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My pals Tito Jankowski and Josh Perfetto have been working for the last, oh, nine months or so on designs for an Open Hardware thermocycler -- basically a Xerox machine for DNA. They've finished their first working prototype, and have set up a Kickstarter project to fund the process of turning this into a full working device that you'll be able to buy for less than $400, or build all by yourself with parts you can easily obtain online. If they can get to $6000, this will happen.

I'm particularly interested in this because its software will be the second real-world demonstration of some of my theoretical work. Some of you might remember Dejector, the "kills SQL injection dead" library I built back in 2005 (and have been really slack about keeping current, though it really needs a serious rearchitecturing). Dejector uses a technique I call "restricted sublanguages" to make sure that SQL queries which don't fit into a very limited (programmer-specified) subset of all possible queries -- that is to say, queries which have had a malicious clause injected into them -- are rejected before they get near the database. The OpenPCR machine is a networked device; you'll be able to plug it into your router and configure a PCR run via a webpage, rather than having to key instructions in on a tiny little keypad. It'll also log data for you (which you can also view in a browser) and, if you want, report results to you over Twitter or SMS.

All this fancy web stuff will be made possible -- and secure! -- through a restricted sublanguage of HTTP which I will be implementing for the AVR series of microcontrollers. (We're actually starting with an Arduino, but we might move to pure AVR by the time we're done.) Your contribution will help go toward making that happen, along with tools for generating custom restricted HTTP sublanguages for other embedded devices. (Networked lab tools are cool; networked lab tools that get hacked to pump out Twitter-spam, not so much.)

If you can spare a few bucks, please kick something in, and please signal boost anywhere you can think of. Thanks!
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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:

Gerard 't Hooft, Nobel prizewinning physicist Bart Preneel, rockstar cryptographer

I'm not sure whether to include Edsger Dijkstra or Guido van Rossum, whose beards seem more distinctive to me
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[ profile] enochsmiles: Crap, the root on this cactus got damaged when you removed the pup. It's going to rot if we don't protect it until it calluses. Do we have any antifungals?

[personal profile] maradydd: No, but let me see what I can do with what we have in the lab.

Google: Why don't you try Bordeaux mixture?

Wikipedia: It dates to 1885, and it's approved for use in organic gardening! You'll need 1g copper sulfate, 1g hydrated lime, and 100mL water.

[personal profile] maradydd: Oh! We have calcium oxide that the Mississippi Lime Company sent us, so I can make calcium hydroxide, and we have copper sulfate from the hardware store.

([personal profile] maradydd disappears into the lab and returns with a 100mL flask of milky blue liquid, which [ profile] enochsmiles pours onto the soil around the cactus.)

Cross your fingers; I hope the cactus makes it. He's older than the cat. We repotted him in a deeper pot (the cat knocked the old pot off the credenza), applied a thin coating of lime to the wound to help it dry out and scab over, and gave him some Bordeaux mixture, so I hope he has a speedy recovery.
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My friend [ profile] 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 [ profile] 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.

[ profile] 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!
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Dear LJ Genie,

I need to have two boxes, one 19 pounds and the other 23 pounds, shipped from Portland to Belgium. Each box is 24" x 24" x 24". Apparently the sizes of the boxes put them into some horrible no-man's-land whereby costs are computed by "volume weight" rather than actual weight -- apparently I could ship 83 pounds worth of stuff for the same price. For the prices that I am being quoted, I could buy one of you Portlanders a ticket to Belgium and have the Portlander in question bring the boxes in lieu of checked luggage. While this idea amuses me enormously, I do not currently have a spare $700 to do this with -- or to ship boxes, natuerlich.

The boxes can arrive pretty much anytime prior to the heat death of the universe (well, okay, sometime this year would be nice), and they'll be full of (well-packed) glass and thus can't be banged around too horribly, but other than that, my main concern is getting them here on the cheap.

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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.
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Whatever that stuff was that had carbonised onto my stove burners, it was no match for concentrated sodium hydroxide and a putty knife.
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...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
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Viewed from human scale to city-block-scale, city streets look well-aligned, on a grid, planned out in meticulous detail. (And they are; city planners and surveyors get paid good money to ensure this.)

Viewed from slightly higher up, they look like slime molds:

A fascinating chapter from a book about our friends the Dictyostelia

Now, what I'd like to know is, what are the self-assembly rules for Dictyostelia? What kind of space do they like to have between them and their neighbors?

Well, thanks to the magic of green fluorescent protein, here's how they come together:

Also, their cell signaling has been caught and immortalized on film:

Thanks, internet!
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Short notice, I know, but this morning at 9am PST/noon EST, Mackenzie Cowell (founder of and I will be on a talk radio program, The Food Chain, discussing the emergent biohacking movement and its possible effects on food. You can listen in on a number of AM radio stations, or over the Internet, and the audio will be available as a podcast later.

Come join in the discussion!

ETA: Well, that went reasonably well -- I was a little startled at first to find out that the station was a FOX News affiliate, but no one called for our heads on platters or anything. I'll post a link to the podcast when it's up, and y'all can listen to Mac sound extremely intelligent and level-headed, Sandra Porter being cautiously enthusiastic, and me waxing far too rhapsodic about molecular computing and epigenetics. ;) Some day I'll remember not to get carried away...
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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.
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Gel electrophoresis is one of the most versatile, widely used tools in a microbiologist's or geneticist's toolbox. It's used for separating out DNA, RNA or protein molecules (that you presumably isolated in a previous step of your experiment) based on their molecular weight, so that you can analyze the molecules, clone them, amplify them with PCR, sequence them, lots of different things.

Electrophoresis does require some equipment to perform -- an inner tray which holds the gel, an outer tray which holds a "running buffer" solution (which keeps things cool and keeps pH stable), electrodes, and a power supply (50V-150V is pretty common). You can buy a gel box from a commercial supplier, though they're not cheap, and a fancy power supply will set you back even more; Bio-Rad has some nice ones, but they run to the thousands of dollars.

Happily, there are solutions for the biohacker on a budget. The University of Utah's genetics department has full specs for how to build your own gel box for about $25 in parts (not counting the power supply, which will run you about $50). The main components are clear acrylic and acrylic cement, which I purchased and had cut to size at TAP Plastics -- they also do mail order. My partner-in-science Tito Jankowski built one too, and did some test runs with food colouring which enabled him to separate the individual dyes which make up different colours. (The molecules in food colouring are pretty small, which is why the bands in Tito's video are a little smeary. He used agarose -- an edible, seaweed-derived polymer which you can find on the shelf in any Asian grocery store, also sold as "vegan gelatin" -- as his gel, and agarose is better suited to larger molecules like DNA. But it's definitely a proof of concept!)

Still, electrophoresis using large rectangular gels has some drawbacks. It's a bit messy, and in order to recover the particular band of DNA you want, you have to slice it out of the gel with a razor blade or something similar. Cleaning up the equipment is also a bit of a pain. If you're using acrylamide or polyacrylamide (common for protein electrophoresis), you need to find a safe way to get the used gel out of the gel carrier and dispose of it properly. Also, while DNA electrophoresis is run horizontally, protein electrophoresis is done vertically, so that means two different pieces of equipment.

This was a recent topic of discussion on the DIYbio mailing list. Ben Lipkowitz wondered whether it would be possible to use a narrow, rigid tube to contain the gel, rather than a big carrier. This would allow for the use of less buffer and lower voltage, since a physically smaller amount of gel is a smaller resistor.

Well, what's a narrow rigid tube that's easy for anyone to acquire? A clear drinking straw! Paper clips make for appropriately sized electrodes, and since a drinking straw is rigid, it can be used in either the horizontal or the vertical orientation. For extra bonus points, when you're ready to cut a band out of the gel, no need for mucking around with razor blades -- just take a (sterile) pair of scissors, snip snip, and you're done! Plus, disposal is extra simple, even with polyacrylamide -- just dispose of the entire straw, gel and all, properly.

Tito Jankowski tried this out, using a single 9V battery as a power supply, and after some debugging, it worked beautifully. (He also used alligator clips as electrodes, and they worked just fine.) We're calling these "keiki gels" because they're so small and cute -- and so simple, even a little kid can do them.

This is crowdsourced science at its very finest. Behold the power of collaboration!

Tito's keiki gels!

ETA: Tito wrote a protocol, doo dah, doo dah
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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.
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Over the last 24 hours I've seen a lot of concern and speculation about what happens if one of my experiments somehow "goes out of control" and turns into some kind of "grey goo" event. It seems that there's a mistaken impression that I'm just randomly mutating things (perhaps with UV stimulation) to see what comes up. This actually couldn't be further from the truth, so let me explain what I'm really doing.

How Your Genes Work can be summed up in a single sentence: "DNA makes RNA makes protein." Your genes are instructions for making several different types of RNA, and those RNA molecules assemble the proteins that your body is made of and which make your body run. Some proteins are structural, some are enzymes used to catalyze chemical reactions (such as digestion), some are used to transport other molecules around (e.g. hemoglobin, which carries oxygen around in your red blood cells) -- proteins are everywhere. So, when I think about something I'd like for a cell to do, I start looking around for relevant proteins.

In the case of "let's detect melamine", I went to MetaCyc -- a browsable database of metabolic pathways -- and looked for proteins which interact with melamine. I found one, called melamine deaminase. It's the beginning of a metabolic pathway called the melamine degradation pathway, which -- go figure -- takes melamine apart. To use this reaction in our detector, we'll need to give some species of bacteria the ability to produce melamine deaminase, which means giving it the appropriate gene. To do that, we either extract the gene from a species that already has it, or we get a lab like IDT to make it for us. Then we insert the gene into a plasmid, which is a circular DNA molecule that a bacterium can "take up" in order to gain some new function.

So, no, there is no deliberate randomness going on here -- rather, it's a concerted effort to make just one type of bacteria do just one additional thing (or, really, some sequence of additional things). The whole experimental setup is also designed so that if I screw something up, the bugs die and that's it. And, naturally, I'm doing everything I can to make sure that stray spores, phages, and other contaminants don't end up in my experiments -- heat sterilization, alcohol sterilization, flame sterilization, you name it.

Do you need to worry about these synthetic bacteria degrading you? Only if you are a whiteboard or certain species of plastic fork.
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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 [ profile] 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! )
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I had managed to run myself out of the petri dishes I'd gotten from AS&S lo these couple of years ago, so I hit up ebay to restock. Found a great price on 60mm x 15mm pre-sterilized plates in packs of 20, so I bought five of them.

Except ... I completely spaced on how small 60mm is. Ergo, I am now the owner of the most adorable little petri dishes ever. They are ever so slightly larger around than the bottom of a Red Bull can. [ profile] whimsywanderer snickered when she saw them. I feel compelled to reassure them that size doesn't matter, we are doing science here.

In the long run I think this will actually be a good thing, as in the very near future I am going to need to use, uh, just about all of them in rather large batches -- possibly 60 at a time -- and there's really no way I could fit 60 full-size plates in my teensy little incubator. It will also mean using up fewer consumables, which is in general a good thing for the budget-conscious citizen scientist.

Science Cat Sasha is, as usual, fascinated with the new arrivals. If he bites holes in the sterile packaging I will be very cranky.

I also snagged the economy size package of graduated 3mL disposable transfer pipettes. With 500 of them, I don't think I will be running out any time soon.
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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.
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Today I went to TAP Plastics in San Francisco and they cut me the plastic pieces I will need to build my very own gel electrophoresis chamber. (Service while you wait, by the way. It took maybe ten minutes, during which time the friend who drove me and I wandered around the store looking at all the cool stuff they had on display and chilling in chairs shaped like giant hands. A+++ will shop there again, if only to spend more time browsing through their photos of neat stuff they made.)

Then I got home and checked the mail and found that my electroporation cuvettes arrived!

Oh, today is a happy happy day. Time to leave positive feedback on eBay for the guy I bought the cuvettes from, fix some lunch, then go down to SuperHappyDevHouse and start building.

*dances the dance of parts that are heeeeeeere!*
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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". ([ profile] 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?)


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