Tuesday, 5 November 2013

"20 scientific facts seldom taught to students" critically reviewed #1 - Abiogenesis

Collyer claims in his first point that "[t]he origin of life is unknown to science. The Law of Biogenesis observes that life only comes from life. Louis Pasteur proved scientifically that life does not come from non-life, a fact that is the basis of the food-canning industry to this day."

His reply makes three main mistakes:
  • He conflates abiogenesis and evolution, which are two different things
  • He uses the argument from personal incredulity, a logical fallacy
  • Finally, he misunderstands the significance of Pasteur's experiment. Pasteur set out to test spontaneous generation – the belief that worms, maggots, flies and other small forms of life spontaneously appeared in rotting food. This is not the same thing as abiogenesis which is the formation of cellular forms of life from prebiotic precursors. Pasteur's experiment did not simulate the conditions of the early earth which is not surprising as Pasteur was not trying to disprove abiogenesis.
 Evolution explains how life diversified and changed over time. Abiogenesis conversely is the field of study which looks at how life appeared from non-living precursors. They are not the same thin. Special creationists frequently make the error of assuming biological evolution is intended as an all-encompassing atheistic theory of everything, explaining not only the origin of species, but the origin of life and the origin of the universe. Once they make this first mistake, they then proceed to find difficulties in unrelated fields such as quantum cosmology or abiogenesis, and claim these are failures of evolutionary biology.

Evolutionary biologists – whose definition of the subject in which they work is the one unqualified critics such as Collyer should be using – define evolution both as the fact of large-scale evolutionary change and common descent, and the mechanism used to explain such change. Abiogenesis is not evolution. It is possible to believe that the first unicellular form of life was specially created, with evolution taking over from there - a position that some evolutionary creationists maintain.

Another blunder Collyer makes is to confuse abiogenesis and spontaneous generation. They are not the same thing. Spontaneous generation refers to the ancient belief that flies and other forms of life could spontaneously emerge from decaying meat. Pasteur’s experiment showed that this was untenable. What he did not do was disprove abiogenesis, which refers to the generation of cellular life from prebiotic precursors and is an entirely different thing to the spontaneous generation of complex metazoan life. or even unicellular life. Pasteur did not disprove abiogenesis as as his experiment was designed to disprove spontaneous generation of complex life, not the formation of cellular life from prebiotic precursors. The concept of abiogenesis most likely was not even on Pasteur's mind, so it demonstrates a poor grasp of both abiogenesis and what Pasteur's experiment was intended to show by Collyer. Research in abiogenesis has advanced considerably from the “primordial soup” idea first advanced independently by Alexander Oparin and JBS Haldane. 

No scientist denies that abiogenesis is still an area in which many problems exist. There is no universally accepted theory for how the protocell was formed from organic molecules, though many hypotheses have been advanced. Some, such as the “RNA world” model [1] argue that nucleic acids formed first, while others postulate the formation of metabolic pathways first. Stuart Kauffman’s work on autocatalytic sets or the Iron-Sulphur world are two prominent examples of this class of hypothesis. However, unlike evolutionary biology, we do not have a rigorous theory. Eugene Koonan summarises current research in abiogenesis in The Logic of Chance:
Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate goal, the origin of life field is a failure—we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. [...]

Not everything is bleak: Major props for the origin of life have been discovered. Certain environments that exist even now, such as networks of inorganic compartments at hydrothermal vents, were likely present 4 billion years ago as well and could be suitable hatcheries for all the earliest steps of the evolution of life, from the synthesis and concentration of monomers to the origin of translation. The RNA World hypothesis that the impressive body of data on the catalytic activities of ribozymes strongly, if not necessarily directly, supports is an attractive - and apparently the only conceivable - way out of the paradoxes associated with the origin of translation.

Still, the difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life. [2]

Biochemist Lawrence Moran states that:
We don't know how life on Earth originated. We're not completely ignorant because we have a good idea of basic biochemistry and we know which enzymes and pathways had to be present in the earliest cells. We're pretty sure that the first life forms captured energy by oxidizing inorganic molecules. We're pretty sure that the first cells formed in the ocean.

We also know from the fossil record that the first organisms were single-celled organisms that resemble modern bacteria in size and shape. We know that they appear more than 3 billion years ago and there were no complex organisms for another billion years. We know that the idea of a primordial soup is nonsense and that speculations about an RNA world are not helpful.

Other than that, all we have is informed speculation. The correct answer to the question of how did life begin is "I don't know." [3]
 Present difficulties in a scientific discipline however do not mean that the problem is insoluble, as even a casual glance at the history of science would reveal. Special creationists such as Collyer appear to be uninformed of the recent work in the subject which makes dogmatism on the impossibility of abiogenesis ill-advised. For example. Lincoln and Joyce recently described the self-sustained replication of an RNA enzyme:
A long-standing research goal has been to devise a nonbiological system that undergoes replication in a self-sustained manner, brought about by enzymatic machinery that is part of the system being replicated. One way to realize this goal, inspired by the notion of primitive RNA-based life, would be for an RNA enzyme to catalyze the replication of RNA molecules, including the RNA enzyme itself. This has now been achieved in a cross-catalytic system involving two RNA enzymes that catalyze each other's synthesis from a total of four component substrates. [4]
Kamioka et al describe the creation of a structure capable of both replicating itself, and catalysing chemical reactions. This is significant for origin of life research, not only because they provide a starting point for creating complex molecules, but because these synthetic replicators have the possibility of mutation. [5]

Then there is the work of Hungarian biologist Tibor Gánti, whose 'chemotron model' provides a compelling model for the simplest system that can be called living.

The chemoton (Ganti, 1984). The metabol ic subsystem, with intermediates Ai, is an autocatalytic chemical cycle, consuming X as nutrient and producing Y as waste material; pVn is a polymer of n molecules of V', which undergoes template replication; R is a condensation byproduct of this replication, needed to turn r into T, the membranogenic molecule; the symbol Tm represents a bilayer membrane composed of m units made of T molecules. It can be shown that such a system can grow and divide spontaneously. (From John Maynard Smith and Eörs Szathmáry, The Major Transitions in Evolution (1995: OUP), p 21)

Gert Korthof, in a review of Gánti's book 'The Principles of Life' observes:
What is the simplest system that still can be called a living system? Plants and animals are composed of cells. Cells are the building blocks of life. So we need to focus on cells. But single cell organisms are still too complex. They can be simplified still further and still be called living. The entity that is stripped of all the unnecessary properties and is still alive is 'minimal life'. Gánti constructed an abstract model that captured minimal life. He called it the Chemoton model. It is composed of 3 subsystems:
1. Chemical motor system: A  soft chemical self-reproducing system capable of synthesising chemical substances for itself as well as for the other two systems [ metabolism. Example: proteins ] 
2. Chemical boundary system: a soft chemical system which is capable of spatial separation, of being selectively permeable to chemical substances, and of growth in the presence of its raw materials [ membrane. Example: lipids ] 
3. Chemical information system: a chemical system which is capable of self-reproduction in the presence of the appropriate raw materials [ information. Example: RNA/DNA ]
Note: the 3 3 components superficially look like the three parts of the prokaryotic or eukaryotic cell: cytoplasm, membrane, nucleus. However, the chemoton model is not a model of the prokaryotic or eukaryotic cell, but a very general model for life; the simplest possible life.
The chemoton model does not contain enzymes (catalysts). It is a metabolism without enzymes. Since there are no enzymes, there is no need for the genetic code. This simplifies the chemoton model significantly. "Gánti liberated himself from the burden of the genetic code" says Szathmáry.

The chemoton model fulfils the 5 absolute life criteria. The chemoton is a unit, because deleting one of its subsystems reduces it to a chemical system. The chemical motor is equivalent with metabolism. The chemical motor is inherently stable (described in the book). The fourth criterion is fulfilled by the information carrying subsystem and the program control is present in the chemoton (described in the book). [6]
Of course, this is a digression from the main point – Collyer's conflation of abiogenesis and evolution, which are two different fields, as well as his  complete misunderstood the significance of Pasteur’s experiment with respect to abiogenesis. The philosopher of biology John Wilkins concludes in an article on spontaneous generation and abiogenesis:
  1. In the initial period of biology it was assumed that life was a special substance, and that it could generate living beings directly. As research into the lifecycles of animals, plants and diseases progressed, it became obvious that modern living forms were always observed to form from existing living forms, and that cells always came from existing cells.
  2. At the same time, it became increasingly obvious that the gap between living things at the chemical level and non-living molecules was decreasing, until it became clear in the mid-20th century that all processes of living things were chemical, and there was no "vital principle" needed for life.
  3. Opposition to abiogenesis has sometimes been due to philosophical or religious principles, but also the state of scientific knowledge at the time. However, it is not feasible now, with our increasing knowledge of the chemistry of life and of prebiotic earth.
  4. None of the people who did crucial experiments on spontaneous generation disproved abiogenesis. At best, they strongly confirmed the hypothesis that modern organisms (mice, maggots, or germs) did not arise in ordinary cases out of nonliving material. Most of the experiments against spontaneous generation were posed against heterogenesis, the doctrine that life could form from the decayed products of living organisms.
  5. Pasteur did not disprove the origin of life by natural means, and the saying "all cells from cells" was not intended to cover the initial period of life on earth. Darwin did not propose a theory of the origin of life in the beginning.
  6. Evolutionary theory was not proposed to account for the origins of living beings, only the process of change once life exists. However, many have thought that the theory of evolution logically requires a beginning of life, which is true. Of those, many have thought that a natural account of the origin of life is necessary, and some have proposed models which have borne up or not as research proceeds. [7]
Collyer begins his twenty point list of "scientific facts seldom taught to students" poorly both by making the classic special creationist mistake of conflating abiogenesis and evolution, and by confusing spontaneous generation with abiogenesis. Then there is his unfamiliarity with the literature on abiogenesis, all of which confirm that Collyer is out of his depth, and hopelessly uninformed. Such a poor start does not bode well for the quality of arguments in his remaining nineteen points.

1. Cech T.R. The RNA Worlds in Context (2011) Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a006742
2. Koonin E.V "The Logic of Chance: The Nature and Origin of Biological Evolution" (2011 FT Press)
3. Moran L "How do the IDiots Explain the Origin of Life?" Sandwalk October 23 2013
4. Lincoln T.A., Joyce G.R Self-Sustained Replication of an RNA Enzyme Science (2009) 323 (5918): 1229-1232
5. Kamioka S et al “Autocatalysis and organocatalysis with synthetic structures” Proc. Natl. Acad. Sci. USA 12 January 2010: 541-544.
6. Korthof G Review: "The Principles of Life" 29th Dec 2003 (updated 19th July 2013)
7. Wilkins JS “Spontaneous Generation and the Origin of LifeThe Talk Origins Archive.