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Biotech AI Science

Computers May Be As Good As (Or Better Than) Human Biocurators 35

Posted by timothy
from the skynet's-nicer-side dept.
Shipud writes "Sequencing the genome of an organism is not the end of a discovery process; rather, it is a beginning. It's the equivalent of discovering a book whose words (genes) are there, but their meaning is yet unknown. Biocurators are the people who annotate genes — find out what they do — through literature search and the supervised use of computational techniques. A recent study published in PLoS Computational Biology shows that biocurators probably perform no better than fully automated computational methods used to annotate genes. It is not clear whether this is because the software is of high quality, or both curators and software need to improve their performance. The author of this blog post uses the concept of the uncanny valley to explain this recent discovery and what it means to both life science and artificial intelligence."
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Computers May Be As Good As (Or Better Than) Human Biocurators

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  • by smoothnorman (1670542) on Saturday June 16, 2012 @05:37PM (#40346713)
    in all my too many years [hack spittoo] of biochemistry bioinformatics bio-whathaveyou this is the first i've heard of the term "biocurators". and i gotta say, i don't like it. no-sir, not a bit.

    "curator mid-14c., from L. curator "overseer, manager, guardian," agent noun from curatus, pp. of curare (see cure). Originally of minors, lunatics, etc.; meaning "officer in charge of a museum, library, etc." is from 1660s." so, "life + manager" or "life + officer in charge of a library" ...nah.

    'geneannonator' ....maybe

      • by PopeRatzo (965947)

        How do you get "translation and integration" from "overseer, manager, guardian"?

        You can use words any way you goddamn please, but you cannot expect the rest of us play along.

        There were plenty of better words to append to "bio-" than "curator" for this purpose. It's nothing more than an effort use the tools of marketing where they don't belong.

        It's a shame that so much science journalism is shit.

        • by Shipud (685171) *
          This is no science journalism. It's the site of the International Society of Biocuration. which has about 1500 members to date. http://colleagues.biocurator.org/affiliations [biocurator.org] it's too bad that you are ignorant of the field: http://www.ploscollections.org/article/browseIssue.action?issue=info%3Adoi%2F10.1371%2Fissue.pcol.v03.i05 [ploscollections.org]
          • Re: (Score:2, Flamebait)

            by PopeRatzo (965947)

            International Society of Biocuration

            Are they also members of the International Brotherhood of Language Wankers?

            I was once a member of the Elks, but guess what? I wasn't really an elk.

            No, really, that's very nice that they have a name for their "International Society" and all, but thanks to my matrimonial duties, I've had to read more scientific papers than I could count (if I could count), and I'm well-versed in the scientific butchery of language. It's partly due to a disease which causes people who are

            • by kermidge (2221646)

              "I've got all sorts of papers to prove it, with fancy embossed stamps...." Beauty of a para.

              My hope, Your Eminence, is that someday you will unbend enough to tell us what you really think.

              I respect English as a tool and as a thing of beauty in it's own way, but not enough to correct my abuse of it. Being simple, I still mourn the death of the adverbial form, and detest the verbification of nouns and such locutions as "going forward", "at this point in time" and "price point."

              • by PopeRatzo (965947)

                Your Eminence, is that someday you will unbend enough

                I would like to unbend, but then it gets caught in the bike's spokes.

            • I was slightly skeptical until you mentioned the tweed coat, and the elbow patches really nailed it down. You should really invest in some briar pipes and Balkan Sobranie.

              This sentence is ambiguous, though: "And despite one (at least) slightly shoddy episode with a fulsome grad student in the early 80's, I've got a stellar reputation in the field." At least one episode, or at least slightly shoddy? Was the the grad student effusive, generous or simply "full and well developed"? Hmm... perhaps the ambiguity

              • by PopeRatzo (965947)

                Was the the grad student effusive, generous or simply "full and well developed"?

                All of the above, if my memory speaks the truth.

                It tends to be a very unreliable narrator, I'm learning.

                But fulsome enough. That's what matters.

            • Now don't get me started on "combinatorics".

              Do you have a better suggestion for the name of that particular field?

              BTW, I know you're at least partly exaggerating for humorous effect, but I have to point out that lines like "It's partly due to a disease which causes people who are expert in one area to spontaneously believe they are expert in any area that they choose, and partly due to post-docs yearning to be special" and "geeks with lab coats and large pores want to clip a form in the back of a journal and send in a money order for $15" don't do a

              • by PopeRatzo (965947)

                I know you're at least partly exaggerating for humorous effect

                "partly"?

                I didn't mean to offend.

                And you're certainly correct that literary critics are among the worst of the lot when it comes to horrible neologisms.

                I believe that combinatorics is among the most beautiful of the Maths. The name is just a mouthful. Bit so is "deconstructionism".

                And regarding my horrible stereotyping of biologists: my beautiful daughter is engaged in the study of biomathematics (which now makes me officially the stupidest

                • Sorry for overreacting. It's a hot button for me, I guess; I do so loathe any manifestation of the pervasive Two Cultures bullshit that I often have a hard time telling when people are joking about it.

    • by Shipud (685171) *
      You must not be reading th etop journals in the field: http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020142 [ploscollections.org]
    • by Yvanhoe (564877)
      I concur. It took me a while to understand that "biostatistics" is simply statistics with no specific mathematical tool...
    • by mcgrew (92797) *

      TFA talks of the Uncanny Valley and little about actual gene sequencing, I didn't read much past the Valley graph; nothing I didn't already know. What did interest me was the two chatbots conversing; it looks like bots haven't improved much since 1983 when I wrote Artificial Insanity on a fantastically underpowered computer. I posted this on my old Quake site ten years ago:

      Alice joined the game
      About 20 years ago, frustrated that otherwise serious researchers and scientests seemingly thought they could progr

    • Did anybody else read this as "Computers May Be As Good As (Or Better Than) Human Binoculars"?
      I thought it meant people with really good eyesight.
  • In fact rather the opposite - it says that the reliability of the machines is 'competitive' or 'rivals' the human curators. That's marketing speak for 'not quite as good just yet'.
    • by Shipud (685171) *
      If you look at the figures, you'll see that the IEA-evidenced annotations outperform the curated ones.
  • by slew (2918) on Saturday June 16, 2012 @07:08PM (#40347399)

    This author seems to have inappropriately compared the "fear" of machines doing better than humans with concept of uncanny valley.

    The concept of the "uncanny valley" is that the affinity of humans for observing the appearance or behavior of a human-like entity (robot, alien, whatever) has this unexpected dip when it is too close to the human behavior (we have this apparent built-in viceral problem with the entity). However, this is only true when it is trying to mimic human-like behaviors. If it's doing something totally different or totally exceeding human behaviors (say distinctly non-human speed, accuracy, strength, appearance, etc), the uncanny valley doesn't say anything about affinity, in fact, if you were to extrapolate the curve out, humans might even have more affinity for these "super-human" behaviors. Maybe that's why many express affinity for live-action versions of comic book super-heros, or airbrushed models in magazines. The behavior is so far from the uncanny valley that it doesn't invoke the supression response that is responsible for it.

    Just like what was once observed with "space-shuttle" pilots, the computers can probably do a better job at this task, but we don't quite trust them yet (for some reason). That's really just the human fear of being replaced by machines, not uncanny valley. Note that the only people fearful about this behavior are the people that are likely to be replaced (and maybe a few that sympathize with them)...

  • by Anonymous Coward

    There are a few people in the world, who work for INSD members like NCBI or EMBL, whose job is "biocuration". It's a rare profession. Having reliable annotations available does not equal to discovering a book. In a car analogy, genes are a list of parts. You know things about the car, but how it works and comes together is up to human ingenuity. In the bioinfo/molbio field that usually means heavy use of OSS and shell coupled with in vitro experiments.

  • Biocurators are the people who annotate genes — find out what they do — through literature search and the supervised use of computational techniques.

    Biocuration means that? I'd have never guessed from the name. Let's face it, literature searching is now something that is thoroughly practical by computer (it's pretty much just like using a web search engine, except over a different digitized corpora) and "supervised use of computational techniques" there makes it sound like they're a bunch of low-level lab technicians. No creativity required at all. Is it any wonder they're being replaced with little more than a shell script? What's more, the computer wi

  • Why not find a way to leverage the advantage of each?

"Pay no attention to the man behind the curtain." -- Karl, as he stepped behind the computer to reboot it, during a FAT

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