kottke.org posts about evolution
Jerry Coyne, University of Chicago professor and author of Why Evolution is True, shares the results of a recent paper called Detection of human adaptation during the past 2000 years. In the study, DNA sequencing was used to find human genes that have changed so quickly in the past 2000 years that the authors conclude natural selection must be responsible.
Now, however, we can, by DNA sequencing, look at DNA directly, and with some fancy statistical footwork, get an idea of which genes have changed in frequency so fast that they must have been due to positive natural selection. That’s the subject of a new paper in Science by Yair Field et al. (reference and free download below). The authors conclude that several traits, including lactose tolerance, hair and eye color, and parts of the immune system, as well as height, have evolved within the last 2,000 years.
Other genes that might have changed during that period include those for infant head circumference, insulin levels, birth weight, and female hip size.
OneZoom is an interactive zoomable map of “the evolutionary relationships between the species on our planet”, aka tree of life. Browsing around is fun, but you’ll want to use the search function to find specific groups and animals, like mammals, humans, and mushrooms. The scale of this is amazing…there are dozens of levels of zoom. (via @pomeranian99)
Photographer Nicky Bay has been documenting an arachnid he calls the mirror spider for past few years. He’s noticed that when the spider feels threatened, it can shift the mirrored plates on its abdomen to reveal itself and make itself look bigger, like a cloaked Klingon ship uncloaking for battle.
For several years, I have been observing the odd behavior of the Mirror Spider (Thwaitesia sp.) where the “silver-plates” on the abdomen seem to shrink when the spider is agitated (or perhaps threatened), revealing the actual abdomen. At rest, the silver plates expand and the spaces between the plates close up to become an almost uniform reflective surface.
Many animals have evolved the ability to camouflage themselves and I’d speculate that is what’s happened to the mirror spider. The mirrored surface reflects the spider’s surroundings and turns it somewhat invisible to potential predators. The mirror system is more complex than an abdomen matching the green of a particular plant, but is also more adaptive — the mirror works equally well on green leaves, brown branches, and black soil. (via colossal)
Update: I misread Bay’s explanation of the spider’s response to threats and have corrected it above. I previously stated “that when the spider feels threatened, it can shift the mirrored plates on its abdomen to make itself appear more reflective”, which is exactly wrong. (via @RLHeppner/status/780921795335581696)
Meet the lichen katydid. Hailing from the forests of Central and South America, this insect has evolved over the millennia to blend in amazingly well with the lichens that populate the forest.
Researchers at Harvard have come up with a novel way of studying how bacteria evolve to become drug resistant. They set up a large petri dish about the same shape as a football field with no antibiotics in the end zones and increasingly higher doses of antibiotics toward the center. They placed some bacteria in both end zones and filmed the results as the bacteria worked its way toward the center of the field, evolving drug resistance as it went. Ed Yong explains:
What you’re seeing in the movie is a vivid depiction of a very real problem. Disease-causing bacteria and other microbes are increasingly evolving to resist our drugs; by 2050, these impervious infections could potentially kill ten million people a year. The problem of drug-resistant infections is terrifying but also abstract; by their nature, microbes are invisible to the naked eye, and the process by which they defy our drugs is even harder to visualise.
But now you can: just watch that video again. You’re seeing evolution in action. You’re watching living things facing down new challenges, dying, competing, thriving, invading, and adapting — all in a two-minute movie.
Watch the video…it’s wild. What’s most interesting — or scary as hell — is that once the drug resistance gets going, it builds up a pretty good momentum. There’s a pause at the first boundary as the evolutionary process blindly hammers away at the problem, but after the bacteria “learn” drug resistance, the further barriers are breached much more quickly, even before the previous zones are fully populated.
In his new book The Kingdom of Speech, Tom Wolfe argues that speech and not evolution is responsible for the many achievements of humans. Wolfe, the author of The Right Stuff and The Electric Kool-Aid Acid Test, went on NPR the other day to talk about the book. This comment about Darwin’s view of speech stuck out (emphasis mine):
He could not figure out what it was. He assumed, because of his theory, that everything evolved from animals. And didn’t even include it in his theory, language, until he decided that it came from our imitation of the cries of birds. And I think it’s misleading to say that human beings evolved from animals — actually, nobody knows whether they did or not. There are very few physical signs, aside from the general resemblance of apes and humans. The big evolution, if you want to call it that, is that this one species, Homo sapiens, came up with this ingenious trick, which is language.
It’s one thing to say that speech did not evolve from the utterances of previous animals and was instead invented by humans, but it’s quite another to assert that humans did not evolve from animals at all.1 Gonna be fun to sit back and watch the controversy roil on this one. (via @JossFong who said “lazy saturday, just listening to @NPR when ….. WHAT”)
There are some things that humans don’t need to survive anymore still hanging around on our bodies, including unnecessary arm muscles and vestigial tail bones.
From It’s OK To Be Smart, a 12-part series explaining evolution.
From the landmark science series Cosmos, Carl Sagan narrates the evolution of humans from the first cells billions of years ago.
Scientists have discovered that an insect has evolved something like a gearbox to coordinate its leg movements while jumping. That’s right, nature invented mechanical gears before man got around to it.
The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box.
Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears — essentially a shock-absorbing mechanism to stop teeth from shearing off.
The gear teeth on the opposing hind-legs lock together like those in a car gear-box, ensuring almost complete synchronicity in leg movement — the legs always move within 30 ‘microseconds’ of each other, with one microsecond equal to a millionth of a second.
This is critical for the powerful jumps that are this insect’s primary mode of transport, as even minuscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” — causing the Issus to spin hopelessly out of control.
“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.
Up until very recently, humans were thought to be the only animals who made and used stone tools, an era in human development that began roughly 3.3 million years ago. But according to this piece at the BBC, some chimpanzees and monkeys in various places around the globe have been using primitive stone tools for hundreds or even thousands of years.
Boesch and his colleagues had previously studied modern chimpanzee stone tool culture in the region. This research revealed that the chimpanzees have an idiosyncratic way of choosing and using their tools.
For instance, chimpanzees will often deliberately opt for particularly large and heavy stone hammers, between 1kg and 9kg, while humans prefer to use stones that weigh 1kg or less. Many of the 4300-year-old stone tools weighed more than 1kg, suggesting they were used by chimpanzees.
Chimpanzees also use their stone tools to crack open certain types of nuts that humans don’t eat. Starch residues on some of the ancient tools came from these nuts.
Together, these findings led to an obvious conclusion: chimpanzees have been using stone tools in the rainforests of Ivory Coast for at least 4300 years.
Because of climate change and other activities caused by humans (invasive species, habitat loss), hybridization of species is resulting in things like super-sized coyotes, pizzly bears (grizzly/polar bear hybrids), and other animals that may not be ideally suited to survive.
Some scientists and conservationists see the coywolf as a nightmare of the Anthropocene — a poster child of mongrelization as plants and animals reshuffle in response to habitat loss, climate change and invasive species. Golden-winged warblers increasingly cross with blue-winged warblers in the U.S. Northeast and eastern Canada. Southern flying squirrels hybridize with northern flying squirrels as the southern species presses northward in Ontario. Polar bears mate with grizzlies in the Canadian Arctic along the Beaufort Sea to produce “pizzly bears.”
All of this interbreeding upsets the conventional notion of species as discrete, inviolable entities. Moreover, some scientists and conservationists warn that hybridization will degrade biodiversity as unusual species are lost to genetic homogenization.
Partly scientists fear hybrids will be less fit than organisms that have evolved in place over eons. And often that is true, but the problem solves itself over time as hybrids lose out in the competitive race for survival.
James Krupa teaches a mandatory biology class at the University of Kentucky and some students have a difficult time because Krupa refuses to shy away from evolution.
Rarely do I have a Kentucky student who learned about human evolution in high school biology. Those who did usually attended high schools in large urban centers like Louisville or Lexington. Given how easily it can provoke parents, the teaching of human evolution is a rarity in high school, so much so in Kentucky that it startled me when I first arrived.
The story of our evolutionary history captivates many of my students, while infuriating some. During one lecture, a student stood up in the back row and shouted the length of the auditorium that Darwin denounced evolution on his deathbed — a myth intentionally spread by creationists. The student then made it known that everything I was teaching was a lie and stomped out of the auditorium, slamming the door behind him. A few years later during the same lecture, another student also shouted out from the back row that I was lying. She said that no transitional fossil forms had ever been found — despite my having shared images of many transitional forms during the semester. Many of her fellow students were shocked by her combativeness, particularly when she stormed out, also slamming the door behind her. Most semesters, a significant number of students abruptly leave as soon as they realize the topic is human evolution.
I personally don’t understand the compatibility of evolutionary biology and Christianity Krupa emphasizes in his class, but I guess it helps to meet people halfway?
This simulator evolves increasingly effective walking creatures through genetic algorithms. After each round, the winners are sent through to the next round and copied by the rest of the competitors, with mutations introduced. At first, the pace of improvement is swift — two orders of magnitude within 100 generations — but slows pretty dramatically after that. (via @nickrichter)
Every year, evolutionary biologist and professor David Barash gives his students The Talk about how evolution and religion do and do not get along.
It’s irresponsible to teach biology without evolution, and yet many students worry about reconciling their beliefs with evolutionary science. Just as many Americans don’t grasp the fact that evolution is not merely a “theory,” but the underpinning of all biological science, a substantial minority of my students are troubled to discover that their beliefs conflict with the course material.
Until recently, I had pretty much ignored such discomfort, assuming that it was their problem, not mine. Teaching biology without evolution would be like teaching chemistry without molecules, or physics without mass and energy. But instead of students’ growing more comfortable with the tension between evolution and religion over time, the opposite seems to have happened. Thus, The Talk.
This is the sort of thing Barash talks about:
The more we know of evolution, the more unavoidable is the conclusion that living things, including human beings, are produced by a natural, totally amoral process, with no indication of a benevolent, controlling creator.
This was one of my favorite scenes the film…Russell Crowe’s Noah telling his children the creation story, which ends up being half supernatural and half evolution.
Worth watching for the special effects alone.
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.
The other day, Bill Nye debated Ken Ham about evolution and creationism. At the event, Matt Stopera asked self-identifying creationists to write question/notes to those who “believe” in evolution. Here’s one:
Phil Plait of Bad Astronomy responded to each of the 22 notes/questions from the creationists. Here’s his answer to the comment above:
I agree; it is amazing! I’ve written about this many times. 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.
Starting with cubes of four simple materials (bone, tissue, 2 types of muscles) and one simple rule (faster bots have more offspring) results in a surprising amount of complexity among walking robots.
Elephants were the “perfect food package” for pre-human hominids (they were slow with a good fat-to-protein ratio) and their extinction in the Middle East (and Africa) caused those hominids to evolve to be more like modern humans.
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.
Evolutionary biologists are increasingly studying organisms (like mice, fish, and bacteria) in urban areas like New York City to find out how they evolve to urban conditions.
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.
Whoa, watch the video at the top of this article to see how the human face develops in the womb from an age of one-month to ten weeks. It all just comes together right at the end!
If you watch it closely, you will see that the human face is actually formed of three main sections which rotate and come together in an unborn foetus.
The way this happens only really makes sense when you realise that, strange though it may sound, we are actually descended from fish.
The early human embryo looks very similar to the embryo of any other mammal, bird or amphibian — all of which have evolved from fish.
Your eyes start out on the sides of your head, but then move to the middle.
The top lip along with the jaw and palate started life as gill-like structures on your neck. Your nostrils and the middle part of your lip come down from the top of your head.
There is no trace of a scar; the plates of tissue and muscle fuse seamlessly. But there is, however, a little remnant of all this activity in the middle of your top lip — your philtrum.
And that’s saying something. But look at this gem of a thread: I like big butts and I cannot lie, but is there some evolutionary reason as to why? Some of the answers:
My homeboys tried to warn me, but that butt you got makes me so confident of your current well-being and future child-rearing potential
So, ladies! (Yeah!) Ladies (Yeah!)
If you wanna roll in my Mercedes (Yeah!)
Then turn around! Stick it out! Even white boys have to make sure that their partner is of high genetic caliber so they can pass on their genes successfully.
My anaconda don’t want none unless you have a high likelihood of producing healthy offspring with a minimal chance of genetic disabilities, hun.
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)
Evolutionary speaking, premature ejaculation may not be such a bad thing after all.
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.)
A recent study indicates that the wing shapes of North American birds are changing in response to deforestation.
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.
In an excerpt from his recent book, The Greatest Show on Earth, Richard Dawkins writes about how wolves evolved into dogs first through self-domestication and then through domestication by humans.
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.
Writing in the New York Times this weekend, Robert Wright attempts to reconcile religion and science. The middle ground is the “built-in” moral sense of our universe, in that the universe builds and rewards organisms that cooperate with one another.
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.