Sunday, October 20, 2019

New genes sometimes emerge in the course of evolution, 'de novo' [culture does something similar]

Adam Levy, How evolution builds genes from scratch, Nature, 16 October 2019:
In the depths of winter, water temperatures in the ice-covered Arctic Ocean can sink below zero. That’s cold enough to freeze many fish, but the conditions don’t trouble the cod. A protein in its blood and tissues binds to tiny ice crystals and stops them from growing.

Where codfish got this talent was a puzzle that evolutionary biologist Helle Tessand Baalsrud wanted to solve. She and her team at the University of Oslo searched the genomes of the Atlantic cod (Gadus morhua) and several of its closest relatives, thinking they would track down the cousins of the antifreeze gene. None showed up. Baalsrud, who at the time was a new parent, worried that her lack of sleep was causing her to miss something obvious.

But then she stumbled on studies suggesting that genes do not always evolve from existing ones, as biologists long supposed. Instead, some are fashioned from desolate stretches of the genome that do not code for any functional molecules. When she looked back at the fish genomes, she saw hints this might be the case: the antifreeze protein — essential to the cod’s survival — had seemingly been built from scratch.

The cod is in good company. In the past five years, researchers have found numerous signs of these newly minted ‘de novo’ genes in every lineage they have surveyed. These include model organisms such as fruit flies and mice, important crop plants and humans; some of the genes are expressed in brain and testicular tissue, others in various cancers.

De novo genes are even prompting a rethink of some portions of evolutionary theory. Conventional wisdom was that new genes tended to arise when existing ones are accidentally duplicated, blended with others or broken up, but some researchers now think that de novo genes could be quite common: some studies suggest at least one-tenth of genes could be made in this way; others estimate that more genes could emerge de novo than from gene duplication. Their existence blurs the boundaries of what constitutes a gene, revealing that the starting material for some new genes is non-coding DNA [...]

But genomes contain much more than just genes: in fact, only a few per cent of the human genome, for example, actually encodes genes. Alongside are substantial stretches of DNA — often labelled ‘junk DNA’ — that seem to lack any function. Some of these stretches share features with protein-coding genes without actually being genes themselves: for instance, they are littered with three-letter codons that could, in theory, tell the cell to translate the code into a protein.

It wasn’t until the twenty-first century that scientists began to see hints that non-coding sections of DNA could lead to new functional codes for proteins. [...]
It turns out that the nature of genes has become problematic:
Studying de novo genes turns out to be part genetics, part thought experiment. “Why is our field so difficult?” asks Anne-Ruxandra Carvunis at the University of Pittsburgh in Pennsylvania. “It is because of philosophical issues.” At its heart is a question that Carvunis has been asking for a decade: what is a gene?

A gene is commonly defined as a DNA or RNA sequence that codes for a functional molecule. The yeast genome, however, has hundreds of thousands of sequences, known as open reading frames (ORFs), that could theoretically be translated into proteins, but that geneticists assumed were either too short or looked too different from those in closely related organisms to have a probable function.

When Carvunis studied yeast ORFs for her PhD, she began to suspect that not all of these sections were lying dormant. In a study6 published in 2012, she looked at whether these ORFs were being transcribed into RNA and translated into proteins — and, just like genes, many of them were — although it was unclear whether the proteins were useful to the yeast, or whether they were translated at high enough levels to serve a function. “So what is a gene? I don’t know,” Carvunis says. What she thinks she has found, though, is “raw material — a reservoir — for evolution”.
I made a similar argument in a recent paper about cultural evolution where, for reasons I explain in the paper, I have adopted the term "coordinator" (as opposed to Dawkins' "meme") for the cultural analog of the gene:
What’s interesting, moreover, is the possibility that a feature that doesn’t have coordinator status at some time may acquire it at some later date. Thus, the tonal trajectory Gershwin used in “I Got Rhythm” didn’t acquire coordinator status immediately. The tune was written for a Broadway musical, Girl Crazy, which opened on 14 October 1930 and was sung by Ethel Merman. The orchestra was led by cornetist Red Nichols and included such eventual jazz luminaries as Benny Goodman, Glenn Miller, Jack Teagarden, Jimmy Dorsey, and Gene Krupa. A bit later in the year Nichols recorded the tune with his own band, the Five Pennies, and with Dick Robertson singing the vocal. It rose to fifth place in the charts. A Louis Armstrong version rose to 17 in 1932.

Had Rhythm Changes acquired coordinator status by that point? I don’t know the relevant musical history well enough to answer that question, though I suspect not. One thing we need to know is when derivative tunes began appearing. Lester Young recorded “Shoe Shine Boy” with Count Basie in 1936 and wrote his own “Lester Leaps In” in 1940, the same year Duke Ellington recorded “Cotton Tail.” These tunes are all based on Rhythm Changes. The existence of “Shoe Shine Boy” in the mid-30s is evidence that at least some musicians had abstracted the chord changes from the whole tune. Does that mean they’d attained coordinator status? I’d say that’s a matter of definition. Obviously more abstracting had been done by 1940. Did audiences routinely recognize the lineage of these derived tunes? I don’t know. Is the question relevant to the issue of coordinator status? Probably not, but I’ve not thought the matter through.

By the mid 1940s, however, enough beboppers had written their own tunes to Rhythm Changes, Charlie Parker in particular, that we can say Rhythm Changes had assumed coordinator status at least within the bebop style, if not within jazz or swing more generally.

This thumbnail analysis suggests that musical coordinators don’t have special formal features. You can’t identify something as a musical coordinator by hearing it. You can only identify it as a coordinator by considering the body of performances in which it functions. Rhythm Changes is the same entity in 1945 as it was in 1930; it has the same characteristics. But it plays a function in the musical world of 1945 that is different from the one it played in 1930. One might even think of this as an example of emergence involving a population of thousands of people interacting with one another through tens of thousands of performances. Some relatively few elements are selected from performances here and there and incorporated into other performances. Those are coordinators.[1]
I then go on to compare my concept of the cultural coordinator with the concept of a dene, a term Evelyn Fox Keller and David Harel coined for the much over-worked (& thus ambiguous) gene[2].


[1] William Benzon, “Rhythm Changes” – Notes on Some Genetic Elements in Musical Culture. Signata 6, Annales des Sémiotiques /Annals of Semiotics: Sémiotique de la musique / Music and Meaning. Per Aage Brandt and José Roberto do Carmo Jr., eds. Presses Universitaires Liège, 2015, pp. 271-285,

[2] E. Fox Keller and D. Harel, Beyond the Gene, PLoS ONE 2(11), 2007: e1231. doi:10.1371/journal.pone.0001231.

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