Fundamentaly biology is about information. An evolving entity must be able to copy itself - it needs the information on how to make a copying machine and it needs to copy this information to its progenitors. Already you can see how this works.
INFORMATION => COPYING MACHINE => COPY INFORMATION
Of course it is much more complicated then that. Take step A (INFO => COPY MACHINE) how do you do that? Well there are other machines that will translate the INFO into MACHINE parts. This process lies at the core of biology, the transfer of information, which is stored in DNA and is coded by the sequence of nucleotides that makes up this polymer, into protein machines, which are long sequences of amino acids strung up to form a protein polymer. This basic process, (Info or DNA => Copying Machines or PROTEIN) is not all you have. For an organism to copy itself it needs energy, but don't worry - some info in your genome codes for those types of machines as well (Info or DNA => Energy Machines or Proteins). And you need to make stuff (Info or DNA => Metabolism Machines or Proteins). And you need machines to make the organism move , communicate ... etc etc. You get the picture. There are a lot of machines in the typical organism. They work together to make the copying machine that can start off with raw materials to make other copying machines and thus other organisms. But the whole network of various machines in one organism is big and it gets messy fast. For example for this to ntwork of machines to function you need machines for this machines for that. Some machines act as garbage collectors and their job is to destroy other machines that need to be trashed. Yet other machines help the newly made machines to work properly. Other machines transport these newly made machines to the right place. Eventually you realize that most of the machines are there to prop the whole system up. And the system is very robust. Take away one type of machine and other backup machines take their place. Heat up the organism so that some machines start coming apart and still other machines march in and help rebuild the decrepit machines. Make too much of one type of machine and monitoring machines will go back to the start of the production line and halt the synthesis of the overstocked item.
All these various machines, this is what your genome encodes. The network of machines is the output.
So lets go back to the study of biology.
INFORMATION (genotype) => MACHINES => NETWORK (Phenotype)
Now lots of people are interested in figuring out the information. What does it say, how does it change? But the biggest problem in biology is not that. The big mystery is how is the INFORMATION translated to make this network of machines, this organic NETWORK that we call the phenotype. And yes it is truly organic (think about it, life = organic). The output is not some pocket watch that is made for some particular purpose with every gear interlocking to give you the time. The output is a survival super machine. It reacts and responds to the environment. It copes with stress. It finds mates (if it is a sexual organism). It multiplies. It eats, sometimes good stuff, often not so good stuff. It runs around, build nests and even pocket watches.
Right now there is a big project going on in the US and around he world. Probably the biggest collective project ever undertaken by humankind. More hours and money have been poured into this endeavour then any other thing we have ever set our mind on. And it is the attempt to understand this:
GENOTYPE => PHENOTYPE
Most of the action doesn't occur on the organismal level. It happens in every single cell. It happens in yeast, in humans, in tissue culture cells, in fly cells, in worm cells. How do you build an organic network? How do these masses of machines work, communicate with eachother to form the edifice that is a single cell?
The first hint is that organic beings are not like pocket watches. In fact the biggest hint is that the network is rigged to be able to cope with changes in the environment. It can be banged up, dipped in toxins, heated, cooled, and at the end of the day (or the week, depending on how bad the damage is) the network not only survives but repairs itself so that it is as good as new. It is the ultimate adaptable survival machine. That is what the nature of our network also know as our phenotype.
NEXT: Why is research dealing with machines that form networks and allow an organism to cope with stress more insightful for understanding evolution then studies involving purely genetic information.
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Interesting angle. I see biology as trying to answer the questions of Diversity (why so many species?) and Adaptation (how do organisms get to be more-or-less well adapted to their environments?). Study of the machines is only one tool in the toolkit used in answering these questions.
Well in many ways the machie network has everything to do with adaptability. In addition I think that the machine network facilitates evolutionary change - that will be the topic of my next post in this series.
Looking forward to it.
Alex,
I appreciate your perspective. I've been involved in a number of biology curricula reform projects where we try and articulate the fundamentals of biology--often we end up somewhere close to where I think I see you going in this post. I've linked to some of your previous postings on our KABT BioBlog and I'll do the same with this one. I am also looking forward to the next in the series.
BW
That's easy: It's because purely genetic information is insufficient to explain how cells function. You know that there is an old literature in developmental cell biology on the interaction between cytoplasmic and nuclear embryological determinants, right?
Well that's a different angle on the entire subject.
To twist your point into what I'm hinting at, all genetic information and the network of machines that is specified by the genome, interact with the environment to produce a phenotype. But you will have a better understanding of how that phenotype was generated by examining the interaction of variable environments with the network rather then the genome.
Evolution involves changes in both genotype and the network - small changes in the genotype are random, but changes in the protein network are skewed. The ability of the network to adapt to the environment also allows for changes in the network itself. It is this adaptive property of the network - the ability to change and to still function - that influences how evolution proceeds.
Great subject Alex, but when I think of "How to Think About Life" I consider that the relevant network is even more complicated than you suggest - since the 10 trillion or so cells (machines) with common genetic code that make up your body are dwarfed in number by the 100 trillion or so bacteria with which they live commensally -- and of course we can't live without them, or many, many other species without which the delivery of ecosystem services would collapse. Also, in the 'how to think about it' department, is the realization that all these networked machines are united together through time. There is an interesting article in the January 11-19 edition of "New Scientist" about how physicists are toying with the possibility that time really doesn't exist, but is simply a product of our minds... the article is about their efforts to design a physics without reference to time... I've always been impressed how we're stuck in the present (try getting out of it), and that the past and the future are truly dependent on memory and imagination. What does it mean if this big network of machines that we know shares common ancestory has always been unfolding in the present, rather than in a linear world of past to future? What does it mean for our self-identity?