Category: Evolution

Hygiene Hypothesis Says Parasites Help the Immune System to Develop

(p. D6) The kakapo, a large flightless parrot that can live 95 years and perhaps longer, is dangerously close to extinction. Once found throughout New Zealand, the population has dwindled to fewer than 150.

Conservation biologists are doing everything they can to keep the kakapo from vanishing. And so, when they discovered a few years ago that a pair of captive kakapos were infected with tapeworms, they did the obvious thing: They dewormed the birds.

Hamish G. Spencer, a geneticist at the University of Otago in New Zealand, thinks that was unwise. If endangered species are going to escape extinction, he argues, they may need parasites to survive.

“Some of these parasites may turn out to be quite good for their hosts,” Dr. Spencer said.

. . .

Evidence accumulated over the decades for what came to be known as the hygiene hypothesis. Supporters argued that over the past two centuries, modern civilization has radically changed our relationship with our inner residents.

For millions of years, our evolving bodies had to strike a tricky balance. We depended on a powerful immune system to fend off deadly infections. But if the immune system were to attack indiscriminately, it could destroy the body’s beneficial bacteria, for example, or damage its tissues with relentless inflammation.

According to the hygiene hypothesis, our ancestors came to tolerate low levels of infection. They even came to depend on parasites to help the immune system develop properly.

. . .

It’s possible, Dr. Spencer said, that the lack of parasites may help explain why some species restoration projects have been disappointing. “There are a number of cases where reintroduced populations haven’t done very well,” he said. “It might be that their immune systems are not very good.”

. . .

A first step, Dr. Spencer said, would be to stop medicating captive animals so freely. “We are arguing against the idea that you just dose the hell out of everything before you put animals back in the wild,” he said.

For the full story see:

Carl Zimmer. “Parasites as Welcome Guests.” The New York Times (Tuesday, April 5, 2016 [sic]): D6.

(Note: ellipses added.)

(Note: the online version of the story has the date March 31, 2016 [sic], and has the title “Tapeworms and Other Parasites Can Make Good Guests.” The paragraph that starts “For millions of years,” appears in the online version, but not in the print version.)

For more on the hygiene hypothesis see the following academic article:

Versini, Mathilde, Pierre-Yves Jeandel, Tomer Bashi, Giorgia Bizzaro, Miri Blank, and Yehuda Shoenfeld. “Unraveling the Hygiene Hypothesis of Helminthes and Autoimmunity: Origins, Pathophysiology, and Clinical Applications.” BMC Medicine 13, no. 1 (2015). DOI: https://doi.org/10.1186/s12916-015-0306-7.

Mitochondria and Chloroplasts Arose Through the Horizontal Evolution of Endosymbiosis

(p. A13) Mr. Mindell, a senior researcher at UC Berkeley’s Museum of Vertebrate Zoology, offers an account of “horizontal” evolutionary processes that are not an alternative to the established view but a tweak and an addition.

. . .

The book . . . offers an updated, more sophisticated appreciation of how some living things, some of the time, exchange genes with members of the same generation.

. . .

Introgression—the mixing of genes between species—has been revealed in human ancestry by the presence, in modern populations, of Neanderthal and Denisovan DNA. Mr. Mindell points to other cases of introgression, including between coyotes and gray wolves and between brown and polar bears. “All hybridization phenomena, including introgression,” he writes, “qualify as horizontal evolution, because genetic material is exchanged between different species, rather than between parents and offspring, the path of vertical evolution. They denote networking rather than branching.”

. . .  . . . inter-species hybridization still has a vertical component. A notable exception is recombination, a process that is widespread in bacteria, archaea and certain viruses. Among these populations, individuals will occasionally connect, exchange genetic material and then go their separate ways: the equivalent of a one-night stand, with important consequences for human health. It is in part because of their penchant for such networking that the viruses that cause AIDS, influenza and Covid-19 are so quick to evolve and thus so difficult to combat.

As “The Network of Life” ably demonstrates, horizontal evolution has shaped ancient processes that have set the stage for life as we know it. Mr. Mindell pays special attention to endosymbiosis, in which one tiny organism comes to reside inside another, sometimes creating a merger. “Some of the most consequential innovations in life’s 3.8-billion-year history,” he writes, “stem from a joining of previously distinct lineages by endosymbiosis.” The process gave rise to mitochondria, the “energy powerhouses” of our cells, and to chloroplasts, the intracellular denizens that enable plants to conduct photosynthesis.

For the full review see:

David P. Barash. “BOOKSHELF; Natural Mixer.” The Wall Street Journal (Friday, June 28, 2024): A13.

(Note: ellipses added.)

(Note: the online version of the review has the date June 27, 2024, and has the title “BOOKSHELF; ‘The Network of Life’ Review: Natural Mixer.”)

The book under review is:

Mindell, David P. The Network of Life: A New View of Evolution. Princeton, NJ: Princeton University Press, 2024.

Some Variants of One Mitochondrial Gene Double Your Odds of Living to 100

(p. D3) . . . what made the great blooming of biodiversity possible? Dr. Lane, building on ideas developed with the evolutionary biologist William Martin, traces its origins to a freak accident billions of years ago, when one microbe took up residence inside another. This event was not a branching of the evolutionary tree but a fusion with, he argues, profound consequences.

The new tenant provided energy for its host, paying chemical rent in exchange for safe dwelling. With this additional income, the host cell could afford investments in more complex biological amenities. The pairing thrived, replicated and evolved.

Today we call these inner microbes mitochondria; nearly every cell in our body has thousands of these energy factories. Dr. Lane and Dr. Martin have argued that because of mitochondria, complex cells have nearly 200,000 times as much energy per gene, setting the stage for larger genomes and unfettered evolution.

. . .

With age, mitochondrial mutations accumulate. Elsewhere, Dr. Lane has pointed to research showing that variants in a single mitochondrial gene halved the prospect of being hospitalized for age-related disease in patients who have them, and doubled the prospect of living to 100. This finding, Dr. Lane believes, could lead to medical advances if we understood how to protect mitochondrial DNA.

“How can we hope to understand disease,” he asks, “if we have no idea why cells work the way they do?”

. . .

Whether research will bear him out remains to be seen, but Dr. Lane’s many predictions, however incredible they seem, are testable and could keep scientists busy for years. As Sherlock Holmes remarked, “When you have eliminated the impossible, then whatever remains, however improbable, must be the truth.”

For the full review see:

Tim Requarth. “Rethinking the Textbook on Life.” The New York Times (Tuesday, July 21, 2015 [sic]): D3.

(Note: ellipses added.)

(Note: the online version of the review was updated July 20, 2015 [sic], and has the title “Book Review: Taking on ‘The Vital Question’ About Life.”)

The book under review is:

Lane, Nick. The Vital Question: Energy, Evolution, and the Origins of Complex Life. New York: W. W. Norton & Company, 2015.

Orangutan Effectively Self-Medicates to Heal Facial Wound

The Food and Drug Administration (FDA) is currently investigating whether Rakus the orangutan conducted a randomized double-blind clinical trial to prove the safety and efficacy of akar kuning before he applied it to his wound.

(p. D3) Scientists observed a wild male orangutan repeatedly rubbing chewed-up leaves of a medicinal plant on a facial wound in a forest reserve in Indonesia.

. . .

“Once I heard about it, I got extremely excited,” said Isabelle Laumer, a primatologist with the Max Planck Institute of Animal Behavior in Germany, in part because records of animals medicating themselves are rare — even more so when it comes to treating injuries. She and colleagues detailed the discovery in a study published Thursday [May 2, 2024] in the journal Scientific Reports.

The plant Rakus used, known as akar kuning or yellow root, is also used by people throughout Southeast Asia to treat malaria, diabetes and other conditions. Research shows it has anti-inflammatory and antibacterial properties.

. . .

Orangutans rarely eat the plant. But in this case, Rakus ingested a small amount and also coated the wound several times. Five days after the wound was noticed, it had closed, and less than a month later “healed without any signs of infection,” Dr. Laumer said.

Michael Huffman, a visiting professor at the Institute of Tropical Medicine at Nagasaki University in Japan, who wasn’t involved in the study, said, “This is to the best of my knowledge the first published study to demonstrate an animal using a plant with known biomedical properties for the treatment of a wound.”

Primates have been observed appearing to treat wounds in the past, but not with plants. A group of more than two dozen chimpanzees in Gabon in Central Africa have been seen chewing up and applying flying insects to their wounds, said Simone Pika, an expert on animal cognition at Osnabrück University in Germany who documented that observation.

For the full story see:

Douglas Main. “Primate Self-Medicates To Heal His Wound.” The New York Times (Tuesday, May 7, 2024): D3.

(Note: ellipses, and bracketed date, added.)

(Note: the online version of the story has the date May 2, 2024, and has the title “Orangutan, Heal Thyself.”)

Laumer’s co-authored academic paper mentioned above is:

Laumer, Isabelle B., Arif Rahman, Tri Rahmaeti, Ulil Azhari, Hermansyah, Sri Suci Utami Atmoko, and Caroline Schuppli. “Active Self-Treatment of a Facial Wound with a Biologically Active Plant by a Male Sumatran Orangutan.” Scientific Reports 14, no. 1 (2024): article #8932.

“Large Citizen Science Projects” Use Data Mining to Explore Risk Factors for Canine Cancers

(p. 2) Every dog has its day, and July 14, 2004, belonged to a boxer named Tasha. On that date, the National Institutes of Health announced that the barrel-chested, generously jowled canine had become the first dog to have her complete genome sequenced. “And everything has kind of exploded since then,” said Elaine Ostrander, a canine genomics expert at the National Human Genome Research Institute, who was part of the research team.

. . .

In the 2000s, scientists identified the genetic underpinnings of a variety of canine traits, including curly coats and bobbed tails. They pinpointed mutations that could explain why white boxers were prone to deafness. And they found that corgis, basset hounds and dachshunds owed their stubby legs to a genetic aberration in a family of genes that also regulates bone development in humans.

These early studies “highlighted both the potential that we could learn from dogs, but also that we were going to need bigger sample sizes to do it really well,” said Elinor Karlsson, a geneticist at UMass Chan Medical School and the Broad Institute. And so, researchers began creating large citizen science projects, seeking DNA samples and data from dogs across the United States.

Pet owners rose to the challenge. The Golden Retriever Lifetime Study, which began recruiting in 2012, has been following more than 3,000 dogs in an effort to identify genetic and environmental risk factors for cancer, which is especially common in the breed. Since 2019, the Dog Aging Project, a long-term study of health and longevity, has enrolled nearly 50,000 dogs.

Dr. Karlsson’s own project, Darwin’s Dogs, is at 44,000 canines and counting. (Some 4,000 have had their genomes sequenced.) Researchers are mining the data for clues about bone cancer, compulsive behavior and other traits.

For the full story see:

Emily Anthes. “Scientists’ New Best Friends.” The New York Times, Pets Special Section (Sunday, June 30, 2024): 2.

(Note: ellipsis added.)

(Note: the online version of the story has the same date as the print version, and has the title “How Science Went to the Dogs (and Cats).”)

Climate-Change-Induced Flooding Blamed for Hurting Tiny Flowers, Instead Helped Them “Flourish”

(p. A10) The whimsical image fit when the state of Vermont announced last month that a plant thought to be locally extinct — false mermaid-weed — had been found through a chain of events that seemed stolen from a fairy tale.

It began with a sharp-eyed turtle biologist for the state, Molly Parren. She had been out surveying the habitat of wood turtles in rural Addison County on May 7 [2024] when she spotted some wild meadow garlic, which is extremely rare, beside a stream. Ms. Parren snapped a photo and sent it to her colleague, Grace Glynn, Vermont’s state botanist.

But when Ms. Glynn opened the photo, another plant, visible in the foreground, seized her attention. She knew at once what it was: Floerkea proserpinacoides, or false mermaid-weed, an herb that had not been documented in Vermont for more than a century, and one that Ms. Glynn had sought in vain for years.

. . .

The day after the false mermaid-weed was spotted, Ms. Glynn rushed to the rural site to confirm its presence in person. She found a dense carpet — “so many plants, it was hard to imagine how they had been overlooked,” she said.

And yet her disbelief was familiar. “It happens a lot, people saying, ‘We couldn’t have missed that,’” she said. “But we do, and we’re humbled over and over — I love that.”

Far from an anomaly, rediscoveries of plants thought to be extinct are a relatively regular feature of field botany.

. . .

Tricky as it is to find elusive species, it is harder to pinpoint why they thrive or dwindle, and how such shifts might be related to a changing climate. Flooding is cited as one possible factor in the disappearance of false mermaid-weed from Vermont. And yet flooding in the state last summer may have helped it flourish by the stream where it was found, Ms. Glynn said, by depositing sediment and creating a more hospitable habitat.

For the full story see:

Jenna Russell. “By a Stream in Vermont, Rediscovering a Plant Last Seen a Century Ago.” The New York Times (Friday, June 14, 2024): A10.

(Note: ellipses, and bracketed year, added.)

(Note: the online version of the story has the date June 11, 2024, and has the title “By a Stream in Vermont, a Glimpse of a Plant Last Seen a Century Ago.”)

Monarch Butterflies Thrive on Poisonous Milkweed

(p. D5) The caterpillar of the monarch butterfly eats only milkweed, a poisonous plant that should kill it. The caterpillars thrive on the plant, even storing its toxins in their bodies as a defense against hungry birds.

For decades, scientists have marveled at this adaptation. On Thursday [Oct. 3, 2019 [sic]), a team of researchers announced they had pinpointed the key evolutionary steps that led to it.

Only three genetic mutations were necessary to turn the butterflies from vulnerable to resistant, the researchers reported in the journal Nature. They were able to introduce these mutations into fruit flies, and suddenly they were able to eat milkweed, too.

Biologists hailed it as a tour-de-force that harnessed gene-editing technology to unscramble a series of mutations evolving in some species and then test them in yet another.

“The gold standard is to directly test mutations in the organism,” said Joseph W. Thornton, an evolutionary biologist at the University of Chicago. The new study “finally elevates our standards.”

For the full story see:

Carl Zimmer. “MATTER; How Monarch Butterflies Evolved to Eat Poison.” The New York Times (Tuesday, October 8, 2019 [sic]): D5.

(Note: bracketed date added.)

(Note: the online version of the story was updated Oct. 3, 2019 [sic], and has the title “MATTER; These Butterflies Evolved to Eat Poison. How Could That Have Happened?”)

The article in Nature mentioned above is:

Karageorgi, Marianthi, Simon C. Groen, Fidan Sumbul, Julianne N. Pelaez, Kirsten I. Verster, Jessica M. Aguilar, Amy P. Hastings, Susan L. Bernstein, Teruyuki Matsunaga, Michael Astourian, Geno Guerra, Felix Rico, Susanne Dobler, Anurag A. Agrawal, and Noah K. Whiteman. “Genome Editing Retraces the Evolution of Toxin Resistance in the Monarch Butterfly.” Nature 574, no. 7778 (Oct. 2019): 409–12.

The “corresponding author” (often considered the primary author) of the article is Noah K. Whiteman, who has published a book that extensively discusses cases such as the monarch butterfly, where a creature has evolved the ability to consume or make use of chemicals that are poisonous to other creatures:

Whiteman, Noah. Most Delicious Poison: The Story of Nature’s Toxins―from Spices to Vices. New York: Little, Brown Spark, 2023.

Egyptians May Have Tried Surgery on Brain Cancer 4,600 Years Ago

(p. D2) Scientists led by Edgard Camarós, a paleopathologist at the University of Santiago de Compostela in Spain, were studying an approximately 4,600-year-old Egyptian skull when they found signs of brain cancer and its treatment.

. . .

Using a microscope, he and Tatiana Tondini of the University of Tübingen in Germany and Albert Isidro of the University Hospital Sagrat Cor in Spain, the study’s other authors, found cut marks around the skull’s edges surrounding dozens of lesions that earlier researchers had linked to metastasized brain cancer. The shape of the cuts indicated that they had been made with a metal tool. This discovery, reported in a study published Wednesday [May 29, 2024] in the journal Frontiers in Medicine, suggests that ancient Egyptians studied brain cancer using surgery. If the cuts were made while the person was alive, they may have even attempted to treat it.

. . .

The new discovery not only expands scientific knowledge of Egyptian medicine, it may also push back the timeline of humanity’s documented attempts to treat cancer by up to 1,000 years.

For the full story see:

Jordan Pearson. “An Ongoing Search: In an Ancient Egyptian Skull, Evidence of a Cancer Treatment.” The New York Times (Tuesday, June 4, 2024): D2.

(Note: ellipses, and bracketed date, added.)

(Note: the online version of the story has the date May 29, 2024, and has the title “Ancient Skull With Brain Cancer Preserves Clues to Egyptian Medicine.” Where the wording of the versions differs, the passages quoted above follow the online version.)

The study co-authored by Camarós, and mentioned above, is:

Tondini, Tatiana, Albert Isidro, and Edgard Camarós. “Case Report: Boundaries of Oncological and Traumatological Medical Care in Ancient Egypt: New Palaeopathological Insights from Two Human Skulls.” Frontiers in Medicine 11 (2024) DOI: 10.3389/fmed.2024.1371645.

On the antiquity of cancer, see also:

Haridy, Yara, Florian Witzmann, Patrick Asbach, Rainer R. Schoch, Nadia Fröbisch, and Bruce M. Rothschild. “Triassic Cancer—Osteosarcoma in a 240-Million-Year-Old Stem-Turtle.” JAMA Oncology 5, no. 3 (March 2019): 425-26.

Bdelloids Frozen for 24,000 Years Return to Life and Reproduce

(p. D2) Bdelloids can . . . come back to life after tens of thousands of years in deep freeze, according to a study published Monday [June 7, 2021] in the journal Current Biology. Bdelloids are one of a handful of teensy creatures, including tardigrades, that are known to survive incredibly inhospitable conditions.

. . .

For the study, scientists collected samples by drilling about 11 feet below the surface of permafrost in northeastern Siberia. They discovered living bdelloid rotifers locked in the ancient permafrost, whose average temperature hovers around 14 degrees Fahrenheit.

. . .

Radiocarbon-dating revealed the bdelloids were 24,000 years old. They then bounced back and were still capable of reproducing once thawed.

For the full story see:

Marion Renault. “The Deepest Sleeper: It Makes Rip Van Winkle Look Like an Amateur.” The New York Times (Tuesday, June 15, 2021 [sic]): D2.

(Note: ellipses, and bracketed date, added.)

(Note: the online version of the story has the date June 7, 2021 [sic], and has the title “This Tiny Creature Survived 24,000 Years Frozen in Siberian Permafrost.” Where the versions differ, in the passages quoted above I follow the online version.)

The study mentioned above is:

Shmakova, Lyubov, Stas Malavin, Nataliia Iakovenko, Tatiana Vishnivetskaya, Daniel Shain, Michael Plewka, and Elizaveta Rivkina. “A Living Bdelloid Rotifer from 24,000-Year-Old Arctic Permafrost.” Current Biology 31, no. 11 (June 7, 2021): R712-R713.

When Ocean Temperatures Dropped 30 Million Years Ago, Some Species Migrated to Warmer Waters; Others Developed New Traits

(p. D2) The Southern Ocean around Antarctica was once warmer. Then about 30 million years ago, the temperature dropped. Few fish could survive temperatures that were just above seawater’s freezing point, and they either migrated to warmer waters or went extinct.

One bottom-dweller held on. Through the power of natural selection, its descendants developed traits that let them survive these unlikely conditions. Today, the Antarctic blackfin icefish, or Chaenocephalus aceratus, thrives in these frigid waters with no scales, blood as clear as water and bones so thin, you can see its brain through its skull.

For the full story see:

JoAnna Klein. “Skullduggery: It’s Not Hard to See How His Brain Works.” The New York Times (Tuesday, March 5, 2019 [sic]): D2.

(Note: the online version of the story has the date Feb. 28, 2019 [sic], and has the title “How the Icefish Got Its Transparent Blood and See-Through Skull.”)

The article quoted above references the following academic article:

Kim, Bo-Mi, Angel Amores, Seunghyun Kang, Do-Hwan Ahn, Jin-Hyoung Kim, Il-Chan Kim, Jun Hyuck Lee, Sung Gu Lee, Hyoungseok Lee, Jungeun Lee, Han-Woo Kim, Thomas Desvignes, Peter Batzel, Jason Sydes, Tom Titus, Catherine A. Wilson, Julian M. Catchen, Wesley C. Warren, Manfred Schartl, H. William Detrich, John H. Postlethwait, and Hyun Park. “Antarctic Blackfin Icefish Genome Reveals Adaptations to Extreme Environments.” Nature Ecology & Evolution 3, no. 3 (March 2019): 469-78.

Giant Bee “Feared Extinct” Is Found Alive

(p. D2) It’s been 38 years since scientists last spotted the insect known as Wallace’s Giant Bee, a rare species found only in a group of Indonesian islands called the North Moluccas. With a wingspan of 2.5 inches and a body the size of a human thumb, it’s considered the world’s largest bee, and was feared extinct.

Those fears can now be somewhat laid to rest. In January [2019], an international team of conservationists found a Megachile pluto, as the species is called, in the wild.

For the full story see:

Douglas Quenqua. “Still Bite-Size: A Bee Absurdly Big, And Surprisingly Alive.” The New York Times (Tuesday, March 5, 2019 [sic]): D2.

(Note: bracketed year added.)

(Note: the online version of the story has the date Feb. 21, 2019 [sic], and has the title “The World’s Largest Bee Is Not Extinct.”)