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Journal Samantha Wright's Journal: Biology Help Desk: Volume 2n+1, n=2 34

Journal by Samantha Wright

I've gotten a couple of requests now for another one of these, so here one is. Please, bring to me your curiosities and questions about the strange and mysterious biological sciences. I can probably answer (or research answers to) most questions. (Also, if you keep missing these, I've decided I'm going to vaguely hint at them in mysterious ways on Twitter (@rhet0rica) from now on. I guess even Twitter has to have some utility.)

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Biology Help Desk: Volume 2n+1, n=2 More

Biology Help Desk: Volume 2n+1, n=2

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  • Hey there.

    Let me first do a little ass kissing, and say that you usually make cogent and thoughtful points in your comments when I see them.

    Enough of that.

    My question is on toxicity and poisoning. I know that movies and TV always exagerate the speed and efficacy of poisons, but I wonder specifically how long in reality it takes to die from acute cyanide poisoning, like when a "secret agent bites his sudicide pill"

    In the movies and TV it never takes longer than ten seconds, but is it really that
    • Ingesting hydrogen cyanide in salt form leads to death after a few minutes. Much more deadly is the inhalation of gaseous hydrogen cyanide, which can cause visible symptoms within a few seconds, because the HCN goes straight into the blood stream. In all cases, however, the onset of death is directly related to the amount ingested. This page [cyanidecode.org] quotes a few ballpark figures for certain concentrations. It is highly unlikely that a cyanide pill could work faster than several minutes, because absorption won't occ

      • Thanks for the answer.

        forgive my ignorance, but what area of biology do you specialize in? I'd rather ask you about stuff you enjoy explaining in the future.

        • It's no problem! My expertise is in evolutionary and analytical genomics, which looks at the history of the tree of life from a nuts-and-bolts perspective, to understand trends in how species and biological features evolve. It's a very unusual vantage point for most people to think about, but it does have the job perk of being completely irrefutable by evolution denialists.

    • Great cyanide question!

      Samantha, thanks for opening up another journal entry for us. I was the anon. reader requesting.

      On the topic of cyanide, can you confirm whether apple seeds, cherry seeds, and peach seeds are poisonous? I don't eat the latter 2, but I do eat the first. I don't need your sources, but would you explain how you know?

      • A lot of plants try to protect their seeds by including cyanide in them, including apple seeds, cherry seeds, and peach pits. Eating a large number of any of them could be potentially dangerous, especially to an infant or elderly person. I had to look this all up, but the important point is that plants know their seeds are tasty and don't want you to eat them. (Well, they've evolved to defend themselves against being eaten because it's bad for their survival.) Most nuts, like peanuts and walnuts, generally

        • Okay. Thanks for both answers.

          I had checked the web before asking, but I kind of gave up early, because I didn't even know where to begin as far as reliability goes.

          The most balanced view that I found was "if the amount of seeds that you eat is the amount in 1 piece of fruit, then you can eat it". That makes sense to me, because of the small dosage. I don't expect the seeds to be filled with cyanide, so I expect the total amount to be very little. Also, the fruit would mix with the cyanide, and act as a buf

  • Heyo -- thanks for the heads-up on Twitter. I'm the sysadmin at a small university department, and I work with scientsts studying gene expression. They're good and patient people, but sometimes I feel a bit like I'm questioning the foundations of their work...which feels either rude or ignorant.

    First off, I'd always been under the impression that DNA was only/mainly used during reproduction -- a cell divides under DNA direction, some bit of the cell is the machinery that makes whatever protein is needed du

    • Hey Aardvark! Happily, the answers to your questions flow from one to the next pretty darn well.

      Deoxyribonucleic acid (DNA) is a long-term storage medium, equivalent in many ways to a hard drive. A single molecule of naturally-occurring, unmutilated DNA (generally called a chromosome) can contain anywhere from a hundred to a thousand genes. The definition of exactly what a gene is differs from place to place, but the important part is that it is a sequence of nucleotides that contains a header and the bluep

      • Many thanks for the explanations!

        The researchers I work with deal with microarray data a lot, and have built a tool to help compare datasets (http://www.chibi.ubc.ca/Gemma). I'm becoming more familiar with the technology as I go along, but the heat maps and the dendrogram legends (is that what they're called?)...man, those are some dense infodumps.

        • One of the most common tasks when looking at microarray data is not just taking one array, but taking a series of arrays: perhaps one per patient (plus a control), perhaps one for each interval along the course of an event (for something really intensive). Part of the reason for this is to help pare down how much data there is; they use simple AI techniques to group different genes together based on how similar their patterns are across all patients. The corresponding heat map generally shows how different

    • Heyo -- thanks for the heads-up on Twitter. I'm the sysadmin at a small university department, and I work with scientsts studying gene expression. They're good and patient people, but sometimes I feel a bit like I'm questioning the foundations of their work...which feels either rude or ignorant.

      First off, I'd always been under the impression that DNA was only/mainly used during reproduction -- a cell divides under DNA direction, some bit of the cell is the machinery that makes whatever protein is needed during its life, and DNA isn't involved much after that. However, I'm starting to understand (I think...) that I've got it all wrong. My understanding now that gene expression can basically turn on a dime, and that *this* is the usual way a cell makes a protein: something happens to a cell, it says "Whoah, I need protein X", and it starts transcribing the DNA so it can manufacture it (modulo things like gene regulation). This process can take very little time (hours or less). Have I got that right?

      Second: one of the things they study is datasets of gene expression in post-mortem brains. (Well, technically I guess I've got that wrong, since genes aren't expressed post-mortem... :-) As I understand it, someone dies -- say, someone with schizophrenia -- their brains are donated to science, and at some point someone does microarray sequencing of blendered neurons. This is compared to brains of control subjects, gene X is found to be over/under-expressed in schizophrenic brains, and so gene X is involved somehow in schizophrenia. (This is a gross simplification, especially in the case of schizophrenia; my understanding is that these signatures cover many, many genes, they're subtle at best, and there's nothing like "a gene for schizophrenia".)

      What I don't understand:

      a) Since time passes between death and sequencing, how much fidelity does/can this have do what was going on at the point of death?

      b) Even if it is a good indication of what was going on at death, how does that relate to a long-term illness like schizophrenia when (assuming I've got this bit right) gene expression can turn on and off in a very short time? I realize there are (ahem) ethical problems with doing brain biopsies on living subjects, and that post-mortem is the best that can be done -- but how good can it be?

      Many, many thanks for your time. Any questions about system administration, let me know. :-)

      Hope you don't mind me hijacking this thread, I think it's a great service Samantha is providing here. I just wanted to add a few comments as someone who has sadly seen alot of sloppy gene-chip experiments going on (but also some very nice ones).

      It's really encouraging to hear that you are taking an active interest in what your scientific collaborators are trying to show. You'll be that much better equipped to help them prove what they want to show if you are roughly on the same page as them - something a

      • Ack! I got carried away. My original intent on replying to this thread was to plug a good book I've been reading that summarizes how all the classic experiments from the 30-60's showed what we know today about how mRNA works and how it is regulated. For me at least, it's much more interesting to read than a dry textbook that just presents the end results as facts handed down from on high (such textbooks also tend to get outdated rather quickly, whereas understanding the logic behind the classic experime

        • With big disorders like autism and schizophrenia, where the underlying causes are so complex that we haven't yet found them, the story generally seems to be the case that we throw microarrays at them just in case, not because we have substantive reason to believe that a hypothesis might be sound. If these studies fail to yield anything, then that's all well and good: we know the problem is either an aberration in the networks which is too complex and subtle for us to detect, or we've narrowed it down to one

          • With big disorders like autism and schizophrenia, where the underlying causes are so complex that we haven't yet found them, the story generally seems to be the case that we throw microarrays at them just in case, not because we have substantive reason to believe that a hypothesis might be sound. If these studies fail to yield anything, then that's all well and good: we know the problem is either an aberration in the networks which is too complex and subtle for us to detect, or we've narrowed it down to one of the other major things that can go wrong, like epigenetics, a good old wholesome mutation (which could be picked up Mendelianly with linkage analysis), environmental exposure, or prions. The language you used was very certain (e.g. 'prove what they want to show') and I just wanted to emphasize that, while such thinking may be the unfortunate reality of grant-writing, determining that schizophrenia can't be detected on a mRNA-based microarray is almost as significant. (As an undergrad I have the luxury of not thinking about the miserable reality of how competitive research can be. Out of the mouths of babes, if you will.)

            Hmmm, I have to disagree here, and not because of cynical grant realities per se. .

            Consider if I was a grant reviewer, and you're proposing to grind up valuable donated brain tissues from dead patients (which is pretty much irreplaceable and in high demand since not alot of people donate their bodies to science anymore). You are proposing an experiment where each sample will require a separate 500-1000K$ genechip to measure the mrna levels (they are not generally re-useable). You need samples from multiple

            • I find it slightly ominous that you call data-driven research a thing of the past; I just got through a course that hailed it as a Big Deal—though the class's attitude was that it was a process for finding a hypothesis, not really testing one. Given that a full human gene expression microarray really is quite excessive for pointing fingers at only a handful of genes (those could be done through much cheaper RT-PCR, after all) my instinct is still to suspect that they're not as organized as you or I mi

              • I find it slightly ominous that you call data-driven research a thing of the past; I just got through a course that hailed it as a Big Deal—though the class's attitude was that it was a process for finding a hypothesis, not really testing one. Given that a full human gene expression microarray really is quite excessive for pointing fingers at only a handful of genes (those could be done through much cheaper RT-PCR, after all) my instinct is still to suspect that they're not as organized as you or I might like them to be—or, at least, they're prepared to fall back, and since they're grinding up such a valuable resource already, decided to go for broke with the gene chips, to make sure any negative confirmations they generate are as useful as possible.

                Don't get me wrong, I think genechips are awesome tools. I've seen some really nice work on elucidating what changes at different points in the cell cycle, for example, that really couldn't have been done with anything else. But just because it's a high-throughput tool that could be used to brute force things doesn't mean we don't have to pay scientists to think anymore. I think genomics really planted the idea in people's heads that if you collected the data first, other people would be able to make it

  • ??? just wondering if our 'logically derived world views' are actually simply biological

    • Culture is its own evolutionary system, created by biology to outsource and speed up all the hard work of evolving. Beyond that point, we have nothing to blame but ourselves. And anthropologists, who study that sort of thing.

      • in other words, if you can analyze and explain the patterns of evolution in biology, can you do the same thing with the patterns of evolution in ... culture, or thought.

        • Ideas and cultures obey Lamarckian evolution rather than Darwinian evolution; that is, they can change in response to pressure without having to go through a reproductive bottleneck. As a result they change pretty darn quickly, although they do obey certain rules too. Linguistics is an easy example of this: languages frequently undergo predictable, one-way changes in pronunciation (e.g. k -> kh -> ch -> s and g -> gh -> y). Unfortunately most of the rules of biological evolution are grounded

        • Sorry to jump in, but I happened to read a neat paper in Nature about something like this a while back. It was called Rise and fall of political complexity in island South-East Asia and the Pacific [nature.com]. TThe article is behind a paywall, but there's a general summary from Wired magazine here [wired.com], and another aimed at fellow researchers here [bluteblog.com].

          My half-assed summary: the researchers use phylogenetic methods -- ways of looking at genomes from organisms and estimating how long ago they had common ancestors (I'm sure S

          • I've dug around in the paper, and I have to admit it's a pretty clever idea to use methods of political organization (e.g. monarchy, duarchy, democracy, oligarchy...) as the 'genome' of each culture. The major reservation I had about the suggestion of using evolutionary methods to study human practices is essentially that there's nothing concrete to really compare, but having this tool helps somewhat.

            That being said, you've reminded me of another field in which phylogeny has been employed for quite some tim

            • Thanks for the term "stemmatics" -- I was familiar w/the concept but knew it as "textual criticism", which I think is probably a great deal more broad than this. What's always bugged me about this concept -- perhaps unfairly -- is whether or not it has any experimental evidence to back it up. My impression is that it's a bunch of heuristics based on a preference for simplicity. Is there any experimental evidence to suggest that texts do grow/change the way these rules say? (I'm not asking for you to chi
              • (Whoops, just saw that you said it was part of textual criticism...)
              • As it so happened, stemmaticists of the day (this is mostly in the nineteenth century) were widely criticized by other textual critics because of their core assumptions, that a text only simplifies as time progresses; it's known now that some hypercorrective scribes might render text more complicated if, for example, an idiom is unfamiliar. On occasion the techniques didn't work because they either supposed that another intermediate copy of the manuscript must have existed (because several derivatives made

  • You mentioned, a while ago, that rinsing gets rid of 90% of the filth on the relevant surface, if I recall correctly.

    What about wiping with a rag, and then rinsing? I ask, because I get the impression that the rag gathers up a lot of filth, but it also releases a little at a time. I wonder if it is worth wiping certain surfaces a certain number of times for optimal cleaning.

    • I'm afraid this question lies outside of my area of expertise (and I would be surprised to hear if there were anyone in whose expertise this lay, outside of, perhaps, radiologists), but presumably successive iterations of wiping things down improve your chances slightly of getting rid of a given particle—unless, of course, it's out of reach. However, I believe the original context we were discussing this in was washing hands without soap, not cleaning a flat surface. Hands are relatively unique becaus

      • Maybe we should ask Mythbusters...This seems like the sort of question that would be in their area of expertise :-]

        • Maybe we should ask Mythbusters.

          That and perhaps it would useful to have a company sell kits that allow us to test and measure.

          A high tech version would be something like an ink that shows up under infrared light. I seem to recall seeing something like that in the news. The person used it to teach kids how to wash hands.

          A low tech version would be nice.

  • Hi again.

    Do you know much about stethoscopes? Do you think that there is any value for average people in buying 1, and then listening to the heart, breathing and circulation on a regular basis?

    I ask because of my general interest in health, and because I have been coughing up phlegm since mid December. I took antibiotics as prescribed and finished them, but it never went away. Other than breathing problems I think that I am fine. I have no sore throat, or runny nose. I only cough when I can't breathe freely

    • I'm afraid I'm not a medical professional, so I can't really comment in this area. To be honest it sounds like you may just be in a really dusty environment. In general, though, when it comes to non-medical folk having access to medical equipment, it's a great way to become a hypochondriac. That's why doctors don't treat themselves!

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