30 April, 2009

Linky Links

You have probably noticed the acute lack of normal science blogging lately. I'm distracted by many things at the moment, including this. I'll be back to normalish soon, probably when I finish my lit review presentation with 3 papers.

1) Eloquence.

2) Admirable. Though as a Mad Scientist I admit that the only one who worries me is Angle Grinder Man, and at that barely. I'm more concerned with Hermitage. And Superbarrio is awesome.

3) Foolish sentimentality.

4) Jazz.

5) Better jazz.

6) Whiny whiners.

7) Poseur.

27 April, 2009

The War Intensifies

It would appear that I have made a grave mistake in underestimating the absolute sinister capacity of Hermitage. Either she is far more wicked than my initial intelligence reports led me to estimate, or I have divulged too many of my personal weaknesses on this blog and she has unscrupulously taken advantage of them.

In either event, what she has done is so...so...fundamentally despicable that I feel a bitter moral vomit rising, although that could just be my wounded ego. For what it's worth, even if it was heinous of her, I have no choice to admire her deft cunning.

What has Hermitage done?

She CAPTURED me! Like a motherfucking flag!

I fully admit that her evil brilliance coincided with unusual foolishness on my part, but in my defense it should be noted that one can't help their fundamental constitution. Cookies are to me like mashing is to potatoes, like bacon is to beans, like LB broth is to E. coli K12. Hermitage knew this, and she took advantage of this. I can't blame her.

You see, she made a cookie and put it in my daily pathways on a PEDESTAL! A pedestal! As a cookie connoisseur, I can't very well pass such a thing up. I fell right into her trap as she lay in hiding, waiting with a baseball bat. She waited until I was distracted by the cookie, then snuck up and BLAMMO! with the baseball bat on my oversized noggin (she could hardly have missed if she'd tried to).

But that's not the worse of it. I didn't even get the cookie before being knocked out because she GLUED IT DOWN!

I woke up strapped into a chair with a headache and a haircut (srsly, WTF, Hermie?) in an OPEN GRAVE.

But it wasn't just an open grave, it was really a giant 2% agarose gel. And she was stomping around in the background, I could just make her out through the agarose walls. She backed a tumbler truck up to the well and promptly flooded it with 1X TAE. She was going to electrophorese me, but being a compassonate megalomaniac, she granted me one last request*.

Naturally, I asked for a cookie.

She had no choice but to oblige.

So I sneaky-like crumbled the cookie up and spit it into the TAE buffer. This saved my life because when she flipped the switch the salt concentrations of the buffer were so screwed up that nothing happened. You see, I know from what Hermitage has revealed on her blog that she is a terrible cook and limited to Ramen and as such there was a 50% chance that she'd mix up the sugar and the salt. Luckily for me, she did. Also luckily for me, nylon rope frays in TAE buffer and I was able to escape.

Revenge will be sweet. Oh, so sweet indeed.

*Regardless of compassion, she was required to as set forth in Section 7.29 of The Nerd Accords.

26 April, 2009

The Ozarks

Ever since I've moved northward to Michigan, this is about the time of the year that I feel homesick. Michigan starts to bloom anemically and I'm reminded of home, somehow. Maybe it's because the snow is gone and so is the wintery bluster, and the watery warmth here echoes of the deep, bone-wrapping cicada heat of the Ozarks summertime. I don't regret moving away, but that doesn't mean I don't miss it.

Figure A: Downtown in the area I grew up. That's the defunct train station. That year the flooding got up to the eaves. When I was in 7th grade I stood on the riverbank and watched the bridge in the background blow up. The area just behind this photograph hasn't been changed since the 1850s--it's still cobblestones and cisterns.

I hold the Ozarks in my mind with a certain tension. On the one hand, there was the simplicity, the friendliness, the summer, the storms. But on the other hand, there was the ignorance, the sprawl, the racism, and the glaring lack of opportunities.

Michiganders always seem taken aback by friendliness, which I don't entirely understand. It's like they just want you out of their way so they can get on with their business. Ozarkians generally seemed to be more cheerful and outgoing, even in tiny one-stoplight towns like Fredericktown, Missouri (population 462 and one old nut, according to the sign welcoming visitors off of Route 67). Of course, this means that Michigan has its advantages for introverts like me, but then again there're also times that you just have to wonder how you managed to run all of your errands without speaking a single word to anyone whereas if an Ozarkian sees you buying something unusual at the grocery store (which in the Ozarks means a leek or anything curry) they're going to ask you what you intend to make with it. Gas stations had delis and tackle shops served delicious breakfast hashbrowns. And of course you could buy anything from a new tactical knife to a horse at a sale barn. At least the Michigan town I live in has a farmers' market; that helps, although I have yet to see livestock for sale there.

And whenever I'm farther south in Michigan where it is just flat plains and swamp, I find myself missing the bluffs and hollers of the Ozarks.

Figure B: Like that. The haze you see here is not morning fog. It's summer noon heat and humidity.

My little brother and I used to do something we'd call "bluff running". In retrospect it was really stupid. Basically we'd find a climbable bluff, race each other to the top, and then race back down skidding along the slick dead leaves and dodging boulders and trees to the bottom. Then we'd find another one and do it again.

And the storms were fucking incredible. Today's storm here in Michigan involved some gray clouds and distant thunder, and a couple outbursts of rain. Compared to Ozark storms (pissed off, sleep-deprived bears), Michigan's are barely-awake fluffy kittens. The Weather Channel talks about supercells in the context of storm formation, basically as powerful little knots of low pressure, but that doesn't translate into seeing a bank of individual supercells breaking over a bluff and crashing down through the holler. That doesn't translate into rain so hard it hurts hitting your skin and wind that whips road signs back and forth. It doesn't translate into writhing arcs of lighting crackling across the horizon, so sharp and constant that you can smell it coming (like scorched copper) and the constant rolling of thunder or the pounding of hail against the windows. Most of all, it doesn't translate into that greenish-orange hue of the clouds or the breakneck train sound of a tornado. I miss these things. Hearing the house pop in the pressure differentials even though windows were cracked open as the driving sound of rain hitting rain hitting puddles leaking in along with the steady growling of thunder are, to me, peace.

And the summertime heat, 40C with 80%+ humidity so thick that it wraps your bones like a warm mud towel, oozing through your pores and back out again. Michigan's summers seem watery and distant, although the cold here has a similar bone-pervading quality (not in a pleasant way, though).

But at the same time, the Ozarks were so deeply anti-intellectual, so intolerant, so absolutely incurious and, well, lazy. These are most of the reasons I packed up and got out at the second opportunity to do so. Driving down backroads it was common to see a stretch of several well-maintained houses, and then one that had burned down or collapsed and just sat there for years. There is only one major research university in the entire Ozarks, Washington University in Saint Louis, and it's a private institution. And at the same time, it was the absolute intolerance and social stratification that stubbornly persisted there that got to me. People would casually drop racial epithets around so often that I grew up not knowing that many of these terms were offensive (e.g., I had believed that "porch monkey" just meant a lazy person until I saw Clerks II), even naming several things with them (there is a rather colorful and deeply offensive term for Brazil nuts used there; I'm not going to repeat it here). And that intolerance didn't end with terms. I distinctly remember my step-mother going into absolute raging hysterics--red-faced screaming, dangerously high blood pressure--when she found out that I was dating an African-American girl in high school, even banning her from the house and from calling (none of which stopped me, of course). Thankfully she'd learned that I was immune to her biases by the time I came back from college for Thanksgiving with a co-habitating African-American girlfriend and kept her mouth shut. But the ignorance wasn't just limited to her, it was also in the evening news with reports of interracial couples' homes being sprayed with violent graffiti and the only mosque in the area being firebombed after Sept. 11th, 2001.

So sometimes I'm torn between the nostalgia of my childhood and the more liberal attitudes of my little corner of Michigan (although perhaps local cracker women should note that trying to flirt with me when I am clearly on a date with a woman of a different race than myself is not cool and doesn't fly, seriously: what the fuck?). But then I have to remember that every good experience of the Ozarks was either internal or within a close-knit group of family and friends whereas most negative experiences were from wider Ozark society. I'm glad I moved for the much greater educational opportunities, but sometimes I miss cornmeal-fried crappie and okra. Here in Michigan you can only find okra served in Indian restaurants, and that's just not the same.

25 April, 2009


In case any of you doubt the awesome hotness of the science I have done this week, gaze upon the picture above and be unimpressed (taken today on an Olympus upright fluorescent microscope). Then click on it to kick it out into a new tab or window much bigger and you'll see just how sweaty-palmed hot this science is.

Don't see it?

Look to the resolution.



This was done using special capillary slides and a Microprobe apparatus and an abbreviated incubation timeschedule. Despite my custom Megablocking Buffer working wonderfully in other micrograph fields, this particular chunk had particularly high background so it's scientifically useless. Still beautiful, though.

Post Script - Toaster has finally gotten a toaster. I've been without a toaster for 8 months, and I've been quite aware of the irony of me, Toaster, not actually having a toaster and being forced to make toast with a skillet or the oven. But this one has 4 slots, and each one is big enough for a grilled cheese!

Nerd Frame 2: The Continuance

7415 3n71r3 p057 w1ll b3 wr1773n 3n 13375p34|<.

4c7u4lly, 1 d0n'7 h4v3 7h3 p4t93nc3 70 d0 7h47, 7h3r34: 4p0l0G135

To those of you who could easily read the above 2 lines: congratulations, you're a nerd. That isn't to say that everyone else who couldn't read them isn't a nerd, just that they've different specialties.

One of the tensions between intellectuals and wider society is that society prescribes a single nerd frame to all nerds irrespective of our diversity. This allows society to get away with marginalizing us stereotypically as unhygienic, cerebral, and weak while we feel unfairly smashed into ill-fitting frames. This dysfunctional dynamic perpetuates nerd isolation and insulation.

In my previous post on this subject, the commentators suggested that nerds are socially isolated because we are unable to climb out of the deep wells of our minds.

But what if the problem is not internal with us, but rather external in that we have no where to climb to?

As nerds we are accused of being insular and having wolf-pack social dynamics (small groups of like-minded nerds with clear hierarchies [who's the PI? who's the most 1337?]). We're also accused of being aloof eggheads with no communication skills. Both of these are true to at least some extent.

Since society is depend upon us nerds for technology, science, medicine, and George Lucas' box office success, why is the onus upon us to make ourselves understandable? It it probably overly idealistic, but I don't think it's unreasonable for society to at least meet us halfway and learn some of our scientific dogma. We as scientists are charged with creating knowledge and disseminating it to the public (which we do to varying degrees of success), but there comes a point at which the knowledge we create simply cannot be watered down any more*. But when we fail to communicate the relevance of what we do to a lazy society, we're just labeled as nerds in the derogatory sense and written off to our labs and equipment.

This is frustrating, and I am frustrated. I want so badly to be able to educate the public, to inspire critical thinking, to share the depth with which I view the world**, at least see questions deeper than "Uh, like, boogers!". But in the end I can't escape my own nerdness. I lack a socially normal frame through which to communicate. I don't have a way to relate to wider society. Save a few well-placed strong blows to my head, I can't un-educate myself and that education has tempered my thinking.

But when coming back to whose frame is best, nerds' or society's, it now boils down to education. If more people were more educated, society's mean frame would move closer to the nerd frame. Then we, as nerds doing science, would be able to keep the flow of information and dialogue going less one-sidedly. It'd be a net bonus.

However, this brings up another question that I'm going to pose to you: does education increase nerdness or is nerdness an inherent and immutable personality trait?

*This is where alternative medicine pseudoscientific quackery is conceived and born.
**Or at least as I like to think so.

24 April, 2009

Verbing Words Fragment

I'd really like to see "science" become a proper verb.

It just seems right. Currently we have to say things such as "I was in the lab all day" or "I researched it quite thoroughly" when we could instead be saying "I was Sciencing all day" or "I Scienced the crap out of it!".

Dearest Nerdy Hordes, let us make it so.

23 April, 2009

Humbly Seeking Advice

OK, so by now it's probably become more or less obvious that I don't blog much about my personal life at all. For all any of you know, I could be the garden gnome in your yard, sneaking in to bang away at your keyboard while you slumber. This isn't because I'm just a brain on a stick, although I'll admit that at times it is nice to retreat into that mode and cavort about in a marshmallow buttercup landscape of knowledge. Rather, I tend to be more of a stubborn introvert like Prof-like Substance, Science Bear, and (my Giga-Nefarious Mega-Archenemy) Hermitage. I'm not comfortable spreading myself out there in public like Dr. Isis and Juniper Shoemaker; it makes me nervous and jittery, although I can turn on the charm as needed and doing so has gotten me out of many scrapes. As such, writing this is somewhat difficult.

It has become starkly apparent that it would be prudent for me to start looking for another job. This isn't due to problems within the lab or with my boss, we all generally get along quite swimmingly and do some really awesome science and I have been lucky enough to get the responsibility to plan, coordinate, execute, and quantify some rather complex experiments. Unfortunately our science doesn't yield publishable results very quickly, and because of this (at least in part) we're not sure how much longer we can keep the lab open. We've been waiting with panicky, bated breath to hear back about the latest grant applications. We're still waiting. I've been nervously checking our reagent stocks and material supplies, questioning whether we really need something at that very moment. Every experiment I have been planning has been as cheap as possible, and I've been afraid to start new projects because I fear wasting precious reagents if it doesn't work. Despite this I have learned a LOT in this job, not least of which has been how to clean up and reorganize the lab's legacy of messy pack rats.

But my boss pulled me into her office today to let me know that, since we've yet to hear about current grant applications, it might be in my best interests to start looking for another job.

I'm hopeful that, what with ARRA and the NIH getting more funds for challenge grants, people will be hiring again. I'm fortunate to live in a town with lots of biotech, both academic and industrial, which is rare enough in the Midwest. Nonetheless, I'm still somewhat at a loss. I mean, I've been looking at the postings, trying to reassure myself at the slightly increased rate of local postings, but still: I really like the work I've been getting to do*. But liking what I've been doing doesn't buy food or pay for rent.

So how best to move forward? Nothing is set in stone here, it's all risk management. But how can I formulate my resume or format my experiences to make then extra shiny? I know that I should personalize the objective in my resume when possible (most internal institution job postings do not include a PI or lab name). But what else can I do? Essentially, how best can I sell my skills and potential to PIs hungry for data?

Let me know what you think, if you'd be so kind. I'd really appreciate it.

*It helps to have an early bird boss who understands that I'm irredeemably a night owl.

22 April, 2009

Tongue Twister of Doom!

[Warning: There is no intellectual content in this post.]

I saw this today and it made me happy. As such, I thought I might share it with all of you to help spread the happiness around.

Well? You happier?

Allergy Inaccuracy (Toaster Burns Bullshit #3)

I need to stop reading anything that appears on the Huffington Post or else I fear the vein running through my right temple will cease merely throbbing and commence with exploding all messy-like everywhere. I sent them some email expressing my anger and disgust over the absolutely abysmal science/medicine reporting standards they apparently have, as have many others in the sciency blogosphere. Apparently they're being reactionary, recidivist bastards because the shit just keeps getting deeper and worse and more stupid that I had believed possible. It is as though Toaster's Stupidity Scale, tempered by the rhetorical vomit and denialist vehemence of the last 8 years, has had to redefine a new Absolute Zero for this kind of stuff.

Not only has the Huffington Post run a poorly informed and incredibly biased article by Jim Carrey (much better known as The Mask and Ace Ventura than a medical expert) on the autism-vaccine link, they're also pimping a link to some site called Intent with an article entitled "The Self Against the Self: Deal With Seasonal Allergies Naturally and Cheaply". The Sciborgs Orac, Abel Pharmboy, and PalMD have ably knocked the wind out of the "ZOMGVAXXIENZ!" argument cloud fogging Mr. Carrey's brain. So I will be burning the latter article.

"The Self Against the Self: Deal With Seasonal Allergies Naturally and Cheaply" contains some vague mystical advice about how to use Zen and Detoxification to get rid of allergy symptoms. It was written by one Debbie Mandel (website), author of several spiritual self-help books, and whose Intent bio says she will help you build immunity to feeling bad. Note that she is not an immunologist, nor even a biologist, but she'll tell you how to build immunity anyway. I wouldn't have a problem with this claim because building immunity can, sometimes, have a different connotation of inuring one against something unfavorable IF she hadn't actually tried, and failed epically, to invoke actual immunology.
Your response to allergens correlates to how balanced you are regarding: eating, exercising, sleeping and stress-management. Allergies are actually an auto-immune response which translates into: the self against the self. [boldface hers]
First the less egregious problem about homeostatic health and allergies: No, allergen responses don't much depend on whether you're stressed out about work or not. Just ask someone with an acute peanut allergy. Allergic responses are, however, modulated through general systemic inflammation if it exists, but this isn't much relevant unless you're morbidly obese (excess fat can increase inflammation).

This second claim, though, is either sheer stupidity or inability to do research. Allergies and autoimmune disorders such as rheumatoid arthritis are NOT the same thing. Some cases of autoimmunity may have similar underlying immune responses as allergy, but this does not mean they are alike. It is true that allergies are an abnormal immune response, but not against the self. Allergens are strictly defined as harmless environmental substances that evoke an immune response as if they were harmful. Or, as a professor once put it, allergens are nonharmful nonself being treated by the immune system as though they are harmful nonself.

The human body, and its immune cells, come into daily contact with millions of nonself molecules and doesn't have an allergic reaction to them. The immune system is generally quite good at distinguishing between what can harm us and what cannot. Allergies arise when the immune system mistakes something that is harmless, like pollen, as harmful and reacts to it.

Here's how allergies basically work (my explanation):
1) Dendritic cells present antigen in MHCII to CD4+ T-cells all the time without much caring what they're presenting. Sometimes harmless antigen gets presented.
2) Some naive CD4+ T-cells are, by virtue of the recombination and mutagenesis that occur as the T-cell receptors are being formed, naturally reactive against that harmless antigen.
3) Harmless antigen-reactive CD4+ T-cells proliferate and usually differentiate into a TH2-type response. The TH2 T-cell phenotype is characterized by secretion of IL-4.
4) TH2 T-cells talk to B-cells and get them to make antibodies against the harmless antigen, now an allergen. Allergen-specific antibodies are usually of the IgE isotype.
5) IgE gets made and secreted into the plasma, where it can become the receptor for mast cells and basophils. Eosinophils get involved in this, too.
6) When an allergen binds mast cell-IgE, it signals the mast cell to release allergy symptom-causing histamines, prostaglandins, and leukotrienes. These chemicals are generally what allergy medications try to work against.
7) Some allergen-reactive TH2 T-cells and their corresponding B-cells will become memory cells, ready to spring back into action at the drop of their allergen.
At no point in this is the immune system reacting against host antigens. In fact, the immune system tries very hard to kill all host-reactive T-cells as they're being made (this results in >99% of all developing T-cells being killed off). If Debbie Mandel had done her research before making up the above assertion, she'd have known better. This is irresponsible, dishonest, and lazy. Although I guess the immune system reacting against harmless environmental substances just isn't as fear-inducing as a self-reactive immune system.
Your response to allergens correlates to how balanced you are regarding: eating, exercising, sleeping and stress-management. Allergies are actually an auto-immune response which translates into: the self against the self. So, it makes absolute sense that when you are intact and whole, your allergies will dissipate and no longer bother you; your immune system will be more vigilant. I present myself as a test case.
It only makes sense if you're poorly informed. Memory immune cells last for many many many years, or else vaccines wouldn't work at all. Presenting herself as a test case is also stupid. How many times do we need to tell people that anecdotes do not equal evidence!?

For years I was an allergy sufferer. My sinus headaches, dizziness, itchy eyes and occasional tiredness always arrived with spring. Every morning I woke up to coffee and Allegra D 180 mg. However, in the past few years I rarely have any symptoms except for the occasional itchy eye and more important, no more killer headaches and sinus pressure!

What has changed? I stopped taking the medication five years ago, ate more fruits and vegetables and basically stopped fighting Mother Nature; I vowed to get along with her no matter what the weather. Brazenly, I went out to my garden, in the trenches, fertilizing, weeding, mulching and pruning without the fear or the expectation of an allergic reaction. I made up my mind not to have any symptoms and oh yes, I almost forgot, I managed my stress.

Note that she doesn't mention how long it took her to stop having symptoms. In all probability, she was quite miserable for the first couple years. What she did here was not Mystical Woo Magic, it was a clumsy and messy version of hyposensitization treatment. In clinical hyposensitization treatment, patients with allergies are inoculated with progressively greater doses of purified allergens. Hyposensitization does not exactly cure allergies, but it does relieve symptoms by skewing the immune response away from a TH2 IgE to a TH1 IgG, which doesn't rely on the mast cells or basophils that can mediate allergic rhinoconjunctivitis. Ms. Mandel would have gotten the same results clinically (but that would have meant vaccine-like injections, which might contain Teh Mercury and Teh Aluminumz! ZOMGs!).

Ultimately, this might have been an interesting and useful article if Debbie Mandel had done their research properly. As it is, her failure to do so has made her writing as flimsy as her detoxicification and Teh Evil Sugarz screeds.

Post Script: Please note that I do not have a problem with people writing about the immune system in the popular media. In fact, I support the information and principles getting more exposure because I think the immune system is The Awesome Eleventy Coolness. If I could, I'd pass out the DC-->T-cell-->B-cell-->antibody dogma in tasty ladlefuls on the street corners if it could be made into a pudding. However, I have a big problem with non-scientists who are completely unqualified trying to assume professional authority and opine about the mechanics of the immune system, or any science for that matter, when they have not done the research thoroughly. That's just irresponsible.

21 April, 2009

Intuitive Medicine (Toaster Burns Bullshit #2)

[Please note that any and all italics or boldface added to quoted text are my additions.]

What the fuck is with new-age looney motherfuckers and their chakra bullshit? Chakras this, chakras that, align your chakras, cleanse your chakras...on and on and on until you want to stab them in the eye with the nearest stick of incense. Unfortunately, chakras are no longer solely the domain of spiritualism or granola crunchers. No, if the Huffington Post is to be believed, then chakras are apparently moving into the mainstream medical establishment under the flimsy disguise of "intuitive medical scanning".

So what is intuitive scanning? Let's allow Huffington Post to explain:
Intuitive body scanning is a technique that can be used to determine medical or health blockages in people and animals. Medical intuitives, professionals who seek to complement traditional medical procedures with this technique, locate body parts that are blocked or in turmoil in order to expedite the healing process...Just as an X-ray machine scans a body in order to gain specific medical details, an intuitive scan works to provide an energetic portrait of the client. The premise is that the physical body has an energy blueprint and so the intuitive scan will look for energy blockages and areas of stress. Good health is, in general, considered to be clear flows of energy between all the chakras and easy, free functioning of all organs and body systems. Because this is an intuitive technique, scans can be done in person or from a distance with equal accuracy.
See a pattern between the bolded text?

Look closely. What do all of the bolded terms have in common?

They're MAGIC! Unquantifiable, unfalsifiable, ephemeral, mystical, MAGIC!!!eleventy

And intuitive medical scanning can even be done from a distance! Holy fuck it must be real if it's that magic! Let's be clear here: the Internet works over long distances. So do rockets. However, spooky energies from the human mind do not exert influence over either immediate or distant states of being, energies, events, or other qualia.

But Huffington Post isn't content to just tell us about the new phenomenon of intuitive medical scanning. No, being the paragon of responsible medical reporting that they are, they also tell us, average Joes and Janes, how to do it at home! Whoopee!

So how does one do an intuitive medical scan?
...perform a scan using inner vision...This technique can be highly accurate, but a bit uncomfortable for anyone who is highly empathic, which is the ability to feel what others are feeling and sensing.
My empathic inner vision is telling me that my stomach chakra wants black olives and cheese, or perhaps a cinnamon raisin bagel with peanut butter. Or a burrito. Maybe my stomach chakra is confused?
Look for knots, dark spots, tension, pain or any area that seems to stand out to you during the scan. Note the spot and then go back and zero in for more detail if you are able. At this point, people who have some medical training can have an advantage because they can sometimes more accurately interpret what organ or system is blocked.
OK, so now it's apparent that my gall bladder is burgeoning with bile salts and stomach acids, that poblano barbecue sauce from last night is chilling in my duodenum, and I'm detecting some major ghrelin production in my stomach lining and...holy fuck it's binding to GHS-R on my arcuate nucleus in my motherfucking hypothalamus!!! Oh, oh, the pain! This must be empathic discomfort...

How do we get rid of this discomfort? Huffington Post is good enough to interview 2 practicioners of intuitive medical scanning for some inside tips and tricks.
My favorite is the Helmet technique. You get a name, city, age, and place a "helmet" of their head on your own. It is a quickie way inside their body. From there, I scan. I can see it in light contrast. I can feel the pain inside me, or the anxiety, or whatever.

I can very quickly (I hate feeling their stuff in me) clear it with breath induced energy spurts. When I feel the release, I know they do. I then remove the helmet, give it back to their body, and physically clear the space around me..especially my head...to regain my Self.

Ah, spurts of energy! Of course! Wait...that sounds rather gross and come to think of it that entire sentence is laden with far too much inneundo for me to stomach (and what the fuck is up with this Helmet shit?). Even more nauseating, however, is that this practicioner can't even keep her mysticism straight:
I will also use a technique where I hold a major chakra, usually foot, to connect (either in person or from a distance) and send a flow of energy from my hands.
Here's a chart of the traditional Indian chakras:

Nothing in the foot.

Of course, logically, this means that they're such a good medical intuitive that they have discovered/invented an entirely new chakra! Holy crapdiddles, she must be great at this.

There is much more, much, much, much more in the original article if you care to slog through it. However, I think I just ran out of sarcasm. To give credit where it is due, however, the author of this piece did include a disclaimer:
Of course, none of this is meant to substitute for traditional medical professional consultations and advice.
Thank you for that much, author. I know that you couldn't help pen such bullshit, for this kind of crazy can only write itself.

20 April, 2009

Developmental Effects of Ambient Air Pollution

ResearchBlogging.orgFirst off, props to Dr. Isis, who in the discussion of her Cairo haze post referenced the work of L. Calderón-Garcidueñas, which set me off into the literature. What I have initially found was sobering.

Air isn't something we often think about. We take it entirely for granted. We complain about how hot or humid it is, but we usually don't have to think about what in that air might be making us, or our children, sick. Those of us fortunate enough to live in Western, industrialized countries really are well-off in that we don't ever really have to pit our own health against the simple act of breathing. Other areas in the world aren't so fortunate.

Dr. Calderón-Garcidueñas' work focuses on the effects of airborne pollutants and particulate matter on the developing lungs of children in Mexico City, Mexico. But her work is actually relevant to anywhere that the air isn't shiny clean.

By radiograph, her team found that children in Mexico City with lifelong exposure to the polluted air had significantly increased rates of lung hyperinflation when compared to age-matched controls from a much less polluted area (Tuxpam, Ver [I'm guessing this is somewhere else in Mexico?]). Lung hyperinflation by itself in one person doesn't indicate a lot, it just means that there is more air in the small alveoli of the lung so it appears larger on a radiograph. This could mean asthma, emphysema, or even lung cancer, but could also just mean the patient was breathing hard. But when there is such a significant (p=0.0004) between groups it becomes indicative of pollution-induced lung dysfunction.

This is in addition to previous work demonstrating that children in this severly polluted area of Mexico City had altered nasal apparatus such that the mucociliary clearing/filter mechanism wasn't working so well as it should be. This is troubling because the loss of the nasal ciliary filter leads to an even greater dose of reactive gasses or particulate matters getting past it into the lower lungs, thus exacerbating the initial problem.

Referenced experiments in this paper showed even more going on. Particulate matter (PM) less than 5um in aerodynamic diameter was found to disproportionately wind up in the alveolar sacks of the lung while PM greater than 10um was found to locate to the proximal bronchioles. PM doesn't seem to affect lung epithelia directly, but it does activate alveolar macrophages to produce inflammatory cytokines (IL-6 and TNF) that utlimately will attract additional inflammatory infiltrate and further damage lung tissues. On the other hand, reactive gasses were found, in vitro and in animal models, to elicit secretion of IL-6, IL-8 (both inflammatory), and fibronectin (involved in repair if tissue damage) in lung epithelial cells.

Together, these 2 overlapping respsonses indicate the air pollution is driving a repetitive damage-repair cycle in lung tissues. Pollution damages lung tissue and activates the immune system to produce and inflammatory response. So the lung tissue tries to repair itself in an inflammed environment, which can lead to scar-like tissue regeneration. The altered tissue regeneration (as in the loss of the nasal cilia above) can lead to lung tissue more vulnerable to subsequent pollution injury. Over time, this kind of cycle leads to long-term tissue remodeling such as increased constrictive reactivity of existing smooth muscle (a hallmark of acute asthmatic responses), increased smooth muscle metaplasia (chronic asthma), eosinophilia (asthma and allergy reactivity), and even destruction of the walls dividing alveoli (a hallmark of emphysema). And what's saddest about this is that moving animal models of exposure to clean air did not completely reverse the exposure-related pathologies, which means that the lung damage will be a life-long legacy of any children that grew up in it.

So take a deep breath, and be thankful it's mostly clean.

Calderón-Garcidue˜nas, L. (2000). Respiratory tract pathology and cytokine imbalance in clinically healthy children chronically and sequentially exposed to air pollutants Medical Hypotheses, 55 (5), 373-378 DOI: 10.1054/mehy.2000.1070

(P.S. - Whomever came to this blog searching for "burning bronchioles so they won't constrict", please don't. I can think of few worse ways to die than by one literally drowning in necrotic, burnt lung tissue while gasping painfully for whatever air they can still get.)

19 April, 2009

Nerd Frame 1

Do we, as science nerds, alienate others as a matter of course? If so, is this a defensive mechanism or a simple inability to climb out of our minds and relate to non-nerds?

I'm not trying to claim that all science nerds are awkward introverts, just some of us. There seem to be some scientists who are very very good at interacting with normal people, but there are just as many, if not more, who wander around public places looking either very confused or somewhat huddled into themselves.

Let's be honest: human social communication is so deep and complex and, frankly, damned weird that some of us will choose to immerse ourselves in protein interaction kinetics instead of going to parties.

What do you think?

(There's a point here that I'll get to later.)

17 April, 2009

Musical Faux Pas

My boss is used to walking in to the lab and hearing this kind of music playing as TechnoGrad and I have extensively programmed several industrial radio channels:

But when TechnoGrad is not there, I tend to listen to more diverse music. Usually this means some wicked drum and bass, blues, or 90s hard rock and I'll Cracker Dance as I do science. But sometimes I put on hip-hop. So of course on the most recent rare occasion when I've got U.S. rap* playing, my boss walks in as Pandora serves up this** (NSFW):


Please also note:
Regular science programming will resume shortly.

*As opposed to UK grimecore rap such as that done by Lady Sovereign, Wiley, Dizzee Rascal, Lethal Bizzle, The Streets, and The Audiobombs.
**Toaster does not endorse or approve the misogyny expressed in this song. He feels guilt for finding the beat catchy.

15 April, 2009

PhizzleDizzle Is Right

Python is a lot more intuitive than Perl. Perl is all twisted up in contractions and brackets and weird contractions whereas Python has just a few punctuation sets and very clear functional parsing. I spent 3h on a Python tutorial and have managed to write scripts that I haven't been able to write even after a couple months of casually studying Perl. The only non-intuitive thing I've found in Perl so far has been trying to link an operation inside of a "while" loop to a condition set outside the loop. With this, it took me about 40min to figure out what was wrong with my script to ask for numbers one at a time until the sum was 100 or greater, because the loop kept quitting after 2 numbers. I think I've got it now.

Bonus: Python can do more than just parse text files. This has been one of my frustrations with Perl so far, I could write a little script to change all the "ae" in a text document to "ä", but when it came to actual utility it was kind of limited. I have no doubt that Perl is useful for large-scale Internet applications, I now think that Python might be a more useful skill to develop. I'm not going to give up completely on Perl, but for the moment Python suits my curiosities much better. There's even a serial.py module that let's Python talk to micro-controllers!

So yes, Phizzle Dizzle was right. Python seems to be just as powerful, more intuitive, and offer a much shallower and less painful learning curve. Also, the IDLE Python GUI is quite nice.

14 April, 2009

Cost of Science

We all know science is expensive. Satellites and particle colliders costs tens of millions of dollars, flow cytometers cost as much as a mansion in Detroit, confocal microscopes can be had for the price of a gently used Cessna. But why is it so expensive?

I understand why large equipement is expensive. A BioRad pentaplex Q-RT-PCR thermocycler system costing $35,000 makes sense given how complex and sensitive it is. A -80C freezer costing $5,000+ makes sense given the sheer amount of materials that go into making it. But it's not just the large equipment that's so expensive. Little, common, everyday scientific supplies are also quite expensive. And disproportionately so.

Fisherbrand sterile Petri dishes cost $0.30 each at list price, and they're really only good for a single use. Acros Organics yeast extract is ~$250/kg at list price. My favorite general dissection scalpel blades (No. 22s), also only good for one use, cost $165 for just 100 blades, and that's Fisherbrand*. Reusable Fisherbrand glass pipettes are $10 each. And sure, base cell culture media are cheap (500ml RPMI $13, 500ml DMEM $4), but when you factor in the cost of adding FBS (~$500/L) to make them complete the costs add up real quick.

In a consumer market these items wouldn't cost nearly so much. 100 straight razor blades, a similar amount and grade of metal as scalpels, cost $9 on Amazon. Fleischman's yeast is $17/kg. Yes, these aren't the same exact products. They aren't specifically made for science, but they are made of similar types and quantities of materials. Does standardization of research supplies really command a 500%+ markup in price? Is the quality really that different?

This adds up to another barrier to entering biomedical research as an amateur, hobbyist, or newly minted PI. Daily disposables cost a busy lab so much money that they can quickly eat through large grants. The thing is, though, is that we're more or less at the mercy of the companies providing these products when they choose their prices. We are a small niche market, and as such the specialization of any product to fit our needs as researchers is going to cost much more than it otherwise would in a larger market.

There are 2 possible solutions to this:

1) More people need to start using scientific supplies for other uses. This will increase competition between Fisherbrand, Denville Scientific, and VWR and force them all to lower their prices. Erlenmeyer flasks are heat stable, so why not use a 2L flask to make pasta at home? Borosilicated tall beakers run about $6 each, and have the advantage of being able to measure the components of your mixed drink in milliliters. If you're worried about your weight, try the Petri dish diet, where you only get to eat a Petri dish's worth of any given food in the space of an hour, so long as that food is not lard of deep-fried chicken skin. I, for one, think that a 10ml glass pipette would make a handy home defense tool shiv.

2) Conglomerate negotiations. The MRU I work at has so many labs that each department has a supplies and ordering coordinator who negotiates special permanant discounts for all supplies needed. With this, the $0.30/Petri dish above becomes $0.10 per. Our black nitrile gloves (what else would a Mad Scientist wear?) cost about $0.01 each rather than the $0.05 listed. In short, the ordering coordinator uses the weight of the institution's aggregated lab purchasing parity to reduce costs across the board.

However, this option isn't really available to individuals, informal groups, or SLACS. Once again raising the costs of admission to basic science.

The high costs of science also don't do much to charm the public when they resent how their tax dollars are being spent (although I really think they should be looking far more angrily to the five-sided building than to ivory towers).

And, finally, a broader question: Do industry labs pay full cost for supplies or do they also negotiate price breaks?

13 April, 2009

Our Shrinking Cloister

I've got a beefy diatribe to spleen out.

I have seen on the Interwebz in the past several months a great deal of discussion about DIY biology research and whether or not it's safe. I've seen big-wiggy biomedical researchers and computer sciencers weigh in on this. I suspect both are missing the point.

Currently, biomedical scientists are arcane magicians working quiet miracles in the shadowy corners of public consciousness. We're nerds of such deep inaccessibility that we become artificers of mythical proportion and prophetic comprehensibility. The public does not understand what we are doing or why it takes so long for progress to be made; we're supposed to produce flash-bang-holy-shit magic tricks on demand even as we dread being questioned why our research matters. The terms we use, the depth of the knowledges that we plumb, the datasets that we construct, the very equipment that we use all serve to enforce an idiosyncratic barrier that requires intelligence, time, and flinty-nosed mule-like stubborness to break into.

This cloister which we've inherited does indeed have its advantages. We can go to work in the lab with other fully competent people whom we may easily assume are familiar with basic genetics and protein dogma. We can develop our presentations with great detail, sculpting each to the level of specialization of each audience. We can dive deeply into a heady rush of informational give-and-take, intellectual play, and experimental thrill. However, I find that this cloister is slowly suffocating us.

When our predecessors enshrined themselves and their disciplines into ivory monoliths of thought, they also shut out nonconformists, radicals, and fundamental innovators. Those that don't deign play the game of academia or lie out the sides of their mouths about career intentions are inevitably shanked with a glass pipette and thrown under the steam roller of their committee's disapproval. An entire industry has birthed itself in response to the standardized demands of academic science, and has made massive profits while doing so (and while it's important to have data standards, it is also true that standards become economic commodities that eventually get more and more expensive to maintain, and are also exclusive of other ways of generating data). By setting the bar for entry to biomedical science so very high, we've effectively shut out everyone who cannot pay to play. This includes independent hobbyists, start-up biomedical firms, and newly minted PIs.

This is due to 2 structural features of academic science:

1) Physical plant/equipment. Think about the sheer variety of specialized equipment that a molecular biology laboratory has. Gel docks, power sources, block heaters, incubators, freezers, microcentrifuges, flow cytometers, UV photoimagers, flow hoods, Bunsen burners, shaking warm water baths, RNase-free chambers, etc. etc. etc.. All of this stuff costs huge sums of money, effectively making the entry costs of biomedical science so very high that no one but the most affluent, in private funds or grants, can hope to even try to play.

This parallels the initial development of computer science. The first computers were so massive, specialized, and expensive that computer science and the study and application thereof were but a fringe niche. Today both are ubiquitous. The fundamentals of computing science haven't changed. But the entry costs have. With the advent of the personal computer costing less and less, more and more nerds have been able to pour into computer science, coding and hacking and building the very environment in which Internet-users dwell. Lowering the entry fees has allowed more people to play and succeed in an arena previously dominated by UNIVACs and their attendant haughty acolytes.

Now, we as biomedical researchers are the high priests of Biology. The knowledge for a talented hobbyist to make real progress exists, as does the capability. The textbooks are written, the databases are public, yet we remain skeptical and the equipment remains prohibitively pricey*.

2) Computer scientists tell their computers what to do and hope they didn't make a mistake. Biologists grope around in the darkness of genetics with enzyme fingers and break something, hope it was what they meant to break, and then hope that it has a measurable outcome. Essentially: they start out knowing what they're doing and we hope we know what we did when we're done.

This also hinders inclusivity in the biological sciences inasmuch as detailed and deep knowledge is required to interpret data or plan a meaningful experiment. Computer science can tinker with code components for a couple hours and a bright person will eventually figure out that $x assigns a variable while @y assigns an array. Meanwhile, the same person could spend weeks, years even, tinkering with E. coli before figuring out that LacI is a protein that acts upon lacZ genetic material.

Unlike the first obstacle, however, this one is much much more difficult to overcome. We could easily rig a water-jacketed incubator by using a styrofoam cooler, Tupperware, and a tropical fish aquarium pump. We can't rig knowledge nearly so easily. To a degree, this is what textbooks are for. Yet at the same time, we've got the most valuable information hidden behind an elaborate series of paywalls.

This also hinders biomedical sciences being relevant. Yes, we know it's important because we work out of compassion, trying to improve knowledge to ease suffering and improve lives. But society doesn't necessarily know that. Sending rockets to the moon was concrete and real and it beat the Ruskies. Growing dynein engines in Petri dishes isn't nearly so concrete. So we're back to being shadowy nerds, toiling on nerdy stuff that doesn't matter. It's here where our cloister begins to strangle us, because when the public does not understand what, why, or how, even to the most shallow degree, what we are doing and what it's potential payoffs are, we have to go on the defensive automatically to keep justifying our labor and its expense.

We'd better serve ourselves by spending more time on the offensive, engaging the public and demystifying what we do, maybe even helping out the DIYers. By embiggening the pool of people thinking about biomedical research issues and increasing the hunger to do something about it we'd be setting up a positive feedback loop, even if some of the greybeards may fear the potential for nontraditional competition. In the end it can only help us, you know?

*To this end I favor the development of biological hacker spaces, similar to those featured at www.hackerspaces.org/wiki. In these, members pay a monthly fee for access to common equipment. This collectivism may be the only viable way to surmount the high entry costs of biomedical research.

10 April, 2009

No Dendritic Cells --> Unchecked CD4+ T-Cell Proliferation --> Autoimmunity --> DEATH

ResearchBlogging.orgDendritic cells (DCs) are the extremely important interface cell type between the innate and adaptive immune systems. Without them, the adaptive immune system has a very hard time getting started and the organism has a much more difficult time fighting off pathogens. But DCs don't just save our lives when we're sick, they also save us from ourselves when we're not. It has recently been found that constitutive knockout of dendritic cells leads to the development of spontaneous fatal autoimmunity.

[Context/background in previous posts on dendritic cells, T-cells, asthma T-cells, and multiple sclerosis autoimmunity.]

As is the case in many immune system pathologies, this comes back to T-cells. In a normal thymus, T-cells are continually proliferating in huge numbers. Each T-cell undergoes Rag-mediated receptor specificity recombination and randomization while it is forming its receptor. This gives rise to T-cells with receptors specific to a massively diverse array of potential antigens and is at the core of how the adaptive immune system recognizes pathogen peptides and fights back against them specifically. However, most of the T-cells that get made are killed off summarily for having receptors that react against self-antigens (meaning peptides native to the organism; called autoreactivity). Although the thymic epithelium is also involved in screening potential T-cells for autoreactivity, DCs are the primary mechanism by which these potentially harmful T-cells are weeded out before they can escape from the thymus differentiated and initiate an autoimmune response. There is even a specialized subset of thymic DCs that express diverse self-antigens to help weed the T-cells reacting against them out, and systemic plasmacytoid and myeloid DCs often circulate through the thymus or lymph nodes bearing chunks of apoptotic self-cells.

This group found a way to constitutively delete DCs. Without the DCs, the CD4+ T-cells of the mice went wild and proliferated massively because they weren't being tested and usually killed anymore (~10-fold more IFNg- and IL-17A-producing CD4+ T-cells in DC- than DC+ mice). This allowed self-reactive T-cells to mature and get out into the circulation, where they infiltrated various tissues and caused massive inflammation. Many of the mice used here died after the autoimmune response had developed. It should be noted that the DC deletion wasn't absolute, IFN-producing DCs were unaffected by their construct and B-cells and some macrophages have been shown to be able to prime T-cells as well, which explains how the CD4+ T-cells were able to fully mature in DC- mice.

Not only did effector inflammatory CD4+ T-cells increase, but Treg cells increased in frequency also, they just didn't seem to be doing much. They seemed to see that effector inflammatory CD4+ T-cells were out of control and tried to proliferate to help curb this, but without DCs they couldn't actually make anything happen. This prompted a quick preliminary search through PubMed and Google Scholar and it looks like the IL-10 that gets produced by Tregs decreases DC maturation from monocytes and encourages macrophage formation instead. It also looks like immature pre-DCs exposed to IL-10 don't express as much CD4/8 or MHCI/II as fully differentiated DCs. This is interesting in that is strongly suggests Tregs don't act directly on inflammatory T-cells, but instead act through DC-mediated pathways.

The group also infected DC- mice with helminths to provoke an immune response and see what happens. Not only were DC- mice unable to clear the infection as DC+ mice were, but DC- also had reduced pulmonary eosinophilia and increased TH1 and TH17 type effector T-cell tissue infiltration (oddly, they didn't report on any TH2 type data, which would have been very interesting). This demonstrated that DCs were absolutely required to mount an effective immune response to infection, which apparently hadn't been definitively shown before (probably because it's hard to knock DCs out; see below).

However, even though DC- mice weren't able to clear a helminth infection, they were able to make antibodies. This defies classical immunology dogma because it is widely supported that T-cells go and activate B-cells to make antibodies after getting primed by DCs. Under some circumstances, e.g., this DC- one, T-cells can still get primed by B-cells or peripheral monocyte populations, which may include the IFN-producing DCs that didn't get knocked out.

To test for antibodies from DC- mice, they used tissue sections from rag-/- mice and immunofluorescently stained them for mouse IgG. Rag is the gene that controls the formation of unique T- and B-cell receptors, and without the rag gene the organism has absolutely no adaptive immune response* and makes no antibodies whatsoever, although they still do have innate immune effector cells. Therefore rag-/- mouse tissues will have no antibodies and no background staining, allowing detection of autoreactive antibodies from the DC- mice. The immunofluorescence staining showed that the targets of autoimmunity varied widely, with some mice autoreactive to nuclear components, others to lamina propria components, and still others to the epithelium itself. Why is this important? Antibodies are the adaptive immune system's signal to the innate immune system that something the innate immune system otherwise wouldn't see as bad is, in fact, bad and should be destroyed. So if something gets antibody bound to it, the innate immune effector cells (i.e., neutrophils, macrophages, eosinophils, even DCs) will recognize it as bad and chew on it. In the case of the DC- mice, the unregulated adaptive immune system wound up labeling the mouse's own tissue as bad and initiated inflammatory responses against it, sort of shooting itself in the foot.

In summary, DCs are important not only to fight off infection, but also to keep the adaptive inflammatory responses in check. Dysregulation or maldevelopment of DCs is therefore a potential target for remediation in autoimmune conditions such as inflammatory bowel disease, rheumatoid arthritis, and multiple sclerosis.

Genetics Addendum: The DC-knockout construct that this group made was really elegant and cool. I didn't mention it above because I wanted to stick to the cool big stuff, but this here is some awesome little stuff. Cre is a recombinase that recognizes floxP sequences. When there are 2 floxP sequences flanking a gene and when Cre gets expressed, it recognizes those floxP sequences and cuts out everything between. This system underpins 17 metric craploads of transgenic mouse studies.

Here, they built a construct where Cre was constitutively (this means always) expressed by a DC-specific promoter. They also stuck in a 3-layer sequence elsewhere on the construct. The outer layer of the sequence consisted of 2 complementary chunks of the sequence for diptheria toxin, the thin middle layer consisted of the floxP sequences, and the inner layer was an erythropoetin resistance gene. So without the Cre, the erythropoetin resistance gene disrupted the diptheria toxin gene. But when Cre got expressed in developing DCs in the bone marrow, the floxP sequences and the erythropoetin resistance gene got cut out and joined the diptheria toxin back into a functional sequence. So then diptheria toxin got made and killed the developing DCs before they could even get out of the bone marrow.

*This makes rag-/- mice popular for studying T-cell behavior. In these experiments, T-cells are taken from a rag+/+ mouse, manipulated according to experimental aims, and injected into rag-/- mice where their behavior and dynamics may be readily observed without native interference.

Ohnmacht, C., Pullner, A., King, S., Drexler, I., Meier, S., Brocker, T., & Voehringer, D. (2009). Constitutive ablation of dendritic cells breaks self-tolerance of CD4 T cells and results in spontaneous fatal autoimmunity Journal of Experimental Medicine, 206 (3), 549-559 DOI: 10.1084/jem.20082394

The End of a Naive Love Affair

I have recently come to realize that one man may only have so many love affairs at once. This is not to say that I have been a skeevy philanderer, just that I now realize that I tried for far too much at once. You see, I'm not the sort of man who is satisfied with limpid, lukewarm love affairs. No, I burn for towering, epic love affairs of grand scope and sweep: steamy and heaving and deep. The kind that steal your breath in thunder and inspire epic poetry and symphonies.

The above realization was inspired by a prior, long overdue, acknowledgment that there was one love affair that I had been poking along for far too long, too stubborn and proud to admit that the free-flowing passion had cooled into quiet despair and subliminal frustration. So, logically, I ended it.

Now she stands in a corner of the room, muttering balefully and gathering dust. Sometimes I have echoes of that former lust, the ecstasy of sliding my fingers gently along her smooth mocha neck, feeling her dulcet murmur against me as my hands slid farther below. But I don't care anymore, for I have more important things to do and can no longer afford to waste my time giving far more than I have ever received in return.

I am speaking, of course, about the violoncello.

Figure A: Baby got back!

I once believed I could wear many many hats at once. While this is topographically possible due to rather large size of my head, it is metaphorically unfeasible. I cannot be a punk rock bassist, industrial electronica composer, death metal guitarist, virtuoso cellist, oddly talented visual artist, polyglot, and console gamer all at once. Especially not when I am enraptured of and captivated by the hot and sweaty passion of Science. I realize that, to be a successful Scientist, I must necessarily place my love for Science above (almost) absolutely everything else. Science is demanding and voracious and will cuckold you in the split millisecond you flinch. But I don't care, I will love it anyway.

However, cello is also a demanding love. Of all the instruments I have ever taught myself to play, it has been by far the most difficult and time-consuming. And I simply don't have the time to devote to it anymore*. What follows is the story of my tumultuous love affair with the cello.

Figure B: Apocalyptica. Eicca Toppinen (far left) is a motherfucking genius.

I was inspired to pick up the cello in addition to other instruments by these guys: Apocalyptica. They were a 4-piece cello metal band from Suomi, now they're 3 cellos + 1 drummer. More specifically, I was inspired by the song: "Path, Vol. 2" from the album Cult, which is still, as far as I'm concerned, their most innovative and daring album to date. I was completely captivated by the sound they had managed to beat out of their cellos and weave into an entirely new music, and I damn near wore that CD out. Other notable tracks from this group that have stuck to me are "Wie Wiet" (Apocalyptica, remake of Quutamo), "Kaamos" (Cult), "In Memoriam" (Cult), and "Toreador II" (Reflections, listen for the cello solo after the violins enter and the subsequent riff).

Cello was also a lot more practical to get around than a double bass, although it must be noted that I miss the automatic hipness that one acquires when playing walking jazz bass lines on a double bass (I never owned my own).

Shortly thereafter I found out about Rasputina.

Figure C: Melora Creager, the brains of Rasputina.

Figure D: Zoë Keating.

I got to see Rasputina live when they were just Melora Creager and Zoë Keating and that drummer guy and I still don't know whether or not I was staring at their cello technique or their corsetry. Zoë Keating has also played with Imogen Heap and has her own solo project.

There is also a cello-alt-rock niche, sort of. To wit, this includes Cursive and Murder By Death.

But that's not all I tried to do with cello. I also discovered what an absolute motherfucking badass J.S. Bach was. Dude was the de facto inventor of modern Western musical tradition. I've found that most people remember Bach for The Well-Tempered Clavier and his solo cello suites (which, by the way, are REALLY difficult). However, when someone mentions Bach to me I immediately think about Lara St. John's recording of his "Double Violin Concerto in D minor", perhaps because I was at one point in a chamber orchestra that tried to play this. It is such a frenetic, complex, yet powerful piece of orchestration. I've heard people obsessed with productivity blather about entering the "flow state". To me, that concerto is the flow state, listening to it is like being back in the heady romance of the initial love affair. I have pulled those notes in the Largo movement from my cello, I tried desperately to keep up and not squeak my strings or hit my fellow ensemble members (it was a small stage) during the Allegro movement. I have played death metal in a band, but Bach was so much deeper and more urgent. With death metal you ask yourself about 2 minutes into any song "Wait a moment, what was I angry about again?", but with Bach, there's no question, you're just in the music, part of it, no longer just an individual but a voice.

Without Bach I would've given up on cello much earlier. However, the fact remained that despite what I wished were true, there was simply no good way for me to devote the time to catch up with my cohort who had been playing with lessons for 15 years already. I saw a fellow group of students play Schubert's "Death and the Maiden", and they fucking rocked it. Looking back, I guess I knew right there that cello would never pay off for me like that because I was too late to the party and had too many other loves in my life to devote myself as much as it required.

Somtimes I still feel the cello notes of classical counterpoint bubbling in me, but more often than not that's backed by an industrial hip-hop beat. I mean, I play bass guitar like I breathe, so I don't need cello.

I do, however, need Science. Come hither, my love!

*This does not in any way mean that Toaster is giving up music, just cello. I have every intention of continuing to make music with bass guitar and computer, and I'm sure as hell not going to stop listening to music. Toaster without music is like powdered water**.

**I actually saw a billboard for Powdered Water in Toldeo, OH. I'm pretty sure it wasn't a joke.

09 April, 2009

Dendritic Cell Phagocytosis of Infected Apoptotic Cells Favors Development of a TH17 Phenotype

ResearchBlogging.orgBackground: TH17 discussed previously here; previous brief run-down of T-cell development here.

TH17 cells are an inflammatory T-cell subtype implicated in acute adaptive immune response as well as chronic autoimmune diseases. We have known for a while now how to create TH17 cells in a dish: just add TGFb and IL-6 (a general T-cell proliferation cytokine such as IL-2 wouldn't hurt either). However, we haven't been very clear on how exactly those kind of conditions would arise in vivo. TGFb is anti-inflammatory and helps slow the adaptive immune response down while IL-6 is pro-inflammatory and revs up the immune system. So how would these 2 molecules be made at the same time? Logically speaking, they wouldn't as it is tempting to think of the immune system as monolithic: capable of one state at a time, either ramping up inflammation or cooling it down. But because TH17 cells have been found in vivo infiltrating tissues and being made in the lymph nodes, and because we haven't yet found any other combination of cytokines that leads to the thorough development of TH17, TGFb and IL-6 must be co-expressed under some condition, somehow.
Before we get there, I'm going to blather at ya'll about dendritic cells for a moment (although I wish I BlogSpot had the functionality to embed this in a text-wrapping box). Dendritic cells (DCs) are the interface between the innate and adaptive immune systems. DCs are phagocytic, meaning they can gobble up pretty much any cell that they see fit to do so to. When they gobble something up, they put it into a special vacuole and crank it through molecular blenders (called proteasomes) to generate short little peptides that they then port back out to their surfaces on major histocompatibility II proteins (MHCII) that T-cells can bind to and recognize. T-cells can't recognize peptides, called antigens here, without the context of MHCII. Correct peptide-MHCII-CD4-TCR signalling tells the T-cell to do adaptive immune stuff that helps the body fight off disease.

Figure A: A dendritic cell grown in vitro on collagen. Note the tentacley things protruding all over the place, those are the dendritic processes. Not all of the dendritic processes in this picture are from that one cell as other dendritic cell bodies are off screen. Picture somewhat altered for better contrast from original Wikimedia Commons jpeg.

DCs also possess Toll-like receptors that recognize PAMPs (pathogen-associated molecular patterns). PAMPs include dsRNA (TLR3), flagellin (TLR5), single-stranded RNA (TLR7), unmethylated CpG DNA (TLR9) and, most importantly here, LPS (TLR4) [LPS is a constitutive component of Gram-negative bacteria, which shed it. It is also known as endotoxin.]. When a TLR binds its ligand, the DC gets activated and migrates to the lymph node where the naive T-cells are hanging out. Once there it secretes various effector cytokines that have specific actions on the T-cells. These cytokines include IL-2, IL-4, IL-6, IL-12, TGFb, TNFa, and a whole other mess of alphanumeric soup noodles.

Anyway, back to the conundrum of how inflammatory IL-6 and anti-inflammatory TGFb get co-expressed and make TH17 cells in vivo. It turns out that infected apoptotic cells can lead to the right co-expression. DC processing of apoptotic cells induces TGFb to throttle down inflammation in case the immune system has gotten too aggressive and is killing off the host organism (as occurs in septic shock). DC processing of non-host infectious agents usually induces IL-6. So when a DC processes an apoptotic cell that was infected with an intracellular microbe of some sort, both stimuli are right there and the DC trundles off to the lymph node making both TGFb and IL-6.

The group in the paper below used LPS-loaded apoptotic B-cells and E. coli-infected apoptotic neutrophils to test this out. They mixed the B-cells and neutrophils with DCs and let them stew for a while as the DC chewed thoughtfully and decided what to do. They then collected the culture medium off fo the DCs, which would contain any differentiation and/or signalling cytokines the DCs secreted in response to the apoptotic cell stimulus. Next, this medium was added to cultures of naive CD4+ T-cells and they sat back and watched what happened via flow cytometry, mRNA expression, and production of phenotypic marker cytokines (specifically, IL-10 and IL-17).

Using unloaded apoptotic B-cells or uninfected apoptotic neutrophils didn't do much by way of making TH17 cells as only TGFb was produced (made Tregs, though, see below). However, this was reversible through complementation with exogenous IL-6. Also, DCs exposed just to LPS such that TLR4 was strongly activated did induce lots of IL-6 production, but this didn't lead to much TH17 production unless IFNg was blocked (this consequently blocks the production of TH1 cells).

It turns out that apoptotic cells also induce a Treg response through TGFb. Tregs are the cells that calm the rest of the immune system down when it's gotten too excited. They are characterized by expression of Fox3p and secretion of IL-10. A sizeable portion of the naive T-cells also made IL-10 and flow cytometric analysis revealed that some had become double T-cells, secreting both IL-10 and IL-17. However, this was only during the initial stimulation of the naive T-cells. Later on, after these now-differentiated T-cells had calmed down, re-stimulation with IL-23 increased IL-17 production and downregulated IL-10 mRNA, indicating that this dual expansion may be a transient phenomenon.

The group replicated their findings in vivo. They used a Citrobacter rodentium model of hemorrhagic colitis in which many cells in the gastrointestinal epithelium go apoptotic and inhibited that apoptosis. Inhibited apoptosis led to lower infiltration of TH17 cells than untreated mice. There were also a bunch of good genetic and chemical controls, but I'm not going to discuss all of that here because 1) it's a LOT of detail and 2) I'm more interested in blathering about the implications of this finding.

Implication 1: Ulcerative colitis
The sick gut cells in ulcerative colitis aren't necessarily infected themselves. But due to the very high native colonization of the gastrointestinal tract by our friendly microbiota, there are always relatively high levels of LPS in the lumen that, presumably, interact with the epithelium. Therefore, at the ulcers, especially those mediated by Helicobacter spp., there is an increased likelihood that responding DCs will encounter both microbial PAMPs and apoptotic cells. This could explain, at least partly, why TH17 cells are heavily involved in the inflammation associated with gastritis.

Implication 2: Cancer
Given that pre-cancerous cells are generally not listening to the cells around them and have higher rates of mutation, it is entirely plausable that some cancer cells with alter the expression patterns of MHCI on their surface, be recognized by CD8+ T-cells, and summarily executed. However, were a DC to encounter this apoptotic body in the abscence of a TLR ligand, it would go to the lymph node promoting development of Tregs for the cancer cell antigens*. While this may be a good thing in preventing autoimmune reactions when T-cells learn the unmutated antigens still present in cancer cells are bad and should be killed, it also brings up the somewhat unsettling prospect that the this leads to immunotolerance of cancerous cells. The immune system is generally the first line of defense against the development of tumors, and if it has specifically learned to not be reactive against them due to Tregs, then the cancer would be allowed to continue growing and mutating without immune system interference. Needless to say, this is ultimately bad for the organism.

Implication 3: Rheumatoid Arthritis
It is known that inflammed tissues produce IL-23, which encourages stable differentiation of TH17 cells and also acts as a chemoattractant for them. I don't think it's unreasonable to think that levels of IL-23, along with NFkB et al, would be elevated in arthritic tissues and that this could lead to infiltration of TH17 cells. Once there, TH17 cells can cause further inflammation, including tissue damage. This in turn would amplify the production of IL-23, which has been shown to decrease IL-10 production and in turn decrease Tregs. This then leads to a dismal scenario in which more and more TH17 cells are being recruited to drive inflammation in arthritic tissue while at the same time stomping on the Tregs that could help break that feedback loop. However, at the same time DCs would be present and processing the apoptotic cells in the arthritic tissues, and then hopefully driving towards TGFb and Tregs.

It should be noted that each and every implication I have put up above could be complete and utter horsefeathers as the immune system is so complex and operates on so many scales that I could very easily be overlooking a key component that makes all of my conjectures seem silly.

Torchinsky, M., Garaude, J., Martin, A., & Blander, J. (2009). Innate immune recognition of infected apoptotic cells directs TH17 cell differentiation Nature, 458 (7234), 78-82 DOI: 10.1038/nature07781

*This happens anyway, MHCI or not. B7.1 and B7.2 (CD80 and CD86, respectively) expression patterns are often altered in chronic myelogenous leukemia and chorionic gonadotropic, which isn't expressed in adults, sometimes pops back up in tumors.

08 April, 2009

Muscle Hypertrophy

ResearchBlogging.orgHaving somewhat recently realized that I don't want to have the awesomely statuesque physique of a stick figure for the rest of my life, I began working out (before and after picture below). I still have no idea how to use most of the equipment in the gym and I'm not going to ask Pikkuveli (="little brother") how to use it just because he has ~130kg of muscle to my paltry ~60kg (we're also the same height: ~2.07m). But I am willing to ask where muscles come from.

So I hit up Current Opinion in Pharmacology and managed to learn something: muscles come from your liver.

Kinda weird, huh?

So here's how it more-or-less works:
1) ghrelin gets made by the fundus of your stomach
2) and binds to GHS-R in the arcuate nucleus of the hypothalamus, which then releases growth hormone in response
3) which travels to the liver and gets it to make up some insulin-like growth factor (IGF-1)
4) which then enters the systemic circulation and
5) acts in concert with local mechano growth factor (MGF) at the skeletal muscle to increase net protein synthesis and myotubule formation

But here's what's really cool and elegant about it: IGF-1 and MGF get made from the same mRNA transcript, just spliced up differently in different tissues.

Figure A: Electron micrograph showing a neuromuscular junction. M = muscle, T = axon terminus, arrow = junctional folds with basal lamina. Scale bar = 3um. Source: Wikimedia Commons.

MGF is produced by skeletal muscle tissue in response to mechanical stress (lifting heavy stuff) and cellular damage (the burn the day after working out) and acts in a paracrine and autocrine manner in and on satellite cells that hang out outside the membrane enveloping the muscle fiber. Satellite cells are mononucleated muscle stem cells. MGF tells them to proliferate and make more of themselves. But in order for this increase in satellite cells to translate into muscle growth, IGF-1 (IGF-1Ea, specifically) has to come along and get the proliferating satellite cells to cross the muscle fiber membrane and merge with each other to form a mature, multinucleated myotubule capable of contracting.

Conveniently enough, MGF levels are increased in skeletal muscle for ~2 days post-workout before tapering off. IGF-1Ea levels are increased for longer than that, so there is a sort of 2-phase muscle growth mechanism at work that smartly regulates itself. If MGF levels didn't taper off, satellite cells would keep proliferating and differentiating to myotubules and we'd drown in overgrowing buffness.

But, it's not quite so simple as that. Skeletal muscles are in a continual state of flux as they tear themselves apart and build themselves back up. The body can stash away amino acids in skeletal muscle or grab them back out as needed to help regulate serum pH. Muscle turnover also helps get rid of old, damaged myotubules and replace them with shiny, new, functionalier ones. Apparently this process takes about 2 weeks (I'm thinking maybe this is a minimum interval for exercise to maintain physique?) and heavily involves myostatin. Natural myostatin knockout mutants include Belgian blue cattle.

Figure B: A Belgian Blue bull (on the right).

Laboratory knockouts of myostatin in mice confirm that no myostatin to help muscle turnover along leads to increased muscle growth, but does not increase strength at all. This is thought to be due to increased accumulation of nonfunctional protein in muscle fibers.

Figure C: Toaster's physique before beginning exercise (left) and after (right).

So right about now my latest MGF pulse should be slowing and hopefully my IFG-1Ea is kicking in to get the new satellite cells that surely must be teeming in my shoulders and triceps fusing into functional new muscle. In the meantime, however, raising my elbows anywhere above shoulder level is rather more painful than I thought it might be. Maybe I shouldn't have done quite so many pull-ups, lat pull-downs, and tricep dips...

GOLDSPINK, G., WESSNER, B., & BACHL, N. (2008). Growth factors, muscle function and doping Current Opinion in Pharmacology, 8 (3), 352-357 DOI: 10.1016/j.coph.2008.02.002

07 April, 2009

Dishonesty In Science Media (Toaster Burns Bullshit #1)

Sometimes one reads things so egregious that they can't help but let out a snarl under their breath at the dishonest pomposity of it. Today I was combing the Huffington Post, hoping, perhaps naively, that there'd be some good science coverage there. Instead, I found this. I did a double take, reading it twice to see if this dude really thought we were stupid enough to buy into his bull. Then I saw that he was in earnest, and I literally roared at the screen. Luckily I am alone in the lab today, or else my lab mates might think me even more daft.

So I turned off the Dr. Dre and turned on Tricky thinking that perhaps it wouldn't seem so stupid after I'd calmed down a bit. I spend 2h splattering data here and there trying to distract myself, but, no, I am still pissed off at this bullshit.

So here is #1 in what is probably going to become a dihearteningly long series:
Toaster Burns Bullshit. Point by point:

(Context: It should be noted that Fred Hahn is pouting, spouting, and posturing here after appearing on the Dr. Oz show.)

What was not discussed, to my great chagrin, was the issue of diet and obesity.

This issue is of great concern to me, having two daughters in public school where the cafeterias are obesity central.

Here we see Fred Hahn trying to scare up some parental street cred. Teh Stupid comes later, so bear with, please.

I was quite shocked that Dr. Oz failed to ask me a single question on the issue. Either he didn't read my book or found what I had to say on the issue too diametrically opposed to his views. But whatever the case may be, he ignored the issue. A shame, because he has the power to sway millions of Americans as to how they should eat for optimal health.

Here's the pouting.

If your child is eating real food, you are on the right track. Real is defined by foods that once either walked, crawled, swam, flew or grew.
Logically, this includes bugs. "Real food" does not include wax fruits, plastic pancakes, or Play-doh. Nor your Doritos. So if you're not banning your children from everything that came in a plastic bag or a can or made your life a little bit easier in any way whatsoever, then YOU'RE DOING IT WRONG!!!11!! And therefore you're obviously a nasty, horrible person who doesn't love your kids as much as Fred Hahn loves his.
If your child is eating food that was manufactured, you are on the wrong track.
See? You're a failure. Shame on you!!!
The mainstay of your child's diet should be fat and protein. Next in line -- vegetables and some fruit.

This is the opening shot of Teh Stupid.

Refrain from grain in all its forms. In the end, grain is nothing more than sugar, and sugar is caustic to the system. Perhaps this is why Dr. Oz did not bring up the issue. He would have had to debate me on this since he supports eating grains and is essentially anti-low carb. Low carb diets have been shown over and over again to be healthful as well as the most potent formula to combat obesity and diabetes.

And here's the rest of the can.

This, right here, is what pissed me off right thoroughly. This is dishonest, and this is bullshit.


C6H12O6 (aq) + 6O2 (g) → 6CO2 (g) + 6H2O (l) ΔG = -2880 kJ per mole of C6H12O6

This is kind of important. You know, it's just the chemical reaction that drives ATP synthesis and allows metazoan cells to live. But, ZOMG!, it starts with SUGAR! And SUGAR is CAUSTIC to "THE SYSTEM"! Therefores, the glycolysis that drives cellular respiration must also be CAUSTIC and that means it's EVIL and is singlehandedly responsible for the obesity epidemic in the U.S.A.! Damn you, thou sinister hexokinase! How could you ever do this to us, o' glyceraldehyde-3-phosphate dehydrogenase!? ZOMG ZOMG ZOMG! Teh Evil Grains!

Figure A: Bread is evil, you just don't know it.

Yes, fats can be oxidized and made into sugar to be used in cellular respiration for energy, but to recommend that children eat a diet primarily made up of fats and proteins is irresponsible and dangerous. Mr. Hahn is making a broad prescription here when a much more nuanced dietary solution is called for (maybe you get that if you buy his book). Letting a child eat lard and Slim Jims fufills his requirements (and both lard and Slim Jims once walked about), but this isn't going to help them at all, and in fact will make them worse off in the long run (if nothing else, due to the nitrosamines in the Slim Jims). Low carb diets work for some obese adults, but that does not make them a panacea, especially not for children who are naturally going to need a diverse array of nutritious foods to develop normally. It is one thing to recommend not allowing kids to eat candy and soda, but it is quite another to tell parents, who may be just as poorly informed as Fred Hahn himself, that the whole wheat bread of their childrens' peanut-butter-and-jelly sandwich is making them fat (more likely to be the minivan and X-box than anything else, really).

FURTHERMORE, since he has demonized natural starches as being nothing more than evil sugar, I find it puzzling that he has not also condemned meats due to their high glycogen content. What's up with this? Just as starch in grains is a polymer of glucose, so too is glycogen, just with a different tertiary structure. Seriously, if you're going to be stupid, please at least be consistent.

It's a tad sad when an expert as famous as he is side-steps science in favor of a personal agenda. This is not to say Dr. Oz is purposefully keeping the truth from the public. It is to say, however, that he has an immense responsibility to learn all there is to know on the subject if he is going to place himself in the public eye and wield such enormous influence.
And here's the egotistical posturing, which Mr. Hahn manages to pull off with all the grace and subtlety of a 4-year-old brat. It is also dishonest for him to try to question Dr. Oz's credibility and authority when he didn't cite a single research article, nor even a newspaper article.

It should also be noted that Fred Hahn is the CEO of Serious Strength* and has never heard the term "conflict of interest" before.

*Located in the Upper West Side and Waldorf-Astoria of New York City, New York. Perhaps the rather insular environment has fostered his ability to deceive those who buy his book, his clients, and maybe even himself. Here's a gem from the Serious Strength website FAQs: "The exercise scientists use a treadmill fatigue/oxygen uptake test to guesstimate a person's level of fitness."