Similarity of human and chimp DNA is down.

[Zaius137]

Loudmouth…

“Why don't you take your own advice. You are the one predicting that none of the unaligned sequence is similar to human DNA.”

Get over it.. because the fact that the chimps genes did not align to human genes as represented in the 2.7Gb/3.1Gb figure. I maintain assumptions can not be made as to their similarity to human DNA, that is unscientific and just opinion. So at most for the time being you cannot assume that these segments align when they do not. At most an 87.5% similarity not the 98.5 similarity, (I believe the lower 62% similarity from the statistical standpoint), not as in the evolution fairytale. I find that the assumption of similarity beyond the science evidence is in fact a biased opinion. This is my last time I deal with you on that subject.

“You are the one claiming that the statistical test is valid. You read it and explain why it is valid.”

Sorry senior not my yob… The author’s validation for his method is his. As a layperson that is not completely ignorant of statistics I can accept it. IMHO

In the rest of your reply I will take it as IYHO… If you want to elevate that assessment you bring up a particular objection and exhaust your understanding of it.

That same old paradigm you have still keeps coming up…

 

[Zaius137]

"In 1998, Carl Woese proposed (1) that no individual organism can be considered a LUA, and (2) that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms.[10]"
Last universal ancestor - Wikipedia, the free encyclopedia”

sfs write that one…

By the way the odds of three universal common ancestors are
1 in 10^3489 times less likely than a single common ancestor. Lets see there are only 10^80 atoms in the estimated known universe… Makes the possibility look rather small unless a Intelligent designer is present.

 

[chris4243]

"In 1998, Carl Woese proposed (1) that no individual organism can be considered a LUA, and (2) that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms.[10]"
Last universal ancestor - Wikipedia, the free encyclopedia”

sfs write that one…

By the way the odds of three universal common ancestors are
1 in 10^3489 times less likely than a single common ancestor. Lets see there are only 10^80 atoms in the estimated known universe… Makes the possibility look rather small unless a Intelligent designer is present.

Who's your most recent ancestor? Your mother, or your father? Do you have a most recent ancestor, or two of them? While bacteria and such don't have sex, they do exchange genes and so they can claim multiple ancestors.

Also, accepting your number of 10^-3489 odds of there being extra common ancestors, that would mean that Creation occurred with only one species and evolved from there.

 

[Loudmouth]

Get over it.. because the fact that the chimps genes did not align to human genes as represented in the 2.7Gb/3.1Gb figure.

Two sequences can share 98% similarity and still be thrown out because of bad alignment. For example, a contig from the chimp genome data could have perfectly matched human sequence, but this contig would have been thrown out if a small subregion of that contig also matched a sequence in a different section of the chimp genome.

Once again, not align =/= not similar.

I maintain assumptions can not be made as to their similarity to human DNA, that is unscientific and just opinion.

What are the assumptions, and why are they unscientific?

So at most for the time being you cannot assume that these segments align when they do not.

That's why they were thrown out. The alignment was ambiguous so it was not used in the comparison to human DNA.

At most an 87.5% similarity not the 98.5 similarity,

The 98.5% is accurate for the sections of chimp DNA that was considered to be accurately sequenced. You still have not given a reason why the other sections of DNA should depart from this number simply because they were poorly read as part of the sequencing process.

(I believe the lower 62% similarity from the statistical standpoint),

Yes, 38% of 30 base pair segments differ by at least 1 base. That is completely consistent with the results listed in the chimp genome paper. That you fail to understand that is your problem, not ours.

I find that the assumption of similarity beyond the science evidence is in fact a biased opinion.

And yet you have no problem pronouncing that 62% similarity is accurate. Go figure.

“You are the one claiming that the statistical test is valid. You read it and explain why it is valid.”

Sorry senior not my yob…

Yes it is. It is your claim. It is up to you to support it. That's how these things work.

The author’s validation for his method is his. As a layperson that is not completely ignorant of statistics I can accept it.

Why do you accept it?

In the rest of your reply I will take it as IYHO…

They aren't opinions. They are facts. You have to get the sequence before you can look for open reading frames. That is a fact.

 

[Loudmouth]

Who's your most recent ancestor? Your mother, or your father? Do you have a most recent ancestor, or two of them?

"Most recent common ancestor" between species always refers to a population, not a single organism. The most recent common ancestor between me and my siblings is my parents. The most recent common ancestor between me and my cousins is the set of grandparents that we share. Surely you understand how this works?

While bacteria and such don't have sex, they do exchange genes and so they can claim multiple ancestors.

They exchange DNA between very divergent species. That is the whole point. Mammals do not. Giraffe DNA does not find it's way into the human genome. Woese correctly argues against a fixed phylogenetic tree at the trunk of life: the split between archae, prokaryotes, and eukaryotes. This in no way puts any doubt as to a common ancestor between humans and chimps. You are taking things WAY out of context.

 

[Naraoia]

I will point to the authors own description of his method:

"For the benefit of readers, I’ll briefly recapitulate the simple comparison algorithm used in my previous test. 10,000 different sequences, each composed of 30 consecutive DNA bases (possible values: A, T, G and C) were randomly selected from chromosome N of genome A. A search for a matching pattern was then performed on the corresponding chromosome N of genome B. A pattern match was deemed to occur only when all 30 base pairs coincided perfectly . . ."

You know what occurred to me?

That for "the corresponding chromosome" to exist in the other genome, they have to be really quite similar.

Just did a bit of looking around on Ensembl, and it appears that human chromosome 1 already has four (well, three and a bit) "corresponding chromosomes" in marmosets. According to this database, only seven out of the 24 distinct human chromosomes map to a single marmoset chromosome (incidentally, the Y chromosome isn't among them). I didn't check the other way round, but some of those are certainly not reciprocal one-to-one matches - see how the chunk corresponding to human chr22 is basically just one end of marmoset chr1.

And we haven't even left the primates.

 

[Zaius137]

Well chris4243 one common UCA is not enough.
The idea of three common ancestors did result from new findings in genetics. We can not come from a single common ancestor. It is amazing what the new evolutionist will believe. There initial arguments always sound so reasonable but when you look closer and really study what they are saying the science always proves them wrong.

Here is the quickest link to look at but there are many more articles.
http://en.wikipedia.org/wiki/Last_universal_ancestor#cite_note-discnews-3

Sorry I have “Wiki” on the brain and linked to it unwillingly.

Here is the link I wanted to use…
http://www.evolutionnews.org/2010/11/douglas_theobald_tests_univers041021.html

 

[USincognito]

The fact that you're citing a C/IDer cite to try and attack the facts in peer reviewed science is almost humorus.

 

[Loudmouth]

Well chris4243 one common UCA is not enough.
The idea of three common ancestors did result from new findings in genetics. We can not come from a single common ancestor. It is amazing what the new evolutionist will believe. There initial arguments always sound so reasonable but when you look closer and really study what they are saying the science always proves them wrong.

We are not discussing the last UNIVERSAL common ancestor. We are talking about the much more recent common ancestor between chimps and humans. Your post is nothing more than a red herring.

 

[Zaius137]

But can you change a monkey into a man.
Let’s talk deleterious mutation rate in chimp and human divergence.

I would like to take up an article by Eyre-Walker & Keightley in Nature magazine.
Eyre-Walker & Keightley, High genomic deleterious mutation rates in hominids, Nature 397, 344 - 347 (1999)

Their proposition basically assumed so may millions of years from a common ancestor of a hominid and so many mutations per generation it would take to achieve a man. Using their numbers, they came up with a number for favorable mutations needed per generation and a number of unfavorable mutations that would be a normal consequence. .

(Their unfavorable number): We will call it U= 1.6 mutations per individual per generation.

Let’s take a quick look at what this number tells us and calculate a number of offspring from a female needed to just maintain a population to a normal level.

B= birth threshold (the number to calculate being the offspring needed per female to maintain a population).

U= Harmful mutation rate (their number).

e^-U is the Poisson distribution in Biology.

An unadjusted number of offspring needed to maintain a population would be 2 (one for the female one for the male).

The adjusted number would then be: B=2e^U

And plugging in the numbers gives:

B=9.9 offspring. So a Hominid female would have to produce 10 offspring just to maintain a level population and this over millions of years. This is absurd… and the numbers get worse if you get real with the evidence. Such as findings that the DNA of Chimps is only 94% instead of 99% the same as Humans and that the oldest Chimp fossil ever found was 520k years old. The “U” is more likely greater than 3. A number of U=3 gives 40 offspring per female.:o

 

[Blayz]

But can you change a monkey into a man.
Let’s talk deleterious mutation rate in chimp and human divergence.

I would like to take up an article by Eyre-Walker & Keightley in Nature magazine.
Eyre-Walker & Keightley, High genomic deleterious mutation rates in hominids, Nature 397, 344 - 347 (1999)

Their proposition basically assumed so may millions of years from a common ancestor of a hominid and so many mutations per generation it would take to achieve a man. Using their numbers, they came up with a number for favorable mutations needed per generation and a number of unfavorable mutations that would be a normal consequence. .

(Their unfavorable number): We will call it U= 1.6 mutations per individual per generation.

Let’s take a quick look at what this number tells us and calculate a number of offspring from a female needed to just maintain a population to a normal level.

B= birth threshold (the number to calculate being the offspring needed per female to maintain a population).

U= Harmful mutation rate (their number).

e^-U is the Poisson distribution in Biology.

An unadjusted number of offspring needed to maintain a population would be 2 (one for the female one for the male).

The adjusted number would then be: B=2e^U

And plugging in the numbers gives:

B=9.9 offspring. So a Hominid female would have to produce 10 offspring just to maintain a level population and this over millions of years. This is absurd… and the numbers get worse if you get real with the evidence. Such as findings that the DNA of Chimps is only 94% instead of 99% the same as Humans and that the oldest Chimp fossil ever found was 520k years old. The “U” is more likely greater than 3. A number of U=3 gives 40 offspring per female.:o

I agree. The paper is indeed absurd. Well done.

Says nothing about evolution, of course, but that's what happens when you critique a paper from 1999 which is years before the human genome or chimp genomes were published, and contains a whole bunch of wildly inaccurate assumptions, like this one:

Mammals are estimated to have a minimum of 60,000 genes

And of course, let's not forget that the entire analysis was based on

our entire sample of 46 genes, which together contain 41,471 nucleotides

Once again, all you have done is proven that this is a crap paper.

I will also take this opportunity to again point out that that actual author of the uncommon descent paper has admitted his 30BP method results in a >98% similarity between chimps and humans. This means that there is only one person on the entire planet that conflates the 62% number from that paper, and that is you, Zaius.

Finally, e^-U generates an exponential decay function. It is not the poisson distribution, in biology or indeed any other branch of science.

 

[cupid dave]

Recent laboratory tests in Russia have shown that Foxes can become dog-ike in only a couple of generations, based upon hormonal changes at first, due to emphasis on emotional intelligence, like the reaction they naturally have to Fear, for example.

This work is claimed to support the theory that wolves became dogs 20,000 years aho as the chinese gradully domesticated the less fearful subjects willing to live closer to the humans.


http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4FF20DD-P&_user=10&_coverDate=02%2F08%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=139aabb18e9d2da08c2c7d15be92ac6c

 

[Loudmouth]

Their proposition basically assumed so may millions of years from a common ancestor of a hominid and so many mutations per generation it would take to achieve a man.

Let's do some calculations of our own. If you don't object, let's use a mutation rate of 100 substitutions per individual per generation, a 25 year generation time, 5 million years since common ancestry, and a steady population of 100,000. Does that sound okay to you? Indels are a bit tougher to model, so we will leave them out for the time being.

At 100 substitutions per individual this comes to 10 million (1E7 in shorthand) mutations per generation. We also have a new generation every 25 years. This comes to 5E6/25 generations since common ancestry, or 200,000 generations. So we have 2E5 generations with 1E7 mutations per generation which comes to 2,000[SIZE=-2] 000,000,000 (or 2E12 in shorthand) total mutations that have occurred in our lineage since common ancestry. That's 2 trillion mutations.[/SIZE]

Now let's look at the difference between the human and chimp genomes. That difference (again, looking at just substitutions for the time being) is 35 million substitutions. If we split half of those differences into each lineage then we are looking at about 17 million mutations needed to get from our common ancestor with chimps to us. That is 17 million out of hte 2 trillion that did occur, or just 0.00085% of the mutations that occurred. That is right. Just 0.00085% of the mutations that did occur were needed. Can you explain to us how this is a problem for evolution?

 

[Loudmouth]

Recent laboratory tests in Russia have shown that Foxes can become dog-ike in only a couple of generations, based upon hormonal changes at first, due to emphasis on emotional intelligence, like the reaction they naturally have to Fear, for example.

This work is claimed to support the theory that wolves became dogs 20,000 years aho as the chinese gradully domesticated the less fearful subjects willing to live closer to the humans.

What does this have to do with the comparison of the human and chimp genomes?

 

[Zaius137]

Blayz…

“Finally, e^-U generates an exponential decay function. It is not the Poisson distribution, in biology or indeed any other branch of science.”

Yes it is the poisson distribution assuming zero occurrences on a given interval (P(0)). If you use the identity I specified it will show occurrences on that interval (P(x)). Look it up for yourself.

“I will also take this opportunity to again point out that that actual author of the uncommon descent paper has admitted his 30BP method results in a >98% similarity between chimps and humans. This means that there is only one person on the entire planet that conflates the 62% number from that paper, and that is you, Zaius.”

And the author does maintain 62% of locating matches between two chromosome comparisons as does the secular view of only differing by 4% would (96% similar). See my previous assessment. See post #137 in this thread.

“I agree. The paper is indeed absurd. Well done.”

Well this paper is peer reviewed and carries with that some authority to this date.

 

[Zaius137]

Loudmouth if you really want to take a stab at the real argument …. Here is a clue…. Synergistic epistasis. By the way my examples are a synthesis of scholarly work reduced to my simple understanding. If you want to take them up properly look up the scholarly arguments please.

 

[Zaius137]

Blayz,
This came from my notes... I don't know where it comes from Originally or if the link even exists anymore.

Application of possion distribution.
Note also that the only variable needed to generate these distributions is m, the average occurrence/interval. Moreover, in biology situations often occur where knowing the probability of no events in an interval P(0) is useful. When a = 0, equation 1 simplifies (Full equation) to:

P(a)=e^-m​

For example, we might want to know the fraction of uninfected cells for a known average (m) multiplicity of virus infection (MOI). Other times, we need to know the average mutation rate/base pair, but our sequencing determines nearly all wild type sequence, P(0). In each case, if we can determine either m or P(0), we can solve for the other.

 

[Loudmouth]

Loudmouth if you really want to take a stab at the real argument …. Here is a clue…. Synergistic epistasis. By the way my examples are a synthesis of scholarly work reduced to my simple understanding. If you want to take them up properly look up the scholarly arguments please.

What does this have to do with the percent similarity between human and chimp DNA?

 

[Blayz]

And the author does maintain 62% of locating matches between two chromosome comparisons as does the secular view of only differing by 4% would (96% similar). See my previous assessment. See post #137 in this thread.

This is word salad. So let's go back to your original assessment in #137

I believe that I made a point from the “Wiki”, "Chimp Genome" and also the "Uncommon Decent" analysis agreed with similar divergences.

Correct.

It is just which one you can accept; either the evolution viewpoint or the statistical viewpoint.

But one sentence ago you admitted they agree. Who cares which you accept when they both say the same thing?

There is also peer reviewed documents that support a 4% divergence which gives the exact figure in the uncommon decent article of 62%.

And here we are, saying they are the same, again.

But the Uncommon decent article does show only a 62% statistical similarity.

It says no such thing. It says 62% of 30BP segments have 100% identity. Which as you have already agreed equates to >98% similarity.

Any way you look at it the estimate between 96% and 99% is just a fairy tale.

Which is supported by the Uncommon descent paper you keep harping on about.

It really is word salad. In one sentence you agree that 62% 30BP match is the same as >98% similarity, and in the next sentence you call it a fairy tale. You agree the two methods are identical then say you can choose which to accept.

“I agree. The paper is indeed absurd. Well done.”

Well this paper is peer reviewed and carries with that some authority to this date.

Nope, it really doesn't. It stops carrying authority the moment it is proven wrong. For this paper, that was 2001. Remember, it's creationists that seem to think famous people have important opinions, scientists care about the data.

 

[Zaius137]

“It says no such thing. It says 62% of 30BP segments have 100% identity. Which as you have already agreed equates to >98% similarity.

“It says no such thing. It says 62% of 30BP segments have 100% identity. Which as you have already agreed equates to >98% similarity.

“It really is word salad. In one sentence you agree that 62% 30BP match is the same as >98% similarity, and in the next sentence you call it a fairy tale. You agree the two methods are identical then say you can choose which to accept.”

First of all I used the 96% assessment not the 98% assessment in the chimp sequencing paper. The 98% gives a statistical match of 62.5%. 94%-95% is given in the following article…

http://www.nature.com/news/2003/030428/full/news030428-3.html

My point is that there is a statistical match in the Uncommon Decent article giving it credibility in its method. When taken segment on segment you only find they are an exact match 62.5% of the time, I maintain you can not call two genomes 98% equivalent if they do not compare segment for segment 98% of the time; the 98% conclusion in the chimp paper is just a bogus evolution fairytale. The problem is that the evolutionist is being misleading in an accurate Interpretation.

By the way the Uncommon Decent analysis used the pre-aligned segments of the chimp genome study from the Web and of course statistically they better match. But how on earth do you get from 98% similar to the real statistical value of 62.5% similar?

Now the evolutionists are further compromised by ignoring the fact that only 2.4Gb of the human 3.1Gb aligned at all. 2.4/3.1 ~ 77%. Sorry but this 23% of the genome can not be ignored. Try ignoring 23% of the book “Huckleberry Finn” and see if you get the same reading.

“Due to the fragmentary nature of the sequence, researchers were only able to align about 2.4 Gb of high quality DNA sequence (about 80% of the human genome). They found that nucleotide mismatches over the whole alignment totaled ~35 million and averaged 1.23%.”

And get this… go ahead and drop or add single nucleotides to increase alignment though coding entry points are all important… I also pointed that fact out early on.

“In addition to mismatches, the chimpanzee and human genomes also differ in their lengths. When aligning any two sequences, it is occasionally necessary to insert or omit a nucleotide (or more) in order to maintain the best alignment.”

http://documents.clubexpress.com/documents.ashx?key=u4FIU0eLuT6SmyXcvLmbCiFa4UnoWsTP3lyArVOo/gM=

The evolution evaluation is nonsense….

"Nope, it really doesn't. It stops carrying authority the moment it is proven wrong. For this paper, that was 2001. Remember, it's creationists that seem to think famous people have important opinions, scientists care about the data. "

By the way arguments against a published work is considered criticism and because they get criticism that does not mean they are wrong.

I think scientists, at least some, care about truth also.