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Monday, August 01, 2011

Carnival of Evolution #38

Welcome to the carnival! This is one of the biggest Carnivals of Evolution we've ever had. It's an exciting and colorful parade of articles about evolution from the month of July 2011.

The last Carnival of Evolution was published on The Lessons of Evolution. For the next one (September 1, 2011) send your submissions to Carnival of Evolution. In case you don't know what a blog carnival is all about, here's a very informative FAQ: Blog Carnival: Frequently Asked Questions.

I hope you enjoy #38. I grouped all the submissions into several categories to make it easier for you to find something of interest. You really should try to scan everything even though this is a very, very, long posting. I think it's the biggest one ever on Sandwalk.

Before we begin, Virginia Hensley at AS DEGREE has some recommendations for us. Check them out if you have a tablet or a smart phone.
20 Incredibly Entertaining iPad Apps for Science Nuts
Science is often an essential part of your education and degree, but it doesn't have to be boring. Science can also be fun through the help of these amazing iPad apps. You'll learn while being entertained.
Engelbert Hudson at Environmental Science Masters suggest some twitter threads you might be interested in following.
33 Environmental Scientists Worth Following on Twitter
Social media is branching out to be more than just places to keep in touch with friends and family. They are great educational tools as well. These environmental scientists post great information on Twitter for those interested in finding out news about the field and other great information about environmental science.


Classification, or taxonomy, is an important part of understanding the history of life. One of my favorite blogs is Catalogue of Organisms by Christopher Taylor ("An inordinate fondness for systematics"). Here are some postings from last month.
The August History of Filter-Feeding Ostracods.
Today's post subject, the Cavellinidae, were a family of ostracods that were around from the Middle Silurian period to the Middle Triassic (Adamczak 2003a). And for those of you unfamiliar with ostracods: you lucky, lucky bastards. They're horrible.
Patterns on a Squill
The south of Africa is one of the world's centres for botanical diversity. Home to an abundance of the floristically wierd and wonderful, you might be surprised to know just how many of your favourite garden plants (assuming that you have favourite garden plants) originate from that part of the world: ...
The Claim-Jumpers and Grave-Robbers of Taxonomy
In a recent paper in Zootaxa (openly accessible), O'Hara (2011) has become the most recent of a number of authors to discuss one of the more irritating taxonomic developments of recent years: the rise of the serial homonym replacer. A taxonomic homonym, in case you aren't already familiar with the term, is when a new taxon is given a name previously assigned to a distinct taxon (usually because the later author is unaware of the earlier usage's existence). Because the various nomenclatural codes require that any name can refer to only a single taxon, the more recently named taxon would generally need to be re-christened if it is to be accepted into polite society.
The Overwhelming Diversity of Life
If there is one thing that most people fail to grasp about biodiversity, it would be that there's just so much of it. It's an understandable failing: I work with biodiversity on a daily basis, and even I find myself constantly startled and awed by this point. So huge are the numbers involved that it's almost counter-productive to simply report them. Humans seem to have a tendency to effectively just lump any number over a hundred or so as simply 'a lot'.
I'm also a fan of Botany Photo of the Day. It often has some interesting evolution stories. Here's a couple from last month.

Ephedra viridis
As the Gnetophyta have some characteristics that are found in one or the other of Pinophyta and Magnoliophyta, some hypotheses suggest the group is an evolutionary link between conifers and flowering plants.
Brighamia insignis
Currently, Brighamia insignis is only found on the island of Kauai, though in the past it was also present on Niihau. It has not been observed on Niihau since 1947, however. The island of Molokai is host to a related species, Brighamia rockii, whose flowers are white instead of yellow and whose seeds are smooth, not bumpy. Both species are adapted to grow on windy sea cliffs, as their thickened stems support them in strong winds and their roots can grow in rocky crevices.
Jennifer Frazer is a science writer with a special fondness for the weird things in biology. She blogs at The Artful Amoeba.

The Jellyfish that Conquered Land — and Australia.
Most people know jellyfish and their ilk — the cnidarians, of sea pen, anemone, coral, and man’o'war fame — live in water and (happily for us) stay pretty well confined to it. But as it turns out, that’s not entirely the case.

In 1935, in a fit of profound naïveté, the government of Queensland introduced the cane toad to Australia to control the insects devouring its sugar cane fields. The result was a biblical-scale plague of the noxious amphibians ...
It's important to have a good understanding of the relationship between various species since that's a reflection of the history of life. It's also important to have the right perspective on life and to avoid the intrinsic bias that we all share: namely, to overestimate the importance of our own species. Psi Wavefunction is an undergraduate with an interest in protists. He/she blogs at The Ocelloid and the first posting is a lesson for all of us addressing the age-old question, "What the heck is a protist?"
Welcome to The Ocelloid!.
Nearly everyone finds wonder in at least some aspects of natural diversity whether it lies in the appreciation of exotic plants, the variety of domesticated breeds or simply enjoying a day off from urban chaos. From colorful venomous frogs to fluffy pandas or the strange terror of deep sea fishes, we are all familiar with the iconic images of our biosphere’s diversity. But the greatest biodiversity lies in the unseen, a world so alien yet so pervasive around us. Microbes, not macrobes, comprise the overwhelming majority of the earth’s biosphere, in quantity, mass and variety. While bacterial microbes are quite familiar to the microbiologist and anyone keen on the study of diseases, much less commonly spoken of are the microbial eukaryotes (and related macroscopic offshoots that are neither plant, fungal nor animal) the protists:
cromercrox identifies as "a Celebrity Nutritionist" who blogs at The End of the Pier Show. This month's contribution to the Carnival of Evolution is a report on the Zoologiclal Society of London's meeting on cryptozoology.
One Of Our Sea Serpents Is Missing
The meeting asked the question – is cryptozoology a science or a pseudoscience? I suspect that most people would veer to the latter view. After all, cryptozoology tends to group with aliens as subjects likely to attract muesli. There is, however, a movement of scientific sympathy towards the study of unknown animals, given that it should be the business of scientists to study unknown things – a tendency with which I have much sympathy, which presumably explains why I was asked to chair the proceedings.


Lot's of people blogged about Xiaotingia zhengi, the new bird-like fossil that resembles Archaeopteryx. The news is that the addition of Xiaotingia to the bird/dinosaur tree confirms the relationship between birds and dinosaurs and confirms the placement of Archaeopteryx as a cousin of modern birds rather than a direct ancestor. PZ Myers has a good description on his blog Pharyngula.
Xiaotingia zhengi
When Xiaotingia's data is tossed into the calculation, though, the results change. Xiaotingia doesn't cluster so tightly with birds; it's a more distant relative. However, Archaeopteryx shares enough significant features with Xiaotingia that they now cluster together, pulling Archaeopteryx out of the basal Aves and into a new classification. It says that Archaeopteryx is now a kind of second cousin, a little less closely related to the birds than previously thought.
The appendix and other vestigial organs aren't exactly "fossils" in the classic sense of the term but I had to put this next submission somewhere! Heather Scoville blogs at Evolution and she addresses a question that's been around for decades—the intelligent design community is especially interested in the answer.
Appendix May Not Be Vestigial After All
Vestigial structures are compelling evidence for evolution. The appendix is usually the first structure we think of that has no function in humans. But is the appendix really vestigial? A research team at Duke University says the appendix just might do something besides get infected.
If you're interested in evolution how could you not be interested in The Cambrian Explosion Song from Kevin Zelnio.

Evolution in Action

Carl Zimmer is a science writer—a very good one. He links from his blog The Loom to an article he published in the July 25, 2011 edition of the New York Times.
The Evolution of New York: My new story for the New York Times
In tomorrow’s New York Times, I’ve got a story about evolutionary biologists who make New York their Galapagos Islands. Working on this story was great fun–I traipsed around Manhattan parks and medians, checking out mice and ants and salamanders. I spoke to other researchers who study plants, fish, and bacteria in and around the city. All of them observe evolution unfolding in what might seem like a very unnatural place. But after four billion years, nothing can stop evolution. Not even New York.
Jerry Coyne is an evolutionary biologist at the University of Chicago. He's the author of Why Evolution Is true and he posts interesting articles about speciation and evolution (and other things) on his blog of the same name—only he insists that you don't call it a blog. (I ignore him.)
Adaptive Hybridization in Mice
One of the newer "expansions" of the modern synthetic theory of evolution is the idea that the genetic variation "used" by either natural selection or genetic drift can arise not just through mutations within a species, but also through hybridization with another species. Hybridization between different species usually yields maladaptive offspring, but occasionally a fertile hybrid can be the source of a new gene that can spread through a species that didn’t originally have it.
One of the most interesting debates in modern evolutionary biology is whether adaptation accounts for all (or most) visible change. The alternative is random genetic drift. This is a topic that interests Jerry Coyne.

The Spirit Bear
So, if the color gives an advantage at fishing and protection from being hunted, why aren’t all the bears in the area white? Even if black bears have an unknown countervailing advantage (like camouflage in the forest), that wouldn’t necessarily keep both color variants in the population: you’d expect the color conferring the highest net fitness to sweep through the population.

The relationship between plants and the microbes that infect them can get very complicated. It's often difficult to tell the difference between a symbiotic relationship and one that mostly benefits the infectious agent. Ford Denison posts at This Week in Evolution and last week he wrote about endocytes.
Beneficial infections?
Endophytes are microbes (often fungi) that infect plants without causing obvious disease. Some endophytes appear to benefit their plant hosts. How do they do this, and why? I will introduce these questions before discussing this week's paper,(Redman et al. 2011) which shows dramatic benefits to rice from particular endophytes.
Jeremy Yoder is a biologist whose specialty if the interaction between species. He has two contributions this month from his blog Denim and Tweed. The first one is about how two different mammals adapt to living at high altitudes.
Of mice and men, making a living in rarefied air
The fundamental problem at high altitude is to pull more oxygen from thinner air. Natural selection is good at solving problems, and it has multiple options for adapting a mammal to thinner air at high altitudes, to the extent that these traits are heritable.
The second article by Jeremy Yoder concerns symbiosis and how scientists can explain why some plants choose some bacteria and vice versa
Choosing your partner is only as helpful as the partners you have to choose from
When you need partners for some sort of cooperative activity—say, teammates for a game of kickball—you'd probably like to have a choice among several candidates. That lets you weigh considerations about kicking strength and running speed—and who promised to give you his dessert at lunch period—to build a winning team. However, if the other team captain snaps up the good players first, the fact that you have a choice among the others might not make much difference.
Sticklebacks (fish) also have to make choices and that's the subject of Emily Weigel's guest posting on the BEACON blog. (BEACON is an NSF (USA) Center for the Study of Evolution in Action.)

The Mating Game
What would a fish say if it could talk? How about, "Hey, baby. What’s your sign?" Male threespine sticklebacks court females in a constant game of flashy zig-zag dances and showing off with the hope that a female will respond favorably. Most of the time, to use the baseball analogy, the male strikes out; that is, the female swims hurriedly away, and the male must go sadly back to the nest alone tonight.

Who wants to get out in the wilderness and take DNA samples from grizzly bears? Kevin Zelnio (EvoECOLab) explains why anyone would want such a dangerous job.
The Reality and Utility of Bear Paternity Tests
The Bear DNA research, more formally known as the Northern Divide Grizzly Bear Project – headed by Dr. Katherine Kendall of the United States Geologic Survey at Glacier Field Station in Montana, used wire traps and video surveillance cameras to capture hair from bears all over the Rockies. It is an ambitious and highly successful program. In its operation has identified nearly every individual bear in the area, estimated to be ~765.
David Winter tells us about his particular passion—which turns out to be pretty weird. It combines snails and bird poop. He sometimes blogs at Scientific American
Bird guts, not muddy feet, may help snails migrate overseas
When I'm not spending my time writing about the weird bugs I find in the garden, or even weirder creatures I just think the world ought to know about, I study land snails from Pacific Islands. That means every time I give I talk I spend the first couple of minutes convincing people that - along with colourful fish, tropic birds and beautiful Hibiscus - land snails are one of the characters tic creatures of Pacific ecosystems. Snails might seem like unlikely overseas travellers, but they've made it to the most isolated and the youngest islands.

Evolution of Behavior/Evolutionary Psychology

Becky Ward reviews a recent paper on the courtship behavior of golden-collared manakins. Becky blogs at It Takes 30. Watch the video.
Dance for Me
Ah, courtship. That crazy time when you’ll do almost anything to show off for your potential mate: drink too much, fight with rivals, play chicken with cars, and generally behave in ways that make you shudder in later life. The courtship rituals of suburbia are complex enough, but they pale in comparison to the behaviors some animals show.
Speaking of birds, have you ever wondered how birds manage to land on a swaying branch? It's a skill that's much like the skill of a baseball outfielder catching a fly ball, at least according to Alex Washoe at Birdland West.
Game Show Pigeons and Ball Playing Dogs
Over at (possibly the coolest domain name ever), Davide Castelvecchi, who is a physical sciences and mathematics editor at Scientific American, has been stirring up controversy recently by revisiting what's known as "The Monty Hall Problem". If you're not familiar with it -- where have you been? It's been discussed over the years everywhere from hard science magazines to Car Talk.
Ford Denison looks at cooperation in human societies—what is the evolutionary advantage of such a behavior? He reviews two papers that address the issue. He blogs at This Week in Evolution.
Evolution of human cooperation
Two papers this week help explain why humans cooperate, even with nonrelatives. Cooperation with relatives (activities that tend to decrease one's own reproductive success, while increasing that of others likely to share many of one's genes) is predicted by "selfish gene" theory, as formalized in Hamilton's rule. I've assumed that cooperation with nonrelatives is a beneficial side-effect of behavioral genes that evolved when most of our neighbors were relatives, as is still the case in parts of the Amazon and West Virginia. But other explanations have been proposed.
Have you ever wondered why bats fly at night instead of during the day? Zen Faulkes (NeuroDojo) looks at a recent paper that tries to answer that question.
Bats marry the night
We know what Bruce Wayne picked as a “creature of the night”: a bat.

But why are bats so strongly nocturnal? Why don’t we see bats out flying around in the daytime (besides a few out on remote islands)? After all, most people can quickly think of one line of birds that is largely nocturnal.

If a bird had flown through Bruce Wayne’s window, we might have had a very different character in stately Wayne Manor.
We have two submissions from Eric Michael Johnson of The Primate Diaries. There are both book reviews with a good deal of editorial comment.
The Science of Sexism: Primate Behavior and the Culture of Sexual Coercion
Primatologists and evolutionary biologists have taken this question seriously and have developed some surprising conclusions that could inform our approach to this issue. Unlike Randy Thornhill and Craig Palmer’s book A Natural History of Rape, a thesis that was criticized by scholars both in biology and gender studies, other evolutionary researchers have developed a much more balanced analysis. One example is from the recent edited volume Sexual Coercion in Primates and Humans by Martin Muller and Richard Wrangham.

Frans de Waal on Political Apes, Science Communication, and Building a Cooperative Society
“It’s the animal in us,” we often hear when we’ve been bad. But why not when we’re good? This is the question that has driven Frans de Waal for the past 30 years. From his pioneering research on alliance formation in Chimpanzee Politics, to reconciliation behavior in Peacemaking Among Primates and Good Natured, to the implications for human life and thought in Primates and Philosophers, de Waal has been seeking to understand the roots of moral behavior in the most political of animals. The theme of his newest book, The Age of Empathy: Nature’s Lessons for a Kinder Society, is the culmination of his work to date and presents a synthesis of the factors that account for cooperative behavior in the natural world.
Let's not ignore the controversy surrounding evolutionary psychology. Jesse Bering is a research psychologist who blogs at Bering in Mind. Here's an old blog posting where he interviews a well-known evolutionary psychologist (Gordon Gallup) and asks the tough question.
Homophobia Phobia: Bad Science or Bad Science Comprehension?
BERING: Evolutionary biologists, but also non-specialists, casually deride evolutionary psychology as generating "just-so stories." Jon Wilkins, for example, of the Santa Fe Institute, reminds us that, "plausibility is NOT scientific proof." Likewise, Yoder layers his critique of your work with references to Brother Grimm​ fairy tales. Larry Moran of the University of Toronto, writes, "Why is it that respected evolutionary psychologists think these just-so stories are an important part of their discipline?"

How has this just-so-story rhetoric affected your research, and what, in your view, are the implications of this type of Gouldian-era language for the discipline as a whole?

GALLUP: Just as the title of my 1996 reply to John Archer implies, everything in science boils down to a matter of evidence. I have never taken the position that plausibility is a substitute for evidence. My 1995 paper along with my reply to Archer is based almost entirely on evidence. It is interesting how my critics tip-toe around the fact that my approach is based on a testable hypothesis, and how they go out of their way to side-step the fact that the data we’ve collected are consistent with the predictions. Whether it is politically incorrect or contrary to prevailing social dogma, is irrelevant. In science, knowing is preferable to not knowing. Minds are like parachutes, they only function when they’re open. If I were a homosexual, I’d want to know about these data.
Kate Clancy is an anthropologist at the University of Illinois. She blogs at Context and Variation where she focuses on "the evolution of human behavior and issues for women in science." Apparently, she's sometimes a bit skeptical of evolutionary psychology.
To save your marriage, hold the mayo… but only if you’re a lady
The data and findings are interesting (even though, controlling for divorce? Really? When studying marriage satisfaction?). The conclusions, however, are troubling. To put it another way: if you write an evolutionary psychology article but the only author you cite who even pretends to be evolutionary is David Buss, I’m probably going to blog about it.
Zen Faulkes is also a little skeptical about some of the evolutionary psychology papers that are being published. Read what he has to say on his blog NeuroDojo.
I will give you a reason to fear the night
I’m puzzled as to why the authors wanted to play up this strange evolutionary psychology angle to the story. Speculative "just so" stories of adaptation seem so insignificant in a project about humans getting attacked and eaten by lions.

Can evolutionary psychology walk the walk over walking?
Robert Kurzban recently defended evolutionary psychology by asking the rhetorical question:
"If you think that we can discover the function of fever, puking, and pooping at the base of a tree, why are other patterns of behavior not susceptible to a similar analysis?"
You can. But there are too many examples of evolutionary biology being applied to human behaviour in an offhanded and slipshod way. For an example, John Bradshaw described this research on the detection of sex from movement.
John Hawks has an appropriately named blog: john hawks weblog. He's mostly interested in human evolution but he approaches it from many different angles. Last month he addressed evolutionay psychology.
Adapting evolutionary psychology
I've written on evolutionary psychology at some length, often in a very critical way (for a good example, check out this post about David Buller's critical work and evolutionary psychologists' lame response). But the idea of niche construction irritates me a lot more than evolutionary psychology ever does.

So I'll take a critical view of the four suggestions put forward by Bolhuis and colleagues as ways to move evolutionary psychology forward: ...


PZ Myers studies the developmental biology of fish at the University of Minnesota in Morris. He's also very fond of cephalopods. PZ has a blog called Pharyngula—a name that reflects his interest in the developmental biology of vertebrates. You may have heard about his blog 'cause he writes awesome articles about evo-devo. He also writes about other things.
A Little cis Story

There is a bit of a debate going on about the relative importance of cis and trans mutations in evolution. Proponents of the cis perspective like to point out that cis mutations can be wonderfully subtle and specific; you can make a change in an enhancer and only modify the expression of the gene in one tissue, or even a small part of one tissue, while changing a trans factor causes changes in every tissue that uses that gene product. Also, most of the cis proponents are evo-devo people, scientists who study the small variations in timing and magnitude of gene expression that lead to differences in form, so of course the kinds of changes that affect the stuff we study must be the most important.
PZ Myers' second contribution was posted on Pharyngula and also on The Panda's Thumb. You're probably going to want to read this one when you see the title.
The greatest science paper ever published in the history of humankind
That's not hyperbole. I really mean it. How else could I react when I open up the latest issue of Bioessays, and see this: Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. Just from the title alone, I'm immediately launched into my happy place: sitting on a rocky beach on the Pacific Northwest coast, enjoying the sea breeze while the my wife serves me a big platter of bacon, and the cannula in my hypothalamus slowly drips a potent cocktail of cocain and ecstasy direct into my pleasure centers…and there's pie for dessert. It's like the authors know me and sat down to concoct a title where every word would push my buttons.
One way of testing the idea that small changes in regulatory pathways can lead to big changes in an organism is to experimentally manipulate a regulatory pathway to see if it can be "switched" to another type of pathway. Stephen Matheson at Quintessence of Dust tells us about a recent paper that does just that.
Evolution cheats, or how to get an old enzyme to do new tricks
Now, kinases tend to be pretty picky about who they stick phosphate onto, and this specificity is known to involve the business end of the kinase, called the active site. The active site is (generally) the part of the kinase that physically interacts with the target and transfers the phosphate. You might think that this interaction, between kinase and target, through the active site, would be by far the most important factor in determining the specificity of kinase function. But that's probably not the case.

Evolutionary Theory

Jerry Coyne is a bit skeptical about so-called revolutions in evolutionary theory. Personally, I think he throws the baby out with the bathwater but see what you think.

BBC Radio 4 tonight: a revolution in evolution? NOT
Over my whole career, but especially in the last half-dozen years or so, I’ve heard that neo-Darwinism (the modern theory of evolution) is either wrong, in a crisis, or about to undergo a profound Kuhnian paradigm shift. And it’s never happened. Neo-Darwinism gets expanded (things like the “neutral theory,” for example, were adopted and largely verified during my own career), but the basic paradigm of mutation, selection, drift, and speciation hasn’t much changed. New findings, like punctuated patterns that appear in the fossil record—patterns once foolishly touted by Gould & Co. as evidence that neo-Darwinism was “effectively dead”—eventually get folded into our current view of evolution, which expands and gets richer. Jerry Fodor and Massimo Piattelli-Palmarini wrote a book claiming that natural selection was theoretically incoherent and not responsible for adaptation, but they were dead wrong.
Bjørn Østman is the fearless leader behind the Carnival of Evolution. He blogs at Pleiotropy and last month he addressed fitness landscapes—a perennial problem in evolutionary theory.
Using deleterious mutations to cross fitness valleys - as misunderstood by ID creationists
This research is part of my PhD thesis which I started in 2007, in part inspired by the creationist claim that deleterious mutations are only bad and prohibits evolution. My first objection was that they can of course exist on the line of descent as hitchhikers - deleterious mutations that go to fixation because they occur in close temporal proximity* to a beneficial mutation, so the combined effect is beneficial. Then I learned about epistasis - the interaction between mutations - which is ubiquitous and essential for non-trivial adaptation. Trivial adaptation is when evolution occurs by accumulating only beneficial mutations, as when a single fitness peak is ascended. But if the fitness landscape is rugged with many local peaks (as it necessarily always is in reality), then it is of great benefit to be able to climb down one peak and up another higher one.

More on high-dimensional fitness landscapes
In a post from a few days ago about a paper I just got published, John Wilkins asked how my work ties in with Gavrilets' stuff on high dimensional landscapes. Here's my answer:

In terms of the discussion about the strength of the metaphor of the fitness landscape, my view is that the people who argue that it's not useful or even misleading are wrong. Yes, some people may take the analogy with a geographic landscape too far.
When we think of evolutionary theory we often think of population genetics and simulations of allele frequency changes. But that's not all there is to evolution. There's a lot of work being done at the level of species and ecology and that's the subject of Nicolas Chaumont's contribution this month. He's a guest blogger at BEACON
Autonomous foraging, speciation and open-ended evolutionary experiments in 3D physically realistic worlds
Everybody I’ve talked to who is aware of Karl Sims’ work on the evolution of his 3D blocky creatures was impressed by the seemingly elaborate behavior they were capable of, despite their simple morphologies. The presentation of his results in 1994 was seen as a technical tour de force. Even by today’s standards, his work remains impressive. I was poised in the summer of 2000 to start a Master’s project at Sherbrooke University in Canada, with the goal of reproducing some of his results. This is how the EVO project has begun. Many students who underwent similar efforts to reproduce Sims’ work typically graduate and move on to a different project. Unlike them, I was fortunate to have Prof. Chris Adami as my Ph.D. adviser who saw how this program could be expanded to study Speciation, and other aspects of Evolutionary Biology.
Artificial intelligence doesn't really have much to do with evolutionary theory, or does it? Arend Hintze, a guest blogger at BEACON, tries to enlighten us.
BEACON Researchers at Work: Developing artificial intelligence
When I am asked what I do, I normally smile apologetically and say something like “Theoretical Biology” or “Computational Biology,” and with a wink of my eye “like biological evolution … only in the computer” followed by a hand waving gesture that looks like me typing. At least that is my way of coping with the problem of explaining what it is that gets me excited, and most people slowly nod their head and respond with an encouraging voice: “In the computer, I see!” and in most cases we change the topic.
Evolutionary theory is always exciting but you ain't seen nothing until you see natural selection as a poem by Kevin Zelnio at EvEcoLab: Agent of Selection.

Molecular Evolution/Genetics

There's a lot of debate these days about the organization of eukaryotic genomes. Is most of it junk or are there important functions hidden in that part of the genome that we haven't characterized? Anne Buchanan is one of the bloggers at the mermaid's tale and she analyzes recent papers on the transcription of the human genome.
Epistemology and genetics: does pervasive transcription happen?
Molecular genetics these days is by and large not hypothesis driven, but technology driven. There is no theory of what we should or must find in DNA. Indeed, there is hardly a rule that, when we look closely, is not routinely violated. Evolution assembles things in a haphazard, largely chance-driven way. Rather than testing a hypothesis, masses of data are collected in blanket coverage fashion, mined in the hopes that a meaning will somehow arise. That this is how much of genetics is now done is evident in this debate.
Ken Weiss also blogs at the mermaid's tale. He has an interesting perspective on what Mendelian genetics means in the genomic age.
Mendelian Inheritance: Basic Genetics or Basic Mistake? Part I: Part II: Part III: Part IV:Part V
Of course all of this is manifestly a Grand Illusion! Even a fertilized pea ovule does not have peas, wrinkled, green, or otherwise! Once the connection between a gene and a trait becomes less than 100%, or once many genes contribute information about a trait, we see how obviously Mendelian ideas were a badly misleading mistake. They were great for providing ways to set up experiments that isolated genetic effects and led to an understanding of genetic inheritance. But they were, from the beginning, very misleading about trait inheritance.

Suzanne Elvidge runs a blog alled Genome Engineering. She blogs extensively about molecular evolution and last month was no exception. She has four articles in this carnival of evolution.
More to the mammoth than meets the eye
The woolly mammoth (Mammuthus primigenius – also known as the tundra mammoth) and the Columbian mammoth (Mammuthus columbi) lived in late Pleistocene North America. Most genetic studies have focused on the woolly mammoth, but research published in Genome Biology shows that the genome of the Columbian mammoth has some secrets to reveal.

Written in our genome
Much of human ancestry is written into our genes, and two papers this month have provided another glimpse into human evolution and dispersal around the globe.

Suzanne Elvidge wrote a new blog post: The impact of new genomes
The modern potato is genetically complex – the researchers predict 39,031 protein-coding genes – and it is polyploid, with four copies of every gene, having undergone two or more genome duplication events during evolution.

The genes of teeth
One of the key characteristics of mammals is that they have mammary glands that allow them to feed their young. These evolved from sweat glands and produce milk that contains casein micelles. This is a casein (milk protein) and calcium phosphate complex that maintains high levels of calcium phosphate, vital for the formation of teeth and bone.

David Winter blogs at The Atavism. Last month he discussed the origin of animals in a series of three postings. The last one was about molecular phylogeny.
Sunday Spinelessness – The first animals (molecular biology)
It’s time to wrap up this series of posts on the origin of animals. If you are just tuning in here, I’ve already decided that early fossils are utterly fascinating but really not much help to us and had a look at some modern organisms that might give us an idea about how the major steps towards multi-cellularity might have been achieved. Today, I’m going to zoom down another level, and see if molecular biology can tell us anything about the first animals.

History of Evolutionary Biology

You know a scientist is famous when their picture is on a postage stamp. The USA can't claim Charles Darwin but they've done the next best thing as Michael Barton reveals on his blog The Dispersal of Darwin.
New USPS American Scientist stamps feature Darwin supporter and botanist Asa Gray
Asa Gray? Hell yes!
"Asa Gray, one of the first professional botanists in the United States, advanced the specialized field of plant geography and became the principal American advocate of evolutionary theory in the mid-nineteenth century."
Here's a few New articles about Darwin and evolution or related from William Bell at The Dispersal of Darwin.

jared h wants you to know about free education opportunities. This is from his blog RICH AS CHOCOLATE. (He forgot to say caveat emptor but maybe that doesn't apply to free things. )
Free College Education from Elite Colleges
Learn about history and evolution from some of the nation's most elite colleges. This article details how you can listen to lectures from every department at college like MIT, Harvard, Stanford, UC Berkeley, and more. All for free.
Ken Cable asks whether Herbert Spenser was a Lamarckian on his blog Kele's Science Blog. He also discusses Lamarckian and Darwinian interpretations of how ant castes work through Spencer and Weismann.
Wait. What? Herbert Spencer was a Lamarckian?
While reading Peter J. Bowler’s The Eclipse of Darwinism, I was surprised to find out that the “social Darwinist”* Herbert Spencer was actually more Lamarckian than Darwinian. He apparently expressed Lamarckian views prior to the 1859 publication of The Origin of Species, and while he accepted Darwinian explanations and the theory of natural selection, Spencer believed Lamarckism – defined (here) as the inheritance of acquired characteristics through use/disuse – was the more important of the two theories.

Ants and Their Castes in the Spencer-Weismann Controversy
As discussed in my last post, Herbert Spencer was a Lamarckian who believed in "inheritance of acquired characteristics" and thought natural selection was "inadequate" for explaining how organisms have evolved. August Weismann contested this; he was known as an "ultra-Darwinian" who believed natural selection explained all biological traits and thought Lamarckism was dead wrong.

Evolution vs Religion

Most of you are aware of the conflict between evolution and religion. It takes many forms ranging all the way from total rejection of evolution (and all of science) to attempts to make evolution and religion compatible. The BioLogos Forum is actively engaged in this struggle and their latest attempt is A Leap of Truth: Evolutionary Creation. Watch the video to see how a number of scientists, theologians, and philosophers deal with the issue of making Christianity and evolution compatible. Then read what Jerry Coyne has to say about all this: Making religious virtues from scientific necessities.

This topic wouldn't be complete without a reference to the Doonesbury cartoon that came out this month: Doonesbury: Sunday July 10, 2011 (Click to embiggen.)

Evolutionary Humor

I promised you a new category for this carnival and here it is. It's a collection of funny things people say about evolution. Most of them are written by creationists. Enjoy.

Toronto Caribana photo credit: CTV News


Alex Washoe said...

Wow. What an incredibly varied and rich selection of articles. I don't know how long it will take me to work my way though these, but I'm looking forward to all of it.

David Winter said...

Superb thanks Larry, great to see how many people are talking about evolution around the place.

I was scared the 'secret' category was going to be narive adaptationist fairy tales and include something I'd written, so nice to see if was just IDiots being IDiotic.

SteveF said...

That's a really great collection. Thanks to all concerned.

Anonymous said...

Darryl Cunnigham asks for some help with a draft on evolution:

Here then is the beta version of my strip about evolution. This is a chapter of the book Science Stories which will be out from Myriad Editions next spring. I'm sure there'll be mistakes here, so do feel free to point them out, so that I can make the necessary changes. Thank you."


suzanne @ Genome Engineering said...

Cracking carnival this month - will be posting it up on Genome Engineering too

Suzanne @ Genome Engineering said...

We've posted on this at

Glen Davidson said...

You know that PZ's calling you a moron, Larry:

Larry Moron went crazy and has created the largest Carnival of Evolution ever.

That's what it says/said before correction

Just to keep things clear for anyone who wouldn't know, it's a typo or autocorrect or some such thing.

Glen Davidson

The Sanity Inspector said...

Excellent job, bookmarked for leisurely perusal. I'm cautious about fossil finds from China, since the locals have been caught forging some sensational finds. Hope this bird thingy is the real article.

Anonymous said...

From this point on, if the next carnival follows your lead, this should be renamed feasting of evolution.


Glendon Mellow said...

Amazing Carnival; I like your commentary and organization, Larry. Could spend all day here.

cromercrox said...

I shall try and inevitably fail to follow Larry's splendid feast with the next edition of the Carnival of Evolution which will be playing at The End of the Pier Show in a few days time.