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Can New Genes Emerge from Scratch?

genes from scratch

Evolutionary theory must account for millions of new, functional genes by chance. Here are some ideas proposed recently for overcoming the huge probability barrier.

In a news feature in Nature, Adam Levy writes about “How evolution builds genes from scratch.” Already he is personifying evolution as a builder. Alarms should go off, but he continues. “Scientists long assumed that new genes appear when evolution tinkers with old ones.” Is he prepping his readers for a falsification of the Tinkering hypothesis? His next sentence tantalizes, “It turns out that natural selection is much more creative.” So now, evolution (and its effective synonym, natural selection) is a creative builder. This demands careful investigation.

Arctic Antifreeze

Levy’s case in point is a gene for antifreeze proteins found in Atlantic cod that survive freezing waters in the Arctic. He claims the gene just popped into existence.

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. By that point, another researcher had reached a similar conclusion. [Emphasis added.]

So How Did This Happen? 

No observation is complete until confirmed by theory, an old reversal of logic goes. Levy goes on to list other candidates for de novo genes throughout the living world. Evolutionists must have missed how simple it is to make new functional genes.

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. 

Genes devolve, he agrees, but sometimes they might innovate, too. If they can arise from scratch by repurposing noncoding DNA, Levy conjectures, this blurs the boundary of what a gene is. He quotes a Chinese geneticist remarking, “The ability of organisms to acquire new genes in this way is testament to evolution’s ‘plasticity to make something seemingly impossible, possible.’” Does this mean it’s time to close up shop at Discovery Institute? The quote harks back to George Wald’s faith that “Given enough time, the impossible becomes possible, the possible probable, and the probable virtually certain.” Perceptive readers should want more evidence before swallowing this new claim of Darwinism’s miraculous powers.

Lest anyone get too hopeful, Levy backpedals a bit:

But researchers have yet to work out how to definitively identify a gene as being de novo, and questions still remain over exactly how — and how often — they are born. Scientists also wonder why evolution would bother making genes from scratch when so much gene-ready material already exists. Such basic questions are a sign of how young the field is. “You don’t have to go back that many years before de novo gene evolution was dismissed,” Baalsrud says.

The basic idea is that “Genes can evolve from non-coding portions of DNA by gaining transcriptions and codons, in either order.” At first, such “proto-genes” might be dysfunctional or disordered, the caption reads in an infographic. But then, if the “proto-gene” gets transcribed, or acquires more codons, selective pressures might refine it into a working gene. In Levy’s imagination, the genome is littered with “junk DNA” just waiting to get its time in the sunshine.

This hypothesis is highly controversial, Levy admits. Given the vastness of sequence space and the tiny portion that is functional, it also seems overwhelmingly improbable, as protein chemist Douglas Axe has shown in his research. Noteworthy in Levy’s article are the frequent hedging words like could and might.

But what of all that noncoding DNA? A design hypothesis that Levy and his protagonists refuse to consider is that the genome has a backup system. What appear to be “junk” sequences flanked by open reading frames (ORFs) might instead be backups of functional proteins socked away for environmental contingencies, hidden by some kind of encryption system. It deserves consideration.

Accentuate the Positive, Eliminate the Negative

Another paper shows how to turn a liability into an asset. McClune et al., writing in Nature, use the vastness of sequence space to propose a different evolutionary hypothesis for de novo genes. Basically, they posit that since orthogonal sequences are unlikely to interfere with existing genes, evolution has a vast playground for inventing new genes.

These results indicate that sequence space is not densely occupied. The relative sparsity of paralogues in sequence space suggests that new insulated pathways can arise easily during evolution, or be designed de novo. We demonstrate the latter by engineering a signalling pathway in E. coli that responds to a plant cytokinin, without crosstalk to extant pathways.

In the lab, they intelligently engineered a signaling pathway, using their minds. Does this prove nature can do it by chance? The absurd conclusion comes from their belligerent faith in the power of natural selection to engineer a functional machine on cue, whenever a cell has a need. This is really quite unbelievable; “sequence space is vast and nature may not have fully occupied or explored it,” they say. Now nature is an explorer! It seeks to occupy, like some pioneer in the wild west wishing to build new towns. 

A Darwinian Twist

The authors mention probability, but with a Darwinian twist:

To assess how crowded paralogues are in sequence space, we sought to engineer protein complexes that are functional but insulated from extant paralogues. If sequence space is densely occupied by existing paralogues, it should be difficult to introduce new insulated pathways…. However, if sequence space is sparsely occupied, new pathways should be easy to introduce, and have a low probability of crosstalk.

New genes should be “easy to introduce,” they think, and are unlikely to interfere due to the vastness of unexplored sequences out there in sequence-space wonderland. Let’s try that with random strings of alphabet letters. Words and paragraphs that mean something new should be easy to introduce. Anyone wish to run that experiment?

In summary, our work highlights the power of using coevolution-guided libraries to investigate protein–protein interactions and supports a model in which sequence space is not densely occupied. The relatively sparse distribution of extant proteins in sequence space presumably reflects their evolutionary history. A previous study indicated that duplicated signalling proteins are under pressure immediately after duplication to change and become insulated, but subsequent movement in sequence space then arises only from neutral changes. Although duplicated proteins are initially subject to selection against crosstalk with each other, each protein is probably not subject to system-wide negative selection or global optimization.

In summary, rather, their work shows undying faith in the power of natural selection to create complex molecular machines and gene networks from scratch. This is how Darwinians explain de novo genes: by the power of faith in imagination.

Photo: Gadus morhua, aka an Atlantic cod, by Hans-Petter Fjeld [CC BY-SA].