Shapiro redux: experiments with bacteria & Yeast (Introduction)

by David Turell , Tuesday, August 15, 2023, 16:31 (256 days ago) @ David Turell

Suport for Shapiro:

https://www.quantamagazine.org/andreas-wagner-pursues-the-secrets-to-evolutionary-succe...

"Quanta spoke to Wagner over the phone recently about his new book, evolution as exploration, and the grand patterns that underlie biology.

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"...when the bacterium Escherichia coli enters the human intestinal tract, the environment contains oxygen. But as it gets deeper into the bowel, the environment starts to lack oxygen. E. coli needs to express different genes depending on whether oxygen is there or not.

"It turns out E. coli has evolved this anticipatory response where as soon as it enters the gastrointestinal tract, it starts to turn on the needed genes before it hits the anoxic zone. Its foresight might have evolved out of the thousands of millions of times it has gone through intestinal tracts: When it gets warm or the pH drops, or whatever it is, then it needs to turn on these genes, because soon it’s going to run out of oxygen.

"We wanted to find out whether you could evolve something like that in the laboratory. So we cycled yeast between different stressful environments. Once yeast went through the cycle multiple times, would they start to turn on the genes for handling oxidative stress [from too much reactive oxygen] before the oxidative stress hit? We found some evidence that they did.

***

"I study evolution...There have been many life forms that were not very successful by any standard when they originated. They didn’t radiate into hundreds of species, and they didn’t cover large areas of the planet’s surface. But wait long enough, and they became very successful.

"The best example is grasses. Today, grasses are one of the most successful families of organisms on the planet. They cover huge amounts of territory on most continents and have evolved enormous diversity, with about 10,000 very different species. They range in size from the tiny tufts of Antarctic grasses to huge bamboo forests in Asia. Grasses are old. We find grass pollen in fossilized dinosaur dung from 65 million years ago. But what’s quite remarkable is that when grasses originated and for many millions of years thereafter, they were just eking out a living at the margins of the biosphere. For that to change, they had to wait literally 40 million years for their spot in the sun.

"We see similar patterns in a lot of organisms. Mammals originated more than 100 million years before they first became successful. Evolution experimented with different mammalian life forms and ways of life, such as flying like bats or water living like otters, or tree living, and so forth. A lot of these originated and went extinct again. They were so unsuccessful that they actually had to be reinvented by evolution. That happened in some mammalian lineages multiple times before mammals became really successful.

"We see analogous phenomena in bees and other insects. So many, many different life forms were not very successful in the beginning and then became successful.

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"It was when we found this kind of phenomenon in the lab that I became interested in it. We took E. coli and exposed them to an environment that contains a lot of an antibiotic called ampicillin. Most of them will die in the presence of that antibiotic. But bacteria are extremely rapid at evolving antibiotic resistance, so within a few weeks, they have absolutely no problem surviving high dosages of it.

"We were interested in other traits that these bacteria acquired as a byproduct of that evolutionary process. To find out what they might be, we exposed the bacteria to hundreds of other toxic environments containing other antibiotics or toxins such as heavy metals or solvents. We knew from previous work that in many of these environments, bacteria could not survive or survive very poorly.

"The important thing to realize is that these bacteria had encountered none of those environments before our experiments. But we found that in 20 or so of these environments, the bacteria could survive pretty well. It was remarkable that as a byproduct of evolution for one thing you get something else altogether. And not just one thing, but multiple viability traits.

"When we see a property that’s evolved in an organism, we have this reflex of thinking that it’s a product of natural selection, right? That at some point, the property was useful to the organism’s survival, and that’s why we see it today. But as these kinds of experiments show, that’s not necessarily the case at all.

[Quanta] "It could have been selection for something completely different."

"Exactly. It could just be a byproduct. And so it’s probably not prudent to always take an adaptationist or selectionist viewpoint. There may be a lot of traits that exist for no good reason at all. (my bold)

***

"It could seem almost like these bacteria are clairvoyant, you know? Like they anticipated that at some point they would need to be resistant against antibiotics when humanity came along, right? But there’s a very mundane explanation that has to do with these latent kinds of traits that we identified in experiments in the lab. So these traits really exist out in nature. They’re not just artifacts of experiments."

Comment: Simple live on-their-own bacteria and yeast must have these abilities to survive and then evolve into our complexity where only minor adaptations can occur. A designer God would naturally do this with simple organisms.