The University of Texas at Arlington: Secrets to “Extreme Adaptation” Found in Burmese Python Genome, UT Arlington Researchers Say

Python said to relive its evolutionary past with every bite.

Does the Burmese python showcase the evolution of snakes every time it swallows an enormous victim? Biologists reporting in the Proceedings of the National Academy of Sciences believe they have discovered that the genetic underpinnings of the python’s ability to accommodate its dinner disclose the secrets of its evolutionary past. Snakes, they suggest, were on the evolutionary fast track, and the huge anatomical and metabolic post-meal adaptations of the python recapitulate that evolutionary history.

KaaKaa, created by author Rudyard Kipling and animated in Disney’s feature film The Jungle Book, is an Indian rock python. Kaa is the same species (Python molurus )as the Burmese python (Python molurus bivittatus) but is a somewhat lighter colored variety. How could this tube-shaped animal hope to digest a boy or the even larger panther Bagheera, as he threatens to do? Snakes are able to engulf and digest enormous prey, and the Burmese python is perhaps the most extreme example, even digesting prey equal to its own considerable body mass.1 Geneticists have revealed how coordination of thousands of genes make the temporary anatomic and metabolic transformation to manage huge meals possible for these snakes. Having learned how the snake genome makes all this possible, they speculate that the evolution of snakes must have happened very fast to produce such prodigious physiologic potential. Image: “Kaa” on Disney Wiki

Common Genes For Uncommon Purposes

Vertebrates have many genes in common. Evolutionary geneticists believe a study of their similarities and differences reveals, not only how the genetic code works, but also how snakes evolved the many characteristics that distinguish them from other vertebrates. These unique abilities have made snakes extremely successful predators, prompting fear of snakes to even be considered a stimulus for the evolution of the primate brain. (To learn more see “Did Snakes Shape Our Brains?”)

“One of the fundamental questions of evolutionary biology is how vertebrates with all the same genes display such vastly different characteristics. The Burmese python is a great way to study that because it is so extreme,” says Todd Castoe, lead author of the PNAS paper about Burmese pythons. “We’d like to know how the snake uses genes we all have to do things that no other vertebrates can do.”

The international group of biologists behind the two published studies reports they have sequenced the genomes of the Burmese python (Python molurus bivittatus) and the king cobra (Ophiophagus hannah). They compared the genomes of the two snakes with each other and with those of other vertebrates—amphibians, reptiles, birds, and mammals. Castoe’s team aligned 7,442 snake genes with comparable genes in the other animals. Then, through statistical analysis they identified hundreds of genetic differences. These genes encode many of the proteins that make snakes like Burmese pythons the unique animals that they are. The researchers believe these genetic differences are the result of an unusually large number of evolutionary changes during the presumed evolution of snakes from non-snakes. Pollock says the large number of evolutionary changes “is extremely impressive, and a surprise even to us.”2

Rather than attributing obvious differences between vertebrates to different ways many of the same basic genes are regulated and expressed, Castoe’s study suggests that a number of other factors contribute to the blueprint for the Burmese python’s phenotype. Thousands of genes must be expressed and their protein production coordinated in order for the python to achieve the physiological adaptations to the python’s enormous but episodic meals. And because these genetic distinctions are responsible for the success of snakes, they presume that those genes and groups of genes evolved to produce a snake ancestor and were then retained through positive selection to produce the modern snake.

Physiologic Remodeling Of The Python

One of the most remarkable abilities of snakes is their ability to swallow and digest large prey despite their tubular shape. This process involves far more than unhinging the jaw and stretching the mouth. In order to consume a chicken or a small pig, a python undergoes “physiologic remodeling.” The metabolic rate skyrockets as much as 44 times its resting rate to digest a big meal.1 This is accompanied by a 35 percent (or more) increase in the mass of its heart, liver, small intestine, and kidneys in just 24–48 hours. The python heart ventricular mass increases about 40 percent.1 This enables the snake’s heart to pump 50 percent more blood per beat than at rest.1 Then after dinner is digested the process reverses. The metabolic rate and organs that temporarily doubled in size return to normal. Large constricting snakes like pythons typically fast, sometimes for weeks or months, after such a feast.

“The Burmese python has an amazing physiology. With its genome in hand, we can now explore the many untapped molecular mechanisms it uses to dramatically increase metabolic rate, to shut down acid production, to improve intestinal function, and to rapidly increase the size of its heart, intestine, pancreas, liver and kidneys,” says coauthor Stephen Secor. Pointing out the potential application of these discoveries to medical science, Secor says, “The benefits of these discoveries transcends to the treatment of metabolic diseases, ulcers, intestinal malabsorption, Crohn’s disease, cardiac hypertrophy and the loss of organ performance.”

Comparative Genomics And The Evolution Of Snakes

Comparison of the python and cobra genomes is an example of “comparative systems genomics,” which coauthor David Pollock defines as “the evolutionary analysis of multiple vertebrate genomes to understand how entire systems of interacting genes can evolve from the molecules on up.” Pollock says, “I believe that such studies are going to be fundamental to our ability to understand what the genes in the human genome do, their functional mechanisms, and how and why they came to be structured the way they are.” Professor Pollock’s remarks illustrate the belief that discovering how genes function reveals not only clues about the present-day structure and function of other organisms’ genes but also truths about their evolutionary origins, in this case, the evolution of snakes.

The most dramatic differences in snakes and non-snakes, the researchers noted, were associated with correspondingly dramatic differences in the genomes. The most extreme differences in physical characteristics, for instance, were associated with either duplicate versions3 of multi-gene families—which is primarily associated with venom production (previously discussed in mambas and to be discussed here next week in connection with king cobras)—or the complete absence of other groups of genes, when compared with non-snakes.

Snakes On The Evolutionary Fast Track

The researchers assume that the presence of multiple copies of the same groups of genes is a result of evolutionary mutation over time rather than a designed feature of the genome. Likewise, they assume that “missing” groups of genes—when compared to non-snakes—were lost over deep time through random evolutionary processes and natural selection. And they believe some special features of snakes were lost in their branch of the vertebrate lineage and re-evolved later. Through molecular clock dating, they assign dates and ascribe great speed to these presumed events in the evolution of snakes. They believe that the acquisition of unique characteristics and their underlying genetic blueprints required that snakes evolve faster than other vertebrates.

Does this mean that snakes have an evolutionary fast track that will continue to enable them to evade threats that endanger them? Commenting on that question, Harvard evolutionary biologist Scott Edwards says that such a comparison would be difficult to make because the researchers are talking about adaptations that still took millions of years to evolve. “Whether they're labile enough to resist all the challenges of habitat loss and climate change is unclear,” Edwards says. “It's a different timescale.”2 Thus the unobservable presumptions about the past—namely the idea that snakes evolved from non-snakes and did so over millions of years—cannot be allowed to make predictions about genomic resiliency in the present.

Designed To Digest

The Burmese python is able to match its metabolic rate and the more plastic features of its internal anatomy to meet its physiological needs more dramatically than any other animal or human. (Humans, as we know, can improve their cardiac efficiency with exercise for instance, but we cannot approach the potential of the python.) These abilities, in addition to the other unique features of snakes’ bodies and senses, equip snakes for life in this post-Fall, sin-cursed world “red in tooth and claw.”4 (We do not know what snakes ate in their original vegetarian state before sin entered the world.) Studies comparing python and cobra genomes and those of other vertebrates have helped determine the genetic features that enable this “physiologic remodeling” and other snake abilities. But nothing about the studies demonstrates the evolution of snakes from non-snakes.

Molecular geneticist Dr. Georgia Purdom of Answers in Genesis explains how the scientists here have leapt from great discoveries to insupportable speculation:

The Burmese python and other snakes have the amazing capability of changing morphologically and physiologically in order to be able to digest large prey. Studies to determine the genome sequence of the Burmese python and king cobra have revealed which genes are responsible for these types of changes. The scientists observed that the phenotypic changes (observable traits) in the snakes were usually due to a change in the expression of these genes. This is an example of good observational science. However, the scientists went one step further into the realm of historical science making the claim that because many mammals also have similar genes that these have been “positively selected” for in the snake evolutionary lineages. While the similarities in genes are observable and real, the explanation for how those similarities came to exist is dependent on the scientists’ worldview—common ancestor or common Designer?

Common Designs and Variations

Vertebrates share certain anatomical designs that they all need. Naturally they also have many similar genes to encode the development of these similar features. Common designs are exactly what we would expect from a Common Designer, our Creator. Furthermore, the defense and attack structures that have enabled snakes to survive in the world of sin and death that ensued after Adam sinned are variations that have occurred within created kinds. Assumptions that the genetic features that make snakes different from non-snakes represent alterations to the genome of ancestral non-snakes are pure speculation. Defining the genetic differences between snakes and non-snakes is not evidence that snakes evolved quickly but only an indication that they are uniquely designed.

Nothing about the unique abilities and anatomy of snakes demonstrates that they evolved from some sort of non-snake. Variations within the genomes of snakes have—like variations in the genomes of other sort of animals—occurred within created kinds. For instance, it appears that the genes that encode the production of certain snake toxins are the same genes that produce various necessary nonpoison-related substances in the snakes’ bodies.5 The current study of the king cobra confirmed this is true in the cobra, the venom being a product of genes that have benign functions elsewhere in the snake’s body.6 Naturally, in a world of violence the fittest survive and the less fit may be eaten, so those snakes with variations that enable them to swallow prey overpowered by either venom or constriction would have a survival advantage. But there is no evidence that those advantageous features arose when some sort of non-snake acquired new genetic information or got rid of some information it already had.

And Don’t Miss . . .

  • This past week we covered two stories regarding human origins: supposed subhuman predecessors and refused human ancestors, and, what else, martian water?
  • Continuing an almost-Eden theme this coming week, we’ll find out more about cobras and their venom and, while we won’t be sewing the leaves together, we will be pondering which came first: the fig or the fig wasp? And who knows what else will be in the News?

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Footnotes

  1. news.nationalgeographic.com/news/2005/03/0302_050302_python.html Back (1) Back (2) Back (3) Back (4)
  2. www.newscientist.com/article/dn24684-snakes-outpacing-other-vertebrates-in-race-to-evolve.html Back (1) Back (2)
  3. Sometimes in biology, genetic duplications do occur and produce variations, but those variations occur within created kinds of organisms. Furthermore, actual duplications do not produce new genetic information of the type necessary for molecules-to-man evolution, just more copies of the same information. Back
  4. Nature did not become “red in tooth and claw” until the curse of death was brought into the world by man’s rebellion against God. This phrase comes to us through the poetry of Alfred Lord Tennyson who used it in his elegy In Memoriam A. H. H., 1850 to describe the apparent conflict between our loving God and the suffering seen in the world around us. Canto 56 describes the man
    Who trusted God was love indeed
    And love Creation’s final law
    Tho’ Nature, red in tooth and claw
    With ravine, shriek’d against his creed.
    The Bible makes it clear that God created the world “very good” (Genesis 1:31), that man’s sin brought the curse of suffering (Romans 8:20–24) and death (Romans 5:12) into the world, and that the love of God through Jesus Christ is the solution (Romans 5:14–21). Back
  5. This discovery of venomous versions of physiologically active molecules and their genetic basis is not confined to snakes but is also found in lizards, even those not commonly thought of as venomous. Furthermore, non-venomous snakes possess nontoxic versions of these toxic molecules. See Mamba Magic and watch for an upcoming News to Know about how this works in the king cobra. Back
  6. phys.org/news/2013-12-rapid-evolution-cobra-venom.html Back