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 | December 5, 2010In the wake of the NASA excitement over the new arsenic study, and my promise to give a detailed review of the paper itself, I have recruited a colleague with strong opinons about the work, a solid chemistry and microbiology background, and "Dr." in front of his name to share his analysis. I will be posting have posted my personal and less-technical take on the whole thing soon, so stay tuned as well.
Dr. Alex Bradley uses modern geochemistry and microbiology tools to study the evolution of life and Earth. He has the following to say about the paper.
There's been a lot of hype around the…
heathero | December 2, 2010Arsenic it is... but the point really isn't arsenic.
That is what Dr. Felisa Wolfe-Simon stressed at the end of the NASA press conference today - that the research being unveiled is just opening the door to other unexamined possibilities for life. She said "I am interested in exceptions, why aren't things constants in nature?"
Her team's new finding is that certain microbes are capable of creating DNA with arsenic rather than phosphorus as the molecular backbone. These are microbes closely related to well known microbes, but their ability to make this substitution is remarkable, and…
kbonham | December 2, 2010(No pun intended)
This just sucks:
As cholera rampages through Haiti, some epidemiologists are warning that the country could face more than half a million cases over the coming year. Yet tracking and treating the disease is proving increasingly difficult as civil unrest grips the county.
As if Haiti hasn't already suffered enough. Vibrio cholerae, the bacterium that causes the disease is transmitted in contaminated water, and can divide rapidly in the digestive tract. The bacterium causes disease by secreting cholera toxin, a group of proteins that hitches a ride into the cell, sneaks…
heathero | December 1, 2010NASA has made a bit of a stir by announcing a press conference for tomorrow at 2pm EST. Scientists are going to reveal some exciting new findings relvent to the search for extraterrestrial life. Some people are anticipating/hoping that they will announce that extraterrestrial life has been confirmed. No one would be more excited than I (I love being able to make silly statements like this) were that the case, but I would bet a lot of money that it is, sadly, not. Don't get me wrong, I am super-excited about this announcement because most likely it is going to deal with extremeophile…
kbonham | November 30, 2010Cancer sucks. I'm sure I don't have to tell you that - it's one of the leading causes of death in developed countries, and our treatment options are pretty thin. Basically, it amounts to cutting out the tumors that can be seen, and then giving a controlled administration of poison in the hopes that the cancer cells die before you do. Don't get me wrong - advances in oncology have saved many lives, but it's no surprise that there's a lot of research happening to find better options.
One promising avenue of study is augmenting the immune system to fight cancer directly. It's known that the…
kbonham | November 29, 2010Did you know that bacteria make up 90% of the cells in your body? That they make up ~5% of your mass? That they colonize you at the moment of birth and are different if you were born via c-section than if you were born naturally?
All this and more in the SITN production, "Our Microbial Organ: The good and bad bugs of the gut." And who's that handsom devil presenting (at least the first part)? Why, it's me!
Part 1: Living in a microbial world
2010 Fall Lecture 7.1: Our Microbial Organ: The Good and Bad Bugs of the Human Gut from Science in the News on Vimeo.
Part 2: Our Microbial Organ
Part 3…
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 28, 2010If you've ever rolled your ankle (as I have many times), you have a visceral knowledge of inflammation. Clinically, inflammation is the redness, swelling, heat and pain that's associated with injury. From an immunologist's perspective, it's the set of molecular events that get the immune system going. All of the clinical systems associated with inflammation are due to increased vascular permeability, which is just a fancy way of saying leaky blood vessels. Actually, "leaky" implies that it's uncontrolled, when in fact there's a very orchestrated set of events that recruit immune cells and…
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 20, 2010This week, I'm going to take a break from vaccines and do some innate immunity. Today's topic: the provocatively named "Inflammasome." This Nature Review from last month focused on inflammasomes and anti-viral immunity, but I think the inflammasome itself needs its own post.
A breakthrough in our understanding of the mechanisms that control the activation of inflammatory caspases came from the identification and characterization of the inflammasome, a large (~700 kDa) multiprotein complex that recruits inflammatory caspases and triggers their activation. Inflammasomes are often defined by…
kbonham | November 17, 2010This is just awesome:
A strain of Escherichia coli bacteria can now solve [sudoku] puzzles
[...]
"Because sudoku has simple rules, we felt that maybe bacteria could solve it for us, as long as we designed a circuit for them to follow," says team leader Ryo Taniuchi.
The mechanism is ingenious and yet straightforward at the same time.
Basically, they have 16 different strains of bacteria, with each initial strain representing a spatial coordinate on a 4x4 grid. Each bacterium has a "4C3 leak" system, which is a chunk of DNA that the team designed that has 4 possible outputs. Depending on…
kbonham | November 16, 2010The last lecture of the Science in the News Fall lecture series is tonight at 7pm in the Armenise amphitheater.
Star Power: New Ways to Harvest Energy From Our Sun
I heard great reviews from people who were at the practice talk, so if you're in the Boston area and interested in alternative energy, come on by. If you're not in the area, don't fret, we'll be posting them online (eventually) too.
Check out the lecture on the Light Amplified by Stimulated Emission of Radiation from week two:
2010 Fall Lecture 5.1 - The Laser Turns 50 from Science in the News on Vimeo.
Part 2: Using Lasers to…
kbonham | November 13, 2010Last week, I talked about strategies to improve vaccine efficacy and safety. Most of those strategies were in the context of standard, inject-into-your-arm vaccines, but what about totally new delivery methods? This week, there was a review in PLoS Pathogens of strategies for generating vaccines that you can swallow:
Enhancing Oral Vaccine Potency by Targeting Intestinal M Cells
The immune system in the gastrointestinal tract plays a crucial role in the control of infection, as it constitutes the first line of defense against mucosal pathogens. The attractive features of oral immunization…
kbonham | November 12, 2010Macrophages are really good at gobbling stuff up. It's all right there in the name - they are big (macro) eaters (phage). I study them in the context of the immune system - one of the things they do really well is eat up bacteria and other pathogens that have found their way into your tissues. As a front line sentinel, they also are capable of kick-starting inflammation and recruiting the rest of the cells necessary to clear an infection. But that's not all, there's more.
Weight loss and lipolysis promote a dynamic immune response in murine adipose tissue
Here we characterized the response of…
kbonham | November 11, 2010Ever wonder what exactly a Toxic Asset is? Follow the engaging story of Toxie the toxic asset on This American Life.
This is just the latest in a series of amazing reporting on the financial crisis from a radio show that is not generally concerned with what would be traditionally thought of as "news." "The Giant Pool of Money," which started this series, is still the best break-down of what caused the financial crisis that I've seen. And a follow-up piece a year later gave even more perspective.
If you read or hear news about the financial crisis but just don't quite get what it all means…