Things you’d think we know… but we don’t.

                “Hey, do you want to be an expert witness?” my husband asked me one night.

                “Maybe,” I answered suspiciously.  “What am I an expert on?”

                “Aluminum,” he said rather matter-of-factly.  I, however, started laughing.

                “Oh, I am?  Says who?”

                “Everyone!  You have a Ph.D. in chemistry!”  I could tell from his response that he wasn’t kidding.  I simply smiled and shook my head.

                “I’m not that kind of chemist,” I explained.  “I do biological chemistry.”

                “Aren’t they same?  Aluminum’s a chemical and you know about chemicals.”

                “Not really,” I sighed.

                Oh, there are so many things that I do not know; my incomplete knowledge of the earth’s soft metals is only the tip of the iceberg.  This exchange highlighted one of the many misconceptions about a regular scientist’s knowledge and skill set.  Having a degree in science doesn’t mean that I know everything about every kind of science.  Physics isn’t the same as either molecular biology or cellular biology, nor are those two the same as each other.  Just as a neurologist has a different knowledge base than an orthopedic surgeon, such does a chemist, biologist, physicist and astronomer.   

                “Okay, can you be an expert on explosives?” he asked with greater enthusiasm.

                I just stared at him blankly.

                While walking around lab this past week, I paid attention to the things that my colleagues and I didn’t know that would probably be interesting to those outside of my field.  We all have notions about other professions.  I’m rather certain that my lawyer husband spends all day/every day reading thick legal books and that my chef brother-in-law has encountered every food-stuff ever to grace this earth.  They can tell you why I’m wrong about them, but I’ll dispel some common misconceptions that I run into about scientists.

We’re excellent at math.

                The first day in my graduate lab, an older student asked me to calculate something.  When I asked for a calculator, he looked at me like I suggested nailing my hand to a wall.  When I mumbled that even a pen and piece of paper would be helpful, he sighed and told me the number I needed with a “do better next time” look.  I was humbled.  And scared.  Was everyone in science like this??

                Turns out, the answer is a resounding no.  Even for the simplest of calculations, I still pull out a piece of paper to set up the basic algebra.  I have to.  Others feel similarly, but choose their gloved hand instead of paper for writing out equations.  While a technician, my boss would often write all over his glove, circle the important numbers, and then promptly throw the glove away before doing the experiment.  He’d then pull out another glove and do it all over again.

                Members of my graduate lab predominantly kept to themselves when doing work, but my post doctoral lab is more … incestuous … about experiments; everyone’s in each other’s business.  In turn, this means that we’re all checking each other’s math.  I’ve become the de facto checker because I’m the chemist; most of the biologists would rather think about more abstract things than if they added the right amount of reagents.  I’m not sure if one of my labmates even owns a calculator – he just avoids experiments that require any kind of quantitation.

We’re not social.

                The stories are out there; I know you’ve heard them.  Little can top the blurb posted on my Facebook wall last week about a lively dinner involving several physicists and my friend Jay.  Apparently Jay discovered that those of the physics variety would rather watch white-water rafting (for hours) on the internet than partake because it was less dangerous.  I believe they also squared away that drugs and rock-n-roll are bad for everyone and that long awkward pauses enlighten even the most dismal dining experiences.  I can’t tell you how hard I laughed at this because, while I understand that these people exist, they are not the norm.  I promise.

                Granted, scientists tend to be a little nerdier than most (we read constantly and understand the terms “nanoparticle” and “western blotting”), but we also have frustrations that drive us to the bars just like the lawyers, med students, and financiers of the world.  I don’t think I’ve ever gone to as many happy hours or been anywhere near as social in my life as I was while working on my Ph.D.  I went out with members of other labs several nights a week and had lively conversations.  Okay, it was a lot about our jobs, but mostly our boss frustrations or teaching nightmares.  We rarely bemoaned that our ethanol precipitations of DNA didn’t work and we most definitely didn’t discuss abstract theories unless to say “It makes no sense!”  Often the loudest or the largest group in our favorite bars, we had befriended most of the bartenders, were well-known and well-liked.

                Life is quieter now that I don’t work at a university, but if getting scientists to some sort of event is necessary, alcohol and not making the topic extra ridiculously nerdy is always a good call; the normals from all labs will be drawn out to have a fun time together.  Unfortunately, those physicists up there won’t make it, but their labmates will and we’ll have a good laugh at everyone’s expense.

We always understand the results of our experiments.

                In a recent group meeting, one of my labmates gave a presentation where he openly stated that he got a result that no one in our lab understood immediately.  It was most definitely the truth because the result was so strange.  My PI announced he was uncomfortable with such a public statement of ignorance and that my labmate should re-tailor this area of the presentation.  Myself and another labmate asked why admitting limited knowledge, especially on something that no one had ever encountered before, was a bad thing.

                The entire point of science is to push the boundaries of what we know and understand.  It’s what makes a graduate student get up at 5am to go to lab or a post doctoral associate cry at night when his data isn’t good enough for a Nature paper.  It’s what we live and breathe on a daily basis.  Sure, we go into an experiment having assumptions on how it’s going to turn out, but that’s most definitely not always what happens.  However, even when we get some screwy results, we are usually able to frame them in the context of previously known science.  But, ever so rarely, we do come across data that defies logical explanation.  In short, the community’s knowledge cannot offer any sort of framework.  These moments are rare and to be celebrated.  It was this type of situation my labmate was describing and we have every right to say “WTF is that?”  

                An undergraduate student at that same lab meeting said her friends often ask her why we haven’t found the cure for cancer yet if we know so much.  The answer is obvious, we don’t know everything yet.  Given the complexities that are constantly being discovered about our cells, proteins, DNA, and environmental interaction, I sometimes wonder if we ever will.

REFERENCES

Me, myself and I

               

You use that in lab?

              Forgive me, but I’m continuing through a busy busy time both in my life and in lab so posts are a bit sporadic and not on topic.  I’ve read several ageing papers and will get to writing those up soon, but since it has been so long since my last post, I needed something quick!  I was oddly inspired for this post today while I was rushing to make a post doc ethics meeting (no jealousy, please).  What inspired me exactly?  This thought:

My nail polish is missing.  I’ll stand on this chair so I can see my shelves clearly and maybe find it.  I don’t want to borrow Tim’s again.

                So, there I was, standing on a swivel chair, hunting through bottles of buffers, random scraps of parafilm, and glassware trying to find my clear nail polish.  My motivating force was avoiding using Tim’s (male, correct).  The whole thing struck me as weird, both the fact that nail polish is an essential laboratory reagent and that I didn’t want to use my male coworker’s stash.  I started to wonder what other things in lab are everyday products that would surprise people.  I have a few!

Nail Polish (clear, thanks!)

                In the Henrietta Lacksseries, I talked about how scientists grow cells in dishes (Figure 63.1).  We give them all sorts of nutrients (called media), place them in incubators at the correct temperature, and let them grow in specially designed (and sterile) cell culture plates.  If I can ever get a camera to work on our microscope, I’ll take some pictures and tell you all about cell culture!  

                Sometimes, we want to do more with cells than merely grow them; sometimes, we want to inspect the cells more deeply.  In my Fluorescent Proteins post, I talked about how scientists can put green fluorescent protein (GFP) inside cells.  I also explained that to “see” the GFP, light of a specific wavelength must be used.  For this reason (among many others) scientists need a way to move cells easily.  Sure, we could walk around with the cell culture plate as shown in Figure 63.1, but you can imagine that with one false move the media would be all over the microscope, which, especially a fancy one with lasers, is terribly expensive.  We’re in the business of trying not to ruin instruments worth more than my house.   

                To circumvent these problems, instead of growing cells directly on the dishes, we place a small coverslip inside the plate.  A coverslip is a piece of glass ~ 0.5” x 0.5”.  Cells will adhere to both the plate and the slip during growth.  When we’re ready, we can take out the cover slip, permanently arrest the attached cells in their current state, and finally place them face down on a microscope slide (Figure 63.2).  Walking around with a microscope slide is easy!  

                We don’t want the cells to dry out on the cover slip.  Between the slip + cells and the microscope slide is a bit of liquid called mounting media.  It keeps the cells somewhat hydrated and in the best possible shape for viewing.  We don’t want the mounting media to evaporate.  To ensure that this doesn’t happen, we paint all sides of the coverslip with nail polish to seal the edges.  Oddly, it has to be clear; colored disrupts our ability to see the cells properly on the microscope.  

Milk (evaporated)

                Scientists commonly use a technique called “Western Blotting.”  I’m not going to get into what all this entails right now; I’ll save it for a much longer explanation in a different post.  Instead, I’m just going to tell you that it involves putting a lot of protein onto a piece of a paper (hence the word “blotting”) and one protein on that paper we’ll call A.  We then place the paper in a liquid containing a different protein called B.  We know that A and B bind each other so B should end up stuck to the paper wherever protein A is found.

                Sounds simple enough, yes?  Not quite.  The paper has a whole lot of other proteins besides A.  Proteins come in all different shapes and sizes.  Some are sticky, some are lonely, and some are really similar to protein A.  Protein B, while very much wanting to hook up with Protein A, can get distracted along the way by all the types of proteins on the paper.  Scientists know this and really want to minimize it so they do something called “blocking.”

                Before adding protein B to the paper, scientists set the paper in some milk, which is full of other proteins.  All those sticky, lonely and similar to protein A proteins on the paper can get together with all the random proteins from the milk.  Then, when protein B is added, the other problematic proteins are otherwise occupied and protein B can find protein A more easily.     

 

               

Acetone

                I do not work in an organic chemistry lab so acetone is not frequently pulled out nor do I know the more fanciful uses for this solvent.  But, I can tell you what I’ve used for it in the past: drying glassware.  Organic labs have lots of glassware (some of it is custom-made for particular experiments; many universities have glass-blowing facilities on campus to help create what the organic chemists need) and it is constantly washed and reused.  This is somewhat different from a biochemistry/molecular biology lab (where I work) because we use a lot of plastics.  The difference?  Sterility.  

                A biochemistry lab needs many things to be sterile because we’re working with living beings (cells, bacteria).  It’s essential to ensure that we aren’t contaminating one growth of bacteria or cells with another.  If we primarily used glass, each piece would need to be washed and sterilized between uses.  This is labor and time-intensive.  Why do that when you can buy a pack of 100 sterile plastic tubes for $40?  

Organic chemists aren’t worried about sterility since they don’t work with live organisms.  Their glassware merely needs to be clean and dry.  After being washed with soap and water, the glassware is usually flushed with acetone and placed in a drying oven.  The acetone serves to rinse out any water left behind.  Acetone evaporates much faster than water so pieces only need to sit in the drying oven for a few minutes to fully evaporate the acetone.  Fully drying pieces covered with water would take much longer.

Acetone is, as many women know, an ingredient in nail polish remover (quite the theme today!).  I know several women who have either flat out used the acetone in lab to take off their nail polish or unintentionally removed it after washing a lot of glassware.

Bleach & Tweezers

                I don’t think either of these products should be surprising.  We commonly bleach anything that has come in contact with bacteria or live cells.  This serves to kill off anything remaining alive before we pour liquids down the sink.  As a technician, I frequently had to go run to the grocery store and pick up bleach because we kept running out.  Tweezers are used for several purposes (all related to picking up things, oddly enough) but one of them is to move coverslips around easily.  We’ve come full circle.

REFERENCES

Me, myself and I

The Hierarchy

              I think most people are somewhat familiar with the chain of command in other jobs: CEO, CFO, other COs, supervisors, superiors, etc.  But, if you have never worked in a lab, I’m assuming you have no idea what the hierarchy is.  The lines are blurry, but I’m going to tell you in general how we all line up.

Principal Investigator- also known as PI

                This is the bossman.  It’s his (or her) lab and solely he is in charge of hiring and firing people within his lab.  He is also the money.  Part of science is applying for grants (asking politely for money) so that labs can be stocked with all sorts of things!  

What kind of things does a lab need?  In addition to all those beakers, flasks and stir bars that most people immediately think of, labs also need freezers, refrigerators, centrifuges, pipettes, cold boxes and all kinds of consumables (gloves, tubes, etc).  A lab will also need chemicals (zomg, chemicals!).   I would estimate that within my current lab, we have ~ 200 different kinds of chemicals in either liquid or powder format.  

A PI will also need a staff because most have to give up doing hands on research and instead become the brain of the operation.  He reads, he pulls information together, he reviews papers and writes.  His staff is almost exclusively doing the hands-on research.  That’s where the rest of these people come in.  I’m going to start at the bottom and work my way up.

High School / Undergraduate Students

                High school students typically come to work during the summers to gain experience and see what it’s like to work in a lab.  I can’t imagine doing that in high school.  I found a lab to be overwhelming after graduating college so kudos to high school students who have the confidence to do this!

                Undergraduate students will spend anywhere from just a semester/summer in a lab to all four years.  Some only work during the school year but others will stay on all summer.  Most will use their research towards their degree (as in writing a thesis at the end of their college career) and the rest are probably looking to put it on their resume/med school application.

Technicians

                This is where I started my life in lab.  Technicians are usually people who have just graduated college with a degree in science.  In my case, I coupled that with not knowing at all what I was doing with my life.  I felt as if I was only qualified to work in a lab so that’s what I pursued.  Typical turnover for technicians is about 2-3 years.  That’s enough time for the newly minted graduate to say “Hey, science rocks!” or “I’m going into finance.” 

 Some technicians are older, however.  They enjoy the work and stay.  I know some career technicians and, quite frankly, they are awesome.  While it’s low on the totem pole, techs are really essential to efficiently running a lab, especially very large labs.

Each lab uses technicians differently, but in general, techs do a lot of lab grunt work.  I was in charge of our personal stockroom and needed to order things in a timely manner so we didn’t run out.  I also had to maintain lab consumables that required a procedure to them.  What the hell does that mean?  I was in charge of preparing tips, stock solutions, and common lab reagents.  These were things that you couldn’t buy directly from the store but had to mix together a few things before it was ready to use.

Most technicians also get to do research.  Their tech responsibilities come first, but that normally can’t fill an entire 40 hour week, so a technician will work with an older lab member on their project and, if they’re confident enough, branch out on a project of their own.  Being a technician is an excellent learning experience for anyone who wants to work in science.  You learn so much and will gain an appreciation for any technicians you meet in the future.

Graduate Students

                I’ve heard them also called “pre-doctoral students,” but that’s just silly.  These are students who have joined a graduate program and will do their doctoral research in the lab.  How long does it take to do all your doctoral research?  It depends, but on average it’s ~ 4-5 years.  I was a graduate student for six years but only five of those were doing research in a laboratory (my first year was all classes and much like college).  I’d say this group is the most stable group in the lab.  They are there for a decent chunk of time and know very well how things run.

                Graduate students are watched in the beginning by older graduate students or post docs, but their goal is to become independent researchers.  They are meeting with other professors out of the lab that govern how their research is going and how they are growing as scientists.  By the end of their time there, they have written and defended a thesis and are ready to become post docs (or give up science all together because they are so burnt out…)

                One small note: different PIs have different traditions for graduating Ph.D.s from their lab.  My PI has us sign the post-defense champagne bottle with our names and defense date.  We were all numbered, as well.  I believe I was the 21^st graduate student to get a Ph.D. in my doctoral lab.  Another PI has the new Ph.D. open the bottle of champagne and wherever the cork hits the ceiling, he must sign his name and date.  Getting my Ph.D. was one of the best days of my life.

Post Doctoral Associates (sometimes also called Post Doctoral Fellows or, more simply, Post Docs)

                These are the lab workers that have defended their Ph.D.s and are continuing to do research (aka – they are totally insane!).  In all but rare cases, these people have left their doctoral labs and picked up research in new labs.  Many stay in the same field but some branch out.  Personally, my doctoral work was in cancer and viruses but my post doctoral work is in cellular signaling.  I wanted to broaden my horizons.  Post docs usually hang around for 2 – 5 years.  Yes, that’s another 2 – 5 years of being a lab rat beyond your graduate work.  You are no longer required to meet with outside professors to check your progress and are considered an independent scientist.

Staff Scientists

                If you’re a post doc too long, the institution you work for will typically rename you a staff scientist.

                Post docs and staff scientists will eventually branch off, start their own labs, and begin this process of getting money, hiring technicians, graduate students and post docs so the cycle will continue.

                Now that I’ve explained the set up. I can explain the list of authors on a published paper.

                Consider this reference (Figure 58.1):

                Anyone can write the paper: graduate student, post doc, staff scientist, technician, even undergrads!  The person who primarily did the work is listed first and the other who helped are listed next.  The final name in the list is the PI in charge of these people.  Sometimes labs collaborate so the last two or three names might all be PIs, but the other ordering of names remains the same.

                Aside from the PI, who is considered the most senior in the lab?  The person who has been there the longest.  If you have a technician in your lab who has been there for 14 years, they are well respected.  If you are a new post doc to the lab, you are relying on the graduate students and the post docs to teach you the ropes.  If you are a new graduate student, you are revering the post docs and elder graduate students.  The lines are blurry but the general hierarchy is there.

                As a final thought for this post, here’s a comic from www.phdcomics.com (love them!)

REFERENCES

Me, myself and I

Inflammatory Reporting about CHEMICALS!

            Okay.  This week requires that you watch a video.  Do it.

               

Fox 29 Investigates: Chemicals On Campus: MyFoxPHILLY.com

            Now that that is done, let’s discuss this “newscast.”  I take several issues with it.  However, I also – shockingly – admit that somewhere in this piece is a point worth discussing, but it’s so buried by inflammatory information that we could cook s’mores on it.

                I chose to point out this video for two reasons.  First, they go after my school.  I went to graduate school at one of these universities that was subject to this “investigative reporting.”  Second, so much of what is said is designed to illicit knee-jerk “ohmygodtheworldisending” responses that I can’t just sit here and pretend that this piece is extolling the truth.  Remember my Thinking Critically post?  Yeah – critical thinking failed these newscasters and anyone who believed their reporting.  So, let’s discuss what is truthful and what is sensationalism here, shall we?

Sensationalism – forgive me, but this part will be obnoxious as is befitting that ridiculous broadcast.

One.  Overall reaction: inflammatory reporting.  

The overuse of the words “chemicals,” “powders,” “liquids,” “acid,” and “flammable” just kill me.  

Let’s start with the word chemical.  People have this idea that “chemicals” are bad.  Yeah – water is a chemical; vitamins are all chemicals; your body is swimming organic and inorganic chemicals.  I’m going to even let you in on a small secret – you have arsenic in your body!  That all natural hair dye people cling to?  Full of chemicals.  Everything on this planet is a chemical so let’s stop thinking that everything labeled a chemical is bad.  It’s not.  If we got rid of the all chemicals, you’d be staring at empty space.  In fact, you wouldn’t be here at all.

As for the next two words, just like in the cooking world, some things are powders and some things are liquids.  It’s hardly surprising that “chemicals” also come in the same formats.

The last two are my favorites.  Scientists are required to label cabinets with the words “acid” and “flammable.”  Not only do laboratory workers need to know these things, but if an accident befalls the lab, emergency personnel need to know the major characteristics of these things!  Acids are reactive and need to be stored separate from bases so they get their own rated (and labeled!) cabinet.  Flammables have a risk of explosion at certain temperatures so they get their own explosion-rated (and labeled!) cabinets.  Good grief.

Two. “We even walked by nitrogen tanks!”  

Yes, yes you did.  Nitrogen is ~80% of the air we breathe.  Those (properly built and designed to hold) nitrogen tanks contain liquid nitrogen.  Yes, liquid nitrogen is extremely cold and will give you burns if you don’t have the proper personal protective equipment (PPE!), but if you’re stupid enough to turn on the tank without knowing what it is – shame on you.  (“We mustn’t touch what isn’t ours.” – Severus Snape.)

But, if you are curious, here is what will happen if you do turn it on: the first thing you’d be greeted with is puffs of white vapor, then the hose from the tank would freeze and finally liquid nitrogen would start to spurt on the floor, but immediately boil back into gaseous nitrogen.  This all takes a few minutes.  I’m telling you, the minute the tank started to choke out vapor, you’d be turning that tank off and going to find someone who knows what’s up long before liquid nitrogen starts coming out.

Three. HYDROCHLORIC ACID (HCL) and ETHYL ETHER (C4H10 O)

If you are going to put the fear of God in people, at least spell the terms correctly.  Hydrochloric acid is HCl.  Yes, the capitalization and lowercase of the letters is important.  Ethyl ether is C₄H₁₀O.  Again, subscripting is important – do a small amount of research on what you’re reporting before you plaster your ignorance on the screen.

Four.  We could have “picked them up, stuffed them in our bags, and walked right out.”

Well, I suppose you could have, but good luck “stuffing” a bottle of concentrated hydrochloric acid in your bag.  I’m willing to bet that you will burn yourself long before you get out the door, which would require a trip to the hospital, and then you’ll have to explain that 4 liter bottle of HCl in your bag.  Enjoy being arrested!

Truth – in a rational and respectful tone

Chemicals are easily accessible. 

This is quite truthful.  The report says that the reporters could simply walk into the chemistry buildings of two universities.  Some buildings have keycards and some don’t.  But, even with keycards, people hold doors open.  I’m sure if they had hung around Drexel’s Science Center (it’s new and gorgeous, by the way!) they would have gotten in.  It’s not horribly difficult to get into a laboratory.  Once in, it’s also not entirely impossible to find a lab with no people in it and nick something.  In theory – it’s really not!

However, labs stock lots and lots of chemicals and, as vigilant as we like to be, these chemicals are in really random orders.  I can’t even find some bottles that I know we have.  To steal effectively, someone would need to be staking out the lab to easily find their target or be an inside person.  I’m not saying a thief couldn’t get lucky on one pass through an unfamiliar lab, though.  Stuff happens.

Laboratory personnel are required to ask unknown people in their lab what they’re up to.  If we feel they are suspicious, we are required to call security (building, campus, etc) and a report goes out to the rest of the building.  

Locking up each and every chemical is not possible.  Scientists use so many different ones all day that those cabinets would be left unlocked for feasibility.  This would be like cooking in a kitchen where the cabinets and the refrigerator needs to be unlocked before opening.  Think about how unrealistic that is.

Locking up labs when we leave for meetings or talks during the day is also difficult.  We could carry keys, but the major problem is one room is not one laboratory.  We share space with other labs and have to be respectful of their schedules, too.  Locking doors also makes collaboration and work between labs difficult – we can’t carry keys to each and every room in the entire building.  Scientists are often in each other’s labs borrowing and using equipment.  It’s not as simple as an office job where you can just shut the door and it doesn’t affect other people.

However, scientist do lock up the most egregious reagents.  For example, I use radioactivity often.  It is under lock and key at all times and we have specific sheets recording its usage.  

Can we do better?  Of course.  Many times we think that someone else in the lab knows who that weirdo person is and we don’t ask.  We should be more open and questioning about unknown people.  We should keep our eyes open to people we aren’t sure belong in the hallways or who are hovering around chemicals.  Definitely.

REFERENCES

Original broadcast: http://www.myfoxphilly.com//dpp/news/local_news/fox-investigates:-chemicals-on-campus#.Tz0bxuvDj00.facebook

Repetition

                This post will be my final one for 2011, which became my inaugural year as a blogger.  I’ve enjoyed being able to share different things about science with all of you, so thank you for reading!  I also like having a place to explain what working in a lab is like every single day.  It’s not quite as exciting as Abby from NCIS would lead you to believe (like - at all), but it’s certainly not bad!  We have the freedom to make our own schedules, we sometimes gather up every item in the lab that matches a post-doc’s shirt color and take pictures, we put dry ice in closed containers to create bombs, we can make water balloon gloves, and we are regularly subjected to meetings about which we know very little but need to act excited.  Most of us are poor actors on that last one.

We do, however, have moments of sheer excitement.  These moments typically follow the endless repetition that is troubleshooting one experiment.  

Let’s review the speed at which scientific research moves by reviewing the breakdown of 2011.

January 2011 – May 2011: completion of one experiment

June 2011 – August 2011: exploring different areas of where my project could go; very little headway on anything.  Cue me having a complete meltdown.

September 2011 – November 2011: Completion of a second experiment

December 2011: Mild troubleshooting, writing a paper

                Okay, look that over.  Two experiments = one mini paper’s worth of work.  It took me five months to complete the first experiment and four months to complete the other.  Yes, they were large and multi-layered experiments that required precise work to get them running properly, but that’s a total of nine months.  I could have grown a functioning human in that amount of time. 

Science is patience.  

And alcohol, which serves to dull the insanity that inevitably follows endlessly repeating the same experiment over and over again.

Okay, let’s discuss why it takes so long.  I’m going to focus on my second experiment and explain, in loose details, about what took three-four months.

Let’s say this experiment required four things: A + B + procedure = results.  This means that I mix A and B together, followed a particular procedure and then was able to see my results.  

Oh man – are you ready?  I first had to make A and B.  Making them is no small feat and required a few weeks worth of work to make them and prove that they were made correctly.  Okay, that’s three weeks there.

Next, I had to perfect the procedure for mixing A and B together.  This means that I take a stab at how the experiment should work.  Then, I look at my results.  Inevitably, they are not great the first time around (if they are, well, you have a horseshoe stuck).  So, I need to tweak it.  For example, I say “Well, maybe I let A and B sit on ice for too long.  Let’s try the procedure again but let A and B sit for a shorter period of time.”  This means I go back and do the same procedure again, but maybe I’ll let them sit for 10 minutes or 15 minutes.  I’ll probably do both and check out my results again.  And I’ll tweak more.

Seriously, perfecting the procedure of an experiment can take anywhere from a few days to a few weeks or even a few months!  For me, perfecting my procedure took nearly two months.  Each and every part of the procedure needed to be tweaked and optimized.  This included how much of A and B were added, the length of time things were mixed together, the time I spent working up the experiment, how I viewed the results, the liquid I used to mix A and B, etc.  Ohmygod.  I’m tired just thinking about it.

The best part?  Sometimes you spend so much time perfecting your procedure that you run out of A or B.  This means you must go back to the beginning and make more.  Sure, let’s add another three weeks!  What’s the difference?

When you finally have perfected your procedure, have enough A and B, and are getting consistent results with your procedure, then you do the real experiment.  Up until now, you’ve been working with controls.  Controls are experiments that follow your exact procedure but you know precisely what the outcome will be.  The real experiment is when you follow your exact procedure and add in ONE extra thing.  If your results change from your controls, then you know it was due to the ONE extra thing.  From this, scientists can draw conclusions about that ONE thing.

For example, let’s say A and B will always bind each other.  We have perfected our procedure to show over and over that A and B will bind each other if and only if both are present.  When we do our real experiment, we add in a small molecule with A and B.  When we see our results, we notice that A and B no longer bind each other when the small molecule is present.  This means that the small molecule inhibits their interaction.

For me, running my real experiments took about two weeks.  

This all adds up to three-four months worth of work.

Sigh.  For these reasons, scientists are constantly working on different projects simultaneously.  If one experiment becomes stuck, the scientist still has another project that may be working and yielding publishable results while the other project is stalled (and vice versa).  Keep this in mind when you hear how much money has gone into research over the course of time and ask yourself why science doesn’t move faster.  All of our results need to be reproducible and above reasonable doubt for working correctly.  The time spent in developing and implementing a solid experiment is necessary.  Also, think about the slow madness that envelops a scientist when they march into work for the third month in a row to perform the exact same experiment with one small difference.  There are many reasons why scientists are sometimes called “mad.” 

A few weeks ago, my boss brought in his son for a Christmas party.  The four year old was walking around the lab looking at our things.  At one point he asked, “Dad, why does Mark have so many of the exact same bottles?”  His father said “Because that’s what science is.  Doing the same thing over and over …and over again.”

Here's to a happy and healthy 2012!

REFERENCES

Me, myself, and I

Funnies.

                It’s the end of the year.  Let’s just have some fun.

                During graduate school, I found Ph.D. Comics to be hilarious and relatable.  If you’ve ever written a thesis or worked on a project with an advisor who seemed like God, you probably can understand the predicament of our heroes here.  

                Unfortunately, July 2010 was over a year ago so I don’t get back there too often.  I caught up on all new comics since February 2011 a few days ago.  I posted a few of the best ones here.

                If you want to read more: www.phdcomics.com

One. Technicians, graduate students, post docs or just lab-hanger ons are required to travel the cheapest way possible to every conference.  Considering conferences are suchabigdeal, we’re traveling a lot without spending any money.  I’ve worked hard to avoid conferences because I don’t like sharing a hotel room with a stranger for six nights.

 48.1: http://www.phdcomics.com/comics/archive.php?comicid=1425

Two. Truth.  Anything could happen outside and those of us in lab wouldn’t know.  I had friends in graduate school without lab windows so they didn’t even know if it rained!  We had an earthquake here in August and most of the people I worked with thought it was someone moving an especially large piece of lab equipment.  Thank God for Facebook or we’d be completely cut off.

48.2: http://www.phdcomics.com/comics/archive.php?comicid=1427

Three. This happens.  Entirely too frequently.

48.3: http://www.phdcomics.com/comics/archive.php?comicid=1429

Four. I wrote a pre-application for a grant several months ago.  Some of the stuff I needed money for was already finished.  Science is a game.  Sadly, I lose often at it.

 48.4: http://www.phdcomics.com/comics/archive.php?comicid=1431

Five. This year, I got married and needed two whole weeks off.  When do you bring that up?  It was unspoken until about a week before I left and that was only because I had a student starting and it became imperative for me to say “Yeah, I’m not going to be here.  Remember?”  Remember?  Like we’d ever had that talk??  Once in graduate school, I actually emailed my boss from Florida saying I wasn’t going to be in that day or the next.  That was kinda low. 

48.5: http://www.phdcomics.com/comics/archive.php?comicid=1432

Six. This is true for some disciplines and most definitely true for my own.  Oddly, in my post doc, I’ve found people whose advisors read their theses multiple times and gave them edits.  My god.  That’s so …unfortunate.

48.6: http://www.phdcomics.com/comics/archive.php?comicid=1441

Seven. I’m so tired of dressing like a college student.  I’m 31.  I don’t want a red X through my business clothes any more.  If you dress nicely in lab people wonder what’s wrong with you.

48.7: http://www.phdcomics.com/comics/archive.php?comicid=1446

9 Years in Science

               I’m going to do something a little different this week.  I’m going to actually use a blog for what it was intended: a place to put thoughts and reflections.  This coming October marks my nine year voyage as a professional scientist (plus 4 years in college makes me 13 years in science!).  As I move into my tenth year, I realize that I don’t know everything about science (judging by my wide-eyed reaction to my boss’s recent words “Want to write a grant?”) but that I know far more than I’d ever give myself credit for (my list for potential blog posts is really long).  But, since readers come here every week to see what I’m talking about, I thought you’d like to know a little bit more about me and, perhaps, my experiences in science.

                I never intended to become a scientist.  At least, I don’t think so now that I’m looking back.  In college, when it came time to pick a major, I was faced with two normal choices: French or chemistry?  I was good at French and mediocre at chemistry.  However, I desperately wanted a major of which I could be proud.  I wanted to look at my diploma and think how awesome it was that I did it (imagine my horrible shock when, at graduation, my diploma did not have my major written on it).  More importantly, I wanted to feel that I got the absolute most out of my college education.  I’m not knocking French majors, here – I’m just saying that I personally felt I could do so much more.   And so, I chose chemistry.  I believe my parents were worried.

                I probably should have been, as well.  While I did just fine in Introductory Chemistry, Organic Chemistry was not my forte.  On my fifth exam when I amazingly wrote all the correct answers to a set of five reactions, my professor wrote on my paper “Congrats!!  You finally did it!”  Yeah.  Lab was also not my strong point (writing an abstract was truly mysterious) and I relied heavily on my lab mate (thank you, Jess!!) to help me through.  However, I loved Physical Chemistry and the higher level chemistry courses I had to take. My later college science years were much better than my earlier ones.

                It was also during college that I had my first run-in with what I like to call “The Old Boys Club of Science.”  I am not stupid.  Science was dominated by men for decades before my time.  Of course there are plenty of women who made important contributions (Roslind Franklin, who never gets any credit and Marie Curie, who gets a lot of credit, for example) but professors were predominantly older males.  Early on, I had thought about becoming a physics major.  Upon meeting with an older, male astronomy professor at my undergraduate university, I was promptly told I was too stupid to be a physics major. 

 Oh man.  Since I was only 18, I really didn’t know how to respond to this and took him at his word.  By my senior year, I knew (a little) better and took his class.  When I got an A, I promptly wrote a review of his teaching and explained that no one should be told they are too stupid to do anything.  

In truth, I don’t know if he said that because I was a woman or if he really thought my grades weren’t good enough.  I do, however, have strong evidence to the former.  Really, though, it doesn’t matter.  The attitude of “You aren’t good enough” should not pervade science (and I'll happily report that I rarely ran into this attitude in chemistry at my undergrad school or in the years since) no matter what the root of feeling is.  Unfortunately, I let this comment bother me for a very long time.

                When I finished college, I had no idea what I was doing.  I mean really – who does?  As with most things that have happened since May 2002, I fell ass-backwards into my next opportunity.  I was only qualified to do one thing: work in a lab (although I’ll debate with you about my level of “qualification” there).  Three months after graduation, I found myself working in a lab at a rather prestigious hospital for a rather prestigious university and mostly wondering how the hell I ended up there. 

                Two years later, I went to graduate school for the wrong reasons.  Everyone will tell you that you should go to graduate school because you have a career goal that a Ph.D. will help you achieve.  You shouldn’t go without thinking about your long term future.  Well, I went because I wondered if I could.  I wondered if my brain would work like all those professors who taught me and the scientists that worked with me after college.  I truly thought they were brilliant and that I was quite the peon.  

                Clearly, a lot of people knew something about me that I didn’t because my ultimate decision came down to: The Johns Hopkins University or the University of Pennsylvania?  (If you read the “About Me” tab, you’ll see where I chose.)  Classes baffled me a bit, but they only lasted one year.  After that, I worked in a lab every day for next five years.  I loved the lab.

I had my own projects, I ran my own experiments, I thought through all my problems and I troubleshooted everything I was working on.  I learned that I didn’t need Jess and it was okay that I didn’t pass Orgo with an A.  None of that mattered any more.  What did matter is that I could look at the problem, think critically about it and come to an answer that was supported by other research and my own experiences.

Graduate school wasn’t about learning science, it was about learning how to learn.  At that level, you are the expert on your projects and no one else knows what you know.  You have to trust yourself and know how to find the right answers because there is no book in which to look.  When I finally figured out the game, I was amazed.  It was so empowering when I understood that, even though my beginning was rough and I felt for sure I could never do it, I had the skills in me all along.  Not only that, but I really enjoyed my work and felt like I was doing rather well with it.

  By the end of my six year graduate school epic journey, I knew I was no different than all those professors that I had so revered in college.  I thought their brains were fundamentally different than mine and that I could only hope to be a little bit like them.  In the end, I was them.  

I tried to make note of these realizations on the dedication page of my thesis by writing:

Why, anybody can have a brain… Back where I come from, we have universities, seats of great learning, where men go to become great thinkers.  And when they come out, they think deep thoughts and with no more brains than you have.

Fleming, V. (1939) The Wizard of Oz

            Or… a more contemporary quote: “Anyone can cook!” – Chef Gusteau

Rosalind Franklin: in short, she provided the data to James Watson and Francis Crick that allowed them to determine that DNA was a double helix.  Her contribution tends to be overlooked.  There is some controversy surrounding Watson/Crick and Franklin and who really discovered what when.  Coinciding with the 50^th anniversary of publishing the structure of DNA, Brenda Maddox published “Rosalind Franklin: The Dark Lady of DNA,” which discussed Franklin’s life and work during those times.

Marie Curie: She loved radioactivity.  Okay, she was awarded two Nobel prizes for her work in physics and chemistry and was the University of Paris’s first female professor.

REFERENCES

Fleming C. (1939) The Wizard of Oz.

Bird, B and Pinkava, J. (2007) Ratatouille.

Me, myself, and I – which has absorbed a lot of knowledge in the past nine years and even before!