Tag: evolution

Sunday Science Poem: Darwin and Happy Endings

Wisława Szymborska’s “Consolation” (2002)
henri_rousseau_-_fight_between_a_tiger_and_a_buffaloEvolution has always been more controversial socially than scientifically. After Darwin published the Origin, the idea that all species descended from common ancestors was quickly accepted by most biologists (though his proposed mechanism of evolution, natural selection, remained controversial until the 20th century). Socially, however, evolution was and remains difficult for many people to swallow. The literalist beliefs of religious fundamentalists of course conflict with evolution. But even among those who don’t have a particular religious axe to grind, discomfort is not uncommon. Evolution in practice is brutal: we posses our unique adaptations – our brains, our opposable thumbs, our ability to talk, to socialize, to feel, see, and touch – thanks to the selective death of billions of organism over eons.

In her hilarious poem “Consolation”, the late Nobel-winning Polish poet Wisława Szymborska ironically contrasts the brutality of the real world in which evolution plays out, with the romantic world we construct for ourselves. She portrays Darwin, the great thinker who first grasped the harsh reality of evolution, as someone who escapes by reading novels with only happy endings.
Consolation

Darwin.
Supposedly for relaxation he read novels.
But he had a requirement:
they couldn't end sadly.
If he happened on one,
he flung it furiously in the fire.

True or not –
I gladly believe it.

Roaming in his mind over so many times and places
looking back on all the extinct species,
such triumphs of strong over weak,
so many tests of survival,
sooner or later all in vain,
that at least in fiction
and its micro-scale
he had a right to expect a happy ending.

And so necessarily: sunrays behind a cloud,
lovers together again, kin reconciled,
doubts dissolved, faith rewarded,
fortunes recovered, treasures dug up,
neighbors regret their mulishness,
good names restored, greed put to shame,
old maids married to respectable ministers,
schemers expelled to the other hemisphere,
forgers of documents cast down the stairs,
seducers of virgins hurrying to altars
orphans taken in, widows embraced,
pride humbled, wounds mended,
prodigal sons invited to the table,
the cup of bitterness poured into the sea,
tissues wet with tears of reconciliation,
universal singing and music-making,
and the puppy Fido,
lost already in the first chapter,
let him run home again
and bark joyfully.

Translation from the Polish by Michael A. White (2016)
Image: “Fight Between a Tiger and a Buffalo”, Henri Rousseau (1908), via Wikimedia Commons.

Impossible

xkcd by Randall Munroe (CC BY-NC 2.5)
xkcd by Randall Munroe (CC BY-NC 2.5)

Turns out biology is hard because biology is hard.

Science for the People: Animal Weapons

sftpThis week, Science for the People is talking about weapons: both the ones that evolve in nature, and those created by humanity. We’ll talk about the arms races that spur the development of horns and claws, warships and nuclear weapons, with Doug Emlen, Professor in the Division of Biological Sciences at the University of Montana, and author of Animal Weapons: The Evolution of Battle.

*Josh provides research help to Science for the People and is, therefore, completely biased.

Where Does the Genetic Code Come From? An Interview with Dr. Charles Carter, Part II

“Translating the genetic code is the nexus connecting pre-biotic chemistry to biology.” — Dr. Charles Carter

Last week we discussed the general question of how the genetic code evolved, and noted that the idea of the code as merely a frozen accident — an almost completely arbitrary key/value pairing of codons and amino acids — is not consistent with the evidence that has been amassed over the past three decades. Instead, there are deeper patterns in the code that go beyond the obvious redundancy of synonymous codons. These patterns give us important clues about the evolutionary steps that led to the genetic code that was present in the last universal common ancestor of all present-day life.

Charles Carter and his colleague Richard Wolfenden at the University of North Carolina Chapel Hill recently authored two papers that suggest the genetic code evolved in two key stages, and that those two stages are reflected in two codes present in the acceptor stem and anti-codon of tRNAs.

In the first part of my interview with Dr. Carter, he reviewed some of previous work in this field. In the present installment, he comments on the important results that came out of his two recent studies with Dr. Wolfenden. But before we continue with the interview, let’s review the main findings of the papers.

The key result is that there is a strong relationship between the nucleotide sequence of tRNAs, specifically in the acceptor stem and the anti-codon, and the physical properties of the amino acids with which those tRNAs are charged. In other words, tRNAs do more than merely code for the identity of amino acids. There is also a relationship between tRNA sequence and the physical role performed by the associated amino acids in folded protein structures. This suggests that, as Dr. Carter summarized it, “Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene.” Perhaps it also suggests – this is my possibly unfounded speculation – that today’s genetic code was preceded by a more coarse-grained code that specified sets of amino acids according to their physical functions, rather than their specific identity. Continue reading “Where Does the Genetic Code Come From? An Interview with Dr. Charles Carter, Part II”

Where Does the Genetic Code Come From? An Interview with Dr. Charles Carter, Part I.

“I’m more and more inclined to think that we can actually penetrate at least some of the steps by which nature invented the code.” — Charles Carter

The genetic code is one of biology’s few universals*, but rather than being the result of some deep underlying logic, it’s often said to be a “frozen accident” — the outcome of evolutionary chance, something that easily could have turned out another way. This idea, though it’s often repeated, has been challenged for decades. The accumulated evidence shows that the genetic code isn’t as arbitrary as we might naively think. And more importantly, this evidence also offers some tantalizing clues to how the genetic code came to be.

This origins of the genetic code has long been a research focus of University of North Carolina biophysicist Charles Carter, and his UNC enzymologist colleague Richard Wolfenden. They authored a pair of recent papers that suggest behind the genetic code are actually two codes, reflecting key steps in its evolution. Dr. Carter kindly agreed to answer some questions about the papers, which present some interesting results that add to the growing pile of evidence that the genetic code is much less accidental that it may seem.

These papers deal with the machinery that implements the genetic code. Conceptually the code is simple: it is a set of dictionary entries or key-value pairs mapping codons to amino acids. But to make this mapping happen physically, you need, as Francis Crick correctly hypothesized back in 1958, an adapter. That adapter, as most of our readers know, is tRNA, a nucleic acid molecule that is “charged” with an amino acid.

But the existence of tRNAs creates another coding problem: how does the right tRNA get paired with the correct amino acid? The answer to this question is at the heart of the origin of the genetic code, and it’s the subject of these two recent papers. More about this story, as well as the first part of my interview with Dr. Carter, is below the fold. Continue reading “Where Does the Genetic Code Come From? An Interview with Dr. Charles Carter, Part I.”