Thursday, March 15, 2012
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
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.
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
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.
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
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.
Sunday, March 11, 2012
Saturday, March 10, 2012
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
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
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 (firstname.lastname@example.org) if you are interested and you should certainly mention you are a CCS student.
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
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
From The History And Evolution Of Banana Hybrids
Monday, March 5, 2012
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
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.
Quoted from (click link to learn more): http://neurophilosophy.wordpress.com/2006/11/20/brainwashed-by-a-parasite/
Sunday, March 4, 2012
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:
This account is from Scientific American but there is also the author's own account, and full details, here.
Saturday, March 3, 2012
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.
Friday, March 2, 2012
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
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.