Thursday, August 16, 2007

Midterm 3 results

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



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.

Wednesday, August 15, 2007

Purple Earth

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!

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Tuesday, August 14, 2007

Dr Fungus

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.

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Monday, August 13, 2007

You say tomato

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

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Sunday, August 12, 2007

Ferrets bounce back

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

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Saturday, August 11, 2007

Evolution's greatest mistakes

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


Friday, August 10, 2007

Science Friday

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

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Thursday, August 09, 2007

Passing gas

Improvements in sampling techniques and mass spectrometry in the last 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 of essential processes?

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

A recent research report shows that herbivore-induced volatile organic compounds elicit a defensive response in undamaged plants (or parts of plants) under natural conditions, and they function as an external signal for within-plant communication.

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

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Wednesday, August 08, 2007

Fog Drip

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

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Tuesday, August 07, 2007

More corpse

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


Monday, August 06, 2007

Frog-killing fungus

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

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Sunday, August 05, 2007

Environmental Forensics

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


Friday, August 03, 2007

When algae go bad

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

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

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Thursday, August 02, 2007

Midterm 2 results

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


Wednesday, August 01, 2007

Titania the corpse flower

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 webpage 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