Sunday, May 31, 2015

HIV and Vaccines

It seems like every week there is some news about an HIV vaccine. There was back in January 1, February with 123,  April that had 123, 4,  May has had 123. There are probably many more that can be found outside of a quick search, but the point is that an HIV vaccine has become one of those science topics that is easy to make a story out of. There are always vaccines in development (even a crowdfunded one) and a vaccine against HIV is something the world needs, so it makes sense that these articles are always being written and read. But like the mouse that has been cured of Alzheimer's you have to wonder if these articles help the public understand anything other than a vaccine is under development. It's interesting to look at science news and how it's presented to the public.

Talking heads - 3minutes (2009)

Ted talk - 20 minutes (2013)

Controversy Surrounding Biological and Environmental Effects of low-level Nuclear Radiation

           I am enrolled in a freshman seminar this quarter titled, “Nuclear Futures: Understanding Global Energy Choices in a Post-Fukushima World.” We met once this past week, and we are going on all-day excursion to the Diablo Canyon Nuclear Power Plant on Tuesday, in Avila Beach near San Luis Obispo (the only nuclear power plant in California). Before our first meeting, we were instructed to watch a few debates between “experts” for and against nuclear power as a reasonable energy alternative. The debates were extremely polarized, and there was one key aspect that sparked my interest. There were massive disagreements about the adverse health effects of “low levels” of nuclear radiation, like the levels of radiation that surround Chernobyl today. I think it’s especially interesting to understand more about the potential adverse health effects from nuclear disasters, because we have a nuclear power plant essentially in our backyard.
            A lengthy report on the catastrophic health and environmental effects of the Chernobyl disaster was published by the New York Academy of Sciences in 2012, and it is quite controversial amidst the nuclear debate. The main controversy surrounds the danger of “low levels” of radiation. According to this report and other anti-nuclear advocates, inhaling such small amounts as one millionth of a gram of plutonium can be devastating. It kills most cells surrounding the area, because it’s an alpha emitter. The surrounding cells that survive mutate, their regulatory genes are destroyed, and years later the exposure can cause all sorts of cancers. This report attributes enormous cancer rates in the regions surrounding Chernobyl to the 1986 disaster, due to the massive incubation time of internal emitters (2 to 60 years). However, nuclear advocates cite the study as an outlier paper and just another fear-mongering fallacy. I think it’s really interesting to try to delve beneath the polarization to the actual scientific truth surrounding this issue. It’s hard to attribute such massive cancer rates to one disaster, because there are so many other factors that can contribute, but the study still seems quite legitimate.
This NY Times article is a good example of the arguments against such studies like the NY Academy of Sciences report:

This is the link to the massive NY Academy of Sciences report on Chernobyl:

A shorter more concise overview of biological and environmental effects of Chernobyl radiation is linked below.

This overview is really interesting and pertains to a lot of topics we’ve covered in CS 20 and CS 30, especially the ecological effects of nuclear radiation. The ecological and evolutionary implications of Chernobyl radiation is a very under-studied issue, but there are all sorts of fascinating evolutionary and ecological questions to be asked about the consequences of low-level radiation on surrounding ecosystems and populations.

Saturday, May 30, 2015

Genetic study on the difference between worker, queen and male bees

I stumbled across the article "From Worker to Queen at the drop of a gene" today while searching Science daily and found this pretty interesting.

The article and study discuss how the genome for male, worker, and queen bees are extremely similar and the differentiation between the roles depends on which genes are activated thought the bee's lifetime. ("The findings suggest that differentiation is not caused by inherited genetic difference, as is typical of most species of animal, meaning that males, which hatch from unfertilized eggs, are genetically very similar to their sisters.") Although the bees are hatched with some slight determination of what their role will be, the events in the lives can change this predisposition and cause certain genes to activate. The behavior and physiology of the male and queen bees hardly overlap. What I found interesting was "the differentiation between the castes in bees is similar to cell differentiation in humans."

the buff tailed bumblebee (used in the study)

Effects of E-cigarrette Vapor on Immune Response

        I found our lecture discussion of the increased prevalence of vaping and its possibly awful health effects very intriguing. I remembered reading a controversial article about vaping causing impairment of various aspects of our immune response, and wanted to know if it was actually true. People naturally think there’s no problem with vaping, because there is no inhalation of smoke involved, but is that really the whole story?
            Despite the lack of smoke and the toxins associated with combustion, E-cigarrette vapor still produces significant effects on the lungs, including inflammation and damage of vital proteins. Though the amount of toxic chemicals in the vapor is over a hundred times less than found in normal cigarettes, the toxins still contain large amounts of free radicals that damage cells, harm DNA, and can be cancer-causing. Some of the potentially toxic chemicals revealed upon analysis of the vapor include formaldehyde, nitrosamines, metals, carbonyls, volatile organic compounds, and polycyclic aromatic hydrocarbons. The levels of these compounds always increase after vaporization, due to heat and/or the voltage from the vaporizer.
            In a study published a few months ago, several groups of mice were extensively tested with exposure to E-cigarrette vapor. They were separated into two groups, one exposed to fresh air for two weeks, and the other exposed to E-cigarrette vapor for the time period. Each group was then separated into two subgroups; one was then exposed to influenza A and the other exposed to Streptococcus pneumoniae (the bacterium that causes pneumonia). Not only did the mice exposed to the vapor experience much more severe infections, but they also revealed physiological changes from the vapor exposure. More specifically, the ability of the mice to rid their lungs of the harmful bacterium was immensely impaired, due to reduced phagocytic capability by macrophages in the alveoli. The main impairment involved with the viral infections was the reduction in several crucial cytokines for immune response, along with the inhibition of pulmonary T-cells that are also crucial to fighting viral infections.
            Not surprisingly, this study was criticized by Tom Pruen, the chief scientific officer for the Electronic Cigarette Trade Industry Association. He claimed that the doses given to the mice didn’t make sense, because they were doses fit for humans. Obviously there are economic motives at play here, but it still does seem that the effects of E-cigarrette vapor on the human immune system remain relatively uncertain.

Two interesting articles from secondary sources are linked below:

One of the main papers that is the source of a lot of the controversy between E-cigarrete companies and health professionals is linked below.

Thursday, May 28, 2015

Related oil spill news

I stumbled along this article describing the consequences of oil spills even years after the initial spill. I know that the recent spill was not nearly as big, but I hope that it does not have a similar effect especially because there are a lot of bottlenose dolphins off of our coast and on the way back to UCSB on the train, I had already seen beached dolphins :(

Deepwater Horizon oil spill contributed to high number of Gulf dolphin deaths

"As part of an unusual mortality event investigation, a team of scientists has discovered that dead bottlenose dolphins stranded in the northern Gulf of Mexico since the start of the Deepwater Horizon oil spill have lung and adrenal lesions consistent with petroleum product exposure according to a paper published today in the peer-reviewed online journal PLOS ONE."

Tuesday, May 26, 2015

Galapagos Volcanic Eruption

Pictured above is the Wolf Volcano, located on Isabela Island in the Galapagos, which erupted yesterday (26 May) for the first time in 33 years.  In the past 200 years, about 50 eruptions have occurred in the archipelago.  The islands are considered young geologically because volcanic formation began around 4 million years ago, and today the Galapagos has some of the greatest volcanic activity in the world.  Because the islands are located above a very hot piece of mantle, volcanic activity is expected to continue for several centuries.

Volcanic activity is most recent in the western islands, making the eastern islands the oldest.  The tectonic plates beneath the islands (and subsequent volcanic activity) move at a rate of about 5 cm per year.  

Pictured below is the Pink Iguana (colonophus marthae), which is found only on Isabela island.  Darwin did not discover the species during his 1820 voyage to the islands; rather, the species was not discovered until 1986.  It was at first thought to be the same species as the Galapagos land Iguana, and only in the past few years has it been determined to be a separate species.  Although the species is only found on this particular island, experts say the pink iguana is not in immediate danger from volcanic activity; instead, experts are more concerned about the impacts of tourism and non-native species.  

3-D Printed Eggs

In biology, we're always trying to find newer and better ways to study animal behavior. Since the 1960s, researchers have studied bird behavior by hand crafting fake eggs. However, this process can be difficult and time consuming, especially when you want to study these birds in large populations. When we went to the museum, we learned about cowbirds. These birds lay their eggs in the nest of other species; sometimes they get tossed out, sometimes they get accepted. Scientists are trying to understand what characteristics of the eggs make the difference. Is it size? The presence or lack of speckles? The color? In this NPR story, Mark Hauber of Hunter College in New York talks about his difficulties in making the traditional plaster eggs, and how new and very available 3-D printing technology has allowed for quick, easy, and consistent creation of these eggs. There are still more steps to take in order to make these fake eggs even more realistic, such as making the shell thinner, but solutions are on the horizon.

Obesity Pandemic

     I enjoyed listening to the discussion in class today about metabolism, food intake, and its relation to the worldwide obesity crisis. This issue is particularly interesting; many people are quite passionate about health and weight loss, and because the results are visible, the subject tends towards being highly opinionated, even polarizing. There are a TON of programs, doctrines, etc. about maintaining a healthy weight, and just as much literature in criticism of these methods.

     In our discussion in class, it seemed to me that every point of disagreement ended in an unanswered question. I believe that we are missing some vital information, that we don't adequately understand the process of taking nutrition and distributing it throughout the body. This is not surprising; the endocrine system is absurdly complex.

     On Netflix, there is a show called Superhumans where Stan Lee (the guy who created The Incredible Hulk, Spiderman, and others) sends a guy around the world to find people who claim superhuman abilities in real life, and puts them under scientific scrutiny. One man they met in Sacramento used pheromones extracted from bees in order to cover his body with over 100,000 bees, without being stung a single time. Incredible.

     If a chemical factor can control this number of bees in such an fashion, it is not unrealistic to assume their role in our body may play as significant a role. Sexual drive, satiation, and emotional states are all regulated by these hormones, and I think it would be difficult to find someone who could consciously control all of these urges. I think people's addiction to fast food is a good example of this; many people understand these foods are unhealthy, yet they still find themselves returning for more french fries. It's difficult even to sit with a group of people eating this food and not end up getting some for yourself.

     However, it is also true that lifestyle and conscious choice has a HUGE role in physical fitness and weight maintenance. Regardless of one's genetic or epigenetic predispositions, a good diet and frequent exercise will almost always yield a healthy weight, when appropriately individualized. If an organism has sufficient but not excessive nutrients, and purpose to allocate them (exercise), it will typically do so and maintain fitness.
     The issue in regards to the obesity pandemic is not, I think, about whether one can maintain a healthy metabolism if they make all the right decisions. Humans are rather imperfect, and make mistakes every day. Public health policy cannot expect the entire population to hold themselves to a specific, individually designed fitness plan that works. This is especially true when mass-produced food means communities receive similar diets. There is a lot of evidence, and has been for some time, that the food industry's use of cheaper (or better mind-controlling) ingredients in food has played a part in this crisis.

     With social tolerance of these establishments that are altering the molecular make-up of the food eaten by the majority of the population, the issue goes far beyond simple personal responsibility. This is especially true in light of the economic factors that prevent access to healthier alternatives. The fact that some of the poorest areas in America (cough...Alabama/Mississippi) are also the most obese supports this premise. If these communities are also lacking in education, which is also more common in areas of low income, they are less likely to even be fully aware of the risks involved with their lifestyle.
     This is one of the functions government was designed for. Yet instead, our elected officials cozy up to the profits acquired by partnerships with the businesses selling the junk. I can't propose a solution to this problem, and I am uncertain how one goes about breaking these enormous financial ties between these "elites". As future scientists, our responsibility is to discover the mechanisms involved in metabolism and weight maintenance, and provide research so irrefutable that the people force their representatives to act.
     I'm taking the Non-Infectious Disease class that John is teaching this quarter, and we covered Diabetes last week. These videos about metabolic disorders and their link to diabetes and obesity were incredibly illuminating, yet simultaneously made me aware of how little we understand. Even aside of the terrible health problems experienced by diabetics and obese individuals, every teenager has either experienced or seen the psychological damage caused by obesity. Think of all the people who might contribute their gifts and ideas to society, but lack the necessary self-confidence due to their superficial appearance. This is certainly a major issue in our post-industrial era.

Thanks for reading my long-winded rant. haha

Matt Pautz

The Global Diabetes Epidemic (NY Times)

Friday, May 22, 2015

So What's Next??

This week while procrastinating for the chem midterm, I delved head first into the science section on Vice, and came across this interesting article. It basically talks about all the crazy things that scientists throughout the world are hoping to accomplish in the future, especially since we have entered what is called the Anthropocene.
The article is pretty short, but the ideas presented on the page are worth looking into on your own. The one proposal I am very skeptical of ever happening is the Incredible Shrinking Man Project, which aims to shrink humans down. Yes, people out there are actually trying to do this, no, they have not made any real progress.
Heres the link to the article on Vice

Wednesday, May 20, 2015

Watch T Cells Hunt Down and Kill Cancer cells

I found this awesome video showing killer T cells at work, like we talked about in class on tuesday
A lab at the University of Cambridge used spinning disk confocal microscopy and lattice light-sheet microscopy to create a 3d live imaging video.

Saturday, May 16, 2015

BIG CRAB!!!!!!

Earlier today as I was walking along the beach, I found two giant dead sheep crabs washed up on shore. Intrigued by the fact that I had never seen crabs this big and this dead, without butter, I decided to research more about them, and why also why they might be dead.
Sheep crabs are the largest members of the California spider crabs. They are slow moving with a carapace that tapers to a point. Juvenile sheep crabs decorate their carapaces in order camouflage themselves, and stop this behavior upon reaching adulthood. At this point their carapaces become covered in a thin film of green algae, which then serves as camoflauge. Males of the species spend winter in deep water, and both genders migrate to shallower water in spring to mate. Females can also store sperm for multiple broods, allowing them to fertilize eggs in the absence of males.
Males of the species are occasionally hunted for their claws, but this has been banned and the market for male sheep crab claws has declined. Sheep crabs are primarily scavengers, but will go after live prey.
Based on this information I cannot reason why the sheep crabs were dead. I tried researching possible reasons, and did not make any head way. Both crabs were intact and showed no sign of attempted predation or any sort of serious trauma. Still it was amazing to see such gigantic creatures washed up on our shore.

Thursday, May 14, 2015

Heroes and horsemen

I can't believe no-one sent me this. It is the most awesome XKCD ever. Click here for the full comic.

Monday, May 11, 2015


A few days ago, a paper was published in Nature, about a new archaea that serves as a bridge between eukaryotes and prokaryotes. The archaeon was discovered in deep marine sediments, near hydrothermal vents by the Arctic mid-ocean ridge (of course). Named after the shape-shifting Norse deity, Loki, the name Lokiarchaea reflects the complexity and confusion surrounding the origin of eukaryotes.

Initial phylogenetic analysis was performed using 16S rRNA gene sequences. Upon the identification of the archaeon, deep sequencing was used for genomic information. Lokiarchaea is monophyletic with eukaryotes. Lokiarchaea show a striking number of similar (genetic) components to eukaryotes.
The paper discusses genes that encode for actin, which is a key structural protein in eukaryotes (phagocytosis, motility, cell division). Lokiarchaea also have genes that encode for multiple GTPase proteins (regulators of actin cytoskeleton), which most bacterial and archaea do code for.

I find it incredible that all of these findings were based purely on molecular work--it would be very cool if someone was able to culture this archaeon...

For the paper, click here.

Sunday, May 10, 2015

Sparklemuffin the Spider

In Intro Bio several weeks ago when our class was learning about biodiversity, a few recently discovered species were mentioned and I was particularly captivated by Maratus jactatus (also known as "Sparklemuffin"), the beautiful creature pictured above.  Sparklemuffin, along with another type of peacock spider, Maratus sceletus (less interestingly nicknamed "Skeletorus," pictured right of Sparklemuffin) were discovered in Australia earlier this year by a UC Berkeley Graduate student.  Both spiders have been found since then in certain parts of eastern Australia.  

There are currently 53 known species of peacock spiders, 20 of which have been discovered in the past 4 years.  Researchers believe that the discoveries will continue.  These spiders are have excellent eyesight and are jumping spiders, meaning that they stalk their prey instead of spinning webs to catch it.  The colorful patterns, in conjuntion with unique mating dances, help male spiders to attract mates.  Below is a pretty cool video of the mating dance for the peacock spider species Maratus speciosus.