Monday, January 27, 2014

More sloth fur

In PLoS ONE this month:
Sloth Hair as a Novel Source of Fungi with Potent Anti-Parasitic, Anti-Cancer and Anti-Bacterial Bioactivity

Apparently the fur hosts a wide range of fungi along with the cyanobacteria and algae.

Saturday, January 25, 2014

Possible Career Paths in Being An Evil Scientist

Options include:
-Making an artificial brain that draws stuff w/ a robotic arm.
-Making a zombie dog head that loves treats.
-Transplanting heads onto new bodies.
-Making it so rampaging bulls won't attack you because you put a device in their heads that can partly control their emotions.

In other words, I am afraid.

Friday, January 24, 2014

de novo origin of genes

Kathy sent me a link to a recent paper in Science describing the appearance of new genes in Drosophila.
“Until recently, de novo origin of genes was considered to be so unlikely as to be impossible,” comparative genomicist Aoife McLysaght of the Smurfit Institute of Genetics at Trinity College in Dublin, Ireland, who was not involved in the study, told The Scientist in an e-mail. “[T]his population level analysis is important because it gives a new insight into the very early stages of the origin and establishment of genes de novo.”

This is pretty exciting stuff. Here's a link to a report in The Scientist and you'll find the Science paper citation there.

Wednesday, January 22, 2014

Whale seminar

I know some of you like the whales. I thought this upcoming EEMB seminar may be of broad enough interest to post here.

Monday, January 27th at 4pm in the MSRB auditorium
Interpreting cetacean behavior around military sonar using suction cup tags

Dr. Alison Stimpert
Visiting Scholar, Vertebrate Ecology Lab, Moss Landing Marine Laboratories

My primary interests lie in the intersection of bioacoustics and
conservation. To study this, I use suction-cup acoustic tags to
correlate sound production with underwater behavior of marine mammals.
Currently, I am focusing on the effects of anthropogenic sound on the
social behavior and foraging ecology of several cetacean species in
southern California as part of the Southern California Behavioral
Response Study (SOCAL BRS). I also maintain a long time research
program on humpback whale acoustic behavior, which has included work in the waters around Hawaii, Massachusetts, Alaska, and Antarctica. Gaining an understanding of the behavioral context of whale sound production will aid our interpretation of how anthropogenic sound in the ocean may affect whale populations, and can also be used in conservation and management strategies for remote monitoring of whale behavior and movements.

Tuesday, January 21, 2014

Hope may be in sight for those of us with a cold *coughcough*

Researchers at the University of Wisconsin-Madison have sequenced the genome for a malicious cold causing virus, but they haven't found out how to inhibit it yet. Sounds like a job for CCS bio students! The link to the Scientific American article is below flubber (aka Rhinovirus C).

Friday, January 17, 2014

Superhabitable worlds

I just heard this story on NPR yesterday and the topic of superhabitable planets is superrelevant to our discussion of what life is and what conditions might exist where it is formed.

 “In their hunt for potentially habitable planets around distant stars, scientists have been so focused on finding Earth-like planets that they're ignoring the possibility that other kinds of planets might be even friendlier to life, a new report says.
So-called superhabitable worlds wouldn't necessarily look like Earth but would nonetheless have conditions that are more suitable for life to emerge and evolve, according to the article published this month in the journal Astrobiology.
"In my point of view, astronomers and biologists are biased," says , an astrophysicist at Canada's McMaster University who is the study's lead author. "These scientists look for planets that are Earth-like."
But it's possible that Earth is actually only marginally habitable by the standards of the universe, says Heller, who points out that our home may not represent a typical habitable world.
He and co-author of Weber State University in Utah have come up with a long list of traits that might make a planet "superhabitable."

The scientific journal article discussed on NPR is available here (just published!).

HellerRenĂ© and ArmstrongJohn. Superhabitable worlds.  Astrobiology. 2014. 14(1): 50-66.

Thursday, January 16, 2014

Blood Falls

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

Apparently no-one has ever made a movie called Blood Falls. They probably should...

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.

Sunday, January 12, 2014

Here's a screen-cap from a really touching video of three sperm whales that adopted a dolphin with a spinal deformation. In the about section of the video there's a little information given about the interaction between the sperm whales and dolphin.

Friday, January 10, 2014

MBARI: Sea Exploration Opportunity

Ever been interesting in working with the Monterey Bay Aquarium Research Institute? I know I have!

Well here is our big chance as undergrads.  Every summer MBARI holds a ten week program where students get the opportunity to work with staff on a self-chosen topic. There are a number of equally rad projects from evaluating deep sea critters to reprogramming AUVs.
$500/week!! (June 9 – August 15, 2014) 

Launching ROV Doc Ricketts

For the full list of potential projects:

Interns must decide on a general topic but can suggest research ideas within the area.  The project must be able to be completed by the end of the ten weeks and any published work will be co-authored with mentor.

Application information (due Feb 13th) can be found at:

I couldn't find the name of this one, so comment if you know!
The only catch, our spring quarter ends a week into the program!  Mega bummer.  My suggestion would be to email the program coordinator George Matsumoto expressing interest in the internship, explaining the schedule overlap, and asking if the program would accommodate for this situation. If you do end up receiving a response, please post it as a comment.

This is a wonderful opportunity for research experience and mentorship!

Thursday, January 9, 2014

Self-sustained Replication of an RNA Enzyme

Now I have to remember all the places in lecture I said I would post a link to the blog. Here's the first I remembered, a 2009 paper in Science

Self-sustained Replication of an RNA Enzyme
RNA enzymes have been made to undergo self-sustained replication in the absence of proteins, providing the basis for an artificial genetic system.
An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other’s synthesis from a total of four component substrates. These cross-replicating RNA enzymes were optimized so that they can undergo self-sustained exponential amplification at a constant temperature and in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about one hour, and can be continued indefinitely. 

Pig's Rump Worm

The mention of the piglet squid reminded me of this fantastic creature.  It may be a little less cute, but just as hilarious.  I hope everyone enjoys this as much as I did.

Wednesday, January 8, 2014

How to post

Here are further details on how to post to the blog (there's also a link on the right hand side) . But this one has added pictures! To illustrate how this works I invited my dog to join. This is what the e-mail looks like. I created a Gmail 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.

Tuesday, January 7, 2014


Welcome CS20 students. You should all have recently received an invitation to join this blog. Please accept this so you can post here.

Here are the links to chosen topic examples I mentioned in class.

Chosen topic example 1
Chosen topic example 2
Chosen topic example 3

The picture that Katie asked about was indeed a squid, a glass squid. Not to be confused with the equally adorable piglet squid.