Bio1blog

Midterm 3 results

2007-08-16T22:09:00.000-07:00

I was e-mailed the mean and the results for each answer for the final midterm but not the histogram. I will get mailed a copy of that but I thought some of you might want to see the rest of the information right away.

The mean was 82% (vs. 81% last year)

I have looked at the answer distribution for all the questions to check for problems and everything looks fine.

Lowest % correct was 57% for Q12 (self-thinning question) and 58% for Q 27 (cutting a shoot question).

Highest % correct was 98% (one question: the fresh fruit question - I'm glad this course has some practical uses!).
I have looked closely at all the questions where either less than two thirds of you got the correct answer (three questions) or more than 20% of you picked a particular incorrect answer (four questions) and don't see any problems.

This time last year: Midterm 3 etc

Sayōnara

2007-08-16T00:23:00.000-07:00

As I may, or may not, have mentioned at the beginning of the class this was my last Berkeley class. After 10 years here, 11 Bio1B summer sessions, 14 semesters of es196, 3 semesters of IB100, 1 semester of ES10, 1 semester of ES100, four freshmen seminars and numerous other guest lectures and things I'm forgetting it is time to move on. UC Berkeley, at least in certain science departments, has a policy of having research faculty teach all classes and not employing teaching faculty except on short term contracts. That's fine, it's their university and they can make the rules. However UC Santa Barbara have offered me a tenured teaching faculty position. I will be able to develop the classes I want, have some security of employment and contribute to course and curriculum development. I'll miss Berkeley and its students but I look forward to the challenges ahead.

Purple Earth

2007-08-15T15:16:00.001-07:00

A fun post to finish with, although if I get an electronic copy of the grade distribution I will post that. I am leaving the University tomorrow so thanks for making my last course enjoyable.

One thing I enjoy about teaching basic biology is finding out how much we don't know and constantly finding fun new hypotheses. Here's one I briefly mentioned today that relates to why plants are green and what life might look like on other planets.

You can find a brief description of the purple planet hypothesis here, the implications of this, and other research, for what life on other planets might be like is discussed here.

This time last year: We beat Turkey!

Dr Fungus

2007-08-14T22:26:00.001-07:00

I know that there are probably more than a few of you who are, or intend to be, pre-med. For your interest and edification I direct you to Dr Fungus - an independent Web site dedicated to providing a wide range of scholarly peer-reviewed contemporary and historical information regarding fungi.

'We seek to promote an understanding of fungi and the ways that fungal diseases of humans, animals, and plants affect people living throughout the world. We provide information to both professionals and the public by making a broad range of mycology-related images and content instantly available via the World Wide Web.'

You can attempt a diagnosis of your fungal infection, read about sick building syndrome, learn about anti-fungal agents and check out their image library.

This time last year: Humongous Fungus
Also check out Campbell 7th, and As requested which are still relevant and, hopefully useful.

You say tomato

2007-08-13T22:42:00.000-07:00

A report published just a few weeks ago revealed the results of a decade-long study evaluating organic versus conventionally grown tomatoes. The study showed that organic tomatoes increased in their concentration of three flavonoids studied over time whereas the levels of flavonoids did not vary significantly through time in conventional tomatoes. Mean values for quercetin and kaempferol in organic tomatoes were 79% and 97% higher than those in conventional tomatoes, respectively.

'Flavonoids are a class of bioactive plant compounds that help protect plants from UV-radiation, chemicals and other environmental stressors. In humans, flavonoids help protect cells against environmental insults that may contribute to chronic disease. Several population-based studies suggest that diets rich in flavonoids may help protect against cardiovascular disease, certain cancers and other age-related conditions, such as dementia. Maximizing the flavonoid content of fruits and vegetables could provide a public health benefit.'

The mechanism involved is suspected to be related to the availability of soil nitrogen. Plants with limited nitrogen accumulate more flavonoids than those that are well-supplied.

You can read a press report on the story or read the research report itself: Ten-Year Comparison of the Influence of Organic and Conventional Crop Management Practices on the Content of Flavonoids in Tomatoes

This time last year: Only you can prevent forests

Ferrets bounce back

2007-08-12T21:25:00.000-07:00

I have to disclose before this post that I'm a huge ferret fan. As you probably know it is illegal to keep ferrets as pets in California. I just checked and Hawaii is the only other state to ban ferrets but several cities also ban them, and Rhode Island will make you buy a 'Ferret permit'. Thanks to Wikipedia I now know that Delta airlines are the only airline to allow ferrets in the cabin during a flight. As I said, I'm a ferret fan but even to me that seems like an accident waiting to happen....

Anyway, the reason for this ferret post is the news this week that the often criticized endangered species act may actually have scored a hit with North America's most endangered mammal, the black footed ferret. This news has numerous links to our ecology lectures, from the way that scientists are estimating the ferret population, to the conservation of endangered species, and the genetic consequences of passing through such a genetic bottleneck.

You can read reports on the research at the LA Times, National Geographic, and many others or read the actual report in the journal Science.

This time last year: Life in a seed

Evolution's greatest mistakes

2007-08-11T23:08:00.000-07:00

There's an interesting article in New Scientist magazine this week on Evolution's greatest mistakes. The article covers seven areas of human biology where evolution has made the best of a bad job, and where it would be hard to argue that any 'intelligent' design has been going on. Unfortunately reading the article requires a subscription to the magazine so from a Berkeley website you may, or may not, be able to read it here. But if not, in the interest of academic debate and in the spirit of fair use, I copy an extract below.

A particularly interesting topic for this class is the discussion of mitochondrial DNA. Bottom line: If you wanted to build humans to last, mitochondria are the last place you'd put DNA.

'Inside every one of our cells are dozens of little sacs called mitochondria, in which sugars are "burned" to produce the energy that powers the cells. The process also produces highly damaging molecules called free radicals, so the interior of a mitochondrion is hardly the safest place for vital DNA - and yet it is home to the genes for 13 crucial mitochondrial proteins.

It's a crazy design: like keeping the repair manual for a steam engine by the furnace, where it inevitably becomes charred and unreadable. The slow loss of function as mutations accumulate in mitochondrial DNA may be the main cause of ageing and, some believe, of many age-related diseases, from diabetes to Alzheimer's.

The DNA is there because of our evolutionary history. Mitochondria are the remnants of a once independent bacterium that formed a symbiotic alliance with our cells around 2 billion years ago. Over time, many of the bacterium's original genes have been lost or jumped to the cell nucleus, but human mitochondria still retain 13 genes.

Anti-ageing research is already exploring ways of moving the remaining genes to the safety of the nucleus. It will not be easy. The 13 genes cannot simply be moved to the nuclear genome, because then the 13 proteins will be made outside the mitochondria where they are needed. A solution might be to get the mRNA recipes for proteins delivered to the mitochondria, so the genes reside in the nucleus but the proteins are still made inside the mitochondria.'

This time last year: the very depressing Eastern Garbage Patch

Science Friday

2007-08-10T19:05:00.000-07:00

The 'internets' get a lot of grief sometimes and so I feel it is my duty to stick up for them whenever possible. Bless those little tubes.

The reason this struck me today was that I was in my car this morning when Science Friday came on NPR. There were two interesting stories of direct relevance to this class but I had other (out of the car) things to do. Thanks to the wonders of the Internet I was able to download the two segments later and listen to them at my leisure.

The first segment (link to mp3 file) concerns the evolution of man. Researchers working in Kenya have found fossils indicating that Homo habilis did not give rise to Homo erectus, as previously thought, but the two existed at the same time, with Homo erectus and Homo habilis both evolving from a common ancestor 2 to 3 million years ago. The paper is to be published in the journal Nature this week.

The second segment (link to mp3 file) described how researchers have been able to extract frozen bacteria up to eight million years old from Antarctic ice samples. They were able to revive the bacteria and the bacterial colonies began to grow again. This research is published this week in the journal Proceedings of the National Academy of Sciences.

This time last year: GM plant escapes into wild

Passing gas

2007-08-09T19:20:00.000-07:00

Improvementsin sampling techniques and mass spectrometry in thelast 20 years have revealed that plants emit a wide range of volatile chemicals such as methanol, acetone, formaldehyde, plus a host of terpenes, phenylpropanoids,benzenoids, and many more. One key question is whether these chemicals perform a function or are the plants just"passing gas" by emitting compounds that are by-products ofessential processes?

In the last decade or so the emitted compounds have been shown to both deter herbivores themselves and attract predatory and parasitic species thatattack herbivores.

A recent research report shows that herbivore-induced volatile organic compounds elicit a defensiveresponse in undamaged plants (or parts of plants) under naturalconditions, and they function as an external signal for within-plantcommunication.

On a related topic, the monarch butterflies that you sometimes see around are not only able to cope with the toxic compounds found in their host plants, milkweeds, but they store them making the larvae and adults distasteful and toxic to their predators.

This time last year: Some like it hot

Fog Drip

2007-08-08T22:08:00.000-07:00

I briefly mentioned today the work of Todd Dawson, a professor in Integrative Biology at UC Berkeley (and past Bio1B instructor) who works on Redwoods. Here are a couple of links if you'd like to read a little further on this interesting topic.

A nice article on the use of fog by plants.
Some of the Redwood research currently going on in Todd's lab.
A UC press report about the use of wireless sensors in the redwood canopy.
Whilst we were speaking today one of Todd's students was presenting a paper on the foliar uptake of fog water by redwood forest plants at the annual Ecological Society of America Meeting, which is going on this week in San Jose. The abstract provides a nice summary of the research.

This time last year: Final Jeopardy

More corpse

2007-08-07T19:01:00.000-07:00

The corpse flower at the Botanic gardens opened today. I was looking for more information about the plant online and found several interesting sources.

First up check out some of the amazing pictures a google image search brings up.

Wikipedia conveniently translates the latin name. ('Corpse flower' is good but I think 'Giant misshapen penis plant' would have been better).

You can read about the efforts at the Huntington library and botanic gardens to pollinate a specimen and circumvent the plants attempts to avoid self-pollination (it involves a bag of apples).

Brooklyn Botanic gardens have a very cool time lapse video of their flower captured over a 12 day period.

But UC Davis wins the prize with a great Titan website, with more information than you could possibly need. Many of your most pressing questions are answered by short videos:
What are the parts of this 'flower' and why do people keep calling it an inflorescence or bloom and not a flower?

What are the insect pollinators of the Titan?

This time last year: Songs of Science

Frog-killing fungus

2007-08-06T22:01:00.001-07:00

When we get to our fungi lecture I won't have more than a few minutes to talk about a strange group of fungi the Chitridiomycota - or the Chytrid fungi. Not included in the Fungi group until recently they are mostly detritivores, living on dead material, but at least one species is pathogenic. The waterborne fungus, Batrachochytrium dendrobatidis, attacks many species of amphibians and is at least partially responsible for a global decline of amphibians.

Work carried out at UC Berkeley and published in PNAS next week now suggests that the fungus may end up playing the bigger role in the frog's demise than previously thought because of the pathogen's ability to spread over long distances and possibly persist in the environment as a consequence of sexual reproduction. A study of the genetics of the fungus provided the first evidence of genetic recombination in B. dendrobatidis, which results in multiple, related genotypes and suggests that sexual reproduction is occurring - even though spores have not been discovered.

This work was carried out in the Briggs lab in Integrative Biology in association with the Taylor lab in Plant and Microbial Biology and is part of a larger project on chytridiomycosis (the disease caused by B. dendrobatidis) and the mountain yellow-legged frog led by Cheryl Briggs, UC Berkeley associate professor of integrative biology.

This time last year: CNR Smorgasbord

Environmental Forensics

2007-08-05T12:24:00.001-07:00

There's an interesting article on the Science website today about Environmental Forensics - a topic I have mentioned several times in class because I presume, with the success of shows like CSI, that it is a topic people find interesting.

The article is actually about the rise of the discipline in Europe but it links to the International Society of Environmental Forensics, which, as the name suggests, is an international organization that provides more information about this emerging field.

This time last year: Deep Green and Dead Zone

When algae go bad

2007-08-03T21:59:00.000-07:00

Algae are like the teenagers of the botanical world. They really do lots of wonderful things - producing oxygen and taking up carbon dioxide for starters (algae, not teenagers) but do you ever hear about these things in the news? Oh no, all you ever hear about are those bad 'toxic' algae.....

Just in today's news there are reports of toxic algae in:
Merseyside, England
Florida
Canada
Nebraska

and the worst part is that most of these bad 'algae' aren't even algae - they are blue-green algae, which are actually bacteria.

This time last year: Beatrix versus the Botanists

Midterm 2 results

2007-08-02T16:08:00.000-07:00

The second midterm has been graded and your GSI's will give you your individual results next time you meet with them. Please don't e-mail me - I don't have the individual results, just the overall summary.

Overall there were 248 students for the second midterm, the mean was 86% (vs 80% for the first midterm) and the median was 89% (vs 84% for the first midterm).

Overall 50% of the class scored in the A range (>90%), 28% in the B range (>80%), 13% in the C range, 5% in the D range and 4% in the F range.

These results are slightly higher than last year(see link below for last years results). Like the first midterm twelve people obtained perfect scores - although I have no idea if they are the same twelve people.

As usual I have looked at the answer distribution for all the questions to check for problems.

Lowest % correct was 49% for Q23 (demographic transition question) and 54% for Q 34 (density dependent mortality in the beetle population).

Highest % correct was 98% (two questions).
I have looked closely at all the questions where either less than two thirds of you got the correct answer (just the two questions mentioned above) or more than 20% of you picked a particular incorrect answer (three questions) and don't see any problems.

Section means were similar and, again, no section was more than 4% away from the overall mean of 86%.

FYI the mean and median for the final midterm are usually closer to the first midterm (ie a mean of around 80-82%) than the second.

This time last year: Midterm 2 Results and Lichens in Space

Titania the corpse flower

2007-08-01T15:02:00.001-07:00

A few days early to be perfectly paced for our lecture material, the titan arum, Amorphophallus titanum, (aka the corpse flower) is expected to bloom at the UC Botanic Gardens this week.

The titan arum is one of the largest and most spectacular blooms in the world, and the specimen at the Botanic Gardens is currently over five feet tall and growing several inches per day. They have set up a webpag e so you can track its progress and visit when it flowers. The picture to the left shows the last titan arum to bloom at the Botanic Gardens

Although the bloom will likely remain for about a week after it opens, the strong stench of dead flesh for which it is named is strong for only about the first 12 hrs after it fully opens. The odor helps the plant attract insects that carry its pollen to other titan arums.

This time last year: Fertilizing the Oceans and Diatom Art

Address the mess

2007-07-31T20:46:00.000-07:00

Something a little lighter for the final ecology post, courtesy of Comedy Central. They invite you to address the mess and find out just how environmentally unconscious you are.

But if I may introduce a slightly serious point, the problem with quizzes like this one (and yes I do know this one isn't meant to be serious), and even the earth footprint calculator, is that they tend to lump all environmental behavior together. This can lead people to think that by recycling, carrying their own coffee mug around and switching off lights they are helping save the planet. I suppose every little helps but it takes an awful lot of little things to make up for some of the big ones and quizzes and surveys like this could do a much better job if they pointed out the impact of each behavior. The earth footprint calculator almost does this on the final page but I don't know why they don't have the 'impact' of each answer pop up as you answer it. It's not as if people are going to cheat on the quiz (are they?) Then it would be clearer that it's nice to recycle but no amount of recycling will make up for even just a few plane trips.

This time last year: Bug Soup and Pathogens determined to attack inside the United States.

Disease snippets

2007-07-30T21:59:00.000-07:00

Just from today:

A cruise liner hit by a suspected outbreak of legionnaires' disease is due to return to Britain today. (July 30)

Russia dealing with Legionnaire's outbreak. (July 30)

Doctors Debate Over Lyme Disease: Patients ache as doctors disagree about whether there is a chronic form of the tick-borne malady. (July 30)

Personal Health Beliefs Are Largely Hit and Myth. False or Outdated Sense Of Risks Is Widespread, Cancer Study Shows. (July 30)

Global Warming Could Harm Health. Evidence Indicates Climate Change Could Affect Individuals, In Addition To Planet As Whole. (July 30)

In addition The Ecological Society of America have a short factsheet on Hanta Virus, to illustrate that even ecological research with no apparent direct applications can sometimes turn out to be of vital importance.

This time last year: The lost Children of Rockdale County and Mad Cow.

Ecosystem services: a primer

2007-07-29T23:30:00.000-07:00

The Ecological Society of America (ESA) provides a nice summary of the idea of ecosystem services at their website: Ecosystem Services: A Primer
Take a look at the article and then at the end you can follow up some of the links. For example there is an interesting interview with Gretchen Daly, one of the authors of an article that attempted to put a dollar value on ecosystem services ($33 trillion if you are curious).

This time last year: Shipbreaking. Not to be confused with Shipbuilding, the Elvis Costello song, that is about the Falklands war, although no-one here seems to know that.

Bee services

2007-07-27T15:16:00.000-07:00

On Thursday I introduced the idea of species as providers of ecosystem services. An example of an ecosystem service is the pollination of our crops that is carried out by insects. The KQED science program Quest recently featured UC Berkeley ecologist Claire Kremen, and her research on bee pollination. In addition, an online-only special features the urban bees of Berkeley entomologist Gordon Frankie.

More snippets

2007-07-26T23:03:00.000-07:00

Vital ecosystem functions, such as sequestering carbon dioxide and purifying water, depend on a larger number of species than previously thought. From a Nature article this month. Read the article here and a news summary here.

The rainforest fragmentation experiment I described in lecture, the one with 1, 10 and 100 hectare plots, is now in danger of destruction itself. The experiment has been going on since 1979 and has produced an invaluable long term data set. The nearby town of Manaus has grown rapidly since being declared a free-trade zone in the 1970s, with a population of 1.7 million people. Settlers are now moving onto the land around the project and raided a research camp last year. A fire lit by the new arrivals also destroyed several study plots. News report from this week and the experiment's web site.

More species than we thought? It turns out we may not even know how many species there are in the places we thought we did know well. Cryptic species – animals that appear identical but are genetically quite distinct – may be much more widespread than previously thought a paper published this week alleges. The findings could have major implications in areas ranging from biodiversity estimates and wildlife management, to our understanding of infectious diseases and evolution. Read the Research paper published last week here. This also means that what I told you about us knowing how many large species there are may also be up for debate. In 2001 a new species of African elephant was discovered, not by looking under bushes, but by genetic analysis of existing African elephants which suggested two groups distinct enough to warrant species status: The African Bush Elephant and the African Elephant. (Research report on the new elephant species).

People consume a massive 24% of Earth's production capacity, depleting species and habitats - and things could get worse if more land is used for biofuel crops. By comparing carbon consumption through human activity with the amount of carbon consumed overall researchers found that humans use 15.6 trillion kilograms of carbon annually. Read the PNAS paper published this month here.

This time last year: Save the Rhino Maggot!, Specicide, Bird Extinction Rates and Snakes on a Plane.

Found today, gone tomorrow

2007-07-25T21:04:00.000-07:00

Hummingbirds are amazing. I must confess that when I first came to California I had no idea that you had hummingbirds here. I can still stare at them in wonderment. They're just so small, and feisty.

A new species of hummingbird, the gorgeted puffleg, has been discovered in the mountains of Colombia, but environmentalists fear the discovery will be short-lived – the bird is already threatened with extinction.

The bird was first spotted in 2005 and new expeditions in 2006 confirmed it as a new species of hummingbird - Eriocnemis isabellae.

Unfortunately it is thought that the bird's range must be very small in order for it to go undiscovered for so long and the bird's habitat is being threatened by slash-and-burn agriculture and encroaching coca fields.

There is a report on the discovery in New Scientist here.

The picture is pretty cool. Something about it reminds me of the infamous youtube praire dog 'dramatic look' video.

This time last year: Rachel Carson, Fred Soper and DDT

Fish Farming

2007-07-24T15:05:00.000-07:00

Perfectly timed for our mutualism lecture is this report from yesterday that the dusky damselfish has joined a select group of species, including humans, ants, and salt-marsh snails, that are known to cultivate beneficial crops. The fish rely on the algae as a source of food, but the algae also benefit because they only survive well if they are farmed. The algae farms are kept both protected and weeded by the damselfish. Unwanted sea urchins and starfish are ejected from the farms, and unpalatable algae are meticulously weeded out to promote lush turfs of the preferred species. When the damselfish are removed from the 'farms' it only takes a couple of days for other grazing fish to move in and obliterate all the algae growing inside the gardens.

This time last year: Mt. St. Helens and Wiki1B again

Encyclopedia of the Environment

2007-07-23T22:00:00.000-07:00

If you have read this blog much you'll know I'm a big fan of Wikipedia. One of the reasons I like it is that it has, largely, emerged organically from the passion of dedicated enthusiasts. It is not being driven by a huge corporation. However as criticisms of Wikipedia grow it isn't clear what will triumph in the long run. Will Wikipedia emerge as a giant in the Google mold, or will it be replaced by more specialized encyclopedias? Numerous contenders are already emerging from the amusing Conservapedia (which always reminds me of Stephen Colbert's quote at the White House Correspondent's Dinner that 'reality has a well known liberal bias') to the more specialized 'Encyclopedia of the Environment' which addresses the issue that Wikipedia is not peer reviewed by having all their articles peer reviewed. Lots of interesting stuff there from classic ecological and environmental papers such as Garret Hardin's Tragedy of the Common's paper to great speeches by Jimmy Carter and Mother Jones, and lots of articles on ecological topics.

Whilst we are on the subject don't forget to check out our very own Wiki1B.

This time last year (another of my favorite posts): Honey Guides, Killer Bees and Land Mines.

Rise of dinosaurs not so rapid after all.

2007-07-22T13:31:00.001-07:00

I didn't want to let this press release from researchers in Integrative Biology at UC Berkeley slip by. They showed, for the first time, that dinosaurs and their non-dinosaur ancestors lived side by side for tens of millions of years, disproving the notion that dinosaurs rapidly replaced their supposedly outmoded predecessors.

The finds, including fossil bones of a new dinosaur predecessor the researchers have named Dromomeron romeri, are described in a cover story in the July 20 issue of Science.

This time last year: 100 Ecological Questions and Global Warming threatens California Wine Industry

Evolution is easy!

2007-07-20T22:43:00.000-07:00

Thanks to the wonderful folks at BoingBoing (a directory of wonderful things) for directing my attention to this fabulous cultural artifact: a Red Queen Barbie doll! Part of a new line of Alice in Wonderland Barbie toys. Buy this one and all your other Barbie dolls will have to run twice as fast just to keep up.

The only disappointment is how, well, static, the Red Queen looks. Perhaps she should come with a catapult launcher.....

Although Barbie is well known for his difficulty with math she has already revealed a fondness for evolution: witness the Paleontologist Barbie. I love the 'Dinosaur Quiz' on the back - 'if you get five or more right you should consider a career in paleontology too!' Sadly the text is too small to read the actual questions. Although I think one of them may be 'What does Dinosaur mean?' Fortunately diligent searching of the ebay archives produces this better image. Now you too can take the quiz and even check the answers to find out if you too can be a paleontologist!

This time last year: Ecological Footprints and Summer Reading part 2

Footprints

2007-07-19T22:32:00.001-07:00

The issues we discussed at the end of today, human population growth and overconsumption, are also neatly summarized in the idea of an 'ecological footprint.' I think this idea is discussed in Campbell but there are several websites that develop this idea. First proposed in 1992 by William Rees, a Canadian ecologist, ecological footprint analysis approximates the human impact upon the environment by calculating the ecologically productive land and marine area required to sustain a population, manufacture a product, or undertake various activities.

I like this Global Footprint Network Site because it lets you see, and calculate if appropriate, world, national and individual footprints. There's lots of interesting stuff here. Check out the World Consumption Cartogram. It's interesting to view this on a national level because some countries and areas will have large footprints because of their large populations and others will have large footprints because of their large consumption.

This time last year: How many people can the earth support?

Worth a thousand words

2007-07-18T14:58:00.000-07:00

If you like your news with cool photographs you should bookmark National Geographic's 'Photos in the News' page.

Here are some recent stories relevant to this class:

New 'Wasp' Orchids tempt male bugs. In a crafty evolutionary hoax, six newly discovered orchid species are shaped like female wasps to trick males into pollinating them.

Baby Mammoth found frozen in Russia. A six-month-old baby mammoth found in Russia's remote Siberian north is the best preserved example of the species ever recovered.

It's those giant penguins again. Two species of ancient penguin have been uncovered in a Peruvian desert, including one that stood almost 5 feet (1.5 meters) tall, a new study reports.

Surprising herds discovered in Southern Sudan. Aerial pictures reveal vast herds of antelope, elephants, and ostriches flourishing in Southern Sudan, despite decades of war.

Amazon expedition discovers dozens of new animals. A flashy purple frog and a kissy-faced catfish are among the 24 new animal species recently discovered by scientists working in the remote highlands of Suriname.

This time last year: Leonard Cohen's March of the Penguin's and Elephants in Space

Rat Reciprocity

2007-07-17T15:44:00.001-07:00

What is it that makes us uniquely human? Is it our intelligence, no, dolphins and monkeys are plenty smart. Is it our capacity for self-awareness? Nope, apes, dolphins and elephants have been shown to be self-aware. Mourning the dead? Nope, elephants do that. In fact we could go through a pretty long list of traits that we might think are uniquely human, only to find one or more animal species that also show this trait. So its a relief to find a study published this week that allows us to hold on to the one trait that, so far at least, remains uniquely human - spite. (Incidentally there are very few scientific experiments I'd want to watch on video but I'd make an exception for this one. Chimps and collapsing tables of food sound like a great combination).

Also, just published, the first evidence of an unusual form of altruism, termed 'generalized reciprocity': Generalized Reciprocity in Rats. In the first example of general cooperation in any animal, rodents helped by unfamiliar rats are found to help strangers themselves.

This time last year: Running after Antelope

Understand the rules before you break them.....

2007-07-16T15:16:00.000-07:00

In a different class I give a lecture on how to give an oral presentation. After going through a pretty big list of do's and don'ts I finish by pointing out that all good speakers will break one or more rules. In my mind though it is still important to understand the rules, not so you can slavishly follow them, but so you know when you are going against convention. Bottom line - always understand the rules before you break them. I think that is generally a good motto for life too.

That is why I go, as clearly as I can, through the scientific method, despite the fact that some fairly influential thinkers have argued that most scientists don't even operate in this way. Again, I would argue that it is vital to understand the rules so that you can see the consequences of breaking them. A noted Berkeley connection is the philosopher Paul Feyerabend who spent three decades associated with UC Berkeley. Feyerabend was critical of not just the idea of the scientific method but was also critical of the idea of the philosophy of science itself - a critical guy. You can read accessible and interesting introductions to his work at both Wikipedia and at the Stanford Encyclopedia of Philosophy. (My definition of 'accessible' is that you can read the article and understand what most of the words mean and the gist of what they are saying. My definition of 'interesting' is that it made me go hmmm.)

If you look at any article in a scientific journal you will also notice that it isn't neatly laid out like the slide I showed with 'Data', 'Hypothesis', 'Prediction' etc. Although these words will be tantalizingly scattered throughout the text. In a bid to demystify the somewhat arcane style of scientific writing, the journal Science has selected a number of scientific articles from that journal and annotated them, illustrating how different parts of each article embody the scientific method. This is part of the 'Keystones of Science project'. Here is an annotated example of the scientific method example titled Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?.

This time last year: Dr Dino versus the Amazing Randi

Evolution Blogs

2007-07-15T22:31:00.000-07:00

For the last evolution post I'd like to recommend a couple of evolution related blogs you may enjoy if you wish to explore some of the topics we touched on, and many we didn't, further.

PZ Meyers Pharyngula blog is self-described as 'Evolution, development and random biological ejaculations from a godless liberal'. That seems to describe it fairly well. PZ Myers is a biologist and associate professor at the University of Minnesota (and the pharyngula period is a stage in the embryonic development of vertebrates).

Speaking of the godless, and I mean that quite genuinely, Richard Dawkins has two websites/blogs that are well worth checking out. The official Richard Dawkins website self-described as 'A Clear-Thinking Oasis' and the Richard Dawkins Foundation for Reason and Science (another Clear-Thinking Oasis'). Richard Dawkins holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University. He came to prominence through his 'Selfish Gene' book in 1976, a book that all Biology undergraduates at my University were recommended to read a decade after its publication - a recommendation I am happy to pass on thirty years after its publication. Lately Richard Dawkins has been rather prominently involved in the debate between creationism and evolution and is often described, usually by others, as an 'outspoken atheist'. His latest book, 'The God Delusion', combines his work on evolutionary biology and his passionate atheism to ask why, if there is no god, a belief in one so widespread and prominent as to be almost universal? In the hands of an evolutionary biologist this turns out to be quite an interesting question.

Onward to Ecology.....

This time last year: What, if anything is a Preble's Jumping Mouse?

When Giant Penguins Roamed the Tropics and other Snippets

2007-07-14T22:32:00.000-07:00

What a great word: 'Snippets'.

A good way to get entertained and keep up with news in the sciences is to read New Scientist magazine. Although it is British, there really isn't an American equivalent and the magazine has become much more international over the last few years. It really isn't that expensive to subscribe especially since it is a weekly magazine but you can also read many of the articles on their website (or in the library copy of course). Although they do have a few longer articles each week, much of the magazine consists of brief news reports on recent research.

Here are a few of the evolution related articles they have published recently:

Gut parasites came from the deep: A genetic comparison finds links between bacteria from deep-sea vents and those from the human body. 7 July 2007

When giant penguins roamed the tropics: Millions of years ago, human-sized penguins roamed the Peruvian coast just 14 degrees south of the equator, according to new fossil evidence. 25th June 2007

Cooler climes help spur on evolution: Tropical hotspots of biodiversity are not the hottest as far as evolution is concerned. 23 March 2007

Looking for larvae in ancestral genes: Did our earliest animal ancestors go through a larval stage, or did that evolve later? 26 January 2007

and one from last year, illustrating the tendency of New Scientist to try and bridge the gap between more popular journalism and science writing. I'm guessing the original research report did not have this title - Mums help chicks if dad was ugly: Females appear to invest extra energy into getting their poorer-quality offspring off to a good start, at least among house finches. 29 September 2006
(I just checked, the title of the research article is: Yolk Antioxidants Vary with Male Attractiveness and Female Condition in the House Finch (Carpodacus mexicanus))

This time last year: Darwin's Finches

Midterm 1 Results - 2007

2007-07-13T11:58:00.001-07:00

The first midterm has been graded and your GSI's will give you your individual results next time you meet with them. Please don't e-mail me - I don't have the individual results, just the overall summary.

However some of you may be interested in this, especially when you have your own grade.

Overall there were 259 students, the mean was 80% and the median was 84%. This difference is typical for skewed distributions and is why the median is a better descriptor. If you got 84% (the median) then half the class scored more than you and half the class scored less.

Overall 37% of the class scored in the A range (>90%), 25% in the B range (>80%), 18% in the C range and 10% each in the D and F range.

These results are similar to previous years (see link below for last years results) with one small exception - a much higher number of students than usual got a perfect score. This year an impressive 12 students got 100% on this midterm. Well done.

As usual I have looked at the answer distribution for all the questions to check for problems.

Lowest % correct was 57% for Q27 (polydactyly in cats - despite the word DOMINANT being in bold capitals, a significant number of people provided the allele frequency that would have been correct if it was a recessive trait) and 50% for Q 37 (the calculation on the seed discarding plant breeder that was meant to be a fairly difficult question).

Highest % correct was 98% (one question).
I have looked closely at all the questions where either less than two thirds of you got the correct answer (6 questions) or more than 20% of you picked a particular incorrect answer (4 questions) and don't see any problems.

Section means were similar and no section was more than 4% away from the overall mean of 80%.

This time last year: Midterm 1 Results and Web Sight

Male killer

2007-07-12T17:29:00.000-07:00

Currently the lead story on the News section on the UC Berkeley Home page is about a study that shows natural selection in action and illustrates the Red Queen principle.

Wolbachia is a is a genus of inherited bacterium that infects a high proportion of all insects. They are the world's most common parasitic microbes and often lead to the death of males.

Over only 10 generations that spanned less than a year, the proportion of males of the Hypolimnas bolina butterfly on the South Pacific island of Savaii jumped from 1 percent of the population to about 39 percent. The researchers considered this a stunning comeback and credited it to the rise of a suppressor gene that holds in check the Wolbachia bacteria, which is passed down from the mother and selectively kills males before they have a chance to hatch.

"To my knowledge, this is the fastest evolutionary change that has ever been observed. This study shows that when a population experiences very intense selective pressures, such as an extremely skewed sex ratio, evolution can happen very fast."
Sylvain Charlat

The actual paper will come out in the journal Science tomorrow.

The fieldwork for this study was carried out on two South Pacific Islands and the researchers were based out of UC Berkeley's Gump Richard B. Gump South Pacific Research Station on the island of Moorea in French Polynesia. I mention this because this field station is also the home for IB 158/ESPM 107 : Biology and Geomorphology of Tropical Islands - a semester long course that spends 9 weeks at the field station.

This time last year: Woof!

Sex, sex, sex

2007-07-11T22:38:00.000-07:00

Science is never so much fun as when it is a little controversial. When you add this to the fact that everybody likes to argue about sex we have a recipe for fun, fun fun.

Just when it looked like the red queen hypothesis was gaining the upper hand as an explanation for the prevalence of sex across the animal and plant kingdoms it has started to struggle to explain why species have so much sex. Why not reproduce asexually most of the time to get the benefits of that strategy and throw in a little sexual reproduction here and there for variety (literally)?

There's a nice essay by Matt Ridley on the PBS Evolution website that discusses the issues we talked about in class.
Here's a BBC report from a paper in 2004 which takes the issue further and asks whether the Red Queen hypothesis can really explain why we have so much sex...
And to bring us up to date here's a link to a report on a paper from 2006 that argues that the Red Queen hypothesis does just fine if we take into account the maternal transmission of parasites.

This time last year: The Demon in the Freezer

Blog fun

2007-07-10T22:58:00.000-07:00

I don't want to make people paranoid but you do leave traces in cyberspace.

I have a simple web counter on this site (click on the number at the bottom of the page, or here, to see it). This is just the free version - the paid version would probably give me much more information. Check it out to see what information ANY website can collect on you.

I don't use it much but it's nice to see that people are using this site. It's also often amusing to see the search terms that bring people here. Last year I started a list of some of the best ones (people search on some very weird things) but here's a few that made me chuckle today. (Although, as you may have noticed, I am fairly easily amused....)

latto first midterm - Nice try buddy.
very fat mouse picture - Okay, who else immediately did a google image search on this?
scorpion chasing duck - What? Why?
zedonk sale

Dominance

2007-07-10T22:27:00.000-07:00

First, be careful when you do a google search on 'dominance'. I'm so naive sometimes.....

Anyhow, an interesting question came up today - what IS dominance? What causes one allele to be 'dominant' to another?

In certain cases it is pretty simple. The production of 'something' tends to be dominant to the production of 'nothing'. So 'wild type' alleles tend to be dominant to mutants that code for nothing. If the allele is coding for the production of an enzyme and a single copy of the allele produces more than enough then the heterozygote and the homozygote will have similar phenotypes - complete dominance. However if the homozygote produces just enough then the half expression of the heterozygote may result in a different phenotype. The pink flowers would be a good example here. The pink comes about by the production of only half as much red pigment.

After this it gets a bit more complicated and was, in fact, the subject of a fairly intense debate in the last century between two giants of the population genetics world: RA Fisher and Sewall Wright. If you are interested in this topic then here are a couple of entries into the literature: a blog post entitled ' Whatever happened to the Fisher-Wright controversy?' and an article in the Journal of Theoretical Biology on 'The Heat-shock Response and the Molecular Basis of Genetic Dominance'.

This time last year: Canterbury Tales

Hox genes

2007-07-09T21:19:00.000-07:00

If regulatory genes can be likened to movie directors then the Homeobox genes (or Hox genes for short) are the Martin Scorsese of the gene world. They certainly get a lot of press and they may well be geniuses.

Hox genes encode transcription factors which switch on cascades of other genes, for instance all the ones needed to make a leg. This means that despite being fairly small (only 180 base pairs long in humans) they can have huge effects.

You can read about the discovery of Hox genes at the Howard Hughes Medical Institute and there are several interesting articles about Hox genes at the Pharyngula blog. Here's one on Hox genesis, and there's an overview of Hox genes here.

This time last year: The Thagomizer

Learn to fish

2007-07-08T21:32:00.000-07:00

There is a very widely known saying:
'Give a man a fish and you feed him for a day. Teach a man to fish and you feed him for a lifetime.'
Variously attributed to 'Unknown', 'Chinese Proverb' or 'Lao Tzu'.

This saying is very pertinent to teaching. Sometimes it's a lot easier to hand out fish! However sometimes it's easy to teach a few fishing tricks. Here's one that you can use for the rest of your Berkeley career, and beyond, that surprisingly few people seem to know about. I may mention this in class on Wednesday but you read it here first.

Now that the Internet has calmed down a bit from its initial birth pangs many sites have fairly reliable url's. These include websites for large classes such as Bio1B. For example the Bio1B website has been http://ib.berkeley.edu/courses/bio1b/ since 2001. You can use a site like the Internet archive to go back in time to look at the site in the past. Why would you want to do that? Well you can easily pull up reading lists from the 6th or 5th edition and you can find some past quizzes that might be useful for review. You don't need to restrict yourself to the summer you can look at sample exams that might have been posted by others that teach this course. Of course they may cover some things we don't and vice-versa but there will be a LOT of overlap - we do compare notes and syllabuses you know!

This time last year: Brave New World

Weird Life

2007-07-07T21:01:00.000-07:00

I don't want to claim to be a good at predicting the future (I'm not) but I do want to say that one of the few predictions I have bored people with for some years is now given some tentative support by a very prestigious group.

“Nothing would be more tragic in the American exploration of space than to encounter alien life and fail to recognize it.”

A report just published the National Research Council (NRC) suggests that the search for extraterrestrial life beyond Earth’s solar system should be widened to include investigations that includes “weird” life. The whole report is available online here or you can read their news report.

Next week we will consider the origin of life, and indeed, what we even mean by life

I think this is post #100. Yay.

This time last year: Missing Links, Transitional forms and the Fishapod...

Spots 'n Stripes

2007-07-06T00:01:00.000-07:00

A student, Raj, sent me a link to this amazing image of a Horse-Zebra cross. The article calls it a Zebrula and if you check Wikipedia you'll see there are a number of Zebra crosses, collectively known as Zebroids:

Zebra (stallion) + horse (mare): zorse, zebra mule, zebrule or golden zebra
Zebra (stallion) + pony (mare): zony
Zebra (stallion) + Shetland pony (mare): zetland
Zebra (stallion) + any ass species (jenny): zebrass
Zebra (stallion) + donkey (jenny): zedonk, zeedonk, zonkey, zebronkey, zebadonk
Zebra (mare) + donkey (sire): zebrinny
Zebra (mare) + horse (stallion): hebra

Apparently they were mentioned by Darwin: in the Origin of Speies he refers to four coloured drawings of hybrids between the ass and zebra. These crosses are usually sterile. The Zorse article has some comments on genetics:

Zebras, donkeys, and horses are all members of the family equus -- equines. Equines can be crossbred to produce hybrids. They are all slightly different in genetic makeup, but still all equines. That is, horses have 64 chromosomes, zebra have between 44 and 62 (depending on species). Zorses can be male or female, but are sterile since their chromosome count is 63.

Just in case you think I get all my information from Wikipedia I'll also refer you to the wonderfully named International Zebra-Zorse-Zonkey Assocation. Lots of information and pictures and even a Zonkey for sale. Where else but at the Spots 'n Stripes Ranch in California. I didn't know I wanted a Zonkey, but now I do.

This time last year: The map that changed the world

Species diversity

2007-07-05T15:42:00.000-07:00

A nice overlap between evolution and ecology is the concept of species diversity. Studying what causes the number of species in a group to increase or decrease is largely the realm of evolution and studying what allows a particular number of species to coexist in any particular habitat is largely the realm of ecology. However, when species get affected by man and are driven to extinction the subject is often of interest to both evolutionary biologists and ecologists.

A nice study reported this week shows that although the loss of species diversity of Tahiti's snails has been high (following the introduction of a predatory snail), the diversity at a larger scale remains because members of each of the major groups (or clades) remain.

'Not much of a consolation, perhaps, but at least in a few hundred thousand years there might once again be the kind of diversity on Tahiti that existed before we arrived.'

High-performing males have underachieving daughters

2007-07-04T21:58:00.000-07:00

An interesting article in Nature last week, summarized here, described how, in red-deer, successful fathers tend to have unsuccessful daughters. In contrast male deer that carried genes that led to greater success in daughters were less successful themselves. This provides an interesting insight into the so called 'battle of the sexes' and may help explain why some genetic variation is maintained in sexual species.

This is relevant to our discussion of sexual selection but we will also return to this topic in the ecology section when we talk about different mating strategies.

Another June has gone by

2007-07-04T21:41:00.000-07:00

Last year I tried to keep this blog class related. I think my only significant lapse was on the 4th of July, so now I'll repeat that with a link to one of my favorite songs. Last year I couldn't find a copy to link to but this year there is a video of Aimee Mann singing 4th of July on Jools Holland's TV show. Enjoy.

This time last year: 4th of July

Scientists change one species to another (cue evil laugh)

2007-07-03T15:30:00.000-07:00

Scientists, oh those wacky scientists, have now transformed one species into another. Craig Venter and his team took the genome of one bacteria and transplanted into another, thus changing it to another species. This research is being reported as the first step in creating an artificial life form from scratch. You can read a BBC report, a report in New Scientist magazine or listen to Ira Flatow talk to Craig Ventner on last week's NPR's Science Friday.

This time last year: follow up on some of the examples from class, Coevolution and Speciation Examples.

Resistance is not so futile

2007-07-02T15:39:00.000-07:00

I could probably post a new link about antibiotic resistance every day. Here's one I noticed today, a report by NPR that Chinese fish imports may contain fluoroquinolone antibiotics - a potentially serious problem since ciprofloxacin, currently often used a last resort, is a fluoroquinolone. You may remember ciprofloxacin, or Cipro, as the drug of choice during the 2001 anthrax attacks.

Some of you may have seen the press reports last week following a new survey of US hospitals that revealed much higher levels of antibiotic resistant bacteria than previously suspected.

Here's a previous post on this topic: Losing the Battle

This time last year: Heterozygote Advantage

and here's a post from approximately this time last year that someone was asking about. Are humans still evolving: Got Milk?

Only vaguely related

2007-07-01T23:38:00.000-07:00

One of the joys of the weekend is catching up on some reading. Although I'm a great fan of the internet I also love magazines. An article in Wired magazine (also available online here) on the advantages humans still hold over computers made me smile. Sometimes people are real smart. You know those little distorted strings of numbers and letters you have to type in on some sites to prove you aren't a robot? Well apparently they are called captchas (Completely Automated Public Turing Test to Tell Computers and Humans Apart). But the next generation of them will be in two parts. The first will be the actual test (which the computer knows the answer to) but the second will be something that couldn't be deciphered by the Internet Archive's project to scan public domain books (a smudged or faded word perhaps). So in the course of everyday transactions millions of people will be helping to correct machine read text. Cool.

Also, in The Week magazine, a weekly compendium of the best US and International journalism, I came across this quote by John Kenneth Galbraith:
"Faced with the choice between changing one's mind and proving that there is no need to do so, almost everyone gets busy on the proof."

This time last year: Family History

Choosing a mate

2007-06-30T21:31:00.000-07:00

One advantage of teaching this course many times is that I'm fairly familiar with the pace we need to go at. One thing I don't like to do is to rush through material at the end of a lecture just to finish off at a particular point. On Thursday I finished whist talking about non-random mating, having covered inbreeding but without covering other types of non-random mating. We will cover this on Monday. Basically ANY form of partner selection will make a mating system non-random. We know this goes on, in humans as well as other animals and plants, but it isn't always clear why particular mates are chosen.

In an interesting recent study that was in the press last week Lynda Boothroyd, in the Department of Psychology at the University of Durham in England, showed that women who enjoyed good childhood relationships with their fathers were more likely to select partners who resemble their dads. In contrast women who have negative or less positive relationships were not attracted to men who looked like their male parents.

In her own words:
' Does this mean that Freud was right? Well no - according to Freud normal people should resolve their 'complexes' in childhood and stop feeling attracted to their parents before puberty. This research shows that we learn what is good in a face partly from the faces of men to whom we have a strong positive relationship. Further research may show whether this is just fathers or, for example, whether elder siblings may play a role.'

This time last year: Extinction Vortex

Fun for all the Family

2007-06-28T17:00:00.000-07:00

Following a link from Pharyngula, another highly recommended evolution related blog, I am pleased to announce that this blog is officially family friendly.

This rating was determined based on the presence of the following words: breast (x1)

Hmmm.

This time last year (one of my favorite posts): Pedigree collapse - you'll never look at bicycles in the same way again.

Me and my budgie

2007-06-27T21:55:00.000-07:00

I thought I'd give you some links to more information about budgie genetics and was thrilled to find a site called 'Me and My Budgie...' What a great name! Sadly I didn't find their genetic information the clearest and many of the links are broken. But still, great name. I hate to sound like a broken record but you could do worse than checking out the Wikipedia article on Budgie Genetics.

This time last year: Thirteen-year old girls storming the Bastille, It's either a thirteen or a forty five or maybe a fish (the color blindness links I mentioned), and The Y Chromosome - More than a Wasteland.

Fair Use and Fat Mice

2007-06-27T20:21:00.000-07:00

Here's a question: What is unusual about this image of the complex interaction between genes and obesity in mice that I used in lecture today?

Give up? The answer is that I had permission to use it. The image was published in PLoS Genetics - a peer reviewed paper published by the Public Library of Science. Not only is the image free for me to use in class but I can link directly to the paper , which is also free for anyone to read.

"everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish."

Unfortunately this is still rather unusual - although hopefully it is a sign of things to come. It is an illustration of how well the policy works that I came across this article because Carl Zimmer, a science writer with an interesting genetics blog, the Loom, wrote about it. He also incuded a link to a recent article he wrote in Discover Magazine entitled Mendel's Mouse that is well worth a read and fits in perfectly with today's lecture.

I mention the issue of copyright because I get frequent requests that I make my Powerpoint slides available to you. I don't do this because I don't have copyright clearance for all the pictures, cartoons, diagrams etc I might use. Whilst it might be fair use to use them once in a lecture (even this is probably debatable) I doubt that would extend to distributing copies. You could argue that I should get permission for all the images I want to use - but this does not seem feasible. Not only would it take up an impractical amount of time but it would prevent me updating lectures. My next task tonight, for example, is to look through tomorrow's lecture and I may well add some new example, as I did yesterday. Getting permission to use images probably requires weeks if not months of time.

This is why I clearly give you the equivalent figure number in Campbell for important figures and provide lecture outlines. Another option would be to just use figures I have permission to use, basically all the figures from Campbell, which would make for a fairly dull lecture. Then I could distribute the slides - but you wouldn't need them because they'd all be in Campbell!

This time last year: Evolution in ten words, The 'theory' of evolution and Summer Reading.

Wallace, no Gromit

2007-06-26T16:09:00.000-07:00

I want to draw your attention to Wiki1B, which is not actually a true Wiki, but is simply the Summer Bio1B lecture outlines linked to appropriate Wikipedia articles. Wikipedia certainly has its critics but I believe it is a tremendously useful resource for introductory classes, allowing you to easily follow up on anything that you find unclear or interesting. It is also a great tool for any curious person. Today it struck me that I didn't know whether Malthus had been as influential to Wallace as he had been to Darwin (I already knew that Lyell had been a tremendous influence to both men). In the past I would have had to go to the library, find some biographies on Wallace, hope they weren't checked out, and then hope that the indexer had done a good job and put Malthus in the index so I didn't have to read the whole book. But now, especially with Wikipedia, it was the work of seconds to pull up the Wallace article and search for Malthus:

'Wallace spent a lot of time at the Leicester library where he read An Essay on the Principle of Population by Thomas Malthus'.'
and
'According to his autobiography, it was while he was in bed with a fever that Wallace thought about Thomas Malthus's idea of positive checks on human population growth, and came up with the idea of natural selection.^'Question answered. Whether Wikipedia is a suitable tool for primary research is a contentious topic but it sure is handy for answering quick questions - most of which I'd never bother to find out otherwise.

Just today Wikipedia helped me find the name of the guy in the hat who won the 800m at the Munich Olympics : Dave Wottle - and there's a link to a YouTube video of the race! I can even make this relevant to the class because slow and steady really DOES win the race sometimes. Although it looks like he sprints past everyone at the end Wottle actually runs a perfectly evenly paced race and it is everyone else who is slowing down.

This time last year: A Wizard did it.

Finding Erasmus

2007-06-25T14:04:00.000-07:00

You can find Erasmus Darwin's work at the Internet Archive Open-Access Text Archive - a wonderful resource with over 200,000 items, most of them out of copyright or otherwise in the public domain.

Here are links to the Temple of Nature, and Zoonomia. Select the format you want to download from the panel on the left.

You can also find Erasmus at Project Gutenberg, the first producer of free electronic books. They have Zoonomia and the Botanic Garden. They also have most of Charles Darwin's books, including the more obscure ones.

Whilst I'm pointing out resources I should also mention Librivox, which provides free audiobooks of books that are in the public domain. This includes a nice reading of Darwin's Origin of Species. (Full title: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.)
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This time last year - The Politics of Mastodon.

Welcome to Summer 2007

2007-06-21T13:56:00.000-07:00

Just checking I could remember the password. Check the main Bio1B site for useful information about the class. Here are the answers to the most frequently asked questions I've been getting (or 'FAQ' as the cool kids say), one for any Berkeley newcomers and one that I got a lot last year.

Q. Can I use Campbell 6th edition?
A. Yes. If you have to buy a book, and especially if you have yet to take other Biology classes (eg Bio1A), then I'd recommend getting the 7th edition even if it costs a bit more. But if you already have the 6th then you don't need to buy the 7th just for this class.

Q. Is there a lab. manual to buy?
A. No. There used to be but all the lab exercises are online now.

Q. When is the final?
A. There is no cumulative final in summer. We have three, slightly longer midterms than in the regular semester. These are held in regular class time on Thursday July 12, Tuesday July 31 and Thursday August 16.

Q. Will there be labs. in the first week?
A. Yes. In fact there are labs and discussion sections on the first day and some of them may take place before the first Lecture. So check the schedule and make sure you don't miss your first lab or discussion section.

Q. Why does the class always start late?
A. Classes at Berkeley start at ten minutes after the hour and end on the hour. We will start promptly each day so please be ready to start at 12.10.

Q. Do I need to have an account to comment on posts here?
A. No, it just looks like you do. When you hit the 'Comment' link at the end of any post a pop-up window should appear. After the space for you to enter your comment is a set of three buttons. You can pick any one of these three (Blogger, Other, or Anonymous). Because the first one seems to be the default it has spaces for your username and password. But if you pick either of the others these disappear. Choosing 'Other' allows you to enter your name, or alias, and choosing 'Anonymous' requires neither.

Buddy Rocks

2007-01-27T15:47:00.000-08:00

For tens of thousands of years humans lived in the landscape without computers, mobile phones or ipods. For much of that time there wasn't formal 'science' as we consider it today - that is an invention of the last few hundred years.

But human survival depended much more on being able to observe, and interpret, the natural environment. If you read the myths and stories of any native culture, the one thing you notice is an extraordinary attempt to explain the world around them.

Today we seem to be losing our ability to interpret the environment. Nowadays we can get food without being able to track prey, distinguish berries, or reliably find edible roots. Part of an ecologists training is to reconnect with this connection to the environment and the first step is to rediscover our powers of obervation.

There was a nice example of this in the Chronicle today. In the northern part of Yellowstone the habitat is mainly sage grassland with scattered Douglas Fir trees. If you look closely at the picture above you'll notice that every single tree is adjacent to a boulder. Coincidence? Friendship? No, the explanation for this pattern, that many people have probably seen without ever noticing, is that the boulders create the only suitable 'safe sites' or microenvironments where the seedlings can survive the harsh conditions.

Losing the battle

2006-10-22T19:31:00.000-07:00

According to a report by the Centers for Disease Control and Prevention released this Thursday hospitals need to step up efforts to prevent infections with drug-resistant "superbugs," which are becoming more and more of a threat to patients, the U.S.

The death toll from hospital acquired infections is larger than most people think. Infections caught in U.S. hospitals now kill 90,000 people a year. This is now more than mortality due to breast cancer (about 40,000 per year) and road accidents (also about 40,000 per year).

In a separate story wounded British troops returning from Iraq have been linked by government scientists to outbreaks of a rare strain of Acinetobacter baumannii, a bacteria that is resistant to antibiotics. At one hospital in Birmingham in 2003 the bacteria went on to infect 93 people, 91 of whom were civilians.

The bacteria is also a concern in the US army, where it has been identified in more than 240 military personnel since 2003, killing five.

Antibiotic resistance is a fine illustration of evolution in action and the conditions and speed under which resistance appears illustrates a number of important features of natural selection.

Two miles underground

2006-10-22T19:13:00.000-07:00

Bacteria don't make it onto the front page of the Chronicle that often - unless they are killing people. Friday's paper has news of the discovery of microbes existing two miles down in the fractured rock of a South African gold mine - a lightless pool of hot, pressurized salt water that stank of sulfur and noxious gases.

Using geologically produced hydrogen and sulfur for energy, such bacteria offer insights into the origin of life and the communities of bacteria that must have existed on the early earth before the atmosphere became oxygen rich. The newly discovered bacteria are distantly related to the Firmicutes division of microbes that exist near undersea hydrothermal vents.

Press reports followed a paper in Science last week.

Cataloguing species

2006-09-26T15:29:00.000-07:00

Many students are surprised to find that there is no central record keeping body for species in the same way that there is for, say, Astronomical bodies. It isn't that the magnitude of the task is that much different - the Catalogue astrographique (Astrographic Catalogue) for example lists over 4.6 million stars.

Fortunately there is now an attempt, Species 2000, to centralize species listings into a single database. The task is large but the sixth (2006) edition of the Annual Checklist, contains 884,552 species, approximately half of all known organisms. Species 2000 is a "federation" of database organizations working closely with users, taxonomists and sponsoring agencies. The goal of the Species 2000 project is to create a validated checklist of all the world's species by bringing together an array of global species databases covering each of the major groups of organisms.

The heat is on

2006-09-11T13:54:00.000-07:00

The cover story in the Economist magazine this week is global warming. The subhead says it all:

The uncertainty surrounding climate change argues for action, not inaction. America should lead the way.

Global warming, a serious environmental issue (perhaps the environmental issue of our time) is also a really nice way to link together the different subjects and lectures in Bio1B: Evolution; plants and ecology.

From the always entertaining Wikipedia:
In one episode of The Simpsons, Homer is travelling by air in first class and says "Look at me, I'm reading The Economist. Did you know Indonesia is at a crossroads?" Four days later, with its customary dry wit, The Economist alluded to the quote, and published an article about Indonesia referring to the "crossroads".

Anemic Phytoplankton

2006-09-05T21:15:00.000-07:00

In the science journal Nature this week is a disturbing report that not only are phytoplankton in the tropical pacific limited by the levels of nitrate and iron in the water, but we have been consistently overestimating how much carbon dioxide they have been taking up because they produce a pigment complex that isn't chlorophyll but shows up just as green in satellite images. Doh!

Pope to publish evolution talks

2006-09-05T20:57:00.000-07:00

There had been some concern that pope Benedict was going to deny evolution and embrace intelligent design. This was based on his inaugural address where he rejected the idea that humans are a product of evolution. But over the weekend Pope Benedict and his former doctoral students held a seminar on evolution. Preliminary reports suggest that the concerns that Pope Benedict was going to support intelligent design were far from the mark.

The minutes, to be issued later this year, will show how Catholic theologians see no contradiction between their belief in divine creation and the scientific theory of evolution, they said after the annual closed-door meeting ended on Sunday.

"When you look at the world and see what appears to be order and design, the conclusion that there is a designer is not a scientific conclusion, it's a philosophical one."

Human Evolution - Instant Expert

2006-08-28T22:16:00.000-07:00

New Scientist have just done one of their Instant Expert guides to Human Evolution. There is also a useful timeline, a nice set of recent articles on human evolution and even 'infrequently asked questions' (in this case: Over the past few hundred thousand years, humans have greatly increased in intelligence and in the size of their brains. As intelligence appears to produce an advantage to survival, I wonder if all animals show a tendency to evolve greater intelligence over time. Or is the value of intelligence overrated?).

Extreme seabed-survival boosts hope of aliens

2006-08-28T22:05:00.000-07:00

Microbes discovered by a lake of liquid carbon dioxide under the sea off Taiwan could help us locate life on Mars, researchers say.
Japanese and German researchers have found billions of bacteria and other tiny organisms living in a layer of sediment which traps the CO2 under the seabed. Their survival in such a hostile natural environment suggests that something similar could be happening on other planets.

New Scientist, 28 August 2006

Fast evolution in mussels

2006-08-28T21:53:00.000-07:00

Invasive crab species in New England have influenced blue mussels in the area to exhibit evolutionary change in as little as 15 years, report U.S. scientists in the journal Science. The change gives the mussels better advantage against the predator crabs.

Reported by the Discovery Channel, NPR and Fox News amongst many others.

Midterm 3 etc.

2006-08-17T14:10:00.000-07:00

Here are the results of the third midterm. Please don't e-mail me for your individual scores, I don't have them!

The overall mean was 81% and the median was 82%.

Nobody managed to get all fifty questions correct this time but four students, in three different sections, got all but one question correct.

Section means were very similar and, yet again, no section mean was more then 3% away from the overall mean of 82%

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

A (ie >=90%) - 31%
B - 37%
C - 18%
D - 8%
F - 6%

I have looked closely at all the questions where either less than two thirds of you got the correct answer (I only have this data by section, but it looks like maybe 4 questions) or more than 20% of you picked a particular incorrect answer (again, maybe 4 questions) and don't see any serious problems.

Well it's been fun. I hope some of you have enjoyed reading the blog. Google's blogger is certainly convenient but I have to say it has the most bizarre spell checker. It's not surprising it doesn't have technical terms in its database but it tries to replace them with amusingly inappropriate terms. Here's a couple I particularly enjoyed:

one of a whole family of defoliants used during the Vietnam war.
is much improved as:
one of a whole family of diplomats used during the Vietnam war.

and humongous fungus.
is alliterative but, again, is much improved as
unionized fungus

John

We beat Turkey!

2006-08-16T16:29:00.000-07:00

The chart shows the proportion of people in numerous countries that answered true (blue), false (red) or unsure (yellow) to the statement:

"Human beings, as we know them, developed from earlier species of animals."

The report was published in Science last week and the full paper is available online. Note that for the precise methodology and questions asked you need to click on the link at the end that takes you to the supplementary material. I mention it because there is some interesting stuff there.

It was widely discussed on the internet, and I'll use this chance to recommend two evolution related blogs, Pharyngula and the Panda's Thumb, both of which reported on it - direct links here and here. It was not widely reported in the mainstream media - although Fox did have an article.

Humongous Fungus

2006-08-15T15:31:00.000-07:00

If you'd like to read a little more about the original humongous fungus there's a really interesting article by Tom Volk, first published in Inoculum in 2002, a decade after the discovery of the fungus. You can read the article online here. The fungus they discovered, an individual Armillaria bulbosa, aka the honey mushroom, was conservatively estimated to be at least 1500 years old and weigh around 100 tons - making it one of the largest and oldest living organisms.

I learned lots of fascinating trivia from this article:

The project was actually an offshoot of a grant from the Department of Defense, which funded a project to study the possible biological effects of ELF (Extra Low Frequency) stations in the Upper Peninsula of Michigan. These ELF stations were built to communicate underground with ocean-going submarines in time of war.

They sampled for the fungus by 'baiting' with tongue depressors. The fungal mycelium quickly colonized the wood sticks.

They were not looking for a large fungus, or even trying to measure the size of any fungus. The project was originally to look at how mitochondrial DNA was inherited in fungi in nature.

When news of the 'giant fungus' broke in the press CNN wanted someone to go out into the woods and wave from the fungus so they could get an aerial picture of the humongous fungus.

Even better, a Japanese businessman called and wanted to build a boardwalk around the humongous fungus and charge people to view the 'pulsating mass of fungus'.

Campbell 7th

2006-08-14T20:01:00.000-07:00

It was brought to my attention that there is a fairly serious error in some copies of the Campbell 7th edition. It doesn't appear to be present in the 6th edition.

In figure 38.4 (The development of Angiosperm Gametophytes), earlier copies of the 7th edition have the haploid and diploid labels reversed. It SHOULD be labeled so that the microsporocyte, megasporangium, megasporocyte and integuments are DIPLOID, and all the other structures are HAPLOID (except the micropyle, which is a gap and so is neither haploid nor diploid!)

As an aside, it can be tricky in the US to tell what printing a book is. However for many books there is a simple code on the rear of the title page that gives you the necessary info. In Campbell you'll find this on page ii just above the Benjamin Cummings logo. You are looking for a string of numbers like:
1 2 3 4 5 6 7 8 9 10 -VHC - 08 07 06 05 04
By taking the lowest numbers you get the printing and year (for some odd reason these numbers are not always in order). So the book I'm looking at was the first printing in 2004. Another copy I looked at in the Bio1B office did not have this mistake and was labeled:
4 5 6 7 8 9 10 - VHC - 08 07 06 05
or the 4th printing from 2005.

So now you know. I suppose if you wanted to get maximum value for your dollar in a used textbook store you would look for later printings hoping that mistakes had been corrected.

As requested

2006-08-14T15:22:00.000-07:00

I do not make my powerpoint slides available to you for one very simple reason - I have not obtained permission to use all the images. To try to make the lectures interesting I pull up all sorts of images from the web and numerous other sources. As long as they don't explicitly request that the image not be copied I don't worry too much for a single in lecture use. However I would not feel comfortable making all these images available to the whole class by putting the powerpoint slides online.

The legally correct solution would be to just use images I have taken myself (the only pictures I take are of Scooter, my dog) or to use those from Campbell (which would make for a fairly dull lecture since you've seen all these images) or to get permission to use all the images I want to use (which would take forever).

So instead I use what I want but don't make the slides available. That is why I have copied much of the text on the slides in the form of the lecture outlines and indicate, wherever possible, equivalent figures in Campbell.

But someone did point out that I could go one step further and make available all the text slides I use and those very few images I make myself. I'm not sure it provides much more than you already have but here are the text slides from the Plant Section powerpoints. (There is also one other image snuck in there that someone requested so I hope you are reading this).

Only You Can Prevent Forests

2006-08-14T15:15:00.000-07:00

Agent Orange was but one of a whole family of defoliants used during the Vietnam war. There were so many in fact that they are known collectively as the "rainbow herbicides": Agent Orange; Agent Purple; Agent Pink; Agent Blue; Agent White; and Agent Green. (Reservoir Dogs enter the Matrix.) They are named, incidentally, not for the color of the chemical but for the color coded stripe on the barrels they came in.

We now know that although the synthetic auxins might have been highly effective they came contaminated with dioxins - causing cancers and horrendous birth defects (deformities so extreme that photographs of affected individuals are often assumed to be faked). Whilst the action of destroying the environment as an act of war is not without ethical issues itself the more pressing matter is the fate of US soldiers, South Koreans (present as US allies in the Vietnam War) and Vietnamese citizens who suffered from the effects of these chemicals.

Thirty years after the end of the war and thirty five years since the widespread use of defoliants, a number of court cases are still pending. Most recently (end of 2005) a suit by a victim's rights group, the Vietnam Association for Victims of Agent Orange/Dioxin (VAVA) had their lawsuit dismissed because Agent Orange was not considered a poison under international law at the time of its use by the US. This, despite accumulating evidence that the companies new about, and kept quiet about, the dioxin impurities:

In March 1965, Dow official V.K. Rowe convened a meeting of executives of Monsanto, Hooker Chemical and others. According to documents uncovered only years later, the purpose of this meeting was "to discuss the toxicological problems caused by the presence of certain highly toxic impurities" in samples of 2,4,5-T. The primary "highly toxic impurity" was 2,3,7,8 TCDD, one of 75 dioxin compounds.

From 'The Story of Agent Orange, from the November 1990 issue of the US Veteran Dispatch Staff Report.'

There is much more about the ongoing Agent Orange issue at numerous websites. As usual Wikipedia is a good entry point.

The US government, is not a party in any of the lawsuits claiming sovereign immunity.

(The title of this entry comes from a sign over the door to the ready room for pilots involved in the defoliation operations at Tan Son Nhut Airport near Saigon. For those of you who are not US residents, it is a play on the words of the famous slogan: Only you can prevent forest fires)

Life in a seed

2006-08-13T19:36:00.000-07:00

Some species of insects complete their entire development in seeds. Protected by the seed coat and nourished by the seed's food supply a developing insect has everything it needs. However these reserves only normally accumulate in fertilized ovules - requiring female insects that wish to lay eggs inside the seeds to either wait until ovules are fertilized (and be able to discriminate), or to lay their eggs earlier and risk many being laid in unfertilized seed. A paper in the Proceedings of the Royal Society last year describes how a host-specific insect, the chalcid Megastigmus spermotrophus that lays its eggs in ovules of Douglas fir has managed to evolve a solution to this problem. This insect lays its eggs before fertilization has taken place in the plant and ovipoisiton of eggs not only prevents the expected degeneration and death of unfertilized ovules, but it induces energy reserve accumulation. Ovules that would otherwise develop as empty seed are redirected in their development by the insect to provide food for the developing larvae. This is the first report of this type of insect-host relationship.

Eastern Garbage Patch

2006-08-12T22:43:00.000-07:00

Just under 100 years ago, in 1909, Leo Hendrik Baekeland invented the first plastic based on a synthetic polymer - Bakelite. Since then plastics have changed our world in a great many ways. The problem is that practically all the plastics we have made in the last 100 years are still with us, particularly those that end up in the ocean where biodegradation, which is slow to begin with, is even slower.

If you've been to a beach in your life you will have seen how much plastic waste washes up. But it turns out this isn't the worst of it. Ocean currents, caused by winds and the earth's rotation, create large circular systems, or gyres. The center of these gyres, thousands of miles from continental land, contain vast accumulations of floating garbage. An accumulation in the large gyre in the pacific is known as the Eastern Garbage Patch. Situated about halfway between California and Hawaii this floating garbage dump is about twice the size of Texas. To save you reading that again I'll just type it again - a floating patch of garbage in the Pacific that is twice the size of Texas. The amounts of plastic involved are staggering, using trawl samples it is estimated that there is already six kilos of plastic for every kilo of naturally occurring plankton.

This plastic is proving disastrous for oceanic islands. For example Midway atoll is littered with decomposing bird remains, piles of feathers and bone surrounding colorful piles of bottle caps, plastic dinosaurs, checkers, highlighter pens, perfume bottles, fishing line and small Styrofoam balls. It is estimated that albatross feed their chicks about 5 tons of plastic a year on Midway alone. Albatross fly hundreds of miles in their search for food for their young and their flight paths from Midway take them directly over the Eastern Garbage Patch. A piece of plastic found in an albatross stomach last year bore a serial number that was traced to a World War II seaplane shot down in 1944.

I find the idea of this vast patch of slowly circling garbage out there in the middle of nowhere to be profoundly depressing.

GM plant escapes into wild

2006-08-11T21:25:00.000-07:00

For the first time in the US a genetically modified plant has escaped into the wild. Even worse it has done it before securing USDA approval. The plant, creeping bentgrass, Agrostis stolonifera, had been modified to make it impervious to the herbicide glysophate and was designed for golf courses and homeowners. Lawn owners would be able to spray lawns to kill off weeds without damaging the grass.

As far as I can tell not a single US media source has picked up on this story. You can read about it in an Australian newspaper and a British Science magazine and, well, that's it.

Although only nine escaped plants have been identified (out of 20,400 plants of various grass varieties sampled) one of the escapees was found over 3.5 kilometers away from where the grass was being grown.

In this case the weedkiller-resistance gene is unlikely to be a particular advantage for this plant in the wild but this discovery doesn't bode well for our ability to contain other genetically moderated crops.

On the more worrying side bentgrass has many close relatives with which it can potentially hybridize. This could add glyphosate-resistance genes to other grass species, some of which are noxious weeds.

Some like it hot.

2006-08-10T21:07:00.000-07:00

From a paper in last week's edition of the journal 'Nature' comes news that some bees may be looking for more than nectar when they visit flowers - they are also looking for warmth. Insects use large amounts of energy maintaining their body temperature and some flowers offer warmth, using color to advertise its presence.

The paper by Adrian Dyer and colleagues describes a controlled experiment that showed that bumblebees preferred to visit warmer flowers, and they learnt to use color to predict floral temperature before landing.

You can access the editorial summary at the Nature site, a news report at the New Scientist website and, if you have a UC Berkeley IP address or a proxy server you should be able to access the article from the nature link.

Final Jeopardy

2006-08-09T20:19:00.000-07:00

When I was younger I was fascinated about how other people's minds worked. I was intensely curious about whether other people had a mind full of junk all the time and whether they were constantly making the same sort of apparently random links and jumps.

I was recently reassured to see this animated cartoon by Scott Bateman which illustrates what happened inside Bob Harris's head when faced with a Final Jeopardy question. (Bob Harris is an American radio commentator, writer, stand-up comedian, Jeopardy contestant and blogger.)

I'm always reminded of this when I try to write exams. It is so difficult to try and step back and see questions as others might see them. I've also been talking with Mike Moser and some others about ways to help people who learn the material, feel they understand it, and yet are disappointed by their midterm results. (There was an earlier blog posting on this if you missed it, and a list of advice is on the Bio1b website.)

Speaking with a couple of separate people this week I realized I need to add a section here on time management. I'll illustrate this for a Bio1B midterm but the principal applies to lots of other exams.

Let's assume that you find 35 of the 50 questions straightforward, they only take you a minute or so, let's say 40 minutes total.

There are another 10 questions that you find harder, maybe they are problems, or take extra reading or calculation. You take two minutes over each of these for a total of 20 minutes.

You now have 20 minutes left for the last 5 questions which you are really puzzling over. It is pretty easy to spend most of this time puzzling over these questions and only leave a few minutes for a cursory check of your answers to the earlier questions. You become obsessed by the harder questions at the expense of checking for errors on the easier questions.

However, if you are anything like me, you have probably made at least half a dozen mistakes on those 35 'easy' questions because you misread the question, filled in the wrong entry on the scantron, failed to notice a negative qualifier etc. etc. Fifteen minutes spent checking your answers will probably bring you much better returns than agonizing over the questions you find hardest.

A better strategy, in this example, would be to allot about 1 minute per question to work through the entire 50 questions. Some questions may take less time but try not to go beyond 1 minute on any question. Cross out answers you know to be wrong as you go along. If you run out of time then put a question mark by your best guess and move on. You should finish this in under 50 minutes. Now split the remaining time in two parts. Spend half the time (15 mins) checking your answers. Make sure you read the question correctly. Look for negatives and qualifiers. In doing this you can take another look at the questions you didn't complete the first time. Something new might come to you. Finally, divide the last 15 minutes between the questions that remain.

Songs of Science

2006-08-08T14:45:00.000-07:00

If you like your education in rhyming form (and who doesn't?) then you'll want to check out the Singing Science Records website. Dozens and dozens of priceless gems from the late '50's and early '60's. Now available in mp3 form.

The one I played at the start of lecture today is near the end of the page ' What Are The Parts Of A Flower?' (links to mp3 file).

'It's time we were explainin' the purpose of the stamen.'

Let me know if you find any more real gems here. I haven't listened to them all. Another of my favorites is How Does A Frog Become A Frog? Although a little skimpy on the details of how a frog actually becomes a frog it makes up for it with a great tune. It reminds me of the 'insane circus' style of music favored by Tom Waits. Come to think of it I bet Tom Waits could do a great version of this.

CNR smorgasbord

2006-08-07T19:30:00.000-07:00

A selection of items gleaned from the CNR website. The first concerns some of the long lived gymnosperms I mentioned today.

From an article in the SF Chronicle last week entitled Performing high-altitude research on global warming:

The famous bristlecones have endured countless challenges over the millennia, yet always seem to muster one more burst of life when spring warms the rocky dolomitic soil. Growing seasons may expand and shrink, but the trees carry on, their growth rings faithfully recording the bad years alongside the good.

From the CNR Breakthroughs magazine is a nice description of an ambitious program to catalogue the DNA of all the species on an entire island - the South Pacific island of Moorea, home to UC Berkeley's Richard B. Gump South Pacific Research station.

Also in the magazine is an article about the Exploring California Biodiversity program which sends Berkeley graduate students to teach in four Bay Area schools. I mention it here because they also involve undergraduates in the program. If you think you might be interested in teaching, or just want to gain some practical experience it is a tremendous opportunity. Check out their website and contact Betsy Mitchell if you are interested (it may be too late for the coming year, but it never hurts to ask).

Dead Zone

2006-08-06T21:02:00.000-07:00

No, not the David Cronenberg movie with Martin Sheen foreshadowing his West Wing presidential role. The dead zone in question is a 70-mile-long zone of oxygen-depleted water, along the Continental Shelf between Florence and Lincoln City in Oregon. It has reappeared each year since scientists first noticed it in 2002. The zone is caused by the action of photosynthetic algae in the water. Explosive blooms of algae eventually die and sink to the bottom, they are then eaten by bacteria which use up the oxygen in the water. This leaves a zone of very low oxygen levels, a so called 'dead zone'. Although these are not toxic algal blooms they are having dramatic effects on the ecosystem causing a massive die-off of fish and invertebrate marine species.

The key question of course is what causes the algae to bloom. In contrast to other dead zones (eg in the Gulf of Mexico) the dead zone on the Oregon coast is not thought to be due to agricultural run off. Attention is now turning to whether it could be climate change related. This combination of catchy name ('dead zone'), dead fish and crabs, financial implications for fishing communities and a global warming tie-in makes for good headlines.

The San Francisco Chronicle today had a report and the story has also been covered by ABC, CBS, the New York Times, National Geographic and many others.

Deep Green

2006-08-05T19:28:00.000-07:00

There are a number of useful resources on the web to help you understand the relationship between the different plant groups and explore their diversity.

The Tree of Life is a collaborative project that provides information about the diversity of organisms on Earth, their evolutionary history and their characteristics. The link above takes you to the main page or you can skip directly to the green plants.

The Green Plant Phylogeny Research Group (Deep Green) is a group that coordinates research into the phylogeny of the green plants. Their website contains a useful hyperbolic tree. Hyperbolic trees are one way to display complex trees clearly.

The Green Tree of Life aims to resolve the primary pattern of evolutionary diversification among green plants. An overview of the results to date can be seen in this poster.

Beatrix versus the Botanists

2006-08-04T11:44:00.000-07:00

When I was a sophomore at college in England I spent a summer working at the Freshwater Biological Association in the English Lake District. The cottage I stayed in was in a tiny village called Far Sawrey. Just down the road is the village of Near Sawrey which contains a small 17th century farm house where Beatrix Potter spent most of her later years, and where she wrote and set her many Peter Rabbit books.

Having mentioned it in class I thought I'd see if I could find out whether Beatrix Potter was happy in her later life or whether she resented being excluded from the male dominated scientific community. Thanks to the wonders of the internet I found a highly relevant book and, even better, the relevant chapter is available online as a sample chapter.

Chapter 1 of Liaisons of Life, Beatrix versus the Botanists, by Tom Wakeford describes Beatrix Potter's encounters with the scientific establishment. Fascinating reading and a picture of science at the turn of the century. Beatrix Potter was facing an uphill battle, not just as a woman in science but also in proposing lichens as a symbiotic and mutualistic association. James Crombie, a prominent English naturalist said:

"A useful and invigorating parasitism who ever before heard of such a thing?"

and he described the relationship as:

"an unnatural union between a captive algal damsel and a tyrant fungal master."

After her aborted scientific career and her successful career as a children's author Beatrix Potter went on to a third, and equally successful career as a sheep breeder and conservationist in the English Lake District.

Lichens in Space

2006-08-03T16:16:00.000-07:00

During the European Space agency's 2005 Foton mission lichens were exposed to space for 15 days. They had to endure a wide range of harsh conditions: a vacuum; wide fluctuations of temperature; the complete spectrum of solar UV light; and bombarded with cosmic radiation. If we were living in a comic book then the lichens would have returned with super powers but here in the real world most people were surprised to find the lichens merely survived. They appeared totally dormant whilst in space but soon revived back on earth.

One conclusion of this experiment is that it appears likely that lichens may be able to survive on the surface of Mars. Although the Martian atmosphere is very thin, it is filled with carbon dioxide, which is necessary for photosynthesis. However, long term survival and growth may be prevented by the low oxygen levels in the Martian atmosphere.

Midterm 2 results

2006-08-03T15:23:00.000-07:00

Here are the results of the second midterm. Again, I can't post your individual results but here is an analysis of the complete data set.

The overall mean was 84% and the median was 86%.

The highest score was 100%, and, again, two students in different sections managed to achieve this.

Section means were very similar and no section mean was more then 3% away from the overall mean of 82%

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

A (ie >=90%) - 38%
B - 37%
C - 17%
D - 6%
F - 2%

There are two issues with individual questions. These changes will be made by your gsi and will not show up on your scantron reports.

Due to the conflicting information presented in Campbell 7th I will accept A or B as answers to question 27 (the island biogeography question).

There was an error on the answer key (my fault, it was due to a last minute change in a question). The correct answer for question 15 (inefficiency of food chain transfer) was B (productivity). Answer C (endotherm/ectotherm) is incorrect. For 152 of you this means your score will go up. My apologies for this mistake.

I have looked closely at all the rest of the questions where either less than two thirds of you got the correct answer (4 questions) or more than 20% of you picked a particular incorrect answer (5 questions) and don't see any other problems.

John

Diatom art

2006-08-02T14:43:00.000-07:00

I love this stuff! If you want to see more then check out Klaus Kemp's work. He has singlehandedly reinvented the 'lost art' of diatom arrangement and taken it to new heights.

There are some beautiful photographs of his work here, that show, at different magnifications, the beautiful structure of the diatom shells.

Definitely a hobby for the patient. Traditionally pig eyelashes were used to collect and place the diatoms because the shells will stick to their oily tips (who knew there was a use for pig eyelashes beyond the obvious pig related one?). The diatom shell is then placed into the mounting material on the microscope slide. Once placed it is hard to make changes........

Fertilizing the Oceans

2006-08-02T14:00:00.000-07:00

The image to the left shows a satellite image of a 150km long phytoplankton bloom created during the 2002 Southern Ocean Iron (Fe) Experiment (SOFex). The arced distribution is due to oceanic currents and the bloom appeared only six weeks after the initial fertilization.

The fertilization involved adding iron to surface waters in two patches, each 15 kilometers on a side, so that the concentration of this micronutrient reached about 50 parts per trillion, increasing the natural level by about two orders of magnitude.

Each of these blooms consumed over 30,000 tons of carbon dioxide, but the crucial question is whether this carbon dioxide would be returned to the atmosphere, or would sink into deep waters as the phytoplankton died. One of the factors that determines which will occur is what type of organisms form the bloom. Diatoms, for example, are relatively heavy and sink easily. But the abundance of diatoms may be limited by silica as well as iron.

The results were published in the journal Science in 2004 and were reported on quite widely by the press. Here is a nice report by the Sciencedaily website.

Pathogens Determined to Attack Inside the United States.

2006-08-01T16:56:00.000-07:00

In June 1996, President Clinton issued a Presidential Decision Directive calling for a more focused US policy on infectious diseases. The intelligence community of the United States is responsible for assessing threats to the United States and in 1999, as part of the US Government's effort in response to the Presidential Directive, produced a report entitled 'The Global Infectious Disease Threat and its Implications for the United States.'

It examines the most lethal diseases globally and by region; develops alternative scenarios about their future course; examines national and international capacities to deal with them; and assesses their national and global social, economic, political, and security impact. It then assesses the infectious disease threat from international sources to the United States; to US military personnel overseas; and to regions in which the United States has or may develop significant equities.

The report was produced by members of the Armed Forces Medical Intelligence Center, the National Intelligence Council and included conclusions from a conference on infectious diseases held jointly with the State Department's Bureau of Intelligence and Research.

You can find it at the CIA webpage as a pdf file but more easily accessible html versions are available.

The conclusions are not optimistic.

Bug soup

2006-08-01T16:18:00.000-07:00

Looking for information to post here has encouraged me to look at Science, Nature, PNAS and several other Journals more frequently than normal. It has surprised me just how many papers are being published that are directly relevant to this course. In PNAS (Proceedings of the National Academy 0f Sciences) next week will be a paper by Mitchell Sogin and others describing a new estimate of the microbial diversity in the deep sea. Only 5,000 marine microbes have currently been named but Sogin's study estimates that the true number of bacterial species living in the ocean could be between five and ten million. You can read the original paper in pdf form or check this link to google news as various newspapers and magazines pick up on the story.

Favorite headlines so far:
Enough to make you swim with your mouth closed
Marine census blows researchers out of the water
Oceans a complex, diverse bug soup

and my vote for least inspired headline:
Scientists` view of oceans might be wrong

Mad Cow

2006-07-31T17:59:00.000-07:00

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

2006-07-31T17:13:00.000-07:00

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.

Shipbreaking

2006-07-30T20:10:00.000-07:00

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.

Snakes on a plane.

2006-07-27T16:36:00.000-07:00

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

2006-07-27T15:59:00.000-07:00

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.

Specicide

2006-07-27T15:58:00.000-07:00

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!

2006-07-27T15:53:00.000-07:00

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?

Rachel Carson, Fred Soper and DDT

2006-07-26T14:48:00.000-07:00

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...

...one 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.

Mt. St. Helens

2006-07-25T16:13:00.000-07:00

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

2006-07-25T15:34:00.000-07:00

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.

Honey guides, killer bees and land mines

2006-07-24T19:41:00.000-07:00

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.

Global warming threatens Californian wine industry

2006-07-23T18:03:00.000-07:00

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.

100 ecological questions

2006-07-23T14:02:00.000-07:00

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.

Giant demon duck of doom

2006-07-22T13:51:00.000-07:00

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.......