In September I wrote an article about a recent experiment at Harvard Medical School in which they created a very large agar plate in order to visualize bacterial colonies evolve drug resistance over time. I was primarily responding to Michael Behe’s argument that this experiment did not show evolution but “devolution.”

Recently Cornelius Hunter over at Evolution News and Reviews (a propaganda blog of the Discotute) wrote a response to my article. Hunter’s response is yet another example of how creationists engage in motivated reasoning and fail to either understand evolution or meaningfully engage with the scientific community. In fact, I found Hunter’s article to be largely incoherent, which is common because creationists are not trying to formulate a coherent scientific theory. They are just trying to provide cover for their ideological beliefs by creating doubt and confusion.

The first actual point I think I can extract from Hunter’s article is that the changes to the bacteria seen in the Harvard experiment were not actually evolution, just adaptation. He writes:

What Novella does not acknowledge, however, is that bacteria adaptation research, over several decades now, has clearly shown non-evolutionary change. For instance, bacterial adaptation has often been found to be rapid, and sensitive to the environmental challenge. In other words, when we look at the details, we do not find the evolutionary model of random variation slowly bringing about change, but rather environmentally directed or influenced variation. That is not evolution. And indeed, the Harvard experiment demonstrated, again, very rapid adaptation. In just ten days the bacteria adapted to high doses of lethal antibiotic. As one of the researchers commented, “This is a stunning demonstration of how quickly microbes evolve.” True, it is “stunning,” but “evolve” is not the correct term. The microbes adapted.

This is one common intellectual trick used by creationists – shift around your definitions as needed in order to manufacture apparent contradictions or at least confusion. Hunter is not working from a coherent operational definition of evolution. He gives no indication that he understands evolutionary theory, but that is hard to know through the fog of motivated reasoning.

Adaptation is evolution. That is, in fact, all evolution is. There are several sources of variation, including several types of mutations (point mutations, gene duplication, deletions, etc.), recombination, and genetic drift. Natural selection acts on that variation so that whatever heritable characteristics happen to provide a survival advantage tend to predominate. This allows for cumulative changes over time that, given a few billion years, can do amazing things.

Populations, however, are always just adapting to their local environment. Hunter is trying to draw a distinction between evolution and adaptation, but there isn’t one. He is hanging his hat on the fact that the bacteria adapted rapidly, and evolution is not supposed to be rapid, but that is nonsense. Given the rapid life cycle and billions of individual bacteria, there is no contradiction with the fact that the bacterial colonies rapidly stumbled upon adaptive mutations.

Hunter falsely assumes that the rapidity with which the bacteria evolved resistance means that the environment was directing the changes seen. This is an unwarranted assumption, and there is no evidence for this. He also falsely states that evolution requires random mutations. This is not true, evolution just requires heritable change under natural selection. If there were a mechanism by which organisms could direct mutations to environmental conditions, that would still be evolution. There is just no evidence that this is actually happening. There is evidence to suggest that the rate of mutations may respond in some circumstances to environmental factors, but not the mutational changes themselves.

Hunter’s mangling of biology continues:

The ability of organisms to adapt rapidly falls under the category of epigenetics, a term that encompasses a range of sophisticated mechanisms which promote adaptation which is sensitive to the environment. Given our knowledge of bacterial epigenetics, and how fast the bacteria responded in the Harvard experiment, it certainly is reasonable to think that epigenetics, of some sort, may have been at work. Such epigenetic change is not a new facet of evolution, it contradicts evolution. Not only would such complex adaptation mechanisms be difficult to evolve via random mutations, they wouldn’t provide fitness improvement, and so would not be selected for, even if they did somehow arise from mutations.

It is simply wrong that the rapidity with which the bacteria evolved resistance implies an epigenetic mechanism. In fact, research so far has shown that antibiotic resistance in bacteria are often due to mutations in the genome, mutations that can, in fact, be passed from one bacterium to another.

It is also true that scientists have identified forms of bacterial resistance that are due to epigenetic factors. Epigenetics, by the way, is part of evolution. It does not falsify evolution, as Hunter claims in his article. Epigenetic factors are simply mechanisms that affect the expression of genes, rather than changes to the genetic code itself.

In order to know if antibiotic resistance is due to genetic or epigenetic changes you have to investigate the exact mechanism of the resistance. You cannot infer an epigenetic mechanism simply from rapidly developing resistance. What scientists do use to infer an epigenetic mechanism is that the resistance rapidly turns off when the selective pressure of antibiotics is removed.

Hunter not only gets this wrong, but he makes an incredible claim, that epigenetic factors cannot be selected for. This is nonsense – epigenetic processes can affect the fitness of an organism and so absolutely can be selected for. In fact, the study I linked above concludes:

In this report we describe the evolution of antibiotic resistance in bacteria mediated by the epigenetic inheritance of variant gene expression patterns. This provides proof in principle that epigenetic inheritance, as well as DNA mutation, can drive evolution.

Hunter seems to be suffering under the false assumption that a heritable change must provide an immediate benefit in order to ever be selected for, but this does not make any sense. Such changes can arise randomly and may even spread through genetic drift, and later an environmental factor can provide the selective pressure. This happens all the time – organisms or populations that happen, through luck, to be better adapted to a new environment will tend to survive.

Every link in Hunter’s chain of reasoning here is demonstrably wrong. Amazingly, Hunter goes onto his next point, directly contradicting the point he just made:

Another problem, one that Michael Behe points out, is that it appears that most of the mutations that occurred in the experiment served to shutdown genes. In other words, the mutations broke things, they did not build things. This is another way to see that this does not fit the evolutionary model. It’s devolution, not evolution.

But wait, Hunter just concluded above that the changes in the experiment must have been epigenetic, now he is acknowledging that they were mutations. This is a classic creationist “kettle defense” strategy. Hunter’s points don’t even have to agree with each other. They each exist in isolation as an attempt to throw doubt on evolution. But let’s move on to this new mangled logic.

As I already stated in my original post, there is no such thing as “devolution.” This is part of a more general strategy creationists use, to focus on one aspect of evolution and complain that it does not explain or accomplish some other aspect of evolution. This is the logical equivalent of arguing that a car could not possibly work because the steering wheel does not propel the car, and the engine is not capable of steering the car.

Evolution creates change, in all directions. Sometimes that change results in greater simplicity, sometimes in greater complexity. Some mutations reduce a specific activity of a protein, others may increase it. Some mutations may truncate a protein so that it does not function at all in its original role. Sometimes genes duplicate, so there are now two genes where there was one before. The second copy of the gene then evolves a new function. Sometimes regulatory genes mutate causing development to take a different path, resulting in new structures. Mutations can certainly “build things.”

The fact that some mutations reduce enzymatic activity in a specific protein is not “devolution” or evidence against evolution, it is simply one of the many things that genetic change can do. Hunter either suffers from a profound ignorance of even basic evolutionary theory, or he is willfully engaging in motivated reasoning, or some combination of the two.

Hunter responds to my correction of Behe’s error (which he is repeating) with two stunning non-sequiturs:

First, Novella ignores the fact that many of the mutations introduced stop codons, and so did not merely slow an enzyme but rather shut it down altogether.

Irrelevant, as I already pointed out above.

Secondly, it is not Behe here who is making the mistake, it is Novella. He says “Evolution is simply heritable change…” But this is an equivocation. On the one hand, evolutionists want to say that shutting down or slowing a gene is “evolution,” but on the other hand, they say that a fish turning into a giraffe is “evolution.” Unfortunately evolutionists routinely make this equivocation. This is because they don’t think of it as an equivocation. In their adherence and promotion of the theory, the distinction is lost on them. All change just smears together in one big long process called evolution. You can see other examples of this here and here.

What? I don’t think Hunter understands what the word “equivocation” means, and is just throwing it out there in desperation. Evolution is any kind of heritable change. This is not an “equivocation,” whatever Hunter thinks he means by that. It simply means that evolution is a complex and multifarious process. It can produce all kinds of change. One tiny branch of this change did result in a fish population eventually giving rise to giraffes. Other evolutionary change provides antibiotic resistance to certain bacterial colonies. So what?

Ironically he comes closest to being correct when he tries to mock evolutionary theory by saying, “All change just smears together in one big long process called evolution.” That’s right. Again, so what? Hunter seems to be stuck on a silly narrow concept of evolution, that it is only about speciation to more complex forms. That is not what modern evolutionary theory holds.

He continues:

The message is clear: This is evolution, the evolution. But it isn’t. There is nothing in these findings that show us how a fish turns into a giraffe.

This is the steering wheel fallacy again. There are multiple lines of evidence for evolution, because evolution is complex. Creationists typically will try to dismiss one line of evidence by arguing that it does not explain a separate line of evidence. This experiment indeed does not show how fish evolved into giraffes. It shows how bacteria can evolve resistance.

Hunter then turns to his final point, an attempt at countering my argument that Behe and others are falling for the lottery fallacy when they argue that a sequence of mutations is too unlikely to occur by chance. My basic point is that Behe is asking the wrong question, what are the odds of this protein, pathway, or structure evolving. He should be asking, what are the odds of any bit of complexity evolving. Hunter says nothing to counter this basic point.

In fact, he gets so incoherent in this section it is difficult for me to know what his point actually is.

This is a terribly flawed argument for several reasons. First, life needs proteins. All life that we know of needs proteins. Thousands of proteins. Yet proteins are far beyond evolution’s reach. It is true, per Novella’s point, that there are a whole lot of ways to make a given protein. There are many, many different amino acid sequences that give you a globin. But “many, many” is like a grain of sand compared to the astronomical amino acid sequence search space. Again, there is no free lunch.

If I am being generous I think Hunter’s point is that, while there may be many possible functional outcomes to mutations in protein sequences, there are many more still that are not viable. I think this is both wrong and irrelevant.

First, every amino acid sequence produces a protein. That’s all proteins are, folded up chains of amino acids. Proteins can potentially serve a long list of functions, structural, enzymatic, signalling, receptor, membrane pore, adhesion, etc. It is probably true that any random sequence of amino acids can potential serve some function, even if it is just to be a glob.

How are proteins “beyond evolution’s reach?” Hunter never makes that point, he just asserts it. He misses the point that evolution is about cumulative change. There are countless cells with countless mutations in countless genes experimenting with new protein structures. Any incremental change that happens to serve some useful function can be retained and built upon. That is the core of evolutionary theory.

Once proteins that can serve a function arise, their basic structure can be preserved, and multiple variations on that theme can arise through mutations. Those variations that function a little better, or happen to serve another function, can also be retained with further variation.

Again, if I am being generous, it seems Hunter is arguing that there are so many potential amino acid sequences that cannot possibly serve any function that random mutation would never stumble upon a useful sequence. Neither he nor any creationist, however, has demonstrated this in any meaningful or rigorous way. They simply wave their hands and appeal to large numbers. And again, they are failing to even consider the potentially huge number of amino acid sequences that can serve any possible function (not just the functions that happened to have already evolved).

Hunter’s attempt at countering this point is laughable:

What Novella is arguing for here is unobservable. He is going far beyond science, into an imaginary philosophical world of maybes. Not only is Novella clearly appealing to the unobservable, but even that doesn’t work. At least for any common sense approach. There is no question that the design space is full of useless blobs of chemicals that do nothing. A speculative claim? No, that is what this thing called science has made abundantly clear to us. Even the simple case of a single protein reveals as much. Only a relatively few mutations to most proteins rob them of their function. Protein function is known to dramatically reduce as different amino acids are swapped in.

This is another creationist tactic – whenever you appeal to logic, they will argue that it is not empirical, even when they introduced the logical argument themselves. It is Behe, and now Hunter, who are arguing (without evidence) that the number of possible amino acid sequences that produce nothing useful overwhelms the number that are potentially useful. I am simply saying that this is not necessarily true, that they are committing the lottery fallacy, and that it is they who have not demonstrated this empirically. Hunter cannot counter my logic, so he basically says that I am appealing to the unknown, which is a non-sequitur.

He does give a glimmer of recognition when he asks of his own position, “A speculative claim?” which he immediately counters with ,”No”. But it is just as speculative as my position – we are both arguing about the probability of any random amino acid sequence serving any possible function. He then doubles down on the original logical fallacy, indicating that he has learned nothing.

He says that, “Protein function is known to dramatically reduce as different amino acids are swapped in.” Sure, for the one current specific function. That is not even relevant to the question of all possible functions, however. Again he is looking back from the perspective of a protein that has already been adapted to one highly specific function. This says nothing about evolving forward to any possible function. Further, once a protein has the tiniest toe hold on a function, enough to provide an adaptive advantage, natural selection kicks in and we can have cumulative adaptive change.

He concludes:

Sure, Novella may be right that there are other, unknown, solutions to life. But that isn’t suddenly going to resolve evolution’s astronomical search problem. The problem was never contingent on the life we observe being the only possible life forms possible.

And yet, every example you and other creationists give to demonstrate that there is a “search problem” commits the lottery fallacy by assuming current life is correct and everything else is “devolution.” You never demonstrate that there is a search problem, or that most amino acid sequences are not potentially useful in some way, or at least enough so that the massive number of cells that have ever existed, with all their genes and proteins, would not be capable of exploring the “space” of possible outcomes to settle on any possible solution (not just the ones we have today).