This chart is a lie

Serial cables are neutral? No way. Chaotic evil. I had to make too many of them. DB9 or DB25, or some ghastly custom pinout some manufacturer saw fit to stick on their device? I’ve encountered lots where all you need is 3 pins — ground, transmit, and receive — but even then you have to worry about whether this is a straight pass-through cable or a null modem cable. Some devices require one or several of the handshaking lines to be enabled — but different machines require different handshakes. Do you need DTR or DCD? Sometimes yes, sometimes no. Then some of those handshake lines are completely redundant, and you can make it work just fine by shorting out the line to one of the other pins.

I remember the bad old days when you’d buy laboratory devices and they’d have some odd connector hanging off the back and there’d be a cryptic pinout diagram in the specs, and you’d have to solder up your own cable for it. It was not a happy time.

Lovely green landscape, charming people, and…a hurricane?

I’m keeping up with the news from Ireland, where Ophelia is rushing up the west coast. Hurricanes and fierce winds and massive storm surges just aren’t what I picture when I envision Ireland.

I hear our national stockpile of thoughts and prayers were seriously depleted by hurricane Maria. Maybe that means we’ll actually have to give appropriate aid where needed.

Just like we’ve been doing in Puerto Rico.

A science video about gonad development

A bit about the early development of human gonads.

A few useful sources:
Sadler TW. 2014. Langman’s Medical Embryology. LWW. ISBN: 1451191642.

Everyone needs to have a copy of Langman’s around. Diagrams in the video were taken from this text.

Sajjad Y. 2010. Development of the genital ducts and external genitalia in the early human embryo. J Obstet Gynaecol Res. 36(5):929-37. doi: 10.1111/j.1447-0756.2010.01272.x.

A good review of the embryonic plumbing.

Zhao F, Franco HL, Rodriguez KF, Brown PR, Tsai MJ, Tsai SY, Yao HH. 2017. Elimination of the male reproductive tract in the female embryo is promoted by COUP-TFII in mice. Science 357(6352):717-720. doi: 10.1126/science.aai9136.

New stuff: a nice example of a female gene product that actively suppresses a male developmental feature.

PZ’s simple curry recipe

I made a curry tonight, and was asked to share my recipe. I was a little reluctant, because this is a really easy recipe, and explaining it will erase my mystique as a cook. But I’m a scientist, not a chef, and we believe in exposing all the mysteries, dammit. So here it is. Bonus: it’s vegan!

Take some extra firm tofu and let it rest under a weight for a while, until it’s extra firmerer.

You’re going to need a small pot. Put a cup of coconut milk in it, and then a couple of healthy dollops of peanut butter, and a variable amount of red curry paste. You get to control the final heat here: add a spoonful or two if you you like it mild, throw in half a tub of the stuff if you want to set the world on fire. Let it simmer until all the chunky stuff melts and you’ve got a nice brownish sauce with rivers of red like blood threading through it.

Now rescue your tofu from the crushing weight and cube it. Slice it into small bits, about the diameter of the tip of your little finger. Use a sharp knife, and maybe you’ll get a finger tip as a standard — you’ll only get to do that twice, so learn fast. Heat up some olive oil in a pan, and fry the tofu cubes up for a while, until they’re getting a toasty brown around the edges. This gives ’em a little more texture. Tofu needs it.

Sad confession. I’d like to add some of those tasty little red dried chilis at this point, and simmer them in the oil with the tofu, but I haven’t yet found any in Morris, so I usually don’t. I should check the Mexican grocery next time.

When the tofu looks good, throw them into the peanut butter/coconut milk/curry paste sauce. Simmer a while. They’ll absorb the flavor and get nutty-spicy.

Get a big white onion and chop it fine. Go ahead and let your tears spatter into it to add a personal touch. Saute in your cooking pot in some olive oil for 5 minutes or so, and then add a healthy dose of grated garlic, like a couple of cloves worth. Add some grated ginger, a bit more than the amount of garlic you added, and swirl it around in the hot oil and onions. Add peanuts. How many peanuts do you like? I throw in a couple of handfuls. Saute some more.

Time to add some spices. If you’re as lazy as I am, just get that yellow curry powder and toss in a couple of big spoonfuls. OK, add another spoonful. Maybe more. To taste. If you don’t have the curry powder, add turmeric and cumin and a bit of ground coriander. Swirl it around until everything is coated and hot, and dump in your coconut milk plus pepper plus peanut butter and tofu. You should get a nice blast of delicious steam in your face.

Really, that might be the best part of cooking this stuff, that moment when you get to breathe in the spices. Sinuses now all clear.

OK, now add a splash of soy sauce, and a couple of splashes of rice vinegar. If you think it’s not robust enough, spritz in some sriracha sauce to invigorate it.

Now we might diverge a bit: I use an instant pot pressure cooker. I just need to zap it at high pressure for 3 minutes or so to turn it into liquid gold. If you’re using a slow cooker, you might need to let it cook for an hour or more. Do the experiment! Do frequent tastings to see how it’s coming along!

Somewhere in here get your rice cooking. I like jasmine rice with this curry.

Final step: add pineapple chunks and simmer for a few minutes. I just use a whole large can of the stuff, but if you want more sweetness, add more (I think Mary wants me to add a couple of pineapples worth). Put it on rice and consume.

Curries are surprisingly easy to make — it’s all in the spices, and they’re easy to come by. I also have a red curry I make with lentils and potatoes, but I’m not telling because I have to keep some secrets.

I could use bigger muscles, but I’m not going to get them with biotech in my garage

Josiah Zayner is a self-proclaimed bio-hacker. He sells CRISPR/CAS9 home gene editing kits, and he goes to conferences where he publicly injects himself with chemicals to modify his own genes. For instance, at a biotech conference, he got up on stage and injected himself with a cocktail to knock out the myostatin gene, to give himself “bigger muscles”.

If you want to genetically modify yourself, it turns out, it’s not necessarily complicated. As he offered samples in small baggies to the crowd, Zayner explained that it took him about five minutes to make the DNA that he brought to the presentation. The vial held Cas9, an enzyme that snips DNA at a particular location targeted by guide RNA, in the gene-editing system known as CRISPR. In this case, it was designed to knock out the myostatin gene, which produces a hormone that limits muscle growth and lets muscles atrophy. In a study in China, dogs with the edited gene had double the muscle mass of normal dogs. If anyone in the audience wanted to try it, they could take a vial home and inject it later. Even rubbing it on skin, Zayner said, would have some effect on cells, albeit limited.

He does not look particularly muscular in his photos.

He’s a snake-oil salesman. He’s doing this demonstration, confident that nothing will go wrong, because he must know that this is a spectacularly inefficient way to use CRISPR/CAS9. I looked over his website, and there’s no information on the frequency of incorporation of his edited sequence into cells, or even on whether they’ve seen any phenotypic effects with this approach. I suspect there’s little effect, which is a good thing. Even if he does get incorporation into some cells, he’s not going to get much of a result — myostatin affects the growth and differentiation of myocytes (it’s not going to do a lot for an adult), and regulates protein synthesis in muscle cells, which could, in fact, promote more ‘bulking up’ of existing muscle mass.

That’s not necessarily a good thing. Cardiac hypertrophy is not something you want to have, and Zayner isn’t exactly controlling delivery of his reagents to specific subsets of muscle cells.

But again, he’s almost certainly not getting enough DNA modification to have either his desired result or a deleterious result. He’s just gambling that the injections will be innocuous enough that they won’t actually do anything except look impressive to the rubes. Here’s hoping he doesn’t get erroneous editing of random cells so that basically, all he’s doing is giving himself a low-dose mutagen.

George Church is the voice of reason on this one.

If you modify your DNA, it’s possible to then sequence your DNA to see if you made the targeted change. But a garage experiment also can’t provide as much information as more conventional methods. “You can confirm that you’ve altered the DNA, but that doesn’t mean that it’s safe and effective,” says George Church, professor of genetics at Harvard Medical School (who also serves as an advisor to Zayner’s tamer kit company, recognizing the value of a biology-literate public in what’s being called the century of biology). “All it does is tells you that you’ve molecularly done the right thing, but it could be unsafe because you’ve also done something off-target. It could be ineffective in the sense that not enough cells were altered, or it’s too late in life and the damage has already been done.” If a baby is born with microcephaly, for example, changing the genes in its body likely won’t be able to change the effects of the condition on its brain.

Zayner’s vial of CAS9 myostatin knock-out juice is really cheap, at only $20. It also makes me wonder about quality control and safety at his workplace, though. I’d worry more about contaminants in a random vial of fluids that I’m expected to inject into my bloodstream than that it contains the latest biotech buzzword.

Changing face of Easter Island

Easter Island has been used as a cautionary tale — the inhabitants denuded the island of palm trees while wasting their resources on colossal religious statuary, and then destroyed themselves in an orgy of self-destructive wars. Only there are a few problems with that myth emerging.

It seems that the palm trees were demolished early in the colonization of the island…not by the people, but by rats that had hitchhiked to the island. The people of Rapa Nui adapted and had a stable agricultural system that allowed them to thrive, and what caused their population to collapse was not internal conflict, but external forces.

Throughout the 19th century, South American slave raids took away as much as half of the native population. By 1877, the Rapanui numbered just 111. Introduced disease, destruction of property and enforced migration by European traders further decimated the natives and lead to increased conflict among those remaining. Perhaps this, instead, was the warfare the ethnohistorical accounts refer to and what ultimately stopped the statue carving.

There’s a lesson here, all right. That lesson is that you should trust the hard work of serious anthropologists who do deep, evidence-based research, rather than the self-serving stories spread by colonial empires or the speculations of dilettantes.