in the beginning

I recently read an article in the guardian about the origins of life which slightly baffled me. So partly as an excerise for myself I copied it below complete with my embedded thoughts as I read it. Please note that these are merely my thoughts on it and it is well possible many are wrong. (Amazingly I am not always right.) It's fair to say I wasn't exactly impressed however to be fair you should probably first read the article for yourself (properly formatted) here. After this you can glance through the article below with my comments bracketted in red and see if you agree or not.

The origin of life is one of the great outstanding mysteries of science. 
(With many proposed solutions that some are happy with.) 
How did a non-living mixture of molecules transform themselves into a living organism?
(This is out and out vitalism, as would seem to infer that a totally synthetic "living" cell is not around the corner which is a brave bet.)
What sort of mechanism might be responsible?
(The same physical and chemical mechanisms that govern the rest of the universe.)
A century and a half ago, Charles Darwin produced a convincing explanation for how life on Earth evolved from simple microbes to the complexity of the biosphere today, but he pointedly left out how life got started in the first place.
(So the author is, thank god, happy with evolution just not the origin of the very simplest life form. We will come back to that later.)
"One might as well speculate about the origin of matter," he quipped. But that did not stop generations of scientists from investigating the puzzle.
(Nor did it stop folk investigating the origin of matter. Unless I missed the all_physics email explaining the missing anti matter issue.)
The problem is, whatever took place happened billions of years ago, and all traces long ago vanished – indeed, we may never have a blow-by-blow account of the process. Nevertheless we may still be able to answer the simpler question of whether life's origin was a freak series of events that happened only once, or an almost inevitable outcome of intrinsically life-friendly laws. On that answer hinges the question of whether we are alone in the universe, or whether our galaxy and others are teeming with life.
(I have no issue with this paragraph bar the odd and obvious opening statement.)
Most research into life's murky origin has been carried out by chemists.
(Hhhm, well most of the research into the origins of molecules that are important to life has. Probably for the same reason most laser research is carried out by laser physicists.)
They've tried a variety of approaches in their attempts to recreate the first steps on the road to life, but little progress has been made.
(If you define success as a page by page chemical history up to living organisms then yes. I would argue the outstanding experiments that produced life-relevant molecules using early earth laboratory conditions or the discoveries of life-relevant molecules in meteorites as more than a little progress but whatever.)
Perhaps that is no surprise, given life's stupendous complexity. Even the simplest bacterium is incomparably more complicated than any chemical brew ever studied.
(This is not entirely obvious to me. At some level Dr. Manhattan's point that to enlightened beings a dead human and a live one have the same number of atoms and hence are just as interesting. The patterns and complexity in a cell are somewhat obvious due to their manifested macroscopic results. Relatedly the inherent sizes and time scales of most biological processes make them amenable to study with current scientific techniques. However at a more fundamental level the quantum mechanical interactions between slowly diffusing molecules in a cell sized drop of water are no less complex or interesting than those in a cell.)
But a more fundamental obstacle stands in the way of attempts to cook up life in the chemistry lab. The language of chemistry simply does not mesh with that of biology. Chemistry is about substances and how they react, whereas biology appeals to concepts such as information and organisation.
(The language only does not mesh only if you don't understand that they are both descriptions that are entirely valid. Many people are capable of holding and understanding both viewpoints and applying insight gained in one language set to the other. I am surprised a physicist does not get this as somewhat famously in physics a particle can be described just as accurately with a wave or particle model.)
Informational narratives permeate biology. DNA is described as a genetic "database", containing "instructions" on how to build an organism. The genetic "code" has to be "transcribed" and "translated" before it can act. And so on. If we cast the problem of life's origin in computer jargon, attempts at chemical synthesis focus exclusively on the hardware – the chemical substrate of life – but ignore the software – the informational aspect.
(This is bizarrely arbitrary which is simple to demonstrate by switching the language. Now: The early molecules experiments were attempting to characterize the probability of a certain type of information structure (life-relevant molecule) arising when other information structures were merged together.)
To explain how life began we need to understand how its unique management of information came about.
(I simply disagree here and I see nothing so far in this article to support his hypothesis that life could only have arisen with our current information management.)
In the 1940s, the mathematician John von Neumann compared life to a mechanical constructor, and set out the logical structure required for a self-reproducing automaton to replicate both its hardware and software. But Von Neumann's analysis remained a theoretical curiosity. Now a new perspective has emerged from the work of engineers, mathematicians and computer scientists, studying the way in which information flows through complex systems such as communication networks with feedback loops, logic modules and control processes. What is clear from their work is that the dynamics of information flow displays generic features that are independent of the specific hardware supporting the information.
(Partly true but again he has not shown in this article anything that justifies the dynamics of information flow being in any way crucial to the origins of life.)
Information theory has been extensively applied to biological systems at many levels from genomes to ecosystems, but rarely to the problem of how life actually began.
(Yet this article seems to know the result of this admittedly non existent research.)
Doing so opens up an entirely new perspective on the problem.
(In his humble opinion as someone who holds such a perspective.)
Rather than the answer being buried in some baffling chemical transformation, 
(only baffling to some)
the key to life's origin lies instead with a transformation in the organisation of information flow.
(No softeners like "maybe" or "could" just a evidence free statement that viewing things his way is the key to understanding life's origin.)
Sara Walker, a Nasa astrobiologist working at Arizona State University, and I have proposed that the significant property of biological information is not its complexity, great though that may be, but the way it is organised hierarchically.
(At last a softener "proposed" bit of a pity it is after all the major claims.)
In all physical systems there is a flow of information from the bottom upwards, in the sense that the components of a system serve to determine how the system as a whole behaves. Thus if a meteorologist wants to predict the weather, he may start with local information, such as temperature and air pressure, taken at various locations, and calculate how the weather system as a whole will move and change.
(With the slight problem that as weather is a non linear system this methodology will simply not work in most cases. Also in a great many emergent systems you simply cannot infer top level system behaviour from examination of smaller constituent elements. An example being how an ant colony responds to floods is not calculable from the respond of a single ant.)
In living organisms, this pattern of bottom-up information flow mingles with the inverse – top-down information flow – so that what happens at the local level can depend on the global environment, as well as vice versa.
    To take a simple example; whether a cell expresses a gene can depend on mechanical stresses or electric fields acting on the whole cell by its environment. Thus, a change in global information (a pattern of force) at the macroscopic level translates into a change in local information movement at the microscopic level (switching on a gene).
(I think the "information" stored in the DNA ie the bit that can evolve and is therefore the important bit when we talk about the origins of life is unchanged, no?)
More generally, a range of signals received from its environment help to dictate how a cell's DNA is distributed and transcribed.
(I am missing now this is relevant to storage or evolution of the information encoded in the DNA base sequence.)
Walker and I propose that the key transition on the road to life occurred when top-down information flow first predominated. Based on simple mathematical models, we think it may have happened suddenly, analogously to a heated gas abruptly bursting into flame.
(An interesting thought that has as far as I can see from this article has no evidence to back it up, yet.)
There is a second distinctive way in which life handles information processing. The language of genes is digital, consisting of discrete bits, cast in the language of a four-letter alphabet. By contrast, chemical processes are continuous.
(Some chemical processes have two stable states and very fast transitions which effectively makes them digital. Most classical digital processes analysed at a sufficiently fast speed are analogue processes with two stable outcomes. It's oversimplistic at this level to merely see digital and analogue as the two options.)
Continuous variables can also process information – so-called analogue computers work that way – but less reliably than digital.
(Are analogue electronics less reliable than digital. If you work with them I think you will know the answer is no they absolutely bloody well are not.)
Whatever chemical system spawned life, it had to feature a transition from analogue to digital.
(Again no softeners just stating his opinion as fact.)
The way life manages information involves a logical structure that differs fundamentally from mere complex chemistry.
(mere complex chemistry being a beautiful oxymoron.)
(or more accurately "I reckon".)
chemistry alone will not explain life's origin, any more than a study of silicon, copper and plastic will explain how a computer can execute a program.
(transistors and thus all modern computers came from the study of silicon, studies of copper allowed early electronics to take place and studies of plastic is what allowed FR4, the PCB material of choice, to be created. After and only due to these scientific advances and many more did modern computational machines become possible. Analysis of an end product of several hundred generations of refinement and optimization by looking at the founding principles is somewhat silly.)
Our work suggests that the answer will come from taking information seriously as a physical agency, with its own dynamics and causal relationships existing alongside those of the matter that embodies it – and that life's origin can ultimately be explained by importing the language and concepts of biology into physics and chemistry, rather than the other way round.
(That information is more important than matter is not a very physical way of looking at the world. Quantum theory is quite clear on the fact that all particles are really probability distributions or information if you prefer. As all matter is "merely" a collection of particles all matter is information. So to rewrite this final paragraph into a more sensible form."Others' work suggests that information can be considered as a physical agency with its own macroscopic dynamics often called matter. Life's origin may ultimately be explained by various constructs from biology, physics or chemistry but they are all equivalent." )