Human chimp gene comparison with other species

[bigore]

Hello,

 

Im new to this forum and i am from holland, so i hope my english is good enough to understand, but i think this is my best bet to get an answer to my question.

 

I'm having an online debat with an creationist, he is a biologist with PHd and all and claims to have an new theory that would blow darwins theory out of the sky.

 

I asked him the question, why do you think we are not descended from apes?In fact, we are apes.

 

His answer is simple, he says that he has studied the human genome and the chimp genome so closely that they could not be related. There are 22.000 genes in the human dna, and 1400 are different with the chimp. So he has based his statement on the fact that there are 1400 different genes between the chimp and human. 6,4% to be precise.

 

Well, im not gonna argue with his statement, but i asked him a counterquestion which could make his statement fall down.

 

He does not have an answer to my question so im gonna ask it here, i hope somebody can help me out.

 

How many different genes are there in different types within kinds. So for example, how many genes differ between a horse and a zebra, or donkey. Or how many genes between an urangatan and chimp. Because if these animals differ also around 1400 genes or more, would make his statement worthless right?

 

I thank anyone who respond in advance:-)

[CharonY]

Without getting into details, I am not sure what kind of phd he holds but this is rather ridiculous. First we do not know the genes in the human genome yet. The 25k or so are just estimates. Identifying genes in a genome is a daunting task and neither in human or chimpanzee it is near completion (if it can be completed at all).

 

A number of 1400 different genes can only be an estimate of an estimate. Even worse, what qualifies as a different gene? For relation purposes the only relevant value is the amount of sequence differences (including indels).

Summarizing, distance can only be estimated by sequence differences, counting genes is ridiculous and apparently there are cheap phds out there.

good night.

Edited October 18, 2008 by CharonY

[bigore]

Thank you for your response, i must say that his statement is not solely based on this argument, but this is one of them. But this statement is not worth looking into i guess?

[Daecon]

I think he may be lying about having a phD...

 

If he was correct the WHOLE scientific community would know about it and evolutionary biologists would be falling over themselves trying to make the best theory to describe the observable data and win the next Nobel Prize.

 

That's why the current theories ARE the current theories, not because they're trying to be anti-creationist, but because they're trying to understand how reality actually really WORKS.

[bigore]

I don't think he is lying about the PHd, but i think it's more ignorance he is proposing. If you are interested in his theory try this link. It is a Dutch site, but his pretentious theory is in english.

 

GUToB

[Sayonara]

I stopped reading on the second line of the first paragraph:

The origin of baranomes cannot be described in scientific terms.

 

This is equivalent to stating "magical processes set life up to be described by the rest of my theory".

 

He loses.

[Daecon]

Well that's just stupid. Of course it can be described in scientific terms otherwise the Universe would never have been able to figure it out and it wouldn't exist.

[bigore]

I stopped reading on the second line of the first paragraph:

 

 

This is equivalent to stating "magical processes set life up to be described by the rest of my theory".

 

He loses.

 

So true, but it's hard for me to debate with him because he goes really technical sometimes where he outclasses me. But the confidence this guy has in his theory is unbelieveble. Especially the genetic redundance part (degeneration of all lifeforms on earth), i can not give good enough feedback to make him doubt his theory. He has "proven" that life was much more complex in the early days then less complex what evolution tells us.

[Sayonara]

It doesn't matter how technical he gets if the basic building block of his argument is magical.

[npts2020]

The bulk of the text seems like mental masturbation but the comments after were hilarious (wish I knew all of the languages). How does this Borger guy know anything about what parts of his barynome (imo same thing as genome only not described by how it really works) are in fact duplicates or non-functional when no scientist I have ever heard of claims to know what even a small fraction are for in any advanced life form?

[bigore]

He is accusing you guys for not knowing your science, this is the article where he refers to

http://www.genetics.org/cgi/content/full/177/3/1941

 

I must admit, it says literally that 6,4% genes are different between humans and chimps, with 678 gene gaines in humans and 740 gene losses compared to chimps. So there is a total of over 1400 genes that differ with chimps.

[CharonY]

No, the article only claims that there are an estimated 1418 genes (mind you, it is just an estimation!) of 1418 genes that are not 1-1 orthologous to each other. Does it mean that there are 6% genome difference?

 

Hell no. Let us do some very basic calculations. The average gene size is roughly 3kb. If we assume (as we do not really know yet!) that there are 22k genes in the human genome, we come to a total sequence size of around 22k x 3kb = 66MB

The human genome is roughly 3000 MB, so the gene content only account for roughly 22 % of the whole genome.

 

Moving on. 1418 gene difference (~ 4MB) would therefore to account for 0.1% sequence diversity. Quite a difference, right?

 

Also he apparently did not quite get the gist of the publication. Or at least chose to misinterpret it.

 

Mind you to calculate whole genome distances is quite complicated. What the paper did, however is to investigate gene loss/gain events, or rather the rates rather than the absolute distance.

 

I just took a look whether this Peter Borger guy is real. Unfortunately he is, though I do hope that he did not really make his PhD in biology (biochemistry would be alright, though).

 

He apparently is affiliated with the ISCID, a group involved in promoting ID (Behe is in the editorial board, btw).

Dear me.

Edited October 20, 2008 by CharonY

[bigore]

No, the article only claims that there are an estimated 1418 genes (mind you, it is just an estimation!) of 1418 genes that are not 1-1 orthologous to each other. Does it mean that there are 6% genome difference?

 

Hell no. Let us do some very basic calculations. The average gene size is roughly 3kb. If we assume (as we do not really know yet!) that there are 22k genes in the human genome, we come to a total sequence size of around 22k x 3kb = 66MB

The human genome is roughly 3000 MB, so the gene content only account for roughly 22 % of the whole genome.

 

Moving on. 1418 gene difference (~ 4MB) would therefore to account for 0.1% sequence diversity. Quite a difference, right?

 

Also he apparently did not quite get the gist of the publication. Or at least chose to misinterpret it.

 

Mind you to calculate whole genome distances is quite complicated. What the paper did, however is to investigate gene loss/gain events, or rather the rates rather than the absolute distance.

 

I just took a look whether this Peter Borger guy is real. Unfortunately he is, though I do hope that he did not really make his PhD in biology (biochemistry would be alright, though).

 

He apparently is affiliated with the ISCID, a group involved in promoting ID (Behe is in the editorial board, btw).

Dear me.

 

Thank you for this new inside of this story, that makes alot of difference indeed. So he's right about the 1400 genes (estimate), but he takes it to literally when saying 6,4% is different between chimps and humans. Because the actual information differs only by an estimated 0,1%, quite a difference indeed.

 

I'm gonna relay your answer to him if you don't mind.

[CharonY]

Sure, though an additional point would be that gene loss and gain events are not really good as distance markers. One of them is simply the identifying those events, another is that the rate of the turnover can be very hard to estimate (the actual point of the paper).

 

Another, possibly more important point might be that it is a complete waste of time. Traditionally ID/creationism proponents rarely do respond to corrections or any arguments. This is sadly also true to some extent to those who actually "believe" in evolution, without actually a deeper knowledge in that matter. And mind you, evolution is a bloody complicated matter since it has departed from the more intuitive Darwinian basics (I am a biologist involved in genomics, though I lack the knowledge of a true evolutionary biologist in that matter).

 

Imagine, for instance, the integration of a virus into the genome. Let us assume furthermore that around 1kb of the virus remains stably in the genome of a population. Now comparing those with and without the virus would yield 1000 additional bases. This is simply not comparable to 1000 individual point mutations. Again the paper's work was not to estimate distances per se, but its point was that in humans they claim to have found an accelerated gene turnover (that is, duplication events and gene losses).

[Blazenarrow]

Without getting into details, I am not sure what kind of phd he holds but this is rather ridiculous. First we do not know the genes in the human genome yet. The 25k or so are just estimates. Identifying genes in a genome is a daunting task and neither in human or chimpanzee it is near completion (if it can be completed at all).

 

A number of 1400 different genes can only be an estimate of an estimate. Even worse, what qualifies as a different gene? For relation purposes the only relevant value is the amount of sequence differences (including indels).

Summarizing, distance can only be estimated by sequence differences, counting genes is ridiculous and apparently there are cheap phds out there.

good night.

 

Wait, i'm sorry but what about the human genome project?

[marnixR]

He has "proven" that life was much more complex in the early days then less complex what evolution tells us.

 

just ask him 2 simple questions : how does he define complexity, and how does he recognise complexity in creatures that have been extinct for 500 million years

 

after all, it's no good comparing present-day "advanced" and present-day "primitive" creatures, because both are thoroughly modern and have a history of 500 million between them and their cambrian predecessor

[Geshenk]

No, the article only claims that there are an estimated 1418 genes (mind you, it is just an estimation!) of 1418 genes that are not 1-1 orthologous to each other. Does it mean that there are 6% genome difference?

 

Hell no. Let us do some very basic calculations. The average gene size is roughly 3kb. If we assume (as we do not really know yet!) that there are 22k genes in the human genome, we come to a total sequence size of around 22k x 3kb = 66MB

The human genome is roughly 3000 MB, so the gene content only account for roughly 22 % of the whole genome.

 

Moving on. 1418 gene difference (~ 4MB) would therefore to account for 0.1% sequence diversity. Quite a difference, right?

 

Also he apparently did not quite get the gist of the publication. Or at least chose to misinterpret it.

 

Mind you to calculate whole genome distances is quite complicated. What the paper did, however is to investigate gene loss/gain events, or rather the rates rather than the absolute distance.

 

I just took a look whether this Peter Borger guy is real. Unfortunately he is, though I do hope that he did not really make his PhD in biology (biochemistry would be alright, though).

 

He apparently is affiliated with the ISCID, a group involved in promoting ID (Behe is in the editorial board, btw).

Dear me.

 

 

Don't know if I should have started a new thread... I'm a novice trying to understand this. I do have some questions.

 

These 1418 genes that have been found not to be orthologous in the two species..... how would this have come about? This is more than just allelic differences right?

 

And how do gene loss/gains happen? If there is a website that I can read to explain this in simple terms I'd be most grateful for a link. Thank you.

[CharonY]

Wait, i'm sorry but what about the human genome project?

What about it?

 

These 1418 genes that have been found not to be orthologous in the two species..... how would this have come about? This is more than just allelic differences right?

Yes. Generally these changes are either caused by loss of genes (the more common phenomenon) or gene acquisition. However, the number in this paper is based on an estimation and is by no means the result of a 1:1 comparison of the complete respective sequences (which is technically rather tricky).

[TheDonner]

Without getting into details, I am not sure what kind of phd he holds but this is rather ridiculous. First we do not know the genes in the human genome yet. The 25k or so are just estimates. Identifying genes in a genome is a daunting task and neither in human or chimpanzee it is near completion (if it can be completed at all).

 

A number of 1400 different genes can only be an estimate of an estimate. Even worse, what qualifies as a different gene? For relation purposes the only relevant value is the amount of sequence differences (including indels).

Summarizing, distance can only be estimated by sequence differences, counting genes is ridiculous and apparently there are cheap phds out there.

good night.

 

http://www.ncbi.nlm.nih.gov/Genomes/

 

there you will find information on both genomes. if 25k is an estimate then why do they teach us in school that the entire human genome has been sequenced? if it was sequenced it wouldnt be an estimate.

 

Although the chimp genome has not been fully completed, you can still determine how similar they are using DNA hybridization, but this is not accurate everytime (some reveal 97% some reveal 98-99%.

 

Im not trying to offend anyone with this post, im just sharing what I have learned here in school. If I am wrong here, please indicate.

 

Doni

[CharonY]

You are wrong. The mere sequence does not directly convey information about what or if they encode anything. This various algorithms are being employed to predict ORFs out of the naked sequences, however, they are still only an estimate unless being experimentally validated at some point.

 

You can imagine the sequence as a series of letters in a foreign language, and it takes enormous work to correctly read the words out of it, and even more to make sense out of these words.