Functional redundancy in duplicates undermines Darwinism

[Atheistoclast]

This great investigative research paper is the basis for my fourth manuscript.

Duplicate genes in yeast were observed to be redundant and did not diverge to become something novel.

http://www.plosgenetics.org/article/...l.pgen.1000113

It is a fascinating insight into what duplicates actually get up to.

[Faid]

Old troll act is old.

Find a new shtick, Bozo.

[Atheistoclast]

Originally Posted by Faid

Old troll act is old.

Find a new shtick, Bozo.

Do you actually have anything to say or offer, geordie-boy?

Use your 6000th post fruitfully.

[Dean W]

I thought the grim reaper was coming for the darwinistas last Christmas. That came and went with nothing at all. Here we are, well into 2010 and all there is is 'Clast jacking off same as always. What's up with that?

[Atheistoclast]

Originally Posted by Dean W

I thought the grim reaper was coming for the darwinistas last Christmas. That came and went with nothing at all. Here we are, well into 2010 and all there is is 'Clast jacking off same as always. What's up with that?

Once the journals allow my papers to be published, the end is inevitable.

Btw, its the grinch ,and not the grim reaper, who appear at Xmastide.

[VoxRat]

Originally Posted by Atheistoclast

...
Once the journals allow my papers to be published, the end is inevitable.

Well, the day any respectable journal publishes one of your "papers", I will indeed look for tell-tale signs of hell freezing over.

[Dean W]

Originally Posted by Atheistoclast

Once the journals allow my papers to be published, the end is inevitable.

Btw, its the grinch ,and not the grim reaper, who appear at Xmastide.

Well, I seem to remember you cackling and posting this:



and this



It's just that you seem like a limp-dick iconoclast is all.

[ericmurphy]

So, of course, since this is a creationist talking, one functional duplicate not diverging means that no functional duplicates can ever, under any circumstances, diverge.

[Entropy]

Originally Posted by Atheistoclast

This great investigative research paper is the basis for my fourth manuscript.

Duplicate genes in yeast were observed to be redundant and did not diverge to become something novel.

http://www.plosgenetics.org/article/...l.pgen.1000113

It is a fascinating insight into what duplicates actually get up to.

By "basis" do you mean that you're just going to paraphrase their data with a bunch of anti-evolution hand-waving?

[Entropy]

Just skimmed it. Its pretty obvious why this is in PLoS and not Nature...

This is a big problem:

First, our measurements of fitness were carried out exclusively in rich medium (YPD). Although work done in this single condition is sufficient to conclude that duplicate genes are highly dissimilar from singleton genes with regard to contributions to fitness, it does not resolve the question of whether duplicate genes gain new functionality. That is, any new functionality acquired by duplicated genes that is only important under alternative environmental conditions would not be detected using this assay. Indeed, several studies show that duplicated genes are often involved in interacting with the environment and managing stress [36],[48].

Only 18% of genes in the budding yeast genome are essential in rich media. An additional 15% show a reduced growth rate in rich media.

Second problem:

The fitness effects of losing the ancestral progenitors are not known.

and

The key assumption in this analysis is that, with respect to the fitness impacts of their deletions, the extant singletons within the proxy set are similar to the genes that produced the extant duplicate genes

How can you tell whether two duplicated genes are functionally diverged when you don't know the effects of deleting the ancestral gene?
They try to get around this with:

Consequently, we developed criteria to choose a proxy set of singleton genes (Dataset S3) that account for the biases among these ancestral progenitors.

So in the absence of the actual ancestral genes, they chose a bunch of other genes who's fitness decreases would stand in? Thats quite a stretch.

[Faid]

Originally Posted by Atheistoclast

Do you actually have anything to say or offer, geordie-boy?

Use your 6000th post fruitfully.

You're right, I'll use it to give an important message.

Old troll act is old.

Find a new shtick, Bozo.

[eversbane]

We had a nice day, yesterday. It was the 100th Birthday for Boy Scouts of America. Since we've got two boys in the system we committed the whole day to scouting activities. It started with a parade at 08:30, followed by a rededication of our boy scout lodge building. Then jamboree all day with a wall climb, tomakawk throwing, rocketry, a scale trebuche', a monkey bridge, a demonstration of wilderness survival (fire starting, constructing a lean-too, etc.), camp cooking (dutch oven cobbler, mmm..), rope making, etc. Then an Order of the Arrow ceremony for some older Boy Scouts and a crossing over ceremony for some Webelos graduating from Cub Scouts to Boy Scouts. Finally, a dinner with speakers, music, skits, etc. All in all, we were going from 07:30 until 21:30. Quite a day.




So... what's this thread about?

[RAFH]

Originally Posted by Dean W

I thought the grim reaper was coming for the darwinistas last Christmas. That came and went with nothing at all. Here we are, well into 2010 and all there is is 'Clast jacking off same as always. What's up with that?

Actually, it was originally Halloween, but he missed that, and several subsequent datelines. He claims he's submitted his 'papers' but I have my doubts. For one thing, I can't see Clastie submitting himself to that sort of professional ridicule.

[Martin B]

*opens thread*

*looks around*

Nope. Nothing good in here.

*leaves*

[rjw]

Originally Posted by Atheistoclast

This great investigative research paper is the basis for my fourth manuscript.

Duplicate genes in yeast were observed to be redundant and did not diverge to become something novel.

http://www.plosgenetics.org/article/...l.pgen.1000113

It is a fascinating insight into what duplicates actually get up to.

Why should duplicated genes have to diverge to become something novel? Why can't a lot of them also switch off?

And where it can be shown that duplicated genes diverged to:-

1) either become something novel, or

2) to share the functions of the original pre-duplicated gene,

what do you say then?



Regards, Roland

[Atheistoclast]

Originally Posted by ericmurphy

So, of course, since this is a creationist talking, one functional duplicate not diverging means that no functional duplicates can ever, under any circumstances, diverge.

Eric seems to think that absence of evidence is not evidence of absence.

That's fine....except in science.

[Entropy]

Originally Posted by Atheistoclast

Eric seems to think that absence of evidence is not evidence of absence.

That's fine....except in science.

Lots of examples of duplicated genes diverging to different functions. My area is cell cycle, but just there you could look at cyclins, cyclin dependent kinases, and the cdc25 paralogues. There are multiple MAP kinase pathways, multiple PI3 kinases, multiple G-protein coupled receptors etc etc.

That this paper didn't find evidence if divergence in yeast is a problem with their methods, not evolution.

[Ved]

Originally Posted by Atheistoclast

Eric seems to think that absence of evidence is not evidence of absence.

That's fine....except in science.

You found a black swan and are using it as evidence that all swans are black.

Do keep the jokes coming...

[SteveF]

Originally Posted by Entropy

That this paper didn't find evidence if divergence in yeast is a problem with their methods, not evolution.

They say:

Additional work is needed to understand discrepancies between our study and various other predictions of new functionality (e.g. [11],[15],[22],[44],[45], although see [46],[47]).

ref 45 isn't a prediction of new functionality as they say, it's evidence of it:

http://kevinbyrne.ie/pubs/ByrneWolfe2007.pdf

In their review of duplication, Conant and Wolfe, say:

Other than the question of dosage balance, one general principle that has emerged from genome-scale studies is that duplicate genes diverge most commonly in their regulation and least commonly in their biochemical function20. Indeed, two recent studies on the yeast WGD have suggested that duplicate genes retain substantial degrees of functional overlap for long periods (as indicated by shared protein-complex membership or by the observation of larger-than-expected double knockout fitness defects for a duplicate pair given the pair's single-gene knockout effects)31, 32. These results reinforce the view that the majority of the gene duplications fixed in the yeast genome did not confer novel functions or have not subsequently diverged substantially in function. But it should be noted that the concepts of novelty and of the function of a gene are open to multiple definitions, and that other results — such as the finding that many WGD loci that are fixed in duplicate in one yeast species are single-copy in others33 — point to a high frequency of neofunctionalization.

ref 31 being the Dean et al paper.

[Ved]

Evolutionary understanding of gene duplication and modification- not smashed.

Common descent- not smashed.

Darwinism- not even dented.

Atheism- not budged a smegging inch.

[Atheistoclast]

Originally Posted by Entropy

That this paper didn't find evidence if divergence in yeast is a problem with their methods, not evolution.

I have presented my evidence. Why don't you present your papers on gene duplication and its relevance to the proteins involved in the cell cycle?

[Atheistoclast]

Originally Posted by VoxRat

Well, the day any respectable journal publishes one of your "papers", I will indeed look for tell-tale signs of hell freezing over.

It'll have to freeze over four times over.

[Entropy]

Originally Posted by Atheistoclast

I have presented my evidence. Why don't you present your papers on gene duplication and its relevance to the proteins involved in the cell cycle?

Quite frankly I have other, vastly more important, things to do than hunt down references in a futile attempt to prove to you that you are wrong.

Here it is in short form: There are about 4 or 6 CDKs in mammals, and like 6 cyclins and 3 Cdc25s. If you look at the sequences of any one of these groups you will find they are related, thus duplicated from an ancestral protein. They have diverged in function.

[ericmurphy]

Originally Posted by Atheistoclast

Eric seems to think that absence of evidence is not evidence of absence.

That's fine....except in science.

Gene families, fucktard.

[Gagundathar Inexplicable]

Clast, you lost way back last year.
Not a single person here actually thinks that a) your 'papers' are worthwhile science, b) that you have actually submitted them, and c) that you have any credentials in any branch of science.

Understand?

We are all laughing at you, you pathetic excuse for a human being.
Grow up, loser.