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Author Topic:   oh look - an observed gene duplication....
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 4 of 43 (23371)
11-20-2002 9:58 AM
Reply to: Message 1 by derwood
11-20-2002 9:32 AM


Allow me to predict any potential attempts at 'refutation':
1. It happened in a lab, so it is really evidence for Design!
2. That is not exactly, precisely what I challenged you to present, so it doesn't count.
3. The researchers had evolutionary assumptions, so it is question begging
4. The mice are still mice, so evolution is still a fairy tale.
5. The whole paper likely contains information contraditory to what you see in the abstract, so I cannot comment on this until I get the paper, and I will never try to get the paper.
Did I miss any?
*******************
6. Williams will say, this is a strawman because clearly if you look at a picture of poodles while playing with a deck of cards you will realize the genetic potential of an ace of spades after a genetic bottleneck while playing keyboards in front of a dead lightbulb and your Ph.D. is from Hasbro from which it can be concluded no information was lost, gained, or maintained
7. Borger will say, the MPG predicted all of this because non-random mutations told me so and I have yet again falsified all biology because I can explain it better than anyone and I don't need to read the paper since it is an evolutionist atheists conspiracy but I will show the evidence for my position in a couple of months even though it should be obvious....but until then I will repeat the same things over and over again because that makes them true

This message is a reply to:
 Message 1 by derwood, posted 11-20-2002 9:32 AM derwood has not replied

Replies to this message:
 Message 5 by Quetzal, posted 11-20-2002 10:14 AM Mammuthus has not replied

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


Message 13 of 43 (23461)
11-21-2002 3:14 AM
Reply to: Message 11 by peter borger
11-20-2002 11:22 PM


Well SLPx...I would say this is number 7 from my addendum to your list
The multipurpose genome (MPG) hypothesis holds that:
M: Already wrong.....define the "purpose of the genome"...or by MPG do you mean miles per gallon
1) DNA sequences within species —-although plastic-- are stable throughout time,
M: Which says absolutely nothing....and ignores hypervariable sequences
2) organisms demonstrate genetic redundancies that reside in the genome without selective constraint,
M: neutral evolution does to....duh
3) adaptive phenotypes are due to duplication and/or shuffling of preexisting DNA elements —either genes or other non-coding elements-- that affect gene expression, or due to loss of (redundant) genes [=degeneration theory],
M: Falsified by point and small and large scale deletion event mutations that also alter phenotype.
4) the function of natural selection is to remove degenerate organisms, and
M: Then why is Williams still around? ...define degenerate
5) there is/has been creation (=creaton interactions with matter in a morphogenetic field giving rise to genes and genetic programs in preexisting genetic programs).
M: So much for your proving anything...without having a loaded crack pipe in your mouth and deeply inhaling...where can the rest of us see morphogenetic fields or creatons?
Predictions of the MPG hypothesis:
1) predicts that within species we do not see abundant variation with respect to genes, and usually such genetic alterations are neutral or degenerate (although distinct alleles can be expected through the principle of degeneration, which is in effect the action of entropy).
It also predicts that all organism --even the simplest-- have an elaborate and accurate mechanism to counteract mutations.
M: This hardly follows from anything in the above tenets you posted...in addition, you have previously claimed that all identity by descent is an illusion so there can be no species...each genome has to be an entity in iteself indepenedent of all others...which falsifies you miles per gallon theory
2) predicts that a considerable part of the genes of any organism can be knocked out without being lethal.
M: And when you put them back in the wild, do thay do better, worse, the same as organisms with the genes?
3) predicts that adaptive phenotypes of organism do never demonstrate new genes.
Falsified..even in primates...syscytin...you are the weakest link..goodbye
4) predicts that organism lacking vital DNA elements are selected against.
M: What is a "vital" element? Or do you mean that when an organism has disruption of say the developmental pathway that leads to heart development this is selected against? Wow..what a novel discovery...
5) predicts that there should be organisms that have not undergone genetic changes (yet).
M: I have not changed genetically in 34 years...wow!
Falsification of the MPG hypothesis:
The concept will be falsified by the observation of the evolution of new genes unrelated to preexisting genes.
M: And by all the rest of the data against almost every one of the hypothesis put forward..
PB:
It will take a while before you will recognise that what you call evolution is 'differential gene expression', usually due to involvement of regulatory mechanism. I already recognised it, since I am in the field of gene regulation, and tried to share this discovery with you. You still are a bit reluctant, but here Dr PAge provides more clearcut evidence that GENE EXPRESSION DOES THE TRICK. Ever expected that? I didn't, till recently.
M: I knew that drugs were freely available in the Netherlands but really Peter..you need to cut back.
PB:
I think Mammuthus will also like this example, since he likes to have proof for the MPG.
M: Then the other half of your post where you actually provide this "proof" must have been cut off from your message..care to re-post it?
[This message has been edited by Mammuthus, 11-21-2002]

This message is a reply to:
 Message 11 by peter borger, posted 11-20-2002 11:22 PM peter borger has replied

Replies to this message:
 Message 23 by peter borger, posted 11-22-2002 8:36 PM Mammuthus has replied

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


Message 14 of 43 (23462)
11-21-2002 3:18 AM
Reply to: Message 10 by joz
11-20-2002 10:22 PM


quote:
Originally posted by joz:
Ok lets see now...
(alphabet soup time)...
Case one.
Two statements:
a)Mr Williams is.
b)Dr Page is not an idiot.
From this we can tell that both Mr W and Dr P exsist and additionslly that Dr P is not an idiot.
Case two.
Same two statements but the phrase "an idiot" is copied from statement b) and appended to statement a)
a)Mr Williams is an idiot.
b)Dr Page is not an idiot.
From these two statements we can see that both Mr W and Dr P exsist and also that while Dr P is not an idiot Mr W is...
Which set of statements do you think contains the most information?
[This message has been edited by joz, 11-20-2002]

*********************
LOL!!!

This message is a reply to:
 Message 10 by joz, posted 11-20-2002 10:22 PM joz has not replied

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


Message 15 of 43 (23467)
11-21-2002 5:03 AM
Reply to: Message 8 by derwood
11-20-2002 3:54 PM


quote:
Originally posted by SLPx:
Well, Fred used #2, and we forget this one:
8. Insult, insult, insult to try to divert attention.

forgot another one...
9. To busy to answer the question even though it is so easy to...
9b. Will post the obvious answer to the questions in a couple of months (since hopefully you will all have forgotten that I said I would)...when asked again I will say I will post the answer in a couple of months (since...etc etc etc.

This message is a reply to:
 Message 8 by derwood, posted 11-20-2002 3:54 PM derwood has replied

Replies to this message:
 Message 18 by Mammuthus, posted 11-21-2002 8:20 AM Mammuthus has not replied
 Message 19 by derwood, posted 11-21-2002 8:22 AM Mammuthus has not replied

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


Message 18 of 43 (23475)
11-21-2002 8:20 AM
Reply to: Message 15 by Mammuthus
11-21-2002 5:03 AM


quote:
Originally posted by Mammuthus:
quote:
Originally posted by SLPx:
Well, Fred used #2, and we forget this one:
8. Insult, insult, insult to try to divert attention.

forgot another one...
9. To busy to answer the question even though it is so easy to...
9b. Will post the obvious answer to the questions in a couple of months (since hopefully you will all have forgotten that I said I would)...when asked again I will say I will post the answer in a couple of months (since...etc etc etc.

**********************
Just thought of number 10 to round out the "ten creationist debating commandments"
10) When you realize that you are completely in error...deny that you ever made the claim or answer posts in complete gibberish (or make references to decks of cards and poodles). Option two, ignore posts exposing your errors.

This message is a reply to:
 Message 15 by Mammuthus, posted 11-21-2002 5:03 AM Mammuthus has not replied

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


Message 22 of 43 (23645)
11-22-2002 2:59 AM
Reply to: Message 20 by joz
11-21-2002 12:32 PM


quote:
Originally posted by joz:
Decks of cards and poodles?
I missed that one but it sounds ammusing, what did he say that time?

*************
His analogies for genetic bottlenecks (which were back assward by the way) used decks of cards "realizing" their diversity and poodles magically turning into St. Bernards

This message is a reply to:
 Message 20 by joz, posted 11-21-2002 12:32 PM joz has replied

Replies to this message:
 Message 25 by Fred Williams, posted 11-23-2002 1:31 AM Mammuthus has replied
 Message 29 by joz, posted 11-24-2002 1:51 AM Mammuthus has replied

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


Message 27 of 43 (23896)
11-23-2002 10:47 AM
Reply to: Message 25 by Fred Williams
11-23-2002 1:31 AM


[QUOTE]Originally posted by Fred Williams:
[B]
quote:
M: His analogies for genetic bottlenecks (which were back assward by the way) used decks of cards "realizing" their diversity and poodles magically turning into St. Bernards
Nowhere do I make even hint at such an idea.
M: Big hint:
FW: Post 81 mol genet evidence for a multipurpose genome
I truly hope you do not have a PhD, because there is simply no excuse for anyone, even an evolutionist, to claim that a bottlenecked animal such as the cheetah has not lost genetic information due to the isolation event and subsequent genetic drift. According to the dream world of Mammuthus, if we isolate the poodle completely, and let it breed only with other poodles, we can eventually get a St Bernard.
M:
This was YOUR attempt in that empty container you call a head of trying to attribute your ignorant incoherent views on population genetics to me. (Note...I NEVER mentioned poodles or dogs for that matter, in any of my discussions prior to this rant of yours. And this was only the first time you brought up dogs to both demonstrate you know nothing about the effect of selective breeding on genetic diversity or dogs for that matter i.e. the dogs "realizing" their potential.
FW:
Please stop parading around with this strawman, now in multiple threads. It’s simply not true, and I do not appreciate you misrepresenting and twisting my words.
M: Oh you mean by demonstratig how you tried and failed to shift the blame for your stupidity to me? Live with it yourself..it is all yours.
FW:
I said dog breeds are essentially man-made genetic bottlenecks, and serve as one way that enables us to SEE some of the diversity inherent in the dog kind.
M: You said no such thing....or do you mean your blatantly incorrect deck of card example? YOU said genetic variation is a result of bottlenecks...you then compounded your error with an equally ridiculous deck of card examples.
FW:Instead of addressing this point you went off on various wild tangents, including this poodle transformation to St Bernard nonsense.
M: The wild tangent was your own as YOU brought up the stupid example in the first place....I am being generous...you have said far more obtuse things than your dog or deck of card analogies.
FW:
It’s become apparent you are not interested in serious debate.
M: It was apparent from the start you were not interested in serious debate. You have 1) not supported any of your claims with any data 2) You almost never actually address any question put to you but wave them away i.e. demonstrating non-random mutations or anything related to the mythical flood/ark 3) when you are shown to be a fool (which is a highly reproducible phenomenon)...you rely on insults or "I am to busy to answer" 4) if you cannot answer a question (which is always) you claim your opposition has said something they have not.
The problem is all on your side Fred.

This message is a reply to:
 Message 25 by Fred Williams, posted 11-23-2002 1:31 AM Fred Williams has not replied

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


Message 28 of 43 (23948)
11-23-2002 3:24 PM
Reply to: Message 23 by peter borger
11-22-2002 8:36 PM


1) DNA sequences within species —-although plastic-- are stable throughout time,
M: Which says absolutely nothing....and ignores hypervariable sequences
PB: Hypervariable sites can of course be explained by protein driven mechanisms. This is non-random mutations (NRM). As mentioned, the Grand Unifying Theory of Biology includes the MPG and NRM. Together they can explain all biological observations.
M: Congratulations Peter...for providing absolutely no evidence for these protein driven mechanisms, and merely repeating your oft falsified MPG hypothesis for the 100th time you win the right to wear a hat saying "space for rent" on it.
2) organisms demonstrate genetic redundancies that reside in the genome without selective constraint,
M: neutral evolution does to....duh
PB: I am not going into genetic redundancies, again. You can ask almost everybody on this site how they falsify evolutionism, since I at least explained it a dozen times.
M: Um...you can ask anyone on this site and they will have just as hard a time finding any evidence for your assertions about genetic redundancies...but if they go through all the threads they will certainly find posts from me, Quetzal, SLPx and others that you have been unable to answer....you have not even begun to explain yourself.
3) adaptive phenotypes are due to duplication and/or shuffling of preexisting DNA elements —either genes or other non-coding elements-- that affect gene expression, or due to loss of (redundant) genes [=degeneration theory],
M: Falsified by point and small and large scale deletion event mutations that also alter phenotype.
PB: No, deletions are part of degeneration theory. That should have been obvious.
M: Hey, YOU put forth the prediction and now you are dancing like a hot potato trying to redefine your theory...there is nothing obvious about your theory Peter other than that it is wrong and not based on scientific principles or observations.
4) the function of natural selection is to remove degenerate organisms, and
M: Then why is Williams still around? ...define degenerate
PB: William is apparently not selected against. Degenerate organisms have negative fitness.
M: Good one Peter...and fitness is? You have shown repeatedly that you don't know what it means...so tell us....how can there be fitness by the way in a Lamarkian scenario like you propose?
5) there is/has been creation (=creaton interactions with matter in a morphogenetic field giving rise to genes and genetic programs in preexisting genetic programs).
M: So much for your proving anything...without having a loaded crack pipe in your mouth and deeply inhaling...where can the rest of us see morphogenetic fields or creatons?
PB: As long as biological phenomena are in accord with the MPG hypothesis it is correct, otherwise I will adapt it. The result of creaton-interactions in a morphogenetic field can be observed every day. Open your eyes and look around you.
BTW where can the rest of us see gravitons?
M: A non answer as I predicted...there is absolutely no evidence for your assertion so you are chickening out and not even debating it...and as you claimed quantum mechanics and the theory of gravity are undisputable facts...I guess now you are going to supply the evidence for both since you claim to have such knowledge..what is the exact mechanism by with gravity works Peter? What makes the theory of gravity and undisputed fact and evolution not..this ought to be a laugher
Predictions of the MPG hypothesis:
1) predicts that within species we do not see abundant variation with respect to genes, and usually such genetic alterations are neutral or degenerate (although distinct alleles can be expected through the principle of degeneration, which is in effect the action of entropy).
It also predicts that all organism --even the simplest-- have an elaborate and accurate mechanism to counteract mutations.
M: This hardly follows from anything in the above tenets you posted...in addition, you have previously claimed that all identity by descent is an illusion so there can be no species...each genome has to be an entity in iteself indepenedent of all others...which falsifies you miles per gallon theory.
PB: It follows from point 1-4.
M: Well since 1, 5, and 4 have already been falsified (1 with help from Fred Williams no less) and you refuse to even speculate at potential data for 5 nothing follows from anything you say.
2) predicts that a considerable part of the genes of any organism can be knocked out without being lethal.
M: And when you put them back in the wild, do thay do better, worse, the same as organisms with the genes?
PB: Knockouts can be oberved in the wild to. The human alpha actinin is knocked out in 18% of caucasians, without any effect on reproductive succes (reference is somewhere on this site).
M: Reference is somewhere..dog ate my homework..etc etc...you did not answer the question.
3) predicts that adaptive phenotypes of organism do never demonstrate new genes.
Falsified..even in primates...syscytin...you are the weakest link..goodbye
PB: No, you say that the syncytin gene has been tranferred by a virus into primates and adopted a new function. I say, the virus arose from the primate genome and captured the protein and uses it in the capsid. My vision is probably correct, since viruses have their origin in the genome. Viruses do not drop out of the sky, that's for sure. In fact your syncytin is an example of a new gene in primates that doesn't have an origin. I take it as evidence for creaton interactions in a morphogenetic field. Thanks for the example.
M: So if someone gets HIV infected they should say oh shit..that damn morphogenetic field? LOL! You have been watching too much teletubbies instead of reading...hint hint..the protein does not act as a capsid..falsified..it works as a sycytiotrophoblast fusion protein...oh yeah..when is the last time a virus "arose" from the primate genome? I guess you will stun us with reams of "evidence" like with all other assertions you make? And viruses don't drop out of the sky? You should believe that! As a creationist you guys all believe that stuff just drops out of the sky when you god takes a leak.
4) predicts that organism lacking vital DNA elements are selected against.
M: What is a "vital" element? Or do you mean that when an organism has disruption of say the developmental pathway that leads to heart development this is selected against? Wow..what a novel discovery...
PB: An element that negatively affects reproductivity.
M: Funny then that balancing selection MAINTAINS lots of lethal alleles in the population in a heterozygous state i.e. CFTR.
5) predicts that there should be organisms that have not undergone genetic changes (yet).
M: I have not changed genetically in 34 years...wow!
PB: So, you will live for ever? Dear Mammuthus, in 34 years you have lost a lot of sensible DNA sequences already. Ever cell division will at least change these sequences at certain spots (due to entropy) and will decrease the length of telomeres. So, your assertion is non-sense.
M: Prove it Peter. Your assertion is nonesense. You do understand the difference between somatic and germ cells being that you are such an expert? .
Falsification of the MPG hypothesis:
The concept will be falsified by the observation of the evolution of new genes unrelated to preexisting genes.
M: And by all the rest of the data against almost every one of the hypothesis put forward..
PB: Like what? Till know it hasn't been falsified.
M: I guess you don't actually read the posts on this forum...nothing you have posted has survived scrutiny.
M: I knew that drugs were freely available in the Netherlands but really Peter..you need to cut back.
PB: I almost laugh my pants off!!
M: Your pants came off? Go to the Is it Science? forum...there is a person posting called Lizard Lips who is really interested in undergarments
PB:
Seriously. Now and then, you really are a comediant. You could perform and make money out of it. Did, you know that The Netherlands have a lot of German Drugs Tourists? I am sure you know.
M: I am not German...but from my interactions with most of them (well except my wife) I think a lot of them must be on drugs
PB:
I think Mammuthus will also like this example, since he likes to have proof for the MPG.
M: Then the other half of your post where you actually provide this "proof" must have been cut off from your message..care to re-post it?
PB: Reread all my 500 -or so- mails.
M: No thanks...most jokes are only funny the first time...except for Revenge of the Pink Panther..I can watch that lots of times and still laugh. Or Monty Python.
PB:
Including at least 10 falsifications of evolutionism and the introduction of a new theory that explains all biology. Frankly, your questioning and scepticism contributed to the improvement of the initial hypothesis. Thanks for the discussions.
M: Honestly Peter, as hard as I have been on you lately I still enjoy the debate...and I end up reading articles on subjects outside what I am researching just to nail you with
PB:
BTW, you were the one that stressed I had to introduce such theory and now you are still not contents. What's the matter with you?
M: I am content that you introduced you hypothesis...I believe I even signalled my approval that you posted you hypothesis..but where did I claim I would agree with it?
Best wishes,
M

This message is a reply to:
 Message 23 by peter borger, posted 11-22-2002 8:36 PM peter borger has not replied

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


Message 30 of 43 (24015)
11-24-2002 7:35 AM
Reply to: Message 29 by joz
11-24-2002 1:51 AM


quote:
Originally posted by joz:
quote:
Originally posted by Mammuthus:
His analogies for genetic bottlenecks (which were back assward by the way) used decks of cards "realizing" their diversity and poodles magically turning into St. Bernards
Hey that last sounds testable....
*stomps off looks hard at his pet poodle*
*Comes back to keyboard*
I reckon hes wrong there bud Biscuit (aforementioned poodle) is still small white and fluffy....
(Oh and before anyone starts mocking my choice of dog they shouild know that poodles are the only sort of dog my wife is not allergic too, that I keep him close shorn rather than having one of those ridiculous show cuts and that teams of poodles (standards) have raced and completed the Iditarod before the injunction that the teams must be northern breeds exclusively.... Pretty tough for a critter that some regard as being at the shallow end of the gene pool).....

+++++++++++++++++++
When you look at Biscuit next time, check to see if he has "realized" his genetic diversity as a dog kind since the ark bottleneck....this is another of Fred's pseudoscience Gilligans Island professor assertions....actually why not ask Biscuit if he has realized his genetic potential? A coherent substantive answer from Biscuit is infinitely more likely than from Fred.

This message is a reply to:
 Message 29 by joz, posted 11-24-2002 1:51 AM joz has not replied

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


Message 32 of 43 (24156)
11-25-2002 3:16 AM
Reply to: Message 31 by peter borger
11-24-2002 10:59 PM


PB: That can hardly be the problem. Evolutionism also relies on processes that haven't been observed. The real problem is that it will never be published in PEER reviewed scientific jounals, since the PEERS are evolutionists themselves.
M: You do know that you can actually suggest to the editors specific referees and also ask that specific reviewers be excluded due to competition? Why not ask for Behe?

This message is a reply to:
 Message 31 by peter borger, posted 11-24-2002 10:59 PM peter borger has not replied

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


Message 35 of 43 (24360)
11-26-2002 3:26 AM
Reply to: Message 34 by peter borger
11-25-2002 11:04 PM


PB:
As soon as the pressure is reduced the duplicated DNA region will recombine out and get lost. That's the reason why wildtype bacteria never demonstrate duplicated genes. I recommend you to read pages 200-202 in Molecular biology of the gene. (Watson JD, et al, ISBN 0-8053-9614-4).
M: Except when it does not happen
Gene 2002 Jul 10;294(1-2):25 Related Articles, Links
A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.
Homma K, Fukuchi S, Kawabata T, Ota M, Nishikawa K.
Laboratory of Gene-Product Informatics, Center for Information Biology-DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Shizuoka, Japan
Pseudogenes are open reading frames (ORFs) encoding dysfunctional proteins with high homology to known protein-coding genes. Although pseudogenes were reported to exist in the genomes of many eukaryotes and bacteria, no systematic search for pseudogenes in the Escherichia coli genome has been carried out. Genome comparisons of E. coli strains K-12 and O157 revealed that many protein-coding sequences have prematurely terminated orthologs encoding unstable proteins. To systematically screen for pseudogenes, we selected ORFs generated by premature termination of the orthologous protein-coding genes and subsequently excluded those possibly arising from sequence errors. Lastly we eliminated those with close homologs in this and other species, as these shortened ORFs may actually have functions. The process produced 95 and 101 pseudogene candidates in K-12 and O157, respectively. The assigned three-dimensional structures suggest that most of the encoded proteins cannot fold properly and thus are dysfunctional, indicating that they are probably pseudogenes. Therefore, the existence of a significant number of probable pseudogenes in E. coli is predicted, awaiting experimental verification. Most of them were found to be genes with paralogs or horizontally transferred genes or both. We suggest that pseudogenes constitute a small fraction of the genomes of free-living bacteria in general, reflecting the faster elimination than production of pseudogenes.
and
Zhu P, Morelli G, Achtman M. Related Articles, Links
The opcA and (psi)opcB regions in Neisseria: genes, pseudogenes, deletions, insertion elements and DNA islands.
Mol Microbiol. 1999 Aug;33(3):635-50.
Primary literature man..primary lit

This message is a reply to:
 Message 34 by peter borger, posted 11-25-2002 11:04 PM peter borger has replied

Replies to this message:
 Message 37 by peter borger, posted 11-26-2002 7:38 PM Mammuthus has not replied

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


Message 36 of 43 (24377)
11-26-2002 6:45 AM
Reply to: Message 34 by peter borger
11-25-2002 11:04 PM


PB:
That's the reason why wildtype bacteria never demonstrate duplicated genes. I recommend you to read pages 200-202 in Molecular biology of the gene. (Watson JD, et al, ISBN 0-8053-9614-4).
M: Oh looky..duplicated genes in bacteria...LOL!
Badel JL, Charkowski AO, Deng WL, Collmer A.
A gene in the Pseudomonas syringae pv. tomato Hrp pathogenicity island conserved effector locus, hopPtoA1, contributes to efficient formation of bacterial colonies in planta and is duplicated elsewhere in the genome.
Mol Plant Microbe Interact. 2002 Oct;15(10):1014-24.
2: Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV.
Lineage-specific gene expansions in bacterial and archaeal genomes.
Genome Res. 2001 Apr;11(4):555-65.
Meinersmann RJ, Hiett KL.
Concerted evolution of duplicate fla genes in Campylobacter.
Microbiology. 2000 Sep;146 ( Pt 9):2283-90.

This message is a reply to:
 Message 34 by peter borger, posted 11-25-2002 11:04 PM peter borger has replied

Replies to this message:
 Message 38 by peter borger, posted 11-26-2002 8:09 PM Mammuthus has replied

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


Message 39 of 43 (24558)
11-27-2002 7:01 AM
Reply to: Message 38 by peter borger
11-26-2002 8:09 PM


quote:
{Entire previous message quoted - Deleted - Adminnemooseus}
+++++++++++++++
LOL!!!!
Meinersmann RJ, Hiett KL.
Concerted evolution of duplicate fla genes in Campylobacter.
Microbiology. 2000 Sep;146 ( Pt 9):2283-90.
PB: Don't have to look up the paper. Concerted evolution = retro-speculation. I predict that if one does a proper study on these genes, it has to be replaced by purifying selection. Probably: neutral purifying selection.
The above reference IS a functional duplicate in bacteria..you said you NEVER see duplicates..your statement is falsified. You now claim you don"t have to look at the reference however, YOU claimed you were able to see through the authors speculation and analyze the data YOURSELF...are you now claiming you can see there raw data without reading the paper? That would explain why you make so many mis-statements. Oh yeah, these references were a few of many papers on duplicated genes in bacteria...poor scholarship leads to poor thinking Peter...you really need to read up before YOU engage in Fundie-christian humbug.
[This message has been edited by Adminnemooseus, 11-27-2002]

This message is a reply to:
 Message 38 by peter borger, posted 11-26-2002 8:09 PM peter borger has replied

Replies to this message:
 Message 40 by peter borger, posted 11-27-2002 6:10 PM Mammuthus has replied

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


Message 41 of 43 (24748)
11-28-2002 5:18 AM
Reply to: Message 40 by peter borger
11-27-2002 6:10 PM


"Campylobacters have two similar copies (flaA and flaB) of their flagellin gene."
PB: They already HAVE two similar genes.
M: So duplicates have to be dis-similar? What kind of sense does that make?
PB: These constraints indicate that flaA is unlikely to have derived from flaB -or vice versa- by duplication and mutation/selection.
M: Um...why?
"Nevertheless, segments of the two genes that are highly variable between strains are conserved between the flaA and flaB copies of the genes within a strain."
PB: Conserved regions taken as proof for duplication? Conserved regions implicate a highly specific function, that's all.
M: Then why are they "highly variable" between strains?
"The patterns of synonymous and non-synonymous differences suggest that one segment of the flagellin sequence is under selective pressure at the amino acid sequence level."
PB: This is evolutionary interpretation. It can also suggest special design in this region. Besides selective pressure of duplicated genes? After duplication the gene is redundant. It will get lost easily, unless the direction of evolution is known.
M: So your argument is that duplications will NEVER be observed in bacteria is now that when found they just have not been removed yet?
"Another segment of the protein is maintained within a strain by conversion or recombination."
PB: Maintained by conversion or recombination? It has been demonstrated for several genes that were said to be in the genome by concerted evolution that gene conversion has to be replaced by purifying selection. However, the MPG says that the genome is maintained by DNA repair mechanism. Even the simplest organism have (unexpectedly) a complete and eleborate DNA repair mecahnism (Eisen et al, PNAS 2002, 99;9509-9514).
M: Actually they said nothing about concerted evolution. Gene conversion is an observed fact as is recombination or do you deny that those processes exist to? Why is it unexpected that simple organisms have DNA repair?
"Comparisons of strict consensus amino acid sequences did not reveal any motifs that are uniquely FlaA or FlaB, but there are differences between FlaA and FlaB in those amino acids available for post-translational modification."
PB: A mechanism preexistent in the genome that contributes to phenotypic variation after genes have been transcribed. It is MPG.
M: It is fantasy land...pre-existent?
"The observed pattern of concerted evolution.."
PB Observed (????) concerted evolution. Nothing was observed here, it is inferred from the data. It IS retro-speculation.
M: An electron has never been observed I guess you don't believe in them either...I guess you are going to retract your papers on gene expression to since you only INFERRED that there were changes and did not observe them.
"..of portions of a structural gene is an unusual finding in bacteria and should be searched for with other duplicated genes. Concerted evolution was unexpected for genes involved in phase variation since it minimizes the antigenic repertoire that can be expressed by a single clone in the face of the host immune response."
PB: Of course it was UNEXPECTED. A careful look will reveal that it is purifying selection. In other words: creation."
M: So now you equate purifying selection with creation? That is indeed strange...what religious fanaticism does to a mind
PB:
I really don't understand the evolutionist's logic. Their conclusions are mind-boggling.
M: Yes it is clear that science boggles your mind..but keep trying.
You want more examples of gene duplications in bacteria that according to you NEVER occur?

This message is a reply to:
 Message 40 by peter borger, posted 11-27-2002 6:10 PM peter borger has replied

Replies to this message:
 Message 42 by peter borger, posted 11-29-2002 12:01 AM Mammuthus has replied

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


Message 43 of 43 (24911)
11-29-2002 7:08 AM
Reply to: Message 42 by peter borger
11-29-2002 12:01 AM


M: So duplicates have to be dis-similar? What kind of sense does that make?
PB: duplicates --the word already spells it-- are the same, otherwise they wouldn't have been called duplicates. It is your hypothesis that similar genes have arisen from duplicates. I don't mind that you believe this but a duplicate is a redundant gene and will get lost if no selective constraint are applied. An increase in DNA content that doesn't convey improved fitness will be selected against. MPG, you know. The fla genes are alternately expressed every ten generations or so. The mechanism of switching from flaA to flaB is unclear, but it is clear that it is the only way to keep the two genes in the bacteria's genome.
M: You used a lot of words but did not say anything Peter. Your claim then is that duplicate genes should not be similar to each other and if they are it is a mere coincidence? In any case, you claimed there are NEVER duplicates in bacteria and that this is a tenet of the MPG yet there they are.
PB: If these constraints are not present the genes deteriorate due to entropy.
M: Funny then that in this case and many others, the genes are still there and even pseudogenes are found.
PB: Conserved regions taken as proof for duplication? Conserved regions implicate a highly specific function, that's all.
M: Then why are they "highly variable" between strains?
PB: Non-random mutations within strains.
M: Ok, yet again, which mutations are non-random specifically? You could also start by showing this with SLPx alignment
Otherwise it is an unsupported assertion.
PB: It can be observed, but it is expected that in the course of time the duplication will get lost. As long as selective constraints favor the duplication it will be part of the genome. As soon as selective constraints are relieved, the duplication is embellishment and will be selected against. Bacteria are able to divide every 20 minutes, Even a slight delay results in the overgrow of the mutant by the wildtype. This is elementary microbiology.
M: Yet duplicates are found (not just this one example) and pseudogenes are found..this is also basic microbio which falsifies your assertion.
M: Actually they said nothing about concerted evolution. Gene conversion is an observed fact as is recombination or do you deny that those processes exist to? Why is it unexpected that simple organisms have DNA repair?
PB: Here I am wrong. Skimmed the abstract to quickly. However, conversion and recombination are highly specific event involving several proteins that are preexisting in the genome. Probably triggered by the environment. It is a non-random 'mutation' event guided by preexisting DNA sequences and proteins. So, it is MPG.
M: Actually niether recombination nor gene converstin is particularly specific. I have not heard that recombination is due to environmental stimuli..at least not exclusively. Gene conversion either. How is it non-random? It is completely unpredictable...this is even testable using jumping PCR methods.
PB: A mechanism preexistent in the genome that contributes to phenotypic variation after genes have been transcribed. It is MPG.
M: It is fantasy land...pre-existent?
PB: How do you think conversions and recombination events are carried out? Utterly at random?
M: Yes, they are random.
PB Observed (????) concerted evolution. Nothing was observed here, it is inferred from the data. It IS retro-speculation.
M: An electron has never been observed I guess you don't believe in them either...I guess you are going to retract your papers on gene expression to since you only INFERRED that there were changes and did not observe them.
PB: 'Observed' suggests 'fact'. However, it has never been observed and will never be observed. In contrast, electrons have been observed as particles and waves. I suggest the following experiment. Take a gene, duplicate it, grow the culture with and without selective constraints, wait for 10000 generations and have a look at the sequences. I predict neutral mutations, duplications and shuffling and no novel genes. What do you predict?
M: Um..the electron "observations" are no more direct than anything in evolution. I am surprised that this eludes you. In any case, in your model, why do you qualify it "without selective constraint"?
M: So now you equate purifying selection with creation? That is indeed strange...what religious fanaticism does to a mind
PB: You know what I mean. Purifying selection is another meaningless term to save evolutionism. Why don't the call it 'creation' (meaning: creaton interactions in a morphogenetic field. Sounds very scientific)
M: Why is purifying selection (also called negative selection) meaningless? Define selection..define fitness. So far basic population genetics principles have been undefineable by you so it is hard to take you seriously when you claim they are meaningless. You have to understand what they intend to describe before you can make a claim that they fail. In any case who are creaton interactions in a morphogenetic field scientific? What is the testable hypothesis? Observations? Is it falsifiable? Apparently not as you NEVER responded to the thread asking you about them.
M: Yes it is clear that science boggles your mind..but keep trying.
PB: Logic science isn't mind boggling, illogic science is.
M: Yeah, non-random mutation, MPG, creatons and morphogenetic fields are highly illogical.
M: You want more examples of gene duplications in bacteria that according to you NEVER occur?
PB: Actually, if you had paid attention to what I write (letter #1, mol gen evidence for the MPG), than you should know that gene duplications are part of the MPG, and are expected to take place upon severe selective constraints.
M: Ah, but I paid attention to what you said to Monkenstick which was that duplications should NEVER be observed in bacteria...that is what I have been responding to.
cheers,
M

This message is a reply to:
 Message 42 by peter borger, posted 11-29-2002 12:01 AM peter borger has not replied

  
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