Monthly Archives: February 2011
‘Twas but a month ago that Kate Clancy stirred up the world of science writers with her post-#scio11-post “Even when we want something, we need to hide it” (which itself was the product of #scio11 discussions weeks before). She certainly didn’t mean to, but it set off a polite firestorm focusing on treatment of women in science and online that is frankly impossible to chronicle. Sheril did a good job of linking to the relavant posts over at The Intersection.
Coincidentally, every watershed moment seems to be given a name, and “KateClancy-et-al-female-scicomm-gate” doesn’t have a good ring to it. Suggestions? Anyway, I found it especially interesting all the men who jumped to defend these women and comment on their plight. It was a true “throwing your cloak over the puddle” moment for the Twittersphere.
Sheril predicted that the enthusiasm would ebb at some point, and being the internet, that has certainly happened. The question that I pose to you is: Now that we are one month on, what have you done about it?
Let me be perfectly clear: I don’t mean to call people out, or act uppity, or make this an “I told you so” post. Read the rest of this entry
This week’s look at what the kids are watching over on Tumblr. Enjoy!
We celebrated Charles Darwin’s birthday with this fun little picture:
ZiaydMD explained how each of the 12 cranial nerves are stimulated when you walk into a Starbucks:
It turns out that Donald Duck invented methylene (and other amazing discoveries) back in 1944?
And some creative inventors have developed TREEPODS for the streets of Boston: Solar-powered, recycled-material, decorative trees that scrub carbon dioxide out of the air and release oxygen:
Finally, if you’ve ever wanted to look at MRI images of your favorite foods in animated cut-aways, well here ya go (thanks to @Katie_PhD):
Paul Revere is riding around science blogs today, and for good reason. The proposed House bill HR 1 is set to cut $1.6 billion from the NIH budget, which is equivalent to 5.2% under current funding levels. As featured by Dr. Isis, Genomic Repairman, PiT, GertyZ (and many others which I am surely overlooking), here is the call to arms from FASEB Prez William Talman:
For months the new House leadership has been promising to cut billions in federal funding in fiscal year (FY) 2011. Later this week the House will try to make the rhetoric a reality by voting on HR 1, a “continuing resolution” (CR) that would cut NIH funding by $1.6 billion (5.2%) BELOW the current level – reducing the budget for medical research to $29.4 billion!
We must rally everyone – researchers, trainees, lab personnel – in the scientific community to protest these draconian cuts. Please go to [this link] for instructions on how to call your Representative’s Washington, DC office today! Urge him/her to oppose the cuts to NIH and vote against HR 1. Once you’ve made the call, let us know how it went by sending a short email to the address provided in the call instructions and forward the alert link to your colleagues. We must explain to our Representatives how cuts to NIH will have a devastating impact on their constituents!
William T. Talman, MD
It has been a long time since anyone has accused Congresscritters of being prescient, rational beings – perhaps possessive of that thing you and I know as a “soul”. I mean, how do they find the time to care about the future of American innovation and competitiveness when they are so busy sending shirtless pics to Craigslist creepers?
Unfortunately, we are notoriously bad at really “getting” the scale of percentages and $ numbers in the billions. Maybe 5.2% doesn’t really sound like the end of the world? So let’s look at it a few other ways. That $1.6 billion cut from the NIH budget is roughly equal to the following:
- The same (in total expenditures) as cutting R&D for the entire CDC, Dept. of Interior and NOAA combined (1).
- The cost of almost three complete Kepler telescope projects (2)
- Half the cost of the entire public Human Genome Project (3)
- Eliminating almost 3,400 currently funded NIH research grants (4)
- And most importantly to people like me: Cutting financial support (tuition/stipends/insurance) for nearly 42,000 Ph.D. students supported by NIH funding. This is well more than half of all Ph.Ds awarded in all subjects in the US (5).
All of those numbers were rounded down to the conservative end of things, which is ironic since the “conservative” end of things on this issue seems to be closer to one’s ass than one’s brain.
So please answer the call to arms, click the links up there and make sure this misguided attempt at fiscal appeasement doesn’t gut an already wounded US R&D outlook. Because besides the NIH, HR1 can get MUCH worse.
First off, did you hear there’s a new New Pornographers video? Might I recommend pressing play and listening to it while reading this post? Because it’s a great track, and every good blog post deserves a soundtrack.
Last week I got a much-respected shout-out from Genomic Repairman, including me in “Who You Should Be Reading: Grad Student Edition”. First off, absolutely correct. You should be reading me!
Second, he pulled something from from my About Me page that I think maybe needs some ‘splaining:
“Joe is a science communicator, not a blogger? Whatever . . . “
I understand the paradoxical bind that this puts you in, because if you look around you’ll find that you are currently on a blog. Furthermore, this blog is written by me, and I just said that I am not a blogger. Is this guy fucking with us? No. Let me explain what I mean . . .
I have run across a lot of very talented Heroes of Science (my name for them, anyway) out there on the internet, and many of them are just amazing. Of course, the medium of choice for disseminating science “a la interwebz” is the blog. Hence so many people calling themselves “science bloggers”. I don’t like that.
To me, the word “blog” really implies the diary formats of Geocities or LiveJournal, actual “Web Logs”. What are you really setting out to accomplish? Just log some intelligent thoughts in reverse chronological order? For most of you, I am willing to bet that you want to communicate science, and writing it on the internet just happens to be your weapon of choice.
Look at it this way: A carpenter is much more than a “hammer swinger”, and a chef is certainly beyond “onion chopper and pan flipper”. If you are a science communicator on the internet, a blog is just a tool. The real mission of a chef is a meal, and your real mission is more than a blog post. I hope.
I am here to communicate science, and like me, you probably don’t stop doing that when you leave the keyboard. You talk to your friends, your family, you teach and you do the research. I think we are all more than “science bloggers”, unless literally all that you do in life is write WordPress posts, in which case you need more help than I can offer you.
It may be semantic, this “blogger or not” distinction. I think it’s more, though. When you put on the uniform, you join the science communicator team, and a blog is just a tool, as is a microphone, a camera, a computer, a search engine, Twitter, PubMed, coffee . . . get what I mean?
My outlook is this: Be more than the blog, and you’ll get more than a blog out of it.
We’ll get to Tumblr another time, and explain “how the fuck that system works”, ok?
On never forgetting where you came from, or whether epigenetic differences in iPSCs are really that bad
Note: The video here contains some foul language. It’s about drug-dealers. So gird your loins and all that before you continue!
At the end of season one of The Wire, Bunk and McNulty are interrogating D’Angelo Barksdale after his arrest for trafficking a big-ass bag of drugs through New Jersey. D’Angelo had grown up in the drug game. His uncle, Avon, ran the business, and D’Angelo was brought up as a cog in the dope machine. But despite his family connections, he grew tired of the violence and the death. He asked the detectives to help him reinvent himself and get out of the game.
“All my people . . . it’s just what we do.”
“I wanna start over, I don’t care where . . . I just want to go somewhere where I can breathe like regular folk.”
Unfortunately, D’Angelo didn’t get to start over. His past kept him from beginning anew, and his history caught up to him in the form of a belt around the neck. A new paper published this week in Nature proves that induced pluripotent stem cells (iPSCs) suffer from the same problem. They never quite let go of where they came from.
The history of iPSCs is written in molecular marks that annotate its DNA. These ‘epigenetic’ changes can alter the way a gene behaves even though its underlying DNA sequence is still the same. They are like Post-It notes – you can stick them to a book to point out parts to read or ignore, without editing the underlying text. Epigenetic marks separate different types of cells from one another, influencing which genes are switched on and which are switched off.
Ecker’s team looked for methyl marks across the entire genomes of five lines of iPSCs, each produced by different laboratories around the world. They also compared these to the methyl marks of adult cells and genuine embryonic stem cells. For each cell line, Lister and Pelizzola looked for methyl marks at 1.17 billion sites across the genome, around 250 times more detailed than the search that Kim did.
At first, the iPSCs seemed to have a spread of methyl marks that looked superficially similar to those of embryonic cells. But when Lister and Pelizzola looked more closely, the cracks started to appear in this tidy picture. The duo found plenty of hotspots around the iPSC genomes that were unusually ridden with methyl marks. None of these marks existed in true embryonic stem cells, and some sat in places that could switch off important genes.
Many of these errors were common to all iPSC lines, and some were unique to individual ones. Around half of them were remnants from the iPSCs past lives, but the other half were fresh mistakes, found neither in the adult cells nor the embryonic ones. In either case, the iPSCs could pass these marks to their own daughters. Any cell that’s born from reprogrammed ones will inherit the same legacy of errors.
Where my interpretation differs is whether to call these epigenetic differences “errors”. Whether something is an error depends on what is “right”. If perfectly replicating an embryonic stem (ES) cell is “right”, then I see why you’d say iPSCs are full of “errors”. Let’s take a closer look at the research and decide whether that name is fair.
In the spirit of LabSpaces “Post Your Screw-Up Day”:
Screw-ups are an integral part of the scientific process. Without them, we would not learn as much as we do (although, graduate students would certainly possess much healthier psychology if they could be minimized). If Alexander Fleming hadn’t erred in sterile technique, we wouldn’t have penicillin, and we’d still be slapping leeches on people and chopping limbs of faster than the hospital tent at Gettysburg.
Speaking of penicillin, that reminds me of a legendary screw-up in our lab from a couple of years ago. It was both potentially lethal and potentially preventable, qualifying both major “Epic Screw-Up Criteria“. It didn’t happen to me (my screw-ups are rarely as entertaining), and I have anonymized it to protect the innocent.
For those of you not well versed in modern molecular biology and biochemistry, many experiments involve taking one or more proteins and putting them in tiny tubes and allowing them to do whatever it is that they do, just in a controlled in vitro environment. Well, these proteins have to be made somehow, and we usually employ yeast or E. coli bacteria to do the job for us. You just shoot a little piece of DNA into them, grow them in certain food under certain conditions, and they manufacture gobs of protein for you to isolate by pulling it out of the mix.
In our lab we do this isolation using an apparatus called a Fast-Performance Liquid Chromatography (FPLC) machine. Essentially, you shoot liquid containing ALL E. COLI PROTEINS + YOUR PROTEIN in one end, various binding columns and filters are applied to the sample, and you get YOUR PROTEIN out the other end. Simple right?
Before you can load the sample onto the FPLC machine, you have to take a big bunch of smelly E. coli culture and break open all the bugs into a suspension. If you’re curious what this smells like, go hang out in a truck stop bathroom. Here’s the thing about E. coli to remember: they live in your bowels, and they are not friendly to other environments. Remember the saga of tainted spinach and lettuce? Unless you want to be affixed to a toilet for 2-3 days, keep E. coli confined to one end of your body.
A post-doc in our lab was doing the usual protein isolation thing, had prepared their E. coli lysate suspension and was getting ready to load it on the FPLC. They were probably having a pretty good day, because they are a very nice person and usually have good days (obvious foreshadowing). The genius who invented the FPLC system decided that it would be a good practice to load it using a syringe, so that’s what we do. Whether or not it’s the best way to do this, in our lab we suck up the E. coli juice using a needle, remove the pointy end and shoot it into the machine port. Of course you never re-cap a needle, right?
Except this time, the post-doc re-capped the needle. Or, more accurately, did NOT re-cap the needle, but instead impaled their hand, injecting 0.5-1 mL of straight, unfiltered E. coli stew straight into their hand. You can imagine what happened next, after the freak-out ceased, and appropriate medical attention was sought:
- Hand swells up to the size of a baseball after a day or so. Smells something like rancid almonds.
- Antibiotics are administered in high doses (thank you Fleming). E. coli happen to thrive at exactly 98.6 F, so this was a challenging battle.
- Antibiotics not working. “Blood poisoning” is a term that was thrown around as a possibility.
- Doctors sliced open the hand, leaving the wound open for about a week in order to, I don’t know, dry out the bugs or pus or something. It was gross. It looked something like this:
Eventually, the infection was controlled, the hand and post-doc were saved, and life continues as we know it today. The protein was later isolated, free of incident, and to this day we take what we have learned and use it to avoid accidents like this in the future.
Oh, who am I kidding?! I see people re-cap needles every freaking day around here! We’re gonna have to do in a scientist before they learn.