98.77% Wrong

I thought they had the Fig Newton of informational type stuff on their side. Can't he perform the irreducibly complex calculations that are required?

How do they explain the one-to-one correspondence between chimp and human chromosomes and bands? Do they have a twisted calculation for that? How do they explain all of the other genetic data such as SINE insertions and mitochondrial DNA? Let me guess...

The comparison I performed was completely different from those usually performed by geneticists, because was purely statistical in nature.

What percentage of the total genome of both chimps, and humans have been compared against each other?

IBelieveInGod said: What percentage of the total genome of both chimps, and humans have been compared against each other?

I'll also point out that one does not need to look at all 3 billion or so bases to estimate a divergence on the scale of 1.25%. Even with 12,000 bases (which is low given modern data), the potential error of my estimate was 0.2%. Thus from my data the net divergence between the species is nearly certain to be between 1%-1.5%.

However, if the two genomes were really 95% similar or more, as is commonly claimed, also a 30BPM statistical test should produce 95% results, and it does not.

What's new about an epic fail?

Any argument put froward by ID or YEC is an epic fail. All are

IBelieveInGod said: What percentage of the total genome of both chimps, and humans have been compared against each other?

And hey, guess what?

If instead of comparing only 30 nucleotides, you compare all (approx.) 3,000,000,000 nucleotides in our genomes, the identity is zero!

By Jove, this mathemajigger has disproved evolution! Praise be to the pink unicorn!

IBelieveInGod said: What percentage of the total genome of both chimps, and humans have been compared against each other?

The error is shockingly crude and childish. The person behind "niwad" is a dolt.

I will break it down to an even simpler analogy.

Imagine two equal length sequences of symbols.

One consists solely of "A"'s. It looks like this "AAAAAAAA....."

The other is 99% A's, but 1% B's. The exact location of the individual B's is not predictable.

A strand of it might look like this "ABAAAAAAAAAAAAAAAAAAA..."

Any dunce can see that if we examine long enough segments, the sequences will be 99% identical. That is, 99% of the time, the symbol at position "n" in the first strand will be identical to the symbol at position "n" of the second strand.

Most people can also see, however, that probability of a sequence of length "m" chosen from one being identical to the same position, same length sequence from the other is (0.99)^m.

Let's imagine a truly asinine person who wants to argue against "the strands look similar theory" for ideological reasons.

He could randomly sample segments of length "m" from either strand and see if they had the exact same sequence as the same position, same length segment from the other strand.

The larger an arbitrarily chosen "m" becomes, of the course, the lower the probability that the entire sampled sequence will be identical between the two.

This is exactly what niwad has done, using m = 30.

To put it another way, his argument is exactly the same as arguing that two equal length series of coin flips will on average be 50% identical, because any given sequence of thirty coin flips has a less than 50% chance of being identical to the next series of thirty coin flips.

I am shocked -- shocked! -- to discover that "nirwad" has made what he believes to be a major innovation in how we compare genomes to quantify difference, has applied it to actual data, but yet failed to submit this breakthrough to a peer-reviewed journal for publication.

Another opportunity to build the scientific infrastructure for ID squandered through an abysmally bad research and publication strategy. It's almost like they don't really want knowledgeable review of their work ...

And of course by "nirwad" I meant "niwrad". My deepest apologies for misspelling the pseudonym.

With all the sincerity I can muster,

SWT

eric said: (in part of a response to trolling by IBelieveInGod): ... Niwrad's entire argument rests on a simple math error.

But then I thought, ah hah, you're making a subtle reference to the fact that Niwrad made and equally simple and stupid error by using randomly-selected 30-base chunks of each chromasome. That is an extremely small percent of each genome to compare against each other.

Our peerless leader Reed Cartwright has pointed out to me that there is also a major response to niwrad's silliness at Todd Wood's blog, Todd being a creationist but an honest biologist.

Todd Wood, the world's only honest creationist*.

Therefore, also, the world's least psychologically tormented, but also loneliest, creationist.

*I count only people who actually had access to an education, but choose to deny scientific reality, as creationists. Historical figures from pre-scientific times, or people who have been involuntarily education deprived, don't count.

I have said before that The Fundamental Misconception of the ID/creationists goes right back to Henry Morris’ pitting the “myth of evolution against the science of thermodynamics.”

Here is niwrad on the thermodynamic argument. It is not surprising that he gets this wrong also.

It is that fundamental misconception that drives all “statistical calculations” by the ID/creationists. They know with out a shadow of a doubt that “everything descends into chaos without a guiding intelligence or program.” It’s because of entropy and the second law, despite the fact that they have learned to say publicly that they don’t believe evolution violates the second law (they have even learned to go out of their way to do some cheap calculations that shows it doesn’t). Nevertheless, their thinking reveals the fundamental misconception is still there.

Therefore all their “statistical arguments” begin by selection, using a uniform sampling distribution, from an essentially infinite set of possibilities. It proves evolutionists wrong 10¹⁵⁰ percent of the time.

Joe Felsenstein said: If niwrad had instead counted the fraction of the 30 that matched, and averaged that, the result would have been closer to 1.23%.

harold said: Todd Wood, the world's only honest creationist*.

Mike Elzinga said: Here is niwrad on the thermodynamic argument. It is not surprising that he gets this wrong also.

mrg said: I looked over it quickly, not trying to dig into an argument that was as specious as it was obscurely phrased, but I noticed he was making a linkup to "creationut information theory (CIT)" in it. MrE, entropy is your hot button. CIT is mine. (Again, pronounced with a VERY soft "c".)

Mike Elzinga said: ID/creationist “information theory” is their “solution” to the “evolution vs. the second law narrative.”

mrg said: From their point of view, it's actually better. The SLOT is well-defined, and any reasonable examination of the SLOT shows that it neither rules out nor confirms evo science.

Why stop at 30-mers? How about comparing 100,000-mers? My genome wouldn't even be 99% similar to my own parents at that level, which means I can't possibly be related to them. Clearly I am the result of immaculate conception, so I'm the new messiah. And I say all Christians should believe evolution is true.

Game. Set. Match.

From that horrible, horrible thread about the SLOT...

Nirwad says, "Maxwell’s demon is a thought experiment and is fictitious, nevertheless it clearly proves that intelligence can counter entropy in principle."

Wow.

Of course what creationists never do when they get upset about the 1% figure and claim it is Much Higher Than That is to compare that figure with the percentage difference with the orang genome or the rhesus macacque genome (gorilla isn’t available yet). Those are of course higher yet, no matter how you calculate the figure, leaving the chimp as our closest relative.

The depressing thing is that a number of people are spending time to refute this nitwit but he'll just let the thread die and then refer back to his "successful counter of the 99% similarity myth" in a few months time. No honor, no shame, not even the slightest cognitive dissonance.

Ben W said: Nirwad says, "Maxwell’s demon is a thought experiment and is fictitious, nevertheless it clearly proves that intelligence can counter entropy in principle." Wow.

Not only are they misunderstanding this data, but they ignore the fact that no matter how close our genomes are to each other, 50 or 60 or 99%, it still means we're... related. How closely or how distantly is hardly the point as far as proving whether or not we are related.

GEORGE said: Not only are they misunderstanding this data, but they ignore the fact that no matter how close our genomes are to each other, 50 or 60 or 99%, it still means we're... related. How closely or how distantly is hardly the point as far as proving whether or not we are related.

Ben W said: From that horrible, horrible thread about the SLOT... Nirwad says, "Maxwell’s demon is a thought experiment and is fictitious, nevertheless it clearly proves that intelligence can counter entropy in principle." Wow.

IBelieveInGod said: We do all have a common Creator:)

RBH said:

IBelieveInGod said: We do all have a common Creator:)

Who made it come out exactly as though evolution were true. Amazing, that. And there are data to suggest that if there were a creator, there were probably many creators, not just one.

I think you're overestimating the probability of a match here. Your calculation would be correct if niwrad were comparing homologous sequences. But he isn't. Instead he's using one 30-base human sequence as a probe into an entire chimp chromosome. If that 30 bases is repeated anywhere in the chromosome, he counts as a match. If there is no exact repeat, no match. About 4% of human sequences are not orthologous to any chimp sequence. I think it's reasonable to suppose that, if there is a related sequence somewhere in the chimp genome, it would be expected to be less similar to the human probe than would a hypothetical orthologous sequence. Then again, many of these sequences would be repetitive, giving us extra chances at a match. In fact, it's hard to figure out the true expectation of this pointless distance measure. Why 30 bases? Why a search limited to one chromosome? Why a 100% identity cutoff? Wouldn't it just make more sense to align the two genomes and do a direct comparison? But of course that's what nimrod is complaining about. Feh.

John Harshman said: Wouldn't it just make more sense to align the two genomes and do a direct comparison? But of course that's what nimrod is complaining about. Feh.

IBIG, Right you are. Evolution is the common creator:)

IBelieveInGod said: We do all have a common Creator:)

DS said: I thought this retard [IBelieveInGod] had been banned from all threads except the bathroom wall. He should definitely be segregated from decent society. He has spewed three hundred and fifty pages of filth all over the bathroom wall. Don't let him do it here.

What gets people put into the Pharyngula killfile dungeon? This is a list of annoyances; it usually takes more than one incident to get thrown in the slammer, though. The people who've been incarcerated are typically persistent and have a known history of pulling these stunts over and over again. Concern trolling: A particularly annoying form of trolling in which someone falsely pretends to be offering advice to favor a position they do not endorse; a creationist who masquerades as someone concerned about the arguments for evolution as an excuse to make criticisms. Godbotting: Making an argument based only on the premise that your holy book is sufficient authority; citing lots of bible verses as if they were persuasive. Insipidity: A great crime. Being tedious, repetitive, and completely boring; putting the blogger to sleep by going on and on about the same thing all the time. Morphing: Changing pseudonyms to avoid killfiles. Slagging: Making only disparaging comments about a group; while some of this is understandable, if your only contribution is consistently "X is bad", even in threads that aren't about X, then you're simply slagging, not discussing. Sockpuppetry: Like morphing, but with a specific intent: creating multiple identities supporting a position to create a false impression of popularity Spamming: Using the comments to sell real estate, mortgage assessments, little blue pills, porn, or Russian mail-order brides. Spammers are not tolerated at all; they are expunged without comment. Stupidity: Some people will just stun you with the outrageous foolishness of their comments; those who seem to say nothing but stupid things get the axe. Trolling: Making comments intended only to disrupt a thread and incite flames and confusion. Wanking: Making self-congratulary comments intended only to give an impression of your importance or intelligence.

RBH said: And there are data to suggest that if there were a creator, there were probably many creators, not just one.

Now I think on it, an additional component of error would be those sequences in the human genome with no homologs at all in the chimp genome. A deletion of even one base in a single-copy sequence in either the chimp or human lineage, for example.

John Harshman said: Now I think on it, an additional component of error would be those sequences in the human genome with no homologs at all in the chimp genome. A deletion of even one base in a single-copy sequence in either the chimp or human lineage, for example.

Ryan Cunningham, posted 9/28/10 12:58 PM Why stop at 30-mers? How about comparing 100,000-mers? My genome wouldn’t even be 99% similar to my own parents at that level, which means I can’t possibly be related to them. Clearly I am the result of immaculate conception, so I’m the new messiah. And I say all Christians should believe evolution is true. Game. Set. Match.

Apologies if this was answered already, here or at UcD:

I know that the "% difference" arguments are always sought and fabricated to promote doubt that "RM + NS" can cause the necessary changes in any imaginable length of time. But was there any mention of whether the supposed alternative occurred "in vivo," or required separate origin (abiogenesis) of both lineages? The reason I ask is that the DI's own Michael Behe was quite clear that the alternative is an "in vivo" process, meaning that the 2 lineages shared common ancestors regardless of whether "RM + NS" produces the differences.

As for the second law arguments, the fact that seeds grow into adult plants, and eggs into adult animals, stops that argument in its tracks, for anybody willing to think.

Evolution is after all a side effect of growth, and any energy associated with it is a tiny fraction of the energy expended for growth.

So that case is closed. (And has been for many decades. Or do I mean centuries?)

Henry J

Reed A. Cartwright said: But such events are rarer than mutations, so wont add to much additional error.

Henry J said: As for the second law arguments, the fact that seeds grow into adult plants, and eggs into adult animals, stops that argument in its tracks, for anybody willing to think. Evolution is after all a side effect of growth, and any energy associated with it is a tiny fraction of the energy expended for growth. So that case is closed. (And has been for many decades. Or do I mean centuries?) Henry J

Here is more of that video of Thomas Kindell

I think there are other links there that get the rest of that entire talk.

John Harshman said: I think you're overestimating the probability of a match here. Your calculation would be correct if niwrad were comparing homologous sequences. But he isn't. Instead he's using one 30-base human sequence as a probe into an entire chimp chromosome. If that 30 bases is repeated anywhere in the chromosome, he counts as a match. If there is no exact repeat, no match. About 4% of human sequences are not orthologous to any chimp sequence. I think it's reasonable to suppose that, if there is a related sequence somewhere in the chimp genome, it would be expected to be less similar to the human probe than would a hypothetical orthologous sequence. Then again, many of these sequences would be repetitive, giving us extra chances at a match. In fact, it's hard to figure out the true expectation of this pointless distance measure.

IBelieveInGod said: We do all have a common Creator:)

I'm just checking, but every one here realizes that niwrad is clearly trolling uncommon descent by posting transparently false analysis and seeing just how many creationist defend his (purposeful) stupidity, right? I mean, seriously, do you think that creationist are as inventive as niwrad? This is original research he did. Creationist rarely (if ever) look at the data, no matter how perversely. Additionally, his name is Darwin spelled backward. niwraD does not believe what he posted. I will bet money on it. It's a good trolling effort, but I don't really think we should be wasting our time talking about how stupid it is. It is meant to be stupid. That is the whole point.

IBelieveInGod said:

GEORGE said: Not only are they misunderstanding this data, but they ignore the fact that no matter how close our genomes are to each other, 50 or 60 or 99%, it still means we're... related. How closely or how distantly is hardly the point as far as proving whether or not we are related.

We do all have a common Creator:)

In other news, bornagain77 has a fairly coherent criticism of the 99% number, in that the 99% number ignores all structural variation. Any sequence which humans possess and chimps do not, or vice versa, is left out of the 99% calculation.

I believe that most of you can see why stating the average similarity of the portion of the DNA which is most similar might be interpreted as slightly miss leading by some.

Now, I don't think there is anything wrong with stating the 99% number, it is a good estimate of substitution rates, but, never the less, SNPs don't make up all the genetic variation in the world.

I am with Dave Ackerman in calling Poes on this one.

The work firewall won't let me get back there but if you go down the comments and look you will find one post where he says that changing the number of pairs closer to 1 will give you the same results as the scientifically presentended 1.2%.

I found that comment odd at the time because it basically admits its all bunk without saying it.

It could still be really just a creationist doing what creationists do best but my vote is that its a POE. Provisional of course. Its so hard to tell with them.

Matt Ackerman said: I'm just checking, but every one here realizes that niwrad is clearly trolling uncommon descent by posting transparently false analysis and seeing just how many creationist defend his (purposeful) stupidity, right?

Of course, what may be more interesting is that the 99% figure really is misleading.

As bornagain77 points out, the 99% figure is a comparison of the portion of the genome which are homologous. In other words, of the portion of the genome which is clearly the same, what percentage of the genome is the same? The 99% figure is meant to be an estimate of the rate of single nucleotide substitutions, and as such is a fine metric, however, much of the genetic variation between humans and chimps occurs as structural variation. In other words genes are duplicated or deleted, and all of the genes which are unique to humans or unique to chimps are left out of this calculation.

Again, this is fine, if what you want to do is estimate rates of single nucleotide substitutions. But there are such events as gene duplications and gene deletions, and I think we ought to be aware that there have been ALOT of duplications and deletions between humans and chimps, which argues that duplicagtions and deletions may just be an important form of sequence evolution. Google AMYLASE some time.

Leszek said: I am with Dave Ackerman in calling Poes on this one.

http://www.ncbi.nlm.nih.gov/pubmed/15716009

Leszek said: It could still be really just a creationist doing what creationists do best but my vote is that its a POE. Provisional of course. Its so hard to tell with them.

IBelieveInGod said: http://www.ncbi.nlm.nih.gov/pubmed/15716009

Mike Elzinga said:

IBelieveInGod said: http://www.ncbi.nlm.nih.gov/pubmed/15716009

Instead of bombing this site with your quote-mining and copy/paste arguments, why don’t you instead show us your level of conceptual understanding of science? I have a paper you can go through where everyone here can look on at the same time and actually evaluate objectively and out in the open whether you understand the concepts. And it is a paper from one of your own. Why don’t you explain and justify for us the concepts there? We will know instantly how you are doing. The last troll like you ran away or tried to change the subject. We think you will do the same.

IBelieveInGod said:

GEORGE said: Not only are they misunderstanding this data, but they ignore the fact that no matter how close our genomes are to each other, 50 or 60 or 99%, it still means we're... related. How closely or how distantly is hardly the point as far as proving whether or not we are related.

We do all have a common Creator:)

On the off chance that no one else has yet pointed this out, we are even more different than you think. Every single chromosome on the chimp is non-identical to the one in human (including the two chimp chromosomes that make up Human chromosome #2). So we are 100% different. (Which should come as no surprise: after all, no intelligent adult person would actually mistake a chimp for a human.)

[BTW, this web site does not work with IE 8.0. comments don't thread right (no separate pages) and you can't post a comment with it.]

I'm having trouble fallowing the term 'one-base pair' Could you set this post up with some illustrations of what exactly was being compared?

Matt Ackerman said: In other news, bornagain77 has a fairly coherent criticism of the 99% number, in that the 99% number ignores all structural variation. Any sequence which humans possess and chimps do not, or vice versa, is left out of the 99% calculation.

It isn't one-base pair; it's one base-pair. A base is one "letter" of a DNA sequence; "pair" because DNA is a double helix, and each base is paired with another on the opposite strand. In a sequence like ACCGATACGTA, each of those letters is a base. It would be paired with (reading in the same direction for convenience) a sequence of TGGCTATGCAT in the opposite strand. Each of those sequences is 11 bases (or base-pairs, if you like) long.

Divalent said: [BTW, this web site does not work with IE 8.0. comments don't thread right (no separate pages) and you can't post a comment with it.]

Matt Ackerman said:

Leszek said: I am with Dave Ackerman in calling Poes on this one.

Dave Ackerman is my brother, do you happen to know him?

RBH said:

IBelieveInGod said: We do all have a common Creator:)

Who made it come out exactly as though evolution were true. Amazing, that. And there are data to suggest that if there were a creator, there were probably many creators, not just one.

However one calculates the percent difference or similarity between humans and chimps, how does that compare with the similarity/difference between chimps and gorillas, or between sheep and goats, or between horses and donkeys?

One might be able to account for there being similarities by appealing to a common designer - a designer working with limitations imposed by the materials being used, or a designer having similar goals for the products - but the interesting thing is that the similarities and differences fall into an overall pattern, known as the "nested hierarchy" or the "tree of life". To the best of my knowledge, no one has ever suggested an explanation of a nested hierarchy which does not involve common descent with modification. (That is, not only for the biological tree, but also for a similar pattern among languages and a similar pattern among manuscript traditions.)

This is a pattern in the world of life which is extremely complex and makes predictions about what will be discovered, and thus cannot be accounted for by "chance" alone. If it is "designed", it is designed to look like common descent with modification.

My take is that who would do all the work to produce utter bullshit? My guess is that the author knew that the methodology was bogus, but that he thought that it could be used to confuse the rubes. He didn't even know what he was comparing his data to. Could anyone that would take the time to do this type of senseless analysis be that clueless? It could be giving the guy too much credit, but he likely knew the results would be bogus.

What would be the point of trying something like this when you could just take known genes and compare them? Heck you can take whole BAC contigs and compare them and get the deletions and insertions too.

TomS said: However one calculates the percent difference or similarity between humans and chimps, how does that compare with the similarity/difference between chimps and gorillas, or between sheep and goats, or between horses and donkeys? One might be able to account for there being similarities by appealing to a common designer - a designer working with limitations imposed by the materials being used, or a designer having similar goals for the products - but the interesting thing is that the similarities and differences fall into an overall pattern, known as the "nested hierarchy" or the "tree of life". To the best of my knowledge, no one has ever suggested an explanation of a nested hierarchy which does not involve common descent with modification. (That is, not only for the biological tree, but also for a similar pattern among languages and a similar pattern among manuscript traditions.) This is a pattern in the world of life which is extremely complex and makes predictions about what will be discovered, and thus cannot be accounted for by "chance" alone. If it is "designed", it is designed to look like common descent with modification.

TomS said: One might be able to account for there being similarities by appealing to a common designer - a designer working with limitations imposed by the materials being used, or a designer having similar goals for the products - but the interesting thing is that the similarities and differences fall into an overall pattern, known as the "nested hierarchy" or the "tree of life". To the best of my knowledge, no one has ever suggested an explanation of a nested hierarchy which does not involve common descent with modification. (That is, not only for the biological tree, but also for a similar pattern among languages and a similar pattern among manuscript traditions.) This is a pattern in the world of life which is extremely complex and makes predictions about what will be discovered, and thus cannot be accounted for by "chance" alone. If it is "designed", it is designed to look like common descent with modification.

TomS wrote:

"One might be able to account for there being similarities by appealing to a common designer - a designer working with limitations imposed by the materials being used, or a designer having similar goals for the products - but the interesting thing is that the similarities and differences fall into an overall pattern, known as the “nested hierarchy” or the “tree of life”. To the best of my knowledge, no one has ever suggested an explanation of a nested hierarchy which does not involve common descent with modification. (That is, not only for the biological tree, but also for a similar pattern among languages and a similar pattern among manuscript traditions.)"

Quite true, however, it's even worse than that. Even if you come up with some post hoc rationalization for the nested hierarchy of genetic similarities, you will never be able to explain why there is also a nested hierarchy of SINE insertions. THese are genetic mistakes. We know the mechanisms by which they occur and their relative and absolute rates. We know that they cause death and disease and we know that they are not going to ever be useful in any way. There is also no known mechanism whereby they can be reversed, so they persist, even through speciation events. This means that they are perfect phylogenetic markers. And the nested hierarchy of SINE insertions also happens to be exactly the same as the nested hierarchy produced by other types of genetic data. So, if you cling to the idea of some kind of intelligent designer, despite all of the evidence to the contrary, you still can't answer the question - why did she copy the mistakes?

IBIG the creationist posted this link -

http://www.ncbi.nlm.nih.gov/pubmed/15716009

IBIG seemed to think that the title supported a vast amount of genetic difference between humans and chimps.

However, let's look at the actual abstract that the link leads to (emphasis mine) -

"Abstract
The chimpanzee is our closest living relative. The morphological differences between the two species are so large that there is no problem in distinguishing between them. However, the nucleotide difference between the two species is surprisingly small. The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species. Still, the number of proteins responsible for the phenotypic differences may be smaller since not all genes are directly responsible for phenotypic characters."

I find this abstract somewhat imprecise - I'd have to read the entire article to understand what metric the authors are using to generate the "80% of proteins are different" statement.

Nevertheless, it is obvious to any reader that the abstract itself merely makes points that are within mainstream science. We all know that humans and chimpanzees share very recent common ancestry, we all know that humans and chimpanzees have similar genomes, and we all know that humans and chimpanzees have many phenotypic differences. There's nothing to support creationism here.

harold said: IBIG the creationist posted this link - http://www.ncbi.nlm.nih.gov/pubmed/15716009 IBIG seemed to think that the title supported a vast amount of genetic difference between humans and chimps. Nevertheless, it is obvious to any reader that the abstract itself merely makes points that are within mainstream science. We all know that humans and chimpanzees share very recent common ancestry, we all know that humans and chimpanzees have similar genomes, and we all know that humans and chimpanzees have many phenotypic differences. There's nothing to support creationism here.

Getting back to niwrad and his error, I am going to even further clarify what - as far as I can understand - he is doing wrong. This will be consistent with my first post but may be more clear to those who lack biology or basic probability backgrounds.

Let's start by looking at what it means when we say that humans and chimpanzees have 98-99% of nucleotides in common.

Humans and chimpanzees share many genes in common. In fact they have very similar chromosome structures and very similar sized genomes, for that matter.

What this means is that it is often very easy to assign a positional identity to a given nucleotide in a the human genome and look at the equivalent nucleotide in the chimpanzee genome, or vice versa. Some judgment is necessary for this process but there are widely accepted and reasonable ways of doing it. This can be done for much less related species, in fact, but it is especially easy to do when species are as close as humans and chimpanzees.

(There are now-antiquated methods of comparing sequence similarity between strands of DNA that don't even involve direct sequencing, and work via hybridization, but I won't bother to discuss that now.)

Since there are four DNA purine and pyrimidine bases, if the human and chimpanzee genomes happened to be similar in size and chromosome organization by coincidence, we would only expect 25% or so of the nucleotides at given definiable positions to be the same between the human and chimp genome. (This is basically true even though the four bases do not occur at exactly equal frequency.)

What we actually see is, if we look at a the human nucleotide at a given definable location, the same nucleotide at the same position in the chimpanzee 98-99% of the time. This is mildly oversimplified but essentially what claims of similar nucleotide sequence mean (obviously).

No evidence can ever "rule out" magical "common design" by an arbitrary trickster deity who would mimic evidence for common descent. However, we can note that common descent would be poorly supported if humans and chimpanzees were extremely different at the genetic level, as all other lines of evidence show them to be closely related. In fact, the new genetic sequencing data, which could have raised doubts, is convergent with all other evidence and adds to the support for common descent.

However, an extraordinarily asinine way of attempting to generate a lower number for nucleotide sequence similarity between humans and chimps would be to play an "apples to oranges" game, and compare, instead of individual nucleotide positions, segments of nucleotides at given positions, calling them the same only if the entire segment is identical. This is apparently what niwrad did. At least that's how it's explained in the post above, and that is consistent with the results he got. If the matching is done correctly - comparing thirty human nucleotide identities to the thirty nucleotide identities at legitimately the same position in the chimp genome - and the definition of "the same sequence" is changed to "segments of thirty must be identical", then, as was pointed out, ony (.9877)^30 "identity" would be expected.

This is extremely obvious.

I'm not sure why this creationist boob stopped at 30. He could have generate an even lower number by using a longer arbitrary segment length (this would also be a good way of demonstrating his error even to a stubborn person - one could show that changing arbitary segment length analyzed had the predicted effect). He could also have generated even lower numbers by doing an apples to oranges trick and comparing non-matched positions.

All such nonsense would be equally worthless. Given the obviousness of the error, it's unclear to me how much self-deception, versus desire to deceive others, is a factor.

That paper is mentioned by several creationists who show no indications of having actually read it. It was brought up by a guy on youtube so many times that I tracked down a copy of it - Eighty percent of proteins are different between humans and chimpanzees (PDF).

Anyone who actually cares to look at it will quickly realize it says nothing like creationists say it does. 80% of proteins are different in that they are not identical (which 20% are), but those that are different mostly only differ by one or two amino acids, highly consistent with inheritance and divergence from a common ancestor.. As Table 4 in the paper there shows, the vast majority of proteins have sequence identities between 98-100%.

IBelieveInGod said:

GEORGE said: Not only are they misunderstanding this data, but they ignore the fact that no matter how close our genomes are to each other, 50 or 60 or 99%, it still means we're... related. How closely or how distantly is hardly the point as far as proving whether or not we are related.

We do all have a common Creator:)

Ron Okimoto said: My take is that who would do all the work to produce utter bullshit? My guess is that the author knew that the methodology was bogus, but that he thought that it could be used to confuse the rubes. He didn't even know what he was comparing his data to. Could anyone that would take the time to do this type of senseless analysis be that clueless? It could be giving the guy too much credit, but he likely knew the results would be bogus. What would be the point of trying something like this when you could just take known genes and compare them? Heck you can take whole BAC contigs and compare them and get the deletions and insertions too.

John said: Anyone who actually cares to look at it will quickly realize it says nothing like creationists say it does. 80% of proteins are different in that they are not identical (which 20% are), but those that are different mostly only differ by one or two amino acids, highly consistent with inheritance and divergence from a common ancestor.

Anyone who actually cares to look at it will quickly realize it says nothing like creationists say it does. 80% of proteins are different in that they are not identical (which 20% are), but those that are different mostly only differ by one or two amino acids, highly consistent with inheritance and divergence from a common ancestor.. As Table 4 in the paper there shows, the vast majority of proteins have sequence identities between 98-100%

What I take away from all this is how very little total change at the level of the genes can result in such large morphological changes. However we measure (or even misrepresent that measure) of genetic differences between humans and chimps, we can't help but notice that chimps are quite drastically different every which way.

I sometimes wonder what would be the minimum genetic difference necessary to cause the maximum morphological difference. Might it be in a gene directing an important stage of development?

Flint said: I sometimes wonder what would be the minimum genetic difference necessary to cause the maximum morphological difference.

Harold said: Another example of outrageously dishonest misrepresentation and quote mining by creationists.

John said: That paper is mentioned by several creationists who show no indications of having actually read it. It was brought up by a guy on youtube so many times that I tracked down a copy of it - Eighty percent of proteins are different between humans and chimpanzees (PDF). Anyone who actually cares to look at it will quickly realize it says nothing like creationists say it does. 80% of proteins are different in that they are not identical (which 20% are), but those that are different mostly only differ by one or two amino acids, highly consistent with inheritance and divergence from a common ancestor.. As Table 4 in the paper there shows, the vast majority of proteins have sequence identities between 98-100%.

If I recall, the mean sequence identity between chimp and human protein-coding sequences is 99.5%, and while the mean doesn't necessarily tell us anything about "the vast majority", I bet the variance isn't all that great. Very few protein-coding sequences will be less than 98% similar. This makes sense if most evolution is neutral (as it almost certainly is). 98.7% similarity is what you get at the neutral rate, and any sequences being conserved by selection, as most protein-coding sequences are, will be more similar than that.

Flint said: What I take away from all this is how very little total change at the level of the genes can result in such large morphological changes.

Ofcourse, I should say, that all of these comparisons are not between 'humans' and 'chimps' but rather between James Watson, the human, and Clint, the chimp. James Watson differs from other humans, and Clint differs from other chimps. so almost any of these comparisons really overestimate the differences between humans and chimps, owing to an inability to infer ancestral states, arising from a sample size of one (ok, it can be slightly larger in some particular studies, but may won't be if you just compare 'the human *cough Watson* genome' to the chimp *cough Clint* genome.')

harold said: John -

Anyone who actually cares to look at it will quickly realize it says nothing like creationists say it does. 80% of proteins are different in that they are not identical (which 20% are), but those that are different mostly only differ by one or two amino acids, highly consistent with inheritance and divergence from a common ancestor.. As Table 4 in the paper there shows, the vast majority of proteins have sequence identities between 98-100%

Another example of outrageously dishonest misrepresentation and quote mining by creationists. Even reading the abstract made it obvious that the authors were making a completely mainstream claim. The work this paper summarizes is of value. Although there's much to be learned about genetics, over the last twenty years, knowledge of genetics and genomics has arguably outpaced everything else. Proteins have taken a back seat for a while, but deserve a lot of study. The actual data is not surprising. Codons in genes should be at least (.9877)^3, or about 97%, identical between humans and chimpanzees; actually more due to selection. And different codons may code for the same amino acid. That may have a very subtle phenotypic impact - if the mRNA strand has to "wait for" a rarer tRNA, subtly different folding or similar things may occur, for example - but it won't change the amino acid sequence. So let's say that if 98.77% of single amino acids are the same, at least 97% of codons are coding for the same amino acid. And that's an absurdly conservative estimate, ignoring synonymous codons and not accounting for selection. As it happens, (.97)^~52 = .2 (creationists - I used something called "logarithms" to figure that out quickly - don't waste your time trying to understand). Now, a 52 AA protein is rather short, but we get a surprisingly reasonable number even using that excessively conservative estimate. And we have to remember that larger proteins often contain repeated domains that are coded for by the same nucleotide sequenc. If we were to set the length of the "average" protein at 100 AA, then a 20% rate of protein sequence identify would imply around a 98.4% identity in individual amino acid sequence. That's highly reasonable, especially given that selection would likely be more selection against point mutations that change AA sequence, than for them. (*Presumably some mutations that change AA sequence were selected for, some of them point mutations, and that's a big part of how we became human.*) So in fact, the "80% of proteins different" metric is nicely within the range of what we would predict from the genome sequence data.

Matt Ackerman said: And this is why I don't like the 99% figure. 5% of the DNA between humans and chimps is 100% different, and the remaining 95% is 1% different. It seems likely that most of the phenotypic differences between humans and chimps arises from the 5% of genes which are unique to humans or chimps, and that the 95% of genes that humans and chimps share are less responsible for phenotypic differences.

Forgive me if I don’t understand what you mean in details. Nevertheless I agree with you that the results of the 30BMP test are not directly comparable to those in genomics literature. The 62% 30BPM similarity is not directly comparable with the 99% identity. We need a corrective coefficient. I agree with you also that such corrective coefficient differs depending on we do a 30BPM or 40BPM or 50BPM test … To understand this I argue according to what I did in #29. Given two supposed genomes that match 99% a 30BPM test gives 70% matches. Since the real test gave 62% my first idea to obtain a 30BPM value comparable to 99% is to apply the simple formula: 99×62/70 = 87.7%. In other words the multiplier coefficient that we must apply to the 62% is 99/70 = 1.41.

Now, I don’t personally believe that humans and chimps share a common ancestry, for a host of reasons that would take me too long to explain in this post.

Michael Roberts said: What's new about an epic fail? Any argument put froward by ID or YEC is an epic fail. All are

http://dictionary.reference.com/browse/froward says: fro·ward    /ˈfroʊwərd, ˈfroʊərd/ Show Spelled[froh-werd, froh-erd] –adjective willfully contrary; not easily managed: to be worried about one's froward, intractable child.

Oh come on. I call POE, again. Darwin spelled backwards! Correction factors so his made up metric can be compared to the way the real scientists do it? Come on, no one can be this stupid. He's just yanking chains, milking it for all it's worth. Has to be a POE.

As for humans and chimps not being related, I pointed out the evidence for that days ago. No amount of hand waving or soul searching is going to make that evidence go away. POE or not, this guy is just plain wrong. I do hope that he realizes that anyone dumb enough to fall for this nonsense probably won't have the sense to understand that they have been duped, even after he fesses up and explains to them that it was all a scam to make them look stupid. That should be worth a laugh, seeing how many of them become POE deniers.

creationists - I used something called “logarithms” to figure that out quickly - don’t waste your time trying to understand)

Creationist: "To understand this I argue according to what I did in #29. Given two supposed genomes that match 99% a 30BPM test gives 70% matches. Since the real test gave 62% my first idea to obtain a 30BPM value comparable to 99% is to apply the simple formula: 99×62/70 = 87.7%. In other words the multiplier coefficient that we must apply to the 62% is 99/70 = 1.41."

JF: "Actually you don’t correct for block size that way. If there is an underlying similarity of p at the one-base level, the probability of a match when there are blocks of B bases is p raised to the Bth power. Call that Q. So to get back to p from Q you just raise Q to the 1/B power. Or use logs and get log(p) by dividing log(Q) by B"

Joe Felsenstein so "niwrad" is not accustomed to "getting" basic scientific facts.

Oh come on. I call POE, again. Darwin spelled backwards! Correction factors so his made up metric can be compared to the way the real scientists do it? Come on, no one can be this stupid. He’s just yanking chains, milking it for all it’s worth. Has to be a POE.

harold said: DS -

Oh come on. I call POE, again. Darwin spelled backwards! Correction factors so his made up metric can be compared to the way the real scientists do it? Come on, no one can be this stupid. He’s just yanking chains, milking it for all it’s worth. Has to be a POE.

"Poe's Law" refers to the general principle that religious extremists are so whacked out that those who try to parody them can't be distinguished from the real thing, and vice versa. This guy could be a parody of sorts, and the discussion so far would still be true (including the fact that anyone remotely familiar with genomic sequencing and/or very basic probability could correct him, and no-one at UD has done so). Bombastic, pompous names are common among narcissistic creationists, so a name that could imply "overturning Darwin" doesn't give me much information. My method of detecting possible parodies, which I believe produces better than random results, is as follows - Just as most racists today deny racism and speak in coded language, most creationists, for whatever reason, choose not to speak openly about the hellfire, brutal executions, obsession with and misinterpretation of the relatively tiny proportion of the Bible that talks about sex, and (in many cases) modern ethnic biases that drive them. They will make not-very-veiled threats ("You'll find out soon!") when provoked, but tend to dissemble away from these topics. Meanwhile, most parodists aren't interested in mimicking dissembling, weaseling, and so on, as that isn't much fun. They prefer to parody the "sinners in the hands of an angry God" type stuff of the past. So when I see someone saying something like "Evolutionists are sodomites who will burn in hell", especially without provocation, I think that there is a reasonable probability that it is a parody. When I see a lot of dissembling, squirming, and weaseling, even when challenged, I know I am dealing with a real creationist. As for this guy, the "great genius who easily overturns science with obviously incorrect math" is a common type of sincere creationist. So who can say for sure?

Nope. You assume that 5% of DNA means 5% of genes, but almost all of that 5% is junk, mostly Alu repeats. Anyway, it’s silly to count each base of that 5% as equivalent to a point mutation, since we can account for all of it by only (!) 5 million mutations, while there are 35 million point mutations.

Matt Ackerman said: My numbers were actually coming from the structural divergence between human and chimpanzees genomes in protein coding regions. Approximately 6% of protein coding genes in human are absent in chimpanzees, and approximately 8% of protein coding genes present in chimpanzees are absent in humans (humans have experienced more lineage specific deletions than chimps) (Demuth et al. The Evolution of Mammalian Gene Families. PLoS ONE 1(1): e85. doi:10.1371/journal.pone.0000085)

If this is parody, my hat is off to niwrad -- he/she has managed to convince the powers that be at UD to let him/her be a blog contributor, not simply a commentator.

John Harshman said: This is a very liberal definition of "gene".

If a recent duplication has produced 2 copies of a gene in the human lineage, are those different genes.

and can chimpanzees be said to lack a gene?

Duplication is an important source of material for evolution, but I suggest that most duplications, like most other mutations, are evolutionarily meaningless.

How many gene deletions separating humans and chimps are of single-copy genes and how many are of recent duplicates?

I do agree that the most interesting questions here are about which differences are functional, and what those functions are. There are uses for distance measures, though.

Demuth et al. said: "In total, our results support mounting evidence that gene duplication and loss may have played a greater role than nucleotide substitution in the evolution of uniquely human phenotypes, and certainly a greater role than has been widely appreciated."

Geneticists may say that deletion of a recent duplicate is indeed loss of a gene, but saying it that way would also tend to deceive a layman into thinking that something important had just happened, like dropping your only copy of, say, cytochrome c. I really do think that most duplicated genes are subsequently deleted, either because they're slightly deleterious or because their loss isn't selected against. And I would further imagine that most of them are pseudogenized (real word?) before they are lost. In some cases, it may be the original copy that's deleted, perhaps even in nearly half of those cases. No matter. None of this prevents gene duplication and loss from being important in evolution, and perhaps more important than point mutations, but I would be interested in seeing the evidence that it's more important.

I do see that about half of all reductions of copy number, during the human lineage, in gene families that are inferred to have been present in the ancestral mammal have resulted in extinction of the family, generally by deletion of a single copy in a family that had been reduced previously to one copy. That doesn't count gene families that weren't in that ancestral mammal, and it doesn't count families that may have had losses but didn't have a net loss, but I'll accept it as an estimate. Can we suppose that most of those losses were in moribund families, i.e. those that humans just weren't using for much?

I read this on uncommon descent and the researcher is showing that humans and primates etc have like templates but the differences could not come from ToE.
This is a line of investigation that others probably will pick up on ape/human sameness claims in time.
As i told him biblical creationists should welcome as close a likeness to primate bodies as possible.
its impossible upon looking at apes to not conclude God simply has one blueprint of life and twists things about. one computer program fits all.
So people were simply given the best type of body in the equation of the blueprint. the ape body. Otherwise an entirely different kind of body would of had to be thought up that still included eyes etc.
Our body is not relevant to conclusions on our origins. Looking for the differences ois a waste of time.

Not being a biologist, I'm confused by the discussion of genes without a discussion of whatever the control areas are called for turning genes on and off.

It seems obvious to me, for instance, that chimp arms are made with very similar genes to ours for all the various protiens-- for hair, nails, bones, muscles, etc. The big difference between us is the longer length of chimp arms relative to the torso and hind legs.

Theoretically, a chimp could have exactly the same genes we do, and still look and act like a chimp, not a human, as different genes are turned on and off at different rates.

So, what are the control areas for the genes called, and how much research goes into differentiating the rates at which genes are turned on and off?

hoary puccoon said: Not being a biologist, I'm confused by the discussion of genes without a discussion of whatever the control areas are called for turning genes on and off. It seems obvious to me, for instance, that chimp arms are made with very similar genes to ours for all the various protiens-- for hair, nails, bones, muscles, etc. The big difference between us is the longer length of chimp arms relative to the torso and hind legs. Theoretically, a chimp could have exactly the same genes we do, and still look and act like a chimp, not a human, as different genes are turned on and off at different rates. So, what are the control areas for the genes called, and how much research goes into differentiating the rates at which genes are turned on and off?

Theoretically, a chimp could have exactly the same genes we do, and still look and act like a chimp, not a human, as different genes are turned on and off at different rates.

Consider that this high figure is obtained under the following conditions very favorable to similarity: (1) the ESM model helps to obtain high value of similarities; (2) the 30BPM test, for definition, is a lavish one because allows a total scrambling of patterns. If one or both of these conditions is not applied the scenario can only get worse for similarity. The conditions #2 implies that to speak of “identity” between genomes is nonsense, despite the high value obtained in the test. Besides 1.27% of difference in 3 billions base genomes makes 38 millions point mutations after all. As a consequence the normalized result of the 30BPM test in no way supports the evolutionist claim of a common ancestor of these genomes. A blind evolution that changes and scrambles 38 millions bases is unthinkable. I am satisfied of this work and wish to thank you for the collaboration.

Ron and Raven--
Thanks for responding. Do you know if anyone is actively working on the specific changes in control regions between chimps and humans?

Also, does anyone else suspect that niwrad is a sock puppet for Dembski himself? That line, "a blind evolution that changes and scrambles 38 millions bases is unthinkable" sounds exactly like his brand of 'let's see how much those rubes will swallow' cynicism. Obviously, whether scrambling 38 million pairs is "unthinkable" depends on how many pairs there are total and how many generations separate chimps and humans. There must be about, what, at least a million generations separating chimps and humans, and three billion base pairs? That comes out to about 13 base pair changes per billion base pairs per generation.

Obviously, whether scrambling 38 million pairs is “unthinkable” depends on how many pairs there are total and how many generations separate chimps and humans.

There must be about, what, at least a million generations separating chimps and humans, and three billion base pairs? That comes out to about 13 base pair changes per billion base pairs per generation.

Do you know if anyone is actively working on the specific changes in control regions between chimps and humans?

Excuse my ignorance, but what is a POE?

Karen S. said: Excuse my ignorance, but what is a POE?

You will also see the term "Loki troll", which is basically the same thing. I tend to prefer it because it's a little more intuitive ... it's more associated with the TALK.ORIGINS forum.

"POE" can be interpreted as "Pretense Of Extremism", but it reality it was orginally expressed by one Nathan Poe. No, it had little or nothing to do with Edgar Allen Poe.

Thanks mrg and Dale Husband for defining POE. I've believed for a long time that a certain poster on
BioLogos named conrad is one of those. (Now I have a word for his kind.) I simply cannot believe that even a fundie could be so butt-clenchingly stupid.

Not being a biologist, I’m confused by the discussion of genes without a discussion of whatever the control areas are called for turning genes on and off.

harold said:

creationists - I used something called “logarithms” to figure that out quickly - don’t waste your time trying to understand)

Maybe someone thought I was being sarcastic. I wasn't. And indeed later, Joe Felsenstein noted this -

Creationist: "To understand this I argue according to what I did in #29. Given two supposed genomes that match 99% a 30BPM test gives 70% matches. Since the real test gave 62% my first idea to obtain a 30BPM value comparable to 99% is to apply the simple formula: 99×62/70 = 87.7%. In other words the multiplier coefficient that we must apply to the 62% is 99/70 = 1.41."

JF: "Actually you don’t correct for block size that way. If there is an underlying similarity of p at the one-base level, the probability of a match when there are blocks of B bases is p raised to the Bth power. Call that Q. So to get back to p from Q you just raise Q to the 1/B power. Or use logs and get log(p) by dividing log(Q) by B"

In fairness, the creationist quoted here did figure out that niwrad was wrong, but was incompetent to correct him.