The reboot of Cosmos has been solid but not spectacular so far, but the second episode contains as solid and clear an explanation of evolution as I've ever seen.
Even if evolution clashes with your world view, this is worth watching if only to understand what you're aligned against (per Bret Victor's advice). The third episode airs on Fox tonight and is about the creation of the scientific method.
Richard Lenski and his team of researchers utilize a clever technique to observe and study evolution of bacteria in realtime. Periodically freezing a sample of the bacteria every few generations allows them to go back in time to study particular traits and to pinpoint when differences occur.
After 30,000 generations, researchers noticed something strange. One population had evolved the ability to use a different carbon-based molecule in the solution, called citrate, as a power source.
Researchers wondered whether it was the result of a rare, single mutation, or a more complex change involving a series of mutations over generations. To find out, one of Lenski's postdocs, Zachary Blount, took some of the frozen cells and grew them in a culture lacking glucose, with citrate as the only potential food source.
After testing 10 trillion ancestral cells from early generations, he got no growth. But when he tested cells from the 20,000th generation on, he began to get results, eventually finding 19 mutants that could use citrate as a power source. The results showed that the citrate-eating mutation was most likely not the result of a single mutation, but one enabled by multiple changes over 20,000 generations.
I agree; it is amazing! I've written about this manytimes. But we know that complexity can arise naturally through the laws of physics. It doesn't take very complex rules to create huge diversity. Look at poker; a simple set of rules creates a game that has so many combinations it's essentially infinite to human experience. We can figure out the rules of nature by studying the way processes follow them, and deduce what's going on behind the scenes. And whenever we do, we see science.
This makes me think of Richard Feynman's ode to the scientific beauty of a flower:
I have a friend who's an artist and has sometimes taken a view which I don't agree with very well. He'll hold up a flower and say "look how beautiful it is," and I'll agree. Then he says "I as an artist can see how beautiful this is but you as a scientist take this all apart and it becomes a dull thing," and I think that he's kind of nutty. First of all, the beauty that he sees is available to other people and to me too, I believe. Although I may not be quite as refined aesthetically as he is ... I can appreciate the beauty of a flower. At the same time, I see much more about the flower than he sees. I could imagine the cells in there, the complicated actions inside, which also have a beauty. I mean it's not just beauty at this dimension, at one centimeter; there's also beauty at smaller dimensions, the inner structure, also the processes. The fact that the colors in the flower evolved in order to attract insects to pollinate it is interesting; it means that insects can see the color. It adds a question: does this aesthetic sense also exist in the lower forms? Why is it aesthetic? All kinds of interesting questions which the science knowledge only adds to the excitement, the mystery and the awe of a flower. It only adds. I don't understand how it subtracts.
When elephants began to die out, Homo erectus "needed to hunt many smaller, more evasive animals. Energy requirements increased, but with plant and protein intake limited, the source had to come from fat. He had to become calculated about hunting," Ben-Dor says, noting that this change is evident in the physical appearance of modern humans, lighter than Homo erectus and with larger brains.
Dr. Munshi-South and his colleagues have been analyzing the DNA of the mice. He's been surprised to find that the populations of mice in each park are genetically distinct from the mice in others. "The amount of differences you see among populations of mice in the same borough is similar to what you'd see across the whole southeastern United States," he said.
BoxCar 2D is a fun little toy: it uses genetic algorithms to evolve little cars that can complete obstacle courses (like the ones you'd find on Cyclomaniacs). If you play this for more than a minute or two, you'll be at it for 30 minutes, easy. (via moleitau)
So given these basic biological facts, and assuming that ejaculation is not so premature that it occurs prior to intromission and sperm cells find themselves awkwardly outside of a woman's reproductive tract flopping about like fish out of water, what, exactly, is so "premature" about premature ejaculation? In fact, all else being equal, in the ancestral past, wouldn't there likely have been some reproductive advantages to ejaculating as quickly as possible during intravaginal intercourse-such as, oh, I don't know, inseminating as many females as possible in as short a time frame as possible? or allowing our ancestors to focus on other adaptive behaviors aside from sex? or perhaps, under surreptitious mating conditions, doing the deed quickly and expeditiously without causing a big scene?
Still, for recreational sex, it blows. (As it were.)
He found that over half of the species he examined demonstrated changes over time with boreal birds developing more pointed wings and temperate birds developing rounder wings. These results support the hypothesis that habitat isolation is spurring evolutionary changes in birds.
Boreal forests have suffered severe deforestation over the past century, and so Desrochers had predicted that increased distances between habitat patches would select for more pointed wings in birds. Pointed wings are associated with more energy-efficient sustained flight.
Recent evidence of horizontal gene transfer -- in which genes are exchanged from other organisms, not from ancestors -- has some scientists thinking that the dominant form of evolution for most of the Earth's history was between non-related organisms and not among ancestors.
In the past few years, a host of genome studies have demonstrated that DNA flows readily between the chromosomes of microbes and the external world. Typically around 10 per cent of the genes in many bacterial genomes seem to have been acquired from other organisms in this way, though the proportion can be several times that. So an individual microbe may have access to the genes found in the entire microbial population around it, including those of other microbe species. "It's natural to wonder if the very concept of an organism in isolation is still valid at this level," says Goldenfeld.
Read on for their hypothesis about how horizontal evolution drove innovation -- development of a universal genetic code and genetic innovation-sharing protocols -- in life forms early on in the Earth's history. Fascinating.
We can imagine wild wolves scavenging on a rubbish tip on the edge of a village. Most of them, fearful of men throwing stones and spears, have a very long flight distance. They sprint for the safety of the forest as soon as a human appears in the distance. But a few individuals, by genetic chance, happen to have a slightly shorter flight distance than the average. Their readiness to take slight risks -- they are brave, shall we say, but not foolhardy -- gains them more food than their more risk-averse rivals. As the generations go by, natural selection favours a shorter and shorter flight distance, until just before it reaches the point where the wolves really are endangered by stonethrowing humans. The optimum flight distance has shifted because of the newly available food source.
I bring good news! These two warring groups have more in common than they realize. And, no, it isn't just that they're both wrong. It's that they're wrong for the same reason. Oddly, an underestimation of natural selection's creative power clouds the vision not just of the intensely religious but also of the militantly atheistic.
If both groups were to truly accept that power, the landscape might look different. Believers could scale back their conception of God's role in creation, and atheists could accept that some notions of "higher purpose" are compatible with scientific materialism. And the two might learn to get along.
This is essentially the subject of the last chapter or two of Wright's The Evolution of God, the only part of this excellent book that I didn't quite buy into, even though I've been thinking about his conclusion quite a bit since finishing the book.
But despite a television teaser campaign with the slogan "This changes everything" and comparisons to the moon landing and the Kennedy assassination, the significance of this discovery may not be known for years. An article to be published on Tuesday in PLoS ONE, a scientific journal, will report more prosaically that the scientists involved said the fossil could be a "stem group" that was a precursor to higher primates, with the caveat, "but we are not advocating this."
Darwinius masillae represents the most complete fossil primate ever found, including both skeleton, soft body outline and contents of the digestive tract. Study of all these features allows a fairly complete reconstruction of life history, locomotion, and diet. Any future study of Eocene-Oligocene primates should benefit from information preserved in the Darwinius holotype. Of particular importance to phylogenetic studies, the absence of a toilet claw and a toothcomb demonstrates that Darwinius masillae is not simply a fossil lemur, but part of a larger group of primates, Adapoidea, representative of the early haplorhine diversification.
Geoffrey West of the Santa Fe Institute and his colleagues Jim Brown and Brian Enquist have argued that a 3/4-power law is exactly what you'd expect if natural selection has evolved a transport system for conveying energy and nutrients as efficiently and rapidly as possible to all points of a three-dimensional body, using a fractal network built from a series of branching tubes -- precisely the architecture seen in the circulatory system and the airways of the lung, and not too different from the roads and cables and pipes that keep a city alive.
From primitive animists to the legends of the first gods, battling like irrational cloud-inhabiting humans over the cosmos, Wright tells the story of how war and trade, technology and human interaction slowly exposed humans to the gods of others. How this awareness led to the Jewish innovation of a hidden and universal God, how the cosmopolitan early Christians, in order to market their doctrines more successfully, universalised and sanitised this Jewish God in turn, and how Islam equally included a civilising universalism despite its doctrinal rigidity and founding violence.
For all the advances and wonders of our global era, Christians, Jews, and Muslims seem ever more locked in mortal combat. But history suggests a happier outcome for the Peoples of the Book. As technological evolution has brought communities, nations, and faiths into closer contact, it is the prophets of tolerance and love that have prospered, along with the religions they represent. Is globalization, in fact, God's will?
I loved two of Wright's previous books, The Moral Animal and especially Nonzero. (via marginal revolution)
A mesmerizing video that shows computer generated geometric shapes that have evolved to walk in all sorts of crazy ways. The shapes are generated using the Darwin@Home software. Some of them resemble young children just learning to walk or crawl. The final "beast" is particularly elegant.
"The only novelty in my work is the attempt to explain how species become modified," Darwin later wrote. He did not mean to belittle his achievement. The how, backed up by an abundance of evidence, was crucial: nature throws up endless biological variations, and they either flourish or fade away in the face of disease, hunger, predation and other factors. Darwin's term for it was "natural selection"; Wallace called it the "struggle for existence." But we often act today as if Darwin invented the idea of evolution itself, including the theory that human beings developed from an ape ancestor. And Wallace we forget altogether.
In fact, scientists had been talking about our primate origins at least since 1699, after the London physician Edward Tyson dissected a chimpanzee and documented a disturbing likeness to human anatomy. And the idea of evolution had been around for generations.
Psychologist Christopher Ryan, author of "Sex in Prehistory," says the desire for sex with more than one person has always been there -- for leaders and followers alike. "The desire is not a function of status or power -- it's a question of availability."
What's relatively new to the human race, he said, is the ability to exercise power and the connection between power and sex.
That's because, for most of human existence, there was only so far a man could coerce others when food was essentially free and hard to hoard. And until relatively recently, sex with multiple partners was the norm. "It would have been very unusual 100,000 years ago for a person to have one sexual partner for 30 years," said Ryan in an interview from Barcelona.
She points out that, while powerful men throughout western history have married monogamously (they had only one legal wife at a time), they have always mated polygynously (they had lovers, concubines, and female slaves). Many had harems, consisting of hundreds and even thousands of virgins. With their wives, they produced legitimate heirs; with the others, they produced bastards (Betzig's term). Genes and inclusive fitness make no distinction between the two categories of children. While the legitimate heirs, unlike the bastards, inherited their fathers' power and status and often went on to have their own harems, powerful men sometimes invested in their bastards as well.
As a result, powerful men of high status throughout human history attained very high reproductive success, leaving a large number of offspring (legitimate or otherwise), while countless poor men in the countryside died mateless and childless.
Yet as biologists have discovered through the application of DNA paternity tests to the offspring of these bonded pairs, social monogamy is very rarely accompanied by sexual, or genetic, monogamy. Assay the kids in a given brood, whether of birds, voles, lesser apes, foxes or any other pair-bonding species, and anywhere from 10 to 70 percent will prove to have been sired by somebody other than the resident male.
Speaking of memes, Susan Blackmore theorizes that humans are just machines for propagating them.
Memes are using human brains as their copying machinery. So we need to understand the way human beings work.
Up until very recently in the world of memes, humans did all the varying and selecting. We had machines that copied -- photocopiers, printing presses -- but only very recently do we have artificial machines that also produce the variations, for example (software that) mixes up ideas and produces an essay or neural networks that produce new music and do the selecting. There are machines that will choose which music you listen to. It's all shifting that way because evolution by natural selection is inevitable. There's a shift to the machines doing all of that.
When asked what the future will look like, she says, "it will look like humans are just a minor thing on this planet with masses (of) silicon-based machinery using us to drag stuff out of the ground to build more machines."
We now have a robust understanding of how sexual pressures -- the pressures to find, impress, and seduce a mate -- influence the evolution of males and females. So much so that if you tell me a fact, such as the average size difference between males and females in a species, or the proportion of a male's body taken up by his testes, I can tell you what the mating system is likely to be. For example, where males are much bigger than females, fighting between males has been important - which often means that the biggest males maintain a harem. If testes are relatively large, females probably have sex with several males in the course of a single breeding episode.
This video is too long and come frontloaded with too much explanation, but like a jelly doughnut, there's some goodness in the middle.
Basically, I simulate clocks as living organisms. Selective pressure is focused on their ability to accurately tell time. NO goal is imposed on the design (you can tell this because every simulation ends with a differently constructed clock). And it works. Clocks evolve through a series of transitional forms: Pendulum, Proto-clock, 1-handed Clock, 2-handed Clock, 3-handed Clock, and 4-handed Clock. Gradually the complexity is built up.
The brisk rate of human selection occurred for two reasons, Dr. Moyzis' team says. One was that the population started to grow, first in Africa and then in the rest of the world after the first modern humans left Africa. The larger size of the population meant that there were more mutations for natural selection to work on. The second reason for the accelerated evolution was that the expanding human populations in Africa and Eurasia were encountering climates and diseases to which they had to adapt genetically. The extra mutations in their growing populations allowed them to do so.
Dr. Moyzis said it was widely assumed that once people developed culture, they protected themselves from the environment and from the forces of natural selection. But people also had to adapt to the environments that their culture created, and the new analysis shows that evolution continued even faster than before.
Duelity is a split-screen movie with one half of the screen showing the six-day creation of the earth & man in scientific terms and the other half showing the Big Bang/evolution origin of the universe as it might have been written in the Bible. (Click on "watch" then "duelity" to get the full effect.) Nice use of infographics and illustration. (thx, slava)
Biologists Helping Bookstores is a guerilla effort to reshelve pseudo-scientific books (books on intelligent design, for instance), taking them from the Science section and moving them to a more appropriate area of the store, like Philosophy, Religion, or Religious Fiction. (via mr)
By now, you've probably heard of the Creation Museum that just opened in Kentucky with the idea that the Bible is "the history book of the universe". Pharyngula has an extensive roundup of information and reaction to the museum, including this inside look at the place. "Journalists, you have a problem. Most of the articles written on this 'museum' bend over backwards to treat questions like 'Did Man walk among Dinosaurs?' as serious, requiring some kind of measured response from multiple points of view, and rarely even recognized the scientific position that the question should not only be answered with a strong negative, but that it is absurd."
Update: An earlier version of this post wrongly stated that Mitt Romney raised his hand when asked about disbelieving evolution...Tom Tancredo was the third person. (thx to several who wrote in about this)
Humans are the animal world's best distance runners...we can run long distances relatively fast without overheating. "Once humans start running, it only takes a bit more energy for us to run faster, Lieberman said. Other animals, on the other hand, expend a lot more energy as they speed up, particularly when they switch from a trot to a gallop, which most animals cannot maintain over long distances." (via beebo)
Although both men and women look at the image of George Brett when directed to find out information about his sport and position, men tend to focus on private anatomy as well as the face. For the women, the face is the only place they viewed. Coyne adds that this difference doesn't just occur with images of people. Men tend to fixate more on areas of private anatomy on animals as well, as evidenced when users were directed to browse the American Kennel Club site.
The cover story in this week's NY Times Magazine is called Darwin's God and covers, from an evolutionary biology standpoint, why people believe in God. Most scientists studying the matter believe that humans have a built-in mechanism for religious belief. For instance, anthropologist Scott Atran sometimes conducts an intriguing experiment with his students:
His research interests include cognitive science and evolutionary biology, and sometimes he presents students with a wooden box that he pretends is an African relic. "If you have negative sentiments toward religion," he tells them, "the box will destroy whatever you put inside it." Many of his students say they doubt the existence of God, but in this demonstration they act as if they believe in something. Put your pencil into the magic box, he tells them, and the nonbelievers do so blithely. Put in your driver's license, he says, and most do, but only after significant hesitation. And when he tells them to put in their hands, few will. If they don't believe in God, what exactly are they afraid of?
Or rather, why are they afraid? One possible reason is that humans are conditioned to be on the lookout for "agents" and we tend to find them even when they're not there:
So if there is motion just out of our line of sight, we presume it is caused by an agent, an animal or person with the ability to move independently. This usually operates in one direction only; lots of people mistake a rock for a bear, but almost no one mistakes a bear for a rock.
What does this mean for belief in the supernatural? It means our brains are primed for it, ready to presume the presence of agents even when such presence confounds logic. "The most central concepts in religions are related to agents," Justin Barrett, a psychologist, wrote in his 2004 summary of the byproduct theory, "Why Would Anyone Believe in God?" Religious agents are often supernatural, he wrote, "people with superpowers, statues that can answer requests or disembodied minds that can act on us and the world."
Another reason for the instinctive religious impulse may be that people are able to put themselves in other peoples' minds, to think about how another person might be feeling or thinking:
Folkpsychology, as Atran and his colleagues see it, is essential to getting along in the contemporary world, just as it has been since prehistoric times. It allows us to anticipate the actions of others and to lead others to believe what we want them to believe; it is at the heart of everything from marriage to office politics to poker. People without this trait, like those with severe autism, are impaired, unable to imagine themselves in other people's heads.
The process begins with positing the existence of minds, our own and others', that we cannot see or feel. This leaves us open, almost instinctively, to belief in the separation of the body (the visible) and the mind (the invisible). If you can posit minds in other people that you cannot verify empirically, suggests Paul Bloom, a psychologist and the author of "Descartes' Baby," published in 2004, it is a short step to positing minds that do not have to be anchored to a body. And from there, he said, it is another short step to positing an immaterial soul and a transcendent God.
There's lots more in the article...it's well worth a read.
Richard Dawkins: Why there almost certainly is no God. "We cannot, of course, disprove God, just as we can't disprove Thor, fairies, leprechauns and the Flying Spaghetti Monster. But, like those other fantasies that we can't disprove, we can say that God is very very improbable."
The AAAS, the organisation which publishes Science magazine, has produced a book called The Evolution Dialogues. "Meant specifically for use in Christian adult education programs, it offers a concise description of the natural world, as explained by evolution, and the Christian response, both in Charles Darwin's time and in contemporary America." (thx, mike)
Profile of Daniel Dennett, "Darwinian fundamentalist" and author of a new book that argues that "religion, chiefly Christianity, is itself a biologically evolved concept, and one that has outlived its usefulness".
Interview with "incompetent design" theorist Don Wise. "The only reason you stand erect is because of this incredible sharp bend at the base of your spine, which is either evolution's way of modifying something or else it's just a design that would flunk a first-year engineering student."
What the hell, Kansas? And those poor science teachers in Kansas public schools...what are they supposed to do? Teaching pseudoscience as real science, that's like asking the math teachers to tell the kids that 2+2=5 because God said so. You can't quit, because then those kids will really be lost. If you don't teach that ID is valid science, you'll probably get reprimanded or fired. So what to do? I have a couple of suggestions:
1) Teach your students about evolution, and then tell them about intelligent design, just as the state curriculum says. Then spend some time going over what science is, what a theory is, and so on. Apply the definition to each. That way, you've taught ID by the books and then demonstrated its relationship to science.
2) Or, as long as you're teaching your students that a higher power designed the world/universe, why not take it a step further and tell them about your personal and scientific belief in The Flying Spaghetti Monster? As long as science can include anything now, why not a supernatural being made from pasta?
In that small, relatively conservative Pennsylvania town, voters booted all eight Republican pro-intelligent design school board members who were up for re-election and replaced them with Democrats who oppose the curriculum policy. Dover is not some bastion of liberal politics; it's more like Kansas than parts of Kansas are.
Why do people believe in God? Evidence suggests that it's partially inherited. "The degree of religiosity was not strongly related to the environment in which the twin was brought up. Even if one identical twin had been brought up in an atheist family and the other in a religious Catholic household, they would still tend to show the same kind of religious feelings, or lack of them."
Is it strange that every time I go into my bathroom and look at the box of tissues sitting on the shelf, I see Charles Darwin looking back at me?
It does look like Darwin, yes? Or have I been reading far too much about science and evolution lately?
Note: My bathroom Darwin orchid has nothing to do with Angraecum sesquipedale, an orchid that Darwin discovered in 1850. At the time, he speculated that in order for the plant to be pollinated, a moth with a 12" proboscis would have to do it, even though no such moth had been shown to exist. This freakish moth was eventually discovered (not in my bathroom) in 1903, 20 years after Darwin's death.
Profile of Robert Trivers who "came up with the first Darwinian explanations for human cooperation, jealousy and our sense of justice that made genetic sense, and he showed how these arose from the same forces as act on all animals, from the pigeons outside his window to the fish of coral reefs".
Richard Dawkins and Jerry Coyne on intelligent design: "You cannot have it both ways. Either ID belongs in the science classroom, in which case it must submit to the discipline required of a scientific hypothesis. Or it does not, in which case get it out of the science classroom and send it back into the church, where it belongs."
An open letter to the Kansas School Board. "Let us remember that there are multiple theories of Intelligent Design. I and many others around the world are of the strong belief that the universe was created by a Flying Spaghetti Monster."
Why intelligent design isn't. "Biologists aren't alarmed by intelligent design's arrival in Dover and elsewhere because they have all sworn allegiance to atheistic materialism; they're alarmed because intelligent design is junk science."