Saturday, March 19, 2016

Loss of Butterflies Species

I was just reading through science daily and I came across the sad news that there is a steady loss of butterfly species due to a variety of factors. These butterfly species are habitat specialists, who require certain larvae host plants and habitat structures to survive. These habitat specialists are very vulnerable and have been a target of numerous nature conservations. Despite these efforts, there observation studies have shown that there is a decline of habitat specialists and the region they are observing, which used to have a diverse butterfly community, has become dominated by a few habitat generalists. Other factors include that ousting of larval host plants due to overfertilization and the ineffectiveness of nature conservation.

-David L.

Saturday, March 12, 2016

Tay Sachs and it's heterozygous advantage, or lack thereof.

Hello everyone!

Earlier in the quarter, we discussed frequency dependent selection, and the advantages of being heterozygous for certain genes. For instance, being heterozygous for sickle cell anemia is beneficial for those who live where malaria is present. Tay Sach's was also mentioned as being beneficial for carriers, but not specified to what and why, so I looked it up. According to random people on the internet, being a Tay Sachs carrier gives slight resistance to tuberculosis, however, when I looked for papers regarding this, I found one that said there was no heterozygous advantage to being a Tay Sachs carrier. Instead, the higher frequency in the Ashkenazi Jewish population is attributed to the founder effect and genetic drift.

Heterochony and Autism

Hello everyone,

During my presentation, I mentioned that there were four phenotypes that the paper described but I only spoke about one. The remaining three can be found here:

The paper is really cool, and I really like how it integrates evolution into brain disease/psych, as we usually wouldn't think to relate the two.

Friday, March 11, 2016

Cool intro article on using satellites to detect the sea floor

Hey guys, If any of you are interested in learning more about satellite detection of the sea floor, you should check out this cool article I found while doing my research for my topic. I think it gives a great initial overview of what altimetry is, and many of the recent advances they are making. I think it's a good, quick read you guys should check out if your interested in the more techy side of marine biology.

Thursday, March 10, 2016

People and Animals

Hey all,

So as I was surfing through YouTube, I found an interesting video that goes over the reasoning behind why humans keep and treat pets the way that they do. They include a historical background on humans and animals and many theories as to why we treat them the way we do today.

The video starts off telling us that, for the most part, humans were on equal terms with animals in the beginning of our existence. A widespread world view that we carried by our "hunter-gatherer" ancestors was animism which is the belief that non-human entities had spirits or souls. Humans respected these non-entities by having things like elaborate rituals for killing other animals for food.

The video then moves to the time period of Aristotle, where there was a new belief that everything in nature served humans and their goals. This lead to movement for using animals mostly of entertainment purposes. Some animals that were used for entertainment in places like the coliseum went extinct due to over-use.

Even more, the development of the geocentric model of the universe further strengthened the view that humans were the most significant creatures. Individuals like Galileo were persecuted for questioning these beliefs and tried for heresy. This persecution however, didn't just end with humans. Animals such as cats were branded as familiars that help witches perform magic. This, along with the widespread fear of witchcraft led to the execution and public massacre of creatures that were thought to be related to magic or supernatural forces.

An important philosopher named Rene Descartes also helped with bolstering the view of the superiority of the human mind. He referred to beasts similarly to inanimate objects that worked more like clocks than life. This continued view of superiority and objectification devalued the existence of non-human creatures around us.

The developments of science in the Age of Reason brought about developments in biology and zoology and returned a perspective closer to our roots with animism. Individuals like Darwin and Wallace created theories of evolution that put us on equal terms with the other species around us. By understanding the mechanisms of evolution and how different species came from common ancestors and how we were all related in some way, humans began having more respect for the animals and creatures around them.

These concepts, facts, and discussions continue further and in more detail in the video and I highly recommend watching it!

-Mitchell Hee

Evolution of courtship behaviors in Drosophila M.

Hey Guys,

This is the paper I was talking about during my presentation about the evolution of courtship behaviors in Drosophila. The sphinx gene regulates courtship and a knock out mutant of the sphinx gene has a higher copulation time with male counterparts, including copulating circles and lines.

More Bird Species Splits!

Hi everyone!
    As you may remember, for my presentation I talked about the split of the Madeiran Storm-petrel (Oceanodroma castro) into (O. castro) and the Monteiro's Storm-petrel (O. monteiroi). Bird taxonomy is still a huge mess and if you're interested, here is a list of proposed species splits that may occur in the near future when additional evidence is acquired.

And here is eBird's (an awesome citizen science site I use frequently to enter my bird observations) most recent taxonomical update.

    As you see, there are still a bunch and undoubtedly there will be more of these cryptic species to be "discovered".

    In other bird news, spring migration is really starting! Saw my first of season Hooded Oriole the other day, while the Northern Rough-winged Swallow have been steadily moving in. My seawatches from Coal Oil Point have also yielded large numbers of Surf Scoter moving north in addition to Gray Whale (at least 6 of them really close to shore on Tuesday!).
Here is an interesting video on the Aquatic Ape Hypothesis:

Here's Something Fun to Inspire You

So Claudia said we were allowed a bit of a stretch for one post. Here is my stretch. Remember how we talked about snails being unable to mate with snails of opposite shell spirals? It reminded me of this video. It is a great and funny video about snails that will hopefully make your day just a little better and perhaps inspire investigations about snails. One thing I found was this article right here which is also interesting. Investigate and comment if you find something in the video hilariously supported or strait up debunked by a paper. Link to the paper I found:

On Thursday last week I mentioned a GM tomato. Having looked it up again, I remembered that it was called the Flavr Savr tomato. What reminded me of it was the discussion of ethylene- a substance that plants create to induce the ripening of the fruit, and that we often spray on fruits like tomatoes so that we are able to pick them while green and then ripen them. The Flavr Savr was invented to get rid of the need to pick tomatoes green and spray them with ethylene. What they did was alter the gene (to my understanding they simply flipped a gene sequence around) to reduce the amount of polygalacturonase produced by the tomato. This is an enzyme that breaks down the pectin in cell walls and contributes to fruit softening. The result was a vine-ripened tomato that stayed significantly firmer than ordinary tomatoes.
Source: Bruening, G., and J. M. Lyons. The Case of the FLAVR SAVR Tomato. Rep. California Agriculture Online, n.d. Web. <>.
Research to control the ripening of tomatoes continues. At UC Berkeley, Athanasios Theologis and colleagues have identified and blocked a gene responsible for ripening. Fruit of this tomato and of similarly modified crops are ripened “on command” by treating on the vine with ethylene, giving freshness, improved flavor and reduced spoilage.

Wednesday, March 9, 2016

Plankton and Their Uptake of Atmospheric Carbon Dioxide.

Hey all!

So I was reading some of my notes from the past lectures and came across one of tangents we made about how scientists have thought about using plankton as a means for absorbing the carbon in the atmosphere. In our discussion, we went over how plankton could absorb the carbon dioxide in the atmosphere and alleviate global warming through depositing the carbon in the atmosphere to deeper levels of the ocean and the ocean floor.

I found this topic extremely interesting because I did a research project for the 2013 QuikSCience Challenge hosted by USC and studied phytoplankton and their potential to mitigate the effects of ocean acidification through their uptake of atmospheric carbon dioxide. Although my proposal was mostly theoretical, it did cover the discussion we had in class: plankton absorbs carbon in atmosphere and lowers the concentration of carbon dioxide, causing a lower amount of carbon dioxide to dissolve into the ocean and acidify the water.

I was interested in some of the negative ecological consequences of using plankton as a means of dampening the greenhouse effect since it seemed like increasing the amount of plankton in the ocean would have a significant affect on marine ecosystems. As it turns out, this use of plankton is a complicated issue. For one, increasing the amount of one type of plankton in the ocean may cause other plankton to die out and therefore reduce carbon dioxide uptake and defeat the purpose of adding plankton in the first place. An article I found talks about how small plankton tend to flourish with higher concentrations of carbon dioxide, but this significant blooming of small plankton led to a reduction in larger plankton species because the small plankton were taking up all the nutrients before the larger plankton.

In another article, a team of researchers discussed how plankton could potentially accelerate the rate of ocean acidification in deeper layers of the ocean, decrease oxygen concentrations in deeper marine ecosystems, and reduce the nutritional quality of plankton. They explained that these were due to the more rapid transport of carbon dioxide to deeper water levels, significantly more decomposition of biomass in the deeper marine ecosystems, and slower growth rates of organisms that fed on these "carbon-infused" plankton.

Check out the articles if you're interested!


Don't Stand Under This Tree in a Rainstorm!

In class a while back I mentioned a tree that if stood under during a rainstorm would give you blisters. Here it is: the manchineel tree aka the little apple of death. The link above is to a paper on some of the effects of manchineels that I think you might find intriguing. The link I will include below is to the site where I obtained this beautiful picture, which also has some fantastic information. Some basic information on the plant include the fact that the fruit was used to poison arrows in some Native American tribes; the fruit which looks somewhat like an apple, is known to do some really nasty things to a persons insides; additionally, the sap from this plant can cause severe eye damage and blistering on the skin, which is why standing under it in rain is a bad idea. Read the sources. These plants are incredible.

Photocredit: Manchineel. N.d. Biologypop. Web

Hello friends!

Recently, it was discovered that farmers have been accidentally creating plants that are genetically engineered for years through grafting.  This article is actually really interesting and shows how natural grafting can lead to GMOs.  It’s a cool read. Enjoy!

Here's the main article

Burgess Shale's Role in Character Design for Cartoon Media

Hey guys!

As the representative art major in the class, I feel a duty to make some connection from our course work to the art world, no matter how tangential it may be.
When John mentioned the Burgess shale fossils, I couldn't help but connect them with creatures- particularly monsters- from movies and games I consumed as a kid. It's great to see media creators with biology experience or interest! There's tons of inspiration to go around.

I've just dug up the first two examples that came to mind. I'm sure there are many more fossil-inspired fictional creatures out there! These are both connected to species found in the Burgess shale mines.

The first is from Pokemon! I'm sure most of us played these games as kids. Though there are several "fossil pokemon," Anorith is clearly designed after Anomalocaris!

The second is a little less recognizable. When I saw Habelia, though, the bumps on its shell in many artists' depictions immediately reminded me of Ohms from Miyazaki's Nausicaa. It does help that the giant arthropods are used as symbols of an ancient, mystical world- not unlike the ocean in the Middle Cambrian period!

It's nice to see fossils and other ancient, unusual creatures outside of Jurassic Park! It shows that even now, many parts of our lives are influenced and affected by the paleontological world. Remember, your work has influence even outside of the STEM sphere!


Research Opportunity for Great Tailed Grackles

(The last post made me realize I could post this here)

Hey guys! If anyone is still looking for a lab, or just something fun to do on weekends, I'm going to start going to the zoo again this Spring Quarter to continue tracking Great Tailed Grackles. Basically I just go to the zoo once a week (free entry, whoo!) and use this phone app to recor what the birds do for ten minute intervals. It's a lot of fun, and even better with a partner along!

Here's Corina Logan's (she's the PA of the project, she was a professor here last year but now she's doing research in the UK) blurb about it.

"The Grackle Project started in Santa Barbara in 2014 to investigate avian cognitive abilities in the lab and field. Currently we are tracking the individually identified (through unique color leg band combinations) grackles using focal follow protocols to gather behavioral data. If you are interested in being considered for a volunteer research position on the project, please see further details about the research at and follow the application instructions"

If you guys wanted to join, I'd suggest emailing Corina soonish so you can go through all the procedures (you need to fill out a health form and I think go to a training about how birds work) to start next quarter. But anyways, let me know if you guys have any questions! I can go on for ages about how cool the birds are.

Good luck on finals!

Research Opportunity for Project Baseline

Hello everyone,

In regards to the Project Baseline post earlier, I actually have a research opportunity for you all! Dr. Susan Mazer and her postdoc Heather Schneider are actually a part of Project Baseline. They recruit a lot of students at UCSB every summer to help with the preservation and curation of wild seeds for the Project Baseline evolutionary seed bank. I actually worked in this lab for a bit, but quit in order to make time for another lab, so I can give you a description of the work you would be doing.

Initially, you start off in the lab cleaning seeds and packaging them for about 8 hours a week and attend lab meetings, where you learn more about the project. I believe that Dr. Mazer said that once involved in the project for a while, there would be opportunities to break away from seed cleaning and packaging and do some field work collecting seeds. So, for those who might be interested in the work that Project Baseline does and want to participate, you should shoot them an email. They generally mass recruit during the end of summer, but of course, if you show interest I'm sure they'll be happy to take you in next quarter, as I know many people have dropped the lab this year. They did require an 8 hour/week commitment when I was with them, so take this in account.


Hi guys,

To study the effects of the environmental change the world is currently experiencing, some scientists have collected a large amount of seeds all across the United States to store for 50 years. They hope that the project "Project Baseline" will show the evolutionary process of plants during environmental change. I think this is a really interesting project, although it would have been more interesting if they included plants experiencing heavy pollution or live in the ozone layer hole area.

Plant Sexuality???

Hello Bio Bloggers!

During week 7, we talked a bit about anther smut, or plant STDs. Turns out, plants actually have sort form of sexuality.... to the extent that 19th century theologians felt the need to denounce the possibility! That's right, theologians were actually worried about the fact that some scientists found plant STD's.... apparently plant sex doesn't fit with strict biblical definitions. Further web-surfing showed that plant sex is also linked to how well plants can defend themselves. Plants such as the evening Primrose have a better chance of defending themselves against caterpillars if they sexually reproduce! As we know, this is due to gene "re-shuffling" that occurs from sexually reproduction. This is a little sneak peak into what I'll be presenting on tomorrow so stay tuned for more :)

*** Look at the pictures at the bottom of the page showing the step by step process of plant sex

See ya tomorrow!
- Katie

Tuesday, March 8, 2016

Quagga: Extant!

Hey guys, thought this would be an interesting video to check out!

In connection with the material we learned about Lazarus species in class, this experiment basically created a man-made version!  Conservationists and scientists are working towards reviving a sub-species of zebra, called a quagga.  These animals used to roam their native South African habitat freely, but were wiped out by colonial hunters in the 19th century.  The final living quagga died in captivity at a zoo in 1883.  The "Quagga Project" has been active for 30 years, selectively cross-breeding zebra with less stripes in an effort to repair the ecological damage done by the hunters.  Looks like they finally did it!

Research Diving

Hey guys,

I know a lot of you guys are SCUBA divers, and maybe also interested in Marine Science. If that's the case then I highly recommend you guys sign up for the Scientific Dive Course here at UCSB. Its an amazing, intensive course, that I'm currently taking, that will train you to become scientific diving certified. With that you can do research dives for many of the marine labs on campus. Many labs go out frequently to do anything from catching fish for classes to just completing surveys of local ecosystems. This course will allow you to help out, and in some cases even get paid to dive, with many labs. The course is offered twice a year, the month before fall quarter starts and during spring break.

If you want to learn more about the course check out this link:

And for those of you interested, but not SCUBA certified, the UCSB Rec Cen also offers a SCUBA class every quarter, not a credit course, that is really great. I got my cert through UCSB and the class was amazing and one of the cheapest options out there for students.

Lotus Land!

Hey everyone!

Hope you guys are studying hard for finals!  I finally had the time to go through my Lotus Land pictures, and I love them.  I thought I’d post some of them here to let you guys reminisce about that awesome trip (and to show those of you who weren’t able to make it some of the cool plants we saw).  I don’t know about everyone else, but I had a blooming’ good time! (no? no one? okay)

At Lotus Land, I was extremely intrigued by the Monstera deliciosa.  Here's a picture to jog your memory!

Bruce had mentioned that the reason for the odd holes in the leaves was so that the plants could be exposed to as much sunlight as possible, since they natively grow in rainforests.  It’s also called the swiss cheese plant (for obvious reasons).  The young plants don’t have holes in their leaves, but the mature ones do.  If you guys want to see the Monstera deliciosa in real life again because it’s so cool, there is actually a set of them outside of Physical Sciences South!  They line the steps and I had been wondering what they were for the longest time.  

Anyway, hope you guys enjoy the pictures of the cool plants!  (If you guys want to see more pictures, let me know.  I have a whole bunch more)


Monday, March 7, 2016

Lazarus Species: Three creatures that came back from the dead

Hey Everyone!

So last week in class, John mention lazarus species which are species believed to be extinct but reappear later. I was curious about some of the recently discovered lazarus species. Here are some of the coolest ones I found.

1. Omura's Whale
Very little is known about this baleen whale as the species was only identified in 2003 and purely form dead specimens. The whale was believed to be extinct but a pod of small fin whales were sighted off the coast of Madagascar in 2013 and after a DNA test the pod was confirmed as Omura's Whale. It resembles a small fin whale and is actually commonly known as the dwarf fin whale since it only grows to about 10m long. They are most commonly found in the eastern Indian Ocean around Indonesia but sighting have been confirmed of the east coast of Africa as well. 

2. Coelacanth

Believed to have gone extinct around the time of the dinosaurs, the Coelacanth was rediscovered in 1938 off the coast of South Africa. This lobbed fin fish is more closely related to lungfish, reptiles and mammals than to the common ray-finned fish. Fun fact: The Coelacanth braincase is 98.5% filled with fat and only 1.5% of the braincase contains brain tissue.

3. Lord Howe Stick Insect

The Lord Howe stick insect, also called the tree lobster due to its freakishly large size, was believed to have gone extinct by 1920 but then was rediscovered in 2001. (lucky us) It is believed to be the rarest insect in the world since only 24 individuals are known to be living on the remnant of a volcano know as Ball's Pyramid off the coast of Australia. These giant insects can grow up to 6in long and although they don't have wings they can run very fast.

If you guys want to learn about a couple more rediscovered Lazarus species check out this link:


Self-Fertilization May Lead to a Shorter Lifespan

Hey CCS gang,
I remember discussing asexual reproduction of plants and a few
organisms as well.  While in class I started thinking to myself about 
whether or not this sort of reproduction would have genetic 
repercussions.  This article addresses my train of thought and
also enlightened me to the fact that self-fertilization in 
Pristionchus nematodes leads to a shorter life-span.
Sorry ladies, at least us men aid in the acquisition of more genetic 
Check it out!


5000 Year Old Trees (and 8 Year Old Me)

When we talked about understanding the age of trees, bristle cone pines were mentioned. I remembered that I actually got to see bristle cone pines somewhere near Mammoth mountain when I was maybe 8 years old. At the time, I did not realize the significance of these trees. I just remember it being extremely cold and windy and thinking they “looked cool.” Now, with more scientific background, I can understand the magnificence of these ancient trees, some of which are nearly 5,000 years old! These gnarled looking trees live so long because of the harsh conditions they grow in. They grow slowly, which makes them develop very dense pest and fungi resistant wood. Their gnarled shapes come from being “eroded” by the elements. This brief article describes some of the oldest bristle cone pines. I have also added a picture of me with my brother and dad from when I visited them (a long time ago). 

-Veronica Russell

Ethephon for Commercial Farming

There are a several classes of important plant hormones that we have discussed this quarter. One of them is ethylene which helps with fruit ripening and leaf abscission. Ethylene is essentially a gas which the fruits on plants emit in order to speed the ripening fruit. Some fruits produce more ethylene gas than others. For example, bananas produce a lot. So, if you want your fruit to last a long time don’t put the bananas in the fruit bowl! The affects of ethylene on plants has been utilized in commercial farming. I found it interesting that they have even developed aqueous chemicals (rather than direct ethylene gas) that can be sprayed on plants to induce ethylene production. Pretty clever. Here is an article discussing the main properties behind one such spray, ethephon.

-Veronica Russell

Gingko bilboa Trees Leave a Legacy

In class within the last couple of weeks we talked about different types of gymnosperms and angiosperms. One of the gymnosperms that we talked about was the  Ginkgo biloba. I thought it was amazing that some of the Gingko biloba trees in Hiroshima Japan survived the atomic bombing during World War II. There are six trees that famously survived the bombing. Although they were severely damaged by the event, later they began to bud again and became a symbol of hope in Japan. This is somewhat of a biologic “miracle.” Today, descendants from these trees are being planted in other locations to symbolize overcoming that event in history. This BBC article briefly discusses the planting of descendants from these Gingko trees in Manchester England which is pretty cool! 

-Veronica Russell

Amber Preservation of Daddy Long Legs

Hey guys,
In class we discussed the different sedimentary levels of rocks, and the fossils contained inside of them.  I'd like to post this in order to clarify what I brought up, and so you all don't think I come up with this weird material on my own.  This is a different sort of fossil for two reasons: the preservation of the remains are encased in an amber tomb, and the spider's 99-million year old remains are viable enough to see an erection.  Another interesting fact is that this specific example of arachnid is now extinct, a distant relative of what we call daddy long legs.


Sunday, March 6, 2016

Further evidence that mimivirus is a fourth domain

Hi guys,

A new paper was just published showing a CRISPR like defense system is present in the mimivirus against virophage that the paper has named a "MIMIVIRE system." CRISPRs as they are currently known, are found in 48% of bacteria and 80% of archaea. The system is capable of recognizing a destroying invading phage DNA that has attached to host DNA. In the paper, strains A, B, and, C of mimivirus were infected with virophage Zamilon, a new virophage that is associated with the strains of mimivirus that causes the mimivirus to stop copying itself. Strain A was not affected by Zamilon and the paper shows a set of proteins made by strain A that was similar to CRISPR system. The paper argues that a defense system like this is unusual to find in a virus as it is more similar to other microbes, suggesting that the mimivirus has gone through a separate evolutionary path, further bolstering the possibility that they belong in a fourth domain branch.

Thursday, March 3, 2016

Plants in Space

A link to a short Science Friday video (it's less than 5 minutes) on growing plants in space.

Better Bannanas

Hi guys!

    We were talking in class the other day about several fruits that are all genetic clones of one another. Bananas were brought up, because they have a pretty interesting story of their own. Basically, there was a completely  different variety of banana we used to eat. You know all those banana flavored candies and things we always complain don't taste like real bananas? Yeah, they're all modeled after the old kind, which was by all accounts better than the current one. What happened though was that they were all genetic clones of one another, but a fungal disease called the Panama disease wiped them all out.

It's a little weird to think that there's a fruit that our grandparents have a completely different perception of, because it was an entirely different species. Granted, we risk the exact same thing happening today, so maybe our grandchildren will be munching on a vastly different kind of banana than we have.


Wednesday, March 2, 2016

Land Plants Return to the Ocean

Hey everyone!
    In class we discussed the movement of plants from aquatic to terrestrial environments. This article I found discussed the opposite, elucidating the genome of Eelgrass, a flowering plant which returned to the ocean. Really interesting read, especially the original article in Nature!

News article

Original article


Cool fossilized nervous system

Hey guys,

So recently there was a 520-million-year-old fossilized nervous system that was discovered. Similar to modern arthropods, this fossil has nerve cords which are similar to spinal cords in vertebrates. They even used fluorescence microscopy to see the evolution of the nervous system and confirming that the ganglia are individual nerves that are fossilized as carbon films. Cool stuff.


Tuesday, March 1, 2016

The Underground Palm Tree Trade

In one of last week's lectures, John briefly touched on the exotic cycad trade. No matter how tangential this relation is, it is related- I recently listened to a podcast focusing on the stealing and illegal sale of palm trees! I thought it would be interesting to learn about the economics behind theft and circulation of exotic plants(beyond The Orchid Thief, of course). 

Here's a link to the episode if you're interested!
And a more general article on the booming cycad trade from NY Times: 


Dog inbreeding

Hey all,

I was lurking through the internet one day and came across an interesting discussion about dog breeding. Dog breeding itself is a concept widely known and understood, but I've always overlooked the idea of possible genetic consequences resulting from pure-breeds. The much rarer and more expensive dogs are often Pure-breeds, and this has created an industry revolved around dog inbreeding. This had led to the rise of many genetic diseases such as those related to eye and heart disease as well as bone and joint disorders. I thought I'd share an article that shares some information regarding the common problems associated with pure-breeds.

Another interesting point that I found through my research is the way humans have "selected" dogs over many generations. Dog breeders have been around for quite some time, but most often their purpose was to select traits is dogs that served a purpose, usually for some work involving strength, hunting expertise, or sense of smell. As we approached modern-day society, we began to focus more on appearance rather than work-related traits. This wouldn't necessarily be an issue, but this focus on appearances has led to the development of appearance characteristics that issue a health burden on the breed. An example is the English Bulldog, which apparently is susceptible to a wide variety of diseases and virtually incapable of mating or birthing without medical assistance. They also live to a median age of 6.25 years. I'd like to share this article from 2012 that makes comparisons to dogs 100 years ago versus modern-day. The author makes very specific analyses based how the breeds have been physically altered and the genetic consequences resulting.