Pharyngula

Genome sequencing is getting cheaper and faster, and more and more people are having it done. A new addition to the ranks is Steve Pinker, who contemplates the details of his personal genome in an interesting essay. It’s got to be fascinating, in a terribly self-centered way — I’d love to have a copy of mine someday. It’s an opportunity to see a manifestation of one’s own lineage, your biological history all laid out for you. There’s the ability to compare with others, and see hints of statistical correlations and associations with specific traits and even, unpleasantly, diseases. Pinker also makes the point that you are not determined by your genome — the man famously has a wild head of hair, and as it turns out, he’s also carrying a bit of sequence that seems to predispose carriers to baldness.

At the same time, there is nothing like perusing your genetic data to drive home its limitations as a source of insight into yourself. What should I make of the nonsensical news that I am “probably light-skinned” but have a “twofold risk of baldness”? These diagnoses, of course, are simply peeled off the data in a study: 40 percent of men with the C version of the rs2180439 SNP are bald, compared with 80 percent of men with the T version, and I have the T. But something strange happens when you take a number representing the proportion of people in a sample and apply it to a single individual. The first use of the number is perfectly respectable as an input into a policy that will optimize the costs and benefits of treating a large similar group in a particular way. But the second use of the number is just plain weird. Anyone who knows me can confirm that I’m not 80 percent bald, or even 80 percent likely to be bald; I’m 100 percent likely not to be bald. The most charitable interpretation of the number when applied to me is, “If you knew nothing else about me, your subjective confidence that I am bald, on a scale of 0 to 10, should be 8.” But that is a statement about your mental state, not my physical one. If you learned more clues about me (like seeing photographs of my father and grandfathers), that number would change, while not a hair on my head would be different. Some mathematicians say that “the probability of a single event” is a meaningless concept.

Another thing I should think having a copy of your genome should drive home is how much of it is incomprehensible; we simply don’t know what most of it does, and even in the example mentioned above, we don’t have a causal relationship between one variant of the rs2180439 SNP and head hair, only a rough correlation. That’s the promise of the future, that we can now get copies of this book of our genome…we just have to get to work learning how to read it.

I’ve got my eye on the progress in genome sequencing. When the price hits $1000 (which isn’t at all unlikely to occur in my lifetime), I know I’m going to have it done, just because it’s a book I’ve been waiting most of my life to read.

Comments

  1. #1 James F
    January 12, 2009

    My DNA
    My DNA
    I want you to play with my DNA….

    (Apologies to Chuck Berry, it’s late)

  2. #2 zaardvark
    January 12, 2009

    I would have to know whether I was predisposed to Alzheimer’s, or not. I might regret it terribly, but not knowing is a bit disturbing, too…

  3. #3 Wowbagger
    January 12, 2009

    PZ Myers wrote:

    we simply don’t know what most of it does

    Well, that’s as good as irrefutable evidence for God then, isn’t it? I mean, if you can’t explain what it does then you can’t argue that it’s not God, can you?

    /desperate gappist rant>

  4. #4 Interrobang
    January 12, 2009

    Despite his statistical likelihood of being bald, he has an astonishing head of hair. Wow. I think I’m in love with (just) his hair…

  5. #5 Don Smith, FCD
    January 12, 2009

    I’d also like to have my sequence but with the current state of health care in the US, I’m afraid that insurers would demand to see it to determine whether to cover you or not.

  6. #6 Cyan
    January 12, 2009

    Methinks Pinker needs some exposure to Bayesian probability and statistics.

  7. #7 Patricia, OM
    January 12, 2009

    My DNA is done on my fathers side. Despite everyone’s honest help here, I still don’t have a rats ass clue on what it means.

  8. #8 Cuttlefish, OM
    January 12, 2009

    The volumes that are written in a strand of DNA
    Are a poetry we thought beyond our reach
    But thanks to all the thinkers reading genomes such as Pinker’s
    We will see how much a molecule can teach.

  9. #9 Jon
    January 12, 2009

    You can get part of it done for US $399.
    https://www.23andme.com/

    I’m sorely tempted. Hell, I was sorely tempted when the kit was still $1,000, but at least then it was prohibitively expensive.

  10. #10 Azkyroth
    January 13, 2009

    Pinker also makes the point that you are not determined by your genome ? the man famously has a wild head of hair, and as it turns out, he’s also carrying a bit of sequence that seems to predispose carriers to baldness.

    Am I misremembering, or isn’t this guy one of the world’s biggest fanboys for the Evolutionary Phrenology view of gender differences?

  11. #11 Bronze Dog
    January 13, 2009

    My cloning tanks are on standby.

  12. #12 Eric TF Bat
    January 13, 2009

    If you have Python installed on your computer, you can always use this instead:

    from random import random
    while 1:
      print "GATC"[int(random()*4)]

    There! I just saved you a thousand dollars!

  13. #13 Patricia, OM
    January 13, 2009

    I’m an epic fail on links, but I’ll try this one for Good Night Sweethearts –
    http://www.youtube.com/watch?v=PdY9ANA_HI&feature=related

  14. #14 Cujo359
    January 13, 2009

    As someone who knows basically nothing about biology, I’d always figured that the genetic cause of baldness would be one of the first things discovered. Supposedly, you can tell you’ll be bald if you’re mother’s brother is bald (naturally bald, of course). If that’s true, then it seems logical that whatever controls that is in the X chromosome, which at least narrows down the search parameters quite a bit.

    Apparently, it’s not that simple.

  15. #15 Mark
    January 13, 2009

    So how will a genome mapping reveal epigenetic effects?

  16. #16 Elisabeth Goodman
    January 13, 2009

    You can in fact have a meaningful amount of your DNA sequenced for $1000 by the new online company “23 and me”. They only sequence select parts, but I would do it if I had $1000 sitting around.

    https://www.23andme.com/

  17. #17 Ronald Brak
    January 13, 2009

    You won’t have to wait long to have your genome sequenced for $1,000 with the cost halving about every two years. A few years might do it. One company claims they will charge $5,000 later this year. We’ll have to wait and see if that’s too optimistic, but prices have come down dramatically and will probably continue to do so.

  18. #18 Galileosreturn
    January 13, 2009

    There is a VERY Good SF movie called Gattica. People pick partners based on their DNA profile and class/status is a issue based on DNA modifications

  19. #19 Gregory Kusnick
    January 13, 2009

    Cujo @ #14: Yes, the major factors controlling male-pattern baldness are on the X (link). The gene Pinker’s talking about (on chromosome 20) is of secondary importance. So the following statement of his doesn’t quite hold up, since pictures of your male ancestors are not good predictors of your own state of baldness:

    If you learned more clues about me (like seeing photographs of my father and grandfathers), that number would change, while not a hair on my head would be different.

  20. #20 Inoculated Mind
    January 13, 2009

    Oh it will get down to $1000 in our lifetimes. And farther down!

  21. #21 nanoAl
    January 13, 2009

    one of the nano-biotech profs at my university is trying build a usb stick that’ll sequence a genome for less than 100$, in a couple of minutes. Its a few years off still. But now that us high tech jerks are into this, moore’s law is taking hold (a bad guess gives it about 5 years for it to come under 1000$). I know I’ll get mine sequenced when its possible, it’d be fascinating and entirely incomprehensible to me. super duper cool

  22. #22 Kel
    January 13, 2009

    I’m in two minds about sequencing my genome. My desire to know is offset by the nature of my mind. If I found out I had a terminal disease, I’d be mortified. Sometimes ignorance is bliss.

  23. #23 Peter Ashby
    January 13, 2009

    @Cujo359
    A bald maternal uncle will increase the chances of you being bald but not make it a certainty. Your mother has two X-chromosomes to dole out and you will get one of them. So you will have a 50/50 chance of inheriting that chromosome. However if your mother’s father is bald as well as her brother you are stuffed, or rather your pillow is ;-)

    For the record my mother’s twin brother was nicely hirsute in later life as was her father. Just to cover chromosome 20 my Dad was well crowned as well. I shall be a silver fox.

  24. #24 Bjørn Østman
    January 13, 2009
    “If you knew nothing else about me, your subjective confidence that I am bald, on a scale of 0 to 10, should be 8.” But that is a statement about your mental state, not my physical one.

    This is dumb. Probabilities are always “subjective confidence.” They are always modified by more information, so if you know nothing else about Pinker, the chance is estimated to be 0.8, If you know he isn’t bald, then the chance that he is is 0.

    What a waste of words from Pinker.

  25. #25 Confused
    January 13, 2009

    I wonder if it includes mitochondrial DNA, and/or copy number variants…

    @NanoAI: Having some insight into DNA/genome handling, I find this USB stick idea highly implausible. Do you have any idea how this concept would work? Are you sure you’re thinking about sequencing?

  26. #26 H.H.
    January 13, 2009

    Some mathematicians say that “the probability of a single event” is a meaningless concept.

    This sounds like a very good response to those who enjoy pretending that our Universe is specially designed, too, by pointing out the “unlikely” probability that it would have turned out this way.

  27. #27 Abie
    January 13, 2009

    @ #18 : The title is GattAca : the name of the place is supposed to be written with bases…
    http://www.imdb.com/title/tt0119177/

  28. #28 Peterte
    January 13, 2009

    Hmmm…. so Steven Pinker wears a hair piece then? Amazing what you can discover with a genome. He seems a bit defensive on it.

  29. #29 Richard Harris
    January 13, 2009

    H.H., the probability of a single event is a meaningless concept…This sounds like a very good response to those who enjoy pretending that our Universe is specially designed…

    If a universe ‘poofed’ into existence out of nothingness, once, then it seems just as likely (probability cannot be computed) that this has happened an infinite number of times, rendering premeditated design superfluous as an explanation for our existence.

    I think that the infinite universes theory is more tenable than the special event universe. Logically, there should be just infinite nothingness, however, as observed, this is not the case. A magic god-thing could bring about a special event universe, but what caused the magic god-thing? Alternatively, there could be a natural process that creates matter-energy, so, in in an infinite volume of nothingness, there must be an infinite number of universes, at any one time, so altogether, that makes an infinity of infinities, assuming that our concept of time is meaningful here.

  30. #30 Holbach
    January 13, 2009

    Good grief, with the religious strickened having their genome sequenced, the thought that religion will survive as long as humans do is horrible to contemplate. Perhaps we can unwire the so-called god genome and be assured that future humans will be free of such superstitious nonsense.

  31. #31 CJ
    January 13, 2009

    Hm…

    My dad recently had a genetic test done. It found that he was homozygous for the A1298C mutation, which results in an abnormal folate metabolism and leads to decreased neurotransmitter levels (up to 30%) even in heterozygous people.

    The lack of neurotransmitters can have results as variant as migraines or snap (fight-or-flight) responses to even mild stress. Coupled with other mental conditions, it can make them much harder to control.

    Because antidepressants work to increase receptors, not the neurotransmitter itself, people who have even one copy of this mutation often do not respond to normal treatments. There’s a new drug, which my brother takes, called Deplin, which has shown to be effective in people with our genotype.

    Obviously I’m at least heterozygous. I haven’t gotten tested myself, and part of it is just out of objection. I don’t have any symptoms for the condition. I’m also one of the calmest, stable people I know.

    I think it goes to show that there’s a great deal of complexity beyond the one-gene explanation to almost any kind of condition.

  32. #32 Ian
    January 13, 2009

    “…he has an astonishing head of hair…”
    It’s not well known, especially by me, but Pinker had all his hair surgically removed and then had it replaced with an exact replica, roots ‘n’ all….

    “Methinks Pinker needs some exposure to Bayesian probability and statistics.”
    He seems rather uninformed about epigenetics, too.

    “If you have Python installed on your computer…”
    I had Monty Python installed on mine. It turned out to be a Complete Waste of Time….

    “I’m in two minds about sequencing my genome…”
    Then you should have it done if only to check for schizophrenia…!

    OK, I’m done!

  33. #33 E.V.
    January 13, 2009

    It’s got to be fascinating,

    in a terribly self-centered way

    ? I’d love to have a copy of mine someday.

    Sheer poetry PZ.

  34. #34 chuckgoecke
    January 13, 2009

    Bjørn Østman, This was from an Op ed piece in the NYTimes. Any verbage that puts statistics in perspective, even if its for the masses, is well spent. This is especially true when considering intelligence and Books like “The Bell Curve”. Ultimately the “n” is one, when you are standing across from someone.

  35. #35 jim
    January 13, 2009

    The report said that 80% of men who have that form of the gene are bald which has nothing to do with Bayesian or frequentist statistics. It is a simple measurement. It was Pinker who turned it into some sort of personal thing. At this point in his life he is not bald, so it appears that he is among the 20% of the population with that form that are not bald.

    I am among about 95% of people with this weenie little Y chromosome to not go to jail.

  36. #36 Rieux
    January 13, 2009

    chuckgoecke @ 34:

    Any verbage that puts statistics in perspective….

    Augh! Sarah Palin, what hath thou wrought?

  37. #37 molecanthro
    January 13, 2009

    PZ…you say “I’ve got my eye on the progress in genome sequencing. When the price hits $1000 (which isn’t at all unlikely to occur in my lifetime)”

    I have to disagree….I’d say within the decade. I work with 454 technology and see that we’re getting more and more data…very quickly. And with the new methods in single molecule sequencing we should be there sooner.

    http://www.sciencemag.org/cgi/content/abstract/323/5910/133
    Science has an article on a new technology which might get there sooner than 10 years…and with deeper coverage.

  38. #38 Grumpy Mr. Gruff
    January 13, 2009

    As mentioned in the NY Times article, the Personal Genome Project (slated to begin enrollment sometime this year) wants 100,000 volunteers (each ready to pay $1000) to have their genomes sequenced. You can register to be chosen for enrollment at the site.

  39. #39 windy
    January 13, 2009

    It is a simple measurement. It was Pinker who turned it into some sort of personal thing. At this point in his life he is not bald, so it appears that he is among the 20% of the population with that form that are not bald.

    Exactly. What’s with the mysticism? Would Pinker call it a “paradox” that there are individual smokers who don’t get lung cancer?

    And chuckgoecke, this isn’t a good way to put “statistics into perspective”. Why does Pinker say that the lactose intolerance prediction is “plausible enough” (but wrong) but the baldness prediction is “flat-out wrong”? What’s the difference if both only predict a RISK of a condition that he doesn’t happen to have?

  40. #40 Nate
    January 13, 2009

    With the rise of personal genome sequencing over the next few years we are going to be seeing more and more of these nucleotide-gazing essays.

  41. #41 chuckgoecke
    January 13, 2009

    Windy, I don’t think the two situations are analogous. Pinker is famous for his magnificent mane, so its quirky that genetic stats point towards him being bald. He is very clearly not bald. I believe lactose intolerance is not a 1 or 0 situation, there are degrees of it. Quite lactose intolerant people can train themselves to tolerate dairy, via diet, building gut flora, etc. It also is not outwardly apparent. Perhaps Pinker is not totally convinced he is completely lactose tolerant; maybe that last banana split didn’t sit quite as well as he’d wished.

  42. #42 Tom
    January 13, 2009

    I wonder what percentage of men with the C version of the rs2180439 SNP have read “Alice in Wonderland”.

  43. #43 Jud
    January 13, 2009

    But something strange happens when you take a number representing the proportion of people in a sample and apply it to a single individual.

    There’s a banner quote for the next time someone starts going off about the usefulness of intelligence tests.

    Oh, and Kel (#22):

    If I found out I had a terminal disease, I’d be mortified.

    There, fixed that for you.

  44. #44 Jon D. Moulton
    January 13, 2009

    You might not have long to wait for that $4000 price, PZ. I was at the American Society for Human Genetics conference in late 2008 and stopped at the BGI booth, where they were offering human transcriptome sequences for $4000. Granted, your introns and UTRs would remain mysterious, but coding sequence might address much of your urge for nucleotidic navel-gazing.

    http://www.genomics.org.cn/en/index.php

  45. #45 meh1963
    January 13, 2009

    As a person gets older, will the telomere damage on their chromosomes significantly affect DNA sequencing? Or, to ask the question another way, would it do to put some tissue on ice now so that it can be sequenced later?

  46. #46 Cruithne
    January 13, 2009

    However if your mother’s father is bald as well as her brother you are stuffed,

    Hmm, I’m forty four and still have a full head of hair, it’s not even graying all that much.
    Having said that, all her family were fat bastids, and I did get hit with that arrow.

  47. #47 SocraticGadfly
    January 16, 2009

    I thought the biggest thing Pinker?s essay showed is that half of what he was talking about.

  48. #48 Alain Renaud
    February 18, 2009

    Myers, do you think getting yours will make you more intelligent or more stupid…
    A. R.

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