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

Samantha Wright (1324923) writes | more than 2 years ago

User Journal 34

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.)

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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Cyanide (1)

ldobehardcore (1738858) | more than 2 years ago | (#38985465)

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 fast? I've tried researching it, and haven't found any time data, but I did find that there are at least two effective or somewhat effective antidotes for cyanide poisoning. This leads me to believe it would have to be on the order of at least minutes in order to merit developing an antidote. If it truly only took 5-10 seconds, the victim would be long dead before you could even find the antidote in the first aid kit.

No need for a car/computer analogy on this one.

Thanks

Re:Cyanide (1)

Samantha Wright (1324923) | more than 2 years ago | (#38985845)

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 occur until it's in the small intestine. (Uncomfortable trivia: a suppository would be faster.) You may also find this [hpa.org.uk] informative.

Re:Cyanide (1)

ldobehardcore (1738858) | more than 2 years ago | (#38985965)

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.

Re:Cyanide (1)

Samantha Wright (1324923) | more than 2 years ago | (#38986355)

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.

Re:Cyanide (1)

eugene ts wong (231154) | more than 2 years ago | (#39003089)

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?

Re:Cyanide (1)

Samantha Wright (1324923) | more than 2 years ago | (#39005595)

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 don't have chemical defences in them because they have different ways of protecting themselves—the hard shell around them.

Re:Cyanide (1)

eugene ts wong (231154) | more than 2 years ago | (#39008179)

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 buffer, in the same way that bread could act as a buffer when alcohol is ingested.

I hope that I'm using the terminology correct.

.
.
.
After writing that, I decided to check Wikipedia. This is an interesting, but slightly off topic quote, "Although usually thought to be toxic, cyanide and cyanohydrins have been demonstrated to increase germination in various plant species.". There was also the application of using it in art. I need to remember that if I decide to write a mystery novel.

Some questions about gene expression (1)

Saint Aardvark (159009) | more than 2 years ago | (#38988965)

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. :-)

Re:Some questions about gene expression (1)

Samantha Wright (1324923) | more than 2 years ago | (#38989775)

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 blueprints for some piece of machinery in the cell (usually a protein.) The header (called a promoter in biological language) is very important and defines many (but not all) of the conditions under which the gene will be expressed, such as growth conditions, different tissues and types of cell, and in plants even the time of day. It also tells the cell where the blueprints start, and that they're there in the first place. These rules are all encoded by special sequences that are physically interacted with by pre-existing pieces of cellular machinery, like physical lock-and-key mechanisms. As a result, like most other things in biology, they have fault tolerances, and many similar keys may partially fit in a given hole.

While DNA replication during cellular reproduction is important, the primary function of DNA is to act as a source for loading up all of these genes and turning them into functional products. The machine that does this is a protein called RNA polymerase. It reads the blueprints (properly called coding sequences) out of genes that the cell has decided should be expressed, and copies them into transcripts made out of RNA. RNA is similar to DNA, except less stable. Everything in a biological cell either degrades inevitably or is programmed to degrade, so that certain problems can go away on their own, and to reduce the amount of effort required to get rid of unwanted molecules.

If the gene in question has a protein (a more efficient and flexible class of molecular machines) as its ultimate product, the RNA molecule will be specially processed into what is called a messenger RNA (mRNA) molecule. This is carried off to a large RNA-based machine called a ribosome. The ribosome interprets the blueprints and produces an unfolded protein, which then assembles itself into the final shape.

All in all, this process can take much less than a second in a bacterial cell, although one of the big bottlenecks is in building up enough messenger RNA to guarantee that a sufficient amount of protein will be produced, and there can be many other surrounding factors that slow everything else down. In larger eukaryotes like humans, we have many tricks for caching mRNAs and inactivated proteins to try and cut down on these delays. The core process is a little slower in humans because we have better separation mechanisms, like the nucleus, through which things must pass, whereas in bacterial cells, a ribosome can be attached to a transcript still coming off the gene. This was demonstrated fabulously in 2004 by MIT's BioBricks course, which produced bacteria that blinked red and green using nothing but a basic genetic circuit at a rate of about 1 Hz, using build-ups of metabolites as the counter for switching between the two colours.

Now, for your next question: when people do gene expression studies, they generally look at the mRNAs, not the proteins, because they're much easier to identify chemically (one of the many advantages of nucleic acids.) In the case of your researcher friends, it really depends on the temperature the bodies were kept at; RNA doesn't degrade at all over the short term if it's kept in a fridge at 0 degrees Celsius. (That being said, the cellular environment is a little more hostile to RNA than specialized storage.) Here are some figures [nih.gov] .

Incidentally, I work with autism researchers (and actually had some lecture examples about schizophrenia treatments...) so I know precisely what's going on here with your last question, "b". While there are some genes turning on and off very rapidly, and some of those may very well contain useful information, your researchers are looking at the genes that don't fit this pattern, and comparing their levels to those found in normal, healthy people. Many of these genes are things that we'd call developmental (they determine how the body should change over time, or help pass messages instructing it to do so), although about a thousand or two of them are what researchers call "housekeeping" or "constitutive": genes that are always active because they must be. Given this knowledge, the next step is to look for discrepancies, find out what genes they're in, and see if they can place any blame if the discrepancy looks like it might be relevant. This technique isn't used in debugging computer programs very often, but it does work there, too. :)

You may have heard the term "microarray" being thrown around in this context, so here's an extra bonus detail: a microarray is a simple device that tells you the expression levels of a bunch of known genes. It consists of a grid of detectors, one detector per gene, and you pour water mixed with mRNAs over it. With a bit of laser voodoo, you can end up with a nice, analogue image that shows the density of each transcript (and hence the level of expression.) Microarray data is notorious for taking up a ridiculous amount of disk space, since the output is a giant raw image that must be reduced into a handful of numbers (one for value, several for quality control) per well.

Re:Some questions about gene expression (1)

Saint Aardvark (159009) | more than 2 years ago | (#38994565)

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.

Re:Some questions about gene expression (1)

Samantha Wright (1324923) | more than 2 years ago | (#38994839)

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 the level of expression is from normal (one common scheme is green=higher, red=lower, although there are tons of others.) It's very rare that someone would look at the whole heat map without an intention of trimming it and crunching it down, or just looking for general trends.

Re:Some questions about gene expression (1)

robotkid (681905) | more than 2 years ago | (#39014519)

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 alot of scientists overlook when they delegate out the technical stuff they don't know how to do themselves. You might find that the group you are working with has some graduate students or maybe postdocs (i.e. probably whoever you have day-to-day contact with who actually does the experiments and hands you with the datasets) that would be much more available to answering your questions than the big bosses who have to consult a calendar to even see if they have time to meet with you.

As a biophysicist (but importantly not a neuroscientist), I can still say that I am not aware of any consensus on what causes schizophrenia other than it must have both a genetic and an environmental component (i.e. having relatives that had it greatly increases your risk, as does certain types of substance abuse). Therefore it is absolutely a central assumption of your collaborators' research that some key component is due to a long-term up or down-regulation of expressed mRNA's, that's certainly not an established fact anywhere in the literature although there is speculation and circumstantial evidence and it might be a favorite hypothesis in the field. I am 100% certain that a large portion of the grant proposal that funded this research was devoted to justifying this assumption and that it will be the first question out of the mouths of peer-reviewer of any papers that come out of it, so I can only assume that very persuasive arguments were made since microarrays are expensive.

I can give an example of an over-simplified hypothesis that, nonetheless, would be a home run to your collaborators if they could prove it. Certain drugs that interfere with neurotransmitter receptors (ketamines?) can induce schizophrenia-like symptoms, so maybe one component of schizophrenia is something that systematically lowers mRNA levels of the neutrotransmitters that interact with ketamines so there are less of them in the brain. It would have to be chronic and long-term to make a huge difference to cognition (surface receptor concentrations take along time to build up as they are expensive to make) so such a scenario would in fact show up in the mRNA levels. Or maybe something upstream that helps promote production of a neurotransmitter (like an activator) gets down regulated and has the same end effect. But I can also make up hypothesis that don't involve mRNA's at all - What if reduced neurotransmitter function is caused by some sort of protein misfolding due to a genetic mutation, so they end up being recycled instead of on the cell surface? Or what if it's an adverse reaction to something else in the environment that interferes with receptor function as opposed to merely diminishing their numbers? As Samantha pointed out, people measure mRNA levels mainly because the technology exists, whereas it simply doesn't for alot of other important processes.

Off the top of my head, there are super-lots of other assumptions that would have to be worked out as well, even assuming there is no significant degradation of the mRNA after death (which as Samantha points out, requires freezing to be absolutely sure, but AFAIK you don't freeze donated organs, since mammalian cells don't handle freezing and thawing very well). Will mRNA expression levels at death have more to do with the dying process than the underlying long-term neurological condition? Would it affect all neurons or just a certain type from a certain part of the brain? What is the false-positive rate on the gene chips themselves? (I've read alot of commercial ones have errors on them). These are all questions that a cell biologist/neuroscientist would be able to answer far better than I (i.e. the lab you are working with). But I would characterize your concerns about "questioning the foundations of their work" as totally legitimate questions since they are relying on you to help them sort the signal from the noise - a task that would be much easier if you know what assumptions are being tested by the controls and where to look first when you get a new dataset.

Good luck with your work!

Re:Some questions about gene expression (1)

robotkid (681905) | more than 2 years ago | (#39014647)

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 experiments will never be outdated).

http://www.amazon.com/RNA-Indispensable-Molecule-James-Darnell/dp/1936113198 [amazon.com]

check your university's library, you ought to be able to get it from interlibrary loan at least.

Re:Some questions about gene expression (1)

Samantha Wright (1324923) | more than 2 years ago | (#39014757)

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.)

Re:Some questions about gene expression (1)

robotkid (681905) | more than 2 years ago | (#39017175)

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 patients to establish a profile that is representative of the disease state (and not specific to one individual). You probably have multiple tissues you could choose from within the brain. You need controls to establish a profile for the healthy state. You need multiple replicates for statistical significance. That's easily in the mid five-figure range for the consumables alone for a single set of experiments, to say nothing of the cost of acquiring and processing the tissues. I'm not going to fund you if you have no hypothesis you are trying to prove other than "we might find something interesting with genechips", that's what we call a very expensive fishing trip. Even if there's lots of grant money around, I will go to the next application in the pile and give the slot to anyone who can convince me they have a hypothesis worth testing (any hypothesis, it doesn't even have to be exciting, it doesn't have to be right, but it should be well thought out).

The drug industry used to do alot of this, what we call "hypothesis-free" research (I think they called it "data driven" research, as in, we'll collect the data first and come up with a hypothesis later). I would argue this doesn't follow the scientific method which allows us to refine a hypothesis given a set of observation until it ends up revealing something new. A well designed experiment will allow you to learn something even if the hypothesis turns out to be false, because it's systematic and tests something from multiple angles, whereas a poorly designed genechip experiment can end up telling us nothing in particular because there's often more noise than signal. . .

Anyway that's my 2 cents. You will certainly see alot of fishing trip type of research out there in the literature, especially from the period when genechips were brand new and you could get anything published just by using one. And there are still plenty of projects like that trying to recruit bioinformaticists to come in and miraculously save the day by finding something interesting in those very expensive datasets that don't show anything (I was in a hospital where they spent a few million dollars taking genechips on all surgery patients pre and post-op, for example, with no particular hypothesis in mind). I suggest avoiding those projects with a 12-foot pole.

Re:Some questions about gene expression (1)

Samantha Wright (1324923) | more than 2 years ago | (#39019819)

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.

Re:Some questions about gene expression (1)

robotkid (681905) | more than 2 years ago | (#39022025)

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 useful later, but then you have the luxury of there being a definite consensus sequence of an organism. With genechips, the results you get can depend alot on where you decide to focus your attention, I would argue if you don't know what to look for you just won't find it.

If these big, multi-center consortium projects had some sort of arrangement where after they identify "interesting" things they could then go in a more detailed study and pick the interesting things apart, that would be something. But they don't, because the people who are good at pushing the technological hi-throughput capabilities are usually not the people who know what a biologically interesting results might look like or where to look for them and that could be fatal if the community these projects are supposed to be serving have no ability to tell the ship it's headed in the wrong direction.

There's a great editorial from a personal hero of mine Sean Eddy (of pFam fame, we overlapped a bit when he was in St. Louis). He has a great point about how science is evolving to where ee completely divorce the people who have the technical knowledge of how to do an experiment with the people who care about the end results and why this might not be such a good idea.

http://selab.janelia.org/publications/Eddy05b/Eddy05b-reprint.pdf [janelia.org]

I was at a conference lately where basically all the bigwigs were predicting the death of data-driven research simply due to a lack of bang for the buck an age of very tight pursestrings and technology that outdates itself in a matter of months. And there was a consortium guy there, whose passionate defense of it was "well, it kept the lights on in my lab so I could do the other cool stuff I wanted to do. Oh, and we standardized on data formats and have a central repository, that's good, right?"

do you think politics is a product evolution (1)

decora (1710862) | more than 2 years ago | (#38989161)

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

Re:do you think politics is a product evolution (1)

Samantha Wright (1324923) | more than 2 years ago | (#38989799)

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.

does it follow similar rules to biological systems (1)

decora (1710862) | more than 2 years ago | (#38990105)

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.

Re:does it follow similar rules to biological syst (1)

Samantha Wright (1324923) | more than 2 years ago | (#38991565)

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 in the immediate nature of how the physics works (e.g. alanine and leucine can be swapped because they're chemically similar) and so don't have any relevance outside of their own domain. The important stuff is very basic and predictable, and much more on the macroscopic scale: quickly-changing things usually survive well, and staid ones don't, unless all of the alternatives are worse.

Re:does it follow similar rules to biological syst (1)

Saint Aardvark (159009) | more than 2 years ago | (#38994671)

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 Samantha could give a better/actually accurate explanation) -- and see if it can be applied to societies to see how they change over time. In this study, they looked at a bunch of different groups in the south Pacific and tested different models about how political organization could change (would people go from loose tribes to highly-organized kingdoms in one step? what about the other way around?). It was interesting stuff.

Re:does it follow similar rules to biological syst (1)

Samantha Wright (1324923) | more than 2 years ago | (#38999053)

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 time—for so long, in fact, that it predates modern biology: stemmatics. This is a technique in textual criticism wherein sequence comparison is employed to figure out which hand-copied version of a book came from which other one, by looking at the mistakes and alterations in wording made by the scribes (many of whom were barely or not at all literate, and hence made predictable errors.) Unlike biological sequence analysis, however, one of the assumptions of biology—that a single split always results in exactly two offspring—is also made in traditional stemmatics, which is often not the case, although the picture is blurred somewhat by the fact that the same mistakes in transcription may readily arise independently if the original document is particularly hard to read.

Re:does it follow similar rules to biological syst (1)

Saint Aardvark (159009) | more than 2 years ago | (#39001121)

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 chip in (although you're welcome to - hey, your journal :-), more just outlining my next bout of reading in my spare time.)

Re:does it follow similar rules to biological syst (1)

Saint Aardvark (159009) | more than 2 years ago | (#39001261)

(Whoops, just saw that you said it was part of textual criticism...)

Re:does it follow similar rules to biological syst (1)

Samantha Wright (1324923) | more than 2 years ago | (#39001537)

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 the same error) or produced lineages that conflicted with other evidence, such as the age of the paper. It gets even worse when you consider the possibility that the original author might be the scribe in some cases; in which case, subtle changes in wording in arbitrary directions might occur, and you're left with the impossible question of which document better reflects the author's intent.

thanks (1)

decora (1710862) | more than 2 years ago | (#39001709)

cool thread , thank you all

Effectiveness Of Cleaning With A Rag? (1)

eugene ts wong (231154) | more than 2 years ago | (#39003101)

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.

Re:Effectiveness Of Cleaning With A Rag? (1)

Samantha Wright (1324923) | more than 2 years ago | (#39005649)

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 because of the complex macroscopic and microscopic texture of the skin, so the knowledge might not transfer. With a smooth, flat surface such as a glass window, there would be no reason not to presume that a good, single sweep with a wet cloth wouldn't pick up everything (except perhaps for artefacts caused by lifting the rag off the glass.)

Re:Effectiveness Of Cleaning With A Rag? (1)

ldobehardcore (1738858) | more than 2 years ago | (#39005837)

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

Re:Effectiveness Of Cleaning With A Rag? (1)

eugene ts wong (231154) | more than 2 years ago | (#39008067)

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.

Re:Effectiveness Of Cleaning With A Rag? (1)

Samantha Wright (1324923) | more than 2 years ago | (#39008115)

You can get a UV lamp for about $25 and a marker that shows up under it for about $4.

Stethoscopes (1)

eugene ts wong (231154) | more than 2 years ago | (#39069745)

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.

The first doctor listened to my breathing and right away said that I had pneumonia or bronchitis, and prescribed antibiotics. I went in again as ordered, and the next doctor said that he couldn't hear anything.

I did develop 1 of those canker sores inside my mouth recently, and my lower leg has been feeling weird flashes of heat in the last few days, but other than that, I think that I'm okay.

Re:Stethoscopes (1)

Samantha Wright (1324923) | more than 2 years ago | (#39070269)

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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