Biochemistry-Official

Hi! Thank you for your question. It’s a big one! I can’t answer it definitively because there’s still a lot to learn about how the chemistry of life began. However, the prevailing theory right now is called the RNA World.RNA is a nucleic acid very similar to DNA, with almost the same set of nucleotide bases. RNA uses adenine, uracil, guanine, and cytosine while DNA uses adenine, thymine, guanine, and cytosine. RNA also has one extra hydroxyl (an oxygen bonded to a hydrogen) group than DNA, so it is slightly less stable. In cells, RNA is more commonly found in short, single-chain strands and DNA is found in long, double-chain helices (your genes!).But the interesting thing about RNA is how it folds. Since it doesn’t have a complementary strand like most DNA, it binds to itself in very interesting shapes. Here’s an example of how a strand of RNA binds to itself - the first image shows which base pairs interact, and the second shows the three-dimensional shape formed. Here’s a link to the paper it’s from.

So I could probably watch this video forever, because it looks like How It’s Made, but for DNA instead of rollerskates or something. The full video is by the Walter and Eliza Hall Institute of Medical Research. Explanation of what’s happening is below the cut.

Since genomes are basically instruction books for making organisms, you’d think that complicated organisms (like people) would have larger genomes than other organisms (like plants and simple animals). But it turns out that isn’t necessarily true! Human beings have roughly 3.2 billion base pairs in our genome, which is about 3.3 Gb of data in every cell. That’s a lot! But it’s nowhere close to the vertebrate with the largest genome: Protopterus aethiopicus, or the marbled lungfish. 

The lungfish has 130 billion base pairs in its genome. Look at that smug face. But she’s still pretty far from the largest confirmed genome. So far, the biggest one that has been found belongs to an organism called Paris japonica.

This week scientists announced something kind of weird: Using the gene editing technique CRISPR, they encoded a series of images and a GIF into the DNA of E. Coli. Scientists have actually been encoding images and basic pieces of information into bacteria for years. But encoding a movie represents a big storage upgrade.

Jurassic Park, Michael Chrichton

tbh anything by Michael Chrichton

Dragon’s Egg, Robert Forward

this book isn’t available in bookstores but you can find it online

Silence of the Lambs, Thomas Harris

 • The Cormoran Strike series by Robert Galbraith (actually J.K. Rowling). A grumpy, ex-military private detective with one leg and a heart of gold solves murders with his secretary/assistant/fellow detective (by the third book) Robin Ellacot. They’re very well written! The third book is the scariest book I’ve ever read.

• The Martian by Andy Weir.  Deserved all the hype it got, funny and fascinating. Better than the movie.

• 11/22/63 by Stephen King.  An English teacher discovers a portal back in time to 1958 and decides to stop the assassination of JFK. A lot of other stuff happens. An accurate-to-the-time-period thriller with some sci-fi thrown in.

• The Moon is a Harsh Mistress by Robert Heinlein. This is a relatively old sci-fi book, but it’s fantastic. It occurs in a future where a prison colony established on the Moon becomes permanent (because people who lived for a long time have trouble adapting to Earth’s gravity and can’t come back). It develops a drastically different society from Earth and eventually rebels. There’s also a sentient supercomputer named Mike. I read it a long time ago but I loved it.

On average how long does a (Masters/PhD) student in your lab take to graduate?

Do you, the PI, do lab work still?

Did any of your students receive fellowships/scholarships/grants that they applied for?

What’s the structure of your lab meetings?

What’s the structure of your individual meetings with students?

Do you travel a lot for conferences?

Do you work from home a lot? (My PI does this a lot and I kinda wish I had known this beforehand, just as a head’s up)

Do you have other responsibilities that remove you from the lab? (ie. if they run a company, do clinical work, teach, etc)

What percentage of your time/resources do you aliquot per project? (Some PIs may spend more time on one project than others)

What are your expectations of students in terms of how long they’re in the lab each day? Do you expect students to work evenings, weekends, and/or holidays?

What are your holiday and sick days policies?

Do you allow students to read papers/do their writing while in lab? (I know one PI in my program who doesn’t allow their students to read papers while in the lab, because lab time is for lab time)

Who will my immediate mentor be in terms of research questions (ie. another graduate student, a post-doc, or the PI themselves)?

Are you familiar with the requirements of my graduate program (ie. committee meeting structures, qualifying exam structure if applicable, how the thesis should be formatted, etc)

This one you may want to ask the current personnel in the lab: Are there any labs/PIs that this current PI isn’t on good terms with? (This is something you may need to know when setting up your committee, for example, or collaborators). 

How do you determine the authorship on papers? (ie. How much work should I do for a project for my name to be on it?)

How many papers do you publish per year? 

How many papers do you expect your graduate students to publish during their time here?

How often do your students go to conferences/present at meetings?

Do you allow your students to have other engagements (like TAing, internships, etc)?

And in general, if you have a huge life event coming up, ask them what the process on that would be. For example, if you’re getting married, or planning on having a child, or have a family member who’s gravely ill, ask them how much time you can take off, etc. If the PI seems really hesitant or put-off by that, that’s something to consider. 

That’s all I can think of.. I’m sure there’s more if anyone else has anything to add. 

anyway, so since water is essentially made up of a gazillion little hexagons, it tends to gather into larger hexagons as it shapes together. this is not visible unless the water is in a solid form, aka ice. when the water is split, it tends to crack around the established hexagons. that bottle rocket exploded in the PERFECT place to show this phenomenon and its geeking me out.