Green marinated chicken

So I won’t pretend to be a whiz at grilling meat. Not even close. But I have had some successes- including this recipe I concocted a few weeks ago then just repeated again tonight for memorial day. It was really putting things together from our garden, but I imagine there could be a lot of variation here. Oh, and it’s easy and absolutely delicious.

Green marinated chicken

  • 2 small sized new onions including greens, peeled*
  • 4 cloves garlic
  • 1/4 cup chopped chivesDSC_6904
  • 2 sprigs of fresh mint (about 10-15 leaves)
  • 3 T olive oil
  • 2 t kosher salt
  • 3/4 cup white wine
  • 2.5 T agave nectar

* you could substitute 1/2 of a regular onion and a bunch of green onions here too.

Put these all in a blender and blend until smooth. Score the tops of about 2 lb skinless-boneless chicken thighs (we got them frozen from Costco) with a sharp knife- 3-4 cuts per thigh and marinate in a zip top bag for 4-8 hours (no reason it couldn’t go longer). Heat grill for 15 minutes with lid closed. Lift the thighs out of the marinade, shake gently leaving a lot of green stuff still on, and grill with lid closed on high for 6-10 minutes on each side. Turn carefully when the underside has started to brown all over, but some regions will stay green too. DSC_6905

I also used the leftover marinade. The first time I used it to marinate slices of butternut squash that I then I then grilled- which was pretty good except that the marinade didn’t really stick that well. Tonight I used some pizza dough we had in the fridge, made small rounds and brushed the tops with the marinade. I put these on the grill – marinade-side down, with lid closed for about 5 minutes, brushed the other side, then grilled for another 5 minutes. These were pretty delicious.

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Start of grilling

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About midway through grilling. The marinade caramelizes really nicely.

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Grilling complete!

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Here are the BBQ rolls I made tonight.

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Here the plating from the first night I made this.

New biosketch format for NIH

Just got word of this from the Twitters- the NIH is announcing rollout of a new biosketch format for grant applications. I thought I’d summarize the information about it here to make things easy.

  1. Starting for grants that would be funded in 2016 (so anything you apply for in 2015 will have this, essentially)
  2. Will be a five page limit (as opposed to 2 page for current format)
  3. Will NOT include a ‘bare’ list of 15 publications
  4. Now includes a new list of up to 5 of your “contributions to science”, which can include up to 4 citations each (your own presumably). So that’s a total of 20 citations you can have.
  5. You will be able to include a link to your full citation list in an online database (NIH resources sciENcv or My Bibliography are mentioned but could be others I guess)
  6. Here’s a template that includes an example new biosketch
  7. More information can be found in the announcement here from the NIH on Salley Rockey’s blog
  8. As it’s being rolled out the requirement for the new format will be stated in the RFA – SO LOOK FOR THIS IN ALL RFAs from here out. Two pilots already have it RFA-CA-13-501 and  RFA-CA-13-502

The upsides: In my opinion the addition of the contributions to science will be the biggest one and should allow you to really highlight your publications (or lack thereof) in appropriate context. Plus space for moar buzzwords!

The downsides: It’s gonna be a pain to write (like a mini grant in there) and reviewers won’t read this one either.

We should F-ing LOVE science

There’s been a recent backlash against a certain kind of science appreciation recently. This sentiment is typified by this (actually pretty funny) comic (see below) and this blog post that’s against the very popular “I F***ing Love Science” website/FB page (and other similar science-themed memes and sites). Consider this as my back-back-lash against that sentiment.

Something has bugged me about this sentiment for awhile and I just put my finger on it. It’s elitism. Them against us. We should want people, LOTS of people, to love science in this way. This superficial, just loving the fun dazzling parts, not down-in-the-real-nuts-and-bolts-of-what’s-happening way. As scientists we REALLY should want people to love science in pretty much any old way they’d like to. Sure, there are real and true and troubling issues with image/content attribution (I’m not talking about that here). Sure, this kind of lovin’ glosses over complicated issues and may hide the actual facts of the matter pretty deep. Sure, there’s misinformation- sometimes harmful- in some of these sound-bite science bits (see my post on the importance of not being a transmitter of misinformation). Sure, we’ve been to school for a gobzillion years and so only WE are the ones that can REALLY appreciate the nuances and subtleties and implications of what’s actually being done. But really… is the love of science exclusive to those of us in the inner circle?

Imagine you’re talking to a kid who is really excited by space exploration. Do you immediately jump on the, “it’s unlikely we’ll ever be able to reach another star or planets outside our solar system”, “faster-than-light travel really might be impossible”, “statistically speaking you will never travel into space”? Do you tell them that they can’t love space exploration, because they really don’t know how it works or the details of how we currently do things? Or do you foster that sense of wonder and the curiosity to explore and discover? If they are serious they will pursue knowledge and experience, and will find out those things by themselves – or will surprise everyone by skipping the part about things being ‘impossible’.

Here’s another way to think about it. I love movies. I don’t want to make movies (well, OK, I do a little), I don’t understand the mechanics of making a movie, I don’t want to think about the day-to-day drudgery of actually being an actor/actress, famous or not (have you thought about it? It sounds positively dreadful and boring), I don’t know the economics of how studios get movies made and the distribution systems. I love movies. I appreciate the whiz-bang parts of movies. I like to be awed by movies and to sit in a dark theater and be transported by my imagination. And here’s a key point: I will pay my good, hard-earned, money to exercise my right to love movies. 

Just substitute architecture, automotive design, music, wine making, etc. for “movies”. Does my lack of knowledge and first-hand experience about any of those areas make me love them (or really, their products) any less? No, of course not. Does it mean that I love them differently than my counterparts who may have a lifetime (possibly pathological) relationship with them? Of course. As it should be.

And those two points are where we, as scientists MUST do better. One, we need to foster the wonder of science, not just in kids but in everyone. It’s OK if sometimes the details are wrong, or the implications are mistaken, or the deep understanding that comes with years of study. And two, we need people, lots of different kinds of people, lots of rich people, to LOVE science and to appreciate science and to have their imaginations captured by science. Because otherwise they won’t see the value in science. And they won’t PAY for science. So we should encourage people to f***ing LOVE science in whatever ways they want.

Comic from (the wonderful) Cyanide and Happiness:

This one goes to 11…

The famous Spinal Tap quote (see the video here) is great because Nigel is explaining how  his amp is better than other rockers since you can turn it up to 11. “Why don’t you just make ten louder and make ten be the top number and make that a little louder?” asks the mockumentarian Rob Reiner. Good question.

The humor in this scene reminds me strongly of this recent paper on the introduction of an artificial nucleotide base pair into a bacteria. Essentially they got a bacteria to incorporate an artificial nucleotide pair into its DNA, it replicates stably (that is, the new pair stays in the bacterial DNA for generations), and its not removed by DNA repair mechanisms that look for problems in the DNA. Novel nucleotides are not new- researchers have created a large number of these and incorporation into DNA has been done in limited ways in test tube (in vitro) systems, not in a living organism. This is really a pretty cool technical achievement – the researchers had to solve a number of complicated problems to get this to work and, more importantly, it’s likely that they got very lucky with their choices (where ‘luck’ here is a combination of knowledge, trial and error, and actual bona fide luck).

The paper itself doesn’t really overstate the implications of this paper. The only implications statement in the paper comes at the end:

In the future, this organism, or a variant with the UBP incorporated at other episomal or chromosomal loci, should provide a synthetic biology platform to orthogonally re-engineer cells, with applications ranging from site-specific labelling of nucleic acids in living cells to the construction of orthogonal transcription networks and eventually the production and evolution of proteins with multiple, different unnatural amino acids.

And all of this seems very reasonable and potentially achievable.

However, as happens with many high profile papers, the press coverage I’ve seen on this is terrible. From Gizmodo touting that “scientists have created alien DNA” (only for a very limited definition of ‘alien’) to New Scientist stating that researchers have expanded the ‘genetic code’ of a bacterium (not really, a code needs to have meaning- that is, to be translatable into something that has meaning, this advance doesn’t yet). However, perhaps the most troubling is coverage from NPR, largely based on an interview with the senior author of the paper. In this piece Floyd Romesburg introduces a simple, and largely apt analogy, for what his work has done:

Maybe you get three consonants and one vowel. Maybe there are some words you can write and you can string them together to make, sort of, primitive stories. But if you could have a couple extra letters, there’s more that you could write. Having the ability to store increased information would allow you to write more interesting words, bigger words, more complicated words, more nuanced words, better stories. – from NPR interview

He goes on to say:

It’s not so much that I think life needs more genetic information but I think that there are things that we could really learn and drugs that could be developed by getting cells to be able to do more

So it’s not a bad analogy, but one where he’s essentially said: “This one goes to 11.” . And it points out exactly why this work is so limited in its implications (exactly the opposite of what he’s trying to point out by using it BTW). They have added, in a very constrained and limited way, added two letters to the standard ATCG alphabet used by nearly all life. Will this introduce the ability to build more complex or useful biological systems? Not in the slightest. Imagine that we added a couple of letters to the English alphabet. Now we give those extra letters to someone like William Shakespeare. Does anyone think that he would be able to do more with more letters? Write better, more complex, more interesting, more profound plays or sonnets? No, of course not. Even if you gave him a whole bunch of new words that contained the new letters (which they haven’t done at all in this paper- they haven’t actually introduced this new addition into the code itself, only into the alphabet), he would likely have produced very similar works. Maybe those works would be slightly shorter, but they would NOT contain more information. Adding a letter to the alphabet doesn’t increase the information or the complexity of the code. It just doesn’t. The computer that I’m writing this on is based on a binary alphabet (1 and 0 are the only letters it uses) and yet I’m able to put these together (with the help of the underlying OS and software) into complicated and information-rich constructs. Having a computer based on 0 , 1 AND 2 wouldn’t help me write this post any more better [sic].

An image of ACTUAL (fictional) alien DNA. This one has a 15 stranded double helix, which CLEARLY makes it more complicated than our humdrum double stranded type. Clearly. (from the movie The Fifth Element)

An image of ACTUAL (fictional) alien DNA. This one has an 8 stranded helix, which CLEARLY makes it more complicated than our humdrum double stranded type. Clearly. (from the movie The Fifth Element)

The idea that this would lead to development of new drugs, new forms of life, new biology is a far, far, far distant stretch that causes confusion and even fear. The problem here is not purely driven by misunderstanding and misrepresentation of the work by scientific journalists (though it looks like there’s some of that) but from the actions and statements of the senior author himself. As I mentioned, this is a sound paper and is pretty interesting- a technical achievement. It may indeed lead to some interesting new discoveries and methodologies that may be broadly applicable. But it’s not alien DNA and it’s not going to help us cure cancer with new drugs, and it’s not going to provide the ability to make the biology more complex, but it might make our rocker friends green with jealousy when we reveal that we have six nucleotide bases compared to their paltry four bases because “these go to eleven” (Nigel Tufnel)

Coincidence

I had a weird thing happen on my way in to work this morning. On the main road just a short distance from my parking lot I noticed that the SUV in front of me had the same three letter combination on their license plate as mine, “YGK”. Then I noticed that the car in front of THEM had the SAME three letter combination! Wow. What are the odds of that happening? Well, I’m not going to tell you the odds of that happening, because I don’t really know. But it did happen. An odd coincidence for sure, but maybe not as cosmically-connected as you might be inclined to think.

First off, let’s think about the odds of drawing the same 3-letter combination from a hat with 26^3 combinations two times in a row (approximating what happened here- because my license plate is fixed). That’s how many different possible 3-letter combinations there are- I suppose probably subtracting one or two for words that aren’t allowed, like “ASS” and, ummm, well maybe there’s another. This is 17,576. The chances of drawing two of the same out of a hat would be 1/17,576 X 1/17,576 – 1 in 300 million. So this means that you could sit and draw letters out of this hat every second (that is drawing two sets of three letters out every second) for about 10 years before you’d be likely to have this happen. Now clearly I’m simplifying here- but still. So for my license plate story I’d be unlikely to have this happen in my lifetime since I’m only driving every now and then and I’m not generally even paying attention to other people’s license plates to see if this has happened or not.

So here are some reasons why it’s not TOO surprising that it did happen. First, assuming all combinations are used, there are 1000 other vehicles in WA state with the same letters, which narrows the field a bit- but only a bit since there are ~6 million registered vehicles (at least in 2012, though some portion of these have the longer 7 number/letter plates). Second, is that it is likely that these are issued in order (though I’m not 100% sure about that, it would seem to make sense) of request. That means that vehicles purchased about the same time as mine (2001) are probably far more likely to have the same set of letters.That’s been about 13 years, which means that those vehicles are going to be of a certain age.  I would also include geography – since that could be another influencing factor as to which numbers/letters you get, but I did get my license plate on the other side of the state. I don’t have a clear idea of how this would bias the probability of seeing three license plates in a row, but it fits in to my next point, which is hidden or partially hidden explanatory variables.

When my wife and I lived in Portland, far before we had such encumbrances as kids to drag us down, we often did a bunch of activities on a weekend. I started to be surprised to notice some of the same people turning up at different places, parks, restaurants, bookstores, museums, etc, far across town. This happened more than you’d expect in a moderately-sized city. Interestingly, in Seattle when we had a kid this also happened. And it happens all the time in our current city(ies), which are much smaller. My idea about this is that it’s not surprising at all. Our choice of activities and times is dictated or heavily influenced by our age, interests, kidlet status, etc. – as are other peoples’. So instead of thinking of the chances of repeatedly bumping in to the same set of people out of the entire population, think about the chances if the background distribution is much more limited, constrained (in part) by those interests and other personal constraints. The probability of this happening then rises considerably because your considering a smaller number of possible people. I’m sure this has been described before in statistics and would love it if someone knew what it’s called (leave a comment).

How does this fit in to my license plate experience? I don’t really have a clear idea, but it is evident that there can be multiple underlying and often hidden explanatory variables that may be influencing such probabilities. Perhaps my work is enriched in people who think like me and hold on to vehicles for a long time- AND purchased vehicles at about the same time. I think that’s probably likely, though I have no idea how to test it. If that’s true then the chances of running in to someone else with the same letters on their plates, or two people at the same time, would have to go up quite a lot. Still, what are the odds?