[DIYbio] Re: How do phenotypes arise from genome?

Well as you may note no one here has been able to definitively answer your question - as indeed nor can I. But I can tell you one thing and that 'things are arranged the way they are due to biochemistry and evolution'. This might seem like a bland and empty statement, but it may not be as empty as you think. Things are arranged the way they are due to a 'happy accident'. Others here have argued for a Turing like map of biochemistry, but for me from a classical perspective this seems too 'purposeful', almost as though there is some overall actor (albeit unconscious perhaps) (or a script) governing the process. It is better in many ways I feel to consider every cell in your body to have arisen (and to be so organised) as a matter of pure chance. A liver cell can no more 'know' where it belongs than can a kidney cell, or a brain cell. It just so happens that the pressures and limitations exerted on evolution have resulted in this very particular conformation of tissues.

A better way to think about this perhaps is to consider how a bacterium might find its way towards a richer source of nutrients either when in culture, or in its natural environment. A great many bacteria use a methodology known as 'quorum sensing' (a form of random walk) to achieve this objective. Although this process may look purposeful, it is nonetheless a fundamentally chance process. The bacteria is in no way concious of it's need for nutrients, nor does it adjust it's course intentionally in pursuit of a favourable outcome. Rather the organism behaves entirely mechanistically in response to a biochemical stimulus - which itself (outside of the lab) is chance in nature. (Indeed all actors in this process are essentially random and/or subject to chance. The bacteria's tissues, its genome (which have simply been 'selected for') the substrate upon which it lives and the nutrient source upon which it depends. It is a matter of the presence (or lack thereof) of a certain type of biochemical gradient that may be unique in each case. Cells like people, also have the capacity to 'recognise' each other, via cell surface proteins and cell binding proteins that only other cells of a similar type can recognise. They can also speak to each other and even to different parts of the same cell, both over short and long distances via the endocrine, intracrine, autocrine, juxtacrine, paracrine (nervous system) signalling pathways. Again while this may appear purposeful, it is important to remind oneself that right down to each individual biochemical interaction taking place in the most minute detail, each one of these processes has arisen as a consequence of chance. Although these pathways may appear more sophisticated than those of the bacteria, it is still possible to recognise a link between this primitive signalling methodology and more recent/more advanced signalling methodologies.

It is very hard to look at this process and at more complex biological arrangements and not see some form of 'organisation' or 'intent'. But its fair to say that all processes like this and all processes where tissues may appear to spontaneously 'self organise' originated in a step by step process and that the ancient ancestor of most modern bacteria was pretty rubbish at sensing the presence of nutrient gradients in its environment. Rather it seems likely that this behaviour emerged only very gradually over countless aeons of time, as a result of endless natural experimentation, overpopulation, extinction, chance and good fortune, as the system that allowed bacteria to become more efficient at 'sensing' nutrients in its environment evolved. Higher organisms after all are not governed by different processes than those that have governed the evolution of bacteria. There is no supplementary 'directed' subtext that governs the evolution of higher life forms.

I know some people will say that since stem cells have the capacity to differentiate into any tissue type that this is evidence that there is some 'direction' in this process. But there is not, as plainly the genome is the source of much of the randomness (in conjunction with external factors) that has resulted in the present state of affairs. Tiny steps, chance and almost unlimited time is what has brought us to this point. If you wish to have a better model for how random systems may display a capacity to self-organise, a better fit would be chaos theory. A sub-branch of Chaos theory is of course fractal theory, although this isn't an area I have a great deal of experience of personally.