Thursday, November 19, 2009

It always comes back to Jurassic Park, doesn't it?

I just got back from a seminar by George Weinstock of Washington University, St. Louis about the human microbiome project. I was planning on doing a blog entry on the human microbiome project--and still will write one--but during the talk I was struck by the amount of data the Wash. U. genome sequencing center was producing, and how a huge percentage of the talk centered on the challenges of storing and processing all that data.

For example, the center needs an additional 4 terabytes of storage each day. They've built an entire storage facility which is in great part air conditioners and electrical equipment to maintain the data storage. It uses the same amount of electrical power it takes to light a New York Skyscraper.

It made me think back to all those Cray supercomputers used to process the ancient dinosaur DNA sequences in that most-influential novel "Jurassic Park" by the late Michael Crichton. The speed of current DNA sequencing technology is blinding in comparison to what those ol' Cray computers would have been capable of. But though the speed of the sequencing has gotten faster, all that data requires a huge space to house the technology to store it.

Wednesday, November 11, 2009

In a world overrun by antibiotics, what are we selecting for?

As a graduate student, I read a lot of self-help books. One of my favorite concepts is from Marcus Buckingham’s “Find Your Strongest Life”:

What does working look like?

It’s a very goal-oriented approach to life. Envision what you want your life to look like, and work backwards from there.

The concept of selection is very similar to the “what does working look like” approach. In my college microbiology class, I was tasked with isolating a microbe—from the environment—that could eat milk (casein proteolysis). So I left an open container of milk out in my dorm room for a week and waited to see what grew. To select for a milk-eating microbe, provide an environment where a milk-eating microbe would do well.

But what does this have to do with the zombie apocalypse that I was rambling on about in an earlier blog entry?

Well, if you want to get humans who are good at surviving zombie attacks, one way to do it would be to flood the world with zombies and see who’s left. If you did that, you’d be selecting for zombie survivors.

But while you would nearly guarantee the remaining humans were zombie-resistant, you would have little control over HOW they were zombie-resistant, or any number of other traits they would possess. You might end up with an excellent marksman, a swift runner, or a violent sociopath. You might find the survivor was just very good at hiding.

So what do antibiotics select for?
When you take antibiotics, you’re basically flooding your microbial world with something deadly. Unless you kill every single microbe, you will select for microbes that survived the antibiotics onslaught. They will survive and multiply in a land empty of competing microbes that used to keep them in check.

I could go on for several more paragraphs about antibiotics, but I’ll try to wrap this up: when you use antibiotics, anything that survives is antibiotic-resistant, but both “good” and “bad” microbes can have that ability. High dosages of antibiotics will kill off more microbes, leaving less to prosper. Using a combination of antibiotics would be like unleashing zombies on the world and then following it up with vampires: while there are citizens uniquely skilled at surviving either monster, there are far fewer individuals who can survive both.

So what happens if the world is full of violent criminals and suddenly zombies kill off a huge portion of civilized society, including law enforcement? Do you think a bad guy or two would survive? Would anyone left standing be able to keep them in check?

Friday, November 6, 2009

Tales from Home Economics UPDATE

After I posted my "Tales from Home Economics" entry, I received an e-mail from my mother-in-law Ellen (her description of yeast producing gas was the feature of that post). Thankfully she was happy about me putting her words on my blog (I have to admit I didn't check beforehand. I am a poor journalist!).

Now, I've never been in her class when she gives the description, so I was excited to get more specific information on what she tells her students about yeast:

When I tell the kids about the yeast they are about to use, I tell them they will first give the yeast a bath and then give the yeast a snack and then the burps come . . . Then I tell them to look very closely after they pour the yeast into the water and maybe they can see the yeasts smiling back at them!!! These poor kids will have a twisted science education by the time they leave my class!

Actually, I think a twisted science education may be just what students need to get excited about science. I think sometimes we get the impression that science only happens in laboratories, and that we need advanced degrees to understand it. But science happens everywhere, and with a little imagination we can understand even the things we can't see with the naked eye.

Although hopefully I won't see the yeast smile before I put them in the oven!