Saturday, 18 January 2014

Why David Pearce's "Evidence for Design" fails to disprove evolution - 2

Pearce’s argument reveals its naiveté in its opening paragraph:

 Science teaching about the natural world invariably assumes acceptance of the theory that organisms changed by an evolutionary process from simple to complex by means of improvements taking place over long periods of time. The idea is so widely accepted that it is rarely challenged. It seems obvious enough in the biology textbook, a progression from microbe to fish, from sea creature to mammal, from fern to flowering plant. Yet looking at the diagram of the evolutionary tree, it is also clear that there are big gaps in the story. (Emphasis mine)[1]
Two things are immediately apparent. The first is his conflation of evolution as fact (reference to evolutionary tree) and evolution as theory (reference to cumulative change over time). Even if the modern synthetic theory was falsified tomorrow, the facts that it explains not only would not go away, but would need to be explained by the successor theory to the MES. Pearce’s failure to properly define evolution in his opening pages undermines the credibility of his attack – he is merely attacking a creationist parody of evolution.

The second problem is his belief in the thoroughly outdated idea of progression in evolution, where evolution is seen as a ladder leading from microbe to man at the top. Evolution is not a ladder, but a tree:

 Thinking of evolution as a progression from simple to complex, or ladder-like, furthers the idea that evolution is lineal and that it should be possible to reconstruct a direct line of ancestors. However, the evolution of life, instead of resembling a ladder, is more similar to a branching bush. Darwin’s…contribution to phylogenetic analysis indeed was to introduce the concept of a branching tree of life, with organisms related through common ancestry (Fig. 1). Each branch on the tree represents a distinct lineage; multiple branches can extend from a common point, joined by a set of characters present in the common ancestor; lineages can also acquire characters that are not shared in a common ancestor. Finally, as a result of extinction, not all lineages persist into the future, as can clearly be seen in Fig. 1. Tree-thinking shifts the focus from looking for fossils of lineal (direct) ancestors to looking for synapomorphies that link collateral (side-branch) ancestors. Your grandmother is a lineal ancestor, your great-aunt a collateral ancestor (Fig. 2), but their lives and times were probably not that different…which means that information about one provides information about the other. Paleontologists do not expect to find the direct lineal ancestor of an extant species…nor do they expect to recognize a direct ancestor as “the ancestor” even if they did find it. However, by understanding the lives and times of the species in its family tree, they can understand what its ancestor would have been like.[2]
Fig. 1
The diagram of divergence of taxa presented by Charles Darwin in On the origin of species (1859)
Fig. 2
Sample family tree for an individual (you) showing your collateral (indicated by dashed lines) and direct or lineal (indicated by solid lines) ancestors

Pearce’s opening paragraph completely fails to define his subject properly, and perpetuates the creationist myth of evolution as a progression upwards from ‘simple’ to ‘complex’. In a few lines, he has telegraphed his scientific ignorance, and destroyed whatever chances he had of being taken seriously.

Abiogenesis is not Evolution


This is sadly not an aberration. In his second paragraph, he employs yet another tired creationist trope, the conflation of evolution with abiogenesis and other separate disciplines:

What about the microbes right at the bottom of the diagram—where did they come from? Cytology, the study of cells, shows that the tiniest microscopic unit of life, once magnified, becomes instantly a whole globe full of intricate specialised parts.[3]

The origin of life is a related but separate discipline known as abiogenesis, and the lack of a universally accepted theory of abiogenesis does not mean that the evidence for common descent somehow is invalidated. Evolution does not explain the origin of life, but the origin of species. Pearce takes his argument to ludicrous extremes by alleging that unsolved problems in atomic physics somehow pose a problem for evolution:
How did the microbe evolve? Was it simply by chance combinations of atoms of nitrogen, hydrogen and carbon in the presence of electricity and heat? How did this produce such complexity? And where did the atoms come from? Even an atom, as an elementary physics course makes plain, is itself an ordered world of enormous power, with many component parts—mesons, protons, quarks and electrons, spinning round in tight orbits held in place by charges so strong that, burst apart, the energy released from a few kilograms could flatten a city and destroy a million people. How did all this energy become locked so neatly into the atom?[4]
I would hardly imagine Pearce would dismiss the fields of inorganic chemistry or metallurgy because he does not know from where the atoms came. Electronics engineers manage to use Maxwell’s equations to design and simulate complex radio frequency devices, despite the fact we don’t know how the electroweak force can be unified with the strong nuclear force. Yet, he thinks our present state of ignorance (or his – one needs to be blunt here) somehow means that common descent suddenly collapses into dust. One hardly needs to take the time to refute Pearce when he does an excellent job of destroying his credibility in his opening paragraphs.

His parody of abiogenesis, “Was it simply by chance combinations of atoms of nitrogen, hydrogen and carbon in the presence of electricity and heat?” is a particularly egregious example of creationist stupidity. No researcher in abiogenesis thinks that a complex single celled organism magically arose in one step from a chance arrangement of atoms. Pearce’s argument yet again betrays his lack of understanding of abiogenesis.

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[5] 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.[6]

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 Pearce 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.[7]

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. [8]

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 metabolic 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 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). [9]

The point of citing Gánti’s chemotron model is not to argue that this is what the earliest living cell would have looked like, but to point out that origin of life researchers do not think that the first form of life was not a complex cell, and did not form magically. Gánti’s chemotron model shows the level of simplicity that origin of life researchers postulate, and these are considerably more simple than obligate intracellular bacteria such as the Rickettsia.

Conspicuously absent are references to experiments designed to shed light on abiogenesis such as Nobel Laureate Jack Szostak, who is one of the leading origin of life experts. Recently, Szostak announced the creation of a plausible prebiotic protocell in which nonenzymatic RNA copying could take place:

Efforts to recreate a prebiotically plausible protocell, in which RNA replication occurs within a fatty acid vesicle, have been stalled by the destabilizing effect of Mg2+ on fatty acid membranes. Here we report that the presence of citrate protects fatty acid membranes from the disruptive effects of high Mg2+ ion concentrations while allowing RNA copying to proceed, while also protecting single-stranded RNA from Mg2+-catalyzed degradation. This combination of properties has allowed us to demonstrate the chemical copying of RNA templates inside fatty acid vesicles, which in turn allows for an increase in copying efficiency by bathing the vesicles in a continuously refreshed solution of activated nucleotides.[10]

In just five paragraphs, Peace has:

  • Failed to properly define evolution
  • Failed to differentiate between evolution as fact and evolution as theory
  • Failed to recognise that the idea of progression alone a ladder is a parody of evolution which is best modelled as a tree
  • Conflated evolution and abiogenesis, and implied that unsolved problems in completely unrelated fields such as nuclear physics somehow pose a probem for evolution.

 Blunders of this magnitude so early in a book destroy the credibility of his argument. There is no way to avoid this fact.

[1] Pearce D “Evidence for Design” p 3

[2] Mead LS “Transforming our Thinking about Transitional Forms” Evo Edu Outreach (2009) 2:310-314

[3] Pearce, op cit p 3

[4] ibid, p 8

[5] Cech T.R. The RNA Worlds in Context (2011) Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a006742

[6] Koonin E.V "The Logic of Chance: The Nature and Origin of Biological Evolution" (2011 FT Press)

[7] Lincoln T.A., Joyce G.R Self-Sustained Replication of an RNA Enzyme Science (2009) 323 (5918): 1229-1232

[8] Kamioka S et al “Autocatalysis and organocatalysis with synthetic structures” Proc. Natl. Acad. Sci. USA 12 January 2010: 541-544.

[9] Korthof G Review: "The Principles of Life" 29th Dec 2003 (updated 19th July 2013)

[10] Adamala K, Szostak JW  Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells Science (2013) 342:1098-1100