Darwinian argumentation is not evolving

Flagellar Diversity Challenges Darwinian Evolution, Not Intelligent Design
Casey Luskin July 22, 2015 3:56 AM |

Over the past week I've been writing about the latest iteration of the Darwinian response to Michael Behe's argument for intelligent design based on what Dr. Behe calls irreducible complexity. I use the word "iteration" not in the sense of our seeing something new, but in the sense that it's another round of the same unworkable objections that we've seen before.

Behe's case for ID goes back nearly twenty years now, yet the objections to it have not evolved much in that time. I have been looking specifically at an article written by biophysicist Matt Baker for the Australian Broadcasting Corporation, "The bacterial flagellar motor: brilliant evolution or intelligent design?," arguing that the flagellum is not irreducibly complex. In the first part of my response I showed how he misunderstands how we test irreducible complexity, and in the second part I showed why the Type III Secretory System cannot serve as an evolutionary precursor to the flagellum.

But Dr. Baker has one other argument up his sleeve to try to show that the flagellum evolved. In his view, God wouldn't have done it that way. Essentially, Baker has imbibed Nick Matzke and Mark Pallen's fallacious theological argument that because there is diversity among flagella, the structure must not have been designed. He writes:

In the aftermath of the first legal challenges to curriculum requirements to teach intelligent design, evolutionary biologists Mark Pallen and Nicholas Matzke wrote "either there were thousands or millions of individual creation events ... or one has to accept that the highly diverse contemporary flagellar systems have evolved from a common ancestor".

Now maybe some (or even most) flagella are indeed related to one another, but there's no reason why a designer couldn't design diverse flagella. After all, in our experience with technological systems devised by human beings, we see incredible diversity! Look at all of the different ways that people have designed cell phones, trucks, or even something as simple as a key. These devices come in all kinds of myriad forms. Diversity doesn't negate design.

Thus, Baker is proffering a theological argument that is simply irrelevant to the scientific case for intelligent design. In reality, flagella are distributed in a polyphyletic manner that doesn't fit what we'd expect from common ancestry:

tim_flag_phyl_500.jpg

Reprinted from Figure 2, Trends in Microbiology, Vol 17, LAS Snyder, NJ Loman, K. Fuetterer, and MJ Pallen, "Bacterial flagellar diversity and evolution: seek simplicity and distrust it?," pp. 1-5, Copyright 2009, with permission from Elsevier.

What you see in the figure above are various major groups of bacteria, represented by triangles (or in some cases written text). They are arranged here according to a standard phylogeny of bacteria. The purple groups have flagella throughout the clade, and the groups with question marks have only a minority of species with flagella within that clade. The white triangles show groups not thought to have flagella.

What's the problem? The groups with flagella are scattered all about the tree and do not form a single monophyletic group. In other words, the diversity of flagella cannot be easily explained by common ancestry. Writing in Trends in Microbiology, the authors of the figure reprinted above explain the problem:

When we attempted to map the known distribution of flagellar genes on to a recently published 'tree of life', instead of a single monophyletic grouping of flagella-bearing phyla, we found multiple apparent points of origin for flagellar systems on the phylogenetic tree (Figure 2). This highlights a fundamental problem with any simple model of flagellar divergence: although there is some agreement as to the existence of bacterial phyla, there is no consensus on the order of their divergence.

The problem here is that flagella do not fit into the nice, neat nested hierarchy that you'd expect from common ancestry. Quite the opposite -- their diversity conflicts with what you would expect from a Darwinian origin of the flagellum. Indeed, the caption for the figure above from the paper states, "Arrows indicate apparent points of origins for flagellar lineages." Common descent predicts there should be just one arrow, but as you can see on the diagram there are five arrows, because there are no fewer than five clades -- widely separated on the tree -- that have flagella. This is not what common descent predicts. Common design, on the other hand would predict that complex features like flagella might be re-used in a manner that doesn't match a nested hierarchy, which is exactly what we see here. Ironically, the nature of bacterial flagellar diversity -- far from being a problem for intelligent design -- is actually a significant problem for Darwinian evolution.

Baker's argument here is ironic. We constantly see evolutionists arguing that homology (i.e., sequence similarity) between proteins is evidence that they evolved. In particular, we see this argument made regarding the flagellum. In fact, in a striking comment that appears after his article, Baker himself states that he feels no obligation to provide anything like a stepwise explanation for the evolution of the flagellum precisely because "commonality" between proteins is sufficient to demonstrate flagellar evolution:

I don't think we need to actually directly show an injectisome can be step by step evolved into a flagellum, the field of experimental evolution is very young! We can look, with greater and greater ease, at the historical genetic record, and look for commonality. This is the basis of most evolutionary genetics. By phylogenetics and common ancestors, we can show that systems share elements, and we do.

Yet in his article he affirmatively quotes Pallen and Matzke saying that the "highly diverse" nature of flagellar proteins also demonstrates their evolution. So now apparently both similarity between proteins and differences between proteins demonstrates evolution. No matter what you find, it demonstrates evolution!

What a sweet deal it must be to be a Darwinian evolutionist. You don't have to provide any evidence that your theory is true (i.e., offer some semblance of a stepwise evolutionary explanation), and no matter what evidence you do find, it is guaranteed to show that your theory is true!

Indeed, Pallen and Matzke's paper presents other related contradictions. They repeatedly denigrate "typological" thinking, stating:

As the great evolutionist Ernst Mayr noted, one of Darwin's greatest achievements was to abolish typological or essentialist thinking from biology; instead, the emphasis in biology is on variation and individuality3. Therefore, when discussing flagellar evolution it is important to appreciate that there is no such thing as 'the' bacterial flagellum. Instead, there are myriad different bacterial flagella, showing extensive variation in form and function.

Since their article is an explicit attack on ID, I suppose their point is that they're trying to tag ID as a form of typological thinking, wrongly suggesting that ID can't accommodate the diversity among flagella. Ironically, however, Pallen and Matkze later admit that "all (bacterial) flagella share a conserved core set of proteins," numbering around 20 proteins, and they further concede that there is a common core of subsystems found in known bacterial flagella:

Three modular molecular devices are at the heart of the bacterial flagellum: the rotor-stator that powers flagellar rotation, the chemotaxis apparatus that mediates changes in the direction of motion and the T3SS that mediates export of the axial components of the flagellum.

There you have it: despite all the apparent "diversity" of flagella, and the evolutionists' distaste for "typological thinking," they admit that all bacterial flagella share a conserved core of about 20 proteins, and a common core (what I would call an irreducible core) of subsystems: a motor, a chemotaxis mechanism, and a secretion apparatus. It seems like the many diverse types of flagella are variations on a common thematic archetype.

And how do we know this core is irreducibly complex? Because the experimental data shows it is. Scott Minnich's genetic knockout experiments on the E. coli flagellum have shown that it fails to assemble or function properly if any one of its approximately 35 structural parts are missing.

Baker discloses none of this, but simply asserts that the irreducible complexity of the flagellum has been refuted:

Typically, intelligent design proponents persevere despite this evidence. They simply adjust their goal posts by selecting other systems to act as poster boys for irreducible complexity. It is difficult to respond to these movable challenges. But as we learn more about the origins of these and other complex systems, we can at least reduce the number of available candidates used to prop up the theory of intelligent design.

Actually ID proponents haven't abandoned arguing for the irreducible complexity of the flagellum because, as we've seen, it was never refuted in the first place. Rather than moving goal posts, we're building a formidable team, as ID advocates have expanded their arguments far beyond irreducible complexity. But I suspect that Dr. Baker doesn't pay any much attention to any of that.

Thus, he closes with a typically inaccurate rant about the dangers of intelligent design:

While all this may seem relatively harmless, the intelligent design movement is well funded, slickly presented, and actively challenges educational curricula in many countries. It is a dangerously well-articulated distraction from the large body of evidence supporting evolutionary theory.

Actually our funding is nothing compared to the wealth of support available to upholders of Darwinian evolution. Setting that aside, consider Baker's claim that ID distracts from the "large body of evidence supporting evolutionary theory." In fact, as we've seen, both evidence and logic contradict Baker's arguments. In fact, he openly refuses to demonstrate what Darwinian evolution requires: a stepwise evolutionary explanation of the flagellum! He apparently wants to blame ID for his failure to make a convincing case.

The world is very different from the one that many Darwin advocates believe they live in. Despite their protests to the contrary, this debate is far from ov