Since Steve has mentioned A. Wagner’s book (which I read, along with his papers), it might be of interest to discuss his theory a bit. What Wagner found (both in theoretical and empirical studies) was that innovation from mutations can happen in most biological systems, including protein function and gene regulatory networks, based on the fact that these systems are fundamentally robust. This means that one or even several mutations are not likely to have any effect on the function of the system. This allows for large number of variants all with the same functional characteristics. But at some point, one additional mutation becomes the straw that breaks the protein back, and either the system fails completely (the most common outcome) or it takes on a whole new function as a result of all the accumulated changes. It’s a good deal more complicated than that, but I find it to be quite satisfying as an explanation for how mutations can produce innovative changes in phenotype (which are then selected for).
In my long-forgotten role as Cassandra yelling about how actual conversations about design ought to go (for Christians), I often referred to Wagner’s work. I have met very few believers who actually understand or care about design (almost universally, Christian talk about “design” is about frantic efforts to find supernatural tasks for gods), but those who do have this interest should focus on the kinds of ideas that Wagner advances.
Oh and, hi Sy! 
bonus forum points for such an apropos literary allusion. 
Wagner states: “adaptations are not just driven by chance, but by a set of laws that allow nature to discover new molecules and mechanisms in a fraction of the time that random variation would take.”
Stephen is the set of laws self-organizing biological networks that guide the creation of innovation - via proteins having differing multiple functions. a duplicated genetic code is duplicated, and a single mutation offers the promise of a new protein with a new function or at least a new protein with the same function?
Does Wagner see the success of evolution as the self-organization of multiple functioning proteins without any external causal influence?
I’m sorry, I couldn’t understand what you were asking.
I don’t recall that he ever committed himself to the existence/non-existence of “external causal influence”. I don’t think it matters for his argument. He also doesn’t limit his ideas to proteins.
@Paul_Allen1 – As fairly recent ‘convert’ to accepting evolutionary science after having been an OEC for something like 36 years prior, you might look at a couple of things that I have come to accept, developed (not exhaustively nor exhaustingly 
) here.
One thing I don’t think that I mentioned there was that the neutral theory of evolution can and does explain how increased complexity can be produced naturally.
Another account – the OP, I mean:
Highly abbreviated:
I would like to hear what Wagner thinks these laws are and how they operate in biology.
If you start with the same genome then there are only a limited number of things it can do. In order to get innovations you need different sequence. For example, there is no way that a fish genome can produce a human. Changes in DNA sequence can produce new functions, change functions, or increase function. This isn’t limited to just proteins since non-coding DNA and functional RNA play a role. A mutation in a gene promoter region can change gene expression profiles which can change phenotype (e.g. lactose tolerance in Europeans).
The laws that govern biological networks are the same laws that drive all of chemistry, so there is nothing “special” about them. What a protein binds to or catalyzes is determined by its chemical properties, and the same applies to DNA and RNA. How an ice crystal organize themselves into interlinked hexagons isn’t that different from how biological networks organize themselves.
Okay there is much confusion here. The primary problem is the failure to understand that the genius of Darwin’s Theory is that it recognizes Evolution is a two phased process. The first phase is Variation where a new allele is produced by genetic changes, often by sexual mixing of genes.
But Variation does not have the final say. Natural Selection does. Variation produces a variant of the existing species, but Natural Selection determines if that variation is viable or not. If that variation is viable , then it might replace the old species, or might break off into a new species. Also Natural Selection might determine that a species is no longer viable and it may go extinct because it is selected out.
Variation produces possible new life forms. Natural Selection determines which life forms are going to survival and flourish. Why is this important? It is important because the earth is constantly changing. The climate is changing. The terrain is changing. The environment is changing.
Suring the time of the dinosaurs the climate changed and the habitat that sustained the dinosaurs disappeared and so did they. Today habitat is disappearing and so are many species. All sorts of changes in the environment force species to change or die out. It is changes in the environment that causes species to adapt and change, as hominids have adapted and changed over many years. .
Regarding evolution spikes - Wagner’s thesis is - a few new proteins offer multiple functions when required - what he calls ‘self-organizing’ biological networks.
Wagner argument is the speed of change. He states new proteins with new functions respond to external changes but falls back onto self-organizing networks. Which I believe is false.
No, that’s really only part of it. His thesis is, as @sygarte discussed above, that biological networks – proteins, RNA, metabolic systems – are robust and can carry very significant amounts of variation while maintaining function. This means that a family of proteins (for example) can support an overall function while existing across a range of forms. The implication for evolution is that new functions and forms are more “nearby” than we tend to think. His recent review article on evolvability is a great summary of these ideas, and his most recent research publication, a few months ago, is about how variation facilitates adaptation.
You misunderstood him. That sentence isn’t very coherent, but it’s wrong. And Wagner’s ideas are supported by lots of hard data. He’s not just theorizing.
Very good article. Thank you
You’re welcome. Glad to discuss the science anytime.
The question that I raised is a very important one. Is Natural Selection based on ecology? Yes or No/
What he says is that variation facilitates adaptation to the environment. Does this mean that organisms are able to anticipate environmental changes so they can anticipate changes in advance? An alternative point of view is the ideas that there are some biological processes that are more flexible and efficient that others, so they are more adaptable to the environment.
Organisms are in constant dialog with the environment in terms of evolutionary change. This means that evolution is not based on random chance, but adaption to the ecology.
No, natural selection is not based on ecology. It is based on fitness, which is based on factors that include the environment (“ecology”) but also include several other key factors. There are many basic types of reading that could lead one to understand why “natural selection is based on ecology” is false. One topic to consider would be frequency-based selection, which is likely based entirely on perception of the phenotype by other organisms.
No, it doesn’t mean that. It means that populations can harbor variation that allows them to adapt to changes using existing resources, instead of “waiting” for adaptive responses to occur genetically.
That is a reasonable approximation of Wagner’s ideas but again, he would not limit this to “the environment.” The milieu in which fitness plays out is much more complex than just the local climate.
Those sentence include a false premise (“based on random chance”) and a false conclusion (“adaptation to the ecology”). The constant repetition of these errors only makes them more cringeworthy.
Evolution will never be about just ecology.
@sfmatheson, and @Paul_Allen1
Ecology is best defined as the study of: The relationships between all living organisms and their environments. The relationships between parasites and their hosts. Aquatic organisms. Interactions between predator and prey populations.
“The perception of the phenotype by other organisms” includes the relationships between all living organisms and their environments; therefore frequency based selection is based on ecology.
Thank you for confirming my understanding of Wagner’s ideas. You are mistaken is thinking that the environment and ecology is limited to local climate. See above.
Evolution is not just about ecology. Natural selection is about ecology. Evolution is about variation and natural selection.
Can a protein anticipate or respond?
Adaption bodes well for climate change?
The danger of climate change is that human pollution is causing it to happen faster and in different ways than it might not happen otherwise. Adaption is change and change is normally disruptive.
We need to show down change and reduce pollution which poisons us and the environment. Too many people do not want to reduce pollution because it is easier and cheaper in the short run not to clean up our messes.
Adaption will happen one way or another, but it might result in extinction.
Living creature3s are not mechanical beings. They interact with their environment i8n a positive manner, not a negative one.