Radio Free Meredith

For free, even. And with a lot of help from physicists all over the world.

Relatedly, I want to start a collection of Famous Dutch-Speaking Scientists With Distinctive Moustaches:



I'm not sure whether to include Edsger Dijkstra or Guido van Rossum, whose beards seem more distinctive to me

My friend feonixrift, who is allergic to latex, recently had an unexpected reaction to a roll of athletic tape that was sold as "latex-free". Whilst commiserating with her, I remarked that there really ought to be a straightforward way to determine whether latex was present in a product or not. Reading about the composition of latex, I noted that allergic responses to latex typically have to do with an antigenic protein in the stuff, and she observed that synthetic elastics shouldn't contain protein. I immediately considered and discarded the idea of an ELISA or a Western blot, since both of those tests are not the kind of thing you can do with common household items. However, a little more research turned up the biuret test, which confusingly uses no actual biuret, but does work as an indicator of the presence of protein and is even kind of quantitative.

The biuret test involves small amounts of copper (II) sulfate and potassium or sodium hydroxide, all reagents which I happened to have in my cellar lab. (I get them at the hardware store; USAians can probably find NaOH as drain cleaner and CuSO₄ as pool algaecide [h/t palecur].) As I had never done a biuret test before and did not know what to expect, I decided to find out what to expect by performing a biuret test on something which I knew had protein in an aqueous solution -- in this case, whole milk.

chocolatecoffee took pictures. ( Here is how you do it. )

It also occurs to me that there are lots of aqueous solutions out there for which protein or an excess thereof is a Bad Thing, e.g., urine. While I do not particularly want to induce proteinuria in myself, I am inclined to find out what my baseline urinary protein levels are like (which will involve working out a way to measure light absorption at 540 nm, i.e., building that spectrometer I've been meaning to build).

More news once I've tested actual latex and some latex-bearing and latex-free athletic tapes. But for now, you can test things for the presence of peptides too!

An enterprising open-source hacker who goes by the moniker Famulus, using polywell plasma confinement, has achieved desktop-scale nuclear fusion.

There are some really lovely photos of plasmas and lab equipment on the blog, and all the STL files for the polywell itself, plus Ruby source code for running the thing, are available on github. Go to.

ETA: That's fusion full stop, not "a sustained fusion reaction producing more energy than is consumed by plasma containment". I'd wager my left temporal lobe that he's running at a net energy loss. However, polywell confinement is one of the more promising technologies out there for net-gain fusion; interested parties should check out the work that EMC2 Fusion is doing.

...wait, I could do 3D "circuit board" design if I could somehow produce the unholy fusion of gEDA and Blender.

If Blender lets you freehand draw on the texture of a surface, that could actually work. omgwtfbbq.

...and then you somehow convert the Blender data file into a knitting pattern, which would in and of itself be a neat little hack, since you could 3D model a garment and then convert it into a pattern ... oh cloning why are you not here yet

I forgot to take my antidepressants today. Maybe I'm actually back to the point where I don't need them anymore. That would be nice.

ETA: apt-get install blender but I am not allowed to play with it till I get more work done, it is a reward

A recent but rapidly growing blog that deserves recognition is Eric Fernandez's DIY Bio 4 Beginners. Eric's been busily trawling the Internets for articles, videos, animations and other great resources for the amateur-biology community. Sometimes it's one link a day, sometimes it's ten -- but the information is great and his enthusiasm is (ahem) infectious. Check it out!

In other news, today I'm off to FOSDEM, especially for David Fetter's talk on OLAP and Common Table Expressions in PostgreSQL. Ever wanted to write a recursive expression in SQL? Now you can, and there are some damn fine reasons to. Representing trees in a database in any useful fashion used to be difficult. Now it's not. This takes data representation to a whole new level.

3. Gel electrophoresis uses ethidium bromide, which is a dangerous chemical. How are you disposing of it safely?

I'm not using ethidium bromide. There are a number of other gel stains which are much safer and easier to work with, such as SYBR-Green and SYBR-Safe. I use GR Safe, which is similar to SYBR stains but even better, because it can be stored at room temperature.

Per standard biosafety practices, I sterilize everything before I dispose of it.

4. Why is there toilet paper sitting on your lab table?

It's absorbent and good for wiping up spills, and it wastes less paper than using full paper towels to wipe up the occasional spill of less than 2mL of liquid. (The paper towels weren't in the frame. Nor was the sharps bin, or the fire extinguisher, or any other safety equipment. It's all within reach, though.)

5. Why are there Ziploc bags sitting on your lab table?

The bacteria I work with -- Lactobacillus acidophilus, Lactobacillus bulgaricus and Streptococcus thermophilus -- are what's called "facultative anaerobes": they prefer environments where there isn't much oxygen. (They'll grow when there's O₂ around, but they won't grow as quickly.) So, when I plate them on a petri dish, I put the finished plate in a Ziploc bag. Then I put some vinegar and baking soda into an empty Coke bottle and capture the generated CO₂ gas in a balloon, squirt the gas into the Ziploc bag, and close it up.

I asked a former boss of mine (a bioinformaticist whose PhD is in population genetics) whether he had any ideas for easy ways to provide an oxygen-free environment for my plates, and he said they used the same Ziploc bag trick when he was in grad school. It's ghetto, but hey, it works.

Once upon a time, there were a boy and a girl. The boy ran a tech conference, and the girl worked for a company that made DNA. She submitted a talk about DNA design software to the conference, and it got in, and she was very, very excited.

While preparing to give her talk, the girl mentioned to the boy that if she only had a salad spinner, she could kick off her talk with a cute demo. "I will find you a salad spinner," said the boy, and he did (thanks to kragen), and the demo was very cute indeed.

After the conference, the boy and the girl got to talking about other amusing things that people could do with DNA, and somewhere in there, someone had the idea that it would be really funny to take Lactobacillus acidophilus, otherwise known as yogurt bacteria, give it the gene to produce green fluorescent protein, and make yogurt with it. Or "glowgurt", if you prefer.

They were, however, rather busy with a number of other projects, both together and separately, and along the line they fell for each other like a ton of bricks and got married.

This is where the story actually starts.

( Scurvy: it's not just for pirates anymore )

( My not-so-clandestine project: the melaminometer. Say that five times fast! )

Do you or someone you know have an ultrasonic jewelry cleaning bath? If you're not using it, can I borrow it for a week or two? If you never use it, can I have it?

It's for Science! Really. I promise. If you are only loaning it to me, I promise not to take it apart or break it, and it will be returned to you in exactly the condition you gave it to me in (or better). I will be putting water and little plastic bottles in it. (There will be Science! inside the little plastic bottles, but they are watertight.)

Yes, I know they cost about $40, but I am a total brokeass. I wouldn't bitch if someone just gave me $40 to buy one with, though.

ETA: Got paid. Bought one. More news, uh, a few days after it shows up.

I have so damn much stuff I have to get done in the next 24 hours but so help me I cannot unglue my eyes from this:



I can see why Dawkins might be a little brassed off about the video's presentation -- it's a balls-out parody of Eminem, and while Eminem does the call-to-arms thing quite well (cf. "Mosh"), his calls to arms invariably involve an element of "shut up and listen to what I say" which I find a bit disturbing. This could well be taken as a slam on Dawkins et al as well; I've heard rumours that the video is actually a viral marketing effort for Ben Stein's upcoming movie "Expelled", which promotes "intelligent design". (spider88 remarked, earlier this evening, "If so, it's backfired.") I won't be surprised if the rumours turn out to be true; equating Dawkins and Eminem as "rebel authoritarians" (i.e., "Here are my revolutionary new ideas intended to destroy the establishment, now take them as gospel and do not question, what do you mean that creates a new establishment?") is probably really funny to folks who think that modern biologists are just mindlessly parroting Darwin.

I do not think that most scientists expect people to listen to them because they are scientists. I think most scientists do expect (perhaps naively) that people will listen to their arguments, recognise that the scientist has undertaken rigorous analytical steps in order to produce those arguments, and evaluate said arguments critically and independently. I also think that most people who aren't scientists are used to people arguing from authority, and interpret scientists' matter-of-factness and lack of weasel-words as authoritarianism. They couldn't be further from the truth, but few take the time to familiarise themselves with the register in question; it's like taking offense to a phrasing which means something derogatory in your dialect but which is totally unmarked in the speaker's.

(Side-note: you will notice that I use the phrase "I think" or equivalent a lot in the remarks above. If you haven't noticed that I try rather hard to make a clear distinction in my writing between points on which I am certain and points on which I am speculating, you either haven't been reading me very long or haven't been reading me very critically, perhaps both. :P )

But anyway, where I was going with this is that I (and my LJ biologist friends thus far, apparently) cannot stop laughing when we watch this thing. Eugenie Scott in a bikini! Blunt-smoking Christopher Hitchens! Daniel Dennett in a pimp hat, waving a cane! Popping and locking Charles Darwin! And on top of all that it's just a dis track that puts Monzy to shame, capturing Eminem's lyrical stylings better than any other nerdcore rap I've seen. We computer scientists have enjoyed the fruits of nerdcore for most of its existence; the biologists have gotten the short end of the stick, even if you count MC Hawking's nods to bio.

(Side-note #2: I wonder if we have so much CS nerdcore because hackers are cocky little fuckers who like to show off and argue -- cf. all the religious wars about programming languages, for instance. [Have we seen a rap battle between proponents of static vs. dynamic or duck typing yet? There should be one. It would be funnier than mailing list arguments.] I've never seen chemists getting into throwdowns about how best to work up a reaction, but then maybe I don't hang out with enough chemists. Anyway, maybe this will kick off a new avenue of creativity in the evolution wars. The voyeur in me can only hope!)

Also, I think PZ Myers and my former boss, Andy Peek, may be long-lost twins. (I dunno. Is PZ Myers 6'3" and built like a linebacker? Some day I want a photo of them together. Evo-devo biologist and population geneticist, separated at birth?)