The second law of thermodynamics and a theory of the origin of life itself

I have in all my time of reading science, and science news, never quite experienced the absolute abstraction of objectivity, as I did this morning. For the first time I found myself emotional, and even partially conflicted, upon reading about Professor Jeremy England, and his approach to explaining the physics of the origin of life.

Professor Jeremy England and his work on A New Physics Theory of Life.

The question of the origin of life, and the origin of selection and evolution, has plagued me for extended periods of time, since I first prepared a paper on evolution as an undergraduate. I have also recently wrote a partially coherent bit about the second law of thermodynamics and biology, which was a subtle attempt at making a connection between the quantum world and biology.

The origin of evolution

It has long been assumed and argued that the origin of the first complex molecules, capable of self replication was the result of a unique set of conditions (primordial soup), and a few strokes of luck (lighting or similar) in conditions thought to prevail on earth around 3.5 billion years ago. This summary explanation accounts for the formation of the majority of amino acids from inorganic precursors, resulting in what is commonly referred to as the primordial soup followed by the “spontaneous” assembly of these components into complex, self replication units, and ultimately, systems of self replicating units. As soon as any of these units can exert some influence on its replication probability, natural selection kicks in and life becomes inevitable.

Where there has been very little investigation from evolutionary biologists, is where the discipline of evolution transitions away from biology and chemistry and enters the realm of quantum physics. The fundamental question about evolution is no longer how complex life forms can evolve from simpler life forms, but rather, how do these first life forms come into existence, and more importantly, why? This raises the question of life itself, and has been addressed by some of history’s most influential figures. Schrödinger himself wrote on this topic.

Selection at quantum level

Now however, Professor England has succeeded in publishing a coherent theoretical model of the origin of life, that relies not on small probabilities and luck, but the notion that the second law of thermodynamics provides the framework that increases the probability of the existence of life. This model does not assume life to be a fortuitous result of “just the right” conditions, but proposes that life is an inevitable result of the same fundamental forces that causes your coffee to cool down.

If my understanding of their thesis, and my intuition serves accurate, then life will result necessarily because the selection between combinations of particles, and their ability to facilitate the distribution of energy, i.e. the second law of thermodynamics. Seemingly complex arrangements of matter at a molecular level, serves to increase the gradient between the various organizational states of energy, and in this manner, the arrangements that are more efficient at distributing energy, become more numerous, as they have a greater probability of existing than alternative arrangements. Selection at quantum level one is tempted to say.

There is more to this argument, as this the spontaneous assembly of complexity is not so uncommon in modern times as you would imagine. Snowflakes have seemingly complex molecular arrangements that cannot be explained unless the probability of their particular [complex] molecular assembly is not overwhelmingly favoured. If snowflakes assemble in complex formation all around the world every day, then it is not a stretch to imaging that there is a fundamental similarity between this and the formation of complex chemical arrangements, such as those required for the existence of life. An example of this is the high probability of the organization of lipid membranes in water into bilayer structures, that are itself a fundamental requirement for the existence of life.

Phospholipid bilayer assembly in water.

The future is exciting

The concept of selection is an enormously powerful concept, and one fundamental to explaining the complexity and diversity of life. However, there is reason to be excited, as the physics of the origin of life, may hold yet more answers about the everyday workings of life. If this model can be extended to include and make room for selection at molecular and quantum level, then we will go a far way to explaining and understanding a whole lot more about ourselves, life in general, and the possibility of life elsewhere in the universe.

Brontosaurus Dolly: Feasibility of dinosaur cloning?

In response to an off topic question, posed during a research methodology lecture, I was humbled by the response of one logically minded undergraduate.

Can we clone a dinosaur? Not as far as I know, but apparently the internet knows more. An Australian billionaire by the name of Clive palmer, has hinted at the possibility of funding research for the purpose of cloning a dinosaur. First of all, we would have to look at a long list of factors governing its feasibility. Initial impressions would suggest that eccentric billionaire, Clive Palmer, is posing a challenge, laced with more humor than sincere ambition. The reality of live dinosaurs should in my mind, present a slightly larger public fascination than even the sensational athletic prowess on display at the recently concluded London Olympics.

Then a student responded, that they have indeed succeeded in cloning a dinosaur, which according to a bit of research, is postulated by some individual, to have occurred at the University of Florida. At first glance, it seemed to be too good to be true, and this opinion has since prevailed.

This publication seems at odds with the research publications and news from the University of Florida’s homepage. I find it strange, that they would have failed to be the first ones to make public this discovery, especially considering the funding (and inadvertent criticism) they would be privy to. But the apparently online-presence-deprived Dr. Norman Trudell, Biology Professor at UF, has neglected several important aspects considering the potential cloning of dinosaurs, and as it may happen, even more recently extinct species, of which he have near complete DNA databases.

But let us steer away from the breaking news of cloned dinosaurs and get into the challenges of feasibility surrounding the cloning of an extinct species.

Is Clive Palmer wasting his time and money? More importantly, is he potentially monopolizing resources that can best be allocated to disciplines related to more pressing public concerns, such as those of cancer and HIV?

The cloning of previous organisms such as the immortally famous (now deceased), Dolly, required some key elements, that is currently in short supply, with respect to dinosaurs. Dolly was cloned using a technique called nuclear transfer, where the nucleus of a somatic cell from primary in vitro cell culture, is introduced to an enucleated oocyte. The oocyte containing a full diploid complement, complete with all associated structural and regulatory protein, is transferred to a surrogate, until it reaches terminal gestational development.

From what I could gather, modern research has not yet produced a complete DNA sequence from any species that has retired from existence during ancient times, which includes many who have gone extinct far more recently than did the dinosaurs. With extensive biological and physiochemical DNA damage that far exceeds 60 million years, I have very little doubt that the scientific community might be expecting the recovery of an intact dinosaur genome any time soon and since we are only just beginning to understand the cellular physiology of extinct animals, the synthesis of a viable genome is as yet, probably even less likely.

According an article published by Nature (Ancient Biomolecules in Quaternary peleocology), we are seeing significant technological advances that increases the rate at which ancient DNA and other biomolecules can be analyzed, yet the National Center for Biotechnology Information (NCBI), does not mention any entry of DNA sequences that is related to the Apatosaurus (Dinosaur postulated to have been cloned).

Even if – with the advances made hitherto – we are capable of extracting sufficient quantities of DNA from paleontological specimens to obtain a complete DNA sequence of some prehistoric species, we would still be very far away from understanding the organization and nuclear morphology of ancient chromatin. I would think that this would make any attempts at cloning redundant. Even if, by some means, assembly of a complete and viable sequence (comparative to that taken from somatic cells in Dolly’s case) could be theoretically feasible (perhaps in cell culture of cells from a species with a close phylogenetic association), there would exist but still, a vast number of challenges in ‘interspecies’ nuclear transfer. There is no telling what difficulties such imperfect chromatin organization could produce, let alone the compatibility, or probable incompatibility of genes and gene products of donor DNA, with cellular components of the oocyte, that has had a hundred million odd years to evolve.

The question remains though, if there should be a public denouncement of this sort of frivolous allocation of resources, to the likes of unrealistic ambition, even if privately funded? This researcher remains a skeptic as to it feasibility, yet I firmly encourage any private funding that will, no doubt, result in the advancement of technologies that could in the future be applied for numerous ambitions, other than frivolity.

In reality, we are unlikely to see this research endeavor materialize to anything more than debated fantasy. Even if Clive Palmer is pursuing this avenue of research merely to satisfy personal curiosity, it may still inadvertently lead to the development of a technology, or even technique, that could justify such expenditure many times over. In any case though, he will be contributing to the advancement of science, or at least propagating some humor in a scientific community, that at times, seems much deprived thereof.