Wednesday, July 1, 2015

Common Creationist Complaint: How did biochemical pathways originate?


Common Complaint: How did new biochemical pathways, which involve multiple enzymes working together in sequence, originate? Every pathway and nano-machine requires multiple protein/enzyme components to work. How did lucky accidents create even one of the components, let alone 10 or 20 or 30 at the same time, often in a necessary programmed sequence. Evolutionary biochemist Franklin Harold wrote, “we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”

Answer:

One of the biggest problems with this question is that it's assuming that each component for each biochemical pathway was created/designed for just that pathway. As it turns out, the components of biochemical pathways actually serve many functions. This plasticity - known as enzymatic promiscuity - is one of the biggest pieces of evidence of the evidence of the pathway's evolution and contributing factors to it's continued evolution. Here's how.

Biochemical pathways are primarily composed of enzymes (a type of protein) acting on substrates. These enzymes catalyze an action that would normally still take place; it would just act slower. These enzymes do not just do one thing; while they usually engage in one primary reaction, they are also involved in other activities that are less important. This flexibility (called enzymatic promiscuity) allows for these enzymes to be incorporated into new metabolic processes as environmental and genetic change occur. 


One of the biggest pieces of evidence for the evolution of biochemical pathways is the different types of functions that the same enzymes perform. Some of the functions they serve are more “primitive” and have been around longer – like basic metabolism – whereas others are more advanced and have recently evolved – like a specific protein that allows for more effective camouflage.

Some may see the complex web of enzyme/substrate interactions with primitive and advanced functions as an irreducibly complex system that could not have happened without divine interference. This is a classic human bias: we manipulate the world around us, creating things more complicated than they were before, and so when we see complexity, we assume that it had to have been created. I wrote about this in-depth here, but here's a snippet explaining why complexity doesn't actually suggest design:


If you really want to think logically, let's do a thought exercise: Imagine you are building a house. With this house, you get to start from scratch. You spend a lot of time planning it out, aiming for simple solutions to complex problems. You know ahead of time how many bedrooms you will end up needing it to have, how many stories, where you want the stairs to go. You plan for energy efficiency, beauty, flow - all at the same time. Once you've got it planned out perfectly, you create it in a short period of time, and you're done.
Now imagine you are remodeling a one-room house. You can only add on bit-by-bit as you need it, and you have to work with what is already available (with the exception of periodic "new" material to work with, let's just call them, oh, mutations). Because you can't sit there and plan it all out for efficiency ahead of time, it ends up very complicated (maybe not dissimilar to the Weasley's "Burrow" from Harry Potter). It might even look so complicated that an outsider looking in might even think that you had planned on it being that way all along.
The first scenario is what we would expect of a "designer God" who planned out everything and then created it instantly while the second is what we would expect from a God working over a long period of time following natural laws (that he himself put in place). And what this reveals is that, far from complexity suggesting design, complexity suggests evolution. The more complicated a system is, the more likely it evolved. After all, why would a designer God have created a 15-step process to create one enzyme when he could have just engineered the perfect 1-step process? These systems are evidence for evolution. A simple, efficient, perfect design would be more indicative of a world created in 6 days designed by an all-knowing God whereas a world full of complexity - the kind of world we live in - is more aligned with a world that was created using evolution as a tool.
Modern biochemical pathways are much more like the second house than the first. Parts are reused, taken from other structures and pathways, tweaked and adjusted. Evolution isn’t so much about “survival of the fittest” – not a Darwinian phrase, by the way – but “survival of the fit enough.” For something to be adaptive, it has to answer the question, “Does it work?” And because sometimes "what works" is a hodge-podge of proteins performing a wide range of functions that they didn't initially perform, we get these complex biochemical interactions. 

The reality is that we don't even have to speculate about whether or not a biochemical pathway could evolve; we’ve witnessed entire pathways evolve in the lab without any help from us. Richard Lenski has been running a continuous 20-year study on 12 initially identical E. coli populations. In addition to a wide range of genetic changes resulting in many different abilities, and one strain has evolved the ability to metabolize citrate - an ability it hadn't possessed before - by creating a transporter protein. There is no reason to think that the ability of evolution to create new biological pathways and proteins is is new today.

[1] 15 Questions for Evolutionists. Evolution: the naturalistic origin of life and its diversity (The General Theory of Evolution, as defined by the prominent past evolutionist Kerkut; see introduction to Origin of life.) by Don Batten