Tag: science

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At Work and Working

Now that I’ve been working at the University of Iowa for over 3 months, I figured I’m past-due to explain what exactly I’m doing. Honestly, it takes about that long when you’re in a new job like this to figure out what’s going on, who you’re working with, and what the general trajectory of the position really is. Suffice to say, it’s all been very interesting thus far and I’m enjoying myself.

As I’ve stated before, I’m a “Postdoctoral Research Scholar” in the College of Pharmacy at the University of Iowa.  A “Postdoc,” as we’re commonly referred to, could be equated with a medical doctor’s “Residency” period.  At this point in the career, you are above a Graduate Student (i.e. no longer taking classes), but you’re still below a full Faculty Member (i.e. no responsibilities with committees, teaching, etc.).  Basically, you have more responsibility and freedom than you did as a Grad Student, but you still report to a mentor for training and guidance.  I have been adjusting to this dynamic over the past three months, but it will probably become more apparent as the school year starts and the graduate students in the lab start attending various functions that I’m not required to attend anymore.

Speaking of which, the other students in the lab are cool.  They certainly aren’t like what I experienced at Saint Louis University (no alcohol allowed on campus…stupid public schools… :-P), but they are a dedicated bunch that do good science.  This is also a larger lab environment than I became accustomed to at SLU, with 4 graduate students and a lab manager (and now a postdoc) in this lab alone, plus all of the other students in the other labs we work with.  The grad students in our lab are working on related, yet different, aspects of Parkinson’s disease, ranging from the effects of neurotoxins on PD-like symptoms to protein binding to dopamine metabolism.  One thing I’ve noticed is that this lab is much more Chemistry oriented than anything we had at SLU.  Considering that I haven’t taken a Chemistry course in over 5 years, I’m having to remind myself and/or re-learn some basic concepts that I haven’t had to use since then.

However, that’s kinda the point of a postdoc.  The general rule of thumb in choosing an appropriate postdoc position is to a). use techniques you already know in a different scientific field, or b). stay in the same scientific field but learn completely new techniques.  I would fit into the latter category, as I’m still working in PD research, but I’m using Chemistry much more than I did in Grad School.  The ability to use mass spectrometry as an analytical technique is especially exciting in that it’s something I’ve wanted to learn more about since Undergrad, but haven’t had access to the equipment to learn on.  Now I do, and I have a variety of scientific questions built up in my head over the past few years of things to look at.

I have just started working on a grant.  The National Institutes of Health (NIH) is the primary government entity that provides scientific research funding, and they offer an F32 grant for Postdocs designed to help defray the cost of their employment, but also provide the funds for you to train in things you don’t know much about.  The application is due in December, so I’ve got some time, but right now I’m working on getting some preliminary data to include in the 6 page research design portion (6 pages is very, very little…I could write 20 pages today on the subject, but figuring out what is important and what isn’t will be the challenge).  The NIH has a relatively high fund rate for F32s, but the award is by no means guaranteed.  I’ve never submitted one before, but I’m going to do my best to write the best one I can.

Regardless, the lab itself is a good learning environment and I’m learning more and more about my co-workers every day.  It took awhile to figure out all of their “inner-workings” (i.e. who will take to my sarcastic personality and who won’t…), but I’m getting closer.  The science itself is very interesting and I feel like I’m learning, hopefully preparing myself for what lies ahead.

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Primer: Mass Spectrometry

These posts, tagged “Primer,” are posted for two reasons: 1). to help me get better at teaching non-scientists about science-related topics; and 2). to help non-scientists learn more about things they otherwise would not.  So, while I realize most people won’t read these, I’m going to write them anyway, partially for my own benefit, but mostly for yours.

My postdoctoral fellowship here at the University of Iowa still involves research on the mechanisms by which Parkinson’s disease progresses, much like my research at Saint Louis University, but I’m employing different techniques.  In an effort to explain those techniques, I’m going to try outlining them here, as it’s a technique that’s “tossed around” on shows like “CSI:” on an almost weekly basis.

Mass Spectrometry is a technology developed over 100 years ago and has been employed by researchers for much of that time.  The high cost of procuring one of these instruments (easily in the $10,000s, if not approaching $100,000+) makes them somewhat difficult to find in the undergraduate setting, and sometimes difficult to find in graduate schools.  Larger institutions, such as the University of Iowa, will have a few of them, but more than likely, you’ll have to share the instrument with quite a few others, not-so-patiently waiting their turn.

The instrument I’m using is called an LCMS-IT-TOF, pictured above.  The acronym stands for “liquid chromatography mass spectrometer – ion trap – time of flight.”  Each section of the acronym represents a distinct component of the mass spectrometer: there are different components that can be inserted to achieve similar analytical results in a different fashion.  Some components are better for some types of analyses, while other components are better for others.

But, in keeping this relatively simple, I won’t go into it each part.  Feel free to check out the Wikipedia article on the subject if you really want to know more about it, but basically, a mass spectrometer is divided into three primary components:

  • A source
  • A mass analyzer
  • A detector

The “source” effectively destroys whatever you’re wanting to look at.  There are a variety of different sources one can have in their configuration (e.g. MALDI, ESI, ACPI, etc.) In my case, let’s say you have a protein you want to investigate.  The mass analyzer can look at it, but the nature of the type of data it provides makes it much easier to break the protein up into smaller bits first.  Therefore, the source breaks up your relatively large molecule of interest (such as the protein in our example) into smaller, more manageable pieces.  As with many other things, taking things in “baby steps” is much easier to deal with.

The “mass analyzer” is necessary to help with sorting of all those small, manageable pieces.  Think of this process like a box of cereal (I know, right?). Specifically, Frosted Mini-Wheats.  When you open the box, you’ll notice that there are mostly fully-formed Mini-Wheats at the top of the box.  As you continue on toward the bottom, you’ll start seeing some smaller pieces, some that may have split in half, for example.  And at the bottom of the box, you’ll see all the individual wheat fibers and sugar frosting.  The same premise holds for a mass analyzer.  All those pieces of protein broken up by the source are in different sizes, and the mass analyzer helps sort them out in such a way that the small pieces, medium pieces, and the large pieces are all separated.  As with the source, there are many different types of mass analyzers (e.g. TOF, IT, Quadrupole, etc.) used to carry out this work, depending on what you’re looking at.

The “detector” is the piece that really gives us the information we want.  After those bits of sample are sorted, they each hit the detector one at a time and the detector tells us what the mass is, typically by actually reading the electrical charge of the sample.  Typically, the source (sometimes referred to as an “ionization source”) introduces a charge to each piece of the sample, allowing for the detector to…um…detect them.  🙂

So, how is my work fitting into this?  Our lab is interested in how a particular molecule, 3,4-dihydroxyphenylaldehyde (DOPAL) may be involved in Parkinson’s disease.  DOPAL is a metabolite of dopamine, the neurotransmitter necessary in order for you to make voluntary movements.  When you run out of dopamine (or the cells that produce it, in the region of the brain where you need it), you get Parkinson’s disease.  Dopamine is present in those cells, which therefore means DOPAL is present, too.  DOPAL is an aldehyde, which means, on a chemical level, it can bind with other molecules relatively easily.  What we want to know is whether DOPAL may bind to proteins within those cells.  This may matter because cells tend to function in certain ways, and if their individual parts (e.g. DNA, organelles, proteins, etc.) get modified somehow, they won’t work properly and, subsequently, the cell will kill itself to prevent further damage to surrounding cells and tissues.

We want to see whether DOPAL binds to any proteins.  If we can find proteins that DOPAL binds to, and if we know what those proteins do inside a cell, then we may be able to a). protect them against DOPAL’s binding, or b). develop drug targets toward those proteins to help prevent them from causing death of the cell.

How does mass spectrometry fit into this equation?  Back to our early example of a protein being introduced into a mass spectrometer.  The instrument will tell us how much a protein weighs on a molecular level.  We also know how much a single molecule of DOPAL weighs.  We can, thus, use a mass spectrometer to see whether the mass of a protein increases when DOPAL is present.  If that occurs, we can show that DOPAL has bound to the protein.  We can also get information as to where on the protein DOPAL bound, or how much DOPAL bound to the protein, and so on.

In the image above (upper left), you can see some vertical lines we refer to as “peaks.”  Each peak represents a single mass of a given protein or molecule.  You can then take that peak and “fragment” it into smaller peaks.  You can do this multiple times (e.g. MS, MS2, MS3 and so on…).  Fragmentation patterns give you an idea as to what makes up a complex molecule.  For example, if you went from MS to MS2 and had a loss of 18, you could say that you lost a water molecule during fragmentation (O=16, H=1…H2O=18).  In the case of DOPAL, we would see an increase in mass (and a shift of the peak) of 151, depending on how DOPAL bound to our protein of interest.

So, basically, that’s what I’m doing in the lab.  There’s quite a bit more to the story than this, but I think I’ve simplified the concepts to a mostly understandable level.

Probably not, though.  🙂

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A Need for Expulsion

Mike has been Facebooking and blogging about the subjects surrounding the material in the Ben Stein documentary, “Expelled: No Intelligence Allowed.” Primarily, Mike got to thinking about it after reading an article by evolutionary theorist, Richard Dawkins, where he says that Stein distorted things Dawkins said in the documentary. Admittedly, Mike hasn’t actually seen the movie (as of this writing), and neither had I when I first read his post, but thanks to the wonders of Netflix Instant Queue, I took the time to watch it.

In his blog post, Mike argues that one of, if not the, primary issue in the debate is a lack of civility, where both sides (Creation vs Evolution) take things so personally that they cannot have a reasonable argument about the matter. I’ll leave that discussion to Mike, however, as my problem with the whole thing is a general ignorance of the definition of “science.”

science –noun

1. a branch of knowledge or study dealing with a body of facts or truths systematically arranged and showing the operation of general laws: the mathematical sciences.

2. systematic knowledge of the physical or material world gained through observation and experimentation.

…

Now, the key in that definition is “…gained through observation and experimentation.” I know I’ve talked about this before (stupid Lee Strobel…), but the definition of science is quite important to understanding what the problem is with the debate.

By the definition put forth above, Intelligent Design (and, relatedly, Creationism) is not science.  I can say this with conviction because I know that in order for it to be science, it must be testable.  If you cannot test a theory, then you cannot consider it science and it must stay firmly in the realm of philosophy.

philosophy –noun

1. the rational investigation of the truths and principles ofbeing, knowledge, or conduct.

…

5. a system of principles for guidance in practical affairs.

Philosophy is very good about providing analysis of an argument.  One could even describe them as “thought experiments,” where one ruminates on a particular moral or existential issue and comes to a conclusion.  However, those conclusions are hardly “evidence,” as they cannot be reproduced by other individuals performing the exact same experiment with the same parameters.  If one person has a “thought experiment,” their experiences in their own lives will inform their conclusions, leading to differences between individuals.  Science, on the other hand, holds specific variables consistent so that any individual can come to the same conclusion, irrefutably.  If I drop a ball in Iowa and you drop the same ball in Missouri, or China, they will both hit the ground in the same amount of time (assuming the ball is held the same way and the height it is dropped from held constant, but only the location of the experiment has changed).

This is, inherently, the issue: Evolution (in the form of Natural Selection) can be, and has been, tested in many, many different ways and it has held up to the toughest of scrutiny; Intelligent Design cannot be tested and, therefore, is not science.  Have all facets of evolution (in the form of Natural Selection) turned out to stand up to that scrutiny?  No, and the Theory of Evolution has been modified when that new evidence has appeared.  I can’t think of a time when Creationism/Intelligent Design has been modified when new evidence has been presented.

Creationists have been trying to get Creationism in public schools for decades, believing that Evolution is not only incorrect, but is somehow anti-Creation.  I’m not going to get into that part of the debate, although I have some pretty clear opinions on it.  I don’t even necessarily have a problem with teaching religion in public schools, as long as they’re all treated equally (i.e. you can teach Christian tenets as long as you also teach the ideas of Islam, Judaism, etc.).  But I do have serious problems with passing off Intelligent Design as science, and serious issues with the people that purport that Intelligent Design should be taught in public schools in science classrooms.

Whether my comments are “civil” or not, I don’t know (they probably aren’t…), but I do know that the proponents of teaching Intelligent Design in science classes are wrong and are doing a disservice to students everywhere.  Science is difficult enough to understand as it is, let alone adding things into the classroom that don’t belong there and simply confuse everyone involved.

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Primer: Pharmacology

These posts, tagged “Primer,” are posted for two reasons: 1). to help me get better at teaching non-scientists about science-related topics; and 2). to help non-scientists learn more about things they otherwise would not.  So, while I realize most people won’t read these, I’m going to write them anyway, partially for my own benefit, but mostly for yours.

Whenever my parents had to try and explain what I was getting my Ph.D. in to their friends or my extended family, the common response would be: “he’s going to be a Pharmacist?” Whenever I’d be asked the question, I’d typically respond with a “sigh” and then continue to say: “The difference is that a Pharmacist sells drugs, and a Pharmacologist makes drugs.” Of course, that’s a simplified definition, but was typically good enough for my purposes.

In actuality, that isn’t completely accurate.  The Dictionary.com definition reads as follows

pharmacology   -noun

the science dealing with the preparation, uses, and especially the effects of drugs.

The Wikipedia article on Pharmacology is also pretty useful, and goes into much greater depth than I prefer to here.  To summarize more broadly, Pharmacology is the study of how drugs work in an organism.  This definition encompasses how a drug gets produced, how it gets into your body, where it goes once it’s in your body, what effect it has once it reaches its destination, and how it ultimately gets out of your body.

According to Goodman & Gilman’s The Pharmacological Basis of Therapeutics (11 ed), the study of Pharmacology can be subdivided into a few different categories, both dependent upon one another.

When a drug enters the body, the body begins immediately to work on the drug: absorption, distribution, metabolism (biotransformation), and elimination. These are the processes of pharmacokinetics. The drug also acts on the body, an interaction to which the concept of a drug receptor is key, since the receptor is responsible for the selectivity of drug action and for the quantitative relationship between drug and effect. The mechanisms of drug action are the processes of pharmacodynamics. The time course of therapeutic drug action in the body can be understood in terms of pharmacokinetics and pharmacodynamics.

So, the study of pharmacokinetics looks at how a drug moves through your body (“pharma” for drug; “kinetic” for movement).  It is important to understand these principles when developing or prescribing a drug.  For example, in the case of sleeping medication, you want the drug to act rapidly in your body so that you fall asleep, however you also want the drug’s effects to last for enough time to keep you asleep…but wear off in time for you to get up the next day.  The study of a drug’s pharmacokinetic properties will help develop treatment regimens that those other doctors (read: M.D.s) can use to prescribe medications accordingly, for whatever the situation calls for.

Pharmacodynamics, on the other hand, looks at how a drug works once it reaches its destination in the body.  Some drugs work primarily in the brain, some in the heart, some in the lungs, and so on.  Many drugs have their function by binding to a receptor on the outside of a cell (example: diazepam [Valium]), perhaps a receptor that is responsible for “exciting” the cell or “depressing” the cell (i.e. increasing a cell’s function or decreasing a cell’s function).  Perhaps Drug A will bind more effectively to that receptor, giving you a more efficient response.  However, maybe Drug B isn’t quite as efficient in eliciting a response.  Along that paradigm, while Drug A may be more efficient, perhaps the desired function by you and your doctor is a more delayed, longer lasting effect, and Drug B could fit that bill (typically, you want anti-anxiety medications to last throughout the day, for example…not just for a few hours).

Knowing principles of pharmacokinetics can help you maximize how much drug gets to the site of action.  Knowing principles of pharmacodynamics can help maximize how much of an effect the drug has once it’s there.  Both of these concepts are essential to effective drug design and usage.

As a brief (yet related) aside, I first became interested in the subject when taking a class on Psychopharmacology in the Psychology department at Truman State.  It was very interesting to learn about how different drugs affect your brain to result in different effects.  For example, a drug like diazepam (Valium) is a drug that’s intended to function as an anxiolytic and sedative.  The basis of its function, however, is that it works on specific receptors that effectively “depress” neurons, limiting their firing ability.  It turns out that function is also quite useful to help prevent seizures, a disorder where neurons fire more often than they should.  So, some drugs that are intended for one purpose can be useful in another, but you need some understanding of how that drug works before you can begin to apply it to another situation.

So, in short, pharmacology refers to the study of how drugs work and, therefore, a pharmacologist works on such things.  I should point out that pharmacists do play an important role in the development of drugs, as well.  Merck and Pfizer employ both Pharmacologists (Ph.D.) and Pharmacists (Pharm.D.), amongst a wide variety of others.

But, they’re quite different in their training.

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Getting To Work

I started working here at the University of Iowa‘s College of Pharmacy on May 10th, so while I’m certainly not familiar with everything yet, I can at least report on some of the new research stuff, as well as the logistical experiences regarding the University of Iowa as a whole. I’ll probably post other tidbits of info about the new job over multiple posts, but for now, I’ll start at the proverbial beginning of the day.

First, let me start by pointing out that parking around the University is nothing short of ridiculous. There simply aren’t enough parking garages close to the buildings for people to park at, which is quite a change from what I’m used to at Truman State or at SLU. Thankfully, Iowa City has done a pretty good job with their Cambus system, which is a free (yes, I said “free”) commuter bus system for any resident of Iowa City or attendee of the University. There are various stops around town, so it actually gets used by a wide range of people. This is my first experience relying on a bus to get to work, however, so things have gotten “interesting” to say the least.

Secondly, let me point out that we live in Swisher, IA, which is a good 10 miles north on I-380 from Iowa City, let alone to the actual University itself. Therefore, due to the parking situation and the driving distance, I decided to start off by parking about halfway down to work at the Oakdale parking lot, a campus outside of town that has bus service, but also has free parking. This worked alright, however, the buses only seem to run every 45-60 minutes, so you really have to be there at a prescribed time, otherwise you’re waiting forever to catch another one. Also, my second day of work, the bus coming to pick us up was in an accident, meaning that the bus that replaced it ended up being an hour late. I ended up driving myself to work and finding a parking lot, which finally cost $15 for the full day of parking.

After that, I signed up for one of the commuter lots closer to campus, one that still has bus access, but the buses come to the lots more often. These lots, however, cost $20 to park in per month. There are two of these lots, both excessively far from campus, but the closer you get, the more expensive the lots become. The next “step up” would be $45/mo, and I’d still end up needing to ride the bus to get to my building. If I read the maps correctly, I’d end up paying $85/mo in order to park in a lot that’s anywhere near walking distance of my building, but it could take years before I’d be eligible to park there. So yeah, I’ve resigned myself to waiting on buses for the foreseeable future, but at least it means I get to listen to more podcasts and use my Nintendo DS more often.

In the afternoon, the bus schedule is also difficult to navigate, but I’m getting better about it. Effectively, for the ride home, I need to be at the stop for either the 4:59 bus or the 5:06 bus…but if I miss those, I have to wait until 5:36 for the next one. After I get on the bus, and get to the car, I still have the 30 min drive home from the parking lot. So yeah, on average, once you take traffic into account at the beginning and end of the day, I’m driving for close to an hour each way every day. That, and I’m staying at work longer than I used to (stoopid real jobs…).

Please keep in mind that this isn’t a complaint: it’s just a reality, and certainly an adjustment I’m having to make as compared to my experience(s) over the last 5-10 years. At Truman, I could either walk from the dorm, or ride my bike to class, taking no more than 5 minutes to get where I needed to go. In order to get to SLU every morning in grad school, I had a 10 minute drive (sometimes less). Going from 5-10 minutes to an hour of transit time is a big jump to make!

Believe you me, though, the amount of time I’m in the car every day makes me ready to have a new one… 🙂

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Crunch Time

December was a pretty crazy month, for many reasons, but I can already see time getting the best of me here in the new year. I’m working on getting things scheduled for graduation, as there’s a timeline of sorts that I have to follow, and I’m getting ready to get this dissertation written. I’m going to turn in my “letter of intent” to the Graduate School at SLU this week to get the proverbial ball rolling, and I have my last committee meeting scheduled for next week to get a date set for my defense. Theoretically, we’re shooting for April to get the defense taken care of, as that should be late enough that I can get everything done (amongst other things…more on that in two paragraphs). I have one paper published and another one ready to go, once I get one last pretty picture of my cells (the microscope I’ve been using is down, so I’m waiting on repairs). Having two papers published should help get the dissertation written almost on its own, so I’m not too concerned about having much writing to do…yet I’m sure the process will be more time consuming than I’m planning for.

I do, however, have a job lined up in Iowa City at the University of Iowa, College of Pharmacy, in the Division of Medicinal Chemistry and Natural Products. Brooke and I both went up in December so I could interview with my new boss, Dr. Jonathan Doorn, while she drove around town seeing if it was a place she’d like to live. The projects running in the lab, the people working there, and the environment in general are quite appealing, and seem like they’ll be good for my career. Brooke has already started looking for jobs up there and has found a few that interest her, so getting this extra time to send out applications and look around at places to live is very, very helpful!

At the same time, Brooke is due to deliver our kid at the end of February, so that is seeming more “real” every day. Dr. Macarthur, my adviser, was also due to deliver her first child on the same day as Brooke, but she went into pre-term labor on December 23rd and now has a son two months early (both Mom and Ian James are doing well)! Ian’s early arrival puts things in perspective, as Brooke could, conceivably, go into labor in less than a month and not be all that early. Or, of course, it could be later as well. In either case, the whole “I’m going to be a Daddy” thing is starting to set in pretty thoroughly, amongst all the other changes that we have in store.

So yeah, basically, everything is getting wrapped up between now and April. In many ways, it feels like graduating from high school or from college where, in that last semester, you feel slightly overwhelmed and unsure of what the future will bring. The addition of a baby into the mix, however, creates a different perspective to work from as, now, child care is a factor, school districts must be considered, doctor’s appointments have to be scheduled, etc.

It’s going to be an interesting semester!

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Denialism

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Jon Stewart had Michael Specter on “The Daily Show” last night, a staff writer for The New Yorker who’s out with a new book, “Denialism.” The sub-title for the book explains what it’s about: “How irrational thinking hinders scientific progress, harms the planet, and threatens our lives.” The interview is about 7 minutes long and covers a wide range of topics, but he mostly focuses on medicine, genetically modified food products, and vaccines.

He begins highlighting how 62 million people have gotten the H1N1 vaccine with no deaths or serious injury, despite half of American adults saying they won’t vaccinate their children or themselves because they believe it to be unsafe. Specter goes on, citing a friend of his that read the book, but still said she wouldn’t vaccinate her child for polio because “there is no polio anymore.” This is true, but only for the United States: polio is still around in other countries where airplanes travel. Similarly, 200,000 people died last year from the measles, another “forgotten disease,” and while none of them were in the United States, it’s not like it would be hard for the disease to spread here.

Specter also talked about how Vioxx “killed” 55,000 people (which, he points out, is the same number of Americans killed in Vietnam), yet Vioxx was never determined to be the sole cause of the deaths: just correlated. Those people had all kinds of other cardiovascular risk factors as well that likely contributed to the deaths. There were millions of other people that were on it and were just fine and benefited from the drug’s actions. Later in the interview, he points out that 45,000-50,000 Americans die in car accidents each year, but we don’t sue the automobile industry or stop using them like we did to Merck after the Vioxx scandal hit. He says, “We know if we lowered the speed limit 10 miles, we would save 8,000 lives, but, we want to get to the mall, so it’s something we’re willing to do.”

The whole vaccine thing just boggles my mind, honestly. A lot of it goes back to the idea of “over-parenting” (there was a nice article in Time Magazine a few weeks ago on that other can o’ worms), where we try to protect our children and ourselves from everything, when statistically, we’ve never been safer than we are now. Vaccines, according to Specter, are probably the single most important health achievement in human history next to clean drinking water, at least so far as the control of disease goes. And yet, there are people out there that continue to believe, against all scientific evidence, that they’re unsafe.

There are a wealth of other crazy beliefs that could be pointed out, of course, like those that don’t believe global warming is occurring (despite all scientific analysis saying it is)…or that mercury in vaccines causes autism, or that the Earth was created in 6 days, or that humans lived with dinosaurs, or that evolution isn’t real, or that the Earth is flat….and so on, ad infinitum…

Ignoring science certainly isn’t the answer. Humanity has developed knowledge over the generations that they’re supposed to use, preferably for the good of everyone. Picking and choosing the science you believe in is ridiculous. If you don’t believe in evolution, then you shouldn’t be allowed to use electricity: science has given us electricity and evolution, and if you won’t take one of those, you can’t have the other.

It’s a pity that rule isn’t enforced, as it would prevent all The Crazies from posting on the internet…

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Travels: Part I

Brooke and I were in different parts of the Midwest last week (or even two weeks ago, almost).  Here’s the first post relating to all that – Brooke’s will follow once she pulls pictures off the camera.

So, I went to Chicago this year for our annual Society for Neuroscience meeting (I only took a few pictures, but here they are if you care…).  We decided to take the train this time around, as something of a change from the typical “hop on a plane” experience.  To be honest, the trip up there via Amtrak was actually pretty nice compared to flying Coach on an airplane: you get much more leg room, slightly more comfortable seats, AC plugins for your laptop (if you want to watch a movie, for example…no WiFi available, sadly…), roomy bathrooms, and a full-service snack car.  The trip was a bit over 5 hours, so it was basically as long as a car ride, but quite a bit more comfortable.

Anyway, we made it to Chicago and got off at Union Station.  Once there, we found a taxi and started heading toward it.  A “gentleman” grabbed our bags and put them in the trunk of the car.  At this point, Dr. Macarthur got in the back seat, and we both noticed that the driver of said car was still in the car, making me wonder who this guy was.  He then demanded a tip.  I was, of course, rather confused by this whole situation, not being used to taxi service in major metropolitan areas, but Dr. Macarthur was kind enough to get rid of him for me.  Once we started driving, Dr. Macarthur told him “Palmer House Hilton” as the destination.  The driver was talking on his cell phone (which he wasn’t supposed to do…), and a few minutes later, we made it to the Hilton Chicago.  Not where we wanted to go.  Then Dr. Macarthur tried explaining this to him, and he actually argued with her about it.  She was not pleased about this, of course.  Long story short, he ended up turning off the meter so we weren’t double-charged, so that was a bit better…  My first exposure to “Chicago,” proper.

The conference itself was pretty good.  Over 30,000 attended, making it pretty crowded.  I wasn’t a huge fan of McCormick Place (the convention center), as it seems pretty poorly laid out (multiple levels, funky entrances, etc.) and not in an area populated by any restaurants, making lunch a bit difficult.  We saw some interesting posters and heard a talk from Dr. Francis Collins, the current head of the National Institutes of Health.  My presentation wasn’t until Wednesday afternoon, the final day of the conference, making me wonder if anyone would still even be around to see my stuff.  Thankfully, I garnered some interest and got to present it multiple times…not as many as last year, but still, much more than I’d expected.

So, we left Wednesday afternoon, again via taxi.  This time, the driver didn’t come to a complete stop at a stop sign, so we got chased by a cop on a 4-wheeler (yes, they have those in Chicago…with sirens…).  The cop was on a power trip, taking advantage of this poor Asian guy that spoke little English.  When the cop went back to his 4-wheeler to input the license and registration information, the driver made the unfortunate choice of getting out of the car to go talk to the cop, who then proceded to yell at the driver: “GET BACK IN THE VEHICLE!  DO NOT EXIT YOUR VEHICLE!”  He knows better now, I guess…  Considering how many people don’t come to complete stops at stop signs, I kinda felt sorry for this particular driver, as he was actually a much better driver than the vast majority of taxi drivers out there, weaving in and out of lanes.  How about you cops on 4-wheelers try picking up some of them, eh?

Finally, we hop on the train for the ride home.  About 5 minutes north of Joliet, IL (which is around 30 minutes outside of Chicago…), we stopped to allow freight traffic to pass by.  Well, they couldn’t re-start our train.  Apparently, one of the computers wasn’t rebooting properly (probably running Windows Vista…).  We spent 2 hours sitting there waiting for the train to get going, and during that time, we were low on power as they’d shut the engines down.  Without power, you a). don’t have lights (making reading difficult) and b). don’t have snack car service, as you can’t use the cash register and can’t use the microwave.   They never actually re-started the train, but instead waited for the next train from Chicago to come down and attach itself to us, so we ended up having two trains heading down to St. Louis, making two stops at each town on the way because there were two trains-worth of people trying to get to their destinations.  Thankfully, Brooke was kind enough to pick us up 2 hours later than planned (12:45 am…).

So, that was my trip.  There were more good things than this (restaurants, some sights, etc.), but these are the more interesting aspects to report.

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Let’s Do The Locomotion

So, tomorrow I’ll be embarking on my first train ride.  Not to say that I haven’t used light-rail metro systems, but this will be the first Amtrak system that I hit up.  I’ll be leaving (eeeaaaaarrrly…) for Chicago to attend this year’s annual Society for Neuroscience meeting.  2008’s was in Washington, D.C. and 2007’s was in San Diego, so Chicago is considerably less interesting to me, but perhaps a train ride will make things a bit more interesting.

We basically decided that, rather than waiting at the airport and flying, we may as well take the 5.5 hr train ride instead.  As I understand it, these trains have quite a bit of leg room (compared to the Coach area of a plane) and a snack car, so it should be more comfortable.

Anyway, I’m looking forward to the trip.  We’ll probably get a chance to head by a few “sights” while in Chicago, as it seems that there is relatively little to see at the meeting on Monday and Tuesday (I present late on Wednesday).  It looks like they put the majority of Parkinson’s-related research on Saturday (when I’m not there) and Wednesday (while I’m also presenting it), so we’ll probably dabble a bit in some posters and then go to Shedd Aquarium or something.

This will also be my last formal presentation of data at a meeting like this, certainly while a grad student at SLU.  I at least think I’m going out with some good work, and the poster looks pretty.  I’ve got some fluorescent images on there to add a bit more color to otherwise boring graphs (I had Brooke help me with some of the color choices, of course, as my Mom saw fit to give me color-blindness…).

Also, as this is my last trip as a grad student, I’ll also be hitting up the NeuroJobs portion of the conference, seeing if I can land a job somewhere.  I’ve sent the resume to a few places, but haven’t really concentrated on it much yet because of various school-related things, and, well, doing experiments and such.  After this week, I’ll be hitting that up in earnest.

Regardless, it doesn’t look like the busy-ness of the last few months is going away anytime soon.  Guess I should get used to it.

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Science Education in the U.S.

I was going to write something about this a few months ago when NPR’s Science Friday did a blurb about it, but they just revisited the same subject again this past Friday and, today, I see another comment from ArsTechnica that goes over the same issue: science education in the United States is sorely lacking and it really needs to get fixed (put simply…).

The basic premise is that there is a divide between those that know science and those that don’t, and that divide is very difficult to surmount. As the ArsTechnica blurb points out, you can look at a set of data (in their example, a graph of CO2 and global temperatures over the centuries) and come to two different, one-sentence conclusions. The correct interpretation, however, takes three paragraphs to explain, and even then, it uses quite a bit of jargon. The problem, therefore, lies in both parties: the scientists can’t explain things succinctly enough to hold the general population’s attention, and the general population doesn’t have enough understanding and background knowledge to “get it” in anything shorter than a few paragraphs. Then, the result is that scientists stop trying to explain themselves and the general population will listen to any interpretation that’s short enough for them to follow, and assume it’s “the whole story.” The vast majority will look for the “quick fix” informative blurb (read: Wikipedia) and won’t, instead, take an extra college-level course in basic biology, chemistry or physics.

You can see the effects of this not only in the climate change “debate” and in such things as the need for vaccinations for young children, or more recently, in the health care debate. Hitting each of those briefly: 1). there is effectively no climate change “debate,” so far as the science goes; 2). the evidence in favor of vaccinating your children is overwhelming, and the evidence against it is ridiculously lacking; and 3). the health care “public option” will not kill your grandmother. These are all examples of very complicated issues that cannot be covered in a 5 min. newscast window to any real degree, BUT if people were educated properly on the background information, it actually COULD, potentially, be explained in a succinct manner.

Obviously, that last example (health care) is only peripherally related to science education, but I think there are plenty of principles from science education that translate into higher learning, in general, and can help promote understanding across the broader population. Not to sound too elitist (which I am…sorry…it’s how I roll), but I’d like to think that my head tends to work in a logical, evidence-based manner: if I’m wrong on a point, for the most part, I’ll accept that I’m wrong when I’m presented with the evidence that proves it. This is also how science works, in general: you put forth an idea (read: hypothesis) and then you look for evidence that supports it, but also for evidence that refutes it. This is the bedrock principle that all of scientific thought is built upon: evidence is required to make a conclusion, otherwise a true conclusion cannot be made and more evidence must be obtained. Things like global warming, evolution and childhood vaccinations have a wealth of evidence in support of them and very little that refute them.

Here we come to the point: the more science-based classes, or education in general, that people experience, the more likely they will be to think in a logical, evidence-based manner and, therefore, should make better decisions about themselves and society. When they are told something on TV or in a magazine or on a blog, they will be more likely to investigate the matter themselves, searching for unbiased, peer-reviewed sources. They will be less likely to listen to the opinions of others without having those opinions backed up by concrete, verifiable, evidence. One would hope that you could simply be “educated” and do all of these things, but there are plenty of “educated” people out there that don’t think very logically and can’t make a reasonable argument for or against a point. More “science-educated” people, however, would potentially help the matter.

Case in point: if anyone had actually bothered to check into the U.S. House bill being shopped around, they would find that there is no such provision for a death panel, as being touted by many on the conservative Right. It just isn’t in there. There’s no evidence to back it up. Yet, because we (read: Americans) are lazy and want things distilled down to a few bullet points, that idea can be propagated and used for nefarious ends.

Anyway, these are just some things I’ve been thinking about recently in dealing with people that are against a public option; and others that believe what they’re told without reading about those things from third-party sources, or at least truly listening to the broad evidence against their view before summarily dismissing it. These are all the type of people that have probably been around since the beginning of time, but I really think that it’s the kind of issue that could be solved by increasing logic-based, science-oriented education not only at the high school level, but especially at the college level. I have no clue how to make that happen unless at the expense of other coursework that is also important, like english, social studies, etc…but maybe it’s the kind of thing where we just need to hire more teachers and start teaching kids 10-11 months out of the year instead of 9 months.

Good luck with that, Andy…