Tuesday, February 28, 2017

Coma Inducing Flowers Grown Next To Bio II

In class today John mentioned that there is a type of plant growing next to the Life Science Teaching Building called Angels Trumpet that is known for its hallucinogenic effects. I was surprised that something like that would be grown on campus so I did some research and found some crazy stuff! Angels Trumpet is scientifically known as Datura Stramonium, and causes anticholinergic effects due to its high content of tropane alkaloids (specifically atropine, scopolamine, and hyoscine). In simple terms, this drug cuts off the neurotransmitter acetylcholine, which is responsible for almost the entire parasympathetic nervous system. According to Diker, a common sign of Datura toxicity is coma! People affected by this drug experience dry throat, raised heart beat (up to 180 bpm), and intense hallucinations. One of the scariest parts of this is that "the effect of Datura is not distinguishable from reality, i.e., the patients have no idea that they are under the influence of a toxic substance" (Diker).

Paper with Datura case studies

I also found a terrifying narrative of a person who took this drug - Story

It is a scary thought that something so intense - a drug where over 80% of the studied patients had to go to the hospital - is growing somewhere I walk every day. I suppose I just never thought twice about the plants that I walked by on my way to class. Anyways, the moral of the story: don't do drugs kids.

Monday, February 27, 2017

Who doesn't like cholera?

Well, most people, but I think it's neat. We briefly talked about it in class, so this isn't completely out of left field. I think the neatest part about cholera is the Bengal (O139) strain, which is fun because emerged in the early 90s, and caused a very nasty epidemic and has been chilling out in India's waterways since, where the populations of the normal (O1) strain and Bengal are cyclic and out of phase with each other (throwback to Red Queen).  This paper is super rad and has something for everyone (evolutions, epidemiology, genetics). And if you have more time/ interest Pandemic: Tracking Contagions, from Cholera to Ebola and Beyond by Sonia Shah is an amazingly written and researched book.

Early Earth's Reducing Atmosphere

A topic that sparked my interest this quarter was the chemical composition of the Earth's atmosphere before the evolution of oxygen creating cyanobacteria. As stated in lecture, scientists already know that the early Earth's atmosphere was reducing. What does it mean to have a reducing atmosphere? To have a reducing atmosphere means the lack of any prominent oxidizers such as oxygen.  During the Hadean period, approximately 4.5 billion years ago, there was no presence of free oxygen. However, scientists do know that during this period the atmosphere was composed of mainly hydrogen sulfide, methane, ammonia, incredibly high amounts of carbon dioxide, and even small amounts of water vapor.
How do scientists know this? How could scientists figure out the main components of our atmophere from 4.5 billion years ago? These questions lead me to do some research and I came across a lab that used the oxidation rates of chromate, zircon, vanadium or igenous rock to provide evidence of early Earth's composition.

If you are interested in learning about these labs and their techniques, there is a link provided below.

Sunday, February 26, 2017

Hints to the Possibility of a Cold Origin of Life

When asked to imagine the origin of life, many things come to mind. Some picture a creator, others a warm primordial soup teeming with organics or a chemically rich environment near a deep sea hydro-thermal vent, while others see it hatching a ride to earth on a comet or asteroid. Yet, most don't picture a cold, icy world fostering the origins of life. Why?

Traditionally, the cold just seems dull or uninviting - it does not appear to be a dynamic situation, it seems rather frozen, sometimes barren and hostile, sitting mostly unchanged throughout time. But guess what? Taking the words of Elsa, the cold never bothered RNA anyway.

More specifically, low temperatures enhance ribozyme activity and catalytic ability - improving RNA polymerization. This does seem somewhat strange though - how would lowering the temperature enhance catalytic ability? We know that the rate of a chemical reaction increases with temperature. However, the low temperature and the eutectic properties of water (waters ability to form a water ice emulsion) strikes a balance between the thermodynamics and kinetics of the RNA polymerization reaction by the ribozyme.

Cold temperatures (particularly cyclic cold conditions where we have freezing and thawing) also drives the formation of complex ribozymes. Now we have a mechanism for the formation of ribozymes as well as a mechanism for the enhancement of there catalytic ability. But why does all this matter? Many researchers now believe that an RNA world was a precursor to the development of the biotic world, RNA being able to self-replicate and catalyze reactions - providing a mechanism upon which different selective pressures could act upon it. While RNA does not tell the whole story, it does give us a mechanism by which genetic information storage could have evolved - as well as how the coupling of genotype and phenotype may have taken place.

Life on earth may or may not have had a cold origin, but this information provides us with some useful insights and ideas that we can draw on when postulating about the nature of the origin of life on our planet and perhaps others. Who knows? Maybe this is just right mechanism for describing how life may have potentially taken hold on some of the icy Jovian moons, the cold subsurface oceans the perfect place for fostering the complex development of an RNA world and the subsequent develop of alien - or not so alien - life.

If you want to read more about RNA and its relationship with the cold, here are some interesting reads:

Friday, February 24, 2017

Inherited worldviews of evolution

Hello everyone,
I am generally interested in the debate between intelligent design(Creationism) and evolution. Some school districts even ruled to use biology textbook(Of Pandas and People) that include both view. Arguments being present both side and let the students choose. Later, the court ruled that violate the establishment clause(no religion in public school) because intelligent design is rooted deep in Creationism, which derivated from Christianity. Now a paper on the philosophical implication of evolution categorizes three inherited worldviews from teaching evolution as a possible theory for the origin of life. They are materialism, theistic evolutionism, and spiritual evolutionism. If you are interested you can search more about all three of them.

This is the link to download the paper:

Press Command-P for a New Layer of Skin

Researchers in Madrid have found a way to print fully functioning human skin from a 3D printer! This new technology will be used to help transplant patients and burn victims, and can be used in the testing of cosmetic and pharmaceutical products. Although the printer is still in the process of being approved, I am incredibly excited about it- this is a huge step in the medical field and so many lives will be saved from this advancement, especially burn victims. The researchers aim to improve the technology and make the printer even more sophisticated, so the printed skin can grow hair, for example. 

Read this short article for a brief summary of how the printer works, or watch the super cool video at the bottom of the page to get a tour of the lab and a verbal explanation of their research (in Spanish!) Want to learn even more?! Click here to read the paper that the article is based off of. 

Thursday, February 23, 2017

Stromatolite Fun

Stromatolites sound a bit boring, and sometimes they are, but they can be observed in present day at Shark Bay (that rhymed)! Here's a study on aaaaaaaaall the factors that shaped the morphology, survivability, and prevalence of the microbial communities that form stromatolites in this bay in the lehnd deown unda' (read as Australia, fair dinkum mate). It gives us clues as to what environments gave rise to microbial mats in the past.


(Click on UC-eLinks, then once on the site, click "Full Text" in the upper left)

P.S. The first name on the authors list sounds like he's really apologetic: E. P. Suosaari, doesn't it kind of read like "soooooo soooooorry"?

Origin of Life on Earth

So remember when we went over the origin of life on Earth and talked about an RNA world? Yes? Remember all the specifics? No? Screw your notes, you can barely read those anyway... if you're like me... So here's a study/review of all that is known on that subject, plus more, for your pleasure. It's from Davis (go UCs!), and it goes over pretty much everything we learned, and beyoooooooond.


Some links for Gymnosperms

Here are the Gymnosperm Videos I mentioned. And if you watched those nicely animated but rather dryly narrated videos here is something completely different.

This is why is is impossible for me to say 'The Larch' with a straight face.

If you need a more basic introduction then here's a nice description of what a trees is. I love the diagram.

Don't forget that if you want to explore any particular topic you can find some ideas by scrolling down to find the 'Labels' on the right hand side of the main page. There are only 4 tagged with the Gymnosperm label but they are all interesting and could suggest areas to explore.

Wednesday, February 22, 2017

Time to migrate!

Two weeks ago, animal lovers in UCSB stepped into one of the most exciting season of 2017 because

"It is time for Gray Whale to migrate!!!!!"

                        Collage of pictures of Grey whale breaching off the cost of Santa Barbara, CA. Picture taken 3-29-07(from Wiki )
Indeed, starting at February, gray whale, as well as other marine mammals( whales, dolphins, seals, sea lions and the occasional sea otters) will pass through Santa Barbara Channel to migrate. According to NOAA's Southwest Fisheries, it is the eastern North Pacific population that migrate passing Santa Barbara's channel, and they actually travel 9,300-12,500 miles in total. Is that amazing? 

Interestingly, there is an organization that is doing survey of migrating gray whale who passing Santa Barbara Channel every year. They have been surveying, counting gray whales for years, and built an online log to record migration. They will upload their observation per day to their website, and also you can view history report of the migration. 
Web: http://www.graywhalescount.org/GWC/The_Count/The_Count.html

Besides, you can choose to read boring words of migration, but you can be one of them to observe by yourself! You can get involved to count gray whales!

click here to see more information. 

BTY, don't expect much to see a gray whale in manz.... I have tried it for a month.....
        but if you see a gray whale from coast of manz, plz tell me.....

A New Ideal Wound Dressing?

So Sphagnum Moss is pretty cool! Between its ability to preserve bog bodies and its effectiveness in preventing infection and helping wound healing it serves quite a lot of purposes. The most amazing effect that it has is that it actually will immobilize bacterial cells and essentially remove all the nutrients it needs to survive. Due to this mechanism - there is no chance of the bacteria/virus from gaining any kind of resistance. Regardless of the pathogen it still needs to move and collect nutrients. In WWI and WWII there was a huge push towards using Sphagnum Moss instead of cotton as a wound dressing since it had been shown to not only heal the wound faster but to significantly lower the chance of infection. Today there are more advanced methods for preventing infection, but I am still curious why no one uses Sphagnum Moss today. It seems like it is ideal, and much better than any gauze or cotton alternative we use today. Anyways, here is the paper that describes its biomedical effects.

"Concerning the wound-healing properties of Sphagnum holocellulose: the Maillard reaction in pharmacology"  (you may need to write in your UCSB perm info for access)

Here's a cool picture of the sphagnum moss releasing leukocytes into a surgically created wound on a pig. The semicircle is the cell wall of
the sphagnum and the black circles are the leukocytes.

Another really cool pic of Tollund Man - an incredibly well preserved bog body due to the tanning effects of Sphagnum Moss.

Big Data on Small Things

So, for all of you botanists and entomologists out there (you know who you are), here is the large communal database that was talked of while we were in the small library conference room:

Global Biodiversity Information Facility (GBIF)http://www.gbif.org/

And, if you are interested in seeing the 3D imaging and reconstruction of insects, it is a service being marketed by CSIRO (https://www.csiro.au/en/Research/D61/Areas/Imaging-and-visualisation/Quantitative-imaging/Bug-scanning) complete with a proof of concept published in PLOS One (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094346).

Tuesday, February 21, 2017

High-Handed Heterozygotes?

Granted, this paper is from 1981 and the results are somewhat inconclusive, but the premise is still interesting. Jews in particular are a rather interesting population because until recently they tended to only mate within themselves, meaning that genetic drift was rampant (and making them perfect for this study on possible heterozygote advantage in not contracting tuberculosis). Unfortunately, this study found no correlation between the two so having Tay Sachs or being a carrier for it still just sucks.

Art of Science

Voting has opened for the 2017 CNSI Art of Science competition at UCSB. Community voting is open to the entire community.

General info here.

View all the entries and vote for your top five here.

(Full disclosure, Grace is a postdoc in my wife's lab. Her painting is freaking awesome though.)

Ubiquitous cephalopod identified

So, if you, like me, were wondering, what that cephalopod that shows up in all the artist depictions of the Ordovician is, it's probably a member of Orthoceras which is pretty neat. If you want to know pretty much everything about it, I suggest you take a look at this paper, which is pretty dense. And if you just want to read something from the 1930s about fossils in China, check this out. They're proposing a new genus for some fossils that kinda look like Orthoceras. 
Charlie Moffatt

Monday, February 20, 2017

Extinct marine reptile that gave live birth!!!!

*I passed this article around to a couple of you but I thought it might be interesting to everyone*

Baby ‘Sea Monster’ Found Inside Fossil Mother

This article is cool for a couple of reasons. One being that its about a super interesting prehistoric marine reptile with a crazy long neck (which is conveniently depicted in the artist reconstruction painting I have tacked on below. John, that one's for you.) Another being that this 245 million year old marine reptile, which belongs to the same subclass as a number of ancient crocodiles and birds, gave live birth rather than egg birth. Although not the only prehistoric reptile to do so, it is one of few which is really interesting when thinking about the evolutionary pressures and changes that brought marine animals to land and how live birth versus laying eggs could have contributed to that transition.

Who runs the world? GIRLS! --> Female Zebra Shark has babies without mating

Asexual reproduction is nothing new, but a shark switching from sexual to asexual reproduction throughout her lifetime certainly is something to question. Leone, a zebra shark living in at the Reef HQ Aquarium in Australia, gave birth to 3 pups in 2016 after being separated from males since 2012. Christine Dudgeon from the University of Queensland conducted a study to test if Leone had been storing sperm for all these years. Using DNA fingerprinting, Dudgeon found that the pups only had cells from mama Leonie- no DNA was found from any other shark. This is the first time scientists have seen this type of asexual reproduction, known as parthenogenesis. Read this Live Science article and read Dudgeon’s paper to better understand why Leonie the Zebra Shark “don’t need no man” in her reproductive life!!

What actually caused the human bottleneck???

Wait. A super-volcano explosion in present-day Indonesia caused the near extinction of the human population and an extreme bottleneck effect?! Sounds crazy. But maybe that's because it is. Check out this really interesting article from BBC about an Oxford research team that published a paper contesting this theory. They studied tiny glass shards found under tens of meters of sediment in Lake Malawi (just west of where Toba, the super-volcano, was located) and reported finding no changes in composition of the sediment that would indicate a significant enough drop in temperature to induce a "nuclear winter" as is thought to have occurred after the eruption. They suggest that the bottleneck effect observed through genetic studies was from mass migrations out of Africa. Could they be right? Does this theory have it all wrong?


Monday, February 6, 2017

In honor of Darwin day

From Bruce, and in recognition of the fact that Sunday Feb 12 is Darwin Day:

Three things you might not know about Charles Darwin