The significance of fitness tradeoffs and compensatory mutations in the evolution of infectious disease

The last couple of decades have seen medical science infused with evolutionary reasoning. This has affected such disparate fields as vaccine design and medical genomics­­[1]. In this post, I will focus on the significance of compensatory mutations and fitness tradeoffs to understanding the evolution of infectious disease.

The imperfection of organisms is often cited as evidence for evolution. This imperfection is obvious from our genomes, which are littered with history – a “genetic book of the dead,” as Richard Dawkins put it[2]. However, even taking the historical explanations of those well-known features into account, organisms are still not ‘perfect,’ and they cannot be. This is because species must compromise, so to speak, when it comes to what traits they will excel in. On the fitness landscape, it is impractical for them to “climb every mountain”[3]. As a result, natural selection leads to specialization as tradeoffs are made between traits. These are known as “fitness tradeoffs.”

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The virtues of science: skepticism and excitement over faster-than-light physics

On this whole ‘faster-than-light’ issue out of CERN, it’s awesome to consider how much proper scientific skepticism is being brought to bear on results from such an incredibly precise and expensive set of instruments, and all because a neutrino traveled a few dozen nanoseconds faster than current physics would predict. Although the results passed the scrutiny of leading European physicists, other researchers are still expecting the results to be replicated before they will “give up on Einstein,” as the choice has been leveled.

If the observations in question are indeed confirmed, it will be extremely exciting! As far as I know, there is no clear consensus on how the aberrant results should then be interpreted. Nevertheless, this whole kerfuffle seems to exemplify the balance Carl Sagan extolled between two key personality traits of the scientist: openness and skepticism.

Before I continue, let me summarize the current situation in particle physics as best I know: A fundamental physical law may have been violated. The raw data came out of state-of-the-art machinery, and were observed by scores of the world’s top experimental physicists before being presented. Because of the extraordinary nature of these researchers’ claims, other scientists are hesitant to accept them prior to their being replicated independently.

And now a summary of where religion finds itself: Countless physical laws may have been violated, including the speed of light, the laws of buoyancy (2 Kings 6:1-7), and Newton’s laws of gravitation (Joshua 10:13). Some have even suggested that our whole understanding of the death process may require a complete overhaul (John 20). There is no quantitative data to check (and don’t even think about trying to replicate anything), but at least one ancient text is known to attest to the aforementioned events. Despite the extraordinary nature of these claims, billions of people express absolute certainty in their accuracy.

“Let there be no doubt that as they are currently practiced, there is no common ground between science and religion… The claims of science rely on experimental verification, while the claims of religions rely on faith. These are irreconcilable approaches to knowing, which ensures an eternity of debate wherever and whenever the two camps meet.” – Neil deGrasse Tyson

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UPDATE: Apparently, OPERA now thinks that the result was caused by “a bad connection between a GPS unit and a computer.” This is complicated by another problem which would have had an opposite effect on the data. They are trying to determine what the net effect would have been.

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http://www.bbc.co.uk/news/science-environment-15017484

http://www.nytimes.com/2011/09/23/science/23speed.html?_r=1&ref=science

http://arxiv.org/abs/1109.4897

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Scientific approach

This is primarily a repost of a guest column I wrote for the University of Maryland’s student newspaper, The Diamondback. It was published back in April following Richard Dawkins’ visit to the campus as a guest of the UMD Society of Inquiry.

Here’s a little background:  Continue reading

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Vestigial Cetacean olfactory receptors

Like most consensus scientific theories, common descent is supported by patterns of evidence rather than by a few disconnected observations. As Stephen Jay Gould said, “We know that the sun is hub of our little corner of the universe, and that ties of genealogy connect all living things on our planet, because these theories assemble and explain so much otherwise disparate and unrelated information—not because Galileo trained his telescope on the moons of Jupiter or because Darwin took a ride on a Galápagos tortoise.”

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Theistic evolution as creationism for academics (part 2)

Biologos, the Templeton-funded brainchild of NIH director Francis Collins, has an article written to defend the fine-tuning argument from the accusation that it is of the God-of-the-gaps form typical of all Creationisms. Their exegesis of the argument begins with the statement, “Unlike a God-of-the-gaps argument, the argument for fine-tuning uses science without divine action to reveal the impeccable precision of our Universe. […] Fine-tuning does not try to draw attention to where science has failed, but rather emphasizes how science has revealed the intricate balance of the universe.” Now reread that passage while substituting the phrase “intelligent design” in place of “fine-tuning” and see how difficult it is to imagine Stephen Meyer writing it. Continue reading

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Theistic evolution as creationism for academics (part 1)

On December 20th 2005, the landmark science education case in Dover, Pennsylvania was settled with the honorable John Jones finding that Intelligent Design (ID) was “not science,” and was unable to “uncouple itself from its creationist, and thus religious, antecedents.”

The key player for the evolution lobby was the National Center for Science Education (NCSE). One of the NCSE’s expert witnesses was Brown University biologist, Ken Miller, who has written extensively on his views regarding Christianity and evolution (most notably in “Finding Darwin’s God”). The fact that Ken Miller is a practicing Catholic seems to have been a key factor in the NCSE’s selection, as it allowed them to decouple evolutionary biology from atheism. (Another witness, a Catholic named Julie Smith, was the parent of a girl who had been labeled an “atheist” for accepting evolution.) Continue reading

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Does science have anything to say about the supernatural?

A good place to start in any productive conversation is to define one’s terms. Carl Sagan said of science, “Science is more than a body of knowledge… It’s a way of thinking; a way of skeptically interrogating the universe.” Science is just a particular species of skeptical inquiry. As the purpose of this post is to investigate the scope of science and whether or not its authority extends to claims of the supernatural, defining what science actually is is of paramount importance. Another similar definition was used by the great paleontologist and author Stephen Jay Gould: “Science is a battery of observational and inferential methods, all directed to the testing of propositions that can, in principle, be definitely proven false.” Curiously, Stephen Jay Gould considered religion to be compatible with his definition of science. In his 1997 book, Rock of Ages: Science and Religion in the Fullness of Life, Gould set out his vision for the relationship between science and religion, known as “Non-Overlapping Magisteria” or “NOMA.” He wrote, “Science tries to document the factual character of the natural world, and to develop theories that coordinate and explain these facts. Religion, on the other hand, operates in the equally important, but utterly different, realm of human purposes, meanings and values–subjects that the factual domain of science might illuminate, but can never resolve.” Today, this idea is commonly phrased as “science and religion are ‘different ways of knowing.’” NOMA is embraced by many theists and atheists who argue for the compatibility of religion and science. This position is commonly known as ‘accommodationism.’ Increasingly, however, religious scientists, progressive theologians and sympathetic secularists seem to be moving away from NOMA and suggesting open interaction between science and religion.

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