99.9% Wrong

Posted 26 May 2011 by Guest Contributor

by Joe Felsenstein,
http://evolution.gs.washington.edu/felsenstein.html Over at Uncommon Descent, "niwrad" is back with more calculations showing that conventional figures for comparing sequences of genomes are all wrong. Last time "niwrad" showed that humans and chimp genomes match only about 62% of the time. The usual figure given is 98.77%. Niwrad did this by taking 30-base chunks of one genome, finding the best match in the other genome, and then asking what fraction of the time there was a perfect match of all 30 bases. That's where the 62% figure comes from. I immediately pointed out here at PT that this was expected and did not represent some insightful new way of calculating these figures. Now Niwrad has turned to comparing two human genomes. The figure for 30-base perfect matches is about 96%. The conventional figure is about 99.9%. Let's see what is expected. If a single base position has a 0.999 probability of matching, two bases have a 0.999x0.999 probability, three bases a 0.999x0.999x0.999 probability. 30 bases then have a probability that is 0.999 raised to the 30th power. Which turns out to be (ta-da!) 0.97. Not a bad fit. Niwrad proudly notes that in the previous discussion

it seemed to me that the general feeling at the end was that my statistical method for performing genome-wide comparisons might have some merit, after all.

(Niwrad must have missed the discussion over here). It does have merit: It's a way of taking a close match and making it sound much less close -- without changing anything. I have a suggestion: why not try 100-base chunks? That way human/chimp match will drop to only about 29%, while human/human will drop to 90%. Or how about 1000-base chunks? (human/chimp would be only about 0.00042 of a percent, and human/human would be down to about 37%). Where will this all end?

72 Comments

Wheels · 26 May 2011

I wonder if he can turn his vast statistical insights to disproving the religion of anthropogenic climate change, now that he's knocked the legs out of Evolutionism. Then the Two Pillars Liberalism will be demolished, like Samson in the temple of the Philistines!

DS · 26 May 2011

Why is it that all creationists are good at is word games and number games? Does this guy really suppose that anyone will be fooled into thinking that humans and chimps are not really related?

Joe Felsenstein · 26 May 2011

DS said: Why is it that all creationists are good at is word games and number games? Does this guy really suppose that anyone will be fooled into thinking that humans and chimps are not really related?

I am unsure what the point of niwrad's latest post is -- unless it is to persuade readers that humans are unrelated to humans.

ben · 26 May 2011

Why not extend the methodology to comparing the entire strand of DNA from each species (so long as we are bent on choosing a methodology which makes no sense whatsoever, to engineer the result we desire)? If there is a single discrepancy between any two bases, the result is a 0% match.

So, as Joe says, no two humans are related to each other, not identical twins or even perfect clones--even they would have some mutations due to methylation, copy number variation, etc., which would cause a mismatch.

This is your brain on ID.

bobsie · 26 May 2011

Could this be an excellent algorithm to accurately predict the magnitude of the ever shrinking creationist brain, maybe?

Les Lane · 26 May 2011

It should surprise nobody the Niwrad gets everything backwards. Nonetheless those who are sure that the existence of monkeys falsifies evolution will likely find his arguments convincing.

Joe Felsenstein · 26 May 2011

Over at Uncommon Descent in Niwrad's thread, a commenter who is supportive of evolutionary biology, “DrREC”, has suggested correcting the percentage mismatches by dividing them by 0.24. This is arbitrary. The proper correction is to start from the fraction of match and take its 30th root. With a match of 96% for 30-base pieces, this yields a match of 0.99864 (a mismatch of 0.00146).

For the human/chimp match of 0.6173 (as given by Niwrad) we get 0.9805, or a mismatch probability of 0.0195 at the single-base level. That is somewhat higher than expected. For the median match (over chromosomes) of about 0.67, the corresponding single base match is 0.9867, for a mismatch of 0.0133.

topquark · 26 May 2011

It's cute watching IDers trying to do science, isn't it? Reminds me of watching three year olds creating artwork with their fingers and a few globs of paint in bright primary colors.

Glen Davidson · 26 May 2011

Is that what they do with their "microevolution"?

Of course not. This is part of their whole idiotic pretense that somehow the same type of evidence that indicates that "microevolution" occurred does not indicate that "macroevolution" happened."

Stark illogic is necessary of ID/creationism.

Glen Davidson

Joffan · 26 May 2011

Joe, I get 0.6173^(1/30) = 0.9840 so a probability mismatch of 1.60%, slightly but not amazingly higher than official stats. I notice his number of trials remained constant despite differing chromosome length - and he had a very low match rate on the Y chromosome, which in any case should surely only count for half? However I weighted the results properly and it made only a slight difference, changing to 0.6260 (mismatch drops to 1.55%).

Otherwise his methodology of using a 30-base stretch is actually quite good, if it is then subjected to the correct probability treatment, since the chance of a random match is vanishingly low - as niwrad confirms directly. The interesting thing which he confirms, all unwitting, is the directness of the match between the chromosomes.

DS · 26 May 2011

Joffan said: Joe, I get 0.6173^(1/30) = 0.9840 so a probability mismatch of 1.60%, slightly but not amazingly higher than official stats. I notice his number of trials remained constant despite differing chromosome length - and he had a very low match rate on the Y chromosome, which in any case should surely only count for half? However I weighted the results properly and it made only a slight difference, changing to 0.6260 (mismatch drops to 1.55%). Otherwise his methodology of using a 30-base stretch is actually quite good, if it is then subjected to the correct probability treatment, since the chance of a random match is vanishingly low - as niwrad confirms directly. The interesting thing which he confirms, all unwitting, is the directness of the match between the chromosomes.

And not only that, but with more comparisons he could actually reconstruct the nested hierarchy of genetic similarities between all living organisms. Now I wonder how he would explain that result? I guess in this case it would be like reinventing the wheel as an oval.

Tex · 26 May 2011

Where will this all end?

The logical end necessarily has to be when we consider 3.2 billion base-pair chunks of the human genome. Then, there will be absolutely no chunks in common with the genome from any other organism, proving once and for all that we are each God's special creation.

Joe Felsenstein · 26 May 2011

Joffan said: Joe, I get 0.6173^(1/30) = 0.9840 so a probability mismatch of 1.60%, slightly but not amazingly higher than official stats. I notice his number of trials remained constant despite differing chromosome length - and he had a very low match rate on the Y chromosome, which in any case should surely only count for half? However I weighted the results properly and it made only a slight difference, changing to 0.6260 (mismatch drops to 1.55%). ...

Thanks, I get the same numbers as you, but somehow when I type them into the comment box they change, and then I subtract in my head using those, and ...

jeff · 27 May 2011

The decay in match rate vs. segment length seems to provide a lot of information about the structure of the genome. Could you describe what is going on in the genome that accounts for this?

Some questions that pop into my mind: What is the segment length to describe a single protein? How many mismatches within a protein give a functionally similar molecule? Is the decay dominated by segments in junk DNA? Is there a critical segment length where the mismatches tell you about different structural aspects of the genome?

sparc · 27 May 2011

One should remember that Uncommondescent.com started as the blog of someone who holds masters degrees in statistics and mathematics and a PhD in mathematics. He is still posting there but obviously doesn't give a shit about other IDiots exposing the vacuity of ID-creationism.

Chris Lawson · 27 May 2011

As DS points out, Niwrad's recalibration is completely irrelevant to the hypothesis of common descent. If he compares humans to chimps, he will find greater similarity than humans to dogs, which will be greater than humans to fish, which will be greater than humans to algae, and so on.

If he uses existing genome databases and applies his personal algorithm, he will still end up reconstructing all the taxonomic hierarchies from first principles and they will look almost the same as the standard evolutionary view. It's like claiming Lyons isn't in France because the Paris-Lyon distance is not the same number in miles and kilometres.

natural cynic · 27 May 2011

jeff said: Some questions that pop into my mind: What is the segment length to describe a single protein?

It varies a great deal. Remember that there are numerous introns of various sizes so a protein that has ~100 amino acids only needs a minimum of ~300 base pairs, but with introns, it might be ~1000 base pairs or more.

How many mismatches within a protein give a functionally similar molecule?

Look at the sequence homology between a "highly conserved" protein like cytochrome c between human and yeast, human and wheat, human and dogfish etc. There are respectively 11, 10 and 6 differences within the first 22 amino acids see here. There can be much greater divergences with other proteins.

Is the decay dominated by segments in junk DNA?

Presumably so, according to theory, with "junk DNA" evolving at a much faster rate.

TomS · 27 May 2011

topquark said: It's cute watching IDers trying to do science, isn't it? Reminds me of watching three year olds creating artwork with their fingers and a few globs of paint in bright primary colors.

I think that you are underrating the esthetics of three year olds. The manipulation of numbers by an evolution denier reminds me of predicting the Rapture.

Dan Gaston · 27 May 2011

jeff said: How many mismatches within a protein give a functionally similar molecule?

As has been said, it really depends on the protein. Some highly conserved proteins only accumulate a relatively small number of substitutions at the amino acid level (3rd codon position mutations at the nucleotide level don't usually lead to a change in the amino acid). Some get quite divergent. Compare human sequences to some of the rapidly evolving unicellular eukaryotes like Microsporidia or say Trichomonas vaginalis and you can see sequence similarities at the amino acid level at only 50% or lower and yet the proteins are still functional and can complement their homologs in yeast just fine. It really all depends on the protein, what it does, how many interactions with other proteins it has, etc.

Dan Gaston · 27 May 2011

sparc said: One should remember that Uncommondescent.com started as the blog of someone who holds masters degrees in statistics and mathematics and a PhD in mathematics. He is still posting there but obviously doesn't give a shit about other IDiots exposing the vacuity of ID-creationism.

His degrees in mathematics never stopped him from playing the exact same stupid word and number games when it comes to probabilities and information theory.

eric · 27 May 2011

jeff said: How many mismatches within a protein give a functionally similar molecule?

All but two amino acids have multiple sequences associated with them. For example, the sequences GCT, GCC, GCA, and GCG all produce alanine. Niwrad's method counts these as differences.

Joe Felsenstein: I have a suggestion: why not try 100-base chunks?

If you really want to see how stupid his method is, try 3-base chunks. Hey look, at position X you use GCT to produce alanine and I use GCG. We are 33% different!!

Joe Felsenstein · 27 May 2011

jeff said: The decay in match rate vs. segment length seems to provide a lot of information about the structure of the genome. Could you describe what is going on in the genome that accounts for this? ...

I have been puzzling about that. There are more direct ways of assessing the distribution of differences throughout the genome, but one issue is simply whether differences are clustered. There are a number of reasons to expect them to be clustered: (1) Variation in degree of conservation of sequences by natural selection. Some sequences have function, some don't, some have more essential function than others. (2) Variation of mutation rates along the genome. (3) Variation of coalescent depth. For closely related sequences such as Human compared to Human, individual loci vary in how closely related they are owing to the random variation of recency of common ancestry due to genetic drift. The genealogical trees of different loci within a species vary. These trees, which are not phylogenies as they are of individual gene copies within one species, are called “coalescents”. So on a priori grounds we expect some clustering of differences. But here's the catch: given the numbers found by Niwrad, there appears to be, not clustering, but overdispersion. Clustering, by concentrating differences, would make the probability of sharing of a 30 base-pair segment greater than we would expect from the degree of single-base similarity. The calculations I have been using here are all based on independence from one base to another along the 30 bases. If that assumption is violated by clustering, we have a greater chance of seeing an identical 30-base chunk. But in the calculations, there seems to be a slightly smaller chance of seeing an unchanged 30-base chunk. So that would hint at differences being, at least slightly, overdispersed (the opposite of clustered). Why? One possible bias in the calculation is that some 30-base pieces do not have counterparts that can be found in the other genome, and those get dropped from the calculation. Wouldn't that bias the frequency of matches upwards? I would guess so. However what is seen is that it is lower then expected. All this needs investigation by more direct calculations than the frequency of 30-base exact matches. The one thing the simple calculations that we have done here show is that a huge difference between the frequency of 30-base matches and 1-base matches is expected, and is not a refutation of the 1-base figure. However the fact that these simple calculations are a bit off in the wrong direction is intriguing.

RodW · 27 May 2011

Why not 3.2 billion bp chunks? Then the similarity of human/chimp drops to 0%? ( come to think of it it drops to 9 long before 3.2 gb

AnswersInGenitals · 27 May 2011

This new mathematical field of Chunkology (which is so new that it is not even in my spelling checker) can lead to some very interesting questions and conclusions. E. g., what is the minimum chunk size needed to show that there is zero similarity between the four gospels, thus demonstrating that the gospels are totally different stories about totally different persons and events?

mrg · 27 May 2011

The first time JF went around on @nirwad's "chunkology" I was puzzled about what was going on until I thought it out for a bit: "Oh. That's really silly."

What is appalling about crackpots is not that they will make blindingly silly arguments, but that when the obvious flaws of the arguments are pointed out to them, they blindly go on with the silly arguments anyway.

One of the advantages of being a crackpot is that people will find it hard to believe that anyone could be so obstinately stupid and be far more patient than is sensible. Thanks to sad experience I am far less patient than I used to be, and my sufferance of fools correspondingly limited.

darwinism.dogBarf() · 27 May 2011

It does have merit: It’s a way of taking a close match and making it sound much less close – without changing anything. I have a suggestion: why not try 100-base chunks? That way human/chimp match will drop to only about 29%, while human/human will drop to 90%. Or how about 1000-base chunks? (human/chimp would be only about 0.00042 of a percent, and human/human would be down to about 37%). Where will this all end?

This is precisely the depth and subtilty of Niwrad's argument all the evolutionists have failed to miss. The greater the chunks of DNA used, the greater the ratio of percentage difference between the human/human and human/chimp comparisons. The broader the scope of the examination, the more different humans and chimps become. The evolutionists have observed H-O in the IR spectra of both water and pee and concluded they are the same thing. However, intelligent design theorists observe the entire spectrum and conclude they are different. This analogy is perfect.

mrg · 27 May 2011

OK, DD, you've shown your hand ... I am wondering how many of the more exciteable Pandas won't notice the cute little double-negative in "failed to miss" and think you're serious.

eric · 27 May 2011

darwinism.dogBarf() said: The greater the chunks of DNA used, the greater the ratio of percentage difference between the human/human and human/chimp comparisons. The broader the scope of the examination, the more different humans and chimps become.

But you forgot the first part: the broader the scope, the more different humans and humans become too. Niwrad's method could be used to show you are not closely related to your own mother. In sane people, this result would be considered a clue that niwrad's methodology is flawed. But creationists look at the human/human and human/chimp results, see one they like, and pretend the other doesn't exist. Ahh, confirmation bias. How do creationists love thee? Let me count the ways.

mrg · 27 May 2011

There's one.

Science Avenger · 27 May 2011

mrg said: What is appalling about crackpots is not that they will make blindingly silly arguments, but that when the obvious flaws of the arguments are pointed out to them, they blindly go on with the silly arguments anyway.

I think of that every time I hear the argument that Human Involvement in Experiments = Evidence for ID, as if intelligence was a magic serum or contagious disease that would cause natural processes to change. It's so obviously goofy its amazing that anyone would propose it once, much less after the glaring flaws are pointed out.

mrg · 27 May 2011

Science Avenger said: I think of that every time I hear the argument that Human Involvement in Experiments = Evidence for ID ...

I always trot out in reply: "So if people make a fire, that proves fires are intelligently designed and so they cannot be explained by science, right?" Does no good. "Dumb looks are still free." Creationists are desperately addicted to reasoning by analogy and are convinced it's a rigorous argument. I'm always careful to say "intelligently designed AND unexplainable by science", since if I don't add the trailer they like to jump to the other foot and play the teleological argument, that natural law reflects design -- of course carefully ignoring the fact that any such argument is irrelevant to the sciences, things work the same whether they were really designed or not.

Karen S. · 27 May 2011

What is appalling about crackpots is not that they will make blindingly silly arguments, but that when the obvious flaws of the arguments are pointed out to them, they blindly go on with the silly arguments anyway.

Just like last Saturday when the world didn't end.

Henry J · 27 May 2011

Just like last Saturday when the world didn’t end.

Or like when the people in Egypt and China didn't notice when they drowned under five miles of water?

Rumraket · 28 May 2011

The evolutionists have observed H-O in the IR spectra of both water and pee and concluded they are the same thing. However, intelligent design theorists observe the entire spectrum and conclude they are different. This analogy is perfect.

Actually, your analogy is flawed because "evolutionists" don't conclude they (humans and chimps) are the same, they conclude they are related. LOL. The point went over your head I'm afraid. Using the same methodology, according to the creationists, you aren't related to your mother either.

Robert Byers · 28 May 2011

The whole presumption in all this, from yEC and ID people too, is that too prove men and primates are not related one must not have a close biological/ genetic match.
Why???
First apes do look greatly like people so that all must submit there is something important about this. Not a happenchance.
Second all creatures look somewhat alike. most have two, eyes, ears, and legs and elbows and butts and noses and hearts, lungs, etc.
There is a dominant theme in nature on form and function despite diversity.

All must submit to either a common origin of creatures(unless glorious convergance) por a common design/program .

The creationist seeks in vain to prove mans biological unique origin if he must prove dna difference with apes.
However close surely its close enough.

The evolutionist works vainly in proving relatedness between us/apes since all creatures are not much different.

All creatures have enough likeness to demand a common blueprint is here on earth.
So this YEC guy welcomes apes being as related as can be.
simply we all have like forms and the ape form , ours, is the best one ONE would pick for a unique being made in the image of GOd.
Otherwise we would have to be breaking the general program of all life just to prove our separation.
What else could be a better body?
YEt having a like body with a ape no more logically suggests relatedness then having eyeballs like a moose would make us cousins.
Evolution is asking people to not look like nature or else they conclude we descend from the rest of nature.
For both sides the option of a common blueprint and therefore best result for flexibility is not being what it should be as the first conclusion or the first thing to criticize.

Its not logical to have a hunch we are related/from primates just because we look the same.
It could only be that way if we were a unique being in the image of God.
Likewise no need to run away from dna likeness to apes.
Its the same body. Its the best body to have. Better then a seal.

Sylvilagus · 28 May 2011

Robert Byers said: Its not logical to have a hunch we are related/from primates just because we look the same.

Thanks for the logic lesson, oh philosopher-king!

It could only be that way if we were a unique being in the image of God. Likewise no need to run away from dna likeness to apes. Its the same body. Its the best body to have. Better then a seal.

Nope. Seals are best. Gotta love seals. It's not logical that seals not have the best body to have. No need to run away from seal dna body differences. Better than primates.

Bobert Ryers · 28 May 2011

Sylvilagus said:
Robert Byers said: Its not logical to have a hunch we are related/from primates just because we look the same.
Thanks for the logic lesson, oh philosopher-king!
It could only be that way if we were a unique being in the image of God. Likewise no need to run away from dna likeness to apes. Its the same body. Its the best body to have. Better then a seal.
Nope. Seals are best. Gotta love seals. It's not logical that seals not have the best body to have. No need to run away from seal dna body differences. Better than primates.

lol

Joe Felsenstein · 28 May 2011

OK, we're into troll-chasing again. I have asked Reed Cartwright to look at this thread and send the trolling and troll-chasing to the Bathroom Wall (I don't have moderation privileges so I can't do it myself, alas).

Karen S. · 28 May 2011

Robert Byers is trolling over at BioLogos. It's hysterically funny! Just look at the Stephen Hawking thread. You'll have to go change into dry pants after reading it.

mrg · 28 May 2011

Rumraket said: The point went over your head I'm afraid. Using the same methodology, according to the creationists, you aren't related to your mother either.

There's two. You need to take your irony supplements.

mrg · 28 May 2011

Karen S. said: Robert Byers is trolling over at BioLogos. It's hysterically funny!

You are easily amused. I sometimes wonder if RB is actually some sort of computer virus, since it would be very easy to write software to replicate his postings using a stock set of phrases and with no great worries about syntax. The problem with that theory is that a computer virus usually has some recognizable point to it.

Science Avenger · 28 May 2011

Robert Byers said: There is a dominant theme in nature on form and function despite diversity. All must submit to either a common origin of creatures(unless glorious convergance) [or] a [STUPID] common design/program.

There, fixed that for ya. You guys always leave that crucial part out. It is stupid to design the human eye with a blind spot, especially given some animals don't have one. It is stupid to design our urinary tract to go through our prostate gland. It is stupid to design our laryngeal nerve to do a loop-de-loop through our chest. It is stupid to design us so that we breath and drink through the same hole in our bodies (as opposed to dolphins), thus making it posssible to choke to death. Repeating these designs in other animals is also the mark of rank stupidity. It's the equivalent of auto manufacturers copying the gas tank design of the exploding Pintos. So cut the crap Byers. Either posit a STUPID designer, or STFU already.

Wolfhound · 28 May 2011

Robert Byers said: Its not logical to have a hunch we are related/from primates just because we look the same. It could only be that way if we were a unique being in the image of God. Likewise no need to run away from dna likeness to apes. Its the same body. Its the best body to have. Better then a seal.

But but but you say that a koala is really just another bear because it's "shaped" like one and that a thylacine is just another wolf because it's "shaped" like a wolf. Same thing with marsupial "mice" just being regular old mice with a twist. So, then, following your own VERY special brand of logic, apes and people are the same "kind" since we're "same shaped", right? The fact that we can't reproduce together has no bearing since, too, koalas and, say, brown bears can't breed successfully, either, even though they are both "bear kind". Right? *I'm not kidding, folks, he really has made this fractally stupid argument concerning "kinds" and marsupials.

mrg · 28 May 2011

Wolfhound said: *I'm not kidding, folks, he really has made this fractally stupid argument concerning "kinds" and marsupials.

I am puzzled that you would think anyone would doubt it.

Glen Davidson · 28 May 2011

Its not logical to have a hunch we are related/from primates just because we look the same.

It's not logical to suppose that humans are related to each other just because they look alike. It's not logical to have a hunch that siblings are related because they have a family resemblance. It's not logical for creationists to suppose that "microevolution" (in its bewildering creationists varieties) occurs just because of the similarities of, say, Darwin's finches. It's not logical to presume that Greek and Latin are related due to similarities in commonly used words. It's not logical to do the science (after the hunch) that demonstrates relatedness of ape and human according to non-functional similarities that are explained only be derivation from a common ancestor. It's not logical to utilize pattern recognition to come up with reasonable inferences based upon what's seen. It is logical, of course, to many creationists, to utilize the evidence of relatedness to show that "microevolution" occurs (never mind that they can't tell us what they mean by it), yet to cut off what this grades into, "macroevolution" as not being demonstrated by the same sorts of familial similarities. It's not logical to do science at all, then. That's always the real conclusion to which creationist "logic" is forced. Glen Davidson

DS · 28 May 2011

Byers may be an idiot, but he has successfully derailed this thread with a single nonsensical post. Not one comment after his has been remotely on topic. We can't really blame Byers for that now can we?

The correct place to respond to trolls is on the bathroom wall, weather the administrators can get their act together or not. Let's help Joe out on this one. (Hat tip to Byers for the foolish spelling error).

Joe Felsenstein · 28 May 2011

DS said: Byers may be an idiot, but he has successfully derailed this thread with a single nonsensical post. Not one comment after his has been remotely on topic. We can't really blame Byers for that now can we? The correct place to respond to trolls is on the bathroom wall, weather the administrators can get their act together or not. Let's help Joe out on this one. (Hat tip to Byers for the foolish spelling error).

Thanks, DS. I know people have more fun telling Byers what they think of him than grappling with similarity of 30-base chunks of DNA. But you are giving Byers and other trolls power to derail the discussion, however much momentary fun it is. Reed is traveling and busy; but I hope he ultimately puts a stop to the trolling and troll-chasing in this thread. As I noted, I do not have the permissions needed; if I did I would be fairly brutal.

George · 29 May 2011

Of course, more simply, if you consider 1 base chunks you get the exact difference. If you consider the entire genome you get 0 matches in all cases I suspect - maybe you would get an exact match in a clone but I suspect not even then.

This is obvious. Thus comparing human to human is somewhat easier as the genomes match up in size quite well. (Except men to women).

But what about a human to an onion. The exact match will be quite low.

So then it becomes a matter of selecting portions to compare. This is a much more interesting analysis. There are similar biochemical systems in all life on earth. How similar the genes for these systems are is interesting.

DS · 29 May 2011

Many other possible mathematical manipulations are also possible. For example, if you take the estimate of 0.985 as the similarity between humans and chimps you can get the following:

Log base 10 = -0.00656

Log base 2 = -0.0218

Natural log = -.01511

Or you could divide by pi and get 0.3135

Or you could do trig functions:

sin = 0.01719

cos = 0.99985

tan = 0.017193

But no matter how you might massage the data, chimps are still the closest living relatives to humans, evolution is still real and all attempts at obfuscation are futile.

Joe Felsenstein · 29 May 2011

DS said: Many other possible mathematical manipulations are also possible. ... But no matter how you might massage the data, chimps are still the closest living relatives to humans, evolution is still real and all attempts at obfuscation are futile.

I think that many creationists, when they insist that the Human/Chimp differences are Much Larger Than That are really trying to give the impression that evolutionary biologists are deliberately propounding fake statistics. In fact, the simple 1-base match, for genomes such as these that can be mostly aligned, is the most straightforward one. The 30-base statistic of Niwrad is misleading. For more distance species, such as the onion that George asked about, the issues of alignment and how one counts insertions and deletions and other rearrangements are serious and not trivial. In fact, onions are diverged from us by about 1 billion years. Most of the genome will have changed so much that no similarity can be detected. Only strongly conserved stretches such as ribosomal RNA sequences and amino acid sequences of slowly-evolving proteins will retain information about relationship.

Joe Felsenstein · 29 May 2011

I meant "For more distant species" ...

mrg · 29 May 2011

Joe Felsenstein said: I think that many creationists, when they insist that the Human/Chimp differences are Much Larger Than That are really trying to give the impression that evolutionary biologists are deliberately propounding fake statistics.

It's a classic "FUD (Fear! Uncertainty! Doubt!)" game played to muddy the waters, targeting to the extent that it is consciously targeting anyone the gallery unequipped with any appreciation of math. "Them scientists have all this fancy math, well golly we'll throw out some fancy math too, and at the very least we can sow confusion." Never mind that those who aren't afraid of math know the creationist argument is silly, just generating noise is all that's needed to do the job.

Wheels · 29 May 2011

I don't think they're doing it on purpose. I think they're genuinely convinced that they've found something that disproves X, whatever X is; they consider the issue narrowly and in isolation because by and large they're NOT scientists, who have to think about the implications of any "new" discovery that overturns conventional wisdom. There is no sanity-check, no cross-reference, no spark that maybe "disproving" the link between humans and chimpanzees will fall apart when the same analysis is done on a wide range of more distantly related organisms to see any pattern of relatedness.

Niwrad in this case simply said "Aha! I've found a method that shows a much greater difference between humans and chimps than Darwinists think! THIS PROVES WE AREN'T RELATED!" The idea of then checking against a guinea pig, a minnow, a planarian, etc. never occurs to them because they just never grokked the whole scheme of nested hierarchies and it doesn't enter into their thinking.

Now someone like Behe should have no excuse, and really shouldn't keep quiet while this stuff gets posted on the official unofficial ID blog. But don't expect anybody from the DI to criticize Niwrad's exercise from their side; there doesn't seem to be anybody checking anybody else's work over there. Unlike science.

DS · 29 May 2011

Joe wrote:

"I think that many creationists, when they insist that the Human/Chimp differences are Much Larger Than That are really trying to give the impression that evolutionary biologists are deliberately propounding fake statistics."

Exactly. But no matter what mathematical shenanigans they try to pull, the basic pattern observed remains the same. The nested hierarchy of genetic similarities between all life forms is exactly what is predicted by evolutionary theory and is completely inconsistent with any rational creationist scenario. Only fools and the willfully gullible would be taken in by mathematical tricks. Modern genetics has dramatically confirmed that Darwin was right. Only sore losers would even attempt to claim otherwise.

This is like watching a defense lawyer try to argue about DNA evidence in a trial by claiming that a random matching probability of one in ten billion isn't good enough because there might one day be more than ten billion people alive.

DS · 29 May 2011

wheels wrote:

"I don’t think they’re doing it on purpose. I think they’re genuinely convinced that they’ve found something..."

You might be right, but I would still like to respectfully disagree. It seems to me much more likely that deep down inside at least some of them must realize that they are being fundamentally dishonest. Otherwise they would publish in mainstream journals, or at least try to. Otherwise, they would listen when some like Felsenstein points out the error of their ways and yet they persist, as if their misconceptions had not already been addressed. Otherwise, they would do the statistical tests required in order to call into question the phylogenies already established by independent data sets for various groups. Otherwise they would address all of the other data sets from which those phylogenies were derived. They have done none of the things that characterize real science or real seeking for truth. All they have done is to confirm their biases at any cost. These are not the actions of intellectually honest individuals.

They certainly might be so deluded that they honestly think that they have found something important, but they sure don't act like they sincerely believe it. They act more like little kids slinging mud and ignoring the people who are politely asking them to stop.

I'm sure Frank or someone will be along shortly to warn us about the pitfalls of trying to read the minds of strangers. But, like the not too bad book says:

"By their deeds ye shall know them."

Their deeds suck.

mrg · 29 May 2011

DS said: It seems to me much more likely that deep down inside at least some of them must realize that they are being fundamentally dishonest.

Err, no, they are SO fundamentally dishonest that they believe they are being truthful no matter what blatantly sleazy games they are playing. Since logic means nothing to them to begin with, they haven't the slightest obstacle to believing anything they want to believe. I do not say this to exonerate them; they are WORSE than conscious liars, every bit as dishonest but also deluded.

Mike Elzinga · 29 May 2011

Wheels said: Niwrad in this case simply said "Aha! I've found a method that shows a much greater difference between humans and chimps than Darwinists think! THIS PROVES WE AREN'T RELATED!"

I am reminded of the “tricks” used by novices who haven’t studied for conceptual understanding in physics. They grab any formula that has the “correct letters” in it. It doesn’t matter if p refers to momentum or pressure, or if it v refers to velocity or volume, etc., they just plug-and-chug the formula and move on. I vaguely remember a conversation – I believe here on PT – in which the “logic” of the creationist reminded me of someone who takes the Pythagorean Theorem (c² = a² + b²) and notes that it is “universally true.” So he grabs the formula, defines c as intelligence, a as weight, and b as age; and proves that the fatter and older one is, the more intelligent one is.

mrg · 29 May 2011

Mike Elzinga said: I am reminded of the “tricks” used by novices who haven’t studied for conceptual understanding in physics.

I recall someone who posted online in all sincerity a refutation of momentum / energy conservation, showing how a rocket flying through space with a certain momentum would lose it all by braking with its rocket engine. It never crossed his mind to consider the momentum of the gases in the rocket exhaust.

Wheels · 29 May 2011

DS said: You might be right, but I would still like to respectfully disagree. It seems to me much more likely that deep down inside at least some of them must realize that they are being fundamentally dishonest. Otherwise they would publish in mainstream journals, or at least try to.

It's not so simple.
1) Most anti-evolutionists are convinced that peer-reviewers are going to dogmatically reject anything which might challenge their "religion" of evolution. Just as Creationist and climate scientist Roy Spencer stopped trying to publish in a proper peer reviewed journal like Nature in favor of refereed Letters format publications (not to slight the publication); he was convinced that a gang of close-minded and close-knit reviewers was going to reject anything he submitted regardless of its merit. People like this are sold on the idea that the scientific establishment is corrupt through and through.
2) To the non-scientist, submitting to a journal can be a mysterious and potentially scary affair. So much easier to make something presentable enough for a blog post with a sciency veneer. After all, real live scientists like Dr. Dr. Dembski post and moderate there, right?
3) I'll go even further and say that a non-scientist's inclination isn't even towards peer-reviewed publication in the first place, simply because that's not what they do for a living and it doesn't weigh on them. 4) Checking their own work rigorously would require some knowledge of how and why scientists do that. Statistical tests, expanding the techniques to different scenarios (in this case comparing more than just humans and chimps), and all that stuff? It doesn't come naturally, that's something you get into the habit of doing with a science background and training. This doesn't excuse Dembski or Behe or any of the IDists claiming to be doing real science because they're "real" scientists, but Niwrad doesn't come off as a scientist here. And frankly, with as much misinformation about the process of science as cdesign proponentsists have slung around, I wouldn't really expect a layman hanging around in those circles to consider all these methodological checks. Their understanding of science stops at back-of-the-envelope, without even understanding how preliminary that is.

Dale Husband · 29 May 2011

Wheels said: 1) Most anti-evolutionists are convinced that peer-reviewers are going to dogmatically reject anything which might challenge their "religion" of evolution. Just as Creationist and climate scientist Roy Spencer stopped trying to publish in a proper peer reviewed journal like Nature in favor of refereed Letters format publications (not to slight the publication); he was convinced that a gang of close-minded and close-knit reviewers was going to reject anything he submitted regardless of its merit. People like this are sold on the idea that the scientific establishment is corrupt through and through.

The whole point of peer review is to halt and expose attempts at corruption among scientists. Only frauds should ever be scared of that.

2) To the non-scientist, submitting to a journal can be a mysterious and potentially scary affair. So much easier to make something presentable enough for a blog post with a sciency veneer. After all, real live scientists like Dr. Dr. Dembski post and moderate there, right?

What, people are not expected to work their butts off to gain fame and fortune? Hey, if laziness worked for Sarah Palin and her daughter Bristol.....

3) I'll go even further and say that a non-scientist's inclination isn't even towards peer-reviewed publication in the first place, simply because that's not what they do for a living and it doesn't weigh on them.

Which is why they do not deserve to be called scientists.

4) Checking their own work rigorously would require some knowledge of how and why scientists do that. Statistical tests, expanding the techniques to different scenarios (in this case comparing more than just humans and chimps), and all that stuff? It doesn't come naturally, that's something you get into the habit of doing with a science background and training. This doesn't excuse Dembski or Behe or any of the IDists claiming to be doing real science because they're "real" scientists, but Niwrad doesn't come off as a scientist here. And frankly, with as much misinformation about the process of science as cdesign proponentsists have slung around, I wouldn't really expect a layman hanging around in those circles to consider all these methodological checks. Their understanding of science stops at back-of-the-envelope, without even understanding how preliminary that is.

And it's not just Creationists we have to worry about. I am always amused at global warming denialists who are not climatologists, but geologists, chemists, or other types of scientific professions that are exactly the sort needed by the FOSSIL FUEL INDUSTRIES! Even before I can dismantle their lame canards, I know I am dealing with conflicts of interest big enough to sail an aircraft carrier through.

mrg · 29 May 2011

Wheels said: 4) Checking their own work rigorously would require some knowledge of how and why scientists do that. Statistical tests, expanding the techniques to different scenarios (in this case comparing more than just humans and chimps), and all that stuff? It doesn't come naturally, that's something you get into the habit of doing with a science background and training.

Yeah, along with this is the crackpot notion of: "All this picky stuff the scientists do is just a smokescreen for their ignorance. I can see the forest for the trees -- I can see the obvious truth that the scientists have blinded themselves from seeing with all their twaddle." And it should be noted that crackpots are not all that shy about trying to shove their views onto the scientific community -- John Baez's well-known "crackpot checklist" was obviously derived from experience with nutjobs thinking they've refuted Einstein and so on. Staggeringly, *I* get missives from such nutjobs, and I'm a nobody -- I tinker with physics on my website, but I have no particular qualifications in the field and have nothing resembling a reputation in it.

mrg · 29 May 2011

One of the other aspects to the matter is the influence of the internet on crackpots. Once upon a time they could mail letters to each other and form small circles of association; but with the internet there's been a democratization of worldwide communications, the lowliest crank now has global reach. Crackpots from all over the planet can band together, collaborate in pumping up the volume on misinformation, and create their own system for its dissemination, even with its own journals. ISCID anyone?

DS · 29 May 2011

Well anyone who doesn't even know what a professional does should realize that they are an amateur. An amateur shouldn't presume to know better than the professionals.

Conspiracy theories are are worthless in science. No matter whether you trust the system or not, if you are not willing to participate within the system you really can't complain about not being taken seriously. All of the great advancements in science were accomplished by people who got the evidence to back up their claims in spite of severe resistance. Claiming that everyone is against you is just a cop out.

Of course creationists many actually believe any or all of these excuses. But once again, at some level, at least some of them must realize that these are just rationalizations.

mrg · 29 May 2011

DS said: An amateur shouldn't presume to know better than the professionals.

I once cited the old saying: "A fool can ask more questions than a wise person can answer." The rejoinder was: "But isn't the reverse also true?" That took me by surprise and I didn't think of the reply until later: No. A fool has an infinite store of answers, easily pulled out of his ass as needed.

DS · 29 May 2011

mrg said:
DS said: An amateur shouldn't presume to know better than the professionals.
I once cited the old saying: "A fool can ask more questions than a wise person can answer." The rejoinder was: "But isn't the reverse also true?" That took me by surprise and I didn't think of the reply until later: No. A fool has an infinite store of answers, easily pulled out of his ass as needed.

Which only shows that you sir are no fool.

MichaelJ · 30 May 2011

The opposite is true as well, for every crackpot there is at least one blog tearing them apart. I think that in the long run it will advantage us more than them.

mrg said: One of the other aspects to the matter is the influence of the internet on crackpots. Once upon a time they could mail letters to each other and form small circles of association; but with the internet there's been a democratization of worldwide communications, the lowliest crank now has global reach. Crackpots from all over the planet can band together, collaborate in pumping up the volume on misinformation, and create their own system for its dissemination, even with its own journals. ISCID anyone?

Henry J · 30 May 2011

The opposite is true as well, for every crackpot there is at least one blog tearing them apart.

But what if they use duct tape on that cracked pot?

mrg · 30 May 2011

MichaelJ said: The opposite is true as well, for every crackpot there is at least one blog tearing them apart. I think that in the long run it will advantage us more than them.

Yeah, thankfully you're right there. I don't worry too much about 911 Troothers because they can't put out a movie like LOOSE CHANGE or the like and not have a website pick it to pieces. Thank Bob the Troothers don't have any big-name advocates -- the most prominent being a retired theology professor and a Hollywood actor noted for his long arrest rapsheet. When Ollie Stone did WORLD TRADE CENTER, there were worries he was going to sell the Troother story to America, but he was surprisingly restrained.

Christopher Booth · 2 June 2011

Karen S. said: Robert Byers is trolling over at BioLogos. It's hysterically funny! Just look at the Stephen Hawking thread. You'll have to go change into dry pants after reading it.

Ok, I went to look at the thread at BioLogos, and the stupidity and the pride in stupidity shocked me, even after years of following Pandas Thumb and Pharyngula, Bad Astronomy, etc. My jaw dropped. I am still staggered. I must thank you for calling my attention to it, but at the same time, part of me regrets having read what I read. [I wrote more, but...'nuff said. Wow. Still gobsmacked.]

harold · 2 June 2011

It's almost impossible to believe that this guy "niwrad" is still pushing this.

These people have no capacity for self awareness whatsoever.

We've been through this before.

If you look at correctly matched parts of the human genome and chimpanzee genome, there is a greater than 98% chance that, at a given individual locus, the base pair will be the same. Let's call that probability "p".

If you want to know the probability that, examining two loci, both will be a match, it is p^2.

If you want to know the probability that, examining "n" loci, all with be matches, it is p^n.

This is probably taught in high school and always taught in basic college statistics, but it is also well understood by many people with little formal education who enjoy games that involve cards or dice. It is very, very basic.

I hate to use insulting language, as it can distract, but for the sake of third party readers, I think it is critical to point out that if English words such as buffoon, moron, imbecile, idiot, jackass, arrogant, delusional, disturbed, pathetic, dull, stupid, egocentric, narcissistic, pitiful, etc, are to be used, they should be used to describe "nirwad".

His argument boils down to "p^n = p^n, therefore magic instead of evolution".

Ron Okimoto · 5 June 2011

Has anyone taken this bozo's side and tried to explain what can possibly be gained by this type of analysis?

Joe Felsenstein · 5 June 2011

There's an even more remarkable statement over at Uncommon Descent right now. Gil Dodgen is, as always, drawing dramatic conclusions that Darwinism has collapsed and that scientists refuse to recognize it (he's very good at drawing that conclusion -- evidence is another matter). Anyway, he opens with a statement that, for once, evolutionary biologists can agree with:

At UD we have many brilliant ID apologists, and they continue to mount what I perceive as increasingly indefensible assaults on the creative powers of the Darwinian mechanism of random errors filtered by natural selection.

I really can't think of anything to add to that.