The Tree of Life

Explore Life on Earth
(or if you need phylogeny help)

"The affinities of all the beings of the same class have sometimes been represented by a great tree... As buds give rise by growth to fresh buds, and these if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications."

Charles Darwin, 1859

Witch trials

Victims of ergotism. Pieter Bruegel painting, Louvre.

Ergot poisoning was certainly common in history, there is no doubt about that. But was it responsible for the events that occurred in Salem and what exactly is the evidence that the fungus was involved?

From The Straight Dope - Were the witches of Salem a result of poisoning with ergot fungus?

In 1976 psychology grad student Linnda R. Caporael proposed the ergotism hypothesis, and history professor Mary Matossian elaborated on it in 1982. The core contentions: A cold winter followed by a moist spring and summer prior to the witchcraft hysteria favored the growth of ergot fungus in rye that the colonists were obliged to eat due to crop failure. Ergot contains toxins known to cause convulsions, hallucinations, and other symptoms similar to those reported by the accusers. 

Doubters were quick to raise objections: Evidence of a cold winter and crop failure is dubious, and none of the accusers displayed the full array of symptoms needed to support a diagnosis of convulsive ergotism. More importantly, the symptoms appeared only at opportune moments during the trials, strongly suggesting a psychosomatic origin if not fraud. The counterarguments seem to have persuaded most historians, but a credulous 2001 PBS documentary has helped keep conjecture about ergotism alive. 

A. Woolf in the Journal of  Clinical Toxicology reaches a similar conclusion. Witchcraft or mycotoxin? The Salem witch trials.

 

The Salem witchcraft trials of 1692 have been studied by many historians looking for the complex social, political, and psychological determinants behind the community-wide hysteria that led to a travesty of justice and the deaths of 20 innocent Puritans. Recently, ergot poisoning has been put forth by some as a previously unsuspected cause of the bizarre behaviors of the young adolescent girls who accused the townsfolk of witchcraft. In this essay the circumstances behind the ergot poisoning theory for this historical event are described. When the evidence is weighed carefully both pro and con, it seems unlikely that ergotism explains much of what went on in colonial Salem.

Read Linnda Caporael's 1976 paper (in Science) and weigh the evidence for yourselves: Ergotism: the satan loosed in Salem?

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

Babbage

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 1/16^th is born
 
Strictly speaking, the actual figure is so long I cannot get it into a line, but I believe the figure 1 1/16^th 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."

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.

Google Doodles

It wasn't that surprising to see Google doodles for Darwin (Feb 12 2009, on his 200th birthday) and for Mendel (July 20 2011 on his 189th birthday) but I was very surprised to see Nicolas Steno show up on his 374th birthday in January this year.
I must confess when I first saw this I wasn't sure whether it was for Steno or William 'Strata' Smith but I like the design. I also like to look at the design notes

Known as the father of stratigraphy and geology, Nicholas Steno worked to understand history by what he could find in the ground. Rather than simply write books about his findings, Steno opted to do his own hands-on research. As an innovative thinker, he disagreed with his contemporaries in thinking that shark-tooth-shaped objects found imbedded in rocks "fell from the sky." Instead, Steno argued that these formations were fossils. His dedication to analysis, critical thinking, and creative thinking make him a great subject for a Google doodle!

Considering Steno's contributions to stratigraphy and geology, I wanted to honor his birthday with a unique take on his work. I knew that the colorful and geeky aesthetic of stratigraphy was the right direction for the doodle, but the team and I weren't sure how to apply it. Should we set the doodle in the middle of the country? Should we relate it to Google culture? Should I just make things up? Below are the exploration sketches.



After consulting a few geology nerds within Google, I decided to set the land in our very own Mountain View! I learned an interesting fact about our home-- there are no dinosaur fossils in the Bay Area (except for Stan of course).

Also staying a little more faithful to stratigraphy graphs, I formed the Google logo as though it was cut from a chunk of three dimensional land. Below are early drafts of the final direction.

Things Darwin didn't say

It's probably safe to say you've made a significant impact on science when people write whole articles on what you didn't say.  In the case of Darwin this isn't actually as odd as it sounds since many people believe he said a lot of things he didn't and still manage to underestimate the importance of what he did say. I think this article from the Guardian (A British Newspaper) is a nice piece of popular science writing.

It ain't necessarily so ...Darwin was no atheist, he didn't say humans came from monkeys, and 'survival of the fittest' - that was someone else's idea. John van Wyhe clears up some myths

Human height

The data on human height I mentioned in class was taken from this fascinating article from the New Yorker on changes in human height, subtitled 'Why Europeans are getting taller and taller—and Americans aren’t.' There is some great writing here and some wonderful images which I confess I shamelessly stole for class.

"Charlemagne was well over six feet; the soldiers who stormed the Bastille a millennium later averaged five feet and weighed a hundred pounds. “They didn’t look like Errol Flynn and Alan Hale,” the economist Robert Fogel told me. “They looked like thirteen-year-old girls.”

American degeneracy

Every time I hear the phrase 'American exceptionalism' I think of Buffon and his theory of American degeneracy. Jefferson's instructions to Lewis and Clark - to seek out Mastodon in the American interior - were provoked by Buffon who had been mocking America as a degenerate continent

"In America, therefore, animated Nature is weaker, less active, and more circumscribed in the variety of her productions; for we perceive, from the enumeration of the American animals, that the numbers of species is not only fewer, but that, in general, all the animals are much smaller than those of the Old Continent."
George Louis Leclerc, comte de Buffon (1707-1788)


The Academy of Natural Sciences has a nice series of webpages entitled 'Buffon's Degeneracy' that descibe this interesting, but often forgotten period in history.

The anteater with a splendid classical background is from Buffon's Histoire naturelle, thirty-six volumes of which were completed during his lifetime and another eight published after his death from material he had prepared.

(Some of this post has been recycled from a post in 2009. I just think it's worthy of repeat.

Mendelian inheritance

It is known that Mendel ordered 40 reprints of the paper that described the results of his now classic experiments, "Experiments on plant hybrids" published in the transactions of the Natural History Society of Brünn in 1866.

He sent these out to scientists he thought would be interested (possibly including Darwin). Only a single scientist responded and, unfortunately he steered Mendel completely wrong.

Karl (or Carl) von Nägeli, of the University of Munich, had previously experimented with hawkweed, a plant that follows an obscure asexual reproductive method. Mendel started experimenting with hawkweed, and began to question his findings from studying peas. He finally gave up all experimentation when he became abbot of the monastery, though he continued to dabble in ornamental horticulture.

Although very few of these 40 reprints survive, in a strange story last year Mendel's original manuscript has surfaced and has become the subject of an inheritance dispute (seriously): A Family Feud Over Mendel’s Manuscript on the Laws of Heredity

In the light of evolution

Posting to a blog every day is an interesting exercise. I'm reluctant to say it has made me a better writer but it has certainly helped me overcome a degree of writers block and procrastination. It also tends to permeate everything I do so I'm constantly on the look out for relevant items to post. Sometimes they just fall into my lap though. Like this article I found on the NCSE website whilst looking for something else. It's an excerpt from a forthcoming book In the Light of Evolution: Essays from the Laboratory and Field. Because the book is a series of chapters by different authors this chapter, by the science writer Carl Zimmer, can be read on its own. It makes a perfect follow up to our lecture on Darwin.

Darwin Under the Microscope: Witnessing Evolution in Microbes by Carl Zimmer

Bad commute

I think I very briefly mentioned in class that a single person, Willi Hennig, is pretty much solely responsible for developing phylogenetic systematics, or what we now call cladistics.

You can read more about him at the Willi Hennig society pages. As well as having helped modern biology take a big leap forward he also seems to have suffered the commute from hell. From 1947 to 1961 he worked, and was in fact director, of the German Entomological Insititute in Berlin. However because of the post-war division of Berlin Hennig ended up living in the American sector and working at the Institute which was in the Soviet sector.

This required 4 hours duration for the way there and returning back home, each day! This situation persisted until 1961 when the Berlin wall was built and hermetically cut off both parts of Berlin from each other.


He had to quit his position when the Berlin wall was constructed though because his commute turned from bad to impossible. Moving to East Germany was not an option because of his anti-communist views and he settled in West Germany. This might have been a good move since the Hennig Society article reveals:

It has recently become known from documents of the East German Secret Service that an official operation of the DDR administration was initiated against WH in 1961 with the final aim to imprison him or take other comparable measures because of his attitudes against the communistic system.

Names and places

Whenever we go to CCBER it reminds me of all the buildings on campus named after people and that I don't have a clue who most of them are. I recently came across the website of The University of California History Digital Archives. This is a great site containing masses of information and you can read about many of the names you see around campus: Vernon Cheadle, Preston Cloud, John Snidecor, Herbert Broida, and many others.

The best stats you've ever seen

I used this video in a different class but I think everyone should see it, and it is relevant to our discussion about human population growth.

You've never seen data presented like this. With the drama and urgency of a sportscaster, statistics guru Hans Rosling debunks myths about the so-called "developing world."

And the best part about it is that the software is now available at the Gapminder website so you can play with it yourself and look at changes through time of all sorts of environmental, social and geographical parameters.

Carrot power

Many people believe that carrots are good for their eyesight. There is a germ of truth in this in that carrots are indeed a good source of vitamin A, and vitamin A is required for, among other things, correct functioning of the visual system. However just because they are required for correct functioning does not necessarily mean that eating more of them will improve your vision. The origin of the myth that carrots are good for your eyesight dates back to World War II and the Battle of Britain that occurred in 1940 and marked a turning point in the war. The Battle of Britain refers to the air battle between the German and British air forces for air superiority. A German victory would have permitted a cross channel invasion of England.

Although the principles of Radar had been known for a long time it was British scientists who produced the first working system, enabling ground controllers to direct British planes to intercept German planes in poor visibility and at night. In order to maintain their advantage the British spread the rumor that their pilots were being successful because of their extraordinarily good eyesight. A feat that was achieved by the mass consumption of carrots. This rumor affected both the Germans and the British. Due to the blackout at night and the frequent requirement to move to air-raid shelters people were keen to improve their night vision and carrots were readily available from allotments and gardens.

I do not know whether the Germans fell for this story. There are a few suspicious parts to it that may not have been fully understood at the time. Or maybe this was a sneaky part of the plan, to encourage German pilots to poison themselves with large amounts of Vitamin A. As Claudia pointed out today, if you want to propose ingesting large amounts of a vitamin you might be better off picking one that is water, rather than fat, soluble. As vitamin A is fat-soluble, disposing of any excesses taken in through diet is much harder than with water-soluble vitamins B and C. As such, vitamin A toxicity can result. This can lead to nausea, jaundice, irritability, vomiting, blurry vision, headaches, muscle and abdominal pain and weakness, drowsiness and altered mental status. Too many carrots will also cause you to turn orange from the accumulating beta-carotene. Another good source, in fact a much better source, of vitamin A is liver. Too much liver is even worse and can kill you quite quickly as Arctic explorers who were reduced to eating polar bear and sled dog liver discovered. Polar bears have very high concentrations of vitamin A in their liver and the native Inuit were well aware of this fact:

After killing a bear, the Inuit ate the meat and used the fur to make warm trousers for men and kamiks for women. An average polar bear would yield three pairs of trousers and one kamik. The only part of the bear that was not used was the liver. This was immediately thrown out, as it could make even the sled dogs violently ill.
From Polar Bear International.

Controversy Over World’s Oldest Traces Of Life

ScienceDaily (Feb. 28, 2009) —
The argument over whether an outcrop of rock in South West Greenland contains the earliest known traces of life on Earth has been reignited, in a study published in the Journal of the Geological Society. The research, led by Martin J. Whitehouse at the Swedish Museum of Natural History, argues that the controversial rocks "cannot host evidence of Earth’s oldest life," reopening the debate over where the oldest traces of life are located.

Featured

Today's featured article on Wikipedia is the History of Evolutionary Thought which looks like it is a pretty nice article. Although there are numerous books on this subject and I'm sure some of them are maybe better, the beauty of Wikipedia is in the hyperlinks and this article is exceptionally well linked.

Despite the warning contained in the article in the previous posting, there is no doubt that Darwin was a fascinating chap.

A wonderful resource is the Darwin Correspondence Project. Darwin was a prolific correspondent (almost 15,000 of his letters survive!) and the website has the full text of 5,000 of them online and searchable. As well as containing some interesting pages (eg. Six things Darwin never said - and one he did), the website also allows you to simply browse and read the letters. Take a dip, meet Darwin the man.

Bone Wars

Today's featured article on Wikipedia is 'Bone Wars' -

...the name given to a period of intense fossil speculation and discovery during the late 1800's marked by a heated rivalry between Edward Drinker Cope and Othniel Charles Marsh. Each of the two paleontologists used underhanded methods to out-compete the other in the field, resorting to bribery, theft, and destruction of bones. The scientists also attacked each other in scientific publications, attempting to ruin the other's credibility and cut off his funding.

Cope and Marsh were financially and socially ruined by their attempts to disgrace each other, but their contributions to science and the field of paleontology were significant, and it provided substantial material for further work—both scientists left behind many unopened boxes of fossils after their deaths. The efforts of the two men led to over 142 new species of dinosaurs being discovered and described. The products of the Bone Wars resulted in an increase in knowledge of ancient life, and sparked the public's interest in dinosaurs, leading to continued fossil excavation in North America in the decades to follow.

Blast from the past:
High-performing males have underachieving daughters

Darwin in National Geographic

A South American gray fox (Lycalopex griseus) yawns as dusk falls on Chile's Torres del Paine National Park. In Voyage of the Beagle, Darwin chronicled his first encounter with another member of the same genus, Darwin's fox (Lycalopex fulvipes): "I was able, by quietly walking up behind, to knock him on the head with my geological hammer. This fox, more curious or more scientific, but less wise, than the generality of his brethren, is now mounted in the museum of the Zoological Society."

National Geographic has a couple of nice Darwin articles this month (of course). Nice light reading but the photos are amazing and you always learn something interesting eg:

Just two weeks before he died, Charles Darwin wrote a short paper about a tiny clam found clamped to the leg of a water beetle in a pond in the English Midlands. It was his last publication. The man who sent him the beetle was a young shoemaker and amateur naturalist named Walter Drawbridge Crick. The shoemaker eventually married and had a son named Harry, who himself had a son named Francis. In 1953, Francis Crick, together with a young American named James Watson, would make a discovery that has led inexorably to the triumphant vindication of almost everything Darwin deduced about evolution.

• Darwin's First Clues: He was inspired by fossils of armadillos and sloths.
• Modern Darwins