Archive for the ‘Evolution’ Category
Fascinating article by James Krupa in Orion magazine:
i’m often asked what I do for a living. My answer, that I am a professor at the University of Kentucky, inevitably prompts a second question: “What do you teach?” Responding to such a question should be easy and invite polite conversation, but I usually brace for a negative reaction. At least half the time the person flinches with disapproval when I answer “evolution,” and often the conversation simply terminates once the “e-word” has been spoken. Occasionally, someone will retort: “But there is no evidence for evolution.” Or insist: “It’s just a theory, so why teach it?”
At this point I should walk away, but the educator in me can’t. I generally take the bait, explaining that evolution is an established fact and the foundation of all biology. If in a feisty mood, I’ll leave them with this caution: the fewer who understand evolution, the more who will die. Sometimes, when a person is still keen to prove me wrong, I’m more than happy to share with him an avalanche of evidence demonstrating I’m not.
Some colleagues ask why I bother, as if I’m the one who’s the provocateur. I remind them that evolution is the foundation of our science, and we simply can’t shy away from explaining it. We don’t avoid using the “g-word” when talking about gravitational theory, nor do we avoid the “c-word” when talking about cell theory. So why avoid talking about evolution, let alone defending it? After all, as a biologist, the mission of advancing evolution education is the most important aspect of my job.
TO TEACH EVOLUTION at the University of Kentucky is to teach at an institution steeped in the history of defending evolution education. The first effort to pass an anti-evolution law (led by William Jennings Bryan) happened in Kentucky in 1921. It proposed making the teaching of evolution illegal. The university’s president at that time, Frank McVey, saw this bill as a threat to academic freedom. Three faculty members—William Funkhouser, a zoologist; Arthur Miller, a geologist who taught evolution; and Glanville Terrell, a philosopher—joined McVey in the battle to prevent the bill from becoming law. They put their jobs on the line. Through their efforts, the anti-evolution bill was defeated by a forty-two to forty-one vote in the state legislature. Consequently, the movement turned its attention toward Tennessee.
John Thomas Scopes was a student at the University of Kentucky then and watched the efforts of his three favorite teachers and President McVey. The reason the “Scopes Monkey Trial” occurred several years later in Dayton, Tennessee—where Scopes was a substitute teacher and volunteered to be prosecuted—was in good part due to the influence of his mentors, particularly Funkhouser. As Scopes writes in his memoir, Center of the Storm: “Teachers rather than subject matter rekindled my interest in science. Dr. Funkhouser . . . was a man without airs [who] taught zoology so flawlessly that there was no need to cram for the final examination; at the end of the term there was a thorough, fundamental grasp of the subject in bold relief in the student’s mind, where Funkhouser had left it.”
I was originally reluctant to take my job at the university when offered it twenty years ago. It required teaching three sections of non-majors biology classes, with three hundred students per section, and as many as eighteen hundred students each year. I wasn’t particularly keen on lecturing to an auditorium of students whose interest in biology was questionable given that the class was a freshman requirement.
Then I heard an interview with the renowned evolutionary biologist E. O. Wilson in which he addressed why, as a senior professor—and one of the most famous biologists in the world—he continued to teach non-majors biology at Harvard. Wilson explained that non-majors biology is the most important science class that one could teach. He felt many of the future leaders of this nation would take the class, and that this was the last chance to convey to them an appreciation for biology and science. Moved by Wilson’s words, and with the knowledge that William Funkhouser once held the job I was now contemplating, I accepted the position. The need to do well was unnerving, however, considering that if I failed as a teacher, a future Scopes might leave my class uninspired.
I realized early on that many instructors teach introductory biology classes incorrectly. Too often evolution is the last section to be taught, an autonomous unit at the end of the semester. I quickly came to the conclusion that, since evolution is the foundation upon which all biology rests, it should be taught at the beginning of a course, and as a recurring theme throughout the semester. As the renowned geneticist Theodosius Dobzhansky said: “Nothing in biology makes sense except in the light of evolution.” In other words, how else can we explain why the DNA of chimps and humans is nearly 99 percent identical, and that the blood and muscle proteins of chimps and humans are nearly identical as well? Why are these same proteins slightly less similar to gorillas and orangutans, while much less similar to goldfish? Only evolution can shed light on these questions: we humans are great apes; we and the other great apes (gibbons, chimps, gorillas, bonobos, and orangutans) all evolved from a common ancestor.
Soon, every topic and lecture in my class was built on an evolutionary foundation and explained from an evolutionary perspective. My basic biology for non-majors became evolution for non-majors. It didn’t take long before I started to hear from a vocal minority of students who strongly objected: “I am very offended by your lectures on evolution! Those who believe in creation are not ignorant of science! You had no right to try and force evolution on us. Your job was to teach it as a theory and not as a fact that all smart people believe in!!” And: “Evolution is not a proven fact. It should not be taught as if it is. It cannot be observed in any quantitative form and, therefore, isn’t really science.”
We live in a nation where public acceptance of evolution is the second lowest of thirty-four developed countries, just ahead of Turkey. Roughly half of Americans reject some aspect of evolution, believe the earth is less than ten thousand years old, and that humans coexisted with dinosaurs. Where I live, many believe evolution to be synonymous with atheism, and there are those who strongly feel I am teaching heresy to thousands of students. A local pastor, whom I’ve never met, wrote an article in The University Christian complaining that, not only was I teaching evolution and ignoring creationism, I was teaching it as a non-Christian, alternative religion.
There are students who enroll in my courses and already accept evolution. Although not yet particularly knowledgeable on the subject, they are eager to learn more. Then there are the students whose minds are already sealed shut to the possibility that evolution exists, but need to take my class to fulfill a college requirement. And then there are the students who have no opinion one way or the other but are open-minded. These are the students I most hope to reach by presenting them with convincing and overwhelming evidence without offending or alienating them.
Some students take offense very easily. . .
And Phil Plait in Slate offers some answers to questions asked by creationists:
After writing yesterday about the now-famous/infamous debate between Bill Nye and Ken Ham, I don’t want to make this blog all creationism all the time, but indulge me this one more time, if you will. On BuzzFeed, there is a clever listicle that is a collection of 22 photos showing creationists holding up questions they have for people who “believe” in evolution.
These questions are fairly typically asked when evolution is questioned by creationists. Some are philosophical, and fun to think about, while others show a profound misunderstanding of how science works, and specifically what evolution is. I have found that most creationists who attack evolution have been taught about it by other creationists, so they really don’t understand what it is or how it works, instead they have a straw-man idea of it.
Because of this, it’s worth exploring and answering the questions presented. Some could be simply answered yes or no, but I’m all about going a bit deeper. With 22 questions I won’t go too deep, but if you have these questions yourself, or have been asked them, I hope this helps.
I’ll repeat the question below, and give my answers.
1) “Bill Nye, are you influencing the minds of children in a positive way?”
I’m not Bill, but I’d say yes, he is. More than just giving them facts to memorize, he is showing them how science works. Not only that, his clear love and enthusiasm for science is infectious, and that to me is his greatest gift.
2) “Are you scared of a Divine Creator?”
No. In fact, if there is a Judeo-Christian god, that would have fascinating implications for much of what we scientists study, and would be a rich vein to mine. Perhaps a more pertinent question is, “Are you scared there might not be a Divine Creator?” There is more room for a god in science than there is for no god in religious faith.
3) “Is it completely illogical that the Earth was created mature? i.e. trees created with rings … Adam created as an adult ….”
It might be internally consistent, even logical, but a bit of a stretch. After all, we can posit that God created the Universe last Thursday, looking exactly as it is, with all evidence pointing to it being old and your memories implanted such that you think you’re older than a mere few days. Consistent, sure, but plausible? Not really.
4) “Does not the second law of thermodynamics disprove evolution?” . . .
If something is a good solution, evolution tends to close in on it, and separate evolutionary paths thus reach quite similar good solutions: the eye, for example, has evolved independently 50 to 100 times. But the eye is a late-comer, evolutionarily speaking, whereas neurons are really basic—i.e., evolved very early, before much branching had been done. But, as it turns out, after some branching, so that we have different sorts of neurons. Emily Singer reports in Quanta:
When Leonid Moroz, a neuroscientist at the Whitney Laboratory for Marine Bioscience in St. Augustine, Fla., first began studying comb jellies, he was puzzled. He knew the primitive sea creatures had nerve cells — responsible, among other things, for orchestrating the darting of their tentacles and the beat of their iridescent cilia. But those neurons appeared to be invisible. The dyes that scientists typically use to stain and study those cells simply didn’t work. The comb jellies’ neural anatomy was like nothing else he had ever encountered.
After years of study, he thinks he knows why. According to traditional evolutionary biology, neurons evolved just once, hundreds of millions of years ago, likely after sea sponges branched off the evolutionary tree. But Moroz thinks it happened twice — once in ancestors of comb jellies, which split off at around the same time as sea sponges, and once in the animals that gave rise to jellyfish and all subsequent animals, including us. He cites as evidence the fact that comb jellies have a relatively alien neural system, employing different chemicals and architecture from our own. “When we look at the genome and other information, we see not only different grammar but a different alphabet,” Moroz said.
When Moroz proposed his theory, evolutionary biologists were skeptical. Neurons are the most complex cell type in existence, critics argued, capable of capturing information, making computations and executing decisions. Because they are so complicated, they are unlikely to have evolved twice.
But new support for Moroz’s idea comes from recent genetic work suggesting that comb jellies are ancient — the first group to branch off the animal family tree. If true, that would bolster the chance that they evolved neurons on their own.
The debate has generated intense interest among evolutionary biologists. Moroz’s work does not only call into question the origins of the brain and the evolutionary history of animals. It also challenges the deeply entrenched idea that evolution progresses steadily forward, building up complexity over time.
The First Split
Somewhere in the neighborhood of 540 million years ago, the ocean was poised for an explosion of animal life. The common ancestor of all animals roamed the seas, ready to diversify into the rich panoply of fauna we see today.
Scientists have long assumed that sponges were the first to branch off the main trunk of the animal family tree. They’re one of the simplest classes of animals, lacking specialized structures, such as nerves or a digestive system. Most rely on the ambient flow of water to collect food and remove waste.
Later, as is generally believed, the rest of the animal lineage split into comb jellies, also known as ctenophores (pronounced TEN-oh-fours); cnidarians (jellyfish, corals and anemones); very simple multicellular animals called placozoa; and eventually bilaterians, the branch that led to insects, humans and everything in between.
But sorting out the exact order in which the early animal branches split has been a notoriously thorny problem. We have little sense of what animals looked like so many millions of years ago because their soft bodies left little tangible evidence in rocks. “The fossil record is spotty,” said Linda Holland, an evolutionary biologist at the Scripps Institution of Oceanography at the University of California, San Diego.
To make up for our inability to see into the past, scientists use the morphology (structure) and genetics of living animals to try to reconstruct the relationships of ancient ones. But in the case of comb jellies, the study of living animals presents serious challenges.
God doesn’t seem to be directly involved, at least not in the common way of thinking about it. Robert Service writes in Science:
The origin of life on Earth is a set of paradoxes. In order for life to have gotten started, there must have been a genetic molecule—something like DNA or RNA—capable of passing along blueprints for making proteins, the workhorse molecules of life. But modern cells can’t copy DNA and RNA without the help of proteins themselves. To make matters more vexing, none of these molecules can do their jobs without fatty lipids, which provide the membranes that cells need to hold their contents inside. And in yet another chicken-and-egg complication, protein-based enzymes (encoded by genetic molecules) are needed to synthesize lipids.
Now, researchers say they may have solved these paradoxes. Chemists report today that a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start. Although the new work does not prove that this is how life started, it may eventually help explain one of the deepest mysteries in modern science.
“This is a very important paper,” says Jack Szostak, a molecular biologist and origin-of-life researcher at Massachusetts General Hospital in Boston, who was not affiliated with the current research. “It proposes for the first time a scenario by which almost all of the essential building blocks for life could be assembled in one geological setting.”
Scientists have long touted their own favorite scenarios for which set of biomolecules formed first. “RNA World” proponents, for example suggest . . .
The exciting thing is that if it’s the result of a natural process, then life must be present across our galaxy and others. Intelligent life, of course, is another story, and is rare even on earth.
It’s amazing what evolution can produce given enough time. Derek Mead reports at Motherboard:
A funny-looking moth has more in common with fighter jets than most of us would ever have guessed: The luna moth’s long, fluttering tail acts like radar-distracting chafffor bats’ echolocation signals, effectively misdirecting the flying mammals to an expendable part of their body. It’s a scene seemingly better suited to Top Gun than the night skies of North America, but hey, the animal kingdom is no stranger to a good arms race.
If you’re a flying insect, having a bat show up on your tail is assuredly more terrifying than a fighter plane. Bats’ echolocation abilities have evolved over millions of years to become incredibly effective at locating and tracking prey, like the relatively noisy fluttering of a moth.
Moths aren’t entirely helpless, however. Many, such as noctuid moths, have simple ears that are tuned to the sonar frequencies of the bats that prey on them. Yet closeto half of nocturnal moth species don’t have those bat-tracking ears. According to new research, the luna moth (Actias luna, family Saturniidae) has evolved a different defense entirely: Its swallow-like tails flap and spin in its wake, creating a confusing mess that bats end up targeting, much like a heat-seeking missile getting misdirected by aerial flares. . .
Continue reading. Video at the link.
Robert Axelrod’s book The Evolution of Cooperation suggested that (in the context of the Prisoner’s Dilemma) cooperation is a winning strategy. (It’s a very interesting book, BTW. It describes a competition of algorithms for playing Prisoner’s Dilemma. One algorithm (by Anatol Rapoport) won the first competition easily. Axelrod (who created the tournament) published the results, including the various algorithms used, then launched a second tournament. Anatol Rapoport was again the winner, using the same algorithm. His book Operational Philosophy had a big impact on me in high school.)
But perhaps cooperation’s victory then was less decisive than we thought. Emily Singer writes in Quanta:
en the manuscript crossed his desk, Joshua Plotkin, a theoretical biologist at the University of Pennsylvania, was immediately intrigued. The physicist Freeman Dyson and the computer scientist William Press, both highly accomplished in their fields, had found a new solution to a famous, decades-old game theory scenario called the prisoner’s dilemma, in which players must decide whether to cheat or cooperate with a partner. The prisoner’s dilemma has long been used to help explain how cooperation might endure in nature. After all, natural selection is ruled by the survival of the fittest, so one might expect that selfish strategies benefiting the individual would be most likely to persist. But careful study of the prisoner’s dilemma revealed that organisms could act entirely in their own self-interest and still create a cooperative community.
Press and Dyson’s new solution to the problem, however, threw that rosy perspective into question. It suggested the best strategies were selfish ones that led to extortion, not cooperation.
Plotkin found the duo’s math remarkable in its elegance. But the outcome troubled him. Nature includes numerous examples of cooperative behavior. For example, vampire bats donate some of their blood meal to community members that fail to find prey. Some species of birds and social insects routinely help raise another’s brood. Even bacteria can cooperate, sticking to each other so that some may survive poison. If extortion reigns, what drives these and other acts of selflessness?
Press and Dyson’s paper looked at a classic game theory scenario — a pair of players engaged in repeated confrontation. Plotkin wanted to know if generosity could be revived if the same math was applied to a situation that more closely resembled nature. So he recast their approach in a population, allowing individuals to play a series of games with every other member of their group. The outcome of his experiments, the most recent of which was publishedin December in the Proceedings of the National Academy of Sciences, suggests that generosity and selfishness walk a precarious line. In some cases, cooperation triumphs. But shift just one variable, and extortion takes over once again. “We now have a very general explanation for when cooperation is expected, or not expected, to evolve in populations,” Plotkin said.
The work is entirely theoretical at this point. But the findings could potentially have broad-reaching implications, explaining phenomena ranging from cooperation among complex organisms to the evolution of multicellularity — a form of cooperation among individual cells.
Plotkin and others say that Press and Dyson’s work could provide a new framework for studying the evolution of cooperation using game theory, allowing researchers to tease out the parameters that permit cooperation to exist. “It has basically revived this field,” said Martin Nowak, a biologist and mathematician at Harvard University.
Tit for Tat
Vervet monkeys are known for their alarm calls. A monkey will scream to warn its neighbors when a predator is nearby. But in doing so, it draws dangerous attention to itself. Scientists going back to Darwin have struggled to explain how this kind of altruistic behavior evolved. If a high enough percentage of screaming monkeys gets picked off by predators, natural selection would be expected to snuff out the screamers in the gene pool. Yet it does not, and speculation as to why has led to decades of (sometimes heated) debate.
Researchers have proposed different possible mechanisms to explain cooperation. Kin selection suggests that helping family members ultimately helps the individual. Group selection proposes that cooperative groups may be more likely to survive than uncooperative ones. And direct reciprocity posits that individuals benefit from helping someone who has helped them in the past.
The prisoner’s dilemma helps researchers understand . . .
And, to provide balance, an example of non-meme evolution: “New class of antibiotic found in dirt could prove resistant to resistance”
And now provide an example of a meme analogue…
And, BTW, how on earth can people deny evolution? I don’t get it.
Emily Singer writes in Quanta magazine:
For 30 years, Gerald Joyce has been trying to create life. As a graduate student in the 1980s, he studied how the first RNA molecules — chemical cousins to DNA that can both store and transmit genetic information — might have assembled themselves out of simpler units, a process that many scientists believe led to the first living things.
Unfortunately, he had a problem. At a chemical level, a deep bias permeates all of biology. The molecules that make up DNA and other nucleic acids such as RNA have an inherent “handedness.” These molecules can exist in two mirror image forms, but only the right-handed version is found in living organisms. Handedness serves an essential function in living beings; many of the chemical reactions that drive our cells only work with molecules of the correct handedness. But the pre-biological building blocks of life didn’t exhibit such an overwhelming bias. Some were left-handed and some right. So how did right-handed RNA emerge from a mix of molecules?
Joyce was able to build RNA out of right-handed building blocks, as others had done before him. But when he added in left-handed molecules, mimicking the conditions on the early Earth, everything came to a halt. “Our paper said if you have [both] forms in the same place at the same time, you can’t even get started,” Joyce said.
His findings, published in Nature in 1984, suggested that in order for life to emerge, something first had to crack the symmetry between left-handed and right-handed molecules, an event biochemists call “breaking the mirror.” Since then, scientists have largely focused their search for the origin of life’s handedness in the prebiotic worlds of physics and chemistry, not biology.
Three decades later, Joyce’s latest research has shown that perhaps life came first after all. Joyce, now at the Scripps Research Institute in La Jolla, Calif., and Jonathan Sczepanski, a postdoctoral researcher, created an RNA enzyme — a substance that copies RNA — that can function in a soup of left- and right-handed building blocks, providing a potential mechanism for how some of the first biological molecules might have evolved in a symmetrical world. The new experiment, published in the November 20 issue of Nature, is reinvigorating the discussion over how life first arose. “They have really opened up a new realm of possible roads,” said Niles Lehman, a biochemist at Portland State University in Oregon who wasn’t involved in the study.
Even more intriguing, Joyce and Sczepanski’s enzyme works differently from other RNA-copying molecules, a discovery that may have profound implications for how life originated. The enzyme is much more efficient and flexible than other RNA-based enzymes developed to date, and it may provide the key to Joyce’s ultimate goal — making life from scratch.
A Crack in the Mirror
Louis Pasteur, the famous 19th-century French chemist, was the first to describe chemical handedness, or “chirality.” He was puzzled by the fact that crystals derived from the dregs of wine twisted light in a specific direction, but the same crystal synthesized in the lab did not. Examining the crystals under a microscope, he discovered that the synthetic chemical came in two mirror-image forms, which canceled out the polarizing effect. The crystal derived from wine had only one.
Scientists later discovered that this bias encompasses the entire living world. Synthetic chemical processes will generate both left- and right-handed molecules. But when nature makes a molecule, the product is either left- or right-handed. For example, all amino acids that are used to make proteins twist light to the left.
Indeed, chirality is an essential component of biochemistry. “It provides a form of molecular recognition,” said Donna Blackmond, a chemical engineer at Scripps and a colleague of Joyce’s. The chirality of a molecule affects how it interacts with other components of the cell. Molecular locks can only be opened with a key of the correct handedness.
Some scientists look to the heavens to explain how this biological bias first arose. . .