Transcription and Translation

Behind the scenes I've been ranting at my Scienceblog neighbours. Since I've been busy writing my k99 grant and have little energy to write about any of the new papers out there I'll repost some of my comments in modified form here.

Why are cell biology, molecular biology, biochemistry, microbiology never covered in the media? I've spoken to so many science journalists - most of whom have no science training. I've come to the conclusion that the barrier is too high - as a result when it comes time to write about these topics, most science journalists end up writing about "genomes" and "junk DNA". These are easy subjects - sometimes they're discussed within the framework of evolution, but never within the context of "how a cell or an organism operates". Think about this - your body makes about 20,000 machines - these cooperate to form functional cells that cooperate to make a body. How do you go from genotype to phenotype? How does it all work? Well more money is poured into this subject then any other topic out there. More man hours are going into this endeavour then any project undertaken by humankind. But you would never guess that from reading most newspapers.

And the stuff is so cool. Within every cell there's a zoo. And within the workings of the cell you can begin to see how life works. You can begin to see how evolution works. The most insightful book on biology written in the past decade was Gerhart & Kirchner's book, The Plausibility of Life. When you go deep down and study the function of those 20,000 coding genes in our genome, you instantly realize that the vast majority of those instructions specify machines that act to regulate cell homeostasis. This includes metabolism, how to copy DNA, how to maintain the DNA, how to divide your DNA, how to change cell shape, how to divide the cell, how to make RNA, how to move RNA, how to assemble proteins, how to fold proteins, how to pump proteins into vesicles, how to modify proteins, how to pinch off vesicles, how to move vesicles, how to fuse vesicles, how to receive signals from the outside, how to interpret those signals, how to respond to stress, how to commit suicide. That's what the genome mostly encodes.

And is it a surprise that humans and worms have all the same types of genes? Is it a surprise that mice and humans have almost the exact same genes?

But how do these cellular processes, the ones closest to the phenotype, collaborate to form a phenotype? That is the beauty of the newest insights from cell biology. These cells that make up our body, they're incredible. They are the most wonderful machines ever. And they are composed of these cellular processes that are extremely robust Rube Goldberg contraptions. And these processes are so neat - most components have backup parts, and many contraptions have backup contraptions. In addition the contraptions talk to eachother and are filled with countless number of feedback loops. And they are intelligible - but it is hard. To fully appreciate what's happening you have to put together countless number of findings. Every week, small bits of the puzzle come out, but if you are some clueless journalist, what would you know?

It is these processes that make cells incredibly adaptable to the environment. Yes that's right, the greatest thing produced by the genotype is adaptability. Nature is not in opposition to nurture, nature is the basis of nurture! These contraptions act as buffers so that the cell does not fall apart when confronted by different situations. But in addition these contraptions make the cell malleable. It takes very little to slightly modify the function of a cell, and they usualy respond in a way tat doesn't compromise their viability or the viability of the organism. In some ways we implicitly understand this idea when we call something organic. In contrast our machines are precision instruments with no adaptability. A cell is not like a watch. The later was built for one purpose and it's construction can only work if all the parts fit exactly. The former is adaptable. You can take things out of a cell put extra things in and not only will the cell be just fine but it can morph into a myriad of functional entities. It can become an inner ear cell, it can make bone, it can be a neuron, it can crawl around - you just have to tweek it a bit by adding just a few extra items and *presto* the incredible cell can do a new trick. Want to change a mouse into a man? Just tweek this cell type a wee-bit, and tweek that cell type a wee-bit and *presto*. The complexity within our genome lies principally in the fact that our cells CAN do this. This ability to be adaptable - this is the primary function of the genome - to build the play-dough of life.

That's the biggest news story that you'll never hear. And it's also the biggest finding that man has made in the past 50 years.

So right now we cell biologists and our morphed cyborg counterparts (systems biologists) are trying to understand not only how these Rube Goldberg contraptions work but what other new Rube Golberg contraptions are out there, how these contraptions talk to eachother and how they achieve their ability to buffer and to be malleable. These are the central questions.