Gene Number Changes Between Humans and Chimps

[mark kennedy]

Some follow up questions for you mark:

Lead on my man!

Do you understand the difference between a nucleotide and a gene?

The four nucleotides that make up the two combinations of base pairs (CG and AT) are what make up the DNA strains in all life.

Do you understand why measurements of the differences of nucleotides would be different from measurements of the differences of genes?

Of course, a single nucleotide substitution would be part of a sequence while genes lose or gain would includes sequences of base pairs that could go on for possibly thousands of base pairs.

Do you understand this:

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?

Neither, you are looking here at a single substitution. The rate of substitution would be 1 in 10 and either synonymous or non-synonymous depending on how it effected the whole sequence.

If we were comparing apples to apples and clearly we are not, the substitution, in the open reading frame of a protein coding gene, would most often result in a truncated protein. This is due to a stop codon being inserted causing a frameshift.

"In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated (in S phase of the eukaryotic cell cycle). Most of these changes are quickly repaired. Those that are not result in a mutation. Thus, mutation is a failure of DNA repair".​

Mutations

Now I have a question for you, do you know when a gene duplication is not a mutation? There is no orthodox answer anymore then there is one for the thought provoking one you copied to the post.

 

[Nathan45]

Mark, you posted a lot of stuff, but none of it is related to my post. I don't think you actually understand the difference between a nucleotide and a gene.

Do you understand the difference between a nucleotide and a gene?

Four nucleotides made up the two combinations of base pairs (CG and AT) are what make up the DNA strain.

That does not answer my question.

a gene is "a segment of nucleic acid that, taken as a whole, specifies a trait" Gene - Wikipedia, the free encyclopedia

Your quote of 94% of genes being identical between chimps and humans, is an apples to oranges comparison of other scientist's estimates of 98% of nucleotides being identical between chimps and humans. This was made clear in the article that you cited in your original post.

Simply put, there are a lot of nucleotides in most genes. The fact that you'd come up with a different percentage measuring nucleotides than genes in unsurprising, because some of the genes that are different between chimps and humans, may share some % of the same nucleotides... so even though the genes are different, some of the nucleotides that make up the different genes are the same.

and the rest of your post has nothing to do with the topic at hand.

 

[mark kennedy]

Mark, you posted a lot of stuff, but none of it is related to my post. I don't think you actually understand the difference between a nucleotide and a gene.

Oh but I do Nathan. There are four nucleotides that are joined together in base pairs and those base pairs come in threes, that is in protein coding genes.

Now there are other kinds of genes but I know the difference between nucleotides and genes.

That does not answer my question.

A gene is not a DNA strand, a gene is "a segment of nucleic acid that, taken as a whole, specifies a trait" Gene - Wikipedia, the free encyclopedia

It was not a real question. A protein coding gene in triplet codons specifies an amino acid sequence that specifies a protein, not a trait.

Your quote of 94% of genes being identical between chimps and humans, is an apples to oranges comparison of other scientist's estimates of 98% of nucleotides being identical between chimps and humans. This was made clear in the article that you cited in your original post.

No, there is a big difference between a single base or nucleotide substitution and a gene loss or gain. That is what you failed to understand about the OP.

Simply put, there are a lot of nucleotides in most genes.

No there are only four nucleotides and two base pairs. It's not in most genes, it's in all of them.

The fact that you'd come up with a different percentage measuring nucleotides than genes in unsurprising, because some of the genes that are different between chimps and humans, may share some % of the same nucleotides... so even though the genes are different, some of the nucleotides that make up the different genes are the same.

and the rest of your post has nothing to do with the topic at hand.

When you finally get to the point where you understand the difference between the single base or nucleotide substitution rate as compared to gene loss or gain we can discuss the importance of the paper.

Look, I know what you are trying to say and your right in a way. What you don't seem to realize is that because there are only four nucleotides that make up all of life there will always be a 25% homology based on nucleotide sequences. The point of the paper is that there are gene losses and gains and until we get to that I think we are just talking in circles.

I really don't like to do this but that is nothing more then an error fabrication

Ad hominems- 6
Rhetorical devices- 4
Error Fabrication-3

There is a substantive point to be made if and only if you can identify how the nucleotide substitution rate differs from the gene loss and gain measurement of the paper cited, quoted and linked in the early posts of the thread.

Pardon the run on sentence but it was vital to clarify the distinction.

Have a nice day
Mark

P.S. Do note that you didn't even try to answer my question. 'Now I have a question for you, do you know when a gene duplication is not a mutation'? Your silence on the primary topic of the thread speaks volumes for the deleterious effects of fallacious lines of reasoning used by evolutionists on this board.

 

[Nathan45]

Look, I know what you are trying to say and your right in a way.

Then you admit, it is correct "in a way" to say that the genomes (based on nucleotides) between chimps and humans are 98% identical. I don't see what this post is for.

What you don't seem to realize is that because there are only four nucleotides that make up all of life there will always be a 25% homology based on nucleotide sequences.

The difference between 25% homology and 98% homology is hugely significant, especially when there are so many nucleotides. And the number is far less arbitrary than basing it on genes, because to identify a gene, you either need to know what a strand of code does or infer the number of genes in a strand through statistical methods (they were doing the later in the paper you quoted). With nucleotides, you can calculate the difference without actually knowing what the code does, therefore it's a much less "fudgeable" (if that's a word) estimate. I don't put any stock in the number of "genes" scientists estimate humans have, and as you point out the estimate keeps changing, however the number of nucleotides is right there for everyone to see.

 

[mark kennedy]

Then you admit, it is correct "in a way" to say that the genomes (based on nucleotides) between chimps and humans are 98% identical. I don't see what this post is for.

That is absurd in the extreme. The Chimpanzee Genome Consortium's comparison of Initial sequence of the chimpanzee genome and comparison with the human genome, conclusively proved otherwise. The only way you get 98% is if you ignore the indels:

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90 Mb. This difference corresponds to ~
3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions. (Nature 2005)​

The difference between 25% homology and 98% homology is hugely significant, especially when there are so many nucleotides.

There are only four nucleotides...are you kidding me.

And the number is far less arbitrary than basing it on genes, because to identify a gene, you either need to know what a strand of code does or infer the number of genes in a strand through statistical methods (they were doing the later in the paper you quoted). With nucleotides, you can calculate the difference without actually knowing what the code does, therefore it's a much less "fudgeable" (if that's a word) estimate. I don't put any stock in the number of "genes" scientists estimate humans have, and as you point out the estimate keeps changing, however the number of nucleotides is right there for everyone to see.

Direct comparison of nucleotides will get you 96%. Direct comparison of genes will get you 96% according to two peer reviewed scientific papers that represent enormous scientific effort and expertise.

Here's the point Nathan, you don't have one. It's late and I'm going to bed and I have to admit that I am very disappointed that you let me set you up so easily.

By the way, saying that based on nucleotide sequences or gene comparisons we are 98% the same as chimpanzees is either an expression of ignorance or deception. In your case I give you the benefit of a doubt and assume the former.

Good night Nathan

Grace and peace,
Mark

 

[AV1611VET]

Pluto?.... who cares? really

It's not so much Pluto, as it is the unanimity here in regards to its demotion.

But, 96% DNA similarity with chimps. Now that's pretty important.

And I'll make the same point as I do with those who say 98% --- that 4% represents a barrier that nature cannot cross.

 

[AV1611VET]

Like creationists here correct themselves?

It is wrong for creations to go vis-a-vis in a public forum.

How many times have I had to correct you and others here, when you refer to"God's Word," instead of your interpretation of scripture?

As I have stated before: I'm not going to preface everything I say with, "In my opinion..."

You guys don't do it, and neither do I.

I think you like bringing up Pluto. You forgot to mention the Space Shuttle and Thalidomide.

The Space Shuttle and Thalidomide don't apply.

Among astronomers, yes. How many astronomers post here? None.

It doesn't matter how many astronomers post here --- that's not the point I'm making.

The point is --- you guys --- are the ones who automatically agreed 100% (and probably still do).

 

[AV1611VET]

Personally I would prefer to substitute the term 'variation' but they thrive on ambiguity

Thriving on ambiguity since 1859!

Personally, I would have used another term, but Mark is more of a gentleman than I am.

 

[AV1611VET]

And AV, for the 1000th time, the designation of pluto as a "Dwarf" planet or a "Planet" is a question of vocabulary not a scientific question. Before, "Planet" didn't have any good definition other than simply being a hardcoded list of 9 planets.

the problem is that they kept finding objects that were like pluto (example, example) and they theorized that there would be hundreds of similar objects, so they had to define "planet" as excluidng pluto or else they'd be liable to call all those other objects "Planets" too, meaning there are actually hundreds of "planets".

The question of whether pluto is a planet or not is not really a scientific question. It's a question of vocabulary. whether you label pluto a planet or a dwarf planet it's still the same as it was before. Nothing changed about our knowledge of pluto when they re-labeled it a dwarf-planet.

This has nothing to do with the point I made.

My point deals with statistics, and in fact, is not even [directly] related to the subject of astronomy.

 

[Assyrian]

Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences The Evolution of Mammalian Gene Families

Direct comparison of nucleotides will get you 96%. Direct comparison of genes will get you 96% according to two peer reviewed scientific papers that represent enormous scientific effort and expertise.

So is there a 1.5 % difference between orthologous nucleotide sequences or isn't there?

You seem to be arguing that the numbers are wrong, that a second method of comparison giving a different number means the first number is wrong. But that does not follow when both methods measure different things. The question should be which is the best method for comparing two genomes?

Clearly creationists will prefer whatever method gives the smallest number, but is it the best way to compare the sequences? A simple nucleotide by nucleotide comparison that ignores the fact that a thousand nuclotides can be changed in a single indel, treating them exactly the same as a thousand single nucleotide mutations, is hardly a good way to compare the two sequences.

When I was a teacher I would sometimes be given essays that were clearly copied from each other. But you don't find the copied essays with a word by word comparison of the whole essay. The copied version could often leave out whole paragraphs and throw in a different introduction or conclusion. Word for word, the two essays might only be 50 or 60% similar. But it is the orthologous paragraphs and sentences that give them away. These were often 98 or 99% similar, with spelling errors or missing words accounting for the difference betweeen the passages.

Which is the best way to copare the essays? The 50% word by word comparison, or the 98% orthologous passage comparison?

 

[Naraoia]

So tell me Mark... is the glass 94% full, or 6% empty? How about explaining the 94% commonality in total genes between humans and a completely unrelated animal that lives in trees?

I like that angle.

I have also noticed this use of semantics or twisting statements on behalf of you and your cohorts. I am glad to see one of you admit it. In fact, I have previously posted a more inclusive list of common creationist skills. Here it is again for your benefit:

Can we please be constructive and return to comparative genomics?

Mark, even if you were correct in your interpretation of these results, so what? 98% or 92%; either way, it's a significant similarity. Especially if these are allegedly separately created creatures that need not have any similarity at all.

It's like with the age of the universe arguments many YEC followers use; "Oh, they say 15 billion years old, but even they admit they could be wrong by a billion years!" It's still well beyond the ~6000 years they bring up.

Word.

I think some of it has to do with what you consider a gene, of course the most important (arguably I guess) are the protein coding genes. The most current count I could find was 20,488 genes but the jury is still out on non-coding RNA.

AFAIK, finding protein-coding genes is also less than straightforward.

These are not genes changed but lost and gained.

So? It's not like gene duplication/loss are rare events.

How many genes are missing between members of the Pan or Gorrilla genus?

I have no idea. Is the gorilla genome even sequenced? (Oops, it seems it is, though still a very rough draft) It's kinda hard to do this kind of analysis without a complete annotated genome sequence, I'd think. And... why is that important again? (You might as well look at rats and mice, since they are compared in the same study and also miss a large number of genes between them.)

I wouldn't expect the difference to be a lot more than between humans and chimps, though, given that gorillas are thought to have branched off only a short time before the human-chimp split, and we had some acceleration after that node.

What do you mean nothing unusual when the name of the paper is 'Accelerated rate of gene gain and loss in primates'?

What I mean is that accelerated evolution is not unique to our own lineage, and I've seen no indication that the gene gain/loss rates involved are impossibly high.

That's not unusual? Bear in mind that 2 mya our supposed ancestors still had chimpanzee size skulls and had just started their threefold expansion of their cranial capacities.

Which, as we've seen in another thread I hope you remember, (1) was gradual all the way from late australopithecines to H. sapiens and neanderthalensis, and (2) only involved a tiny increase each generation.

What's the connection between the blown up human brain and the differences between the human and chimp genomes anyway? (Apart from the fact that, if I recall the genome study correctly, many families that expanded in humans are nervous system-related.)

 

[Naraoia]

Neither, you are looking here at a single substitution. The rate of substitution would be 1 in 10 and either synonymous or non-synonymous depending on how it effected the whole sequence.

How does that mean that two 10-character long strings that differ at one position are not 10% different when compared at that level?

(BTW, it's affected. To effect something is to cause something to happen.)

If we were comparing apples to apples and clearly we are not, the substitution, in the open reading frame of a protein coding gene, would most often result in a truncated protein. This is due to a stop codon being inserted causing a frameshift.

Sorry, this is just wrong.

A frame shift is, well, a shift in the reading frame. That is, codons start in different places than they did before. A substitution (exchanging one base for another) will not cause a frame shift unless it happens to create a start codon "out of phase" with the original reading frame or something - and then only if the new start codon is actually used as a start, which it'll most likely not be unless it's very close to the "real" start and surrounded by the right stuff, from what I've learnt about translation.

Sure, substitutions can create premature stop codons, but not by frame shift. I also doubt that that would be the most common result of substitution, since there are only three stop codons as opposed to 61 "sense" codons. There are simply many more ways for a non-stop codon to mutate into another non-stop codon.

Indels, on the other hand, do cause frame shifts if their length is not a multiple of three. Incidentally, what you've illustrated with that nice picture is this, not substitution, and in its original location, the image specifically illustrates indels.

Now I have a question for you, do you know when a gene duplication is not a mutation?

Uh... I thought any change to DNA sequence was a mutation

 

[Hespera]

This is all you will do in this thread because, well...it's all you do. Do note the constant use of the pronoun 'you' and the absence of anything remotely substantive or on topic.

Ad hominems- 6
Rhetorical devices- 3
Error Fabrication-2

Actually I can do way more than point out how you don't restrict yourself to the truth, but then, others are dealing well enough with the "substance" of your ideas.

The thing is, you are like "dad" in that you think you have hit upon some idea that will invalidate evolution. His is that science can't prove to his satisfaction that there was a "same state past". Yours is more nebulous, but it involves an amateur's misunderstanding of genetics and math. Both of you try to bolster your arguments with an aggressive, overwrought writing style.

Unfortunately for both of you, the very bias of which you accuse others precludes your ever seeing anything but what you want to see. Your arguments are further weakened by a bombastic writing style which is made laughable by inept use of English.

Now, as I said, others are doing fine trying to point out where you are wrong in your assessment of the origins of H. sapiens. I think its a complete waste of time to do that. You wont ever accept that you are wrong.

Actually, it was a kind of test I ran on you, when I called you on your canard about how every chimp fossil that is dug up is immediately classified as human / human ancestor.

Your response could have been to say, honestly, that it was an exaggeration to make a point. Fair enough, as a rhetorical device, though it isnt much of a way to advance a serious discussion. Instead, first you defended it as true, then changed it a bit and defended that. Now your version of it is that I twisted your words (another falsehood). There was no need to twist anything, and I didn't; your words speak fine for themselves.

The statement was as untrue as 2+2=5, but having made it, you have to stick to it. (why is that?) Then, you call me a name (amusingly misspelled, but still name-calling) and say you didnt call names, all in one post. Call you on that, and you ignore the substance, as you always accuse others of doing, and try to turn it around on me. (why cant you admit that you do name- calling?)

Anyway, I dont see any point it addressing the rather complex subject of the post as long as you continue to be unwilling to admit to error in even the simplest and most obvious things.

 

[Split Rock]

So tell me Mark... is the glass 94% full, or 6% empty? How about explaining the 94% commonality in total genes between humans and a completely unrelated animal that lives in trees?

Rhetorical device, with this kind of question no satisfactory answer is expected, possible or ever accepted. It's hopelessly circular.

There was nothing at all rhetorical or circular about my question. While I did not expect a satisfactory answer from you, I was willing to hear one. Clearly, you have no answer. Neither does any other creationist. Of course, we have an answer... you just don't like it. The genetic similarities between us and chimps are because we are closely related species. Just as the genetic similarities between a father and son indicate genetic relatedness.

 

[mark kennedy]

And I'll make the same point as I do with those who say 98% --- that 4% represents a barrier that nature cannot cross.

It certainly can be but my thing is this. If they make the argument that we must be related because you are so close genetically and then it is found that we are actually three to four times more different, doesn't that argue against common ancestry?

Now if they want to make the argument that we did evolve from ape ancestors then the molecular mechanism for the adaptive evolution required is key. They use variations of Darwin's theme of natural selection and when genes show huge differences they just call it accelerated evolution or positive selection. With no directly observed or demonstrated mechanism you have an a priori (without prior) assumption.

There are limits but they want to differ to time what is rightfully attributed to the Creator.

Grace and peace,
Mark

 

[Skaloop]

It certainly can be but my thing is this. If they make the argument that we must be related because you are so close genetically and then it is found that we are actually three to four times more different, doesn't that argue against common ancestry?

Now you're playing number games by switching reference points. Three to four times more different? How about only four to five percent less similar? Same numbers used, different implicated significance.

I am 6-feet tall. I have a friend who is 5-feet tall. I have another friend who is 4-feet tall. Saying that my second friend is, relative to me, twice as short makes no sense. Saying she is two-thirds of my height does.

And still, whether it's 98% or 94% or even as low as 80%, that's still 98/94/80 percent more than would be expected if the two creatures were created separately and individually by an entity who can do anything.

 

[atomweaver]

It certainly can be but my thing is this. If they make the argument that we must be related because you are so close genetically and then it is found that we are actually three to four times more different, doesn't that argue against common ancestry?

You still ask that question, as if there actually were only one method for measuring genetic similarity.

Here are ten numbers;

12, 10, 8, 6, 10, 11, 14, 11, 7, 12

Is the average of these numbers the mean; 10.1, the median; 10.5 or the mode; 11?

Your correct answer should be "that's a trick question, atomweaver, there are (at least) three different ways you can mathematically determine the average of a set of numbers. Mean, median, mode; each is an average, but none of these choices precludes the others from being mathematically correct." It seems like Mark has decided in advance that those calculations of genetic similarity which distance humans from chimps are more correct than other calculations. But this is as absurd as saying that the mean, above, is more correct than the median or mode.

 

[Hespera]

You still ask that question, as if there actually were only one method for measuring genetic similarity.

Here are ten numbers;

12, 10, 8, 6, 10, 11, 14, 11, 7, 12

Is the average of these numbers the mean; 10.1, the median; 10.5 or the mode; 11?

Your correct answer should be "that's a trick question, atomweaver, there are (at least) three different ways you can mathematically determine the average of a set of numbers. Mean, median, mode; each is an average, but none of these choices precludes the others from being mathematically correct." It seems like Mark has decided in advance that those calculations of genetic similarity which distance humans from chimps are more correct than other calculations. But this is as absurd as saying that the mean, above, is more correct than the median or mode.

He has decided in advance how this whole subject has to come out, based on how he interprets the bible.

Its too bad, because enthusiastic amateurs often enough make real contributions to science. Maybe he will yet; lets hope so.

Of course, one of the first thing a researcher has to be able to do is look at data objectively, and to always be prepared to recognize / accept that they are wrong about something.

As per my exchange with MK, he seems incapable of conceding he is ever wrong about anything, so his chances of ever doing any worthwhile research is very limited.

 

[BananaSlug]

Meh, I had a fun discussion with him in another thread. I'm wary about starting another one for fear of it getting erased during another format change. Plus spending 3 hours to refute a single post gets annoying.

Last thing I can remember saying is I find it funny that he cannot accept a 200cc increase from H. habilis (612) to early H. erectus (~800) but he can easily accept a 600cc increase from early H. erectus to modern H. sapiens.

 

[Hespera]

"Plus spending 3 hours to refute a single post gets annoying. "

Cast not thy pear;s?