tronvillain

I just thought I'd point out that orangutangs are extremely different from the other three species socially, being solitary by nature.

Choccy

I'll second that. I'm mostly lurking here, but I've learned a lot from these discussions. So in short: Thanks guys!

Choccy

Bait

Hi Oolon,
Actually I'm not trying to dent you guys pointthat much, just trying to show a different view. I read some of the Ed Max response of the Plaisted.Max debate. Here's a couple of points I saw (noticed):

David A. Plaisted
3. Mutations are not completely random. It's possible that the same kinds of mutations tend to occur in the same way (for example, where the DNA folds, or whatever. Dan Hughes also suggests that DNA might tend to adopt a low energy state.) This could explain many common errors. Note that mutations in a population can be expected to obey more regularities than those among individuals, because of the similarities in survival benefits and the laws of large numbers

Ed Max response ;
Your point #3 (mutations are not completely random, so some shared mutations may have occurred independently) is a theoretical possibility, but where is the evidence that would support it if it were true? In fact, scientists cataloging the gene mutations that cause specific genetic diseases have found scores of different mutations can inactivate particular genes; so you might have a difficult time making your case that any particular shared mutations were due to independent non-random events. Your argument also overlooks my section 5.9, in which I point out that for the case of retroposon insertion, identical independent insertions have not been observed even in individuals of the same species.

My comment: Mr. Max seems first admits that theoretically Mr. Plaisted’s suggestion is possible. But then he states “so you might have a difficult time making your case that any particular shared mutations were due to independent non-random events”. So he is stating that it would be hard to show that mutations occur in any other way than randomly.
Then Max states in his rebuttal of item 7, “But his calculations are precisely appropriate for demonstrating that it would be impossible for random mutations to produce a pseudogene IN THE ABSENCE OF SELECTION FOR FUNCTION”.

This means that unless there is a selection for a function, a reason if you will, then the likelihood of identical independent insertions, creating shared random mutations among even the same species would be highly unlikely, if not impossible, which is exactly what Mr. Plaisted stated.
Mr. Plaisted noted that “Note that mutations in a population can be expected to obey more regularities than those among individuals, because of the similarities in survival benefits and the laws of large numbers”.
This in itself would be selection for function…the function of survival, which Mr. Max recognized as a mechanism for producing a functional gene in his rebuttal of item 7.
Mr. Plaisted stated that it (mutations) would happen between populations more often than in individual cases, because of the similarities in survival benefits, so Mr. Max’s point that retroposon insertion not being observed in individuals of the same species is really a moot point.

David A. Plaisted
7. Something has to appear in the nonfunctional part of the DNA. Why should it be one thing rather than another? Just by chance (accident) there are likely to be sequences that resemble genes, but this says nothing about their origin. Do we expect that the Lord would have deliberately avoided common subsequences at common locations just so that we would not think there was common descent?

Ed Max response ;

Your point #7, suggesting that a pseudogene could have evolved from meaningless DNA to resemble a functional gene by successive random mutations is preposterous, and that is why I dismissed this possibility in my section 4.7.
Indeed Dr. Gish provides many calculations that demonstrate how impossibly unlikely such an event would be. His calculations are completely inappropriate to explain the probability of evolving a FUNCTIONAL gene because he ignores the evolutionary mechanism of multiple iterations of selection for tiny improvements of function.
But his calculations are precisely appropriate for demonstrating that it would be impossible for random mutations to produce a pseudogene IN THE ABSENCE OF SELECTION FOR FUNCTION, which is what you propose.


My comment: Mr. Max argues that pseudogenes, or evolving functional genes do occur as a result of selection for function. He allows Mr. Gish’s calculations to demonstrate the impossibility of the production of pseudogene’s unless there is a reason to do so (in nature). But then he states “His calculations are completely inappropriate to explain the probability of evolving a FUNCTIONAL gene because he ignores the evolutionary mechanism of multiple iterations of selection for tiny improvements of function. “ Would not adding into the equation of the evolutionary mechanism of multiple iterations of selection for tiny improvements of function actually increase the odds of seemingly random mutations…pseudogenes? What I mean is that it is common for nature to try several solutions to a nature survival problem, eventually keeping one, and the rest dying out (discarded) or actually stored in the genetic codes. That is what natural selection is all about…right? The argument then returns to Mr. Plaisted’s points in item no. 3, that mutations are not completely random. It appears what Mr. Plaisted is getting at is that the “errors” and the non-functional genes may be a case of where God (or nature if you prefer), made a solution to a survival problem in nature, and when not needed any more, deactivated it, and stored it for future use or manipulation.

Put way more simply, the common ingredients of a cake may be eggs, milk, chocolate, flour, sugar, vanilla, salt, etc baked at a certain temperature for a specified amount of time. You can also combine salt and eggs, fry them and make a totally different food. Yet again, combine the chocolate, sugar, and milk, heated to make a third (hot cocoa)…and so on. The ingredients are exactly the same, prepared different, some ingrediants left out (different sequence, nonfunctional genes?). You can change the receipt of the cake very slightly (about 1% difference?) and get a loaf of bread (add yeast, take out chocolate)…a totally different food? It does not mean that the bread is a descendant, or comes from a chocolate cake. Better yet, is the common ancestor of all of the foods possible… flour? Then what about the hot cocoa?


David A. Plaisted:
8. Let us consider humans and apes. Since they are so similar, one would expect that they had many similar genes at the creation in similar locations in the genetic material. Also, with the change in environment since then, one would expect that some of these genes would no longer be necessary, such as the gene for synthesizing vitamin C, and that there would be a few such genes in common between apes and men. Now, point mutations arise all the time, and if they are fatal or harmful, they will disappear from the population (have a small frequency). If they are neutral, they can be passed on. So it is reasonable that point mutations inactivating the vitamin C synthesizing genes would occur in both humans and apes, and be preserved in both, since these genes have little benefit now. Thus we would get a pseudogene in the same location in humans and apes. It could have been present in the individuals on the ark, for example. This probably would occur for a few other genes, as well. For organisms that are less similar, this still could happen, but less often. So we would expect to find a pattern of common pseudogenes that reflects the similarity between organisms, but not as an evidence of common descent

Ed Max response;
Your point #8 suggests that humans and chimps may share pseudogenes for vitamin C metabolism through independent mutations resulting from loss of selective pressure to preserve functional genes, or even through selective pressure to inactivate the genes (your point #9). I fully agree that this is possible; indeed the history of galactosyltransferase genes appears to follow a very similar scheme (as I pointed out in the box to section 4.1). But as I mentioned above, when scientists examine the mutations in a particular human gene to understand the cause of a genetic disease, they generally find that many different mutations that can inactivate a gene. Therefore, as I mentioned in section 4.1, if primates closely related to humans have the SAME crippling mutations in their LGGLO pseudogenes as we see in the human pseudogenes, this finding would support the evolutionary model. As I pointed out, the data on this question are not yet available for the LGGLO pseudogenes, but in other shared pseudogenes identical crippling mutations clearly favor evolution (see my section 4.2).

My comment: Mr. Max first agrees with Mr. Plaisted’s point, even mentioneing that “indeed the history of galactosyltransferase genes appears to follow a very similar scheme”, but then reverses himself by stating “if primates closely related to humans have the SAME crippling mutations in their LGGLO pseudogenes as we see in the human pseudogenes, this finding would support the evolutionary model”.
This is not necessarily so because it could also just indicate that primates and humans just shared the same selective pressures, which could have merely been a product of a common environment.

Ed Max ;
Your point #10--that we should not speculate on the relationships between living organisms because these relationships reflect Divine ideas--seems to be a purely theologic argument, which I cannot comment on from a scientific perspective except to say that it sounds rather anti-science to me. (Are the relationships of living forms any more the product of the mind of God than are the laws of physics? Isn't most of theology and religion an attempt to understand what might be called the mind of God?)

My comment: Yes, theology and religion is an attempt to understand the mind of God, and science, whether admitted or not, is an attempt to understand the methods and workings of God (with or without the word God…replace with the word nature). Which is why I can state that I believe that science and religion does not have to be at odds with each other. If looked close enough, they may actually be complimentary. I think it is the lack of understanding of each, (both sides) and each other that causes the majority of conflict….not anti-science, not anti-God

There’s other parts of the Plaisted/Max debate I can comment on, but haven’t got through it all yet.

Bests,
Ron

Happy Wonderer

Um, question from the back of the lurker's peanut gallery. The sequences posted look to be extremely similar to me, I don't see vast differences from a layman's point of view.

(Bait says:"
Look at the DNA cytochrome C sequences/matches of a rhesus monkey compared to a chimpanzee. Vast differences (much more than between human and Chimp), but basic physical features of the rhesus monkey and chimps are closer...Should they not be more similar to each other if your hypothesis is true?

Chimpanzee: mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgiiw gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne

Rhesus monkey: gdvekgkkif imkcsqchtv ekggkhktgp nlhglfgrkt gqapgysyta anknkgitwg edtlmeylen pkkyipgtkm ifvgikkkee radliaylkk atne ")

Rearranging the above sequences in a fixed-width font and with line breaks in arbitrary (but not misleading, it is to be hoped) places reveals:

[code]
Chimpanzee: Mgdvekgkki fimkcsqcht vekgg
Rhesus monkey: gdvekgkkif imkcsqchtv ekgg
*

Chimp: khktg pnlhglfgrk tgqap
Rhesus monkey: khktgp nlhglfgrkt gqap

Chimp: gysyt aanknkgiiw gedtl
Rhesus monkey: gysyta anknkgiTwg edtl
*

Chimp: meylen pkkyipgtkm ifv
Rhesus monkey: meyle npkkyipgtk mifv

Chimp: gikkkee radliaylkk atne
Rhesus monkey: gikkke eradliaylk katne
</pre>[/quote]

Looking closely (sorry for the tiny type) you see two letters that are different and the spaces are off by one character.

Questions: What do the spaces represent? Is there a signicance to the fact that they occur no more than one character apart from the other species?

Thanks!

HW

[ March 11, 2002: Message edited by: Happy Wonderer... Man, finally got the formatting right but now I lost half of the post. Grrrr. ]

[ March 11, 2002: Message edited by: Happy Wonderer ]</p>

Bait

Hi Happy,
Someone, I think on this thread, told an analogy to computers, how sometimes sequences are added to merely delay a command. I think this is a real good analogy that might (could be) be applied to DNA sequences. We know of non-functional "junk" DNA genes and sequences, which are at the moment inoperative and of those that are functional. IF the non-functional DNA is there mainly maintained by nature (I prefer God) for a delay, so the functional "command" DNA aligns as needed to perform a certain function, then the non-functional DNA actually has a function...yes? They could also be stored sequences...like keeping foods in your pantry, to be used if needed at a later time.

BTW, when I say by chance...is that not what "random" really means?

Really though, I mis-stated when I said the word "vastly"...when I should have said they are more different. Someone pointed that out to me...thank you.

theyeti & Choccy,
Thank you for the compliment, I prefer polite disagreements, and really don't mind even getting shot down if it's civil. Anger, hatred, name calling, etc. really solves, and proves nothing. I had a wise lady once tell me that wise man is one who surrounds himself with smart people...who disagree with him. I agree, and further like to add that it also increases the mind power (by natural selection?)

It may be the 'morrow before I can get around to continuing...I haven't gone though.
Ron

Looking closely (sorry for the tiny type) you see two letters that are different and the spaces are off by one character.

Questions: What do the spaces represent? Is there a signicance to the fact that they occur no more than one character apart from the other species?

Thanks!

HW

[ March 11, 2002: Message edited by: Happy Wonderer... Man, finally got the formatting right but now I lost half of the post. Grrrr. ]

[ March 11, 2002: Message edited by: Happy Wonderer ]</strong>[/quote]

theyeti

Nothing. The spaces are just there to make it easier to read. I think that's GCG format. There are other formats, like fasta and pir, that either don't have spaces or have them spaced differently. In the data you have above, the spaces are shifted for the rhesus monkey due to a missing amino acid, but it means nothing in regards to the rest of the sequence. In fact, the chimp and rhesus monkey sequences only differ in that the rhesus is missing the N-terminal methionine. I didn't notice it before, but they are almost identical.

Welcome, by the way.

theyeti

Daggah

Well, see, that's the often-held misconception about evolution. Yes, the mutations are random - but evolution itself is not. I'm not saying it's guided, but natural selection negates the randomness aspect by counting the hits and ignoring the misses. (And it's a fallacy of logic when we do it! Damn nature, gets away with everything. ) Cumulative selection is very powerful, in fact.

Think of it with this analogy: if I flip a coin a hundred times in a row, then what are the chances of me getting all heads? It's rather unlikely. According to my calculator, the odds of it happening are 1 in 1.2676506 x 10^30 - not good odds. But what if I go one at a time, flipping my coin, and if it lands on heads, I mark it down - my selection process is filtering out the tails and retaining the heads. Obviously if I do this, I will have to flip the coin more, BUT I am going to get 100 heads eventually. I'm not saying that this is analogous to evolution; all I'm saying is that, in a way, it's analogous to cumulative selection, and helps to demonstrate how evolution itself isn't random, even if it isn't a guided process (I don't necessarily have to "aim" for 100 heads with this procedure, so it's essentially unguided too.) Do you see where I'm coming from now?

lpetrich

The spaces are just for convenience; they are put at every 10th amino acid. And you are quite correct at doing the realignment; I'd done that for some other examples in a posting that I can't recover.

theyeti

Ron, none of this really makes any sense. That's the problem with using analogies to things like computer code; DNA is not the same as a computer code. It is a molecule whose properties depend on the chemical/physical reactions that it partakes in. I know of no way in which "junk" DNA can "delay" other DNA from doing what it does. (Okay, possibly introns, but we were talking about pseudogenes.)

I have heard creationists claim that maybe pseudogenes were backup copies that could be brought back to function sometime in the future. This argument is usually contradictory though. It's claimed that the backup is needed because mutations will disrupt the functional genes. But then the same mutational process will take the already disfunctional gene and make it functional again? This is an evolutionary process anyway, and it's inconsistent with creationist claims about the supposed inability of new functional DNA ("information") to evolve.

There isn't any evidence that "junk" DNA does anything, though it's likely that structurally speaking, the rest of the genome has evolved to take the extra DNA into account, so that removing huge portions of it would be disruptive. However, its very clear that the sequences are functionally uncessary, and since that is what's at issue here, even if there is a structural function it would not diminish the evidence for common descent. (Also remember, as I stated earlier, we know how these sequences originate. So most of these objections not only require an origin without any evidence, they are forced to ignore the mechanisms that we see happening now.)

theyeti

Valentine Pontifex

Your oil paintings do not form unique natural strictly-nested hierarchical groupings either. Get it through your head that the commonality of material is but a small and unimportant part of the evidence, the pattern is what is important.

(Of course we are ignoring that paintings sometimes come in "mixed mediums" that materials (paints) in even "normal" paintings varies to a considerable degree.)