My post last week elicited a number of sharply critical comments from conventional evolutionary thinkers, most notably from my University of Chicago colleague Jerry Coyne on his Why Evolution Is True website. Let me respond and add four additional points.
1. The comments from Jerry Coyne and other orthodox critics on his website showed that they misunderstood my point completely. Apparently, all they could see was an assault on natural selection as a valid concept. Consequently, they confused the fixation of novel hereditary features, where selection plays an important role, with the origination of novel features, where selection does not (indeed, by definition, cannot) play a role. This distinction was pointed out most clearly on the blog by Victoria Alexander. My argument remains that the innovative process in evolution is rapid natural genetic engineering rather than gradual selection of small changes over long periods of time. This argument does not deny a role for selection. I simply assert that it is unrealistic to ascribe a creative (virtually deus ex machina) role to natural selection.
2. In his 2006 book on computational evolution, Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution, Richard Watson points out limitations of Darwinian-style hill climbing by successive accretion of small changes. This "accretionist" process is not well-suited to solving complex problems in silico. A superior computer evolution method is what Watson calls a "symbiogenetic" approach. In symbiotic evolution in silico, different parts of the problem are solved separately, and solutions are then combined symbiotically to generate novel combinations that could not evolve by accretion. This process has intriguing parallels with protein evolution by exon shuffling. Watson's work is also available online in his 2002 thesis.
3. I neglected to make it clear that Alfred Russell Wallace often viewed natural selection as a purifying and stabilizing force, not a creative one. In his seminal 1858 paper, "On the Tendency of Varieties to Depart Indefinitely from the Original Type," he wrote:
The action of this principle is exactly like that of the centrifugal governor of the steam engine, which checks and corrects any irregularities almost before they become evident; and in like manner no unbalanced deficiency in the animal kingdom can ever reach any conspicuous magnitude, because it would make itself felt at the very first step, by rendering existence difficult and extinction almost sure soon to follow.
The idea of selection as a feedback governor inspired Gregory Bateson to call Wallace the first cybernetician.
4. Other contemporary geneticists and evolutionists have taken a similar view to mine about the molecular origins of evolutionary novelties. An extensive and periodically updated bibliography on this subject can be found here . Some pertinent references include:
"Engineering is the discipline, art, skill, profession and technology of acquiring and applying scientific, mathematical, economic, social, and practical knowledge, in order to design and build structures, machines, devices, systems, materials and processes."
In other words... his "intelligent engineers" would have to have "scientific, mathematical, economic, social and practical knowledge" that would allow it to solve an evolutionary problem that puts selection pressure on the individuals of a population.
What are the chances that there is a molecular agent at the cell level which INTELLECTUALLY UNDERSTANDS classical mechanics, thermodynamics, its own molecular biology, the molecular biology of pathogens, astronomy and geophysics (especially the chain of events after asteroid impacts and large scale volcanism) and that can react by constructing a different version of itself that is better adapted to these processes?
Or maybe he doesn't mean such an intelligent engineer AT THE CELL LEVEL, after all? Maybe he means an "intelligent engineer" permeating the universe? Or maybe even one that created the universe?
Who knows... I am having trouble figuring out what he really means by that.
An easy example of independent action : a normal person will have trouble to jump off a roof.His muscles freeze and he cannot do it. If he is in distress, or drugged he can.
The human body cells seem to have access to what our brain receives as "information from the
outside" and may take action,even before the brain has considered action. For instance : in case of imminent danger.
In the male/female context : the instant movements of the face,the heart,the feeling,the genitals are not decided by the brain.The body cells have seen/heard/smelled it instantly and decided :this is it.
When it comes to evolution ,the cells do the work ,they know the details.They are large communities with excellent resources.
Our medical people would be wise to study them a lot more and stop posioning them as often happens through lack of understanding.
:-)
Is my understanding correct, or are you really arguing that natural selection cannot introduce novel features? Because, not-an-expert as I may be, I feel like there's evidence to the contrary, even within Watson's 2002 thesis that you provided.
By definition, natural selection does not introduce variation or novel features. It acts after the fact to screen variants and novelties for adaptation to existing conditions. Natural selection can only serve as a creative force on the basis of gradual accumulation of multiple small changes, as Darwin says in the quote from my previous posting. If change is rapid or massive, the novelty results from the processes generating variation. In the case of DNA changes, the underlying engines are natural genetic engineering systems. The genome sequence record documents many examples of rapid, often genome-wide modification at key points of evolutionary change. So I raise the question as to whether we have not made a mistake in ascribing a creative role to natural selection, when its function is really to eliminate novelties that do not contribute to or detract from adaptation. Moreover, I do think natural selection has often been invoked in a Deus ex Machina fashion to account for major transitions by gradualist models. If you think I am wrong in raising this question, please provide the counterexamples demonstrating a creative role for natural selection.
Which, of course, rests on the assumption that the mapping between genome and phenome is a continuous function. Of course, Dr. Shapiro, you know that's not the case, so why bother using such an argument? Small changes in the genome not only can, but often do end up in large changes for the individual, thus even random mutation and selection are rapidly probing the evolutionary "phase space" of a species. Any such rapid change can be adopted in just one generation, and given enough selection pressure, spread very quickly over whole sub-populations.
"In the case of DNA changes, the underlying engines are natural genetic engineering systems."
Your use of "engineering" is very loose here. An engineer works from a set of requirement documents and uses physics, chemistry, mathematics, information theory etc. to THEORETICALLY develop a model of a workable solution, then uses simulation to test a virtual prototype and then uses test environments to test a real prototype. None of what you are describing here works in any way, shape or form like engineering. So why use the term "engineering", then?
Because there is nothing in the available record to indicate otherwise? Unless you are willing to violate Occam's razor to push an unnecessary explanation, of course...
"Moreover, I do think natural selection has often been invoked in a Deus ex Machina fashion"
It seems to me that you are the only person here who is pushing such a solution... natural selection is a minimalist explanation, requiring nothing but observed facts, whereas the "intelligent engineer in the cell" is a questionable concept that violates both the definitions of "intelligent", "engineering" as well as the observed functions of these cell mechanism.
Now, I really, really doubt that the people who do actually think about "intelligence" (as in human or even higher intelligence), see much of that in these kinds of very limited information processing systems...
So it's a matter of perception... Dr. Shapiro sees an automaton and, because it can do a trick or two (that's all they do), he calls it "intelligent". I see an automaton (stochastic or deterministic) and I see some of the most trivial information processing structure imaginable and I really don't get too excited about it, as I am used to dealing with these things in my job all the time and they really don't do much for me in terms of "intelligent engineering".
If I want to get some really amazing stuff out of an algorithm, I turn to genetic algorithms, which, despite being much harder to describe mathematically, have a lot more "creativity". And I like creativity, it beat's the finite "intelligence" of an automaton any time.
I'm not a biologist so my apologies if I'm asking something that would be obvious to one. What do you mean by the phrase "natural genetic engineering"? Are you implying that there is an intelligent agent driving these changes?
I am saying that genome change is an active, regulated, non-random cell process rather than a series of stochastic accidents. Change is initiated in response to challenge, can be targeted within the genome, and occurs in ways that we know have produced novel combinations of molecular functions in evolutionary history. The details are laid out in my book. I call the various processes that cells use to change their genomes "natural genetic engineering."
Molecular biology has also illuminated cell sensory, communication, information-processing and decision-making capabilities. The book explain how cells monitor their environments, their genomes and their internal processes so that appropriate action can be taken when necessary to maintain survival, reproduction and even change when it is important. Altogether, I have applied the word "cognition" to these cell capacities.
The question I raise now is -- how far does cell cognition extend into the regulated process of natural genetic engineering? Does it enhance the probabilities of making functional innovations? Does it help produce changes that have a better possibility of meeting ecological challenges? These are questions subject to empirical testing, and I lay out a couple of tests in my book.
If you read the book or look at the material posted online at http://shapiro.bsd.uchicago.edu/evolution21.shtml, you will get a clearer and more detailed sense of my argument. Then we can engage in further discourse over whether or not the cell constitutes an intelligent agent.
So nuclear or chemical mutation, as used as research tool and to generate new cultivars is not a random process on the genetic level? What are the active, regulated, non-random cell process leading to the resulting, rather random looking, changes in the genome?
"Change is initiated in response to challenge, can be targeted within the genome, and occurs in ways that we know have produced novel combinations of molecular functions in evolutionary history."
How would the genomes of the surviving species have foreseen the necessary genetic changes to cope with extinction level events and climate change that let some thrive and many others die off?
"I call the various processes that cells use to change their genomes "natural genetic engineering.""
So it's just about the name, then? And how would this notion differ from Lysenkoism? Would that be a truly novel concept, then, or just a new name for a rather old one?
NEO-DARWINISM: “all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; . . . the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms”
By “similar naturalistic mechanisms” most neo-Darwinists mean “devoid of design or rational purpose“. Any statement about purpose or design in nature is a philosophical assumption, and materialism is the philosophical positions being debated. I’m a non-materialist, myself, but I am turned off by the emotional arguments presented by materialists. For instance, Jerry Coyne’s criticism of Shapiro’s work. Coyne admits he hasn’t read Shapiro’s book, but still feels qualified to criticize it.. Coyne states:
“Shapiro’s piece then rapidly goes downhill as he starts repeating creationist arguments.”
Anyone sceptical of “random mutation and natural selection” as an explanation of biological diversity is usually accused by Neo-Darwinusts of being a “creationist”. (I was once called “an ignorant creationist pig”.)
I am a political liberal, religious agnostic. I do not believe in a personal god. I do believe volition, consciousness and purpose are innate aspects of living systems.
Berthajane Vandegrift
A Few Autistic Questions about Freud, Marx and Darwin
:-)
But the truth of your statement depends upon how you define animal. If you include every animal down to microorganisms you'll find that most animal species have no mouth or eyes. But that's a semantic difference in defining "animal".
Think Professor Shapiro is enjoying a semantic argument with his colleagues. What is a unique trait? For example the start of the evolution of eyes is presumed to be a single light sensitive cell on the surface of an organism. That's a unique feature that becomes more common through evolution. Next there's an organism with two light sensitive cells on its surface. Thats a unique trait which becomes more common through evolution. And so on until you have a complete eye. Every step on the way was a unique trait and none of the traits changed, they just became more or less common.
If you call eyes a feature, then natural selection surely plays a role in their origination through evolution, even though every step along the way requires genetic change. A debate over the relative importance of two things that are essential to a process doesn't seem to lead much of anywhere.
It would seem likely that much of evolution does occur in small steps, but occasionally a mutation sets of a chain of rapid (geologically speaking) evolution. A change in a controller gene, or possible a modifier gene might have such an effect.
If you look at http://shapiro.bsd.uchicago.edu/TableII.7.shtml, you'll see that genome change does not occur constantly but is subject to triggers by various kinds of stimuli, generally stresses that threaten reproduction.
Am I missing something here?
Pretty sure the standard model of Darwinian evolution has new traits arising by mutation and recombination, not selection. But I might have been reading that wrong for the last 40 years.
What has changed in the last 40 years is that we now know genome change is not the result of random accidents. Change results from the regulated action of natural genetic engineering systems. Cells cut, splice and otherwise restructure their genomes in a responsive manner. The evidence is in my book, "Evolution: A View from the 21st Century" (http://www.amazon.com/Evolution-View-Century-Press-Science/dp/0132780933/ref=cm_cr_pr_product_top) and in the material posted in the links at http://shapiro.bsd.uchicago.edu/evolution21.shtml .