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Author Topic:   molecular genetic proof against random mutation (1)
peter borger
Member (Idle past 7665 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 151 of 274 (18783)
10-02-2002 12:11 AM
Reply to: Message 147 by Mammuthus
10-01-2002 4:45 AM


Dear mammuthus,
If an utterly hypothetical gene duplication --that has been proposed to explain the incongruence of gene trees and species trees-- is not to be found in the genome than something is wrong with the method. It is proof against common descent beyond any doubt, the rooting of gene trees cannot overcome it. The theory falls. That's it. Better get used to it.
best wishes,
Peter

This message is a reply to:
 Message 147 by Mammuthus, posted 10-01-2002 4:45 AM Mammuthus has not replied

peter borger
Member (Idle past 7665 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 152 of 274 (18787)
10-02-2002 12:28 AM
Reply to: Message 147 by Mammuthus
10-01-2002 4:45 AM


Dear Mammuthus,
You say:
"Ever going to present your hypothesis with the supporting data, how the theory is falsafiable, yada yada yada?"
I say:
Good to have you back. How was the holiday? Convention?
In your absence I presented some sort of hypothesis. It says that all organsims have a multipurpose genome and that adaptations to environment can be induced either randomly, or by non-random protein/RNA mediated mechanism. It holds that there should be a lot of redundant genes in the genome of any organism. That is exacly what we observe. In contrast, the hype of evolutinism doesn't have an explanation for redundant genes. So, that in support of my hypothesis. Furthermore, by now I presented 4 examples that cannot be explained by random mutation, but rather involves non-random mechanisms. These examples are the 1G5 gene, the primate ZFY region, the redundant alpha actinin genes, and today I mailed to SLPx that the DNA shuffling in ticks and lizards is exacly identical. These examples all point in the direction of non-random evolution. The overturn of an established paradigm takes time, I know.
best wishes,
Peter

This message is a reply to:
 Message 147 by Mammuthus, posted 10-01-2002 4:45 AM Mammuthus has replied

Replies to this message:
 Message 154 by Mammuthus, posted 10-02-2002 4:21 AM peter borger has not replied

peter borger
Member (Idle past 7665 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 153 of 274 (18808)
10-02-2002 3:33 AM
Reply to: Message 133 by derwood
09-17-2002 10:42 AM


Dear SLPx,
You wrote in a previous mail I didn't see yet:
"--------------------------------------------------------------------------------
quote:
--------------------------------------------------------------------------------
Originally posted by peter borger:
I say:
"Read something on neutral evolution (NT). You will find out that according to NT genetic change is expected on third positions in AA codons (due to redundancy in the genetic code). They are not present for the major part of protein coding genes. I think that's a bit peculiar in the light that it took these organsims millions of years to evolve."
best wishes
Peter
--------------------------------------------------------------------------------
Hi Peter,
I was hoping that you could point out where in Kimura's works he explains that genetic change is expected on third positions in AA codons. I think what the creationist is doing is engaging in a classic cart-before-the-horse misrepresentation here.
But, please, Peter, prove me wrong. I possess a collection of Kimura's works, and I am fairly certain that I will have the paper(s) you cite."
I say:
It is known that the redundancy in the genetic code leads to neutral positions on the third positions of codons. For instance, the aminoacid leucine can be coded by 6 different codons including CUU, CUC, CUA, CUG. A look at these 4 codons reveals that the third letter of the code is unimportant for determining the aminoacid. This is known as "wobble in the anticodon". The same accounts for the aminoacids valine, serine, proline, threonine, alanine, arginine, and glycine. So, these positions are not under selective constraint (neutral positions) and are expected to behave accordingly. I don't know whether Kimura also had these positions in mind, but I do.
best wishes,
Peter

This message is a reply to:
 Message 133 by derwood, posted 09-17-2002 10:42 AM derwood has replied

Replies to this message:
 Message 157 by derwood, posted 10-02-2002 10:13 AM peter borger has replied

Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 154 of 274 (18811)
10-02-2002 4:21 AM
Reply to: Message 152 by peter borger
10-02-2002 12:28 AM


Hi Peter
[QUOTE]Originally posted by peter borger:
[B]Dear Mammuthus,
You say:
"Ever going to present your hypothesis with the supporting data, how the theory is falsafiable, yada yada yada?"
I say:
Good to have you back. How was the holiday? Convention?
*************************************+
Thanks. Holiday actually. Went to Spain to tilt at windmills
In your absence I presented some sort of hypothesis. It says that all organsims have a multipurpose genome and that adaptations to environment can be induced either randomly, or by non-random protein/RNA mediated mechanism.
Problem 1: this is the same old issue of your using an inappropriate definition of random mutation. For example, if a portion of a gene is wrapped around a histone in such a way that it is more or less likely to suffer demethylation it will radically change the probability that you get C to T transitions. However, the C to T transition is still random.
Problem 2: Define protein/RNA mediated mechanism of mutation generation. If you mean the lack of proof reading functions of reverse transcriptase for example the higher rate of mutation generated is fully expected and non-random.
It holds that there should be a lot of redundant genes in the genome of any organism.
Big problem 3: How do random or non random mutation in any way account for redundant genes? There is no connection between the first and second part of your hypothesis. Redundant genes have been known to evolutionary biologists for decades and have presented no problems for the theory. I can think of lots of ways off the top of my head for how do generate duplications and redundancy. And to use your own oft fallacious logic, until you prove each gene is really redundant and not in some way involved in another slightly different funcition your hypothesis is dead
That is exacly what we observe. In contrast, the hype of evolutinism doesn't have an explanation for redundant genes.
Problem 4: or 3b if you will. This statement is false.
So, that in support of my hypothesis.
Problem 5: this sentence makes no sense.
Furthermore, by now I presented 4 examples that cannot be explained by random mutation, but rather involves non-random mechanisms. These examples are the 1G5 gene, the primate ZFY region, the redundant alpha actinin genes, and today I mailed to SLPx that the DNA shuffling in ticks and lizards is exacly identical. These examples all point in the direction of non-random evolution.
Problem 5: On multiple occassions it had been pointed out to you that your definition of non-random is wrong and is in conflict with what statisticians and evolutionary biologists use. That you choose to ignore this fact does nothing to further your cause or support your beliefs.
The overturn of an established paradigm takes time, I know.
It takes even longer when there is no compelling hypothesis or data with even a billionth of the support evolution has
best wishes,
M

This message is a reply to:
 Message 152 by peter borger, posted 10-02-2002 12:28 AM peter borger has not replied

Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 155 of 274 (18812)
10-02-2002 4:25 AM
Reply to: Message 150 by peter borger
10-01-2002 10:42 PM


quote:
Originally posted by peter borger:
Dear Joe,
I am still writing/thinking about my opus magnum. Every now and than, I mail to proevolutionary boards/evolutionary biologists to test some examples/ideas. As you can see from this board the resistance is overwhelming. Of course, I consider all comments carefully since I like to know what to expect, and how to improve it. Prior to launching, better prepare carefully.
Whether or not it will be a scientific publisher depends on guys like Mammuthus and SLPx, since usually such guys comprise the proevolutionary editorial board. Did you know that before Behe published his book it was reviewed by several scientific editors. One of them was against publishing since it would question the current paradigms. Apparently, in his land of evolution there is no freedom of thoughts.
best wishes,
Peter

**********************************************************
Ah Peter, resorting to personal attacks on my and SLPx integrity as reviewers to further your agenda? I reject papers when the data is bad or the conclusions are not supported by the data. I don't reject papers because an author has a different opionion than I do. I would actually think from your postings that you would be more likely to indescriminatley reject papers that conflict with your religious worldview regardless of the science behind them.
Ciao
M

This message is a reply to:
 Message 150 by peter borger, posted 10-01-2002 10:42 PM peter borger has replied

Replies to this message:
 Message 161 by peter borger, posted 10-03-2002 1:23 AM Mammuthus has replied

derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 156 of 274 (18835)
10-02-2002 10:08 AM


Peter the false witness boy:
"BTW, I discussed this already with Dr page himself and he couldn't address it beyong 'maybe it isn't properly rooted'."
This is entirely untrue. I have mentioned that I would like ot discuss this, but PB never has, not with me anyway. I have never made such a reply.
Peter B has taken the route of the desparate creationist, putting words in the mouth of his opponant (see especially his last post to me!) and engaging in dishgonesty.
We should all be wary of this.

Replies to this message:
 Message 160 by peter borger, posted 10-02-2002 8:10 PM derwood has replied

derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 157 of 274 (18836)
10-02-2002 10:13 AM
Reply to: Message 153 by peter borger
10-02-2002 3:33 AM


Please not the sections in bold:
quote:
Originally posted by peter borger:
Dear SLPx,
You wrote in a previous mail I didn't see yet:
"------------------------------------------------------------------
quote:
----------------------------------------------------------------------
Originally posted by peter borger:
I say:
"Read something on neutral evolution (NT). You will find out that according to NT genetic change is expected on third positions in AA codons (due to redundancy in the genetic code). They are not present for the major part of protein coding genes. I think that's a bit peculiar in the light that it took these organsims millions of years to evolve."
best wishes
Peter
----------------------------------------------------------------------
Hi Peter,
I was hoping that you could point out where in Kimura's works he explains that genetic change is expected on third positions in AA codons. I think what the creationist is doing is engaging in a classic cart-before-the-horse misrepresentation here.
But, please, Peter, prove me wrong. I possess a collection of Kimura's works, and I am fairly certain that I will have the paper(s) you cite."
I say:
It is known that the redundancy in the genetic code leads to neutral positions on the third positions of codons. For instance, the aminoacid leucine can be coded by 6 different codons including CUU, CUC, CUA, CUG. A look at these 4 codons reveals that the third letter of the code is unimportant for determining the aminoacid. This is known as "wobble in the anticodon". The same accounts for the aminoacids valine, serine, proline, threonine, alanine, arginine, and glycine. So, these positions are not under selective constraint (neutral positions) and are expected to behave accordingly. I don't know whether Kimura also had these positions in mind, but I do.
Why is it that I have come to expect this sort of thing from Peter B, creationist?
Oh, I know - its the whole creationist thing...

This message is a reply to:
 Message 153 by peter borger, posted 10-02-2002 3:33 AM peter borger has replied

Replies to this message:
 Message 159 by peter borger, posted 10-02-2002 8:00 PM derwood has replied

derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 158 of 274 (18852)
10-02-2002 11:43 AM
Reply to: Message 146 by peter borger
10-01-2002 2:42 AM


quote:
Originally posted by peter borger:
Dear SLPx:
THIS IS WHAT YOU WROTE. MY RESPONSE IS IN CAPITAL LETTERS< SO YOU WILL NOT GET CONFUSED.
Thanks, Pete. I do find your posts most confusing.
quote:
quote:
----------------------
Originally posted by peter borger:
Dear SLPx,
I had a bit of time to spare so I read a couple of articles you refered to in an attempt to disprove non-random mutations.
----------------------------------------------------------------------
SLPx:You mean the ones that you had already claimed in fact support your version of non-random mutations? You hadn't even read them yet, but were claiming them as support for your position?
I'm shocked!
Guess I hit that nail on the head, eh "Peter"?
I say:
Why reiterate this, while I already explained to you that the article you referred to was in a mail to Fred Williams not a message addressed to me, so I missed it (look it up, if you like, it was a Science paper in a mailing to Fred. But anyway, it is nit-picking)
----------------------------------------------------------------------
SLPx:
I have no need to look it up. It is right here:
http://EvC Forum: molecular genetic proof against random mutation (1) -->EvC Forum: molecular genetic proof against random mutation (1)
Message 96. I DIRECTLY address you in reply to a request from you. You replied in Message 97 that these citations support your position. As is so common with creationists, you then actually went on condescendingly how I must not understand the content of the papers (message 102, Aug.22) and such.
Yet it was not until SEPTEMBER 12 that you actually even read the papers! (YOUR message 123 in the linked thread).
So, "Peter B", your 'memory' is a bit clouded.
MY RESPONSE:
THE ONLY ONE HERE TO MISREPRESENT THINGS IS YOU. iF YOU GO BACK IN THE THREAD THAN YOU WILL FIND OUT THAT I REFFERRED TO THE SCIENCE PAPER IN YOUR MAIL TO FRED. THIS MAIL CAN BE FOUND IN THIS THREAD #52, THE CAIRNS EXCERPT. SO NEXT TIME BEFORE YOU START TO BLAME ME READ BACK AND PREPARE PROPERLY.
You know, it is the strangest thing. Looking at my post #52, I did indeed post a reply to Williams with a link to a Science article containing information on Cairns. But if one looks at the links to replies in the bottom of that post, one sees that you did not respond to it until post #123. This of course is well after I had already reposted a quote from that source and supplied several abstracts to papers that provide direct evidence against 'directed' mutations - the ones you claimed were in fact evidence for them.
While I see that I was in error in so far as interpreting your post #123 and #126, I maintain that you did not read, or perhaps understand, the implications of the abstracts I posted in #96. One has to be a dogmatist extraordinaire to believe that papers explaining how mutations occurred genome-wide really indicate a non-random mechanism.
quote:
You have: 1)Tried to misrepresent the situation by claiming that I was writing to Williams, not you. That is demonstably false. 2) You arrogantly and overconfidently implied that it was I that had not read the papers or could not understand them when in reality it took you nearly a month to get around to looking at them DESPITE the fact that you had previously proclaimed them supportinve of your claims, and then still ignored the fact that not of them even comes close to supporting the notion of 'directed mutation' as you describe it.
Nitpicking, indeed...
quote:
----------------------------------------------------------------------
quote:
----------------------------------------------------------------------
One of the guys in field of hypermutations says in the article that you refer to says:
"Over the past decade, researchers have been dissecting the molecular underpinnings of these so-called adaptive mutations. And within the last 2 years, they have made impressive strides. They have found, for example, that although these mutations are not directed to particular genes, as Cairns originally suggested, they don't uniformly pepper the bacterial genome either. "There are hot and cold regions for hypermutation," says Rosenberg, who is now working on defining these regions. "All regions are not equal.""
If I understand his last sentence properly, he says: "All regions are not equal"
MY RESPONSE:
THIS CAN BE FOUND IN MAIL #52 TO FRED, THE CAIRNS EXCERPT. NOT IN A MAIL TO ME.
Yes, I see that now. My sincere apologies. However, again, I quoted from that article in a message directed to you, to which you responded immediately with some nonsense about the articles really supporting non-random mutation. And again we see that the creationist hangs his hat on what might be, rather than what is.
quote:
In my opinion not equal means that a mechanism (=non-random) is involved, isn't it?
----------------------------------------------------------------------
If by mechanism you mean some guiding force, I say LOL!
I say:
The driving force could be the environment that induces certain proteins (e.g. polymerases) that carry out the mutations.
----------------------------------------------------------------------
And how does your 'conclusion' of non-random mutation falsifying NDT follow from that? In your selective readings of the papers I cited, did you not notice that the mutations were not centered - directed - specifically to the genes 'needed'?
Or did that slip by your razor-keen scientific insight?
I say:
Probably prokaryotes differ from eukaryotes in this respect (although they have lots of redundant genes too). In comparison, it was long thought that prokaryotes do not have introns, but now we know that some have. So, a mechanism not optimal/fully present in prokaryotes may be fully operative in eukaryotes.
----------------------------------------------------------------------
Just so stories form the creationist. You have learned well from creationist Spetner, who also had no actual supportive evidence for his fairy tales occurring in multicellular eukaryotes.
MY RESPONSE:
YOU ARE WRONG. WHEN SPETNER WROTE HIS BOOK (BEFORE 1997) THESE EXPERIMENTS HAD RECENTLY BEEN PUBLISHED, SO SPETNER WAS PRETTY UP TO DATE WITH HIS BOOK.
I am wrong? Well, then, Peter B., please supply us with the documentation for non-random mutations occurring in multicellular eukaryotes that result in phenotypic change. The best he could do was some pap about sea gull wings... Which of course had no genetic analysis in its support...
Spetner the creationist could not do this then, and he has not done it yet.
Help him out.
quote:
THAT THE MECHANISM IS NOT EXACTLY AS HE (AND CAIRNS) THOUGHT IT WAS, IS NOT SURPRISING SINCE NOTHING IN BIOLOGY IS AS WE EXPECT IT TO BE.
So he was wrong then. Good to hear you say that.
quote:
FURTHERMORE, THE CAIRNS INTERPRETATION IS ONLY A MINOR POINT IN SPETNER'S BOOK SO YOU CANNOT REJECT HIS ENTIRE BOOK ON CAIRN'S PARTIAL RECANTATION.
I didn't. Indeed, the Cairn's bit was mentioned in regards to "non-random mutation" in general, not to anyone's vanity press book targeting a lay audience.
quote:
BETTER READ HIS BOOK INSTEAD OF ONLY HIS OPPONENTS. AND WHY DO YOU THINK THERE HAVE BEEN CARRIED OUT SO MANY EXPERIMENTS TO FALSIFY CAIRNS INTERPRETATION?
In reality, so many experiments were carried out to see if he was right (he wasn't), not to try to disprove him.
quote:
THE NDT WOULD HAVE FALLEN, AND THAT IS EXACTLY WHY YOU OBJECT/DENY THE NON-RANDOMNESS OF MUTATION IN THE 1G5 GENE. AND THAT'S WHY NDT BLOCKS SCIENTIFIC PROGRESS.
What progress would be made by accepting a fringe idea on non-random mutation? I object/deny it because as I have repeatedly explained and supplied references for, the idea of non-randomness is not what it is made out to be by folks like you.
quote:
quote:
----------------------------------------------------------------------
you quote:
----------------------------------------------------------------------
You say:
If by mechanism (ahh - I love the sound of a semantics game coming!) you mean a tendency to do one thing over another, than of course., However, as has explained to you repeatedly on this board, there are simple physicochemical reasons for mutations occurring in some areas over others.
I say:
"Molecular mechanism in biology usually involve proteins and/or RNA molecules. If so, all necessities are present in the genome"
---------------------------------------------------------------------
LOL! Yeah, I guess those "kinds" must have been jammy-packed with all sorts of genes that they didn't need and that are, dammit, no longer present in their in-kind descendants...
I say:
Loss of genes is a common mechanism in evolutionism[sic] to explain observations. There is even a discipline in evolutionism that postulates utter hypothetical gene additions and gene deletions to reconcile gene trees with species tree.
----------------------------------------------------------------------
Please expand on this. Please provide citations, as well. Also, please explain why it is that you believe that all gene trees should be exactly the same.
MY RESPONSE:
ANY RECENT BOOK ON MOLECULAR EVOLUTION HAS A CHAPTER CONCERNING ‘RECONCILIATION OF GENE TREES WITH SPECIES TREES'.
They do? Examples please.
quote:
ACCORDING TO EVOLUTIONARY BIOLOGISTS, GENE TREES HAVE TO BE IN AGREEMENT WITH SPECIES TREES.
This is a major misrepresentation on your part, Peter B. It is outright false.
Your credibility - what little you may have once had here - is now completely gone.
quote:
WHY? OTHERWISE ALL GENES LYING OUT PROVIDE FALSIFICATIONS OF COMMON DESCENT.
This is just asinine, and indicative of your dogmatic ignorance. Any text on molecular evolution not only explains why discrepencies exist, they actually predict that more will be found.
quote:
YOU CAN FIND THIS HIGHLY DISPUTABLE MATHEMATHICAL TRICK FOR INSTANCE IN 'MOLECULAR EVOLUTION, A PHYLOGENTIC APPROACH by R. PAGE'. WHAT EVO’S DO IS THE OTHER WAY AROUND REASONING. THEY CLAIM THAT SINCE EVOLUTION IS TRUE, THE EVIDENCE FOR PUTATIVE DUPLICATIONS IS SIMPLY THE INCONGRUENCE BETWEEN THE GENE AND THE SPECIES TREE. I OBJECT TO SUCH SIMPLISICISM.
I object to your idiocy, but it won't get me anywhere. Is it a 'trick'? That sounds awfully inflammatory, Peter B. Perhaps you don't understand statistics? Or maybe the workings of genomes? Well, either way, your claims are getting more and more bizarre and more and more desparate.
quote:
FOR EXAMPLES: (http://taxonomy.zoology.gla.ac.uk/rod/papers/page97mpe.pdf).
The abstract:
"The processes of gene duplication, loss, and lineage
sorting can result in incongruence between the phylogenies
of genes and those of species. This incongruence
complicates the task of inferring the latter from the
former. We describe the use of reconciled trees to
reconstruct the history of a gene tree with respect to a
species tree. Reconciled trees allow the history of the
gene tree to be visualized and also quantify the relationship
between the two trees. The cost of a reconciled
tree is the total number of duplications and gene losses
required to reconcile a gene tree with its species tree.
We describe the use of heuristic searches to find the
species tree which yields the reconciled tree with the
lowest cost. This method can be used to infer species
trees from one or more gene trees."
Whats your point?
I am constantly amazed at how the creationist interprets 'explanations' as 'excuses' and the like. Pitiful, really.
quote:
quote:
----------------------------------------------------------------------
You say:
Water tends to collect in low areas rather than high ones.
Are you going to suggest that some Ubermensch plays a role in that, too?
I say:
You use similar faulty analogies as Mark24. You cannot compare gravity and protein mediated mechanism. I know you have to use such analogies, since you need naturalistic explanations for NDT. However, if all things are in the genome to respond to environmental change, a naturalistic explanations is untenable."
----------------------------------------------------------------------
You say:
My "analogy" was not to NDT, rather it was to demonstrate that there are perfectly natural reasons for apparently 'specified' outcomes. As is so often the case, the creationist Reads too much into posts and tries to make much of their shallow comprehensive skills.
I say:
Here you demonstrate again your condescending (dumb and dumber, remember) overconfinced attitude.
No, it is a valid conclusion.
quote:
----------------------------------------------------------------------
You may recall that I was not the one claiming that articles that I had not read support my position. THAT is overconfidence. Also, I was not the one that 'explained' that perhaps I didn't understand what was in the articles... the ones that you hadn't yet read...
The analogy was clear, and it fulfilled its purpose. That you could not understand it has nothing to do with anyone's overconfidence, real or imagined.
quote:
----------------------------------------------------------------------
Challenge me and I will falsify common descent beyond doubt. I will open a new thread, if you like.
----------------------------------------------------------------------
Consider this a challenge. Similar to the other challenge that you suggested, discussing gene trees and such.
I think I will find your beyond-doubt falsification most informative, and will gingerly forward it to the appropriate authorities such that we can immediately informa those thousands of scientists that utilize evolutionary theory in their research that they are going about their work all wrong.
MY RESPONSE:
THE MOLECULAR GENAEOLGY OF INTERLEUKIN-1-beta demonstrates an aberration from the species tree.
So?
quote:
quote:
----------------------------------------------------------------------
And concerning the Uebermensch: you were the one that introduced space-aliens to explain genes in humans not present in apes. I can think of several better 'scientific' non-testable explanations.
----------------------------------------------------------------------
I did no such thing. Please stop misrepresenting me and trying to erect straw man arguments.
MY RESPONSE;
YES, YOU DID. IN RESPONSE TO THE GENES PRESENT IN HUMAN NOT PRSENT IN MAN.
What genes might be present in humans but not in man, I wonder...
quote:
quote:
----------------------------------------------------------------------
You say:
I am still waiting for your unequivocal evidence that these unused but maybe someday necessary genes are in the genomes of all creatures......
(Creatures? When did you become a creationist? )
----------------------------------------------------------------------
When did you become such a moron?
MY RESPONSE:
JUST KIDDING.
I see...
quote:
quote:
---------------------------------------------------------------------
....just waiting for that one lucky mutation - in the right conditions, of course - to be turned on.
I say:
Redundant genes are 'non per niente' in the genome. Yes, my hypothesis of "(non-)random mutation in a multipurpose genome" is ALMOST as incredible as evolutionism. Probably we have to wait for another decade and we will know. At least if the appropriate experiments are carried out. That is: the comparison of subspecies with related species. That is not: the comparison of individuals of distinct species.
----------------------------------------------------------------------
How do you propose this comparison be done?
MY RESPONSE:
AS DEMONSTRATED FOR THE 1G5 GENES IN A LARGE AMOUNT OF SUBPOPULATIONS.
What do you mean sub-population?
quote:
I AM INTERESTED IN THE SEQUENCES OF ONE PARTICULARE GENE (SAY HEMOGLOBIN OR CYTOCHROME C) THROUGHOUT THE DIFFERENT HUMAN SUBPOPULATIONS. I WONDER WHETHER THESE DATA ARE PRESENT INLITERATURE?
I don't know about that particular gene, but Paabo's group has done an extensive study on the mitochondrial genome and, why, it must be a mere coincidence, the findings fit wquite nicely with evolutionary hypotheses.
quote:
quote:
----------------------------------------------------------------------
You say:
Your silly (and typically overconfident) position simply supports something I have believed for some time now - evolutionists base their thoughts on what is known, creationists base theirs on what is not.
I say:
The real silly thing is that even the major part of the tiny bit that we know from the genome does NOT point in the direction of evolution.
----------------------------------------------------------------------
And there is the gem - that nugget of creationist stupidity that pops its head out once in a while.
I wonder what your more knowledgible and rational colleagues would think if they knew that you were writing - and apparently believe - something so asinine?
I guess you didn't realize that all those duplicated genes actually fit quite well within an evolutionary framework? Nah - you are a creationist, and your personal opinions are the REALLY important things! facts be damned!
quote:
----------------------------------------------------------------------
(ever heard of the second DNA associated code of transcription? And there may even be a third code involved in coactivation of transcription. Firstly, there is NO evolutionary explanation for the first code. And now we find that the first code gives rise to a second code through possible another code. So you better present a pretty good story to explain this by a random mechanism).
----------------------------------------------------------------------
Frankly, no, I have not heard of this. Please provide some verifiable documentation that I can check to see if your depiction of this is accurate.
MY RESPONSE:
I ALREADY GAVE THE REFERENCES. I AM WAITING FOR A REPONSE.
I am still waiting for your hypothesis...
A response to what? Let me guess - that falsifies evolution too?

This message is a reply to:
 Message 146 by peter borger, posted 10-01-2002 2:42 AM peter borger has replied

Replies to this message:
 Message 162 by peter borger, posted 10-03-2002 3:37 AM derwood has replied

peter borger
Member (Idle past 7665 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 159 of 274 (18913)
10-02-2002 8:00 PM
Reply to: Message 157 by derwood
10-02-2002 10:13 AM


Dear SLPx,
Yes, Mister SLPx, these postions are NOT under selective constraint and are per definition neutral. I guess, mister Futuyma forgot about this, I don't. Why don't you just simply address my comments in a scientific way and try to convince me, instaed of repeating that I am a creationist. I am always open for good scientific arguments.
best wishes
[This message has been edited by peter borger, 10-02-2002]

This message is a reply to:
 Message 157 by derwood, posted 10-02-2002 10:13 AM derwood has replied

Replies to this message:
 Message 165 by derwood, posted 10-03-2002 12:53 PM peter borger has replied

peter borger
Member (Idle past 7665 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 160 of 274 (18914)
10-02-2002 8:10 PM
Reply to: Message 156 by derwood
10-02-2002 10:08 AM


Dear SLPx,
I referred to Roderick Page, the author of "Molecular Evolution, A Phylogenetic Approach".
Sorry for confusing you. I mentioned that I --before registration to this board-- I had a lot of private conversations with evolutionary biologists. As soon as I mentioned the current problems in evolution theory and demonstrated this with examples from literature, there was silence. So I know what I'm talking about.
Best wishes,
peter

This message is a reply to:
 Message 156 by derwood, posted 10-02-2002 10:08 AM derwood has replied

Replies to this message:
 Message 164 by derwood, posted 10-03-2002 12:49 PM peter borger has not replied

peter borger
Member (Idle past 7665 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 161 of 274 (18948)
10-03-2002 1:23 AM
Reply to: Message 155 by Mammuthus
10-02-2002 4:25 AM


Dear Mammuthus,
If you feel offended: Sorry for that. It happens to me a lot. Try to be a stoic, that helps. And thanks for clearing things and for your comments on the hypothesis. I will take them in consideration. The more scientific comments the better.
Best wishes
Peter

This message is a reply to:
 Message 155 by Mammuthus, posted 10-02-2002 4:25 AM Mammuthus has replied

Replies to this message:
 Message 177 by Mammuthus, posted 10-07-2002 10:40 AM peter borger has replied

peter borger
Member (Idle past 7665 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 162 of 274 (18955)
10-03-2002 3:37 AM
Reply to: Message 158 by derwood
10-02-2002 11:43 AM


dear SLPx,
In response to your comments on my previous mail:
You say:
Thanks, Pete. I do find your posts most confusing.
I say:
That is because it involves thinking beyond the current paradigm.
You say:
You know, it is the strangest thing. Looking at my post #52, I did indeed post a reply to Williams with a link to a Science article containing information on Cairns. But if one looks at the links to replies in the bottom of that post, one sees that you did not respond to it until post #123. This of course is well after I had already reposted a quote from that source and supplied several abstracts to papers that provide direct evidence against 'directed' mutations - the ones you claimed were in fact evidence for them.
I say:
Thanks for admitting you were wrong. I agree on the other mail.
You say:
While I see that I was in error in so far as interpreting your post #123 and #126, I maintain that you did not read, or perhaps understand, the implications of the abstracts I posted in #96. One has to be a dogmatist extraordinaire to believe that papers explaining how mutations occurred genome-wide really indicate a non-random mechanism.
I say:
I know the implications, and I just wait and see for more experiments on the 'hot' regions.
You say:
Yes, I see that now. My sincere apologies.
I say:
Accepted
You say:
I am wrong? Well, then, Peter B., please supply us with the documentation for non-random mutations occurring in multicellular eukaryotes that result in phenotypic change. The best he could do was some pap about sea gull wings... Which of course had no genetic analysis in its support...
Spetner the creationist could not do this then, and he has not done it yet.
Help him out.
I say:
I already helped him out by showing some interesing examples of non-random mutation (although they are not accepted by some evolutionists, including yourself). So, more research in this particular area will be revealing. I predict: Within 10 years non-random mutations will have their place in NDT.
my quote:
--------------------------------------------------------------------------------
THAT THE MECHANISM IS NOT EXACTLY AS HE (AND CAIRNS) THOUGHT IT WAS, IS NOT SURPRISING SINCE NOTHING IN BIOLOGY IS AS WE EXPECT IT TO BE.
--------------------------------------------------------------------------------
So he was wrong then. Good to hear you say that.
I say:
The original proposal was false. I just wait and see what the hot regions imply. Maybe it implies an indirect mechanism.
my quote:
--------------------------------------------------------------------------------
FURTHERMORE, THE CAIRNS INTERPRETATION IS ONLY A MINOR POINT IN SPETNER'S BOOK SO YOU CANNOT REJECT HIS ENTIRE BOOK ON CAIRN'S PARTIAL RECANTATION.
--------------------------------------------------------------------------------
you say:
I didn't. Indeed, the Cairn's bit was mentioned in regards to "non-random mutation" in general, not to anyone's vanity press book targeting a lay audience.
I say:
At least somebody who tries to educate the lay audience in an anti-nihilistic way. My objections to the hype are all the extrapolations from it. That is, the BullS..T I hear on the television and read in the papers. You --as a respectable scientist-- should also object to that.
quote:
--------------------------------------------------------------------------------
BETTER READ HIS BOOK INSTEAD OF ONLY HIS OPPONENTS. AND WHY DO YOU THINK THERE HAVE BEEN CARRIED OUT SO MANY EXPERIMENTS TO FALSIFY CAIRNS INTERPRETATION?
--------------------------------------------------------------------------------
In reality, so many experiments were carried out to see if he was right (he wasn't), not to try to disprove him.
I say:
Maybe they didn't perform the right experiments yet. I think a lot more is going on in this operon than we think there is. And what about the cryptic genes? The distinct stopcodons alternated by sense DNA are nor merely for show. I persist, there is a mechanism that can drain this well, and it will be found. Maybe it cannot be found in the laboratory. Maybe one has to look in subpopulations of extant organisms.
my quote:
--------------------------------------------------------------------------------
THE NDT WOULD HAVE FALLEN, AND THAT IS EXACTLY WHY YOU OBJECT/DENY THE NON-RANDOMNESS OF MUTATION IN THE 1G5 GENE. AND THAT'S WHY NDT BLOCKS SCIENTIFIC PROGRESS.
--------------------------------------------------------------------------------
You say:
What progress would be made by accepting a fringe idea on non-random mutation? I object/deny it because as I have repeatedly explained and supplied references for, the idea of non-randomness is not what it is made out to be by folks like you.
I say:
I said this with the 1G5 gene in mind. Denial of observations does not bring science any further.
You say (about reconsiliation of gene and species trees):
They do? Examples please.
I gave you the IL1-beta incongruence. One should be sufficient.
my quote:
--------------------------------------------------------------------------------
ACCORDING TO EVOLUTIONARY BIOLOGISTS, GENE TREES HAVE TO BE IN AGREEMENT WITH SPECIES TREES.
--------------------------------------------------------------------------------
you say:
This is a major misrepresentation on your part, Peter B. It is outright false.
I say:
Please elaborate a bit on it. References etc.
You say:
Your credibility - what little you may have once had here - is now completely gone.
I say:
My credibility within the evolutionary community is about zero, I guess. But, so what, I go for truth, not for 'evolutionisms just-so stories'.
my quote:
--------------------------------------------------------------------------------
WHY? OTHERWISE ALL GENES LYING OUT PROVIDE FALSIFICATIONS OF COMMON DESCENT.
--------------------------------------------------------------------------------
you say:
This is just asinine, and indicative of your dogmatic ignorance. Any text on molecular evolution not only explains why discrepencies exist, they actually predict that more will be found.
I say:
Listen Mr SLPx, I don't adhere any dogma's. I just stand up against nihilism. And as I see it, molecular genetics points in the direction of 'creatons interacting with matter in a morphogenetic field'. And you have to present pretty strong arguments to convince me of the opposite.
And now I am curious what the hype has invented now to predict discrepancies. So, explain plus references please. (BTW, "to predict discrepancies". Hear what you are implying: 'our hype predicts that phenomenon X may be found and otherwise the opposite of X may also be found.' I call that HUMBUG)
my quote:
--------------------------------------------------------------------------------
YOU CAN FIND THIS HIGHLY DISPUTABLE MATHEMATHICAL TRICK FOR INSTANCE IN 'MOLECULAR EVOLUTION, A PHYLOGENTIC APPROACH by R. PAGE'. WHAT EVO’S DO IS THE OTHER WAY AROUND REASONING. THEY CLAIM THAT SINCE EVOLUTION IS TRUE, THE EVIDENCE FOR PUTATIVE DUPLICATIONS IS SIMPLY THE INCONGRUENCE BETWEEN THE GENE AND THE SPECIES TREE. I OBJECT TO SUCH SIMPLISICISM.
--------------------------------------------------------------------------------
I object to your idiocy, but it won't get me anywhere. Is it a 'trick'? That sounds awfully inflammatory, Peter B. Perhaps you don't understand statistics?
I say:
No, your are not going to hide behind statistics. That's another trick to not answer. Besides, statistics has nothing to do with putative duplications that are not present.
you say:
Or maybe the workings of genomes? Well, either way, your claims are getting more and more bizarre and more and more desparate.
I say:
That the claims seem bizarre is due to the shortcomings of evolutionism on the level of the genome.
my quote:
--------------------------------------------------------------------------------
FOR EXAMPLES: (http://taxonomy.zoology.gla.ac.uk/rod/papers/page97mpe.pdf).
--------------------------------------------------------------------------------
The abstract:
"The processes of gene duplication, loss, and lineage
sorting can result in incongruence between the phylogenies
of genes and those of species. This incongruence
complicates the task of inferring the latter from the
former. We describe the use of reconciled trees to
reconstruct the history of a gene tree with respect to a
species tree. Reconciled trees allow the history of the
gene tree to be visualized and also quantify the relationship
between the two trees. The cost of a reconciled
tree is the total number of duplications and gene losses
required to reconcile a gene tree with its species tree.
We describe the use of heuristic searches to find the
species tree which yields the reconciled tree with the
lowest cost. This method can be used to infer species
trees from one or more gene trees."
you say:
Whats your point?
I say:
My point was the incongruence of the IL-1beta family and the absence of the duplication. The only putative duplication to be found in this region is the one that gave rise to human IL-1alpha. Maybe reread my point. And I am not the desperate one.
You say:
I am constantly amazed at how the creationist interprets 'explanations' as 'excuses' and the like. Pitiful, really.
I say:
Better try to convince me with a scientific explanation instead of these evo-blahblah.
quote:
I say:
Here you demonstrate again your condescending (dumb and dumber, remember) overconfinced attitude.
--------------------------------------------------------------------------------
You say:
No, it is a valid conclusion.
I say:
Based on what? Could you please lead me through your thoughts and how you draw such conclusions.
quote:
---------------------------------
peter borger writes:
THE MOLECULAR GENAEOLGY OF INTERLEUKIN-1-beta demonstrates an aberration from the species tree.
you say:
So?
I say:
Why did you cut of this falsification of common decent. It was the quintessence. Maybe you could respond to it in a scientific way.
quote:
----------------------------------------------------------------------
And concerning the Uebermensch: you were the one that introduced space-aliens to explain genes in humans not present in apes. I can think of several better 'scientific' non-testable explanations.
----------------------------------------------------------------------
I did no such thing. Please stop misrepresenting me and trying to erect straw man arguments.
MY RESPONSE;
YES, YOU DID. IN RESPONSE TO THE GENES PRESENT IN HUMAN NOT PRSENT IN MAN.
--------------------------------------------------------------------------------
What genes might be present in humans but not in man, I wonder...
I say:
Obviously, you have a very selective memory. The gene in the LCR16a segment: present in human not in apes.
You say:
How do you propose this comparison be done?
MY RESPONSE:
AS DEMONSTRATED FOR THE 1G5 GENES IN A LARGE AMOUNT OF SUBPOPULATIONS.
--------------------------------------------------------------------------------
You say:
What do you mean sub-population?
I say:
Remember the Ig5 gene and the peculiar results that gave when the authors compared subpopulations. That's where my discussion started 3 months ago.
quote:
--------------------------------------------------------------------------------
I AM INTERESTED IN THE SEQUENCES OF ONE PARTICULARE GENE (SAY HEMOGLOBIN OR CYTOCHROME C) THROUGHOUT THE DIFFERENT HUMAN SUBPOPULATIONS. I WONDER WHETHER THESE DATA ARE PRESENT INLITERATURE?
--------------------------------------------------------------------------------
You say:
I don't know about that particular gene, but Paabo's group has done an extensive study on the mitochondrial genome and, why, it must be a mere coincidence, the findings fit wquite nicely with evolutionary hypotheses.
I say:
Is this really your response? Could you give me the references of Paabo studies. Was it caried out in subpopulations.
And you write:
"I wonder what your more knowledgible and rational colleagues would think if they knew that you were writing - and apparently believe - something so asinine?"
I say:
Nice try to stop me from doing. My colleagues like new ideas.
Ye, why not publish somewhere that i'm an ass. That would be fun, isn't ist. You could join Schrafinator's club.
You say:
I guess you didn't realize that all those duplicated genes actually fit quite well within an evolutionary framework?
I say:
And this shows your lack of knowledge on the topic. Once more for you:
There is NO association between genetic redundancies and gene duplications. So how exactly does it fit in? Please explain, and send a letter to Nature, since you are the first one.
quote:
----------------------------------------------------------------------
(ever heard of the second DNA associated code of transcription? And there may even be a third code involved in coactivation of transcription. Firstly, there is NO evolutionary explanation for the first code. And now we find that the first code gives rise to a second code through possible another code. So you better present a pretty good story to explain this by a random mechanism).
----------------------------------------------------------------------
Frankly, no, I have not heard of this. Please provide some verifiable documentation that I can check to see if your depiction of this is accurate.
MY RESPONSE:
I ALREADY GAVE THE REFERENCES. I AM WAITING FOR A REPONSE.
--------------------------------------------------------------------------------
You say:
I am still waiting for your hypothesis...
I say:
You could have found it if you actually were reading my posts.
You also say:
A response to what?
I say:
It once more demonstrates your lack of knowledge on contemporary biology. Notably it was published in Science 2001. Everybody reads Science! Except ostriches, I guess.
Best wishes,
Peter

This message is a reply to:
 Message 158 by derwood, posted 10-02-2002 11:43 AM derwood has replied

Replies to this message:
 Message 170 by derwood, posted 10-04-2002 2:28 PM peter borger has replied

Dr_Tazimus_maximus
Member (Idle past 3217 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 163 of 274 (18989)
10-03-2002 10:52 AM
Reply to: Message 144 by peter borger
09-27-2002 6:37 PM


Hi Peter, the largest problem with your statements concerning mutation and randomness appear to me to be a confusion with respect to: 1) randomness with an equal probability of a specific occurance over the range of possibilities, 2) randomness with a non-equal proability of a specific occurance over a range of possibilities, 3) and a non-random occurance of a specific possibility over a range. I am sure that there is a better statistical means of saying this, my stats are self taught although sufficient to compile, analyze and submit clinical and production data through the FDA. NDS deals with the second, not the first as you seem to be indicating. In fact, every reference that you have pointed out supports this treatment of the results far more than number 3 (your apparent approach). The Science paper on Histones, which I had on hand, is very supportive of this interpretation as well. The higher rate of mutations in actively transcribing genes has been well known for years. The fact that both the primary and secondary structure of genes play a role in the probability of a mutational event at those sites is also well known. The mutational frequency that everyone talks about is an average of the much higher probability sites and the much lower probability sites. Your directed mutation seems to me to be nothing more than the increased probability based on structural features and is therefor not in conflict with NDS at all.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 144 by peter borger, posted 09-27-2002 6:37 PM peter borger has replied

Replies to this message:
 Message 167 by wj, posted 10-03-2002 11:57 PM Dr_Tazimus_maximus has replied
 Message 181 by peter borger, posted 10-07-2002 9:30 PM Dr_Tazimus_maximus has not replied

derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 164 of 274 (18998)
10-03-2002 12:49 PM
Reply to: Message 160 by peter borger
10-02-2002 8:10 PM


quote:
Originally posted by peter borger:
Dear SLPx,
I referred to Roderick Page, the author of "Molecular Evolution, A Phylogenetic Approach".
Sorry for confusing you. I mentioned that I --before registration to this board-- I had a lot of private conversations with evolutionary biologists. As soon as I mentioned the current problems in evolution theory and demonstrated this with examples from literature, there was silence. So I know what I'm talking about.
Best wishes,
peter

Yes, of course. Because after all, the dogmatic evolutionists are afraid to discuss the falsifications of their pet theory.
I rather believe that when it became clear that you were not really intereste din any rational discourse - as one can see form your TalkOrigins feedback and your posts here - that they decided to stop wasting time on you.

This message is a reply to:
 Message 160 by peter borger, posted 10-02-2002 8:10 PM peter borger has not replied

derwood
Member (Idle past 1876 days)
Posts: 1457
Joined: 12-27-2001


Message 165 of 274 (18999)
10-03-2002 12:53 PM
Reply to: Message 159 by peter borger
10-02-2002 8:00 PM


quote:
Originally posted by peter borger:
Dear SLPx,
Yes, Mister SLPx, these postions are NOT under selective constraint and are per definition neutral. I guess, mister Futuyma forgot about this, I don't. Why don't you just simply address my comments in a scientific way and try to convince me, instaed of repeating that I am a creationist. I am always open for good scientific arguments.
best wishes
[This message has been edited by peter borger, 10-02-2002]

Odd - this does not even address what I wrote.
YOU wrote that Kimura claimed this and that, then later admiotted that it was what YOU had in mind.
I simply demonstrated the inconsistency, Mr.Borger.

This message is a reply to:
 Message 159 by peter borger, posted 10-02-2002 8:00 PM peter borger has replied

Replies to this message:
 Message 166 by peter borger, posted 10-03-2002 10:21 PM derwood has replied

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