Freethought & Rationalism Archive

gallo · 05-06-2003, 06:07 PM

Researchers in Japan and UCSD Discover Novel Role For Pseudogenes

Already heard from a creationist about this. I think his point was that "junk DNA" really has a function.

Kevbo · 05-06-2003, 06:09 PM

Quote:

Already heard from a creationist about this. I think his point was that "junk DNA" really has a function.

Which is funny, because it makes the genetic component of evolutionary theory even more robust.

WinAce · 05-06-2003, 06:27 PM

Goodie. Unfortunately for your creationist friend, the strength of pseudogenes as evidence for evolution isn't affected one iota by finding a role for them in biology. This ties in with the old creationist canard of vestigial meaning functionless.

Doubting Didymus · 05-06-2003, 06:45 PM

Note that the article reports a function for ONE pseudogene. No doubt others will be found to have functions, but this is not by any means a function found for ALL 'junkDNA'. The inefficiency argument against design still stands strong, naturally. (and the common ancestry evident in pseudogenes would remain even if all pseudogenes had functions.

RufusAtticus · 05-06-2003, 07:10 PM

Socrates brought this up on TW last friday or so by quoting from the news article that accompanies the paper, and excising all the information that pertained to the actual study. Here I will quote from the paper itself.

Quote:

With these studies, we have uncovered a mechanism of gene regulation of a coding gene, Makorin1, by a transcribed non-coding pseudogene Makorin1-p1. Makorin1-p1 must function as an RNA, as it cannot code for a protein. Protection from mRNA decay of Makorin1 by Makorin1-p1 was easily reproduced by expression constructs in several cell lines and in transgenic mice, suggesting that this type of regulation may be a general phenomenon. Although the precise enzymatic mechanism is unknown, one possibility is that a trans-acting RNA-destabilizing factor�which is able to bind to the 5' UTR of Makorin1 and Makorin1-p1 transcripts�is in limiting amounts or temporally and spatially regulated. Expression of the Makorin1-p1 transcript may titrate out this factor, thus increasing wild-type Makorin1 mRNA stability in a developmentally regulated and tissue-specific manner.

In general, the mammalian genome contains a large number of pseudogenes (20,000 in the human3) compared to other organisms. Although functions of pseudogenes have not been characterized, some proportion of them are transcribed8. Other expressing pseudogenes may have important functions, like Makorin1-p1. Pseudogenes are functionally less constrained, and have accumulated more mutations than translated genes. If they have some functions in gene regulation, this property would allow more rapid functional diversification than protein-coding genes. In addition, some genetic phenomena that exhibit incomplete penetrance might be attributed to 'mutation' or 'variation' of pseudogenes.

See the paper did not find a function for a single-copy pseudogene like the GULO or urate-oxidase pseudogenes in human.

gallo · 05-06-2003, 08:24 PM

As I pointed out, the creationist's assertion that "...the [article] provides more evidence that much of the so-called "Junk DNA" has important function" goes beyond the information in the article. The article provides evidence that one pseudogene in mice has an important function. It certainly indicates an avenue for further research. There may be more, maybe not. They may exist in other species, maybe not.

But "junk DNA" isn't even a clearly defined "official" term anyway. To me it always meant non-coding DNA. Introns are junk DNA but it is unknown whether they serve a function. At least it is unknown to me if something has changed recently.

Of course, some segments of DNA seem to be obvious junk without function, either coding or regulatory.

S2Focus · 05-06-2003, 08:34 PM

...never seem to look like this?

"Researchers at the Institute for Creation Research and Answers in Genesis Discover Novel Role For Pseudogenes"

Quote:

Originally posted by gallo
Researchers in Japan and UCSD Discover Novel Role For Pseudogenes

Already heard from a creationist about this. I think his point was that "junk DNA" really has a function.

gallo · 05-06-2003, 09:50 PM

Oh poop!

I already answered.

Why didn't I think of that?

Wounded King · 05-07-2003, 01:01 AM

I always thought of Junk DNA as the DNA that just didnt do anything so all the regulatory sequences, chromosome stabilising repeats, small interfering RNA genes and such like can hardly be classified as Junk. As has been pointed out there are a large number of roles for non coding DNA. Now if the pseudogene had been non transcribed, that would have been weird.

It would be naive to think that we know all there is to know about gene regulation but at least the scientific community keep finding stuff out.

MortalWombat · 05-07-2003, 07:18 AM

What this paper shows is that a non-protein coding gene can be co-opted by the cell to perform a useful function.

In sort of reverse way, this has happened before. Here is a link to a paper from a former colleague of mine in which he has identified a gene in rodents which is about 96% identical to the opposite strand of a central region of the large ribosomal RNA, and this gene encodes a protein which actually regulates rRNA transcription.

Since rRNA genes have been around a lot longer than the eukaryotic RNA polymerase I transcription machinery, one can assume that the eukaryotic cell has found a novel way to turn a normally non-protein coding gene into a protein coding one.

05-06-2003, 06:07 PM	#1
gallo Regular Member Join Date: Jun 2001 Location: Houston, TX, US Posts: 244	Researchers in Japan and UCSD Discover Novel Role For Pseudogenes Researchers in Japan and UCSD Discover Novel Role For Pseudogenes Already heard from a creationist about this. I think his point was that "junk DNA" really has a function.

Thread Tools	Search this Thread
Show Printable Version	Search this Thread: Advanced Search

05-06-2003, 06:27 PM	#3
WinAce Beloved Deceased Join Date: Feb 2002 Location: Carrboro, NC Posts: 1,539	Goodie. Unfortunately for your creationist friend, the strength of pseudogenes as evidence for evolution isn't affected one iota by finding a role for them in biology. This ties in with the old creationist canard of vestigial meaning functionless.

05-06-2003, 06:45 PM	#4
Doubting Didymus Veteran Member Join Date: Jul 2002 Location: East Coast. Australia. Posts: 5,455	Note that the article reports a function for ONE pseudogene. No doubt others will be found to have functions, but this is not by any means a function found for ALL 'junkDNA'. The inefficiency argument against design still stands strong, naturally. (and the common ancestry evident in pseudogenes would remain even if all pseudogenes had functions.

05-06-2003, 08:24 PM	#6
gallo Regular Member Join Date: Jun 2001 Location: Houston, TX, US Posts: 244	As I pointed out, the creationist's assertion that "...the [article] provides more evidence that much of the so-called "Junk DNA" has important function" goes beyond the information in the article. The article provides evidence that one pseudogene in mice has an important function. It certainly indicates an avenue for further research. There may be more, maybe not. They may exist in other species, maybe not. But "junk DNA" isn't even a clearly defined "official" term anyway. To me it always meant non-coding DNA. Introns are junk DNA but it is unknown whether they serve a function. At least it is unknown to me if something has changed recently. Of course, some segments of DNA seem to be obvious junk without function, either coding or regulatory.

05-06-2003, 09:50 PM	#8
gallo Regular Member Join Date: Jun 2001 Location: Houston, TX, US Posts: 244	Oh poop! I already answered. Why didn't I think of that?

05-07-2003, 01:01 AM	#9
Wounded King Veteran Member Join Date: Mar 2003 Location: Edinburgh Posts: 1,211	I always thought of Junk DNA as the DNA that just didnt do anything so all the regulatory sequences, chromosome stabilising repeats, small interfering RNA genes and such like can hardly be classified as Junk. As has been pointed out there are a large number of roles for non coding DNA. Now if the pseudogene had been non transcribed, that would have been weird. It would be naive to think that we know all there is to know about gene regulation but at least the scientific community keep finding stuff out.

05-07-2003, 07:18 AM	#10
MortalWombat Veteran Member Join Date: Apr 2001 Location: St Louis area Posts: 3,458	What this paper shows is that a non-protein coding gene can be co-opted by the cell to perform a useful function. In sort of reverse way, this has happened before. Here is a link to a paper from a former colleague of mine in which he has identified a gene in rodents which is about 96% identical to the opposite strand of a central region of the large ribosomal RNA, and this gene encodes a protein which actually regulates rRNA transcription. Since rRNA genes have been around a lot longer than the eukaryotic RNA polymerase I transcription machinery, one can assume that the eukaryotic cell has found a novel way to turn a normally non-protein coding gene into a protein coding one.

Freethought & Rationalism Archive

The archives are read only.