Thursday Quote Du Jour: Nature is no dummy

I stumbled upon this quote, in all places, on the lid of my yogurt

Nature is pleased with simplicity.  And nature is no dummy. 

-Issac Newton

 

Now, any one who believed nature to be simple, much less pleased with simplicity, has never studied Biochemistry.  Nothing in how nature works at the microscopic/molecular level is simple.  It’s actually quite astounding how complicated the things are that we observe as the simple color blue, eating a ripe apple, or even just breathing.  It may appear simple because we are only seeing the outcome of a million things happening “behind the scenes,” as it were, to make these things possible and we have grown up taking them for granted.  But, I assure you my friends these simple actions are not simple at all.

So, sorry Mr. Newton.  Had you known about Biochemistry you would not have felt this way about nature loving simplicity.  But you were most definitely right in that she is no dummy.

By the way, I actually did well on my first Biochem test.  I’m no mother nature, but not so much a dummy either.  I was a nice four points above the average.  While my teacher was disappointed with what she felt was a low average, in a tough subject that gets the short end of the the homework time stick, I was pleased to be above average, even if just by four measly points.

Constellations in my Borrelia

So, do any of you ever wonder what I do when I’m in my Lyme Studies lab?

I know, you have been dying to know!

Mostly I count Borrelia burgdorferi, the primary bacteria responsible for Lyme disease in the U.S.  There are other Borrelia species that also cause Lyme disease, but most are not found in my neck of the woods.

In general Borrelia are thin spiral shaped bacteria that swim about independently.  However, they do also form clusters of varying size.  I don’t know why for sure, and I don’t know if anyone else does either.  They might and I just haven’t stumbled on that information yet.

Anyway, I am responsible for a strain that has been genetically engineered to express a green fluorescent protein that makes it glow green.  This has many practical applications, it makes them much easier to see for sure, it also makes it easier to tell if the bacteria is alive as dead bacteria don’t make glowing green protein, they don’t make anything if they are dead.

So every week I gaze into a microscope and check for itsy-bitsy green lines on a field of black.  A healthy bacteria culture has millions or even billions of the little critters all swirling about doing their little bacteria thing.  Often there are so many it looks like the depths of outer space, if the stars, planets, galaxies and nebulae were all fluorescent green anyway.  To see them well it is best to turn off the lights in the lab to reduce the ambient light which can interfere with catching a glimpse of the faint green glow, so it really does often feel like star gazing through binoculars.  The other day it so strongly put me in mind of star gazing that I started looking for shapes in the “constellations” of bacteria.

Lo an behold I found Ursa Major!

I think I just discovered the evolution of Bear-relia!

Love is in the water

It occurred to me that I forgot to share a very important update in the wake of Constitution Day.

I’m sorry if you’ve all been on tenterhooks with anticipation to know the outcome of my fish experiment.

So last week Thursday I got to genetics lab and found that Verda and Rudy didn’t spawn.

*sad face*

But apparently odds for a single couple spawning aren’t that stellar.  Out of all the different classes doing this project there were 60 something “fish couples” and only 12 produced baby fish.

I ended up having a pretty cool Genetics lab anyway.  We got to look at the baby fish (called larva, apparently) under these special microscopes.  You can see fish larva with the naked eye, but they are super tiny, think smaller than the size of an eyelash.  Mostly they are clear, but you can see some of their skeletal and muscular system which give that appearance of a very fine, small, black eyelash.  However, under the microscope you can see all the details.  You could see their eyes and fins move and you could see their gills flap.  If you were looking at a fish that had inherited the fluorescent genes, you could put on a special light and see the colors glow.  It was cool.

As my couple didn’t couple, I had to pick from some fish belonging to other students.  So I picked a purple to wild type cross to look at under the scope.  I reasoned that, because it is thought that the purple fish are actually that color because they get a red transgene and a blue transgene that sort of combine to form an intermediate color (thinking back to your color wheel from your art class days, red+blue=purple, right?),  if you cross a purple fish with a natural wild type fish, in theory, you shouldn’t get any purple fish because, due to the nature of genetic inheritance, your purple parent fish can only pass on one blue gene or one red gene per offspring.  For the same reason you won’t expect any wild type fish, because the transgene is believed to be dominant over the wild type, or normal color, gene.  So every egg gets one one wild type gene from the wild type parent and one color transgene from the purple parent, either red or blue, that will mask or dominate over the wild type gene.

This couple only produced three babies.  But seeing as we were looking at tiny larva, they all looked the same at first.  While it is not impossible to end up with three that all look the same, I couldn’t see any real color at all.  I was hoping to find a nice combination of red and blue fish.

And, guess what?  There was one red, one blue and one wild type.

An exciting curiosity.  While I got both colors, I also got an unexpected wild type.

It seems as though we have to write a little research paper about our fish experiment.  Because this couple only had three babies, it’s not really enough to judge accurately what inheritance patterns are present.  And, there is that errant wild type larva.  It turns out that the professor had two tanks of other purple to wild type crosses she spawned the night before, she’s putting them aside for me and I can use those progeny, too, which will hopefully give me a larger pool of progeny to base a paper on.

Biology is so cool.  This is why I put up with all the school crap.

One fish, two fish, red fish Glo-fish

In genetics lab we are studying transgenic glo-fish.  To learn about gene inheritance, we are experimenting with crossing glo-fish with different phenotypic traits in order to assess whether the genes which encode for those traits follow Mendalian ratios.  Transgenes are not native genes, but in this case, are genes taken from other species which have the ability to create fluorescent proteins.  So, our fish glow under black light and have bright Kool-aid like colors in white light.

Tomorrow we find out if love was in the air.  That is, did my fish do *IT* and make baby glo-fish.

I chose to cross Verda:

A green fluorescing fish with Rudy:

A red fluorescing fish.

My camera phone doesn’t take the best photos, but I think you can kinda see what I’m dealing with.  Any bets on what our babies will look like?

Tuesday Titters: assorted funnies

I have a smorgasbord of comics I’ve downloaded over the years.  For any of you who are worried about proper citation, I have none so read at your own risk…

In honor of my Genetics class:

In honor of Biochem class:

In honor of Virology class:

And you make the big bucks?

We all know the professorial realm of academia is full of hacks.  We all know that students ultimately pay the price for their professor’s laziness/ineptness.  Every semester I have at least one textbook example (no impending pun intended).

So, my Virology class meets the first time today at 11 am.  Yesterday the professor sends us an email that says, essentially, you will need this virology textbook (included a link to Amazon).  And, by the way, you can’t get it at the campus bookstore even if you want to pay the outrageous prices they charge, so you will have to find a copy online, either at this link or elsewhere.

Now, riddle me this:  How is it that my biochem teacher could notify her students back in JUNE to say this is the textbook, it is expensive if you buy it from the campus bookstore, if you want to shop around and order it from a cheaper online bookstore do it early so it can be shipped to you before class starts, why can’t my virology teacher have his act together earlier than the day before class starts?

Not off to an inspiring start, if you ask me.

Tuesday Titters: Yesterday was my first Genetics lecture, so naturally here’s a chromosome joke

What is the fastest way to determine the sex of a chromosome?

Pull down its genes.