Even if you end up with an irreducibly complex system by removing parts from scaffolding, you still had to build the scaffolding. How does unguided evolution build the scaffolding by adding parts?
Müller introduced this concept way back in 1918, and did so in the following scientific paper: Genetic Variability, Twin Hybrids and Constant Hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918)
Here is the relevant quote :
Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect upon which it produced upon the 'reaction system' that had been brought into being by the many previously formed factors in cooperation; thus, a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent upon the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery
Behe's Critics' Scaffolding Falls Down
In their response to Michael Behe in Quarterly Review of Biology, Maarten Boudry, Stefaan Blancke, and Johan Braeckman raise a common objection to irreducible complexity, claiming that even if an irreducibly complex system cannot function if it loses parts, it might still function if it gains parts. The problem is that this "scaffolding" argument lacks biological analogues. If we trace backward along the evolutionary pathway, perhaps the system first gains parts until there is a sort of "scaffolding" supporting the final structure, and then it loses parts until the scaffolding is gone. They write:
As early as the beginning of the 20th century, geneticist Herman Muller explained how biological systems that depend on the complex "interlocking" actions of many different components could come about by evolutionary processes: "Many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former" (Muller 1918, pp. 463-464). Thus, redundant complexity can eventually generate IC (under the weak interpretation). More recently, biochemist and molecular biologist A. G. Cairns-Smith proposed the analogy of "scaffolding" in the construction of an arch to explain the evolution of systems that are IC according to Behe (Cairns-Smith 1986; see also Orr 1997; Pennock 2000). A classical stone arch is IC in the weak sense, because the structure will collapse as soon as one removes either the keystone or one of the other stones. The support of scaffolding is necessary in building a stone arch, but once the arch is completed, the scaffolding can be safely removed. In a similar vein, a biochemical structure may have functioned as a scaffold in the evolution of an IC system before becoming dispensable and disappearing. That is, "Before the multitudinous components of present biochemistry could come to lean together they had to lean on something else" (Cairns-Smith 1986, p. 61).
This argument makes a valid point insofar that gradual evolution can remove parts in addition to adding them. However, I've heard this point made before, and in each case I've asked defensors of evolution to give me a biological analogue for the "arch" or scaffolding. It sounds nice in theory, but I have never been provided with a single specific real world example where this argument might actually have some relevance to the real world of biology.
And there's another problem with the scaffolding objection. Behe defines irreducible complexity as requiring as requiring not just one part, but "several well-matched, interacting parts." Even if you end up with an irreducibly complex system by removing parts from scaffolding, you still had to build the scaffolding. How does unguided evolution build the scaffolding by adding parts?
In that regard, adding parts to build scaffolding may be more complicated than ID critics would admit. Adding a part isn't always that simple, even if it isn't indispensible. Sometimes simply getting a functional protein-protein interaction is beyond the reach of Darwinian evolution. In 2004, Behe and Snoke published a paper in Protein Science reporting results of computer simulations and theoretical calculations. They showed that the Darwinian evolution of a simple functional bond between two proteins would be highly unlikely to occur in populations of multicellular organisms. The reason, simply put, is because too many amino acids would have to be fixed by non-adaptive mutations before gaining any functional binding interaction. They found:
The fact that very large population sizes--10^9 or greater--are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10^8 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.
(Michael J. Behe & David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues,"Protein Science, Vol 13:2651-2664 (2004).)
According to this data, chance mutations are unlikely to produce even two required non-adaptive mutations in multicellular diploid species within any reasonable timescale. This answers the third question: getting multiple specific non-adaptive mutations in one individual is extremely difficult, and more than two required but non-adaptive mutations are likely beyond the reach of multi-cellular organisms. Studies like this show that the actual ability of random mutation and unguided selection to produce even modestly complex new genetic functions is insufficient.
In other words, there is too much complex and specified information in many proteins and enzymes to be generated in humans by Darwinian processes on a reasonable evolutionary timescale, even given the actual age of the earth. Simply adding a functional part in the hopes of building scaffolding might be far beyond the reach of Darwinian evolution.
The Mullerian two-step 1
With Behe's error now in hand, we immediately have the following embarrassingly facile solution to Behe's "irreducible" conundrum. Only two basic steps are needed to gradually evolve an irreducibly complex system from a functioning precursor:
Add a part.
Make it necessary.
It's that simple. After these two steps, removing the part will kill the function, yet the system was produced directly and gradually from a simpler, functional precursor. And this is exactly what Behe alleges is impossible.
As a scientific explanation, the Mullerian two-step is extremely general and powerful, since it is independent of the biological specifics of the system in question. In fact, both steps can happen simultaneously, in a single event, even a single mutation. The function of the system can remain constant during the process or it can change. The steps can be functionally beneficial (adaptive) or not (neutral). We don't even need to invoke natural selection in the process — genetic drift or neutral evolution will do4. The number of ways to add a part to a biological structure is virtually unlimited, as is the number of different ways to change a system so that a part becomes functionally essential. Plain, ordinary genetic processes can easily do both.
Example 1: The stone bridge
Feature theory and the two-step hypothesis of Müllerian mimicry evolution 2
The two-step hypothesis of Müllerian mimicry evolution states that mimicry starts with a major mutational leap between adaptive peaks, followed by gradual fine-tuning. The hypothesis was suggested to solve the problem of apostatic selection producing a valley between adaptive peaks, and appears reasonable for a one-dimensional phenotype. Extending the hypothesis to the realistic scenario of multidimensional phenotypes controlled by multiple genetic loci can be problematic, because it is unlikely that major mutational leaps occur simultaneously in several traits. Here we consider the implications of predator psychology on the evolutionary process. According to feature theory, single prey traits may be used by predators as features to classify prey into discrete categories. A mutational leap in such a trait could initiate mimicry evolution. We conducted individual-based evolutionary simulations in which virtual predators both categorize prey according to features and generalize over total appearances. We found that an initial mutational leap toward feature similarity in one dimension facilitates mimicry evolution of multidimensional traits. We suggest that feature-based predator categorization together with predator generalization over total appearances solves the problem of applying the two-step hypothesis to complex phenotypes, and provides a basis for a theory of the evolution of mimicry rings.
As can be inferred, the solution is just theoretical. There is no real-life evidence that evolution could act in the proposed fashion of " major mutational leap ".
"Complexity by Subtraction": In Evolutionary Biology, a Devilishly Subversive Suggestion 4
In another paper 3, we read that : it is not known which aspects of predator psychology cause the initial mutant to be perceived by predators as being similar to the model, leaving open the question of how the crucial first step of mimicry evolution occurs.
In "Complexity by Subtraction," they argue that rather than being built up as normally imagined by Darwinists, from simple to complex, evolution may happen the opposite way. Starting out with something highly complex, there follows a loss of complexity, and you end up with an evolutionary product that is simpler and more streamlined. Where did you get the highly complex beginning? That must remain the usual free gift. From the Abstract:
The standard [Darwinian] thinking could be right, even in general. But alternatives have not been much discussed or investigated, and the possibility remains open that other routes may not only exist but may be the norm. Our purpose here is to introduce a new route to functional complexity, a route in which complexity starts high, rising perhaps on account of the spontaneous tendency for parts to differentiate. Then, driven by selection for effective and efficient function, complexity decreases over time. Eventually, the result is a system that is highly functional and retains considerable residual complexity, enough to impress us.
The problem is always explaining how biological information or function is built up in the first place.
Instead of emerging by gradually and incrementally adding new genes, cells, tissues or organs over time, what if some so-called "irreducibly complex" structures came to be by gradually losing parts, becoming simpler and more streamlined? Think of naturally occurring rock arches, which start as cliffs or piles of stone and form when bits of stone are weathered away. They call the principle "complexity by subtraction."
This is all very revealing. In the geological context, we know very well how, as a starting point, "cliffs or piles of stone" form. It's readily comprehensible how, worn by water or weather, an arch may appear. In the biological context, we do not know how the starting point -- functioning "genes, cells, tissues or organs" -- got there.
An Absurd Charge
In my previous critique, I explained that Boudry, Blancke and Braekman would effectively place neo-Darwinism in an unfalsifiable position. To further give a sense of the mindset of Behe's critics, consider the following:
Boudry, Blancke and Braekman charge that Behe makes an "absurd demand" simply for stating: "Not only would I need a step-by-step, mutation by mutation analysis, I would also want to see relevant information such as what is the population size of the organism in which these mutations are occurring, what is the selective value for the mutation, are there any detrimental effects of the mutation, and many other such questions."
Apparently for these critics, Behe is "absurd" for actually expecting neo-Darwinian evolution to present a convincing case. Thankfully, some scientists are interested in actually testing these questions, even when they are difficult. As discussed above, Michael Behe and David Snoke have performed tests that address the plausibility of Darwinian processes producing new protein-protein interactions under reasonable timescales and population sizes. Doug Axe's recent paper in BIO-Complexity also addresses such questions. Both papers are showing that to simply produce modestly complex features that require multiple mutations to yield any function, one quickly exhausts the probabilistic resources available in the history of the earth.
In contrast, it seems that Boudry, Blancke and Braekman would just give up and say (my paraphrase): "if neo-Darwinian evolution is too hard to test, we should just assume it's true." Only a die-hard ID-critic would find it "absurd" to actually test neo-Darwinian explanations on a mathematical level.