 I made a video a few months back about bacterial chemotaxis, responding to an article on the Discovery Institute blog by Jonathan M. He has since responded, and I have been requested to respond to him, to maintain the dialogue, which I am happy to do. Dear Jonathan, let me first get a few things straight. I am not the same person as Agent Orange 20. I am not Zachary Moore. No idea where you got that impression. If your attempt was to disclose my personal details, what we on YouTube call dock-dropping, mission not accomplished, let's start by detailing your counterpoints. Point one, chemotaxis can be described in mathematical or engineering terms, therefore it is intelligently designed. Point two, irreducible complexity is perfectly compatible with diverse forms of the system with differential fitness. In other words, just because there are almost as many ways to steer a bacteria as there are species of bacteria doesn't mean that each of those ways isn't intelligently engineered. Point three, in contrast to my assertion, knocking out a single gene usually disrupts the function of a pathway. In other words, these systems must be irreducible because every gene is essential. Point four, intelligent design creationism can be argued positively by the appearance of real engineering hallmarks. Point five, neo-Darwinian synthesis cannot explain the existence of multiple coordinated changes that facilitate novel utility. Let's knock down the easy ones, especially one in four. The appearance of design is what organisms are, in a way, designed, in the sense that the processes of life are an optimization routine. This is demonstrated in artificial evolutionary algorithms when a process of diversification is matched by a process of competitive selection. The result is an optimization. NASA engineers used these algorithms to control elements of the space shuttle, rational drug designers used it to improve drug compound libraries, and computer scientists used it to optimize database searches. The appearance of design is not enough. We need to differentiate between top down and bottom up design. Top down suggests that something is designed with a purpose in mind. Bottom up design is starting with existing structures and allowing their repetitive diversification and competitive selection to find a point of increased fitness. Which of the two better describes the chemotaxis pathways? I think the point is well illustrated with a fitness landscape. If you're not familiar with these figures, there are a graphical way of representing fitness in response to genetic variation. In the case of key A and key Y, two key components in chemotaxis, Jonathan M's assertion is that the only acceptable fitness is a sharp-sided peak at some optimal point, suggesting that any changes are deleterious and that there is no easy path from the outer periphery of low fitness to the point of maximum local fitness, which would be consistent with top down design. The only way for a bacteria without all the components for chemotaxis to acquire them would be the intervention of a magical being because there is no gentle slope to allow for natural selection to drive up this peak. Let's quote Jonathan's definition so you don't think I'm distorting this. The key to finding characteristic of an irreducibly complex system is that multiple coordinated and non-adaptive changes are required to attain novel utility. On our graph, that means a non-climable slope, or a peak surrounded by a trough, neither of which is seen in the case of chemotaxis. There appears to be a lot of different ways that bacteria can bring together these genes into a useful network. My assertion is that there are multiple shallow-sloped regions where a bacteria can be very fit, achieve its goals, and reproduce itself, yet there is still room for further improvement. In fact, I would say that there are multiple local points of fitness, and that explains why there is so much diversity in how bacteria navigate along chemical gradients. This is much more consistent with bottom-up design, where existing structures may only give a very weak advantage, may only move the bacteria a few points up the fitness slope, but that slow path is still favored evolutionarily. It's worth noting that the authors of the papers cited by Jonathan agree with me, and not with Jonathan. He quotes them for their use of engineering jargon to describe the control systems of flagellum, but he carefully excises all references to the likely evolutionary explanations for the appearance of bottom-up design. Let's quote some of the parts of the papers that he carefully excised in his long block quotes on his blog. From the 2011 May article by Hamada et al. in Plus Computational Biology, it is likely that the two chemotaxis pathways initially evolved independently, and then became part of the same organism by horizontal gene transfer. Thus one would possibly expect either full connectivity or complete isolation of the two pathways until a further mutation occurs. And their final concluding sentence. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in robust functionality in more complex signaling pathways and in improving their performance. Contrast this idea to Jonathan's model of the single steep fitness peak required of irreducible complexity. Instead what is presented as a gentle climb up a fitness slope and a different local maxima on a landscape. As to Jonathan's assertion that removing a single gene usually makes the system cease to function. In the very paper he cites. The authors created four models where a single gene was deleted, and they found that one such deletion no longer functioned in the same way, but that it was still able to sense but rotated its flagella at a different frequency. This is a great example of what's wrong with the idea of irreducible complexity. It's unfalsifiable. Jonathan would no doubt say that the bacteria minus the gene in question no longer functions in the same way as the wild type, but the point is that the pathway still contributes to the fitness of the organism, which is precisely how evolution works. The bacteria can still respond to chemical stimuli. Jonathan complains in his article that neo-Darwinian synthesis can't explain the step by step process that led to the current complex control system in certain bacteria. And I say that he'd have to close his eyes, stick his fingers in his ears, and hum really really loud to avoid the truth presented in the very articles he cites. This is directly to you Jonathan, and I hope you'll respond. Your counter argument is very weak sauce. A system that can be configured in thousands of ways and still function to improve the fitness of the organism that possesses it is not irreducible. Yes, it is complex, and yes, it was designed, but by a tinkerer, not a de novo designer. You can describe it in engineering terms or model it mathematically. We can do the same for erosional geology, for the weather, or for quantum physics, and they can look quite elegant. But I presume you don't invoke the supernatural to explain clouds or riverbeds. Don't make the same mistake as Paley in his walk along the heath. Don't confuse complex for artificial. Give natural processes a little credit. They can do astounding things. Thanks for watching.