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Retire this science idea, Edge: That there is a common toolkit of conserved genes


From the “What science ideas to retire” file, evolutionary biologist Seirian Sumner tells the Edgesome revealing things about common descent and the inheritance of genes:

Genes and their interaction networks determine the phenotype of an organism—what it looks like and how it behaves. One of the biggest problems in modern evolutionary biology is understanding the relationship between genes and phenotypes. The prevailing theory is that all animals are built from essentially the same set of regulatory genes—a genetic toolkit, and that phenotypic variation within and between species arises simply by using shared genes differently. Scientists are now generating a vast amount of genomic data from an eclectic mix of organisms. These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes. Instead, we need to turn our attention to the role of genomic novelty in the evolution of phenotypic diversity and innovation.

“These data are telling us to put to bed the idea that all life is underlain by a common toolkit of conserved genes”? Isn’t that common ancestry she is talking about? Demonstrated by conserved genes? That’s the idea due for retirement? Okay, she notes the conserved genes, but says,

We can now sequence de novo the genomes and transcriptomes (the genes expressed at any one time/place) of any organism. We have sequence data for algae, pythons, green sea turtles, puffer fish, pied flycatchers, platypus, koala, bonobos, giant pandas, bottle-nosed dolphins, leafcutter ants, monarch butterfly, pacific oysters, leeches…the list is growing exponentially. And each new genome brings with it a suit of unique genes. Twenty percent of genes in nematodes are unique. Each lineage of ants contains about 4000 novel genes, but only 64 of these are conserved across all seven ant genomes sequenced so far.

“Novel genes” are essentially “created” genes. (That is why works of fiction are called “novels.”) That certainly reduces the explanatory power of what we can expect to find learn from the study of the evolution of, say, ants. She then says,

Darwinian evolution explains how organisms and their traits evolve, but not how they originate. How did the first eye arise? Or more specifically how did that master regulatory gene for eye development in all animals first originate? The capacity to evolve novel phenotypic traits (be they morphological, physiological or behavioural) is crucial for survival and adaptation, especially in changing (or new) environments.

Hmm. It’s not at all clear that Darwinian evolution does explain how traits evolve if genes can simply appear from nowhere. “Random mutation” has clearly meant minor, survivable mutations of existing genes that confer a small advantage. If indeed “Each lineage of ants contains about 4000 novel genes, but only 64 of these are conserved across all seven ant genomes sequenced so far,” why would anyone look to Darwin’s theory to explain anything much about the history of ants?

She suggests a role for junk DNA,

The over-abundance of non-coding DNA in genomes is less puzzling, if they are a melting pot for genomes to exploit and create new genes and gene function, and ultimately phenotypic innovation. The current thinking is that genomes are constantly producing new genes all the time, but that only a few become functional.

and ends on an apparently conciliatory note:

Our story started simply: all life is a product of gentle evolutionary tinkering of a shared molecular toolkit. The unimaginable time has arrived where we can unpack the molecular building blocks of any creature. And these data are shaking things up. What a surprise? Not really. Perhaps the most important lesson from this is that no theory is completely right, and that good theories are those that continue evolving and embracing innovation. Let’s evolve theories (keeping the bits that are proven correct), not retire them.

What she has described is obviously more than tinkering; it sounds like a factory belt churning out new models.

Now here’s the problem: We tend to think theories should be useful. What exactly, in her model, does neo-Darwinism explain or predict that would justify keeping the “bits” that are proven correct? What bits are these? We can keep something around forever, like an 8-track tape deck, but if someone is asking us to actually incorporate it into what we are doing today …

Well, readers, we live in interesting times.

Note: Her comments on the role of gene duplication are valuable too.

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Jerry Coyne has a response to the article: bad answers about evolution- no science just bald declarations. For anyone who cannot post on Jerry's blog, this is a good opportunity to call him out. Joe
So, again correct me if I'm wrong, but it sounds like Ms. Sumner is from the Punc. Eq. school of thought? De novo genes popping magically out of the junk DNA soup? Lizard laid an egg and out popped a bird? Interesting times, indeed. drc466

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