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Kindle Notes & Highlights
by
Addy Pross
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January 29, 2020 - May 12, 2021
What is no less remarkable is that modern biology appears to be happily meandering along its current mechanistic path with most of its practitioners indifferent, if not oblivious, to the shrill cry for reassessment.
there is no élan vital, that living things are made up of the same ‘dead’ molecules as non-living ones, but somehow the manner in which those molecules interact in a holistic ensemble results in something very special—
to merge biology into chemistry rests on the idea that there is a kind of stability in nature that has been previously overlooked, one I have termed dynamic kinetic stability.
the recent description of life by Carl Woese: ‘Organisms are resilient patterns in a turbulent flow—patterns in an energy flow.’
Within biological systems catalysts play a crucial role and are called enzymes.
Replicating chemical systems will tend to be transformed from (dynamically) kinetically less stable to (dynamically) kinetically more stable. That selection rule is in some sense an analogue of the Second Law, the selection rule in the regular chemical world. In both worlds chemical systems tend to become transformed into more stable ones, but as the two worlds are each governed by a different kind of stability, the selection rule in each world is different—thermodynamic stability in the ‘regular’ chemical world, dynamic kinetic stability in the replicator world.
When a number of different replicating molecules all compete for the common building blocks from which they are constructed, the faster replicators out-replicate the slower ones so that over time the slower replicators will tend to disappear.
As Leslie Orgel, the eminent British chemist and leading origin of life researcher, once put it: ‘Just wait a few years and conditions on the primitive Earth will change again.’
The real challenge is to decipher the ahistorical principles behind the emergence of life, i.e., to understand why matter of any kind would tend to complexify in the biological direction. It is this ahistorical question,
What laws of physics and chemistry could explain the emergence of highly complex, dynamic, teleonomic, and far-from-equilibrium chemical systems that we term life?
systems chemistry deals with the class of simple replicating molecules and the networks that they create. That area of study, still in its infancy, has already revealed that reactivity patterns observed in such systems are quite different from those we find in ‘regular’ chemistry,
despite major differences in the essence of their chemistry, all contend that holistic autocatalysis (a catalytic cycle that achieves closure)—in what might be thought of as a primitive metabolism—preceded the subsequent incorporation of a genetic capability. Second, all presume that the organization required to generate metabolic function came about spontaneously, or through random drift.
But, as has been pointed out by several leading origin of life researchers, in particular Shneior Lifson46 and Leslie Orgel,47 that idea is highly problematic. It’s the Second Law problem again.
Tibor Ganti, a Hungarian chemical engineer, recognized the problem over thirty-five years ago when he stated that ‘living systems have special properties which arise primarily not from the substances of the system, but from their special organizational manner.’
Jacques Monod in his classic Chance and Necessity considered the problem of teleonomy as the ‘central problem of biology’.10 As Monod put it: how could purposeful systems have emerged from a universe with no purpose? But the minimal attention that has been directed toward this ‘central problem’ suggests that the scientific community considers the problem solved (or uninteresting) and has accepted the ‘emergent property’ explanation.
Darwinism did bring about a sense of unity within biology, but the troubling consequence of that unification, of enormous value in itself, has been a growing isolation of the subject from the physical sciences to which it must necessarily connect.
when the two RNA molecules were allowed to replicate and evolve in the presence of not one, but five different substrates, the two RNAs were able to coexist, but in an unexpected way. Initially the two RNA molecules utilized all five substrates in varying degrees in order to replicate. After all, all five were present and therefore all five could be utilized to some extent. But here is the punch line: over time each RNA molecule evolved so as to optimize its replicative ability with respect to different substrates.
holistic replication is the norm in biology; that’s what cells do when they replicate—the system as a whole makes copies of itself, as opposed to each individual component within the cell copying itself. So what is the significance of this result? Simply this: what one simple replicating entity could only do inefficiently, a more complex one was able to do more efficiently.
Cooperation is win-win. No wonder cooperation is endemic in the biological world—biologists call it symbiosis.
The conclusion seems clear: complexification, primarily through network establishment, appears to be the mechanism for the transformation of simpler chemical replicators into more complex biological ones.
But how is this different from emergent complexity? They sound synonymous
If a further reminder of the special nature of the replication reaction is needed, consider a single replicating molecule, weighing just 10-21 grams. If it were to replicate once a minute, then, in under five hours that replicating molecule would have grown (in principle, of course) into a mass exceeding that of the entire universe!
While consciousness is certainly a characteristic of life, it is not an essential one, as it is only associated with advanced life forms. Accordingly, we have not dealt with
On what possible basis does he say this? Such humanist arrogance,
