Monday, April 30, 2012

Mouse to elephant

I was wrong, you CAN go from mouse size to elephant size. The catch is that it will take 24 million generations! A curious fact is that the reverse, elephant sized to mouse sized, only takes 100,000 generations.

Research published in the Proceedings of the National Academy of Sciences (The maximum rate of mammal evolution) describes increases and decreases in mammal size following the extinction of the dinosaurs 65 million years ago.
The asymmetry between rates can potentially be explained by distinct but not necessarily mutually exclusive mechanisms. One possibility is that there are fewer physical, biological, and environmental constraints to decreasing as opposed to increasing size. Pedomorphic processes are good candidates as mechanisms of size reduction, because all animals must pass through a smaller size during their ontogeny. We hypothesize it is easier to halt the developmental program and reproduce early than to grow larger and delay maturity. Another possibility is that selection favors size decreases because smaller animals have higher rates of reproduction with life histories characterized by rapid maturity, high birth rates, and short lifespans. Finally, decreases in size may reflect adaptation to a more generalized ecological niche, whereas increases in size require novel adaptations to obtain more food and space to fuel higher whole-organism metabolic rates.

Sunday, April 29, 2012

Fasting for Lent forces hyenas to change diet

In Ethiopia, members of the Orthodox Tewahedo Church stop eating meat and dairy products during a 55-day fast before Easter. As a result, spotted hyenas too change their eating habits – from scavenging waste from butchers and households to hunting – new research in the British Ecological Society's Journal of Animal Ecology has found.

The results showed that when humans stop buying, eating and discarding animal products the hyenas' eating habits change significantly: before Lent, 14.8% of hyena droppings contained donkey hairs, during Lent this increased to 33.1%, falling again to 22.2% once the fast was over.
According to Yirga: “Our study shows a remarkable change in the hyenas' diet – we found that hyenas around Mekelle mainly scavenge waste from butchers and households but during fasting donkeys provided an alternative food source.”

Gidey Yirga et al (2012).'Adaptability of large carnivores to changing anthropogenic food sources: diet change of spotted hyena (Crocuta crocuta) during Christian fasting period in northern Ethiopia', Journal of Animal Ecology, April 2012.

Saturday, April 28, 2012

Norwegian sludge

Sometimes the oddest corners of biology research can suddenly hit the headlines (okay, the science headlines).

Mankind's remotest relative is a very rare micro-organism from south-Norway. The discovery may provide an insight into what life looked like on earth almost one thousand million years ago. 

 or, as ScienceDaily put itRare Protozoan from Sludge in Norwegian Lake Does Not Fit On Main Branches of Tree of Life

Friday, April 27, 2012

Human physiology in action

9am tomorrow (Saturday 28th). Details here.

Thursday, April 26, 2012

What's inside an elephant?

Thanks to a link on BoingBoing I just discovered John Hutchinson's blog, rather accurately titled 'What's in John's Freezer' since it is 'about celebrating the joy and wonder of organismal morphology, which researchers’ freezers help preserve.'

There's also a fair bit of morphology and physiology and lots of revealing (pun intended) photographs such as this X-ray of an elephant's foot - revealing a surprisingly human bone structure.

But for the real fun it gets a little gory. What is inside an elephant? Guts, lots of guts. No seriously, more guts than you are imagining.

Wednesday, April 25, 2012

Late heavy bombardment update

New research reveals that the Archean era -- a formative time for early life from 3.8 billion years ago to 2.5 billion years ago -- experienced far more major asteroid impacts than had been previously thought, with a few impacts perhaps even rivaling those that produced the largest craters on the Moon, according to a paper recently published online in Nature.

They found that approximately 70 (and 4) dinosaur killer-sized or larger impacts hit the Earth (and Moon) over a span that lasted between 3.8 and 1.8 billion years ago.

The implication of such enormous impacts over the Archean era is unknown, but some are believed to have released nearly 500 times the blast energy of the Chicxulub impact. (aka the one that wiped out the dinosaurs)

"It will be interesting to see whether these mammoth events affected the evolution of early life on our planet or our biosphere in important ways," says Bottke. 

Quotes are from the ScienceDaily report and the original paper is here:
An Archaean heavy bombardment from a destabilized extension of the asteroid belt. Nature, 2012

Tuesday, April 24, 2012


If you like your computing old school style then you may recognize this picture as the world's first computer - designed by Charles Babbage in the early 1820's. Well over a century ahead of his time.

Although he never completed the full machine in his lifetime he did produce prototypes, full plans and many of the parts. His first machine had 25,000 parts and weighed 15 tons. This, his second, the famous "Difference Engine No. 2" is 11 feet long with 8,000 parts and weighs only 5 tons. It was finally constructed according to his plans in 1991.

I've been reading about Babbage recently in James Gleick's new(ish) book - The information: a history, a theory, a flood - and there are a couple of gems I thought I'd share.

Babbage briefly became an actuary working for the new Protector Life Assurance Company where his job was to compute the statistical tables laying out life expectancies - the 'Life Tables.'

One of the problems of being somewhat ahead of your time is that you are somewhat ahead of any audience. Babbage received this rejection letter from The Edinburgh Journal of Science in 1821. Notice that it not only rejects Babbage's ideas for a series of paper but seems to preemptively reject ANY paper by him. But they put it so nicely...

It is with no inconsiderable degree of reluctance that I decline the offer of any Paper from you. I think, however, you will under reconsideration of the subject be of the opinion that I have no other alternative. The subjects you propose for a series of Mathematical and Metaphysical Essays are so very profound, that there is perhaps not a single subscriber to our Journal who could follow them.

And finally, Babbage would, I think have loved population biology and the mathematical description of populations. Here's part of a letter said to have been written to Tennyson by Babbage after reading his poem 'The Vision of Sin' 

Every moment dies a man,
Every moment one is born.

"If this were true, the population of the world would be at a standstill. In truth, the rate of birth is slightly in excess of that of death. I would suggest that the next version of your poem should read:

Every moment dies a man,
Every moment 1 and 1/16th is born
Strictly speaking, the actual figure is so long I cannot get it into a line, but I believe the figure 1 1/16th will be sufficiently accurate for poetry."

This may be apocryphal though since another version of the letter has the same idea but rather different text:

"I need hardly point out to you that this calculation would tend to
keep the sum total of the world's population in a state of perpetual
equipoise, whereas it is a well-known fact that the said
sum total is constantly on the increase. I would therefore take the
liberty of suggesting that, in the next edition of your excellent
poem, the erroneous calculation to which I refer should be corrected
as follows:--

Every moment dies a man,

And one and a sixteenth is born.

I may add that the exact figures are 1.167, but something must, of
course, be conceded to the laws of metre."

Monday, April 23, 2012

Robert Trivers

I posted this to Gauchospace for Kathy's new seminar class but I just realized we don't have much (any?) overlap between the two classes and it is relevant here too.

The paper this week for that class was a classic by Robert Trivers on parental choice of sex ratio in offspring. This is a topic that I mentioned very briefly last quarter, at least for halpodiploidy, and we will retrun to briefly in our animal behavior lecture.

In doing some background reading on Robert Trivers I came across an interesting quote about him from an article in the Guardian newspaper:

"Robert Trivers could have been one of the great romantic heroes of 20th-century science if he'd died in the '70s, as some people supposed he would."

It made me realize just what an extraordinary flourishing of creative, and often very novel, thinking he had over a period of a few years with seminal papers virtually every year of the first half of the seventies (1971 - Reciprocal Altruism, 1972 - Parental Investment and sexual selection, 1973 - sex ratio of offspring, 1974 - Parent offspring conflict, 1976 - Haplodipoidy and social insects). In many ways this is the sort of creativity associated with mathematicians who often do all their important and novel work early in their career.

Here's a section from a Boston globe article on Trivers in 2005:

Rebuffed in his demand for early tenure, he left Harvard in 1978 to teach at the University of California, Santa Cruz. He befriended Huey Newton and joined the Black Panthers. He all but stopped publishing. As the literary agent John Brockman put it when introducing Trivers at a recent talk, ''Over the years there were rumors about a series of breakdowns; he was in Jamaica; in jail. He fell off the map.''
His ideas, however, seemed to do just fine without him. In the 1970s, Trivers published five immensely influential papers that braided genetics into behavioral biology, using a gene's-eye view of evolution to explain behaviors from bird warning calls to cuckoldry to sibling rivalry to revenge. According to David Haig, a Harvard professor of biology and a leading genetic theorist, each paper virtually founded a research field. ''Most of my career has been based on exploring the implications of one of them,'' says Haig. ''I don't know of any comparable set of papers.''

In 1976 Trivers wrote the introduction to Richard Dawkins "Selfish Gene' and tossed out this gem:

'(I)f, (as Dawkins argues) deceit is fundamental to animal communication, then there must be strong selection to spot deception and this ought, in turn, to select for a degree of self-deception, rendering some facts and motives unconscious so as not to betray - by the subtle signs of self-knowledge - the deception being practised. Thus, the conventional view that natural selection favors nervous systems which produce ever more accurate images of the world must be a very naive view of mental evolution.'

Here he is at a TEDx conference in Jamaica expounding on the self-deception idea 35 years later.

Sunday, April 22, 2012

New skin for the old ceremony

Green Anole lizard shedding its old skin, Photograph by Michael Walker, Photo of the day at National Geographic for April 7t.

Saturday, April 21, 2012

Mangy wolves

Well we did mention the Yellowstone wolves in the last lecture, and we did mention high technique techniques becoming available in ecology so I think this is nicely relevant.

Scientists in Yellowstone are using thermal imaging cameras to evaluate the condition of the wolves.

“Thermal imagery of wolves allows us to not only document the extent of hair loss caused by mange, but also to determine the actual loss of heat, and energy, associated with the different stages of infection. A great side benefit is that this is a noninvasive way to study the disease and its effects. We don’t have to capture wild wolves to do this.”

The only downside is that the thermal imaging cameras are still pretty expensive and bears have a tendency to trash them...

Friday, April 20, 2012


It's a repeat but some of you sounded interested in this experiment so I thought I'd put the links up again.
The classic whole lake experiments Claudia referred to were published in Science as Eutrophication and Recovery in Experimental Lakes: Implications for Lake Management. The lead author, David Schindler, was elected to the National Academy of Sciences in 2006 and they have a nice profile of him that explains some of the background to the experiments and their impact.

Aerial photographs captured the dramatic results: the phosphorous-treated half of the lake had become green and murky because of algal blooms, whereas the other half of the lake remained clear. Pictures can speak a thousand words, and the stark contrast of the two sides of Lake 226 caught the public's eye and policymakers' collective ear.

Thursday, April 19, 2012


Re-wilding North America: Nature 436, 913-914 (18 August 2005) North America lost most of its large vertebrate species — its megafauna — some 13,000 years ago at the end of the Pleistocene. And now Africa's large mammals are dying, stranded on a continent where wars are waging over scarce resources. However much we would wish otherwise, humans will continue to cause extinctions, change ecosystems and alter the course of evolution. Here, we outline a bold plan for preserving some of our global megafaunal heritage — one that aims to restore some of the evolutionary and ecological potential that was lost 13,000 years ago, and which offers an alternative vision for twenty-first century conservation biology.
Definitely one of the more controversial Nature papers of recent years. Just Google Pleistocene rewilding for lots of links. Or go to the Wikipedia article for lots of links and this handy guide for who replaces who:
  • African Bush Elephant (as a proxy for the extinct Columbian mammoth)
  • Sumatran Elephant (as a proxy for the extinct American Mastodon)
  • African Forest Elephant (as a proxy for the extinct Pygmy Mammoth of Channel Islands of California)
  • Mountain tapir (as a proxy for the extinct California tapir)
  • Bactrian camel (as a proxy for the extinct camelops)
  • Capybara (as a proxy for the extinct species of North American capybara)
  • Onager (as a proxy for the extinct species of North American horses/asses)
  • Grant's Zebra (as a proxy for the extinct Hagerman horse)
  • Asiatic Cheetah (as a proxy for the extinct American cheetah)
  • Barbary Lion (as a proxy for the extinct American lion)
  • Siberian Tiger (occurred in Alaska during the Pleistocene; might also serve as a proxy for the extinct American Lion)
For a contrary view see Pleistocene Park: Does re-wilding North America represent sound conservation for the 21st century? in Biological Conservation

Wednesday, April 18, 2012

A broken system

Opinion: Academic Publishing Is Broken
The current system by which academics publish their scientific discoveries is a massive waste of money.
 Not the first article on this topic, and certainly not the last, it does serve as a nice introduction if you've never thought about it that much.

With government-funded researchers providing the writing, the editing, the reviewing, and even most of the formatting, you might think that the publishers who benefit from all this would be able to do their part very cheaply, and that subscription prices would be low and falling fast. Not a bit of it: at a time when library budgets are being progressively squeezed, Elsevier—the biggest of all the academic publishers—reports a 2011 profit of £768 million on revenue of £2,058 million, an astonishing 37.3 percent, compared for example with Apple’s 24 percent profit margin in their record-breaking 2011. This makes 2011 the fifth consecutive year in which Elsevier’s profit margin has increased.

Tuesday, April 17, 2012


A satellite view of penguin colonies in Cape Colbeck, Antarctica.

Some fun papers of relevance to this class I missed out on posting whilst I was visiting the old homeland:

Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. 
In a study published in the journal Proceedings of the National Academy of Science, scientists from the Max Planck Institute for Marine Microbiology in Bremen and Greifswald University, together with colleagues from Freiburg, Italy and the USA, have revealed that a small marine worm, faced with a scarce food supply in the sandy sediments it lives in off the coast of Elba, must deal with a highly poisonous menu: this worm lives on carbon monoxide and hydrogen sulphide.

The Sex Determination Gene Shows No Founder Effect in the Giant Honey Bee, Apis dorsata.
By mating with nearly 100 males, queen bees on isolated islands avoid inbreeding and keep colonies healthy. The results, published in the current issue of PLoS ONE, focused on giant honey bee colonies on Hainan Island, off the coast of China. Since these bees have long been separated from their continental cousins, it was thought that the island bees would be prime candidates for inbreeding as well as having very different genes, said Zachary Huang, Michigan State University entomologist.

and from National Geographic (this is relevant to our next class):
Emperor Penguins Counted From Space—A First

Talk about a bird's-eye view—scientists have taken the first-ever penguin census from space.
What's more, the high-resolution satellite images reveal that there are twice as many emperor penguins in Antarctica than previously thought, a new study says.Scientists have snapped penguin pictures from space before. But the new work used a technique called pansharpening, which offers high enough resolution for the scientists to differentiate between penguin poop, ice, and the birds themselves.

Monday, April 16, 2012

It's that time of the year again...

Yes, it's grad student appreciation week next week. No, really.

As part of this year's festivities they are holding a free screening of the PHD movie in Corwin Pavillion at 4pm on Tuesday April 24th.

If you don't read PHD comics then you should - especially if you intend to go to grad school. If you want a flavor then try the 200 most popular comics.

I haven't seen the movie but I believe that all the actors and actresses are PhD or graduate students, many from Caltech where it was filmed.

Sunday, April 15, 2012

Advanced dinosaurs

I confess that one of my interests is in  seeing how science papers are reported by the press. Sometimes the connection between the paper and the story that is reported is a little tenuous to say the least.

For example, would you have reported this paper in the Journal of the American Chemical Society:  Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth

in this way:

Could 'Advanced' Dinosaurs Rule Other Planets?
New scientific research raises the possibility that advanced versions of T. rex and other dinosaurs -- monstrous creatures with the intelligence and cunning of humans -- may be the life forms that evolved on other planets in the universe.

The authors of the paper do set themselves up for this by including this by slipping in this rather far-reaching statement at the end of the paper:
An implication from this work is that elsewhere in the universe there could be life forms based on d-amino acids and l-sugars, depending on the chirality of circular polarized light in that sector of the universe or whatever other process operated to favor the l-α-methyl amino acids in the meteorites that have landed on Earth. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them. 

Friday, April 13, 2012


Bruce sent me these. Have a good weekend.

Thursday, April 12, 2012


When Olivia mentioned she'd be going to Antarctica with the Hofmann lab I immediately thought of this video which was made by the multi-talented Henry Kaiser. Perhaps most famous for his guitar playing he also works as a research diver and underwater filmmaker. This ten minute film is a great introduction to life at the McMurdo station (surprisingly similar to any research station but with more facial hair and a heartier breakfast buffet) and diving under the ice. The Hofmann lab is prominently featured.

Tuesday, April 10, 2012

Smart octopus tricks

I'm back. Did you miss me? I'm reluctant to start with repeat but here's a most spectacular octopus camouflage video. I like the way the octopus gets a round of applause.
Of course as biologists we want to look a little deeper. The cool bit is that it gets even more amazing as you think about it more closely. As PZ Myers pointed out on his blog, the octopus needs to do four things to achieve this trick:
  1. It needs good visual system. In order to match the background you need to be able to see it. To match it well, you need to see it well.
  2. To pull off the fast change you need a fast connection from the brain to the color changing organ.
  3. Speaking of which, yes, the octopus needs organs that can change color. Cephalopods have tiny, discrete sacs of pigment scattered all over their body, each one ringed with muscles that can close the sac to conceal the pigment, or expand the sac to expose the pigment.
  4. Finally, the octopus needs a set of rules, an algorithm, so it can translate what is sees with its eyes into a visual pattern that hides the animal.
For more information check out the website of Roger Hanlon at Woods Hole Marine Biological Laboratory. The New York Times had a nice article on his lab recently, Revealed: Secrets of the Camouflage Masters. For a more scientific, but still very accessible treatment, see Cephalopod dynamic camouflage, in Current Biology.