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Author Topic:   oh look - an observed gene duplication....
derwood
Member (Idle past 39 days)
Posts: 1457
Joined: 12-27-2001


Message 1 of 43 (23360)
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?

Emphases and comments in italics mine:

**********************************************************************
Dev Biol 2002 Sep 1;249(1):96-107

Duplication of the Hoxd11 gene causes alterations in the axial and appendicular skeleton of the mouse.

Boulet AM, Capecchi MR.

Howard Hughes Medical Institute, Department of Human Genetics, University of Utah, School of Medicine, Salt Lake City, Utah 84112-5331, USA.

The Hox genes encode a group of transcription factors essential for proper development of the mouse. Targeted mutation of the Hoxd11 gene causes reduced male fertility, vertebral transformation, carpal bone fusions, and reductions in digit length. A duplication of the Hoxd11 gene was created with the expectation that the consequences of restricted overexpression in the appropriate cells
would provide further insight into the function of the Hoxd11 gene product.
Genetic assays demonstrated that two tandem copies of Hoxd11 were functionally indistinguishable from the normal two copies of the gene on separate chromosomes with respect to formation of the axial and appendicular skeleton. Extra copies of Hoxd11 caused an increase in the lengths of some bones of the forelimb autopod and a decrease in the number of lumbar vertebrae.

Point 1: 'New information' is NOT required to alter phenotype. One leg knocked out from the YEC information hawks...

Further, analysis of the Hoxd11 duplication demonstrated that the Hoxd11 protein can perform some functions supplied by its paralogue Hoxa11. For example, the defects in forelimb bones are corrected when extra copies of Hoxd11 are present in the Hoxa11
homozygous mutant background.

Point 2: The presence of a duplicate 'fixes' problems caused bya mutated gene. Beneficial in anyone's book. Both legs gone, YEC information hawk goes tumbling down...

Thus, it appears that Hoxd11 can quantitatively compensate for the absence of Hoxa11 protein, and therefore Hoxa11 and Hoxd11 are functionally equivalent in the zeugopod. However, extra copies of Hoxd11 did not improve male or female fertility in Hoxa11 mutants.

Oops - missed this 'excuse': It isn't all good, so the 'challenge' was not met. Right?

Interestingly, the insertion of an additional Hoxd11 locus into the HoxD complex does not appear to affect the expression patterns of the neighboring Hoxd10, -d12, or -d13 genes.
******************************************************************

Still waiting for lab reports of creation ex nihilo by the deity depicted in the bible, lest YECism is false...


Replies to this message:
 Message 2 by Quetzal, posted 11-20-2002 9:46 AM derwood has responded
 Message 4 by Mammuthus, posted 11-20-2002 9:58 AM derwood has not yet responded
 Message 6 by Fred Williams, posted 11-20-2002 1:19 PM derwood has responded
 Message 9 by Tranquility Base, posted 11-20-2002 6:40 PM derwood has responded
 Message 11 by peter borger, posted 11-20-2002 11:22 PM derwood has responded

    
Quetzal
Member (Idle past 4035 days)
Posts: 3228
Joined: 01-09-2002


Message 2 of 43 (23365)
11-20-2002 9:46 AM
Reply to: Message 1 by derwood
11-20-2002 9:32 AM


Yeah, you missed at least one:

6. All of which proves the multipurpose genome (because of the duplications) and falsifies evolutionism.


This message is a reply to:
 Message 1 by derwood, posted 11-20-2002 9:32 AM derwood has responded

Replies to this message:
 Message 3 by derwood, posted 11-20-2002 9:52 AM Quetzal has not yet responded

  
derwood
Member (Idle past 39 days)
Posts: 1457
Joined: 12-27-2001


Message 3 of 43 (23369)
11-20-2002 9:52 AM
Reply to: Message 2 by Quetzal
11-20-2002 9:46 AM


quote:
Originally posted by Quetzal:
Yeah, you missed at least one:

6. All of which proves the multipurpose genome (because of the duplications) and falsifies evolutionism.


Silly, silly me.....


This message is a reply to:
 Message 2 by Quetzal, posted 11-20-2002 9:46 AM Quetzal has not yet responded

    
Mammuthus
Member (Idle past 4638 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 yet responded

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

  
Quetzal
Member (Idle past 4035 days)
Posts: 3228
Joined: 01-09-2002


Message 5 of 43 (23373)
11-20-2002 10:14 AM
Reply to: Message 4 by Mammuthus
11-20-2002 9:58 AM


[This message has been edited by Quetzal, 11-20-2002]


This message is a reply to:
 Message 4 by Mammuthus, posted 11-20-2002 9:58 AM Mammuthus has not yet responded

  
Fred Williams
Member (Idle past 3019 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 6 of 43 (23389)
11-20-2002 1:19 PM
Reply to: Message 1 by derwood
11-20-2002 9:32 AM


Dear Mr “Tree Rings = Code” guy,

Please show me anywhere in the history of the internet where I claimed duplications have not been observed. Since you save all my writings this should be easy. Let me help you. Put all my posts in the same folder. Then do a FIND on “duplication”. Read them to see if I ever claim duplications haven’t been observed. No luck? Then please dismantle your strawman and return it to the closet.

quote:
Point 2: The presence of a duplicate 'fixes' problems caused bya mutated gene. Beneficial in anyone's book. Both legs gone, YEC information hawk goes tumbling down...

LOL! So where is the new information?!

Keep trying, Dr Tree Rings.


This message is a reply to:
 Message 1 by derwood, posted 11-20-2002 9:32 AM derwood has responded

Replies to this message:
 Message 7 by derwood, posted 11-20-2002 3:25 PM Fred Williams has not yet responded

    
derwood
Member (Idle past 39 days)
Posts: 1457
Joined: 12-27-2001


Message 7 of 43 (23399)
11-20-2002 3:25 PM
Reply to: Message 6 by Fred Williams
11-20-2002 1:19 PM


quote:
Originally posted by Fred Williams:
Dear Mr “Tree Rings = Code” guy,

Please show me anywhere in the history of the internet where I claimed duplications have not been observed.


I never said you did, Moderator 3. Of course, you asked for an 'example' of a gene duplication and subsequent mutation conferring an advantage. I provided one, you tack on the extra criterion about 'observed.' That is the creationist way.[quote]
Snip implicit attemtp to make face-saving accusation by Oil-of-hyssop-is-50%-antibacterial guy.

quote:

quote:
Point 2: The presence of a duplicate 'fixes' problems caused bya mutated gene. Beneficial in anyone's book. Both legs gone, YEC information hawk goes tumbling down...

LOL! So where is the new information?!

Keep trying, Dr Tree Rings.


Oh look - yet more additional criteria!

Mam and questzal - we all missed the obvious one:

8. No new information by my personal defintion.

That is (one of the) the point, totally lost on Mr.SNPs-are-removed-from-phylogentic-analyses.

The points are:

The gene duplication conferred an advantage ('fixed' problems caused by mutant genes); therefore, it meets your criterion re: advantage

Gene duplication - observed - can alter phenotype.

"New information required by evolution" mantra rendered moot.

It is obvious that a one-trick pony such as yourself would do his darndest to tryt to dodge the issue.

But your tactics are transparent.

And a bit sad.

Not to mention predictable.

The creationist Jerry Bergman said it best:

"A key to success is knowing what one can speak authoritatively about and knowing where one's limits of knowledge and expertise are. All of us have opinions which lie outside of our area of expertise. Most intelligent people are cognizant of this fact and therefore usually avoid pontificating on areas they know little about."

So please Williams, stop the pontification.


This message is a reply to:
 Message 6 by Fred Williams, posted 11-20-2002 1:19 PM Fred Williams has not yet responded

Replies to this message:
 Message 8 by derwood, posted 11-20-2002 3:54 PM derwood has not yet responded

    
derwood
Member (Idle past 39 days)
Posts: 1457
Joined: 12-27-2001


Message 8 of 43 (23400)
11-20-2002 3:54 PM
Reply to: Message 7 by derwood
11-20-2002 3:25 PM


Well, Fred used #2, and we forget this one:

8. Insult, insult, insult to try to divert attention.


This message is a reply to:
 Message 7 by derwood, posted 11-20-2002 3:25 PM derwood has not yet responded

Replies to this message:
 Message 15 by Mammuthus, posted 11-21-2002 5:03 AM derwood has responded

    
Tranquility Base
Inactive Member


Message 9 of 43 (23412)
11-20-2002 6:40 PM
Reply to: Message 1 by derwood
11-20-2002 9:32 AM


SLPx

I didn't check to see which category my answer comes under but I have spent a lotof time pointing out that we agree with everything you say on alellic copies and changes. We point out that that is not the primary differnce between genomes. It's the banks of new pathways which include new gene families - that's where we disagree with you!


This message is a reply to:
 Message 1 by derwood, posted 11-20-2002 9:32 AM derwood has responded

Replies to this message:
 Message 16 by derwood, posted 11-21-2002 8:16 AM Tranquility Base has responded

  
joz
Inactive Member


Message 10 of 43 (23432)
11-20-2002 10:22 PM


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]


Replies to this message:
 Message 14 by Mammuthus, posted 11-21-2002 3:18 AM joz has not yet responded

  
peter borger
Member (Idle past 5828 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 11 of 43 (23444)
11-20-2002 11:22 PM
Reply to: Message 1 by derwood
11-20-2002 9:32 AM


Dear Dr Page,

It was already recognised by Quetzal (although it neither falsifies nor verifies evolution), but thanks for your marvellous example demonstrating the MPG in action. All your points were predicted by the MPG. See my letter #1 mol gen evidence for a MPG thread for these predictions. And that should be expectd from a good scientific theory: it should have predictive power.

The multipurpose genome (MPG) hypothesis holds that:

1) DNA sequences within species –-although plastic-- are stable throughout time,
2) organisms demonstrate genetic redundancies that reside in the genome without selective constraint,
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],
4) the function of natural selection is to remove degenerate organisms, and
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).

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.
2) predicts that a considerable part of the genes of any organism can be knocked out without being lethal.
3) predicts that adaptive phenotypes of organism do never demonstrate new genes.
4) predicts that organism lacking vital DNA elements are selected against.
5) predicts that there should be organisms that have not undergone genetic changes (yet).

Falsification of the MPG hypothesis:
The concept will be falsified by the observation of the evolution of new genes unrelated to preexisting genes.

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.

I think Mammuthus will also like this example, since he likes to have proof for the MPG.

Best wishes,
Peter

[This message has been edited by peter borger, 11-20-2002]


This message is a reply to:
 Message 1 by derwood, posted 11-20-2002 9:32 AM derwood has responded

Replies to this message:
 Message 13 by Mammuthus, posted 11-21-2002 3:14 AM peter borger has responded
 Message 17 by derwood, posted 11-21-2002 8:19 AM peter borger has not yet responded
 Message 33 by Budikka, posted 11-25-2002 1:22 PM peter borger has responded

    
monkenstick
Inactive Member


Message 12 of 43 (23458)
11-21-2002 1:22 AM


borger,if you're referring to regulatory evolution, its not a new idea - its also entirely consistent with NDT
  
Mammuthus
Member (Idle past 4638 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 responded

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

  
Mammuthus
Member (Idle past 4638 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 yet responded

  
Mammuthus
Member (Idle past 4638 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 responded

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

  
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