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Author Topic:   Is convergent evolution evidence against common descent?
randman 
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Posts: 6367
Joined: 05-26-2005


Message 286 of 311 (216061)
06-11-2005 2:15 AM
Reply to: Message 283 by mark24
06-10-2005 6:36 PM


Re: Inconsistent?
Mark, cladograms based on CytoC alone do not provide identical cladograms as other molecular and morphological data. I ran a search and comparison for:
human
kangaroo
horse
rattlesnake
turtle
Sequence 1: humanctochrome>CMFADRWLFSTNHKD 443 aa
Sequence 2: kangaroocytoC>GDVEKGKKIFVQKCAQ 34 aa
Sequence 3: horsecytochromeC>MFINRWLFSTNHK 444 aa
Sequence 4: RattlesnakeCytoC>GDVEKGKKIFSMK 34 aa
Sequence 5: Turtle>GDVEKGKKIFVQKCAQCHTVEKG 34 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 20.5882
Sequences (1:3) Aligned. Score: 92.7765
Sequences (1:4) Aligned. Score: 20.5882
Sequences (1:5) Aligned. Score: 17.6471
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 20.5882
Sequences (2:4) Aligned. Score: 73.5294
Sequences (2:5) Aligned. Score: 88.2353
Sequences (3:2) Aligned. Score: 20.5882
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 20.5882
Sequences (3:5) Aligned. Score: 17.6471
Sequences (4:2) Aligned. Score: 73.5294
Sequences (4:3) Aligned. Score: 20.5882
Sequences (4:4) Aligned. Score: 100
Sequences (4:5) Aligned. Score: 76.4706
Sequences (5:2) Aligned. Score: 88.2353
Sequences (5:3) Aligned. Score: 17.6471
Sequences (5:4) Aligned. Score: 76.4706
Sequences (5:5) Aligned. Score: 100
This has a kangaroo very closely related to the turtle (88), and fairly close to the rattlesnake (73.5), and more so than to humans, another mammal, (20.582), and that the kangaroo more closely related to the turtle than the 2 reptiles are to each other.
Maybe I made a mistake, but this does not match at all.
Moreover, it is common knowledge there is significant debate between morphologists and molecular systemists in which data is correct.
You need to own up to that and quit pretending there is no debate on this issue.
This message has been edited by randman, 06-11-2005 02:16 AM
This message has been edited by randman, 06-11-2005 02:18 AM

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Modulous
Member
Posts: 7799
From: Manchester, UK
Joined: 05-01-2005


Message 287 of 311 (216065)
06-11-2005 2:49 AM
Reply to: Message 286 by randman
06-11-2005 2:15 AM


Re: Inconsistent?
I think you might have got it wrong. Cytochrome c is 104 amino acids long isn't it? You seem to have ones that are 443 aa and 34 aa long. Here is a human to turtle comparison.

This message is a reply to:
 Message 286 by randman, posted 06-11-2005 2:15 AM randman has replied

Replies to this message:
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randman 
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Posts: 6367
Joined: 05-26-2005


Message 288 of 311 (216067)
06-11-2005 2:51 AM
Reply to: Message 287 by Modulous
06-11-2005 2:49 AM


Re: Inconsistent?
see corrected post on CytoB 2 posts down.
Edited this one out due to incorrect name and error as Mondulous figured out. Thanks Modulous.
This message has been edited by randman, 06-11-2005 03:40 AM

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Modulous
Member
Posts: 7799
From: Manchester, UK
Joined: 05-01-2005


Message 289 of 311 (216068)
06-11-2005 3:05 AM
Reply to: Message 288 by randman
06-11-2005 2:51 AM


Re: Inconsistent?
I see your problem. Look at your kangaroo cytochrome b. You got it from this page right? Look at the organism type: ="Lerista bougainvillii"
What is "Lerista bougainvillii" - looks like an Australian Lizard to me, quite different from a kangaroo (though it can be found on kangaroo island)
The biggest correlation then looks like a turtle and a skink. Both reptiles, in accordance with predictions. I didn't check your other sequences.

This message is a reply to:
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AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 290 of 311 (216070)
06-11-2005 3:10 AM
Reply to: Message 288 by randman
06-11-2005 2:51 AM


Topic!
The bioinformatics thread was spun off to keep this type of post out of this thread. Please keep it there. Thank you.

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randman 
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Posts: 6367
Joined: 05-26-2005


Message 291 of 311 (216076)
06-11-2005 3:27 AM
Reply to: Message 289 by Modulous
06-11-2005 3:05 AM


Re: Inconsistent?
It looks like the site will give you wrong data for common names. I looked up and ran the scientific names though, and got the following. Please note that "alligator" is alligator snapping turtle, aka Macroclemys temminckii.
Maybe this has an error too, but it definitely does not correspond to current cladograms.
Sequence 1: humanCytoB>MTPMRKINPLMKLINHSFI 308 aa
Sequence 2: rattlesnakeCytoB>MMQTMTGFFLAIH 155 aa
Sequence 3: redkangaroo>MTNLRKTHPLIKIVNHSF 311 aa
Sequence 4: alligator 198 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 58.7097
Sequences (1:3) Aligned. Score: 75.6494
Sequences (1:4) Aligned. Score: 77.7778
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 61.2903
Sequences (2:4) Aligned. Score: 62.5806
Sequences (3:2) Aligned. Score: 61.2903
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 77.2727
Sequences (4:2) Aligned. Score: 62.5806
Sequences (4:3) Aligned. Score: 77.2727
Sequences (4:4) Aligned. Score: 100
>humanCytoB>MTPMRKINPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDASTAFSSIAHIT
RDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFLYSETWNIGIILLLATMATAFMGYVLPWGQMSF
WGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFFTFHFILPFIIAALAALHLLFLHETGSNNPLG
ITSHSDKITFHPYYTIKDALGLLLFLLSLMTLTLFSPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTI
LRSVPNKLGGVLALLLSILILAMIPILHMSKQQSMMFRPLSQSLYWLLAADLLILTWIGGQPVSYPFTII
GQVASVLYFTTILILMPTISLIENKMLK
>rattlesnakeCytoB>MMQTMTGFFLAIHYTANINLAFSSVIHITRDVPYGXIMQNLHTISASLFFICIYIHIARGLYYGLYLNKE
VWLSGTALLITLMATAFFGYVLPWGQMSFWAATVITNLLTAIPYLGTTLTTWLWGGFSINDPTLTRFFAL
HFILPFIIISLSSIHIILLHNEGSNNPLGTNSDIDKIPFHPYHSYKDVLMITSMITLLLLILSFSPSLLN
DPENFXKAXPXXTPQ
>redkangaroo>MTNLRKTHPLIKIVNHSFIDLPAPSNISAWWNFGSLLGACLIIQILTGLFLAMHYTADTLTAFSSVAHIC
RDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKETWNIGVILLLTVMATAFVGYVLPWGQMSF
WGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFAFHFILPFIITALVLVHLLFLHETGSNNPSG
INPDSDKIPFHPYYTIKDALGFMLMLLILLTLALFSPDMLGDPDNFSPAKPTEHSSHIKPEWYFLFAYAI
LRSIPNKLGGVLALLASILILLIIPLLHTSKQRSLMFRPISQTLFWILTANLITLTWIGGQPVEQPYIII
GQVASISYFLLIIVLMPLAGLFENYMLEPKW
>alligator snapping turlte>MATNLRKTHPMMKIINNSFIDLPSPSNISAWWNFGSLLGTCLIMQTITGIFLAMHYSPDISMAFSSITHI
TRDVQYGWLIRNMHANGASLFFICIYLHIGRGLYYGSYLYKETWNTGVILLLLTMATAFMGYVLPWGQMS
FWGATVITNLLSAIPYIGSTLVQWIWGGFSVDNATLTRFFTLHFLLPFTIMGLAMVHLLFLHETGSNNPT
GLNSNSDKIPFHPYFSYKDLLGLILMLSLLLTLALFSPNLLGDPDNFTPANPLVTPPH
Humans are more related to alligator snapping turtles than a red kangaroo, aka Macropus rufus, according to this?
This message has been edited by randman, 06-11-2005 03:42 AM

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randman 
Suspended Member (Idle past 4889 days)
Posts: 6367
Joined: 05-26-2005


Message 292 of 311 (216077)
06-11-2005 3:49 AM
Reply to: Message 235 by Wounded King
06-09-2005 11:41 AM


Re: Genomic data on a marsupial
WK, how about comparing the genomes of a opossum, human, kangaroo, mouse, and turtle?
I don't really know of a placental couterpart to the opossum, but seeing the data on these, if done, might shed some light on the process. Or, pick some others. Basically, whatever is available, but the fact humans are probably available, and the opossum as your post indicates. It ought to be informative to see how some others come out that are somewhat in-between.
The turtle is just to throw a curve in there and see what happens.

This message is a reply to:
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Replies to this message:
 Message 301 by Wounded King, posted 06-11-2005 8:17 PM randman has replied

mark24
Member (Idle past 5185 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 293 of 311 (216079)
06-11-2005 4:00 AM
Reply to: Message 284 by randman
06-11-2005 12:45 AM


Re: Inconsistent?
randmnan,
Sure Mark, after you calculate the odds as I asked you, of the chances of the ear bones independently evolving from chance, mutations and natural selection.
I have already told you I have no idea of the odds, neither do you.
However, I have been asking why unrelated data sets should show similar patterns for many posts now, so if anyone gets to adopt the childish, "I asked first" mentality, its me, OK?
Now, I ask again:
mark writes:
Please explain why cetacean milk caseins, long & short interspersed elements, & morphology must mutate/evolve is such a way as to place them in the artiodactyl order, since it seems so inevitable to you?
Please explain what it is about cytochrome c's primary structure, NADH's primary structure, & morphology that makes the 8 taxa phylogeny cited return identical cladograms.
Please be specific.
Mark
This message has been edited by mark24, 06-11-2005 04:05 AM

There are 10 kinds of people in this world; those that understand binary, & those that don't

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Replies to this message:
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randman 
Suspended Member (Idle past 4889 days)
Posts: 6367
Joined: 05-26-2005


Message 294 of 311 (216081)
06-11-2005 4:07 AM
Reply to: Message 293 by mark24
06-11-2005 4:00 AM


Re: Inconsistent?
Markm first off, your stance that molecular evidence all supports morphological "trees" is untenable. There is no debate on that.
On the data you showed, that shows very little. Heck, I just ran some data on the same program for CytoC and CytoB and got totally different results from what your scenario predicted.
So the short answer is that your questions are wrong because your data is wrong.
Please explain why cetacean milk caseins, long & short interspersed elements, & morphology must mutate/evolve is such a way as to place them in the artiodactyl order, since it seems so inevitable to you?
First off, what do you mean by "seems so inevitable to you"?
Secondly, I hear you claiming that the morphological analysis agrees with the molecular analysis that place the cetaceans and hippos as one monophyletic group, and that's where you are wrong.
The morphologists disagreed with the molecular systemists. I don't know why you don't just up and admit this. You continually base your entire argument and participation in this thread on a factual error on your part, falsely claiming the morphology and the molecular data agree here on whale evolution when they do not.
It is unbeleivable to me that after all these posts, you still ignore the debate between morphologists and molecular systemists, and erroneously claim they have always been in agreement in this matter.
This message has been edited by randman, 06-11-2005 04:19 AM

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randman 
Suspended Member (Idle past 4889 days)
Posts: 6367
Joined: 05-26-2005


Message 295 of 311 (216083)
06-11-2005 4:22 AM
Reply to: Message 293 by mark24
06-11-2005 4:00 AM


Re: Inconsistent?
Please explain what it is about cytochrome c's primary structure, NADH's primary structure, & morphology that makes the 8 taxa phylogeny cited return identical cladograms.
They don't. I don't see why you don't get it. Anyone can draw a cladogram after the fact to match the molecular data, and that's what molecular systemists do.
That doesn't make it congruent with the morphological data. But don't take my word for it. Read the following:
Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids.
Taylor and Francis reference
(edited by AM to reduce reference length)
http://diglib1.amnh.org/novitates/i0003-0082-344-01-0001.pdf
The origin of late Neogene Hippopotamidae (Artiodactyla) involves one of the most serious conflicts between comparative anatomy and molecular biology: is Artiodactyla paraphyletic? Molecular comparisons indicate that Cetacea should be the modern sister group of hippos. This finding implies the existence of a fossil lineage linking cetaceans (first known in the early Eocene) to hippos (first known in the middle Miocene). The relationships of hippos within Artiodactyla are challenging, and the immediate affinities of Hippopotamidae have been studied by biologists for almost two centuries without resolution.
Just a moment...
This message has been edited by randman, 06-11-2005 04:29 AM
This message has been edited by AdminNosy, 06-11-2005 09:53 AM

This message is a reply to:
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mark24
Member (Idle past 5185 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 296 of 311 (216086)
06-11-2005 4:28 AM
Reply to: Message 294 by randman
06-11-2005 4:07 AM


Re: Inconsistent?
randman,
Heck, I just ran some data on the same program for CytoC and CytoB and got totally different results from what your scenario predicted.
Post them.
They don't. I don't see why you don't get it. Anyone can draw a cladogram after the fact to match the molecular data, and that's what molecular systemists do.
They don't "draw a cladogram after the fact". Have you learnt NOTHING? The data, regardless of whether it sequence data or morphological data, have similar algorithms applied to them like clustal, in order to derive a cladogram/tree.
You also ignore the fact that in most cases the morphological data & conclusions predated the molecular. This is why molecular data is forcing changes in our conclusions, remember?
The rest of post 293 has already been dealt with at length. Focussing on the incongruence at the expense of the congruent, again. Yada, yada, yada. If you remember, all you could manage in response to that post was accuse me of not accepting that molecular data warrants clade placement changes when I explicitly said a much in a previous post.
Mark
This message has been edited by mark24, 06-11-2005 04:40 AM

There are 10 kinds of people in this world; those that understand binary, & those that don't

This message is a reply to:
 Message 294 by randman, posted 06-11-2005 4:07 AM randman has replied

Replies to this message:
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randman 
Suspended Member (Idle past 4889 days)
Posts: 6367
Joined: 05-26-2005


Message 297 of 311 (216088)
06-11-2005 4:31 AM
Reply to: Message 296 by mark24
06-11-2005 4:28 AM


Re: Inconsistent?
You also ignore the fact that in most cases the morphological data & conclusions predeated the molecular.
Read my edits above.
Also, I am not ignoring that fact. That's the whole point. The morpholigical data and trees disagree with the molecular, and the molecular has caused a revision in the data.
Maybe we are talking past one another. You claim to have run some data that produced a cladogram that matched the current phyologenies, probably of a molecular systemist.
Well, duh! He's already run that data and used it to advance his cladogram. That's why they matched 100%.
But that doesn't mean it matches the morphological data.
There is no amazing statistical fact here. You ran molecular data and compared the results with those that ran the same data with the same results. No wonder it was 100%!
Also, I did post the data. Read the thread and the new thread.
But rereading your post, I see where you are admitting that there are changes in the clades, that disagreement between molecular and morphological systamists is indeed real. Good.
As as why CytoC and NADH should parrallel one another, it could be something related to how they interact within the DNA. From what I can tell, all of the molecular data does not fit as nicely as those 2 did on your data. Why not look a little more deeply?
This message has been edited by randman, 06-11-2005 04:35 AM
This message has been edited by randman, 06-11-2005 04:53 AM

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mark24
Member (Idle past 5185 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 298 of 311 (216091)
06-11-2005 5:03 AM
Reply to: Message 297 by randman
06-11-2005 4:31 AM


Re: Inconsistent?
randman,
randman writes:
Heck, I just ran some data on the same program for CytoC and CytoB and got totally different results from what your scenario predicted.
Post them.
Post the data.
Well, duh! He's already run that data and used it to advance his cladogram. That's why they matched 100%.
No, the data has algorithms applied to it & is congruent to a greater or lesser degree with other data, or it isn't.
Or are you suggesting this is one big lie? That the figures are massaged to look congruent?
Post 215's 100% congruence is a lie, too? How did I manage to pull that off & make it congruent with the pre-Heniggian expectation?
How did Masato Nikaido, Alejandro P. Rooney, and Norihiro Okada, manage to pull off an overall congruence with Giessler? Same for John Gatesy, Cheryl Hayashi, Mathew A. Cronin, and Peter Arctanderg's study?
But that doesn't mean it matches the morphological data.
I look forward to your explanation of why camels, pigs, peccarries, mysocetes, odontocetes etc always fall within artiodactyla, rather than: Perissodactyls, paenungulata, rodentia, chiroptera, primates, carnivora, xenarthra, ameridelphia, australidelphia, multituberculata, docodonta, triconodonta, symmetrodonta, enantiothornes, hesperornithiformes, icthiornithiformes, anseriformes, galliformes, podicepiformes, gaviiformes, sphenisciformes, pelecaniformes, procellariformes, gruiformes, charadriiformes, columbiformes, ciconiiormes, falconiformes, strigiformes, caprimulgiformes, apodiformes, coraciiformes, piciformes, passeriformes, pelycosauria, therapsida, testudines, araeoscelidia, younginiformes, placondontia, nothosauria, plesiosauria, sphenodontia, squamata, prolacertiformes, crocodilia, pterosauria, saurischia, ornithischia, aistopoda, nectridia, microsauria, temnospondyli, gymnophiona, urodela, anura, anthracosauria, seymoriamorpha, diadectomorpha, thelodonti,heterostraci, arandaspida, astraspida, galeaspida, osteostraci, ctenacanthiformes,hybodontiformes, xenacanthiformes, symmoriformes, eugeneodontiformes, petalodontiformes, iniopterygiformes, chongrenchelyformes, ptyctodontida, rhenanida, acanthoraci, petalichthyida, phyllolepida, arthrodira, antiarchi, saurichthyiformes, paleonisciformes, pholidopleuroformes, perleidiformes, peltopleuriformes, pynodontiformes, parasemionontiformes, amiiformes, osteoglossiformes, anguilliformescrossognathiformes, ellimmichthyiformes, clupeiformes, esociformes, gonorhynchiformes, cypriniformes, charachiformes, siluriformes, salmoniformes, stomiiformes, aulopiformes, myctophyformes, polymiciiformes, percopsiformes, ophidiiformes, lophiiformes, gadiformes, atheriniformes, cyprinodontiformes, beloniformes, beryciformes, lampridiformes, zeiformes, gasterosteiformes, dactyliopteriformes, scorpaeniformes, perciformes, pleuronectiformes, tetraodontiformes, diabolepidida, dipnoi, porolepiforms, rhizodontiformes, osteolepiforms, pandericthyida...
Mark

There are 10 kinds of people in this world; those that understand binary, & those that don't

This message is a reply to:
 Message 297 by randman, posted 06-11-2005 4:31 AM randman has not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 299 of 311 (216100)
06-11-2005 6:14 AM
Reply to: Message 291 by randman
06-11-2005 3:27 AM


Re: Inconsistent?
The site didn't give you the wrong data. You simply didn't bother to check that the results you looked at were actually what you wanted.
The site did exactly what you wanted, found you a database entry with the words 'Kangaroo' and 'Cytochrome B'. The entry for the lizard was from a species found on Kangaroo island.
If you want to ensure that it only looks for kangaroo in the context of the organism the sequence is derived from you need to put in a slightly more sophisticated search such as 'macropus[organism] Cytochrome c'. The '[organism]' limits the search for the species name to one field in the database. You were on the right lines looking for the latin rather than common names, that is a much more reliable term for searches.
TTFN,
WK

This message is a reply to:
 Message 291 by randman, posted 06-11-2005 3:27 AM randman has not replied

RAZD
Member (Idle past 1395 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 300 of 311 (216165)
06-11-2005 12:57 PM
Reply to: Message 80 by randman
06-05-2005 5:45 PM


Re: common descent goes deeper
Pardon the time taken to respond. I lost my internet service at home and it has taken a while to replace it.
randman, msg 80 writes:
but could you back up "the 98% DNA sequences" comment for me?
There are a number of sources, and some disagreement on the actual percentage, but all pretty much agree that it is between 97% and 99%.
A quick google will find several resources for this information, including a link to a popular (meaning written for general audience) book called What It Means to Be 98 Percent Chimpanzee: Apes, People, and Their Genes (click for amazon link)
this is a pdf paper:
Page Not Found | University of Chicago
that I have a little trouble with (another paper asserts chimps are closer to gorillas than to humans), and they make a distinction about "functional" DNA rather than all DNA (which would include junk sections that would still have similar mutations from a common ancestry)
but even that other paper lists the commonality between humans and chimps at 98%:
http://www.newsroom.ucr.edu/cgi-bin/display.cgi?id=875
it just says that:
"The explosive expansion of the DNA repeats and the resulting restructuring of our genetic code may be the clue to what makes us human," Dugaiczyk said. "During the same amount of time, humans accumulated more genetic novelties than chimpanzees, making the human/chimpanzee genetic distance larger than that between the chimpanzee and gorilla."
this site:
http://www.cnpt.embrapa.br/redbiobr/nov_1020.htm
gives some further background for comparing human chimp gorilla and orangutan DNA
There are also some known mutations (like the loss of vitamin C making ability) that are shared by chimps and humans.

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