molecular genetic evidence for a multipurpose genome

quote:

---

Originally posted by Fred Williams:
...I wanted to play in a band (which I did for 17 years, then I grew up ).

---

Let me guess - you are an 'expert' keyboard player, too?

quote:

---

Originally posted by peter borger:
Dear mark,

​

You write:

​

Peter,

​

Provide ONE example that hasn't been trounced, or retract this ridiculously overconfident claim. Sheesh.

​

I say:
1) the redundant Src kinase family,
2) the redundant alpha actinin family,
3) the 1G5 gene in D melanogaster
4) the swim reflex in conjunction with the gag reflex in newborn
5) the ancient mtDNA (is still open for discussion)
6) the ZFY region (nobody responded)
7) the ZFX gene/exon
8) the IL-1beta incongruence (and more)
9) the LCR16a gene
10)the wollemi's invariable DNA

​

And probably more.

---

Well, there is at least one lie....

Can't remember which thread this should go in, so am posting it in several...

quote:

---

Originally posted by Fred Williams:

​

Maybe Scott is ready to shatter the world with the example he implies he has in his hand. Let’s see if he plays the card, or keeps us all in suspense!

---

What example? Oh yes - an example of a gene duplication and subsequent mutation that conferred a benefit to the population.The series of gene duplications in what we now call the beta globin gene cluster, a group of 5 genes and a pseudogene. Epsilon-globin, which is expressed in the embryo, has a higher affinity for oxygen than does the adult-expressed beta and delta globin, thereby making it easier for an embryo to gets its 'fair share' of oxygen. Epsilon arose via a duplication from other genes starting with proto-beta.Healthy embryos make for healthy offspring, and healthy offspring are beneficial to the population.What about an insertion that confers pesticide resistence?A Single P450 Allele Associated with Insecticide Resistance in Drosophila
P. J. Daborn,1 J. L. Yen,1 M. R. Bogwitz,2 G. Le Goff,1 E. Feil,1 S. Jeffers,3 N. Tijet,4 T. Perry,2 D. Heckel,2 P. Batterham,2 R. Feyereisen,5 T. G. Wilson,3 R. H. ffrench-Constant1*
Science 297:2253-7.Some interesting findings:From the abstract:"Transgenic analysis of Cyp6 1 shows that overtranscription
of this gene alone is both necessary and sufficient for resistance. Resistance and up-regulation in Drosophila populations are associated wit a single Cyp6 1 allele that has spread globally. The is allele is characterized by the insertion of an Accord transposable element into the 5' end of the Cyp6 1 gene."From the paper:"First, resistance to DDT was wide-spread, as expected, and second, resistance can persist in laboratory strains in the absence
of pesticide selection, which suggests that little or no fitness cost is associated with this mechanism.""The observation that the nucleotide sequence around the first intron in Cyp6g1 (291 bp away from the site of the insertion) is identical in all the resistant alleles supports the concept of this global spread and suggests strong linkage disequilibrium or hitchhiking of nucleotide variation with the spread of DDT resistance."I was especially interested in your Information Theory expertise on this, because: there is no change in the expressed protein, just more of it, and this confers an advantage. Is this 'new information'? If not, why not? If it is, how is so when the expressed protein has not changed?The ref for how Gene duplication can result in altered phenotype is at the office, will post that later.But I did come across this pertinent ref (pay attention Freddie and Borger), emphases mine:
*************************************************Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification.
Proc Natl Acad Sci U S A 2002 Feb 19;99(4):2164-9Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth JR.Department of Biology, University of Utah, Salt Lake City, UT 84112, USA.When a particular lac mutant of Escherichia coli starves in the presence of lactose, nongrowing cells appear to direct mutations preferentially to sites that allow growth (adaptive mutation). This observation suggested that growth limitation stimulates mutability. Evidence is provided here that this behavior is actually caused by a standard Darwinian process in which natural selection acts in three sequential steps. First, growth limitation favors growth of a subpopulation with an amplification of the mutant lac gene; next, it favors cells with a lac(+) revertant allele within the amplified array. Finally, it favors loss of mutant copies until a stable haploid lac(+) revertant arises and overgrows the colony. By increasing the lac copy number, selection enhances the likelihood of reversion within each developing clone. This sequence of events appears to direct mutations to useful sites. General mutagenesis is a side-effect of growth with an amplification (SOS induction). The F' plasmid, which carries lac, contributes by stimulating gene duplication and amplification. Selective stress has no direct effect on mutation rate or target specificity, but acts to favor a succession of cell types with progressively improved growth on lactose. The sequence of events--amplification, mutation, segregation--may help to explain both the origins of some cancers and the evolution of new genes under selection.********************************************Looks like the ball is in William's court now.Let the hand waving, insults, backpedalling, and story-telling begin!

Everything, it seems, can be used by the creationist as 'evidence' for their preferred hocus pocus...That you do not accept the valid explanations presented for the lack of polymorphism in a ZFY intron in humans is your issue. You can claim that you have one 'example' of your 'non-Darwinian' beliefs, sadly, one such anomoly, if we are kind enough to grant it to you in the hopes of going on, is hardly sufficient to topple NDT or 'prove' whatever it is you believe in.

quote:

---

Originally posted by peter borger:
Dear Dr Page,

​

Your examples are all in accord with the multipurpose genome. Lets start with your reference:

​

From the abstract:

​

"Transgenic analysis of Cyp6 1 shows that overtranscription
of this gene alone is both necessary and sufficient for resistance. Resistance and up-regulation in Drosophila populations are associated wit a single Cyp6 1 allele that has spread globally. The allele is characterized by the insertion of an Accord transposable element into the 5' end of the Cyp6 1 gene."

​

What does the MPG hypothesis predict (see mail #1):

​

The concept 'multipurpose genome' holds that:
1) DNA sequences —although plastic-- are stable throughout time,

---

Amazingly, that is what NDT says!

quote:

---

2) organisms demonstrate genetic redundancies that reside in the genome without selective constraint,

---

Amazingly, that is what NDT says!

quote:

---

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],

---

Amazingly, that is what NDT says!
Well, accept for this 'degenration theory' - since this is labelled a 'theory', perhaps you can point in the direction wherein I can read for myself what must be voluminous documentation for this theory.Of course, adaptive evolution results in an accumulation of new genetic information. But you knew that....

quote:

---

4) the function of natural selection is to remove degenerate organisms, and

---

Amazingly, that is what NDT says! Of course, the "non-degenrate" or better adapted organisms are selected for. So far, all I see is a co-option of NDT .

quote:

---

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).

---

Now here is where you go off the deep end.Evidence for "creatons" please.Evidence for morphogenic fields, please.Evidence that you are refilling your prescriptions, please.

quote:

---

Point #3 predicted your observation.

---

It did? Can I see the documentation for this? Hindsight is, afterall, 20/20. I would like to see the paper outlining the likely pesticide resistence strategies encumbent upon mosquitos having a multipurpose genome.Thanks.

quote:

---

So, I do not see a problem for the MPG hypothesis here. The other examples are similar. They all involve differential gene regulation. As predicted by the MPG hypothesis.

---

Yeah, I guess no evolutionary biologist/geneticist had ever even thought about differential gene expressions.Wow. I guess NDT is all wrong...So, how does that fare for the creationist information arguments?

quote:

---

The ball is back in 'your' ZFY region.

​

Best wishes,
Peter

---

Already addressed. You have taken the "fingers in ears shouting LALALALAL" approach. What could I possibly add?[Fixed quoting. --Admin][This message has been edited by Admin, 11-12-2002]

quote:

---

PB: 5) Is evolution a phenomenon driven by random mutation?
YES

​

PB: Apparently NOT, judging from examples like the alpha actinin genes, the ZFY region, the 1G5 gene, etcetera.

---

Here is your big chance, Pete.
I have offered it to you before, and like all creationists before and likely all that will follow, you simply ignored it.Go here:http://www2.norwich.edu/spage/alignmentgam.htmApply your amazing scientific insights as they pertain to MPG.Analyze the sequence data there, and tell us all:Which of those nucleotide sites represent non-random changes.Which are evidence for MPG.Which are anomolous for MPG.Surely, you can do this.

duplicate[This message has been edited by SLPx, 11-12-2002]

quote:

---

Originally posted by peter borger:

​

However, are you a neutralist or a selectionist?

​

Best wishes,
Peter

---

Informed scientists understand that the two are not mutually exclusive.

quote:

---

Originally posted by peter borger:
Dear Dr Page,

​

I had a look at the sequences.
Easy to explain. Non-random in conjunction with random mechanisms give the illusion of common descent. I will study these sequences in detail, and respond to it next month (or so).

​

Best wishes,
Peter

---

Great deduction.Now tell us all which ones are which.You must be able to do this, lest your 'theory' be vacuous.

[QUOTE]Originally posted by Fred Williams:
[B]

quote:

---

What example? Oh yes - an example of a gene duplication and subsequent mutation that conferred a benefit to the population. The series of gene duplications in what we now call the beta globin gene cluster, a group of 5 genes and a pseudogene. Epsilon-globin,

---

MEGAROTFL! I must say you are consistent! Perhaps you should let me write your posts for you, I know what you are going to say before you say it! [/quote]Oh, you are so clever Fred! You knew I was going to write this? Why didn't you pre-resond, then?

quote:

---

Following is an important question for Scott to answer for the audience.

​

Scott, please tell the audience when you believe this duplication + subsequent mutation event occurred? Thanks!

---

I will go with the evidence. You will go with your fairy tale protection.http://opbs.okstate.edu/~melcher/PE/PE41.html"The phylogenetic distribution of globin genes is consistent with their degrees of divergence."There is lots more, of course, but most is farily technical and I know that it is over your head.No time line is mentioned there - but the time does not really matter, does it? You are just producing your usual red herrings, or is it double standards? For do you not assume a priori that the earth is no more than 10,000 years old (talk about megaROFTLMAO!) whenever you engage in your little ego-stroking fests?The difference is, Williams, I can actually produce evidence supportive of my claims.You produce accusations, repeated assertions, and bombast.What Williams the creationist does not understand is that there are valid reasons for accepting the time frame.As I indicated before - let the hand-waving and dodging begin.No legitimate rebuttal? Insult insult insult! Accuse of 'fallacious reasoning'! Yeah, thats the ticket to Heaven!

quote:

---

(I’m swamped, but will try to get to FK’s strawman and other replies tomorrow)

---

I take it then that you are just going to ignore the other aspects of my post?Perhaps you are not the genetics and information theory expert that you tell everyone you are...So, were you ever planning to support your claims?Or are you content to just do your little flame dance?

quote:

---

Originally posted by peter borger:
Dear Dr Page,
At least the MPG hypothesis predicts properly. Something NDT/evolutiomnism lacks completely.

​

best wishes,
Peter

---

If you say so...Apparently, you are the only person in the world that knows this.

quote:

---

Originally posted by Fred Williams:

​

You are on a road to nowhere, the information-less abyss. Scott on the other hand provided a hypothetical example of what I have said all along would constitute a gain in information by most info scientist standards (a substantial improvement over his tree rings = code goofiness).

---

"Hypothetical"? You mean the situation for which there are literally hundreds of published papers on? I am still waitiing for legitimate scientific support for your many delusions of importance.

quote:

---

Too bad though that Scott was engaging in his characteristic begging the question fallacy.

---

Only according to you. That really doesn't mean much. At least I do not need to rely on repeated assertions for my "evidence."

quote:

---

Anyway, here’s the target: gene duplication followed by subsequent mutation that provides a new benefit to the population as a whole. Find this, and you have a BINGO. I’ve spotted you the BING. Just go find the O!

---

So, as is a common creationist tactic, you have set up an impossible 'challenge.' Apparently, you want something to occur meeting the above criteria in 'real time.' Informed and rational creationists know that this is an unrealistic and therefore fallacious challenge.

quote:

---

quote:

---

I am just presenting a scenario that is possible.

---

​

In science, if something is observed countless times over throughout time with no observed exceptions, it qualifies as a Law of Nature.

---

Is that so? Perhaps you can provide some documentation for this.
Of course, I have no doubt that you do not really mean that. Think about it - are you sure you want to take such a position? It will do some damage to your fellow creationists' pet 'theories'...

quote:

---

It also means it is justified to declare the opposite is impossible. It is impossible to let go of a rock off a building and not have it drop to the earth. It is also impossible for new information to be created naturalistically.

---

Bullshit. You saying this over and over does not make it so. Ask Dr.Tom Schneider. Ask Kimura. And indeed, ask yourself.
You just said that it is possible, but now you say it is impossible. And you believe it impossible because you personally have not had your 'challenge' met...
What fluff...

quote:

---

If you guys can produce evidence in the lab of something similar to Scott’s fantasy, then you would have found ONE example of new info in the genome. But you can’t even produce ONE example, despite countless experiments on various rapidly reproducing species. This is a bad sign for evolution. It means evolution of new complex organs and features is impossible.

---

ROTFLMAO!Tell us all, wizard, how many lab experiments have verified ANY aspect of your religious fantasy? How many 'kinds' have been descended from some original stock via loss of information that was already there?What a joke.Of course, what the creationist demonstrates is that he still does not understand how genomes operate, and I suspect that is why he is ignoring my other citation.Gene duplications - even without subsequent mutation - can alter function and phenotype. How does that fit your precious "information theory"? According to other creationist information hawks, duplicating genes does not increase information. And when I have asked them the same questions, they clam up, too.

quote:

---

Yet another bad day for evolution.

---

The level of delusion displayed by the creationist is truly phenomenal.By the way - if tree rings are not 'coded information', what are they?I don't think you understand the amount of 'information' tree rings possess.That or you are not this 'expert' you keep telling people you are...

quote:

---

Originally posted by peter borger:

​

M: 1. the entire intron is not neutral..you do know that there are conserved features of introns?..guess not.

​

PB: And that would invalidate all studies on neutral evolution, isn't it? So, you have to either deny Kimura's theory or you have to deny common descent.

---

You have never read even one of Kimura's papers, have you?
For if you had, you would know that NT does NOT deny selection, nor does selection deny neutrality.And you wonder why I don't take you seriously?

quote:

---

Originally posted by peter borger:
Dear dr Page,

​

In reposne to

​

Originally posted by peter borger:
However, are you a neutralist or a selectionist?

​

Best wishes,
Peter

​

----------------------------------------------------------------------
----------

​

You say:

​

Informed scientists understand that the two are not mutually exclusive.

​

My reponse:

​

Could you please point out where I say that they are mutually exclusive? It is a common characteristic of evolutionism to conlusion-jump. You once more proof it here,

​

---

Why are creationists so purposely obtuse and thickheaded?If you do not think that they are mutually exclusive, why did you ask?If you think differently, why did you reply to Mam that conserved regions in introns refute the NT?You could at least try to be consistent in your rants.

quote:

---

Originally posted by Fred Williams:

​

LOL! Come on guys, you're killing me!

​

Itzpapa, please tell us when this event was observed in the lab. Tanks a bunch!

---

So is observing something in a lab your new criterion for scientiific validity?Or just when your 'challenges' have been via observations in nature?Because, if you are going to use observation in a lab as your key scientific criterion, which you seem to be doing, I will like to see the documentation for the observation - in a lab - of creation ex nihilo of a 'kind' by Yahweh.

quote:

---

What is ironic about your citation is that it is actually evidence for adaptive mutation.

---

The irony is too rich...[This message has been edited by SLPx, 11-14-2002]

[QUOTE]Originally posted by Fred Williams:
[B]

quote:

---

Gene duplications - even without subsequent mutation - can alter function and phenotype. How does that fit your precious "information theory"? According to other creationist information hawks, duplicating genes does not increase information. And when I have asked them the same questions, they clam up, too.

---

Yea, right. O’le Scott shut ‘em up! The truth is, this is a no-brainer. For your answer, why don’t you ask Tom Schnieder if he thinks gene duplications alone represent increased information.[/quote]Why don't I? Maybe because that is not what I asked."How does that fit your precious "information theory"?is what I aksed. Please do not continue to toss out your red herrings to cover the apparent fact that you have no answer when, as an expert in information theory and genetics, you should.If you cannot explain the impact on the flow of information in a genome during the phenotypic shift caused by a gene duplication, then just say so.

quote:

---

quote:

---

By the way - if tree rings are not 'coded information', what are they?

---

​

Do you know what a code is? Can you speak tree?

---

Thyats right - I forgot that you are an "expert" in Gittian Information Theory. The 'theory' conjured up by a creationist, for creationists.Because, after all, if the 'code' didn't come from humans of the deity that mooned Moses, it cannot really be a code.Funny thing - your boy John Paul said that they do contai information - 'code', if you will... but that it took a person to get the information out of it (duh).But that brings up another point - the ole' cretin definition game. Make up your own defintions that favor cretinism. Thats the ticket!Like I said, I guess you just have no clue how much 'information' there are in tree rings, if you know what to look for.