Thursday, January 31, 2013

Are blonde's dying out?



Permit me a repeat but I thought some of you may find this interesting. The idea that 'recessive' genes will somehow be lost from the population (simply because they are recessive) is quite persistent. They may be lost by genetic drift or by selection but, as you should have seen today, being recessive actually helps you if you are at a selective disadvantage because the heterozygotes are not selected against and they each contain a copy of the recessive allele.

In 2002 there was a series of stories in the press announcing that blondes were dying out. A typical story from the BBC:
Blondes 'to die out in 200 years'.
The proposed mechanism for this loss of blondes was simply that the gene was recessive

..too few people now carry the gene for blondes to last beyond the next two centuries.   The problem is that blonde hair is caused by a recessive gene.


But, as we saw, Hardy and Weinberg cleared that up for us over 100 years ago. An allele will not decline in frequency simply because it is recessive.

The story appeared to originate with the World Health Organization, although suspiciously, no scientists were named. It subsequently turned out the whole story was dubious if not fake. The WHO eventually issued a press release: 

''W.H.O. has no knowledge of how these news reports originated,'' said  the organization, an agency of the United Nations based in Geneva, ''but  would like to stress that we have no opinion of the future existence of  blonds.''

Because news stories tend to have a cyclical life of their own this story has resurfaced a number of times since 2002.

Skip forward a few years  to 2005 and a series of press reports on a similar fate for redheads:
Gingers extinct in 100 years, say scientists    
This time the story can be chased back to a misreporting of a story in National Geographic and the 'Oxford Hair Foundation' - funded by a manufacturer of hair dye.

I used to have blond hair but it died out....

Wednesday, January 30, 2013

Spirit Bears

A white mother Spirit bear and a black cub offspring; the father must have been black and the cub is a heterozygote for the coat color polymorphism. This picture really reminds me of the old Polar Bear joke which is not really suitable for printing here...

It's Carl Zimmer again with a really nice practical example of one of the simulations we will look at in class tomorrow - the interplay between genetic drift and natural selection: Snow Coyotes and Spirit Bears

The Bear part of the story is based on this paper in the journal 'Evolution': POPULATION GENETICS OF THE WHITE-PHASED “SPIRIT” BLACK BEAR OF BRITISH COLUMBIA

The Spirit (or Kermode) bear is a white-phased black bear found on the northwest coast of British Columbia, and is one of the most striking color polymorphisms found in mammals. A single nucleotide polymorphism at the melanocortin 1 receptor gene (mc1r) locus is the cause of this recessive w variant. Recently, evidence suggests that the white color provides a selective advantage during salmon hunting. Here we examine the effects of favorable selection, gene flow, genetic drift, and positive-assortative mating in an effort to understand the establishment and maintenance of this polymorphism and the observed heterozygote deficiency for mc1r but not for microsatellite loci. It appears that genetic drift was important in the establishment of the w allele and that the selective advantage was important to counteract immigration from populations without the w allele. Positive-assortative mating can result in a deficiency of heterozygotes but needs to be quite high to result in the large deficiency of heterozygotes observed, suggesting that other factors must also be contributing. Examination of population genetic factors, singly and jointly, provides insight into the establishment and maintenance of this unusual polymorphism.

Tuesday, January 29, 2013

Agua Pura

From Kathy Foltz:
CCS Students - here is an opportunity to put your interests in science, conservation, education and outreach to good use!
I am the Key Leader for a county-wide Science, Engineering and Technology committee through (UC based, cooperative extension service) Santa Barbara County 4-H. We are looking for one or two adult volunteer leaders to head up a youth 4-H Environmental Stewardship (water conservation) project, "Agua Pura." The volunteer leader(s) could be an undergraduate or graduate student or any community member. Responsibilities include meeting regularly with 4-H youth (typically about ages 9-16) who are enrolled in the project and coordinating community outreach events. The project itself teaches the participants about watershed and water quality issues, but focuses on having the youth then teach others in the community about water conservation.

SB County 4-H is looking for one or two adult volunteers to head up this program - ideally someone with a passion for science education and conservation as well as outreach. 4-H uses an Experiential Learning model for all of its educational activities.  Please contact Kathy Foltz (foltz@lifesci.ucsb.edu) if you are interested.

More information about 4-H and the Agua Pura project can be found here:

http://www.sb4h.org/County_4-H_Projects/County-wide_Projects/New_Countywide_4-H_Environmental_Stewardship_Project/

We periodically have opportunities for UCSB students to get involved on other science projects as well. Please contact me if interested.

Thanks!
Kathy Foltz
MCD Biology
CCS Biology
UCSB
foltz@lifesci.ucsb.edu

Monday, January 28, 2013

Discover the Natural Reserve System


Here's a great opportunity to find out about some of the research going on at UCSB's many natural reserves.

Discover the Natural Reserve System:
A Conference Celebrating the UCSB NRS
PROGRAM for February 8, 2013
University of California Santa Barbara
Bren School of Environmental Science and Management

Even if you can't make it to the talks you could check out the poster sessions - there are 32 posters in each session and its a very efficient way to find out about a whole bunch of research on campus. Plus you can meet the grad students involved and ask them questions.


8:45 – 9:00 WELCOME TO NRS DAY: Dr. Patricia Holden, Director,
UC Santa Barbara Natural Reserve System

9:00 – 9:30 Dr. Cristina Sandoval, Director, Coal Oil Point Reserve, UC Santa Barbara
The Recovery of the Western Snowy Plover at Coal Oil Point Reserve

9:30 – 10:00 Dr. Carla D’Antonio, Environmental Studies Program, and Department of
Ecology, Evolution and Marine Biology, UC Santa Barbara
Interpreting Livestock Grazing Effects on Grassland Composition

10:00 – 11:00 POSTER SESSION ONE (Abstracts will be posted by January 14)

11:00 – 11:30 Dr. Kevin D. Lafferty, United States Geological Survey and UC Santa Barbara
This Nature Reserve is Full of Parasites!

11:30 – 12:00 Dr. Tim M. Tinker, United States Geological Survey and UC Santa Cruz
The Sea Otters of Central California: Keystone Predators and Indicators of
Nearshore Ecosystem Influences

12:00 – 1:30 LUNCH BREAK – Lunch is on your own

1:30 – 2:00 Dr. Lynn H. Gamble, Department of Anthropology, UC Santa Barbara
Human Adaptation During the Middle Holocene on Santa Cruz Island

2:00 - 2:30 Hank Pitcher, College of Creative Studies, UC Santa Barbara
Painting on a Reserve

2:30 – 3:30 POSTER SESSION TWO (abstracts will be posted by January 14)

3:30 – 4:00 Dr. John M. Melack, Bren School of Environmental Science and Management,
and Department of Ecology, Evolution and Marine Biology, UC Santa Barbara
From Snowmelt to Saline Waters: Studies of Lakes in the Eastern Sierra Nevada

4:00 – 4:30 Dr. Peggy L. Fiedler, Director, UC Natural Reserve System
The UC Natural Reserve System at 48 Years (and Counting)

4:30 – 6:00 WINE RECEPTION

Sunday, January 27, 2013

The origin of Eukarytotes

Carl Zimmer's 2009 essay for Science magazine on the Origin of the Eukaryotes is well worth reading.

If the eukaryote cell hadn't evolved, we wouldn't be here to discuss the question of how it originated. In the eighth essay in Science's series in honor of the Year of Darwin, Carl Zimmer describes one of the most important transitions in the history of life: the origin of cells with a nucleus, which gave rise to every multicellular form of life.

Saturday, January 26, 2013

Don't abuse your antibiotics! Your intestinal bacteria will be unhappy with you.

http://mic.sgmjournals.org/content/156/11/3216.short

Epigenetic news

A paper in Nature this week, Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine, provides important details for how epigenetic information could be inherited.


Dr Jamie Hackett from the University of Cambridge, who led the research, said: "Our research demonstrates how genes could retain some memory of their past experiences, revealing that one of the big barriers to the theory of epigenetic inheritance -- that epigenetic information is erased between generations -- should be reassessed."
...
"However, it is not yet clear what consequences, if any, epigenetic inheritance might have in humans. Further studies should give us a clearer understanding of the extent to which heritable traits can be derived from epigenetic inheritance, and not just from genes. That could have profound consequences for future generations."

Friday, January 25, 2013

Science communication


Both these talks sound really interesting.

Dr. Jennifer Gardy will be giving seminars next Thursday and Friday at 1:30pm. The Thursday seminar (Thursday, Jan 31 MRL 2053 at 1:30 pm) "Science Communication: Lessons Learned from My Weird Career" addresses effective scientific communication, and the Friday seminar (Friday, Feb 1 ESB 1001 at 1:30 pm) "Outbreak: The Sequel – Using Next-Gen DNA Sequencing to Understand Infectious Disease Transmission" is a bit more technical. There is also the opportunity to meet and chat with Dr. Gardy about everything from her research career to here wide-ranging scientific communication experience (TED talks, television appearances).

Dr. Gardy is the head of the British Columbia Center for Disease Control's (BCCDC) Genome Research Laboratory and also an Adjunct Professor in the Department of Microbiology and Immunology at the University of British Columbia (UBC). For her PhD work, she studied bacterial genomics and bioinformatics-based predictive methods at Simon Fraser University. During her three year post doctoral work, she studied mammalian innate immune response at UBC. Currently, at BCCDC, Dr.Gardy work on genomic epidemiology on organisms such as tuberculosis and influenza. Dr. Gardy bio also states that she is "a passionate science communicator involved in a number of science media projects, including regular appearances on CBC Television's documentary series The Nature of Things."

Dr. Gardy's BCCDC website: http://www.bccdc.ca/util/about/UBCCDC/People/Faculty/DrJenniferGardy.htm
Dr. Gardy's website: http://jennifergardy.com/

Thursday, January 24, 2013

Evolution of Dog

Even Darwin, who got most everything else right, underestimated the power of selection when it came to man's best friend.

Darwin thought that dog breeds differed so much that they must have been derived from different ancestors.

Nevertheless he speculated what it would mean if we could show that they were derived from a common ancestor:

if… it could be shown that the greyhound, bloodhound, terrier, spaniel and bull-dog, which we all know propagate their kind truly, were the offspring of any single species, then such facts would have great weight in making us doubt about the immutability of the many closely allied natural species

Genetic data now provides strong evidence that ALL dog breeds are descended from the Gray Wolf in a process of natural and artificial selection that took a mere 14,000 years to go from wolf to Chihuahua or from wolf to Poodle, or from wolf to Shar-Pei, or from....

How to post

Here are more explicit details on how to post to the blog . Now with added pictures! To illustrate how this works I invited my dog to join. This is what the e-mail looks like. I created a Yahoo e-mail account for my dog and it didn't go in the spam folder there but you should check there if you didn't receive an invite.


Click on the link and you'll be taken to a page like this

If you already have any sort of account with Google (Google, G+, Blogger, Gmail) then you can probably just sign in on the right hand side. If you don't then click SIGN UP at the top right. This only takes a few minutes and very little personal information. (I managed to sign my dog up with no problems)

You should then be able to accept the invite. You can then either go straight to the blog or, once you are logged in, if you open the ccsblog in a separate window you should see that you are logged in at the top.


Now you can click on New Post (top right) and this will bring up a new window where you can compose your post.


Once you are done just hit the orange 'Publish' button. I've also highlighted the other two buttons you may want to use - to add a picture or a link.

It's that easy.

Wednesday, January 23, 2013

Strain 121


Vent chimneys with tubeworms on the Juan de Fuca Ridge.
The tops of the chimneys are too hot for animals. 

There's an article about Geogemma barossii, aka Strain 121, at Microbe Wiki but it doesn't contain a lot of information. I found this article at Microbe News Network more interesting. Click for the full article, I've only posted an excerpt.

World’s Hottest Microbe: Loving Life in Hell

Move over, Pyrolobus fumarii. A new entry for the record books has just been discovered. The hottest organism known to man has been isolated from a thermal vent deep in the Pacific Ocean.


The previous record-holder, P. fumarii, could live at temperatures as high as 113 °C (235 °F), well above the boiling point of water. But the new microbe, for now called “Strain 121,” thrives at 121 °C and can even survive for two hours at 130 °C.

The new organism is also unusual because it relies on iron to digest food and produce energy. Such organisms show promise in generating electricity from waste products and in removing radioactive metals from the environment.

“No one had ever seen a bug like this before,” says Derek R. Lovley of the University of Massachusetts in Amherst, who along with colleague Kazem Kashefi reported their discovery in Science. Researchers believe that many high-temperature microbes rely on iron to grow, but none had ever been isolated or cultured until now.

“The trick was to grow it in the presence of iron,” says Lovley. Many underwater structures are rich in metals and the microbes that live there are likely to use things like iron in their metabolism, he says.
...
In addition to their possible use in cleaning up toxic wastes and in generating energy, the microbes may also yield useful substances and pharmaceuticals with commercial and technological applications, such as heat-resistant enzymes that can be used in detergents.

Tuesday, January 22, 2013

Rogue scientist

I've always been fascinated by the idea of rogue scientists. I had presumed that they existed only in the comic books but now we have a real one, Russ George, who dumped 100 tons of iron sulphate in the Pacific Ocean off the British Columbia coast last July without the knowledge or consent of the Canadian government. The end result was an algae bloom covering more than 10,000 square kilometers of ocean.

There have been a number of articles on this incident (eg Geoengineering: Testing the Waters in the New York Times) but the most interesting is the one in Scientific American because they interview the man himself: Pacific Ocean Hacker Speaks Out. Is Russ George a "rogue geoengineer," salmon savior or something else?
Lots of interesting questions are asked:

  • Any concerns about possible side effects like dead zones?
  • Any concerns about the legality of this effort?
  • Can ocean fertilization really help combat climate change on any significant scale?

Monday, January 21, 2013

Slothfulness

Given the poor quality of much science reporting in the mainstream media I shouldn't complain but I can't quite tell whether this article from the Guardian newspaper is making more fun of sloths or the people that study them.


Sloths simply can't get away from scientists -
They have studied their locomotion, snoozing patterns, social lives, appetite and hair. Yes, scientists are fascinated by sloths.

At least they link to the primary research articles. Some of these look quite interesting.

Three-Dimensional Kinematic Analysis of the Pectoral Girdle During Upside-Down Locomotion of Two-Toed Sloths

Use of hands and feet of two-toed sloths during climbing and terrestrial locomotion
and the follow up paper
Use of hands and feet of three-toed sloths during climbing and terrestrial locomotion.

Disgusting appetite: Two-toed sloths feeding in human latrines.
I wish I hadn't clicked on that one. It's got pictures.

Sunday, January 20, 2013

Cheating algae

A lecture or two early for this link but I thought it was an interesting story and I'm not very good about remembering to post things later. From Science Daily, original paper reference below.

Cheating is a behavior not limited to humans, animals and plants. Even microscopically small, single-celled algae do it, a team of University of Arizona researchers has discovered.
...

Driscoll isolated several strains of the species, Prymnesium parvum, and noticed that some grew more quickly and do not produce any of the toxins that protect the algae against competition from other species of algae.
"When those 'cheaters' are cultured with their toxic counterparts, they can still benefit from the toxins produced by their cooperative neighbors -- they are true 'free riders,'"  Driscoll explained.


I like the paper title too: ALLELOPATHY AS AN EMERGENT, EXPLOITABLE PUBLIC GOOD IN THE BLOOM-FORMING MICROALGAPRYMNESIUM PARVUM.

Saturday, January 19, 2013

Get your nerd on


Get Your Nerd On: Desire, Passion And The Scientific Bookstore

A tribute to the scientific bookstore - a dying breed I'm afraid.

The pleasure of the technical/scientific bookstore is a rare and elusive thing. It's like spending your life in a foreign country, only to find a store full of books written in a native tongue that you never knew about. To find a new store can be the highlight of a trip. Over the years my friends and I have exchanged stories and the addresses of our favorite bookstore finds around the world.

Although the Internet has brought us many wonderful things (witness the last post) it has brought about the demise of many used and specialty bookstores. Santa Barbara used to have literally dozens of used bookstores and even Isla Vista had several. A few remain in Santa Barbara but Isla Vista's are long gone.

Friday, January 18, 2013

That is how a seahorse do



On the topic of biodiversity (?) here's a new True Facts video from zefrank1. I think it's largely true although that's not the case with all his True Facts videos. I have my suspicion about some of the facts in the True Facts about Morgan Freeman video. Although the animal ones all seem to be more or less true. Like he says in the one about the baby echidna 'It's difficult to make shit up about the echidna because it's so damn weird.'

Thursday, January 17, 2013

Blood falls

Blood Alley, Blood Diamond, Blood Red, Blood Simple, Blood Ties, Blood Work, Bloodbrothers, Bloodfist, Bloodline, Bloodsport.

Huh, apparently no-one has ever made a movie called Blood Falls.

The Blood Falls story, that is pictured in your textbook, is highlighted in a news report at the NSF website: Unusual Antarctic Microbes Live Life on a Previously Unsuspected Edge.

The News report was inspired by an article in Science entitled: A Contemporary Microbially Maintained Subglacial Ferrous "Ocean"

An active microbial assemblage cycles sulfur in a sulfate-rich, ancient marine brine beneath Taylor Glacier, an outlet glacier of the East Antarctic Ice Sheet, with Fe(III) serving as the terminal electron acceptor. Isotopic measurements of sulfate, water, carbonate, and ferrous iron and functional gene analyses of adenosine 5′-phosphosulfate reductase imply that a microbial consortium facilitates a catalytic sulfur cycle. These metabolic pathways result from a limited organic carbon supply because of the absence of contemporary photosynthesis, yielding a subglacial ferrous brine that is anoxic but not sulfidic. Coupled biogeochemical processes below the glacier enable subglacial microbes to grow in extended isolation, demonstrating how analogous organic-starved systems, such as Neoproterozoic oceans, accumulated Fe(II) despite the presence of an active sulfur cycle.

Wednesday, January 16, 2013

Correction

The part of my brain responsible for storing the details of TV shows seems to be deteriorating. In some ways this is good because it means I can watch shows again and enjoy them without remembering what happens but it's also frustrating at times when trying to recall something.

The House episode I was trying to recall in class was actually an episode of Grey's Anatomy (series 5 episode 9) where Joshua Malina (Will Bailey in The West Wing) quite memorably says 'No poo for you' when fighting with this partner  about whether to, err, 'donate' a faecal sample.

I'm glad I cleared that up. You kids don't know how lucky you are to have an internet that will, ultimately, answer any question, no matter how few facts you remember.

If you want to read more about this technique then the Wikipedia article is a good starting point: Fecal (faecal) microbiota transplantation (FMT) also known as a stool transplant. And if I'd gone there in the first place I could have found this:
The procedure was performed in an episode of Grey's Anatomy - In the Midnight Hour, season 5, episode 8 where a woman receives a "poop transplant" from her husband.

Tuesday, January 15, 2013

More on conjugation

Apparently in 1958 you still got your Nobel Prize notification by Telegram.

I was following up on some questions during and after class today and found some interesting papers I thought I'd pass on. The first is a 2011 review in Frontiers in Microbiology, Horizontal Gene Exchange in Environmental Microbiota. This comes closest to an overview of the question 'How common is conjugation (and other methods of horizontal gene transfer (HGT)) in prokaryotes?

The main aim of this review is to give a brief account of the occurrence and diversity of MGEs (Mobile Genetic Elements) in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.
...
The high rate of horizontal gene exchange in natural ecosystems is evident from both retrospective and prospective types of studies. The microbial world around us can be seen as a giant microbiome, with the continuous flow of genes between its different compartments. 

The second paper I found provides at least a theoretical answer to why plasmids may persist in a population without either going to fixation (ie 100% of individuals have plasmids) or extinction. From the journal Genetics in 2007: The Persistence of Parasitic Plasmids.

Plasmids thus make a major contribution to the accessory gene pool, but they are also considered to impose a fitness cost related to plasmid carriage and the time and resources required to replicate extra DNA. The precise magnitude and consistency of the fitness cost imposed by plasmids are currently a matter of debate.
...
In addition to conferring a potential fitness cost, plasmids may be lost stochastically during bacterial reproduction by failing to segregate into one of the daughter cells during binary fission.
...
(A) combination of fitness cost and stochastic loss should, over time, act to remove plasmids from the bacterial population. Much attention has therefore been focused on the nature of the opposing forces that act to maintain plasmids, and two such forces are widely considered important: the rate of infectious (horizontal) transfer between bacteria (in this case the dynamics are similar to the trade-offs in parasite–host dynamics) and the strength of the selective advantage conferred by plasmid genes. There are reasons to doubt the ability of either of these forces to maintain plasmid-bearing cells indefinitely.

The paper goes on to reexamine a model for plasmid persistence and conclude that:

In sum, we find no evidence to support the claims that a strong selective advantage or population heterogeneity is required for the maintenance of plasmids in bacterial populations and argue instead that even costly plasmids may persist in homogenous populations through undamped or (more realistically) damped oscillations with the plasmid-free class.

Monday, January 14, 2013

Pubic service announcement


Well in case you hadn't read the news, or noticed all the sick people, it's a pretty bad flu season this year. It's already shaping up to be worse than 2009 in terms of total cases and the virulence is actually worse as this year's strain appears to be quite nasty.

Google's flu tracker now has data by state and by cities and is a great illustration of using our search data for public good. Google can track flu trends several weeks before healthcare data is available simply by tracking the search terms people use (see 'How does this work?')

Here's a public service announcement from the executive director of UCSB student health.


Due to the increasingly serious influenza illnesses spreading across the country, we encourage all students and staff to receive a flu shot as soon as possible. Faculty & staff are encouraged to obtain their shots from their local healthcare providers, and many retail pharmacies also offer flu shots.

Student Health will be offering special times when flu shots for students can be obtained quickly without appointments in the Student Health Classroom on Tuesdays or Fridays 1:30 - 3:30pm. 

Alternatively students may obtain flu shots at our regularly scheduled Immunization Clinics Monday - Friday 10:00 am - 12:00pm & 1:30 - 3:30 pm; check in at the designated Immunization computer in the Student Health lobby. There is no additional cost for students with UC SHIP insurance, and for other students the cost is $20 and is billed to BARC.

Symptoms of flu include fever, cough, fatigue and joint aches. Medications can be prescribed to shorten the course of the illness if treatment begins within the first 48 hours, but otherwise the treatment is rest and over-the-counter painkillers. Most cases of flu don’t need to see a doctor unless there are serious symptoms, or can come in the first 2 days of illness when prescription medications may shorten the course of illness.

Please DO NOT GO TO CLASS OR WORK when you are ill to avoid spreading illness to others! The best way prevent the spread of illness is by avoiding others when ill, covering your cough and washing your hands. You should not have intimate contact or share cups or food utensils with people who are ill. Further information can be found at http://studenthealth.sa.ucsb.edu and http://www.flu.gov.             

Sunday, January 13, 2013

Chosen topic - example 3

Okay, I think this will be my final example and it illustrates how to get to something interesting as quickly as possible.

One thing I hope you do is to jot down words and phrases in class that didn't get much explanation that sounded interesting.

On Thursday I think I mentioned that coacervates were one type of protobiont. And that's all I said about them!

So, assuming I'd written down 'coacervate??' in my notes here is how I would proceed.

As I mentioned in class Wikipedia is a great place to start. Their page on Coacervates is okay and tells us a bit more. In the first paragraph it includes this intriguing statement that links us back to Oparin:

Coacervates were famously proposed by Alexander Oparin as crucial in his early theory of abiogenesis (origin of life). This theory proposes that metabolism predated information replication. The debate as to whether metabolism or molecules capable of Template replication came first in the origins of life remains open[1]
[1] Origins of Life and Evolution of the Biosphere, Volume 40, Numbers 4-5, October 2010 , pp. 347-497(151)

So after less than 5 minutes at Wikipedia it's off to a paper in 'Origins of Life and Evolution of the Biosphere'. Which turns out to be a fascinating journal. [You'll need to access this through the libraries e-journals for full access - if you are off campus use the libraries off-campus login].

The reference turns out to be to a Special Issue: Workshop OQOL’ 09: OPEN QUESTIONS ON THE ORIGINS OF LIFE 2009. but the papers are only conference abstracts.

It looks like they have this as the theme of their conference every year though and the 2012 conference is now published and has more complete papers.

Some of these look fascinating:
How Does Biology Emerge From Chemistry?
and many more.

My point is that you should get to this point in 10-15 minutes and now you can start to select a paper or two to read more thoroughly

Oh, and if you still wanted to read about coacervates and haven't been sidetracked by something else (my inevitable fate) then you could search this journal for that term giving you 15 results.




Saturday, January 12, 2013

Chosen topic - example 2

Another good source for inspiration for your weekly research is ScienceDaily. If you want to be a complete science nerd (and that's cool these days) you can make it your homepage because it changes constantly.

You can search the site to find recent science news on topics we have covered. For example a search on 'Panspermia'  would lead you to three articles  and this one, Evidence Of Liquid Water In Comets Reveals Possible Origin Of Life, from 2009 looks interesting. Remember that this is a news site though, so remember to follow the links back to the original article, here Liquid water and organics in Comets: implications for exobiology.

You can also just browse the site by topic to see what catches your interest. So for this week's topics you might want to browse The Origin of Life or even Extrasolar Planets.

Friday, January 11, 2013

Conservation and restoration

We will be visiting the Cheadle Center for Biodiversity and Ecological Restoration later this quarter but I thought I'd post details of their Conservation and Restoration seminar series for those of you with an interest in this area. In the past we have had students whose research interests are in molecular biology but who like to get their hands dirty with some practical conservation and restoration for fun.

This seminar series is a good way to hear about projects without the pressure of taking a whole class. You CAN take the whole series as a class for 2 units or you can just drop in to any seminar that sounds interesting.

Seminars are 6-7pm Monday evenings in CCBER Classroom - Rm 1013 harder south.

Each quarter the class has a different theme and this quarter the theme is California Channel Islands  Restoration.

This coming Monday's talk (Jan 14) is:

 Kathryn McEachern: Islands in transition: Studying and managing vegetation on the northern Channel Islands

Kathryn has been running the vegetation monitoring program for Channel Islands National Park for about 20 years and has some  interesting data to present.

The schedule for the rest of the quarter is:

Jan. 21  – MLK Holiday

Jan 28: Tim Handley : Twenty-plus years of vegetation change on Santa Barbara and Santa Rosa Islands: Monitoring methods and ecological results

Feb. 4. Denise Knapp: Ecosystem restoration on Catalina Island: Assessing threats and maximizing benefits

Feb. 11 – John Knapp: Invasive Species Monitoring and Management on Santa Cruz Island

Feb. 18th  - President’s Day – Holiday

Feb. 25th – David Mazurkeiweiz: Seabird nesting habitat restoration: Scorpion Island and Santa Barbara Island

March 4th – Ken Niessen – Optimizing Restoration Choices on Santa Rosa Island

March 11th – Emily Schultz: The effect of introduced herbivore removal and climate change on Santa Rosa Island plants with a focus on Jepsonia malvifolia demography

Thursday, January 10, 2013

Chosen topic - example 1

I thought I'd illustrate the 'Chosen topic' idea a bit more by giving you some examples as we go along. What we don't want you to do is to spend your time reading and writing about the basics. We want you to get to something fun, new and cutting edge as soon as possible.

So, for example, you might wonder what's new in the field of abiogenesis research? Because I know this is a very hot topic I'm going to start with a simple Google scholar search restricted to 2013 on that single term. I can widen that to 2012 if I don't find anything. You can do the same thing in Web of Knowledge.

http://scholar.google.com/scholar?as_ylo=2013&q=abiogenesis&hl=en&as_sdt=0,5

Although that only produces 5 hits from 2013 (it increases to 138 if you include 2012) we have a couple of interesting prospects.

The first, a paper entitled A review on the spontaneous formation of the building blocks of life and the generation of a set of hypotheses governing universal abiogenesis looks interesting. Neither the link nor the UC e-link brought the paper up for me but, undaunted, you can cut and paste the title into regular google and up pops the paper at the first link (you could also hunt it down via WoK or the citation and library).

I got lucky first time here. That paper looks well worth a read and it proposes a set of five hypotheses that govern abiogenesis.

Your investigation can now take off in various directions. In some cases you might want to investigate the response to a paper (might be too soon for this one). You might want to follow up some of the references in the paper if you find a particular part of the paper interesting. Or, if it hasn't gripped your interest yet, you could take a step back and browse the latest edition of the journal it was in 'The International Journal of Astrobiology'.

Oh and those five hypotheses are:


. Any celestial mass that has a body of liquid water and therefore has access to energy, will form at least the building blocks of life, if not life itself.

. The major component of any life form anywhere in the universe will be H2O.

. Any organism, anywhere in the universe, will be carbonbased.

. All life in the universe will be composed of nucleic acid based molecules as its code for life.

. The cell is the universal unit of life.


Wednesday, January 9, 2013

MCDB seminar

MCDB SEMINAR THURSDAY!

Thursday, January 10, 2013
12:30-1:30 PM
LSB 1001 (Rathmann Auditorium)

Seminar Speaker:
Vicente Torres, M.D., Ph.D.
Mayo Clinic, Rochester, MN

Talk Title:
Targeting cAMP related Pathways in Cystic Disease” Hosted by: Thomas Weimbs


Tuesday, January 8, 2013

Experiment Exploded ! ! !


Here's the link to the Miller-Urey experiment simulator I mentioned in class. Not only is this a fun little simulation but it is also a snapshot of how the internet looked 10 years ago with tiny videos in mpg format!

Still fun though. See how many goes it takes you to actually simulate the experiment correctly.

Friday, January 4, 2013

Start the quarter with a bang


For everyone who has ever wondered what it would be like when a 500km diameter asteroid crashes into the earth here's a simulation. Asteroids of this size would have impacted the earth during the late heavy bombardment I mention in the first class. If you go to YouTube to watch it you can click a little link to watch it in high def. (highly recommended). You might also want to wait until you can crank up the speakers. The perfect soundtrack to the end of the world.

Also this is an opportunity to remind you that as we go through the course you can click on the labels at the bottom of the posts to review past postings. For example as well as my yearly version of this post the Abiogenesis label has a small, but interesting, collection of posts