Daily Archives: June 9, 2017

I

often think about the long and winding road from organic compounds floating in the so-called primordial soup to humans. Lately Ive been wondering if microbes helped drive the bus.

Even just a few years ago, that would have been a truly ludicrous idea. But thanks to our growing understanding of the human microbiome, it could represent a thrilling example of evolutionary symbiosis that has mutually benefitted humans and their microbial passengers.

Our bodies are made up of many more microbial cells than human cells. Thousands of species of bacteria, fungi, viruses, and other microbes live almost everywhere in and on our bodies, including the digestive system, nose, and skin, to name just a few. Some of the earliest research showed that the microbes that live in our digestive systems help us digest food, make some of the vitamins we need, and balance the immune system.

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Since then, weve learned that these microbes, collectively called the microbiome, can affect body weight, susceptibility to cancer, and even behavior. The gut microbiome interacts with its host using signaling networks that employ the immune system, hormones, and the nervous system. In short, it has a profound effect on our overall health.

Another kind of superbug: Seeking an edge in the elite athletes microbiome

Ive been studying the microbiome for more than 20years. My research team at Massachusetts Institute of Technology explores how microbes help keep us healthy. Weve learned that our daily diet and habits dramatically influence our microbiomes. Weve specifically studied aspects of wellness in mice (which often make good stand-ins for humans) that are influenced by diet and microbes, including healthy skin, a slender physique, and breeding success across generations. Several findings from our work make me think that microbes helping steer the evolution of humans isnt such a far-fetched idea.

For starters, in our glow of health study, we fed to mice bacteria extracted from human breast milk. This dietary addition gave them thicker skin, more lustrous fur, and, in females, more acidic vaginal mucus. That change in mucus is correlated with increased fertility in mice and in humans.

Or take the case of oxytocin, sometimes called the love hormone. In humans, oxytocin not only stimulates reproductive behaviors, but also induces childbirth, releases breast milk, bonds babies with their moms, and joins couples in monogamy to share child rearing. Oxytocin promotes nerve growth, fosters creativity in the brain, and serves as glue for complex mammalian social networks that have been integral in evolving social organizations. When fed to mice, certain kinds of bacteria found in human breast milk elicit production of oxytocin in the brain and bloodstream.

Likewise, testosterone levels in mice soar after eating these bacteria. Such microbe-treated mice display larger testicles with higher sperm counts and also build extra muscle. The resulting mouse swagger would give these mice a competitive edge in combat and romance, letting them spread their genes and microbes more widely and for a longer time. During bad times, these microbiome-related changes could provide a huge survival advantage for both the host and its microbial allies.

Even thyroid hormone, sometimes called the gas pedal that controls the bodys metabolism and thus body temperature, is influenced by our resident bacteria. It makes sense that heat-loving (thermophilic) bacteria originally dwelling in decaying swamp plants would try to set the body temperature of their new hosts so they could live year-round in total comfort with a competitive edge over other microbial interlopers. This stabilized host environment could then have chaperoned the evolution from external egg laying to internal placental pregnancy. As a bonus for microbes, by increasing mother-infant intimacy, internal pregnancy abets the transfer of microbes from mother to child, and thus the creation of future suitable dwellings for the mothers microbial descendants.

It turns out that our minuscule microbial manipulators also boost levels of a transcription factor (a protein that helps turn the instructions of DNA into body-building proteins) called Forkhead Box N1. It helps build tissue in the thymus gland that produces specialized immune cells that sustain pregnancy in mammals. Thanks to the exquisitely synchronized immune interactions choreographed by this tissue, the immune system doesnt swarm and kill sperm cells or the developing fetus. Instead, it opens the door to internal fertilization and lengthy pregnancy while still combating invading bacteria and other pathogens.

Microbe-stimulated Forkhead Box N1 is also involved in the growth of body hair which, along with the production of thyroid hormone, supports the stable body temperature (called endothermy) needed for an extended pregnancy. Forkhead Box N1 is also implicated in the development of mammary glands. Its just a small stretch to imagine that microbes helped modify sweat glands into lactating breasts in order to create a yummy and nutritious food for human infants and at the same time spread their own microbial sprouts to future generations.

Interestingly, mouse moms consuming probiotic bacteria from human breast milk actually take better care of their infants and are less likely to eat them compared with untreated mice or those eating other types of diets. Following this line of reasoning, the bacteria help make more mice and thus more future microbe hosts.

The idea that humans are a kind of deluxe love bus for microbes sounds preposterous, even diabolical. But maybe its actually a winner for everyone.

Susan E. Erdman, DVM, is a principal research scientist and assistant director of MITs Division of Comparative Medicine.

Susan E. Erdman can be reached at serdman@mit.edu

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Did the microbiome help drive human evolution? - STAT

June 9, 2017 by Ricki Lewis, Phd, Plos Blogs A coyote (Canis latrans)

Are the red and eastern wolves separate species, or hybrids with coyotes? And what has that got to do with climate change? Actually a lot, in illustrating what scientific inquiry is and what it isn't.

Comparing canid genomes

A report in this week's Science Advances questions conclusions of a 2016 comparison of genome sequences from 28 canids. The distinction between "species" and "hybrid" is of practical importance, because the Endangered Species Act circa 1973 doesn't recognize hybrids. But DNA information can refine species designationsor muddy the waters.

At first, genetic marker (SNP) studies hinted at a mixing and matching of genome segments among coyotes, wolves, and dogs. Then came full-fledged genome sequencing.

Last year Bridgett M. vonHoldt, head of Evolutionary Genomics and Ecological Epigenomics at Princeton and colleagues, scrutinized the 28 full genome sequences for signs of "lack of unique ancestry." They compared the genomes of 3 domestic dog breeds (boxer, German shepherd, and Basenji), 6 coyotes, a golden jackal from Kenya, and various wolves to 7 "reference" genomes from 4 Eurasian gray wolves (to minimize recent mutations) and 3 coyotes. The conclusion: lots of genes have flowed from coyotes and gray wolves into the genomes of the animals that became what we call red and eastern wolves, in different proportions.

A bit of background.

Classifying these animals based on geography and visible traits gets confusing, with all the overlaps and shared DNA sequences. Apparently various pairings can successfully mate but probably don't do so very much in the wild when populations are large. Tracking genomes reveals a classic cline, in the parlance of population genetics, with coyote gene introgression into wolf genomes rising from Alaska and Yellowstone (8-8.5%), to the Great Lakes (21.7-23.9%), to Ontario (32.5%-35.5%), and to Quebec (>50%). (BTW the Basenji, the barkless dog, is 61% gray wolf.)

Paul A. Hohenlohe of the University of Idaho and colleagues maintain that the 2016 findings actually support 2 hypotheses: recent admixture (hybridization) or that red and eastern wolves are distinct species. Actually it's 3: hybridization might have happened a long time ago, something that following genes with known mutation rates might reveal.

The new paper challenges the 28-genome comparison:

Dr. vonHoldt's team responded to Dr. Hohenlohe's team's comments, reiterating that the results show red wolf and eastern wolves are "genetically very similar to coyotes or gray wolves," reflecting recent hybridization.

Discussion of wolf classification goes back a quarter century, and this trio of papers is only a recent glimpse of the debate. But I love the respectful back-and-forth of the efforts to extract a compelling narrative from the data that might be what actually happened. Multiple interpretations of the same data and amending interpretations as new data accumulate is the very essence of the scientific process.

Anti-science rhetoric

Let's reframe the wolf papers using the language of the popular climate change discussion.

Are Hohenlohe and his co-workers "coyote deniers?"

Do vonHoldt and her colleagues "believe in" wolf-coyote couplings and Hohenlohe et al don't?

The science of wolf origins is clearly not "settled" for science is NEVER settled. Facts aren't proven, but instead evidence demonstrated and assessed, from both experimentation and observation. The information from tested hypotheses may be so consistent and compelling that it eventually builds to gestate a theory, or even a law, that then explains further observations. But to get there, science is all about asking questions. As I've written in all 35 or so editions of my various textbooks, science is a cycle of inquiry.

In fact the history of genetics is a chronicle of once-entrenched dogma changing with new experiments and observations. I was in grad school when Walter Gilbert's famed "Why Genes in Pieces?" was published. The classic paper introduced introns, the parts of genes that aren't represented in the encoded protein. It was an astonishing idea circa 1978, but with compelling evidence. Yet even Mendel's pea crosses sought an alternate explanation for the prevailing notion that traits simply disappear between generations.

Before I'm hurled insults, let me assert that although my expertise isn't in climate science, I think that the evidence very strongly supports the hypothesis that the planet is warming at an accelerated rate compared to some other times. And fossil fuel use is likely a partial cause, not just a correlation or association, because the relationship is linear and a mechanism plausible. But I don't "believe" in global warming as if it is the tooth fairy or a deity.

I cringe when politicians and celebrities appoint and anoint themselves experts on climate change, then use language that illustrates profound unfamiliarity with the ways of science.

Why did Eddie Vedder begin his speech at the Rock and Roll Hall of Fame induction ceremony for Pearl Jam with "climate change is real?" He's a musician, not a meteorologist. Why not, "semi-conservative DNA replication is real?" Or "hydrogen bonds are real?" "Noble gases are real?"

I've long had a problem with the term "climate change," because of course climate changes! Why would it ever be static, given weather ups and downs?

Climate dynamics are a little like the composition of blood, or any other manifestation of biological homeostasis. Have a complete blood count at various times and, if you're healthy, results are likely to be within a narrow normal range. Ditto blood sugar, liver enzymes, serum cholesterol level. But steady blood counts don't mean that the same blood cells hang out forever. Bone marrow stem cells continually pump out blood cell progenitors as the older specialized cells die off. Natural systems change over time, with fluctuations large and small.

Climate always has and always will change.

We can learn about normal blood circulation by studying off-kilter situationsleukemia, infection, anemiawithout fear of being labeled a "denier." It's not only a scientifically inappropriate term, but one that is offensive to some, with its echoes of the Holocaust.

I'm interested in other times deep, geologic time, not the president's simplistic reference to the next century when the climate warmed at the rate that it is doing so now. How long did the warming escalate and persist? What forces or events might have precipitated warming? What factors accompanied its ultimate reversal as ice ages neared? By asking questions we can learn what we can expect from nature, so that perhaps we can better understand what we can do to counter the warming trend.

And so those who claim to believe in climate change and vilify those who ask questions might learn a lesson in what science actually is from the elegant discussion of wolf origins.

Explore further: Study doesn't support theory red and eastern wolves are recent hybrids, researchers argue

This story is republished courtesy of PLOS Blogs: blogs.plos.org.

A team led by University of Idaho researchers is calling into question a widely publicized 2016 study that concluded eastern and red wolves are not distinct species, but rather recent hybrids of gray wolves and coyotes. In ...

Research by UCLA biologists published today in the journal Science Advances presents strong evidence that the scientific reason advanced by the U.S. Fish and Wildlife Service to remove the gray wolf from protection under ...

Scientists have successfully produced hybrid pups between a male western gray wolf and a female western coyote in captivity.

Today's Great Lakes gray wolf, de-listed by U.S. officials as an endangered species, probably is a hybrid and no longer the historic animal, biologists said.

Wolves and other top predators need large ranges to be able to control smaller predators whose populations have expanded to the detriment of a balanced ecosystem.

Wolves in the eastern United States are hybrids of gray wolves and coyotes, while the region's coyotes actually are wolf-coyote-dog hybrids, according to a new genetic study that is adding fuel to a longstanding debate over ...

Flatworms that spent five weeks aboard the International Space Station are helping researchers led by Tufts University scientists to study how an absence of normal gravity and geomagnetic fields can have anatomical, behavioral, ...

The diverse 'coats' which protect a deadly microbe from our immune cells are generated by a 'hotspot' of rapidly evolving genes, a study has found.

(Phys.org)A group of scientists from several institutions in Germany has suggested that extinct animals that are resurrected through scientific means be given a tag on their name to indicate their origins. In a Policy ...

It's well known that young babies are more interested in faces than other objects. Now, researchers reporting in Current Biology on June 8 have the first evidence that this preference for faces develops in the womb. By projecting ...

(Phys.org)A small team of researchers from Austria and Sweden has found that ravens are able to remember people who trick them for at least two months. In their paper published in the journal Animal Behavior, the group ...

Sex-changing fish exhibit differences in androgen receptor (AR) expression in muscles that are highly sensitive to androgens (male sex hormones) and essential for male courtship behavior, according to a Georgia State University ...

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How did a review of wolf studies turn into a "climate dynamics" rant?

Really tired of these spoiled whelps that think the world hangs on their every thought. And don't expect a moment's gratitude for the fact that the author was trying to be even handed on the subject. That's the thing with the alt-right and evangelicals where they will always have an advantage. No one else is that rude.

"Climate change "deniers" aren't as dangerous to our children as is science illiteracy." Odd statement. Like there's a difference. All 'deniers' are either science illiterate, or act that way in a conscious scam to appeal to those...that are scientifically illiterate. It's like saying gravity isn't nearly as life threatening as falling out of a window.

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Wolf evolution and 'settled science' - Phys.Org

Nigel Dodds and Arlene Foster, DUP deputy leader and leader

Charles McQuillan/Getty Images

By Frank Swain

Having failed to win an overall majority in the UKs general election, Theresa Mays Conservative party is hoping to foster an informal coalition with Northern Irelands Democratic Unionist Party (DUP). Members of the party have taken controversial stances on everything from climate change to evolution, with one assembly member being unaware that heterosexual people can contract HIV. Here are five things you need to know when it comes to science and the DUP

The party has a history of speaking out against climate change. Senior member Sammy Wilson has called climate change a con, and described the Paris Agreement as window dressing for climate chancers. During his time as Northern Irelands environment minister, he said that people would eventually look back at this whole climate change debate and ask ourselves how on Earth we were ever conned into spending billions of pounds on the issue.

It isnt just Wilson though in 2014, DUP ministers tried to oppose proposals to introduce local measures against climate change in Northern Ireland.

Northern Ireland remains the only part of the UK where women cannot access abortion unless their life is endangered by pregnancy a legal situation that is incompatible with the European Convention on Human Rights, according to a Belfast High Court ruling in 2015.

But on taking leadership of the party in 2016, Arlene Foster promised to block any attempt to change these laws, telling reporters I would not want abortion to be as freely available here as it is in England.

Foster did, however, say she might consider an amendment in cases of rape. But the DUPs Jim Wells formerly the health minister for Northern Ireland opposes abortion even in these circumstances.

DUP assembly member Thomas Buchanan has previously called for creationism to be taught in schools. In 2016, he voiced support for an evangelical Christian programme that offers helpful practical advice on how to counter evolutionary teaching. He has expressed a desire to see every school in Northern Ireland teaching creationism, describing evolution as a peddled lie.

Buchanan told the Irish News Im someone who believes in creationism and that the world was spoken into existence in six days by His power, adding that children had been corrupted by the teaching of evolution.

The DUPs leader narrowly survived a no-confidence motion following a disastrous attempt to bolster green energy in Northern Ireland by providing subsidies for wood burners. Arlene Foster introduced the scheme in 2012 when she was head of the Department of Enterprise, Trade and Investment. The original budget was 25 million, but a lack of price controls meant that, over five years, almost 500 million went up in smoke.

Last year, DUP assembly member Trevor Clarke admitted that he had thought only gay people could be infected with HIV, until a charity explained otherwise. He made the comments during a parliamentary debate around a campaign to promote awareness and prevention of HIV in Northern Ireland and to increase support for those living with HIV.

Read more: How YouGovs experimental poll correctly called the UK election

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Five things you need to know about DUP politicians and science - New Scientist