Funding science

As a scientist I have found that funding is everything.  To do good science you need  money and lots of it.  Everything is expensive.  People, equipment (dear lord…), consumables, time, everything is much more expensive than pretty much anyone outside of science would think.

So how should the government decide which scientist should be funded and which shouldn’t?  It’s not an easy issue and it’s one that has been debated for a long time, but it has recently ended up in the NYT and it really began to piss me off.  Essentially, I believe people don’t have a realistic view of what scientific progress is: slow and steady with the occasional breakthrough.  Those outside of science (and some idiots within our own ranks) seem to think that only breakthroughs are worth the money and that we should then fund all the people who think way out of the box and have radically new ideas.

However, there is a reason these people don’t get funded by governmental agencies very often.  While the work COULD POTENTIALLY be high payoff, such research is characterized to be very risky.  Why?  This could be for any number of reasons: little background data, implausible mechanism of action, little to no experience in the field, etc.  These are, in my opinion, very good reasons for not funding scientific research because the very nature of science is extremely CONSERVATIVE.

Now, I know what you’re thinking: “Conservative?  But I thought Conservatives hated science and did everything they could to undermine it.”  In that sense you’d pretty much be on point, but I’m not speaking of conservative in a political sense.  Science makes slow and steady progress because by it’s very nature a lot of data must be backing a certain idea in order for it to be accepted by the scientific community.  This makes it much more difficult (but not impossible) for incorrect ideas to take hold.

This is why I don’t feel bad for the researchers spotlighted in the article as being “ahead of their time” or “revolutionary” or whatever term you want to use.  Take Dr. Jaffe for example.  Here is a woman who has been dealing with the grant system for two and a half decades and she thinks it’s unfair that her grant was rejected out of hand because she had no preliminary data?  Pardon me, but she’s a fucking moron if she actually believes that.  “Of course I don’t.  I need the grant money to get them [the preliminary data].”  Fuck her, that’s not how funding agencies work and she knows it.  She’s just trying to be the victim here.

How it really works is that you use grant money that you already have to do quick, exploratory pilot studies to see if your ideas actually have any merit.  If they do then you write up a grant and include your pilot study as the preliminary data and submit it.  Funding agencies will then decide if your work looks promising or not and decide your grant’s fate.  But to submit a grant with insufficient (or nonexistent) preliminary data and then blame the funding agency for not giving you money is absolutely fucking ridiculous.  Sure, the funding situation is far from perfect, but you know the rules so you have to play by them.  If you don’t then you have no room to complain.

Who cares?

Michael Jackson died and I don’t care.  Yes, he was a great entertainer who many people, but not me, cared about.  But what did he really do to deserve this public spectacle?  In my opinion we should mourn his death like it was any other and save our praise for people who have devoted their lives toward bettering those around them and by extension the human race.

/rant

Natural substances/products and a common claim

Don’t fall for nonsense, just because a product is found in nature does not mean it is good for you or is any better than man-made substances.  When people mention that something is “natural” in order to make you more interested in it they conveniently want you to forget that there are a lot of natural substances that are potent enough to kill you hundreds of times over.

Also, remember that the danger is in the dose.  Normally toxic substances can be harmless in small amounts and typically safe substances can be very toxic in large doses.  We put toxic substances into our bodies every day and most people will never see the effects of them because they are in such small doses.  This whole concept is why the EPA and other agencies can post acceptably safe levels of things such as mercury, arsenic, dioxins, etc.  A “natural” product doesn’t necessarily have safe levels of ingredients

And while I’m on the subject, if you ever see a product that claims to “boost your immune system” run away from that product.  What the hell does that statement even mean?  First, the company that is promoting their product would have to show that it somehow modulates some part of the human immune system (increasing T-cells?).  They would then have to show that the modulation their product induces actually has the desired effect on whatever problem/disease it is trying to alleviate/cure (because you can’t just assume that an increase in something in the immune system is actually going to change the immune system – a bit counter-intuitive, but that’s how science works).

Personally, I stick to well-known, tried-and-true drugs, and I think you should too.

A problem

I’ve really been trying to write stuff lately but to no avail.  Everything I come up with just seems to be a rant of some sort and I really don’t want this blog to go in that direction.  I’ll try harder to figure stuff to write about in the future.

Improving science literacy – part 6

A Primer on Mutations

You shouldn’t necessarily be afraid of mutations; they can, in fact, be your friend. Like pretty much everything else in this world it depends on the context.

The first thing you should understand from the last post is that DNA doesn’t do a whole lot by itself. Instead, the DNA strands act through RNA to create proteins. It is these proteins that do all of the important work in your body which biologically matter. Through the hard work of many scientists we’ve known the secret code (see below) for a while now and it turns out to be fairly simple: a group of three nucleotides in a row (AAA, AAC, AAG, and so forth) code for a single amino acid (along with a few that code for when the the protein should start and stop).

(source)

Each of these groups of three nucleotides (also known as triplets) is called a “codon.” Get it? Code. Codon. See, science occasionally makes sense. So, lets use some actual codons in a quick example: (please note, this isn’t exactly correct, but it’s being used only as a simplified example so it’s okay)

———DNA ———————-> RNA —————-> Protein

AAG GTT CTC ATG ————————————-Phe-Gln-Glu-Tyr

——————————- UUC CAA GAG UAC

So, these twelve nucleotides of DNA code for complementary nucleotides of RNA. Groups of three nucleotides of the RNA strand code for singular amino acids and we’re left with a protein made of four linked amino acids.

Now that you know generally how this process works you can being to understand what mutations actually are and how they function. Mutations actually come in quite a few flavors: point, deletions, insertions, inversions, duplications, etc. However, all follow the same general principles, so if you understand one you will most likely understand the others by their name alone (which describe exactly what is happening to the DNA). So, I’ll explain two types and let you figure out the rest. If you can’t just ask me to explain it in the comments.

Point Mutations: Changing a single nucleotide in the original DNA can have either a dramatic effect or none at all depending on what has changed.

———DNA ———————-> RNA —————-> Protein

AAG GTT CTG ATG ————————————-Phe-Gln-Asp-Tyr

——————————- UUC CAA GAC UAC

See how changing that one little nucleotide in the DNA completely changed the protein?  That could have one of three biological effects: it could completely destroy the function of the protein, it could have no (significant) effect on it’s function, or it could actually improve the function of the protein (yes, it actually does happen, but that’s a whole other story…).

———DNA ———————-> RNA —————-> Protein

AAA GTT CTC ATG ————————————-Phe-Gln-Glu-Tyr

——————————- UUU CAA GAG UAC

This is called a silent mutation because while the DNA suffered a mutation it had no effect on the final makeup of the protein and is therefor neutral in regards to evolution.

Deletion: This is exactly what it sounds like.  Most times only one nucleotide is removed so that’s what we’ll focus on.

———DNA ———————-> RNA —————-> Protein

AAG GTT –TC ATG ————————————-Phe–Gln–Ser–

——————————- UUC CAA –AG UAC

This is called a reading frame shift.  Just getting rid of a nucleotide doesn’t change the fact that codons are needed for the final protein to be translated from the RNA.  Instead, it shifts the code one nucleotide over (and since three are needed for an amino acid, in our example there is RNA overhang that essenatially does nothing).

I hope this makes a little bit of sense and begins to open your eyes to the wonderful world of genetics.  Of course, the way this actually goes down is much more complicated and nuanced, but I feel my explanation is a good introduction to any interested lay person (as I hope all of you are).  As before, any and all questions are welcome.

Cleaning day

Instead of writing like I wanted to I have spent most of the day cleaning my apartment so that it can be shown to other potential renters/buyers.  I still have quite a bit more to do, so I don’t think I’m going to be able to write anything tonight.

On a side note, my landlord’s realtor uses AOL.  WTF?  I didn’t know I was living in 1995.

Improving science literacy – part 5

It’s all about relationships: DNA, RNA, and proteins

Words like DNA, RNA, and protein are thrown around all the time, but what does it all mean?  What’s the relationship between them?  It’s basic biology that can help everyone understand their own bodies and the biological world around them better.

DNA is essentially a very long chain of repeating units called nucleotides (also called “bases”).  There are only four of them in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T).  DNA is actually two strands of what are called “complementary bases.”  Essentially, that means the strands are set up like this:

strand 1: AGTCTCAGG
strand 2: TCAGAGTCC

See how the A’s only line up with the T’s, and the C’s with the G’s?  That’s due to how they bond on a molecular level, and that isn’t really important in our discussion.  Just remember that the curvy (C and G) and straight letters (A and T) go together and you’ll be just fine.

RNA is the single-stranded cousin of DNA and is also made up of four nucleotides, except one (thymine) is replaced with another (uracil – U).

Proteins are complex molecules made of a string of subunits called amino acids.  All of the various proteins in your body are made up of only 20 amino acids arranged in varying order and length.

The simplified chain of events goes like this:

transcription                                translation
DNA ————————–> RNA —————————-> protein

Transcription: DNA literally unzips it’s two strands for a short time in order for a complementary strand of RNA to be made.

Translation: Using the RNA as a template, amino acids are lined up and formed into the protein that was originally coded by the DNA.

Here how it looks in all of it textual, non-graphical glory (courtesy of me).

DNA ————————- DNA+RNA —————- Protein made using RNA
AGTCTCAGG ————-> AGTCTCAGG ———————-> PROTEIN!
TCAGAGTCC ————-> UCAGAGUCC ——————–> UCAGAGUCC

Summary: DNA codes for information and uses RNA as a middleman to produce proteins.  Simple, huh?  Of course, it’s not quite that simple, but that’s the gist of it and now you know just enough to be dangerous discussing this among non-biologists at a party.  Gotta be slightly drunk though.

Make sense?  Any questions?  If you do have some be sure to ask because Saturday (I hope) I will expand upon this gift of knowledge and teach you all about the dreaded MUTATIONS.

I think the chicken thighs need a picture

So I added one.

Dijon braised chicken thighs

This is easy, I swear. The only problem is that I don’t really use recipes, so writing one poses some problems. I’m also still trying to polish this dish so there’s still some issues I’m working out (like seasoning). However, it’s still a simple, delicious, and cheap dish that can absorb some blows and is easily adjustable to suit your taste. So keep it my way or change it, I don’t care, just enjoy it!

Reagents:
1T dijon
3-4c chicken stock (HOMEMADE, I take no responsibility if this dish sucks because you used canned or boxed stuff)
0.5 onion (or equivalent of shallots) – small dice
1 large carrot – small dice
3 cloves garlic – minced
1tsp thyme
(maybe a little cream)
2 slices thick cut bacon – small-medium dice
4-6 bone-in chicken thighs brought to ~room temp. (I deskinned them, but that’s just me)
1c dry white wine

Equipment:
Large frying pan
2.5-3 qt. dutch oven

Protocol:
1. Put the frying pan over medium-low heat
2. Add the bacon and render as much fat as possible
3. When rendered, remove the cooked bacon and reserve
4. Add the diced onion and carrot to the rendered fat
5. Cook ~5min and preheat the oven to 400deg.

6. While the onion and carrot are cooking add the dijon to the stock pot
7. Whisk in a very small amount of chicken stock (note: don’t add more than two tablespoons of stock to mix in with the mustard or it won’t mix in smoothly, trust me)
8. Add the rest of the chicken stock, the thyme, the reserved bacon (and the cream if you chose to add it)
9. Bring to a simmer
10. Add the minced garlic to the onion and carrot mixture in the frying pan and cook until just fragrant
11. Put the cooked onion, carrot, garlic mixture into the chicken stock mixture

12. Quickly season the chicken with salt and pepper then sear them ~2 min. each side just to get some nice color on them (may have to do in two batches)
13. Add the chicken to the dutch oven
14. Deglaze the frying pan with the wine – make sure to scrape up ALL the fond – and add it to the dutch oven
15. (at this point the chicken should be mostly submerged in the stock mixture, but since I don’t measure anything and you don’t have the same equipment I do you can add more stock to the pot to get the right volume. don’t worry, it’ll still taste good in the end)
16. Add the top and throw in the preheated oven for 1 hour

Serve as is, with a side of mashed potatoes, pasta, or whatever you like. Personally, I removed the chicken into a covered bowl and strained the braising liquid. Then, I took the solids, put them into the food processor and processed them until smooth then added them back to the braising liquid. I then cooked that for a few minutes over medium heat and strained it yet again so I was left with a luxurious and slightly thickened sauce. I then served the whole dish over egg noodles. Classy.

I’m gonna use this dish to bag me a new woman.

New recipe

So last night I just wanted to throw something together, so I gathered all the crap in my fridge I wanted, and needed, to get rid of, devised a plan to deal with them, then did it.

And it was heavenly.

I have no idea how it turned out so well, but it did. It’s not perfect (or fully written out yet) and I’m currently doing what I can to make it better, so I won’t post it quite yet but I will describe what it is. Essentially, it’s chicken thighs braised in a liquid of chicken stock, dry white wine, dijon mustard, thyme, and some aromatics. It was relatively quick, incredibly easy, and delicious.

Now wipe up that drool and eagerly anticipate the recipe 🙂