Saturday, April 30, 2011

Static apnea

On Tuesday we will start our physiology section and Claudia will be talking about respiration. To get you pumped up (pun intended) I thought I'd post this video of what I only just discovered was a sport - static apnea. Basically this is floating face down in a swimming pool whilst holding your breath - quite possibly the most boring sport in the world to watch (it makes cricket look exciting) but physiologically quite interesting. For example if you watch the video you'll notice a demonstration of what I think is glossopharyngeal insuffation - this is a method of pumping additional air into the lungs widely used by reptiles and amphibians (picture a frogs bulging neck) but not by humans. Until a few decades ago when free divers discovered that by using the tongue as a piston an additional liter or so of air can be forced into the lungs. Don't try this at home though, rupturing the lung is a real possibility unless you work up to it.

How long can you hold your breath? A minute? A minute and a half?

What do you think the world record is. Four minutes? Five minutes? TEN minutes? Think again.

Curiously the techniques involved don't involve keeping the brain alive without oxygen, that's simply not possible, but getting oxygen to the brain even though you aren't breathing


Thursday, April 28, 2011

Very different but very cool

Two totally different critters I mentioned today. First up the slime mold.



and then the cephalopod - master of camouflage.

Rock-Paper-Scissors Tournaments Explain Ecological Diversity

Directly relevant to our discussion of ecological diversity, is this hot-off-the-press research co-authored by UCSB ecologist Jonathon Levine.

The mystery of biodiversity –– how thousands of similar species can coexist in a single ecosystem might best be understood as the result of a massive rock-paper-scissors tournament, a new study has revealed.

From the UCSB pub, "Coastlines":

According to classical ecology, when two species compete for the same resource, eventually the more successful species will win out while the other will go extinct. But that rule cannot explain systems such as the Amazon, where thousands of tree species occupy similar ecological niches.

The childhood game of rock-paper-scissors provides one solution to this puzzle, report researchers at UC Santa Barbara and the University of Chicago in the Proceedings of the National Academy of Sciences. A mathematical model designed around the game's dynamics produced the potential for limitless biodiversity, and suggested some surprising new ecological rules. Read the article here.

The link to the original source, published in PNAS is here.

Wednesday, April 27, 2011

Museum event

Bruce forwarded this. It sounds like an interesting

The next Friends of the Santa Barbara Museum Library Lecture is Wednesday, May 11th at 7:00 PM. The evening will feature Curator of Malacology, Paul Valentich-Scott and Elizabeth Garfinkle, a San Roque High School student. Theirs is a unique research story. Read about it below.

Not just your everyday new species How does a small clam from deep water off Baja California end up being a local sensation with a Santa Barbara teenager? Collaborators Paul Valentich-Scott, Curator of Malacology, and Elizabeth Garfinkle, a junior at San Roque High School, will present their recently published research describing a new species of clam. The pair will discuss the initial discovery of the new bivalve and its surprising links to the past of central California.

Elizabeth is one of the few high school students globally who has described a new species. Her achievement has been chronicled in many local media outlets from San Luis Obispo to Los Angeles. She took top honors at the 2011 Santa Barbara County Science Fair for this unique project. Come meet Paul and Elizabeth and learn more about the exciting journey that led to a new species being described in a zoology journal from New Zealand.

Admission is free but you need to make a reservation by e-mailing Terri Sheridan at tsheridan@sbnature2.org or (805) 682-4711 ext. 134

Tuesday, April 26, 2011

What is peer review?

I thought this article on peer review was interesting and well written. You may know most of this by now but some of it may surprise you.

For the most part, scientists are not formally trained in how to do peer review, nor given continuing education in how to do it better. And they usually don't get direct feedback from the journals or other scientists about the quality of their peer reviewing. Instead, young scientists learn from their advisors—often when that advisor delegates, to the grad students, papers he or she had volunteered to review. Your peer-review education really depends on whether your advisor is good at it, and how much time they choose to spend training you.

Sunday, April 24, 2011

Time Lapse Fungi


I found this website that contains time lapse movies of fungi, molds, bacteria, slime molds and insects. Its pretty cool to see the time lapse of the Rhizopus on the strawberries and there are a few cool videos of the Pilobolus. This is so related to Thursdays lecture I couldn't help but be intrigued and a little grossed out by how successful these guys are at what they do. If you watch the Pleurotus djamor clip you will never look at an old book the same. Check it out!

Friday, April 22, 2011

Two seminars for Monday 25th April

Next week's EEMB Seminar speaker will be Dr. Stephanie Pau, who is currently a post-doc at NCEAS. Her research incorporates field studies with remote sensing and paleo-ecological methods in order to investigate ecosystem responses to climate variability. Stephanie's talk is titled:
"Investigating diversity and ecosystem function at multiple spatial and temporal scales"
The seminar will take place on Monday April 25 from 4-5pm in the MSRB auditorium.


CCBER is pleased to announce that our Monday evening seminar will feature local botanical expert,
Mary Carroll who will focus on identifying local grasses.
Monday 25th, 6-7pm, Harder 1013.

Thursday, April 21, 2011

Speaking of ecosystems...

By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific.

"We found that the combination of microbes in the human intestine isn't random," says Peer Bork, who led the study at EMBL: "our gut flora can settle into three different types of community -- three different ecosystems, if you like."

Report at ScienceDaily and the paper, Enterotypes of the human gut microbiome, is published in nature this week.

Monday, April 18, 2011

Omnivore

I'm all for education in cartoon format but Slylock Fox always confuses me. As the Comics Curmudgeon points out, if the rules are suspended for half the characters - the fox is a detective, the mouse wears pants and the pig grows tomatoes, why should we assume that in this universe the snake is a carnivore and the raccoon is an omnivore? I hope that the solution to this conundrum would be obvious to any biologist - if the cartoonist has shown their teeth then we could have been confident in the identity of the omnivore.

Sunday, April 17, 2011

Human records

I don't know if anyone watched the London Marathon today. The BBC kindly made it available on the web on demand so you could watch the whole thing at your leisure. The stellar field this year led to a resurgence of interest about whether a sub-2 hour marathon will ever be run. Personally I think people underestimate the significance of the 4 minutes improvement it will take. However watching Emmanuel Mutai storm the second half of the course today led me to believe that maybe I'll see it in my lifetime. He ran the last 12km at a 2:02 pace (and promptly threw up the moment he crossed the line). To run a sub-2 hour marathon would require over 26 consecutive 4:35 miles. That's under 69 seconds for each quarter mile - approximately a lap of a track. Try it. For 69 seconds. Now imagine two hours of it. Humans are, or can be, extraordinarily good distance runners. Why?

Anyway, when we talk about human physiology, which we will shortly, it is always interesting to consider the human superlatives, Haile Gebrselassie or Usain Bolt.

But what is equally interesting is the revolution that is taking place further back in the pack. Virtually unreported in the media was the new world record by Canadian Ed Whitlock in the Rotterdam marathon last week. Whitlock ran 3:25:43. A very nice but utterly unremarkable time you might think. But Ed Whitlock is 80. He beat the old 80-84 world record by almost 15 minutes and Whitlock is not unique. The gains made at older age groups are really amazing. This, of course, is actually much more relevant to most of us - gains made in medical understanding affect both our longevity and also the quality of our life.

For an equally inspiring female example check out this New York Times article on the amazing 91 year old Olga Kotelko: The Incredible Flying Nonagenarian.

When the efforts of medical science converge to simply prolong existence, you envision Updike’s golfer Farrell, poking his way “down the sloping dogleg of decrepitude.” But scientists like Taivassalo and Hepple have a different goal, and exercise — elixir not so much of extended life as extended youthfulness — may be the key to reaching it. James Fries, an emeritus professor at Stanford School of Medicine, coined the working buzz phrase: “compression of morbidity.” You simply erase chronic illness and infirmity from the first, say, 95 percent of your life. “So you’re healthy, healthy, healthy, and then at some point you kick the bucket,” Tarnopolsky says. “It’s like the Neil Young song: better to burn out than to rust.” You get a normal life span, but in Olga years. Who wouldn’t take it? 

Thursday, April 14, 2011

The Song of the Dodo: Island Biogeography in an Age of Extinction


This book deals with many of the studies Claudia talked about in class on Thursday. It may be a bit long to count as a light read, it’s about 600 pages, but the author makes it funny and portrays the information in the form of stories and personal accounts. For anyone who is going into ecology, or is already in ecology, this is kind of a must read. It is a wonderful way to be introduced to some major studies and the people who conducted them. I found it super fun to read and packed full of cool biology facts. The author's other books are also wonderful works of biology writing.

Today's Miscellany

Don't forget next TUESDAY you will be writing about a selected research topic in class (it's on your syllabus).

A few items Claudia mentioned today that are buried here on the blog somewhere.
You may have received an e-mail from Bruce about tomorrow's meeting (Friday noon in room 143) with a CCS bio alum. Brendan Borrell (CCS Biology '99, UC Berkeley PhD in Biology '06 ) will talk about how he made the leap from science to journalism, demystify the logistics of surviving as a freelancer in New York, and share stories of reporting from the Bolivian chaco, the Australian rainforest, and the phosphate mines of Morocco.
    Finally I think Kathy may have also e-mailed you about her summer class but here are the details:

    MCDB 161L: Research Immersion in Molecular Biosciences
    Offered: Summer Session A,  June 20 – July 29,  2011
    Developed as part of the $1,000,0000 UCSB-HHMI initiative, this is an intensive (6 unit) undergraduate laboratory course covering basic approaches to research in molecular biosciences using model systems. In addition to the laboratory techniques, students learn hypothesis building, experimental design, data analysis and interpretation, as well as presentation skills. The 6-week course (Summer Session A) is taught in three modules, each based on current interdisciplinary biomolecular and biomedical research being conducted on the UCSB campus.  This is a unique opportunity for UCSB undergraduate students to obtain practical training that will help them prepare for careers in biomedical research.

    For more information and to apply to enroll in the course, see the attached flyer and the website:

    http://hhmi.mcdb.ucsb.edu/course/mcdb161

    Kind Regards,
    Kathy Foltz

    Wednesday, April 13, 2011

    Lotusland photo quiz

    Two very nice pictures from Rebecca. Those are ants inside the flower in the second picture, the third picture is just a close up. Speaking of species interactions, which we will, what do you think the ants are doing? ie who is gaining and who is losing in this interaction? More importantly how would you design an experiment to test your hypothesis? What would your treatments be, what would your control be and what would you measure?




    Tuesday, April 12, 2011

    Lotusland redux

    I just unearthed my camera to take some pictures and when I came to download them I found some Lotusland pictures which have just been sat there. I'm sure some of you took some good pictures. Why not post your best ones or send them along for me to post. I rather like the light in the picture above.

    Monday, April 11, 2011

    Biomagnification of Toxins in Marine Food Webs

    The Interdepartmental Graduate Program in Marine Sciences is sponsoring a special seminar that is of potential interest across a broad span of biology (see Abstract). Dr. Trapido-Rosenthal is visiting UCSB for Friday's Symposium honoring Professor Dan Morse (Hank earned his PhD with Dan in 1985).  We hope you can join us for this seminar.

    _______________________________________________
    Special IGP Marine Science Seminar

    Thursday, April 14, 2011
    12 noon
    MSRB Auditorium
    (pizza lunch following, on MSRB 2nd floor balcony)

    Henry (Hank) Trapido-Rosenthal
    Associate Research Scientist
    School of Ocean and Earth Science and Technology
    University of Hawaii


    Biomagnification of Toxins in Marine Food Webs

    ABSTRACT
    Some dinoflagellate algae and cyanobacteria produce toxins that have human health endpoints after being biomagnified as they move upwards through marine food webs. We are studying two of these toxins: (a) ciguatoxin, which is produced by dinoflagellates in the genus Gambierdiscus, and which causes poisoning in humans who eat toxin-containing reef fish; and (b) β-methylaminoalanine (BMAA), a “nonprotein” amino acid which can be produced by some cyanobacteria, and which can have neurotoxic effects on organisms at higher trophic levels after food web biomagnification. In this talk, I will first describe the results of our work with ciguatoxin here in the Hawaiian Islands. I will then describe work being done by ourselves and our international colleagues to address some mysteries associated with the ways in which BMAA is biomagnified and exerts its toxic effects.


    PUBLICATIONS
    Bienfang, P.K., DeFelice, S.V., Laws, E.A., Brand, L.E., Bidigare, R.R., Christensen, S., Trapido-Rosenthal, H., Hemscheidt, T.K., McGillicuddy Jr., D.HJ., Anderson, D.M., Solo-Gabriele, H.M., Boehm, A.B., and Backer, L.C. (2011) Prominent human health impacts from several marine microbes: History, ecology, and public health implications. Int. J. Microbiol., ID 152815, 15 pages.
    Venn, A.A., Loram, J.E., Trapido-Rosenthal, H.G., Joyce, D.A., and Douglas, A.E. (2008) The importance of time and place: How genetically-different Symbiodinium algae are distributed in a variable coral reef symbiosis. Biol. Bull., 215:243-252.
    Loram, J.E., Boonham, N., O’Toole, P., Trapido-Rosenthal, H.G., and Douglas, A.E.  (2007) Molecular quantification of symbiotic dinoflagellate algae Symbiodinium in corals. Biol. Bull., 212:259-268.
    Loram, J.E., Trapido-Rosenthal, H.G., and Douglas, A.E. (2007) Functional significance of symbiont clade in a coral reef symbiosis. Molec. Ecol. 16: 4849-4857.
    Venn, A.A., Wilson, M.S., Trapido-Rosenthal, H.G., Keely, B.J., and Douglas, A.E. (2006) The impact of coral bleaching on the pigment profile of the symbiotic alga Symbiodinium. Plant, Cell Env. 29:2133-2142.
    Yasuhara-Bell, J., Yang, Y., Barlow, R., Trapido-Rosenthal, H., and Lu, Y. (2010) In vitro evaluation of marine microorganism extracts for anti-viral activity. Virol. Jour. 7: 182-193.
    Anderson, P.A.V., and Trapido-Rosenthal, H.G. (2009) Physiological and chemical analysis of neurotransmitter candidates at a fast excitatory synapse in the jellyfish Cyanea capillata (Cnidaria, Scyphozoa). Invert. Neurosci. 9:167-173.
    Toledo, G., Green, W., Gonzalez, R., Christoffersen, L., Podar, M., Chang, C., Hemscheidt, T., Trapido-Rosenthal, H.G., Short, J.M., Bidigare, R.R., and Mathur, E.J. (2006) High throughput cultivation for isolation of novel marine organisms. Oceanography 19:120-125.
    Owen, R., Mitchelmore, C., Woodley, C., Trapido-Rosenthal, H., Galloway, T., Depledge, M., Readman, J., Buxton, L., Sarkis, S, Jones, R. and Knap, A. (2005) A common sense approach for confronting coral reef decline associated with human activities. Mar. Pol. Bull. 51:481-485.
    Trapido-Rosenthal, H. G., Zielke, S., Owen, R.J., Buxton, L., Boeing, B., Bhagooli, R., and Archer, J.A. (2005) Increased zooxanthellae nitric oxide synthase activity is associated with coral bleaching. Biol. Bull. 208:3-6.

    Rebecca Skloot

    The last CCS Distinguished Visiting Fellow for 2011 will be  Rebecca Skloot, author of 'The Immortal Life of Henrietta Lacks'.  Ms. Skloot will be available for a special question and answer session  Tuesday morning , April 12th 10:00 - 11:00 AM in the CCS Art Gallery.  This event is open to CCS Students and Faculty.


    In order to generate lively discussion, Ms. Skloot requests that you attend the Campbell Hall Lecture the prior evening (4/11 8PM Campbell Hall) to avoid duplicating Questions & Answers raised there.  The CCS special engagement on April 12th is specifically for Rebecca to go deeper into the discussion of the book with students and faculty.  In preparation, it is also asked that you acquaint yourself with the FAQ page on Rebecca's website:

    A limited number of free tickets are available for the event at Campbell Hall.  Please see Casey in Room 102 CCS (casey.moreau@ccs.ucsb.edu).  These will be available on a first come, first served basis.

    Saturday, April 9, 2011

    Cool Endosymbiotic Algae in a vertebrate!


    This article discusses a pretty interesting case of endosymbiosis, the first of its kind seen in vertebrates. I am very curious about how the algae actually gets in their cells and if there is some bizarre vertical transmission mechanism as mentioned in the article.

    Don't worry it's short, no TLDRs!

    Original paper is here.

    Friday, April 8, 2011

    Proteus

    Kathy sent this on:

    Chasing Haeckel - A documentary centered on Ernst Haeckel's drawings of radiolarians sets the unity of art and science in motion



    Selections from the the film Proteus, a documentary concerning the life, work, and philosophy of Ernst Haeckel, a 19th century naturalist. The film tells of the man's character and influences while using his detailed engravings of Radiolaria, single celled marine organisms, to make animated progressions

    Thursday, April 7, 2011

    Awesome summer opportunity


    Awesome opportunity. Get involved in research, see beautiful places, get fit, and help save a declining amphibian species. What more could you ask?

    Andrea needs help with back-country field work studying disease dynamics in mountain yellow legged frogs. The work will involve hiking, backpacking, catching frogs and testing them for chytrid infection, and collecting water samples. Contact Andrea directly if you are interested: andrea.jani@lifesci.ucsb.edu

    How to post to the Blog

    This information will be archived as one of the links on the right hand side.

    HOW TO SIGN UP TO POST TO THE BLOG
    You all received an invitation to join the blog at the start of the Winter quarter. If you need me to send a new invite just let me know.
    The invite comes as an e-mail from google with the heading: 'You have been invited to contribute to John Latto's blog'
    This will contain a link. (The information that follows is what I think happens but if it is different just follow the instructions). If you click on the link you will have two choices:
    If you already have a Google account just log in with your username and password and follow the instructions.
    If you don't have a Google account then click the link to sign up for an account. This requires very little in the way of information - just a valid e-mail, the password you want, and the name you want to use. I think you will then get sent an e-mail with a link to click on to validate your account.
    If you haven't received that e-mail then check your spam folder since it is an automated e-mail it may have been filtered out as spam.


    HOW TO POST
    Adding posts is really easy. Starting from scratch you would go to:
    http://www.blogger.com
    and sign in at the top with your Google username and password.

    You should then see the dashboard with the EEMB40 Blog. Click on 'New Post' and a simple word processor type screen will come up. Adding a text only post is as simple as typing it and hitting 'Publish Post'. You will probably also want to add links though (the whole point of the blog really) and adding links is very easy. Just highlight the text you want linked and click the word 'link' on the toolbar at the top of
    the entry form. Just cut and paste the link in directly from your browser, including the http://.

    Further buttons at  the top allow you to format the text, add pictures, spell check and, usefully, remove all the formatting from any section. You can preview posts before publishing them if you wish. Oh and the spellcheck is automatic and very easy to use but comes up with some very strange and amusing corrections for words it doesn't know. It is a good idea to test any links after you have posted to make sure they work (and work as you expect).

    Let me know if you have any questions. Rather than give a big long tutorial on how to use the blog publisher  I suggest you just play with it and then ask questions. It is very easy to delete posts, and preview them before you publish, so you can practice without messing anything up. 

    Tuesday, April 5, 2011

    E.O. Wilson on saving life on Earth


    What great opportunities to see E. O. Wilson: this Thursday at CCS from 4-5 in the art gallery (free), and/or at Campbell Hall at 8pm ($15). Hope you will take advantage.

    To inspire you, here is his biography. And here is an interview of E. O. Wilson on “Bill Moyers Journal”

    And finally, in 2007 he won the prestigious TED prize.

    See his TED talk and what he wants to do with his $100,000 prize money: