What struck me first about Okbay et al. 2016 was the sheer number of people who had worked on it–2 pages worth of authors and affiliations! Now, having lots of authors can be great because:
1) they can collect TONS of data
b) they bring together complementary expertise/resources
BUT science is expensive and there are limited resources ($$$, time, lab space, research positions, etc.) to go around so we need think about how we’re allocating those precious dollars.
So let’s decide whether the extraordinary amount of money that must have been spent on this study was worth it.
This article was called Genome-wide association study identifies 74 loci associated with educational attainment. What was this study about?
These biologists were looking for sequences in the genome that varied between those individuals that had little education and those who had finished many years of school. These sequence changes are called single nucleotide polymorphisms or SNPs (pronounced “snips”).
Say hypothetically that the scientists had found a gene in which most people who had a PhD had a T in one specific spot whereas most people who hadn’t finished high school had a G. This would be great evidence that that gene affects educational success and that changing that specific letter in the gene affects something in the body (probably the brain) that drives an individual along their educational path.
The authors identified 74 gene sequence changes that seemed to make a difference for education. On its face, that’s quite exciting! But how much can we actually predict by knowing what sequences someone has in these 74 genes?
What did these authors actually look at? They were testing a variable called educational attainment, which is number of years of schooling. They found that together the 74 genes sequences can predict about 3-9 weeks worth of educational attainment.
This is troubling for at least 2 reasons:
1) Number of years of schooling is only one measure of educational success. Did these students learn? Did they remember and apply the knowledge? Did they think critically and learn to communicate effectively?
2) 3-9 weeks is not a meaningful amount of time. If we care about education, it’s because people can achieve more with more education. And sure, people with a college diploma tend to do better than people who didn’t graduate high school. But is 9 weeks (which was their upper range!) going to make a substantial difference in one’s earnings/meaningfulness/ability to give back to society?
And sure, if there was a single gene that predicted 3-9 weeks worth of achievement, fine, perhaps that would be something interesting. But these are 74 genes that you have to combine to even see this measly effect.
Other potential problems (a couple extra are described in the video):
1) This study was done on white guys, all over 30 years old. Let’s just set aside for a minute the fact that this is in no way representative of the general population. Instead, as Bill Nye (who I once hugged!) would say:
When we think about education, we’re trying to help the next generation. So how relevant are these findings to a population that grew up in a totally different environment? (just one example: Today’s kids are born holding a smartphone and that access to technology is totally changing education!)
2) These findings are statistically significant but not meaningful. This is a complicated topic that you can learn more about here, but the takeaway is that the statistics here say that while these findings are likely reliable (=you’ll see them over and over again if you keep testing the same question), they don’t actually matter. That is, the independent variable only predicts a small amount (~3%) of the dependent variable. (And that’s not even getting into the fact that this is a correlative study not a causative one, so the words “independent” and “dependent” are pretty questionable.)
3) The authors found that the implicated genes are mostly involved with neural development, but there’s no indication of whether that was their hypothesis or whether they just tested all the possible pathways and only showed us the ones involved in neural development? Deciding ahead of time what hypotheses to test is important for avoid introducing common statistical biases, and we don’t know if the authors did that.
4) If it’s true that this collection of genes makes a difference for how the brain develops, how is it that this difference only changes educational attainment by a few months? How are cells changing their function in a way that has such a small effect?
Are you convinced that 9 weeks worth of extra education is something to get excited about? To pile this many resources into? To publish in Nature, which is a big deal?
And here’s the catch: it was already known going into this study that >80% of educational success is predicted by nurture, not nature. So why aren’t we pouring more resources into understanding and solving the environmental factors that affect education in a huge way? Especially since we’re going to be hard-pressed to change people’s genes large-scale (even if we wanted to), but we can do a hell of a lot to change their environment.
Please chime in with thoughts, corrections, criticisms, or thoughts about:
a) educational studies
b) allocation of resources
c) publishing in Nature
d) nature vs. nurture
f) anything else!
I’m a big fan of openly discussing and accepting mistakes and failure (ever heard of a resume/CV that includes failures?). These tubes are an example of a mistake I made, as all 3 tubes were supposed to have 3mLs like the middle one). This mistake was no big deal and easily reversible. But like everyone else, I’ve made plenty of mistakes and had failures that have set me back much further. The PhD in Progress podcast calls failures “secret learning” and I love that! Let’s embrace secret learning opportunities.
Note: It’s especially important to be open about failures and rejection if you’re mentoring because your mentees need to get over their fear of failure.
I embrace mine so much so that I recently performed at an open mic a story about how I embrace my experiences with failure. If you’d like to read that story, get in touch!
One of my favorite parts of doing our research involves “dissecting” bags of 4 cells on Petri dishes. They each started as a single diploid cell, underwent a form of cell division called meiosis (the same process that makes sperm and egg cells), resulting in 4 haploid cells.
We use a microscope with a teeny needle controlled by a joystick to move individual cells to specific spots on a Petri dish so we can follow them individually. The different cells have different combinations of gene flavors, so we can then choose exactly which ones we need for our later experiments.
It took a while to learn how to do it correctly and quickly! Once I did, I started enjoying the process.
Heads up to my non-scientist audience: This post is aimed at undergrad/grad school researchers who are already familiar with biology and are trying to understand how a common DNA isolation protocol (called a miniprep) works. That’s why there’s a bit more jargon in this post, which you know I usually try to avoid. Feel free to ask me to clarify or give a non-scientist explanation for anything in this post, or you can just skip this one and enjoy my posts that are aimed at non-scientists.
You’ve done a miniprep or maybe a thousand of them! But you might not know how it works. Each kit is a little different but they all follow the same basic principles.
So let’s talk about what the whole goal is—what are we doing here? You do minipreps to isolate DNA. Not just any DNA—we’re looking for small circular pieces of DNA, called plasmids. Plasmids are incredibly useful tools for biologists! We can use them to put almost any gene we want into the organism we’re studying!
You’ve learned that every organism has a genome, and every cell within the organism has that same genome. Cells read the code of the genome to determine which proteins to make. In addition to the DNA in their chromosomes, bacteria naturally produce these circular pieces of DNA called plasmids. Researchers have taken advantage of the fact that bacteria make these plasmids and carefully manipulated them so that we can now express any gene we want by placing it in a plasmid and transforming it into bacteria.
Once we’ve inserted a plasmid with our gene of interest into bacteria, we can take use rapid bacterial growth to make up huge amounts of the gene we want. Then we explode their cells and extract the plasmid DNA. Once we have the DNA we can do whatever we want with it. For example, we could introduce it into yeast or mammalian cells, or cut out just the portion of this plasmid we want and fuse it to another piece of DNA to make a brand new plasmid.
So, we’re ready to miniprep the bacteria that are living in our culture tube. But how did we get here?
You started with a plate that had a culture of bacteria growing on it. Each colony started as a single cell that grew and divided outward until it became a mass that’s large enough for you to see with the naked eye. You then jabbed a stick into it that has a small number of cells on it, and poked that into a small amount of liquid media in a test tube. That media has lots of nutrients for our bacteria to grow. Now it’s been growing overnight and the few cells you put in have multiplied and multiplied.
Let’s get started! We begin by centrifuging the culture we grew up, using rotational force to pull the heaviest items to the bottom.
Now, you can see that the cells have all been pulled down and the media is at the top. We’ll take off the media and now we just have lots of bacterial cells in our tube.
Now we begin messing with our cells. First, we have to resuspend them into liquid. We use a solution that has
the sugar glucose to maintain osmotic pressure (so the cells don’t explode or shrivel!)
the buffering agent Tris to maintain the pH at a moderately basic level, and
the acid EDTA to weaken the cell envelope. The EDTA will also prevent enzymes called bacterial nucleases from degrading the DNA in later steps.
Next, we’re going to explode the cells! Except, we’re scientists, so we call it lysis. For this, we use a detergent called SDS, which dissolves cellular lipids, including ones in the cell membrane. The solution also has sodium hydroxide which is so basic and thus harsh that all the chromosomal DNA separates into single strands. In contrast, the plasmid DNA is so tightly coiled up that its two strands will be able to stay together.
Next, we’re going to get rid of everything other than the DNA we want, in a process called precipitation. That just means we’re taking something that was dissolved and making it solid again. The solution we use has acetic acid (which you may know as the main ingredient in vinegar) to bring the pH back to neutral. The neutral condition is much less harsh on the DNA, so the chromosomes can become double-stranded again. But the huge pieces of chromosomal DNA can’t come back together neatly as double stranded DNA because of their size, and they get tangled up.
In addition to acetic acid, the precipitation solution also has the salts potassium acetate and guanidium hydrochloride. The columns we use for minipreps have the compound silica in them to bind DNA. Guanidium hydrochloride’s job is to strip water off the silica in the column and off of the DNA. Now that both the silica and the DNA are lonely, they’ll interact with each other. There are also potassium ions in the solution, which form a bridge between the DNA and the silica column. Finally, the solution has the molecule acetate to interact with SDS, lipids, and proteins and pull them out of solution. This whole mess also takes with it the chromosomal DNA, which is all tangled up. The whole thing looks white and goopy.
Next, we do a wash with ethanol. This removes salts as well as any SDS that’s lingering. If we don’t do this, some later applications like restriction enzyme digests won’t work as well.
Finally, we’re going to force our plasmid DNA to move from the silica column above to a solution which will end up coming down into the tube below. We call that eluting. This solution is designed to protect the DNA. Its low salt concentration helps release the DNA from the silica column. The buffering agent Tris maintains the pH at 8, which is just slightly basic. Just like in the solution we used to resuspend our cells, we again use EDTA. EDTA binds magnesium and other ions with a positive charge of +2, so that bacterial nucleases can’t use them to help degrade DNA.
After the solution sits for a few minutes, we do one last spin in the centrifuge and there you have it, your plasmid DNA is in the solution in your microcentrifuge tube!
Get in touch: How are you going to use the DNA you isolated? What other uses can you brainstorm? What other lab protocols do you want to learn about? Also please let me know if you want to make any corrections or add any more info to this explanation.
Thanks to all of the students in Dr. Ella Tour’s Recombinant DNA Techniques class who participated in filming the video explaining this process. I can’t wait till it’s ready to be released!
You down a shot of vodka and then after you start to wonder how many calories it has. You pull out your smartphone and check…100? What, it’s just clear liquid? How is that possible? It doesn’t have any sugar, fat, or protein and isn’t that where calories come from?
To understand this, let’s start by making sure we understand what calories are, and why high-calorie items get turned into fat. We know that foods with lots of sugar, fat, or protein have lots of calories. Calories are a unit of energy. Molecules we eat that provide more calories give the body more ability to do work, in this case, to run its cells.
Your cells need a LOT of energy; they’re constantly making and breaking down proteins, reading their genes, and fighting off invasions. Zooming out from cells to organs, two major hotspots for energy use are your muscles and brain. Both use tons of energy! And that’s just under normal conditions; when something goes wrong in your body, your cells go into overdrive trying to get back to status quo.
So how does food give us energy? It all comes down to a molecule called ATP. (Scientists just love their acronyms, don’t they?) ATP stands for adenosine triphosphate but it could also stand for ALL THE POWER. The bonds in ATP store lots of energy. You can think of ATP like a rechargeable battery: you use up the energy by breaking bonds and recharge them by rebuilding those bonds.
The fat you eat is broken down into fatty acids and glycerol. Fatty acids are turned into water and carbon dioxide. (Yep, the same carbon dioxide that is messing with our ozone.) This happens by processes called beta-oxidation and the Krebs Cycle, both processes that make that powerful molecule ATP. The other molecule I mentioned that’s made when you break down fat—glycerol—also feeds into energy-generating processes that make ATP.
Now, how are carbohydrates used for energy? Carbohydrates (or carbs as we tend to call them) are big molecules that are made up of smaller molecules of glucose and other sugars. Carbs are broken down into glucose molecules, which are used in a pathway called glycolysis to make ATP.
So, how is the ALL THE POWER—I mean adenosine triphosphate—used? I’ll give you just a few examples. Our cells use ATP to move molecules across their membranes and to assemble and disassemble the cell’s skeleton. ATP is also used as a signal within and between cells. The last uses I’ll mention are that ATP is used to make DNA and proteins. As you can see, ATP is pretty important.
So, what happens when you have plenty of energy in the form of ATP? This high energy state promotes pathways that make the fat molecules in your fat cells.
Your fat cells get bigger, and so do you. “Not that there’s anything wrong with that!” Ok I couldn’t help but throw in that old Seinfeld reference. Whether there’s something wrong with being fat is a way complicated medical and societal issue that we’ll come back to on another day.
Ok so now you have a bit of a sense of how the energy from food can get stored as fat. But we talked about how you can get energy from foods with sugar or fat, but alcohol doesn’t have those things.
So what’s up? Even though alcohol doesn’t have sugar, fat, or protein, your body turns the alcohol into something that gets broken down and produces ATP in the process. These ATP molecules are why alcohol has calories. The alcohol that’s in your beer and cocktails is ethanol, which has 2 carbons, 5 hydrogens attached to those carbons, and a hydroxyl group. A hydroxyl is an oxygen and a hydrogen bonded together, and it’s this hydroxyl group that makes ethanol an alcohol.
As you sip on your vodka cocktail, your body is ingesting ethanol, which gets turned into acetic acid in a process that makes ATP. (Fun fact: acetic acid is the main ingredient in vinegar!) The acetic acid is then broken down by the Krebs Cycle, yielding even more ATP molecules.
Another way of looking at energy production is how many kilojoules a process makes. You’re familiar with kilojoules, even if you don’t know it. That’s because a kilojoule is about a ¼ of a dietary calorie. To understand how we count the calories we get from a shot of vodka, you need to know that chemists measure quantities in amounts called “moles.” It’s really similar to how we measure eggs in dozens, except that a mole of something is way way way more than a dozen. If you want to know how much bigger, if you divide a mole by a dozen, the number you get has 22 zeros!
A shot has 1.5 oz, and there’s about a 1/3 of a mole of ethanol in a shot of 40% vodka. The process of metabolizing a mol of ethanol makes 1,325kJ of energy for our bodies. So a shot of 40% vodka has about 400kJ or 100 dietary calories.
What else has 100 calories? 2 cups of strawberries, 1 medium sweet potato, 1 slice of cheese, and 1 slice of bread each has 100 calories. But today we’re talking about beverages. You can find 100 calories in 4 oz. of wine, 7 oz. of beer, 8 oz. of soda if you’re going the non-alcoholic route, or of course, 1 shot of vodka.
Now you understand why this clear colorless beverage can have so many calories—it’s because it provides the body with molecules that feed into energy-producing pathways. So, if calories are something that matter to you, maybe pass up the soda mixer and use seltzer water instead.
And if you had trouble following this math, don’t feel bad. I skipped lots of steps in my simplified explanation, and this stuff is way complicated!
Thanks to Dr. Phil Kyriakakis, Ray Mak, and Alina Sokolskaya for their helpful comments in the writing process.
Still confused about something? Have more questions? Or do you want to add any info, notice any errors, or just want to give me some feedback or ideas for future podcast episodes or blog? Let me know!