On the Origin of Snakes

New studies of snakes and their genes are surprising scientists with stories of “rapid evolution.”  Some findings offer potential for human health.

Snakes made headlines in scientific papers in the last couple of weeks.  With the publishing of genomes for the king cobra and the Burmese python, scientists are gaining opportunities to update their evolutionary stories with new data.

PNAS published findings from the king cobra genome.  Of interest is “dynamic gene evolution and adaptation in the snake venom system,” assuming cobras evolved from other snakes.  By comparing the venom delivery system with those of other vertebrates (with the platypus being the only mammal), they constructed a story of an “evolutionary arms race” between predator and prey.  They also argued for cases of gene duplication and neofunctionalization.  Speaking of the venom itself, the team said that “snake toxin genes evolve through several distinct co-option mechanisms and exhibit surprisingly variable levels of gene duplication and directional selection….”  Referring to the snake’s “complex biological weapons system,” they pointed out the functional significance not only of genes but of microRNAs.  They also found all but one of the Hox gene sequences related to amniote limb development.

PNAS also published findings from the genome of the Burmese python, one of the largest snakes in the world.  As with the king cobra, this species shows adaptation due to more than just genes.  “Snake phenotypic novelty seems to be driven by the system-wide coordination of protein adaptation, gene expression, and changes in genome structure,” they said, claiming these have evolved by strong positive selection.  They found, for instance, “massive rapid changes in gene expression that coordinate major changes in organ size and function after feeding,” adding, ” Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology.”  The team compared the Burmese python with the king cobra and other snakes, finding the species highly adapted for its feeding habits.  Describing “extensive adaptive redesign of snake metabolic pathways” as products of evolution, though, confuses adaptation with the mechanism for its origin.

PhysOrg summarized these papers, focusing on the “rapid evolution of cobra venom.” Readers may be unfamiliar with the fact that evolutionists are puzzled by the origin of venom.

In particular, lead author Dr Nick Casewell and his colleagues were interested in how the cobra’s venom evolved. It contains dozens of highly specialised toxins, and exactly how this complex brew could have come about has long been a puzzle.

Analysing the newly-sequenced cobra genome confirmed the hypothesis that the individual toxins that make up the venom developed from proteins that originally evolved for unglamorous day-to-day tasks elsewhere in the body.

The evolutionary story says that genes for the “unglamorous” proteins duplicated many times, with duplicates free to evolve other functions – a process dubbed neofunctionalization.  It does not explain, however, the simultaneous adaptive evolution of the venom delivery system, the behavior for injecting it, and mechanisms the snake uses to protect itself.

The concept of an “evolutionary arms race” also enters the story.  “Venomous snakes rely almost totally on their venom to kill prey, so prey immunity would be a disaster; to avoid that risk, the venom has to keep developing new tricks.”  To whatever extent that occurs, it would only involve changes to the brew, not changes to the “complex biological weapons system” itself.  Another extreme adaptation is seen in the Burmese python, which can alter its metabolic pathways by 150% after feeding, then return to normal, supposedly co-opting other genes in the body for its “extraordinary capacity to change its whole body to deal with the situation.”  New Scientist added to the tale of these snakes “outpacing other vertebrates in [the] race to evolve,” calling this “evolutionary nimbleness.”  Someone even found a way to bring global warming into the story:

This evolutionary nimbleness may make snakes more able to adapt to future challenges too, says Scott Edwards, an evolutionary biologist at Harvard. However, he adds, snakes’ “fast” evolutionary changes still took millions of years to accumulate. “Whether they’re labile enough to resist all the challenges of habitat loss and climate change is unclear,” he says. “It’s a different timescale.”

Of more practical import is how to protect humans from snakebite.  These papers may help with the development of antivenom compounds to help reduce the 100,000 annual snakebite victims around the world.  Science Magazine ran a special section on snakes this week.  “Exotic, elusive, and dangerous, snakes have fascinated humankind for millennia,” the news focus began.  Amid adventure stories of those who study snakes (some of whom were bitten in the process), and repetition of the evolutionary themes, one article stood out as very different: “From Toxins to Treatments” by Kai Kupferschmidt.  The subtitle reads, “Researchers are hoping to find lifesaving drugs in the deadly venoms from snakes and other animals.”

We’ve seen efforts to use the world’s deadliest substances for good before.  Cone snails and other venomous creatures have proved invaluable as sources of health-giving compounds.  Botulin toxin is one clear example that is in widespread use today.  Kupferschmidt tells of other developments that seem almost miraculous in the use of poison to give life.  While “Nature has had millions of years to perfect this molecular sabotage and turn snakes into accomplished killers” on the one hand, “more and more researchers are studying venom’s powers to heal rather than harm.”  The unique proteins in venom are being viewed as a library of useful chemicals to alter biological processes in healthy ways.  Some 40 million such compounds await study in the some 170,000 venomous species of animals, from centipedes to gila monsters to the platypus.  Interesting factoid: “There are only 1500 species of venomous snakes, but 50,000 species of venomous spiders,” one researcher noted, emphasizing that the library is extensive in that wing.  Spiders may have even more distinct proteins in their venoms than the 250 or so in a snake venom.

What can these compounds do for good?  “Ziconotide, a peptide in cone snail venom, was approved in 2004 to treat chronic pain; exenatide, isolated from the saliva of a venomous lizard called the Gila monster, has become a blockbuster drug for type 2 diabetes.”  One peptide from cobra venom is 20 to 200 times more effective than morphine, without the side effects and addiction.   It’s time to explore this “toxic treasure trove” systematically, one expert advises.  A day may come when your doctor plays snake and lets his hypodermic needle substitute for snake fangs, to deliver toxin-derived agents of healing to your body.

Update 12/06/13: Elizabeth Pennisi wrote a summary of the findings for Science Magazine.  At one point she related the current just-so story about snake origins:

Snakes have slithered their way through oceans and across all the continents save Antarctica; their 3000 species have infiltrated nearly every conceivable habitat from termite mounds to rainforest canopies. But they got their start in a specialized niche where legs were a handicap. A few researchers think snakes first evolved while living in water, but most now contend that they originated from lizards that went underground (Science, 8 November, p. 683). There, they acquired not just the serpentine body type, but also an economical metabolism able to deal with low oxygen levels. Eyes weren’t needed, so they degenerated. When snakes surfaced again, lacking limbs for capturing prey, some species evolved venom instead. And they developed visual systems quite different from those of their lizard relatives.

But this answer raises numerous questions.  How did they “acquire” these things?  Did they “evolve venom” on purpose?  If they were able to “develop visual systems” a second time, why didn’t they also “develop” legs?  (It would seemingly be a simpler task if the Hox genes for them still existed.)  Readers might well wonder if this explanation is any more credible than a certain story of a serpent being cursed to crawl on its belly.

This is a very intriguing subject that plays on our fears as well as our hopes.  It also crosses over into questions about theodicy.  Why would an all-loving Creator make such potent agents of suffering and death?  While we can admire the design of a king cobra, and even see its fearful kind of beauty from a safe distance, it’s hard to endure the agonizing screams of a person dying from its bite.

There are many works on theodicy that are better prepared to deal with these questions than space allows here.  Suffice it to say that these findings support the idea that systems designed for good in the initial creation could have easily been switched over for punishment after the Fall into sin.  Indeed, only the Judeo-Christian worldview supplies the grounds for understanding good and evil.  If it evolved, it’s not evil; whatever is, is – stuff happens.  The Bible contains a coherent (if not exhaustive) account of the entry of sin, its consequences, and its cure.  Only the Bible has a Savior, the Lord Jesus Christ, the Creator-Redeemer, who suffered more than any man.  Now, He offers forgiveness, love, and abundant life now, with pain-free joy and glory in heaven, without all these punishments.  There’s a happy ending in Christianity that no other worldview or religion can offer.

So what we see in snake venoms are alterations to good proteins – some of which are regulated by other molecules.  Although God made some drastic changes to living things in the Genesis account, they were for the most part modifications of good things.  As such, some of them can be modified back for good, as scientists are now learning how to do.  After all, a peptide is not evil in itself.  It’s what the peptide does in another animal’s systems that determines whether there is healing or pain.  This realization can awaken new ways of thinking about natural evil.

For Bible believers, we might note that the origin of snakes cannot be simplistically explained by the story of the serpent in Genesis 3.  One cannot say that the judgment on the serpent (Satan) applied to all snakes; that would be reading more into the account than is presented (after all, other creatures, like worms, slither on the ground, too).  The judgment was announced specific to that serpent, the devil, so called the serpent again in the last book of the Bible, Revelation.  We just don’t have enough information to know if snakes were similar before the Fall.  Given their amazing designs for traveling and sensing their environment, one could be justified in believing they were part of the amazing diversity of animal life in the “very good” creation before sin, before some of them became agents of judgment.  For this reason, herpetology is certainly a worthwhile scientific endeavor that should be encouraged.  Instead of forcing the genomic data into evolutionary stories, theist herpetologists might examine non-Darwinian mechanisms for adaptation over shorter periods of time than millions of years, calling attention to built-in designed mechanisms for rapid adaptation.  Theists will also have all the more reason to find healthful applications of scientific knowledge gained, motivated by a share of God’s compassion and mercy for the suffering.