Oolon Colluphid

Not really...

Ah, Plaisted. Ron, I suggest you read the article <a href="http://www.talkorigins.org/faqs/molecular-genetics.html" target="_blank">Plagiarized Errors and Molecular Genetics</a>, and especially the link to that author’s <a href="http://www.talkorigins.org/faqs/molgen/plaisted.html" target="_blank">response to Plaisted</a>.

As Max states:

And how does the claim of undiscovered functionality dent my point? There are millions and millions of small repeats in organisms’ DNA. It’s not completely random garbage, it’s repeats of untranscribed bits. And it’s passed down generations. Sometimes with changes

At the very least, it is an extreme oddity of design, an oddity in need of explanation. Do you have one to offer, other than "because that’s how god wanted it"? Because evolution has a simple explanation, based on the masses we do know about genetics.

Oolon

RufusAtticus

Please provide your model of special creation that explains the observed phenomena better than descent with modification from a common ancestor, i.e. evolution.

You appear to be advocating that similar designs are the result of a common designer. There are many problems with this from the start.

• Pantheism: Do dissimilar designs imply different creators?
• Identity: What evidence do you have that divine creators even exist?
• The Tree: The relationships of organisms do not fit design/niche. For instance, aquatic organisms, like whales, are more related to land animals than other aquatic animals.

Would you care to provide us with a rigourosly defined model for special creation, along with the evidence that supports it and examples of evidence that would disprove it?

Thank you.
-RvFvS

Daggah

It's a good question, but still, it isn't a matter of not knowing what the DNA does, it's a matter of knowing that the DNA itself is inoperative - it doesn't code for any amino acids!

theyeti

That's a good question. Generally speaking, if a), the DNA doesn't code for a protein, or codes for a severly truncated one and b) removing the DNA has no effect, then you can consider it nonfucntional. However, there's more. We know in nearly every case exactly how such DNA originated. Processes pseudogenes, for example, leave tell tale signs of how they were inserted into the genome. All processed pseudogenes have a degenerate poly A tail, are flanked by tandem repeats, and are almost always truncated at the 5' end (Alu sequences are an example of this). These facts are a smoking gun that tells us that the (pseudo)gene came from a reverse transcribed RNA and was inserted into the genome randomly (there are a handful of functional retrogenes that originated in this way). Not every pseudogene is a processed pseudogene. Some come from duplication of the DNA by unequal crossing over. In this case, the pseudogene is always near it's parent sequence; again, we know how these things originate, and we have seen them do so in the laboratory.

So when you see two organisms with the same pseudogene in the same location, it's a sure bet that they came from common ancestry; the odds of this occuring independently are astronomical. Likewise, if we were to see shared pseudogenes in organisms that we don't think could be related by common descent, it would falsify evolution. But we don't see this.

See <a href="http://www.talkorigins.org/faqs/molgen/" target="_blank">Plagiarized Errors and Molecular Genetics</a>. This was the article that Plaisted was trying to rebut. Max wrote a rebuttal of the Plaisted article here: <a href="http://www.talkorigins.org/faqs/molgen/plaisted.html" target="_blank">A Response to David Plaisted</a>.

edited to add: I just noticed that Oolon already posted those links. Damn you Oolon.

theyeti

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

theyeti

Pot...Kettle...Black.

scigirl

Well duh, I already figured out that you are way more interested in making personal attacks, and replying to people who make attacks on you,than actual science. But if you ever actually want to learn about science, check out <a href="http://www.gate.net/~rwms/EvoEvidence.html" target="_blank">http://www.gate.net/~rwms/EvoEvidence.html</a> It will surprise and stun you.

Several of us here have repeatedly demonstrated undenyable proof for evolution, and THIS is your answer?
Mwa ha ha. Or it could be. . . we are RIGHT! Did you consider that option? What freaking propaganda? If by propaganda you mean undisputed scientific data, sure I'll agree with you.

Randman, read your reply to me again - I provided evidence, and you admitted that you will never even look at it!

At least we click on your links and make an effort to understand your arguments. Indeed, I'm sure we understand your side better than you do, since you don't seem to understand one thing about science.

How would you even know that, since you just admitted to ignoring the facts?

Yes it is rather silly how much time we have all spent with you, instead of doing more worthwhile activities like picking lint out of our pockets. But doesn't that clue you into something?! The fact is, we DO care what society thinks. I personally become very angry and sad when I read your treatises on how "scientists are all lying to you." Why? Because I am actually a scientist, and I happen to give a shit. How would you feel in our shoes? Wouldn't you want to defend your career? Wouldn't you want to correct misconceptions and lies put forth about your field?

Evolution is not our religion, randman. But people here do have a passion for seeking the truth. Check out a christian e/c debate sometime - like the one on the baptist board. If we acted like you have been acting there, we would have been banned by now. They censor a lot of stuff, and outright delete it if they feel it's necessary. Now, if YEC is the truth, why do they feel the need to do that?

You know what I think? You should set up a formal debate with one of us, and we will only stick to science. No ad homs, no insults, just straight data. I think you couldn't handle it for two seconds.

Are you up for the challenge?

scigirl

Bait

Daggah,
Yes, human and chimpanzee cytochrome C matches each other exactly. That just means these two species uses oxygen in the exact same way because cytochrome C is a gene which has to do with how one uses oxygen.

The fact that the sequences are similar in apes and humans still doesn’t prove evolution theory (nor does it necessarily disprove it). The DNA sequence, (as an example) of NPKKYIPGTKM appears in most life forms, which would indicate to me that it is an essential sequence for life in general. 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 to each other than from chimp to human (bone structure, skull shape, dental arcade, feet/hand shape, brain structure, and many other physical features. So why are the sequences between Rhesus monkey and chimpanzee so different? 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

Further, there is a 98.5% match between humans and Chimpanzee DNA, but a 99.9% match between the DNA of different human individuals. The individual differences, including maleness and femaleness is largely attributed the remaining 0.1% of the DNA. That would mean that a 1.5% difference is actually a HUGE difference, would it not?

To further illustrate…Humans and chimpanzees have approx. 3.5 billion (3,500,000,000) nucleotide positions each. 1.5% difference is the difference of 525,000,000 nucleotide positions. It only takes 3,500,000 (the 0.1%) positions to account for all of the differences that occur between each of the individual humans in the world. That includes eye color, skin color, shapes of faces, noses. height, weight, hair, etc.

So lets do some other comparisons. Gorilla’s and Oragutans generally look and act similar to chimpanzee’s, correct? All three knuckle walkers, all three are tree climbers, though gorillas spend much more time on ground than the other two, all three have very similar dental arcades, skull shapes, hairy bodies, non-opposing thumbs, feet shape, etc…right??? None of the three are true bipedal’s…right? It would seem logical that gorilla’s should be closer to humans than chimps are since gorillas actually spend more time on the ground than any of the other apes, which logically would lend itself to the development of bipedal mobilization (walking upright on two feet). Also orangutans should be closer to chimps than chimps to humans just based on the physical features...right? So the evolutionary sequence should seem to go (based on physical features) orangutan, chimp, gorilla, man.

Ok, lets look at the DNA facts then. The difference between a chimp and human is about 1.5%. The difference between a chimp and an orangutan is 2.1%. So a chimp is a closer relation to humans than they are to orangutan’s? Is that what you are saying? Then why do not humans and chimps look closer alike than chimps and oragutans? The difference between Chimps and Gorilla’s is 0.8%…but gorilla’s are ground dwellers, and chimps are tree dwellers, and gorillas are closer in size to humans than are chimps. But then again, why is there only a 1.5% difference between humans and chimps, but a 2.3% difference between a gorilla and humans. Again, the percentage difference between humans and gorillas are roughly the same as between chimps and orangutans...so why are the physical features of the three types of apes more similar to each other and so different from humans? I haven’t even mentioned the differences between the rhesus monkey and the other three apes and humans.

Matches to humans: 98.5% chimp, 97.7% gorilla, 96.4% oragutan. Then we can assume that the sequence of evolution would then be 1st.came orangutans, then 2nd. came gorillas, then came chimpanzee’s, then came humans…based strictly on DNA evidence…right? But from what I understand it doesn’t work that way. Explain why it DOESN’T work that way. It’s all by chance…right??

Dr. David Heaf : co-ordinator of the International Forum for Genetic Engineering : <a href="http://www.anth.org/ifgene" target="_blank">www.anth.org/ifgene</a>
wrote: (at <a href="http://www.anth.org/ifgene/heaf3.htm)" target="_blank">http://www.anth.org/ifgene/heaf3.htm)</a>

He’s also quoted as saying:
URL source of this article : <a href="http://www.anth.org/ifgene/heaf3.htm." target="_blank">www.anth.org/ifgene/heaf3.htm.</a> Originally published in New View, 4th Quarter, Autumn 2000, pp 7-12

Also, from your own evidence, really look close at those chromosome strands. Parts do match, but other parts has to be folded in order to match. The matching parts are not in the same location, in the same manner. Some scientists suggests that the human strands fused or as you said yourself :
But the differences between the apes and humans are obvious. Perhaps the real truth is they are of different lineage, and the “apes” just have similar sequences at different junctions of their DNA.

In a later post you said :
But then the question becomes “what makes you sure that either haemoglobin or fibrinopeptide are wrong in it’s estimate of evolutionary relationships? Maybe they are actually correct, but you do not want to see it because it would lend evidence to opposing views. Maybe they are really not related (the dog and the rat), but as a coincidence are similar in make up. Any discrepancy should worry you, because it may be the evidence of separate, but similar beginnings of the different life forms. Maybe they do not converge at all, and maybe their similarities ARE just coincidence. Maybe the genetic makeup that seems to point to man (or any animal for that matter) is merely a coincidence…after all, are not you (and others) saying that evolution is really a matter of chance anyway?

Going back to the similarities in chromosomes between humans and apes, could not those similarities then , (per your statement above), be expected??

And again you said:

QUOTE]
The probability of getting this result by sheer luck is very small indeed: the number has 31 noughts after the decimal point. We should not be surprised if we fail to get agreement quite as perfect as this: a certain amount of convergent evolution and coincidence is only to be expected”[/QUOTE]


uh, if I read right, that’s 1 in 10000000000000000000000000000000 chances that all five trees would be identical. But does not the evolution theory depend on sheer luck to make it work??? Is that not what “chance” means? Your statement that your model placed
QUOTE]
All the five molecules agree in placing human, chimp and monkey close to each other, but there is some disagreement over which animal is the next closest to this cluster: ”[/QUOTE]

But as I’ve shown above, the DNA sequences for Rhesus Monkey and Chimps are vastly different.


In an exchange concerning panspermia Feb. 2, 2000, between Jon Richfield and Brig Klyce, Jon Richfield said it best : (whole essay can be found at <a href="http://www.panspermia.org/replies3b.htm)" target="_blank">http://www.panspermia.org/replies3b.htm)</a>
QUOTE]
“Now let's talk monkeys. Lots and lots of monkeys with infinite stamina and lots and lots of typewriters; very, very good typewriters with lots and lots of consumable supplies. After something like 1e1e7 keystrokes (sure; call me a liar for the sake of a few googols!) we get a complete Shakespeare, right? Maybe. (With MY luck, don't rely on it!) OK, but what else do you get on the way? Any half Shakespeares? Any other full Shakespeares in different sequences? What? Not even a Pushtu Limerick? How about a few Spencers, Schillers, Semmelweisses or Skytbalies?
(Skytbalie never *actually* existed, but he is the fellow who *would* have written the definitive, cogent explanatory treatise on the nature of mind, its generation and predictive physics if he *had* in fact existed. His work would have made Einstein look like Enid Blyton for depth and like a nineteenth-century political-theoretic tract for clarity and cogency. Unfortunately, if he *had* been real and he had gotten round to writing it, the non-existent Skytbalie would have written his non-existent tract in his non-existent mother tongue of Strondskrif, so no one could have read it, since we have no such language. However, who is in a position to deny that this tract may have appeared in the by-products of our monkeys' output, and maybe there would also be a fortuitous dictionary... into the other non-existent language of Gageluid!)
See? All that Good Stuff may be cramming our monkeys' output and we are not even assuming anything heuristic about their products. Looking through that mass, we would find the Shakespeares and Schillers and so on, while in some other universe these would be sifted out unrecognised, while the delighted Strondskriftish would exclaim over the Skytbalie tracts. There could be many different systems, mutually irrelevant, but intrinsically viable, given a fair chance.

We have no way of knowing what the frequency of meaningful RNA, DNA or peptide chains may be within the space of accessible sequences, combinations and configurations, very likely with strongly heuristic associations. Must I necessarily be wrong to guess at frequencies of one in millions or billions? Tell me why. (Careful! If Strondskrif had indeed been our language (and who are you to say it is intrinsically a lesser probability than English) then Skytbalie's works would have been far more recognisable to us than Shakespeare's. Trying to generate a text in a particular language might be infeasible; generating a text in any extant language might be only a few orders of magnitude easier, but generating a text in something that might in principle be viable as a language, given a suitable semiotic environment might not be ridiculously difficult at all.)”[/QUOTE]

Explain these if you will.

Ron

Daggah

Bait, however, you have to realize that only a small portion of cytochrome C is actually necessary for its function.

Actually, I didn't say it -proved- evolution by itself. It does present compelling evidence. And no, the differences between the rhesus monkeys and chimpanzees don't hurt my hypothesis; they're obviously less closely related than are chimps and humans. Note that they are still fairly similiar. Did you note the pattern that one sees when one looks at the other cytochrome C sequences?

Yes, I see the differences, and furthermore, we would EXPECT to see differences - just not so significant a number that it's hard to hypothesize that those differences could arise from small amounts of cumulative change.

Not really huge. But hey, look at a chimp and then look at a human - they obviously don't loop *exactly* the same. One should then proceed to compare the percentage matches of humans and other animals - do humans more closely resemble frogs, for example? No.

Actually, no. You're assuming that I'm saying that the chimps are man's ancestor, when in fact, man's ancestor is ape-like, and the chimps, gorillas, and orangutans evolved from that ape-like ancestor themselves. Not all of these species evolved in exactly the same way, so no, the conclusion that man should be most like an orangutan does not really follow.

(the next point is answered above)

NO, it is not "all by chance." Mutations are what we would call random, but natural selection is a selection process, and is thus the opposite of random.

I hope I helped.

Daggah

Sorry, I hit the quote link and assumed I got it all:

And none of the differences are inconsistent with observed phenomena.

Why is the pattern so consistent? Against all odds, the relationships seem to be mostly consistent. As Dawkins said, perfect relationships can't be expected. However, again, the evidence is extremely consistent, and I don't see any better explanation for this consistency.

And again, evolution is not "chance."

Actually, no, you've only demonstrated that the DNA sequences are MORE different, not "vastly" different. If the DNA sequences for a frog (for example) and a human were more similiar than a rhesus monkey and a chimp, you'd have something.

Bait, I don't see the need to explain your quote, in light of the huge amount of consistency we see among this type of evidence.

theyeti

But the differences in sequence do not alter function. This has been proven by putting a human cytochrome C in yeast, where it works just fine. There is no reason why the cytochromes from various organisms should be identical or different, aside from common descent and subsequent mutation. And there's certainly no reason that they should differ in a way that parralles morphological divergence.

What can be said is that it's entirely consistent with it, and almost impossible to explain otherwise.

That's an amino acid sequence, bub.

Does it appear in most life forms? Where did it come from? (That's not a rhetorical question, I'm just not sure where you got this example.) Anyway, there are highly conserved regions of some proteins that are found within all life. This means that these sequences are not tolerant to mutation. But this is not the case with cytochrome C, as shown by the numerous variants and transgenic experiments.

That's because humans and chimps are more closely related than chimps and rhesus monkeys.

I doubt that this is the case. Maybe you know something that I don't, but I would bet that a morphological analysis of chimps, humans, and rhesus monkeys would put chimps and humans as sister groups, with resus monkeys as the outgroup. In fact, since this was the case prior to molecular sequencing (I think), then I'm pretty sure that chimps are more morphologically similar to humans. Remember, your subjective views of how they "look" can be misleading.

In terms of morphological differences, maybe. Afterall, we see plenty of differences between us and chimps, so therefore small genetic changes can make a big difference. However, most of the differences between us and chimps are in non-functional DNA. It also bears mentioning that humans and chimps are not that different. On the chemical, cellular, tissue, organ, etc. level, we are identical. Most of our DNA is involved in keeping up with that stuff; a relatively small % of DNA regulates larger developmental patterns, and it is in this DNA that we are different from chimps. BTW, the differences between male and female have to do with the presence of absence of the Y chromosome, not DNA seqence similarity.

Yes, but they also look and act similar to humans. Chimpanzees, more so to humans, I think, than to the others.

Actually, there's a lot of diversity with the locamotive modes, here. I'm not very knowledable about these sort of things, but gorillas are true knuckle walkers whereas chimps are somewhat in between. Chimps, more than gorillas, walk upright on ocassion. (Just going from memory here). However, when doing phylogenetic analysis, you can't just pick and choose certain characters. You need to take all characters into account, and I'm pretty sure that chimps are closer to humans than to gorillas, but I could be wrong. Hair, for example, is something that all of us have. The fact that chimps and gorillas both have longer hair is phylogenetically uninformative.

Quote:

It would seem logical that gorilla’s should be closer to humans than chimps are since gorillas actually spend more time on the ground than any of the other apes, which logically would lend itself to the development of bipedal mobilization (walking upright on two feet).

Now you're getting into ecological stuff. Ecological niches can't really be used for phylogenetic analysis, because closely related species can vary widely in terms of their ecology. It is widely thought that humans evolved bipedality because our ancestors moved out onto the African plains. Gorillas live in the jungle, and thus there is no selective pressure to evolve bipedality.

I don't think so. You would need to show us a morpholgical cladogram to make your case here, and I don't think the ones that have been made show what you think they should show.

Yes, I think that's the accepted hypothesis.

Who says they don't? Ron, I think you're using your incredulity here. You may not think that humans and chimps look alike, but biologists don't use superficial looks to make that determination. They use bone and organ structure, and quantitative measurements that are not based on subjective interpretation.

Again, both ecological niche and size cannot be used for phylogentic analysis. Various dog breeds vary tremendously in size, but are all very closely related.

I think I've pretty much dealt with this. I might be wrong, but why don't you show us a cladogram that places gorillas and chimps as sister groups? I've never seen one. At any rate, I should mention that discrepancies sometimes do happen. Since mutation is a stochastic process, some lineages will recieve more mutations than others, just due to chance. This is why you need to utilize a large data set and lots of characters before you can make a good phylogenetic tree. Also, parallisms and reversals are known to happen; there's just no way around that. Again, you've got to use a big enough data set to prevent any discrepancies. Non-functional DNA is useful because there is no selection pressure that can cause parallelisms or reversals; any of these happen by chance and can be overcome by using more data.

I think you've got it a little confused. The evidence shows that chimps and humans contain the most recent common ancestor (circa 6Mya). The chimp/human lineages share a common ancestor with gorillas a little further back, and the chimp/human/gorilla lineage shares one with orangutangs even further back still. However, they are all "modern" organisms who have been evolving since their divergence with each other. I don't know what's not clear about this.

The Dr. Heaf quotes do no damage to the evidence of shared DNA. Actually, his claims are misleading and I would dispute them at length (for example, all proteins that have an effect on DNA come from DNA! Furthermore, no protein is known to change the DNA sequence in a deterministic manner.) But for now, it's sufficient to say that it's irrelevant.

First of all, those "obvious" differences are your subjective interpretation, as I've said before. When one starts looking at us in detail, the differences seems insignificant next to the extremely large number of similarities. Secondly, as already pointed out, it would make no sense for humans and apes to have similar non-functional DNA. As I wrote in my last post, we know where most of this DNA comes from, and since it's inserted randomly, it would take an outrageous coincidence, or a deceptive deity, to find the same ones in the sames places without common descent.

Again, minor descrepancies are not only accounted for, but expected. In fact if we did not see such descrepancies, we would find it odd because that would mean that mutation was uniform instead of random. It would also mean that there are no parallelisms or reversals, which we know can and do happen. The way to get around this is to use lots of proteins and DNA sequences, and they provide a highly statistically significant tree. This would not be possible if the descrepancies were major and frequent.

It is absolutely impossible, statistically speaking, that those similarities are a coincidence. The chances of that happening would be so slim that it would never happen once in a trillion universes. The only way around them is to propose a deceptive deity, and that carries its own set of problems.

Yes, they are expected through common descent, and nothing more. Some amount of similarity may come about by chance, but almost certainly not the level that we observe. Remember, it's more than just similarity; the presence of teleomeric sequences in the middle of the chromosome is a smoking gun telling us that it was a fusion. All that can be said at this point is that common descent is the best explanation by far. No other "theory" can account for the data.

There is a little confusion here. That huge number above is the chance of those trees being identical by coinicidence. This is why we reject coincidence as an explanation for their matching up. Itstead, we think that they were derived from common ancestry, and thus a decidedly non-random distribution is expected. However, "chance", as you're using it below, is in relation to the nature of mutation, and has nothing to do with the matching trees (except as I said before, the randomness of mutation can produce minor descrepancies.)

They aren't that different at all (assuming that you're referring to the cytochrome C amino acid sequences). Just looking at them, they appear to be better than 90% identical, which is quite high. Remember, we expect chimps and rhesus monkeys to be more different than chipms and humans.

That quote from the panspermia board is 1) irrelevant to the topic at hand and 2) seems to support the opposite of your case. The statement, "but generating a text in something that might in principle be viable as a language, given a suitable semiotic environment might not be ridiculously difficult at all.)" seems to say that abiogenesis may not be unlikely.

theyeti

P.S. Ron, I would like to thank you for your politeness and willingness to discuss the evidence without resorting to ridicule, etc. Recent events have shown that not every anti-evolutionist is capable of that. In the end, you may not agree with us, but at least you're showing respect for our position, and I appreciate that.

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