New genes

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New genes

Postby Chris Sergeant » Fri Dec 19, 2008 1:50 pm

An interesting article in the New Scientist discusses how new genes evolve. As more species are sequenced, it becomes possible to use the data to identify the mutations behind the individual gene changes. Gives a much richer and quantifiable picture than before. The data is illustrating the significance of some of the mechanisms. Thus:
Gene duplication has been found to be nearly as common as single letter changes. Provides much raw material for evolution to work on.
10% of the new genes studied in fruit flies were the result of retroposition.
60 or so new genes in human ancestors from retroposition of gene duplicates around 45 my ago.
470 examples of duplication followed by frameshift mutation for new genes in human genome.
The origin of the antifreeze protein in an Antarctic icefish, from a gene originally coding for a digestive enzyme.
New human genes identified with a contribution from non coding DNA. 6 being since the divergence from chimps.
Researched fruit fly genes evolving from junk DNA. The ancestral non-coding sequences have been identified in 8 cases.
It has been found that lots of junk DNA can be accidentally transcribed to RNA, making it more likely to be translated into protein.
Humans with around 400 smell receptors, all duplicated from 2 in fish from 450 my ago.

Retroposition occurs when an RNA copy is translated back into DNA and inserted elsewhere in the genome. If near a promoter, can be activated at a different phase of development or in different tissue.
Frameshift mutation moves the start point for reading by a base or 2.
http://www.newscientist.com/article/mg2 ... volve.html
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Postby Chris Sergeant » Fri Sep 04, 2009 12:28 pm

AT LEAST three human genes evolved "from scratch" via mutations in non-coding stretches of DNA, a process thought to be virtually impossible until recently. The genes evolved since human and chimp lineages split and so are unique to us.
Such "de novo" gene evolution was once thought impossible because random mutations are highly unlikely to produce a DNA sequence that encodes a protein of any length, let alone a protein that will be transcribed by cells and do anything useful. But in 2006, several de novo genes were discovered in fruit flies. Since then, it's become clear that genes do continually evolve in this way.
http://sciencenow.sciencemag.org/cgi/content/full/2009/901/2
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Postby Chris Sergeant » Fri Sep 04, 2009 12:30 pm

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Postby marcsurtees » Thu Sep 10, 2009 7:39 am

Chris Sergeant wrote:The quotes were actually from
http://www.newscientist.com/article/mg2 ... -junk.html


Hi Chris,

This is interesting stuff. But there are a couple of assumptions that should be acknowledged here.
One is that humans & chimps evolved from a common ancestor.
The other is junk DNA.
Both of these are questionable. It which case these "new" genes are in fact genes unique to humans. It is worth noting that the mechanistic problems with deriving genes de-novo are acknowledged and this lends support to the alternative hypothesis, that we are actual unrelated to chimps.

Following on from the realisation that our DNA is actual about 30% different from chimps, its good to see more research that highlights the differences between humans and apes.
Marc
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Postby psiloiordinary » Thu Sep 10, 2009 1:50 pm

Hi Marc,

Those aren't assumptions - one is supported by lots of lines of evidence and the other isn't what you purport it to be anyway.

Can you guess which is which?

Regards,

Psi

BTW I'm in Edinburgh for the evenings of the 23rd and 24th sept - fancy that pint?
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Postby marcsurtees » Thu Sep 10, 2009 4:35 pm

psiloiordinary wrote:Hi Marc,

Those aren't assumptions - one is supported by lots of lines of evidence and the other isn't what you purport it to be anyway.

Regards,

Psi

BTW I'm in Edinburgh for the evenings of the 23rd and 24th sept - fancy that pint?


Lets just take the DNA difference. For a long time we we told that the 1% to 1.5% difference was good evidence that we are related to chimps. Now we find that the difference is nearer 30% and no-one bats an eyelid.

As for junk DNA, its about time people stopped using the term and stick to non-coding DNA (although that is a bit of a misnomer as well) as it appears that most of it is transcribed but not into protein. A much better term would be one that captures the fact that it has regulatory and other functions.

As for a pint the 24th - sounds good after 8pm (where is "local" in Edinburgh), or would you like to come to the Sheep's hied in Duddington. A good choice of real ale.
Marc
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Postby psiloiordinary » Thu Sep 10, 2009 6:40 pm

marcsurtees wrote:
psiloiordinary wrote:Hi Marc,

Those aren't assumptions - one is supported by lots of lines of evidence and the other isn't what you purport it to be anyway.

Regards,

Psi

BTW I'm in Edinburgh for the evenings of the 23rd and 24th sept - fancy that pint?


Lets just take the DNA difference. For a long time we we told that the 1% to 1.5% difference was good evidence that we are related to chimps. Now we find that the difference is nearer 30% and no-one bats an eyelid.

As for junk DNA, its about time people stopped using the term and stick to non-coding DNA (although that is a bit of a misnomer as well) as it appears that most of it is transcribed but not into protein. A much better term would be one that captures the fact that it has regulatory and other functions.

As for a pint the 24th - sounds good after 8pm (where is "local" in Edinburgh), or would you like to come to the Sheep's hied in Duddington. A good choice of real ale.


Hi Marc,

You are quoting different people talking about different parts of the DNA. You need to bear in mind that sometimes they will be talking about just the coding sections etc.

A creationist did write in to the OU to complain about just this point which we picked up on our blog here;

http://bcseweb.org.uk/blog/2009/05/18/a ... ng-around/

I can bring the book with me if you like - it is part of the degree I am doing.

You also need to remember that, unlike your religious claims to inerrancy, science progresses as more evidence comes in. I don't think you can find any seriously made claims from any scientists that we have nothing left to learn about DNA!

As for a pint, I will drop you a note nearer the time but I usually stay in the Roxburghe or somewhere near Charlotte Square. Happy to take a recommendation on the venue.

Regards,

Psi
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Postby marcsurtees » Fri Sep 11, 2009 10:18 am

psiloiordinary wrote:You are quoting different people talking about different parts of the DNA. You need to bear in mind that sometimes they will be talking about just the coding sections etc.

Yes of course you are right, depending on the sample one takes one gets 0% to 30% difference. But the 30% figure takes in as much of the genome as possible, and is therefore associated with the minimum amount of sampling error.

psiloiordinary wrote:A creationist did write in to the OU to complain about just this point which we picked up on our blog here;
http://bcseweb.org.uk/blog/2009/05/18/a ... ng-around/
I can bring the book with me if you like - it is part of the degree I am doing.

You have to admit that the title is a little provocative, after all evolutionists claim that we are 100% ape, so the title does seem to be promoting the myth of 1% (a phrase first coined by an evolutionist... oh dear quote mining again!)
Anyway I would be grateful for a look at the book.
I got so much out the latest evolutionist book that I read (Prothero, 2007) that I might buy a copy of 99% as well.

psiloiordinary wrote:You also need to remember that, unlike your religious claims to inerrancy, science progresses as more evidence comes in. I don't think you can find any seriously made claims from any scientists that we have nothing left to learn about DNA!

I believe in the inerrancy of scripture... not the inerrancy of Marc, and I agree that we all have lots to learn about DNA.
Marc
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Postby psiloiordinary » Mon Sep 14, 2009 6:40 am

Hi Marc,

I don't find the title provocative at all.

We are classified as an ape so in that sense we are 100% ape, by a particular measure of DNA we are 99%, as long as you don't need your science to be complete in one book headline (something I don't think can be done) then I can't get excited about it.

BTW the book is available outside the course anyway £14.99.

I will bring it with me.

Regards,

Psi
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Postby Chris Sergeant » Fri Sep 18, 2009 1:11 pm

Marc,
Regarding your presumption about Junk DNA, it does state in one of the papers that:
In the other primates, the equivalent DNA sequences contained differences that would halt protein production early on, so the sequences are non-coding in these species. Crucially, chimps, gorillas, gibbons and macaques share some of these differences, meaning that, in our shared ancestor, these sequences were non-coding as well.
The researchers conclude that three of these non-coding sequences must have mutated in humans and become capable of coding for the short proteins at some point since we diverged from chimps six million years ago (Genome Research, DOI: 10.1101/gr.095026.109). While at least half the non-coding DNA in humans is junk with no function, it is not clear whether the non-coding DNA from which the genes evolved had any function.
To clarify your confusion over 98.5% similarities etc, you could read “The Greatest Show on Earth”. Pages 317 to 320 talk about this area in layman’s terms.
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Postby Roger Stanyard » Fri Sep 18, 2009 1:19 pm

Marc Surtees claims <blockquote>Lets just take the DNA difference. For a long time we we told that the 1% to 1.5% difference was good evidence that we are related to chimps. Now we find that the difference is nearer 30% and no-one bats an eyelid. </blockquote>

Oh, I see. The scientists are stupid and 70% commonality shows we are not related to chimps, the world is 6,000 years old and Noah's Ark story is "true".

Not much of a scientific position, is it?
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Postby Roger Stanyard » Fri Sep 18, 2009 1:26 pm

marcsurtees wrote:
You have to admit that the title is a little provocative, after all evolutionists claim that we are 100% ape, so the title does seem to be promoting the myth of 1% (a phrase first coined by an evolutionist... oh dear quote mining again!)</quote>

Oh, I see. We are not apes. So what is your definition using taxonomy - how does that incorporate you're non-existant definition of "kinds"

marcsurtees wrote:I believe in the inerrancy of scripture... not the inerrancy of Marc, and I agree that we all have lots to learn about DNA.


Oh, I see. You don't accept any science that contradicts your personal religious opinions. A bullying and cowardly copt out of a fundamentalist ideologue. You would feel at home in a Marxist-Leninist or Trotyskyite group (or, perhaps, with Paul Garner in the BNP).
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Postby marcsurtees » Sat Sep 19, 2009 9:47 am

Roger Stanyard wrote:Oh, I see. We are not apes. So what is your definition using taxonomy - how does that incorporate you're non-existant definition of "kinds"

We share some similar design features but the many differences between apes and humans is a very good case for humans being a separate kind.

Roger Stanyard wrote:Oh, I see. You don't accept any science that contradicts your personal religious opinions. A bullying and cowardly copt out of a fundamentalist ideologue. You would feel at home in a Marxist-Leninist or Trotyskyite group...

Actually personal religious opinions don't come into it and as a scientist, I accept any scientific fact.
The only bullying I see on this forum comes from you.
Marc
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Postby Roger Stanyard » Sat Sep 19, 2009 11:49 am

marcsurtees wrote:Actually personal religious opinions don't come into it and as a scientist, I accept any scientific fact.
The only bullying I see on this forum comes from you.


So it's not your "personal opinion" that the Bible is inerrant and therefore you need take no personal responsibilities for your religious position? Your positon on young earth creationism has nothing do do with your personal religious beliefs?


Lying bastard.

"We vas only obeying orders.
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Postby Steve660 » Wed Oct 07, 2009 4:55 pm

Lets just take the DNA difference. For a long time we we told that the 1% to 1.5% difference was good evidence that we are related to chimps. Now we find that the difference is nearer 30% and no-one bats an eyelid.


What's your source for this claim? I suspect you've got the numbers muddled. Or some other creationist has and you've just repeated the error. The numbers may be referring to two separate things. In terms of base pairs, human & chimp DNA are indeed about 1.5 % different. Not 30 %. In terms of genes the number will be much higher, maybe 30 %, because it takes only one base pair to be different for the gene to be counted as different. Perhaps it should be that 30 % of the genes are different, and they differ by about 1.5 % of their base pairs. Unless you define what exactly each number refers to the argument is highly misleading. Like so many creationist arguments.
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