Genes and Environment

In my Biology and Cognitive Science of Communication course last year, one of the #1 themes–one of perhaps 5 ideas that I really hoped students would understand by the end of the course and take away with them–is the notion that genes/innate biology and environment have, for the most part, mutual effects on outcomes (including/especially behavior) that cannot be parceled out in to X% and Y%.  That is, the interaction between genes and environment is usually much more important than either by itself.

Of course, this is not always true.  There are extreme versions of both–single-gene traits (e.g., color blindness, Huntington’s Disease, many others) and trisomies (e.g., Down Syndrome) obviously have a very large, direct effect on outcomes.  Likewise, extreme environmental circumstances (e.g., Fetal Alcohol Syndrome, head trauma, sensory deprivation) can have large, direct effects.

But for the most part, it’s an interaction–and that’s an easy, glib line to memorize, but I think it took students awhile (and, for that matter, it took me a long time) to really grasp what that means.  But this morning I was perusing my new 23andme.com* results and I came across a good example.  Below the cut is copy pasta of one of my results, “Response to Diet.”  This result reports on 3 SNPs (essentially, genes) that research shows to be associated with the link between diet and obesity.

Now, 23andme.com calls these “preliminary results” because each link only has one approved study that goes with it, and there are a host of statistical issues with the way that much research is done on gene effects (basically, it’s correlational data mining, so unless you have MANY studies showing the same association repeatedly, there’s always the possibility that a given result is a chance fluke rather than an actual relationship).  But let’s pretend for a moment that they’re associations that can be taken at face value.

Each of these genes has 3 known variants (this is not the only way it can happen, but it’s usual for the SNPs that 23andme reports).  Scientists doing gene studies compute odds of whatever outcome they’re interested in (e.g., obesity, Parkinson’s Disease, etc.), comparing the less usual variants (i.e., mutations) to the most common variant (i.e., “normal”).  Sometimes the mutation seems to be protective–it does better than the most common variant (e.g., it is correlated with lower odds of heart disease than the general population), but often the mutation is associated with higher odds of things you don’t want.

The results below the cut are interesting because they specifically relate to response to diet–that is, how my body interacts with the environment. Thus, these aren’t “obesity” genes in the simplistic sense–having a given variant causes obesity–but they are (perhaps) genes that determine how I metabolize different kinds of foods, and thus what kinds of foods are likely to help me lose weight or make me gain weight.**

So the genes themselves are not causing weight loss/gain.  Neither is my diet alone.  You can’t say it’s 30% genes and 70% environment.  It’s genes AND diet (environment).  The effects of the genes are conditional upon what food I eat, and the effect of food I eat is conditional upon my genes.  Their effects cannot be separated.

I think this is also interesting to interpret the wide variety of fad diets out there, and how so many people can swear that a given fad diet is THE way to lose weight because it worked very, very well for them.  How can Atkins work for some people, and low-fat diets work for other people?  I suggest that those people have different genes like the ones below (assuming this research pans out).  This isn’t even that earth-shattering of an idea–maybe some people store carbs more easily than others, whereas some people store fats more easily than others.  Human metabolism is ridiculously complex–you learn the Krebs cycle in high-school or freshman Bio and think that’s complex?  That’s just baby stuff, and really scientists have only scratched the surface of figuring out how we do the biochemical wonders that we do.***  It’s no surprise, to me at least, that the wide range of individual differences in diet efficacy could have some underlying genetic cause.

And my particular results affirm why I have personally had success with low-fat diets and not with low-carb diets (that, and I’m also a carrier for MCAD deficiency–which apparently even carriers have lower-than-typical MCAD levels, so eating very few carbs tends to do things like make me faint).

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* If you are not familiar, 23andme.com is a company that, for a fee and a container of spit, tells you about your genes.  They only provide results that are based on some baseline level of expert-vetted (as well as peer-reviewed, published) research.  For that reason, though their information about my genes doesn’t change, they periodically update what given results MEAN based on new research.  You can also download the full result that lists every gene that they genotyped, which despite the fact that it is not a full sequence, is 8MB of text–that’s a lot.

** I phrase things this way because I am currently, um, larger than I would prefer to be–curse you, baby weight that never left!!–but the reverse is obviously also true if you are one of those folks who have trouble keeping weight on.

*** You know what’s scary, that I did not know prior to being married to someone in Big Pharma?  A great many drugs on the market have unknown or only theorized mechanisms.  They don’t really know how they work.  Drugs are developed by testing a bunch of molecules (usually, ones that have something in common with another drug/compound that is already known to work) to see which ones are biologically active, and out of those which ones do the things that we want with the fewest side effects (in a very simplistic nutshell).  It’s very much “throw stuff, see what sticks.”

[See below for my 23andme "Response to Diet" results]

United Airlines sucks for traveling with children

I have been meaning to regale our story about traveling on United Airlines over Winter Break, but for awhile I was too angry to write this without including a bunch of inappropriate language.  I have calmed down, but it is still worth writing in case I ever suffer amnesia and think it might be a good idea to book a flight on United.

(I should note that we fly with the kid a lot. In her 2 years, she has been on at least 25 flights including connections. It always goes as smoothly as one can expect with a small child, and the only reason we’ve ever had to dread flying with her in the past is getting a metric ton of baby gear–and, when she was younger, breast milk–through security.)

I don’t know if it’s United’s policy to not let you choose seats on flights they plan on overbooking, or if the flights were already overbooked when I bought the tickets, but we were unable to choose seats for our flights to and from Denver for the holidays.  In the past, this would have been a minor annoyance, but while traveling with a toddler…well, I assumed it would still be merely an annoyance, because for some bizarre reason, I assumed that with all of today’s technology at their disposal, any intelligently designed system would not allow a 2-year-old child to be seated alone.

Hahaha.

APA style

In a hypothetical reality where I have the kind of free time to devote to nerdy sidequests personal crusades, I would put serious effort into reforming APA formatting guidelines.

APA 6 already made some good headway in this area, especially in the reformatting of levels of heading.  I know that people who had already become set in their ways didn’t like that, because everyone hates memorizing new arbitrary rules of style.  But aside from recent modifications, APA formatting guidelines exist because of typewriters.  Before APA 6, you had a complicated set of headings that involved ALL CAPS and italics (formerly underline) because caps and underline were all you could do on a typewriter.  Now we have fancy-schmancy things like bold, so headings can actually stand out from the body text.  Yay!

But lots of things remain from the old typewriter days.  Does anyone know why we have a running head and define it on the first page?  It’s because in the old days scholars would send in typewritten manuscripts with a title page identifying author info.  The editor pulls off the title page and sends the anonymous manuscript out to reviewers (by mail!), then gets it back with actual red marks on it and needs a way to match it back up with identifying information.  I know there are still a couple Luddite journals out there that take paper submissions (I don’t know how many of them use APA style, however)–but by and large this is a completely unnecessary practice that continues out of tradition.  

But who cares–how hard is it to just type up a running head? No big.  What is perhaps more significant is the resistance of APA to put figures and graphs inline with the text.  Really? We still need to attach them to the end?  This practice dates to when you would have attached ACTUAL PHOTOGRAPHS, hand-drawn graphs and figures, output from a “supercomputer,” etc. that you needed to attach to your typewritten manuscript (and that would be captured to print in the journal with a camera… with film).  Now it’s actually (arguably) easier to put these things inline than it is to attach them to the end of the manuscript–especially if you’re using reference-management software or automatic endnotes that seem to think it knows better than you where things should be placed, making it difficult to put things in a single document AFTER the refs or endnotes.  Moreover, it is a LOT easier for reviewers to check your tables and figs when they are presented in with the text than when they are at the end of the document, especially when they are reviewing docs on a computer or tablet (as is increasingly the case).  

So yeah… this is my dream, this is my quest.  If I had the kind of time that Don Quixote did, anyway.

Optimize my tablet!

I have recently acquired an iPad and I would very much like recommendations on how to maximize my tablet experience.  Entertainment is good, and toddler apps are great, but mostly I’m looking for productivity lifehacks.

Right now, the three apps that I’m using almost primarily (aside from Mail, Safari, iCal) are Flipboard for passive reading, iAnnotate PDF for active reading (highlighting & notes, etc.), and Notes Plus for notes, to-do lists, scribbles, etc.

I signed up for an Instapaper account, but I’m not sure I’m going to use it, so I’m hesitant to buy the app .  But I think it would be good to get an offline reader of SOME kind, because I’ve got the WiFi model.

Also, a tangent:  I was really mad that for a long time, you couldn’t tether the iPad to the iPhone without a jailbreak.  Apparently this issue is fixed (see also this).  I will update both devices and find out.  My fangirlishness faith trust in Apple may be restored, ish.

/tangent

Ahem.  So, yeah… any recs?

Quack science and medicine

I’m doing a poor job at keeping up my blog (funny how teaching 2 classes and working on a dissertation will do that) but I wanted to share this link and this link to pharma chemist Derek Lowe talking about quack science and medicine, because it’s pretty much exactly what I would say. Especially the stuff about the quest for “natural.”

Natural isn’t necessarily good for you. Lots of natural things are poisonous. They don’t want to be eaten/ingested.

Also, a big point that Derek mentions just briefly but that I think is really important is the (false) idea that we are, by default, perfect and healthy. Modern medical interventions, “lifestyle” problems, bad upbringing, or other human mistakes are required in order for poor mental or physical health to result, and we would all be happy, well-adjusted, and cancer- and disease-free if we would shun the evil ways of modern science/industry and get back to living/eating/bathing/parenting the way that Nature intended.

There’s this related idea out there that it is possible to optimize. That there is some ‘perfect’ way to live, and if you can just find that perfect way, you will have perfect health and well-being. I actually think this kind of thinking comes about from living in a technological society surrounded by things that are designed to function in a particular way, and if you use them correctly, they’re not supposed to break (and if they do, you can collect on that warranty and get a new one). But our bodies aren’t warrantied. They’re not even designed to work properly. They’re designed (by natural selection) to work WELL ENOUGH, MOST OF THE TIME, to have babies that survive to do the same thing. That’s it.

And nature can only work with what it’s given. It doesn’t design out of whole cloth. We’re really just a set of kludgy hacks–unlike in software development, nature can’t say “Screw backwards compatibility–we’re going to do a complete architectural redesign with the next version, because that will let us have better features and performance!” Nope, you get whatever features and performance are possible within the constraints of the current system. Slowly. Incrementally. And non-intelligently (so even if a better system is THEORETICALLY possible given the current system, if the cards don’t end up falling that way, it doesn’t happen).

So there aren’t guaranteed to be “natural” solutions to any of your problems… in fact, there aren’t guaranteed to be medical solutions (another weird thing I see a lot–anger if there is nothing a doctor can do for someone, even in non-life-threatening circumstances, because “they should be able to fix you”).

Personally, I can’t wait for cyborg bodies.

Tennessee’s New Monkey Bill

Right now there’s a bit of a storm in a teacup about a bill introduced in Tennessee–original home of the Scopes Monkey Trial–that putatively would protect teachers from being sanctioned if they refuse to teach evolution, or if they teach intelligent design, or if they don’t worship the Flying Spaghetti Monster.

On one hand, after reading the full text of the bill (it’s very short), I’m a little confused. The bill states that educators

“shall endeavor to create an environment … that encourages students to explore scientific questions, learn about scientific evidence, develop critical thinking skills, and respond appropriately and respectfully to differences of opinion about controversial issues”

and that

“teachers shall be permitted to help students understand, analyze, critique, and review in an objective manner the scientific strengths and scientific weaknesses of existing scientific theories covered in the course being taught,”

while explicitly clarifying that these protections do not apply to religious ideas (as if the number of times the word “scientific” is repeated does not make that clear).

So I’m having a hard time seeing what the fuss is about. Most stories seem to be downright misinterpreting it. One editorial concedes that the actual language of the bill refers to protecting science education and not religion–but then goes on to suggest that this is doublespeak that somehow contains a hidden loophole, and the intent is really “to replace scientific principle with religious ideology.” (Moreover, I’m not sure how a bill that encourages critical teaching and protects teachers from sanction for encouraging discussion–essentially, protecting their speech–is “an attack … on First Amendment guarantees of speech and religious freedoms.” I don’t know how this would be true even if this bill really DID explicitly allow/encourage teaching “alternative theories” to evolution, unless it required doing so.)

On the other hand, there is something really powerful about false controversy, and this bill explicitly uses evolution and global warming as examples of “controversial” science topics. Both happen to be excellent examples of false, intentionally manufactured scientific controversy where, in actuality, no scientific controversy and only political controversy exists.* This bill reifies these topics’ “controversial” label. In fact, what makes me skeptical about this bill is that (as many point out in these hand-wringing articles) if it is being honest about its intent, the bill is unnecessary. But if it is being disingenuous, I want to know what kind of voodoo turns

“This section only protects the teaching of scientific information, and shall not be construed to promote any religious or non-religious doctrine, promote discrimination for or against a particular set of religious beliefs or non-beliefs, or promote discrimination for or against religion or non-religion”

into something that promotes “an atmosphere in which myths and fairy tales would prevail over science.” I mean, I know I’m not a lawyer and all, but that is some truly amazing doublespeak.

 

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* If you think I’m sounding like a paranoid conspiracy theorist here, read Frank Luntz’s leaked 2002 memo to G.W. Bush, especially pp. 137-143. Apparently Luntz has changed his tune, because he has started using his opinion-creation powers for good rather than evil.

That/which

I haven’t updated here in awhile, and I really do have things that I want to say. Trouble is, I’m supposed to be working on my dissertation proposal. Writer’s block is a drag, and I’m in arguably the most epic existential-crisis-producing stage of the academic doctorate. What do I do to mitigate the effects of an existential crisis? Surf the internet until my eyeballs fall out.

While engaging in such rampant time murder, I came across a brief online article that repeatedly included sentences of the following form: “There are multiple companies out there, which secretly exploit starving puppies in third-world nations.”* So.

That/Which

That: I have some pants that are too big for me.

The that clause is called a restrictive clause. It modifies the preceding noun (in this case, pants) to specify certain boundary conditions (restrictions) that are important to the sentence’s meaning. Without this that clause, I just have some pants–which is true, but is not the point of this sentence.

Which: I gave some of my pants, which were too big for me, to Goodwill.

In this sentence, the point is that I gave some of my pants to Goodwill. It also happens that all of these pants that I gave to Goodwill were too big for me. For this reason, the “too big for me” clause is nonrestrictive. Nonrestrictive clauses are a type of nonessential element–a part of the sentence that you could leave out without changing the meaning of the sentence. For this reason, it is set off with commas.

The thing is, unless you’re a stickler prescriptivist, it doesn’t actually matter which word you use, because lots of very good professional writers just always use “which.” What does matter, in terms of meaning and understandability, is your comma usage. Unfortunately, that’s where MS Word’s too-smart-for-its-britches grammar check trips people up. I imagine the online article I came across was a victim of Word, which tells you to put a comma before “which” even if you’re using the clause restrictively. So to go back to my fake example, because it is set off with commas, the starving-puppies clause is nonrestrictive–in other words, that sentence means that all companies secretly exploit starving puppies in third-world nations.

Bottom line:

If you’re interested in using that/which “correctly”: use that where you don’t set off its clause with commas (i.e., in essential clauses), and which where you do (i.e., in nonessential clauses). If you have reasonably good comma usage, this rule of thumb will not fail you.

If you’re not that confident about your comma usage, but Word tells you that you need a comma before your “which,” don’t just blindly add the comma. Only set a phrase off with commas if it is giving you “extra” information about something else in the sentence.

* This is not an actual sentence from the article. Obviously.

Quick link…

This Jezebel post* asking whether students are crazier than ever includes a similar argument to my “Are students dumber than ever” post — yes and no. Yes, they’re more likely to have severe mental illness. No, it’s probably not caused by the stress of college life; it’s probably because more people, including people with mental illness, are getting access to higher education.

* [Warning: Jezebel uses f-bombs.]

A friend stirs up my outrage – to boycott Petsmart

I will begin with a letter I wrote, and then explain how I got here. This letter is to support my friend’s boycott of PetsMart. Basically, for people who don’t want to click the link below and read her long blog post, her cat Ei[se]nstein died during a grooming appointment. They had just moved, so he had a clean bill of health from a vet only a few months prior, and he had been remarkably tolerant of grooming for a cat — he was a Persian and she kept him shaved down, so it was quite routine for him to be groomed. This cat was Miranda’s only local friend because she had just moved to Bloomington, Indiana, for graduate school. (And I would like to remind anyone from PetsMart corporate who may end up reading this — if it were not for people who perceive pets to be close friends and family, you would not have a business.) Worst of all, when her cat died, the employees at this PetsMart location left her with her raw grief in a public area, with no offer of comfort or support, and with no offer to figure out what happened (well, except the vet tried to sell her an autopsy!). In what seems like an effort to cover their own butts, they only offered statements that all boil down to “Sometimes these things happen.”

Before this gets all tl;dr, I encourage anyone reading this to join me in signing Miranda’s petition and boycotting PetsMart until this situation is addressed.

To Whom It May Concern:

I am a proud former employee of PetsMart, and friends with many other current and former PetsMart employees, some of them groomers. For this reason, I am writing you today in hopes that PetsMart will address a situation that occurred in December 2008 at one of your Indiana locations. Specifically, as outlined in a blog post online (http://mirandathom.blogspot.com/2010/06/most-important-recommendation-i-can.html), a friend of mine lost her cat while he was in the care of PetsMart groomers. This incident—both the pet Einstein’s death and the way his caretaker Miranda was treated—reflects poorly on PetsMart as an organization and on its current and former employees. Until this incident receives due attention, I will cease doing business with PetsMart, and will encourage my friends and family to do the same. My own blog post on the matter can be seen at http://amberwb.wordpress.com/2010/07/22/a-friend-stirs-up-my-outrage/.

Thank you,

Amber Westcott-Baker

So, how I got here… It’s kind of interesting to me (as a researcher of attitudes and attitude change) that I’m having a hard time summarizing my former position or how I got here (ah, consistency bias).

I didn’t originally want to support this boycott. As a former PetsMart employee, I did not like the way my friend characterized this incident as “PetsMart killed my cat,” rather than some specific PetsMart groomers killed her cat. My initial position was that the organization PetsMart is separate from the action of its individual employees when those actions break with store policy–which certainly would be the case if, as she suspects, the groomers gave her cat a sedative or did anything else other than groom her cat.

However.

What I failed to consider before was the fact that an organization is made up of its employees, and its actions are the summed actions of its members. If those employees did break with store policy, were they held accountable? Does PetsMart have a SOP for handling a pet death? If so, why was it not followed in her case? (I am assuming it wasn’t, because the way she was treated reeks of diffusion-of-responsibility — no one seemed to know what to do or how to respond.) Are records kept of deaths, and are they investigated in any way? From my experience as an employee and friend of groomers, I know that sometimes pets die from stress or overheating — rarely, but it does happen. What I don’t know is whether there is a standard way of handling it.

I wanted to view her incident as unique, not a symptom of a systemic problem with PetsMart as an organization. However, the way that she was treated in the aftermath of Ei[se]nstein’s death makes this an organizational issue. It means that when anyone takes their pet to PetsMart and the worst happens, no one in the organization will know what to do or how to respond to real grief at the loss of a family member. It means that the bereaved will have no way of knowing whether their pet died of natural causes (stress, some underlying condition) or mistreatment/neglect unless they have their wits about them enough to preserve the pet’s remains, have an autopsy, perhaps hire a lawyer… which, BTW, are all things that only people of privilege have the social and economic capital to do.

Miranda has her own list of things she wants to happen to resolve this situation. Personally, at the very least I want someone from PetsMart to acknowledge and sincerely apologize for her loss. I want them to investigate this PetsMart location and the number of pet deaths that have taken place there. I want them to develop Standard Operating Procedures and actually train their employees to deal with pet deaths–or, if they have these procedures and training policies in place already, investigate why they were not followed in Miranda’s case.

Until that happens… PetsMart, you’re dead to me.

Broken systems: Teaching evaluations

Teaching evaluations are a broken system.

For those not familiar, pretty much all colleges and universities have course evaluations at the end of a term where students have the opportunity to provide anonymous feedback about the course and the teacher.  It’s usually a bunch of bad survey questions, and, at least on my campus, you’re ranked relative to other profs or TAs in your department and in the campus at large.

A couple problems with this. First, the numbers are meaningless unless they are compared to something else (indeed, many of the questions here are phrased specifically as “how would you rate [blah] compared to other [blahs] on campus?”, making them especially meaningless standing alone), but comparing everyone against each other is a zero-sum game. No matter how good your teaching is on campus, there are going to be people on the bottom of the distribution.

Survey numbers in general are a really bad way of getting high-stakes data (for one, there’s a self-selection bias in completing it at most schools), and even worse is using data from a “survey” that has had very little thoughtful survey design and no validity checks put into it. And these data are high-stakes–the more teaching-oriented the school, the more high-stakes they are. But the students don’t know this… nearly always these surveys are phrased in terms of “opportunities to improve the course,” but behind the scenes they are used in hiring, merit-raise, and promotion decisions. It might be interesting to run a study (too lazy to see if one has been done already, though I wouldn’t be surprised if it has)–rate a professor with the framing of the instructions emphasizing course improvement or with emphasis on hiring/raise/promotion opportunities. I mean, it’s kind of amazing to me that we don’t disclose how this data is used.

That brings me to the last point: the asymmetrical nature of the feedback. Teachers have to give high-stakes, potentially ego-threatening feedback to students (in the form of grades and evaluation of student work), sometimes to their faces and always non-anonymously, but students are given the opportunity to provide high-stakes, threatening feedback anonymously. Most or all schools have students complete the evaluation before the final grades are released (but the teacher doesn’t receive the results until after); but obviously they don’t complete it before they have received grades and feedback on everything else in the course thus far. Clearly students will provide feedback differently if the professor/TA/whoever knows who they are–that is the whole point of anonymous feedback, to get their “real” opinion. But there is not such thing as a “true” opinion, and the asymmetry of evaluation opportunities is potentially harmful. For one, it leads to grade inflation and softening of course material–when the class is too hard or students don’t all get As, course evaluations go down. Course evaluations are high-stakes. So instruction becomes subservient to the anonymous feedback of students, who, just like on the internet, will say the kinds of things or provide the kinds of ratings that they would never dream of saying to someone’s face. Here’s a gem from the most recent teaching evals for my husband’s cousin, who is a professor of media comm: “Dr. [cousin] wears baggy pants that looks like he’s wearing a diaper.” On one hand, maybe he didn’t know and who else is going to tell you that? On the other hand–really?? This how seriously his students take these evaluations; this what will (partially) decide his next merit review?!