Wednesday, August 06, 2014

When will they ever learn?

On most days I'm an optimist. I think that eventually the truth will win out and all you have to do is convince people that they are misguided. That's why I spend so much time discussing the view of Intelligent Design Creationists. On the good days, I firmly believe that if I can show them what science is all about then they will come around to accepting evolution.

I cherish a few modest successes over the years. For example, a few months ago I tried to teach David Klinghoffer and his friends about modern concepts of evolution and genetics. The example I used was the 98% sequence similarity between the human and chimp genomes. I showed him that the similarity is quite consistent with our understanding of Neutral Theory and random genetic drift [Why are the human and chimpanzee/bonobo genomes so similar?].

A remarkable thing happened. Some of the Intelligent Design Creationists on Evolution News & Views (sic) and Uncommon Descent actually agreed with me! They tried to explain to their fanatical friends that chimps and humans really do share a common ancestor and that the differences between them are explained by evolutionary theory. (I've included links to all the posts at the bottom of this post.)

Just when you think you are making some progress, the IDiots prove you wrong. Yesterday on Uncommom Descent there was a post on the topic of the similarity between chimps and humans [At last, a proposed answer re 98% human-chimpanzee similarity claim]. The author was probably Barry Arrington posting as "News." Here's the relevant part of that post ...
From this comment (by Gordon Davisson, in response to this post):
In other words, I’m agreeing with Denyse here:
BUT claimed 98% similarity due to a common ancestor (a claim that hundreds of science writers regularly make, in support of common descent) *undermines anything else they have to say on the subject.*
I do not know how to put the matter more simply than this: A person who does not see the problem is not a credible source of information.
He responds:
…just disagreeing about which side is not credible. Take the 98% similarity figure as an example: one of the basic principles of science is that you must follow the evidence. If the evidence supports the 98% figure, and that conflicts with your intuition, then you either have to throw that intuition into the trash bin, or stop claiming to be doing science.
No. Absolutely not.

One should never discard intuitions formed from experience, especially about vast claims. Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science.
This is called, among other things, wanting to have your cake an eat it too. The IDiots want you to believe that they accept all of modern science and that their "theory" is consistent with the evidence.

On the other hand, if the science of genetics leads to conclusions that contradict your "intuition" then the science must be wrong.

We've known for decades that this is how the IDiots really think but it's interesting to see someone like Barry Arrington express it so openly.

Now all we have to do is sit back and wait for the more intelligent IDiots to point out that we've been through all that a few months ago and Barry's intuition is wrong. Instead, what we're seeing is Barry Arrington doubling down [Sun orbits Earth vs. Chimps are people too – the differences].

This is not a good day. It's hard for me to remain optimistic.

An Intelligent Design Creationist explains why chimpanzees and humans are so similar
IDiots respond to the evidence for evolution of chimpanzees and humans
A creationist illustrates the argument from ignorance while trying to understand population genetics and Neutral Theory
Breaking news: Creationist Vincent Torley lies and moves goalposts
Vincent Torley apologizes and claims that he is not a liar
Vincent Torley tries to understand fixation
On the frustration of trying to educate IDiots
Why creationists think they are more open-minded than scientists
What would happen if Intelligent Design Creationists understood evolution?
Branko Kozulic has questions about fixation
Branko Kozulic responds
Branko Kozulic responds: Part II


  1. When will they learn? Never.

    Generally speaking, you are not dealing with rational people who can evaluate evidence on its merits. No, they already know the Truth (TM) and everything must be shoehorned to fit that Truth. And, in the case of people like Arrington, it is tied in to a comprehensive world view that includes their politics. They have so much invested that it's just impossible to get through to them. You might as well argue with brick walls.

  2. I'm pretty sure the author is not Arrington, but Denyse O'Leary, Canadian journalist, telling us we must throw out "genetic science." She has made this demand, quite comically, many times before.

    The style is not like that of Barry Arrington, ethically challenged accountant and employee of Rep. Michelle "President Obama will steal refugee children for secret medical experiments" Bachmann.

    O'Leary is the gift that keeps on giving.

    The Discovery Institute employs this moron and pays her a real salary. Not monopoly money either. They couldn't scrape the barrel any more so they knocked it over and employed an isopod dug up below it.

    Larry, please improve your formatting, as your indentation does not clarify who is saying what.

    1. It could be Denyse but it's not really her style either. I agree that it doesn't sound like our lawyer friend but if they insist of anonymous posts then I'm going to attribute everything stupid to Barry Arrington until he disavows it.

      Larry, please improve your formatting, as your indentation does not clarify who is saying what.

      Check the original. If you can figure it out, let me know. (That's more like Denyse!)

    2. Larry: "I'm going to attribute everything stupid to Barry Arrington until he disavows it."

      O'Leary identified herself as the author. In your second link, O'Leary refers to "my" quote, meaning the absurd quote from your first link, "One should never discard intuitions formed from experience, especially about vast claims."

      The second link is signed "O'Leary for News."

    3. It's Denyse O'Leary who posts as "News". Others sign their OP pieces as "Jonathan M", "vjtorley", "Barry Arrington", etc.

  3. "No. Absolutely not.

    One should never discard intuitions formed from experience, especially about vast claims."

    Great. Am I the only one now wondering what, exactly, is the nature of the writer's experience relating to chimpanzees in general and their genome in particular?

  4. I'm reminded of the old joke that ends "Who are you going to believe, me or your own lyin' eyes?

    One might however interpret this all very charitably (though I would not) as an example of Bayesian reasoning. Anonymous has a very strong prior against human/chimp similarity. It would take very strong evidence to change the posterior. Of course we might wonder where that prior came from or whether he/she had ever actually looked at the evidence.

    1. Another old joke: A man runs into an old friend and exclaims "Bill, I heard that you had died!". Bill replies "As you can see, I'm very much alive." "Impossible!", the man says, "the person who told me is much more reliable than you!".

      The chimps-are-obviously-different-from-humans argument will be convincing to millions, but it is simply an appeal to personal incredulity. The writer of this piece is in what grade at school?

    2. 63 year old Canadian journalist, with no science degree, demands that science labs and research funding be taken away from succesful scientists and given to political antiscience extremists based on their religious beliefs. So naturally, the Discovery Institute pays her to promote their agenda.

  5. No. Absolutely not.

    One should never discard intuitions formed from experience, especially about vast claims.

    I wonder what Barry or Denyse think of Quantum Mechanics, then. But I guess that doesn't conflict that much with baby jesus so everything's fine.

    Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science.

    - Listen you all! Throw all your genetics/evolution theory nonsense into the trash! It's so obviously wrong!
    - Huh, why?
    - Just look at how chimps are so obviously unlike humans!
    - Huh, in what way?
    - In any way that matters!!!

    I don't know if I should laugh or cry.

    1. News said:

      "Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science."

      Hmm, I find myself thinking about the alleged similarities between humans and 'God' (and which 'God'?). 'God' allegedly lives in the sky somewhere, is invisible, has unlimited knowledge and powers, can read minds, is eternal/infinite, indestructible, uncaused, and perfect, and a bunch of other stuff that is unlike humans, yet humans are allegedly specially created in 'God's' image, at least according to christians. If humans are specially created in 'God's' image, shouldn't humans be exactly like 'God'?

  6. Larry and I disagree as to whether it's O'Leary or Arrington, but let's compare this comedy gold which was definitely written by O'Leary to today's comedy.

    Here O'Leary explains precisely what "experience" gave her the "intuition" that tells her she must "discredit genetics" (all of it-- she really does mean throw out the whole science of genetics, because of the 98% similarity bugbear).

    The "experience" she speaks of is that a lady don't want to $%&! no monkey. I'm not kidding, this is really the "experience" she's got as her proof for throwing out genetics.

    O'Leary: ...her editor had demanded that I account for the fact that humans share 98% of our DNA with chimps.

    …If both [man and chimp] are more than 30 years old, and are normal specimens, how many people will believe that they are 98% identical?

    What woman, otherwise consigned to being a spinster, would marry the chimp if she didn’t get the man? After all, the chimp is supposedly 98% of a man.

    Actually, the chimp isn’t a man at all. He belongs in the wilds, or a preserve, or a zoo somewhere... Every woman in the world knows this.

    None are the least bit interested in the chimp...

    So, my question is, what is this 98% similarity thing based on, other than to discredit genetics?

    [Just a hack writer, but … question. By Denyse O'Leary. 31 March 2010.]

    There you go, Larry! You and all the other geneticists, you're all finished. You're exposed as frauds, and your whole phony science of genetics is "discredited" as a big hoax because... Denyse O'Leary don't wanna hump no monkey.

    1. And now I find myself hoping that the unshakable intuition is not based on actual experience.

    2. Sometimes I do wonder if, back in high school perhaps, Denye O'Leary had a terrible crush on a Pan troglodytes, but it was sadly unrequited as Bobo was more interested in the head cheerleader instead-- and ever since that moment, Denyse has carried a terrible grudge against his whole genus and its damned DNA!

      She'll show Bobo who's really the summit of creation!

  7. AMEN. The truth will win out. thats why there is a revolution going on and doing fine in our time.
    Looking alike is not evidence of common descent. including the reasons, genes, for looking alike.
    All biology looks alike. Its off the same rack.
    A creator with a common design would make biology look alike.
    by the way us looking like apes is a great YEC point.
    We are the only creatures that look like another creature while being very different in nature .
    This because we could not have our own body to show our true identity.
    We are made in gods image and so very special. God can't have a biological representation of himself on earth and so neither do we.
    sO we were simply given the best body type for fun and profit. The ape body.
    Yet its not evidence of common descent because of looks. Morphological or genetic.
    Its just a line of reasoning. Gene likeness also is just a line of reasoning that it means common descent. Yet how else could it be if we look alike?
    ID/YEC/evolutionists all should say what percentage would be suggestive of not being related to apes if genes is the qualification.
    i welcome 100& looking like apes. We have a ape body. Not our own body for humans.
    However looking alike is not biological scientific evidence even if we were from common descent.
    Science demands accurate methodology.

  8. O'Leary: "One should never discard intuitions formed from experience, especially about vast claims."

    Nobody at the Lunacy Institute can truly accept that proposition.

    I have no experiences of a disembodied, Uber-intelligent, infinite, omnipotent, omniscient, all-loving and immortal mind, existing in the absense of a physical brain, outside of time and space, which loves me and wants to make me live forever in eternal happiness in an alternative spirit-dimension called "paradise", which can also simply wish, WISH entire universes into existence out of absolute non-being.

    Quite frankly, all my intuitions and experiences are protesting this idea as the ultimate "vast" claim. All my intuitions tell me this is simply childish wishful thinking.

    1. In fact, since extraordinary claims require extraordinary evidence, I'm at a loss trying to envision what kind of evidence could ever sufficiently establish the existence of this absurd entity.

    2. Theistic evolutionists like Ken Miller would say that "God is beyond all evidence" and "Our methods and instruments are not powerful enough to detect God."

    3. "Our methods and instruments are not powerful enough to detect God."

      Odd, isn't it, that just a couple of thousand years ago eyeballs, ears , and the normal human sense of touch were (reputedly) well sufficient to detect the presence of the Almighty and various miracles, whereas today, other than images on a variety of foodstuffs (e.g., burnt tortillas), electron microscopes, radio telescopes, and the most sensitive CCD detectors are insufficient.

  9. ""God is beyond all evidence" and "Our methods and instruments are not powerful enough to detect God."

    Isn't that convenient.

    1. I'm leaving my Fiat car in my driveway for a few decades hoping it will evolve into a Rolls Royce. After all, they are 98% similar in construction and assembly instructions so it's inevitable if I leave it long enough.

    2. The reason organisms evolve is that they die but leave offspring which are slightly different than their ancestors, because of mutations. Those differences some times have adaptive potential, i.e. they are subject to natural selection.

      Do cars undergo meiosis or mitosis? Do cars undergo cell division? Do cars have genes? Do cars have sex? Do they undergo spontaneous mutations? Do cars undergo genetic recombination during meiosis? Do cars even reproduce at all?

      Then why the fuck would any one think that your car would start changing if just left alone?

      Holy shit what a stupid point you made.

    3. Pauline, you just brought attention to the vast difference between intelligent designed objects which don't evolve, like your car, and biological organisms, which do evolve. The gap between the complexity of biology and the complexity of intelligently designed objects, like your car, is so large as to be unbridgeable.

      The difference you brought attention to is the fact that your car has no sex organs, whereas animals and plants do; your car does not reproduce and make copies of itself, but organisms do; your car has no genome, but organisms do; your car's offspring don't exist and can't be defined, so we can't measure how different its offspring might be from its parents, but biological organisms have offspring and we can compare the genomes of parents and offspring and measure the mutation rate.

      Although you mistakenly give your car-- a single object-- as an example of "evolution", in fact evolution happens to populations, not single organisms. A single Tiktaalik does not evolve into an amphibian, rather, what evolves is a population which may have hundreds of thousands or millions of individuals.

      For your car, "genome" and "mutation" are indefinable and unmeasurable. For biological organisms, we have measured their mutation rates and observed the evolution of new complexity and increased information.

    4. So Pauline, my assessment of your true motives months ago after a long discussion here at this forums that you were being dishonest and not really interested in learning anything actually turned out right, right? It's the only possible explanation for your extraordinarily idiotic comment. Only Denyse could do worse (Byers doesn't count). But watch out, Arrington is close.

  10. One of the creationists at the forefront of the claim that humans and chimps are far less similar than 98% has been the notorious Jeffrey Thomkins.

    Earlier this year he published a "paper" which exposed the massive flaw in his algorithm which computes the similarity between humans and chimps.

    He was looking specifically at the GULO pseudogene and he made the astounding claim that for this sequence (28,800 base pairs), his algorithm had computed that humans and chimps were only 84% identical.

    I downloaded the exact sequences he was working with and counted up the differences for myself. There were 519 SNPs and 61 indels making them 98% identical. Astoundingly Jeffrey (using his algorithm) had arrived at a number which was over 7x the actual mutation count!

    He made similar erroneous claims (with results just as ridiculous) for gorillas and the 13,000 bases upstream of GULO for both chimpanzees and gorillas.

    I have been trying to get Jeffrey to acknowledge his errors for months now (see discussion here) and to date his is still obstinate about his algorithm being correct and basic maths being wrong.

    It's worth a read for an insight into the mind of a creationist "geneticist".

    1. Could you briefly explain just what his distance measure is?

    2. Here's the paper

      GULO (28,800bp), Human - Chimp: 84% identical
      GULO (28,800bp), Human - Gorilla: 87% identical
      13,000 bases upstream, Human - Chimp: 68% identical
      13,000 bases upstream, Human - Gorilla: 73% identical

    3. Hey, Ace of Spades, you're not the same person as Ace of Clades [AronRa], I guess?

      We should all read your comment at Uncommon Descent where you not only show creationist chimp-human DNA "similarities" are garbage, and expose Jeffrey Tomkins, but (heroically) attempt to figure out how they got their garbage numbers! Detective work...

      I'll tweet your comment from DiogenesLamp0.

    4. As mentioned above, Ace of Spades posted at Uncommon Descent a detailed debunking of Jeffrey Tomkins on human-chimp similarity being "84%".

      Tomkins did in fact post a brief reply at UD, in which he did not explain, or even get close to explaining, why his published numbers are so different from what they appear to be just by eyeballing the sequences. He simply calls AceofSpades' analysis "amateur armchair" and "bogus" but does not explain how his own numbers are larger by factors of 7x or 15x.

      Scientific fraud by Tomkins? There's no reason not to think so, considering that he refuses to make his work reproducible-- but another possibility is that (like other creationists before him) he deliberately designed an algorithm to grossly overestimate the sequence differences between nearly identical sequences, so that each insertion (or unsequenced data, which is an issue with gorilla and chimp) is effectively counted multiple times. So one "N" (unsequenced nucleotide) will effectively count as 7 or 15 differences in Tomkins' shit algorithm.

      The only response from UDites is typical moronic and uncurious sycophancy from BornAgain77:

      Dr. Jeffrey Tomkins, thank you so much for taking the time to clear that up. ,,, Darwinists have been trying to diss your work ever since it came out. I have to admit that I did not know which data set to believe, theirs or yours, until I watched your interview with Ian Juby. I then knew that you are a man who knows exactly what he is doing in this field and who takes his research seriously. Thanks again.

      It's not just that they don't know any science-- it's that they're not even curious about science.

    5. John Harshman, to answer your question about his distance measure, I'll copy in Tomkin's reply to AceofSpaces at UD:

      See if you can figure out what his distance measure is. Be aware that in the past, to pump up the dissimilarity between humans and chimps, creationists (like Niwrad at Uncommon Descent) would take a window of, say, 50 nucleotides and slide it over the human and chimp genome and if any nucleotides within the window (even just one) were different, the creationist would count the whole 50 nucleotides as different. I suspect that Tomkins did something similar when he refers to "sequence slicing the large contiguous sequence into optimized slice sizes", whatever that means.

      Also, he just deletes all the N's (unsequenced nucleotides), and the chimp and gorilla sequences were not fully sequenced and had more N's, so that probably threw off his ability to align his "optimized slices", whatever they are.

      Note that the chimp has more N's than the gorilla, and like Ace, I bet this is the explanation why the idiot Tomkins counts the gorilla as more similar to humans than the chimp is to humans.

      Jeffrey Tomkins: The BLASTN analyses done in this paper were performed after stripping all N’s from the data set and sequence slicing the large contiguous sequence into optimized slice sizes – all done on a local server using optimized algorithm parameters. My data not only takes into account gaps, but sequences present in human and absent in chimp, and vice versa. Doing an amateur armchair analysis on the BLAST web server with default parameters never designed for a one-on-one large scale genomic regional comparison as noted in the comment above by aceofspades25 is bogus. Of course, if the paper was actually read in it’s entirety in regards to the above comments this would have been obvious.

      Also, as noted in several evolutionary papers, which I cited in my paper, the large scale comparison and major differences in structural variability surrounding the GULO regions between humans and great apes in the intronic areas has been noted before. Interesting that the misleading post by aceofspades25 did not make note of that. My paper was in fact accurate in all respects and true to previous findings published by evolutionist themselves. My work just hashed out and exposed what was already known, but never previously elaborated upon because it shows just another aspect of what a complete fraud the human evolution paradigm truly is.
      [Tomkin's reply to AceofSpaces at UD]

    6. At Reddit, AceofSpades has effectively proven that Tomkins' bullshit similarity figures are due to him improperly handling the parts of the chimp genome that were N's, not sequenced yet. Tomkins' paper highlighted a region of what he calls "extreme discontinuity" and it's the N-part of the chimp sequence. Bizarrely, Tomkins' figure still shows small regions of "alignment" inside the UNSEQUENCED part of the chimp genome, so he is clearly pulling some bullshit with slicing sequences into fat windows and aligning them individually.

      Here is Ace's killer comment at Reddit-- Tomkins was initially responding to AceOfSpades, but then bailed after this killer comment, I wonder why?-- and I recommend you click on the links which conveniently show images of the alignments. Tomkins is toast!

      AceofSpades: Here is the BLAT result showing that they are 98% identical.

      Here is an image of the aligned sequences, clearly showing that your region of "extreme discontinuity" corresponds to a large gap (unsequenced region) in the chimpanzee genome.

      The MUSCLE algorithm made a few mistakes in the alignment and so it is far from ideal, but it still shows sequences that are 97.98% identical.

      This diagram shows the regions where the MUSCLE algorithm could and couldn't align the sequences.

      Here is your region where you claim there is "extreme discontinuity". As you can see, this region is perfectly continuous at the start and then we run into a large section where the chimp genome hasn't been sequenced. I am rather curious as to how your diagram is showing small regions of alignment within this area when the chimp genome hasn't even been sequenced here.
      [AceofSpades debunks Tomkins' 84% GULO similarity at Reddit, Tomkins never responds]

    7. Thanks for the summary Diogenes, that all sounds about right.

      No, I'm not AronRa :)

    8. Reading Tomkins' "papers", I can't figure out how he measures distances. Nor can I figure it out from the bits you quote. If you understand this, please explain.

  11. I would like to suggest a challenge for creationists:

    Pick 10 positions from the regions suggested below. For each of these 10 positions, make a prediction of how similar you think these sequences will be in Chimpanzees.

    For each of your chosen positions, I will personally go and retrieve 5000 nucleotides from either side.

    I will then take these 10 sets of 10,000 nucleotides and blast them against the chimpanzee genome to find the matching sequences and I will personally demonstrate a sequence similarity of about 98%

    Requests to compare regions around centromeres or defunct centromeres will be ignored since these are rich in Satellite DNA, meaning that multiple matches will likely be found.

    Here are the regions I invite you to choose positions from:

    Chromosome 1: 5 million - 240 million
    Chromosome 2: 5 million - 240 million
    Chromosome 3: 5 million - 190 million
    Chromosome 4: 5 million - 188 million
    Chromosome 5: 5 million - 170 million
    Chromosome 6: 5 million - 160 million
    Chromosome 7: 5 million - 150 million
    Chromosome 8: 5 million - 140 million
    Chromosome 9: 5 million - 130 million
    Chromosome 10: 5 million - 130 million
    Chromosome 11: 5 million - 130 million
    Chromosome 12: 5 million - 120 million
    Chromosome 13: 30 million - 110 million
    Chromosome 14: 20 million - 100 million
    Chromosome 15: 20 million - 100 million
    Chromosome 16: 5 million - 85 million
    Chromosome 17: 5 million - 80 million
    Chromosome 18: 5 million - 75 million
    Chromosome 19: 5 million - 55 million
    Chromosome 20: 5 million - 60 million
    Chromosome 21: 15 million - 45 million
    Chromosome 22: 20 million - 45 million

  12. I noticed this in the Tomkins essay:
    "Of particular note is the growing data set showing that cartilaginous and non-teleost bony fish species are able to synthesize vitamin C while no known teleost (ray-finned) fish has this capability, which is associated with the complete absence of the GULO gene (Drouin, Godin, and Page 2011; Wong et al. 2013; Yang 2013).The complete lack of GULO genes in all studied teleost fish genomes thus far is highly significant because they make up about 95% of all fish taxon (Yang et al. 2013). The key question from a grand evolutionary perspective is how did these genes completely disappear during macroevolution in teleost fishes and then reappear in other metazoan lineages later on?"
    I wonder which 'metazoan lineages' he was thinking of. I wonder if he looked at figure 2 in the Drouin paper he cited.

  13. Similarity is not interesting, what is, is functionality - is this GULO region serves any function or not? If not, how come it remained so identical for so long?

  14. It didn't remain any more identical than random accumulation of neutral mutations indicates. You can do sequence comparisons between quite divergent species of mammals and see how it is basically just becoming increasingly divergent over time, at a rate of mutation that strongly indicates the total absene of purifying selection.
    This link gives a nice overview of that evidence: The pseudogene GULOP.