Gene Number Changes Between Humans and Chimps

[mark kennedy]

The last thread I participated in had an Opening Post that was passing off the same of propaganda of humans and chimps being '98% the same'. What was revealing about that is that not one evolutionist corrected it and most of the regulars knew it was bogus. It has been conclusively demonstrated that this is wrong but those who peddle this, flawed homology argument, always have one refuge from the facts. The 98% homology rule holds since most of the differences are in non-coding regions. The truth is slowly coming out, this isn't true either:

ScienceDaily (Dec. 20, 2006) — Approximately 6 percent of human and chimp genes are unique to those species, report scientists from Indiana University Bloomington and three other institutions. The new estimate, reported in the inaugural issue of Public Library of Science ONE (Dec. 2006), takes into account something other measures of genetic difference do not -- the genes that aren't there...

...The researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent. Human-chimp Difference May Be Bigger​

Think I'll keep a running total this time, usually the first few posts are simple ad hominem attacks. These are then followed by rhetorical questions (basically asking questions that go in circles). There will always be one troll who continually bombards the creationist with as much rudeness and contradiction as the forum rules will allow.

One of the mainstays of this forum is finding an error, usually by creating one through semantics or twisting statements.

Ad hominems
Rhetorical devices
Error Fabrication

Now when we get past all of that the benign scientific type will enter, inquire of the resident trolls what the trouble is and proceed to reinforce their arguments no matter how fallacious.

Other then that, anyone who has something substantive to contribute to the thread I'd be interested in whatever you have for me.

Have a nice day
Mark

 

[Hespera]

The last thread I participated in had an Opening Post that was passing off the same of propaganda of humans and chimps being '98% the same'. What was revealing about that is that not one evolutionist corrected it and most of the regulars knew it was bogus. It has been conclusively demonstrated that this is wrong but those who peddle this, flawed homology argument, always have one refuge from the facts. The 98% homology rule holds since most of the differences are in non-coding regions. The truth is slowly coming out, this isn't true either:

ScienceDaily (Dec. 20, 2006) — Approximately 6 percent of human and chimp genes are unique to those species, report scientists from Indiana University Bloomington and three other institutions. The new estimate, reported in the inaugural issue of Public Library of Science ONE (Dec. 2006), takes into account something other measures of genetic difference do not -- the genes that aren't there...

...The researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent. Human-chimp Difference May Be Bigger​

Think I'll keep a running total this time, usually the first few posts are simple ad hominem attacks. These are then followed by rhetorical questions (basically asking questions that go in circles). There will always be one troll who continually bombards the creationist with as much rudeness and contradiction as the forum rules will allow.

One of the mainstays of this forum is finding an error, usually by creating one through semantics or twisting statements.

Ad hominems
Rhetorical devices
Error Fabrication

Now when we get past all of that the benign scientific type will enter, inquire of the resident trolls what the trouble is and proceed to reinforce their arguments no matter how fallacious.

Other then that, anyone who has something substantive to contribute to the thread I'd be interested in whatever you have for me.

Have a nice day
Mark

Looks like the running total on ad homs is 4, so far. Did I miss one?


1. not one evolutionist corrected it and most of the regulars knew it was bogus.

2. those who peddle this, flawed homology argument, always have one refuge from the facts.

3. always be one troll who continually bombards the creationist with as much rudeness and contradiction as the forum rules will allow.

4. resident trolls what the trouble is and proceed to reinforce their arguments no matter how fallacious.

 

[atomweaver]

The last thread I participated in had an Opening Post that was passing off the same of propaganda of humans and chimps being '98% the same'. What was revealing about that is that not one evolutionist corrected it and most of the regulars knew it was bogus. It has been conclusively demonstrated that this is wrong but those who peddle this, flawed homology argument, always have one refuge from the facts. The 98% homology rule holds since most of the differences are in non-coding regions. The truth is slowly coming out, this isn't true either:

ScienceDaily (Dec. 20, 2006) — Approximately 6 percent of human and chimp genes are unique to those species, report scientists from Indiana University Bloomington and three other institutions. The new estimate, reported in the inaugural issue of Public Library of Science ONE (Dec. 2006), takes into account something other measures of genetic difference do not -- the genes that aren't there...​

*thweet* 10 yard penalty; Unnecessary use of the Ellipsis.

ScienceDaily (Dec. 20, 2006) — Approximately 6 percent of human and chimp genes are unique to those species, report scientists from Indiana University Bloomington and three other institutions. The new estimate, reported in the inaugural issue of Public Library of Science ONE (Dec. 2006), takes into account something other measures of genetic difference do not -- the genes that aren't there.

That isn't to say the commonly reported 1.5 percent nucleotide-by-nucleotide difference between humans and chimps is wrong, said IUB computational biologist Matthew Hahn, who led the research. IUB postdoctoral researcher Jeffery Demuth is the paper's lead author.
"Both estimates are correct in their own way," Hahn said. "It depends on what you're asking. There isn't a single, standard estimate of variation that incorporates all the ways humans, chimps and other animals can be genetically different from each other."

Bold emphasis mine. Thanks for the article, Mark. It's own content refutes your assertions, saving us the effort.


​

 

[mark kennedy]

Looks like the running total on ad homs is 4, so far. Did I miss one?


1. not one evolutionist corrected it and most of the regulars knew it was bogus.

When Time and Nature Web Focus said that we are 98% the same as chimpanzees in our DNA, is that a true or false statement?

2. those who peddle this, flawed homology argument, always have one refuge from the facts.

With that omission you managed to surgically remove the whole point, the 6% difference is in the genes. So that's one ad hominem and one rhetorical device.

3. always be one troll who continually bombards the creationist with as much rudeness and contradiction as the forum rules will allow.

It would appear that you have point on that.

4. resident trolls what the trouble is and proceed to reinforce their arguments no matter how fallacious.

So far I'm three for four and that's from the first response.

Ad hominems- 2
Rhetorical devices- 1
Error Fabrication

Do notice that the content of the quote, article and paper is utterly ignored and her attack is stickily ad hominem or 'to the man'.

Have a nice day
Mark

 

[mark kennedy]

Bold emphasis mine. Thanks for the article, Mark. It's own content refutes your assertions, saving us the effort.

*Tweet* Quote out of context, incomplete point, replay first down.

Public Library of Science ONE (Dec. 2006), takes into account something other measures of genetic difference do not -- the genes that aren't there.

Just to put this in context we originally were thought to have 30,000 genes, now it's less the 20 k. At one time estimates of how many genes absent in the chimpanzee and present in the human genome was around 50, now it's in the hundreds.

That's why I keep coming back, you guys make it so easy. The first one is a sly but empty attempt at error fabrication, the second one was clearly a rhetorical device meant to dismiss the point of the OP without a hearing. Both are fallacious and so far not a single substantive response, you usually don't start getting those until at least the second page.

Ad hominems- 2
Rhetorical devices- 1
Error Fabrication-1

Initial Resident Bombarder - Hespera

All we are missing is the benign scientific type who comes in and reinforces your fallacious attacks.

Have a nice day
Mark

 

[PhilosophicalBluster]

Mr. Kennedy, you seem to have ignored atomweaver's post...

Anyway, the reason for the differences in the two measurements (98% and 94%) is because they are effectively different scales. See, the 98% measurement is in reference to each nucleotide that makes up the gene. So out of all the bases in ours and an ape's genetic code, only 2% are different.

However

The 96% measurement is referring to the whole genes, not the individual nucleotides. From what I've gathered, (somebody correct me if I'm wrong) the differences in nucleotides are spread out across different genes. In other words: a small amount of different nucleotides can make a gene different. This gives the difference in the two measurements. They are both correct. Arguing this would be like me trying to argue that a shrub is one yard high, and you saying that is incorrect because the shrub is actually three feet high. Or if you're in Europe, 1,000 meters and not 1 kilometer.

 

[Hespera]

*Tweet* Quote out of context, incomplete point, replay first down.

Public Library of Science ONE (Dec. 2006), takes into account something other measures of genetic difference do not -- the genes that aren't there.

Just to put this in context we originally were thought to have 30,000 genes, now it's less the 20 k. At one time estimates of how many genes absent in the chimpanzee and present in the human genome was around 50, now it's in the hundreds.

That's why I keep coming back, you guys make it so easy. The first one is a sly but empty attempt at error fabrication, the second one was clearly a rhetorical device meant to dismiss the point of the OP without a hearing. Both are fallacious and so far not a single substantive response, you usually don't start getting those until at least the second page.

Ad hominems- 2
Rhetorical devices- 1
Error Fabrication-1

Initial Resident Bombarder - Hespera

All we are missing is the benign scientific type who comes in and reinforces your fallacious attacks.

Have a nice day
Mark

It is not an ad hom to quote what you said. Review the dictionary.

Are you going to keep a running count of all the name calling you do?

How about if you just start over, with some data, should you have some, and not start out with all the personal stuff?

 

[Skaloop]

Here are two series of three multi-digit numbers:

128-396-2475
128-397-2475

Based on the individual digits, what percentage difference is there between the two series? 1/10, so 10%.

Based upon the whole numbers themselves, what percentage difference is there between the two series? 1/3, so ~33%.

Which answer is correct?

 

[Assyrian]

When Time and Nature Web Focus said that we are 98% the same as chimpanzees in our DNA, is that a true or false statement?

With that omission you managed to surgically remove the whole point, the 6% difference is in the genes. So that's one ad hominem and one rhetorical device.
It would appear that you have point on that.
So far I'm three for four and that's from the first response.

Ad hominems- 2
Rhetorical devices- 1
Error Fabrication

Do notice that the content of the quote, article and paper is utterly ignored and her attack is stickily ad hominem or 'to the man'.

Have a nice day
Mark

What is wrong with addressing a major portion of your post which was made up of an ad hom attack complaining of ad homs and rhetorical devices? It certainly had me checking my irony meter for damage.

You actually had two replies, one from hespera commenting on your ad hom ad homs, and a second reply from atomweaver deaing with the rest the post. Sound to me like your whole post was covered between the two. Why complain that hespera only dealt with one part?

The researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes)

So these 698 genes come from duplicates of existing genes we share with chimps? Doesn't that mean each of these genes is only a small pecentage different from the chimp version?

 

[mark kennedy]

Mr. Kennedy, you seem to have ignored atomweaver's post...

No I haven't, the first one was a joke and the second he just bolded a couple of sections. In response I quoted the article in context that specifically identifies how their approach is different.

Anyway, the reason for the differences in the two measurements (98% and 94%) is because they are effectively different scales. See, the 98% measurement is in reference to each nucleotide that makes up the gene. So out of all the bases in ours and an ape's genetic code, only 2% are different.

I think you need to read the paper because they are talking about birth and death rates for genes. For instance:

Of particular note is the gain of nine genes in the centaurin gamma family (humans have 15 copies, none of the other mammals has more than 7). (Cited and linked above)​

However

The 96% measurement is referring to the whole genes, not the individual nucleotides. From what I've gathered, (somebody correct me if I'm wrong) the differences in nucleotides are spread out across different genes. In other words: a small amount of different nucleotides can make a gene different. This gives the difference in the two measurements. They are both correct. Arguing this would be like me trying to argue that a shrub is one yard high, and you saying that is incorrect because the shrub is actually three feet high. Or if you're in Europe, 1,000 meters and not 1 kilometer.

What we have here is not two kinds of measurements, this is a clear error fabrication. The 96% has been known since at least 2005, if you add up single nucleotide (or base pair) differences the, '98% the same holds'. When you add in the gaps (erroneously called indels because they are thought to have resulted from them) it jumps another 2% to 3% and dwarfs the single base substitutions.

Now when looking just at the genes that are lost or gained they come up with 96%. Of course the highest gain/loss is in the lineage leading from the LCA of chimpanzees and humans.

Ad hominems- 2
Rhetorical devices- 1
Error Fabrication-2

Initial Resident Bombarder - Hespera

 

[mark kennedy]

It is not an ad hom to quote what you said. Review the dictionary.

It's not a substantive point either, it is an obvious attempt at mirroring criticism aimed directly at you.

Are you going to keep a running count of all the name calling you do?

I haven't called anyone names but that's two ad hominems in this post alone.

How about if you just start over, with some data, should you have some, and not start out with all the personal stuff?

I started off with data and have linked to the news article and even the PLoS paper. You would not so much as comment on the 'data' because that's not what you do.

Ad hominems- 5
Rhetorical devices- 1
Error Fabrication-2

Initial Resident Bombarder - Hespera

 

[mark kennedy]

What is wrong with addressing a major portion of your post which was made up of an ad hom attack complaining of ad homs and rhetorical devices? It certainly had me checking my irony meter for damage.

The question is rhetorical and clearly goes in circles. Adding a clutch phrase and reinforcing the Bombardment regardless of the content.

You actually had two replies, one from hespera commenting on your ad hom ad homs, and a second reply from atomweaver deaing with the rest the post. Sound to me like your whole post was covered between the two. Why complain that hespera only dealt with one part?

Exact same thing but since you used it twice I'm counting it twice.

So these 698 genes come from duplicates of existing genes we share with chimps? Doesn't that mean each of these genes is only a small pecentage different from the chimp version?

I cannot find a single use of the word duplicate in the paper, care to expand on that a little?

Ad hominems- 5
Rhetorical devices- 3
Error Fabrication-2

Initial Resident Bombarder - Hespera

 

[Naraoia]

Mark, as you yourself say, estimates of gene number still change by thousands (I've recently heard one that puts our gene number close to that of fruit flies, under 20k). OK, chimps have no orthologues of what, 1500ish human genes? What does that mean if we don't even know how many genes either species has?

Also, I see that these are not singletons, but all members of gene families (the study didn't look at singleton genes at all). They were gained by duplication. Nothing out of the ordinary is going on, it seems. Furthermore, it seems that the number of these duplications is in absolutely the right ballpark as far as "evolutionary" expectations are concerned:

Recent gene duplicates are estimated to have arisen in the human genome at a rate of 0.009 /gene/million years (my) [15]. Using this rate, we would expect there to have been 1,188 new gene duplicates in the human genome since our split with chimpanzee (0.009 duplications/gene/my * 22,000 genes * 6 my). Assuming equal numbers of gene gains and losses and similar rates of turnover in chimps, the total number of genes in humans not present in chimps would be 2,376 (or ~11% of all genes).

(Apparently, rats and mice also differ by thousands of genes (figure 1). Fortunately, nobody cares just how similar the rat and mouse genomes are.)

 

[Naraoia]

I cannot find a single use of the word duplicate in the paper, care to expand on that a little?

Are we not reading the same paper?

 

[Hespera]

I haven't called anyone names but that's two ad hominems in this post alone.

Initial Resident Bombarder - Hespera

So that isn't name calling?

I guess you better start tallying your falsehoods?

 

[PhilosophicalBluster]

No I haven't, the first one was a joke and the second he just bolded a couple of sections. In response I quoted the article in context that specifically identifies how their approach is different.

My apologies, when I began writing that post you had not yet answered him.

I think you need to read the paper because they are talking about birth and death rates for genes. For instance:

Of particular note is the gain of nine genes in the centaurin gamma family (humans have 15 copies, none of the other mammals has more than 7). (Cited and linked above)​

​

I'm not quite sure how that makes my point any less valid. Could you please explain it to me?

What we have here is not two kinds of measurements, this is a clear error fabrication. The 96% has been known since at least 2005, if you add up single nucleotide (or base pair) differences the, '98% the same holds'. When you add in the gaps (erroneously called indels because they are thought to have resulted from them) it jumps another 2% to 3% and dwarfs the single base substitutions.

Now when looking just at the genes that are lost or gained they come up with 96%. Of course the highest gain/loss is in the lineage leading from the LCA of chimpanzees and humans.

Isn't that about what I said?

Ad hominems- 2
Rhetorical devices- 1
Error Fabrication-2

Initial Resident Bombarder - Hespera

Well technically, Hespera was quoting the ad homs made by you... so technically doesn't that make you the 'Initial Resident Bombarder'? And wouldn't 'Error Fabrication' mean making a fake error? That almost sounds like a double negative. Maybe you should just put 'Error' or 'Fabrications' instead, because putting them together is misleading.

 

[Hespera]

Well technically, Hespera was quoting the ad homs made by you... so technically doesn't that make you the 'Initial Resident Bombarder'? And wouldn't 'Error Fabrication' mean making a fake error? That almost sounds like a double negative. Maybe you should just put 'Error' or 'Fabrications' instead, because putting them together is misleading.

Actually, if you want to get technical, I dont think any of us could really be called a "bombarder"

Bombarder definition:
A very large transformer used in the processing of neon electrodes. Typically Available in 7,000 – 15,000 volt models.


Perhaps the intent was to say "bombardier"; but in the face of such as attributing the ad hom not to the person who said it but the one who points it out, it may be a fabricated error and it may not. Its hard to say.

A thread that starts out with name calling, ad homs and falsehoods may have nowhere to go but up. We shall see. Cessation of same would be an excellent start on moving to civil discourse on actual issues.

 

[atomweaver]

Here are two series of three multi-digit numbers:

128-396-2475
128-397-2475

Based on the individual digits, what percentage difference is there between the two series? 1/10, so 10%.

Based upon the whole numbers themselves, what percentage difference is there between the two series? 1/3, so ~33%.

Which answer is correct?

They both are, of course. Excellent post, Skaloop.

The calculations of percentage differences in genomes is similar to that of accounting/bookkeeping in business; depending upon your methodology and your metrics, you can come up with various figures that represent the fiscal (un)health of a company. In accounting, there are generally accepted standards and practices that allow for an understanding of numbers. No such standards exist with respect to comparing genomes, and so the methodology always matters to the latter, even when it is not made explicit.

Mr. Kennedy would take two different "genome accounting methodologies", and attempt to declare one value as false the basis of the results given from the other. Its as ignorant as saying "the Gross Profit of company XYZ is a lie!!!!", because its Net Profit after interest and taxes is so much smaller. Such comments show a general (deliberate?) ignorance of the fact that these are two different calculations... related, but different.

 

[Naraoia]

Now when looking just at the genes that are lost or gained they come up with 96%. Of course the highest gain/loss is in the lineage leading from the LCA of chimpanzees and humans.

I've just spotted this, and I think it's not entirely clear.

The highest of what set, and by what measure? It would be helpful if you clarified this so that detailed knowledge of the paper isn't necessary to know what you mean.

 

[Assyrian]

The question is rhetorical and clearly goes in circles.

Whether it is a rheorical question or not, it made a point that you did not answer. You complained about herspera addressing a major part of your post. I don't see any basis for that, and called you on it, but it was your reply and it was up to you to justify it if you thought it was a good response to her post.

A brief analysis of someones grammatical construction or highlighting techniques is not the same as answering their point.

Adding a clutch phrase and reinforcing the Bombardment regardless of the content.

The 'clutch phrase' does nothing to lessen the irony of you complaining about ad homs in the middle of an ad hom attack on people before they even replied.

Exact same thing but since you used it twice I'm counting it twice.

Ad hominems- 5
Rhetorical devices- 3
Error Fabrication-2

Initial Resident Bombarder - Hespera

Initial? Check the OP. Do you really think this helps your argument Mark?

I cannot find a single use of the word duplicate in the paper, care to expand on that a little?

The researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent.
​