, see Chou et al. 2002. Inactivation of
    CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. PNAS 99:11736). For your other perplexities, don't forget the basic tenet; e.g. what about whales and the loss of external legs: do you really think their ancestors lost the legs while still on ground? or the ancestors of ground tetrapodes lost the ability to breathe under water while still in water?! Face it: all ancestors of extant species have been fit.

    ReplyDelete
  142. M. Dionis posted:
    "Do you really believe that not giving a quick answer to a rather long list of questions you rose indicates inability to answer?!"

    Anyone can answer concerning ANY one. That would be fine.
    Moran listed a number of losses.
    Can anyone take any one of those losses and say if it occurred at the time of Australopithecus?
    And if that loss did not occur in Australopithecus, when did it occur and in what creature?

    People keep pretending that they cannot answer anything because they do not have time to answer for all the losses. Just take one.

    ReplyDelete
  143. http://email.eva.mpg.de/~paabo/pdf1/Chou_Inactivation_PNAS_2002.pdf

    "Thus, we used independent molecular approaches
    to estimate that the inactivating mutation in the hydroxylase occurred just over 2 mya. No single one of these approaches is free of potential error. However, when taken together, they allow us to reasonably date the inactivation of the hydroxylase to the period just before the appearance of Homo."

    "It is intriguing to note that, in all mammals studied so far (1), including the chimpanzee (4), the amount of Neu5Gc in the brain is always very low, no matter what the levels are in other organs of the body. This seems to be explained by selective down-regulation of CMAH gene expression in the mammalian
    brain (44). A potentially testable hypothesis is that the low levels of residual brain Neu5Gc in other mammals somehow limited
    brain expansion and that the human CMAH mutation released our ancestors from such a constraint.
    We are therefore studying the effects of Neu5Gc overexpression in the mouse brain and exploring how Neu5Gc expression might affect the biology of neural cells and molecules."

    Very interesting.

    ReplyDelete
  144. http://www.genetics.org/content/172/2/1139.full

    "The human CMAH gene is inactivated by deletion of the 92-bp exon (exon 6) that encodes an active center for the enzyme (CHOU et al. 1998; IRIE et al. 1998; VARKI 2002). HAYAKAWA et al. (2001) studied the genomic sequences around exon 6 of various primate species and found that whereas the exon and a nearby AluSq element are present in all nonhuman primates, they are completely replaced by a young AluY element in humans."

    "CMAH is one of several human-specific functionless genes that have been caused by disruption or deletion of the coding frame and such loss of function might play some roles in evolution of human characteristics (VARKI 2004). These human-specific functionless genes include those for T-cell receptor gamma chain V10 (ZHANG et al. 1996), some olfactory receptors (SHARON et al. 1999; GILAD et al. 2003), type I hair keratin (WINTER et al. 2001), myosin heavy chain (STEDMAN et al. 2004), SIGLEC13 (ANGATA et al. 2004), and bitter taste receptors (CONTE et al. 2003; GO et al. 2005). Unlike CMAH, however, the others are generally members of multi-gene families with potential functional compensation by other paralogs."

    ReplyDelete
  145. M. Dionis, you posted:
    "... or the loss causes an adaptive advantage (as for the CMP-N-acetylneuraminic acid hydroxylase, see Chou et al. 2002."

    Can you please explain how the loss caused an adaptive advantage?
    In what way was the deletion of CMP-N-acetylneuraminic acid hydroxylase an "adaptive advantage"?

    ReplyDelete
  146. anonymous writes:

    M. Dionis, you posted:

    "... or the loss causes an adaptive advantage (as for the CMP-N-acetylneuraminic acid hydroxylase, see Chou et al. 2002."

    Can you please explain how the loss caused an adaptive advantage?

    In what way was the deletion of CMP-N-acetylneuraminic acid hydroxylase an "adaptive advantage"?

    The potential adaptive advantage that has been hypothesized is a role in expansion of brain size in human evolution subsequent to australopithecines.

    But as with many things in evolution and genetics, this is not a simple story. The same loss has been implicated as possibly making Type 2 diabetes more likely in humans. Type 2 diabetes is sometimes referred to as "adult onset" diabetes because symptoms may only manifest in adults, particularly overweight adults.

    So the same loss might be an adaptive advantage if it allowed brain growth post-partum as hypothesized by Chou et al., but turn into an adaptive disadvantage for modern humans in whom long life with excess calorie intake is presumably more common than for our ancestors over 2 million years ago.

    ReplyDelete
  147. Jud wrote:

    The potential adaptive advantage that has been hypothesized is a role in expansion of brain size in human evolution subsequent to australopithecines.

    But as with many things in evolution and genetics, this is not a simple story.[...]


    I gave the reference in order to hint out an exciting possibility: would it be proven that this loss played a role in crucial human brain size increase started with the genus Homo, that would mean the hugest adaptive advantage of them all, our intelligence, which would clearly outbalance any other minor disadvantage. But this remains still an educated guess; when speaking about advantage of this gene loss, there is a prosaic aspect which was already convincingly argued, i.e. resistance to at least some common pathogens conferred by very low levels of the binding molecule Neu5Gc: "[...] many major pathogens and their toxins gain access to their mammalian hosts by binding to cell-surface sialic acids. The microbial binding proteins involved in such interactions can show exquisite specificity for the precise structure and linkage of the sialic-acid target (Sharon, 1996; Karlsson, 1998; Varki, 1997, 1999b). Thus, the hu3man loss of Neu5Gc would have conferred protection from animal pathogens that prefer to bind to this sialic acid, while enhancing the success of pathogens that prefer to bind to Neu5Ac. [...] It is clear that certain microbes causing serious diarrheal diseases in farm animals like cows and pigs have a strong preference for Neu5Gc [...], and humans are thus immune to infection." The two sides of the story are particularly obvious in dealing with malaria: "The merozoite form of this organism that invades red blood cells uses cell-surface Neu5Ac as one of its targets for initial binding [...]. Since chimpanzees appear to be resistant to this form of malaria (Ollomo et al., 1997), it is possible that the P. falciparum merozoite receptor proteins do not recognize Neu5Gc. Conversely, the merozoite
    stage of the phylogenetically related Plasmodium reichenowi that infects chimpanzees (Qari et al., 1996; Escalante and Ayala, 1994) might recognize Neu5Gc preferentially." (the quotes are from a slightly outdated but still information-rich article: A. Varki - Loss of N-Glycolylneuraminic Acid in Humans: Mechanisms, Consequences, and Implications for Hominid Evolution in Yearbook of Phys. Anthrop. 44:54-69, 2001; some more recent papers are M. Martin et al. Evolution of human-chimpanzee differences in malaria susceptibility: Relationship to human genetic loss of N-glycolylneuraminic acid PNAS 102/36:12819-12824, 2005, A. Varki -Multiple changes in sialic acid biology during human evolution, Glycoconj J 26:231-245, 2009 A. Varki - Uniquely human evolution of sialic acid genetics and biology, PNAS 107 suppl. 2:8939-8946, 2010, containing for instance a proposed complex evolutionary scenario linking human-specific changes in Sia-related genes).

    Anonymous wrote:

    Can anyone take any one of those losses and say if it occurred at the time of Australopithecus? [...] Just take one.

    So you're not happy with dates provided for GULOP loss (~61 MYA BP), the keratin pseudogene inactivation (~240 KYA BP) or 92-bp CMAH gene deletion (~3 MYA BP)?! What about all metazoan being unable to produce lysine, a loss to be thus dated many hundreds of MYA BP (just an example)?!

    ReplyDelete
  148. It sounds like:
    The deletion was not of value at the time it occurred (in fact it was deleterious) but was valuable in the later expansion of the brain.

    Interesting. Not in accord with evolution theory, but certainly interesting.
    But I expect we will start to hear the just-so stories and the excuses.

    ReplyDelete
  149. http://email.eva.mpg.de/~paabo/pdf1/Chou_Inactivation_PNAS_2002.pdf

    "Thus, we used independent molecular approaches
    to estimate that the inactivating mutation in the hydroxylase occurred just over 2 mya. No single one of these approaches is free of potential error. However, when taken together, they allow us to reasonably date the inactivation of the hydroxylase to the period just before the appearance of Homo."

    It would be more correct to say that the inactivation of the hydroxylase occurred at the appearance of Homo.

    The deletion was part of the package of changes that took place at the time of the origin of humans.

    ReplyDelete
  150. I had posted:
    "The deletion was part of the package of changes that took place at the time of the origin of humans."

    It would be more accurate to say that the deletion was part of the package of changes that took place at the time of the origin of PRE-humans. Pre-humans, such as homo sapiens (not including homo sapiens sapiens).

    The other gigantic leap occurred at the origin of homo sapiens SAPIENS.

    ReplyDelete
  151. Anonymous wrote:

    It sounds like:
    The deletion was not of value at the time it occurred (in fact it was deleterious) but was valuable in the later expansion of the brain.


    Deeply wrong.
    1. We humans cope fairly well with Neu5Ac instead of Neu5Gc: there is nothing in the articles I mentioned which would suggest/imply this deletion was intrinsically lethal;
    2. The information provided suggest there were advantages and disadvantages of the deletion linked to different pathogen binding and resistance to diseases; some now unthinkable experiments were performed after WWI and the results are fair and square: "humans could not be infected with parasitized chimpanzee blood" (with P. reichenowi), as stated by M. Martin et al.;
    3. The still hypothetical role in brain size increase has yet to be supported by an underlying mechanism; anyway, if proved, the advantage of having bigger brains should have been effective from the very beginning (of course, it would be a clear misrepresentation of how evolution works to think that brain size should have a sudden macroscopic bound from 500 to 1500 cc when deletion occurred).

    Not in accord with evolution theory, but certainly interesting.

    It sounds more like: "not in agreement with my [i.e. yours] own idea about what evolution theory would predict". It is actually all on the contrary.

    It would be more correct to say that the inactivation of the hydroxylase occurred at the appearance of Homo.

    It would be still more correct to read the articles first: "Our original estimate of CMAH inactivation was 2.8 MYA (Chou et al. 2002). This was based on the assumption of the 5.3-MY divergence time between the human and the chimpanzee. Recent findings of more ancient hominid fossils pushed the assumed divergence time back to 6–7 MY (Haile-Selassie 2001; Burnet et al.
    2002; Haile-Selassie et al. 2004). If we assume a 6-MY divergence time, our estimate of CMAH inactivation time (T) becomes 3.2 MY and that of TMRCA in the sample becomes 2.9 MY, suggesting that the deletion mutation fixed in the human population long ago." (T. Hayakawa et al. - Fixation of the Human-Specific CMP-N-Acetylneuraminic Acid Hydroxylase Pseudogene and Implications of Haplotype Diversity for Human Evolution DOI:10.1534/genetics.105.046995 - 2006). Would you be so kind to tell us when exactly would you place "appearance of Homo" in order to fit the best estimate?!

    I am still curious to find out what's your point, now that you were provided the required information.

    ReplyDelete
  152. Even more precise:
    It would be more accurate to say that the deletion was part of the package of changes that took place at the time of the origin of PRE-humans. Pre-humans, such as homo sapiens, and the other homo lines (not including homo sapiens sapiens).

    ReplyDelete
  153. M. Dionis posted:
    "1. We humans cope fairly well with Neu5Ac instead of Neu5Gc: there is nothing in the articles I mentioned which would suggest/imply this deletion was intrinsically lethal".

    Note the dishonesty.
    I never said it was "intrinsically lethal".
    This is a very old tactic - make up something and attribute it to someone. Notice how M. Dionis just slips it in.

    I am familiar with all the tricks.
    But now we will hear all the excuses and self-justifications.

    ReplyDelete
  154. Anonymous writes:

    It sounds like:
    The deletion was not of value at the time it occurred (in fact it was deleterious) but was valuable in the later expansion of the brain.

    Then, quoting a scholarly article:

    "However, when taken together, they allow us to reasonably date the inactivation of the hydroxylase to the period just before the appearance of Homo."

    But mere working scientists are no match for Anonymous' keen mind:

    It would be more correct to say that the inactivation of the hydroxylase occurred at the appearance of Homo.

    So Anonymous must forcibly misread the references (contradicting himself in the bargain - note the difference between his first note saying the genetic change was immediately deleterious and only later favorable, and his second note saying the genetic alteration was simultaneous with the beneficial change causing the appearance of Homo) to try to make them evidence for design rather than evolution. Not the least bit surprising.

    Well, I'm going to take my cue from the Bible here, and not "cast [my] pearls before [Anonymous], lest [he] trample them under [his] feet." That is, what I say below, I do not say with any hope whatever that Anonymous would engage in any sort of illuminating discussion. But I shall "cast my bread upon the waters," so that if anyone does wish to engage in fair and interesting discussion, they are warmly invited to do so.

    The additional information M. Dionis provides shows yet another example of why any reasonable understanding of genetics precludes a belief in design. The fact that so many genetic changes have multiple effects, various of which may be deleterious and various advantageous, depending on the local environment (M. Dionis brought up malaria - how about sickle cell trait for a dramatic illustration of a genetic change with both advantageous and deleterious aspects?) that no designer would ever choose such a complex, chaotic and imperfect system as the toolbox for designing new species.

    ReplyDelete
  155. Anonymous writes:

    The other gigantic leap occurred at the origin of homo sapiens SAPIENS.

    Such a gigantic leap that neither you nor a scientist would be able to tell any difference between the "last" homo sapiens and the "first" homo sapiens sapiens. Such a gigantic leap that they could interbreed with each other and produce live offspring and were thus not different species under the "biological species concept."

    ReplyDelete
  156. M. Dionis asks about the timing of the appearance of Homo.
    Can anyone help him with that?

    According to wikipedia the estimate is:
    http://en.wikipedia.org/wiki/Homo

    "Homo habilis lived from about 2.4 to 1.4 Ma. Homo habilis evolved in South and East Africa in the late Pliocene or early Pleistocene, 2.5–2 Ma, when it diverged from the Australopithecines."

    "It was considered to be the first species of the genus Homo until May 2010, when a new species, Homo gautengensis was discovered in South Africa, that most likely arose earlier than Homo habilis.[22]"

    ReplyDelete
  157. Here is a basic way to understand this:

    "Archaic Homo sapiens is a loosely defined term used to describe a number of varieties of Homo, as opposed to anatomically modern humans (Homo sapiens sapiens), in the period beginning 500,000 years ago. The term is typically taken to include Homo heidelbergensis, Homo rhodesiensis, Homo neanderthalensis and sometimes Homo antecessor.[1]

    The creatures that are called "archaic homo sapiens" are PRE-HUMANS. They are characterized by the package of losses and expanded brain. They originated in what evolutionists call a saltation.

    The next leap forward occurred with the origin of "homo sapiens sapiens". Again another saltation.

    Whether evolution theory can explain this evidence is another question.

    ReplyDelete
  158. Anonymous wrote:

    I never said it was "intrinsically lethal"

    No, you didn't and I didn't mean it, it was a slip. Read again the phrase with "deleterious" instead of "lethal" and forget about useless comments.

    M. Dionis asks about the timing of the appearance of Homo.

    Nope. I was asking about *your own version* of human lineage timeline ("when exactly would *you* place") since I'm pretty aware of the timings currently supported by paleontologists and they don't support your claim ("the inactivation of the hydroxylase occurred at the appearance of Homo").

    The creatures that are called "archaic homo sapiens" are PRE-HUMANS.

    It depends what do you mean by "human". For biologists, all the members of the genus Homo are humans. Would you be so kind to substantiate your own definition?!

    They are characterized by the package of losses and expanded brain.

    You seem to have behind here a full theory nobody is aware of. Please enumerate those losses which characterize the pre-humans in your proposed theory, their occurrence dates and their consequences. For which concerns the "expanded brain", please give a touch of concreteness to your model and give us the limiting sizes for the characteristic brain of "pre-humans" and the criteria used to establish them.

    They originated in what evolutionists call a saltation.

    Where from did you got the "saltation" characterization? Please explain which were the numerical parameters taken into account and why do you label their continuous variation in time as "saltation".

    The next leap forward occurred with the origin of "homo sapiens sapiens". Again another saltation.

    The same key questions are still valid.

    ReplyDelete
  159. Anonymous writes:

    The creatures that are called "archaic homo sapiens" are PRE-HUMANS. They are characterized by the package of losses and expanded brain. They originated in what evolutionists call a saltation.

    The next leap forward occurred with the origin of "homo sapiens sapiens". Again another saltation.

    References?

    By the way, whether or not people who actually know something about evolutionary theory consider these saltation events, what I said in a previous comment stands: Neither you nor a scientist would be able to tell any difference between the "last" homo sapiens and the "first" homo sapiens sapiens; they could interbreed with each other and produce live offspring.

    Do you disagree with this? Are you proposing a G- err, the Designer - created Adam and Eve sort of scenario?

    ReplyDelete
  160. M. Dionis.
    Think these things out for yourself.

    Give some thought to your assumption about the "continuous variation in time".
    But only if you wish.

    I am not presenting the details of this, since I know from lots of experience that that just leads to further argument.
    If these ideas interest you, then good. If not, then just let it go.
    With your knowledge, you could give all the supporting details if you had the will to do it. But of course I do not expect that.

    ReplyDelete
  161. Here is the saltation I am referring to:
    http://en.wikipedia.org/wiki/Behavioral_modernity
    "There are two main theories regarding when modern human behavior emerged.[2] One theory holds that behavioral modernity occurred as a sudden event some 50 kya (50,000 years ago) in prehistory, possibly as a result of a major genetic mutation [change] or as a result of a biological reorganization of the brain that led to the emergence of modern human natural languages.[3] Proponents of this theory refer to this event as the Great Leap Forward[4] or the Upper Paleolithic Revolution."

    AND

    There was a saltation at the origin of PRE-HUMANS as well.

    ReplyDelete
  162. Just to make this clear:
    PRE-HUMANS = Homo (non homo sapiens sapiens)
    HUMANS = homo sapiens sapiens

    PRE-HUMANS originated in a saltation.
    HUMANS originated in a saltation ("the great leap forward").

    ReplyDelete
  163. Anonymous wrote:

    Give some thought to your assumption about the "continuous variation in time".
    But only if you wish.


    Well, mutations do continuously occur, it's a matter of chance whenever an occurred mutation will trigger evolutionary advantage and/or will be fixed within a population, but since the numbers are high on a geological timescale, the phenotypal variations related to those mutations which got fixed appear rather continuous on the same timescale.

    Here is the saltation I am referring to: http://en.wikipedia.org/wiki/Behavioral_modernity

    Oops, you were referring to one saltation? From "The next leap forward occurred with the origin of "homo sapiens sapiens". Again another saltation", one would be tempted to infer that you were really speaking about two saltation events.

    Quoted by yourself, the well-known scientific ultimate source Wikipedia says about your saltation event: One theory holds that behavioral modernity occurred as a sudden event some 50 kya (50,000 years ago) in prehistory, possibly as a result of a major genetic mutation [change] or as a result of a biological reorganization of the brain that led to the emergence of modern human natural languages.. I'm fine with that, since it refers to the essentially cultural event called "Upper Paleolithic Revolution". It is advocated that a possible (neither sure, nor even identified) cause of this event could be some biological change. That would make 1 (one) hypotetical biological variation leading to many collateral dam... results. :)
    Now, if you look in the very same Wikipedia page you will see that the theory of the Great Leap says: "According to this model, the emergence of anatomically modern humans predates the emergence of behaviorally modern humans by over 100 kya." That is not consistent with your own words about the saltation event: as you said, the leap should coincide with the origin of Homo sapiens sapiens (which are anatomically modern humans). So you should decide once for all what event are you taking about: emergence of anatomically or behaviorally modern humans?!

    AND
    There was a saltation at the origin of PRE-HUMANS as well.


    Erm, there were after all two saltation events?! OK, let it be so. Are these pre-humans characterized by... "the package of losses and expanded brain. They originated in what evolutionists call a saltation" you were talking about?! Then please explain which are those (genetic?!) losses you have in mind (up till now, there has never been brought into discussion any loss having occurred precisely at the eve of the genus Homo) and make up the "package". I repeat myself: I have a pretty fair picture of what science says about our ~6 MYA of evolution, what I want to clear out is your own picture which looks somehow different. It would be very useful even to you to define a timeline and to put your meaningful events on it at the right moments (of course, I assume you don't like confusional states and you want to posess coherent knowledge of what you're taking about).

    ReplyDelete
  164. http://www.genomenewsnetwork.org/articles/2004/03/25/prehumans.php
    "About 2.4 million years ago, pre-humans diverged from their ape-like brethren, losing their prominent jaws and developing the larger skulls associated with physical and, later, intellectual advancements. Now, a team of scientists reports that it all started with a mutation [change] that caused weaker jaw muscles in some of the apes."

    This is part of the package of changes that occurred in the saltation origination of PRE-HUMANS.

    ReplyDelete
  165. M. Dionis is still struggling to grasp the idea of two saltations.

    Is there anyone else who wishes to contribute?
    I am still hoping that Dr. Moran will contribute.

    ReplyDelete
  166. Anonymous wrote:

    Just to make this clear:
    [...]
    PRE-HUMANS originated in a saltation.
    HUMANS originated in a saltation


    OK, at least you have set your point on that: you stand for two leap events.

    M. Dionis is still struggling to grasp the idea of two saltations.

    Actually I am still in that good mood in which I'm willing to try to give a meaning to your rather confusional posts. Give me another reason to change it.

    "[...] Now, a team of scientists reports that it all started with a mutation [change] that caused weaker jaw muscles in some of the apes."

    This is part of the package of changes that occurred in the saltation origination of PRE-HUMANS.


    OK, that makes 1 (one) another mutation which supposedly played a role in favoring larger skulls & brains.

    Let me synthesize a kind of timeline including also discussed issues (the list is by no means exhaustive):

    - more than 600 MYA BP: somewhere on the metazoan lineage, the ability to synthesize lysine and other amino-acids is lost
    - ~61 MYA BP: on ancient Haplorrhini branch, a mutation occurs inactivating the GULOP gene
    - ~6 MYA BP: a branch of terrestrial Hominins separates; they will adopt soon bipedalism, a key factor allowing skull size increase;
    - ~3 MYA BP: a deletion occurs in Australopithecine CMAH gene triggering usage of Neu5Ac instead of Neu5Gc, with possible consequences in brain size increase;
    - ~2.4 MYA BP: first Homo genus fossils; another mutation which supposedly caused weaker jaw muscles and allowed skull size increase; here you might want to insert other "package losses"
    - ~0.24 MYA BP: keratin pseudogene inactivation;
    - ~0.15 MYA BP: anatomically modern humans; here you might want to insert other "package changes"
    - ~0.05 MYA BP: behaviorally modern humans.

    You should still clear out what exactly do you intend by "packages" (actually they contain one single biological event) and how are these related with the losses mentioned by Dr. Moran. Concerning the current scientific viewpoint on the issue, I find these phrases particularly illuminating:

    "Current evidence suggests that human evolution occurred over more than 5 million years, and that different events were spread across this time, so that there cannot be a single explanation for all of human evolution.
    [...]
    over the course of primate evolution there is a sustained pattern of increased brain size, intelligence, behavioral flexibility, and social complexity. Many of the anatomical traits observed and inferred in the fossil record are correlates of this overall pattern. In this context, humans can be said, by and large, to have extended the pattern of primate evolution, rather than to have set if off on another course. [...] Differences between humans and other primates are ones of degree, not kind.

    A threefold increase in absolute brain size occurred during the past 3 million years. Whether this increase took place gradually [...] or episodically [...] is a matter that will be settled only with the discovery of additional, accurately dated fossils."
    (R. Lewin & R.A. Foley - Principles of Human Evolution, 2nd ed. - Blackwell 2004)

    You should notice that even if you stick to think about the brain size increase as a leap-varying parameter (a still debatable position), this poses no problem to evolution theory. I suggest you as nice further readings the works of S.J. Gould and N. Eldredge, the promoters of "punctuated equilibrium" in evolution.

    ReplyDelete
  167. Here is a reference o the PRE-HUMANS I have been referring to:

    http://www.genomenewsnetwork.org/articles/2004/03/25/prehumans.php

    "About 2.4 million years ago, pre-humans diverged from their ape-like brethren, losing their prominent jaws and developing the larger skulls associated with physical and, later, intellectual advancements. Now, a team of scientists reports that it all started with a mutation [change] that caused weaker jaw muscles in some of the apes."

    This is part of the package of changes that occurred in the saltation origination of PRE-HUMANS.

    ReplyDelete
  168. Here is a reference to the PRE-HUMANS I have been referring to:

    http://www.genomenewsnetwork.org/articles/2004/03/25/prehumans.php

    "About 2.4 million years ago, pre-humans diverged from their ape-like brethren, losing their prominent jaws and developing the larger skulls associated with physical and, later, intellectual advancements. Now, a team of scientists reports that it all started with a mutation [change] that caused weaker jaw muscles in some of the apes."

    This is part of the package of changes that occurred in the saltation origination of PRE-HUMANS.

    ReplyDelete
  169. "A threefold increase in absolute brain size occurred during the past 3 million years. Whether this increase took place gradually [...] or episodically [...] is a matter that will be settled only with the discovery of additional, accurately dated fossils."

    The word "episodically" is a reference to the SALTATION which took place at APPROXIMATELY 2.4 MYA at the origin of PRE-HUMANS.

    ReplyDelete
  170. The EXPANSION of the brain took place at the origin of the PRE-HUMANS and later there was an exceptionally significant change and re-organization that took place at the origin of HUMANS.

    http://en.wikipedia.org/wiki/Behavioral_modernity
    "There are two main theories regarding when modern human behavior emerged.[2] One theory holds that behavioral modernity occurred as a sudden event some 50 kya (50,000 years ago) in prehistory, possibly as a result of a major genetic mutation [change] or as a result of a biological reorganization of the brain that led to the emergence of modern human natural languages.[3] Proponents of this theory refer to this event as the Great Leap Forward[4] or the Upper Paleolithic Revolution."

    ReplyDelete
  171. Anonymous wrote:

    The word "episodically" is a reference to the SALTATION which took place at APPROXIMATELY 2.4 MYA at the origin of PRE-HUMANS.

    Ummm. No.
    If you read repeatedly and carefully enough the quoted phrase, you will undoubtedly notice it refers to a process spread over 3 MYA: (average) brain size increase in human lineage, from Australopithecines to modern Homo sapiens. This proces certainly did not happen just around ~2.4 MYA BP as you seem to believe, but it took all the time. What the two quoted phrases say is bassicaly this:
    1. over the last 3 MYA, the brain triplicated its size on modern human lineage [through various Homo intermediates]. Brain size is just a numerical biological parameter, not a "package" of several genetic changes hypothetically occurred over night, so it does not fit well your initial claims.
    2. there is a debate about the character of this variation: available data doesn't allow yet to decide with a minimum of pertinence whether the gradual or the episodical scenario reflects better the actual situation. It is thus senseless to claim that the episodical scenario should be true just because you think it fits better your own biased preconceptions.
    3. even if we accept for the argument that the increase in brain size occurred episodically, this does not yet mean there was an unique variation episode which:
    a) was a saltation event;
    b) took place ~2.4 MYA BP.

    In order to clarify your ideas, you might try to pun on a graphic the following three functions:
    1. f:[0,3] -> R , f(x) = (2/3)x + 1
    2. g:[0,3] -> R
    g(x) = 1 for 0 <= x < 1/2
    g(x) = (4/3)x + 1/3 for x <= 1/2 < 1
    g(x) = 5/3 for 1 <= x < 3/2
    g(x) = (4/3)x - 1/3 for 3/2 <= x < 2
    g(x) = 7/3 for 2 <= x < 5/2
    g(x) = (4/3)x - 1 for 5/2 <= x <= 3
    3. h:[0,3] -> R
    h(x) = 1 for 0 <= x < 1/2
    h(x) = 5/3 for 1/2 <= x < 3/2
    h(x) = 7/3 for 3/2 <= x < 5/2
    h(x) = 3 for 5/2 <= x <= 3

    All three functions exhibit an increase from 1 to 3 spanned over an interval of length 3 and all three functions assume the same intermediate values for intermediate integer values of x.
    The function f is linear and is thus a model of gradual increase (there can be also other models but for illustration purposes f is just fine)
    The functions g and h have horizontal portions (i.e. there are subintervals on which the variation of x doesn't affect their value), therefore they are both valid examples of episodical increase.
    On another hand, both f and g are continuous (that is: no jump in the values) while only h exibits three sudden variation episodes with saltation. Therefore "episodical scenario" does not necessarily imply h-like functions (i.e. non-continuous step functions, with saltation): it may design very well a g-like function (continuous and with extended stasis moments).

    The brain size average we consider for our real data are:
    A. afarensis ~400 cc
    H. habilis ~700 cc
    H. erectus ~900 cc
    H. sapiens ~1350 cc
    We must keep in mind that these are averages of notable variance data, and the set of available intermediate taxons used for estimations is very limited. Hence, while data fits with highest probability an increasing trend, the details of this trend (and specifically its graduality or episodicity) are still far beyond the resolutive power of statistics: we are only in position to assert some approximate intermediate values at some approximate intermediate time values.

    After getting this point well, feel free to expose the required information about the two "packages" you claim coincident with saltations.

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  172. It looks like the folks here do not like where the evidence is leading us and they have just gone quiet.
    I am familiar with that tendency on this blog.

    The two major "saltations" (as evolutionists call them) contradict evolution theory. We need an entirely different explanation.
    The packages of changes are not coincidences. And they are not random
    We are forced to an explanation based on intelligence - the intelligence of Nature and the intelligence of the cell.
    Of course I do not expect people here to acknowledge this.

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  173. A. afarensis ~400 cc
    H. habilis ~700 cc
    H. erectus ~900 cc
    H. sapiens ~1350 cc

    We see 3 distinct categories:

    Australopithecines ~400
    Pre-human ~700 - 900
    Human ~1350

    I have no problem with that. It fits with the two saltations I have talked about.

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  174. So M. Dionis has produced more material that supports the two "saltations" I have been talking about.

    ReplyDelete
  175. Anonymous wrote:

    It looks like the folks here do not like where the evidence is leading us

    It looks like nobody sees how on earth can you misunderstand the evidence to such tremendous extent. I'd rather call it "silence heavy with meaning".

    The two major "saltations" (as evolutionists call them) contradict evolution theory.

    Were them two "saltations", they still wouldn't contradict evolution theory. If you keep arguing nonsense, I'll suggest you again and again to read the works of S.J. Gould and N. Eldredge. Gould was a biologist particularly annoyed by creationist/ID claims that his theory (punctuated equilibrium) could ever be used as argument against evolutionism, I might abe tempted to answer with some particularly acid quotes from his writings.

    We need an entirely different explanation.
    The packages of changes are not coincidences. And they are not random


    This would be the right moment for you to explain what exactly do these "packages" contain (still asking). Up till now, the two advocated "packages" of changes contain one hypothetical biological change each. If you won't get out with other details, you can't really expect to be taken seriously when claiming talking about science.

    We see 3 distinct categories:
    Australopithecines ~400
    Pre-human ~700 - 900
    Human ~1350


    I see three labels. What exactly is described under these three labels is a matter of personal preference, not of science.

    I have no problem with that. It fits with the two saltations I have talked about.

    It fits nearly everything.
    Oversimplifying, the problem to be answered is: find the shape of a function given its value in 4 points. How can that be done? Simple answer: based on what you know, you can't. The three functions introduced in my previous message were a trivial example of different kinds of functions which take the very same 4 given values in the 4 integer points on the definition interval. Of these, the first is linear (there is no function more gradual than linear variation), the second exhibits episodical increases but no "jumps" since it is continuous and perfectly gradual on its increasing portions, and only the third is discontinuous with saltation in some intermediate points. There is no way to decide based on the 4 given values whether the variation should look more like f, g, or h, therefore it is ridiculous to claim that the 4 points "fixed" by data should necessarily imply any saltation.
    The most plausible scenario in data analysis is linearity; if linear variation is not sufficient, all usual fitting methods still assert either known regular functions, with simple shapes and no discontinuities, or one looks for decomposition on some basis set of regular functions. The only reason to think about eventual function jumps would be to get its values in really many other intermediate points and to notice something odd. This is what the phrase "Whether this increase took place gradually [...] or episodically [...] is a matter that will be settled only with the discovery of additional, accurately dated fossils" essentially says. Moreover, in our real case the intermediate points are not determined with ultra-high accuracy since at present we dispose only of a very reduced set of skulls enough complete to enable brain size estimation, because the skulls pertain to individuals not to be confused with the statistical average, because their datation is affected by errors (it is not an ideal point on the real time axis but rather a confidence interval); the variances on both axes and the statistical interpretation of the results really don't allow to notice anything else than the increasing trend and no peculiar reason to think about jumps in brain sizes at specifical intermediate time moments.
    I strongly suggest you to graphic the three functions from my last message before any other worthless assumptions about saltation scenarios.

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  176. M. Dionis posted:
    "We see 3 distinct categories:
    Australopithecines ~400
    Pre-human ~700 - 900
    Human ~1350

    I see three labels. What exactly is described under these three labels is a matter of personal preference, not of science."

    At least you recognize the three categories.
    That is good - even if you pretend not to see much more.
    But it is tiresome talking with someone who is just pretending.

    Is there anyone else who wishes to contribute?

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  177. Anonymous wrote:

    At least you recognize the three categories.

    No; as you could notice if reading carefully, I simply aknowledge you are using three labels. Were you stating "the oranges are blue" I'd aknowledged: "I see you claim that oranges are blue". Of course, taking notice of your claims doesn't mean agreeing with them: you should be as (un)happy with me saying "I see three labels" as with "I see you claim that oranges are blue".
    Actually, asserting some labels is always subjected to some arbitrariness. As Jud already put it, "neither you nor a scientist would be able to tell any difference between the "last" homo sapiens and the "first" homo sapiens sapiens". There is usually no saltational gap between succesive species identified as such with conventional labels (as "H. erectus" or "H. sapiens"), there is always the interbreeding possibility within the unit of evolution (population). Do some homework and read about how ancient Greeks solved the bald man paradox more than 2000 years ago: it will provide you lots of useful information:

    But it is tiresome talking with someone who is just pretending.

    Now that's very odd. I am for now the only person on this blog disposed to pay you my $0.02 of attention and to fight against the temptation to depict your scientific competence level with the appropriate labels everybody is now aware of. You could at least try to help me doing so by displaying a minimum of non-mantra feedback. For instance, you could explain what exactly those "packages" consist of (you cannot seriously keep takling abou them and mean one hypothetical change for each), and what are the reasons (if any) to think that brainsize variation was more saltational rather than gradual since the available data can be fitted with thousands of variational shapes (picking graduality has the huge mathematical advantage to keep out unjustified informational input, i.e. it supposes the minimum set of extra assumptions & parameters).

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  178. M. Dionis is having trouble seeing the three categories.
    Anyone else having the same difficulty?

    ReplyDelete
  179. Anonymous wrote:

    M. Dionis is having trouble seeing the three categories.

    In the world of science (to which it happens I belong), when an objection is raised it is examined by the person whose opinion it concerns. If there is a definite answer to the objection, this answer is clearly stated and debated (hopefully reaching a rational consensus on the issue, in one sense or the other). If there is no definite answer, usually one labels the issue as "under debate" and looks out for additional information (if any available). What does not happen is that the criticized opinionist continues to speak without any reaction at all.
    In your particular case, it happens I raised a mathematical objection to your data interpretation and you systematically refuted to examine it. Mathematics is not a matter of opinion and the intuitive examples I gave should be enough even for any average-skilled college teenager to take note that there is a definite answer invalidating your position: it's just a matter of not being too lazy and using the large size brain you're endowed with (as result of our species evolutionary path) for a minute of unbiased reasoning. Since you obviously didn't tried to understand what I said, our conversation cannot lead anywhere, and since my time is way too limited to spend it in the hopeless enterprise to determine you to think at least 10% as a scientist, my contribution to this thread ends here (unless you will prove constructively to have understood the mathematical meaning of my objection and refer it in annother eventual message).

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  180. ...and using the large size brain you're endowed with (as result of our species SALTATIONAL evolutionary path) for a minute of unbiased reasoning.

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  181. M. Dionis has already said that if the development of humans did take place in two giant saltations, that would not contradict evolution theory.
    So it is odd that he fights that idea so hard.
    There must be some other reason why he is unwilling to analyze the idea objectively.

    By the way, I am not interested in a mathematical distraction. I am interested in looking at the actual evidence as we see it in the fossil record and the genome.

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  182. http://en.wikipedia.org/wiki/Saltation_(biology)
    "In biology, saltation (from Latin, saltus, "leap") is a sudden change from one generation to the next, that is large, or very large, in comparison with the usual variation of an organism. The term is used for occasionally hypothesized, nongradual changes (especially single-step speciation) that are atypical of, or violate, standard concepts - gradualism - involved in neo-Darwinian evolution.

    Soren Lovtrup, a biochemist and embryologist from Denmark, believed that macromutations interfered with various epigenetic processes, that is, those which affect the casual processes in biological development. This is in contrast to the gradualistic theory of micromutations of Neo-Darwinism which claims that evolutionary innovations are generally the result of accumulation of numerous very slight modifications. Lovtrup also rejected the punctuated equilibria of Stephen Gould and Niles Eldredge claiming it was a form of gradualism and not a macromutation theory. Lovtrup defended many of Darwin's critics including Schindewolf, Mivart, Goldschmidt, and Himmelfarb"

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  183. http://en.wikipedia.org/wiki/Macromutations
    "Many dramatic mutations [changes] induced [intentionally] by X-rays in the laboratory are now known to involve deletion or rearrangement of entire genes",

    And

    http://en.wikipedia.org/wiki/Behavioral_modernity
    "There are two main theories regarding when modern human behavior emerged.[2] One theory holds that behavioral modernity occurred as a sudden event some 50 kya (50,000 years ago) in prehistory, possibly as a result of a major genetic mutation [eg. change/deletion] or as a result of a biological reorganization of the brain that led to the emergence of modern human natural languages."

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  184. Anonymous wrote:

    M. Dionis has already said that if the development of humans did take place in two giant saltations, that would not contradict evolution theory.

    It depends on the meaning you attach to the word "giant" (in this thread, this is the first time you used it). Until you will state clearly what exactly these hypothetical saltations consist of (in the genome and/or the phenotype) one cannot discuss anything. OTOH, the major "sudden" (in geological terms) evolutive changes we know of, don't contradict evolution.

    So it is odd that he fights that idea so hard.
    There must be some other reason [...]


    This fragment is crucial for characterizing your approach.

    My position can be synthesized as follows:
    1. Yes, there is a reason I cast a heavy doubt on the idea.
    2. No, the reason has nothing to do with its hypothetical implications concerning evolution. It is related to the total lack of either proofs or significant indications supporting the "saltational" scenario. From my point of view, it is symptomatical for your approach that you depict my criticism as "odd": you would expect me to criticize the scenario only for supporting evolutionism. Actually, I support or criticize an idea if I find serious arguments in favor of or against it respectively, not because I like or dislike its consequences. To put it in another way: I support the idea I will never be able to travel with a speed of 1000*c with respect to the Earth not because I'd dislike exploring the Galaxy but because there are serious reasons to think that the massive particles my body is made of can only acquire speeds inferior to c.

    By the way, I am not interested in a mathematical distraction.

    That should read: "I am not interested to understand the mathematical reason for which my reasoning supposedly fails". And that's precisely the reason you fail when dealing with science.

    the actual evidence as we see it in the fossil record and the genome.

    The actual evidence does not point towards a saltational scenario (and the maths were brought here to explain you why). The evidence doesn't exclude absolutely that kind of evolutionary path, but (as for any scientifical "doesn't exclude that...") you shouldn't take that as a positive indication. As hinted, there is a mathematical reason to prefer neutral scenarios (graduality or smooth continuous paths) over saltations. Moreover, there are biological reasons to reject huge instantaneous evolutionary jumps for animals (they could not successfully mate with older genome sexual partners).
    The case would be definitely decided if we would dispose of a complete fossil record of the human lineage (i.e. all generations from say some Australopithecine ancestor to a Homo sapiens). For obvious reasons, this is not possible. We are even very far from having a perfectly known fossil coverage of a statistically significant number of intermediate evolutive steps: with 10 or even better 20 regularly time-spaced complete fossil records, one could already have a sharper resolution but this is still not the case.

    http://en.wikipedia.org/wiki/Saltation_(biology) [...]

    Having a definition of a hypothetical idea and mentioning some guys who support it does not constitute an argument.

    http://en.wikipedia.org/wiki/Behavioral_modernity

    Having a definition of a hypothetical idea and mentioning there are persons supporting it does not constitute an argument (and you repeated yourself, but failed again to mention the other theory exposed on the wikipedia entry).

    Not having a clue about what are the supposed genetical mutations (no, the ones Dr. Moran mentioned have nothing to do with), not explaining which were their so huge consequences for the human lineage, and not presenting any kind of positive evidence pointing in the favor of saltational moments constitute key arguments against the scientifical status of any theory of this kind.

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  185. M. Dionis posted:
    "Not having a clue about what are the supposed genetical mutations (no, the ones Dr. Moran mentioned have nothing to do with).."

    Concerning the mutations that Moran mentioned - when did each occur and in what creatures (genus, species) did each occur? Start with a couple of them.
    Please support your opinion with links.

    We both know you cannot answer those basic questions.
    For evolutionists this is all unknown. It is all taken on faith.

    ReplyDelete
  186. Here is an interesting study:

    http://www.sciencedaily.com/releases/2011/06/110613012758.htm
    "Although most of our variety comes from reshuffling of genes from our parents, new mutations are the ultimate source from which new variation is drawn. Finding new mutations is extremely technically challenging as, on average, only 1 in every 100 million letters of DNA is altered each generation.

    1 in every 100 million per generation!

    Evolution theory depends on these 1 in every 100 million mutations per generation!
    What a laugh.

    The idea of gradual accumulation explaining the changes we see in the fossil record, is completely impossible at that rate.

    People should really think about the significance of this.

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  187. http://www.sciencedaily.com/releases/2011/06/110613012758.htm
    "Although most of our variety comes from reshuffling of genes from our parents, new mutations are the ultimate source from which new variation is drawn. Finding new mutations is extremely technically challenging as, on average, only 1 in every 100 million letters of DNA is altered each generation.

    Let's make sure this is perfectly clear.

    The article says two things:
    1. only 1 in every 100 million letters of DNA is altered each generation.

    AND

    2. new mutations are the ultimate source from which new variation is drawn.

    So variation is dependent on the 1 in a 100 million letter changes per generation.
    Can people wrap their minds around that? And see how impossible evolution theory is?

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  188. Anonymous the IDiot says,

    Let's make sure this is perfectly clear.

    The article says two things:
    1. only 1 in every 100 million letters of DNA is altered each generation.

    AND

    2. new mutations are the ultimate source from which new variation is drawn.

    So variation is dependent on the 1 in a 100 million letter changes per generation.
    Can people wrap their minds around that? And see how impossible evolution theory is?


    Let's assume, for the sake of argument, that the number is correct. What that means is that each person will be born with a single mutation in a 100 million bp stretch of DNA.

    If two people are counted then together there will be two mutations in that stretch of DNA.

    Now, let's consider the entire population of the USA, which we will round off to 300 million. (I'm trying to keep these numbers as simple as possible because I'm talking to someone who is intellectually impaired.) There will be 300 million mutations in that stretch of DNA.

    What does that mean? It means that in just one country there will be enough variation to ensure that every single base pair in a 100 million bp stretch of DNA will be mutated three times. It means that somewhere in the USA one of the three other nucleotides is likely to be substituted at every single position.

    If you extrapolate that to the entire genome it means that every possible non-lethal mutation is present in the population multiple times.

    Scientists have wrapped their minds around that fact for fifty years. It's one of the reasons why evolution is so very probable. IDiots, on the other hand, seem incapable of grasping even the simplest concepts in evolution.

    Isn't that strange?

    ReplyDelete
  189. Oh that Moran is a wily guy.
    He presents his argument in terms of the 300 million people in the United States.
    But of course in evolution history we know that groups were not huge like that. Far, far, far from it.
    What size groups are we talking about?
    Anyone can contribute on that question.
    We might be talking about a group of primitive creatures that became horses. How many in such a group? Being generous perhaps 500? 1,000? 2,000?

    How about tribes of pre-humans? Groups of 50? 100? 500?

    Do people see the trick that Moran is playing here.
    I have found him trying these kinds of tricks quite often.

    Moran makes his living from teaching these ideas. For him the motivation to present these tricks is VERY high.

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  190. Here is another humorous thing.
    Before the study, the popular idea was that there were twice as many mutations.
    This study shows that there are perhaps half.
    But people do not pause for a second. They use the same arguments.
    It seems that the actual number does not matter.
    Only half as much as previously thought - NO PROBLEM.
    This is very typical of thinking based on FAITH.

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  191. anonymous says,

    Do people see the trick that Moran is playing here.
    I have found him trying these kinds of tricks quite often.


    TRANSLATION: Anonymous was so wrong that has to resort to distractions and diversions to avoid looking like an idiot.

    ReplyDelete
  192. I see that Moran is going to try to bluff it out.
    Not much else he can do I guess.

    But I am interested in someone realistically presenting how the supposed evolutions occurred.
    What were the sizes of groups?
    How many changes would there have been using the 1 in 100 million figures?
    What is the probability of the changes occurring as evolution theory imagines?

    ReplyDelete
  193. Anonymous the IDiot asks,

    But I am interested in someone realistically presenting how the supposed evolutions occurred.
    What were the sizes of groups?
    How many changes would there have been using the 1 in 100 million figures?
    What is the probability of the changes occurring as evolution theory imagines?


    Wait a minute. Thought you already knew the answers to those questions. Isn't that why you said,

    So variation is dependent on the 1 in a 100 million letter changes per generation.
    Can people wrap their minds around that? And see how impossible evolution theory is?


    Make up your mind. Is it impossible or not?

    ReplyDelete
  194. Moran is being very careful to avoid dealing with the issue I have brought up.
    I do not expect him to.
    Can anyone else contribute?

    ReplyDelete
  195. sez moran: "Make up your mind. Is it impossible or not?"
    Objection, sir! Assumes organ not in evidence!

    ReplyDelete
  196. Anonymous wrote:

    Concerning the mutations that Moran mentioned [...]

    I can live with you changing the subject for hiding your inability to answer the question (you should still emphasize at some point of the discussion those supposed genetical mutations occurring in your so-called "packages" in order to get a minimal credibility), but I wonder how can you cope with your own intrinsically unfocused approach!?

    [...] when did each occur and in what creatures (genus, species) did each occur?

    The issue was already addressed; after I wrote "in order to save everybody's time I suggest you to focus on a few losses mentioned by Dr. Moran" you stated: "Anyone can answer concerning ANY one. That would be fine.
    Moran listed a number of losses.
    Can anyone take any one of those losses and say if it occurred at the time of Australopithecus?"

    We discussed rather extensively the CMAH gene inactivation which occurred around 3MYA BP on the human lineage (that is: in some Australopithecine branch). We discussed also extensively the GULOP loss which occurred around 61MYA BP in ancient Haplorrhini lineage. Dr. Moran mentioned the essential amino acids (the synthesis of which cannot be generally achieved in metazoans); among these I singled out lysine (see e.g. J.C. Sumathi et al - Molecular Evidence of Fungal Signatures in the Marine Protist Corallochytrium limacisporum and its Implications in the Evolution of Animals and Fungi, in Protist 157/4 363, 2006: "Protists and metazoans have lost the ability to synthesize lysine, which is an essential amino acid for these organisms"), but the affirmation stands also for the other amino acids (you can check a comprehensive table with subsequent references in D.W. Gietzen & Q.R. Rogers - Nutritional homeostasis and indispensable amino acid sensing: a new solution to an old puzzle, Tr. Neurosc. 29/2 91, 2006). We humans share with most other Metazoans and all Vertebrata the inability to produce Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan and Valine: the inactivation dates hugely predate existence of Mammals (not to mention Australopithecines). You weren't happy with the provided information; will you now stop claiming you've not been answered and make your own homework (i.e. answer the questions having been repeatedly asked)?!

    Start with a couple of them.

    Feigning you have not been answered is a a ridiculous policy since any Ctrl-F search in this thread with the keywords from the above paragraph invalidates your claim. Let's count: GULOP -> label 0 since is the subject of the original post, CMAH -> 1, lysine -> 2; now you have been informed about other 8 amino acids which makes a total of 10.

    Please support your opinion with links.

    If you aren't able to find them by yourself from the clear references I gave, then you may try
    http://www.sciencedirect.com/science/article/pii/S1434461006000460
    http://www.sciencedirect.com/science/article/pii/S0166223605003255

    We both know you cannot answer those basic questions

    Errrm... you were talking while in front of the highly-reflective surface of a glass, weren't you?!

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  197. Here are my questions:

    What size groups are we talking about?
    Anyone can contribute on that question.
    We might be talking about a group of primitive creatures that became horses. How many in such a group? Being generous perhaps 500? 1,000? 2,000?

    How about groups of pre-humans? Groups of 50? 100? 500?

    Just pick any creature and provide answers on these questions. The numbers will never be exact of course but ballpark numbers will get us started.

    These seem like pretty basic questions for evolutionists who purport their is evidence backing their theory.

    But I expect we will see a continuation of tap-dancing on these basic questions.

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  198. Moran referred to the 300 million people in the US and posted:

    "Scientists have wrapped their minds around that fact for fifty years. It's one of the reasons why evolution is so very probable."

    In other words according to Moran, "scientists" (ie. evolutionists) have been thinking that because the probabilities in a group of 300 million people is high, therefore evolution theory is probable.

    If he really means that, then evolutionists have all made the same mindbogglingly foolish error that Moran has made. They have all used an irrelevant and incorrect number like 300 million as the size of groups that in the past are claimed to have evolved.

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  199. It is just amazing how much idiocy can IDiots pack in their comments. Try keeping asking questions about little details. After they get answers they can't further twist they will go further asking for the quantum level details of how those mutations occur, and demand that because the quantum mechanics and quantum chemistry questions have not being answered evolution is impossible.

    But it is much easier to answer than try and show how every possible mutation might exist in current humanity (which Anus. The IDiot took to the extreme that, if every mutation might exist today, thus no mutation existed if the population was smaller than that). Here is a simpler answer: OK, I have no idea which mutations occurred, nor how many were available in the wolves ancestral to our dogs. However, it is undeniable that we have produced lots of dog breeds. Many with characteristics not found in any wolf. Thus, no matter how much you mislead those mutation calculations, those dogs are still here, we still see enormous variation in populations, and you cannot claim that humans are using magic to make those new dog breeds, can you? Thus, the answer must be there in the biology of natural variation. Asking for quantum level details won't change the hard facts: we have bred dogs, we have evolved, we have common ancestry with the other apes, there is no need for magic to explain any of it. Live with it and stop being an imbecile. get some education in something other than rhetorical trickery.

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