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.

Comments

  1. #1 pough
    January 15, 2008

    Think about this – your body makes about 20,000 machines – these cooperate to form functional cells that cooperate to make a body.

    Break out the canaries, boys, we’re goin’ quote-minin’! ;-)

  2. #2 Gary Greenberg
    January 15, 2008

    This is a good post drawing attention to the absence of a genetic code or blueprint. It is all very probabilistic.

  3. #3 apalazzo
    January 15, 2008

    I’ve had enough of this quote-mining mentality. Materialism undermines religious and creationist thought more then any other idea. Life is not vitalistic but instead reducible to a plethora of molecular interactions. Vitalism is the real illusion that most religious (and many non-religious) individuals have. Materialism is not an argument for design.

  4. #4 Acme Scientist
    January 15, 2008

    So what is the biggest story never covered by the mass media? That the Nature vs. Nurture debate is over? That Nature is Nurture?

  5. #5 Coturnix
    January 15, 2008

    Oh, I have always preferred the Rube Goldberg metaphor to the clock metaphor.

  6. #6 apalazzo
    January 15, 2008

    Acme,

    Exactly! Anyone who says “Nature vs Nurture” just doesn’t get it. We have countless mechanisms to respond to nurture – it’s in our nature!

    Coturnix,

    If only William Paley was around, we would show him that even our internal clocks aren’t watches!

  7. #7 bayman
    January 15, 2008

    What about the (genetically-determined) limits to what nurture can achieve, those which are imposed by nature? A boy and raised or “nurtured” by wolves for example, does not grow a tail. Organisms do indeed consist of immutable phenotypic aspects, and how they are specified by genomic sequence is not going to be answered by some hand-waving about adaptability. (Although I wish it could be)

  8. #8 apalazzo
    January 15, 2008

    Bayman,

    Yes, there are limits to the adaptability – but also the adaptability expresses itself in particular ways. The whole genes vs environment is a over-facile attempt to understand how organisms develop. Individuals will gain weight if they are placed in a colder climate, but they won’t grow more hair. Why? It’s not nature it’s not nurture. It is our gene-determined Rube Goldberg contraptions responding to changes in environment.

  9. #9 bayman
    January 16, 2008

    Fair enough – that’s an important point to be made. But I’d still like to know how to turn a man into a wolf – or a stegosaurus for that matter. :)

  10. #10 apalazzo
    January 16, 2008

    Because our cells are so tweek-able it take relatively few genetic changes to accomplish transformations such as this.

    It’s been clear for a while that there is a core set of genes that don’t vary much between most eukaryotes – it is these elements that provide the cell/organism the ability to buffer changes and also be malleable. Those changes may come in two forms. There are changes in peripheral genetic elements – the ones that guide our cells to become a human and not a wolf. And there are environmental changes.

    What are these peripheral genetic changes? Some would claim that they are DNA regulative elements (enhancers, promoters) that act to turn genes on or off. Some would say that they are transcription factors that regulate the transcriptional landscape. Some would say that they are signalling genes that allow cells to communicate with one another and interpret their signals.

    So yes genetic alterations do affect the organism, but it’s only through our core (and relatively unchanging) genetic elements that allow individuals to evolve in response to those changes AND adapt to different environmental cues.

  11. #11 Drugmonkey
    January 21, 2008

    oh for…

    JHCoafPS, where to start.

    Look, I’m the first to bag on idiot journalists not gettin’ science. but. come. on. nobody but nobody likes the geek-away details and elegance the way scientist do. else they’d be…wait for it…scientists.

    One thing all scientist could stand to do, yes even bloggers, is to get out a little more. Talk to people that don’t understand what you do, don’t understand the process of science, may not even be much brighter than average but, btw, pay your salary through taxes.

    Do a little one on one research into your presentation to the guy on the next barstool. Where do the eyes start to glaze over? That’s where you’ve lost ‘em. What do they ask a question about? That’s what they get. The point is not to get all enraptured about why you like your science but to figure out what captivates them!

    Admittedly, I usually get to talk about stuff that people already have some ideas on but believe you me, even talkin’ drugs, ADHD, etc there is a “glaze-over” point that we scientists are more likely than not to hit…

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