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Some recent DNA threads

by eyepopslikeamosquito (Chancellor)
on Apr 29, 2012 at 06:19 UTC ( #967903=monkdiscuss: print w/replies, xml ) Need Help??

I couldn't help but notice a number of questions in the past week or so supposedly from University researchers in the technical field of Bioinformatics/Genomics. At least they were asking questions about DNA. Unfortunately, most of these threads seem to be dominating the "worst nodes of the week" page. For example:

Now, I'm an ignoramus in these fields but I expected that if you were a researcher in such fields you would be really, really smart with an ability to learn new things quickly. Unfortunately, what I've observed in the above threads is the exact opposite. Moreover, university researchers are expected to publish papers, so I would have expected sound written English skills, which are also conspicuously absent from the above threads. Is it that they are so short of people in these fields that almost anyone can do it? Or maybe these questions are from B-grade students masquerading as researchers? I used to have enormous respect for such researchers but now I'm really surprised, confused and saddened. So if anyone has a plausible explanation, especially a monk who is a Bioinformatics/Genomics researcher, I'd love to hear it.

Update 18 May: another barrage from supriyoch_2008:

And a new player anisha3:

And a new player RRK:

Replies are listed 'Best First'.
Re: Some recent DNA threads
by aaron_baugher (Curate) on Apr 29, 2012 at 15:10 UTC

    The poor English skills struck me too. Yes, there are surely non-native-English speakers in the field, but we're still talking about very educated people. When I deal with educated people in other fields who have learned English as a second language, they'll occasionally get tripped up by an odd preposition usage or something, but in general their grammar is solid. Their English will strike me as stilted, but never sloppy.

    So my guess is that at least some of these questions come from contracted programmers who got stuck with a Perl task despite having little or no experience with the language. If the researchers are hiring large coding companies, the work may be farmed out to wherever they've been able to find the cheapest coders this week. Even a well-respected company like IBM is starting to develop a reputation for high turnover, under-qualified coders, and poor communication skills, because they've made earnings-per-share (and thus cost) their primary concern.

    So that's my guess: some guy who hasn't had his job for long and is already looking for a better one gets passed a task because he mentioned Perl in his job interview, and now he's stuck. He doesn't have the time (or incentive) to spend a few weeks really learning the language. He doesn't even have a few days to try things and wait for the back-and-forth here as people help him fix his errors. He just needs the code.

    Aaron B.
    My Woefully Neglected Blog, where I occasionally mention Perl.

      They can get some help even with a sloppy description of their needs, but they can't get the code if they are unable to explain what is it to do. If I would need help and would have to ask in a language I'm not fluent in I'd do my best to explain with examples what it is I need. Simple sentences, careful spelling (as far as I can) and never ever any "cool" l33t5p33k. And I would mention I'm struggling with the language.

      But then I come from a place where it's considered more acceptable to say "I don't know this" than to claim I'm an expert in a field I've hardly heard of and fail miserably to fulfill the promises.

      The person you mention in your guess deserves to fail and the manager that hires him or the "outsourcing" company AGAIN deserves to be fired.

      Enoch was right!
      Enjoy the last years of Rome.

Re: Some recent DNA threads
by moritz (Cardinal) on Apr 29, 2012 at 10:49 UTC
Re: Some recent DNA threads
by marto (Bishop) on Apr 29, 2012 at 14:01 UTC

    I know very little about this field of study. I do know that a university local to me have recently begun bioinformatics electives. I'm sure this happens every term and isn't unique to this establishment. The students have no Perl (or in the majority of cases any programming) experience, the course is very poor but this is something which is being addressed in the near future. I don't agree that all of these posts are coming from 'researchers' (or people pretending to be researchers) or that everyone in the field must be 'really, really smart'.

    I'm sure people who spend long periods of time here begin to notice trends in popularity of certain topics, bioinformatics being one of them. To me this is hardly surprising. Like a lot of people using Perl to solve a problem, they're not computer science students, or employed to write code they're just trying to achieve a goal. Some could care less how this is achieved.

    When people show up here with a vague specification or check list of goals they want to achieve I tend to advise the walk "before you can run" approach of learning the basics of the tools being used. Sometimes people don't want to hear this, often because they just want the end result rather than to learn from the journey. I find failure to do so results in thread after thread of the same question being posted, see davidos reply to How can I count the number and kinds of letters at 1st, 2nd and 3rd positions of 3-letter words in a string?, which is one of the threads you mention.

    To address some other points you raise, not everyone speaks English fluently, they may not be writing papers or sitting courses in English, simply trying to ask questions in English here. See List_of_languages_by_number_of_native_speakers. There may be a shortage of people working in this field, even if this is the case it doesn't necessarily mean that these questions are from industry/academic professionals.

      The problem is not unique to Perl, nor to recent history. A few interesting MJD articles:

      In the case of these bioinformatics questions, I tend to agree that they're not the result of some highly intellectual researcher who happens to be so frazzled by some problem that he finds himself posting incoherent and poorly-specified problems to PerlMonks. It is far more likely that the undergraduate class BIO239, required as a prerequisite for an associates degree in Medical Records Processing has suddenly added a section on automating genome searches with Perl. The professor enjoys Perl as a hobby, and actually understands some of it, but not well enough to effectively teach non-programmer undergrads how to (a) feel the same passion he has for this hobby, and (b) how to become programmers, and Perl programmers at that, in the course of a few weeks.

      Repeat some variation on this theme across a bunch of universities, community colleges, and degree mills throughout the world, and it's not surprising we get a few kooky posts here as a result.

      As often as I can, I try to just ignore them and move on. Sometimes they pose interesting problems if you can see through the haze of the poster's misunderstanding of programming and/or the problem domain. In those cases, occasionally I'll take a shot at it just out of curiosity. Sometimes I'm feeling good-natured, and try to encourage the poster to learn how to learn Perl so that he can answer the question himself. And sometimes I fire off some pissy comment, realizing about a half second after clicking 'create' that I shouldn't bother, and really shouldn't lower myself.

      I do miss the days when we were frequented by people who just loved Perl because of how cool it is. It may be my imagination, but it seems that it's becoming harder (not only here... just about everywhere) to find the really thought-provoking and interesting posts.


        I do miss the days when we were frequented by people who just loved Perl because of how cool it is. It may be my imagination, but it seems that it's becoming harder (not only here... just about everywhere) to find the really thought-provoking and interesting posts.

        I miss those times too. Though looking around at a few home nodes, it seems that many of those people still visit this place -- though perhaps less frequently than previously -- but for the most part, they no longer post.

        It would be interesting to know why that is.

        With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
        Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
        "Science is about questioning the status quo. Questioning authority".
        In the absence of evidence, opinion is indistinguishable from prejudice.

        The start of some sanity?

Re: Some recent DNA threads
by BrowserUk (Pope) on Apr 29, 2012 at 12:10 UTC

    I find it intriguing that these stalwart "throw me a fish" guys have suddenly started turning up here so soon after the recent 965211 discussions. Maybe they read those and concluded we were all an easy touch here?

      But doesn't that assume a level of effort on their part that is contrary to the empirical evidence we have seen so far?

      Elda Taluta; Sarks Sark; Ark Arks
      My deviantART gallery


        Its easy to live the good life by taking jobs off, and getting stackoverflow and PM to do you job for zilch. Only the suckers dumb enough on stackoverflow and PM would hand out the trade secrets.
Re: Some recent DNA threads
by Anonymous Monk on Apr 29, 2012 at 06:33 UTC
Re: Some recent DNA threads
by sundialsvc4 (Abbot) on May 07, 2012 at 21:01 UTC

    Never overlook the “accounting reality” angle.   Which says that (and I am very sorry to have to say it, in consideration of everyone involved):   I don’t have to know what they are actually doing ... cheapest labor wins.

    The simple reason why I say that “I am very sorry to have to say it” is that ... there exists a very influential segment of our business population that was trained-up in a hypothetical “business” world in which Companies™ make Widgets™.   The only differentiator that actually matters, in their hypothetical world, is:   unit labor cost.

    In other words ... “Be afraid.   Be very afraid.”   You are (correctly!!) telling me that, not only do you know more than three people who cost one-sixth as much as you do, but you can accomplish more, too.   But, the only thing that I see is “a way to reduce unit labor costs by 50%.”   Even if those three people require half-again as much time to fumble their way through to an acceptable-enough solution, I have reduced labor costs by at least 25% and I have removed from the payroll, at a single stroke, one “cost center” that cost six times more.

    Surely, I am due a fat promotion.

    Yes, you are absolutely right that “it sucks to be any one of those three people!”   But no one ever got rich by consigning people to a fate that they deserved.   “The numbers say that,” not only have I just reduced labor-costs by a whopping 25%, but I have also eliminated the organization’s dependency upon one expensive labor-unit (with an atttitude...) and replaced it with a pool of labor that is more-or-less completely interchangeable.   I have eliminated the business requirement for Shakespeare and replaced it with ... Haplorrhini.   My business goal is to sell tickets, to fill every seat in the Old Globe Theater and to sell lots of wine in the process ... not to create a lasting work of literature.

    Now, please!!   Before you dismiss this posting as a rant and with “you must be an [!!] and obviously completely full of [!!!!]” ... I want you to please, for once:   Stop and.   Be afraid.   Become very afraid.   One hundred fifty years ago, you could have been an expert third-generation gunsmith who was utterly certain that Mr. Eli Whitney was similarly full of [!!!].

      Be afraid. Be very afraid.
      Being afraid does not help you think clearly. It actually does the opposite. If you have a sound argument, you don't need to rely on an emotional response. Even if you do need to rely on an emotional response, subtlety will work better than just telling your audience what you want them to feel.

      - Boldra
        "Be Afraid. Be Very Afraid" is a colloquialism and should not be taken literally. It's downright scary that some of you are. Well, not really, but that's another colloquialism. Ironic given that poor "written English skills" are part of the OP's complaint.

        Elda Taluta; Sarks Sark; Ark Arks
        My deviantART gallery

        I do not intend here to be a fearmonger, not in the literal sense, but I do intend to plainly say that there is a reason why people who seem remarkably uninformed in programming of all sorts are successfully flooding into the market and displacing people who know how to do the same job better and faster.   Therefore, if you are (of course...) such a person, actually on either side of that fence, you have a selling job to do.   Labor cost is the number-one component of any white-collar type operation, so you have to be able to argue the case that, even though you “cost more,” you cost less.   Meanwhile, if you are on the other side of that equation, you have a far more difficult problem:   having displaced yourself or been displaced thousands of miles from home, you have been dumped into a situation where you might not be expected to succeed because you are, well, interchangeable.   I have had the opportunity to talk with a lot of very smart men and women who are in that situation right now.

        Being a student of history as an avocation, I find eerie but familiar parallels with the past in today’s labor relations in this professional-market segment.

      One hundred fifty years ago, you could have been an expert third-generation gunsmith who was utterly certain that Mr. Eli Whitney was similarly full of [!!!].

      Eli Whitney died in 1825, 187 years ago

Re: Some recent DNA threads
by bulk88 (Priest) on Apr 30, 2012 at 05:26 UTC
    The worst posts are the ones where you know the OP isn't a native english speaker. With how crass these foreign english posts are, I have to wonder, how do these non natives speak in their native languages? If they wrote their post in their native language, and send it through Google Translate would it have the same level of entitlement, cluelessness, and hostility? Who are the customers of these fake programmers? For some reason I am picturing programmers chained to desks with sipper water bottles in a concrete bunker with guards and nightsticks and attack dogs.

      Racist much?

        Racist much?

        While that post has a bad smell, its not exactly racist