Campus Life Electronics research stories

A Good Day

I got up at 7 am this morning and got to work by eight.

I wore real shoes (not flip-flops) for one of the first times since I moved to Berkeley.

I work in a goverment building, with sign in sheets, and ID badges, and filters on the internet.

I didn’t even get the chance to talk to my new PI today, but I had the e-mail he’d sent me about my rotation project, so rather than sit around and waste time I started to work on it.

Did you know FT has 13 homologs in rice? And I found even more homologs in maize and mapped them on to the tree of rice genes using reciprical blasting.

The other people in this lab are really nice too. Two post-docs and one other grad student.

When I got home I realized I was babbling at my roommate about my exciting first day. We tend to be introverted around the apartment most of the time. I hope she doesn’t think I’m going insane.

To celebrate I cooked delicious pseudo-monty burgers (two plain patties left over from stuffed burgers on saturday, fried in a pan with a whole lot of extra spices.)

I also got an internet server working on my low power linux computer! It required a bit of tinkering to get around using the standard http port (most ISPs block connections on this port for residential costumers to discourage people from hosting web pages at home (like I just did!)). The page itself is just a proof of concept… I still haven’t figured out what I want to host at home (rather than using the hosting account I use for this blog) but it’s another advantage of an always on computer.

And for the record…I was able to bypass the filters at work. There’s no reason to, since I really don’t need access to facebook at work, but the point is, I can. And apparently people there have been trying to for over a year. (Some people really need their facebook.)

Photo Posts Plants research stories

The same stuff as rainbows

Thinning out my corn seedlings today I was struck by the fact that is:
Is made of the exact same stuff as this:

Plants may grow out of the soil, but when you’re holding a whole big mass of them, the weight in your hand came from nothing more than water, air, and light. The same stuff as rainbows.

I remember the first time I learned about that in high school biology. A guy in Europe weighted a pot full of dry soil, then planted a seed in it, watering only with distilled water. Over several years the seed grew into a large tree, which he finally uprooted, carefully rinsing off all the soil from the roots. After it had dried, he reweighed the soil, and found its mass almost identical to what it had been before he planted the tree. That very real, very solid, tree, made of nothing but water, air and sunlight.

Campus Life research stories

Weekend Update

It’s been a long week. I’ve been doing a lot more lab work this week (which has been great!) as I’ve learned more about the lab, and am able to work longer without having to ask questions. Coursework has also gotten more intense this week. We finished up our module on Genetics and Development on Tuesday, and started Computational Biology on Thursday.

So now I’m relaxing on the futon watching the Discovery Channel documentary on the frozen baby mammoth. They’ve got a big machine that takes the tissue down to -140 and grinds it automatically. I’m envious. But they’re using the same PCR machine I was using this week! Now on to 454 sequencing of the mammoth genome! It’s a hokey documentary (they keep having CGI mammoths wander into their interviews with scientists), but I’m enjoying it.

Hope to return to the Berkeley farmers market tomorrow. Maybe there will be a new mystery vegetable tomorrow.

Book Reviews research stories

Tomorrow’s Table

Believe it or not plant geneticists and the organic movement do share share common ground. It is the realization that conventional agriculture (meaning high input, in the forms of pesticides, energy intensive synthetic fertilizer, and drawing more water out of aquifers every year than is replaces by rainfall) is not going to be sustainable over the long term. I just finished reading a book that makes the case to proponents of organic agriculture that genetic modification of crop species can be a beneficial and powerful tool for developing a more sustainable, lower input system of agriculture that can still feed the six and a half billion people alive on the earth today, and the billions more than will be born in the coming decades. The book is called Tomorrow’s Table: Organic Farming, Genetics, and the Future of Food, and it’s written by a husband and wife who personally straddle the divide between the two movements. She’s a professor working with rice at UC-Davis, and he manages and teaches organic farming.

The first part of the book is really an introduction to the ideas behind organic farming and genetic modification. I think I’ve got a pretty good background and I’ll admit I skimmed quickly over chapters like “the tools of genetic engineering.” The real substance of the book is in the second half where the authors address some of the frustratingly common arguments used by those who vehemently oppose genetically engineering crops (for example: safety, pollen drift, intellectual property) and go on to talk about the benefits GM crops can and do bring to the environment, consumers, and growers.

While the authors do a good job of making the point that GM crops really are compatible with the principles of the organic movement, I obviously already agreed with the value of GM crops. What won me over about this book was the way Pamela Ronald describes the delicate dance of a plant biologist drawn into a discussion of genetic engineering with friends or family who are firmly convinced of the danger or immortality of the technology.

If you’re interested in the subject, a good short read that summarized a lot of the points in Tomorrow’s Table is an op-ed piece Pamela Ronald wrote for the Boston Globe called The New Organic. (I read the article before Tomorrow’s Table came out, and went straight from reading the article to pre-ordering the book on amazon.) Pamela Ronald also has recent started her own blog.

In closing I’d like to quote another plant scientist blogger who I’ve discovered (while searching for the link to the Boston Globe article): “I want people to know that I’m here. I am a scientist, I am reasonable, and I am a good person. . .I believe that the two types of scientists and farmers (sustainable agriculture and genetic engineers) need to communicate and work together. . .The partnership can only happen if every scientist and every person on each side of the issue works to share and understand each other.” – Anastasia at

research stories

Of Genetics and Bears

One of John McCain’s signature issues is the wastefulness of government spending and one of the issues he’s getting a lot of play with is a government funded study of the genetics of bears in Montana. A description like “the genetics of bears” leaves a lot to the imagination so I looked up what the study actually entailed. They’re using wire traps to collect hair from grizzly and black bears in the wild and then using the samples to study the population structure. From the article I found in scientific American, it looks like they’re only looking at species (grizzly vs. black), gender, and number of individuals in the population. I can see why this is interesting from an ecological perspective, but I thought they were going to be doing deeper genetic analysis. 

Congress gave 4.8 million dollars to the bear genetics study, though McCain says 3 million in his speeches. With that much money, and the rapidly dropping cost of 454 and solexa technologies, a grant that size should have made it possible to shotgun sequence DNA from a number of individuals generating gigabases of data. Assembling the genome of the grizzly bear probably wouldn’t have been feasible within the 4.8 million dollar budget budget, but the data set generated could have been used for all sorts of studies. Looking at how much genetic diversity is present in different sub-populations. Looking for previous bottlenecks in grizzly bear populations. Identifying alleles of genes under positive selective pressure in the population. Testing if one set of alleles has been under selective pressure in the time frame since humans crossed the land bridge into the Americas, and a different set was under selective pressure previously. Alternatively, after mapping a number of single nucleotide polymorphisms (Spots in the genetic code occupied by different genetic bases (A, T, C and G) in different individuals, it should have been possible to develop a quick and (relatively) cheap test to identify different individuals. All the estimates I was able to find put the grizzly bear population in Montana at 1000 or less, meaning the cost per individual of this population count was over 5,000 dollars. My girlfriend informs me there are several ways to estimate a population cheaply and efficiently, such as recapture percentage.

My point here is that 4.8 million to study the population genetics and genomics of bears is completely justified, but there are probably cheaper ways to do a simple population census. Just to be clear, given that bears are an endangered species in Montana, there’s no question that a good population census was needed. McCain, however, sounds like he doesn’t think any study of bears is worthwhile. “I don’t know if it was a paternity issue or criminal, but it was a waste of money.” I guess funding genetic research into wildlife is wasteful by definition? Or maybe he means any genetic research except human genetics?

McCain seems opposed to basic research, and Hillary Clinton and Obama mention science as little as possible one way or the other. I’ve decided the reason I like Al Gore is that he actually comes across as smart and interested in research, but interestingly enough he only let that aspect of his personality emerge after he gave up on being president. What it comes down to is that the sort of person I wish was running this country is by definition unelectable.