Monday, July 31, 2006

Mad Cow

I'm convinced that it is getting harder and harder to tell stories in The Onion from real stories. The US has long maintained that there is no Mad Cow disease in the US. Critics had argued that the level of testing was far too low to actually detect it if it was present. Eventually the Agriculture department increased the testing rate - and lo and behold they discovered infected cows (you probably read about this in the press because other countries now banned US beef).

In the news just a few days ago was an announcement from the agriculture department that they would scale back testing for BSE (the technical name for mad cow disease) by 90%. NINETY PERCENT! I'm no expert but I'm guessing that they won't find as many of those pesky infected animals that cause export bans.

If you think this is bad then check this out. Individual farmers or companies who want to carry our further testing on their own animals at their own expense are prohibited from doing so by the Agriculture department because 'it could make consumers think that untested beef was not safe.'

As usual if you don't know much about Mad Cow disease, BSE, CJD etc then Wikipedia is a better place to start than a google search.


The Lost Children of Rockdale County

I'm pretty unshockable but I found the PBS show on an outbreak of syphilis in Georgia pretty amazing. Although the show was aired in 1999, thanks to good old PBS you can access a lot of information about it at a website dedicated to the show and even read a complete transcript.

The website will also give you access to details about the actual investigation of the outbreak, the techniques used and the results. For example this paper shows the complete network visualization of the outbreak I presented in class.

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Sunday, July 30, 2006


I can't remember where I first saw Edward Burtynsky's Shipbreaking photographs but these haunting images have stayed with me. The one reproduced above looks like a scene from the Trojan war but these are in fact some of the world's largest ships being disassembled, largely by hand, in some of the world's poorest countries. The scenes Burtynsky shot were in Chittagong, Bangladesh but similar scenes can be found at Alang, India.

Following the Exxon Valdez oil spill in 1989 there has been increased pressure to phase out the vulnerable single-hulled ships and replace them with safer double-hulled tankers. This might seem like a good idea but the problem comes about when the old ships are broken up. A single oil tanker can contain literally tons of toxic material (eg 7000 kg of asbestos) and in Chittagong and Alang, the workers have virtually no protection from toxic, and other, hazards, and the waste itself often ends up on the beach or in the ocean.

A series of articles on the international shipbreaking industry by Gary Cohn and Will Englund of The Baltimore Sun won a Pulitzer prize in 1998 and you can read the series here. The article on Alang is perhaps the most relevant. More recently in 2006 Foreign Policy magazine had a short photo essay on the ship breaking beaches of Chittagong. Greenpeace has an informative website and an ongoing campaign around the shipbreaking issue

I think the sad moral of this story is that one apparently simple change (a move to safer ships) can create a toxic nightmare in a number of poor countries. Cleaning up this mess (literal and metaphorical) isn't going to be easy. This sort of consequence very much reminds me of the ecological consequences we see when we mess around with food webs by introducing alien species or driving species to extinction. There. I made it relevant right at the end.


Thursday, July 27, 2006

Snakes on a plane.

I will be out of e-mail and computer contact on Friday and Saturday so there won't be any more updates here until Sunday. But I just made several postings to give you some interesting material to read and consider.

If you do much reading on the internet then you can't have failed to notice the excitement over one of the most anticipated movies of recent times, and possibly the best title for a movie ever - Snakes on a Plane.

To make this, just a little bit relevant to Bio1B you can read an interesting interview with the snake wrangler over on the National Geographic Website.

If you don't know what the excitement is all about then check out the Wikipedia entry for the movie, or the 'Snakes on a Blog' page.

Bird extinction rates

A recent paper in the Proceedings of the National Academy of Sciences estimates that bird extinction rates may be much worse than had been estimated. (I told you we didn't know.) In the revised calculations as many as 12% of existing species are estimated to be in danger of extinction by 2100. This revised estimate for birds is particularly alarming because people value birds and they attract a lot of conservation money.

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Are there species that we should deliberately drive to extinction? Before you say no, try reading Olivia Judson's controversial article in the New York Times entitled 'A bug's Death: Should we send the malaria mosquito the way of the dodo?' . In this article she advocates the extinction, or "specicide", of thirty mosquito species through the introduction of recessive knockout genes".

Would this be the first step on a very slippery slope (a lot of people hate snakes, many people dislike spiders etc. etc.) or would the ends justify the means - eliminating the mosquitoes that vector malaria would save at least one million human lives every year?


Save the rhino maggot!

Everybody knows that the big critters, especially if they are cute, attract the conservation dollars (the so called charismatic megafauna). But why should this be so?

An interesting article, available online here, highlighted the unfortunate plight of the parasites of endangered species. From the endangered rhino maggot of the title to the lice that are specific to the Califonian condor, these species are not just overlooked but they are sometimes destroyed in our attempt to breed 'healthy' individuals in captive breeding programs.

For every animal facing extinction there is an entire world of other species living on and inside it that depend on them for survival, and may be equally endangered. Should conservationists be just as worried about the fate of these parasites as they are about the survival of their hosts?


Wednesday, July 26, 2006

Rachel Carson, Fred Soper and DDT

In the last few years Rachel Carson was named as one of the '100 most influential people of the last century' by Time magazine and then her book Silent Spring, was named as one of the 'Most Harmful Books of the 19th and 20th centuries' by a panel of 15 Conservative Scholars.

But this is nothing compared to the reception Carson got when the book came out. From the Time magazine article:

Carson was violently assailed by threats of lawsuits and derision, including suggestions that this meticulous scientist was a "hysterical woman" unqualified to write such a book. A huge counterattack was organized and led by Monsanto, Velsicol, American Cyanamid - indeed, the whole chemical industry - duly supported by the Agriculture Department as well as the more cautious in the media.

You may wonder, as I did, what is so dangerous about Carson's book? Many of her companions on the list of 'harmful books' are more predictable (Karl Marx, Adolf Hitler and Mao Zedong are the top three). The argument, presumably, is that by starting a campaign that ultimately led to the banning of DDT in many countries, Carson's book led, indirectly, to increased rates of disease as a major tool in the war against insect transmitted diseases was removed.

But what is interesting is that if you actually read the book, nowhere does it call for the banning of DDT. For example at the end of her section on DDT she says:

Practical advice should be "Spray as little as you possibly can" rather than "Spray to the limit of your capacity."

Sound advice.

But if you are ready to have some of your preconceptions about DDT challenged you might want to read this article from the New Yorker magazine about Fred Soper... of the unsung heroes of the twentieth century. With DDT as his weapon, Soper almost saved the world from one of its most lethal afflictions. Had he succeeded, we would not today be writing DDT's obituary. We would view it in the same heroic light as penicillin and the polio vaccine.


Tuesday, July 25, 2006

Mt. St. Helens

Last year was the 25th anniversary of the Mount St. Helens eruption. Since that time scientists have been monitoring the colonization of plant and animal species as the ecosystem undergoes succession.

A report in National Geographic suggests that succession has been far less predictable than expected and has proceeded at different speeds in different areas.

The USDA maintains a good website about the Mount St. Helens National Volcanic Monument that has some good links to information on the eruption and the recovery of the communities.

Mount St. Helens is named after, Alleyne Fitzherbert, 1st Baron St Helens of St Helens in the County of Lancaster. This is the same, rather dismal, northern British town I grew up in. Having spent so much time on Wikipedia lately I couldn't resist looking it up. I was most amused to find the following item listed under 'Trivia'.

Residents of St Helens are known as "Woollybacks" which is an offensive term.

It's been a long while since I'd heard that term...


Wiki1B again

In a monument to stick-to-it-evenness I have finished the Wiki1B project I was working on. It's available here. Let me know if you find it useful.

It's been a while since I so seriously underestimated how long a task would take. I thought it might take a couple of afternoons and maybe have a few hundred links. In its current state it took, let's say, a bit longer than that, and has somewhat over a thousand links.

Monday, July 24, 2006

Honey guides, killer bees and land mines

The story of the honey guide and the honey badger (aka the ratel) is an interesting one, but is it true? It is frequently reported in text books but there appears to be little evidence that the birds actually guide the ratels to the bees nests. Birds are certainly found when ratels tear into the nests but that doesn't indicate they helped the ratel get there.

There is no doubt, however, that the honey guides can lead people to birds nests and their behavior has become quite sophisticated. The Boran people of northern Kenya are able to summon the birds to their camp before a bee hunting expedition by giving a particular whistle. So honey guides do have a mutualistic association - but with humans rather than ratels. Whether this evolved from a prior relationship they had with the ratel is currently unknown.

When I mentioned this today I suddenly wondered whether it would be possible to use honey guides to detect Africanized bee nests (aka killer bees). When killer bees first invade a new area there is a considerable economic cost as farmers and other outdoor workers need to be more careful. Like land mines, much of the economic cost comes about as the cost of farming increases and people are denied access to certain areas. Fortunately this probably isn't necessary. Most human incidents with Africanized bees occur within a couple of years of the bees' arrival and then subside as the bees interbreed with local bees - especially if beekeepers cull the queens of the most aggressive strains.

Curiously, the aggression of Africanized bees may be due to the ratel. The colony most likely to survive a ratel attack was the fiercest one and so natural selection strongly favored fierce bees. European bees did not have to contend with anything quite as vicious as the ratel.

On the subject of land mines it is interesting to note the number of biological alternatives that are now becoming available for demining areas (a need that is sadly increasing - mines are still being laid 25 times faster than they are being cleared). Since it costs one to two million dollars to clear a single square kilometer of land there are obvious benefits to any cheaper, more accurate and safer method than demining by hand. Hitting news headlines within the last few years have been the Gambian pouched rat, which can sniff out mines, and the humble Arabidopsis (or cress) which has been manipulated to create a strain that changes color to red in response to the nitrous oxide that leaks from landmines and other explosives. The picture at the top of this post shows the quite dramatic color difference.

In a strange coincidence, the oddly shaped South African Infantry Fighting Vehicle is called the Ratel, after the animal - which has a reputation as a ferocious fighter. It's an odd shape because the bottom of the hull is angled in a v shape to deflect mine blasts.


Sunday, July 23, 2006

Global warming threatens Californian wine industry

When we talked about species distributions I mentioned that one of the reasons for studying distributions was that many would be changing due to the effects of global warming. Well, a paper in the latest Proceedings of the National Academy of Sciences looks at how climate change might affect the areas suitable for wine production in the US. Grapevines are very susceptible to high temperatures and typical global warming scenarios lead to a reduction of the areas suitable for premium wine by up to 81%. This could obviously have significant consequences for the Californian economy.

The story has been picked up by the The San Francisco Chronicle and New Scientist Magazine, amongst others.

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100 ecological questions

The latest issue of the Journal of Applied Ecology contains an interesting article:
The identification of 100 ecological questions of high policy relevance in the UK. Ecologists hope the list will have a major impact on both science and policy and in the press release they liken the list to the 23 mathematical problems David Hilbert posed at the Second International Congress of Mathematicians in Paris in 1900. This list had a major impact on mathematics throughout the twentieth century.

The list is interesting to browse through (the link above takes you to the complete paper) because it really does help to highlight how little we know in ecology.


Saturday, July 22, 2006

Giant demon duck of doom

A few years ago scientists in Australia described a particularly large example of a Thunder Bird, an extinct group of large (up to 3m tall and 500kg), carnivorous birds. For many years it was assumed these birds were related to other large flightless birds, such as emus, cassowaries and ostriches. However as further specimens accumulated opinions changed and it is now thought that the similarities between these groups are the result of similar adaptations following the loss of flight. The latest idea is that thunder birds actually evolved early in the lineage that includes waterfowl. Because of its large size, carnivorous habits and its waterfowl ancestry, the Australian find was nicknamed the 'Demon Duck of Doom.' Which, of course, guaranteed a bumper crop of press reports.

Now, from the same site, paleontologists are reporting flesh eating 'Killer Kangaroos' with wolf like fangs. Only a week old the story has already been picked up by a number of media sources. The message to paleontologists everywhere is clear - if you want some attention in the media find a carnivorous species from a group that is usually perceived as herbivorous. Bonus points if people already find the group funny. I'm off to look for a carnivorous cow.......


Friday, July 21, 2006

Summer Reading part 2

To match the previous, evolution related, posting I was going to recommend two more books, one graphic novel and one more conventional book. But I can't manage to restrict myself to a single graphic novel - there's too many good ones out there on environmental issues and ecology. For reasons that could take (and probably have taken) a whole thesis to examine, a number of comic book characters regularly cover environmental topics: Swamp Thing, Toxic Avenger, Dr Strange and the Silver Surfer to name just four.

But perhaps the most environmentally conscious 'super hero' is Paul Chadwick's Concrete. In two different graphic novels he addresses first the environmental movement as a whole (particularly the more radical side) and then he takes on population growth (again addressing some of the more radical viewpoints). In both books, the readers responses give valuable additional viewpoints.

Japanese manga comics have also covered environmental issues. Perhaps the best example is Nausicaa of the Valley of the Wind. I don't think I could begin to summarize the story. Oh, go on then: Joan of Arc like character helps defend people and planet, including lots of giant insects and toxic fungi, from warring factions. The story is collected in a 7 volume set or you can rent the movie, based around the first two books, by fimmaker and illustrator Hayao Miyazaki.

If you want to read an actual book, I'd like to recommend Laurie Garrett's 'The Coming Plague: Newly Emerging Diseases in a World out of Balance'. We won't cover this topic until our final lecture but in many ways this book shows some of the practical applications of the material we cover. If you are interested in public health you really should read this book. The paperback is a bargain at a little over $10 for a 768 page monster and I have a spare copy if anyone wants to borrow one.


Ecological footprints

An 'Ecological Footprint' is the amount of land and water area a person or a human population would need to provide the resources required to sustainably support itself.

The term was first coined in 1996 by Canadian ecologist William Rees and his graduate student Mathis Wackernagel. It has proven to be a useful educational tool, especially now that you can easily use websites such as this one to calculate your own footprint.

If you haven't already played around with a site like this you might like to have a go. It only takes a couple of minutes and the answers to 15 questions. Take a look at some of the FAQ's, they do help to make you think about some of the concepts. This all relates back to the very last few minutes of class when I was pointing out that it is not overpopulation itself that is the problem but overconsumption.


Thursday, July 20, 2006

How many people can the earth support?

The book I briefly mentioned at the end of class today was 'How many people can the earth support?' by Joel Cohen. Although it is ten years old now there isn't really another book like it and the points it makes are still relevant.

You can read an interview with Joel Cohen here that nicely summarizes some of the points in the book.

You might think that we'd be able to calculate the earth's carrying capacity and you certainly wouldn't be alone. From the interview:

People see the title, How Many People Can the Earth Support? and they ask me "What is the answer?" And my answer is: we have to understand the question better. What choices do we want to make?

You have to ask how many people can the Earth support at what average level of material well being? Do people want to have a lot of food, with animal foods included, or just vegetarian food? Do people want their clothing to be cotton or wool or synthetic fibers? Do people want to drink river water or Perrier water?
etc. etc.


Wednesday, July 19, 2006

Leonard Cohen's March Of The Penguins

Penguin's - adorable flightless comedians of the Antarctic. Leonard Cohen - the adorable flightless poet from Canada. Put them together and you get something truly disturbing.

Penguins keep cropping up in this class. We mentioned them a couple of times in the evolution section and, when you think of it, they have a pretty interesting life history strategy. I expect the penguin references will decline in the plant section.


Elephants in space

Actually that's a NASA headline, not mine. It turns out they aren't currently planning to put any elephants in space. In fact elephants are waaaay back in the queue - just ahead of whales, poison ivy, ferrets and killer bees.

The article and the NASA project concerns the viewing of elephants from space. The Wildlife Conservation Society (the people who run the fabulous, conservation oriented, Bronx Zoo amongst other things) have been collaborating with NASA to see if wildlife counts from space would be feasible. High definition photographs were taken of the Bronx Zoo itself by the Quickbird satellite, 450km vertically overhead. The advantage of taking photos of the Zoo for testing is that these could be ground truthed by taking photographs at ground level at the same time (see images above with 3 items: a clearing, a tree and a fence labeled in each).

The advantages are obviously many, from less disturbance of the animals to cheaper research.

Imagine being able to monitor a herd of elephants in the Serengeti, or a flock of endangered flamingos in Bolivia, from a lab in New York. This technology may allow us to do just that.
Dr. Eric Sanderson, WCS landscape ecologist

Satellite imagery resolutions are continuously improving. Typical resolutions today are about 1m (i.e. each pixel represents a square 1m on a side) and 0.5m resolution is probably close. Military satellites almost certainly have better resolution - perhaps as good as 5 or 10cm. With this sort of resolution you could spot, but not definitively identify some of the world's biggest insects! (But not if they were hiding under a leaf of course). I think ecologists will need to be out there in the field for a long time to come......


Tuesday, July 18, 2006

Can I eat the scorpion now mom?

A paper in this week's Science, and in fact the current banner headline story on the Science website (likely to change in a day or two), concerns the behavior of meerkats.

Perhaps surprisingly there is little evidence for teaching in nonhuman animals. In this study, by researchers at the University of Cambridge in England, adult meerkats in the Kalahari were shown to teach their pups how to deal with scorpions and other prey.

After all if part of your diet consists of deadly scorpions and you are born clueless it might be a good idea to get some pointers from an experienced relative. Meerkats are social animals that live in groups of around forty. Some of the teaching is carried out not by the parents but by helpers. These helpers are likely to be closely related to the pups they are teaching so this is a nice example of kin selection at work. There is a good summary of the research at the National Geographic website.

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Running after Antelope

You may be familiar with the radio show This American Life. If not, then you'll just have to listen to it because it is hard to describe. Each week they have a number of stories loosely based around a theme.

Around here you'll find it on 88.5 KQED at noon on a Saturday and again at 10pm. Even better they stream practically all their shows on the web.

Back in 1997 one of their perennial favorites Scott Carrier told a great story about his attempt to run down an antelope. (It's actually the second story in the show but takes up the majority of the hour long show). For reasons a little too complicated to explain Scott and his brother are trying to show it would have been possible to hunt down antelope on foot simply by doggedly chasing them until the antelope become exhausted. Listening to this story made me realize yet another advantage to group living when it comes to defending against predators. After chasing a pair of deer for some hours they round a corner to find the two deer they were chasing had merged with another group of deer. This group then merged with yet another group. After repeated merging like this they found it impossible to know which deer they had been chasing which made it impossible to single out and chase down any particular individual.

But don't take my word for it, listen to the story. It's got some interesting observations on biology, grad school and life generally and it is a great example of storytelling.


Monday, July 17, 2006

Dr Dino versus The Amazing Randi

Offering a prize is one way to attract a lot of publicity. Unfortunately not all prizes are created equal.

Let's compare the prizes offered by Kent Hovind (aka 'Dr Dino'), a creationist, who is currently offering $250,000 for scientific evidence of evolution with the prize offered by James Randi (aka 'The Amazing Randi') who has one million dollars to anyone who can prove they have 'supernatural powers.

The first one sounds easier doesn't it? But like all offers you need to read the small print. To satisfy Hovind you would have to show, and I quote:

* NOTE: When I use the word evolution, I am not referring to the minor variations found in all of the various life forms (microevolution). I am referring to the general theory of evolution which believes these five major events took place without God:
1. Time, space, and matter came into existence by themselves.
2. Planets and stars formed from space dust.
3. Matter created life by itself.
4. Early life-forms learned to reproduce themselves.
5. Major changes occurred between these diverse life forms (i.e., fish changed to amphibians, amphibians changed to reptiles, and reptiles changed to birds or mammals).

Wow. That suddenly got a lot harder. In fact it can now be argued that to satisfy Hovind you would need to prove not only that God didn't do the aforementioned five acts but that he couldn't have done so. This would imply that God is not omnipotent, so satisfying Hovind may involve proving that God does not exist. Christian theists have already pointed out that the only way to truly know whether God exists or not is to be omniscient - that is to be God yourself!
Enough. This is clearly just a publicity stunt. If you do want to read more you can find a nice summary and links at the talkorigins site. Bottom line, if you want to play in the Science sandbox you need to play by the rules.

The offer by James Randi is actually far more interesting. In order to get Randi's million bucks all you need to do is show a single convincing case of a supernatural power (eg. Dowsing. ESP. Precognition. Remote Viewing. Communicating with the Dead . Homeopathy. Faith Healing. Astrology. Prophecy. Levitation. Reflexology. Clairvoyance. Graphology. Numerology. Palmistry. Phrenology.) What is a convincing case? One that is clearly shown cannot be a trick.

The interesting bit to me is in the correspondence between the James Randi Educational Foundation and the claimants as they try to agree on a testing protocol (look at the ones with the most replies for the most interesting debate). This has a lot of relevance to today's discussion on putting your hypotheses to rigorous tests. Psychics may be able to read your mind but they may also be able to read your body language or just plain cheat. If you give them easy tests then passing them doesn't really reveal very much. A good test is one that can distinguish real psychic powers from cheating. I admire Randi for putting his money on the line in this way. Not only is he inviting believers in the paranormal to put themselves to the test but he is also saying that he does not believe he can be tricked. It probably helps that Randi was a magician himself and is, I imagine, hard to fool.


Sunday, July 16, 2006

What, if anything, is a Preble's Meadow Jumping Mouse?

This last evolution posting before we head into the ecology section is a good one. It's got everything: evolution; ecology; current events and a mouse that can jump.

The Preble's meadow jumping mouse (Zapus hudsonius preblei) is a small mouse, about three inches long, but with a six-inch long tail. They get their name from the fact they can use their large hind legs to jump 18 inches into the air. The mouse is not a distinct species but is on the endangered species list because it is recognized as a distinct subspecies.

For some years the mouse, found in Colorado and Wyoming, has been on the federal endangered species list. Its declining numbers are probably due to habitat loss and much of the remaining mouse habitat is also under threat. Its preferred habitat is a narrow band of land along the eastern edge of the Rocky Mountains that is being keenly eyed by developers.

A subspecies, by definition, differs morphologically from members of other subspecies of the species. Subspecies may, in some cases, be on their way to forming full species. In other cases they may not ever form separate species but will contain important genetic variation. Although the endangered species act preserves both species and 'subspecies' there is no clear definition of how distinct a 'subspecies' has to be before it deserves separate protection. In the current case opinions are sharply divided over whether the Preble's Jumping Mouse is distinct enough from the more common Bear Lodge meadow mouse. The story was summarized by the Jackson Hole Star Tribune last week because the US Fish and Wildlife Service had convened a panel of scientists to review the evidence. A google search on the mouse will show the history of the debate.

This may sound like a small academic debate but it could have important outcomes for how the endangered species act is interpreted in the future. Genetic data is becoming increasingly important in deciding what is a valid subspecies but there are no guidelines for how much genetic difference is required between two populations for them to be considered different subspecies.

There are a lot of issues here, some of which we touched on and some of which we will touch on in the ecology section. It is important to realize that we may not currently have enough information to make these decisions.

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Saturday, July 15, 2006

Darwin's Finches

Hot off the presses is a new paper about Darwin's Finches published in the journal Science this week and reported on in the San Francisco Chronicle yesterday.

Darwin's Finches are a group of 14 closely related birds found on the Galapagos Islands whose beaks have adapted to the foods found on the specific islands they live on. Darwin did not initially realize that these birds were closely related and only later did the work of others convince him that this was so. Darwin then speculated that all these birds must have once had a common ancestor.

For the last 33 years Peter and Rosemary Grant have been studying Darwin's Finches on the Galapagos Islands. In the current paper they describe how the new colonization of one island by a species of finch (Geospiza magnirostris) led to a rapid evolution of a finch that was already present on the island (Geospiza fortis).

The newly arrived species of finch was able to break open and eat large seeds three times faster than G. fortis could. Over the years 2003 and 2004 little rain fell and competition for food was fierce. The only G. fortis to survive had short beaks and fed on smaller seeds where they did not compete with the larger billed G. magnirostris.

This is an example of both directional selection and character displacement. Although this is almost certainly common in nature it is rare that scientists are on hand to document it, and it may be rare that it happens this quickly.


Friday, July 14, 2006

Midterm 1 results

I thought some of you may be interested in the results of the first midterm. I obviously can't post your invidual results, and, in fact, don't have them, but I do have an analysis of the complete data set.

The overall mean was 80% and the median was 83% (for skewed distributions like this the median is a better description of the 'typical' value than the mean.)

Highest score was 100%, and two students in different sections managed to achieve this - well done.

Section means were very similar and no section mean was more then 3% away from the overall mean of 80%

The histogram of scores is above and the breakdown by grade is below.

A (ie >=90%) - 31%
B - 31%
C - 17%
D - 12%
F - 9%

Looking at the individual questions I see no problems. Lowest % correct was 53% for Q6 (a calculation), Q37 (a calculation) and Q43 ('what evolved before what' question). These were all meant to be hard questions.
Highest % correct was 97% (two questions).
I have looked closely at all the questions where either less than two thirds of you got the correct answer (5 questions) or more than 20% of you picked a particular incorrect answer (8 questions) and don't see any problems.



Web sight

At around the same time I was telling you about the coevolution of spiders and their prey scientists were reporting the discovery of the worlds oldest spider web. Preserved in a large blob of amber the web and the insects caught in it have now been dated to the early Cretaceous - about 110 million years ago.

Although the web is not complete enough for scientists to reconstruct it, enough remains to suggest this was not just a collection of strands and was probably in one plane like an orb web.

As you can imagine finding fossilized spider webs is unusual. We do know that fossilized spiders have had spinnerets for producing silk for closer to 400 million years.

There is a report on the research in New Scientist magazine.


Thursday, July 13, 2006

Woof !

Well, the evolution part of the class is over but I'm going to spend the next few days posting links to evolution related news from the last few weeks to show you what an interesting and dynamic science evolution is before we start on the next section. It isn't just a set of facts, although, for obvious reasons, that is how it can tend to come across in class.

Up first is the evolution of the dog. (The photo is from CuteOverload - the only place to go when you need some cute.)

As we have mentioned several times Darwin was a very smart and perceptive guy. But when it came to dogs even Darwin underestimated the power of selection (here artificial selection rather than natural selection). Darwin thought that the current array of dog breeds must have been descended from a number of different wild canine species such as such as jackals, coyotes and wolves. We now know this is not the case and all 350+ distinct breeds are, in fact, descended from one species, the grey wolf. This raises the question of just where all the variety in dogs came from.

A paper in Genome Research on June 29th of this year by Matthew Webster of Trinity College Dublin, Ireland, and colleagues at Uppsala University in Sweden has proposed an explanation. They analysed the complete mitochondrial DNA genome in 14 dogs, six wolves, and three coyotes. This data suggests that mutations in the canine genome have played a bigger role in dog evolution than previously thought. Natural selection usually weeds out mutations in wild species if they offer no survival advantage. But if that pressure is removed, these mutations will get passed on. This provided dog breeders with a wide inventory of traits in the DNA to exploit. Others disagree, Webster et al. only studied mutations in mitochondrial DNA, which tends to accumulate more quickly than in nuclear DNA which forms the largest part of the genome. Far fewer mutations may have occurred in genes in the nucleus compared with mitochondria. Much of the variation we see in dogs may have to do with pre-existing variation from the ancestral wolf-dog population.

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Wednesday, July 12, 2006

The Demon in the Freezer

In these days of gene splicing, genetic engineering, cloning and DNA fingerprinting it is easy to overlook the simple power of selection. I was just reminded of this by reading Richard Preston's book about bioweapons - the Demon in the Freezer. (I like the way he gets a quote from Stephen King on the back of the jacket - 'One of the most horrifying things I've ever read in my whole life.' It's like the official stamp of scary).

In chapter 4 he describes the Soviet bioweapons program at the Biopreparat facility and how this came to the attention of the UK and the US in the late 1980's via a couple of high profile defectors. First Vladimir Pasechnik and later Ken Alibek. Ken Alibek is a whole other story, it's hard not to admire a man who is now regarded as a great humanitarian and philanthropist but was once responsible for making weaponised smallpox by the ton. The relevant bit here is the description of how the Soviet Union created antibiotic resistant strains of plague - the Black Death that killed a third of Europe back in the 1300's:

One of the principal weapons was genetically modified (GM) plague that was resistant to antibiotics. The Soviet microbiologists had created this GM plague with brute-force methods: they had taken natural plague and had exposed it again and again to powerful antibiotics, and in this way they forced the evolution of drug-resistant strains.

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Tuesday, July 11, 2006

Canterbury Tales

There are two ways to be successfull. You can be super-genius-freaky-smart and think of something before everyone else has thought of it. In this case you run the risk of being excommunicated, burnt at the stake, ridiculed or just plain ignored. I'd like to say this was no longer the case but I can't. If you are ahead of your time you run this risk.

The other way to be successful, that often avoids the unpleasant fates I just mentioned, is to take the advances someone has made in one field and apply them to a new field. Given the specialization of disciplines there are an increasing number of possibilities for such inter-disciplinary transfers. This applies to the arts just as well as it does to the sciences.

Which brings me to something I mentioned in class today. The application of cladistic techniques to textual analysis. It turns out that the analysis of Chaucer by cladistic techniques has gone from strength to strength. They have their own website now and the project must be reaching it's first decade anniversary soon.

Textual analysis using cladistic techniques has become an accepted technique these days and has been used on texts ranging from old Norse manuscripts to the New Testament.


Monday, July 10, 2006

The Thagomizer

As some of you have probably noticed I do like a good cartoon and I try to have a relevant cartoon to start every lecture. I was delighted to find out recently that Gary Larson (of Far Side fame) has inadvertently given paleontologists a new term. The original caption for the cartoon to the left was:

"Now this end is called the thagomizer, after the late Thag Simmons."

Apparently the collection of spikes on the tail of dinosaurs like Stegosaurus did not already have a name. So, in a nice nod to Gary Larson, the term 'Thagomizer' has been adopted as a genuine anatomical term, and has been used by multiple authorities, including the Smithsonian Institution.


Sunday, July 09, 2006

Brave New World

When considering hybridization it is important to note that the biological species definition refers to the potential to interbreed in nature. This specifically excludes whatever technologies we may develop to allow such hybridization in the laboratory. The few cases of animal hybridization observed in the wild (see last posting for links to two insect examples) are interesting partly because they are so unusual.

The accompanying photograph of a frog and mouse is classic tabloid bait and switch. The mouse is trying to avoid a flood - check out the link, apparently it is a real, unstaged photograph from flooding in India. There are no frog/mouse hybrids in nature - think of all the potential isolating mechanisms.

But it seems to be human nature that we are fascinated by the potential of hybridization - from the mythical Chimera, with a lion's body a serpent's tail and a goat's head to the pot-bellied elephant in Southpark. If we move from nature into the laboratory then we can circumvent a great number of the potential isolating mechanisms and it seems that much is possible.

Here are some recent news articles. These are generally not true hybrids as we have been talking about them but I'm including them here to show just what is now possible in combining organisms in the laboratory. The one thing they have in common for me is that my response is invariably the same. First shock at what is now possible, then an understanding of the potential benefits, and finally sadness at realizing that with the potential shock value of newspaper headlines much of this research may be in serious peril.

1) Mice have been used to produce viable monkey sperm using tissue transplanted from the testes of macaques. The work may be very useful in helping conserve endangered species on the brink of extinction. It might also be possible to grow human sperm in mice, although the team agree this would be a controversial move. An experiment that would raise concerns is genetically engineering mice to produce human sperm and eggs, then doing in vitro fertilization to produce a child whose parents are a pair of mice.

2) At Stanford University in California an experiment might be done later this year to create mice with human brains. They have already created mice with brains that are about one percent human and later this year will conduct another experiment where the mice have 100 percent human brain. Before being born, the mice would be killed and dissected to see if the architecture of a human brain had formed. Weissman said he's not a mad scientist trying to create a human in an animal body. He hopes the experiment leads to a better understanding of how the brain works, which would be useful in treating diseases like Alzheimer's or Parkinson's disease.


Saturday, July 08, 2006

Mouse rides frog (oh, and hybridization too)

As I mentioned in class National Geographic is not just for Dentists waiting rooms, yard sales and dusty cabins.

The writing is always good and the photographs are usually stunning. Even if you don't get the print version their website is worth frequent visits. You can download hundreds of their photographs as wallpaper and can read lots of short articles on recent research.

(The mouse rides frog explanation is here.)

Also in the news right now is an interesting story about hybridization. In a mechanism much like Mendel (and even Linnaeus later in his life) had speculated it appears that sometimes a new species CAN be created by the hybridization of existing species. Although examples are known from the plant kingdom this is the first time anyone has thoroughly documented animal examples. Shown last year for Drosophila a paper published in Nature just a few weeks ago gave a second animal example, this time in a South American butterfly species.

Such hybridization is only likely to occur between closely related species (think about the many possible isolating mechanisms between most species) so don't expect frog/mouse hybrids any time soon.


Friday, July 07, 2006


As I was using Wikipedia to get some information on the recent 'fishapod' find for the last blog entry it occurred to me that Wikipedia is now stable enough and complete enough to make a very useful resource for Bio1B. Although I'm sure you are all capable of looking up items on your own it would be highly useful if the lecture outlines were hyperlinked to the approrpriate entries.

Well, it seemed like such a good idea I thought I'd make a start but this is going to take some time! In the meantime I may as well post what I have since some of you may find it useful for reviewing the Evolution section. I only got through six lectures so far but I'll update the file as I get through more.

Missing Links, Transitional forms and the Fishapod

Paleontology hit the headlines a couple of months ago when paleontologists discovered a fossil fish, Tiktaalik roseae, that showed the beginnings of digits, wrists, elbows and shoulders, as well as a skull, neck and ribs that resemble those of tetrapods like today's familiar four-legged land animals. Paleontologists suggest that it was an intermediate form between fish which lived about 385 million years ago, and early tetrapods which lived about 365 million years ago. Its mixture of fish and tetrapod characteristics led one of its discoverers, Neil Shubin, to characterize Tiktaalik as a "fishapod". Like any self-respecting Fossil Tiktaalik has its own homepage.

The story raised some interesting debate about what is meant by the term 'missing link' - a term that sees more use in the mainstream media than the scientific literature. A better term would be 'transitional form'. The Wikipedia article on Transitional Forms has a nice set of figures showing the number of Hominin species known to science in 1850, 1900, 1950 and 2002 - illustrating how our knowledge has steadily increased and although there are still 'gaps' in the record these gaps become smaller and smaller through time.

A popular term to designate transitional forms with is 'the missing link'. The term is especially used in the regular media, but is inaccurate and confusing. This is partly because it implies that there was a single link missing to complete the picture, which now has been discovered. In reality, the continuing discovery of more and more transitional fossils is further adding to our knowledge of evolutionary transitions.


Thursday, July 06, 2006

The map that changed the world

For more on William 'strata' Smith and how he produced the first geological map and yet ended up in debtor's prison and homeless for ten years I recommend Simon Winchester's book 'The map that changed the world: William Smith and the birth of modern geology'.

Or you can read an article for free and see the maps here.

(I'd also recommend another book by Simon Winchester 'The professor and the madman' - a tale of murder, insanity, and the making of the Oxford English Dictionary.)

Wednesday, July 05, 2006

Got Milk?

People are always interested in human evolution. Are we still evolving is a common question. Here is a very recent example of human evolution that was the subject of a paper by a professor and an undergraduate student at Cornell just last year.

Although all mammalian infants drink their mothers' milk, humans are the only mammals that can drink milk as adults (despite their well known fondness for the product most cats are also lactose intolerant). But not all of us can digest milk. In fact most adults in the world, about 60%, are lactose-intolerant: the majority of humans stop producing significant amounts of lactase sometime between the ages of two and five. Lactase is an enzyme required to digest milk. A relatively recent genetic change caused some populations, including many northern Europeans, to continue producing lactase into adulthood; these lactose-tolerant populations are the exception and not the rule. Lactose intolerance is an autosomal recessive trait, while lactase-persistence is the dominant allele.

It has been known for some time that people from different parts of the world have very different rates of lactose intolerance - ranging from 2% intolerant in Sweden to 98% intolerant in Thailand and 100% in Native American populations.

The Cornell study published last year showed that
it is primarily people whose ancestors came from places where dairy herds could be raised safely and economically, such as in Europe, who have developed the ability to digest milk. The mutation that originally produced the lactose tolerant gene (or rather the lactase-persistence gene) is thought to have occurred as recently as 4000 years ago. You can read more about the story at the Wikipedia lactose intolerance entry.


Coevolution and Speciation examples.

Some links to further information on some of the examples I mentioned today.

The Madagascar Star Orchid story is described, and you can see further pictures, both here and here.

There's a nice article here that covers the role of linguistics in studying the initial peopling of the Americas.

The snail shell coiling example is described here.

There are several nice articles on the web on the evolution of the Hawaiian Drosophila. Here is one I found interesting, with some general background, and there are some nice pictures on the PBS Evolution website as part of their Adaptive Radiation Gallery.


Tuesday, July 04, 2006


One of the advantages of having a multiple choice exam is that I get abundant feedback on how many people got every question right, what proportion picked each answer etc. I was looking through the results of last years exam as preparation for writing this years and although I had always realized that people found genetic problems difficult I didn't realize the magnitude of the effect until I decided to quantify it.

If I crudely divide the questions up into three categories and calculate the average percentage of people that got questions in that category correct I get something like:

Genetic problems requiring calculations - 54%
Genetic problems requiring just logic or punnet squares etc - 73%
Everything else - 82%

Another way of looking at this is that although only perhaps ten questions fall into the first two categories the average person will lose 1/3 of the total points they lose on these ten questions alone. Hmmm.


Monday, July 03, 2006

Exam Tips and Tricks

Mike Moser and I were talking about what we could do to help some of the people who are clearly interested in the subject matter of Bio1B and work hard, yet are dissapointed by their midterm grades. Others seem to get good grades with less effort. Some people, it seems, are just better at exams than others. So to help level the playing field I thought I'd try to compile a list of exam advice, tips, tricks, whatever you want to call them. I have focussed particularly on multiple choice exams because that's what we have in Bio1B but many of the principles apply to other types of exam.

Brett has posted the list I came up with to the Bio1B website here.

To most of you, I hope, most of these are common sense. My reason for posting here is to request your input. Any good tips and advice I'm missing? You can e-mail me direct or post a comment here. (Bio1B is NOT graded on a curve so you are not decreasing your own fitness by helping your fellow students!)


4th of July

Today's the Fourth of July
Another June has gone by
And when they light up our town I just think
What a waste of gun powder and sky.
(Aimee Mann - 4th of July)

I have to confess I'm really not very big on patriotism - neither for the country of my birth, nor for the country I now live in. I just don't feel it myself and, like Samuel Johnson, am a little wary of those who claim patriotism as their motive.

So I won't be celebrating too hard tomorrow (in fact I'll most likely write the first midterm) but I'll probably manage to play a 'patriotic' song or two.
Any other suggestions for ironically patriotic songs? (Extra points if a presidential candidate has tried to co-opt them).

You know I thought I had a tenuous link to the class when I started writing this but it escapes me now.

Enjoy the holiday.


Heterozygote Advantage

One of the important things to realize about heterozygote advantage is that it doesn't matter how disadvantageous the homozygous form is, as long as the heterozygote has an advantage over the other homozygote. Or, as Campbell puts it:

Although the fitness advantage to the heterozygotes is much smaller than the disadvantage to the homozygotes, there are so many more heterozygotes than homozygotes that the aggregate benefit of the allele in the population balances, its aggregate harm.'

The classic example is sickle-cell anemia and malaria and this is the only example that seems to fulfil the criteria for heterozygote advantage and be well understood.

Other possible examples are:

Cholera and Cystic fibrosis. When you have Cholera, a toxin is produced by the bacteria which binds to the small intestine, interfers with fluid channels, and causes the body to pump out large amounts of chloride ions and water. In the absence of medical inervention many individuals die from dehydration. Mice (used here as a model system) that are heterozygous for the Cystic fibrosis gene only pump out half as much water and stay better hydrated during Cholera infection. The hypothesis is that, like sickle cell anemia, the Cystic fibrosis gene will be found at higher concentrations where Cholera was most prevalent in the past. But there are some problems with the hypothesis. Perhaps the largest are that Cholera is not thought to have been around long enough to lead to the relatively high frequencies of cystic fibrosis in caucasian populations and there is some evidence the allele had high frequencies before the emergence of cholera. The same allele has been hypothesized to also confer some protection against other diseases that lead to diarrhea and dehydration (eg Typhoid fever and E.coli)

A third possible example of heterozygote advantage is Tay Sachs disease in European Jews originally from Eastern Europe. Heterozygotes are hypothesized to be more resistant to Tuberculosis, which had a high prevalence in this area in the past.

(Speaking of Tuberculosis, check out yesterday's Doonesbury cartoon)


Sunday, July 02, 2006

Family History

'Whenever families gather, the Surgeon General encourages them to talk about, and to write down, the health problems that seem to run in their family. Learning about their family's health history may help ensure a longer future together.'

Although we are increasingly aware of how genetics affects our health, most of us are relatively unaware of our family's health history. The U.S. Surgeon General's Family Health History initiative aims to fill this gap by providing tools to help in the recording and disseminating of your family history.

The program was introduced at Thanksgiving 2004, the online tools were provided for Thanksgiving 2005 and I'd like to give them a little publicity for the 4th of July 2006 - another holiday when many families gather together.

Whilst some illnesses may have relatively simple Mendelian genetics, others have a more complex set of causes. If you'd like the facts about what we currently know about the genetic contribution to almost any disease (from A-alphalipoprotein Neuropathy to YY syndrome) I'd recommend the Genetics Home Reference site - a part of the National Library of Medicine's web site.


Saturday, July 01, 2006

Extinction vortex

One of the problems of a species becoming rare is that it has to contend with all sorts of additional problems that it didn't have to when it was common.

'Artificial insemination has been considered since the 1990s as a way of reducing inbreeding, but has been hindered by the difficulty of collecting sperm. Early attempts used a fake female kakapo mounted on a radio-controlled toy car, which would approach a male in the midst of his lek display.'

Such is the lot of the unfortunate Kakapo - a species of nocturnal, flightless parrot found only on new Zealand. You know you are in trouble as a species when you all have individual names (unless your species happens to be Homo sapiens). The poor Kakapo, with only 86 individuals alive, all of whom are named, suffers from the effects of genetic drift, inbreeding and demographic stochasticity. We discussed the first two of these on Thursday - genetic drift is a problem because it is likely to lead to the fixation of alleles and the reduction of genetic diversity and inbreeding is a problem because it may lead to an increase in recessive genetic disorders. Demographic stochasticity refers to the random fluctuations in population size and structure that will occur as the population gets smaller (in some ways analagous to genetic drift). For example in 1977, the last 18 Kakapo on an island population in New Zealand were all male.

This increase in problems for a species as it gets rare has been termed an 'extinction vortex' - although how general this is is something of a hot issue.

Hot off the press. Check this out in the library: Quantifying the extinction vortex, Fagan WF, Holmes EE, Ecology Letters 2006, 9:51-60