Carnival of Evolution, No. 67 — Wallace centenary edition

Charles Darwin's Tree of Life metaphor (from 1859) has become world-famous. However, Alfred Russel Wallace, who independently developed the idea of evolution by means of natural selection, had already used a very similar image in 1855, when he noted: "the analogy of a branching tree [is] the best mode of representing the natural arrangement of species ... a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled oak ... we have only fragments of this vast system, the stem and main branches being represented by extinct species of which we have no knowledge, while a vast mass of limbs and boughs and minute twigs and scattered leaves is what we have to place in order, and determine the true position each originally occupied with regard to the others".

This past year has been one in which many people commemorated the death of Wallace (1823-1913), and so it seems appropriate to join them for the final summary of 2013's posts at the Carnival of Evolution.

Wallace spent 1848-1852 collecting in the Amazon, and 1854-1862 doing the same in South-East Asia. He is best known today for his studies of biogeography, but he also worked on what we now call environmental issues, and even what is now known as exobiology. More controversially, he also involved himself in social criticism, and atheistic spiritualism. At his death, he was as well known as any living biologist; but since then he has sadly been eclipsed by Darwin.

This month's blog posts

Wallace was interested in origins, of course, so we can start the list of evolution posts with that topic.

Darren Naish at Tetrapod Zoology discussed a new species of perissodactyl from the Amazon (A new living species of large mammal: hello, Tapirus kabomani) (submitted by Donald Prothero). New mammal species are rather rare these days, but Wallace would not have been surprised to find them in the Amazon.

At the Panda's Thumb, Wilson Sayres asked: Why sequence the manatee genome? (submitted by Ryan Gregory). In spite of being aquatic mammals, manatees are more closely related to elephants than they are to dolphins or whales. Gert Korthof then took us to the origin of life (New Szostak protocell is closest approximation to origin of life and Darwinian evolution so far), discussing the creation of a prebiotically plausible protocell, consisting of a fatty acid vesicle in which RNA replication occurs autonomously without the help of enzymes.

Kathy Orlinsky at The Stochastic Scientist then takes us to the origin of genetic variation, noting that for mitochondria DNA mutations might not be so random after all.

1848

Wallace studied adaptations, among other things, so we can now proceed on to that topic.

GrrlScientist was formerly one of the mainstays of the Carnival of Evolution, but she then drifted off into natural-history blogging, instead. However, this month she reported on a study of hummingbird species living at high altitudes (How do hummingbirds thrive in the Andes?). They have independently evolved hemoglobin with enhanced oxygen-binding properties, so they can thrive in oxygen-poor environments.

Ed Yong at Not Exactly Rocket Science considered the evolution of the two of the oddest mammals, the platypus (How the platypus and a quarter of fishes lost their stomachs) and the koala (Organ helps koalas bellow at elephant pitch).

Tim Eisele at The Backyard Arthropod Project talked about the options available for getting yourself through the winter when you are a living organism (Winter is the enemy).

At Eco-Evo Evo-Eco, Steven Brady contemplated why wood frog populations seem locally maladapted to roads (Homage to the Island of Misfit Toys) (submitted by Ben Haller), and Andrew Hendry considered the question of whether adaptation is driven by many genes of small effect or by a few genes of large effect (Epic wrap battles of Christmas).

Wallace's main collecting interest was beetles

Processes were at the heart of Wallace's evidence for evolution, so we should look at this topic, too.

Caroline Tucker at The EEB & Flow looked at an example (Ecological processes may diffuse through evolutionary time: an example from Equidae) of how patterns of trait divergence and adaptive radiation can evolve as a result of diffusion evolution, rather than from a single strong ecological pressure (submitted by Bradly Alicea).

At Synthetic Daisies, Bradly Alicea examined the nonlinear evolutionary dynamics of Mexican cavefish (Dragons, sandpiles, and cavefish: an evolutionary inquiry), considering both the Sandpile and the Dragon King statistical models for the developmental changes that made them eyeless.

Kim Gilbert at The Molecular Ecologist asked the question: How prevalent are non-overlapping generations?, which is of obvious importance for evolutionary modeling, and found that there is no known answer.

At The Genealogical World of Phylogenetic Networks, David Morrison asked a phylogenetic question: Is rate variation among lineages actually due to reticulation? He decided that it might be, but for most studies it is simply an untested assumption that it isn't.

1862

Selection involving groups was a bit out of Wallace's line, but it is prominent these days.

At Evolution in Structured Populations, Charles Goodnight noted that kin selection can be useful for developing an intuitive or qualitative grasp of social evolution, but for many reasons it fails when it is applied to the real world (Now I know I am "El Lobo Solitario"). He then considered the phenotypic view of evolution, by assessing the adaptive role of religion in providing cohesion in societies (Group selection and religion) (submitted by Bjørn Østman).

Wallace's global biogeographical regions

Now we come to those posts about the broad range of applications of evolutionary ideas.

Sarah Bodbyl at the BEACON blog asked about whether plants experiencing rapid loss of their pollinators are able to adapt and maintain viable populations by increasing their ability to reproduce without pollinators (Mating system evolution).

At The Mermaid's Tale, Anne Buchanan noted that genes associated with domestication and diversification have been identified with fine-mapping or genome-wide association studies, thus distinguishing artificial selection from natural selection (What domestication can and can't tell us about evolution). Then, Ken Weiss asked: "Every trait is due to natural selection!" .... often said, but is it true? This is belief in a form of very strong determinism, which he investigates in relation to the human thumb.

Carl Zimmer at The Loom pointed out that one of the best places to survey the sloppy creativity of evolution is inside your own nose (The smell of evolution).

Noah Reid at Nothing in Biology Makes Sense highlighted one of the more popular topics of the news, blog and twitter world in late November, which concerned a proposed phylogeny of the well-known folk tale about Little Red Riding Hood (Learn the origins of fairytales with this one weird trick!). However, The Genealogical World of Phylogenetic Networks has countered with a post about The phylogenetics of Little Red Riding Hood, in which it is shown that studying the evolution of folk tales requires knowledge of the time direction of evolutionary change — and it appears that the proposed phylogeny might be wrong.

1895

Finally, here are some miscellaneous blog posts about evolution and blogging.

PZ Myers, the grumpy old man at Pharyngula, critiqued a paper on the human brain that apparently has no data, or a hypothesis that makes sense (Frugal to the point of vacuity).

At the Tumbld Thoughts microblog, Bradly Alicea looked at the nature of blogosphere academic activity, and its relationship to open-source publishing (Blogosphere review).

Finally, every month has its drinking vessel in which the waters become stormy. Recently in Aeon magazine, science writer David Dobbs published an article (Die, selfish gene, die) in which he noted that: "The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong." This has generated a number of responses (as submitted by Ryan Gregory and Bjørn Østman), including those by PZ Myers from Pharyngula (Higher order thinking), Annalee Newitz from io9 (It's time to get skeptical about "the selfish gene"), and Larry Moran from Sandwalk (Razib Khan doesn't like Gould and doesn't like new-fangled ideas) (all of them arguing in favor of Dobbs, to one extent or another), and from Jerry Coyne from Why Evolution Is True (David Dobbs mucks up evolution, part I; and part II) and Razib Khan from Gene Expression (There is no revolution in genetics; and Evolutionary orthodoxy may be boring, but it is probably true) (who are against). David Dobbs has replied, as has Richard Dawkins.

Coda

Well, that's it for this month. While you wait for the next edition, you will find the Carnival of Evolution on Facebook and Twitter, as well as at the official Carnival of Evolution blog. Past posts and future hosts can be found on the Carnival index page.

The host of next month's Carnival will be Byte Size Biology.

You can submit posts for the next edition using the Carnival submission form (which requires you to log in), by commenting at the Carnival facebook page, or by sending an email to Bjørn Østman.

The network history of the Carnival of Evolution

We recently hosted the 52nd edition of the Carnival of Evolution here at this blog, and since then I have done a bit of digging into the history of the Carnival (or CoE). I am sharing here some of what I found, mostly numbers.

The Carnival of Evolution was founded at the end of August 2008, by Daniel Brown, then of the Biochemical Soul blog. Most blog Carnivals seem to last for only a few issues, but the CoE has continued for more than 50 editions as a monthly summary of "all that is best in evolution blogging". Indeed, it is the only Carnival currently listed as "active" in the Science category, out of the 48 that have existed at one time or another (see this 2009 blog post by Grrl Scientist on the demise of science carnivals).

For longevity, it cannot yet compete with some other biology carnivals, such as I and the Bird, which appeared for 149 fortnightly editions from July 2005 to April 2011, but it has lasted better than most other carnivals — there are 2,964 carnivals listed, but only 136 of these posted an edition during Aug-Oct 2012. For example, the 51st edition of the CoE celebrated precisely 4 years, while the 52nd edition appeared after 1,500 days of continuous blogging. The early editions were intended to be fortnightly, but after a missed hosting early on (at the Life Before Death blog) the plan was changed to roughly monthly intervals, as shown in the first graph.

Frequency histogram of the times
between CoE editions.

The first 18 CoE editions were administered by the afore-mentioned Daniel Brown; but circumstances change for most bloggers, and so he passed the baton to Bjørn Østman, who has carried it since then. There have been 47 different host blogs for the 52 editions — Biochemical Soul, Carnival of Evolution, Greg Laden's Blog, Observations of a Nerd and Quintessence of Dust have all hosted twice. Furthermore, as individuals, Daniel Brown hosted 3 times, and Bjørn Østman, Greg Laden, Steve Matheson, Christie Wilcox and Psi Wavefunction (the Scarlet Pimpernel of evolution blogging) have each hosted twice (not always at the same blog!).

Unfortunately, not all of the 52 Carnivals are still available at the original blogs — number 13 was at a now-deleted blog, the blog hosting number 37 is now access-restricted, and the blogs for numbers 7, 9, and 15 no longer have links to the relevant pages. Fortunately, two of these Carnivals have been archived at the Internet Archive Wayback Machine (#9 and #15), and one is available in a slightly re-formatted form at the blog aggregator Planet Atheism (#37). As for the extinct two, Pleiotropy has a sample list of some of the post topics for #13; but for #7 the only information available is that it was "a short but sweet edition".

This issue raises the related question as to the fate of the 47 blog hosts since their Carnival hosting. As far as I can tell, 1 has been deleted, 1 is now restricted access, 11 have stopped new posts, 5 have continued in another form (eg. another name or address), and the remaining 29 are extant. This shows some remarkable longevity in evolution blogging.

I have looked through the 50 available Carnivals, and I can report as follows. (Note: In the following I took a restricted view of "blog posts" as not including press announcements, of which there have been quite a few.)

There are 283 separate blogs mentioned in the Carnivals, although several of these blogs were moved and/or renamed versions of other blogs, as bloggers tend to move about a fair bit. Of these blogs, 161 (57%) were One Hit Wonders (ie. they were featured only once), as shown in the second graph.

Frequency histogram of the number of
Carnivals in which each blog was cited.

The two blogs with the highest number of Carnival appearances are: Pleiotropy (by Bjørn Østman, naturally!), which was featured in 68% of the Carnivals from number 9 onwards; and NeuroDojo (by Zen Faulkes), which was featured in 69% of the Carnivals from #11 onwards. A special mention should also go to Living the Scientific Life (Grrl Scientist), which was featured in 62% of the Carnivals during numbers 1-29 (she has now drifted into a different form of blogging).

A separate issue is how many actual posts were contributed by each blog (some people blog a lot more than others), which is shown in the third graph.

Frequency histogram of the total number
of posts cited for each blog.

The record of 52 posts is held by The Mermaid's Tale (present from Carnival #30 onwards), which is a multi-author blog (Anne Buchanan, Holly Dunsworth, Ken Weiss), giving them an advantage quantity-wise (and also in diversity of subjects). Mind you, the sole-authored NeuroDojo has 51 posts and Pleiotropy has 49! The record of 10 posts cited in one Carnival is held by Sandwalk (Larry Moran), which was the "specially featured" blog in Carnival #28. Sandwalk also contributed 7 posts to Carnival #50, while The Loom (Carl Zimmer) contributed 6 to #31, and The Mermaid's Tale contributed 6 to #33.

Frequency histogram of the number
of blogs cited in each Carnival.

If we look at these data the other way around, we can contemplate the number of blogs cited per Carnival, in the fourth graph, and the total number of posts cited per Carnival, in the fifth graph.

Frequency histogram of the number
of blog posts cited in each Carnival.

The maximum number of blogs cited in any one Carnival is 44 and the record number of posts is 69, both held by The Dispersal of Darwin (Michael Barton), the host of Carnival #31. (This Carnival also produced the greatest number of One Hit Wonders.) The minimum number is 6 for both criteria, interestingly enough in Carnival #6. The highest average number of posts per blog was 2.1, in Carnival #33 (41 posts cited from 20 blogs).

Fortunately, the number of posts has shown a steady upward curve, as indicated in the sixth graph, although not always at the one-blog-post-per-day rate set in the earliest days. However, over the past 20 Carnivals there has been an average of 1.06 blog posts cited per day of passing time, so we are certainly  holding our own.

The steady growth of the CoE through time.

That's enough about the numbers. What themes have been employed by the CoE host bloggers to present their Carnival? The idea of theme-based presentations was introduced by Daniel Brown in CoE #10, but they appeared only sporadically until CoE #44, since when they have become de rigueur.

The themes we have had are (in order): Darwin's journal, phylogenetic analysis, superstars, a real carnival, Feed Your Head, a football game, a Darwin letter, the Origin of Species, a scientific conference, a conference slide presentation, phylogenetic trees, a newspaper report, an Icelandic saga, mousetraps, a set of teaching modules, Darwin's Restaurant, and phylogenetic networks. Clearly, invention is the name of the game. The most inventive may well be Adrian Thysse's slide presentation in CoE #45; while probably the most outrageous came from Psi Wavefunction in CoE #20, who performed original phylogenetic analyses of the blog posts while claiming no prior knowledge about how to do it!

Finally, and most importantly, we can ask: How has the Carnival of Evolution changed through time? This is precisely what a phylogenetic network is designed to tell us, as shown in the final figure, which is based on a phylogenetic analysis of the data concerning which blogs were cited in which Carnivals.

NeighborNet graph of the similarity relationships between the
Carnivals. The data being summarized are the number of posts
from each blog. So, in the data matrix each row is a Carnival
and each column is a blog, with the data in each cell being the
number of posts. The length of the terminal branches of the
network roughly reflects how many blogs were featured,
whereas the intricate network of inter-connecting lines
indicates the complex patterns as to which blogs were

featured in which Carnivals. Note that #7 and #13 are absent.

As you can see, the analysis shows that there has been a gradient through time. For example, the first 12 Carnivals are at the bottom-right of the diagram and the most recent 12 are at the upper-left of the diagram, with the others arranged in between. (Note that they are not in perfect order.) This means that the blogs being cited have greatly changed through time. For example, none of the blogs featured in the first three Carnivals re-appeared among the most recent four Carnivals.

The biggest change appears to have occurred with Carnival #31. This is indicated by the big gap in the diagram between Carnival #28 and #31 (it is arrowed). Presumably, this had nothing to do with the CoE host (the afore-mentioned Dispersal of Darwin), but has more to do with the time, which was the end of 2010. The world of social media was changing rapidly at that time, and several of the bloggers either stopped blogging or moved house.

It is tempting to interpret the relationships among the blogs in more detail, but that might be tempting fate. I will content myself with pointing out that, in the diagram, the sister to my blog (#52) is Pharyngula (#48), which must be an example of the well-known phylogenetic artifact of long-branch attraction.

Anyway, that's all there is in my network history of the ongoing Carnival of Evolution. Congratulations to all of the people involved in this successful Carnival; but someone else will have to write the centenary history, when it falls due.

Carnival of Evolution, Number 52 — the Network Edition

Welcome to the 52nd edition of the Carnival of Evolution, hosted here at The Genealogical World of Phylogenetic Networks blog.

Exordium

For those of you not familiar with the Carnival of Evolution, at the beginning of every month the Carnival provides a collection of some of the most interesting of the recent blog posts about biological evolution. The Carnival is hosted by a different blog every month: last month's Carnival can be found at The Stochastic Scientist blog; and next month's Carnival will be hosted by the Sorting Out Science blog at the beginning of November.

The theme for the presentations this month is, of course, phylogenetic networks. You can skip straight on to the blog posts if you are familiar with such networks.

Introduction to phylogenetic networks

For those of you not familiar with phylogenetic networks, the host blog this month is about the use of networks in evolutionary analysis, as a replacement for (or an adjunct to) the usual use of phylogenetic trees. The 46th edition of the Carnival of Evolution (hosted at the Synthetic Daisies blog) provided a good introduction to trees in the study of evolution, which are used as a metaphor for branching genealogical history. In this blog, we take evolutionary trees to the next logical stage — reticulating networks.

Networks have received considerable attention in the recent biological literature, not least in microbiology (where horizontal gene transfer is often considered to be rampant) and botany (where hybridization has always been considered to be common). It has also received increasing attention in the computational sciences.

Networks are acknowledged to have two main uses within phylogenetics: (i) exploratory data analysis, in which conflicting data patterns are displayed and their quality and quantity assessed; and (ii) evolutionary analysis, in which the historical (genealogical) patterns involve not only vertical descent (parent to offspring) but also reticulations due to horizontal processes (such as horizontal gene transfer, hybridization, recombination, and genome fusion).

A network is thus more general than a tree (or "more complete"), because it is a tree that also has reticulations. For example, the Decision Tree presented with the Carnival of Evolution #46 might look like this if it was a network:

Note that for some of the leaves there are multiple paths through the network from the root, whereas a tree is restricted to a single path between any two points. This is the essence of why networks are being introduced into evolutionary studies, because the evolutionary history of many organisms involves complex pathways of "descent with modification" (as Darwin put it).

If you would like to know more about this blog, then the simplest access is via the various Pages, listed at the top of the right-hand column, which gather together the blog posts related to particular topics. The most popular blog posts for non-specialists are in the History and the Analyses sections, as well as in the Tattoo section; so please take a look around the blog while you are here.

This month's Carnival posts

For this edition of the Carnival of Evolution, the featured posts have been incorporated into a series of phylogenetic networks. Each network represents a typical topology that you might encounter in the scientific literature, illustrating the relationships between the blog posts. I have been somewhat selective this month, by not including anything about the ongoing arguments between evolutionists and creationists.

Posts about networks

To get the Carnival off on the right foot, we will start with a collection of blog posts that are themselves about biological networks. They are all different, and not all of them involve phylogenetic networks, so they display the diversity of what networks are used for in biology. The network shown here is a NeighborNet, which connects the topics based on overall similarity.

Franklin Harold, guesting at the Small Things Considered blog, discusses the evolution of the eukaryotes in Begetting the Eukarya: an unexpected light. The eukaryotes originated from the fusion of several genomes, so that the Tree of Life is not a tree at that point in evolutionary history. Sadly, in this blog post the suggested alternative image to a tree is not a network but "a pointed Gothic arch thrusting out of the prokaryotic underbrush", which you will have to check out for yourselves.

John Hawks, at his personal blog, introduces us to the world of human evolution when he explores Denisova at high coverage. The archaic Neandertals and Denisovans have recently been shown to have been involved in gene flow with early modern humans, which re-writes the story of human evolutionary history.

The Genealogical World of Phylogenetic Networks then asks, in light of this information, Why do we still use trees for the Neandertal genealogy? Clearly, a network is more appropriate than a tree for phylogenetic analysis when there is horizontal gene flow.

Razib Khan, at the Gene Expression blog, develops this theme in Across the sea of grass: how Northern Europeans got to be ~10% Northeast Asian. He takes us into more modern times when he ponders recent evidence concerning the evolutionary relationships between Neolithic farmer migrants and the indigenous Mesolithic southern European populations.

Dienekes Pontikos, at his Anthropology Blog, then ponders Structural stability and ancient connections between languages, in which a phylogenetic network is used to discover unexpected geographic clusters of similarity among the families of modern languages.

On a related topic, Jeremy Yoder, The Molecular Ecologist, considers Genes...in...space! by looking at ways to summarize multivariate geographical patterns among human genotypes. Sadly, this inadvertently demonstrates just why one should not use Principal Components Analysis for this type of data analysis — the right idea but the wrong tool. The second axis of the ordination is frequently nothing more than a quadratic function of the first axis (ie. a mathematical artifact), as shown clearly by two of the three ordinations reproduced in the blog post. This is one of several reasons why we should use a network instead of PCA.

Bradly Alicea, writing at the Synthetic Daisies blog, then moves away from phylogenetic networks and into gene regulatory networks, with Cascades in common: biological network function in evolution. He connects these networks to biological evolution by pointing out that they contribute to both adaptive variation and to variation between species.

Finally, the ever-present Bjørn Østman, from the Pleiotropy blog, considers Epistasis in evolution. He uses genetic interaction networks to look at epistatic interactions (which are non-additive interaction effects resulting from mutations) and their role in evolution, particularly in adaptation and speciation.

Human evolution

Human evolution is always of interest to humans, and so there is a steady stream of blog posts about this topic every month. The network shown here is a Recombination network, with the converging pair of arrows indicating, in this case, a topic that combines two of the others.

This month, Kathy Orlinsky, writing as The Stochastic Scientist, discusses recent evidence that Our methylomes make us human. One explanation for how humans and chimpanzees can be so different when their genomes are so similar is that the DNA methylation of their genes is different.

On a slightly more tasty note, Heather Pringle, from The Last Word On Nothing blog, considers The sweetness of human evolution. The search for a honey diet has probably played a much more complex (and interesting) role in human history than you have heretofore realized.

Writing at the Nothing in Biology Makes Sense! blog, Jonathan Yoder then muses, appropriately enough, about the Evolution of diabetes? Type 2 Diabetes is a highly multifactorial disorder, so don't expect an answer any time soon.

Gunnar De Winter, masquerading as The Beast, The Bard and The Bot, then contemplates fatty brains and what their genes might tell us about history, in Once upon a (complicated) time in Africa.

Next, Faye Flam, from the Planet of the Apes, ponders What whales tell us about the evolution of menopause. Very few species have a long post-reproductive period for females, and these include several species of whale as well as humans, so a comparative analysis might be very revealing.

Ed Yong, over at the Not Exactly Rocket Science blog, continues the cetacean theme with Same gene linked to bigger brains of dolphins and primates — in this case, the title says it all.

Finally, Helen Thompson and Shankar Vedantam, writing at The Salt blog, reflect on How food and clothing size labels affect what we eat and what we wear. This is my personal favorite post of the month, because it tells us everything we need to know about human evolution.

The study of heterozygosis

Bodies are interesting things, especially the differences between males and females, and this month we have a few blog posts about that topic. The network shown here is a Hybridization Network, in which the paired arrows indicate three hybridization events, in this case showing hybridization of topics based on sex (male versus female).

PZ Myers, over at the Pharyngula blog, shows a great interest in reconstructing reproductive anatomy, in O brave new world that has such penises in't. I'm sure that you will be just as interested in regrowing penises as he is.

Emily Weigel, on the other hand, shows that the Beacon blog is more interested in Maternal effects — mothers have more of an effect on their offspring than most daughters ever want to admit.

As a compromise position, Jerry Coyne, at the Why Evolution is True blog, contemplates A gynandromorph cardinal. Externally, one half of the bird is male and the other half is female, divided lengthwise! A similar thing happens in fruitflies, although they take it to the extreme.

Marc Srour, over at the Teaching Biology blog, then muses about Wolbachia: the ubiquitous male-killing, feminising parasite, which has at least four different ways to alter the insect host's reproduction in order to increase its own maternal transfer.

Finally, Suzanne Elvidge, at the Genome Engineering blog, reports about Men on your mind: male DNA in women’s brains — this concerns the first description of male microchimerism in the female human brain.

Evolutionary theory

Theory is either fascinating or terribly dull, depending on whether you like to spend your time in the pub or in the field. There is room in the world for both types of scientist, and this collection of posts comes from the former group. The network shown here indicates that there is no particularly close relationships among the blog posts.

Joachim Dagg, living in the Mousetrap, starts us off by conducting a Thought experiment about recombination. The resulting conclusion is that the maintenance of sex is a problem distinct and separate from the maintenance of recombination rates.

Jeremy Yoder, still at The Molecular Ecologist blog, reflects on the problem of Isolating isolation by distance — in population genetics, can we distinguish isolation by distance from population structure? The answer appears to be rather complicated.

Ford Denison, at the This Week in Evolution blog, provides us with some thoughts that the editor excised from his book on Darwinian Agriculture, when he asks Biomimicry of forests or trees? The answer is presented as a Galilean dialog between an engineer and a couple of expert biologists.

Andrew Hendry, contributing to the Eco-Evolutionary Dynamics blog, ponders the difficulty of making arguments for biodiversity preservation solely from a consideration of ecosystem services, in Ecosystem disservices and assisted elimination.

Finally, The Genealogical World of Phylogenetic Networks reflects on Metaphors for evolutionary relationships, which surveys the rich world of evocative metaphors used in evolutionary studies.

Evolution in practice

This collection of posts comes from those scientists who have been contemplating the evolving world from inside the lab or out in the field. The network shown here is a Median Network, which simply displays all of the character-state differences between the posts (the central structure is a cube in this case).

The Mostly Open Ocean blog muses about Rapid speciation in starfish. There have been profound changes to life history in the two daughter species arising from the recent speciation event, involving selection on many morphological and physiological traits.

Carl Zimmer, weaving at The Loom blog, revisits one of his favorite experiments in The birth of the new, the rewiring of the old. The experiment is Richard Lenski's 24-year study of evolutionary change in Escherichia coli, which now encompasses an unheard-of 55,000 "generations". The results to date are, to say the least, fascinating.

Ken Weiss, contributing to The Mermaid's Tale, discusses the opposite trend in Evolving...to stay the same? — the horseshoe crab seems to have changed very little for 150 million years.

Jerry Coyne, still at the Why Evolution is True blog, reflects on the same phenomenon in Horseshoe crabs aren’t really "living fossils", but he elaborates instead on some of the differences between the fossil and contemporary species.

Finally, Greg Laden, popping up at the 10,000 Birds blog, contemplates The incredulous New Caledonian crows, which apparently can distinguish the concept of an Unknown Causal Agent from that of a Hidden Causal Agent, which most animal species cannot do.

The ENCODE debacle

The network shown here is a Horizontal Transfer Network, with the two dashed lines showing the transfer of text (quotations) in this case.

Early in the month we saw what may well be the nadir of scientific journalism, when the ENCODE (Encyclopedia of DNA Elements) consortium provided the excuse for a media blitz associated with the co-ordinated release of 30 papers in some of the high-profile genome-oriented journals. Most notably, the media reports focussed almost entirely on the apparently new claim that 80% of human DNA is not "junk" (as opposed to the previous claim that 80% is junk DNA). This new claim rests almost entirely on a re-definition of "junk DNA" rather than any new data about DNA function, so this is not much of a contribution from the ~400 ENCODE people, let alone a good reason for a media bombardment. Not unexpectedly, the blogsphere exploded with outrage at the distortions involved in the media reporting. A few selected blog posts are included here to commemorate the event.

Mike White, sitting in The Finch and Pea pub, sets the scene with ENCODE media fail (or, Where’s the null hypothesis?). Michael Eisen, at the It Is NOT Junk blog, then starts the attack on the media with This 100,000 word post on the ENCODE media bonanza will cure cancer, while Larry Moran, strolling on the Sandwalk, develops the attack with The ENCODE data dump and the responsibility of science journalists. Ryan Gregory, from the Genomicron blog, then weighs in with A slightly different response to today’s ENCODE hype, as does PZ Myers, popping up at the Panda's Thumb, with The ENCODE delusion. Sean Eddy, at his Cryptogenomicron blog, presents a DNA-researcher's perspective by asking incredulously ENCODE says what? Finally, Ewan Birney, the bioinformatician co-ordinating the ENCODE project, presents My own thoughts at his personal blog.

Genome science reporting can only get better, and less embarrassing, from here on. However, the simple fact that several reputable science journal editors got together to orchestrate the release of the papers on the same day, thus unnecessarily delaying the publication of some of the papers (by several months), strikes me as outrageous. (Casey Bergman, at the brilliantly titled I Wish You'd Made Me Angry Earlier blog, discusses this in The cost to science of the ENCODE publication embargo.) The possibility of a media extravaganza seems to have loomed larger in the minds of the editors than did their journals' role in communication among scientists. We take them seriously, so why can't they do the same for us?

Terminus

Well, that's it for this month. While you wait for the next edition, you will find the Carnival of Evolution on Facebook and Twitter, as well as at the official Carnival of Evolution blog. Past posts and future hosts can be found on the Carnival index page.

Next month's Carnival will be hosted at Sorting Out Science. You can submit posts for the next edition using the Carnival submission form (which requires you to log in), or by sending an email to Bjørn Østman.