Carnival of Evolution 50: The Teaching Edition

Welcome to the 50th edition of the Carnival of Evolution! In keeping with the name of the blog, this edition will have an educational theme to it. The posts are categorised into modules. Each module has an introduction by me about why it’s important to learn about it, and each post has a short blurb by me on the post’s content and, if appropriate, personal comments. I include a further reading list with links to relevant books and review papers for further discussion/background information. Most of these papers are behind draconian paywalls. If you don’t have institutional access, my e-mail can be found here. Just saying.



Module 1: The Boundaries of Life

The prerequisite for biological evolution is life, so while the question of the origin of life isn’t necessarily an evolutionary one, the origin of life is equal to the origin of evolution. In this module, you will learn about questions being asked pertaining to life and its origin.

  1. Defining life foolishly – Bjørn Østman (Pleiotropy)

Before discussing any subject, the terms must be defined. And so it is with “life”, which has always proven to be a problem in this respect. From the high-school definition to the minimalistic properties ascribed by origin of life researchers and astrobiologists, definitions of life come a dime a dozen. In this post, Bjørn presents a compelling case against the most common definition of life as “anything that evolves”.

Chapter 2 of Luisi’s 2006 book, The Emergence of Life, has an excellent overview of the definitions of life.

For a historical perspective on the definition of life, see Tirard et al. (2010).

  1. NASA Confusion About the Origin of Life: Part II – Larry Moran (Sandwalk)

In this post, Larry Moran rightfully criticises the multitude of stories that come out every few weeks about how we can find clues to the rigin of life on Earth in meteorites that seeded the Earth’s oceans with biomolecules. He correctly asserts the superiority of the metabolism-first scenario for the origin of life (a view that, if personal experience is anything to go by, is virtually unknown among the lay public).

Philips (2010) wrote a neat article outlining the pros and cons of the RNA world and the metabolism first hypotheses for the origin of life.

Martin et al. (2008) review why hydrothermal vents are seen as very likely locations for the origin of life, as opposed to some primordial soup.

  1. Was the Origin of Life a Lucky Accident? – Larry Moran (Sandwalk)

A perspective by Larry Moran, based on an article by Nick Lane, about the probability of larger cells evolving convergently on some other planet. While life can originate “easily” anywhere with suitable chemistry, the origin of eukaryotes is a “lucky accident”, to use their words. While I agree, the perspective can be seen as limited, as there can surely be other ways to get cells more complicated than prokaryotes, other than symbiosis with mitochondria.

De Duve (2007) provides the current concensus on the origin of eukaryotes.

Module 2: Zoology

The Metazoa may be just one single taxon in the grand scheme of life, but they are the most visible and well-studied one. Hence they deserve their own module, where specific animal evolution-only posts belong.

  1. The hummingbird that wasn’t – Anne Buchanan (The Mermaid’s Tale)

Sphingid adults are typically large moths, so large that some can be confused with hummingbirds. In Europe, we have Macroglossum stellatarum, the hummingbird hawkmoth. The Americas have their own hummigbird mimic, Hemaris thysbe, the hummingbird clearwing moth, pictured in this post by Anne Buchanan. She uses it as a jumping point to discuss how this mimicry could evolve – is it really hummingbird mimicry, or is it convergent evolution due to sharing similar food plants, or merely coincidence? Read the post for the pros and cons of each possibility.

I couldn’t find any papers dealing with this issue. Personally, I would say it’s mimicry, simply because it takes a bit more than coincidence for the same morphology to evolve independently on two continents. However, as the post says, there isn’t much of an adaptive gain in looking like a hummingbird.

For an overview of mimicry, check out this oldie but goodie: Malcolm (1990).

  1. Speciation in Bears – Larry Moran (Sandwalk)

This post by Larry Moran summarises a kerfuffle that’s been going on for the past couple of years about the origin of polar bears, demonstrating the frailty of phylogenetic hypotheses (especially when they’re supported by just a couple of sequences, and especially with mitochondrial DNA).

The papers referred to in the post serve as the further reading suggestions.

  1. Evolution’s Witness: book review – Matt Young (Panda’s Thumb)

The evolution of the eye is a favourite creationist trope. They trot it out with glee, thinking they’ve ensnared us with the irreducible complexity of this wonderful organ. Except that it’s not really that wonderful, and it most definitely is not irreducibly complex. In case you don’t find the simplistic explanations found on the internet about eye evolution satisfactory, then get the book reviewed in this post by Matt Young. It also receives a glowing recommendation from me: it’s a very comprehensive book about the evolution of eyes.

Fernald (2000) and Arendt (2003) are good reviews of eye evolution.

Gehring (2004) has a historical perspective on the various thoughts about the origin of eyes.

  1. Why You Can’t Fake A Good Horn – Carl Zimmer (The Loom)

Dung beetles are some of the best organisms to use in class projects at all levels. Easy to maintain, they can be used for all sorts of ecological experiments, from navigation to life cycle changes. Many male dung beetles also grow horns, and these can be used to study sexual selection: the horns are used in male dominance fights (and, in some species, there is a hornless male form that sneakily copulates with the female while the macho beetles are being idiots outside). In any case, beetle horns have become model systems in evo-devo. In this post, Carl Zimmer describes new research showing that the growth of the horn in rhinoceros beetles is correlated with larval hormone levels. In nature, this is correlated with amount of food eaten – so a beetle that can’t get lots of food will get a small horn, and so is likely to lose the sexual selection fight.

Mocjek et al. (2007) write about the use of beetle horns in evo-devo.

The relation of horn length with hormone levels extends to other horned beetles, e.g. Emlen & Nijhout (1999) for dung beetles.

Module 3: Behaviour

The days when it was thought that animals are simply machines that unthinkingly respond in a single way to stimuli are long gone. Animals are actively intelligent, and the posts in this module reflect the evolution of that intelligence.

  1. Animal Personality, Ecology, and Evolution – The Beast, the Bard and the Bot

“Personality” is a finnicky term, often overloaded with anthropomorphism. Yet it’s certainly true that animals exhibit individual behavioural differences – this would be a working definition of personality. In this post, the Beast, the Bard and the Bot summarises 14 traits identified by a recent review paper as contributing to the evolution of animal personalities.

Dingemanse et al. (2009) offer a perspective for the study of animal personality.

Dingemanse & Réale (2005) summarise the fitness effects of personality.

Wolf et al. (2007) find that life history plays a large role in the evolution of animal personalities.

  1. The dolphin’s genome and the evolving brain – Suzanne Elvidge (Genome Engineering)

Besides their misleading cuteness, dolphins have always attracted attention for their high intelligence. In this post, Suzanne Elvidge reports on an analysis of natural selection acting on the dolphin genome, identifying what genes have played an important role in dolphin evolution. Among them are indeed genes linked to intelligence and the brain, as well as metabolism-related genes.

Marino (2002) wrote about the intelligence of cetaceans and how it compares to primate intelligence. See Marino (1998) for a comparison of their relative brain sizes.

  1. What makes our language abilities unique? Or are they? – Anne Buchanan (The Mermaid’s Tale)

The diversified vocal grunts of humans are an integral part of what makes human sociality so successful – the possession of a language makes for easy communication, after all. It’s long been known that other animals can also communicate with language, from the dance language of bees, to the songs of whales, to the chirping of birds. The latter are mentioned in this post by Anne Buchanan, where she discusses whether the human ability to develop and interpret complex languages really is unique.

Tecumseh Fitch (in press) is a paper, grounded in evolutionary theory, showing how much of what is considered “unique” in human language is actually not unique to humans.

Bolhuis et al. (2010) point out various apparent convergences between bird language and human language.

  1. One way to successfully invade a habitat: eat the competition – Jeremy Yoder (Denim and Tweed)

Ladybirds are another one of those vicious animals that are yet found to be cute. In this post, Jeremy Yoder describes a new study on ladybird behaviour, research that implies that the invasive ladybirds introduced everywhere for aphid biocontrol (Harmonia axyridis) are so effective because they also get rid of other predators.

For more wanton destruction by Harmonia axyridis, see Gardiner & Landis (2007).

Giorgi et al. (2009) have information on food preferences among ladybirds.

Module 4: Human Evolution

Humans are not really such interesting animals, but egocentrism has made their study a very active field (YMMV). They can bge used as models for studying the evolution of brain and behaviour, as well as the intersection between sociality and ecological success, and they’re poster children for the effect of climate changes on geographical distribution.

  1. Mapping the genome of the hunter-gatherer – Suzanne Elvidge (Genome Engineering)

The Mesolithic was one of the pivotal moments in human evolution (at least in Europe), when the transition to agriculture started taking place. In this post, Suzanne Elvidge reports on the sequencing of both the mitochondrial DNA and the genome of two human remains from this time period, laying the ground for future research on the genomic consequences of agriculture.

Tresset & Vigne (2011) provide an overview of the Meso-Neolithic transition in Europe.

The study by Pinhasi et al. (2005) traces the original spread of agriculture in Europe.

  1. Out of Africa: Startling New Genetics of Human Origins – Gary Stix (Talking back)

This post is an interview of Sarah Tischkoff, leader of a group that recently published a genomics paper analysing the genomes of Pygmy, Hadza, and Sandawe individuals (all African tribes). The results are very interesting, with numerous evidence for natural selection acting on their genomes. Most cool, however, is the finding that there was interbreeding happening between humans and some unknown archaic hominin. To me, the most important question here is about the implications of such interbreeding on species concepts used in human palaeontology – interbreeding means that there was no reproductive isolation. So were these archaic hominins really different species? How did all this hybridisation happen?

African genome reveals hunter-gatherer’s ancestry – Suzanne Elvidge (Genome Engineering)

Suzanne Elvidge reports on the same study mentioned above, with more details on the results.

Green et al. (2010) reported the draft sequence of the Neandertal genome, with the surprising revelation that there was interbreeding between Neandertals and modern humans, so this is a very relevant comparison case.

Module 5: Pressing Problems in Evolution

In this module, classic problems of evolution are introduced. These are subjects that have been debated for decades with both theoretical and empricial work, with still no satisfying end in sight. I recommend to all undergrads or even high school graduates to inform themselves about these debates, and then try and wrangle their own opinion and justify it. Whether you’re right or wrong is irrelevant; just the process of thinking critically about these subjects will help you hone your biological mindset.

  1. Evolution of aging talks at Evolution 2012 in Ottawa – R. Ford Denison (This Week in Evolution)

The evolution of aging is one of the classic problems of evolution. Is it merely a side-effect of natural selection acting strongest on young individuals? Does it arise because of wear and tear? A combination of both? Or something else entirely? Every month, there’s bound to be several papers published that brings up new aspects to the debate. In this post, R. Ford Denison summarises the talks given at the recent evolution conference in Ottawa, thus giving us an insight into the latest findings from this very active field of research.

Hughes & Reynolds (2005) provide a masterful review of the various dominant theories about the evolution of aging. Finch & Ruvkun (2001) do the same for the genetic basis of aging.

Chapter 10 by Marc Tatar in the 2001 book, Evolutionary Ecology, has a comprehensive look at the results of many case studies in the evolution of aging.

  1. Argument maps for the paradox of sex, pt. 2 – Joachim D. (Mousetrap)

The evolution of sex is another one of the classic problems in evolution. Why does sexual reproduction persist, when its costs amount to double that of asexual reproduction due to the need to produce males and females? Does the gained genetic diversity from recombination outweigh this double cost of meiosis and so lead to the maintenance of sex? In this post, Joachim D. considers the effect of gamete size, specifically as argued by two of the leading evolutionary biologists who concerned themselves with this issue, John Maynard Smith and George C. Williams.

Meirmans & Strand (2010) give a historical overview of the main debates that occurred on the topic of sex, and considers how to deal with all the different proposed hypotheses.

Stearns (1990) is pretty old, but it’s a good summary of the various hypotheses, most of which are still valid nowadays.

Chapter 2 in Sherratt & Wilkinson’s 2009 book, Big Questions in Ecology and Evolution, deals with the origin and evolution of sex.

Module 6: Evolution in Deep Time

The fossil and geological records, incomplete as they are, provide the only undisputed source of information on the path evolution took place from the origin of life to now. As such, it’s integral for every (evolutionary) biologist to be acquainted with both historical geology and with palaeobiology (the study of evolutionary patterns in time), if only to get the proper perspective of life on Earth.

  1. Evolving fungi stop the creation of coal – Suzanne Elvidge (Genome Engineering)

The coal forests of the Carboniferous flourished in the tropical, humid climate zones of the time, and persisted until climatic changes wiped them out. In this post, Suzanne Elvidge reports on the sequencing of 31 fungal genomes, with one notable result being that genes responsible for the ability of white rot fungi to decompose lignin arose in the Carboniferous, coincident with the collapse of the rainforests, implying that they also played a role in the decline of the forests. It’s a very interesting study, although I must profess that I am not a fan of molecular clocks (what was used to find out when these fungal genes evolved).

For more on the transition away from the Carboniferous rainforests, see DiMichele et al. (2009).

DiMichele et al. (2010) summarise the evolution of the palaeoclimate around the rainforest collapse.

Blanchette (1991) summarises how white rot fungi manage to degrade lignin.

  1. Fuzzy thinking about fuzzy dinosaurs – Troy Britain (Playing Chess with Pigeons)

Creationist blather is often interesting to read. On the one hand, it makes one despair at the state of very basic science education in certain parts of the world (including the part I reluctantly call my home). On the other hand, their screeds can serve as excellent starting points for teaching evolution. I often use creationist texts when teaching in order to demonstrate just how derived real evolution and its surrounding disciplines are from the ridiculously ignorant caricatures drawn up by creationists. This post by Troy Britain is a perfect example of such a use. It’s a wonderfully detailed passage-by-passage takedown of a misrepresentation of a recently-published dinosaur and its implications for the evolution of feathers. The post is good because it doesn’t just rebut Luskin’s points, but also provides additional information on the evolution of feathers, one of the most booming areas of dinosaur research of recent years, fueled by the many, many findings of feathered dinosaurs from China.

The post cites several papers and book chapters. I would add the third chapter by O’Connor et al. of the 2011 book Living Dinosaurs, where the context for the origin of feathers in dinosaurs is given in as much detail as you could ask for.

Module 7: Molecular Evolution

Evolution at the molecular level is a different beast than evolution at the organismal level (although there is a bridge between them, a bridge I’m currently working to document), but it’s a beast that must be studied because it’s what gives evolution so much power in other biological fields – the ability to find homologues, to predict the presence of protein sequences, and other such important activities all flow out of the study of molecular evolution, nowadays booming with the ever-cheapening access to sequencing technology. The ubiquity of free databases also makes molecular evolution a favourite for quick, bioinformatics-based, demonstrations of evolution in classrooms.

  1. The Evolution of Enzymes from Promiscuous Precursors – Larry Moran (Sandwalk)

In this post, Larry Moran outlines the two ways by which enzymes evolve after gene duplication: a highly-specific enzyme gets duplicated and the duplicate catalyses a related reaction; or an unspecific enzyme gets duplicated and its duplicate catalyses specific reactions. I guess it’s like the evolution of ecological specialisation, except at a tiny level.

This is far out of my field, so I don’t have anything specific to suggest. Gherardini et al. (2007) point out that convergence in enzyme evolution is common, it can be tied to the post.

  1. Better Biochemistry: Good Enough Enzymes – Larry Moran (Sandwalk)

In this post, Larry Moran looks at the performance and efficiency of enzymes, and looks at the two main philosophies in explaining evolutionary patterns: adaptationism vs. non-adaptationism. Adaptationists are those who see natural selection acting to optimise everything, while non-adaptationists are those that view everything as working just enough for survival, no more. Read the post to see how these contrasting views would interpret the enzyme efficiency data.

No discussion of adaptationism would be complete without a reference to the classic Spandrels paper by Gould & Lewontin (1979). A must-read by any biologist.

Nielsen (2009)‘s update on the Spandrels paper looks at adaptationism in genomics and molecular evolution – very relevant to this post.

  1. Do Invasive Mitochondria Spread by Drift or Selection? – Larry Moran (Sandwalk)

Mitochondrial DNA is commonly used for phylogenetics and phylogeogeography (note: don’t use it for arthropods!), yet we now know (see further reading) that mtDNA exhibits some strange evolutionary properties that can compromise its use in such studies if not properly accounted for. This post by Larry Moran highlights one such property that has been causing trouble recently: the transfer of mitochondrial genes from one species to another. He proposes that a research program should be set up to investigate just how this can happen – is it just a random event, or is it natural selection acting to fix those mitochondrial genes? If it’s the latter, how exactly do these genes confer fitness advantages?

The problematic nature of mitochondrial DNA, contrasted with nuclear DNA, can be read about in Ballard & Whitlock (2004).

See the other post about speciation in bears (Zoology, post 2) for mtDNA naughtiness.

Module 8: Evolutionary Theory

The public face of evolution is what’s seen in the posts above – pretty animals, dinosaurs, charismatic, showy stuff that can be stuck on TV. Underlying the proper study of all that is masses of mathematics that I lump together as “evolutionary theory”, the gritty details of how gene frequencies change across time and populations, the mathematical visualisation of landscapes (fitness landscapes, morphological landscapes), the modelling of evolutionary processes. In my experience, evolutionary theory tends to be the largest stumbling block that turns students away from being evolutionary biologists (they tend to turn to the naturalistic fields of ecology, zoology, or palaeontology instead). The posts here show some examples of evolutionary theory in action.

  1. Crossing valleys in fitness landscapes – Bjørn Østman (Pleiotropy)

The idea of visualising fitness of populations and species as peaks in a “fitness landscape” is the brainchild of Sewall Wright, and has since become a powerful concept, if a bit abstract. Basically, the entire landscape represents all the genetic possibilities. A peak represents a high fitness value (at that single point in time; environments change and fitness tags along). How evolution acts to get species to climb up a peak is one of the active areas of research. It’s in this context that Bjørn Østman describes some of his own research on the features of the fitness landscape and provides a nifty overview of how it changes over time.

The post has a reference list.

Arnold et al. (2001) describe how these landscapes can be used to study the bridge between micro- and macroevolution, which is one of my own pet subjects.

  1. They also serve: Adaptation from standing variation – Jeremy Yoder (Denim and Tweed)

In this post, Jeremy Yoder describes how adaptations occur at the genetic level – how natural selection leads to mutations getting selected for and fixed in a population. Specifically, he focuses on adaptation occurring from the standing variation present in a population, in other words, the genetic variability already found in a population, without the addition of novel, flashy mutations.

The post contains a reference list.

Barrett & Schluter (2008) is a review of the exact same topic.

The model of adaptation presented by Orr & Unckless (2008) is also relevant, taking into account both standing variation and novel mutation.

  1. Searching for Ronald Fisher (at #Evol2012) – John Stanton-Geddes (Nothing in Biology Makes Sense)

This post by John Stanton-Geddes is an editorial on the genotype x phenotype research he saw presented at the Ottawa evolution conference, with an outlook for the future that involves moving beyond just looking for single genes causing single phenotypes, to start looking at the broader, more complicated picture that makes up most of biology.

Dowell et al. (2010) is a tiny paper, but the results underline the need to look at polygenic effects.

Salazar-Ciudad et al. (2001) provide a framework for the intersection of GxP research and developmental biology, which is where this research should head in order to uncover the origins of evolutionary novelties.

Module 9: Evolution at Large

From the direct applications in agriculture, medicine, and linguistics to the more abstract derivations used in economics, evolutionary theory has always been coopted by other fields and disciplines. Ever since Darwin’s Origin, evolution has been discussed in society. In all these cases, the quality of the discourse varies wildly, from the solid science behind domestication and Darwinian medicine, to the inane ramblings of creationists. The point is that evolution has never been some isolated field of research, detached from the rest of the world as with many other fields of research. It’s always been part of the popular discourse, and so it’s the duty of evolutionary biologists and educators to make sure the quality of that discourse remains at a high enough quality. The posts here revolve around this theme of evolution out in the public, away from the realm of the lab and field.

  1. Evolutionary trees: old wine in new bottles? – David Morrison (The Genealogical World of Phylogenetic Networks)

Tree-thinking is one of the most basic skills any (evolutionary) biologist must learn, preferably at the middle school level (or even earlier). It’s something I always emphasise in my own teaching at all levels, and I always find it worrisome when I find undergrads who can’t properly interpret a tree (it’s a very common occurrence). It’s a bit of a difficult concept to get across because of the ubiquity of popular ideas of evolution as progression, remnants of outdated concepts. In this post, David Morrison brings up another source of confusion: phylogenetic trees themselves, and their pictographic evolution reflecting and reinforcing these outdated concepts. The historical perspective here is very interesting, and the points raised very valid.

The post has an extensive citation list.

For more on teaching tree-thinking, see Meiser (2010) and Sandvik (2008).

  1. ISMB 2012 Vignettes Pt. 3: Swag – Iddo Friedberg (Byte Size Biology)

In a perfect demonstration of the ignorance of tree-thinking apparent in popular imagery of evolution, Iddo shows us pictures of merchandise acquired at the ISMB 2012 conference, including a human evolution bumper sticker portraying the “march of progress”, with chimps at the back slowly changing into humans at the front. This graphic is wrong on so many levels – humans didn’t evolve anagenetically, the last common ancestor wasn’t chimp-like, it stinks of progression. The post has effective takedowns.

Klein (2009) has a much more accurate phylogeny of humans. What it makes up in realism, it loses in marketing appeal and photogenicity.

  1. What Can YOU Do to Support Intelligent Design?”– Troy Britain (Playing Chess with Pigeons)

My experience with creationists allows me to draw the general conclusion that they come in three types (YMMV): the exploiters, the willfully ignorant, and the brainwashed. The first is the type that preaches creationism; the second is the one that follows creationism and, when pushed, starts preaching it and ignores all the counter-evidence. These two often overlap, and arguments with them benefit no one but bystanders. The third group is why debating with creationists is necessary: these are the ones who have never been exposed to any other points of view by virtue of their crappy educational system – and there are quite a lot of them. In this post, Troy Britain highlights what Casey Luskin (the creationist Discovery Institute’s lackey) considers to be good support for creationism, and shows that it basically boils down to “keep people brainwashed”. It’s both cynical and very telling. Troy also has some good words to say about why scientists should bother dealing with creationists (can be extended to other charlatans too).

  1. The banana genome: Saving the nation’s favourite fruit? – Suzanne Elvidge (Genome Engineering)

Popular reports about the supposed imminent demise of bananas come out once in a while, fueled by the knowledge that the common yellow banana comes from monocultures that can very easily be destroyed by any new disease or pathogen. In this post, Suzanne Elvidge reports on the sequencing of the wild banana’s genome and what it tells us about the domesticated banana.

A review of the history and future of domesticated bananas can be found in Heslop-Harrison & Schwarzacher (2007).

  1. Robot Reproduction, as seen on TV – Bradly Alicea (Synthetic Daisies)

Fictional biology is pretty cool. As a teenager, I actually started making a rather detailed Pokémon zoology textbook, complete with anatomical diagrams. Did you know that Charizard had a symbiotic relationship with methanogenic bacteria? That’s how it could produce fire. Pokémon “evolution” is actually a process very similar to eusocial insect caste changes, and caused by a certain hormonal threshold being passed. Still no word on how Pokéballs work as a habitat though. I also have stuff on the biology of the Diclonius and the evolutionary dynamics that will allow them to get rid of Homo sapiens by widespread hybridisation. In any case, in this post, we see evidence of robot genetics and their life cycle, from Futurama.

Wait for my books to be released by some stupidcrazyawesome publisher if you want further reading.

Module 10: Philosophy

Every science student should have a grounding in the philosophy of science, as well as the philosophy of their respective discipline, if only so that they learn about the basis behind the scientific method and how it should ideally be applied. Extending beyond these necessary rudiments is a matter of personal taste. In my own teaching, I only stress the philosophy of science, of biology, and of statistics (at the very least, the distinction between frequentism and Bayesianism has to be understood by any modern biologist).

  1. Standards for evolutionary inference: some happy place between Baba Brinkman and Dick Lewontin. – Andrew Hendry (eco-evolutionary dynamics)

Idealism is a fickle thing. We all have our own ideals, but it’s not very often that reality allows us to live up to them. And so it is with science, as Andrew Hendry points out in this post, where he gives a personal retrospective on the standards for evidence demanded by people as different as Dick Lewontin, Rosie Redfield, and Baba Brinkman. His points about how different study approaches require different standards of evidence resonates with my own experience, both in palaeontology and with Recent organisms.

Any philosophy of biology textbook will have a discussion on inference, and the standards of evidence needed for proper inferences. I recommend Rosenberg & McShea’s Philosophy of Biology: A Contemporary Introduction (2007) and Hull & Ruse’s The Cambridge Companion to the Philosophy of Biology (2007), both have good sections on the topic.

Module 11: History

In my opinion, the history of biology (and of science in general) should always be taught to biology students. In universities, it should be a required course. It’s not only fascinating, but knowing the details of how current theories came to be, and what was discarded as a result of their emergence, is knowledge that completes a scientist’s worldview. After all, we’re all standing on the shoulders of giants. If we don’t know who those giants are and what they did, we’d be pathetic scientists by not being curious enough.

  1. Creationist foists “fraudulent” embryo picture on his readers – Troy Britain (Playing Chess with Pigeons)

In a giant win for irony documented in this post by Troy Britain, the Institute for Creation Research accuses one of my favourite scientists of all time, Ernst Haeckel, of having faked human embryo drawings while showing a fake picture of a human embryo. I have no idea what that thing is that they picture. I’ve seen the development of animals from over 20 phyla, and nothing ever, ever looked like that. Anyway, the faked embryos accusation is an all-too-common one, used as a jumping point for arguing against the idea of a phylotypic stage in development. Read the post for an effective dissection of this argument.

Richards (2008) has a summary of the whole faked embryo drawings issue.

Reviews for and against the existence of phylotypic stages: Hall (1997) for, Richardson et al. (1997) against.

For fellow Haeckel fans, Richards’ 2009 book, The Tragic Sense of Life, is a must-read.

Module 12: Teaching Evolution

As a biology educator, I can safely say that teaching evolution is by far more challenging than teaching any other area of biology, because it doesn’t only involve maths and charismatic organisms. A different mindset is needed in order to think in evolutionary terms, and this mindset has to be cultivated and groomed by both the educator and the student. A complete evolutionary biology teaching program requires a blend of dry lecturing, mathematical problems, and hands-on experimentation and fieldwork. The posts in this module are excellent teaching posts that I recommend saving for future use (with attribution as necessary, of course).

  1. More on Evolving Computer Programs – Mike Vollmer (Recurial)

As a small-time programmer, I fully realise the power of computers in both teaching and understanding evolution. It’s certainly easier and cheaper to demonstrate the principles of evolution with a couple of lines of code than by growing bacteria for thousands of generations. In this post, Mike Vollmer writes up an excellent introduction to coding simple evolutionary programs and what they can show.

Check out Java for the Study of Evolution, a series of PDFs freely available at that link. They have exercises using Java to demonstrate principles of evolution, much like what is written in the post (check out Vol. 7). I know, Java is the black sheep that nobody wants of programming languages, but it’s all I can offer.

  1. You can’t ban redheaded sperm – David Winter (The Atavism)

David Winter gives an excellent working example of how to teach Hardy-Weinberg equilibria. The sections of any evolutionary biology curriculum dealing with genotype frequency changes et al. are always, in my experience, the most challenging to teach, mostly because biology students tend to be less maths-inclined (a broad generality, but certainly applicable to certain segments of biologists!). So they will either want to simply substitute numbers in equations without thinking of what they’re doing, or they will simply switch off at the sight of any larger equation, no matter how simple it actually is (and the Hardy-Weinberg stuff is relatively simple). This post gets it right by giving tangible examples instead of just abstract letters (I’m no pedagogist, but I’m sure this is what turns people off of maths).

Any evolutionary biology textbook will have a section on Hardy-Weinberg equilibria. My textbook of choice is Futuyma’s 2009 Evolution.

  1. Welcome to Life, A Guide for New Members of Species Homo Sapiens – Ryan Somma (ideonexus)

Teaching evolution to children is a special challenge (personal experience). The difficulty is compounded by the lack of children’s books with evolution-related material. There’s no problem finding things about wildlife, nature, or dinosaurs, but books explicitly about evolution are rare indeed (at least in English; there are several in French). This is why this book should be welcomed. Download it from the link.

Richard Dawkins has written the hands-down best children’s science book, The Magic of Reality (2011), including evolution of course. Fully recommended for anyone even up to middle school age (heck, I enjoyed reading it too).

Extracurricular Activities: Conference Reports

The past month saw several conferences take place. Most relevant is the evolution one in Ottawa which looked like a must-attend event. The blogosphere reaction (andtales from colleagues who went) attest to that. The blog posts here are the ones that deal with these conferences, either compilations of talks, reactions to talks, or simply a look at the social side. No further reading lists to give here.

Overview of the Artificial Life (ALife) 13 Conference – Bradly Alicea (Synthetic Daisies)

This post by Bradly Alicea covers several sessions that took place from this recent conference in Michigan. It’s quite an interdisciplinary event, with sessions on protocells, collective animal behaviour, and experimental and programmed evolution. Very interesting stuff.

#Evol2012: Ottawa in retrospect – Jeremy Yoder (Denim and Tweed)

Jeremy Yoder gives his personal take on the large Ottawa evolution conference, including a link to his own slideshow. I’m glad to read that it was open to social media. I haven’t been to many conferences (why are they so expensive?), but those few that I went to either had no wi-fi, or were simply shut off to social media (Twitter, live-blogging, that kind of thing). Nice to see things changing; maybe in the not-so-distant future, we’ll even have routine conferences delivered directly by livestreaming (not an original idea), slashing the exorbitant cost of these events to let more people participate (at the considerable expense of networking though).

#Evol2012 Molecular Ecology Symposium: Your overconfidence is your weakness – Jeremy Yoder (Nothing in Biology Makes Sense)

In this post, Jeremy Yoder zooms in on the molecular ecology symposium of the Ottawa evolution conference, and the talks given there. I’m not so well acquainted with molecular ecology, but it’s nice to see that they look critically at their methods. It’s something every field should do.

#Evol2012: Inversions and spruces and tethered snails – Jeremy Yoder (Nothing in Biology Makes Sense)

In this post, Jeremy Yoder describes some of the talks from the first day of the Ottawa evolution conference, including talks on chromosomal inversions, spruce pine adaptation, radish domestication, and the relation between dispersal ability and predator-prey response.

#Evol2012 Nothing in biology makes sense, except in the light of good models. – Noah Reid (Nothing in Biology Makes Sense)

Two talks from the conference are highlighted in this post by Noah Reid: a phylogenetics talk, and one on modeling genetic differences under isolation. What unites them is that the presenters apparently did a great, concise, and clear job of presenting their mathematical models. Anyone who manages to pull that off deserves a tip of the hat. I personally can never do it in a Powerpoint presentation. When I must, I whip out a prepared R session with saved functions and derive it on the spot. It works well, but is also very risky, so I can’t recommend the method. If you’re curious as to how they pulled it off, there is a link to Carl Boettiger’s slides (phylogenetics talk) in the post.

Evolution and Poutine – Larry Moran (Sandwalk)

There are two purposes to science conferences: getting to hear the latest findings and goings-on before they’re published, and networking – getting to know other researchers (which can potentially lead to new collaborations). So don’t miss out on the various lunches and dinners, they’re as much a part of it as the pure science.

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I hope this was a pleasant edition, and that your schedule and bookmarks folders are filled for the next few days.

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