Category Archives: Those Other Sciences

The gay gene

I was having a discussion with a friend at the bar the other night and the topic of personality came up. We were mainly discussing how much of it can be/is determined by genetics and I began wondering about the genetics of homosexuality. In particular, I just wondered if being gay was genetic or not.

In reality, I don’t really care if being gay is genetic. Gay people ARE people and therefore deserve to be treated with the same respect and dignity as anyone else, but my question still remains. I’m merely curious about how much of someone’s personality can be considered “genetic.”

I’m of the belief that genes don’t determine, but clearly influence, aspects of personality. (See what I did there? Being vague is what I do best) I’m still not sure of how to proceed with clearing this up in my own head. Any of you have legitimate ideas?

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Filed under social, Those Other Sciences

Recent happenings

I honestly don’t really know what to write about.  So much has happened/been happening that it’s hard to figure out even where to begin.  I guess since it’s freshest in my mind I’ll write a little bit about grad school first.  For the past few months I have been working in a lab as a temp because my grad student status doesn’t officially begin until September 1st.  Unfortunately, that means I have to stop working in said lab at the end of August.  Even worse, it means that I have to get my ass in gear and write up a lab report summarizing my research so that this will count as one of my mandatory three lab rotations (though I’m going to do four).  This is a problem because in addition to all the work involved in “my” project my boss has made me take over parts of three other projects that no one wants to do (I’m decent at a particularly finicky and tedious technique that involves a lot of front end work that no one else wanted to do).

Because of this situation I have a very odd problem.  I’ve been generating data like it’s my job (literally and figuratively… wait, nope, just literally) but I haven’t learned anything new.  I’ve missed the big picture.  I feel like a lab tech again.   Such feelings are not good when one is in grad school.  So for the past week I’ve been trying to play catch-up and figure out what my results have added to this particular field and while I’ve been having success in doing so there’s just so much more I need to learn before I feel comfortable with it.  Maybe it’s a lost cause and no one really expects me to know all that I expect myself to know, but since those people aren’t telling me otherwise I am just going to assume I do.  Well, grad school is off to a fantastic start!  Can’t wait for more of this!

Sarcasm aside I actually can’t wait for the school year to begin.  I haven’t been intellectually stimulated in years and very much look forward to the challenges that await me in classes that range from how to build a patch-clamp rig so we can study individual ion channels on the surface of an axon to how large-scale neural circuits underlie complex behaviors.  It’s gonna be awesome and I am truly excited for the long term, but now is all I know and now sucks.  Oh well, it will get better soon.  It always does.  In the meantime I’ll just listen to a little M83, Drive-by Truckers, Broken Social Scene, and MGMT to get me out of this funk.

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Filed under crazy, grad school, life, marriage, music, sleep deprived, Those Other Sciences

Ultranerd post – feel free to skip

I fully endorse Bio-Rad’s CFX96 and accompanying iScript cDNA Synthesis Kit and SsoFast EvaGreen Supermix.  What literally took me three full days using Invitrogen’s kits took me FOUR HOURS using Bio-Rad’s equipment and reagents.  The PCR efficiencies are ~20% better than SYBR Green Supermixes, Ct values are lower when running a head-to-head comparison (even handicapping the Bio-Rad reagents), run times are less than 40 minutes, and the data is cleaner!  I started and completed a project in one afternoon.  Fucking incredible.

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Filed under animal research, grad school, life, Those Other Sciences

So sad

I gave a quick presentation at my lab meeting this afternoon and felt sad when I realized that all the work I have done over the past month and a half could be reduced to four bar graphs on a single powerpoint slide.  It was the saddest presentation I have ever given or witnessed.  Here is one-fourth of that work.

Sad

It wouldn’t have been so bad if I had some cool pictures of neurons, but no such luck.

Oh, and today I found out that I make less as a grad student than I was on unemployment.  That’s a fun fact to learn.  Fuck.

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Filed under animal research, crazy, grad school, just sad, life, Those Other Sciences

A post worth reading, I promise. You’ll learn a some important things.

In place of the post I was going to write about my fantastic weekend I decided to write one about (go figure) evolution, religion, and my mom.  The idea about this post came about through a conversation I had with my parents over dinner and the ride to the bus station.

A reoccurring theme in my time since college has been a low-intensity war between me and my mother over our disagreements in the science vs. religion wars.  This current episode was sparked by an article in my parent’s local newspaper by an old scientist with “fifty years experience” whatever the hell that means (couldn’t find it online, but I’ll add a link if I do in the future).  I read his opinion piece and much of it made perfect sense.  He correctly, if simply, described what science is and then went off the deep end.  Huge jumps of logic were made by describing biological features and then, with no explanation given, attributing those features to his idea of God (which happens to be the standard Christian one).  This gentleman then finishes his article by calling evolution an “invalid theory” and attributing everything to God.

I think my mother thought she had me cornered when she had me read this op-ed.  I mean, here is a guy who apparently has some credentials (but so do these people, and they’re all nutjobs) and is arguing against what she believes to be my position.  Largely, she was correct in that assumption, but when it comes to something as complex as science and religion the devil is in the details.  Through the conversation I had with my parents (though mostly my evangelical mother) I had to continually correct a number of false ideas about their understanding of science.  Namely, science never does, and never can, PROVE something.  This is a subtle, yet critical point about science that is often overlooked by those not intimately involved in the process.  Over and over I had to correct my mother when she said the word “prove” because science doesn’t “prove” anything (at least in the strict definition of the word).  The word “prove” can be, and often is, used colloquially within certain circles out of simplicity.  If I find, through rigorous scientific trials, that there is less of a certain protein in cell A I will often tell other scientists that I “proved” it because I know they understand what I mean.  However, outside of those circles syntax and semantics become increasingly important and slip-ups need to be corrected.

(I swear this rambling is going somewhere.  This is getting to the crux of my argument with my mother.)

While most people are taught about the scientific method at some point very few are taught about the basic premises of the philosophy of science.  One premise essentially states that natural processes have natural causes (go figure).  This is called methodological naturalism and is the basis of scientific thought.  My mother has a problem with this premise because it leaves no place for a god to exert it’s will upon the natural world.  Now, this is a very important distinction that I am going to explain.  Gods are, by definition, SUPERnatural (OUTSIDE/ABOVE nature) while methodological naturalism (science) is based only upon nature.  Therefore, if you add the premise of a SUPERnatural being in a scientific argument you invalidating it due to one of your premises being inherently flawed.  Science has no preconceived notion about the existence of a supernatural being (one may or may not exist), but it acts as through all natural processes have natural causes.

That was my mother’s main problem (though she had many others), but I was able to get through to her.  I made her honest as a Christian by admitting that her problems with science, and particularly evolution, were not scientifically based, but were instead based only on theology.  Science didn’t back her story up, so she decided to believe what she wanted to in order to continue believing in her idea of God.  I showed her what science has proven beyond a reasonable doubt (but not an unreasonable doubt) and she has decided to reject it based on her understanding of the Christian God.

It was a very difficult two hours explaining this to my parents, but in the end it was all worth it.  My mother is no longer delusional about science and I am happy with my efforts to defend what I have come to know and love, but I can’t help but feel a bit sad at my mother’s dismissal of the only way of truly knowing what goes on in this world around us.  It’s sad really, and I hope other Christians (and all other followers of religions) can one day be as truthful as my mother and admit that they don’t “believe” in evolution based solely on theological principles and stop hiding behind pseudoscience in order to sound more legitimate.

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Filed under Biology and Evolution, christianity, crazy, home, religion, Those Other Sciences

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.

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Filed under animal research, cancer, social, Those Other Sciences

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).

codon(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 GTTTC ATG ————————————-PheGlnSer

——————————- UUC CAAAG 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.

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