Later On

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Archive for the ‘Evolution’ Category

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:

Abstract

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

Is Consciousness An Illusion?

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In the NY Review of Books Thomas Nagel reviews a new book by Daniel Dennett (whom I wish had known about back when he started):

From Bacteria to Bach and Back: The Evolution of Minds
by Daniel C. Dennett
Norton, 476 pp., $28.95

For fifty years the philosopher Daniel Dennett has been engaged in a grand project of disenchantment of the human world, using science to free us from what he deems illusions—illusions that are difficult to dislodge because they are so natural. In From Bacteria to Bach and Back, his eighteenth book (thirteenth as sole author), Dennett presents a valuable and typically lucid synthesis of his worldview. Though it is supported by reams of scientific data, he acknowledges that much of what he says is conjectural rather than proven, either empirically or philosophically.

Dennett is always good company. He has a gargantuan appetite for scientific knowledge, and is one of the best people I know at transmitting it and explaining its significance, clearly and without superficiality. He writes with wit and elegance; and in this book especially, though it is frankly partisan, he tries hard to grasp and defuse the sources of resistance to his point of view. He recognizes that some of what he asks us to believe is strongly counterintuitive. I shall explain eventually why I think the overall project cannot succeed, but first let me set out the argument, which contains much that is true and insightful.

The book has a historical structure, taking us from the prebiotic world to human minds and human civilization. It relies on different forms of evolution by natural selection, both biological and cultural, as its most important method of explanation. Dennett holds fast to the assumption that we are just physical objects and that any appearance to the contrary must be accounted for in a way that is consistent with this truth. Bach’s or Picasso’s creative genius, and our conscious experience of hearing Bach’s Fourth Brandenburg Concerto or seeing Picasso’s Girl Before a Mirror, all arose by a sequence of physical events beginning with the chemical composition of the earth’s surface before the appearance of unicellular organisms. Dennett identifies two unsolved problems along this path: the origin of life at its beginning and the origin of human culture much more recently. But that is no reason not to speculate.

The task Dennett sets himself is framed by a famous distinction drawn by the philosopher Wilfrid Sellars between the “manifest image” and the “scientific image”—two ways of seeing the world we live in. According to the manifest image, Dennett writes, the world is

full of other people, plants, and animals, furniture and houses and cars…and colors and rainbows and sunsets, and voices and haircuts, and home runs and dollars, and problems and opportunities and mistakes, among many other such things. These are the myriad “things” that are easy for us to recognize, point to, love or hate, and, in many cases, manipulate or even create…. It’s the world according to us.

According to the scientific image, on the other hand, the world

is populated with molecules, atoms, electrons, gravity, quarks, and who knows what else (dark energy, strings? branes?).

This, according to Dennett, is the world as it is in itself, not just for us, and the task is to explain scientifically how the world of molecules has come to include creatures like us, complex physical objects to whom everything, including they themselves, appears so different.

He greatly extends Sellars’s point by observing that the concept of the manifest image can be generalized to apply not only to humans but to all other living beings, all the way down to bacteria. All organisms have biological sensors and physical reactions that allow them to detect and respond appropriately only to certain features of their environment—“affordances,” Dennett calls them—that are nourishing, noxious, safe, dangerous, sources of energy or reproductive possibility, potential predators or prey.

For each type of organism, whether plant or animal, these are the things that define their world, that are salient and important for them; they can ignore the rest. Whatever the underlying physiological mechanisms, the content of the manifest image reveals itself in what the organisms do and how they react to their environment; it need not imply that the organisms are consciously aware of their surroundings. But in its earliest forms, it is the first step on the route to awareness.

The lengthy process of evolution that generates these results is first biological and then, in our case, cultural, and only at the very end is it guided partly by intelligent design, made possible by the unique capacities of the human mind and human civilization. But as Dennett says, the biosphere is saturated with design from the beginning—everything from the genetic code embodied in DNA to the metabolism of unicellular organisms to the operation of the human visual system—design that is not the product of intention and that does not depend on understanding.

One of Dennett’s most important claims is that most of what we and our fellow organisms do to stay alive, cope with the world and one another, and reproduce is not understood by us or them. It is competence without comprehension. This is obviously true of organisms like bacteria and trees that have no comprehension at all, but it is equally true of creatures like us who comprehend a good deal. Most of what we do, and what our bodies do—digest a meal, move certain muscles to grasp a doorknob, or convert the impact of sound waves on our eardrums into meaningful sentences—is done for reasons that are not our reasons. Rather, they are what Dennett calls free-floating reasons, grounded in the pressures of natural selection that caused these behaviors and processes to become part of our repertoire. There are reasons why these patterns have emerged and survived, but we don’t know those reasons, and we don’t have to know them to display the competencies that allow us to function.

Nor do we have to understand the mechanisms that underlie those competencies. In an illuminating metaphor, Dennett asserts that the manifest image that depicts the world in which we live our everyday lives is composed of a set of user-illusions,

like the ingenious user-illusion of click-and-drag icons, little tan folders into which files may be dropped, and the rest of the ever more familiar items on your computer’s desktop. What is actually going on behind the desktop is mind-numbingly complicated, but users don’t need to know about it, so intelligent interface designers have simplified the affordances, making them particularly salient for human eyes, and adding sound effects to help direct attention. Nothing compact and salient inside the computer corresponds to that little tan file-folder on the desktop screen.

He says that the manifest image of each species is “a user-illusion brilliantly designed by evolution to fit the needs of its users.” In spite of the word “illusion” he doesn’t wish simply to deny the reality of the things that compose the manifest image; the things we see and hear and interact with are “not mere fictions but different versions of what actually exists: real patterns.” The underlying reality, however, what exists in itself and not just for us or for other creatures, is accurately represented only by the scientific image—ultimately in the language of physics, chemistry, molecular biology, and neurophysiology.

Our user-illusions were not, like the little icons on the desktop screen, created by an intelligent interface designer. Nearly all of them—such as our images of people, their faces, voices, and actions, the perception of some things as delicious or comfortable and others as disgusting or dangerous—are the products of “bottom-up” design, understandable through the theory of evolution by natural selection, rather than “top-down” design by an intelligent being. Darwin, in what Dennett calls a “strange inversion of reasoning,” showed us how to resist the intuitive tendency always to explain competence and design by intelligence, and how to replace it with explanation by natural selection, a mindless process of accidental variation, replication, and differential survival.

As for the underlying mechanisms, we now have a general idea of how they might work because of another strange inversion of reasoning, due to Alan Turing, the creator of the computer, who saw how a mindless machine could do arithmetic perfectly without knowing what it was doing. This can be applied to all kinds of calculation and procedural control, in natural as well as in artificial systems, so that their competence does not depend on comprehension. Dennett’s claim is that when we put these two insights together, we see that

all the brilliance and comprehension in the world arises ultimately out of uncomprehending competences compounded over time into ever more competent—and hence comprehending—systems. This is indeed a strange inversion, overthrowing the pre-Darwinian mind-first vision of Creation with a mind-last vision of the eventual evolution of us, intelligent designers at long last.

And he adds: . . .

Continue reading.

Written by LeisureGuy

20 May 2017 at 2:09 pm

How can a bunch of cells do what humans do?

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If you look at a human cell by cell, you see a great number of little organic factories, busily at working making and using proteins, metabolizing fuel via the energy-rich molecules that the mitochondria make from nutrients, and basically following a path of least effort, with no consciousness whatsoever.

But pile up enough of these cells, organize them appropriate, and you have someone writing thoughts in a language that the cells have created over time, with someone else reading it and understanding the thought.

Somehow it seems weird that languaage, thought, music, and human culture and knowledge in general can come to be from cells, given that cells basically know nothing. Emergence is really amazing. No matter how much you studied cells and how they are hooked up, it is hard to see how you could predict human knowledge and activity.

Written by LeisureGuy

16 May 2017 at 9:01 am

Ancient stone carvings confirm how comet struck Earth in 10,950BC, sparking the rise of civilisations

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Sarah Knapton reports in the Telegraph:

Ancient stone carvings confirm that a comet struck the Earth around 11,000BC, a devastating event which wiped out woolly mammoths and sparked the rise of civilisations.

Experts at the University of Edinburgh analysed mysterious symbols carved onto stone pillars at Gobekli Tepe in southern Turkey, to find out if they could be linked to constellations.

The markings suggest that a swarm of comet fragments hit Earth at the exact same time that a mini-ice age struck, changing the entire course of human history.

Scientists have speculated for decades that a comet could be behind the sudden fall in temperature during a period known as the Younger Dryas. But recently the theory appeared to have been debunked by new dating of meteor craters in North America where the comet is thought to have struck.

However, when engineers studied animal carvings made on a pillar – known as the vulture stone – at Gobekli Tepe they discovered that the creatures were actually astronomical symbols which represented constellations and the comet.

The idea had been originally put forward by author Graham Hancock in his book Magicians of the Gods.

Using a computer programme to show where the constellations would have appeared above Turkey thousands of years ago, they were able to pinpoint the comet strike to 10,950BC, the exact time the Younger Dryas begins according to ice core data from Greenland.

The Younger Dryas is viewed as a crucial period for humanity, as it roughly coincides with the emergence of agriculture and the first Neolithic civilisations.

Before the strike, vast areas of wild wheat and barley had allowed nomadic hunters in the Middle East to establish permanent base camps. But the difficult climate conditions following the impact forced communities to come together and work out new ways of maintaining the crops, through watering and selective breeding. Thus farming began, allowing the rise of the first towns.

Edinburgh researchers said the carvings appear to have remained important to the people of Gobekli Tepe for millennia, suggesting that the event and cold climate that followed likely had a very serious impact.

Dr Martin Sweatman, of the University of Edinburgh’s School of Engineering, who led the research, said: “I think this research, along with the recent finding of a widespread platinum anomaly across the North American continent virtually seal the case in favour of (a Younger Dryas comet impact).

“Our work serves to reinforce that physical evidence. What is happening here is the process of paradigm change.

“It appears Göbekli Tepe was, among other things, an observatory for monitoring the night sky.

“One of its pillars seems to have served as a memorial to this devastating event – probably the worst day in history since the end of the ice age.”

Gobekli Tepe, is thought to be the world’s oldest temple site, which dates from around 9,000BC, predating Stonehenge by around 6,000 years. . .

Continue reading.

Written by LeisureGuy

1 May 2017 at 11:28 am

Climate denial in schools: Diseducating the young

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Emmalina Glinskis reports in Vice News:

Legislation proposed across the country since Donald Trump’s election threatens to bring climate change denial into the classroom under the guise of “academic freedom.”

Currently, six states have legislative measures pending or already on the books that would allow anti-science rhetoric, including the rejection of global warming, to seep its way into schools’ curricula. While these types of proposals have become fairly routine in certain states, some of the most recent crop have advanced farther than in the past.

Senate Bill 393 in Oklahoma, for example, would permit teachers to paint established science on both evolution and climate change as “controversial.” The “controversy,” however, doesn’t really exist — more than 97 percent of actively publishing, accredited climate scientists agree that global warming trends over the past century are directly attributable to human activity. And some teachers might already be misleading students.

Since its initial proposal in early February, the bill passed out of the Senate and into the House, where it circumvented the House Education Committee and now heads for a full House vote.

“It’s important to note that this exact bill in Oklahoma has been proposed in the past seven times, and it’s only this year, at a time when there’s federal policy that’s egregiously anti-science, that the bill made it so far,” said Lisa Hoyos, the director of Climate Parents, a Sierra Club–affiliated organization that supports climate change education. In fact, the bill’s sponsor, Republican Sen. Josh Brecheen, has introduced similar legislation every year since 2011. He’s said he wants “every publicly funded Oklahoma school to teach the debate of creation vs. evolution.”

A bill similar to Oklahoma’s is currently working its way through the Texas Legislature. And Florida has two bills pending aimed at letting local residents object to the use of certain instructional materials, such as textbooks that teach human-induced climate change, in public schools.

Some states are passing resolutions, which have a less direct influence but send strong signals about where the state Legislature stands on climate change. In February, Indiana successfully passed its Senate resolutionsupporting teachers “who choose to teach a diverse curriculum,” giving climate denial and creationism the chance to enter classrooms. A similar “academic freedom” resolution has already made its way through the Alabama House. Finally, Idaho locked in a legally binding Senate resolution in March that deletes material about climate change and human impact on the environment from the state’s science standards.

“Academic freedom bills are the new normal,” said Glenn Branch, deputy director for the National Center for Science Education. According to him, state legislators across the country have filed over 70 academic freedom bills since 2004. That’s when state-level legislation began using vague language to protect teachers’ “academic freedom” by permitting educators to teach about the “strengths and weaknesses” of existing scientific theories. The bill pending in Texas, for example, includes “climate change, biological evolution, the chemical origins of life, and human cloning” among its controversial theories.

“We’re very familiar with this type of language, and it has clearly morphed from the anti-evolution education perspective into the anti-climate change perspective,” said David Evans, executive director of the National Science Teacher Association, which played a key role in shaping the Next Generation Science Standards. The standards, adopted by 18 states and Washington, D.C., since 2015, included the first-ever recommendations for students to learn about human-induced global warming.

These old proposals are being made new again along with a stark ideological switch at the federal level. The president has called climate change a “hoax.” The EPA administrator doesn’t believe carbon dioxide contributes to global warming. And the White House’s continued rollback of environmental regulations reflects those viewpoints. In fact, a series of Pew studies shows 2016 marked the largest gap yet between Republicans and Democrats over belief in human-caused global warming.

“It’s no coincidence when you have an administration banning climate science material from federal websites that science deniers in states would feel emboldened. But at the end of the day, it’s our kids that get shortchanged,” Hoyos said. Her organization, Climate Parents, is circulating a petition — with over 2,250 signatures so far — that urges Republican Gov. Mary Fallin to veto Oklahoma’s bill and stand by the science standards she passed in 2014.  . .

Continue reading.

America seems determined to move from reality to delusion, in this case prompted by the fossil-fuel industry, which sees reality as having an adverse impact on profits. But delusion has its dangers, as our grandchildren will know from bitter experience.

Written by LeisureGuy

1 May 2017 at 11:11 am

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