Friday, November 02, 2007

"Computational Thinker" Thinks About Medicine

Some of the herpes viruses that are being studied at Stanford as suspects in chronic fatigue syndrome are described as remaining dormant in the body after a person recovers from infection, in specific parts of nerve cells or bone marrow, though sometimes reactivating. (The better-known members of the herpes family include the viruses that cause chicken pox and mono, in addition to the ones people actually call "herpes".) People are familiar with shingles being a reactivation of the dormant chicken pox virus.

I read about "dormant" viruses and wonder what does "dormant" actually mean to doctors and scientists? Is it completely asleep and immobile, nonfunctioning and nonreproducing, not doing anything to the human body? Is it the exact same virus entities from say fifty years ago in somebody's body reawakening after fifty years, and none of them woke up during that time in between? If not, that would mean they reproduced somewhere along the way.

What happens to all of the microbes when a body fights off infections? What happens when you take an antibiotic? Is the reason why people usually stay well after recovering from infections because antibiotics or the immune system kill every single one of the bacteria possibly located in the body? What would a random doctor or medical scientist answer to these questions?

Me thinking, thinks that well, these are cells and molecules, antibodies and antigens, flowing through blood and lymph and whatever in the body. They are actually objects and not magic nor abstract ideas. Physics, chemistry, and statistics apply. What are the chances that antibodies and antigens will perfectly collide such that every single one of the infecting microbe is killed before it gets to reproduce? Why do low levels of antibodies remain after an infection has been fought off?

My imagination plus logic thinks that viruses and other microbes in the body probably behave like chemical reactions with equilibriums that shift in response to various factors in the environment. Are "dormant" viruses actually "dormant," or are they just in an equilibrium in very small numbers against the immune system? I'm picturing visible infection as analogous to those pH experiments everyone does in high school chemistry where you drip one drop of acid or base at a time into a beaker of some pH-detecting liquid that changes color suddenly from clear to pink after one particular drop.

Viruses are known to be linked to some types of cancer, but interestingly there hasn't been much attention on the viruses as active causes of the disease and targets for treatment. Sometimes I think this is an example of lack of thought.

Here's an interesting article on a new discovery:

Kill the Virus, Stop the Cancer

And here's the research paper from the cool open access PLoS journals:

Treating Cancer as an Infectious Disease—Viral Antigens as Novel Targets for Treatment and Potential Prevention of Tumors of Viral Etiology

There have been a lot of news articles on the following big study which includes the conclusion that eating more meat increases the risk of cancer.

Doctors, Dietitians Stand Behind Fat/Cancer Link: Most Physicians Applaud New Report; Meat Groups Oppose Recommendations

In the meat and vegetables area, it's not enough to just eat more vegetables, you have to eat less meat too. That's one possible factor to explain different results from different studies, such as one I recently read about finding that doubling fruit and vegetable intake did not have an effect, and another finding that a diet heavy in vegetable-y foods lowered risk compared to a diet heavy in meaty foods. Seemingly conflicting research study results actually have logical explanations that should be figured out, and which probably actually turn out to be key information.

Okay, it's a vague link, but I thought this article on the need to teach and apply computational thinking in sciences and life in general is interesting. "Computational thinking" seems to be a term describing basic logic and problem solving skills, useful and needed for just about everything, but not taught or practiced very much outside of computer science and engineering.

Computational Thinking
, Jeannette Wing
Official Google Blog: About the Google Education Summit


Mai-Sie said...

"Viruses are known to be linked to some types of cancer, but interestingly there hasn't been much attention on the viruses as active causes of the disease and targets for treatment. Sometimes I think this is an example of lack of thought."

Not necessarily just simple lack of thought. The whole immunotherapy thing (whatever the target might be) is relatively new. If the infusion of modified antibodies was becoming a routine therapy for people with any diseases, then it would be a lack of thought. But it's still a relatively new/experimental/specialized/limited therapy.

It's at least partly because there just haven't been terribly good treatments for viruses. Even the ones that are clearly known to cause cancer. Hepatitis B-liver cancer, HPV-cervical cancer, no debate there. Effective Hep B antiviral medicines are relatively recent developments, and "effective" actually means they only suppress the virus and don't manage to eradicate and cure. So, the strategy for "treating" the cancers has been prevention.

This is the case even for viruses that don't definitely cause cancer but cause some other disease that people would want to eradicate. Like HIV, or Hepatitis C.

As for the "dormant" issue, I think what they mean is what you say, a kind of equilibrium. That's the only way it would make sense with the explanations that often stressors or things that suppress the immune system would cause a flare. Because those would be affecting the host, not the virus, so it must be a disturbance of the equilibrium. Of course, I wouldn't be surprised if many docs also think "dormant" is just magically asleep or something.

As for infections staying in some low equilibrium in belief would be that's probably not the case, at least with bacterial infections and even many viral infections...because otherwise all those people who get immunosuppressive treatments would probably die almost instantaneously from all the 100s of infections they've had in the past flaring up.

dancing dragon said...

The virus-cancer article is interesting because it presents their research as a fundamentally different approach even within radioimmunotherapy against tumors because it targets viral antigens instead of human antigens. Reading the article gives me a sort of ahah moment, why didn't we think about that before, which probably could be said for many big discoveries.

These are interesting thought exercises. The microbe-immune system equilibrium abstraction, not having a "backwards reaction" but reproduction, can theoretically go to zero. It's an interesting exercise for trying to understand how things work to try picturing the one last sole survivor of a microbe species in the body and how the immune system would find and eliminate it, and then picture what makes the difference between microbes that can be fully eliminated and the ones that are dormant or chronic infections.

Interesting also because it's virtually impossible to prove that there are zero of a microbe in the body, and that gives room for a lot of possibilities.

BadTux said...

Viruses are kinda an odd thing because they aren't actually alive. They're just little snippets of genetic material in a package. They don't reproduce or anything, they penetrate into the body's cells, replace the genetic mechanisms inside those cells with their own, and then use the cell's own reproductive mechanisms to reproduce. After a while the cell dies due to using up all its energy to reproduce virus material, bursts to let the newly-produced virii out, and you have an itchy nose drooling virus-filled goo all over the place.

Your body's immune system actually doesn't do anything about the virus when it fights off the viral infection (assuming it does). Virii operate on a level far smaller than white blood cells are capable of doing anything on. What your body's immune system does is target virus-infected cells and kill them before the virus can reproduce, via targeting proteins associated with the virus that infected cells have on their surface.

So when a virus is dormant, basically what this means is that it's laying low. It's not infecting cells, so the body's immune system can't do anything about it. Because it's not alive, it can stay dormant for years with no problems. As far as I know they still haven't figured out the mechanisms via which some virii, like herpes, can lay low for sometimes years then suddenly erupt again when conditions are right. But then if you added up all the stuff we really know about what constitutes biological life in one hand, and what we don't know in the other hand... well, actually, you'd need a dump truck or two for what we don't know. We are still many years away from being able to create life from raw chemicals in a test tube, if we ever can.

- Badtux the Biology Penguin