Category Archives: Evolution

Blog For Darwin


From Blog For Darwin:

February 12th-15th, 2009 participating bloggers around the world will be celebrating the bicentenary of Charles Darwin’s birth (February 12th, 1809) with a BLOG SWARM, in which posts will be aggregated on BLOG FOR DARWIN to be kept as a resource for educators, students, and others.
CLICK HERE or read below to learn how you can participate!

Yes, there’s a month left, but I hope you participate.

Darwin Bicentenary

2009 is the 200th anniversary of Darwin’s birth and 150th anniversary of the publication of the Origin of Species, so a lot of organizations are going full steam in promoting science, evolution and the history of science this year. Here are some of the examples:
The New Scientist has published Darwin’s dangerous idea: Top 10 evolution articles (see Larry for some commentary).
Nature is ready for the celebration with a special page – Darwin 200 – collecting all the articles. Check out the most recent one – 15 evolutionary gems (pdf)
Over on The Loom – a three-part interview with Ken Miller on evolution and the demise of Intelligent Design Creationism:
Smoke and Mirrors, Whales and Lampreys: A Guest Post by Ken Miller
Ken Miller’s Guest Post, Part Two
Ken Miller’s Final Guest Post: Looking Forward
And of course, expect a lot of activity on The Beagle Project Blog and, donate to the Beagle Project.

On Gould and rates of evolution

Three Obligatory Readings of the Day:
Brian Switek: Stephen Jay Gould’s view of life
Larry Moran: An Adaptationist View of Stephen Jay Gould
Greg Laden: How fast does evolution happen?

Evolutionary Psychology – why it is fundamentally wrong

Larry, Amanda, John, Mike and others are comenting, quite positively, on the recent Scientific American article – Evolution of the Mind: 4 Fallacies of Psychology by David J. Buller. And I agree – this is an excellent, well-deserved and well-thought smack-down of Evolutionary Psychology and I am happy that it appears in a popular magazine and is spreading around the blogosphere.
The Fallacy 1 – Analysis of Pleistocene Adaptive Problems Yields Clues to the Mind’s Design – is my favourite counter-argument when I hear someone offering an EvoPsych-style Just-So-Story, but the other three just as interesting and important:

Of course, some speculations are worse than others. Those of Pop EP are deeply flawed. We are unlikely ever to learn much about our evolutionary past by slicing our Pleistocene history into discrete adaptive problems, supposing the mind to be partitioned into discrete solutions to those problems, and then supporting those suppositions with pencil-and-paper data. The field of evolutionary psychology will have to do better. Even its very best, however, may never provide us knowledge of why all our complex human psychological characteristics evolved.

James Holland Jones wrote an interesting commentary on the article that in some details disagrees with Buller and, if anything, makes an even more potent criticism of EvoPsych:

I happen to think that the whole sex-differences in sexual preferences thing is the most overplayed finding in all of evolutionary science. In class, I refer to this work as Men-Are-From-Mars Evolutionary Psychology. The basic idea is to take whatever tired sexual stereotype that you’d hear in a second rate stand-up comedian’s monologue, or read about in airport bookstore self-help tracts and dress it up as the scientifically proven patrimony of our evolutionary past. Ugh.

Read both the Buller article and the Jones post in their entirety – they are excellent and provide a food for thought as well as ammunition for your next duel against one of the ‘true believers’ in EvoPsych.

Bizarre Squid Sex (no video)

In National Geographic:

A new investigation into the tangled sex lives of deep-sea squid has uncovered a range of bizarre mating techniques. The cephalopods’ intimate encounters include cutting holes into their partners for sex, swapping genders, and deploying flesh-burrowing sperm. These and other previously unknown reproductive strategies were documented in a survey of ten squid species living worldwide at depths of between 984 and 3,937 feet (300 and 1,200 meters). Study leader Henk-Jan Hoving, a Ph.D. student at the University of Groningen in the Netherlands, examined squid caught during research voyages as well as preserved museum specimens.

Of course, you can find many more examples of Weird Cephalopod Sex on Pharyngula….

Scientific American – special evolution issue

January issue of Scientific American is devoted to Darwin’s 200th birthday and contains several excellent articles. Check out The Latest Face of Creationism in the Classroom by Glenn Branch and Eugenie C. Scott for starters.
But beware, there are other (and I would say better) ways of thinking about some of the issues in some of the articles, so check out what Larry has to say about Why Everyone Should Learn the Theory of Evolution and Testing Natural Selection. You may not agree 100%, but you need to think about it.

Both Male-Male Competition and Mate Choice are parts of Sexual Selection

Beaked Whales’ Tusks Evolved Through Sexual Selection Process:

For years, scientists have wondered why only males of the rarely seen family of beaked whales have “tusks,” since they are squid-eaters and in many of the species, these elaborately modified teeth seem to actually interfere with feeding. A newly published study help explain the evolutionary origin of these distinctive “tusks” in beaked whales, a rather mysterious family of whales that live in the deep oceans. Although the tusks are known to be used in competition between males, another purpose seems to be to attract female beaked whales – and to avoid mistakes in choosing a mate.

Hmmm, I have read Darwin’s “Descent of Man” and the take-home message from it was that, if there is a big difference in a trait between males and females, then sexual selection is the first, default hypothesis. Why should this one be a ‘surprise’?
I think they mangled their terms – both ‘male-male competition’ and ‘female choice’ (or ‘male choice’ in some species) are aspects of sexual selection. What they were trying to say is not that the sexual selection hypothesis is new for tusked whales, but that they discovered that the tusks are also a part of ‘mate choice’, and not only ‘male-male competition’. Nice finding, but not that surprising.

Darwin’s Sacred Cause

Peter McGrath, Michael Barton and Mike Haubrich brought my attention to a new book by Adrian Desmond and James Moore. Their previous biography of Darwin is arguably the best (and there are hundreds of Darwin biographies out there, many more to be published next year as well). The new book, Darwin’s Sacred Cause is a result of a lot of study by the duo, especially since the publication of all the Darwin’s correspondence. The new thesis is that the driving force behind Darwin’s work on evolution was his disgust with racism:

“This book, by Darwin’s most celebrated modern biographers, gives a completely new explanation of why he came to his shattering theories about human origins. Until now, Desmond and Moore argue, the source of the moral fire which gives such intensity and urgency to Darwin’s ideas has gone unnoticed. By examining minutely Darwin’s manuscripts and correspondence (published and unpublished) and covert notebooks, where many of the clues lie, they show that the key to unlocking the mystery of how such an ostensibly conservative man could hold views which his contemporaries considered both radical and bestial, lay in his utter detestation of slavery. Darwin’s Sacred Cause will be one of the major contributions to the worldwide Darwin anniversary celebrations in 2009.”

From the interview with the authors:

What do you think is the most surprising element of this book?
Our revelation that much of Darwin’s research over many years was about race. There was no ultimate difference for Darwin between a `race’ and a `species’, so his work on `the origin of species’ was also about the origin of races, including the human races – `man’ was never an exception for him. And while most of Darwin’s research was implicitly about human origins, the extent of his explicit interest in combating racist science is a real surprise. The fact that his most intense phase of work on racial questions came as the United States hurtled towards civil war, a war that the humanitarian Darwin dreaded, adds poignancy to the moral dimension of his research.
What sort of reaction are you anticipating from the scientific community? The history community? The evangelical community?
Many scientists will welcome a `moral’ Darwin’ to confound his religious critics; others will resent our polluting Darwin’s pure science with `extra-scientific’ factors and will declare his anti-slavery beliefs irrelevant. Historians may be more positive, if only because Darwin’s Sacred Cause locates Darwin for the first time on the well-trodden historical fields of transatlantic slavery, slave emancipation and the American Civil War. And those who study the history of `scientific racism’ will have a new Darwin to reckon with. Evangelicals may feel distinctly queasy, not least because William Wilberforce, the Clapham `Saints’ and others they revere as religious ancestors once supped happily with the freethinking Darwins and saw them as allies in the anti-slavery crusade. Darwin’s words, `More humble & I believe true to consider [man] created from animals’, will pose a challenge to every creationist.

Yup. I guess the Creationists will not be happy with the book. It appears to be a must-read for me, though. For you, too, I hope.

Everything you always wanted to know about the Evolution of the Eye

Evolution: Education and Outreach, Volume 1, Number 4, is a thematic issue – 26 articles on the Evolution of the Eye. It’s Open Access so you can download and read all the articles.

New journal: Ideas in Ecology and Evolution

Ideas in Ecology and Evolution is a new Open Access journals which is also experimenting with the review process.
Bob O’Hara and commenters go into details. I hope it does not end like Medical Hypotheses: a great source of blog-fodder for snarky bloggers and not much else. We’ll keep an eye….

The world that contains giant spherical bunnies and poisonous birds is worth living in

And blogging about! Obligatory readings of the day:
The Evolution of Poisonous Birds:

This research elegantly demonstrates that the evolution of just one character — in this case, toxicity — can profoundly affect the evolution of a suite of other characters, ranging from body size and behavioral traits to ecological niche.

Allen’s Rule, Phenotypic Plasticity, and The Nature of Evolution:

Within species … across clines or subspecies … this raises very significant (and addressable) questions regarding adaptation in the genetic vs. the ontogenetic realms. If Allen’s rule is primarily an ontogenetic effect in some species, one can still consider the possibility that it is adaptive, but the nature of adaptation becomes somewhat more nuanced. Which is appropriate, because adaptation is probably never as straight forward as the textbook version of it towards which we tend to gravitate.

Beagle Project liveblogging the visit to the Darwin exhibition

Go here (requires a 5-second process of signing up for FriendFeed, a move you will not regret, if you want to comment instead of just reading) and participate in liveblogging as the Beagle Project crew visits the opening of the Darwin exhibition.

Aerosteon riocoloradensis – the new dinosaur with hollow bones

I always get excited when Paul Sereno publishes a paper in PLoS ONE and today is one such day – his third paper in this journal within a span of less than a year (the first was the paper with detailed description of Nigersaurus and the second was the article on Green Sahara cemeteries). Today’s paper is also the second time PLoS ONE publishes a taxonomy paper, i.e., a monograph that describes a new species:
Evidence for Avian Intrathoracic Air Sacs in a New Predatory Dinosaur from Argentina:

Background
Living birds possess a unique heterogeneous pulmonary system composed of a rigid, dorsally-anchored lung and several compliant air sacs that operate as bellows, driving inspired air through the lung. Evidence from the fossil record for the origin and evolution of this system is extremely limited, because lungs do not fossilize and because the bellow-like air sacs in living birds only rarely penetrate (pneumatize) skeletal bone and thus leave a record of their presence.
Methodology/Principal Findings
We describe a new predatory dinosaur from Upper Cretaceous rocks in Argentina, Aerosteon riocoloradensis gen. et sp. nov., that exhibits extreme pneumatization of skeletal bone, including pneumatic hollowing of the furcula and ilium. In living birds, these two bones are pneumatized by diverticulae of air sacs (clavicular, abdominal) that are involved in pulmonary ventilation. We also describe several pneumatized gastralia (“stomach ribs”), which suggest that diverticulae of the air sac system were present in surface tissues of the thorax.
Conclusions/Significance
We present a four-phase model for the evolution of avian air sacs and costosternal-driven lung ventilation based on the known fossil record of theropod dinosaurs and osteological correlates in extant birds:
(1) Phase I–Elaboration of paraxial cervical air sacs in basal theropods no later than the earliest Late Triassic.
(2) Phase II–Differentiation of avian ventilatory air sacs, including both cranial (clavicular air sac) and caudal (abdominal air sac) divisions, in basal tetanurans during the Jurassic. A heterogeneous respiratory tract with compliant air sacs, in turn, suggests the presence of rigid, dorsally attached lungs with flow-through ventilation.
(3) Phase III–Evolution of a primitive costosternal pump in maniraptoriform theropods before the close of the Jurassic.
(4) Phase IV–Evolution of an advanced costosternal pump in maniraptoran theropods before the close of the Jurassic.
In addition, we conclude:
(5) The advent of avian unidirectional lung ventilation is not possible to pinpoint, as osteological correlates have yet to be identified for uni- or bidirectional lung ventilation.
(6) The origin and evolution of avian air sacs may have been driven by one or more of the following three factors: flow-through lung ventilation, locomotory balance, and/or thermal regulation.

Wow! Read the whole thing!
For more, read Greg Laden’s thoughts.

Historical biogeography of Madagascar

From SCONC:

Wednesday, Sept. 24
Noon, with free lunch
Sigma Xi pizza lunch with Anne Yoder, director of the Duke University Lemur Center: “Historical biogeography of Madagascar: using genes to study the evolution of an island.”
3106 E. Hwy 54, RTP

How to BLAST Sarah Palin

Jonathan describes, step by step.
I wonder if there are any palindromic sequences to be found?

Will you be the 900th….

clone of Professor Steve Steve? Ehrm, the 900th Steve on the listing of the Project Steve?

Sigma Xi Pizza Lunch – Lemurs

Message from Sigma Xi:

You may know that Duke University is home to the Duke Lemur Center (http://lemur.duke.edu/), the world’s largest sanctuary for rare and endangered prosimian primates. But do you know its research? For a glimpse, attend Sigma Xi’s first 2007-2008 pizza lunch at noon, Wednesday, Sept 24. Center director Anne Yoder will speak on the “Historical bio-geography of Madagascar: Using genes to study the evolution of an island” as well as field your questions.
Pizza lunch is free. RSVPs required to cclabby AT amsci DOT org. Directions to Sigma XI: http://www.sigmaxi.org/about/center/directions.shtml.

Why should evolution be taught in the classroom?

A very nice column by Olivia Judson:

The third reason to teach evolution is more philosophical. It concerns the development of an attitude toward evidence. In his book, “The Republican War on Science,” the journalist Chris Mooney argues persuasively that a contempt for scientific evidence — or indeed, evidence of any kind — has permeated the Bush administration’s policies, from climate change to sex education, from drilling for oil to the war in Iraq. A dismissal of evolution is an integral part of this general attitude.
—————–
But for me, the most important thing about studying evolution is something less tangible. It’s that the endeavor contains a profound optimism. It means that when we encounter something in nature that is complicated or mysterious, such as the flagellum of a bacteria or the light made by a firefly, we don’t have to shrug our shoulders in bewilderment.
Instead, we can ask how it got to be that way. And if at first it seems so complicated that the evolutionary steps are hard to work out, we have an invitation to imagine, to play, to experiment and explore. To my mind, this only enhances the wonder.

What she said….

The Horse Exhibit at the AMNH

One of the cool perks of being a scienceblogger and going to a meetup this year was the opportunity to go and see the Horse Exhibit at the American Museum of Natural History in New York City and to recieve (as we were not allowed to take pictures in there) a CD with some of the pictures. You can also see a lot more text and pictures, pretty closely following what is on the exhibit itself, on the excellent Horse Exhibit wesbite.
So, on Saturday afternoon, after the Meet-the-Readers event, several of us got on the subway and went up to the Museum. And I was not disappointed. You know I love horses and have been voraciously reading about them all my life. Yet, I still learned a thing or two new to me at the exhibit. The first thing one sees when entering the room is this huge and beautiful diorama, with various species of now-extinct equids:
weprettysorryweextinct.jpg
The exhibit itself put a lot of effort into dispelling the old textbook notion of a linear progression (from Eohippus to Equus caballus) of the horse evolution, the ‘ladder’, and tries to present the more realistic way of thinking about it as a ‘bush‘ (I am surprised Brian never moved that post to his new blog) with many twigs, and with many species of horses living simultaneously in many parts of the word.
The video (featuring, I think, Ross MacPhee) next to this part of the exhibit, explained how scientists figure out these things, like ages of fossils and genealogical relationships between extinct species – a good antidote to the inevitably static nature of the exhibit, i.e., the Facts, as opposed to the Process.
A similar video about the way scientists study the early domestication of horses serves the same function – it shows the method by which we get to know what we know, not just what we know. The portion of the exhibit about domestication, as well as the one on the natural history (evolution, behavior, extinct and living relatives, etc.) were very well done – there were no usual factual errors that often creep into such exhibits, books etc.about horses.
The rest of the exhibit was devoted to the relationship between horses and humans – how the two species affected and changed each other over the past six millennia. From the use of horses for food, bones, hair and milk, through domestication, riding, driving, warfare and work and today – to sport and the protection of the horses. How horses were bred for different purposes at different times, for instance for large size and carrying ability:
myknightwaskindaheavybutsoami.jpg
…or for high speed needed to deliver mail from East to West Coast:
ponyexpressridershadhardbottoms.jpg
It was great fun, especially seeing this together with some knowledgeable SciBlings like Brian, Grrrl, Josh and others who will probably write their own reviews soon. If you can come to NYC before January 4th 2009, make sure you take some time to see this exhibit. Perhaps it will go on a tour of other cities afterwards. In the meantime, peruse the Horse Exhibit wesbite for more information.

Green Sahara Cemeteries

ResearchBlogging.orgI’ve been saving this picture for more than a year, not showing it to anyone or posting it anywhere online, not wanting to break the embargo:
Gobero%20girl.jpg
This was a picture I took of one of the fossils brought to SciFoo’07 by Paul Sereno and Gabrielle Lyon, together with the skull of Nigersaurus.
Apparently, while digging for dinosaurs in Niger, Paul and the crew discovered an enormous and fascinating archaeological site – Gobero. They teamed up with anthropologists and archaeologists and spent two digging seasons analysing the site. The first results of this study are now finally published in my favourite journal – PLoS ONE:
Lakeside Cemeteries in the Sahara: 5000 Years of Holocene Population and Environmental Change

Background
Approximately two hundred human burials were discovered on the edge of a paleolake in Niger that provide a uniquely preserved record of human occupation in the Sahara during the Holocene (~8000 B.C.E. to the present). Called Gobero, this suite of closely spaced sites chronicles the rapid pace of biosocial change in the southern Sahara in response to severe climatic fluctuation.
Methodology/Principal Findings
Two main occupational phases are identified that correspond with humid intervals in the early and mid-Holocene, based on 78 direct AMS radiocarbon dates on human remains, fauna and artifacts, as well as 9 OSL dates on paleodune sand. The older occupants have craniofacial dimensions that demonstrate similarities with mid-Holocene occupants of the southern Sahara and Late Pleistocene to early Holocene inhabitants of the Maghreb. Their hyperflexed burials compose the earliest cemetery in the Sahara dating to ~7500 B.C.E. These early occupants abandon the area under arid conditions and, when humid conditions return ~4600 B.C.E., are replaced by a more gracile people with elaborated grave goods including animal bone and ivory ornaments.
Conclusions/Significance
The principal significance of Gobero lies in its extraordinary human, faunal, and archaeological record, from which we conclude the following:
1. The early Holocene occupants at Gobero (7700-6200 B.C.E.) were largely sedentary hunter-fisher-gatherers with lakeside funerary sites that include the earliest recorded cemetery in the Sahara.
2. Principal components analysis of craniometric variables closely allies the early Holocene occupants at Gobero with a skeletally robust, trans-Saharan assemblage of Late Pleistocene to mid-Holocene human populations from the Maghreb and southern Sahara.
3. Gobero was abandoned during a period of severe aridification possibly as long as one millennium (6200-5200 B.C.E).
4. More gracile humans arrived in the mid-Holocene (5200-2500 B.C.E.) employing a diversified subsistence economy based on clams, fish, and savanna vertebrates as well as some cattle husbandry.
5. Population replacement after a harsh arid hiatus is the most likely explanation for the occupational sequence at Gobero.
6. We are just beginning to understand the anatomical and cultural diversity that existed within the Sahara during the Holocene.

Triple%20up.jpg
You can see more pictures and the background story on the Project Exploration site.
Greg Laden has already posted about it, and I hope other bloggers will as well.
I am not an expert on human evolution, but if I understand correctly, the information gathered at the site shows that Sahara was going through cycles: being very dry for some time, then having lakes and forests for some time, then getting dry again, etc. During dry periods, no humans lived there. During wet periods, this place was inhabited by humans – but not the same kinds of humans!
The earlier group, if I understand this right, were large, strong humans who subsisted on large game hunting and harpooning huge Nile perch. They are direct descendants of early human ancestors, i.e., they have evolved in Africa, and only their later descendants went out of Africa to Middle East, Europe and beyond.
The latter group came to the site about a 1000 years later. They were smaller and more gracile, made tools, ornamented their pots in very different ways, they kept animals, did some fishing, perhaps some agriculture. They buried their dead on beds of flowers. They may have, but I am not sure about this, be descendants of Eurasian humans, i.e., they may have come back from the Middle East or Europe into Africa and settled there.
Triple%20down-reverse.jpg
The National Geographic story about the finding is a riveting read – I strongly suggest you read it whole. And I hope you read the paper itself (it is NOT a tough slog through highly technical lingo) and see all the additional information about human remains, artefacts, animal and plant remains, and new methods of analysis. And I hope you post comments, ratings and notes on the paper and, if you blog about it, send trackbacks.
Reference:
Lakeside Cemeteries in the Sahara: 5000 Years of Holocene Population and Environmental Change by Paul C. Sereno, Elena A. A. Garcea, Helene Jousse, Christopher M. Stojanowski, Jean-Francois Salieege, Abdoulaye Maga, Oumarou A. Ide, Kelly J. Knudson, Anna Maria Mercuri, Thomas W. Stafford, Jr., Thomas G. Kaye1 , Carlo Giraudi, Isabella Massamba N’siala, Enzo Cocca, Hannah M. Moots, Didier B. Dutheil and Jeffrey P. Stivers. PLoS ONE 3(8): e2995. doi:10.1371/journal.pone.0002995
.
Update – more coverage:
Anthropology.net: The Kiffian & Tenerean Occupation Of Gobero, Niger: Perhaps The Largest Collection Of Early-Mid Holocene People In Africa
Greg Laden: Stone Age Graveyard Reveals Lifestyles of a Green Sahara
Pharyngula: I wish I was a Paleontologist
Sociolingo’s Africa: African archaeology Niger : Saharan cemetery dig report and paper
Ontogeny: Burial site offers rare glimpse of daily life in the stone-age Sahara
Pro-science: Stone Age graveyeard found in Sahara
Knight Science Journalism Tracker: AP, Chicago Trib, New Scientist, NYTimes, etc: Dino hunters find, instead, an ancient human graveyard in the Sahara
L.A.Times: Archaeologists get a glimpse of life in a Sahara Eden

When science bloggers publish, then blog about it ;-)

On Tuesday night, when I posted my personal picks from this week’s crop of articles published in PLoS ONE, I omitted (due to a technical glitch on the site), to point out that a blog-friend of mine John Logsdon published his first PLoS ONE paper on that day:

It’s a updated and detailed report on the ongoing work in my lab to generate and curate an “inventory” of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life cycle.

Here is the paper (and check John’s post for his experiences publishing in PLoS ONE):
An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis:

Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)–which represent the majority of eukaryotic ‘supergroups’. We surveyed genomes of animals, fungi, plants and protists for meiotic genes, focusing on the evolutionarily divergent parasitic protist Trichomonas vaginalis. We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange. Overall, this expanded inventory of meiotic genes forms a useful “meiosis detection toolkit”. Our analyses indicate that these meiotic genes arose, or were already present, early in eukaryotic evolution; thus, the eukaryotic cenancestor contained most or all components of this set and was likely capable of performing meiotic recombination using near-universal meiotic machinery.

The Genius of Charles Darwin

Not on US television (Channel 4 in the UK only):

Part 1
Part 2
Part 3
Part 4
Part 5
[Via]

Domestication – it’s a matter of time (always is for me, that’s my ‘hammer’ for all nails)

Since this article came out in The American Scientist (the only pop-sci magazine that IMHO has not gone downhill in quality over the past decade) in early 1999 (you can read the entire thing here (pdf)) I have read it many times, I used it in teaching, I discussed it in Journal Clubs, and it is a never-ending fascination for me. Now Andrew and Greg point out there is YouTube video about the fox domestication project:

Back in the 1950s, Dmitri Konstantinovich Belyaev started an experiment in which he selectively bred Silver Foxes, very carefully, ONLY for their tameness (and “tameness” was defined very rigorously in terms of type and speed of response, distance that triggers aggression, etc.).
What happened really fast in this experiment is that many other traits showed up, seemingly out of nowhere, in the subsequent generations. They started having splotched and piebald coloration of their coats, floppy ears, white tips of their tails and paws. Their body proportions changed. They started barking. They improved on their performance in cognitive experiments. They started breeding earlier in spring, and many of them started breeding twice a year.
Most of the people reacting to this experiment invoked pleiotropy, i.e., how changes in one gene affect expression of many other genes. See this NYT article for instance. However, even while I was reading it for the first time, my mind screamed – development! And not just development, but more specifically, heterochrony – change in timing of developmental event.
If you alter the expression of one of the genes that affects developmental timing, you affect all sorts of things.
For instance, when the neural crest cells migrate they become melanocytes in the skin – if due to changes in timing they are late to arrive to some distal parts, e.g., paws and tail-tips, those part will be white. Neural crest cells also migrate to become the adrenal medulla – that little part of the body that releases (nor)epinephrine (adrenaline). If fewer of those cells arrive there on time, less the animal will show stress-response later in life.
There appears to be tight correlation between timers that act on different scales, e.g., developmental and circadian timing, circadian and fast behavioral timing, circadian and seasonal timing, etc.
I always wished I could get a lab, some foxes, an IACUC approval and some money to run these animals through a battery of standard experiments comparing dogs, wild foxes and domesticated foxes on all sorts of parameters of circadian rhythms, photoperiodism (they did change their seasonality patterns of breeding, after all), etc.
The bottom line is that a subtle change in timing of expression of a single developmental gene, something one can select for by choosing one of the traits (in this case a behavioral trait), will affect the change in timing of expression in many other genes. The difference between wild and domesticated foxes may not be in any DNA sequence at all – it could presumably be all epigenetic (see also). Sequence differences would arise later, as the two populations are not inter-mixing any more (for 60 years now).
When you put together development, genetics and evolution, you can see that big changes (or, really, any changes at the very beginning of the evolutionary change) in DNA sequence are not necessary for big changes in entire suites of phenotypic traits. But in the 1950s, the bean-bag deterministic genetics was the norm, so the Belyaev experiment was a big jolt to the scientific community in the West (not so much for the Russian evolutionary biologists, though), so we need to look at this experiment through a decent grasp of history.
Now, I’d like to know what is the state of the experiment today. Ten years ago, the project appeared doomed – they had to sell foxes for fur in order to keep going at a small scale. Has this been fixed? Has anyone from the West help finance the continuation of the project? Has anyone in the West acquired some of the foxes and continued with the project? What are the recent developments?

Good science on the blogs these days!

Broca’s Area, 1865:

This doesn’t sound too out there to us now, but at the time it caused a lot of controversy. The problems wasn’t the localization to the inferior frontal lobe, it was Broca’s claim that it was the LEFT inferior frontal lobe. This didn’t sit well with a lot of scientists at the time. It was pretty accepted that, when you had two sides or halves of an organ, the both acted in the same way. Both kidneys do the same thing, both sides of your lungs, and both of your ovaries or testes. Your legs and arms will do essentially the same thing, though due to handedness (or footedness), you may have more strength or dexterity on one side. Therefore, if the left part of your brain was involved in language, the right must be also.

Operant and classical learning can be differentiated at the genetic level:

Learning about relationships between stimuli (i.e., classical conditioning) and learning about consequences of one’s own behavior (i.e., operant conditioning) constitute the major part of our predictive understanding of the world. Since these forms of learning were recognized as two separate types 80 years ago, a recurrent concern has been the issue of whether one biological process can account for both of them. Today, we know the anatomical structures required for successful learning in several different paradigms, e.g., operant and classical processes can be localized to different brain regions in rodents and an identified neuron in Aplysia shows opposite biophysical changes after operant and classical training, respectively. We also know to some detail the molecular mechanisms underlying some forms of learning and memory consolidation. However, it is not known whether operant and classical learning can be distinguished at the molecular level. Therefore, we investigated whether genetic manipulations could differentiate between operant and classical learning in Drosophila. We found a double dissociation of protein kinase C and adenylyl cyclase on operant and classical learning. Moreover, the two learning systems interacted hierarchically such that classical predictors were learned preferentially over operant predictors.

This food doesn’t taste right … or is it me?:

Flavor is a result of what happens with taste-receptors in the mouth (including but not exclusively those on the tongue) and with olfactory receptors. The 40 or so kinds of taste-receptors interact with the chemicals in what you’re tasting (yes, all your food is made of chemicals!) and create a nerve impulse that sends a signal to the brain. Meanwhile, the 300 or so olfactory receptors send their own smell-signal based on the volatile components of your food. The taste-signal and the smell-signal are correlated in the brain to make the flavor you’re experiencing.

Evolving snake fangs:

I keep saying this to everyone: if you want to understand the origin of novel morphological features in multicellular organisms, you have to look at their development. “Everything is the way it is because of how it got that way,” as D’Arcy Thompson said, so comprehending the ontogeny of form is absolutely critical to understanding what processes were sculpted by evolution. Now here’s a lovely piece of work that uses snake embryology to come to some interesting conclusions about how venomous fangs evolved.

The Evolution of Cats: Sabertooth vs. Regular:

There are two kinds of “true cats”. Cat experts call one type feline or “modern” partly because they are the ones that did not go extinct. If you have a pet cat, it’s a modern/feline cat. This also includes the lions, tigers, leopards, etc. The other kind are called “sabercats” because this group includes the saber tooth. It is generally believed but not at all certain that these two groups of cats are different phylogenetic lineages (but that is an oversimplification).

Male fish deceive watching rivals about their top choice of females:

They say that all’s fair in love and war, and that certainly seems to be the case of Atlantic mollies (Poecilia mexicana). These freshwater fish are small and unassuming, but in their quest to find the best mates, they rely on a Machiavellian misdirection.

CLOACA, the Defecation Device:

This made me wonder – what exactly IS poop? Other than having a vague idea of nutrients, bacteria, and fiber, I had never deeply contemplated it before.

Obligatory Readings of the Day: Darwin and Evolution

Olivia Judson has, so far, posted four parts of her Darwin series. We (“we” meaning “bloggers’ including myself) have already commented on some of these, but here is the entire series (so far, I hope there will be more) for ease of use:
Darwinmania!
An Original Confession
Let’s Get Rid of Darwinism
A Natural Selection

Cool bloggy miscellanea

Scientific Collectivism 1: (Or How I Stopped Worrying and Loved Dissent):

I want to bring up a discussion about what I perceive is a dangerous trend in neuroscience (this may be applicable to other areas of science as well), and that is what I will term “scientific collectivism.” I am going to split this into two separate posts because it is so long. This first post is the weaker arguments, and what I see are the less interesting aspects of scientific collectivism-however, they deserve a discussion.

What will you be? and the related Friday Poll: Tinker, Tailor, Biologist, Researcher. So, how do you call yourself when you are introduced to a stranger?
A little muddled (especially in not making sufficient distinction between peer-reviewed Journals and pop-science magazines), but an interesting look from the outisde in: The High Cost Of Science:

Let’s say, for the sake of argument, that you are interested in science and you want to learn more about it. Maybe you’re tired of creation vs evolution debates and you want to do the research yourself, or maybe you just want to become a more informed citizen. Whatever your reasons, you have a few options but none of them are all that appealing.

Online Alarm Clock which, once set, does not need to be online in order to ring on time. Does it work on an iPhone?
Fair Use Rights:

Intellectual property, copyright, creative commons, copyleft, open access… These are all terms high on the science and other agenda these days. For example, public-funded scientists the world over are calling for research results to be available free to them and their peers for the public good and for the good of scientific advancement itself. Librarians likewise are also interested in the fullest dissemination and sharing of knowledge and information, while user-creators and the new breed of citizen journalists that are the result of the Internet Age are also more liberal in their outlook regarding the proprietary nature of creative works.

Survival of the Abudant: Mutational Networks Constrain Evolution:

What has been found over the last few years is that these neutral mutations occur in networks. That means that there are little fleets of genotypes, all of the same “fitness”, that have overlapping series of neutral mutations. Most of these fleets are small, but a few are larger, and its the larger fleets of genotypes that the researchers in this study focused on. The large networks tend to be adjacent to a pretty large number of phenotypes. So you have all these little neutral mutations, next to RNA with a wide variety of phenotypes. Do these little neutral mutations influence evolution after all?

The Kudlow Year:

We’ve had a terrible year. Obvious problems remain, along with whatever else lurks beneath the waterline. Wall Street showed some optimism about the future yesterday, but we’ve still got a long way to go. A lot of this boils down to arithmetic. Pay more attention to the numbers and less to ideologues on teevee or the web who try to tell you different.

Scribd and Lulu partner:

Print-on-demand publisher Lulu (which offers an OA option for content providers) and document sharing site Scribd are partnering, according to ReadWriteWeb. Lulu will begin making some of their OA content available in Scribd’s iPaper format (a “sort of a YouTube for PDFs”), including utilizing iPaper’s ability to embed AdSense ads within the documents.

Rational Voters?

The underlying assumption, of course, is that issues matter, that voters are fundamentally rational agents who vote for candidates based on a coherent set of principles. In other words, they assume that my political preferences reflect some mixture of ideology and selfish calculation. I’ll vote for the guy who best matches my geopolitics and tax bracket.
The problem, as political scientist Larry Bartels notes, is that people aren’t rational: we’re rationalizers. Our brain prefers a certain candidate or party for a really complicated set of subterranean reasons and then, after the preference has been unconsciously established, we invent rational sounding reasons to justify our preferences. This is why the average voter is such a partisan hack and rarely bothers to revise their political preferences.

I Like My Facts Well Done and Humorless. The funny take on Sizzle.
PhysioProf rants and raves on Feministe for a couple of weeks or so. Check the tribal wars in the comments!
A pierced scientist? AKA, I need a mentor:

It occured to me yesterday that I have a lot of questions to ask and nobody to go to for answers. I really need a mentor of some kind. I mean, I have an academic advisor, but he’s an old white man who doesn’t make any attempt to engage me in conversation. He’s very standoffish and business-oriented whenever I meet with him, which I think has been once a year for the last three years. I doubt he knows my name. And I have Dr. Calhoun, my research advisor, who I’m starting to warm up to a little bit but I’m not really at the point where I can ask him the kinds of personal questions that are the most burning. I doubt I’ll ever be able to not be intimidated by him, especially since I found out he’s the chair of the graduate admissions committee.

Evolution: Education and Outreach

The third issue of the Open Access journal ‘Evolution: Education and Outreach’ has been published, and it is again full of good, thought-provoking articles. You can see them (for free, of course) if you click here.

Darwinist

Olivia Judson is absolutely right – let’s get rid of the terms “Darwinist” and “Darwinism”. She writes, among else:

I’d like to abolish the insidious terms Darwinism, Darwinist and Darwinian. They suggest a false narrowness to the field of modern evolutionary biology, as though it was the brainchild of a single person 150 years ago, rather than a vast, complex and evolving subject to which many other great figures have contributed. (The science would be in a sorry state if one man 150 years ago had, in fact, discovered everything there was to say.) Obsessively focusing on Darwin, perpetually asking whether he was right about this or that, implies that the discovery of something he didn’t think of or know about somehow undermines or threatens the whole enterprise of evolutionary biology today.

I am glad to see that John Wilkins, Jonah Lehrer and Brian Switek also agree with this, though each one cites a somewhat different reason for it. Many of those reasons have been put together into a table form (with deep explanations) by Wilkins before – a good reference for the future, something to bookmark.
Brian Switek says, and I agree that at least for us in the USA, this is the most pressing reason to abandon the terms:

I’ve never liked the term “Darwinism.” To me it has always been more of a watchword that might indicate that I was talking to a creationist, a term I generally do not encounter unless I’m reading or hearing an argument against a straw-man version of evolution. (I’m not a big fan of “evolutionist,” either.) It may have been useful in the past, when evolution by natural selection (as popularized by Darwin) was competing with other systems like Neo-Lamarckism and orthogenesis, but today it doesn’t have any relevance. (It should also be noted that A.R. Wallace wrote a book on natural selection called Darwinism. Despite his own work on the same subject he calls evolution by natural selection “Darwin’s theory.”) If anything it continues the myth that Darwin is the be-all and end-all of evolutionary science, and while he certainly deserves a lot of credit On the Origin of Species is not some kind of secular Bible where every word is dogma.

According to Blake Stacey (and I have heard this before), the terms is used much more widely in the UK, including, until recently, by Dawkins who should have known better about the power of words:

I’ve written before about the different ways people define the word Darwinism and its close relatives. The short version is that American biologists and other academics don’t seem too likely to use the word: they just like to say “evolutionary biology” and be done with it. In the U. S. and A., hearing the word “Darwinism” is a pretty sure sign you’re dealing with a creationist, or at least a person whose knowledge of science derives too much from creationist misinformation. Over in Britain, serious academics still use the word, as do people who appear fairly pro-science (maybe there’s some kind of national pride thing going on?). One can still see negative uses of the D-word over in the UK, of course, particularly from people who confuse “social Darwinism” with actual biology or radically misinterpret kin selection and the “selfish gene” idea, but sorting out all their problems would require a book of its own.

Perhaps, I thought, this is because Darwin was British, so there may be an element of national pride involved. But then, smalled nations with even bigger reasons to push national pride, would have gone further than this, yet I have never heard a Serb proclaim to be a “Teslaist” or “Milankovichist”.
I have ranted about this before (e.g., here, here and here). For instance, here I wrote:

Bashing evolution is an example of phatic language. Words like “Darwinist” and “evolutionist” that are never used by actual evolutionary biologists serve as code-words for belonging to the Creationist Village, just like saying “Democrat party” instead of “Democratic party” immediatelly signals one’s political party affiliation (GOP). These two words, ending with “-ist” also serve to provide equivalency between creationist belief and evolutionary methodology, infering that evolutionary theory is a religious belief instead of a method for understanding the material world. If the two are seen as two opposed religions, they can have a war on equal footing in which “my religion is better than yours” contest can take place and Christians, due to sheer numbers and the tight community spirit are confident in victory. This kind of rhetoric also allows the creationists to show up on TV as equals to evolutionary biologists, as the naive media misreads phatic language as logical language and, following the American fairness sentiment, indulges in destructive “He said/She said” pseudo-journalism.

And here I wrote:

I am not an “evolutionist”. I am not a “Darwinist”. I am a biologist. Thus, by definition, I am an evolutionary biologist. Although my research is in physiology and behavior, I would never be able to make any sense of my data (or even know what questions to ask in the first place) without evolutionary thinking.
As I am also interested in history and philosophy of biology, I consider myself a Darwinian. But not a “Darwinist” or “evolutionist” – those two words are Creationists’ constructs. They arise from the basic misunderstanding of evolution. Being religious believers they cannot fathom that people can operate outside of the realm of belief, thus they assume that evolution is a belief, akin to and in competition with their belief.
I do not believe in evolution. It is not something you believe in or not: it is something you understand or not. I judge the evidence. If I think it is fishy I will delay my judgement until more data comes in. If the evidence looks good, I will tentatively and temporarily accept it as correct until more data come in. Evolutionary biology is sitting on such large mountains of strong evidence collected over the past 150 years that it appears impossible that over the next 150 years we will be able to collect an equivalent amount of data challenging it in order to question the validity of evolutionary theory. It is one of the strongest supported theory in all of science. For all practical purposes, evolution (as in “common descent”) is a fact, an d natural selection is the strongest of several mechanisms by which evolution operates. There is nothing controversial about this.
——-snip—————
Those two terms (“evolutionist” and “Darwinist”) have lately also been used on purpose, as code-words for their own audience. They understand that using these terms implies (and turns on a frame of mind in the listeners) that evolution is a religious belief. It is similar to the way I think of myself as a member of the Democratic Party, but Republicans prefer to use the Luntzism “Democrat Party”. It’s all about framing the debate.

Note a little difference between me and Olivia here. I want to preserve one of the three words – Darwinian, but only in the sense of “Darwinian Scholarship”, i.e., the historical and philosophical study of the history of evolutionary thought, rightfully centered around Darwin, and including the world he lived in – the Victorian England. Darwin is a gold mine for scholars. He was a little, let’s say, anal-retentive, so he preserved all of his correspondence, his papers, books, notebooks and diaries. Hundreds of biographies of Darwin have been published, in addition to book about Darwin, about the history of evolutionary thought, biographies of other players (e.g., Huxley, Wallace, Lamarck). I doubt that there is any other aspect of history that is known and studied more than British aristocracy of teh 19th century, so the context for Darwin’s life and work is well understood. The Darwinian Industry has enough material to keep thriving for decades to come.
However, another important reason is the one that Jonah Lehrer empasizes:

My problem with “Darwinism,” then, is the exact opposite of Judson’s. She dislikes “Darwinism” because she thinks the noun is applied too broadly, so that Darwin gets implicit credit for things like population genetics. But I think that “Darwinism” misleads because it causes people to underestimate Darwin’s real achievement, which is far grander than merely getting people to believe that species change. If “Darwinism” should be a synonym for anything it should be the ideology of unrepentant materialism, which is the underlying philosophy of modern science.

I completely agree. Actually, in a very old post I wrote something similar:

What we, who consider ourselves rational are, is not Aristotelian, but Darwinian. What????!!!!! Forget Darwin’s contribution to biology, or the misuse of his name by eugenicists and social-Darwinists of all kinds. The greatest contribution of Darwin is the way we in the Western world THINK! We require data! Give me information! Empirical proof! Statistics! At least give me polls! Before Darwin, people thought their great ideas in the seclusion of their homes and published books. It was my word against your word. Many philosophers became famous this way. Descartes and others started, earlier on, asking for empirical proofs but nobody provided them. Darwin did – he showed how philosophy is done! There were evolutionary theories before him, written by Erasmus Darwin, Lamarck, Chambers and others that were laughed out of court. Everyone took “The Origin” seriously because it provided a consilient set of proofs: not just internal logic of the argument (many earlier philosophies had that) but a link to the reality of the world. That was the Day One of the Age of Rationality. If asked who my favourite philosopher was, I would have said Darwin and lost the Presidency that very moment! But it is true. The Western world lives in a Darwinian worldview – the worldview of empiricism.

Origin of Life

Nick Matzke wrote an excellent update on what we know about the Origin of Life:

Here is a short list of things we have discovered or confirmed in the last 50 years or so pertaining to the origin of life. In my opinion all of these points have reached high enough confidence that they are unlikely to change much with future discoveries, and our confidence in them does not depend in uncertainties in the remaining unanswered questions.

I agree with him that, in confrontations with Creationists, we should not secede the origin of life to then (i.e.., “evolution only covers what happens once Life already exists). When I teach BIO101, I always cover the current ideas about the Origin of Life, and Nick’s post will be helpful for me next time to get my lecture up to date (and perhaps give it as “supplemental reading” to the students).

Chatting about Epigenetics

Abbie and PZ chat about the recent discoveries in biology, how exciting those discoveries are, and how annoying it is when Creationists try to put a damper on such excitement:

A flounder with a half-moved eye

What a delightfully obvious and visually compelling example of a transitional fossil! A flatfish in which the eye migrates from one side to another, but not quite as much as in the modern flounder. Carl Zimmer and Ed Yong have the details and explanation.

Happy 150th Birthday to the Principle of Natural Selection!

On this day 150 years ago essays by Alfred Russel Wallace and Charles R. Darwin were read at the meeting of the Linnean Society in London. This was the first time in history that the idea of natural selection was presented to the world.
George Beccaloni and Wesley R. Elsberry wrote excellent pieces commemorating the anniversary.

Darwin Ceiling at the Museum

Anne-Marie found this article:

London’s Natural History Museum is to decorate the ceiling of one of its major rooms with a permanent art installation, inspired by evolutionary theory, in honour of Charles Darwin’s bicentennial. The 10 shortlisted entrants have now been announced and their ideas are on display.

You can see a slideshow of the proposals, but the article does not say exactly who is doing the choosing. Some internal committee, public at large?
Which proposal do you like the best? Perhaps we can influence the choosers if we write about this all over the blogs.

Evolutionary Medicine

Bjoern Brembs alerts me to a cool new paper (OA so you can read the whole thing) – The great opportunity: Evolutionary applications to medicine and public health by Randolph M. Nesse and Stephen C. Stearns:

Evolutionary biology is an essential basic science for medicine, but few doctors and medical researchers are familiar with its most relevant principles. Most medical schools have geneticists who understand evolution, but few have even one evolutionary biologist to suggest other possible applications. The canyon between evolutionary biology and medicine is wide. The question is whether they offer each other enough to make bridge building worthwhile. What benefits could be expected if evolution were brought fully to bear on the problems of medicine? How would studying medical problems advance evolutionary research? Do doctors need to learn evolution, or is it valuable mainly for researchers? What practical steps will promote the application of evolutionary biology in the areas of medicine where it offers the most? To address these questions, we review current and potential applications of evolutionary biology to medicine and public health. Some evolutionary technologies, such as population genetics, serial transfer production of live vaccines, and phylogenetic analysis, have been widely applied. Other areas, such as infectious disease and aging research, illustrate the dramatic recent progress made possible by evolutionary insights. In still other areas, such as epidemiology, psychiatry, and understanding the regulation of bodily defenses, applying evolutionary principles remains an open opportunity. In addition to the utility of specific applications, an evolutionary perspective fundamentally challenges the prevalent but fundamentally incorrect metaphor of the body as a machine designed by an engineer. Bodies are vulnerable to disease – and remarkably resilient – precisely because they are not machines built from a plan. They are, instead, bundles of compromises shaped by natural selection in small increments to maximize reproduction, not health. Understanding the body as a product of natural selection, not design, offers new research questions and a framework for making medical education more coherent. We conclude with recommendations for actions that would better connect evolutionary biology and medicine in ways that will benefit public health. It is our hope that faculty and students will send this article to their undergraduate and medical school Deans, and that this will initiate discussions about the gap, the great opportunity, and action plans to bring the full power of evolutionary biology to bear on human health problems.

Taz – in the mouse!

funny pictures

PLoS ONE just published a very exciting paper – a regulatory sequence from the genome of a preserved Tasmanian wolf was inserted into a mouse and shown to have the same function:
Resurrection of DNA Function In Vivo from an Extinct Genome:

There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

The Open Sleep Journal and The Phylogeny of Sleep Database

One of the latest additions (just two days ago, I think) to the Directory of Open Access Journals is a journal that will be of interest to some of my readers – The Open Sleep Journal. The first volume has been published and contains several interesting articles. One that drew my attention is The Phylogeny of Sleep Database: A New Resource for Sleep Scientists (PDF download) by Patrick McNamara, Isabella Capellini, Erica Harris, Charles L. Nunn, Robert A. Barton and Brian Preston. It describes how they built a database that contains information about sleep patterns in 127 mammalian species. The Database itself can be found here and one can search it by species, by what was measured, by physiological or environmental conditions in which sleep was measured, etc. It has links to research on everything from platypus and echidna, through humans and kangaroos, to elephants, giraffes and sloths.
Since one of the stated projects that will come out of the database is a publication of a book on the Evolution of Sleep, I looked around to see if they are interested in anything else apart from mammals. Looking at the Projects page, I see they intend to add birds to the database later on. But that is not enough. Sleep did not suddenly appear full-blown in mammals and separately in birds. There is a long history of sleep research in reptiles, amphibians and fish, as well as – more recently – in insects like cockroaches, honeybees and Drosophila. In order to study the origin, evolution and adaptive function of sleep we have to look at its precursors among the invertebrates, not just focus on mammals and birds.

Friday Weird Sex Blogging – Corkscrewing

Friday Weird Sex Blogging - CorkscrewingYou really think I am going to put this above the fold? No way – you have to click (First posted on July 7, 2006):

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Hot Peppers – Why Are They Hot?

TITLE(First posted on July 21, 2006) Some plants do not want to get eaten. They may grow in places difficult to approach, they may look unappetizing, or they may evolve vile smells. Some have a fuzzy, hairy or sticky surface, others evolve thorns. Animals need to eat those plants to survive and plants need not be eaten by animals to survive, so a co-evolutionary arms-race leads to ever more bizzare adaptations by plants to deter the animals and ever more ingenious adaptations by animals to get around the deterrents.
One of the most efficient ways for a plant to deter a herbivore is to divert one of its existing biochemical pathways to synthetise a novel chemical – something that will give the plant bad taste, induce vomiting or even pain or may be toxic enough to kill the animal.

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Jablonka & Lamb

Anne-Marie wrote an excellent review of Evolution in Four Dimensions by Eva Jablonka and Marion Lamb.
I tend to think that the use of the term “neo-Lamarckism” (just like the use of “neo-Darwinism“) is unnecessary as it will raise hackles and start linguistic battles instead of invite people to investigate new ways of thinking and new additions to the body of evolutionary theory.
Yes, we now understand that genes are necessary, but not sufficient, for heritability and we are increasingly including development in our accounts of evolution. And as much as I like the Developmental systems theory (DST), I don’t think it needs a new name – it is just an addition to our thinking about biology, a newish and promising angle to use when looking at Life.

Patricia Brennan on bird genitalia

News from SCONC:

On Thursday, March 27 at 4 p.m., the Zoology Department at NCSU will host a seminar from Patricia Brennan of Yale University entitled “The Biology of Avian Genitalia: Form and Function.” Brennan’s work on the genital anatomy of waterfowl has revealed the existence of a “sexual arms race” between males and females. Unlike 97 percent of bird species, male waterfowl have a phallus, and it can range “from a half-inch to more than 15 inches long.” The seminar will be held in 101 David Clark Labs. Refreshments will be served in the lobby at 3:45.

Related:
Friday Weird Sex Blogging – The Birds Do It….
More on duck phalluses and uteri

Evolution: Education and Outreach

The second issue is now available online. Open Access. Most articles are highly ‘bloggable’.

Olduvai George on NPR

I was lucky to be in the car at the right time this morning to catch a story about Mastodons in Manhattan: A Botanical Puzzle, i.e., why honey locust trees in NYCity have long thorns – an interesting story (click on the link and click on “Listen Now”) which, among others, features our blog-friend Carl Buell.

Good news

The Florida Board of Education passed new science standards.

DNA barcoding

I tried to understand what DNA barcoding is, as everyone is talking about it. And I tried reading a couple of papers about it – I am a biologist, so I should have understood them, but nope, I was still in the dark.
So, what does one do? Waits for a science blogger to explain it. And so it happens, Karen explained it yesterday. I read it. Slowly and carefully. Only once. And I grokked it all!

Tiktaalik on audio

Karl Mogel interviews Neil Shubin. Paleontology makes testable predictions, with cool results.

Darwin Day in the Guardian

Karen is excited this morning, reading the enormous Guardian edition full of good Darwiny goodness, chockful of articles by Dawkins and many others, as well as extracts from Darwin’s works.
The only part I find a little too narrow is The best Darwinian sites on the web which mentions only a small handfull of such sites, e.g., Darwin Online, Darwin Correspondence Project, Darwin Day Celebration, AboutDarwin.com and Darwin Today (the last one yet to launch next month). I know, I know, these are the biggest and bestest, but there are so many others that I feel are snubbed by being left out – they should at least have been linked from a sidebar or a box. How about Talk Origins, Panda’s Thumb, The Dispersal of Darwin, The Beagle Project and The Beagle Project Blog, The Friends of Charles Darwin, or hundreds of other links you can find, for instance, here?

2008 Darwin Day Symposium ‘Origins and Evolution of Early Life’

If you liked Sigma Xi last weekend, and if you are in the Triangle on February 8th, and if you are interested in the origin and early evolution of life on Earth (and potentially elsewhere), you will love attending the NESCent symposium on the topic:

The National Evolutionary Synthesis Center invites you to the 2nd annual Darwin Day Symposium. Carol Cleland, Mark Bedau, Janet Siefert, Abigail Allwood, Andrew Roger and Laura Landweber will be talking about their research in early life, generating life and astrobiology. This day-long program is open to the public and will be held at the Sigma Xi Headquarters in Research Triangle. Space is limited so register early! (There is no charge for registration.) For more information, visit the web site at:http://www.nescent.org/news/DarwinDay2008.php.

The Hopeless Monster? Not so fast!

Olivia Judson wrote a blog post on her NYTimes blog that has many people rattled. Why? Because she used the term “Hopeful Monster” and this term makes many biologists go berserk, foaming at the mouth. And they will not, with their eye-sight fogged by rage, notice her disclaimer:

Note, however, that few modern biologists use the term. Instead, most people speak of large morphological changes due to mutations acting on single genes that influence embryonic development.

So, was Olivia Judson right or wrong in her article? Both. Essentially she is correct, but she picked some bad examples, overgeneralized a bit, over-reached a little and she used the dreaded term that was bound to shut down all rational processes occurring in some biologists’ brains. Remember that she wrote to general audience. If she took time and space to explain all the nuances and details she would have lost her audience somewhere in the middle of the second paragraph. I think that her post explains the topic just fine for the intended audience, pointing out that not all evolutionary changes take millions of years of imperceptible change – some do, indeed, happen relatively abruptly (yet it can be explained completely mechanistically, not giving Cdesign Proponentsists any hope). Not every day, but they do.
So, who jumps first into the fray with an angry rebuttal – one of the Usual Suspects: Jerry Coyne in a guest-post on The Loom:

Unfortunately, her piece is inaccurate and irresponsible, especially for a journalist with a strong science background (Judson has a doctorate from Oxford). I’ve admired Judson’s columns and her whimsical and informative book Dr. Tatiana’s Sex Advice to All Creation. But this latest posting is simply silly. As an evolutionary biologist, I’m used to seeing our field twisted out of shape to satisfy the demands of journalists who love sensational new findings–especially if they go against long-held Darwinian beliefs like the primacy of gradual, stepwise evolution. But I’m not used to seeing one of my own colleagues whip up excitement about evolutionary biology by distorting its findings.

Unfortunately, in bashing Judson along with making legitimate points (how many people will ignore this caveat in their responses?), Coyne ends up being more wrong than she is. And his intended audience is, arguably, better scientifically educated than hers – it’s the Scienceblogs.com readers, not NYTimes. While bashing her head into a rock, Jerry makes visible his emotional enmity towards everybody who has a bigger picture of evolution than he has and has at their disposal both a methodological and a conceptual toolkit that Jerry lacks.
Before you jump on me, read the historical reviews of the concept of the Hopeful Monster by Brian and John. Then, read Greg and Razib who are far too lenient on Coyne but add good points of their own. Finally, read PZ Myers and especially Larry Moran for a clear explanation of the entire set of issues – the history, sources of current emotional disputes, and the current science. Reading all of these is essential to understanding the claims in this post as I do not have space/time to repeat all of their claims at length – so click on the links and read first before commenting.
In a back-and-forth with a commenter, Coyne defends himself that he is talking about the changes in genes, not evolution. This just shows his bias – he truly believes that evolution – all of it – can be explained entirely by genetics, particularly population genetics. His preferred definition of evolution is probably the genocentric nonsense like “evolution is a change of gene frequencies in a population over time”. I prefer to think of it as “evolution is change in development due to ecology” (a softening of Van Valen’s overly-strong definition “evolution is control of development by ecology”). Population genetics is based on the Hardy-Weinberg equilibrium – pretty much all of it is a build-on and embellishment of it. Population geneticists tend to forget, once they get into complex derivations of HW, that HW has about a dozen completely unrealistic assumptions underlying it. Now, in a case-to-case basis, some of those assumptions can be safely ignored, some can be mathematically taken care of, but some are outside of the scope of mathematics (or at least the kind of math that can be integrated into the development of HW). Those are ignored or dismissed and, if this is pointed out by those working on evolution from a Bigger Picture perspective, met with anger.
When Goldshmidt’s book The Material Basis of Evolution was reissued, Stephen Jay Gould wrote a lengthy Introduction. About a dozen years ago I checked the book out of the library and skimmed the book itself. I read Gould’s intro very carefully (I wonder if it is available somewhere online for free? Update: Gould’s introduction is available online here, hat-tip to Michael Barton.). It is also worthwhile to read Gould’s 1980 essay The Return of Hopeful Monsters keeping in mind that evo-devo was barely beginning at the time (yes, it is 28 years old, so do not judge it by current knowledge – put a historian’s cap on when reading it).
In his Big Book, Gould wrote:

“By proposing a comprehensive formalist theory in the heyday of developing Darwinian orthodoxy, Richard Goldschmidt became the whipping boy of the Modern Synthesis–and for entirely understandable reasons. Goldschmidt showed his grasp, and his keen ability to utilize, microevolutionary theory by supporting this approach and philosophy in his work on variation and intraspecific evolution within the gypsy moth, Lymantria dispar. But he then expressed his apostasy by advocating discontinuity of causality, and proposing a largely nonselectionist and formalist account for macroevolution from the origin of species to higher levels of phyletic pattern. Goldschmidt integrated both themes of saltation (in his concept of “systemic mutation” based on his increasingly lonely, and ultimately indefensible, battle to deny the corpuscular gene) and channeling (in his more famous, if ridiculed, idea of “hopeful monsters,” or macromutants channeled along viable lines set by internal pathways of ontogeny, sexual differences, etc.). The developmental theme of the “hopeful monster” (despite its inappropriate name, virtually guaranteed to inspire ridicule and opposition), based on the important concept of “rate genes,” came first in Goldschmidt’s thought, and always occupied more of his attention and research. Unfortunately, he bound this interesting challenge from development, a partially valid concept that could have been incorporated into a Darwinian framework as an auxiliary hypothesis (and now has been accepted, to a large extent, if under different names), to his truly oppositional and ultimately incorrect theory of systemic mutation, therefore winning anathema for his entire system. Goldschmidt may have acted as the architect of his own undoing, but much of his work should evoke sympathetic attention today.”

So, Coyne’s Gould-bashing, as Larry Moran demonstrated, is just petty and baseless sniping by one scientist of limited scope at another who actually “got it”.
I thought the discussion so far has been far too tame. So, here is the red meat! I want to see a real fight – a blogospheric war that brings in some serious traffic, OK?

New Journal Club on PLoS ONE – Chimps exchange fruit for sex

A paper published back in September – Chimpanzees Share Forbidden Fruit by Hockings et al. is getting renewed attention these days.
Rebecca Walton has compiled links to the recent media and blog coverage of the paper (including those by my SciBlings Afarensis, Greg Laden and Brian Switek), the peer-reviewer’s comments have been added to the paper, and The Animal Cognition Research Group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany has posted a series of comment as part of a Journal Club on this paper.
Now, all you need to do is join in the conversation – log in (or register if you have not done it already) and add your thoughts about chimps sharing forbidden fruit to the comments, ratings and annotations on this paper. If you decide to write a blog post, please send a trackback or, if that fails, leave us the link to your post in the comments on Rebecca’s blog post.

Grapevine Genomes

Two grape genomes were published this year, one in Nature, the other in PLoS ONE. Larry Moran explains the methodologies and results of both and discusses the trustworthiness of each. The Nature paper is explained in The Grapevine Genome, and the PLoS ONE paper is discussed in The Second Grapevine Genome Is Published. Obligatory Readings of the Day.