Science Process
kbonham | April 13, 2011Yesterday was my birthday, and I tend to use this time in April to re-up my commitment to all of those resolutions that I failed at around Jan 5th.
And add a new one: Data is the name of the game.
- Millions of cells in the incubator? Check!
- Freshly-made solutions and buffers? Check!
- 10-15 Western blots/week? Check!
- Will to live? Fading... but still there!
There's nothing worse than this phase in a scientific process. I know the answer to my question and now I just need to generate a few figures that are presentable for publication.
For instance:
That's a loading control for an assay…
kbonham | March 14, 2011Tomorrow, as part of the @ASBMB "Hill Day," I'm headed to capitol hill to meet with my congressman and my senators (or more likely their staff) in order to plead for science funding. If you pay any attention to politics, you know that congress has been locked in budget battles for months, and since government grants account for the vast majority of basic science research have a pretty large stake in this fight.
One Republican proposal out of the house (that was defeated in the senate) cut over $1 billion of NIH spending. I doubt this is out of malice, but when trying to reduce spending when…
kbonham | March 11, 2011For those of you don't already have some affliction (facebook, reddit etc) that sucks up all the time you should really be working, try:
The Power of Research!
I didn't get very far, but only because I have real lab work to do. It seems silly to procrastinate by doing a virtual research project. It seems like a cool idea though - anything to get the general publish* public to sympathize with researchers is a plus in my book.
Let me know how it goes (also... if you choose immunology as a specialty, one of the options is a TLR research project, I must approve).
*Freudian Slip?
heathero | February 18, 2011I got to spend last week in sunny California. I forgot how wonderful it is to sit and eat lunch outside! I was participating in a workshop held at the Department of Energy's Joint Genome Institute (JGI). The workshop was entitled Microbial Genomics and Metagenomics. Basically I spent the week learning about different tools that are available to help biologists deal with the data flood that has come out (and continues to flow faster and faster) of sequencing technologies that continue to get faster and cheaper.
Since microbes are not exactly easy to observe with ones eyes,…
kbonham | February 11, 2011At the superbowl party at my house last weekend, most folks didn't really have a stake in who won. But several friends were rooting for Pittsburg to loose, largely due to their quarterback, Ben Roethlisberger. In case you don't pay attention to sports news (like me), Roethlisberger was twice accused of rape/sexual assault in the last two years. When folks were talking about it, I foolishly said something along the lines of, "well, what were the cirumstances of the rape?"
The Daily Show - Rape Victim Abortion FundingTags: Daily Show Full Episodes,Political Humor & Satire Blog,The Daily…
kbonham | February 10, 2011My common New Year's resolutions (get more exercise, keep my lab notebook up to date, etc) rarely make it off the starting block. In this I am hardly unique, and there are very good reasons why, so I usually also try to make one major, sort of intangible resolution. This year for instance (largely because of reading this book), I decided to try to be wrong more often. More precisely, I'm trying to want to change my mind.
It's hard to know how well this is going (with all of the things I'm not changing my mind about, it's obviously because I'm right), but alas, all my other resolutions have…
kbonham | January 23, 2011Mark Henderson of The Times is embarking on (what I think is) a great project - highlighting the contribution that the science savvy can have and are having on public discourse.
The intersection of science and politics is a growing interest of mine, though I don't have nearly as much credibility as many others around the blogosphere (but give me a break - I'm still in grad school). Go help him out, he wants to know
* What are the best examples of geek activism, what have they achieved and what can we learn from them?
* What else can geeks do to hold politicians and civil servants to…
kbonham | January 20, 2011The heavy hitters in the science publishing business are taking notice.
This critical onslaught was striking -- but not exceptional. Papers are increasingly being taken apart in blogs, on Twitter and on other social media within hours rather than years, and in public, rather than at small conferences or in private conversation.
Like everything else in the modern world, old orthodoxies are going to have to change. I would love to accelerate this process, but it's going to be an uphill battle.
This article in Nature discusses a GWAS (genome-wide association study) that supposedly linked a…
kbonham | January 2, 2011Like so many things, the problem is best explained with an analogy. Imagine a car parked in a dark garage (if you're a mechanic by hobby or trade, make it a computer). Someone hands you keys to the car, a flashlight and a piece of metal that she says belongs to a car similar to the one in the garage. Now, your task is to figure out what that the piece of metal is, and what it's for. Replace car with organism, piece of metal with gene and make the flashlight a whole lot smaller, and you have an idea of what biological research is like. For decades, those wanting to study human genes were like…
kbonham | December 15, 2010If you've had your head in the sand for the last 2 weeks, you might have missed the story about arsenic in bacteria and the resulting controversy. If you did go read Ed Yong first.
In an editorial published today in Nature, the editors make a similar point to the one I made yesterday, namely that it's hypocritical for the authors of this paper to parade their research in front of the media to great fanfare, and then refuse to respond to legitimate criticism in the media.
In response to the arsenic bacterium claims, bloggers and researchers raised serious and thoughtful reservations about the…
kbonham | December 13, 2010In last week's editorial in Science, Bruce Alberts starts with a point that I think few here would disagree with: decisions in government need to be data-driven, and based on the best science available. This point has been made before, and it's certainly crucial, but the more crucial point is why the government currently doesn't pay much attention to science, and why there is wide-spread misunderstanding of what science means.
Most Americans have never met a scientist, and despite having been "taught science" at school, most have no real idea of how a scientific consensus is reached through…
kbonham | December 12, 2010Sometimes, when I take a step back and look at the ways that we can manipulate life, I'm astounded. We can breed mice that lack any gene we want. We can also insert new genes, and have them only express in certain types of cells or only at certain times. This is routine. We can make design viruses to insert genes into human cells to cure, cure debilitating diseases.
We have bacteria that play sudoku, and we have mice born with two fathers. We can make corn express toxins from Bacillus that only kill pests, and tobacco and cats that glow green (through two different mechanisms even).
Our…
kbonham | December 11, 2010The "Science and the Public" story of the year might just be Arsenic using bacteria. Certainly, Alex's critique has been the most popular post on this blog since we started and has received quite a bit of attention from other bloggers as well as in conventional media.
This might be a teachable moment in science communication, but even though it's clear that this wasn't handled particularly well, it's hard to see how things can be done better in the future. Heather's follow-up post is a great summary of how science works in the real world, but I think it also illustrates a fundamental…
kbonham | December 8, 2010Sorry for the radio silence on my part lately. My house got broken into... again... and I'm dealing with the fallout.
I'm thinking about a post on knowledge, where it comes from, what it's good for and if it matters. But before I write it, I'd like to get your input.
What do you think "knowledge" is? Is it different than Truth?
Do you agree with the idea, "Ignorance is Bliss"? Is it ever? What about, "Where ignorance is bliss, 'tis folly to be wise?"
What does it mean to be wrong?
heathero | December 5, 2010If you read Alex Bradley's guest post calling into question the claims of the recent Science paper stating the existence of microbes that can substitute arsenic for phosphorus in their DNA you might be wondering what to take away from it all, if the scientists can't even agree on whether the study is valid or not. I would like to take this opportunity to reflect on the scientific process and hopefully explain why this type of intellectual discourse demonstrates the strength of the scientific process rather than being an example of scientists not knowing what they are talking about.
Here's the…
heathero | November 29, 2010Bioluminescince is amazing. I have seen it first hand barely noticeably in the wake of a ship at night, from a laboratory culture in a large flask, filling a Puerto Rican bay such that every fish darting or rain drop falling glows blue, and most recently in a 2 hour light show viewed through the window of the Alvin submersible on my descent into the Pacific ocean. I can tell you that it is always a crowd pleaser. The fact that microbes have generated biochemical pathways to produce light is amazing and awe inspiring. It may also, have some practical use for people, eventually.
Picture…
kbonham | November 22, 2010Most of my favorite long-standing discussions with friends and family tend to resolve around definitions. My good friend Paul and I have had hours upon hours of discussion about the nature of the universe - he calls his perception of the order of the universe "god," and I call myself an atheist (interestingly, that picture was taken by Paul), though in practical terms I don't think our beliefs are really that far apart. He says his definition allows him to engage with religious people, I say it just causes confusion.
In my first year of graduate school, I used to argue endlessly with my class…
kbonham | November 10, 2010When a paper in Molecular Cell starts with
Science, this very creative human endeavor to understand the nature of the reality that exists independently of ourselves, is impossible. By "impossible," I am not saying "very, very difficult," although it is that, as well.
you just know you're in for a treat.
He lists 6 things to remember when stressed, but I identified most with the first:
Thing #1. You Are Not in Control of the Answers
I contend that this is one of the greatest sources of stress in our professional lives. As scientists, we don't ask for much: we want to have some good ideas (see…
kbonham | September 14, 2010[This post was originally published at webeasties.wordpress.com]
Back in July I wrote about an editorial published in Nature about the future of science communication and what place blogs had in that future. Though I agreed with them that blogs are a great resource, I also thought that they were being a bit disingenuous about their desire to relate with the public considering that almost all of their material is locked behind a paywall, so the public doesn't have access. I even wrote a comment to that effect on their website:
It's all well and good to talk about public accessibility of…
kbonham | June 30, 2010[This post was originally published at webeasties.wordpress.com]
Considering the forum, you can probably guess my answer, but it seems the editors at Nature agree... sort of:
Institutions need to recognize and to encourage such outreach explicitly -- not just as a matter of routine, but specifically highlighting and promoting it at times of relevant public debate or when the interests and voices of scientists need to be promoted. Web 2.0 doesn't yet have what it takes to add significant value to open academic discourse, but it can surely make a difference to the public accessibility of…