Later On

A blog written for those whose interests more or less match mine.

Archive for the ‘Science’ Category

How dead is the Great Barrier Reef?

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Written by LeisureGuy

25 May 2017 at 12:58 pm

Trump Administration Says It Isn’t Anti-Science As It Seeks to Slash EPA Science Office

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Actions speak ever so much louder than words. Lisa Song reports in ProPublica:

When the city of Toledo temporarily lost access to clean drinking water several years ago after a bloom of toxic algae, the Environmental Protection Agency sent scientists from its Office of Research and Development to study health effects and formulate solutions.

The same office was on the front lines of the Flint water crisis and was a critical presence in handling medical waste from the U.S. Ebola cases in 2014.

Thomas Burke, who directed ORD during the last two years of the Obama administration and was the agency’s science adviser, calls the office the nation’s “scientific backstop in emergencies.”

President Trump’s 2018 budget would slash ORD’s funding in half as part of an overall goal to cut the EPA’s budget by 31 percent.

A statement from EPA Administrator Scott Pruitt did not directly address the cuts to ORD, but offered broad defense of the proposed agency budget, saying it “respects the American taxpayer” and “supports EPA’s highest priorities with federal funding for priority work in infrastructure, air and water quality, and ensuring the safety of chemicals in the marketplace.”

ORD has no regulatory authority, but it conducts the bulk of the research that underlies EPA policies. ORD scientists are involved in “virtually every major environmental challenge the nation has,” Burke said. Diminishing the role and input of the office, he said, risked leaving the country “uninformed about risks and public health.”

“In time, you’re flying blind,” he said. “Everything becomes a mystery.”

Trump’s budget, released Tuesday, reflects the president’s wish list. The numbers likely will change by the time it goes through the congressional appropriations process, but the proposed cuts are consistent with the administration’s push against environmental regulation and scientific funding. Many of the cuts fall on agencies involved with climate change research, including the EPA, the National Oceanic and Atmospheric Administration, the National Science Foundation and the Department of Energy.

Mick Mulvaney, director of the White House Office of Management and Budget, told reporters in a Tuesday briefing that the budget reduces climate science funding without eliminating it.

“Do we target it? Sure,” Mulvaney said in response to a reporter’s question. “Do a lot of the EPA reductions aim at reducing the focus on climate science? Yes. Does it mean that we are anti-science? Absolutely not. We’re simply trying to get things back in order to where we can look at the folks who pay the taxes, and say, look, yeah, we want to do some climate science, but we’re not going to do some of the crazy stuff the previous administration did.”

Much of the EPA’s climate research takes place in the Office of Air and Radiation, which is separate from ORD. But ORD studies the strategic, long-term effects of climate change, including the effects on agriculture and the oceans, Burke said.

Christine Todd Whitman, a former EPA administrator who worked for George W. Bush from 2001 to June 2003, said the proposed ORD cuts are more drastic than anything she can remember.

Whitman said she expects Congress will restore much of the funding, but she worries about the message behind the budget.

“A budget to me was always a policy document,” she said. Regardless of what Congress does, this administration’s policy “indicates to me [that] they’ll be looking for other ways to … stifle the research and slow it down,” she said. . .

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Written by LeisureGuy

24 May 2017 at 2:48 pm

Trump wasn’t always so linguistically challenged. What could explain the change?

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Sharon Begley writes at STAT, a national publication focused on finding and telling compelling stories about health, medicine, and scientific discovery:

It was the kind of utterance that makes professional transcribers question their career choice:

“ … there is no collusion between certainly myself and my campaign, but I can always speak for myself — and the Russians, zero.”

When President Trump offered that response to a question at a press conference last week, it was the latest example of his tortured syntax, mid-thought changes of subject, and apparent trouble formulating complete sentences, let alone a coherent paragraph, in unscripted speech.

He was not always so linguistically challenged.

STAT reviewed decades of Trump’s on-air interviews and compared them to Q&A sessions since his inauguration. The differences are striking and unmistakable.

Research has shown that changes in speaking style can result from cognitive decline. STAT therefore asked experts in neurolinguistics and cognitive assessment, as well as psychologists and psychiatrists, to compare Trump’s speech from decades ago to that in 2017; they all agreed there had been a deterioration, and some said it could reflect changes in the health of Trump’s brain.

In interviews Trump gave in the 1980s and 1990s (with Tom Brokaw, David Letterman, Oprah Winfrey, Charlie Rose, and others), he spoke articulately, used sophisticated vocabulary, inserted dependent clauses into his sentences without losing his train of thought, and strung together sentences into a polished paragraph, which — and this is no mean feat — would have scanned just fine in print. This was so even when reporters asked tough questions about, for instance, his divorce, his brush with bankruptcy, and why he doesn’t build housing for working-class Americans.

Trump fluently peppered his answers with words and phrases such as “subsided,” “inclination,” “discredited,” “sparring session,” and “a certain innate intelligence.” He tossed off well-turned sentences such as, “It could have been a contentious route,” and, “These are the only casinos in the United States that are so rated.” He even offered thoughtful, articulate aphorisms: “If you get into what’s missing, you don’t appreciate what you have,” and, “Adversity is a very funny thing.”

Now, Trump’s vocabulary is simpler. He repeats himself over and over, and lurches from one subject to an unrelated one, as in this answer during an interview with the Associated Press last month:

“People want the border wall. My base definitely wants the border wall, my base really wants it — you’ve been to many of the rallies. OK, the thing they want more than anything is the wall. My base, which is a big base; I think my base is 45 percent. You know, it’s funny. The Democrats, they have a big advantage in the Electoral College. Big, big, big advantage. … The Electoral College is very difficult for a Republican to win, and I will tell you, the people want to see it. They want to see the wall.”

For decades, studies have found that deterioration in the fluency, complexity, and vocabulary level of spontaneous speech can indicate slipping brain function due to normal aging or neurodegenerative disease. STAT and the experts therefore considered only unscripted utterances, not planned speeches and statements, since only the former tap the neural networks that offer a window into brain function. . .

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Videos of Trump speaking, then and now, at the link.

Written by LeisureGuy

24 May 2017 at 11:40 am

Why Chocolate May Be Good for the Heart

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I file this under “good news.” Nicholas Bakalar reports in the NY Times:

Eating chocolate has been tied to a reduced risk of heart disease. Now scientists have uncovered one possible reason.

Using data from a large Danish health study, researchers have found an association between chocolate consumption and a lowered risk for atrial fibrillation, the irregular heartbeat that can lead to stroke, heart failure and other serious problems. The study is in Heart.

Scientists tracked diet and health in 55,502 men and women ages 50 to 64. They used a well-validated 192-item food-frequency questionnaire to determine chocolate consumption. During an average 14 years of follow-up, there were 3,346 diagnosed cases of atrial fibrillation.

After controlling for total calorie intake, smoking, alcohol consumption, body mass index and other factors, they found that compared with people who ate no chocolate, those who had one to three one-ounce servings a month had a 10 percent reduced relative risk for atrial fibrillation, those who ate one serving a week had a 17 percent reduced risk, and those who ate two to six a week had a 20 percent reduced risk.

Dark chocolate with higher cocoa content is better, according to the lead author, Elizabeth Mostofsky, an instructor at Harvard, because it is the cocoa, not the milk and sugar, that provides the benefit. Still, she warned about overindulgence.

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Written by LeisureGuy

24 May 2017 at 9:51 am

Posted in Food, Health, Science

Why a Paleolithic diet is not practical

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I do restrict my carbs severely (generally under 30g/day), so in terms of a diet high in fat and low in carbs, the Paleolithic diet is similar (in macronutrients) to any low-carb, high-fat diet. However, the Paleolithic diet has as its goal to eat like humans did when they were gatherers and hunters, before they were relied on herds of domesticated animals (goats, sheep, cattle) or agriculture. So both Paleolithic dieters and I avoid grains (high in carbs) and beans (same), but I can eat cream and butter and they cannot.

But the reason it is impractical is that virtually all of the plant foods in the store are not like they were in the old days, due to centuries of selective breeding. For an example, look at the Paleolithic version of the banana. That is a far cry from a modern banana.

Or take the Paleolithic version of the carrot, which again looks like little more than a weed.

You can see more photos of Paleolithic area vegetables here. The watermelon is particularly pitiful

Written by LeisureGuy

24 May 2017 at 8:46 am

The Thoughts of a Spiderweb

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God, I love Quanta. Here’s another great article, this time by Joshua Sokol:

Millions of years ago, a few spiders abandoned the kind of round webs that the word “spiderweb” calls to mind and started to focus on a new strategy. Before, they would wait for prey to become ensnared in their webs and then walk out to retrieve it. Then they began building horizontal nets to use as a fishing platform. Now their modern descendants, the cobweb spiders, dangle sticky threads below, wait until insects walk by and get snagged, and reel their unlucky victims in.

In 2008, the researcher Hilton Japyassú prompted 12 species of orb spiders collected from all over Brazil to go through this transition again. He waited until the spiders wove an ordinary web. Then he snipped its threads so that the silk drooped to where crickets wandered below. When a cricket got hooked, not all the orb spiders could fully pull it up, as a cobweb spider does. But some could, and all at least began to reel it in with their two front legs.

Their ability to recapitulate the ancient spiders’ innovation got Japyassú, a biologist at the Federal University of Bahia in Brazil, thinking. When the spider was confronted with a problem to solve that it might not have seen before, how did it figure out what to do? “Where is this information?” he said. “Where is it? Is it in her head, or does this information emerge during the interaction with the altered web?”

In February, Japyassú and Kevin Laland, an evolutionary biologist at the University of Saint Andrews, proposed a bold answer to the question. They argued in a review paper, published in the journal Animal Cognition, that a spider’s web is at least an adjustable part of its sensory apparatus, and at most an extension of the spider’s cognitive system.

This would make the web a model example of extended cognition, an idea first proposed by the philosophers Andy Clark and David Chalmers in 1998 to apply to human thought. In accounts of extended cognition, processes like checking a grocery list or rearranging Scrabble tiles in a tray are close enough to memory-retrieval or problem-solving tasks that happen entirely inside the brain that proponents argue they are actually part of a single, larger, “extended” mind.

Among philosophers of mind, that idea has racked up citations, including supporters and critics. And by its very design, Japyassú’s paper, which aims to export extended cognition as a testable idea to the field of animal behavior, is already stirring up antibodies among scientists. “I got the impression that it was being very careful to check all the boxes for hot topics and controversial topics in animal cognition,” said Alex Jordan, a collective behaviorist at the Max Planck Institute in Konstanz, Germany.

While many disagree with the paper’s interpretations, the study shouldn’t be confused for a piece of philosophy. Japyassú and Laland propose ways to test their ideas in concrete experiments that involve manipulating the spider’s web — tests that other researchers are excited about. “We can break that machine; we can snap strands; we can reduce the way that animal is able to perceive the system around it,” Jordan said. “And that generates some very direct and testable hypotheses.”

The Mindful Tentacle

The suggestion that some of a spider’s “thoughts” happen in its web fits into a small but growing trend in discussions of animal cognition. Many animals interact with the world in certain complicated ways that don’t rely on their brains. In some cases, they don’t even use neurons. “We have this romantic notion that big brains are good, but most animals don’t work this way,” said Ken Cheng, who studies animal behavior and information processing at Macquarie University in Australia.

Parallel to the extended cognition that Japyassú sees in spiders, researchers have been gathering examples from elsewhere in the animal kingdom that seem to show a related concept, called embodied cognition: where cognitive tasks sprawl outside of the brain and into the body.

Perhaps the prime example is . . .

Continue reading.

Fascinating article and reminded me of this recent book and review.

Written by LeisureGuy

23 May 2017 at 12:11 pm

The energy expansions of evolution

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Olivia P. Judson writes in Nature:


The history of the life–Earth system can be divided into five ‘energetic’ epochs, each featuring the evolution of life forms that can exploit a new source of energy. These sources are: geochemical energy, sunlight, oxygen, flesh and fire. The first two were present at the start, but oxygen, flesh and fire are all consequences of evolutionary events. Since no category of energy source has disappeared, this has, over time, resulted in an expanding realm of the sources of energy available to living organisms and a concomitant increase in the diversity and complexity of ecosystems. These energy expansions have also mediated the transformation of key aspects of the planetary environment, which have in turn mediated the future course of evolutionary change. Using energy as a lens thus illuminates patterns in the entwined histories of life and Earth, and may also provide a framework for considering the potential trajectories of life–planet systems elsewhere.

Free energy is a universal requirement for life. It drives mechanical motion and chemical reactions—which in biology can change a cell or an organism1,2. Over the course of Earth history, the harnessing of free energy by organisms has had a dramatic impact on the planetary environment3,​4,​5,​6,​7. Yet the variety of free-energy sources available to living organisms has expanded over time. These expansions are consequences of events in the evolution of life, and they have mediated the transformation of the planet from an anoxic world that could support only microbial life, to one that boasts the rich geology and diversity of life present today. Here, I review these energy expansions, discuss how they map onto the biological and geological development of Earth, and consider what this could mean for the trajectories of life–planet systems elsewhere.

In the beginning

From the time Earth formed, around 4.56 billion years ago (Ga), two sources of energy were potentially available to living organisms: geochemical energy and sunlight. Sunlight is a consequence of the planet’s position in the Solar System, whereas geochemical energy is an intrinsic property of the Earth. Geochemical energy arises when water reacts with basalts and other rocks8,​9,​10. These water–rock reactions—which continue today11—generate reduced compounds such as hydrogen, hydrogen sulfide, and methane8,​9,​10. Oxidation of these compounds releases energy, which organisms can capture and store in the form of chemical bonds. Although sources of geochemical energy can be at or near Earth’s surface, they need not be: many are deep within the planet, out of reach of sunlight.

Assuming that life did not parachute in, fully formed, from elsewhere, a number of authors12,​13,​14,​15 have argued that the transition from non-life to life took place in the context of geochemical energy, with the ability to harness sunlight evolving later (Fig. 1). Consistent with this, both phylogenetic16 and biochemical13,17 evidence suggest that the earliest life forms were chemoautotrophs, perhaps living by reacting hydrogen with carbon dioxide and giving off acetate, methane and water13,16. Mounting evidence18,​19,​20,​21,​22 suggests that the transition from non-life to life may have taken place before 3.7 Ga—a time from which few rocks remain23.

(i) Life emerges; epoch of geochemistry begins. (ii) Anoxygenic photosynthesis: start of energy epoch 2, sunlight. (iii) Emergence of cyanobacteria. (iv) Great Oxidation Event: energy epoch 3, oxygen. (v) Probable eukaryotic fossils appear. (vi) Fossils of red algae appear. (vii) Start of energy epoch 4, flesh. (viii) Vascular plants colonize land; fire appears on Earth. Finally, the burning logs indicate the start of energy epoch 5, fire. The dates of (i)–(iii) are highly uncertain. For (i) I have taken the earliest date for which there is evidence consistent with life20. For (ii) I have taken the earliest date for which there is evidence consistent with photosynthesis18,19,21. For (iii), I have marked the date currently supported by fossil evidence for the presence of cyanobacteria (see main text, ‘Cyanobacteria and the oxygenation of the air’). Tick marks represent intervals of 25 million years. Figure drawn by F. Zsolnai.

Energy epoch one: geochemical energy

Analysis of biochemical pathways suggests that, under favourable environmental conditions, early autotrophs could readily have adopted a heterotrophic lifestyle, feeding on the contents of dead cells24. At this time in Earth history, oxygen was at trace levels25, so the first ecosystems would have been anaerobic.

Early ecosystems may have quickly diversified to take the form of a microbial mat, where the waste products of one group of life forms feed the metabolism of another26,27. Such an arrangement generates layered communities of organisms, each layer having a different metabolic speciality28,29. In anaerobic ecosystems of this type, mobile predation is essentially nonexistent: growth rates are so low that hunting and consuming other organisms doesn’t yield enough energy30. Viruses, however, are likely to have been an important force from early in the history of life31. They act as agents of death—and by lysing cells, they would have provided additional sources of organic carbon to heterotrophs. Viruses also transport genes from one host to another, and thus may have enabled the spread of evolutionary innovations. Many of the coevolutionary selection pressures of the modern biosphere would have been minimal (for example, predation and the opportunity to live inside other organisms) or absent (for example, sexual selection).

The niches available would have been those near sources of geochemical energy, suggesting a patchy, local distribution of life. Consistent with this, geochemical models32,​33,​34 suggest that the productivity of the biosphere before it was powered by the sun would have been at least a thousand times less than it is today, and may have been one million times less.

Owing to the scarcity of rocks from Earth’s remote past, the impact of early life on the planetary environment is also hard to assess. Life inevitably creates a suite of changes in its environment (Box 1), and the establishment of life would have initiated biogeochemical cycling, but owing to the low productivity of the biosphere, the initial effects are likely to have been small32,​33,​34. . .

Continue reading.

Written by LeisureGuy

22 May 2017 at 2:09 pm

Posted in Evolution, Science

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