Thursday, March 19, 2009

Courses, schedule and research opportunities

A number of items:

1/ From Kathy: If you have an advisee looking for a challenging, literature-based, grad seminar style course in S09, I am offering one on the topic of "cell death" and am happy to have ccs students enroll in it through MCDB 194X (2 units). They just need to contact me for an add code. It meets Mondays at 10 AM. I posted a description on the ccs bulletin board and Les sent out an email advertising the course as well.

2/ A general heads up (also from Kathy):
MCDB is working on revising curricula and one of the main goals is to spread out the upper division course offerings across all quarters a bit more (right now, many are bunched in Winter qtr). The most immediate change that might affect our CCS Bio students is that MCDB 112 (Dev Biol) will be offered in FALL 09 (instead of W10), so be aware. The lab (MCDB 112L) will remain a Winter 2010 offering for the moment. Some of the micro courses (such as MCDB 139, medical microbiology) are likely to redistribute as well, and I'll keep everyone posted as I become aware of the changes. For students who are likely to want to take a number of MCDB upper div courses, my advice is to have them get at least 1 qtr of genetics under their belts asap as it seems most faculty really want to see this as a prep for many upper division courses.

3/ A grad student was asking me about whether there were any CCS students interested in a plant based research project. If you are let me know and I'll put you in touch. They were interested in collaborating to put in an application for a Worster award. These awards support the development of graduate and undergraduate research through a mentoring program that pairs an undergraduate with a graduate student mentor during the summer. Stipends this year will be approximately $6000 for each team ($3000 for the graduate and $3000 for the undergraduate). Applications for this award are due by Friday, April 3, 2009.

4/ Sunmer research experience for undergraduates based in Dublin.

Collections-based Biology in Dubin (CoBiD) provides an exciting research environment, with experience both in high quality laboratories in the science departments in University College Dublin, and important international research centre in the National Museum of Ireland (Natural History) collections in Dublin city centre. Diverse research projects are offered, with topics ranging from systematic biology— including traditional and molecular techniques— to ecology and population genetics. Students will work side-by-side with curators and senior scientists and will be involved in all aspects of collections-based research including collection and curation of specimens, participation in field expeditions, and dissemination of scientific results through oral presentation and publication.

The deadline is in two weeks. See website for more info.

Saturday, March 14, 2009


I am going to take a brief break from posting here every day. I will be around on campus all next week, if you need to see me for anything, but will then be out of the the country for a week before racing back to continue our tour of Biology in the Spring quarter. Good luck with finals and have a safe and fun break.

Thursday, March 12, 2009

Stupid octopus tricks

Well, since I'm not the only one feeling the cephalopod love, here's one more for you. As was noted, octopuses are notorious for escaping from tanks since they are agile, clever and have no rigid skeleton - allowing them to squeeze through practically any gap that they can squeeze their brain through.

This is actually more than just a stupid pet trick since it really helps to remind you that, in water at least, a hydrostatic skeleton, like that of an octopus, can be very impressive and allow sophisticated, rapid and powerful movement.

Wednesday, March 11, 2009

Octopuses in disguise

Once you start posting cephalopod videos it's hard to stop. This one is a nice overlap between diversity and next quarter's physiology though.

Getting a paper published in science as a grad student. Excellent.
Giving it a cool title: Underwater Bipedal Locomotion by Octopuses in Disguise. Even better.
Capturing the whole thing on video. Priceless.

Tuesday, March 10, 2009

Cthulhu hates Chordates

Having just enthused about Cephalopods I was delighted to come across this picture in the news today. I'm a big fan of obscure jokes and this placard, at a counter demonstration to the hateful Fred Phelps, who was at the University of Chicago yesterday, is excellent. Fred Phelps and his church, the Westboro Baptist Church are (in)famous for their protests which usually involve a lot of placards along the lines of 'God hates gays', 'God hates the world' or 'God hates you'.

This parody is great since it requires you to know something about HP Lovecraft to know that Cthulhu is very Cephalopod like AND to know that Cephalopods are most decidedly not Chordates. In addition, the Lovecraft Cthulu WAS evil and probably does hate Chordates. Kudos.

MTA. A comment from the signmaker: I decided that if the Mighty Tentacled One had to hate a chosen group, it would be one outside of it's representative clade, and deuterostomes wouldn't fit on a sign.

Cephalopod star

There are a lot of amazing octopus videos around. Here's the most famous camouflage one:

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

Monday, March 9, 2009


This week sees a little flurry of seminars:

Monday March 9th, 4-5pm, MSRB Auditorium
"Variation in Resilience and Species Interactions Among Southern Californian Kelp Forest Ecosystems"
Anne Salomon

Tuesday, March 10, from 8 to 9 p.m in Broida Hall, Room 1610.
Public Lecture and Demonstrations
'Journey to the Heart of the Electromagnetic Spectrum'
Would you like to know how doctors might one day be able to see through bandages? To learn about this and many other technological breakthroughs, you are invited to attend "A Journey to the Heart of the Electromagnetic Spectrum." The event is designed for anyone who is curious, regardless of technical background, and will be presented by Mark Sherwin, Professor of Physics and Director of the newly formed Institute for Terahertz Science and Technology.

Tuesday, March 10, ESB 1001, 11:00 AM
Mellichamp Chair in Systems Biology Search Seminar
"Nature, nurture or just dumb luck: gene expression variability and cell fate"
Arjun Raj, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA

Thursday March 12, MCDB Seminar , 3:30pm LSB Auditorium (1001)
“Dying Young as Late as Possible: Regeneration, Planarians and Stem Cells”
Alejandro Sánchez Alvarado, Ph.D.
Howard Hughes Medical Institute, Dept. of Neurobiology & Anatomy
University of Utah School of Medicine

Sunday, March 8, 2009

Wolfram Alpha

Kathy sent me some information about a new tool from Wolfram (the people that make Mathematica). It is called Wolfram Alpha and promises to change the way we use the internet for research. At the moment there is more hype than actual information but Kathy saw a demo and was impressed. Basically it looks like a search engine but instead of just searching for websites with keywords it will take questions in natural language and return answers, provided the data is available, even if no-one has addressed that question before.

There is clearly a huge market for such a tool. Currently there is a ton of data out there on the internet - but unless someone has already asked your question you are out of luck in getting a quick easy answer. Say I want to know the relationship between seed size and mature plant size, or how stomatal density varied over the Cenozoic, or how VO2 max varies with animal body size. Unless someone has already asked these questions I would be left to combine data sets on my own. If this product lives up to its promise it will present the data to me - and in graphical form. Cool. I'm sold. I like the last line in the blog posting:

I think it’s going to be pretty exciting. A new paradigm for using computers and the web.
That almost gets us to what people thought computers would be able to do 50 years ago!

Saturday, March 7, 2009

Things Darwin would not say

In honor of the 200th anniversary of Darwin's birth, New Scientist magazine had a competition to come up with the best 'Thing you would never have heard Charles Darwin say about evolution.' Out of 900 entries the winner was:
'Finches eh? Seen one, seen 'em all'

Also in New Scientist this week The Last Word, where readers send in questions and then others submit answers, has:

I have always been fascinated by evolution, and while I can usually see why and how certain characteristics evolved in different species, I'm confused by whales and dolphins. How did their breathing holes evolve, bearing in mind their ancestors were land mammals?

You can see the answers submitted to date here.

Friday, March 6, 2009

Marine Biologist

A little something for the weekend.

Combine this with UCSB Marine Biologist Milton Love's little essay on some good, and not so good, reasons to be a Marine Biologist.

Oh and can a golf ball really block the blowhole of a whale? You're CCS students, you should be able to take a crack at that question

Thursday, March 5, 2009

Signs point to sponges

Just a few weeks ago there was a nature paper based on 'chemical fossils': Fossil steroids record the appearance of Demospongiae during the Cryogenian period.

MIT, where some of the researchers are based, had a press release: Signs point to sponges as earliest animal life 'Chemical fossils' provide evidence for first multicelled creatures.

The Cryogenian is that period in the Precambrian era when there was an extensive series of severe ice ages - often referred to as 'snowball earth'.

Soft-bodied animals such as sponges are very rarely preserved as fossils, so finding evidence of their early appearance required some clever detective work. The key turned out to be an examination of unusual chemicals: steroids of a particular type produced abundantly by sponges but virtually never by simpler organisms.

Studying an unusually well preserved long sequence of strata found in Oman, the research team was able to extract these "chemical fossils" from a large number of samples spanning a range of tens of millions of years -- before, during and after the Ediacarian period. This provided clear evidence that sponges must have evolved long before the great variety of multicellular organisms that proliferated at the dawn of that period.

At that time in geological history, the Earth was just coming out of the last of its "snowball Earth" phases, when the entire planet was shrouded in ice. Since the new findings show that complex life seems to have begun tens of millions of years before that, that means these organisms were able to survive through that extreme episode of glaciation, something that many scientists had thought was impossible. This provides new evidence that the freezing was not absolute, but instead left some open patches of water.

"There's plenty of evidence in these rocks that there were places on Earth where life was flourishing" during this snowball episode, known as the Cryogenian, Summons says. "There must have been some refugia. Life certainly didn't shut down."

Wednesday, March 4, 2009

Fossil Fish Brain

The structure of the skull (foreground) of a 300-million-year-old iniopterygian fish from Kansas remotely related to living ratfish is elucidated thanks to holotomography, a technique based on synchrotron X-ray phase contrast imaging (background), and yields the first hint at an exceptional mineralization of the brain (orange). (Credit: PNAS/Philippe Janvier (CNRS, Museum National d'Histoire Naturelle))

I think this must be the 300 million year old fish brain that was mentioned on Tuesday. Although it is the first time that the soft tissue of such an old fossil brain has ever been found it sounds like it is also one of the first times people have used sophisticated imaging techniques to look inside the fossil skull.

(S)cientists used the technique of absorption microtomography to study different samples. One sample, stemming from Kansas (US), revealed a peculiar structure: it was denser than the surrounding matrix that fills the braincase, and which is made of crystalline calcite. In order to elucidate its structure in detail, they decided to use a second technique, X-ray holotomography. Surprisingly, the results showed a symmetrical and elongated object placed in the same position as a brain would have been.

Tuesday, March 3, 2009

Carbon dating and global warming

The prodigious mobilization of science that produced nuclear weapons was so far-reaching that it revolutionized even the study of ancient climates. Nuclear laboratories, awash with funds and prestige, spun off the discovery of an amazing new technique — radiocarbon dating.

The discovery of carbon dating is an interesting story in its own right and is described in several places, for example here. It is also described here, at the American Institute of Physics, part of a rather nice collection of essays on the discovery of global warming. The ratio of C-14 to C-12 on earth has varied significantly during the Earth's history. This variation is due to changes in the intensity of the cosmic radiation bombardment of the Earth, and changes in the effectiveness of the atmosphere in deflecting that bombardment. To compensate for this variation, dates obtained from radiocarbon laboratories are now corrected using standard calibration tables.

It was particularly interesting that, as Stuiver had suspected, the carbon-14 wiggles correlated with long-term changes in the number of sunspots. Turning it around, Suess remarked that "the variations open up a fascinating opportunity to perceive changes in the solar activity during the past several thousand years." The anomalies were evidence for something that many scientists found difficult to believe — the surface activity of the Sun had varied substantially in past millennia. Carbon-14 might not only provide dates for long-term climate changes, but point to one of their causes.

Monday, March 2, 2009

How plants make decisions

In the early edition of PNAS this week is Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity.

This paper describes how plants balance the tradeoff between growth and defence. The same light sensor that detects other plants crowding in and gives the signal to switch on the synthesis of the plant growth hormone auxin reduces the plant's responsiveness to the hormone jasmonic acid, which orchestrates the synthesis of a whole array of defensive chemicals.

Coupling shade avoidance syndrome with the regulation of resource allocation to defense could provide a major selective advantage for plants growing in the wild, but might increase the vulnerability of densely planted crops to insects.

Hmm. I guess this is more relevant to next quarter but I thought it was an interesting paper. Here are a couple of past posts of more relevance to our current topics:

Sunday, March 1, 2009

Toco Toucan Tradeoff

A Toco Toucan at London Zoo.

I was doing some reading about Toucans. I confess I was never this enthusiastic as a student but these days I seem to be finding everything interesting. Anyway, I came across this curious conservation paper: Conservation puzzle: Endangered hyacinth macaw depends on its nest predator for reproduction.

In the Pantanal wetlands of Central Brazil, the endangered hyacinth macaw (Anodorhynchus hyacinthinus), the largest psitacid in the world, makes its nest almost exclusively in natural hollows found in the manduvi tree (Sterculia apetala). The recruitment of manduvis greatly depends on the seed dispersal services provided by the toco toucan (Ramphastos toco), responsible for 83.3% of the seed dispersal. The toco toucan, however, is responsible for about 53% of the preyed eggs, resulting in a case of conflicting ecological pressures in which the reproduction of the hyacinth macaw is indirectly dependent on the seed dispersal services of its nest predator.