Jan 13 2015

Chimp and Human DNA

I was recently asked to respond to an apologist page that  challenged the scientific claim that human and chimpanzee DNA are very similar, which is evidence that we are descended from a recent common ancestor. You have probably heard the claim that human and chimp DNA are 96% the same. The apologist was referencing the work of Jeffrey Tomkins in his “peer reviewed” study showing that there is only 70% similarity. In fact, the the DNA of chimps and humans are so different, Tomkins claims, that there would not have been enough time for evolution to account for all the changes.

This is what I like to call, “sophisticated nonsense.” The very purpose of pseudoscience such as this is to confuse the public with complicated arguments that only scientists are likely to understand. We can turn such pseudoscience, however, into teachable moments.

For background, it is helpful to understand that there is no completely objective way to come up with one number that represents the percent similarity between the DNA of two species. There are just too many different choices to make in terms of how to count similarity. For example, how do you count chromosomal differences? Do you just compare the sequences of genes in common? What about insertions, gene duplications, and deletions? Do you line up sequences to their best match and just count point mutations? Do you count non-coding segments?

There is no one right way to do it to give a definitive answer of similarity. However, if you have a specific question in mind, then the method you choose should be designed to answer the question.

In this case we do have a very specific question – how recent, according to a comparison of human and chimp DNA, is the most recent common ancestor likely to be? What geneticists do to answer this question is take segments that the two species have in common, line them up, and then count point mutations. They then can calculate, given known mutation rates, how long the two samples of DNA have been evolving away from each other. Each species is accumulating new mutations over time at a fairly predictable rate.

Doing this kind of analysis has yielded a variety of answer, from 8-13 million years ago. The range is due to the way in which the comparisons were made and how the mutation rates were calibrated. Also, when an ancestral population splits into two is not always a clean event. Different populations can have decreased interaction over millions of year, with occasional back breeding before the split is final. So a genetic split of 13 million years is still compatible with fossil evidence of a split 8 million years ago.

What about the percent? With this type of analysis scientists come up with a range, about 95-98% similarity between human and chimp. The average number of 96%, derived after the complete mapping of the chimp genome, is now generally accepted. But this number is just representative. It depends on what you’re looking at. Some genes are highly conserved, others less so.

So how does Tomkins come up with 70%. Well, he is not comparing point mutations of aligned segments. He is comparing chromosomes to see how many segments line up to some arbitrary amount. As many others have already pointed out, this result is not wrong, it’s just irrelevant. Well, it might also be wrong. Others have found it difficult to reproduce his results. But even if his analysis is accurate, it is simply the wrong analysis to apply to dating the last common ancestor.

To explain the problem further, he is applying mutation rates for point mutations (changing a single base pair) to other types of mutations, like gene duplications or insertions, that might change thousands or millions of base pairs with a single mutation. He is essentially treating a single mutation that results in the insertion of 10,000 base pairs into the genome as if it were 10,000 separate mutations of single base pairs.

How did he get such a blatant error past peer-review? Well, that is the reason for the scare quotes around “peer-review” above. He published in a young-earth creationist rag, Answers Research Journal. He published ideologically motivated nonsense in an ideologically motivated journal, the purpose of which is that creationists can go around citing peer-reviewed papers to befuddle non-scientists.

It works. The apologist to whom I was asked to respond was doing just that on his Facebook page, bludgeoning any commenters with his peer-reviewed source.  The average Facebook commenter is not going to spend the time to do the requisite searching, coming up with half a dozen references to give proper background to the science, and specific sources addressing the Tomkins paper. Even if they tried, without a sufficient background in science it may be difficult to understand the logic behind interspecies DNA comparisons to calculate last common ancestor.

That is why it is perfectly reasonable to side with the scientific consensus, even when someone confronts you with apparently sophisticated arguments or evidence. It is also reasonable to dismiss evidence because the source is obviously ideological or does not seem reputable.

Unfortunately, those types of judgments can sometimes be complex also, and sometimes sophisticated nonsense works its way into reputable journals. There is no simple algorithm you can apply. Sometimes you just have to have a working knowledge of the science. You may also rely upon proven trustworthy sources, but then you susceptible to overreliance on authority.

The pseudoscientists have a distinct advantage here. All they have to do is muddy the waters and sow doubt and confusion.

There are some fairly reliable red flags that can help, however, and we discuss these often. Sources that are obscure, seem ideologically bound, or have direct commercial interests are suspect. Extreme minority opinions are probably in the minority for a reason. Invoking conspiracy theories to explain rejection by the mainstream scientific community is almost certainly nonsense. Invoking unseen, magical, mystical, or paranormal powers or effects is a huge red flag.

In the end, for the non-expert, it is best to use a combination of methods. Examine claims for these and other red flags. Rely upon trusted scientific sources, but also make an effort to understand the scientific basics so at least you can apply a basic smell test to claims. And of course there are now many scientists and experts on social media who would be happy to dissect such claims, so use them as a resource.

Unfortunately, well organized pseudosciences like creationism have their own experts, their own social media warriors, and now even their own peer-reviewed journals, institutions, and other trappings of legitimacy. They have been unable to gain acceptance by mainstream science through evidence or argument, and so they have simply created a bizarro world alternative in which they are correct. They no longer have to convince actual scientists, they can simply talk to each other and generate sophisticated nonsense to confuse the public.

24 responses so far

24 Responses to “Chimp and Human DNA”

  1. dbfinneyon 13 Jan 2015 at 10:46 am

    Steven, thanks for this.

  2. John Danleyon 13 Jan 2015 at 12:03 pm

    Trying to employ a reasonable doubt wedge strategy to usurp ancestral chromosome fusion is a mug’s game. Of course, was there ever any doubt that Tomkins was tendentiously unreasonable given his mere-reviewed protocol?

  3. DevoutCatalyston 13 Jan 2015 at 1:44 pm

    A different trajectory, but it might be fun for you to tackle Jeffrey Schwartz from the University of Pittsburgh. Scientific American fawns over his book The Red Ape,

    http://www.amazon.com/Red-Ape-Orangutans-Origins-Revised/dp/0813340640/ref=sr_1_14?ie=UTF8&qid=1421171963&sr=8-14

    Schwartz appears to me a crank.

  4. BillyJoe7on 13 Jan 2015 at 4:55 pm

    DC,

    I’m not sure if that would be worthwhile. “The Red Ape” was written in 2005, and it was a reprint of his earlier book written in 1987. The more recent version has only 6 reviews in 10 years.

  5. BillyJoe7on 13 Jan 2015 at 5:07 pm

    SN: “This is what I like to call, “sophisticated nonsense”.”

    Congratulations on the coining of a phrase.
    It accurately and concisely captures the activity in question.

    (Jerry Coyne has “coyned” his own phrase: “sophisticated theology”.
    The added nuance is that the theology espoused by “sophisticated theologians” bears no resemblance to the theology of the common believer, making it nonsense even for them.)

  6. MaryMon 13 Jan 2015 at 7:27 pm

    I love the phrase “sophisticated nonsense” too. I see it all the time, but didn’t call it that.

    The best description I’ve seen of that before was here:

    The talking point on one side is just complex enough that it’s both intelligible–even somewhat intuitive–to the layman and sounds as though it might qualify as some kind of insight. (If it seems too obvious, perhaps paradoxically, we’ll tend to assume everyone on the other side thought of it themselves and had some good reason to reject it.) The rebuttal, by contrast, may require explaining a whole series of preliminary concepts before it’s really possible to explain why the talking point is wrong. So the setup is “snappy, intuitively appealing argument without obvious problems” vs. “rebuttal I probably don’t have time to read, let alone analyze closely.”

    http://scienceblogs.com/mikethemadbiologist/2009/04/20/the-asymmetry-of-bullsh-t-and/

  7. Jared Olsenon 13 Jan 2015 at 11:38 pm

    Is the nonsense *in general* getting more sophisticated?
    Or do these “sophisticates” just pop up from time to time?

  8. BillyJoe7on 14 Jan 2015 at 6:10 pm

    It’s certainly getting more impenetrable and obtuse.

  9. ccbowerson 14 Jan 2015 at 9:57 pm

    Fortunately, identifying most sophisticated nonsense does not require much digging if you have a good basic understanding of the topic, and have reasonable critical thinking skills.

    The trickier sophisticated nonsense often involve topics made unnecessarily complex while having ideological implications. These conditions alone should be a clue to be on the lookout for motivated reasoning, if not intellectual dishonesty.

  10. Jared Olsenon 15 Jan 2015 at 12:01 am

    I guess it’s inevitable that they’d up their game in response to greater skeptical activism, but I still find it worrisome.
    I think it’s already very difficult to engage the layperson in science and critical thinking, and as the arguments become more complex and opaque, it’s just gonna get tougher.

  11. arnieon 15 Jan 2015 at 8:04 am

    I’ve noticed in my conversations with nonsense and woo sophisticates, they behave much in the manner of bacteria in response to arguments based in science and critical thinking. They desperately mutate their more complex, sciencey, but still nonsensical verbiage in an effort to reinforce their resistance to evidence and logic.
    Hopefully, the long term persuasive power of evidence and logic will erode the resistance of enough of their invasive “bacteria” sufficiently to gradually provide increasing immunity to their destructive impact for increasing numbers of our species.
    Not easy, but can’t give up our own efforts as well as appreciation for dedicated contributors like Steven.

  12. arnieon 15 Jan 2015 at 8:07 am

    Change “bacteria” in my first sentence to “antibiotically challenged bacteria”

  13. Jared Olsenon 15 Jan 2015 at 3:34 pm

    @Arnie: Agreed. And good analogy. Particularly ironic in regards to evolution deniers!

  14. arnieon 15 Jan 2015 at 5:07 pm

    Jared,

    Yes, very ironic!

  15. mattartaraon 15 Jan 2015 at 5:24 pm

    Nice Post! especially liked the “sophisticated nonsense” like many!! LOL
    I am from Argentina luckily here the creationism is almost nonexistent, i think it has to do with the fact that the protestant church doesn’t have too much force here; but i have seen this kind of nonsense in people using pseudo science in the anti-vaccine movement.
    I think is really worst, because they really are putting mainly kids in danger.
    The worst part of this, is people citing this kind of works in facebook even without even looking at the sources.
    One more thing to add to “how to spot” this kind of pseudo science that i have seen, is that they often cite just one part of a really good scientific paper or just a tiny part of the conclusion that supports his side of things, the rest of the paper can arrive to an opposite conclusion, but if a person do not look any further than this it seems that support an opposite view.

  16. ccbowerson 15 Jan 2015 at 5:55 pm

    A few things realted to that bacteria analogy. One is that the more convoluted the nonsense, the less assessible the message. So hopefully, the more that motivated reasoning (in response to evidence and arguments) complicates their message, the more convoluted the message becomes. The mental gymnastics should become more evident as more evidence and good arguments accumulate.

    The group of people we are talking about it pretty small… pseudointellectuals that are interested in building complex arguments to protect their ideologies. There is no point to using too much energy to educate that group. Their issue is not of education, but motivation and ideology.

    As a group, the readers of this blog (and skeptics in general) are more likely to encounter the sophicated nonsense group, because we are a self selected group who may engage those individual. Despite this, however most people (the general population) do not have a sophicated understanding of these complex topics, and have opinions that are not well informed on these issues. It is this group for which education and argument may have a chance, at least over time.

  17. arnieon 15 Jan 2015 at 6:22 pm

    CC,
    Thanks for your very relevant elaboration. Excellent additional points which reflect some of what I had in mind in referring to the “erosion” of their impact on others as our accumulating science based, and increasingly clear and convincing, message forces ever more convoluted responses from that group of which the general public will be increasingly unable to make any sense.

  18. BillyJoe7on 15 Jan 2015 at 6:37 pm

    CC & arnie.

    Me too!

    “theology espoused by “sophisticated theologians” bears no resemblance to the theology of the common believer, making it nonsense even for them”

    Seems we’re basically agreed on that point. (:

  19. Jared Olsenon 15 Jan 2015 at 8:42 pm

    @CC That’s an interesting point, I’d not thought of that.
    But..I’m not convinced. What you say hinges on the public’s knowledge
    of what Steve calls “neurological humility” which IMO is pretty lacking.
    For motivated reasoning to be evident, one must be aware such a thing exists.
    In all of my encounters,the most difficult thing to get across
    is our ability to fool ourselves into believing what we want to believe.

  20. grabulaon 15 Jan 2015 at 10:13 pm

    @CCBowers

    “Fortunately, identifying most sophisticated nonsense does not require much digging if you have a good basic understanding of the topic, and have reasonable critical thinking skills.”

    I’d say just reasonable critical thinking skills is the minimum required. If you don’t enough about the sbuject then a good critical thinker will look into the subject to get that better understanding.

  21. ccbowerson 15 Jan 2015 at 10:26 pm

    Jared – the motivational reasoning itself does not have to be evident to the average person, but like the religious analogy BJ7 mentioned- the sophisticated nonsense that becomes sufficiently convoluted will look more and more like nonsense even to the people who agree ideologically.

    Small correction. The term he uses is “neuropsychological humility.”

  22. ccbowerson 15 Jan 2015 at 10:41 pm

    grabula –

    I did say basic understanding. Without a basic understanding, even looking into a complex topic can be a bit much for the average person, and when looking into a subject it can be difficult to get the proper perspective without a broader understanding. Sometimes critical thinking is enough, but I would never rely on that alone. It is necessary, but often not sufficient.

    This reminds me of a related issue: I do not think that critical thinking skills alone are enough for many complex subjects (outside of the sophisticated nonsense discussion). The problem I often see are people who have some critical thinking skills, who think this is enough to evaluate topics for which they are not sufficiently knowledgeable in. This can get pretty close to the Dunning-Kruger effect. It can be tricky to navigate complexity without more than a basic understanding, and for some subjects even being an expert in an adjacent field is sometimes not enough. This is particularly true in sciences or applied sciences, (e.g. GMO and certain alt. med nonsense even among skeptics)

  23. Jared Olsenon 16 Jan 2015 at 12:54 am

    Fair enough CC, I hope you’re right! But I’m pessimistic.
    BTW thanks for the correction ☺

  24. ccbowerson 16 Jan 2015 at 10:32 pm

    Jared – I don’t think your pessimism is very far from my perspective. I have just adjusted my expectations =)

Trackback URI | Comments RSS

Leave a Reply

You must be logged in to post a comment.