If you are referencing a specific study, it is important to put the actual study. A few imprecise sentences are never enough to be able make sense of anything in biology. Here is the study:
The ability to adapt to changes in the function of gene regulators, as opposed to structural genes, is a crucial aspect of evolutionary change. Taylor et al. mutated a central regulator for the formation of flagella in the bacterium Pseudomonas fluorescens . They then put the mutated flagella-free bacteria under strong selection pressure to regain mobility. The mutated bacteria regained the lost flagella, and motility, within 4 days. Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis. The mutations increased the levels of the co-opted regulator, then altered its specificity for the flagella pathway.
http://science.sciencemag.org/content/347/6225/1014
To be clear, the genes for flagella were not delete. A key regulator (a protein that controls production of the flagellum RNA from DNA) was deleted, and this protein is not part of the flagellum itself. It also was very easy to recover this. Given that most human-chimp differences are changes in regulation, this is an example of the sort of evidence that makes the molecular basis of human evolution seem very easy.
It is also an example of something called “exaptation” where parts of a cell are easily repurposed for a new use. This means that evolution often does not have to start from scratch, but can just compose things together. A very interesting study.
It has nothing to do with whether or not mutations are random or not.
Yes, it is true that he is playing word games. Conceptually he is talking about the same thing, but he does so with an abuse of terminology. Stochastic = random. Directed randomness just says there is an order to the randomness that is beneficial, which is obviously true.
This is where he becomes incoherent and is abusing terminology. This is demonstrably false. His imprecision in language is creating immense confusion. As I said several times, there is both order and randomness in mutations. It is true that some of that order places mutations more frequently in some locations, and can be biased towards benefit. This order, however, does not meant they are not random.
Both can be true at the same time, so it does not follow that “variation is not random with respect to location or function.” Such a statement is false.
Both can be true. Mutations are both ordered with respect to location and function, and also random with respect to them. We can even quantify how much. That is exactly what we do. Both are true at the same time. In fact, we can even study how the order of mutations evolves to be more beneficial over time (the evolution of evolvability). The fact there is order does not mean there is no randomness. There are patterns in the randomness that correlate with function and location, but there still remains a great deal of randomness.
Moreover, this is not my idiosyncratic definitions. This is, actually, part of information theory. We can actually quantify how much randomness (entropy!) there is in a distribution. In no distribution to which Nobel has referred that there is no randomness. Period. Therefore he is false if he “denies randomness with respect to location.”
That being said, you are only reporting his views. It is also possible you are misquoting him. Though, given what I’ve seen from Shapiro, @Perry_Marshall, a EES, it is more likely he is abusing the terminology for rhetorical effect, to the point of miscommunication science and creating an avoidable conflict.
I disagree, and have explained why. However…
I have no problem with this. There is still randomness, but the shape of the distribution is such that it improves likelihood of meeting a functional goal. There is still randomness, but there is a pattern in the randomness. If Nobel says there is no randomness, Nobel is unequivocally false.