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

What does water look like?

         At birth, 80% of a baby’s weight is due to water; as an adult, 70% of the body is water.  ~ 70% of the earth’s surface is covered with water; all of the fresh water underground will add up to more than is available on the surface.

                Water’s cool.  In the Soap! post and the Hand Sanitizers vs. Soap post, I discussed how water can hang on to certain other kinds of molecules and pull them places.  In the case of soap, water pulls the soap from our hands and flushes it down the drain.  

                Water’s necessary.  Some of the enzymes in our bodies require water to function.  Dehydration is a serious problem that can lead to death.  A human can survive for a few weeks without food, but only a few days without water.

                But, what does water look like?  Many people know that a water molecule is comprised of one oxygen atom and two hydrogen atoms, but how are they arranged?  Are they just stuck together arbitrarily?  Where are the electrons?  What’s going on there?

                Okay.  Let’s start with a guided tour of an atom.

                We’ll start deep in the center of an atom at the nucleus (Figure 56.1).  Here is where we will find protons, neutrons, some forces called the strong nuclear force and the weak nuclear force and just a lot of stuff.  The nucleus of an atom is quite dense – meaning, there’s a whole lot of mass in a really small space.  Let’s get out of here.

                Upon leaving the nucleus, you will now encounter mostly empty space.  Electrons are flying around (not exactly willy-nilly, but also not in “orbits” like planets around the sun), but the vast majority of the space is empty.  Think of an atom as the fenced in yard of a home and two kids as the electrons.  The fence determines the size of the property and the kids are allowed to run anywhere within the fence.  If you just stand there, a kid will eventually run by you, but you’re mostly standing there alone.  That’s what it’s like to stand among the electrons.

                The left of Figure 56.2 gives you a closer look at the atom oxygen.  It has eight electrons roaming around its nucleus.  However, two of these eight are too close to the nucleus to really be bothered by anything so we are only going to consider six of its electrons; these six are called oxygen’s valence electrons.  Valence electrons are those that are involved in forming bonds with other atoms.

                The right of Figure 56.2 shows hydrogen.  It only has one lonely electron floating around, so hydrogen has one valence electron.

                So how does all this jazz fit together?  Bonding is all about sharing of valence electrons.  In the case of water, one oxygen atom offers six electrons and each hydrogen atom offers one electron each.  So, we have three atoms and eight electrons that need to be arranged between them.

                Let’s start with what we know: the oxygen binds both hydrogens and the hydrogens do not bind each other.  This makes oxygen the central atom.  So… let’s draw it in the middle and place each hydrogen on either side to make a schematic of one water molecule (Figure 56.3).

                Now we have to fill in those eight electrons.  In chemistry, electrons hang out in areas called orbitals.  Orbitals are areas of space that electrons are likely to be found.  I’m not going to go in depth about them because, quite frankly, they are a smidge complicated.  I’m going to keep things straightforward here!  Each orbital can hold two electrons.  

                How many electrons do we have between the oxygen and hydrogens?  Eight.  

                Since each orbital can hold two electrons and we have eight, we need four orbitals around our oxygen*.

                Electrons all have a negative charge.  Like charges repel so these orbitals need to be situated around the oxygen as far from each other as possible.  The best way to do this is to have a tripod + camera situation, as shown in Figure 56.4.  The center of the tripod is the oxygen and the three legs plus the arm sticking up with the camera represent the orbitals.  I’ve redrawn the schematic with this orbital arrangement in mind (Figure 56.5).

               

                Now we fill in our electrons; two per orbital. Look at Figure 56.6.

                Ta-da!  That’s water!  That’s three dimensional water! 

                People tend to draw water like a bent line or refer to water as “bent.”  Looking at Figure 56.7 helps explain why.  If you are looking strictly at the atoms, you will see one oxygen atom with two hydrogen atoms placed slightly lower.  You will not see the orbitals just containing electrons because they are considered part of the oxygen atom. 

                In the Soap! post, I specifically drew water as a large center circle with two smaller circle slightly lower on either side.  I was trying to accurately represent how water looked in real life. 

 

No, you can’t see water molecules with your eyes, but now you know what it would look like if you could.  Interestingly, the bent shape of water lends itself to many of water’s wonderful properties, but that is definitely a topic for another post.

*  For the more science-y among us: I realize that this sentence is very very simplified.  It’s a backhanded and not entirely accurate explanation of VSEPR Theory, but I did not want to get into that here, especially since I’ve never explained electron configuration, Lewis dot structures or orbital shape.  To get through all that just to explain water would be overkill.  If I ever do explain those topics, I will certainly link back to this post and offer a more in depth explanation.  Until then – this is what I thought would get the point across as simply as possible.

* - For any chemistry students who stumbled upon this, read your text book to get a handle on VSEPR Theory!  You should know and understand electron configuration, Lewis Dot structures, orbital shape, the Pauli Exclusion Principle and Aufbau's law before looking at VSEPR or MO Theory.   Or taking a test.

Valence electrons: electrons that are involved in bonding with other atoms

Orbitals: areas of space where electrons are likely to be found.  They are three dimensional areas (like a sphere) and not two dimensional circular orbits (like the plants going around the sun).

REFERENCES

http://www.allaboutwater.org/water-facts.html

 

Zumdahl, Steven S. “Chemical Principles, 4^th Edition” (2002) Houghton Mifflin Company, Boston, MA.

One is Fun!

The more that you read, the more things you will know.  The more that you learn, the more places you'll go! -- Dr. Seuss, I Can Read with My Eyes Shut!

Happy Birthday to my little blog today!

Thinking Critically

                I like to send links of random things to my sister and my husband.  Last week, I sent my sister an article about how Leah Messer miscarried.  I was only mildly surprised that, two days post-miscarriage, this information was floating around the internet.  Apparently, my sister was a bit more shocked.

                “Where do you find this stuff?” she asked me.

                “The interwebz.  It’s full of information from people willing to share too much.”

                It was that statement, along with a controversial blog post that roamed around Facebook and other blogs a few weeks ago, that made me want to discuss thinking critically.  We all do it to some degree every day.  I have to do it every day at work… “Did I address this variable correctly?”  “Did the author really make their case?” “What isn’t being said in this presentation that I need to figure out before I decide if this speaker is completely full of it?”

                It’s exhausting.  My head is tired.  My husband wants to put on the Republican debates at night and I beg him to turn them off – I can’t listen to any more people who need their true meanings deciphered or read between any more lines.  

                The internet is full of information.  Some of it is contained on really awesome websites.  Some of it is on sites overrun with flashing advertisements.  Some of it comes from pretty little blogs with flowers while some comes from simply designed sites with one random black and white picture.  Some of what is written is fact, some is opinion, some is one person’s idea of fact and another is the same story from a different perspective.  Some information is meant to inflame feelings in readers while others are simply meant to inform.  If one story has 4 likes and another has 447 likes, neither one is necessarily more correct than the other.  If one blog has 2 followers but another has 2061 followers, the second blog isn’t necessarily posting more accurate information.  Deciphering which website means what is an interesting and daunting task.

                A few weeks ago, a blog post from an irate mother circled the web.  The story was picked up by other blogs and written about.  One blog with well over 2000 followers picked up the story and wrote an equally impassioned story agreeing with the mother and begged readers to sign a petition.  As is common in the blog world, I commented on her lack of information from the other side of the story.  I wasn’t alone – several people commented in suit.  Sadly, never once did the blogger acknowledge our protests, admit that perhaps she jumped the gun, or say anything other than to promote her own blog and her own viewpoint.

                This kind of writing is dangerous.  Not the opinion piece – everyone has their right to an opinion – but the fact of where it was written, the position the original writer was in, and the actions of the readers she influenced.  Critical thinking failed everyone in that situation and the result was a huge amount of misinformation being spread like a cancer over the internet.  Many people went for the easier, kinder, knee-jerk reaction instead of stopping and thinking "Some of this story isn't really adding up, can I ask a question?"

                Why am I writing about this? 

                Because I’m going to lay my cards on the table now: I strive for excellence, fairness, and accurate passage of information with my blog.  All my posts are referenced for a reason – I want what I write be transparent, questioned and researched further if anyone feels that I’ve stated something incorrectly.  My credentials are placed on this site not so that people will blindly parrot everything I say, but so that I can be taken more seriously and perhaps encourage those who want to learn more about various scientific topics.  I beg you to read both my blog and all information with a critical eye.

                I’m going to promise my readers a few things:

One. I have a good understanding about the things I write and I am not “winging it.”

Two. If you feel I have inaccurately posted something, tell me.  I’ll happily fix my errors or discuss with you the issue.

Three. I will always post sources for my posts that are not from questionable sites.  I pull a lot of from The Mayo Clinic, PubMed, textbooks, and my own background.  

Four.  Opinions creep in no matter how hard I try to stay unbiased.  However, some things just rub me the wrong way or inspire me and you will see that reflected in my words.  But, should I post about any flat out controversial topic, I will be sure to state as such at the beginning.  I welcome opinions from the other side on those matters.

                My blog will be turning 1 on February 7^th.  I’m so proud and happy of this site that I can’t even describe it to you.  I hope you stick around and I hope that if you have any suggestions for topics that you will pass them along to me.

--  Amedeo

Here’s a picture because I think all my posts need at least one little picture…

 It’s soooo fluuuuufffy!!!

-Coffin and Renaud. "Despicable Me" (2010).