Tuesday, November 30, 2010

Pink Dolphins!

Almost as much fun as pink elephants! ;)

Medical Skepticism and Dr. Oz

I think that it is fair to say that a lot of the New-Agey, hippie, touchy-feely woo-tastic type beliefs in terms of medicine and nutrition either originated in or were propagated by the San Francisco Bay Area. I know a LOT of hippies that live here (my parents are hippies. I'll get to them by and by) that swear by things like healers and parasite cleanses and various other bits of woo.

My parents are hippies. (see? Told ya!) I grew up taking vitamins for everything from colds to cramps. I went to my first chiropractor's appointment by the age of 12. I still feel weird taking analgesics.

I was introduced to the nature of the vitamin industry at a nutritional seminar at Fresno State. The researchers had done nutritional studies on geriatric model mice in order to determine why geriatric animals have a difficult time keeping weight on. After tweaking the genes of the mice to promote obesity, they had supplemented the mice with a particular fatty acid in order to see if it helped improve appetite and weight retention. Unfortunately their results were inconclusive, but it opened the doors for further study.

In the Q&A session, the topic of the vitamin industry came up. Now mind you, this is a group of professional research scientists that basically dumbed down their research in order to make it accessible for the average biology undergrad to understand. I had a brief conversation with the presenter where he basically concluded that vitamins are pretty much a scam if you have a varied diet and that they should not be trusted because manufacturers can and do put anything in there and the FDA has no power to regulate.

Fast forward 7-8 years. I ran into an old friend of mine on Facebook who claimed that her 3 year old son got autism from his vaccines. I didn't know very much about the topic, but I did what any scientist does when presented with a question for which she has no answers: I did some research. I asked the lady how she knew the vaccines caused the condition and she sent me links from Age of Autism, Safe Minds, and some odd independent researchers. I hunted through the data there and concluded that it was mediocre at best and lies at worst (in fact it's all lies, really.) I did my own digging and I came up with the delightfully quirky Respectful Insolence.

Orac was my first glimpse into a world that I hadn't dipped a toe into for quite some time: the world of science based medicine. I jumped in and read everything that I could get my hands on. My brain seemed to like being dusted off and the cobwebs removed. I worked at an incredibly dull job that really required me to turn my brain off to be happy, and I guess it got to be habit. Thanks to him and a few others, I was inspired to go back to school and get my medical degree.

But I digress. There are scads of websites out there that have all the information on vaccines and whatnot that you need to know. Quackwatch is a great one. Respectful Insolence is another. I also like What's The Harm?, Autism News Beat, Code For Life, and The Truth About The Evils of Vaccination.

What is the difference between these people and the idiots I mean folks at Age of Autism and Safe Minds? These people are scientists and practicing medical professionals that base their practices on sound science-based medicine. AoA and SM do not.

What does this mean? It means that they base their conclusions about treatments and medications on sound scientific well-developed research that has been published by reputable scientists with no glaring conflicts of interest in reputable top-tier journals that has passed the vetting process by the scientific community. Science is a process, a long slow arduous one, and conclusions come gradually. Even an excellently developed and well-laid out paper will be met with cautious enthusiasm if there is only one set of data to back it up. One paper does not mean this is true always. Two? Closer. Ten? Much closer. A hundred? It becomes accepted fact. Science is slow for just this reason: it prevents us from jumping to conclusions about how things work until they have been rigorously tested.

Bottom line: Are vaccines safe? Yup. Are they thoroughly tested? Yep. Do they cause neurological conditions such as autism? Nope.

But much like the biological refutation of creationism, it gets discredited, cherry picked, and sneered at by the fundamentalists that have something to profit by propagating these outright lies.

Often what these people do is sell things like autism 'treatments' and 'cures' to credulous and terrified parents. Autistic children can be very difficult to handle, and require a lot of time and money in order to help them gain something close to normal function. What people like Joe Mercola and Mike Adams and other scumbags do is peddle expensive treatments to parents who will try just about anything to 'fix' their 'broken' child. This can include things like putting an industrial chelator into a supplement form (chelators draw out heavy metals and can be used for heavy metal toxicity clinically, but it can be incredibly damaging for a growing child because some heavy metals are necessary for development: magnesium and calcium come to mind)  or using a drug that is used to chemically castrate sex offenders and those suffering from prostate cancer. (I hope I don't have to explain why messing with the hormones in a growing body is a very very bad idea)

And now we move on to the vitamin industry. In 1993 a piece of legislation was passed that prevented the FDA from regulating vitamins, minerals, supplements, and basically allowed the vitamin industry to self-regulate. But because the vitamin industry stands to profit egregiously, and indeed has: (Americans spent $26.9 billion on supplements in 2009 (from the Nutrition Business Journal)) the chances of that happening are slim to none. It is a repeated tale in America: give companies that can become megarich from shady business practices the chance to self-regulate and all kinds of abuses crop up.

What kind of abuses? Well, since the labels are not regulated by the FDA, they can put anything in their vitamins and herbal supplements. They often do. Hormones have been found in vitamins. The potency of vitamins is also dicey. The gram weight on the label can mean anything, but the part that your body can actually use (called bioavailability) varies wildly. In other words, the label may or may not have anything to do with reality. And frankly, the jury is still out on whether you really need supplementation anyway.

A fantastic overview of what might be in supplements can be found here.

The problem is that the FDA can't do anything about these abuses because of this bit of legislation. It took nearly 10 years to get Ephedrine off the market because the burden of proof of harm is on the FDA, not on the supplement company.

Pretty much the only thing the FDA can regulate are the claims made on the label. Even this, though, they seem powerless to do much about, because some of the claims you seen on supplement packages are absurd to say the least. But so long as they have the Quack Miranda Label on the package somewhere, the FDA seems hamstrung.

And so we return to my wonderful family. I love them dearly. But I get slightly concerned about where they are throwing their money if they have a subscription to Joe Mercola's blog and I see them get supplement shipments regularly. I have gently tried to explain why they should be a bit more careful about where they buy their supplements (or if they need them at all) and they pooh-pooh my concerns.

Somehow I doubt that they will pay any more attention to me if I have MD after my name.

I have given up trying to argue the point with them. But in an oddly defensive manner they brought up Dr. Oz as being a real genuine medical professional that they actually agree with. I didn't have an opinion on Dr. Oz because I didn't know much about him. But they were talking about how common sense he was about things like diet and exercise (A little side rant: I hate how alties claim that normal doctors don't care about the whole person. Of course we do! Of course there is nothing wrong with a sensible diet, lots of exercise, and proper hydration. Of course this is advice that normal doctors should be giving their patients. But by claiming that we want to 'medicate away' every ill the alties make themselves sound more caring and speshul. Grrr.) I told them that it sounds reasonable. But I was still skeptical.

But being the scientist I am, you know where that led. Yay for research!

The wonderful thing about Respectful Insolence is that if the person in question is a woomeister, quack, or otherwise has a reality problem, Orac will have written about them. And Dr. Oz has his own category. This doesn't bode well for Dr. Oz. In fact, he has merited multiple helpings of Insolence since the beginning of this year. I like this one in particular since Orac seemed to wrap up everything he has said about Dr. Oz in one nice tidy package of Insolence.

Now the next time my family brings up Dr. Oz, I know what to say: He's a quack.


It isn't often that I stumble on a fantastic webcomic that is spot-on about skepticism, atheism, and religion. But Ape Not Monkey somehow manages it, and is incredibly funny to boot. I loved this comic in particular, but I highly recommend reading the whole archive. Enjoy!

Monday, November 29, 2010

We Be Trollin'

I don't have this problem just because my readership isn't that wide. But I do know a number of people that have to deal with stupid trolls. And it is for them, dear readers, that I post this.

From The Mouths of Babes

Sunday, November 28, 2010

As Promised: Adult Content!

But not quite what you may think. Because I'm studying neurosciences, this is a fantastic article. Enjoy!

Making Fun of Faux News: A New Holiday Tradition

This is delightfully tongue-in-cheek. Enjoy!

Christopher Hitchens On Christmas

Atheist Holiday Song

I found this and it made me laugh. Enjoy.


A Christmas Carol Lyrics


Celebrations of The Season

Over at I H8 Religion, folks are chiming in on why or how they celebrate the season. I thought that I'd weigh in a smidge.

I was raised in a Buddhist household. Both of my parents were recovering Christians and probably wanted to shuck the trappings of their former religion. The only monkey wrench in that particular equation was my grandmother.

My grandmother was an amazing woman. I loved her dearly and I miss her painfully this time of year. All of our holiday activities centered around her. I would spend the night at her place before Thanksgiving and I would help her get the turkey in the oven and clean and set up before people arrived for dinner. We would go help with her tree and I would often help her wrap her gifts. She made her own bows to put on packages.

I'm sure that my Christian grandmother was heartbroken at the prospect of not being able to spoil her new grandchildren rotten on Christmas. After my grandfather died she often said how we kept her going. I'm sure that my parents relented in order to make her happy. Buying gifts and all that was very stressful for my mom because my grandmother rather cracked the whip over her, but I do know that she likes the holiday.

My grandmother was a true Christian, never pushing it on us, and she was charitable and generous. She read bits of the bible to me every morning because it was part of her daily ritual. It was more like she was sharing her life with me and less that she was trying to indoctrinate me. I liked having her read to me, and there are lyrical parts of the bible and psalms that are quite pretty.

Up until she passed away my grandmother was active at the food pantry at the church-run community center. She organized the boxes of dry good donations into portions for needy families. Even when her hands were too twisted and weak with arthritis to drive she would get a ride with other folks from the church and go to work.

My last memory of my grandmother was spending time at her house watching the football game between Fresno State (my alma mater) and Georgia Tech. (my sister's alma mater) This was after Christmas, and before New Year's. She taught me how to make her wonderful Christmas toffee. That was a lovely day. I was away at school when I got the news that she'd had a stroke.

When she died, we were at a loss as to what to do. So much revolved around her. That first year was an awkward attempt to keep going. But we did and we somehow managed.

This is what the holidays mean to me. It means spending time with family that I love, exchanging gifts that come from the heart, having good food and good times together. Now that I have a husband it means even more to me, because his memories of the holidays are a reflection of his scarring childhood. All I ever wanted to do was help him see that the holidays can be positive.

This year I am on an extremely limited budget because of my loans and all, and so I figured out how to make everyone's gifts. I feel like it means more this way anyway.

I still make toffee every year, and I know that grandma would be happy that we've carried on and done as well as we have.

Friday, November 26, 2010


I finished the last of my applications today.

I discovered that the most difficult aspect of these applications was selling myself. I felt like I was bullshitting everything, but my friends told me to not undersell myself, and to not exaggerate but speak plainly that I would be a credit to any university that accepts me.

I tried to do this in a way that hopefully did not seem like ton of crap. Selling but not overselling myself was a tough order.

I am really glad that I finished everything.

I have a ton of homework to complete before I return to school on Monday, but in the meantime I think I will knit a bit more and watch this excellent video from TED.

Tuesday, November 23, 2010

Center For Inquiry

Meat For The Masses

I love meat. I have a degree in Animal Science from Fresno State University. In order to get this degree, I had to take a Meat Science course that followed the animal all the way from slaughter to processing. We had to cut up a lamb for a final project. I've seen chickens hung upside-down, stunned, slaughtered, and processed.

If that experience wasn't enough to make me go vegetarian, nothing ever will.

It sounds a lot worse than it is. Like any capitalist venture there are those that abuse the system (and the animals) and the beef lobby is incredibly powerful in this country. But the truth is that there are multiple safeguards in place to make sure that the animals are treated as humanely as possible. And we are approaching a time of year when people eat a lot of meat, for Thanksgiving and the winter holidays.

And so I want to bring this up, because I think that it's important. I refuse to eat kosher meat. I also refuse to eat veal, but that's another story. The conclusion at the end is very poignant. Go have a look see.

Skepticism In Christianity

Or lack thereof, I should say.

Unsure of the source, but I found this on I H8 Religion. Enjoy.


Yet another gem from I H8 Religion.

A powerful post on the proselytizing and the attempted takeover of the military by Christianity by Atheist Oasis. It is long but well worth checking out.

And if you do, and can spare anything to help Rock Beyond Belief, go do so.


This is particularly interesting to me because I am considering a career in the military. The benefits available to an Army doctor are really quite appealing. Considering that the average medical education in this country costs about $300,000, working for the Army for 4-8 years after residency in exchange for excellent benefits, free housing and no debt seems rather fair. Plus it would look great on a resume.

But all that aside, the culture in the military is interesting to me. It is the result of groupthink, of subsuming one's own self for the betterment of the group. It seems as if people are encouraged to just go along with the group and not raise too much noise or fuss.

I would not just sit there and take it, though.

Friendly Atheist At It Again

This is so worth sharing. Thanks again to Friendly Atheist for being his usual wonderful self and saying things that I often lack the words for.

I know people who seem to think that we're such dicks because we speak our minds and respect the person but not the beliefs. We're such assholes.


Ahh, it's been nice doing a whole lot of nothing. Actually, that's not really true. I've been getting a lot of knitting done, planning out holiday gifts (as a poor student I'm glad that I'm so crafty) and spending lots of quality time with my husband.

I know I have posts and all kinds of goodness promised. I will try to catch up on all of the content that I want to write about. Life just got so busy and I just needed some time to catch up on sleep and do a fair bit of nothing for a while.

I haven't even been keeping up on my reading list. That shows you how disinclined I've been to touch the computer. ;)

I hope all of the Americans have a lovely Thanksgiving full of wonderful food and great family memories. Love and happiness to all.


Saturday, November 20, 2010

Thursday, November 18, 2010

Paleontology, Anyone?

I love Jerry Coyne's blog Why Evolution is True. I have noticed, after watching and reading things about Pharyngula, Orac, and Coyne, that scientists tend to be completely and utterly sentimental saps. I know I am. And I think it is very sweet.

Anyway, enjoy this exploration of the life of a giant shrimp from nearly 450 million years ago.


Midterms And Mormons

Crazy week, but fortunately things should be quieting down enough after tomorrow's exam so that I can get some serious autonomic nervous system content up in this hizzouse.

I H8 Religion FTW! I live in San Francisco where Mormans tend to be shunned, so I'll never get to use this, but it amused me greatly anyway.

I have a feeling that if I haven't gotten an invitation to submit supplemental application to a school by now, then I won't period. Which is slightly disappointing, but I did submit apps to 5 schools out of the 16 that I applied to. That's not bad.

Anyway, I am taking a knitting break, and then I'm back to homework. Ciao!

Tuesday, November 16, 2010

Excuses Excuses

I am just exhausted with all the stuff I have going on right now, and frankly I wonder if I'm not getting under the weather. More substantial posts might have to wait until after my Physics midterm.

Part three of the conversation between Bible Belt Atheist and the Muslim. Enjoy.

I am sick and tired of Catholics telling me not to tar all of them with the same brush because of "a few" child molesters. I mean, really. The basis of this person's argument was that there are other people doing it too, so nah. Big deal. Other people don't claim to be the infallible word of god and its vicar on earth, and still hide child rapists all over the globe. Seriously, it is difficult to claim the moral high ground if you know that they guy you are sending to Oregon raped a few kids. And I'd be delighted to not tar them all with the same brush if they were, you know, actually doing something about it. Like demanding jail sentences. Or refusing to tithe. Or walking, which a lot of them are doing. I just wish more of them would demand change. The ones who stay, I mean. Protesting by walking is pretty effective.

Ugh. The person who overheard the argument said to me "Let the meek inherit the earth. The rest of us will travel to the stars."

Monday, November 15, 2010


There is a fascinating discussion going on over at Bible Belt Atheist (I really enjoy his clear, concise explanations to theists and non-theists alike) that one cannot understand the Koran (or Qur'an as this guy spells it)unless you read it in the original Arabic.

BBA goes on to refute that, quite neatly.

I get where the guy is coming from.... sort of. Some nuances are definitely lost in translation, and one could definitely argue that holy books are ultimate propaganda machines because of varying bizarre translations designed to say what translators wanted it to say. (For more on that go see Bart Ehrman's excellent lecture series on the topic: Misquoting Jesus. This is only part 1 of 10, but it is well worth the 100 minute watch)

But that kind of specious reasoning only holds if one is arguing AGAINST the validity of these books, not for. What this guy seems to be saying is that somehow maliciously the book was mistranslated to give Muslims a bad name. Which makes no sense whatsoever, because historically translations were used in an effort to conceal discrepancies and fix little scriptural mistakes in these kinds of texts. BBA goes off and finds 6 different translations of the same passage. Guess what? With some subtle differences, they all say the same thing. Imagine that.

But then the guy goes on to draw all sorts of absurd conclusions from this idea, like the idea that in order to be objective one must be a theist and other nonsense.

Objectivity =/= belief. Sorry, no can do. The closest one can get to this idea is to be skeptical. Skepticism is the closest we can get to be objective. Believing in something and then hunting for evidence to back up your beliefs is not, I'm afraid to say, objective. It is the story of every creationist ever. It is the story of every vaccine denier ever. Of every 9/11 truther, moon-landing denier, birther, woo-meister, crackpot theory ever.

Richard Dawkins

My husband really dislikes Richard Dawkins. He says that Dawkins comes off as an ass and a bully. I do think that it is easy to come to that conclusion if you only see one or two videos of Dawkins, particularly the video of him telling and older Scottish gentleman that he is hallucinating his personal relationship with Jesus.

I think that ridicule is an effective way of confronting ridiculous religious beliefs, and that Dawkins does an excellent job of it. By the time people realize they are being mocked, it can make them think more about their position.

But Dawkins has a lot to say about biology, about the natural world, and I've seen many of his lectures on the human mind and the origin of religiosity and refuting creationism.

I got this from Friendly Atheist. It is well worth looking at. Enjoy!

Sunday, November 14, 2010

Cardiac Physiology!

So I have an exam on this stuff tomorrow, and I thought that talking about it would help me solidify a lot of it in my mind.

So here's a picture of a heart:

I really like this picture because it shows you the atria, ventricles, and valves, as well as the attached vasculature. I got this from an NIH-NIAAA website.

So here we go: BLOOD. We've got about 18 liters of the stuff (I've said it before and I'll say it again: I HATE English measurements. USA, get into the 21st century already and get with metric!) all circulating around. It goes from out heart to our extremities, drops off nutrients, exchanges gases, and comes back to the heart. First it goes into the right side of the heart, which pumps it into the lungs. From the lungs it goes into the left side of the heart and then it gets sent out to the extremities again.

The diagram shows you how it works: into the right atrium via the inferior and superior vena cava,  (these are veins, which return to the heart) into the right ventricle, and then to the lungs via the pulmonary artery (pulmonary = lungs. Cardiopulmonary system means the heart (cardio) and lungs (pulmonary)) then into the left atria from the pulmonary veins, then into the left ventricle and then out into circulation via the aorta. Arteries carry blood away from the heart.

 Our heart is one big pump. And it generates a lot of pressure, almost 120 times as much pressure as the atmosphere at sea level. (EDIT: ACK! This is so wrong! Sea level pressure is 760 mm Hg. Pressure inside the aorta just after systole is 120 mm Hg. So it is quite a bit of pressure, just not as much as atmospheric. Game on.) And because fluid movements are generally dictated by differences in pressure, our blood gets coaxed along where it needs to go via a gradient of pressures, between our heart, lungs, veins, and arteries.

Let's look at the left side of the heart. It works exactly the same on the right side but it's a bit simpler to look at the left side of the heart. Blood is coming into the pulmonary vein from the lung. The pressure goes up because the volume goes up. (If you aren't familiar with Boyle's law, it might make sense for you to go look at that for a moment and then come back. Bear in mind that in physics, gases and liquids in motion are known as fluids) As the pressure goes up, a gradient between the pulmonary vein and the left atrium is building. Finally, a high pressure is reached, the valve between the vein and the atrium opens, and blood rushes into the atrium.

See the valve on the diagram between the atrium and the ventricle? It has 3 names. Annoying, isn't it? It is the atrioventricular valve, the bicuspid or the mitral valve. (because it looks like a mitre, a bishop's hat. Stupid religious imagery) It has 2 cusps or flaps of skin that open and close the valve, and are attached to collagenous strings called chordae tendonae. These strings anchor the valve to the heart muscle at little nipple-like protrusions called papillary muscles. This setup reinforces the valve. When the pressure gradient between the atria and ventricle is at a certain point, the valve opens, and blood rushes into the ventricle.

Point of interest: the valve between the right atrium and the right ventricle is the tricuspid or atrioventricular valve. Instead of two flaps of skin opening and closing the valve, it has 3, though it still only has 2 chordae tendonae.

Now the ventricle is filling, and when it can hold all that it can hold (about 135 mL of blood) the mitral valve closes. The ventricle now has greater pressure than the pulmonary veins, but the mitral valve, due to its anchoring system, prevents blood from going back into the atrium. As we age and if we are genetically predisposed to heart failure, these valves don't close very well and don't prevent backflow. This can lead to fluid building up in the lungs, a condition known as congestive heart failure.

As the blood hits the mitral valve, wanting to go back to the atrium, we hear a 'lub' sound with a stethoscope.

The left ventricle wall contracts, and the blood pressure forces the aortic semilunar valve, the valve between the left ventricle and the aorta, to open and the blood is pushed out at rather high pressure. The pressure is now greater in the aorta than in the ventricle, but the valve has two cups on either side that is forced closed with the weight of blood. The sound blood makes when it hits the cups is 'dub'. You can hear it with a stethoscope.

The amount of blood that is in the left ventricle when it is done filling (during the heart relaxation phase, diastole) is 135 mL. The amount of blood that is forced out with each contraction (systole) is 70 mL. This is the stroke volume. 65 mL of blood is left in the left ventricle after each heartbeat. This is the end systolic volume. That means that the heart operates at 55% efficiency, also known as the ejection fraction.  Cardiac output is the measure of how many milliliters of blood is pushed out of the heart every minute. So if the average human's heart rate is 60 beats per minute, and each heartbeat (or stroke) pushes 70 mL out of the heart, 4200 mL of blood/1 minute would be the cardiac output.

I think that tomorrow after my exam I'm going to talk a little bit about the autonomic nervous system control of heart rate. Till then, wish me luck on my exam!

VERY Funny Standup Bit

I got this from I H8 Religion (seriously, go check this guy out, he is too funny and delightfully non-PC) and I laughed like crazy. Enjoy!

Saturday, November 13, 2010

Jon Stewart on The Rachel Maddow Show

This is excellent and well worth watching. He clarifies a number of points that I think were lost in the kerfuffle of the Rally. Enjoy.

Cardiac Physiology

I will do the promised post on cardiac physiology, starting with how blood moves through the heart and how the valves operate, but every time I think about the nervous control of the heart (originating with the medulla oblongata just superior to the brain stem which regulates the cardiac control centers and the involvement of the autonomic nervous system) I can't help but think about that episode of Pinky and The Brain where they sing about parts of the brain.

And because I'm awesome, look what I found. While I'm putting together another post for you, enjoy a small piece of my childhood.

Friday, November 12, 2010


I must admit that having a following is giving me an excellent impetus to finish some of the content that I keep promising but, for reasons relating to school and all of the hundreds of other things I am doing right now, just don't get to in as timely a fashion as I want.

Last time we were talking about C3 convertase, an enzyme that is made differently by each pathway, but each pathway does, in fact, make it.

What differentiates the pathways, I should mention, is how each pathway is activated. The classical pathway is activated by interaction with Immunoglobulin G and M that have interacted with antigen. How that comes about will be the topic for another discussion. The lectin pathway reacts with a sugar that is often found on the coats of pathogens known as mannose. The alternative pathway spontaneously forms the C3 convertase, unlike the others which are triggered by the above interactions, but the difference is that unless there are certain molecules on the pathogenic membrane (lipopolysaccharides, glycoproteins, etc.) to interact with, the C3 convertases break down and don't do anything.

A side note: immune diseases are caused when these kinds of molecular interactions either don't take place or the control mechanisms preventing the immune system from functioning in the absence of pathogens are faulty. Some nasty diseases can be caused if complement goes haywire or doesn't function.

The classical pathway takes longer to respond because it is a little dependent on all of the processing and presentation that happens in order to get IgG and IgM that have been exposed to antigen. However, the alternative pathway is extremely fast. My immunology professor said that it reacts in a matter of minutes, whereas other parts of the immune system can take days to respond.

Once the C3 Convertase is achieved, still more reactions occur and still more cleavages of proteins occur in cascade fashion until a C5 Convertase is made. All 3 pathways make C5 Convertase, which is important to make a molecule of different complement proteins called a Membrane Attack Complex, or MAC. It is thought that the MAC physically punches holes in pathogenic membranes, lysing the cells by doing damage to the cell wall.

Typical of biology, systems are made to be efficient and minimize waste (well, except for B and T cells) and complement is no exception. In the progressive cascade involving cleavages of different proteins and the creations of enzymes that help make the final product, the cast off bits of proteins have important immune functions of their own. The lectin and classical pathways create molecules that are important for the inflammatory response, useful for heating the local tissue in order to make the areas inhospitable to pathogens. They synthesize molecules that make the epithelium of capillaries leaky, allowing fluid into the tissues and helping to bring in other cells that are important for immune responses like macrophages, neutrophils, mast cells and basophils. They even make proteins that can help macrophages and neutrophils phagocytize pathogens by 'marking' them for destruction. Complement proteins also create anaphylotoxins, implicated in anaphylaxis or severe allergic reactions because of signaling molecules that induce mast cells and basophils to dump their granules full of histamine. Histamine is important in inflammation, as a protective measure. Too much of this, or inappropriate reactions, can cause anaphylactic shock. Anaphylaxis can be fatal.

I hope you enjoyed my discussion of complement. It is a very lengthy topic, and breaking it down to simple terms was challenging. But I think I'm getting the hang of this, and I had fun doing it. I would like to talk about blood moving through the heart and differential pressures at some time today.


Janeway’s Immunobiology, 7th edition by Murphy, Travers, and Walport. Garland Publishing, 2008
Medical Microbiology, 6th edition by Murray, Rosenthal, and Pfaller. Elsevier/Mosby, 2009

And Since We're On The Subject....

This is what a potassium channel looks like. Enjoy.

I Haz Follower?

Hello to my follower person! Hope you like the weather over here. :) By all means, feel free to communicate and say hello, or to recommend my blog to others.

I plan on finishing complement today, and putting up a discussion on cardiac physiology. It'll give me practice for my exam on Monday.

Hopefully sometime next week I can talk about X-rays and CT before my physics exam.

But, because I have someone who is watching, I thought I would do something a little special right now and include a little neurophysiology. It is, after all, one of the most interesting things about physiology in general. At least to me.

Robert MacKinnon won the 2003 Nobel Prize in Chemistry for helping to isolate and describe the crystalline structure of potassium channels. Potassium channels are extremely crucial to our normal function. This is a fascinating paper that details his approaches and gives some background on the problem. Right now, visualizing ion channel structure is very difficult. They are miniscule and isolating them without destroying the structure is painstaking. He has gotten the closest to imaging the channel. Go and enjoy.

Thursday, November 11, 2010



And if you've never read A Softer World....well, you probably haven't lived. Enjoy.

Statistics and Veterans Day

So today is Veteran's Day in the US. It is a national holiday set aside to remember and honor people who fought for the freedom of this country. Well, supposedly.

You see, I think that once upon a time, soldiers did fight to keep this country free. World War II is the primary example. But round about the Korea war or the Vietnam war, we stopped doing that and started sending troops to other areas of the world on police missions. The validity of these missions can definitely be debated at length. I still wonder if Christopher Hitchens, a man I respect greatly for his erudition and his sense about the world, can truly be wrong about overturning Saddam Hussein, but we obviously went about it all wrong.We may have removed Hussein, but what kind of life did we supply those people in exchange?

And now as I approach a decision to serve as an Army doctor, I honor those who gave their time and lives for this country. They deserve our greatest respect. I have multiple family members who served: my father, my deceased grandfathers, my uncle, and I married into a military family. My husband went to a military high school. My father in law was a Marine in Vietnam. My mother in law had brothers who served at Air Force Bases. And my brother in law served in the Coast Guard for years.

I think that, whatever your opinion may be of the military, that scorn or derision or whatever should be pointed more at the policies that use it as a law enforcement tool. We went into Iraq for entirely the wrong reasons, and and now we have to get out of there while leaving chaos in our wake. We need to more closely scrutinize the decisions that may lead us as a country to use the military.

On a completely different note, I found this over at Darwin Killed God. I found it very interesting, and worth chewing over. Enjoy.

Wednesday, November 10, 2010

Religion And Neuroscience

I like this because it mixes neuroscience, my career choice, with religion, something that I enjoy seeing though a scientific eye.



Real life snuck up on me something fierce, what with homework, applications, orientations, and dear friends having their baby. It has been an interesting week, let me tell you.

I am about 5 days away from launching into more midterms. Physiology and physics. I'm pulling a reasonable grade in both but I could do better. There is a fair bit of pressure on me here to perform well because I'm basically between grades at this point.

I was accepted into a clinical research internship at San Francisco General Hospital, sponsored by UCSF. I am really excited about this. Basically my job consists of approaching patients in the emergency department that fit specific profiles and asking them to consent to participate in various studies. The two that hold my interest the most involve blunt trauma and HIV testing.

Because of the confidentiality agreements that I made, I'm not permitted to talk about specific patients. What I can do, however, is discuss my experiences working around an ER (obviously I'm not a doctor, so I am not trained to assist in an emergency or anything like that) and what I see on a daily basis. I can't wait to get started. I spent quite a bit of time in a veterinary ER, and I have a feeling that I will adjust rather well.

I also have been doing rather well at chipping away at my applications. I got three done, and am working on the last two. I was thrilled when I got a secondary application invitation from Stanford, which is my first choice.

Applications are an odd duck. Sometimes they give you an enormous amount of room to finish what really can be summed up in a sentence or two. Sometimes the questions are so unlike everything that I have answered before that I am just taken aback and really need to consider my response. The more I do the easier it gets, but I doubt it will ever really be easy.

On a slightly different note, I am gathering my materials and letters and preparing for application to grad school. 3 local universities have my interest: Stanford, UCSF and SFSU. I was considering USF but they are really expensive. I have to investigate their biology programs, because I still really want to apply for grad studies in neuroendocrine physiology. The deadline for SFSU is the earliest one, being in February, and unlike med school they aren't rolling admissions. This means that in February they begin to sift through applications. I am pretty confident that I will get in to SFSU, since I have made so many contacts in the department.

Well, I'm off to school. Hopefully I will be able to finish complement and have a physiology post by Friday.

Tuesday, November 9, 2010

Very interesting assessment of the rally. I agree with an awful lot of what Maher has to say.

Monday, November 8, 2010


So I finally got in contact with one of the schools that I had applied to. The good news is that they want a supplemental application, which is fantastic! This means that they liked my application and want to learn more about me.

The bad news is that the supplemental application must be in by the 15th. Hence the post title.

I am very behind on a lot of things, and I know I promised a completion of the complement post. But hopefully I will be able to get back on track soon.

In the meantime, I do hope you enjoy this.

Sunday, November 7, 2010


So I find myself feeling awkward while writing my applications. I am trying to strike the correct balance of playing to my audience (there go the reviewer's bullshit meters again) and my desire to write an essay that reflects my best qualities.

Writing these applications is not easy. If they were, everyone would be a doctor. While that may not be such a bad thing, with general practitioners in such desperate short supply, the truth is that they make these things tough to assess the dedication and thoughtfulness of all of their applicants.

When looking at statements like "Why should YOU get into such and such University" the first thing that comes to mind is "Because I'm awesome."

Not exactly what they want, I'm sure. I have a reasonably good idea of what they want, but then it becomes an exercise in putting enough of myself and my spirit, intelligence, dedication, and passions into the format to make it more appealing than all the other hundreds that they have to read.

How do I stand out? How do I stand out more than the other guy? Do I bother with that so much and just try and get my own point and perspective across? Should I try and do both? What kind of balance must be struck?

It is an odd juggling act. I want to get in, but not for any reason other than the fact that I would be an excellent doctor. And I want my essays and my interviews to reflect that.

Cephalopod Sunday

Because of various things, I'm behind right now. I am hoping to catch up today, since my plans to go to the park with my husband have been rained out. But in the meantime, here is something that I hope you will enjoy.

Friday, November 5, 2010

Topics In Medicine

Man there is a lot that I want to talk about, from topics from class, to filling out my applications, (which feels more and more like I'm playing to my audience in a vaguely guilty fashion) to medical ethics.  I'm not 100% sure if I'm going to get to all of them, really (I want to finish complement, talk about heart physiology, do a quick and dirty overview of eicosanoids, and whine about filling out rather tiresome applications) but I'm going to try and get to the more time-sensitive ones first, like the ones that affect my grades and my application deadlines.

White Coat Underground is a wonderful blog about topics in science-based medicine and medical ethics. I particularly enjoy his posts on the latter, because I think that in our litigation-happy culture, we need to think about these things. We also don't want to repeat mistakes of the past.

I worked in veterinary clinics for years. I saw a lot of disease and suffering and death. When one is exposed to such things on a regular basis, you have to figure out how to justify it somehow. How do you get through a day when you have to euthanize parvo puppies because the owner can't afford the treatment? It is difficult and can be heartbreaking.

Euthanasia isn't part of the medical dialogue (yet) like it is with veterinary medicine. In emergency cases people just work the best way they can, as fast as they can. A patient's life must be saved. Period.

In situations where the person is sick and lingering, the decision must be made about how to spend those last few months. Doctors approach the situation from the perspective that every bit of extra time is worth it in order to allow the patient to spend it with loved ones, doing the things they enjoy, and the illness is managed rather than treated.

I think that it is very important to have and maintain an open dialogue with your patients. Telling someone that they are going to die soon cannot be easy, but it is important to make certain that the patient understands all of the options, even at the risk of overwhelming them with information. They need literature to take home, something to discuss with their loved ones, and your phone number. Tell them that you can talk to them and make sure that their questions are answered. This is the only way that they can make an informed decision.

The ability of patients to have that kind of informed decision-making, to be able to enjoy those last few months with their families and friends, is, in my opinion, what makes it a little easier. All doctors have to be around and see suffering on a daily basis. Death isn't easy for anyone, but it is comforting to know that the patient knew the options and was able to go for the one that best suited them. That situation is impossible without informed consent.

And PalMD did an excellent job of framing the question. Go have a look-see.

Wrapping Up Vaccination Awareness Week

Stay tuned for a discussion of heart physiology. I am having an exam on this material in about a week, so I thought this would be an excellent way to review.

Until then, enjoy the last few days of Vaccine Awareness Week, courtesy of Orac, here and here

And thanks to Orac's rather wide readership I stumbled on this blog, which I have really enjoyed so far. Since the topic today is Vaccine Awareness Week, I will post this link, but I suggest further reading. The gentleman is very good at communicating difficult facts, and I could probably learn a great deal from him in terms of how to write a good scientific article.

And from Pharyngula, I found this wonderful opportunity! Except that, due to the time differences, I'll be in class or at my orientation and so will miss the entire thing. But that doesn't mean that you can't give it a try!

Happy Friday!

Thursday, November 4, 2010

Where All Da Wimmin At?

With all the sexism and outright misogyny that is rampant in religions, you would think that this would not be the case.

And guess what. It isn't. That lady just didn't look very hard, or was very eager to cast atheists in a negative light. Because any movement that isn't religious looks bad when it isn't inclusive of women, right?


Yeah, It's Kind Of Like That

Just A Quickie

I'm studying for my neurosciences exam, so the more substantive posts will have to wait. I really want to talk about synapses, my favorite subject in class.

But, since I am on a bit of a break and found this, I really wanted to share. There are times when people say things in a much more elegant and eloquent way than I can think of, and this is one of them.


Wednesday, November 3, 2010

Vaccine Awareness Week

It's Vaccine Awareness Week over at Respectful Insolence. I am enjoying Orac's series very much, and I thought I'd share his posts from Saturday, Sunday, Monday,  and today.

I got started on all of this (and actually it woke up an interest in real science that I think had been sleeping for years) when an old friend found me on Facebook and started talking about all of this 'vaccines cause autsim' nonsense. I instinctively knew that her position was BS, but frankly I didn't know very much about it. So I did what anyone would do under the circumstances: I Googled it.

Lo and behold. Enter Orac.

This caused a flood of new scientific data for me, and I spent a HUGE amount of time reading everything I could get my hands on. It's like working in veterinary clinics had starved my brain of nutrition for so long, and I was desperately hungry to feed my intellect. Once I had literally read the entire Respectful Insolence archive (5 years or so) I hungrily devoured the content at Pharyngula and all of the other blogs that I now happily and proudly link to on the left of this post.

It inspired and fed my skeptical sensibilities. The facets of scientific argument and scientific inquiry came out from where they'd been stored for years, and by dint of new knowledge and a new awareness got a spit shine and polish.

This experience actually helped me sort out and come to grips with my lack of religious belief. I had the time to consider (here a word that means mull, chew over voraciously, discuss at length with a very patient husband, and settle on a conclusion) how I felt about religion and being an atheist. And I must say that it makes me very happy indeed.

Funny story: I made a comment on an old friend's Facebook on how the Huffington Post (what Orac calls a villainous hive of scum and quackery; guaranteed to make me smile) bears at least some of the responsibility for the pertussis outbreak in Southern California for propagating misinformation and scare tactics on vaccines. Someone else who saw that post vigorously denied what I said, and went on (after multiple arguments) to quote Joe Mercola at me to say that vaccinations aren't really down, that outbreaks follow cycles, and that it is because of the urban poor. (We'll leave the racism and class stereotypes for another post, shall we?)

Let's be crystal clear here. Someone quoted Joe Mercola at me. To defend Huffpo.

It burns.
I do not like this word.To me it is a word that has been too often used by the religious to mean or imply faith without evidence. It is not a word that I think should be used to explain science.

I do not like this word. To me it is a word used to denote the religious beliefs in their texts, revelations, personal relationships with their gods, etc. I do not like the implication that if one uses it in the context of science, that scientists use similar means to come to scientific conclusions.

Facts and evidence are means by which scientists explore their worlds. Faith and belief are the tenents of the religious. I do not think that faith and belief are part of science.

When I discuss science I do not like to use those words. I use words like know, or trust. I cannot be an expert in all fields. There are thousands of scientists out there, many of whom are experts in their fields. I trust their knowledge because their knowledge is reportable, checkable, falsifiable, understandable within the greater context of the whole. If a scientist makes a claim, I can check it. I can ask them how they know that. I can ask them to explain and I can verify their facts.

I have a responsibility as a scientist to discard ideas in the face of greater knowledge. If 1 paper came out about how mammograms detect breast cancer early, was published in a top-tiered journal by scientists and researchers with good credentials and no conflicts, reviewed by good scientists, I would be hopeful with the caveat that it was later confirmed. If 5 papers came out saying the same thing, I would be less skeptical, and more willing to accept it as fact. If 100 papers came out, then it would most likely be an established scientific fact and would (and should) be implemented in hospitals as part of a diagnostics regimen.

But if our knowledge began to point in the direction that it may have fewer benefits than previously thought (due to better technology or more sensitive screens) then I should understand the reasons and cases where this might be the fact, and change my protocols accordingly.

In all of these cases I have the ability and knowledge to do research on all of the conclusions elucidated by the papers and come up with facts. I can check their numbers, carefully comb their conclusions, and decide whether the research is sound and solid. These facts can either refute or agree with the papers.

Does any of this rely on faith or belief? I do not think so.

Other people use faith and belief to mean what the dictionary definition of the word means, and I sometimes have a difficult time making that leap. I should make a point to ask people what they mean by their use of that word.

I think that where this pure and reasonable pursuit of knowledge breaks down is when we as people cannot leave our egos or own dogma out of the discussion. I am not very good at that. I sometimes cannot see other people's perspective over the sight of my own navel. I get offensive or defensive. I color the argument. It took a very heavy cluebat from my husband for me to understand how I was approaching the problem.

I am making a very concerted effort to take much more time to listen to other people's perspectives and to fully understand their argument before I say anything. This has gotten me into trouble recently, and I need to correct that.

As a scientist, I should always be open to reconsider or re-evaluate what I know. Ego (which I have in spades) should be left out of the equation. My being right isn't nearly as important as fact, and I should have known this already.

In Reason,

Rally To Restore Sanity And/Or Fear

I watched it live streaming on Comedycentral.com. I laughed, I clapped, I danced and I sang along. I had a blast.

I think that I was hoping that Stewart would provide real world solutions to some of the problems that we as a country are facing. I didn't realize until later that that wasn't the point of the rally, though it did make his message fall a little flat. It felt a little hollow, unfortunately, because it felt like it was all show with very little substance.

But as a friend of mine pointed out, I missed the point a bit.

I am all for sanity in discourse. And it is high time we found that in this country. He was talking about laying down a groundwork for how we work out issues and come to compromises in politics. There are some things that I don't think we should be compromising on (gay marriage, rights to contraception and abortion, separation of church and state, teaching real science in our classrooms, for example) but the discourse we have now, shouting and screaming epithets at each other, are getting us nowhere.

And a friend of mine sent me this, which I enjoyed very much.

Tuesday, November 2, 2010

The Big Atheism Post

I was raised Buddhist in what is arguably the most liberal city in the Western Hemisphere: San Francisco. My parents were both raised Christian: my dad was Lutheran and my mom was mainstream Protestant. Both rejected their faiths and converted to Japanese Buddhism before I and my sibling were born.

Japanese Buddhism is weird. Buddhism is all about the illusion of reality. What I was taught to believe, however, was not that reality is an illusion, but that we are our own personal god, and life is about being the very best god that you can be. Along with that is the other stuff typically associated with Buddhism: reincarnation, living a good life, being the change that you want to see in the world. We did a kind of focused meditation/chanting/prayer that was developed and meant to be a way to channel your energy into something positive. Energy and karma were really big focuses of our belief. Negative energy was bad karma. The universe was almost perceived as a living breathing entity that provided energy that we could use. As a sort of thanks, energy was supposed to be put back into the universe in the form of kindness and good deeds.

I never really took it very seriously. As a kid I thought it was a game. I was always encouraged to chant more, but I think my parents remembered how forcefully Christianity was pushed on them and they shied away from being too strong about it.

That isn't to say that I didn't participate in activities. I sure did. I was in the choir, the orchestra, and the hip-hop group. I got to meet the head of the organization ( but it wasn't the first time. I met him in utero, about 3 months before I was born) and he was a very lovely gentleman. His wife was so sweet and supportive.

But like any organization that has a strong central leadership and draws on ancient traditions, it had its flaws. It was terribly sexist and ageist. It was very difficult for a young woman who was growing up faster than her peers to be stuck with people that she couldn't relate to. My sister was learning to play trumpet, and she wanted to play in the jazz band. But she was female, so she couldn't. And she couldn't play in the fife and drum corps, because she played trumpet. People were supposed to report to senior members for 'guidance'. I think my mom strongly disliked the organized proselytizing that was required of people. I was told some incredibly demeaning things about my gender when I was very young. It was about then that I made the decision never to involve myself with anything that told me I was inferior because of my gender.

Combine this with a deep seated suspicion and dislike for organized religion that my father had inculcated in me at a very young age. I remember walking into the kitchen and watching him watch the news of the pope going to some 3rd world country and telling everyone there to 'be fruitful and multiply.' My father was sickened by the abuses of religion, and still is.

Fast forward. The year is 2005. The place is Fresno, the California Bible Belt. I was sitting in a Philosophy of Religion class taught by a gay ex-seminary student (who'd been kicked out for being gay) being lectured on the glories of god by a couple of rather frightening fundamentalists. I was the only Buddhist in the class. There were 3 Jewish kids, a Mormon, and the rest were Catholic or Evangelical.

I am a scientist. I require empirical, reproducible evidence for knowing what I know. The fundamentalist chap was demanding to know why I believed in reincarnation if I required evidence for everything. I sat there and a slow smile spread over my face. I look at him and said "You know, I don't know why." He thought he had triumphed and pushed his case, trying to make the final case for his religion. I didn't know it at the time, but I had simply taken the last step necessary to reject all religion.

Let me tell you, there were some rather scary people in that class. They pulled out all of the creationist canards and threw them at me. I was asked to read a book called "The Case for Christ." I stopped 50 pages in because I couldn't continue to read such utterly fallacious and vapid material. They threw the 2nd Law of Thermodynamics at me (really? Lame) and said they could see micro but not macro evolution. I got asked the "Why are there monkeys?" question so many times I lost count.

The great thing about that class was that my professor encouraged discussion but never let me feel (or get) ganged up on. It was easy to do. I was outnumbered by about 23 to 1. But he called the 3 most vocal fundamentalists out if they got too outrageous in their claims with his flawless memory and grasp of scripture.

I happily and comfortably eschewed religion. I am a little uncomfortable around the overtly religious. I spent several years never really making the final push to atheism until everything I knew about science and my demands for evidence crystallized into something that made a great deal of sense to me. I spent a lot of time watching Richard Dawkins and Christopher Hitchens videos. I was needlessly self-righteous and proselytized until I realized that I was being horrendously hypocritical.

I do not think that science and religion are compatible. In my opinion, it involves a rather serious cognitive disconnect to believe something that has no evidence and then demand evidence for something else. I think that while religion and science are two different ways of knowing the world, science is the one actually grounded in reality, in the here and now. And my primary problem with religion is that it is used as an excuse to do harmful things. The bottom line for me is that if it is harmful, if it removes or denies rights, and if I am forced to behave or live in a certain way because of the legislation of someone else's morality, then I am not okay with it. Evolution should be taught in science class because it is science.Creationism, if it is taught, should be taught in philosophy class because it is not science.

I have friends that are religious or spiritual. My husband is a little spiritual, though he mostly agrees with me on religion. I bear no ill will to people who are religious, but I will defend my views and ask pointed questions when it is brought up. I don't think that religious views are all that worthy of respect, but I will respect the person that holds them. Everyone deserves respect, but if you have silly ideas I will point out that they are silly or that I disagree, and I will try to be extremely clear when I explain why.

I try to live my life in the very best way that I know how: with compassion, integrity, and a dedication to reality. I have a lot of love to give: to my husband, my family, my friends, to nature and the natural world. I try very hard to be a moral, ethical person.


Immunology Tuesday!

I've been playing with the look of the blog. I'm not 100% happy with my header image, just because I had to contort it so much to do what I wanted. I may end up playing with other synapse images I have just to see if I can make them work.

Today is Immunology Tuesday, and I thought I'd kick things off with some microbiology which will segue nicely into today's topic: complement. Friday's topic is going to be intercellular signaling, so that comes together nicely, I think.

I thought I'd begin with a lovely blog I stumbled on, courtesy of erv, also of SciBlogs. He seems to take a pathogenic approach to immunology. I've seen a couple of different approaches besides that, mainly specific functions of cells and regulation of gene expression. His blog's name is We Beasties, which always makes me smile.

Last semester I attended a microbiology seminar (to my chagrin I cannot find the seminar details, and so sadly cannot direct you to the gentleman's site) led by a wonderfully jovial speaker who did research into microbial genome plasticity. He knew he was addressing an audience of students and faculty, so he spent a good 15 of his 45 minutes talking about some basics in microbiology. He talked about some of the diverse forms, functions, and environments of prokaryotes, and the fact that we are made up of more prokaryote DNA than we are human DNA. Interesting concept.

Typical labs tend to coddle and spoil their colonies of microbes, simply in order to keep enough specimens alive for whatever purpose. He opted to starve his colonies  of E.coli and see what resulted. This means that no additional nutrients were added to the plates or broth used to culture the colonies. To his great surprise, a number of things came up. For one thing, colonies hit the death phase of microbial growth, which resulted in about 98% dieoff, and then the colony recovered. The growth remained pretty steady after that.

Another unexpected outcome (although in retrospect perhaps not) came from an experiment they conducted where, after the death phase, colonies from 1 day old cultures were plated with 10 day old cultures. And the older colonies outcompeted the younger ones. Why might that be? Probably because they'd had more time to allow mutations to spread through the colony.

And my were there a LOT of mutations! Some of the most bizarre looking organisms came from this experiment. E. coli with long filaments, odd shapes, and even enormous sizes were found. The large cells were curious. In a starvation situation, it makes sense to try and get small, because you don't require as much nutrition to survive. But the researchers postulated that perhaps the large cells were able to out compete their smaller neighbors (though if they'd found evidence of phagocytosis they'd probably have the Nobel by now).

Analysis of the genome before and after the death and steady state phases revealed dropped segments of unnecessary genes, upregulation of metabolic genes that helped the bacteria process what little nutrition there was available, and an overall massive genome plasticity.

This seminar was really incredible. And one of the things that I might like to study in grad school is how the genome changes in starvation conditions and with exposure to low levels (as in, mortality less than 100%) of antibiotics. Also, I'm pretty sure that E. coli were chosen because they are hardy and easy to cultivate. I might like to look at more pathogenic and more fragile species that are more difficult to cultivate. If there is one thing I learned from this experiment and a semester of medical microbiology, though, it is that bacteria are tough little critters.

Moving on from microbiology, we come to our immunology topic for today: complement. Complement is amazing because it isn't even a finely honed system of cellular responses. Complement is a system of molecules. That's it.

Complement is considered part of the non-specific (or innate) immunity, because it does not generate a specific response depending on the type of pathogenic attack, and does not adapt itself to different types of immune stress. It is consistently synthesized and distributed and is the very first responder when the mechanical defenses of the immune system are bypassed.

Complement precursors are synthesized by the liver and white blood cells that are resident in tissue, such as macrophages and neutrophils, and circulates through the bloodstream.When activated (typically about 5-10 minutes after infection is detected) it is cleaved in a series of enzymatic reactions. The type of cleavage and the enzymes used in the reaction are dependent on the type of infection.

There are three pathways to complement activation. The classical pathway (so named because it was discovered first), the alternative pathway (probably discovered second) and the mannose-binding lectin pathway (so named because it reacts to a specific sugar on the outer coat of certain pathogens) all come to make their own variant of C3 convertase, which kicks off the cascade, but diverge depending on the series of proteolytic cleavages.

Stay tuned for part 2! 


Janeway’s Immunobiology, 7th edition by Murphy, Travers, and Walport. Garland Publishing, 2008
Medical Microbiology, 6th edition by Murray, Rosenthal, and Pfaller. Elsevier/Mosby, 2009

Monday, November 1, 2010

Application Process

Much like the difficult school curriculum, the grueling MCATs, and the competition, the application process involved in getting into medical school is probably designed to weed out those that don't REALLY want to do it. There is, I think, a certain level of dedication that is required to deal with a primary application, secondary applications, interviews, and then the nail-biting tension of waiting to see if you got in.

In the spirit of weeding out the wafflers (because if it meant being closer to their dream of going to med school no one would really mind, right?) the application designers want everything just so. This meant tedious hours of entering in each and every course taken over one's entire post-secondary academic career, logging and tagging them and filing them just so. Many were the times I sighed as I was about to begin a new entry and wonder why they couldn't just read the transcripts.

The tagging process, I know, is useful to them as they determine the science, non-science and total GPA. It saves them work, and probably me money, as otherwise I would have to pay for the average time it took to calculate all of that.

The essays were interesting studies in composing. I wrote and edited and re-wrote and edited some more, in search of the elusive goal known as the perfect essay. Because I am me, I went with a science-centered approach. Compassion for my patients is not even a question (I worked veterinary for quite a while. If that doesn't develop compassion in a person nothing will) so I chose to talk about my dedication to and my understanding of the role of science in medicine.

Once my application was submitted I had to wrangle my professors and advisors to write me letters. Herding cats, I tell you. The last of my letters was submitted today, if that is any indication. It can be tough as deadlines approach to keep the calm, polite tone one really should use when addressing professors that are doing you a favor instead of screaming hysterically because if they are a day late you will have an aneurism.

But I'm better now.

Ahh, supplementary applications. Delightful. They are rather similar to the original, except that each school has a specific format and set of questions for you to answer. I am trying to put my very best foot forward (partially because I'm certain that good reviewers can smell bullshit a mile away) and answer the best I possibly can.

I was invited to submit 4 supplemental applications. I'm waiting to hear back from the schools that are in processing, so this isn't half bad.

Grad school is a whole other ball of wax. The more I study the more interested I am in research. I did not apply to MD PhD programs this year, mainly because I don't have a lot of experience in the research field. There is a part of me that wonders if maybe I shouldn't go to grad school even if I do get into an MD program. It might be foolish of me to do so, but I am really excited at the potential for learning.

If I don't get into med school, I will probably get into grad school at State, because besides my grades and my letters, I have contacts in the biology department with professors that I think will be interested in sponsoring me.

And so in the meantime I am finishing up everything that I can do with my supplemental applications and keeping a close eye on my application status. There's that whole school thing, too, but that's a given, I think.


More About Frames

I must have been tired last night when I put up my post on reading frames. One thing that I have quickly realized is that writing about scientific topics is very difficult to do well. Biology is a field with a great deal of detail, and everything is interconnected. Where do I start when I talk about transcription and translation? The definition of a nucleus? What a ribosome is? You see my problem.

I think that it may well be easist to provide further reading suggestions from Bioweb or various other sources and simply discuss the topic that I am interested in discussing, rather than starting at the very beginning.

With that in mind, I began learning about reading frames when we were talking about hypervariability in B- and T-cell receptors. These hypervarible loops on the receptor surface allow for an enormous diversity in the ability of these cells to detect antigens. What is amazing to me is that we have a codified system within our genome, expressed by parts of our immune system, that actually allows for the limited re-writing of the genome. This further allows for a limited restructuring and variability of the proteins on the cell receptor surface. What results is our ability to detect and build immune responses to each type of immune invader. The picture is a bit larger than that, but maybe I'll do a series on immunology.

One possible course of study for grad school is the plasticity of genes expressed by organisms that survive attempted killing by antibiotics and how these genes allow them to evade the defense mechanisms of the host. Understanding like this can help us develop more effective vaccines and more promising antibiotics. Antibiotic resistance is a huge problem in the medical field, and a mechanism that allows us to completely bypass an organism's ability to build resistance would be ideal. Currently we have discarded early versions of some antibiotics simply because we have better synthetic ones that don't have the track record of increasing resistances.

Mutations resulting from the misreading of reading frames are fascinating to me, because so much is dependent on how the nucleotide sequence is "read" and where the starting points are. Misreading the sequence or copying errors like adding or deleting a nucleotide can have devastating effects on the organism or none at all. Frameshifts are particularly interesting to me, because they can be lethal or produce high morbidity in nature. They involve deletions or insertions of nucleotides that throws off the reading frame (Remember, the frame is the group of codons that codes for a protein, and codons are triplets of nucleotides. I think I was off in my previous definition) and so there is either one too many nucleotides or an extra one. While the code is very redundant (there are 64 codons for 20 amino acids) if the frame is thrown off the stop codon will not be read properly, and then all kinds of havoc will ensue.

Further Reading: Immunology: Hypervariable Loops
Cell Biology: Reading Frames and Frameshift Mutations


During protein synthesis, the DNA template is transcribed and translated to produce a strand of amino acids, which is folded (or not) depending on interactions and how the strand is processed. The result of these processes is a protein. Some proteins are finished during this process, and some are enzymatic precursors that are finished by interactions with their environment.

During translation a codon, made up of three nucleotides, determines which amino acid is going to be added to the chain. The reading frame is the way in which the strand of nucleotides is read. The beginning of the strand determines the frame for the rest of the strand, as the frame goes from codon to codon.

 Further information and explanation can be found here. 

I chose this name because I wanted something somewhat obscure, a bit more memorable, and very geeky. Plus I really like the play on words that makes it sound more literary than scientific.