ODDS&ENDS: The Evolution Of Evolution

Inheriting the windbags

THE SET-UP: Here’s a headline I didn’t expect to see in the 21^st Century:

Teaching Evolution Has a Bright Future in the U.S.

It’s perplexing that a quarter-century marked by quantum leaps in science is also one in which evolution isn’t a square-one fundamental of science education. It’s even more perplexing given that we’re approaching the 100 year anniversary of the Scopes Monkey Trial.

Amazingly, though, it’s taken this long for the deputy director of the National Center for Science Education to see a “bright future” for those charged with the daunting duty of introducing America to a principle established in the 19^th Century. And that’s in spite of its repeated corroboration by fossil evidence, by genetic evidence and by real-time observation.

But that’s where we are folks.

Writing in Scientific American, Glenn Branch traces the “evolution” of post-Scopes attacks against evolution. The Tennessee law John T. Scopes violated was finally repealed in 1967. But that wasn’t the end of Christian recalcitrance. Ironically enough, evolution’s opponents have, as Branch cleverly writes, “adapted in response to legal setbacks” to their “religiously motivated attempts to undermine the teaching of evolution in the U.S.’s public schools.”

According to Branch, we’re currently in the third “wave” of counterattacks against teaching basic science:

The new strategy was not to ban or to balance the teaching of evolution but to blunt it by requiring, or more commonly permitting, teachers to misrepresent evolution as scientifically controversial. A handful of states—Mississippi, Louisiana and Tennessee—presently have such laws on the books. It is difficult to challenge these laws as unconstitutional in the abstract without a teacher who actually claims their protection to proselytize against evolution to their students.

On the brighter side, it looks like acceptance of reality is growing organically:

[W]hile in 2007 a bare majority of [high school biology teachers] reported that they emphasized the scientific credibility of evolution while not emphasizing creationism as a scientifically credible alternative, in 2019 it was a commanding majority, 67 percent, who did so.

That said, there’s still plenty of room for teachers to evolve:

[E]ven in the 2019 survey, 17.6 percent of high school biology teachers—more than one in six—reported emphasizing, wrongly, that creationism is a scientifically credible alternative to evolution. Many of those teachers were creationists themselves: 10.5 percent of respondents indicated that they personally agreed that “God created human beings pretty much in their present form at one time within the last 10,000 years or so.”

It’s both notable and not coincidental that the US House Of Representatives is currently led by a “Young Earth Creationist.”

Speaker Mike Johnson is a “Young Earther” who also hails from a state currently leading the effort to topple the Wall of Separation. Louisiana Governor Greg Landry’s flamboyant effort to post the Ten Commandments in schoolrooms is designed, however unintelligently, to spawn a Supreme Court showdown. Christian politicians in Texas and Oklahoma are making similar efforts to force religion into school curricula and the courts. And it’s in the courts that Branch sees potential problems “in light of the Supreme Court’s recent abandonment of the legal tests” that litigants used to defeat “the second wave of attacks on evolution education.”

Given where we are in the third wave, it’s hard to see the “bright future” teased in the headline, but Branch finds it nonetheless:

Acceptance of evolution became a majority position among the American public more than a decade ago, according to multiple independent polls, and there are signs of a shift even among religious communities that have been traditionally hostile to evolution.

I guess that’s “something,” but the zealotry of both Trump-connected Evangelicals and the Supreme Court’s majority makes it hard to be sanguine about the future. But Branch has faith in his fellow Americans’ and the inevitability of science. He’s certain that “someday every student in the U.S.’s public schools will be in a position to appreciate that nothing in biology makes sense except in the light of evolution.”

And maybe that’s the real impediment … maybe we don’t want to “make sense” of biology or face the possibility that we are inescapably tethered to the fate of a planet we are actively despoiling and denuding. Speaker Johnson doesn’t think he is “of this Earth” … he believes this planet is merely a means to an end … as in the End Times … and for him and millions more like him, there’s no real need to save it or the variety of life it sustains from human appetites … they only need their savior to save themselves. - jp

TITLE: How Neanderthals Kept Our Ancestors Warm
https://nautil.us/how-neanderthals-kept-our-ancestors-warm-1185278/

EXCERPTS: Early humans and Neanderthals hooked up outside of Africa, including in Europe, from about 50,000 to 43,000 years ago. (They mated in the Middle East as far back as 100,000 years ago.) In the recent Science paper, researchers show that Neanderthal genes related to skin color, metabolism, and immune function seemed to be the most common across the sample of early humans.

“Because Neanderthals were living outside of Africa for several thousand years before modern humans arrived there, they presumably were adapted to the climate and adapted to life outside Africa,” says geneticist Manjusha Chintalapati, a former postdoctoral fellow at the University of California, Berkeley, who is now at the company Ancestry DNA. “So when Neanderthals and humans interbred, genes were passed on to humans that helped them adapt to that climate and spread across the world.”

Similar findings have been reported before in other papers. But none had ever examined such a large sample of human DNA. The authors of the Science paper examined 59 previously sequenced ancient Homo sapiens who lived in Europe and Western and Central Asia over the past 45,000 years, and the complete genomes of 300 contemporary humans.

“The novelty in our study comes from the fact that we looked at these Neanderthal ancestry segments in all samples,” Chintalapati says. “Our study shows that these regions were at high frequency since probably a hundred generations after the initial event. So that was probably quite beneficial to humans.” The Neanderthal variants related to skin color conferred lighter skin, which likely made it easier to absorb vitamin D—crucial for bone health—in conditions of low sunlight.

Tony Capra, an evolutionary genomics professor at the University of California, San Francisco, has no doubt that a small portion of Neanderthal DNA likely made a big difference in Ice-Age Europe. He has spent the last decade combining high-powered computational techniques, genetic sequencing, and medical records databanks to analyze the effects of Neanderthal DNA on contemporary humans.

He has found, among other things, that the DNA affecting metabolic pathways—biochemical reactions linked together in a cell—changed the way most modern humans break down fat. Since the game these humans hunted in colder climes tended to have fatty deposits to keep them warm, genetic variants that might have helped early humans more quickly process fat for energy would have given them an edge.

Neanderthal DNA also likely helped modern humans survive threats that went beyond the challenges of the cold climate. One intriguing variant identified by Capra in 2016 relates to blood clotting. Using medical records, Capra and his team linked the variant to thrombosis, which can increase the risk of a heart attack or cancer.

But it’s not hard to imagine how humans might have benefited from having it, says Chris Stringer, an evolutionary anthropologist at London’s Natural History Museum. Life was rough then. “People were hunting dangerous animals,” Stringer says. “They were working with sharp stones for tools that could cut them. Women were giving birth without medical support. [They] picked [the variant] up because to have a gene that actually sped up the process of blood clotting was good news 50,000 years ago.” But modern sedentary lifestyles and longer lives come with a great risk of thrombosis.

The variant, which also would have reduced the risk of infection by quickly sealing wounds, is just one of many that helped the body fight environmental pathogens, Stringer says. The most powerful genetic Neanderthal signals found to date have been in the immune system. Since Homo sapiens evolved in Africa, most of the natural defenses to pathogens and parasites they developed were endemic to the local conditions. Neanderthals had evolved defenses against microscopic threats in the new environment.

TITLE: Scientists Discover Bacteria Trapped in Endless Evolutionary Time Loop
https://www.sciencealert.com/scientists-discover-bacteria-trapped-in-endless-evolutionary-time-loop

EXCERPTS: Lake Mendota in Wisconsin is transformed by the changing seasons – covered by ice in winter, and by algae in summer – and a new study shows how these cyclical shifts are putting the lake's bacteria into evolutionary loops.

Led by researchers from the University of Texas at Austin, the team behind the study analyzed 471 lake microbe samples collected across 20 years, looking at genetic variations within and between species through time.

The data showed thousands of bacteria species evolving through the generations, then evolving back to a virtually identical state as the seasons shifted. As microbes live just a few days, we're talking about genetic evolution crossing thousands of generations within the span of one year.

These cycles repeated year on year too, like a video played through and then played backwards, back to the original starting point. Of the 2,855 bacterial genomes studied, cyclical seasonal changes were found in 80 percent of them.

"This study is a total game changer in our understanding of how microbial communities change over time," says marine scientist Brett Baker, from the University of Texas at Austin.

"This is just the beginning of what this data will tell us about microbial ecology and evolution in nature."

As environmental conditions changed, the analysis showed, different bacterial strains were able to thrive and become dominant – only to lose ground to other strains as the seasons changed back. Around 20 percent of the studied species showed a more sustained pattern of genetic change, spanning decades.

This was particularly evident in 2012, when the lake experienced a summer that was hotter and drier than normal. The team noted a substantial shift in genes handling the bacteria's nitrogen metabolisms that year – most probably because of lower levels of nitrogen-producing algae, resulting from less water flowing into the lake.

The findings suggest ecology and evolution seem to go together rather than operating distinctly – and that's an important perspective for researchers, especially when studying a planet that continues to heat up.

" Climate change is slowly shifting the seasons and average temperatures, but also causing more abrupt, extreme weather events," says Rohwer.

"We don't know exactly how microbes will respond to climate change, but our study suggests they will evolve in response to both these gradual and abrupt changes."

TITLE: Creature hiding in California lake reveals evolutionary secrets from 650 million years ago
https://www.thebrighterside.news/post/creature-hiding-in-california-lake-reveals-evolutionary-secrets-from-650-million-years-ago/

EXCERPTS: Mono Lake, nestled in California’s Eastern Sierra Nevada, is a haven for unique life forms. Its iconic tufa formations and thriving populations of brine shrimp and alkali flies showcase an ecosystem adapted to the lake's hypersaline, alkaline waters.

Now, researchers from the University of California, Berkeley, have identified a microscopic organism in this extreme environment that could illuminate the early evolution of life.

The discovery is a single-celled organism called a choanoflagellate, a group that holds special significance in the study of evolution. Although not animals themselves, choanoflagellates are the closest known living relatives of animals. Their biology offers vital clues about the transition from single-celled to multicellular life.

What sets this particular species apart is its microbiome. Unlike other choanoflagellates, which typically consume bacteria, this species forms a stable, physical association with its bacterial partners.

This makes it the simplest known organism to host a microbiome, providing researchers with an unprecedented opportunity to study how early interactions between single-celled organisms and bacteria influenced the evolution of complex life, including animals.

“Very little is known about choanoflagellates, and there are interesting biological phenomena that we can only gain insight into if we understand their ecology,” says Nicole King, a professor of molecular and cell biology at UC Berkeley and an investigator for the Howard Hughes Medical Institute.

King and her team study choanoflagellates as models for ancient life forms that once inhabited early oceans. Their findings offer a window into the evolutionary processes that eventually gave rise to multicellular organisms.

Mono Lake’s extreme environment, characterized by high salinity and toxic substances such as arsenic and cyanide, may have driven the evolution of this distinctive species.

Dubbed Barroeca monosierra, this choanoflagellate demonstrates how early life forms not only survived in harsh conditions but also developed symbiotic relationships with bacteria. These relationships may have been pivotal in shaping the complex microbiomes that are now integral to animal life, including humans.

The choanoflagellate was first discovered nearly a decade ago, when Daniel Richter, then a UC Berkeley graduate student, brought back a vial of water from a climbing trip to the Eastern Sierra Nevada. Under the microscope, the water teemed with life, particularly large, beautiful colonies of choanoflagellates.

These colonies, composed of nearly 100 identical cells, formed a hollow sphere that twirled and spun as the individual cells used their flagella for movement.

King noted the similarity between these colonies and a blastula—a hollow ball of cells that forms early in the development of animal embryos. "One of the things that's interesting about them is that these colonies have a shape similar to the blastula," she said. However, it wasn’t until years later that the research team realized the full significance of the colony’s structure.

Graduate student Kayley Hake revived the choanoflagellates from a freezer and discovered something unexpected: DNA was present inside the hollow sphere, where there should have been no cells. After further investigation, she identified this DNA as bacterial, marking the first time bacteria had been observed living inside a choanoflagellate colony rather than being consumed by it.

Hake’s work uncovered not just bacteria, but also a network of extracellular matrix structures inside the colony. These structures appeared to be secreted by the choanoflagellates and could serve as a habitat for the bacteria. This was a major breakthrough because no one had ever documented a choanoflagellate forming a stable, symbiotic relationship with bacteria.

Jill Banfield, a UC Berkeley professor and pioneer in the field of metagenomics, collaborated with King’s team to identify the bacterial species found both in Mono Lake water and inside the choanoflagellate colonies. Metagenomics allows scientists to sequence all the DNA in an environmental sample and reconstruct the genomes of the organisms living there.

Banfield’s lab identified several bacterial species in the lake’s water, and Hake determined which of these were also inside the choanoflagellates. The bacterial populations inside the colonies were distinct, suggesting that some bacteria thrive better than others within the oxygen-poor interior of the colony.

While it’s still unclear whether the bacteria are being farmed by the choanoflagellates for consumption or simply taking refuge from the harsh environment of Mono Lake, King believes future research will reveal more about the interactions between these organisms. "Much of this is speculation," King admitted, but she is hopeful that the findings will provide important clues about the evolution of life on Earth.

Previous studies in King’s lab have already shown that bacteria can influence choanoflagellate behavior, including stimulating mating and encouraging the formation of colonies. Barroeca monosierra will likely serve as a new model system for studying the interactions between eukaryotes (organisms with complex cells) and bacteria, as well as the role bacteria played in early animal evolution.

King’s work, along with that of her colleagues, could help answer fundamental questions about the relationships between early life forms and their microbial companions—relationships that likely paved the way for the human microbiome and the complex interactions between animals and bacteria that we see today.