Archive for the ‘Evolution’ Category
Amanda Gefter has an interesting interview with Donald Hoffman in Quanta:
As we go about our daily lives, we tend to assume that our perceptions — sights, sounds, textures, tastes — are an accurate portrayal of the real world. Sure, when we stop and think about it — or when we find ourselves fooled by a perceptual illusion — we realize with a jolt that what we perceive is never the world directly, but rather our brain’s best guess at what that world is like, a kind of internal simulation of an external reality. Still, we bank on the fact that our simulation is a reasonably decent one. If it wasn’t, wouldn’t evolution have weeded us out by now? The true reality might be forever beyond our reach, but surely our senses give us at least an inkling of what it’s really like.
Not so, says Donald D. Hoffman, a professor of cognitive science at the University of California, Irvine. Hoffman has spent the past three decades studying perception, artificial intelligence, evolutionary game theory and the brain, and his conclusion is a dramatic one: The world presented to us by our perceptions is nothing like reality. What’s more, he says, we have evolution itself to thank for this magnificent illusion, as it maximizes evolutionary fitness by driving truth to extinction.
Getting at questions about the nature of reality, and disentangling the observer from the observed, is an endeavor that straddles the boundaries of neuroscience and fundamental physics. On one side you’ll find researchers scratching their chins raw trying to understand how a three-pound lump of gray matter obeying nothing more than the ordinary laws of physics can give rise to first-person conscious experience. This is the aptly named “hard problem.”
On the other side are quantum physicists, marveling at the strange fact that quantum systems don’t seem to be definite objects localized in space until we come along to observe them — whether we are conscious humans or inanimate measuring devices. Experiment after experiment has shown — defying common sense — that if we assume that the particles that make up ordinary objects have an objective, observer-independent existence, we get the wrong answers. The central lesson of quantum physics is clear: There are no public objects sitting out there in some preexisting space. As the physicist John Wheeler put it, “Useful as it is under ordinary circumstances to say that the world exists ‘out there’ independent of us, that view can no longer be upheld.”
So while neuroscientists struggle to understand how there can be such a thing as a first-person reality, quantum physicists have to grapple with the mystery of how there can be anything but a first-person reality. In short, all roads lead back to the observer. And that’s where you can find Hoffman — straddling the boundaries, attempting a mathematical model of the observer, trying to get at the reality behind the illusion. Quanta Magazine caught up with him to find out more. An edited and condensed version of the conversation follows.
QUANTA MAGAZINE: People often use Darwinian evolution as an argument that our perceptions accurately reflect reality. They say, “Obviously we must be latching onto reality in some way because otherwise we would have been wiped out a long time ago. If I think I’m seeing a palm tree but it’s really a tiger, I’m in trouble.”
DONALD HOFFMAN: Right. The classic argument is that those of our ancestors who saw more accurately had a competitive advantage over those who saw less accurately and thus were more likely to pass on their genes that coded for those more accurate perceptions, so after thousands of generations we can be quite confident that we’re the offspring of those who saw accurately, and so we see accurately. That sounds very plausible. But I think it is utterly false. It misunderstands the fundamental fact about evolution, which is that it’s about fitness functions — mathematical functions that describe how well a given strategy achieves the goals of survival and reproduction. The mathematical physicist Chetan Prakash proved a theorem that I devised that says: According to evolution by natural selection, an organism that sees reality as it is will never be more fit than an organism of equal complexity that sees none of reality but is just tuned to fitness. Never.
You’ve done computer simulations to show this. Can you give an example?
Suppose in reality there’s a resource, like water, and you can quantify how much of it there is in an objective order — very little water, medium amount of water, a lot of water. Now suppose your fitness function is linear, so a little water gives you a little fitness, medium water gives you medium fitness, and lots of water gives you lots of fitness — in that case, the organism that sees the truth about the water in the world can win, but only because the fitness function happens to align with the true structure in reality. Generically, in the real world, that will never be the case. Something much more natural is a bell curve — say, too little water you die of thirst, but too much water you drown, and only somewhere in between is good for survival. Now the fitness function doesn’t match the structure in the real world. And that’s enough to send truth to extinction. For example, an organism tuned to fitness might see small and large quantities of some resource as, say, red, to indicate low fitness, whereas they might see intermediate quantities as green, to indicate high fitness. Its perceptions will be tuned to fitness, but not to truth. It won’t see any distinction between small and large — it only sees red — even though such a distinction exists in reality.
But how can seeing a false reality be beneficial to an organism’s survival?
There’s a metaphor that’s only been available to us in the past 30 or 40 years, and that’s the desktop interface. Suppose there’s a blue rectangular icon on the lower right corner of your computer’s desktop — does that mean that the file itself is blue and rectangular and lives in the lower right corner of your computer? Of course not. But those are the only things that can be asserted about anything on the desktop — it has color, position and shape. Those are the only categories available to you, and yet none of them are true about the file itself or anything in the computer. They couldn’t possibly be true. That’s an interesting thing. You could not form a true description of the innards of the computer if your entire view of reality was confined to the desktop. And yet the desktop is useful. That blue rectangular icon guides my behavior, and it hides a complex reality that I don’t need to know. That’s the key idea. Evolution has shaped us with perceptions that allow us to survive. They guide adaptive behaviors. But part of that involves hiding from us the stuff we don’t need to know. And that’s pretty much all of reality, whatever reality might be. If you had to spend all that time figuring it out, the tiger would eat you.
So everything we see is one big illusion?
We’ve been shaped to have perceptions that keep us alive, so we have to take them seriously. If I see something that I think of as a snake, I don’t pick it up. If I see a train, I don’t step in front of it. I’ve evolved these symbols to keep me alive, so I have to take them seriously. But it’s a logical flaw to think that if we have to take it seriously, we also have to take it literally.
If snakes aren’t snakes and trains aren’t trains, what are they?
Snakes and trains, like the particles of physics, have no objective, observer-independent features. The snake I see is a description created by my sensory system to inform me of the fitness consequences of my actions. Evolution shapes acceptable solutions, not optimal ones. A snake is an acceptable solution to the problem of telling me how to act in a situation. My snakes and trains are my mental representations; your snakes and trains are your mental representations.
How did you first become interested in these ideas?
As a teenager, I was very interested in the question “Are we machines?” My reading of the science suggested that we are. But my dad was a minister, and at church they were saying we’re not. So I decided I needed to figure it out for myself. It’s sort of an important personal question — if I’m a machine, I would like to find that out! And if I’m not, I’d like to know, what is that special magic beyond the machine? So eventually in the 1980s I went to the artificial intelligence lab at MIT and worked on machine perception. The field of vision research was enjoying a newfound success in developing mathematical models for specific visual abilities. I noticed that they seemed to share a common mathematical structure, so I thought it might be possible to write down a formal structure for observation that encompassed all of them, perhaps all possible modes of observation. I was inspired in part by Alan Turing. When he invented the Turing machine, he was trying to come up with a notion of computation, and instead of putting bells and whistles on it, he said, Let’s get the simplest, most pared down mathematical description that could possibly work. And that simple formalism is the foundation for the science of computation. So I wondered, could I provide a similarly simple formal foundation for the science of observation?
A mathematical model of consciousness.
That’s right. My intuition was, there are conscious experiences. I have pains, tastes, smells, all my sensory experiences, moods, emotions and so forth. So I’m just going to say: One part of this consciousness structure is a set of all possible experiences. When I’m having an experience, based on that experience I may want to change what I’m doing. So I need to have a collection of possible actions I can take and a decision strategy that, given my experiences, allows me to change how I’m acting. That’s the basic idea of the whole thing. I have a space X of experiences, a space G of actions, and an algorithm D that lets me choose a new action given my experiences. Then I posited a W for a world, which is also a probability space. Somehow the world affects my perceptions, so there’s a perception map P from the world to my experiences, and when I act, I change the world, so there’s a map A from the space of actions to the world. That’s the entire structure. Six elements. The claim is: This is the structure of consciousness. I put that out there so people have something to shoot at.
But if there’s a W, are you saying there is an external world?
Here’s the striking thing about that. I can pull the W out of the model and stick a conscious agent in its place and get a circuit of conscious agents. In fact, you can have whole networks of arbitrary complexity. And that’s the world.
The world is just other conscious agents?
I call it conscious realism: Objective reality is just conscious agents, just points of view. Interestingly, I can take two conscious agents and have them interact, and the mathematical structure of that interaction also satisfies the definition of a conscious agent. This mathematics is telling me something. I can take two minds, and they can generate a new, unified single mind. Here’s a concrete example. We have two hemispheres in our brain. But when you do a split-brain operation, a complete transection of the corpus callosum, you get clear evidence of two separate consciousnesses. Before that slicing happened, it seemed there was a single unified consciousness. So it’s not implausible that there is a single conscious agent. And yet it’s also the case that there are two conscious agents there, and you can see that when they’re split. I didn’t expect that, the mathematics forced me to recognize this. It suggests that I can take separate observers, put them together and create new observers, and keep doing this ad infinitum. It’s conscious agents all the way down.
If it’s conscious agents all the way down, all first-person points of view, what happens to science? Science has always been a third-person description of the world. . .
Why don’t they just feed us kibble? It’s going in that direction. — Jaw-dropping story of a Silicon Valley juice-box startup
Yes, really. Read this NY Times article by David Gelles: what sure seems like a crackpot money-sinkhole of an idea is sold on the basis of machine feeding, more or less. From the article:
By some measures, Juicero is very much on trend. Soylent, a liquefied meal replacement, is already popular among single-minded coders too busy to eat. Chime, a device meant to brew Indian chai, will soon be on the market. A company called Tovala is raising money on Kickstarter, hoping to build a hybrid microwave and toaster, and also sell specialized meal packs.
You have to read the article to believe it.
BTW, note also in the article this very clear depiction of meme competition and evolution (and dead-ends).
To succeed, Juicero will have to buck these trends, and also clear a more pedestrian hurdle — persuading people to pay a premium for another kitchen doodad. “Seven hundred dollars for a small cooking appliance is extremely high,” said Virginia Lee, beverage analyst for Euromonitor. “There are a lot of appliances competing for counter space, never mind the wallet.”
And I personally, as a type-2 diabetic (and I’ve heard that there are more than a few of us around), juice is contraindicated: a type-2 diabetic needs the fiber that the Juicero discard and definitely doesn’t need the quickly-digestible high-carb product. So I think the reception might be substantially underwhelming. But I’m sure he’s made his bundle, which is what the whole exercise seems to be about, unless it actually is to move us all closer to a piped-in diet of kibble and sludge.
One thing about evolution: it may be blindly responding to the current environment, but it never ever stops—and over (long periods of) time, it does produce amazing results.
Take food. I recently blogged how some humans have genetically adapted to vegetarian diets. That makes sense if for many generations a regional group of humans subsist on a vegetarian diet: those who can get more nutrients from non-meat foods will then have a survival advantage, so that tiny mutations and changes in that direction tend to accumulate. At one extreme of this in the animal kingdom, you have animals that can detrive nutrients from bamboo (like the giant panda), a food with not much nutritional density.
And natural selection also favored those among the Inuit who could best tolerate the high-meat, high-fat diet on which they subsist, so they evolved to do some tricks with the available foods.
And then another obvious example occurred to me: how a mutation for lactose tolerance conveyed a survival advantage to some groups and enabled some humans to digest milk as adults. (More (and better) information here.)
I continue to be unable to understand how so many in the US can deny the truth of evolution when the evidence is so overwhelming and the idea makes so much sense. But I suppose I could say the same about global warming.
Certainly humans (and other predators) find hope a survival advantage. I’ve watched my cats check certain spots for prey, day after day, despite prey never being present. But predators that lose hope—that give up looking—would not survive so well as those that always continue looking, despite many failures. So hope certainly would seem to convey a survival advantage and thus be favored by natural selection.
As this article points out, attributing events to a conscious agent that has a purpose also offers a survival advantage, even though the result is many false positives (since most events are random and lacking in purpose—e.g., the tree that topples onto your car in a windstorm: it’s not doing that for a purpose, it just happened. It’s not because (for example) you overdrew your account at the bank or were mean to your kids, but it might feel that way—particularly if you already harbor beliefs in a conscious controlling superpower.
Sarah Emerson writes at Motherboard:
More than eight in ten people worldwide have some sort of religious belief, according to a Pew Research Center study. Approximately one third of those people are Christian.
Even though the percentage of people who identify as atheist is on the rise, the world is an overwhelmingly devout place.
And while science versus religion has been debated since classical antiquity, we’re still a long ways off from definitively knowing how and why the human species came to attribute its existence—and the creation of everything in the universe—to spiritual entities we cannot see, and cannot prove to be real.
One theory, as illustrated in this short video from New Scientist’s Explanimator series,presents the possibility that religion emerged a long time ago as an evolutionary adaptation. According to this argument, early forms of organized religion were necessary for the building of clans that helped to ensure the long-term survival of large groups of people. Religion encouraged clans to unite around a shared belief or ritual, and allowed for the cultivation of community practices like foraging for food, hunting, and sharing childcare duties. These things would have given religious groups a key advantage over their competitors.
So as these clans continued to thrive and survive, their genes were passed on, and religion was selected for by evolution, according to the video. Clans, over time, grew into large communities that supposedly benefited from the stability that a shared faith provided, until religion eventually appeared in some form throughout every human society.
No matter how we ended up like this, our brains do seem biologically wired for religion, the video adds. “Many think our brains evolved to assume that things that happen in the world have a purpose, and if that purpose is mysterious, perhaps an unseen supernatural agent is at work.”
The argument here is that humans are “strongly attracted to explanations of events in terms of agent action—particularly events that are not readily explained in terms of ordinary causation.” Existential threats scare us, and we desire tools that help us reason with them.
Religion is therefore much like language. Humans aren’t born with an innate knowledge of French, English, Chinese, or whatever. But we are born with the ability to learn those languages based on the societies into which we are born or raised, the video adds. They help us to make sense of the world around us. Likewise, none of us are born believers, but we can pick up our faiths depending on whether or not we’re raised to believe.
It’s pointed out that religion came to be so diverse because of the different needs of different types of societies. Agrarian tribes, for example, believed in gods that represented the things they found important such as crops, water, or fire. While larger, sedentary civilizations often worshiped entities responsible for protecting elements like human affairs [e.g., a god of war – LG].
But the larger these communities grew, . . .
Ariana Eunjung Cha reports in the Washington Post:
Why is it that some people can stay healthy only by sticking to a strict vegetarian diet? Why is it that others can eat a steak a day, remain slim, avoid heart disease and feel like a million dollars? The answers may lie in your heritage.
Cornell University researchers have found a fascinating genetic variation that they said appears to have evolved in populations that favored vegetarian diets over hundreds of generations. The geography of the vegetarian allele is vast and includes people from India, Africa and parts of East Asia who are known to have green diets even today.
Researcher Kaixiong Ye said that the vegetarian adaptation allows people to “efficiently process omega-3 and omega-6 fatty acids and convert them into compounds essential for early brain development.”
Omega-3 is found in fish, whole grains, olive oil, fruits and vegetables, while omega-6 is found in beef, pork products and many packaged snack foods such as cookies, candies, cakes and chips, as well as in nuts and vegetable oils.
Nutritionists believe that getting a good balance of these two types of fatty acids in the diet is essential to staying healthy. The body can’t produce these substances naturally, so it must get them from food.
Omega-3 is anti-inflammatory and helps regulate metabolism, which affects a wide range of functions in the body. In recent years, supplements rich in omega-3 have been trendy, based on the idea that it may reduce risk of heart disease. (The Food and Drug Administration says the evidence supports this theory but isn’t conclusive.) Omega-6 contributes to inflammation and plays an important role in skin and hair growth, bone health and reproductive health. Inflammatory responses are essential to our survival. They help fight off infections and protect us from injury. But if the response is excessive, it can lead to all kinds of problems and may contribute to a higher risk of heart disease, cancer and Alzheimer’s disease.
Studies have suggested that humans evolved on a diet with a ratio of omega-6 to omega-3 essential fatty acids of 1:1 but that the Western diet has a ratio that is closer to 15 or 16:1. The Mediterranean diet, in contrast, is closer to having an equal balance of the two and is recommended by many doctors.
But this new study, funded by the National Institutes of Health and the U.S. Department of Agriculture, shows that different people may need radically different ratios of the substances in their diet depending on their genes, and it supports the growing evidence against a one-size-fits-all approach to nutrition and for highly personalized advice.
The existence of the vegetarian allele implies that, for people with this variation, straying from that diet — by eating a lot of red meat, for example — may make them more susceptible to inflammation, because their bodies were optimized for a different mix of inputs.
The research, published Wednesday in the journal Molecular Biology and Evolution, involved two parts. . .
One standard argument from those who don’t understand and thus disbelieve evolution is that they would believe if any transitional species could be discovered—e.g., of the transition of the ancestors of modern whales moving from land-dwelling to sea-dwelling. Of course, whenever such fossils are found, the goalposts are moved, and some additional thing must be found.
One biggie, of course, which is of interest to believers in evolution as well as skeptics of it, would be the discovery of fossils showing the transition of vertebrates from sea-dwelling species to land-dwelling species, and lo! such a species has been found still living.
Obviously, this small (5-cm) fish is not the ancestor of current land-dwelling vertebrates, but it exemplifies the evolutionary transition from swimming in water to walking on land. It’s a fascinating discovery, reported in the NY Times by Carl Zimmer:
It’s one of the most famous chapters in evolution, so familiar that it regularly inspires New Yorker cartoons: Some 375 million years ago, our ancestors emerged from the sea, evolving from swimming fish to vertebrates that walked on land.
Scientists still puzzle over exactly how the transition from sea to land took place. For the most part, they’ve had to rely on informationgleaned from fossils of some of the intermediate species.
But now a team of researchers has found a remarkable parallel to one of evolution’s signature events. In a cave in Thailand, they’ve discovered that a blind fish walks the way land vertebrates do.
The waterfall-climbing cave fish, Cryptotora thamicola, has even evolved many of the skeletal features that our ancestors did for walking, including a full-blown pelvis.
“It’s really weird,” said John R. Hutchinson, a biologist at the Royal Veterinary College at the University of London who was not involved in the new study. “It’s a good example of how much fish diversity there’s left to be discovered.”
Drop an ordinary fish on the ground, and it will flop around helplessly: Its fins are adapted for pushing against water, not fighting gravity.
The early land vertebrates, known as tetrapods, evolved adaptations that enabled them to move efficiently over solid ground. A pelvis joined their hind limbs to their spines, for example. Their vertebrae grew flanges so that they interlocked, helping the spine hold itself stiff and straight even when being pulled down by gravity.
These adaptations led tetrapods to walk in a distinctive fashion, moving their forelegs and hind legs together in a cycle. Early tetrapods probably walked much the way salamanders do today, bending their trunk from side to side as they traveled.
All tetrapods descend from a single ancestor — a single lineage of fish that managed to spread on land. Some other fishes evolved vaguely similar ways of moving around.
On coral reefs, for example, frogfish can push off surfaces with their fins. They have a gait that looks something like a slow-motion walk. But they can manage this movement only underwater.
Other fish can move on land, although none of them use a tetrapod gait to do so. Some simply squirm, while others, like mudskippers, rely on their front fins as crutches. In Hawaii, the Nopili rock-climbing goby climbs up rock faces by using its mouth as a suction cup.
The waterfall-climbing cave fish is leaps ahead of them, it turns out. Pale and blind, the two-inch-long fish feeds on microbes and organic matter growing on the cave walls. It was discovered in 1985, deep inside a system of caves in northern Thailand, and has been found nowhere else.
While other fish in the caves enjoy a life in quiet pools, the waterfall-climbing cave fish clambers up slick rocks as water crashes over it. . .
Continue reading. At the link, a GIF of the little guy in action.
Obviously the transition this little fish represents was long ago accomplished, but evolution doesn’t care: evolution is blind. The variations that result in a survival advantage will have more progeny, and that’s the story of evolution: the process never stops and never is directed at any particular goal. It just churns away and the survival advantages produce the pressure that helps the variations that have such an advantage. If conditions change, which variations are helpful also change.
I have to say I simply cannot grasp the logic (if any) if those who disbelieve in evolution. I do not see how they can have the slightest grasp of modern biology, which shows evolution’s work on every hand. It must be that such skeptics simply are ignorant of biology, which of course makes one wonder how they can believe that they are in a position to judge the reality of evolution. I suppose it’s the Dunning-Kruger effect at work: great confidence because the level of knowledge is so tiny.
Once you have a replicator that allows occasional variation, evolution kicks in and the process of natural selection effectively pushes things along, whether it is lifeforms or memes. But how to get that first replicator. Emily Singer interviews David Deamer in Quanta:
For the past 40 years, David Deamer has been obsessed with membranes. Specifically, he is fascinated by cell membranes, the fatty envelopes that encase our cells. They may seem unremarkable, but Deamer, a biochemist at the University of California, Santa Cruz, is convinced that membranes like these sparked the emergence of life. As he envisions it, they corralled the chemicals of the early Earth, serving as an incubator for the reactions that created the first biological molecules.
One of the great initial challenges in the emergence of life was for simple, common molecules to develop greater complexity. This process resulted, most notably, in the appearance of RNA, long theorized to have been the first biological molecule. RNA is a polymer — a chemical chain made up of repeating subunits — that has proved extremely difficult to make under conditions similar to those on the early Earth.
Deamer’s team has shown not only that a membrane would serve as a cocoon for this chemical metamorphosis, but that it might also actively push the process along. Membranes are made up of lipids, fatty molecules that don’t dissolve in water and can spontaneously form tiny packages. In the 1980s, Deamer showed that the ingredients for making these packages would have been readily available on the early Earth; he isolated membrane-forming compounds from the Murchison meteorite, which exploded over Australia in 1969. Later, he found that lipids can help form RNA polymers and then enclose them in a protective coating, creating a primitive cell.
Over the past few years, Deamer has expanded his membrane-first approach into a comprehensive vision for how life emerged. According to his model, proto-cells on the early Earth were made up of different components. Some of these components could help the proto-cell, perhaps by stabilizing its protective membranes or giving it access to an energy supply. At some point, one or more RNAs developed the ability to replicate, and life as we know it began to stir.
Deamer thinks that volcanic landmasses similar to those in Iceland today would have made a hospitable birthplace for his proto-cells. Freshwater pools scattered across steamy hydrothermal fields would be subject to regular rounds of heating and cooling. That cycle could have concentrated the necessary ingredients — including both lipids and the building blocks for RNA — and provided the energy needed to stitch those building blocks into biological polymers. Deamer is now trying to re-create these conditions in the lab. His goal is to synthesize RNA and DNA polymers.
Quanta Magazine spoke with Deamer at a conference on the origins of life in Galveston, Texas, earlier this year. An edited and condensed version of that conversation follows.
QUANTA MAGAZINE: What have been the biggest accomplishments of researchers seeking to understand life’s origins? What questions remain to be solved?
DAVID DEAMER: We have really made progress since the 1950s. We have figured out that the first life originated at least 3.5 billion years ago, and my guess is that primitive life probably emerged as early as 4 billion years ago. We also know that certain meteorites contain the basic components of life. But we still don’t know how the first polymers were put together.
Scientists disagree over how to define life. NASA has come up with a working definition: an evolving system that can make more of itself. Is that sufficient?
Life resists a simple abstract definition. When I try to define life, I put together a set of a dozen properties that don’t fit anything not alive. A few of them are simple: reproduction, evolution, and metabolism.
Many scientists study individual steps in the emergence of life, such as how to make RNA. But you argue that life is a system, and it began as a system. Why?
DNA is the center of all life, but it can’t be considered alive even though it has all the information required to make a living thing. DNA cannot reproduce by itself. Put DNA in a test tube with water, and it just slowly breaks into different pieces. So right away, you see the limitation of thinking about single molecules as being alive.
To get a bit of what we call growth, you have to add the subunits of DNA, an enzyme to replicate the DNA, and energy to power the reaction. Now we have molecules that can reproduce themselves if they have certain ingredients. Are they alive yet? The answer is still no, because sooner or later the subunits are used up and reproduction comes to a screeching halt. So how do we get to a system that’s really alive? That’s what we and others are trying to do. The only way we can think of is to put DNA into a membranous compartment.
Why are compartments so important? . . .