Thursday, March 15, 2012

Wrap up

Thank you one and all for your presentations today. Excellent timekeeping by everyone and  such a diverse range of topics.

If you did not receive your Multiple Choice Quiz back that means that it was all present and correct - good work.

After ten weeks of daily posts (a habit is a powerful thing) I'm going to take a break from posting here every day but will return next quarter.

Good luck with your finals and have a fun Spring Break. Here's a final Spring Break related topic from a paper in Science this week that the media are naturally picking up on: 
eg in the Washington Post - Real barflies: Study explains why male fruit flies turn to alcohol when they can’t have sex
 The actual paper in Science is here: Sexual Deprivation Increases Ethanol Intake in Drosophila
(my new favorite paper title)
and there's a commentary on the paper here: Sexually Rejected Flies Turn to Booze

Offer a male fruit fly a choice between food soaked in alcohol and its nonalcoholic equivalent, and his decision will depend on whether he's mated recently or been rejected by a female. Flies that have been given the cold shoulder are more likely to go for the booze, researchers have found. It's the first discovery, in fruit flies, of a social interaction that influences future behavior. 

Wednesday, March 14, 2012

Evolving Economics

On the Origin of $pecie$

My parents religiously watch PBS NewsHour, sometimes even over dinner. Throughout high school I would watch it with them, and I have grown to miss hearing about the latest news that PBS covers daily. I recently heard about a popular new book by naturalist and economist Bob Frank, who in his book relates the evolution of species to the market economy. This greatly interested me, since I plan to relate biology to another field like sociology. When my Dad called me and told me about Tuesday night’s PBS coverage of Bob Frank’s The Darwin Economy: Liberty, Competition, and the Common Good I went to the PBS website and watched the episode. In his interview, Bob Frank explains his comparison of Darwin’s evolutionary theory with the market economy. He even goes as far to say that the honor of being regarded as ‘The Father of Economics’ should be bestowed upon Charles Darwin. Frank uses Darwin’s theory of evolution to describe the negative effects of competition on a species. This is described by traits favored by the gene pool that help a species in one aspect of life but hinder them in another. Frank uses the example of male Elk – those with larger antlers than their competitors win battles between males, so that mutations in the species that coded for larger antlers are very strongly favored. Generation by generation, Elk antlers have grown in size so that now bull elk have massive four-foot long antlers. These antlers are great for winning interspecies battles, but horrible for retreating into cover when being chased into a dense forest by a pack of hungry wolves. The bull Elk’s antlers get tangled in low hanging branches, and the animal is slowed down and more easily killed by its predators. This phenomenon of evolution captures the conflict between individuals and the group. From an economic standpoint, the survival of the fittest comes at a cost to the 99%.

Frank uses a particular species of seals as another example. In this species of seal, 4% of the males father 88% of the offspring. This can be related to humans in the sense that the children of the rich often become rich themselves, due to connections fostered for them by their wealthy and powerful parents. In modern societies, incomes concentrated at the top, cause the rich to continue spending patterns, consequently raising the bar for the standard of living of that society. This reality relates to why money conditions in the middle class have become more difficult since the 1950’s. As the rich continue to build larger mansions, people’s standard of living goes up, causing middle class families to spend possibly 50% more on a house than is affordable.

Frank concludes by stating that there are two sides to market economics: the invisible hand of competition which makes companies and their products more ‘fit’, and the helping hand of the group and the government, which is supposed to impose regulations when the cost outweighs the benefits. Chief competitors such as Henry Ford and Steve Jobs can be compared to the individuals within a species that benefit from a small mutation. These mutations not only help individuals, but they also promote the prosperity of the species by leaving copies of that mutation to be passed down to generations to come; in economic terms: the greatest good for the greatest number.

Mmm pie

Welcome to Pi day - a favorite holiday among geeks, according to CNN, whose article is actually quite interesting explaining several interesting uses of pi, including finding planets, DNA folding and drug design.

On a vaguely related note (drug design) next week's MCDB seminar is a little different in that the speaker is from industry.

Thursday, March 22, 3:30pm - 4:30pm, Rathmann Auditorium (1001 LSB)

Timothy W. Behrens, MD, Senior Director, ITGR Human Genetics
Genentech, Inc.

Developing biomarkers for inflammatory diseases

In this presentation, Tim Behrens will discuss overall strategies for developing biomarkers that predict treatment effects in autoimmune and inflammatory diseases, and provide examples of the application of this approach in rheumatoid arthritis and asthma.

Short Bio:
Dr. Timothy Behrens moved to Genentech in 2006 following 20+ years in academia, with a focus on three major themes: 1) development of B lymphocytes; 2) genetics of human autoimmune diseases, especially systemic lupus erythematosus; and 3) identification of biomarkers for lupus and rheumatoid arthritis. Recently, Dr. Behrens has been particularly intrigued by the problem of applying cutting-edge genetic and proteomic technologies into the clinic to answer important questions like 'How active is the disease in this patient?' and 'How likely is this patient to respond to a particular drug?'

Tuesday, March 13, 2012

Google Doodles

It wasn't that surprising to see Google doodles for Darwin (Feb 12 2009, on his 200th birthday) and for Mendel (July 20 2011 on his 189th birthday) but I was very surprised to see Nicolas Steno show up on his 374th birthday in January this year.
I must confess when I first saw this I wasn't sure whether it was for Steno or William 'Strata' Smith but I like the design. I also like to look at the design notes

Known as the father of stratigraphy and geology, Nicholas Steno worked to understand history by what he could find in the ground. Rather than simply write books about his findings, Steno opted to do his own hands-on research. As an innovative thinker, he disagreed with his contemporaries in thinking that shark-tooth-shaped objects found imbedded in rocks "fell from the sky." Instead, Steno argued that these formations were fossils. His dedication to analysis, critical thinking, and creative thinking make him a great subject for a Google doodle!

Considering Steno's contributions to stratigraphy and geology, I wanted to honor his birthday with a unique take on his work. I knew that the colorful and geeky aesthetic of stratigraphy was the right direction for the doodle, but the team and I weren't sure how to apply it. Should we set the doodle in the middle of the country? Should we relate it to Google culture? Should I just make things up? Below are the exploration sketches.

After consulting a few geology nerds within Google, I decided to set the land in our very own Mountain View! I learned an interesting fact about our home-- there are no dinosaur fossils in the Bay Area (except for Stan of course).

Also staying a little more faithful to stratigraphy graphs, I formed the Google logo as though it was cut from a chunk of three dimensional land. Below are early drafts of the final direction.

Monday, March 12, 2012

Ancestry inference

EEMB's departmental speaker today will be John Novembre. Dr. Novembre is a professor at UCLA. His research combines theoretical population genetics and statistical genetics to investigate questions in evolutionary genetics, focusing on human evolutionary history and using data from second generation sequencing.  The title of his talk is "Ancestry inference and population genomics: Insights to recombination, migration, and rare variant diversity.

4pm in the MSI auditorium (ground floor) as usual.

Sunday, March 11, 2012

Earth's history in cake

You should probably review this fantastic cake before our class on Tuesday. Mmmm cake....

Saturday, March 10, 2012

Shiny birds

According to a new study, Microraptors—four-winged, feathered dinosaurs that lived 125 million years ago—sported Earth's earliest known iridescence, as pictured in this illustration.

Recent research suggests the pigeon-size Microraptor's feathers glimmered black and blue in sunlight, like feathers of modern crows or grackles.

The findings are the earliest evidence of iridescence in any creature-bird or dinosaur, said study leader Julia Clarke, a paleontologist at the University of Texas at Austin.

National Geographic has the cool pictures and this week's Science has the original article: Reconstruction of Microraptor and the Evolution of Iridescent Plumag.

Friday, March 9, 2012

Big dino

Was there a general trend towards larger size in dinosaurs, and if so why?

In addition to this question, why were some dinosaurs massive and what allowed them to reach such huge sizes.

For the answers to all these questions and more check out Rise of dinosaurs reveals major body-size transitions are driven by passive processes of trait evolution in this months Proceedings of the Royal Society B.

There's also a commentary on the DiscoveryNews website.

Benson and colleagues Roland Sookias and Richard Butler analyzed more than 400 species spanning the Late Permian to Middle Jurassic periods. The animals' pattern of growth during 100 million years supports a theory called "passive diffusion." This just means that various evolutionary lineages did a bunch of different things, from growing larger to growing smaller.
The findings counter a theory known as "Cope's rule," which claims that some groups, such as dinosaurs, tended to always evolve bigger bodies over time.
"Several aspects of dinosaurian biology may have allowed them to obtain larger maximum sizes than any other land animals," Benson said.
"For example, in many dinosaurs, parts of the skeleton contained air, and we think they had an efficient bird-like lung. These features helped them to support their weight on land more easily, and made their respiration and heat exchange more effective than in mammals."

Thursday, March 8, 2012

Research opportunity in the evolution of genomes

Steve Proulx, a Professor in EEMB, is looking for a couple of undergrads interested in research to join his lab.

Steve's interests are focused on understanding the evolutionary forces that structure genomes. Do genomes evolve to be robust? How do multi-gene families form? How does gene regulation evolve? Should regulation be simple or involve complex feedbacks? What evolutionary forces act to shape the machinery of DNA replication, transcription, and translation?

His lab website is here. You should contact Steve directly ( if you are interested and you should certainly mention you are a CCS student.

Your inner fish

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

Neil Shubin wrote a popular science book  'Your Inner Fish' which is a very easy and highly recommended. We tend to focus on those areas where we have 'improved' on our fish-like ancestors (walking upright, doing pushups, inventing calculus etc) but what I found fascinating, was a discussion of olfaction (smelling) and how it's all been downhill since our aquatic past.

The human genome only contains about 23,000 protein-coding genes - which itself is an amazing fact. The other 98.5% of our genome consists of non-coding genes, regulatory sequences, introns and endogenous retrovirus sequences.

About 1,000 of those 23,000 protein-coding genes code for different odor receptors but less than half of them are functional in modern humans. Which says a lot about the importance of different senses in the evolution of humans from an aquatic ancestor (smell) to a terrestrial life (vision). Our evolutionary history is revealed in our genes.

Finally, Neil Shubin, appeared on the Colbert Report in 2008 and did a pretty good job.

(Parts of this post were recycled from previous blog postings).

Wednesday, March 7, 2012


File this under 'more than you wanted to know' but since somebody asked and because I needed to get it straight in my own head here is the answer to whether plant cytokinins are the same as animal cytokines.

Cytokinins are a class of plant growth substances that promote cell division, or cytokinesis from the Greek cyto- (cell) and kinesis (motion, movement), in plants. Kinetin is an example and so is zeatin (pictured, found in maize).


Cytokines from the Greek cyto-, (cell); and -kinos, (movement) are small cell-signaling protein molecules that are secreted by numerous cells of animal immune systems and are a category of signaling molecules used extensively in intercellular communication. Although they have a rather wide variety of effects they do sometimes trigger differentiation of cells. The most widely known cytokines are the various interferons.

So both animals and plants use signalling molecules to stimulate cell division. In animals the term 'Cytokine' is now used more broadly and encompasses compounds that don't just lead to cell division. As far as I am aware the specific compounds used by animals and plants are completely different - the name Cytokinin/Cytokine describes a function rather than a specific molecular structure so I suppose its possible there is a compound that acts as both a cytokinin in plants and a cytokine in animals. There are about 200 compounds classified as Cytokinins and, I think, a somewhat larger number of Cytokines.

Tuesday, March 6, 2012


Those first bananas that people knew in antiquity were not sweet like the bananas we know today, but were cooking bananas or plantain bananas with a starchy taste and composition. The bright yellow bananas that we know today were discovered as a mutation from the plantain banana by a Jamaican, Jean Francois Poujot, in the year 1836. He found this hybrid mutation growing in his banana tree plantation with a sweet flavor and a yellow color-instead of green or red, and not requiring cooking like the plantain banana. The rapid establishment of this new exotic fruit was welcomed worldwide, and it was massively grown for world markets.

From The History And Evolution Of Banana Hybrids


Here are a few pictures I took during our trip...

Monday, March 5, 2012

Worster awards

You may be familiar with CCS's SURF awards but another source of funding for summer research is the Worster awards. These only apply to those working with grad students in them labs of EEMB faculty but that includes numerous CCS students and CCS students ARE eligible to apply (and several of them have won this award in the past). Even if it is not suitable this year you may want to bear it in mind for future years.

The text below is copied from an e-mail from Craig Carlson (ie applications go to his mailbox not mine!).

The Worster family has again graciously given EEMB a gift to go towards graduate / undergraduate research pairing fellowships. As in previous years, this award is to support the development of graduate and undergraduate research in ecology, evolution and/or marine biology through a mentoring program that pairs an undergraduate with a graduate student mentor during the summer. All graduate students that have their thesis committee chaired by an EEMB faculty member are eligible to apply for this award. We anticipate that stipends this year will be $6000 for each team ($3000 for the graduate and $3000 for the undergraduate, to be paid during the summer). We anticipate that we will be able to fund 5 teams this coming summer. Applications for this award (electronic, Word or PDF files AND a printed copy delivered to my office or placed in my EEMB mailbox) are due to me by Friday, April 6st, 2012. Please be sure to send and to deliver both electronic and hard copies. Please include:

1. Brief (2 pages, prepared by the graduate student) description of the research project and how the undergraduate student will participate in it.
2. CV of the graduate student, including progress toward his/her degree and any prior mentoring experience. 3. A brief statement from the undergraduate regarding his or her professional goals and how the research experience will prepare him/her to meet them. Undergraduates are expected to complete a senior honors thesis during the 2012-2013 or 2013-2014 academic year and express their intent to do so. In addition, undergraduate promise, experience, and GPA in their major will factor into the decision for funding.
4. Letter of support from the grad student's major professor. Please note that recipients will be obligated to write a summary of their team's progress and accomplishments at the end of the summer. These summaries will be sent to the Worster’s in the fall as part of a package thanking them for this important gift.

Undergraduates who will graduate in June 2011 are NOT eligible for this award. If you have any questions, please don't hesitate to contact me. -- Craig A. Carlson Department of Ecology, Evolution and Marine Biology University of California Santa Barbara, CA 93106
The carpenter ant in the picture on the right (genus Campanotus) has fallen victim to parasitic fungi of the genus Cordyceps, which manipulate the behaviour of their host in order to increase their own chances of reproducing. The spores of the fungus attach themselves to the external surface of the ant, where they germinate. They then enter the ant’s body through the tracheae via holes in the exoskeleton called spiracles. Fine fungal filaments called mycelia then start to grow inside the ant’s body cavity, absorbing the host’s soft tissues but avoiding its vital organs.

When the fungus is ready to sporulate, the mycelia grow into the ant’s brain. The fungus then produces chemicals which act on the host’s brain and alter its perception of pheromones. This causes the ant to climb a plant and, upon reaching the top, to clamp its mandibles around a leaf or leaf stem, thus securing it firmly to what will be its final resting place.

The fungus then devours the ant’s brain, killing the host. The fruiting bodies of the fungus sprout from the ant’s head, through gaps in the joints of the exoskeleton. Once mature, the fruiting bodies burst, releasing clusters of capsules into the air. These in turn explode on their descent, spreading airborne spores over the surrounding area. These spores then infect other ants,completing the life cycle of the fungus. Depending on the type of fungus and the number of infecting spores, death of an infected insect takes between 4-10 days.

Quoted from (click link to learn more):

Sunday, March 4, 2012

Evolution with all kinds of cute

How do you make an authentic evolution animation?  Quite simply: you allow it to evolve.  Tyler Rhodes, a student in the animation program at Virginia Commonwealth University, wanted to create an animation that wasn’t simply linear, but instead represented the true ‘tree-like’ process of evolution.  So he enlisted the help of elementary school students from William Fox Elementary School and the Patrick Henry School of Science & Art, and involved them in a type of game.
“Much like the whispered game “telephone” where one person whispers a message down the line until it’s very different by the end due to small “mutations” along the way, I would create a game of telephone using visual imagery.”
Tyler began the game by sketching a nondescript salamander-like creature:
He then had various groups of students make copies of this sketch, knowing that the copies would contain subtle differences.  The natural variation in the ‘progeny’ created from the first salamander sketch was used to determine the survival of the fittest.  Tyler would ‘kill off’ 98% of the organisms and start the process again, this time working from the sketches that ‘survived’.  In subsequent iterations he would throw out curveballs like desertification or a volcanic explosion (subsequent to the sketching), which would help the group decide which animals were best suited to survive.  They would then take these environmental changes into account when sketching their next creatures.

This account is from Scientific American but there is also the author's own account, and full details, here.

Pelagibacter Ubique

Well this is just a tad tardy, but here it goes anyway! 

Toward the beginning of the quarter, Latto mentioned Pelagibacter Ubique while lecturing on proteobacteria. He told us that this organism was overlooked until 2002 but it is quite possibly the most common organism on Earth

I read about a study on P. ubique; turns out this little guy is pretty badass! 
P. ubique has the smallest known genome (only 1,308,759 base pairs) and smallest number of genes (just 1354 open reading frames) out of all free living microorganisms! (To give you an idea of how small this little guy is, its genome makes up 30% of the cell volume.) But most other microorganisms with small genomes can't do what P. ubique can! P. ubique has complete biosynthetic pathways for ALL 20 amino acids and ALMOST ALL cofactors! 
You are probably wondering how such a small genome codes for everything a free living organism needs. 
It is because P. ubique doesn't have any duplicate gene copies, viral genes, or junk DNA (it doesn't have any introns, pseudogenes, transposons inteins etc.) WOW! That's quite a genome! 

P. ubique makes up to 50% of ALL CELLS in the temperate ocean! Because the genome is so small, it is easily copied and duplicated. 
Because there are so many, one would think mutation would be a problem, but it hasn't! It is thought to be due to the fact that the cell is self sufficient, but there hasn't yet been research to explain this phenomenon! 

Follow this link to learn more about our tiny, amazing friend!! 

Saturday, March 3, 2012

The bachelors

Here are the three large specimens of Encephalartos woodii seen at Lotusland. These have a fair claim to be among the world's rarest plants because they are extinct in the wild and the last known specimen, from which all garden specimens derive, was male.

The Cycad Garden has been called a “million dollar garden” because its development coincided with the auction of Madame Walska’s enormous jewelry collection, which fetched nearly that amount.

Kew Gardens in London has another large specimen of Encephalartos woodii and their website has some interesting information on it, and on rare cycads and cycad collecting.

In 1895, a single clump of this cycad was discovered by John Medley Wood on the edge of a forest in South Africa. In 1903, Wood sent his deputy, James Wylie to collect some of the smaller offsets for cultivation in the Durban Botanic Garden, where they survive to this day. More offsets were collected from the wild until finally in 1916, the Forestry Department collected the last remaining stem, making the species extinct in the wild. To date, no other wild specimen has been discovered. Two more male cycads have been found that resemble E. woodii but are not identical. All of them are male. The successful cultivation of offsets of the original plant has ensured the ex-situ preservation of this enigmatic species.
The search for a female
Although the area in which the original Wood’s cycad was discovered is well explored, it is yet to be thoroughly surveyed. Consequently, there is still hope that a female plant will eventually be found, and that could reproduce with the growing population of male clones in cultivation. Alternatively, there is a remote possibility that one of the plants in cultivation will undergo a spontaneous sex change, as has been documented in a few cases in other cycad species. Meanwhile, efforts are being made to create a female plant by crossing Wood’s cycad with the closely related E. natalensis. By successively backcrossing the female hybrid offspring with male Wood’s cycads, the aim is to eventually produce a ‘pure’ female. The project has currently created second generation crosses.

Cycad collectors
The rarity of these cycads is part of their appeal to a network of smugglers and thieves, who try to evade restrictions placed on plant movements by the CITES treaty. The other is a network of willing and obsessive buyers who grow their collections in secrecy to avoid having their own illegal plants removed. Enormous sums of money change hands, and because of the rarity of the species and their colourful history, offsets can sell for as much as $20,000 each.
It is therefore not surprising that theft is a serious problem. It is so serious that the San Diego Police Department in southern California assigned an officer to 'cycad beat' to monitor these precious plants. Elsewhere in the Hollywood Hills, Brad Pitt, Oprah Winfrey, David Bowie and Kevin Costner are among the celebrities that cycad-sellers report as collectors. ''I planted a huge grove of them in Brad Pitt's garden,'' says Jay Griffith, his landscape designer. ''And Brad flipped. He kept saying, 'I want more and more.' To me, they are most majestic when you plant gobs of them. You expect a triceratops to come around the corner and just gobble them up.'' Brad is not infringing any regulations though: his cycads are the commoner cycad species, Cycas revoluta, the so-called sago palm.

Friday, March 2, 2012

Lotusland 2012

Unlike 2010 when it rained we had beautiful weather this year. Check out the posts here and here for some photos of the gardens in the sun and rain in 2010.

Post some pictures from this year if you took some good ones (when you click the photo icon in the posting screen this will give you the option to upload a photo). Or you can just send them to me and I'll post them.

Here's a brief article about the Lotusland gardens and their founder, Ganna Walska, Forget About Rubies – She Wanted Cycads from the Christian Science Monitor.

Thursday, March 1, 2012

Private life of plants

It's shocking to realize that David Attenborough's Private Life of Plants is now 17 years old but it is still one of the most captivating documentaries on plant growth, morphology, ecology and evolution. Time-lapse photography is used extensively throughout the series and reveals plants as much more complex organisms than we generally think.

There are six episodes in total and they are well worth watching but for the condensed version there are a number of clips available online.