Lion cub vs. GoPro

September 28, 2014 • 4:56 pm

Now that we have the GoPro camera (a great invention, whose only downside may be the tendency of people to care more about the video than the experience), we’re going to see a whole lot more video closeups of animals in the wild.  Here’s one by photographer Chris Bray with the following information (among other stuff):

While running one of our five 2-week photo safaris to Kenya in 2014, we attached a GoPro camera to a remote control car and drove it up to a lioness with cubs, stopping at a distance where they still showed no interest, and then jiggled the car around just enough to invoke the cubs curiosity. Two of the three cubs then came over and investigated it for 20min, before growing bored and tired and falling asleep back with mum. Our 8th safari to Kenya, we had off-road permits and filming permits for this national reserve, and two very experienced driver guides, used by Nat Geo, Imax and BBC. See our YouTube channel for other footage like from last year where a lioness carried the GoPro camera away, and an elephant stomped right next to it.

The cub’s attempt to roar at the end is ineffably cute.

And behind the scenes (missing the roar for some reason):

h/t: Merilee, Michael

David Barash on the incompatibility of science and faith

September 28, 2014 • 11:59 am

As I mentioned two posts ago, David Barash, a biologist at the University of Washington who works on animal behavior and evolution, has a post in today’s New York Times, “God, Darwin, and my college biology class.”  It’s basically an argument for the incompatibility of science and religion, and I like it a lot, not the least because I agree with him 100%.

But there’s one thing about his piece that bothers me: Barash’s article is about how he tells his animal behavior class that science and religion are incompatible. In other words, he’s making theological arguments at a public university. But first let’s back up and see what he says.

Barash discovered that a lot of his students aren’t comfortable with evolution because it contravenes their religious beliefs. He thought that, as his course progressed, the facts would win out and the discomfort would dissolve. It didn’t. Therefore, Barash decided to have what he calls “The Talk” with his students, telling them directly how evolution clashes with religion.  In The Talk, he considers and then discards Steve Gould’s NOMA gambit (see two posts back), an argument claiming that science and religion each have important and non-overlapping roles to play, the former in ascertaining facts about the universe, the latter in arbitrating meanings, morals, and values. Barash:

There are a few ways to talk about evolution and religion, I begin. The least controversial is to suggest that they are in fact compatible. Stephen Jay Gould called them “nonoverlapping magisteria,” noma for short, with the former concerned with values and the latter with facts. He and I disagreed on this (in public and, at least once, rather loudly); he claimed I was aggressively forcing a painful and unnecessary choice, while I maintained that in his eagerness to be accommodating, he was misrepresenting both science and religion.

In some ways, Steve has been winning. Noma is the received wisdom in the scientific establishment, including institutions like the National Center for Science Education [NCSE], which has done much heavy lifting when it comes to promoting public understanding and acceptance of evolution. According to this expansive view, God might well have used evolution by natural selection to produce his creation.

. . . So far, so comforting for my students. But here’s the turn: These magisteria are not nearly as nonoverlapping as some of them might wish.

. . . As evolutionary science has progressed, the available space for religious faith has narrowed:

Indeed. As I’ve harped on incessantly, religion makes many existence claims about the real world or the real Universe. That’s one reason why NOMA has been heavily criticized by theologians, who resent being told that they can’t say anything about what exists. (This will all be hashed out in The Albatross.)  And NOMA is indeed the received wisdom by science organizations like the NCSE, the National Academies, and the American Association for the Advancement of Science, which even has a Templeton-funded “Dialogue on Science, Ethics, and Religion program“—something wildly inappropriate for such an organization.

But Barash, to his credit, is no accommodationist, and in The Talk he points out three areas in which science and religion make incompatible claims. (The indented discussion below is my writing, not Barash’s.)

  • The argument from complexity. As we all know, evolution dispelled this most powerful argument for God when Darwin showed that “design-like” features could arise from a purely naturalistic process. This conflicts with creationist religion, though Barash doesn’t mention that many more liberal faiths simply say that evolution happened but God either set it in motion, knew it would happen, directed it toward specific ends (i.e., H. sapiens) or intervened in subtle and undetectable ways.  In this sense the conflict between science and faith can be somewhat resolved, though such theistic accommodationism still requires that we abandon naturalism. If you’re a true naturalist, theistic evolution is still incompatible with science. If you argue that God set up the universe knowing in advance that evolution would occur but didn’t intervene (and that’s claimed by a fair number of believers), then there’s not really any practical incompatibility, for the difference between that and naturalistic evolution is nil.
  • Human exceptionalism.  Barash notes that there is no evidence that humans are special in any supernaturalistic sense: “. . we are perfectly good animals, natural as can be and indistinguishable from the rest of the living world at the level of structure as well as physiological mechanism.” Again, if you think humans were a teleological goal of evolution, requiring God’s planning or intervention, or have souls or a kind of behavior (say, morality) that can’t be explained by naturalistic processes, then yes, human exceptionalism is incompatible with science. If you think, though, that humans were simply an inevitable or likely result of a naturalistic process, the incompatibility is barely discernible.
  • The existence of evil. This, to me, is the most powerful of Barash’s arguments for incompatibility between science and religion. Theists must perforce explain evil—both “moral” evil (humans doing bad things to other humans) and “natural” evil (diseases like childhood cancer, earthquakes, and other stuff that kills innocent people)—as part of God’s plan. There’s no easy way to reconcile these with a loving and all-powerful god, though the entire discipline of theodicy is devoted to the effort. I haven’t yet seen a successful reconciliation, and theists know, deep in their hearts, that the problem remains. But such “evils” are, as Barash explains, easily understandable in a naturalistic universe: they’re an inevitable result of either evolution, physics, or geology.

Barash ends The Talk this way:

I CONCLUDE The Talk by saying that, although they don’t have to discard their religion in order to inform themselves about biology (or even to pass my course), if they insist on retaining and respecting both, they will have to undertake some challenging mental gymnastic routines. And while I respect their beliefs, the entire point of The Talk is to make clear that, at least for this biologist, it is no longer acceptable for science to be the one doing those routines, as Professor Gould and noma have insisted we do.

He’s absolutely correct here, both in highlighting the tortuous arguments of accommodationists and in saying that the brief of scientists is not to reconcile religion with science. We shouldn’t be doing theology.

But in fact, and this is my beef (a small one, like a filet mignon): Barash may not be accomodating science with religion, but he’s still discussing their relationship, and his view of their incompatibility—in a science class. I wouldn’t do that, especially in a public university. One could even make the argument that he’s skirting the First Amendment here, mixing government (a state university) and religion. After all, if Eric Hedin can’t tell his students in a Ball State University science class that biology and cosmology are compatible with belief in God, why is it okay to say that they’re incompatible with God?

While I do touch lightly on the religion/science issue in class when discussing the historical evidence for evolution—by saying that Darwin’s arguments won the day because the facts he adduced did not comport with the creationist views of the day—that’s about as far as I’ll go. It is my job to teach science, not to discuss the religious beliefs of my students, to show how science opposes them, or to try to tell them they can have Darwin and Jesus, too.  I am not there to dispel any discomfort that arises when some students realize that religion doesn’t sit so nicely with evolution. I am there to teach them the latest ideas and facts about evolution, period. If students ask me, “Well, Professor Coyne, how do you think that relates to religion?”, I’ll tell them that if they want to discuss it, I’ll be glad to make an appointment to talk in my office.

In other words, while I think Barash is 100% right, and that religion and science are indeed incompatible in critical ways (see The Albatross), I think he needs to knock off giving The Talk. It is not science, but a form of theology or philosophy.  By all means let him trumpet his views in The New York Times, as he did so well, or any other similar venue. I admire him for standing up to public opinion and accommodationist organizations like the NCSE. But I’m not so sure that this stuff belongs in a science class. Nevertheless, if Barash insists on giving The Talk, he might as well make the other big refutation of NOMA: religion isn’t the only repository for thinking about meanings, morals and values. For surely the students have heard about something called “philosophy.”

h/t: Tom C. and many other readers who called Barash’s piece to my attention.

 

Two videos on Islam: Bill Maher and Hitchens

September 28, 2014 • 10:08 am

Here are two videos that deal at least partly with the claim that violent Islamic radicals aren’t “really Muslim.”

The first is a new video from Bill Maher’s show taking as a starting point the Pennsylvania kid recently arrested for posting with a Jesus statue in a compromising position (see my post here). What I didn’t realize, but Maher did, was that although penalizing the kid for that act was wrong, doing something similar in a Muslim country would inevitably result in your death. Maher then decries cultural relativism and adds a few harsh words for the Yale atheists who objected to Ayaan Hirsi Ali’s talk at their school.  I have to say, I’m a big fan of Maher when he talks about religion, for he speaks the truth.

And here’s an old clip of Christopher Hitchens on Islam and the Caliphate. At 5 minutes in, he takes up the claim that jihadis and extremist Muslims don’t represent the “real Islam.” Clearly very ill, having lost his hair to chemotherapy, he had lost none of his fire.

h/t: John, Malgorzata

My take on NOMA: an old book review

September 28, 2014 • 8:36 am

Several readers called my attention to a nice essay by biologist David Barash in today’s New York Times, an essay whose theme is the incompatibility of science and religion. In it, Barash takes out after Steve Gould’s accommodationist stance of Non-overlapping Magisteria, or NOMA, adumbrated in detail in Gould’s 1999 book Rocks of Ages.

When that book came out, the Times Literary Supplement asked me to review it, and I obliged them. When I read David’s piece I remembered that review,  but when I tried to find it online I discovered that it has vanished. One can’t even see it in our library subscription to the TLS archives, as it’s cut off on the scanned page. Therefore, it has disappeared from the universe, perhaps remaining only on microfilm or in those libraries that have paper copies of the TLS.

As I want to discuss Barash’s essay later today, I thought that first I’d simply republish the essay I sent to the TLS. I believe a few words might have been changed before publication, or some sentences omitted by the editor, but my criticisms of NOMA haven’t much changed.

I also see in the draft below the beginning of my battle against accommodationism, for when I wrote this in 2000 I was not much concerned with the relationship between science and religion. And I was less “strident” then, for I no longer think that it’s useful to have a “dialogue” between science and religion. Now, of course, accommodationism occupies a great deal of my time, and a discussion of NOMA will be part of The Albatross.

This, then, is a draft of what was published in the Times Literary Supplement on June 9, 2000 (pp. 28-29). It is not word-for-word identical to that article, but I want the essay deposited where I (and others) can find it easily. That would be here. Reading the first paragraph, I find that I, like Gould, have entered philosopause.

Is NOMA a no man’s land? 

 by Jerry A. Coyne

Rocks of Ages: Science and Religion in the Fullness of Life
by Stephen Jay Gould
1999; The Library of Contemporary Thought; Ballantine Publishing Group
241 pages; $ 18.95 (US)

Like everyone else, scientists have midlife crises, but ours do not generally involve red sports cars. Rather, we are seized by the urge to forsake our daily tasks and embrace one or another of the great metaphysical problems that have engrossed philosophers and theologians throughout the ages. The result is often a big book dealing with the human condition. So common is this tendency that it has acquired a name: philosopause. Unfortunately, philosopausal tomes are often amateurish, fated to become the dustiest items on the library shelves. After all, a lifetime spent driving a taxi is probably better preparation for tackling the great questions of humanity than is a lifetime spent peering through the microscope.

If anyone could buck this trend, it would be Stephen Jay Gould, the polymathic paleontologist famous for his popular writing about evolution. In his new book, Gould sets aside his usual topics and turns to one that older scientists can rarely resist: the relationship between science and religion. Sadly, I must report that Gould has foundered on Rocks of Ages, adding little to the work of those who have already addressed this perennial problem. Well intentioned though it is, and often couched in Gould’s characteristically lively prose, this slim volume is as slight in scholarship as it is in size. Ultimately, Rocks of Ages is a repository of sound ideas that are not new, and new ideas that are not sound.

Gould begins by observing that both science and religion sometimes overstep their boundaries, with religion in effect making scientifically testable statements about nature, and scientists inferring ethical or social beliefs from nature. An obvious example of the former is American creationism, recently notorious for its successful crusade to downgrade evolution in the Kansas school curriculum.   Scientists, on the other hand—particularly those adhering to “evolutionary psychology”—sometimes try to base moral or social precepts on our evolutionary history.

Using examples drawn from Darwin, Galileo, Cardinal Newman, and other scientists and theologians, Gould shows that these territorial violations have occurred throughout history. His purpose is to prevent their recurrence by proposing a principle of reconciliation called “Non-Overlapping Magisteria,” which he saddles with the awkward acronym of “NOMA.” This principle leaves both religion and science with important but distinct tasks:

“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.” [p. 4)]

Gould grants these magisteria equal status and asserts that we must accept the values of both. He calls for intense dialogue between religion and science, not to unite them, but to encourage greater harmony and mutual understanding.

This is a worthwhile suggestion, and is nearly as old as science and religion themselves. But Gould goes further and runs into trouble. First, he never defines “religion.” Although what we think of as “science” is fairly well delimited, “religion” can mean many things, including religious institutions themselves, church doctrine, beliefs of prominent theologians, practices of ordinary religious people, and so on. Gould’s failure to clarify this key term in his argument is disturbing in itself, but causes terminal confusion when combined with the second problem: his unwillingness to stick to a single notion of NOMA. Instead, he offers several versions that are used interchangeably.

He first conceives of NOMA as a utopian vision. In an ideal world, religion and science would logically form harmonious, nonoverlapping realms of activity. If this was all Gould were saying, we could accept it as a pleasing platitude and pass on. However, he believes that this utopia must be realized:   science and religion should be structured to allow peaceful coexistence. He therefore redefines NOMA as “the potential harmony through difference of science and religion, both properly conceived and limited.” [p. 43]. The word “proper” is the red flag here. Imagining “proper” science is easy—the vast majority of scientists are happy to pursue their calling as an entirely materialistic enterprise. But what is “proper” religion? It seems to be religion that does not overlap science.

Unfortunately, real religion is frequently and stubbornly improper, for the religious beliefs of many people are in absolute conflict with the findings of science. Evolution provides the most prominent example—not only fundamentalists, but also many mainstream Protestants and Catholics, Mormons, Jehovah’s Witnesses, Orthodox Jews, Native Americans, Scientologists, Muslims, and Hindus, subscribe to creationist narratives. Beliefs about human origin are not the only religious violations of NOMA. Christian Scientists, for example, entertain a spiritual theory of disease, and many Hindus share Glenn Hoddle’s belief that disability is a sign of past spiritual transgression.   The fact is that religions worldwide often stray into scientific territory, sometimes with tragic results. Who knows how many have died because a bacillus is misdiagnosed as spiritual malaise?

Gould apparently limits religion to the views of liberal Western theologians, many of them agnostics in all but name. But of course there is far more to religion than the opinions of scholars. Religion encompasses beliefs that help people make sense of personal reality, regardless of whether these beliefs overlap with science. By casting himself as the arbiter of “proper” religion, Gould simply redefines terms to satisfy his utopian vision. Thus NOMA undergoes another metamorphosis—from an achievable utopia to an actual description of reality. That is, the apparent clashes between religion and science create genuine discord, but in reality involve neither science nor religion. Referring to those who oppose religions with naturalistic tenets, for example, Gould notes:

“If these colleagues wish to fight superstition, irrationalism, philistinism, ignorance, dogma, and a host of other insults to the human intellect (often politically converted into dangerous tools of murder and oppression as well), then God bless them—but don’t call this enemy “religion.” [pp. 209-210]

Improper intrusions of scientists into meaning and morals are fairly rare, and nearly all of us decry or rebuff them. But many religious people will surely be insulted to hear that NOMA requires them to abandon essential parts of their faith. Nevertheless, that seems to be Gould’s prescription.

Gould’s example of an illusory violation of NOMA is American evangelical Christianity and its belligerent creationism.   To maintain the reality of NOMA, he contends that creationism is neither proper religion nor even an outgrowth of religion (“Religion just can’t be equated with Genesis literalism. . .” [p. 209]). To support this view, he first argues that creationists form only a vocal minority of American believers and are nearly absent elsewhere. There are indeed relatively few creationists who try to sneak their misguided “science” into public schools; yet surveys consistently show that nearly 50% of Americans believe that humans were directly created by God within the last 10,000 years, and 40% think that creationism should replace evolution in the biology classroom. Without the support of this silent plurality, creationists would be powerless. Gould also demotes creationism by noting that its opponents include “the great majority of professional clergy and religious scholars.” [p. 129] Again, “religion” is construed as the views of intellectual theologians. Finally, he maintains that creationism is actually a sociopolitical movement having nothing to do with real religion. Many of us who have fought creationism would disagree. Indeed, so would creationists themselves, who sincerely believe that teaching evolution undermines Biblical authority, morality, and the spiritual meaning of life. But Gould is right to recognise that fundamentalist views have sociopolitical repercussions. In a speech that would seem surreal anywhere but in the United States, Congressman Tom DeLay pointed an accusing finger at Darwin after the Littleton, Colorado school shootings: “our school systems teach the children that they are nothing but glorified apes who have evolutionized out of some primordial soup of mud.”

Questionable analyses similarly characterize other arguments given by Gould. I limit myself to one example: his claim that religion is (and should be) the main source of morality. This assertion ignores an intense debate about the wellsprings of ethical belief. Does religion directly create moral views, or does it only codify and buttress morals taken from secular sources? There may be some ethical beliefs deriving largely from religion, but in many cases (e.g., the idea of equal rights for women and ethnic minorities, and of the immorality of slavery) one can argue that religious institutions simply embraced earlier changes in secular morality. And I need hardly point out that atheists are not automatically amoral.

Gould senses this difficulty, but again finesses it by redefinition, claiming that all ethics is really religion in disguise.   To distinguish the two, he says, is to “quibble about the labels,” and he decides to “construe as fundamentally religious (literally, binding us together) all moral discourse on principles that might activate the ideal of universal fellowship of people.” [both quotes from p. 62] Well, if this is religion, we can guiltlessly forsake Sunday services for a lively discussion in the pub.

Gould owes his readers more than oversimplified and dubious arguments cobbled together in the name of a good cause. Short though it is, Rocks of Ages is a scrappy affair, seemingly assembled in haste. Three of the chapters are stitched together from his earlier essays, and the seams are readily discernible. The writing, too, is well below Gould’s usual high standards; all too often his pen seems to be on automatic pilot (e.g., “Science and religion interdigitate in patterns of complex fingering, and at every fractal scale of self-similarity.”). [p.65]

In the end, Rocks of Ages is an unsatisfying quarrel about labels and not a substantial contribution to the science/religion debate. And NOMA ultimately becomes an irritating acronym for a utopia that, like all utopias, never did and never will exist. Religion will forever encroach on the territory of science, and scientists will forever wave a flag against creeping obscurantism. As Isaiah realized when prophesying harmony among the beasts, it takes a miracle to reconcile the irreconcilable: “And the lion shall eat straw like the ox.”

 

Guest post: Why the genetic code is not universal

September 28, 2014 • 6:16 am

JAC:

In this post, Matthew—who has considerable expertise in this area—answers a student’s question about the genetic code that was sent to me yesterday. I immediately handed it off to Matthew, who was nice enough to turn the answer into a post.  He is, of course, writing a popular “trade” book abut the genetic code.

In case you’re not sure what is meant by the “genetic code,” it refers to how the sequence of bases in DNA (there are four such bases) are translated into amino acids, the constituents of proteins and the products of most genes.  As Matthew describes below, it’s a “triplet” code: each adjacent group of three DNA bases codes for a single amino acid.  Since there are four bases, there are 64 possible triplets (“codons”) that, in total, code for 20 amino acids. That means that some amino acids are coded for by more than one triplet sequence.

Here is the code based on the RNA translation of the DNA (DNA is transcribed into RNA before it is translated into proteins). For any sequence of three bases, you read the first one down the column to the left, the second across the top, and the third on the column on the right.  So, for example, CAU would be “His,” or the amino acid histidine. “Stop” refers to stop codons: when the process of protein-making in the ribosomes encounters this codon, the translation is stopped and the string of amino acids ends.

It is the near-universality of this code (Matthew’s post is about the rare exceptions) that gives us confidence that modern life traces back to a single ancestor. If there was more than one origin of life, and its descendants independently developed the DNA—>protein system, it would be very unlikely that all modern species would have the same code.

genetic_code

 

by Matthew Cobb

Glendon Wu, an immunology PhD student at the University of Pennsylvania, wrote in with a question. He was in a lecture the other day and learned that mitochondria – small energy-producing structures found in the cells of all multicellular organisms and also some single celled organisms like yeast (this group is called the eukaryotes) – contain a different genetic code to the rest of us. In other words, your cells contain two different versions of the genetic code – one for your human DNA, the other for the DNA in your mitochondria. Glendon was understandably intrigued about this and wanted to know more.

As it happens, I’m just putting the finishing touches to a popular science book about the race to crack the genetic code (Life’s Greatest Secret). Although the historical part finishes in 1967, the final three chapters bring the story up to date, which includes the existence of alternative genetic codes. What follows is an adapted version of part of one of those chapters.

The genetic code is contained in your DNA, and consists of 64 different three-letter ‘words’ (known as triplets or codons), 61 of which code for the 20 amino acids your body uses to make proteins, and three of which say ‘stop’. One codon codes both for an amino acid and for ‘start’.

We have four different kinds of letter (A, C, G and T in our DNA; as the genetic message is expressed, it passes into RNA, where T is replaced by U), so with four possible letters in each of three positions in a codon, we have 4 x 4 x 4 = 64 different codons.

In 1967, the last word of the genetic code was deciphered. Appropriately enough, it was the third stop codon, which reads UGA (for complicated reasons it was nicknamed opal). Everyone working on the genetic code assumed that the code would be universal, that is, all life on Earth would use the same way of representing amino acids in DNA and RNA. As Jacques Monod put it in 1961, ‘what is true for E. coli is true for an elephant’.

In November 1979, a group at Cambridge discovered that human mitochondria, UGA does not encode stop but instead produces an amino acid, tryptophan. Not only is the genetic code is not universal, the same organism can contain two different genetic codes, one in its genomic DNA, the other in its mitochondria.

This fact tells us something fundamental about the history of life on our planet. In 1967, the US biologist Lynn Margulis began arguing that mitochondria were not merely micro-structures within our cells, but were remnants of an independent single-celled organism that had fused with the ancestor of all eukaryotic organisms, billions of years ago, probably as part of a symbiotic relationship. She was not the first to come up with this idea – in the early years of the 20th century both Paul Portier and Ivan Wallin suggested that mitochondria might be symbionts.

Margulis argued that these symbiotic bacteria subsequently found themselves trapped in every one of our cells and lost all their independence, but not their own, separate genome – a tiny ring of DNA about 16,500 bases long (in comparison, the human nuclear genome contains about 3 billion bases). It appears that all mitochondria, in all the eukaryotes on the planet, have a common ancestor that was alive over 1.5 billion years ago.

Similar things happened in plants, which gained their power-generating chloroplast organelles in a similar way. In both cases there are arguments over exactly what kind of microbe fused with what, and above all the speed with which it took place, but most scientists now think that there was a single event, which enabled what was effectively a hybrid organism to grow larger and to acquire the energy required by more complex organisms.

The extremely small nature of the mitochondrial genome, and its peculiar use of codons, can be explained in terms of the history of this symbiotic relationship. The mitochondrial genome codes for very few proteins – most of the other genes were lost before or shortly after fusion with our ancestors or were incorporated into the genomic DNA of the host – so the appearance of new codons in mitochondrial DNA through mutation would not have had an important effect on the symbiont, most of whose needs were provided by the host cell.

Mitochondria are not alone in having an unusual genetic code. In a series of discoveries beginning in 1985 it was found that single-cell ciliates – tiny organisms like Paramecium – show variants of the nuclear genetic code that have appeared several times during their evolution. In some species of ciliate, UAA and UAG code for glutamate rather than stop, with only UGA encoding stop, while in others UGA codes for tryptophan.

In a few rare instances in single-celled organisms without a nucleus, UGA and UAG have even been recoded by natural selection to code for extra amino acids, not normally found in life – selenocysteine and pyrrolosine, respectively. A recent study of 5.6 trillion base pairs of DNA from over 1700 samples of bacteria and bacteriophages isolated from natural environments, including on the human body, revealed that in an important proportion of the sequences, stop codes had been reassigned to code for amino acids, while an investigation of hitherto unstudied microbes revealed that in one group UAG had been reassigned from stop to code for glycine.

More than 15 alternative or non-canonical genetic codes are known to exist, and it can be assumed that more remain to be discovered. The non-canonical codes almost always involve the reassignment of stop codons; this may indicate that there is something about the machinery involved in stop codons that makes them particularly susceptible to change, or it may simply be that as long as the organism can still code stop using another codon, reassigning one stop codon to an amino acid does not cause any important problems.

The exact process by which codon change takes place has been the focus of a great deal of theoretical and experimental research, with a number of hypotheses put forward to explain how variant codes might arise.

The current front-runner is called the codon capture model, and was first put forward in 1987 by Jukes and Osawa. According to this model random effects such as genetic drift can lead to the disappearance of a particular codon in a given genome; similar effects than those that lead to the codon being captured by a tRNA that codes for another amino acid.

A recent experimental study of genetically engineered bacteria in which some codons had been artificially replaced supported this model, and even suggested that reassignment of codons could be advantageous in some circumstances, providing the organism with expanded functions.

The responses of scientists to the non-universality of the genetic code reveal something important about the nature of biology. It was completely unexpected, and went against all the assumptions of all the researchers who had been studying the genetic code, showing that Monod was wrong – what is true for E. coli is not necessarily true for an elephant. But despite this revolution, the basic positions established during the cracking of the genetic code remained intact.

The strict universality of the code was not a law, nor even a requirement. The only requirement is that any divergence from this assumption can be explained within the framework of evolution, and through testable hypotheses about the history of organisms. This has been amply met.

Although the genetic code is not strictly universal, there is no dispute that life as we know it evolved only once, and that we all descend from a population of cells that lived over 3.5 billion years ago, known as the Last Universal Common Ancestor, or LUCA. The alternative codes are what are called derived features – they have appeared after all present life evolved.

The fact that all organisms use amino acids with a left-handed orientation, and the universality of RNA as a way of stringing amino acids together to make a protein are both very strong arguments that support this hypothesis. In 2010 Douglas Theobold calculated that the hypothesis that all life is related ‘is 102,860 times more probable than the closest competing hypothesis.’

The variations in the code that have been discovered can be explained either in terms of the deep evolutionary history of eukaryotes – thereby revealing the thrilling fact that our evolution has hinged on the chance fusion of two cells – or in something recent and local in the life-history of a particular group of organisms, which is what seems to have happened in the case of ciliates.

Hope that answers the question, Glendon!

Readers’ wildlife photos

September 28, 2014 • 5:09 am

I think you guys are getting spoiled with all these high-class photos every day. Perhaps you’re getting jaded? There are several unknown species to identify in the series of photos below.

First, from reader Michael Day:

I’ve attached some pictures I thought you might enjoy. The “main” picture in this set is of a caterpillar–I believe it is either a tomato or tobacco hornworm–in the genus. This particular one is heavily burdened with cocoons from a parasitoid wasp of some type. Interestingly, this caterpillar was on a beautyberry bush in the flower bed by our driveway here in Watkinsville, GA (very close to Athens, GA). I’ve included a photo of our beautyberry bushes in case you aren’t familiar with them (genus Callicarpa). They are a native Georgia plant and are a common in many yards around here.

Can readers identify the caterpillar and the parasitoid? The end of this grisly interaction is shown below.

photo 1

 

photo 2

As a bonus, I’ve included a photo of a black swallowtail butterfly (Papilio polyxenes) on butterfly bush (Buddleja davidii) in our front flower bed.

photo 4

THE AFTERMATH!

(Sept. 17): Earlier this month I sent you an email (“Parasitoids et al.”) that included a picture of a caterpillar (Manduca sp.) with numerous parasitoid wasp cocoons on its back. Well, just today (9/17/14) I noticed the remnants of the parasitized caterpillar were still hanging on the same leaf, and it’s obvious the wasps have emerged.

photo

Here’s a reptile to identify, from non-biologist reader Robert Seidel.

It’s not exactly spot-the-reptile, but pretty close. This one was posing for me during a recent trip to Cyprus. Don’t ask me about species name and binominal, I’m only a geologist (the rock is plagiogranite, cutting the basalt of a sheated dike sequence). Maybe a reader can help.
Well?
Zypern Echse - 2
Sorry about the quality. For compensation, you get a cat [Felis catus]. This belongs to someone from the residential we stayed at, and I was privileged to be her assigned petter each evening. And yes, she really is called Fluffy!
Zypern Fluffy
And from Stephen Barnard in Idaho, a bull elk.
My d*g spooked this bull elk (Cervus canadensis) this morning. [JAC: This was a few days ago.]
Bull elk Barnard
 A mated pair bald eagles (Haliaeetus leucocephalus):
RT9A6140
And a bird. I had lost the notes giving the identification, but some reader correctly identified this as a Marsh Wren (Cistothorus palustris). As Stephen subsequently emailed me when confirming the ID:
They’re common here, but tend to be elusive, hiding in the reeds. I called this one out by  playing its call on my iPhone. I photographed this one from a float tube in the creek. I’ve noticed that birds are less spooky when you approach in a float tube rather than on foot.
RT9A6099

 

Sunday: Hili dialogue

September 28, 2014 • 3:44 am
It’s walnut season in Dobrzyn, and Hili is schooling Cyrus. A note of explanation: when I told Malgorzata that she and Andrzej didn’t “break loose from a different food chain” from that occupied by Hili and Cyrus, but were on a different food chain, she explained:
Basically, you are right but there is a Polish saying “to break loose from a Christmas Tree” which means more or less “to be a bit crazy” or “silly”. In Polish, of course, this connection is obvious and Hili’s answer does not mean that we are on a different food chain but hints that being on the food chain we are on is just crazy and incomprehensible for a cat.
With that out of the way, on to the dialogue:
Cyrus: Why are they collecting all these walnuts?
Hili: Because they broke loose from a different food chain.
P1010712
 
In Polish:
Cyrus: Po co oni zbierają te wszystkie orzechy?
Hili: Bo oni się urwali z innego łańcucha pokarmowego.

Music and love

September 27, 2014 • 2:35 pm

It struck me today, as it does occasionally, that nearly all popular songs have the same theme: love.  New love, enduring love, broken love, all-you-need-is love, and so on.  Yes, the Beach Boys sang about cars and Steely Dan about god knows what, but they’re the exceptions.

Now why is this? The easy answer is that love is perhaps the most intense of human emotions (verging on psychosis when it’s new), and it’s a happy emotion. People want to write about what occupies them, and what pleases people and stirs their emotions. That’s why we don’t get many songs about death (unless it’s the death of a loved one, like “Last Kiss”) or depression. On the other hand, a substantial proportion of songs about love are about lost love, i.e., they’re songs laden with misery.

I’m not conversant enough with the history of music to know whether the proportion of popular songs devoted to love has changed over the centuries, although I know that some nice love songs (i.e., “The Water is Wide”) are at least four centuries old.  Hell, I don’t even know what popular music was in medieval times.

So my question is this: why love? If the apocryphal Martian zoologist were to come to Earth, and discovered that we have music and we have love and other emotions, as well as food and machines and cats, but the zoologist didn’t really know Earth languages, could it predict that most music would be about love? I don’t know Bulgarian (though I’ll soon learn a few phrases for my trip), but I can confidently predict, knowing that Bulgarians fall in love, that most Bulgarian popular songs will also be about love.

p.s. While a lot of poems are about love, too, I’d guess that this is a much smaller proportion than one sees with songs.