My writing here has lapsed again, because unfortunately when things get crazy this activity has to be the first one to go. (Well, that and the volunteering, which I have had to give up for the time being.) My anxiety got out of control last week for the first time in months, and I thought I might decide to put writing on hiatus altogether, and that I would sit out the next season of hockey. Then I had a rethink and decided that this would be precisely the right time to try to re-establish some balance, when things feel the most out of control, rather than completely immersing myself in the thing that is stressing me out (the lab).

But I did need a bit of a break, so I’ve taken a quiet two weeks, not pushing myself to get up for yoga and rather sleeping an extra hour, and coming home from work and turning off the brain. Consequently I’m almost caught up on watching Lost, which actually probably contributes to my anxiety because that show is totally infuriating. How I love Sawyer though. I think it’s the dimples and the nicknames.

We saw at the end of the last lesson that protons and neutrons each weigh approximately one atomic mass unit (amu, unit “u”), while electrons in comparison weigh only 1/2000th of that.  Formally, an amu is defined as the exactly 1/12 the mass of carbon-12.  Let’s look at how atomic number, mass number, and the numbers of the subatomic particles  are related.  

X represents the element’s chemical symbol found in the periodic table, while A is the atomic mass and Z is the atomic number (also sometimes known as the proton number). For instance, represents the element carbon - “C” in the periodic table - which has 6 protons and a mass of 12 amu.

Because we know that protons and neutrons are the only subatomic particles that count towards the atomic mass and each has a mass of one amu, we can calculate that the number of neutrons in this atom is 6.

A - Z = # neutrons
12 - 6 = 6

II. Isotopes

It is important to note that all atoms of a given element will always have the same number of protons. Carbon always has 6, oxygen always has 8, uranium always has 92, and so on. If the number of protons changed, we would have a different element entirely. Number of protons therefore gives the atom its identity.

In contrast, atoms of the same element can have different masses. For example, while most naturally occurring carbon has a mass of 12 u (carbon-12), there also exists a significant amount of carbon-13 and carbon-14, which you may have heard of in the context of radioactive dating of ancient artifacts. Atoms that have the same number of protons but different masses are called isotopes.

Where does the change in mass come from?  By process of elimination - the difference can’t be in the protons because it would change the atom’s identity, and it can’t be in electrons because they don’t weigh enough - we know it must be a difference in the number of neutrons that gives us isotopes.

If we use the A minus Z method on carbon-14, we see that this molecule has 8 neutrons.

Note: it’s important not to confuse isotopes with ions!  An ion, or charged atom, results from a gain or loss of electrons.  In an electrically neutral atom, the number of protons will equal the number of electrons. Because electrons are negatively charged, gaining one makes the overall charge of the atom more negative, while losing one makes it positive. A sodium (Na) ion which has lost one electron would be represented this way:

Q: How many protons does this atom have?
A: Eleven (the atomic number or proton number)

Q: How many neutrons?
A: 23-11 = 12

Q: How many electrons?
A: 11-1 = 10

III.  Real Atomic Masses

In practice, observed atomic masses must take into account all the masses of the naturally occurring isotopes. To calculate this value, we use a weighted average based on the relative abundances of the isotopes.

atomic mass = (fractional abundance of isotope 1 x mass of isotope 1) + (fractional abundance of isotope 2 x mass of isotope 2) + … +

(This is the same calculation you must undertake to calculate your grade point average, “weighting” each grade with the units of credit for the corresponding class.)

IV. Homework!

1. a. How many protons, neutrons, and electrons are in an atom of ?
b. How about ?

c. And ?

2. If 98.892% of carbon atoms are carbon-12, with a weight of 12 u. and 1.108% are carbon-13 with a mass of 13.00335 u, calculate the atomic mass of naturally occurring carbon.

One of my undergraduates is giving his first lab meeting on Thursday.  I am way more nervous than he is.  It stems from not feeling comfortable with the analysis myself; I have so little background in behavior.   In fact that’s part of the reason I asked our PI for a lab meeting in the first place, to discuss the issues I feel that we’re having in getting the most meaning out of the data.  But PI is excited to see the results, and thus undergraduate and I are going to have a pre-meeting meeting at my insistence to make sure that at least his presentation is organized and clear even if everything in it is meaningless.

On Saturday a colleague from whom I needed technical advice came to my lab with his three year old daughter.  She used my highlighters to color on all of the paper in the recycle pile and then decorated them with all the colored lab tape.  I guess I should just be thankful she didn’t decide it would be fun to pull out all the cotton balls to set free the little bugs.

I.  Early Chemistry

For example, In 1774, Antoine Lavoisier proposed the following:

It is always true that the total mass of substances formed by a chemical reaction is the same as the total mass as the reactants before the reaction happened.  In other words, matter can neither be created nor destroyed in a chemical reaction.  This is the Law of Conservation of Matter. It means that in any chemical reaction, if you can find a way to measure exactly how much of every reactant you start with, and exactly how much of every product you end up with, you would find the masses of each group added all together would be the same.

If AB + DC –>  AC + BD, then Mass (AB + DC) = Mass (AC + BD)

In approximately 1805 Joseph Proust described an initial version of what we now know as the Law of Definite Proportions:  All samples of a compound have the same composition - that is, they have the same proportion of elements by mass.

For example, let’s think of one everybody knows, H₂O.  Every water molecule has a ratio of 2 hydrogens to one oxygen.  If we were to, say, add an extra oxygen to the molecule to make it H₂O₂, we would now have hydrogen peroxide - which you can use to bleach your hair or clean out your earwax, but you wouldn’t want to drink or swim in.  Hereby we see that if we change the ratio of atoms in the compound, we change the identity of the compound.  Sometimes dramatically.

Then there’s good old John Dalton and his Atomic Theory, put forward in the early 1800’s:

1. Chemical elements are composed of atoms, which are not created or destroyed in chemical reactions.
2. All atoms of the same element have the same mass and other properties, but are different from atoms of every other element.
3. Atoms combine in simple, whole number ratios to form compounds.

p.s. John Dalton was an English teacher!

II.  Subatomic Particles

The ancient Greeks thought atoms couldn’t be divided.  Now we know they’re made of protons, neutrons, and electrons.  (Which are themselves made of still smaller particles, but that’s a way more advanced lesson.)

The particles we know as electrons were first discovered by Michael Faraday about a century and a half ago, when he called them “cathode rays” because they emanated from the negative end of a cathode ray tube.  J.J. Thomson took over from there and established their charge/mass ratio and declared they were fundamental particles of all atoms.  Robert Millikan established the charge of the electron, which is -1.6 x 10^-19 coulombs.

Ernest Rutherford, beginning in 1909, set out to learn something about the position of electrons in atoms and ended up discovering protons.  In his famous “gold foil” experiment, Rutherford fired positively charged particles at a thin sheet of, well, gold foil.  The results are as follows:

• Most of the particles passed straight through the foil undeflected.
• Some were slightly deflected; a few were severely deflected.
• About 1 in 20,000 bounced right back like a rubber ball hitting a wall.

One of the most famous quotes in chemistry belongs to Rutherford.  After the gold foil experiment he said of the bounced-back particles, “It’s about as credible as if you had fired a 15-inch shell at a piece of tissue paper and it came back and hit you.”

The explanation for this bounce-back phenomenon was that the positively charged particles were encountering another positive charge which was repelling them back the direction they came from.  In other words, 1 in 20,000 of the particles Rutherford fired were hitting the nuclei of the gold atoms head-on.

This experiment led Rutherford to propose the nuclear atom, where the mass and positive charge are concentrated at the center, or nucleus, of the atom while the negatively charged electrons are outside of it.  The magnitude of the positive charge is different for the atoms of each element, and is about one half the atomic weight.  Atoms are mostly empty space and are electrically neutral.

III.  Summary

Protons
Electric charge = 1.602 x 10^-19
Atomic charge = +1
Mass = 1 atomic mass unit
Location = nucleus

Neutrons
Electric charge = 0
Atomic charge = 0
Mass = 1 atomic mass unit
Location = nucleus

Electrons
Electric charge = -1.602 x 10^-19
Atomic charge = -1
Mass = 0.0005 atomic mass units
Location = outside the nucleus

“[The economic stimulus package] includes $300 million to buy new cars for the government, $8 billion for high-speed rail projects, such as a ‘magnetic levitation’ line from Las Vegas to Disneyland, and $140 million for something called ‘volcano monitoring.’ Instead of monitoring volcanoes, what Congress should be monitoring is the eruption of spending in Washington, D.C.”

Thank you Governor Jindal for reminding me how obnoxious anti-science sentiment can be.  You know, I do understand that it might on the surface seem like those aren’t the first projects we should pick to stimulate the economy, but I feel like he hasn’t thought about it for more than 4 seconds or so.  I mean, aren’t high speed rail lines a GOOD thing?  They’re energy efficient, aren’t they?  Better than flying or driving?  And people need to be employed to build them?

“Something called volcano monitoring”?  Is it. . like. . . hard to understand what that means? And wouldn’t we. . . like to know. . . if a volcano is about to erupt?

It’s firing at about 3.3Hz, mixed tonic (the single spikes) and bursts (the parts that look like somebody with a mohawk stuck their finger in an electrical socket).  This cell lasted almost half an hour - this is a ten second sample.

11:45-1:15 Seminar (Chris Miller)

1:15-2:30 Recording

2:30-3 Lunch/Email/Internet

3-6 Fly work/impromptu meeting with PI

6-6:30 Planning project for undergraduate #3

6:30-7 Fly flipping

Notes:  So today I tried putting the recording first so as to make sure I would get to it.  Well, I definitely did get to it, but it resulted in unacceptably high stress levels and rushed fly work.  In a way it was good because it forced me to streamline and just get rid of some lines that I know deep down aren’t worth my time but that my pack rat nature wouldn’t, until today, let me abandon.  Undecided on where to go on that from here.

I learned today that I will be sans work study students until Wednesday, which means part of my Monday or Tuesday will have to go to fly flipping.  One more thing to take into account.

Started to teach electrophysiology to undergraduate #2 today.  I’m optimistic he might be able to become our lab’s second physiologist, especially given the upcoming summer.

Way more work left to do tomorrow than I’d hoped, but I’m fried.

2.  There is a mother/daughter pair on my hockey team.  The mother is our team captain and is about my mother’s age, and the daughter is in college.  Seeing them together, talking about laundry or sarcastically sniping at each other, makes me miss my mother.  It’s approaching ten years now since I lived close enough to see my mom all the time.

3.  I actually have two confirmed purely social events on my calendar in the next week.  This may be unprecedented;  what is even more astounding is that I’m actively looking forward to both of them.   On the other hand, I love today because there is absolutely nothing written in the box for today.  Glorious.

4.  www.environmentalgraffiti.com has recently become one of my favorite websites.  The pictorial nature top tens can hold my attention for way too long, but I mean come on… crater lakes!  Underwater volcanoes!  Awesome.  Plus, this story.  Ha.

9:30 - 10:30 New Solutions

10:30 - 11:00 Fly work

11:00 - 11:05 Yogurt

11:05 - 12:30 Electrophys prep and Undergraduates

12:30 - 2 Attempted recordings and Undergraduates

2 - 2:20  Lunch and reading Ashburner’s Drosophila

2:20 - 3:45 Wrapped up in Ashburner’s Drosophila … oops

3:45 -4  Downloaded an audiobook about Kant

4 - 6  Attempted recordings (absorbed nothing of audiobook about Kant)

6 - 7  Catching up on articles

Notes:

Got a lot done for a day with three undergraduates.  They’re all starting to get the hang of their respective tasks and projects - yay!

I actually had a second day in a row of recording time!  I think I got two with data worth using.  Tomorrow we’ll try for three in a row, but no promises.  The cells are much like people in that they display no sense of urgency when there is no time pressure.  I seem to get more nice cells when I only have 90 minutes to devote to trying.

Not to mention how you come home smelling sometimes.  You know you live a weird life when the smell of ethanol makes you think not of an awesome party you went to over the weekend but the research grade of it you use to fill an Erlenmeyer full of dead flies.

One of the rare bright spots in terms of lifestyle is that, unless you work for an M.D. or just a PI who is a real outlier, you get to set your own schedule.  There are a lot of reasons for this, one being that science just ain’t a 9 to 5 job.  You do your work when stuff is ready, and you keep doing it till you’re done, because things in science don’t usually stay “shovel ready” for that long, to borrow a phrase from current economics.  Another is that scientists tend to be individuals both in their personalities and in their work environments.  I mean, there are collaborations and meetings and stuff, but a lot of the time it’s just you and your notebook and whatever apparatus and materials you happen to be working on that day.  It doesn’t really matter if it’s 10AM on a Tuesday or 8PM on a Sunday.  I’ve worked in a 10m x 10m room all day with three other people and said like four words to them.  I even liked most of them, we were just doing our own things.

Another reason is that most people who go into and stay in science are really, really passionate about it.  They actually want to be there all the time because science is one of their favorite things to do.  And so you have this very strange phenomenon where, although theoretically we can take breaks and vacations whenever we see fit, and work semi-reasonable sets of hours, most of us. . . just don’t.

With this utter lack of structure to rein one in, there is a huge variety that manifests in terms of individual schedules.  I, for example, on weekdays like to leave my apartment around 9AM and come home at approximately 7PM.  This allows me to miss both rush hours (on the roads and on the bike trail, depending how I go that day) and stay up a little late to spend time with Dana.  Then there are weekends as necessary, of course.

But it can actually be quite a hard thing to figure out what are the correct limits in terms of person-hours.  You have to balance the culture of your institution and the culture of your individual lab with your own needs, which is of course a category with 15 thousand subdivisions that require serious prioritization.  For example, at my graduate school in Manhattan after hours and weekends were vastly more common than they are here in laid-back California, and my boss was a workaholic.  Thus, even though I work 50+ hour weeks these days, it feels not only totally manageable but also sometimes like glorious freedom.  Sometimes.

But some nights I find myself, at let’s say 6PM or so, thinking, “Okay, so which of my personal priorities is more important right now, spending an hour screening this last tray of flies or making sure to get an oil change before they close tonight so my car doesn’t die on the side of the highway tomorrow on my way to hockey?”

It’s not always as straightforward as it sounds.  Nor is the decision to spend an afternoon each week volunteering outside of the lab and every Saturday as an SAT tutor.  And the work-life dilemmas are in another realm entirely for those brave, crazy souls who decide to have kids and be grad students, postdocs, or new PI’s at the same time.  And a lot of the PI’s I know, let’s face it, don’t or didn’t have lives and are proud of that, because every ounce of their energy went to getting the career they have now.

I can categorically say without any shred of doubt that if I do not have extracurricular activities in my life - and I don’t mean my partner or my friends, I mean other STUFF I care about doing - I get mentally unhealthy.  It’s not an easy balance for me nonetheless.   I think I inherited my father’s Midwestern work ethic, and then of course my graduate school conditioning makes me feel like I am never, ever working hard enough.  My solution for the time being is just to do a whole lot of everything.  I make a lot of lists.  And I feel more alive than I have since… well, maybe ever.  Even while I know it isn’t sustainable.

My point is that the one bonus to the scientific lifestyle isn’t always such a bonus (even though I do love being able to sleep until 8AM).  For people with a passion, working in a highly competitive market, the freedom to work as we choose sometimes means working… well, a lot.