Snake Bite Shock for Creationism

King Cobra (Ophiophagus hannah)

You know, sometimes, challenging creationist loons and putting up facts for them to either explain away, or more often, ignore all together, feels a bit like shooting fish in a barrel. A proud contempt for learning and an admiration for the moral and intellectual bankruptcy which means they aren't bothered about being right or wrong, must be such great assets for them. No wonder they seem to positively delight in displaying them, yet never enter into serious debate about the biological facts.

Take for example something that struck me in a long and very readable article in New Scientists by Bob Holmes this week about the evolution of snakes. (Unfortunately, this sits behind a paywall but articles like this justify my decision to stump up the £44 per year). The article discusses many aspects of snake evolution, most of which would precipitate ophidiophobia in any dedicated creationist, but the observation which is guaranteed to push any creationist into deep denialism concerned the evolution of snake venom.

Burmese python (Python bivittatus)

The article relates how a team from the Naturalis Biodiversity Centre in Leiden, Netherlands, led by Freek Vonk have identified the venom genes in the cobra and compared them to the Burmese python (a non-venomous constrictor) and an anole lizard. They found that there is nothing especially remarkable in these genes, which are common in all cells. In Bob Holme's words, "the cobra seems to have assembled its venom bomb from household materials". They are almost all simple adaptations of genes that deal with routine matters in cells. What seems to have happened is that these genes were replicated several times in snakes and have so been free to mutate over time. Natural selection has then selected for those which give cobras an advantage.

Abstract
Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates. In contrast to the platypus, the only other venomous vertebrate with a sequenced genome, we find that snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection that correlate with their functional importance in prey capture. The enigmatic accessory venom gland shows a very different pattern of toxin gene expression from the main venom gland and seems to have recruited toxin-like lectin genes repeatedly for new nontoxic functions. In addition, tissue-specific microRNA analyses suggested the co-option of core genetic regulatory components of the venom secretory system from a pancreatic origin. Although the king cobra is limbless, we recovered coding sequences for all Hox genes involved in amniote limb development, with the exception of Hoxd12. Our results provide a unique view of the origin and evolution of snake venom and reveal multiple genome-level adaptive responses to natural selection in this complex biological weapon system. More generally, they provide insight into mechanisms of protein evolution under strong selection.

Significance
Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced the genome of a venomous snake, the king cobra, and assessed the composition of venom gland expressed genes, small RNAs, and secreted venom proteins. We show that regulatory components of the venom secretory system may have evolved from a pancreatic origin and that venom toxin genes were co-opted by distinct genomic mechanisms. After co-option, toxin genes important for prey capture have massively expanded by gene duplication and evolved under positive selection, resulting in protein neofunctionalization. This diverse and dramatic venom-related genomic response seemingly occurs in response to a coevolutionary arms race between venomous snakes and their prey.

Freek J. Vonk, et al
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
PNAS 2013 110: 20651-20656.

Now, that process of gene replication creating a freedom for evolution to 'experiment' by random mutation and natural selection, without the mutation doing any harm, is familiar enough to anyone who understands evolution and explains the evolution of very many enzymes, metabolic processes and internal cell structures like flagella, although you will find creationists trying to argue that all mutations must be harmful so evolution must be impossible.

No! That isn't the problem for creationists in this article. The problem they have is hinted at in the last sentence in the paper quoted above. It is to explain why most advanced snakes have very complex venom, and not just a simple, single-substance venom that would kill its prey just as surely, such as you might expect an intelligent designer to provide it with - if an intelligent designer actually wanted venomous snakes killing its other creations in the first place, that is.

The reference to a 'coevolutionary arms race' explains this very readily and simply in terms of Darwinian evolution, because, as Bob Holmes also points out, prey species could quite easily evolve resistance to a single toxin. In fact, Darwinian evolution would almost guarantee that they did. So what snakes have counter-evolved in this evolutionary arms race is a cocktail of different toxins to counter this tendency in their prey species, so making it much more difficult for them to evolve resistance.

Okay, I can almost hear creationists who have got this far getting ready to argue that this ability to produce a cocktail of toxins is something any intelligent designer could come up with. However, and this is the catch, why would it need to? Why would an intelligent designer need to provide snakes with the ability to circumvent their prey species' ability to evolve resistance? Is the intelligent designer working in a natural world subject to Darwinian Evolution after all, and only bothering about venomous snakes?

Answers below, please.

Incidentally, the same paper reports that the team identified genetic coding sequences for the hox genes normally responsible for limb development in amniotes, with the absence of only one. Briefly, hox genes are genes that switch stages of development on and off in the developing embryo. The development of major structures like limbs is controlled by a set of hox genes. It seems very clear that snakes were once limbed vertebrates and the loss of limbs was due to the breaking of a single gene. Why would an intelligent designer give it the ability to make limbs in the first place, then simply break that ability? It would be like a designer designing a radio complete with the old Mullard valves, then simply breaking one of the pins to stop them working when transistors came along but continuing to fit them anyway - something that wouldn't surprise us in the least if done by an unintelligent process like Darwinian Evolution, but makes no sense at all as the actions of an intelligent designer.

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