Freethought & Rationalism Archive

monkenstick · 10-22-2002, 03:46 PM

*frolics in the vanderzyden-free land of psuedogenes*

Valentine Pontifex · 10-22-2002, 04:03 PM

Quote:

Originally posted by monkenstick:
<strong>*frolics in the vanderzyden-free land of psuedogenes*</strong>

Are you planning to make a web version of this?

monkenstick · 10-22-2002, 04:16 PM

yeah, I just have to find time - i've had an assignment due every friday for the past 5 weeks and swot-vac is in two weeks - I've done some phylgenetic trees - but I think i'm doing something wrong because phylip is grouping chimps with gorillas, even though the gorilla sequence has a large insertion (think it might be to do with clustalx's alignment) - other than that the tree topology seems to match the accepted species tree quite nicely - the new world monkeys split off first, then the gibbons and then the hominidae

Coragyps · 10-22-2002, 04:58 PM

Quote:

swot-vac is in two weeks

Damn! That sounds painful!

We'll wait for the website; <fatherly voice> studies come first</fatherly voice>

rafe gutman · 10-22-2002, 05:12 PM

i'm not sure if this will work (or if it's legal):

[Edit by Kevin Dorner: Sorry to have to be a party-pooper, but it isn't, so I have removed the image link. To be specific, any deep-linking of images is not permitted, and I even have a legal precedent: Kelly v. Arribva Soft Corp. , 280 F.3d 934 (9th Cir. 2002.) but if it were an image that anyone could view, then it is usually overlooked; however in this case it is supposed to require a paid registration to view, so it definitely is a copyright issue. Sorry 'bout that.

From the link below that rafe posted to the abstract, the article can be read for 24 hours for $5 U.S.]

can you guys see the picture?

[ October 22, 2002: Message edited by: Kevin Dorner ]</p>

Doubting Didymus · 10-22-2002, 06:00 PM

I can see it.

monkenstick · 10-22-2002, 06:16 PM

yeah, thats the tree I got - mind if I steal that pic for a website? - phylip's output options just confuse me

Blinn · 10-22-2002, 06:39 PM

Care to explain that? Is that a single gene? It appears to be urate oxidase?

[ October 22, 2002: Message edited by: Zetek ]</p>

monkenstick · 10-22-2002, 06:52 PM

sure, at node A, theres a split between the new world monkeys (baboon, rhesus monkey, crab eating(?) monkey) and the old world monkeys. All the old world monkeys on the tree subsequent to node A have an inactivated urate oxidase - the new world monkey urate oxidase remains functional. At node B - the species diverge again - the gibbons have a different premature stop codon to the hominadae group. So it appears the inactivation of urate oxidase occured somewhere prior to node B - the fact that the stop codons are different between the gibbons and the hominidae indicates that the inactivation probably first occured in the promoter region - then later on the gibbons and the hominidae acquired premature stop codons separately

rafe gutman · 10-22-2002, 08:13 PM

monkenstick, i got the picture from the paper where those sequences came from:

<a href="http://www.molbiolevol.org/cgi/content/abstract/19/5/640" target="_blank">http://www.molbiolevol.org/cgi/content/abstract/19/5/640</a>

i'm not sure of the legality of putting the image on your website. i don't think they'd really care, since you aren't trying to distort their claims or anything, but just be forewarned.

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10-22-2002, 03:46 PM	#11
monkenstick Regular Member Join Date: Jul 2002 Location: Australia Posts: 214	frolics in the vanderzyden-free land of psuedogenes

10-22-2002, 04:16 PM	#13
monkenstick Regular Member Join Date: Jul 2002 Location: Australia Posts: 214	yeah, I just have to find time - i've had an assignment due every friday for the past 5 weeks and swot-vac is in two weeks - I've done some phylgenetic trees - but I think i'm doing something wrong because phylip is grouping chimps with gorillas, even though the gorilla sequence has a large insertion (think it might be to do with clustalx's alignment) - other than that the tree topology seems to match the accepted species tree quite nicely - the new world monkeys split off first, then the gibbons and then the hominidae

10-22-2002, 05:12 PM	#15
rafe gutman Junior Member Join Date: May 2001 Location: La Jolla, CA Posts: 72	i'm not sure if this will work (or if it's legal): [Edit by Kevin Dorner: Sorry to have to be a party-pooper, but it isn't, so I have removed the image link. To be specific, any deep-linking of images is not permitted, and I even have a legal precedent: Kelly v. Arribva Soft Corp. , 280 F.3d 934 (9th Cir. 2002.) but if it were an image that anyone could view, then it is usually overlooked; however in this case it is supposed to require a paid registration to view, so it definitely is a copyright issue. Sorry 'bout that. From the link below that rafe posted to the abstract, the article can be read for 24 hours for $5 U.S.] can you guys see the picture? [ October 22, 2002: Message edited by: Kevin Dorner ]</p>

10-22-2002, 06:00 PM	#16
Doubting Didymus Veteran Member Join Date: Jul 2002 Location: East Coast. Australia. Posts: 5,455	I can see it.

10-22-2002, 06:16 PM	#17
monkenstick Regular Member Join Date: Jul 2002 Location: Australia Posts: 214	yeah, thats the tree I got - mind if I steal that pic for a website? - phylip's output options just confuse me

10-22-2002, 06:39 PM	#18
Blinn Veteran Member Join Date: Aug 2001 Location: Ohio, USA Posts: 1,162	Care to explain that? Is that a single gene? It appears to be urate oxidase? [ October 22, 2002: Message edited by: Zetek ]</p>

10-22-2002, 06:52 PM	#19
monkenstick Regular Member Join Date: Jul 2002 Location: Australia Posts: 214	sure, at node A, theres a split between the new world monkeys (baboon, rhesus monkey, crab eating(?) monkey) and the old world monkeys. All the old world monkeys on the tree subsequent to node A have an inactivated urate oxidase - the new world monkey urate oxidase remains functional. At node B - the species diverge again - the gibbons have a different premature stop codon to the hominadae group. So it appears the inactivation of urate oxidase occured somewhere prior to node B - the fact that the stop codons are different between the gibbons and the hominidae indicates that the inactivation probably first occured in the promoter region - then later on the gibbons and the hominidae acquired premature stop codons separately

10-22-2002, 08:13 PM	#20
rafe gutman Junior Member Join Date: May 2001 Location: La Jolla, CA Posts: 72	monkenstick, i got the picture from the paper where those sequences came from: <a href="http://www.molbiolevol.org/cgi/content/abstract/19/5/640" target="_blank">http://www.molbiolevol.org/cgi/content/abstract/19/5/640</a> i'm not sure of the legality of putting the image on your website. i don't think they'd really care, since you aren't trying to distort their claims or anything, but just be forewarned.

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