Monday, April 7, 2008

Lab meetings aren't ALL bad


Okay, before I begin I'd like to say something. I do not intend to begin the majority of my blogs with the word, "Wow"... but it just seemed to fit my mood today... and last week... and quite likely sometime in the immediate future... but I do not intend to make its usage a regular occurrence.

But it may turn up from time-to-time.


We had a lab meeting today. Usually, I would do my best to not make it obvious that I am falling asleep while the other students give updates on their "oh so interesting" projects ::cough, cough:: and then wait for my PhD to let me know that our research has been delayed AGAIN because the fluorescent microscope is improperly calibrated, or the anesthetics have not arrived, or another lab used our rats, or something...

But today was different.

I could tell something was up when I got there and my PhD was waiting for me (he has a tendency to run late). Instead of going through the monotonous Weekly Update he announced immediately that our grant proposal had been accepted!

Now for us, this is REALLY BIG NEWS!

See, unless you work in a gov't lab (and even when you DO work in a gov't lab) almost the only way that you can get funding to perform your research (other than selling prescription medications for outrages prices) is to apply for grants from the gov't and other organizations. Every month or so my PhD writes a couple of grant proposals (basically an outline of what we'll do with the money) and sends them in. I get to see them all, because I proof-read and edit the grant proposals.... and we just got one!

Of course a great deal of this money will go to things like the general operation of the lab, our income, etc but there is a small amount of money set aside specifically for a project that I designed... a project that I included in the grant proposal (and I'm pretty sure that my project is the only thing that got us this grant...).

Assuming my PhD doesn't kill me for adding my project to the proposal without asking him, some exciting things could happen Very Soon.

Friday, April 4, 2008

Once upon a time in an RNA world...

So what is an RNA world anyway?

Well, that's both more and less complicated a thing than you might think. First lets talk about your genetic material, the stuff that makes you who you are.

See, you DNA is the medium used to store your genetic code. It is the book upon which the story that is YOU has been written. Now, if you want to share portions of a book with your friends you don't rip out the pages, do you? I hope not... you either have them buy their own copy of the book (unfortunately human cloning isn't legal in the States) or you make a copy of the page(s) you want to share with them.

This copy of the page is akin to your RNA. Now the copy doesn't have all the information, and it is more likely to be broken down, degraded, or outright destroyed than the book with its heavy binding. Much like RNA is a more transitory molecule than DNA... it breaks down easier and is not as stable.

Well, DNA store the information in each of your cells and uses cellular machinery to make RNA copies of the instructions that need to be carried out.

Well that fact raised a lot of questions. See, RNA is ubiquitous to all forms of life. The DNA ~> RNA cycle is also ubiquitous to all forms of life (we are excluding viruses from this discussion for the time being). DNA acts ONLY as a storage device (in most cases) and RNA is the functional form of genetic material in a living creature.


Because RNA came first.

::ducks bits of rotten veg and cans being thrown at him by the conservative scientists and religious fanatics in the audience::

See, RNA was the most likely form of genetic material to have evolved initially: It is the simpler genetic molecule (DNA is actually a modified form of RNA) & it is the most diverse form of genetic material capable of storing and transferring genetic information, transporting amino-acids (as in the case of tRNA), structural activities, and even enzymatic activities.

When life first evolved, there were no molecules available to carry out these functions. Over time, other molecules evolved that can do the job more efficiently or more effectively, but none of them are capable of doing ALL of them, except RNA. It was the evolution of RNA that allowed for the first truly LIVING organisms to exist, evolve, and develop more advanced forms of structure and catalytic activity (in the form of proteins) and safer genetic storage techniques (DNA) furthering the evolution of RNA and organisms extensively.

Now for many of you, this is a moot point. Whether RNA or DNA came first is of little importance... or perhaps you don't even believe in it at all. And, I guess, that is your right. If you want to believe that the sun does not shine or that water is not wet, then who am I to tell you any differently.

But there are those who take matters such as this far more seriously than you or I... the same type of people that try to ban evolution in our schools, animal testing in our laboratories... the type of people willing to commit acts of violence against organizations, and people, who try to advance these types of studies.

But, no worries. I'm only a student after all... who'd want to come after me.

Thursday, April 3, 2008

Ribosome = Ribozyme


So for those of you who are now looking at your screens with a puzzled look and trying to figure out exactly why you made the effort to check out my second blog... allow me to illuminate that statement.

You see, the ribosome is a macromolecular machine, meaning that it is larger than an individual molecule (e.g. water or ethanol) but is smaller than, say, a living cell. There are hundreds and sometimes thousands of ribosomes active in any one of your living cells, and it is their job to read strands of messenger RNA (which is transcribed in the nucleus of the cell and is a literal carbon copy of a portion of your DNA) and turn that mRNA (as messenger RNA is called) into a chain of amino-acids (the building blocks of proteins).

So without the ribosome you would be unable to produce proteins that are necessary for everything from structural roles such as cellular skeletons and collagen, to signaling roles in the brain played out by neurotransmitters, to hormonal changes throughout the body, to the numerous catalytic activities that proteins undergo every moment of every day.

Now, until fairly recently the ribosome (which is made up of protein subunits bound to a special type of RNA called, you guessed it, ribosomal RNA or rRNA) was thought to gain its catalytic powers from the proteins and that the rRNA was there simply to provide a binding site for the mRNA that was to serve as the template.

Well, apparently that is not the case.

The current theory that is being bandied around in the scientific community is that the ribosomes actually take their catalytic properties from this rRNA and that the proteins provide significant structural and binding support to the macromolecule during protein synthesis.

Basically what this is saying is that RNA is not only capable of catalysis, but that it is most likely the first form of catalytic biological molecule to have EVER existed!

And when you are trying to convince people of an RNAworld, you need every bit of help you can get.

Wednesday, April 2, 2008

Welcome to My World

Hello world.

I'm quite obviously new to the whole "blog-o-sphere" but decided that now was the time to get involved.

So where do I begin?

For some, the best place to start is the beginning. I however will start at the middle, and we'll see how things go from there. RNAworld is a place where I hope to share the wonders of the scientific world with all the rest of you, and chronicle my adventures in uncovering the mysteries of our past. Exciting, huh?

If you haven't already guessed, I'm a bit of a science freak (I prefer biology and chemistry but I'm down for anything) and evolution is a major hobby of mine. I know, most people will tell you how they like to go hiking, back-packing, walking on the beach at sunset, etc... but I figured I might as well be honest with you all. I do all those things, but evolution is still my hobby.

I find that far too many people have a misconception as to what evolution ACTUALLY is. They seem to think that when a species evolves it means that individual organisms become something else. That is as far from reality as Tom Cruise! (no hard feelings Tom, I love your movies and everyone has the right to believe whatever they want... but you just act really crazy sometimes) Anyway, evolution in a broad sense is a change in allelic frequency in a population over time.


Basically, lets pretend there is a population of 100 flowers, 1/2 red and 1/2 white. When those flowers reproduce lets say that only 25 red flowers are produced while 75 white flowers are produced. (we're going to assume that red v. white is controlled by one gene and that the gene follows simple dominance patterns) then the new population of flowers would have a different frequency of red genes and white genes... right?

We'll assume that it does. So the population has evolved. Over time this population might evolve to a point where there are no longer ANY red flowers at all... or other events might occur that drive the evolution in the other direction. It can all get very exciting!

But to tell you the truth, my real love is genetics. That's why I'm so interested in evolution, because you can study it by studying the genetics of organisms. And when you combine evolution with genetics you undoubtedly get RNA (ribonucleic acid), the first form of genetic material to evolve on the planet... at least, we think it is.

We use DNA (essentially just modified RNA) for our genetic material now (primarily because it is loads more stable than RNA) but if something needs doing, its the RNA that gets it done. There is even RNA that has the properties of enzymes, referred to as enzymatic RNA or sometimes as ribozymes.

I guess I'm a little bit like RNA, slightly unstable but that's what helps me do my job.

Well this has been fun. Check back in for the next installment of RNAworld!