February 7, 2019 | David F. Coppedge

Snake Bites Darwin

The origin of snakes and snake venom has become more puzzling to believers in Darwinian evolution.

(Note: For explanation of our usage of Darwin, Darwinism and Darwinian, see footnote.)

If snakes evolved from lizards, there should be fossils showing the transition. There should also be genetic changes evident between lizards and snakes. Often in biology, things turn out too complicated for simple stories.

Does Darwinism Explain Snake Limblessness?

Research explains how snakes lost their limbs (Fundação de Amparo à Pesquisa do Estado de São Paulo). Scrutiny is advised whenever science claims to “explain” something. Writer José Tadeu Arantes begins not with an explanation, but an assertion:

Snakes and lizards are reptiles that belong to the order Squamata. They share several traits but differ in one obvious respect: snakes do not have limbs. The two suborders diverged more than 100 million years ago.

The Brazilian researchers at FAPESP, led by postdoc Juliana Gusson Roscito under the supervision of Miguel Rodrigues, Professor at the University of São Paulo’s Bioscience Institute (IB-USP), compared genes between snakes and one species of lizard, the tegu lizard, as well as some other animals. Roscito also compared genes of species that lost eyes. That’s when things got messy. These stories of lost organs did not involve genetics alone, but also epigenetics: issues of gene regulation. Instances and functions of cis-regulatory elements (CRE’s) are more difficult to discern.

From a computational standpoint, CREs are not as easy to identify as genes. Genes have a characteristic syntax, with base pairs that show where the genes begin and end. This is not the case for CREs, so they have to be identified indirectly. This identification is normally based on the conservation of DNA sequences among many different species.

Gene conservation, though, entails belief in evolution: i.e., that “conserved” genes were so important that they were preserved by natural selection over millions of years. Already some Darwinian circular reasoning is involved in the conclusions, because genetic differences could be due to other causes than common ancestry. The method used by the team seems reasonable only when evolution is assumed.

“Using the tegu genome as a reference, we created an alignment of the genomes of several species, including two snakes (boa and python), three other limbed reptiles (green anole lizard, dragon lizard and gecko), three birds, an alligator, three turtles, 14 mammals, a frog, and a coelacanth. This alignment of 29 genomes was used as the basis for all further analyses.”

The researchers identified more than 5,000 DNA regions that are considered candidate regulatory elements in several species. They then searched the large database using ingenious technical procedures that are described in detail in the article and obtained a set of CREs the mutation of which may have led to the disappearance of limbs in the ancestors of snakes.

They found mutations in one particular CRE in snakes they believe is involved in the loss of limbs, because mice with the snake version were born almost limbless. The classical neo-Darwinian approach of looking for mutations in selected genes is now complicated by looking for mutations in epigenetic factors.

A regulatory element can activate or inhibit the expression of a gene in a certain part of the organism, such as the limbs, for example, while a different regulatory element can activate or inhibit the expression of the same gene in a different part, such as the head. If the gene is lost, it ceases to be expressed in both places and can often have a negative effect on the organism’s formation. However, if only one of the regulatory elements is lost, expression may disappear in one part while being conserved in the other,” Roscito explained.

Sounds simple enough; but Roscito cautions, “However, this CRE is only one of the regulatory elements for one of several genes that control limb formation.” It appears premature to say that this finding “explains how snakes lost their limbs.”

To see why, consider a mutant snake born without limbs. Would it survive? And even if it survived, would it mate with a limbed lizard, and pass on limblessness to all the offspring? How could a limbless male mount a female? Why would such a physical deficiency become established in a lizard population? In the case of blind cave fish, eyes are no longer needed, and other existing organs take on the needed senses for viability. The mouse with the snake CRE, however, was definitely impaired in “fitness” for its environment.

Along with limb loss, the snake would have to evolve new behaviors and new methods of locomotion. The capabilities of snakes are staggering in their variety and complexity, from flying through the air, to living in the ocean, and inhabiting environments as diverse as deserts and tropical jungles. They also exhibit enormous variations in color, patterns and sizes. If a mutation in one regulatory element caused loss of limbs in snakes and yet led to tremendous success, why aren’t there thriving examples of limbless dinosaurs, limbless birds and limbless primates? Remember, too, that the mutations had to affect the germ line or would vanish when the first snake died.

The paper in Nature Communications shows that Roscito and the co-authors realize that a single CRE change is inadequate to explain why snakes lost their limbs. In the paper, “Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution,” they can only say that the candidate CRE they studied appears to be “associated” with limb loss in snakes. There are many complications, like pleiotropy (a change in one gene affecting other genes) that must be considered when trying to turn association into causation – or into explanation.

The loss of a complex phenotype is one extreme case of morphological evolution. Upon phenotype loss, we expect a different evolutionary trajectory for the genetic information underlying this phenotype. On the one hand, the integrity of developmental genes should be maintained over time due to selection on those gene functions that are not related to the lost phenotype. On the other hand, modular cis-regulatory elements associated specifically with this phenotype may directly contribute to its loss and are expected to evolve neutrally afterwards. This should result in sequence divergence and thus decay of regulatory activity over time…. However, recent studies found that numerous other limb enhancers are nevertheless still conserved in snakes, despite limb reduction in this lineage dating back to more than 100 Mya, possibly due to pleiotropy of regulatory elements that drive expression in other non-limb tissues. Thus, it remains an open question whether phenotype loss is generally associated with widespread divergence of the cis-regulatory landscape.

While they may have accounted for conservation of a genetic loss, nowhere in the paper do they use the term “positive selection” to account for the many other phenotypic innovations that had to occur for limbless lizards to thrive as snakes. Is it not just as scientific to infer that snakes came fully formed as thriving creatures, with their different CRE’s and all?

Does Darwinism Explain Snake Venom?

Misti Crane writes for Ohio State that “Rattlesnake venom” comes in forms that are “mild, medium and wicked hot.” Even within a species or genus, “Lizard-killing ability varies from snake to snake.”

In a surprising evolutionary twist, a new study suggests that while one rattlesnake may routinely feast on lizard meat, its seemingly identical neighbor snake might strike and strike and never kill its would-be reptilian prey.

The first-of-its-kind research reveals significant venom variation within populations of Florida pygmy rattlesnakes, showing that effectiveness against one type of prey differs widely among individuals and opening up questions about why this variation exists.

Evolutionists usually had accounted for the differences in snake venom by studying the prey available in different environments. Crane says “that made good intuitive sense, because they were living in different environments, with different dietary options at the ready.” Consequently, herpetologists spent their time comparing species rather than watching for differences within species. H. Lisle Gibbs, the senior author of the study, shared the surprise.

“This is a whole new way of looking at how evolution operates on venom that we haven’t considered,” he said. “There’s a new act in this evolutionary play that we didn’t know about until now.

For evolutionists, this must be baffling, because snakes diverged from lizards 100 million Darwin Years ago. Why aren’t the less-fit snakes long extinct? Individual pygmy rattlesnakes differ by as much as fourfold in their ability to kill prey with their venomous bites. Admittedly, these evolutionary biologists have no explanation.

Gibbs and team could turn from their evolutionary focus and work to help mankind. “Aside from broadening scientific understanding of evolution, this work could one day help inform efforts to develop drugs based on venom – an area of pharmaceutical research that has already shown benefit in cardiovascular disease and could prove important in the treatment of pain and neurological disorders, as well as other human diseases, Gibbs said.”

Snakes are wonderfully designed, yet fearsome, creatures. Their colors, varieties, sizes and behaviors astonish all who learn about them. Some snakes can be kept as pets and held in the hands with perfect safety; others cause great pain and suffering and death. Creationists struggle to explain these realities, too, from the brief Biblical account provided. Everything was very good in the beginning; did some species of snake exist then? It seems unlikely that “the serpent” in chapter 3 was the father of all snakes (where was the female?).

As with all cases of “natural evil” from viruses to man-eating tigers, we don’t know everything. In last year’s film The Riot and the Dance, Dr. Gordon Wilson showed many fearsome creatures and discussed some of these questions. Viewers watched as he came dangerously close to some deadly cobras and held other organisms that, if not handled carefully, could kill. In many creatures, we observe fascinating design coupled with extreme danger. Given what has been revealed about the curse due to sin, and the creation groaning in pain in the current epoch (Romans 8:18-25), and the promise of a new heaven and new earth without pain and suffering, we have enough general information to trust God and wait for the redemption of creation. But for any mockers who think the Stuff Happens Law created snakes by mistake, the articles above show that evolutionists have no answers. When it comes to snakes, we can all agree on one thing: while explaining them is hard, observing and learning about them to help alleviate suffering and create cures for disease is a better way to spend our time.

Footnote on use of “Darwin” in CEH: The term Darwin serves as a shorthand metonymy for all that his view entails, much as the term Newton serves as a convenient shorthand for all that Newtonian physics entails. We realize that evolutionary thought has come a long way since Darwin’s Origin of Species, just as physics has progressed far beyond Newton’s Principia. It could be argued that Newton was not a Newtonian in the way some of his followers were, and Darwin was not a Darwinian in the way some of his followers feel. Nevertheless, there are certain features of Darwinism that all modern evolutionists believe: namely, universal common ancestry by unguided material processes, such as natural selection. “Darwin” becomes the face of those beliefs. Our criticisms of “Darwin,” including the cartoons, are not personal attacks on Darwin the man, since he is long dead, but on the worldview by which he made it possible to become (to mutate Richard Dawkins’ statement), an intellectually fool-filled atheist.

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