Category: Biology

Body of Proof: “Going Viral”

Ah, a club. Perfect place for an outbreak. Hmm. Date rape drug?

I’m glad Peter has the sense to recognize the symptoms. But hasn’t he caught whatever it is, at this point, from holding Dani?

It is just too convenient that three new patients show up just as Kate says that there ought to be a lot more sick people. Or maybe I mean, the one person just showed up, but the other two were there before and happened to be in the same isolation unit? That should mean that they recognized the commonalities and did have more sick people — 4 total — and one more person does not suddenly an epidemic make, if 4 didn’t.

They can’t seriously be wearing that protective gear and still be letting their hair down! I mean, at least Kate’s hair is in a reasonable ponytail, but shouldn’t they look more like they’re in surgery, with caps?

Why doesn’t Curtis already see that Ethan has a point? He was Chief ME at some point, so it’s not like he’s some dumb intern or someone without medical training, like Peter.

I feel fairly certain that they don’t have an autoclave there under the bench (who puts an autoclave there?), and even if they did, autoclaves are not randomly portable that way. Seriously.

Kate brings her own blood to the analyst? Why would you let someone who’s potentially infected have the chance to swap out fluids for a negative test result?

“Remind me to never investigate a plague again” is the best line ever, hehe.

May I point out that not everyone on the team may want to be working in BSL-4? Like Ethan??

If the team’s been keeping the news of the deaths and outbreak quiet, how would Youtube know to send it to them specifically?

I wonder if they quarantined or otherwise screened the relatives of the deceased? Also, “will you please explain to him how the internet works?” is also a great line. Delivered just right.

How can Curtis tell Ethan to just relax? Ethan should keep calm, yes, but he should go fix his suit, shouldn’t he?

I am confused why the FBI guy doesn’t even ask for an ETA on the lab results to confirm meningitis before telling her “no we’re not confirming it before telling the public what we think it is.”

Is Kate taking off her gloves without exiting BSL-4? I can’t tell. But I do like the way she’s not telling anyone, trying to squeeze out the blood, looking for blood in her innermost glove, etc, because those are all fairly typical reactions.

I find the interrogation scene with the teenager somewhat unlikely, but his sarcasm is at least on the mark, and the reactions within it sensible and entertaining. And thank you for pointing out why it can’t possibly be airborne, because Megan never explained it to anyone and it didn’t make sense for her to just expect that the non-medical people would get it and believe her without an explanation.

How does being through decontamination guarantee that you won’t catch it afterwards? *raises eyebrow*

I sort of think that the eyes are much more evidently jaundiced than bloodshot. Also why wouldn’t patient zero be dead by now, given that the subsequent cases have all died? Either that or he’s probably recovered. What is the mortality rate on this, anyway?

Why isn’t Kate in on that meeting, anyway? And… the terrorist isn’t still out there, because he’s presumably either dead or recovered and no longer infectious, I would think?

Episode break!

Is the CDC guy not a doctor, and he’s just a researcher? There’s no way.

That sort of makes sense, the way they say it: first some internal bleeding, then more internal bleeding that shows some of the other symptoms they observed (like the purpura that they didn’t re-mention), hypotensive shock, and cerebral/pulmonary edema before death. But why did they make Kate look so shocked as she looks around the isolation ward?

Really? The FBI guy’s going to be the first one to figure out that the terrorist might be dead already?

Go Peter! Also, making progress with syringes, good. And yay Kate for noticing Trevino, because I, at least, find it hard to keep track of the number of days that have passed in a TV show.

It seems sooo unlikely for the terrorist to have somehow figured out a way to stay alive longer without some kind of trial-and-error testing, and for that you’d have seen deaths beforehand. But it is sort of awesome that Trevino is a “walking pharmacy” (on 17 different drugs for various reasons).

Really, are they going to go to a shot of an empty bed (presumably Trevino’s) during the terrorist call just because the ME’s office happened to call right then and name Trevino as their suspect? He’s in isolation! I get that the bar is near the hospital, but how do you expect him to have gotten out, seriously?

Why are they pointing at the two “electron microscope” images as if they indicate that the two samples are clearly from different people? And why do they then point at the images as they mention the interferon and how the one sample’s supposed to have more of it that clusters more or whatever?

Marburg is not the “bastard cousin” of Ebola. (I mean, calling it a “bastard” makes it sound like it’s engineered, doesn’t it?) Nor is it nastier, if I recall correctly. Also there are more than 3 filoviruses. Also also the mortality rate for Marburg is not as high as they’re making it seem with their “they all died!” statements every now and then. Also also also the symptoms don’t seem as bad as I thought they ought to be for Marburg. They’re definitely not as bad as the symptoms for Ebola, though at least Stafford (the CDC guy) said the words “unmentionable orifices” a little earlier.

That is sooo not adequate consent. True consent means that the subject actually understands the risks involved, and given how quickly Trevino is given the vaccine (behind Megan’s back during the few moments she takes to talk to Kate), it seems incredibly unlikely that he understands the risks.

Stafford’s explanation of why he picks Trevino is totally unreasonable: even if the biology made sense, the math wouldn’t. First of all, vaccines don’t “target virus particles” or anything. But even if they did, his argument that a higher viral load would make it “easier” for the vaccines to “target” the virus particles is only saying that more virus particles would be reached, but the percentage would presumably be similar and there would be more virus particles left at the end, still. And it’s a vaccine, which is preventative, so the earlier you get it, the more chance it has of working. Why does this not make it into anything?

Why is Peter not wearing gloves? I understand that the file is supposed to be clean, but I wouldn’t trust that, with Marburg on the loose….

Ah, closing shot of the terrorist watching the school, setting up for “he’s going to target the kids next! Oh no!” But I wonder what he’s really going to target, because an older, sick man would sort of stand out in an elementary school, and it’s not like kids all play on the same playground toy or anything.

Yay bed bugs. And haha, Megan looks all indignant as Johnson (the head FBI guy) brings Peter along to the hotel but not Megan.

Guys, if you shoot him his blood will aerosolize. (I was wondering, earlier, why Bud was carrying a shotgun when they stormed that abandoned warehouse.)

And now, because they’ve been trying to make us believe that Marburg has a nearly 100% mortality rate, they can’t just let Kate be one of the three out of four survivors (that’s what I recall Marburg’s mortality rate being, anyway). And I guess they’re going to play off the rest of the survivors as “they didn’t actually have Marburg”?

Yay for the inevitable happy ending, though Dani’s death at the beginning was quite a shock. I feel like usually TV shows put the shocking death in the middle or at the end of the episode instead of at the beginning, and I’m not sure whether putting it at the beginning is better (because that’s where you least expect it) or not as good (because you have the rest of the episode to distract you while your subconscious processes most of it for you).

Biology BS Filter and … Why It Sucks To Be A Girl?

From my personal class (-i bio):

Me: I should have something better than a generic BS filter.
Ian: bullshit?
Me: Yes.
Me: I often can tell when people are bullshitting about basic biology, but asking me to spew it and remember terminology off the top of my head is somewhat more difficult. Then again, I learned most of that stuff >9 years ago, and last ~reviewed it >6 years ago, so … can I be forgiven for being rusty?

This seems like a similar problem to how Real Mathematicians tend to lose practice with arithmetic and are slower at it than an elementary school student might expect a person “who does math all day” to be. Over my years in the laboratory, I’ve spent more time dealing with immunology- and cancer-related terminology than the basic terminology taught in general/introductory biology classes, so while I can mostly remember what various terms mean when they’re being used to explain things to me, and thus can detect BS reasonably well, I probably couldn’t actually explain some basic biology terms the way that I feel that I ought to be able to.

I feel guilty about this, but it really is a matter of practice and common usage, I think. Most of that basic biology is stored in my implicit memory, so recalling it from no particular starting point is difficult. So while I feel guilty for not knowing basic terms/principles as well as I could, the only real solution is to use them more often, or else spend time reviewing them (which, in my opinion, setting aside chunks of time for is silly, since the time could probably be more effectively used and/or the material could be more efficiently reviewed).

I vaguely wonder if this is related to language usage. There is this common phenomenon that one remembers a foreign language much more quickly than might be expected when immersed in the environment, and I feel that it is similar (for me, at least, and probably for many/most other people as well) both with languages and different kinds of jargon. For example, I’m reasonably confident that it would take me some time rambling/thinking about immunology before I could just spew about it and use the jargon as fluently as I did when I was actually doing immunology work, but it would come back to me faster if I were inserted into an environment where other people were throwing around jargon (although it would take considerably less time in both cases for cancer terminology, I imagine).

Of course, this is just a specific area of general knowledge recall, I suppose, although I am inclined to say that knowledge recall is slightly more explicit than implicit. Then again, the split between explicit and implicit memory is probably not that distinct for specific topics (e.g. some of my biology knowledge is probably explicit, and some of it is probably implicit), and implicit memory can be analyzed to make it explicit, which is what teachers who are “experts” in a field but relatively new to teaching (e.g. me) do in order to be able to convey it to their students; for that matter, it is how people communicate ideas in general, to some extent.

Speaking of which, I’ve been asked to enumerate/expound upon the reasons “Why It Sucks To Be A Girl.” (Feel free to contribute additional reasons/comments or ask for clarification in the comments.) Having at it, then (disclaimer: I do not guarantee the veracity of the statements below, nor even that they accurately represent my opinions; spending time trying to figure out how to address every edge case or wording ambiguity is not part of the exercise here, nor is it something I’m willing to spend time on right now, and besides, these are very much intended to be broad, sweeping generalizations that don’t hold water in the face of anecdata) ….

Girls are generally expected to dress “better” than guys, or have a better fashion sense, or something. For guys, it seems more acceptable to dress casually, because they have more of a need for functionality, while girls are here just to look pretty. For example, guys can claim to need to carry tools around on their belts, whereas if a girl wants to, she meets more resistance. Another observation that has been made time and time again is that while wallets made for girls/women are at least the same size, if not larger than, wallets that are made for guys, the pockets in girls’/womens’ clothing are considerably smaller than the pockets of guys’ clothing. What does this mean? Essentially, girls are forced to carry purses (or backpacks). I don’t know about the rest of you, but personally, I rather dislike purses. What else…oh yeah, what’s with this whole high heel thing? There’s so much suggestion in the media that this/that is more attractive/feminine, but how it is practical AT ALL? Moving on to makeup…it really just gets everywhere. Do I really want lipstick smeared everywhere after kissing, or foundation smeared everywhere if I want to rest my head on someone’s shoulder? And eye makeup? Gets into your eyes and dries them out. Very irritating, both physically and otherwise. And how does this all play out in a work environment? I’ve been told that more attractive women get paid more and promoted more. While this is probably true for both men and women, it feels more excusable for men to be slightly more unkempt/disorganized. And don’t even get me started on things that are actually biologically-related…(although here I go anyway:) when women moved into the workforce and we finally got to the point where men stopped freaking out about it, society basically seemed to say, “Fine, you want to work and all that? You still have to deal with all of this childbearing/child-rearing crap.” (Yes, “crap” is probably not the word I want, or maybe I am using it to refer to the negative aspects of pregnancy and “womanhood” and such.) So prime time for reproduction for women falls somewhere in the twenties, which is also the point at which careers are supposed to be worked on heavily and possibly take off. What happens if you wait on one or the other? Waiting to work on one’s career generally works less well than in theory, because going back to school/work is *very* hard after children. Waiting to have kids is also less-than-ideal because of the increased risk of things going wrong in the pregnancy. And doing both at the same time…I think the solution of most women in such a position is to hire a (live-in) nanny, which, some of those mothers say, gives them less contact with their children than they might like. The other solution, of course, is heavier involvement from the father, but that depends heavily on the relationship. Anyway, this basically segues to the whole double-standard in society that so many people have remarked upon between men and women. Sure, sexism is much less prominent these days as compared to some number of decades ago, but the double standard is still there, and it sucks.

First Post!

So I guess I’ve decided to name this blog “SHM”, which stands for “Somatic Hypermutation” (and not “Simple Harmonic Motion” — sorry for all the fans of The Other SHM). Here comes the stream-of-consciousness word vomit of the why: Somatic mutations aren’t passed on — they take effect locally and don’t bother anything else in the body or future generations. Somatic hypermutation, more specifically, is one of the two processes that comprise affinity maturation, which is what happens when your body is reacting to an antigen that it has seen before. It’s called affinity maturation because your body is creating a bunch of new antibodies (well, antibody-producing cells, actually) that are all slightly different but still mostly attuned to recognize the particular antigen (somatic hypermutation), and then selecting for the ones that have a higher affinity for the antigen (clonal selection). Thus, affinity maturation is part of the immunological process that allows your body to “remember” antigens, and this blog, so far as I can tell at the moment, is going to serve as a memory dumping site bank for my random thought processes that I never seem to be able to remember once they’ve concluded themselves.

It’s kind of silly, actually — I’ll have some minor epiphany at the end of a thought process, and then forget that I’d ever thought about it until someday, maybe, when I start thinking about it again. Considering how many random thought processes I have about various topics, my remembering these minor epiphanies happens less often than I might like, because they’re not accessible to me when I’m trying to randomly brainstorm things, as, for example, for writing blog posts…uh oh. I think I see a problem here…. I guess I’d better hope that my longer trains-of-thought happen when I’m in front of a computer, although they rarely do, and this is exactly why I have this problem…. *shifty eyes*

Anyway, so I think I’ve kind of veered off-topic, except not, because the post was originally about the blog and the rationale for naming, wasn’t it? While I’m at this whole word-vomiting thing, though, I think I will ramble a little more about immunology.

I have a number of allergies, and it’s gotten to the point where I’m tired of just avoiding them and want to try getting rid of them (there are some other reasons and complicating factors, but anyway). I’ve been testing myself for allergies by exposing myself and checking for known reactions, but sometimes it’s hard to tell whether the things I notice are psychosomatic (stress aggravates allergy symptoms, after all) or whether they’re actually physically triggered. I mean, ideally I won’t eat more than the minimum to be sure that it’s an allergic reaction, but it’s kind of hard. Also, it’s somewhat cost-inefficient to obtain food for testing (that is, if I end up not being able to eat it because I am allergic, it’s a waste to just throw the rest away), so I try to do it as the opportunity arises to take part in the eating of $food.

So this plan of getting rid of allergies pretty much involves an elimination diet. I am not convinced that it will work, but I think that it is worth a try, maybe? I’m told that one of the CMEs our freshman year went on an elimination diet for some amount of time (O(1 year), maybe?), and afterwards she could eat anything again. So here’s my reasoning: allergic reactions are generally IgE-mediated. Pharma companies do make anti-IgE antibodies that cause them to be targeted for destruction, but this is generally inadvisable as a course of action for treating food allergies, and IgE antibodies are not terribly well-understood either; they seem to play a role in cancer detection (although the data supporting that theory is inconclusive). The drug is also rather expensive, and your body will just keep producing those antibodies anyway.

From a different angle, then: the half-life of IgE antibodies is approximately 2 days for unbound antibodies and up to several weeks for bound antibodies. Allergens present in the body stimulate T cells, B cells, mast cells, and basophils. T cells and B cells aren’t involved in the acute response, but basically, the T cells stimulate naive B cells to secret antibodies, and then other T cells signal the B cells to switch isotypes and produce IgG, IgA, or IgE antibodies instead of IgD or IgM antibodies, resulting in mature B cells that just churn out antibodies (and daughter B cells that do the same, of course). Mast cells and basophils, which are what actually cause imflammation and other acute reactions, get coated in the IgE antibodies that become bound when the allergen/antigen enters the body. Where am I going with this? Essentially, the idea is to eliminate the cells that play a role in producing the allergic response by not stimulating their proliferation until they die out.

Will it work? I don’t know. The human body has been known to produce antibodies that react to antigens last encountered more than thirty years prior, but not all antibodies hang around that long. And since allergies are so poorly understood…I really just don’t know.

The other possibilities that are out there involve building insensitivity to the antigens, which start off exposing you to small amounts of allergen and increasing the dosage with time to reduce the symptoms of the allergic reaction(s). (It’s  like in Le Comte de Monte Cristo / The Count of Monte Cristo, when M. d’Avrigny gives M. Nortier — who in turn gives Valentine — slowly increasing amounts of poison and the recipient’s system slowly builds resistance, except that was resistance to a toxin/poison, and this is immunotherapy to effect reduced sensitivity.) Sublingual immunotherapy is more widely administered in Europe than in the U.S., but it’s gaining popularity here and seems promising. The other option is allergy injections, which require a long-term commitment and are also not recommended for food allergies; they are generally used to treat pollen/dust/etc allergies, but given that there is a possible connection between food and pollen allergies, it’s certainly worth a try. One of the major concerns with injections, however, is the reason for the long-term commitment: pollen allergies vary by region, so different formulations are used in different areas depending on the local flora. Thus, changing environments that require a different formulation will render the former injection course less effective, and adjustments have to be made, etc etc, that just make it too complicated a problem to deal with unless absolutely necessary; hence, the long-term commitment requirement.

More research is necessary; more testing is necessary; I certainly would rather have a wider set of options open to me while I am on my elimination diet, if at all possible, so eliminating various foods as allergen suspects is tedious, frustrating, painful to some degree, but hopefully useful in the end.

[Edit:] I think that with this skin, writing out “Somatic Hypermutation” doesn’t look as bizarrely unbalanced, so the name of the blog is hereby officially changed! (At least until it lives up to its name, changes its skin, and wants a balanced title again ^_^)

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