….Nevertheless, there is a second, and arguably deeper, mystery associated with the Cambrian explosion: the mystery of how the neo-Darwinian mechanism of natural selection and random mutation could have given rise to all these fundamentally new forms of animal life, and done so quickly enough to account for the pattern in the fossil record. That question became acute in the second half of the twentieth century as biologists learned more about what it takes to build an animal.

In 1953 when Watson and Crick elucidated the structure of the DNA molecule, they made a startling discovery, namely, its ability to store information in the form of a four-character digital code. Strings of precisely sequenced chemicals called nucleotide bases store and transmit the assembly instructions—the information—for building the crucial protein molecules that the cell needs to survive. Just as English letters may convey a particular message depending on their arrangement, so too do certain sequences of chemical bases along the spine of a DNA molecule convey precise information. As Richard Dawkins has acknowledged, “the machine code of the genes is uncannily computer-like.” Or as Bill Gates has noted, “DNA is like a computer program, but far, far more advanced than any software ever created.”

The Cambrian period is marked by an explosion of new animals exemplifying new body plans. But building new animal body plans requires new organs, tissues, and cell types. And new cell types require many kinds of specialized or dedicated proteins (e.g., animals with gut cells require new digestive enzymes). But building each protein requires genetic information stored on the DNA molecule. Thus, building new animals with distinctive new body plans requires, at the very least, vast amounts of new genetic information. Whatever happened during the Cambrian not only represented an explosion of new biological form, but it also required an explosion of new biological information.

Is it plausible that the neo-Darwinian mechanism of natural selection acting on random mutations in DNA could produce the highly specificarrangements of bases in DNA necessary to generate the protein building blocks of new cell types and novel forms of life? 

According to neo-Darwinian theory, new genetic information arises first as random mutations occur in the DNA of existing organisms. When mutations arise that confer a survival advantage, the resulting genetic changes are passed on to the next generation. As such changes accumulate, the features of a population change over time. Nevertheless, natural selection can only “select” what random mutations first generate. Thus the neo-Darwinian mechanism faces a kind of needle-in-the-haystack problem—or what mathematicians call a “combinatorial” problem. The term “combinatorial” refers to the number of possible ways that a set of objects can be arranged or combined. Many simple bike locks, for example, have four dials with 10 digits on each dial. A bike thief encountering one of these locks faces a combinatorial problem because there are 10 × 10 × 10 × 10, or 10,000 possible combinations and only one that will open the lock. A random search is unlikely to yield the correct combination unless the thief has plenty of time.

Similarly, it is extremely difficult to assemble a new information-bearing gene or protein by the natural selection/random mutation process because of the sheer number of possible sequences. As the length of the required gene or protein grows, the number of possible base or amino-acid sequences of that length grows exponentially. 

Here’s an illustration that may help make the problem clear. Imagine that we encounter a committed bike thief who is willing to search the “sequence space” of possible bike combinations at a rate of about one new combination per two seconds. If our hypothetical bike thief had three hours and took no breaks he could generate more than half (about 5,400) of the 10,000 total combinations of a four-dial lock. In that case, the probability that he will stumble upon the right combination exceeds the probability that he will fail. More likely than not, he will open the lock by chance.

But now consider another case. If that thief with the same limited three hour time period available to him confronted a lock with ten dials and ten digits per dial (a lock with ten billion possible combinations) he would now have time only to explore a small fraction of the possible combinations—5,400 of ten billion—far fewer than half. In this case, it would be much more likely than not that he would fail to open the lock by chance.

These examples suggest that the ultimate probability of the success of a random search—and the plausibility of any hypothesis that affirms the success of such a search—depends upon both the size of the space that needs to be searched and the number of opportunities available to search it. 

In Darwin’s Doubt, I show that the number of possible DNA and amino acid sequences that need to be searched by the evolutionary process dwarfs the time available for such a search—even taking into account evolutionary deep time. Molecular biologists have long understood that the size of the “sequence space” of possible nucleotide bases and amino acids (the number of possible combinations) is extremely large. Moreover, recent experiments in molecular biology and protein science have established that functional genes and proteins are extremely rare within these huge combinatorial spaces of possible arrangements. There are vastly more ways of arranging nucleotide bases that result in non-functional sequences of DNA, and vastly more ways of arranging amino acids that result in non-functional amino-acid chains, than there are corresponding functionalgenes or proteins. One recent experimentally derived estimate places that ratio—the size of the haystack in relation to the needle—at 10⁷⁷non-functional sequences for every functional gene or protein. (There are only something like 10⁶⁵ atoms in our galaxy.)

All this suggests that the mutation and selection mechanism would only have enough time in the entire multi-billion year history of life on Earth to generate or “search” but a miniscule fraction (one ten trillion, trillion trillionth, to be exact) of the total number of possible nucleotide base or amino-acid sequences corresponding to a single functional gene or protein. The number of trials available to the evolutionary process turns out to be incredibly small in relation to the number of possible sequences that need to be searched. Thus, the neo-Darwinian mechanism, with its reliance on random mutation, is much more likely to fail than to succeed in generating even a single new gene or protein in the known history of life on earth. In other words, the neo-Darwinian mechanism is not an adequate mechanism to generate the information necessary to produce even a single new protein, let alone a whole new Cambrian animal….

[….]

Of course, many scientists dismiss intelligent design as “religion masquerading as science.” But the case for intelligent design is not based upon religious or scriptural authority. Instead it is based upon scientific evidence and the same method of scientific reasoning that Darwin himself used in the Origin of Species. 

In rejecting the theory as unscientific by definition, evolutionary biologists reveal a deep a priori commitment to methodological naturalism—the idea that scientists must limit themselves to materialistic explanations for all things. Yet, we know from experience that certain types of events and structures—in particular, information-rich structures—invariably arise from minds or personal agents. Indeed, no thinking person would insist that the inscriptions on the Rosetta stone, for example, were produced by strictly materialistic forces such as wind and erosion. Yet, by insisting that all events in the history of life must be explained by reference to strictly materialistic processes evolutionary biologists preclude consideration of a designing intelligence in the history of life, regardless of what the evidence might indicate. 

This commitment to a wholly materialistic account of the origins of life also helps to explain the reluctance to criticize the Darwinian theory publicly. Many evolutionary biologists fear that if they do so they will aid and abet the case for intelligent design—a theory they disdain as inherently unscientific. Those of us who support the theory of intelligent design advocate a more open approach to scientific investigation. Not only do we think the public has a right to know about the problems with evolutionary theory, we also think that the rules of science should allow scientists to “follow the evidence wherever it leads”—even if it leads to conclusions that raise deep and unwelcome metaphysical questions.

(AMERICAN SPECTATOR)