mattbell | Entries tagged with bio

Avatar is worth seeing as a demo reel for state-of-the-art filmmaking technology that will completely revolutionize the industry and will eventually trickle down to independent filmmakers over the next 20 years or so. The movie was visually so stunning that I managed to more than tolerate a thoroughly mediocre plot. Lots of people have written about the special effects, the plot, and the issues of race the movie brings up. My questions is...

So, could a world like Avatar evolve?

The conclusion is very surprising.

( Very minor spoilers and a lot of fun speculation )

Since I last checked a year ago, the price of a thorough (but not complete) genome scan has dropped to around $400, and there's a lot more useful documentation tying it to specific conditions. There's also the Genetic Nondiscrimination Act, which provides some protection from employer or insurance company discrimination based on genetic conditions. (I say "some" because they can still discriminate based on diseases caused by genetic defects once any symptom of the disease is present)

Logically, this seems like a good idea. If I know more about my risk levels on various preventable diseases (eg heart disease), I can focus my attention on ameliorating the biggest risk factors. Even if a disease is nonpreventable (eg Huntington's), it will help me better maximize my level of enjoyment of my life by not working my ass off and building up savings for a retirement that's never going to come.

However, I will say that, viscerally speaking, this is scary. There's a certain dread in finding out a piece of your own fate. I faced this fear when looking for prior art on things I was looking to patent or when doing STD testing the first couple of times. This is bigger though -- it's a potential threat to my dreams and plans for my life. It could also have an impact on marriage, kids etc, plus I could find out things that may be affecting other memebers of my family.

Of course, logic brain points out that these threats are there whether I look or not. The one semi-legitimate thing I'd worry about is that by being an early adopter of genetic testing, I could scare off potential mates. If I have a few known bad genes (and almost everyone does), I might be "scarier" than someone who hasn't had genetic testing.

Most mainstream people adopt the same "what I don't know can't hurt me" approach with sex and STD testing. They will gladly have sex with a stranger, no questions asked, but may be scared off by someone who had regular testing and discovered (and cured) some outbreak of an STD years ago. Fortunately, I'm not so into mainsteam people.

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Anyway, I'm going to do it. Most of my fears appear to be of the "head in the sand" variety as opposed to legitimate fears. But don't ask me if I found anything scary in my genome. If I want to tell you, I will.

A few days ago I was talking with some friends about how people don't really know where their foods come from and how they're made. I'd especially love to see a giant flowchart around milk products, with cow/goat/sheep milk at the top and all the different cheeses at the bottom. A friend mentioned seeing one on a billboard in Canada, but I couldn't find any images of it online. I did find this, which is painful to read but provides the relevant info:

Here's another one that focuses more on the protein vs fat broken out of the milk.

I'd love to have these charts for various different types of food. (corn and corn products, beef, ice cream/gelato, wheat, rice, soybeans and all that processed vegetarian stuff). They'd make nice posters.

Update: Here's a way better one, via [Bad username or unknown identity: easwaran �.� ]

Suppose your house (say, the one I'm living in now) has an ant problem. Suppose you toss some food out and the ants get to it. The ants take your food back and turn it in to more ants. How many more ants?

Energy conversion across trophic levels in the food chain is around 10%, an ant in this part of the world weighs around 0.2mg, and a typical apple weighs around 300g.

So... if the ants eat the whole apple, they can use it to make 150,000 more ants. Fucking ants.

While the transmission rates per sex act for HIV are roughly known, they are not known for all the other lovely STDs out there (herpes, gonohhrea, syphilis, HPV etc). This knowledge would be really valuable in fighting the spread of these diseases. But hey, I know a place where I can gather a ton of data. If the prostitutes in Amsterdam are having large (and meticulously recorded) amounts of regular always-protected sex, we can get a good sense for the transmission rates of various STDs with a condom. If we assumed that the clients had STD infection rates similar to or greater than the general male population (a reasonable thing to assume) then we could get an upper bound on STD transmission rates per sex act for all the major STDs. My guide on the tour thought this was unliekly – prostitution is still heavily stigmatized in Holland, and most prostitutes do not like any invasions of their privacy, especially an expiriment that tracked them over time.

The most interesting thing in Budapest for me was seeing a large number of people who resembled a Hungarian woman I dated back in college. Her look was fairly distinctive. Although I cannot easily describe it, I know it when I see it. What's interesting is that while 15% or so of the residents looked very close to the way she looked, the rest didn't resemble her at all. In a country with a long history of continuous habitation by the same group, there are probably substantial subgroups within each ethnic group – eg, the peasants kept separate from the noblemen, people from within a particular guild tended to intermarry etc.

Update: Accordiang to my Hungarian-Italian couchsurfing host, after a particularly devastating war many centuries ago, Hungary “purchased” a million peasants from Romania. So that might account for some of the genetic diversity. Ah, serfdom.

It turns out that having unhealthy, inflamed gums dramatically increases the risk of heart disease. Study here.

From a programmer's perspective, the body is an enormous hack. All the components are deeply interdependent, causing weird and unusual bugs and linkages. Given that the body was programmed by a genetic algorithm and not a skilled intelligent designer, it's not surprising. There's probably mild selection pressure for more cleanly programmed organisms, but the common programming technique of building a better and cleaner "version 2.0" program from scratch is simply not available to evolution!

Here's how the linkage works:

Unhealthy gums have constant bacterial infections, which cause inflammation as well as an easy path for foreign bacteria to enter the bloodstream. The constant inflammation puts stress on the body, since it's constantly fighting an infection. This stress leads to the release of hormones that cause heart disease.

Inerestingly, the vast majority of gum disease is caused by a single species of bacterium that eats sugar and secretes tooth-dissolving lactic acid. Some enterprising genetic engineers have designed another bacterium that can live in our mouth and secrete a chemical that kills these bacteria. I'm a little wary of their solution, but it serves as an example of the wide variety of creative solutions that genetic engineering affords us.

I stumbled upon a totally appropriate follow up to my post from earlier today... A company is developing a blood test chip that will screen for the presence of various proteins that indicate cancer infections.

http://www.technologyreview.com/biomedicine/21676/

It only needs one drop of blood, and could cost just a few dollars.

It's an island south of the Arabian peninsula belonging to Yemen. It's been called the Galapagos of the East. A friend of mine told me about it.
I think I might just have to stop there on my trip 'round the world.
Here's why:

Socotra - Dragon's Blood tree by Valerio Pandolfo

Yemen, Socotra, Ar-Ar 12 by nidodipoiane

My high school biology teacher showed us this during a slow day in Bio AP.

What you're about to see is the process of messenger RNA transcription into proteins, as explained by interpretive dancers.

"Only rarely is there an opportunity to participate in a molecular happening" :D

The dance part starts at 3:00 or so. The whole thing was a collaboration between the Stanford Chemistry and Drama departments in 1971.

Two companies -- 23 and Me and deCODEme, just started offering personalized genetic testing. The era has arrived sooner than I expected.

For $1000, they give you a vial to spit in, and a couple of weeks later you can log on to their website and find out your genetic risks for various diseases -- eg heart disease, diabetes, and more.

They don't sequence your entire genome, but they do look at over 500,000 polymorphism sites on the gene.

Some things I noticed:

- DeCODEme seems to be a aimed more at a tech-literate audience, while 23 and Me seems to be much more aimed at a biotech-phobic audience.

- You really have to dig to find out exactly what kind of report you get, and even then it's unclear what you will learn. It appears that deCODEme has the wider list of diseases they screen for. ( Our current list of diseases includes: Age-related macular degeneration, Asthma, Atrial fibrillation, Breast Cancer, Celiac Disease, Colorectal Cancer, Exfoliation Glaucoma XFG, Inflammatory Bowel Disease, Multiple sclerosis, Myocardial Infarction, Obesity, Prostate cancer, Psoriasis, Restless legs, Rheumatoid arthritis, Type 1 Diabetes and Type 2 Diabetes.) However, since both sites gather lots of data, they may be able to tell you about the risks for other diseases in the future.

- Both companies are taking a very conservative approach to what for many is a touchy subject. They have some of the most consumer-friendly privacy policies I've seen, and explicitly call out that they won't ever tell insurance companies what they find without your permission. They provide ways for you to hide your identity when doing the test. DeCODEme has also made an explicit policy of not telling you anything about genetic diseases that you can't do anything to prevent. Thus, they are driven towards vague, nonmedical assessments of risk.

- Both companies have an opt-in social network component. This component is designed to help you, for example, connect with other people who have a high risk of diabetes and form a support group. As

frogpyjamas pointed out, people could also use the social network feature to create groups with goals like "I have a perfect genetic profile and I'm looking to breed... let's create a new master race". It's the basic dystopian Gattaca scenario... don't just Google your date -- submit their saliva sample for genetic testing!

I'm strongly considering trying deCODEme, but I'm trying to figure out exactly what I'd be getting for my money. Any expert opinions out there?