Welcome to the Thirty Sixth Carnival of Evolution. The world of blog carnivals is in a state of flux and uncertainty these days, with the distinct possibility of a mass extinction just around the corner. One of the oldest, longest running, and most important carnivals, I and the Bird, issued its last issue only a few days ago, and the Keepers of the Carnival of Evolution themselves are said to be thinking about ways that this whole carnival thing can be made to work better. That could, I suppose, mean killing it and replacing it with something else. We are hopeful that this will not be something monstrous. Well, actually monstrous would be fine, I suppose, just highly unlikely to found a new species of scientific social networking.

With that thought in mind, I’d like you do to me a favor. If you are into evolution (which you probably are because you are reading this post) then help promote excellent evolution blogging. Do you have a facebook account? Good. Open up a selection of the following posts and if you like them or find them interesting, post them on your wall. Let your facebook friends see some of this interesting blogging. Do you tweet? Then tweet them! Oh, and go ahead and facebook-share and tweet this very carnival. Stumble, Digg, Reddit, Whatever. The idea is go get the word out that there is some interesting stuff to read, about evolution, on the intertubes. We want Evolution Blogging to be more linky and socially networked than other topics such as, well, creationism for example. This carnival is a pretty darn good listing of what has come out over the last few weeks across the blogosphere. So, your job as a lover of and promoter of evolution is to use this list of blog posts as a kind of todo list … working off this list, promote the posts.

I’ve taken a very straightforward approach to the carnival, which is my style; I let the posts speak for themselves. So, in the following listing you’ll see the title of each post and a brief excerpt. Click on the title to see the post. The categories into which I’ve divided the post make total sense and form a very good taxonomy of evolution blogging. For some of the posts. For others, the categories suck. It is not easy making categories for this sort of writing, as many of the posts are so darn multifarious, which is a good thing.

And now, the carnival:

Hard Core Theory, Genetics, Mutations

When does a beneficial mutation fail to benefit?

Every time a cell divides is an opportunity for mutation, creating new genetic variation that may be beneficial, may be harmful, or may make no difference at all. In sexually reproducing species, the fate of a useful new mutation is relatively straightforward. If it overcomes the vicissitudes of genetic drift, the mutation will spread through the population as recombination swaps it into different genetic backgrounds, so that on average the mutation spreads or disappears on its own merits.

Mutational predictability and robustness of genetic circuits

Besides its numerous applications, synthetic biology is also a powerful system for studying evolution. After finishing my graduate work doing experimental evolution in Richard Lenski’s lab, I was intrigued by the possibility of being able to assemble large numbers of BioBricks together on plasmids and watching how these modular DNA sequences change over time. I decided that my project should tackle one of the biggest problems in synthetic biology, evolutionary stability of genetic circuits, while at the same time involve the study of evolution.

Are antibiotics weapons, signals, cues, or manipulation?

Sometimes, there are more than two possibilities.

Many bacteria make antibiotics which, in high doses, kill other bacteria. But microbiologists have noticed that, at lower doses, antibiotics may change gene expression or alter behavior, without killing. So, they suggest, maybe antibiotics are mainly “tools of communication,” rather than weapons.

Maybe, but…

Mapping fitness: ribozymes, landscapes, and Seattle

So, we’ve looked at three significant articles in the last year or so on fitness landscapes, in which talented scientists explored the relationships between genotype and phenotype, on scales barely imaginable just a decade ago. All three studies were carried out in Seattle, Washington, within just a few miles of Biologic Institute, where the scientists of the intelligent design movement work on questions of the same ilk. If those scientists really want to be taken seriously, if they really seek to understand how structure and function and evolution are related, they’ll have to …

Blind fish in dark caves shed light on the evolution of sleep

If a mutation disrupts a gene that is not being used, natural selection will have no restoring effect. This is why fish that adapt to a lifestyle of darkness in a cave tend to lose their eyes. There is no longer any advantage to having eyes, and so the deleterious mutations that creep in are no longer being weeded out. Think of it as the ‘use it or lose it’ school of evolution.

Ratcheting up some splice leaders: a note on directionality

… Ciliates run two nuclear genomes, trypanosome kinetoplasts contain a chainmail suit of RNA editing circles and dinoflagellates are just weird in every genome compartment they have. Their plastids contain tiny minicircles often containing but a single gene, capable of “rolling” transcription where the minicircle is much like a Mesopotamian cylindrical seal, leaving a concatenated repeated string of genes on the transcript….

Sticky proteins, complexity drama and selection’s blind eye

Constructive neutral evolution is one mechanism of complexity increase without any associated increase in fitness – or, in other words, non-adaptive complexity gain. Basically, a random interaction between two proteins can lead to a fixed dependency if this interaction compensates for a mutation that was otherwise lethal – termed ‘pressuppression’. In this way, previously unnecessary dependencies accumulate…

Kin Selection (or not)

When nice guys finish first: a lesson from tiny robots

People used to talk about such altruistic behavior as being ‘for the good of the species’. But this explanation does not work. Natural selection does not operate at the level of species, it is solely concerned with the reproductive success of the individual. Any gene that inclines an individual to be more concerned with the welfare of the species than with their own welfare is not going to get very far.

The Central Dogma Strawman

Whenever you’re trying to promote a new idea it’s nice to have a scapegoat to beat up on. You’re going to get a lot more attention if you can demonstrate that your latest results overthrow some key scientific concept that everyone took for granted. If you can’t find a real “key concept” then the next best thing is to make one up.

Ecology and evolution

Released from predators, guppies reshape themselves–and their environment

Consider a population of guppies living in the Aripo River in Trinidad. They have a happy existence, as far as guppies can be happy, but their lives are shaped by the constant threat of larger, predatory fish. The river runs clear over a colorful gravel bed, and guppies who stand out against that background are eaten quickly. Even guppies whose coloration helps them blend in have to be ready to make a break for it if a predator shows up. All in all, a guppy’s chances of surviving to mate depends most on its ability to hide from bigger fish, and to swim quickly when it can’t hide.

Ecology of an evolving bacterium

Every day, human activities release a wide variety of chemical compounds into the environment, from fertilizers and pesticides to pharmaceuticals and industrial waste. Many of these compounds are produced only by humans and not otherwise found in natural environments. While some chemicals are benign, others are harmful to human and ecosystem health. For example, over 200 industrial chemicals present in the environment have been identified as neurotoxins that may cause learning disorders, cerebral palsy, and delayed development. Naturally, there is strong interest in removing these harmful compounds from the environment.

Microbes with ESP

Microbes that see the future

Quite a few stories have come out recently about microorganisms that use one type of stress as a signal that they should prepare themselves for another stress. For example, an Escherichia coli bacterium on a piece of the salad you ate for lunch (let’s hope normal E. coli, not the pathogenic sort) may find itself traversing your digestive tract. One of the first things it can observe about its new environment is that the temperature has gone up; soon afterwards, the level of oxygen goes down. It turns out that the transcription of genes associated with dealing with oxygen starvation is induced by an increase in temperature.

Applied Evolution

Pregnancy, Evolution, and Nutrition Data

My recent post outlining my own pregnancy prompted a lot of questions about whether the primal diet is safe for pregnant women. The fear is that they might end up deficient in some nutrients if they don’t follow the advice of their doctors to eat whole grains and the government guidelines to eat 6-11 servings of them per day.

The Paleolithic Prescription: A Program of Diet & Exercise and a Design for Living

I’m not recommending the book as a self help guide, but rather, as a way of linking the scientific evidence for human diet and activity, based mainly on work with living foragers, with your own process of making choices.

Hybrid history of North American cattle

In the ranch lands of Texas it can feel like cattle have always been a part of the western landscape. However, neither domesticated cattle (Bos taurus) nor their wild ancestor, the auroch (Bos primigenius), are native to the Americas¾there were no cattle prior to 1493. The first cattle were brought by Christopher Columbus on his second voyage across the Atlantic to the Caribbean island of Hispaniola, what is today Haiti and the Dominican Republic. The cattle he brought were likely from the Canary Islands, off the western coast of Africa, then a Portuguese colony, which were in turn probably descended from animals of Portuguese origin. The imported cattle reproduced rapidly, and by 1512 importation of cattle by ship was no longer necessary. Caribbean cattle were introduced into Mexico in 1521, and had reached north into what is now Texas and south into Colombia and Venezuela within a few decades (Barragy 2003).

Plasmid evolution is the key to fighting antibiotic resistance

We are in the midst of a medical crisis. Even though we have more antibiotics on the market than ever before, our ability to effectively combat antibiotic-resistant pathogens is constantly decreasing. While many people know that bacteria are becoming increasingly resistant to antibiotics, it is not common knowledge just how they are adapting so rapidly.

Coevolution of hyenas and their beneficial, odor-producing bacteria

…perhaps … all, animals can be appropriately viewed as supraorganisms. A supraorganism is an organism that is actually a composite of multiple contributing organisms. Consider yourself, for example….

Fish Physiology

A bunch of hot heads

It turns out that lamnid sharks are not the only creatures in the pelagic realm that can operate above the ambient temperature. It seems that many pelagic species express some form of control over their internal temperature and that that control is expressed in a surprising diversity of forms and functions.

Crayfish Sex

Another (occasionally) parthenogenetic crayfish

I not sure how to describe the sound I made when I saw the title of this paper, but it was not a quiet sound. I immediately thought, “This is huge.”

A new paper in PLoS ONE reports that spinycheek crayfish (Orconectes limosus) can reproduce by parthenogenesis

Human Evolution

Did humans lose dominance?

An extensive critical review has just been published online in advance of publication for Biology and Philosophy. The title is “Evolution and the loss of hierarchies: Dubreuil’s Human evolution and the origin of hierarchies: the state of nature” by Catherine Driscoll.

The Evolution of Common Sense

The reliability of common sense is an issue for philosophers and cognitive scientists alike. Philosophers debate whether or not ordinary objects, the objects of common sense such as Eddington’s Table 1, can be said to be real or exist.

Still think you have free will?

So, apparently, do some robots. Well, simulated robots, anyway.

Specifically, scientists in Lausanne, Switzerland, built some robots that were designed to seek small disks, which we will call “food.” … The robots had wheels, a camera, and something that passed for a nervous system.

Darwinia

Scientists Take Charles Darwin on the Road

“I want to send our scientists to rural schools and communities around the U.S. to talk about evolution for Darwin Day 2011.” Jory Weintraub’s words hung undigested in the silent air of the management meeting at our North Carolina center last July.

“You want to send our scientists where?” I jested. “On purpose?”

child-sized depictions of charles darwin to grow on

…the adventuresome seafaring young Darwin didn’t seem to make much of an impact with my Discover with Mr.Darwin particular child reader at home, who, I realized one day when I saw a new computer art picture appear on the computer desktop, had come up with an illustration of Darwin on her own that seemed to owe less to the conventional voyage thematic than it did to three different, more original takes that a handful of children’s authors had created.

The Darwins at Malvern: the Water-Cures

… When his dearest daughter, Annie, fell ill in 1851, Darwin brought her to Malvern, where Dr Gully was sure he could cure her. After a week she seemed to be improving, and Darwin left her to return home, confident he’d soon return to Malvern to find her quite recovered, but instead he was summoned back within a fortnight because she was getting worse. He went alone, as his wife, Emma, was heavily pregnant and unable to travel….

How the Victorians Learned about Darwin’s Theories: Popularizing Evolution

Here’s a 2010 talk by historian of science Bernard Lightman, How the Victorians Learned about Darwin’s Theories: Popularizing Evolution (mp3), from Discover Yale Digital Commons

VIDEO: Images of Darwin and the Nature of Science

“Today, Charles Darwin is the iconic founder of evolutionary theory. But it hasn’t always been so. William Kimler, a historian at North Carolina State University, charts the changing image of Charles Darwin through time.”

Time and Deep Time

How did animals evolve? — A matter of perspective

am always fascinated by how different angles of attack on a scientific problem can lead to different solutions. One example of this phenomenon that I encountered recently concerns the evolution of the first animals.

On the Reasons Why We Need A New Supereon

The largest unit of defined geologic time is the supereon. Only one is defined, the Precambrian spanning from the formation of the Earth to right before life goes crazy in the Cambrian explosion (4.6 billion years ago to 542 million years ago). Oddly, there is no other supereon after the Precambrian, just the Phanerozoic eon ranging from the Cambrian explosion to the present. The Precambrian can be broken into three eons, Hadean, Acrhaean, and Proterozoic. Life as cyanobacteria first appears in the fossil record 3.5 billion years ago during the Acrhaean. Molecular estimates place life starting around 3.97 billion years ago. Did you get all that?

Elephants

Elephant Evolution

… Apart from their use as instruments of war, Elephants have been – in various times and places – objects of reverence, beasts of burden and symbols of imperial might. The caliph Harun-al-Rashid gifted an albino elephant named Abu-Abbas to Charlemagne as a token of friendship. Legend has it that Charlemagne later called upon Abbas in a tremendous battle against the Viking Danes. That’s epic.

Basic Concepts and Pedagogy

The F-words of Evolution

Getting things wrong is bad enough, but scarier ramifications occur when wrong-headed evolutionary thinking, based on what or who is “favored” or “fittest,” is used to support apathy or to justify hateful and violent behavior between humans.

Why moths lost their spots, and cats don’t like milk. Tales of evolution in our time.

In the children’s game of hide-and-seek, it doesn’t matter much whether you win or lose. In the animal kingdom, however, the stakes are significantly higher. If you’re found, you’re food.

Brains

Mammals’ Big Brains Began With a Sniff

While dinosaurs ruled the world some 200 million years ago, a group of nocturnal, shrewlike proto-mammals unwittingly sniffed out a strategy for survival that eventually led to the evolution of larger brains. Fossil skulls of two ancient, mammal-like reptiles suggest that natural selection for a keener sense of smell was the initial spur behind bigger brains in early mammals, according to a report online today in Science. “Mammals didn’t get our larger brains for thinking,” says co-author Zhe-Xi Luo, a paleontologist at the Carnegie Museum of Natural History in Pittsburgh, Pennsylvania. “We got it for a more urgent and more basic need–our sense of smell was far more important.”

Genes and languages evolving in parallel

The Caucasus region covers the borders of Europe and Asia, bordered by Turkey, Iran and Russia. There is a huge diversity of language in this area, with the languages falling into three main groups. A team of researchers at the Research Centre for Medical Genetics, Russian Academy of Medical Sciences, have looked at the languages in the North Caucasian group and spotted a link with the genetics of the population.

Extinction

Tales of Extinction: 7 Animals that You’ll Never See on Safari

Take a step back in time to discover some incredible African animals that lost out in the game of evolution.

Blog The Controversy

There’s something fishy about that fish

Institute for Creation Research President Dr. John Morris has taken to recycling; in this case he’s dusted off some nonsense from an article he wrote 3 years ago titled “Evolution’s Biggest Hurdles” (Morris 2008) and repackaged it as “The Biggest Problems for Evolution” (Morris 2011).

Sorry Brunswick County, ID STILL Not Science

Dear Editor,

Kathryn Jacewicz’s April 19 story on Brunswick County Commissioners’ attempt to wedge creationism into the educational fabric of the public school system is very troubling for the parents and students of Brunswick County. Such a proposal severely threatens students’ future marketability as professionals in science and technology.

Wait, what?

Intelligent Design creationist Denyse O’Leary, in the midst of rationalizing (over at Uncommon Descent) why ID creationists spend all their time attacking science rather than doing science, has provided yet another example of how antievolutionists are pretty much pathologically unable to portray evolutionary theory (or its supporting evidence) accurately…

Are the top universities in the United Kingdom abandoning the teaching of evolution?

Yes, according to U.K. creationist YouTuber davemakesawave who started leaving comments in response to a short video I did regarding so called “polystrate” fossils and the claims creationists make about them. However this post, as the title suggests, is not about “polystrate” fossils; for those interested in them I suggest the following links as good starting places.

The Carnival of Evolution home page is here. There, you will find instructions for submitting to the carnival, an existential discussion of carnivals, and when it is known, the location of the next carnival should there be one. The previous carnival of evolution, which is still quite current, is at Lab Rat. Please check it out.

The images used above are culled and modified from Darwin Online.

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