Chemistry Becomes Biology – Notes

The Nobel biologist Francois Jacob expressed it rather poetically: ‘the dream of every cell, to become two cells’.

 Put a bacterium in a glucose solution in which the glucose concentration is variable and the bacterium ‘swims’ toward the high concentration region. That phenomenon is called chemotaxis.

Chiral nature - Many of the molecules found in living systems are chiral, meaning that the molecule’s mirror image is not superimposable on the molecule itself.  
one chiral molecule is labelled D (for dextro, or right-handed) and its mirror image, L (for levo, or left-handed), based on its spatial relationship to the organic substance, glyceraldehyde.  that given enough time, that material of single chirality will become racemic, meaning that the material will end up consisting of equal quantities of D and L forms

Within living systems only one chiral form of the two possible chiral forms is present—biological sugars are almost invariably D-sugars, while amino acids are almost invariably L-amino acids. Living systems are universally homochiral

The essence of Aristotle’s teleological view—that there is an underlying purpose to the workings of nature, that purpose governs the cosmos as a whole.

 nature is objective , that there is no underlying purpose to the natural order. 
Jacques Monod, in fact, considers that idea the single most important idea offered by man.
 generation later Jacques Monod, the Nobel biologist, in his classic 1971 monograph Chance and Necessity ,reaffirmed the existence of a deep physics–biology divide,
Simply put, how could function and purpose have emerged from an objective universe devoid of function and purpose

NASA definition of life: Life is a self-sustained chemical system capable of undergoing Darwinian evolution .

Wittgenstein -  ‘whereof one cannot speak, thereof one must be silent’.

 The essence of the reductionist approach is simply: ‘the whole can be understood in terms of the interaction of its constituent parts’. thought termed holism , whose philosophy can be summarized by the simple statement: ‘the whole is more than the sum of its parts’, and so appears to negate the reductionist view. Holism contends that within complex systems in particular, unexpected emergent properties arise that cannot be derived by examining the individual components of the system

 Reduction in its various forms and subforms, was, is, and will likely remain the central conceptual tool in scientific endeavour. To the extent that the ‘what is life’ question can be satisfactorily resolved, I believe it can only be through a fundamentally reductionist approach—by seeking the underlying connections between chemistry and biology, by identifying the process responsible for biological complexification


the essence of life will be found to lie in the dramatic difference between the rates of catalytic and autocatalytic reactions.  The difference comes about because in the autocatalytic reaction, the rate of product formation proceeds exponentially , whereas in the catalytic reaction the rate of production proceeds linearly.

 In 1967 , Sol Spiegelman a microbiologist at the University of Illinois, performed one of the truly great classic experiments in molecular biology when he carried out molecular replication in a test tube. Spiegelman simply mixed an RNA strand with free floating building blocks from which the RNA is itself built up, an enzyme catalyst to speed up the reaction, and lo and behold, the RNA strand ended up making copies of itself

 In fact in 1986 , a dramatic step forward was taken when the leading German chemist, Gunter von Kiedrowski, was able to carry out the first molecular replication reaction without any enzyme present to facilitate the reaction (i.e., no biological assistance)—finally pure replicative chemistry


A replicating system that acquires an energy gathering capability by a chance mutation would be more stable in a DKS sense and would therefore be selected for over one without that capability.
 
The moment some non-metabolic (downhill) replicator acquired an energy-gathering capability, could be thought of as the moment that life began.

 The Second Law of Thermodynamics is, of course, fully applicable to replicating systems, but the enormous kinetic power of replication ends up seemingly circumventing that ubiquitous Second Law.


 In the world of replicating systems, matter is stable (in the sense of being persistent) if it does react, to make more of itself. And in this persistent sense, matter that is better at making more of itself is more stable than matter that isn’t. That is the essence of the DKS concept

 Biology then is just a particularly complex kind of replicative chemistry and the living state can be thought of as a new state of matter, the replicative state of matter.

Working definition of life : a self-sustaining kinetically stable dynamic reaction network derived from the replication reaction.