In his recent review (Genome Biology and Evolution, first published online January 24, 2012, doi:10.1093/gbe/evs008) of Professor James A. Shapiro’s new book, Evolution: a view from the 21st century (2011, FT Press: Upper Saddle River, N.J.), Adam S. Wilkins expresses his disagreement with Shapiro’s decidedly un-Darwinian view that natural selection’s importance for evolution has been hugely overstated:
My final disagreement with Jim [Shapiro]’s general argument concerns a truly fundamental point, however: the dismissal of natural selection as a shaping force in evolution. Thus, it is stated, at the very start of the book (top of p. 1): “Innovation, not selection, is the critical issue in evolutionary change. Without variation and novelty, selection has nothing to act upon.” While all evolutionists would agree whole-heartedly with the second sentence, most would reject the first. The matter of selection is then virtually ignored until the final section of the book. There we read, as one of nine bullet-points that summarize the core message: “The role of selection is to eliminate evolutionary novelties that prove to be non-functional and interfere with adaptive needs. Selection operates as a purifying but not creative force [emphasis added].”
Natural genetic engineering
Commenting on this claim, Wilkins highlights the fact that any adequate theory of evolution will have to account for the fact that cells are capable of what Shapiro calls “natural genetic engineering” – genetic change which is created by cellular systems, often in response to environmental challenges. What Shapiro is claiming, in a nutshell, is that cells are, to a large degree, capable of engineering their own evolution. In Wilkins’ words: “The cell is thus its own agent, its own engineer.” Or as Stephen Talbott puts it in a recent article for The New Atlantis (Fall 2011), entitled, Evolution and the Illusion of Randomness, “organisms are masterful participants in, and revisers of, their own genomes, taking a leading position in the most intricate, subtle, and intentional genomic ‘dance’ one could possibly imagine,” which enables the organism to respond “intelligently, and in accord with its own purposes, to whatever it encounters in its environment, including the environment of its own body.” That’s certainly a pretty impressive feat.
In his review, Wilkins acknowledges himself to be persuaded of the reality of natural genetic engineering, by virtue of the sheer weight of scientific evidence put forward by Shapiro (and by other scientists before him):
Altogether, the evidence marshalled in the book for genomic responses and remodelling in response to environmental and developmental cues is a long and impressive one. It includes such phenomena as: the gene rearrangements essential to and ubiquitous within the mammalian adaptive immune system; the restructuring of ciliate macronuclei; changes within the genomes of sporulating bacteria; the yeast mating type system; massive genome “restructuring” during plant hybridization; hybrid dysgenesis in Drosophila; a host of transposon and retrotransposon-mediated genetic changes in plants and animals; and much more… The general argument of the book, buttressed by all these examples – that genomes can be highly responsive to environmental influences, becoming “reformatted” to greater or lesser extent – is clearly important. It is not wholly new, however. It was made previously by Lynn Caporale (Caporale, 1999) and by Eva Jablonka and Marion Lamb (Jablonka and Lamb, 1995, 2005)…
How did cells originally acquire the ability to direct their own evolution?
However, what Wilkins finds puzzling is that Shapiro, having assembled a veritable mountain of scientific evidence that living things possess the remarkable ability to reformat their genomes in response to environmental changes, turns his back on what Wilkins regards as the only possible scientific explanation for their having this ability – namely, natural selection. The only alternative is Intelligent Design, which Wilkins regards as some kind of mystical mumbo-jumbo:
…[W]ith respect to this issue of selection, one might add that, in terms of Jim [Shapiro]’s particular thesis, it is hard to understand how cells could have the very capacities for “natural genetic engineering” attributed to them without those capacities having been evolved, in some manner and over long evolutionary spans, by natural selection. The evolution of such capabilities, favouring the process of “evolvability” (the capacity to give rise to new properties), is a fascinating subject, mentioned explicitly though only briefly in the book, and deserves more attention than it has traditionally received. Again, the only alternative for the origination of these capabilities, if one discards natural selection as the generative agent, is some supra-natural force, a position that I am certain is not being advocated here.
Given that cells are indeed capable of natural genetic engineering, could it be the case that cells are intelligently designed to evolve? And why might one prefer this hypothesis to the notion that cells acquired the ability to engineer their own evolution as a result of natural selection?
Natural genetic engineering is a striking and unexpected ability of living things, if Intelligent Design is not true
One reason for taking the Intelligent Design hypothesis seriously is that as I pointed out in my recent post, The Big Picture: 56 minutes that may change your life, the sheer complexity of the first self-replicating system, and the information needed to build it, imply Intelligent Design – a point that was tellingly made by Professor John C. Walton, a Fellow of the Royal Society of Chemistry, in a recent talk he gave on the origin of life. (Note: Before you play this video, press the PAUSE button and wait about two minutes, until the gray bar at the bottom has finished scrolling across to the right. Then press the PLAY button to start the video.) Professor Walton also argued that any hopes of beating the colossal odds against random formation of replicating RNA is based on ideology rather than science, and that no chemically or geologically plausible routes to nucleotides or RNA strands have ever been developed.
But if it is wildly unlikely that self-replicating systems developed from non-living matter without the need for an Intelligent Designer, it is even more unlikely that organisms with the startling ability to engineer their own evolution would have developed in this fashion.
Putting it another way: it is very easy to imagine a planet where life evolved, without subsequently evolving the ability to direct its own evolution, as life on Earth can. This invites the question: how did we get so lucky?
Intelligent Design overcomes two major objections to natural genetic engineering
Another good reason for supposing natural genetic engineering to have been intelligently designed is that if this was the case, then it would suffice to overcome two major objections to this evolutionary mechanism, which Wilkins highlights in his review:
The first concerns transmissibility of the induced genetic changes to future generations. Many of the phenomena involving multicellular organisms discussed extensively in the book involve DNA arrangements within the somatic cells and nuclei of those organisms… Being purely somatic, however, they are not transmitted to the next generation, and hence lack direct evolutionary potential. Indirect consequences of those genomic changes, affecting survival and ultimately “fitness” are, of course, a different matter…
Secondly, amongst the genomic remodelling events described here that can be transmitted across generations, none relate directly to developmental/morphological evolution, the main focus of traditional evolutionary biology. Instead, many of the phenomena listed that possess such direct evolutionary potential take place within the context of host-parasite “arms races”… Hence, there are (as yet) no cases of precisely targeted evoked genetic variation, to create specific new gene alleles, in response to environmental hazards…
However, if natural genetic engineering is the outcome of a program originally designed by an Intelligent Agent, then precisely targeted evoked genetic variation would not be so surprising after all. Indeed, it would be expected. Again, an intelligently designed program could allow organisms to pass down induced genetic changes to future generations, if they proved to be highly advantageous.
So, what might an Intelligent Design hypothesis of natural genetic engineering look like?
Living things are designed to evolve: Perry Marshall’s Intelligent Design hypothesis
Author Perry Marshall, in his blog article, Testable Hypothesis for Intelligent Design, Part 1, over at Cosmic Fingerprints.com, puts forward a testable Intelligent Design hypothesis, based on his belief that “evolution is an engineered process and is programmed to happen; and that the program itself is intelligent and operates in a top-down fashion”:
1) Evolutionary adaptation is the work of a “Mutation Algorithm.”
Cells employ a built-in algorithm, which engineers re-arrangement of Mobile Genetic Elements (as observed by McClintock and Shapiro). Genes and Chromosomes are re-arranged in a fantastically beautiful process which produces useful adaptations and new species.
I call this the Mutation Algorithm. It is a program which attempts to evolve when necessary and computes the optimal path to a desired result. This algorithm is described as exhibiting some form of intelligence.
This Mutation Algorithm, in combination with natural selection, explains what random mutation and natural selection cannot.
2) The Mutation Algorithm tests design options like blades on a Swiss army knife. DNA has a huge “bag of tricks” and is able to mix and match combinations of eyes, feet and claws, joints, digits, hair, skin and fur colors and patterns, switching out different “blades” as environments change.
It builds animals on a common chassis of head, spine, heart, lungs, stomach and limbs.
It ferociously defends this core chassis from being corrupted by random mutations, while switching out different variables in the head, spine, heart etc.
3) The Swiss army knife “blades” include variables that adjust the structure of incredibly complex systems with simple changes.
For example the length of a giraffe neck could be “dialed in” by a single gene which controls the length of nerve fibers, muscles, esophagus and number of vertebra, all at the same time.
This explains both small and large variations in species. DNA fills the ecosystem with every imaginable variety of life because it’s designed to.
It adjusts these variables until the creature is maximally adapted to its environment.
4) The Mutation Algorithm is normally at rest. It goes to work whenever the population is under extreme stress. This is why we see the pattern of “punctuated equilibrium” in the fossil record.
There are long periods of stability where there is no change, because the Mutation Algorithm is dormant. When there is a crisis, it activates and begins to test novel features.
5) The Mutation Algorithm operates within populations, not just individuals.
The Mutation Algorithm catalogs past mutation attempts so that it does not get “stuck” repeating past failures. Organisms somehow share information so that they can collectively test a wider variety of mutations than any one organism could attempt.
Efforts to find a mechanism by which organisms share this information will eventually be rewarded. And the mechanism that is discovered will be as surprising and revolutionary to biology as Einstein’s theory of relativity was to physics.
6) Evolutionary pathways are not random and purposeless, they are mathematically optimized in advance to reach desired destinations in the smallest possible number of steps.
An analogous process is the Taguchi method used in Quality Control, which creates a very small set of manufacturing experiments, which represent a very large number of possible manufacturing combinations.
It systematically tests them via a “design of experiments” process, then generates a new design which is a nearly optimal combination.
Thousands of possible design combinations are evaluated with only a few dozen tests….
I invite you to consider that DNA does something very similar with arrangements of modular biological components, literally calculating and anticipating possible evolutionary steps. It senses inputs from its environment and optimizes the experimental process….
My hypothesis is that DNA operates much the same way as a Kaizen / Six Sigma manufacturing operation. DNA not only actively participates in the mutation process, it also monitors the natural selection process.
I hypothesize that the genome got from single cells to humans in an incredibly short period of time – that 3 billion years from cells to mankind is an engineering feat of the highest order. That such a feat required the most advanced forms of optimization and as little waste as possible.
Perry Marshall’s hypothesis sounds like a very attractive one. It’s testable, and its explanatory power is very broad. Marshall also manages to provide a mechanism – an intelligently designed “Mutation Algorithm” – which overcomes a vital flaw of Darwinian evolutionary models: their inability to explain how evolution proceeded from microbe to man in the space of just a few billion years.
Intelligently designed evolution takes just the right amount of time to account for life on Earth
Mathematician Gregory Chaitin pointed out this glaring defect of neo-Darwinism, in a talk he gave at PPGC UFRGS (Portal do Programa de Pos-Graduacao em Computacao da Universidade Federal do Rio Grande do Sul.Mestrado), in Brazil, on 2 May 2011, entitled, Life as Evolving Software, which I blogged about here. During his talk, Chaitin (who is a Darwinist) acknowledged that Darwinian evolution seems to take far too long to generate the variety of life-forms we find on Earth today, judging from the software models he has developed, with the aim of putting Darwinian evolution on a mathematically rigorous footing and demonstrating its feasibility:
So what happens if we do that, which is sort of cumulative random evolution, the real thing? Well, here’s the result. You’re going to reach Busy Beaver function N in a time that is – you can estimate it to be between order of N squared and order of N cubed. Actually this is an upper bound. I don’t have a lower bound on this. This is a piece of research which I would like to see somebody do – or myself for that matter – but for now it’s just an upper bound. OK, so what does this mean? This means, I will put it this way. I was very pleased initially with this.
Exhaustive search reaches fitness BB(N) in time 2^N.
Intelligent Design reaches fitness BB(N) in time N. (That’s the fastest possible regime.)
Random evolution reaches fitness BB(N) in time between N^2 and N^3.
This means that picking the mutations at random is almost as good as picking them the best possible way. It’s doing a hell of a lot better than exhaustive search. This is BB(N) at time N and this is between N squared and N cubed. So I was delighted with this result, and I would only be more delighted if I could prove that in fact this [here Chaitin points to Darwinian evolution] will be slower than this [here he points to Intelligent Design]. I’d like to separate these three possibilities. But I don’t have that yet.
But I told a friend of mine … about this result. He doesn’t like Darwinian evolution, and he told me, “Well, you can look at this the other way if you want. This is actually much too slow to justify Darwinian evolution on planet Earth. And if you think about it, he’s right… If you make an estimate, the human genome is something on the order of a gigabyte of bits. So it’s … let’s say a billion bits – actually 6 x 10^9 bits, I think it is, roughly – … so we’re looking at programs up to about that size [here Chaitin points to N^2 on the slide] in bits, and N is about of the order of a billion, 10^9, and the time, he said … that’s a very big number, and you would need this to be linear, for this to have happened on planet Earth, because if you take something of the order of 10^9 and you square it or you cube it, well … forget it. There isn’t enough time in the history of the Earth… Even though it’s fast theoretically, it’s too slow to work. He said, “You really need something more or less linear.” And he has a point….
The time has come for scientists to publicly acknowledge that any version of evolution which is not intelligently designed – be it Darwin’s or Shapiro’s – (i) couldn’t possibly work in the time available; (ii) is incapable of generating the massive cellular and morphological changes that have occurred in the history of living things; and (iii) fails to acount for the emergence of the remarkable ability of organisms to reformat their genomes in response to environmental changes and thereby direct their own evolution.
Before I finish, I’d like to draw readers’ attention to one more prediction made by Perry Marshall’s model of intelligently designed evolution: the “Swiss Army knife” that he describes must have been there from the very beginning. If early fossil organisms were discovered that lacked the ability for natural genetic engineering, that would falsify his hypothesis.
So, what do readers think of Perry Marshall’s “Swiss Army knife” model of intelligently designed evolution? I’d like to invite readers to have their say, and subject Marshall’s model to the detailed scientific scrutiny it deserves.