 The Discovery Institute, on a blog deceptively called Evolution News and Views. In one of their recent posts called Engineering at its Best, Jonathan M. discusses the emergence of irreducibly complex systems within irreducibly complex systems in the chemotaxis of bacteria. What he's talking about are how bacteria move along chemical gradients to find food. Jonathan goes on to cite these signaling cascades as evidence of brilliant engineering, which he cites as positive indication of intelligent design. What we are now observing is the existence of irreducibly complex systems within irreducibly complex systems. How random mutations coupled with natural selection could have assembled such a finely set up system is a question to which I defy any Darwinist to give a sensible answer. The sad thing about such a challenge is the intellectual laziness it depends on. Evolution of signaling is its own field. Even the specific proteins that guide bacteria up chemical gradients have a body of literature that detail their evolutionary history. I found no fewer than 35 papers specifically giving evidence for their origin and emergence by natural processes. How did the bacterial chemotaxis system evolve? Specifically, the methyl accepting chemotaxis proteins cited by Jonathan. I'm going to try to make the science accessible as best I can for a very high level topic in molecular biology. The intelligent design creationists rely on the befuddlement of their target audience using scientific sounding terms to support their pseudoscience agenda. Are MCP pathways irreducibly complex? MCPs are methyl accepting chemotaxis proteins. That means they are analogous to switches embedded in the inner cell membrane that turn on when they sense a certain type of chemical like a sugar or fat molecule, food in other words. The on switch is the accepting of a methyl group, a single carbon molecule, usually a methyl ester. And that on or off state is transmitted through a series of different proteins until it has the desired effect which in this case is to alter the swimming behavior of the bacteria driving the flagellum in different ways. This pathway allows a bacteria able to move under its own power to find food. There's also a second activity and it allows the bacteria to avoid something, a repellent, by a behavior called tumbling. Let's imagine a human analog to a cell, a little robot capable of following a chemical trail. You wire the wheels to run forward when it senses table sugar and run backward when it senses vinegar. Simple enough, right? A single specialized process, a way to transmit the signal and it would be simple enough to design such a device. But that's not what we find in the MCP pathway. They're a series of interacting proteins, one class of which have the prefix key for chemotaxis. So the members are named key A, key B, key R, key W, and key Y for example. Here's where we run into the first problem with Jonathan's argument. Not all bacteria have this full pathway. In some bacteria, key A and key R are sufficient. In some, different partners match up or at different ratios. In some bacteria, key A can interact with itself instead of the protein it's paired with and others. In other words, this is not an irreducibly complex system because we find it fully functional, missing several components, and there is no single consensus about what is required. My second complaint is that the members of the pathway have some ambiguity and overlap of function. Each of the genes in the pathway contain conserved domains and probably arose by gene duplication and divergence through the evolution of bacteria and archaea. There are dozens of papers reconstructing this, testing it in evolutionary computer models, and the data matches very nicely with the predictions. My third objection is that removing a single component rarely disrupts the function of this pathway. For example, when scientists knocked out some of the key genes in E. coli, the standard lab bacteria, they can still sense some molecules but not others. This is not a fragile system. Multiple components of the pathway have to be knocked out of the genome of an organism adapted to use them in order to fully disrupt function. It's trivial to see that an organism can survive without any one of these components, so it can hardly be called irreducibly complex. Using our analogy of a chemical sensing robot, it would be like finding three sugar sensors welded together in one robot and a vinegar sensor with reverse polarity in another, and some robots have a sensor that doesn't really do much except pass the electrical signal along. Another has the sensor directly mounted on the wheels with no wiring. This is not what we expect from intelligent engineering. Once an optimal solution is designed, coming up with a variety of non-optimal approaches, apparently frozen in time or inherited from earlier designs, is unlikely. My fourth objection is the nested hierarchy of chemotaxis genes. With biological organisms, we have the added context of knowing how these organisms are related to each other, and the genes for chemotaxis show the same nested hierarchies so universally seen in comparative genomics. Together, this change over evolutionary time, this narrative of conserved functions and new capabilities spanning millions or billions of years of genetic variation, does not describe what we know of engineering with purpose. It only makes sense if the designer of these structures is an unintentional process that causes periodic divergence and extinction of individual structures and organisms. The appearance of design here is of lots of independent processes, unconnected to each other, where intelligent design creationism posits a single, unifying supernatural origin of biological structures, a supreme single engineer. Evolution proposes a landscape of little tinkerers. They take what their ancestors gave them, make small modifications here, add a new what's it there, remove a little bit over there. What we see in chemotaxis is a million crazed engineers working from different ancestral blueprints, co-opting structures, duplicating and deleting them, not a single blueprint of optimal design. If God, oops, the intelligent designer, wished to indicate her presence, all she needed to do was create one gene that every organism on earth possessed without variation, a supernatural barcode or RFID, that would be unexplainable, that would be a divine miracle. The actual picture is of a natural process, are millions of independent tinkerers, miraculous in its own way, in that through striving to survive, it explores all the possible ways that life can evolve. Thanks for watching.