Start 2011 off with some evolution, the Carnival of Evolution!

Here it is – to start off the new year – the 31st edition of the Carnival of Evolution! (CoE is on Twitter, @CarnyEvolution)

To start off this edition, let me remind you that, yes, evolution kicks ass!

Two evolution-related topics have received much attention in December, not only for their interesting nature, but how the media has spun the conclusions of the research.

First, the arsenic-based life:

Pharyngula: It’s not an arsenic-based life form (oh, sorry!) & There are people meaner than I am; Homologous Legs: When life gives you arsenic, make arsenate-backboned DNA, non-alien Halomonadaceae!; The Loom: Of Arsenic and Aliens & What the critics said; Sandwalk: Arsenic and Bacteria; Byte Size Biology: A new life form? Not so fast; oh what the heck, just check out Bora’s post of links to lots more about this!

Second, some anthropology news:

The Loom: Meet the Denisovans, the newest members of the human tree of life, Denisovans: Ordinary humans with extraordinary genes? & Oldest Homo sapiens fossil? Journalistic vaporware; Laelaps: A Fistful of Teeth – Do the Qesem Cave Fossils Really Change Our Understanding of Human Evolution?; and Gene Expression: The paradigm is dead, long live the paradigm!

And now to the rest…

Science

Kele’s Science Blog, The Mario Genome!: “While I am sort of familiar with the idea of genetic algorithms, and many are cooler than what this does, I think the Mario Genome easily illustrates what the idea is all about to someone with little prior knowledge.”

Smithsonian, The Top Ten Daily Consequences of Having Evolved: “all species inhabit bodies imperfect for the lives they live. Our own bodies are worse off than most simply because of the many differences between the wilderness in which we evolved and the modern world in which we live. We feel the consequences every day.”

john hawks weblog, The Denisova genome FAQ: “Today, a paper by David Reich and colleagues presents the nuclear genome of the Denisova pinky bone. This is the second “whole genome” of an apparently extinct population of Pleistocene humans. This genome is nearly as distinct from Neanderthals as the draft Neanderthal genome is from living people.”

National Center for Science Education, “Molecular Insights” videos on-line: “Featured are four exciting speakers whose research in molecular evolution is revolutionizing our understanding of familiar and compelling examples of evolution.”

Neurotic Physiology, Friday Weird Science: Female Orgasm, Evolutionary Byproduct? Or not?: “Evolutionary biologists have debated the “purpose” of the female orgasm for a good long while. They have debated WHAT the purpose is, to be sure, but even more so, they have debated whether there IS one. Is the female orgasm just an evolution byproduct?”

The Atavism, Sunday Spinelessness – The origin and extinction of species: “Extinction is a natural part of life, and the fate of all species eventually, but when it’s driven by human short-sightedness and robs us of not just a wonderful product of nature but a window through which we might have understood nature’s working it’s very hard to write about.” (this could go in the History section, too)

Anthropology in Practice, The Evolutionary Roots of Talking With Our Hands: “The role of gestures in communication has been on my mind recently because my goddaughter is just beginning to communicate beyond crying and laughing. She recently celebrated her first birthday, and she’s begun to speak her first words. It’s extremely exciting. I find it really interesting that she points with increasing frequency to emphasize her exclamations—Elmo isn’t just a word, he’s a recognizable part of her world, from the decorations that were a part of her birthday celebration to her stuffed muppet that laughs when shaken. Her gestures help her bridge a communication gap.”

Why Evolution Is True, “Reinforcement” and the origin of species: “Curiously, though, the “reinforcement” seen in the wild applies to gametic isolation but not sexual isolation.  While sexual isolation (mate discrimination) quickly became stronger in forcibly-coexisting lab populations, it’s no stronger in nature in areas where the species coexist than elsewhere.  It’s a mystery to us why both forms of isolation evolve so quickly in the lab but only one is seen in co-occurring populations in nature.”

archy, Blood of the mammoth: “Catastrophists love frozen woolly mammoths. It doesn’t matter what their preferred catastrophe is–Atlantis sinking, falling ice moons, the Noachian flood, abrupt changes of the Earth’s axis, or a near miss by a pinballing planet disguised as an ancient Near Eastern god–at some point, they will trot out the frozen mammoths as proof positive of their theory. Frozen mammoths have already been spotted milling around 2012. What is it about mammoths that make them so attractive to catastrophists?”

13.7 – Cosmos and Culture, Our Family Tree: Chimps, Bonobos And Our Commonality: “So here’s the six-million-dollar question: What was the human-chimp-bonobo MRCA like? A great ape for sure. But what about behavior? Was it Homo-like? Pan-like? And what do we mean by such distinctions?”

Quodlibeta, Island of the Hobbits: “My best guess – going on past performance – is that the culprit is a yet to be discovered species, Hamster Giganticus, which polished off the islands inhabitants in a violent feeding frenzy and died of starvation shortly afterwards. The evidence will arrive any day now, you’ll see.”

Greg Laden’s Blog, There are two species of African elephant: “Everyone knows that there are two kinds of elephants in this world: Asian and African… Once again, everything you know is wrong. But you knew that.”

Denim and Tweed, Under the mistletoe, coevolution is about s and m: “Plants and plant products, from sprigs of holly to pine boughs, have been traditional winter holiday decorations since before Christmas became Christmas. Nowadays, if we don’t resort to plastic imitations, we deck our halls with garlands from a nursery and a tree from a farm. But seasonal decorations have natural histories apart from mantelpieces and door frames—ecological roles and, yes, coevolutionary interactions with other species.”

Denim and Tweed, Coevolutionary constraints may divide Joshua trees: “Scientists love it when the real world validates our more theoretical predictions. It helps, of course, if those predictions are rooted in the real world to begin with. This is more or less what happened in my own research, with results reported in two just-published scientific papers.”

The Mermaid’s Tale, A new broom sweeps gene?: “The idea that strong directional or ‘positive’ selection favored a single gene grew out of the Mendelian thread, but nobody in quantitative genetics (such as agricultural breeders or many working in population genetics theory) and those who understood gene networks, should have known that most of the time, especially given the typical weakness of selection, selection would not just find and fix a single allele in a single gene.”

The Mermaid’s Tale, Should we cut Darwin out of parts of the human skin color story?: “But it’s difficult to go into the details and nuance of these issues about skin color variation and vitamin D while introducing evolution to students. For many of my students, this is the first time that they’ve learned about evolution in a scholarly setting and we perform activities to illustrate the differences between Lamarckian evolution and Darwinian selection. Of course we also discuss all the known evolutionary forces—mutation, gene flow, drift, and selection—not just selection.”

Why Evolution Is True, New genes arise quickly: “What role does the appearance of new genes, versus simple changes in old ones, play in evolution? There are two reasons why this question has recently become important… The first involves a scientific controversy…   The second controversy is religious.”

Wired Science (Brian Switek of Laelaps), 6 Strange Fossils That Enlightened Evolutionary Scientists: “Even so, Darwin brought the subject of evolution to the forefront of Victorian science. And with an eye toward evolution, his colleagues began to pick through the traces of ancient life for clues about how organisms changed. This is a gallery of some of the key fossil species that have both confounded and inspired scientists in their efforts to understand the history of life and, placed in context of what we know today, have confirmed Darwin’s vision of a branching tree of life produced by natural selection.”

360 Degree Skeptic, Insight into the Minds of Turtles and Dogs: “Because most animals behave in a way foreign to our own minds, we tend to overlook and belittle what is going on in their minds. So to speak. The following two studies got my primate brain thinking about the minds of other species.”

Dr. Carin Bondar, The Fish-Stache: A Whole New Level of Sexual Selection: “Sexual selection is alive and well in the animal kingdom… Case in point: males of the Mexical guppy Poecilia sphenops seem to get by just fine with a little peach-fuzz on the upper lip. Yes, you read that correctly. Researchers hypothesized that epidermal outgrowths on the upper maxilla of these male fish (aka fish-staches) may be a sexually selected characteristic.”

Lab Rat, Levels of evolution: “From a bacteriologists point of view this is a fascinating example of just how variable a single strain of bacterial species can be. From a medical viewpoint it’s more worrying. The ability of highly virulent bacteria to chop out large portions of their genome and pass them onto other, potentially non-virulent strains could help to spread not just antibiotic resistance, but also other tricks like biofilm formation and different enzymes which help the bacteria to cope with antibiotic challenges.”

Teenage Atheist, Unintelligent Design: Blind Cave Fish: “When discussing evolution with Creationists, I love to bring up the case of the Mexican Tetra, more commonly known as Blind Cave Fish. These fishy critters are wondrous emblems of the blind processes of evolution and prove to be conspicuous hollows in the Intelligent Design movement.” (this post could go in the Culture Wars section, too)

Pharyngula, The molecular foundation of the phylotypic stage: “Two recent papers in Nature have examined the real molecular information behind the phylotypic stage, and they’ve confirmed the molecular basis of the conservation.”

The Scientific Fundamentalist, Is This Why Teenage Girls Don’t Swoon for Middle-Aged Billionaires?: “The parent-offspring conflict theory of mate choice that Bram Buunk and his students have been advancing for the last several years questions the assumption of individual mate choice commonly used in evolutionary psychology. The pioneering work of David M. Buss and others since then all implicitly and explicitly assumes that men and women choose each other in mate selection according to the criteria that they consider important. Buunk and others question this assumption of individual autonomy in mate choice, and instead suggest that, both throughout human evolutionary history and in most traditional societies in the world today, parents may have exerted significant influence and control over their children’s mate choice.”

Pharyngula & Why Evolution Is True both discuss why “There’s plenty of time for evolution.”

NeuroDojo, The lonely places: Where could life exist, but doesn’t?: “While as a biologist, even microbes would be a spectacular finding, the question of whether habitats are vacant for complex, multicellular life is almost as interesting. And if Mars is ever found to support microbial life, why doesn’t it support macroscopic life?”

Pleiotropy, Pleiotropy is 100 years old: “This year, the term pleiotropy was defined 100 years ago, and Frank Stearns, graduate student at the University of Maryland biology graduate program has written a perspective in Genetics, which I highly recommend.”

Kele’s Science Blog, Of Lobsters, Sticklebacks, and Google Chrome: “The following is the last take-home essay for my developmental class. This essay is about the concept of modularity and how it is being used in biology today. It’s fairly basic stuff and if you are reading this blog, you probably know most of it already! I do hope you find the comparison to Google Chrome convincing though.”

Genome Engineering, Oh darling I love your bacteria: “Fruit flies (Drosophila melanogaster) can be annoying in the summer when they cluster round the kitchen compost crock, but they are also a vital weapon in evolutionary and genetic research. Research published in PNAS has suggested that fruit fly evolution may be driven by something as simple as diet and bacteria.”

Greg Laden’s Blog and Pharyngula both look at whether it’s okay to use term “missing link”

History

Brian Switek (Laelaps) for Smithsonian, Guest Blog: Breaking our link to the “March of Progress”: “I hate the phrase ‘missing link’. It immediately sends up a red flag in my mind, and is almost always a sure indicator that the person employing it has only a very superficial understanding of the way evolution works. To understand why this is, however, we have to inspect the intellectual baggage that the phrase carries with it.” (I reviewed Switek’s first book, Written in Stone, here)

Evolving Thoughts, Darwin’s motivation: “For some time now I have been convinced that Darwin’s original and most pressing problem was not adaptation. It was the existence of taxonomic diversity.”

Whewell’s Ghost: [Review] Wiker “The Darwin Myth”: “But all of this serves as a mere 134 page prelude to real argument that Wiker wishes to make. Three chapters (“What to make of it all”, “Darwin and Hitler”, “Christianity and Evolution”) repeat a series of creationist canards. Natural selection is a tautology. Darwin lied to himself when he felt that morality and natural selection could co-exist. Darwin’s ideas led to, or supported, eugenics, Nazism, abortion, euthanasia, sex education and contraceptives for the poor, and pornography.  Indeed, Darwinism can be used to justify cannibalism.”

The Dispersal of Darwin, This is why history of science is important

History of geology, Island Life: “Even the first naturalists noted that islands display important peculiarities in the animals and plants found on them, but it was only with the formulation of Darwins and Wallaces theory that these phenomeas could be explained.”

History of geology, The greatest show on Earth: “But Darwin’s theory by killing many of the old monsters created a lot of new ones. It is interesting to note that the classic cryptid monsters in modern pop culture since the late 19th/ early 20th century are in fact such “missing links” as imagined by the layman. Cryptozoologists are searching, based on presumed sightings, for Bigfoot, Sasquatch, Orang-Pendek and other cryptids, all described as the classic ape-man creatures. Even if all these creatures lack physical evidence, the theory of evolution somehow provided to these animals a plausible background.”

Culture Wars

National Center for Science Education, Top Ten Evolution Stories of 2010

Sandwalk, Students vs Icons of Evolution: “Students have to read Icons of Evolution and write an essay analyzing the arguments in one of the chapters (their choice). They have no problem recognizing the flaws in the logic and the outright mistruths in that book. For typical university students with a rudimentary understanding of evolution it’s like shooting fish in a barrel. The Discovery Institute sees it differently but they must live on another planet.”

World of Wonders, How Does Understanding Evolution Make Us Better Citizens?: “It is not so much our understanding of the fact of evolution that is so important to being an informed, responsible citizen. It is our understanding of how we know that evolution is a fact that is critical.” (want to understand evolution better, then check out Understanding Evolution, which just won a Science Prize for Online Resources in Education for 2010)

Dipping in the Toe, On Evolution: You are a Mutant: “The problem was there was a point that could have been made – perhaps a clarifying moment for some in the audience – to wipe away one of the very many misunderstandings surrounding evolution. Neither you, nor I, have ever (in the biological sense) evolved. You were born, you live, you die. And, genetically speaking, the essence of the physical “you”, your body, is a result of that one one event, when you were first conceived. What your body became was locked in at that moment. Yes, environment and other factors have their roles – some quite dramatic, but the genetic component is the core of it all. From birth to death, YOU do not evolve. But… when you were conceived and then born, there was something different about you. Something that does have to do with evolution. I’ll tell you what it is…”

National Center for Science Education, “Evolution and its rivals”: “‘Evolution and its rivals’ — a special issue of the philosophy journal Synthese focused on the creationism/evolution controversy — was just published.”

Skeptic, Top Ten Myths About Evolution: “This concise pamphlet provides answers to common objections to evolution, such as: If humans came from apes, why aren’t apes evolving into humans?; Only an intelligent designer could have made something as complex as an eye; The second law of thermo-dynamics proves that evolution is impossible; Evolution can’t account for morality; and more…”

The Panda’s Thumb, Chapman U. welcomes Evolution Education Research Center: “I’m particularly happy to see this because a few years ago, as readers will recall, the Chapman Law Review published a terrible creationist article. As an alumnus, I was so embarrassed to see the school’s name on such a piece of tripe that I responded with an article of my own. It’s nice to see Chapman step up for science!”

The Mermaid’s Tale, Encounters with Evolution… or… the Ark-etype of ignorance: “In the foreseeable future, it’ll be us Americans who are sitting around a meagre campfire gnawing raw meat (probably rat-meat, or maybe just McBurgers), while people in other countries, who value real education, will be dining on caviar…..and smiling patronizingly at our plight.”

Homologous Legs, The ID community isn’t Lönnig from their mistakes: “Once again, a touted “pro-ID, peer reviewed paper” hasn’t made a positive case for its favoured hypothesis. It’ll be interesting to see how much positive publicity this paper will get in the ID community, but it deserves no praise from the scientific one.”

Homologous Legs, BIO-Complexity’s opinion on intelligent design isn’t complex: “As you can see, all of the editorial board members (expect one) are either sympathetic to or supporters or proponents of intelligent design. The odd one out is Branko Kozulic, about whose ID viewpoint I could find very little. I doubt he’s a hardcore ID critic, however. So, make up your own mind: do you think BIO-Complexity is a journal with an editorial board that has “a wide range of views on the merit of ID”, or is it simply another place for ID proponents to submit “research” to uncritical peer review and pass it off as legitimate science?”

Miscellany

World of Wonders, Lamarck is Alive and Well Living in Language: “And yet, nearly three centuries after his birth, we describe evolution with language that more closely suggests Lamarck’s idea than Darwin’s. We write that ‘snakes modified their lungs—one lung has been slimmed and elongated and the other reduced to a functionless relic.'”

Charlie’s Playhouse, Winners of the Evolution & Art Contest!: “In this contest we asked kids to think of an animal alive today, imagine a bunch of them stranded in a different environment, and draw a picture of how the animal might evolve to fit its new environment after a long time. And boy, did the kids think, imagine, and draw!” (interviews with two of the winners, here and here; and my own son’s entry)

She Thought, My 5 year old just worked out evolution: “I don’t mean she’s intuited natural selection or anything like that, she’s 5 and not even I’m that deeply into Mummy pride.  And honesty compels me to admit that we’re just a little bit into ‘science activities’ around here so she probably has a head start on 99% of the population.  But I can track the way her understanding has developed and it’s fascinating to see.”

Richard Dawkins, “History of the Earth” in C Major:

The Flying Trilobite, Calvin Mellow: this is a wonderful, evolutionary welcome to a new life (congratulations, Glendon!)

Drawing Files, THIS JUST IN: Reviews!: “We are tantalizingly close to having a finished book! Here are the first two reviews of Evolution: The Story of Life on Earth. So far so good!” (the NCSE has a free preview)

Jon’s Blog, Best Birthday Gift: “Marvel Apes: The Evolution Starts Here”: “The best part this series of one-shots, IMHO, was a serial about the time that Charles Darwin pissed off the Ancient One (Earth’s now-deceased Sorcerer Supreme) and got mystically exiled to the Planet of the Marvel Apes for a couple weeks.  He immediately drew the attention of L-ook-i (God of Mischief), who proceeds to split Darwin into three forms (Human Darwin, Ape Darwin, and Future Human Darwin).  Eventually, Future Human Darwin uses super-science to transform Human Darwin into the Low Evolutionary and super-evolved hijinks happen.  I won’t spoil how things turn out, though I will gleefully reveal that at least one of these three Darwins survives the storyline and is traveling the cosmos and just begging to return to someday to comics.”

There were some fun evolution-themed images and cards for the holiday season: Need some holiday cards…, With Frosty in mind…, Tree, from xkcd, and Darwin Phylogenetic Christmas tree

Why Evolution Is True, Redundant parts: “We are bilaterally symmetrical, bipedal organisms descended from bilaterally symmetrical fishes. In some cases having two of something isuseful.  Our two eyes give us binocular vision, but we have two not because of that facility, but because our fishy ancestors had two eyes that enabled them to see, nonbinocularly, on both sides of their bodies.”

Babel’s Dawn, Riding A Two-Horse Shay: “David Sloan Wilson has an online essay, ‘Take the Evolution Challenge,’ calling for the extension of “evolutionary theory beyond the biological sciences to include all things human.” It is a radical proposition, perhaps overstated as a way of encouraging people to take the idea to its limit. I’m not sure what new insights the theory of evolution has to offer a history of, say, the crusades, but you never know. And I have to say that I have been amazed by how much I have clarified my understanding of language simply by taking an evolutionary approach to its origins. It turns out that evolutionary theory forces a series of questions that, at least in the study of language, pays off handsomely. So, despite my uncertainties, I want to endorse Wilson’s call. No study of anything human should ignore what evolutionary theory has to offer.”

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Thus ends this New Year edition of the Carnival of Evolution. The next edition will be hosted by Jeremy Yoder at Denim and Tweed. Submit your posts on this page. Take note, also, that CoE is seeking help in creating another logo.

Happy New Year!