Science – Page 41 – Southern Fried Science

Surviving Grad School: A Practical Guide to an Impractical Lifestyle

January 10, 2013January 10, 2013 Andrew Thaler 1 Comment

Science

Ah, graduate school. For approximately 5 years you will live awash in the intellectual stimulation that comes with the pursuit of knowledge. You will learn more than you ever have before. Now at the forefront of the human data engine, you are not just being taught, but pushing the limits of human understanding imperceptibly, but significantly, … Read More “Surviving Grad School: A Practical Guide to an Impractical Lifestyle” »

This Week in the Deep

January 5, 2013January 25, 2013 Andrew Thaler

Science

New and noteworthy publications in deep-sea science for the week of December 31st, 2012.

PLoS One: How Deep-Sea Wood Falls Sustain Chemosynthetic Life

Large organic food falls to the deep sea – such as whale carcasses and wood logs – are known to serve as stepping stones for the dispersal of highly adapted chemosynthetic organisms inhabiting hot vents and cold seeps. Here we investigated the biogeochemical and microbiological processes leading to the development of sulfidic niches by deploying wood colonization experiments at a depth of 1690 m in the Eastern Mediterranean for one year. Wood-boring bivalves of the genus Xylophaga played a key role in the degradation of the wood logs, facilitating the development of anoxic zones and anaerobic microbial processes such as sulfate reduction. Fauna and bacteria associated with the wood included types reported from other deep-sea habitats including chemosynthetic ecosystems, confirming the potential role of large organic food falls as biodiversity hot spots and stepping stones for vent and seep communities. Specific bacterial communities developed on and around the wood falls within one year and were distinct from freshly submerged wood and background sediments. These included sulfate-reducing and cellulolytic bacterial taxa, which are likely to play an important role in the utilization of wood by chemosynthetic life and other deep-sea animals

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The ten best and worst events in shark fisheries management of 2012

January 4, 2013October 27, 2013 Guest Writer 1 Comment

Conservation, Science

Sonja FordhamPresident, Shark Advocates International — Sonja Fordham
President, Shark Advocates International

Sonja Fordham founded Shark Advocates International as a project of The Ocean Foundation in 2010 based on her two decades of shark conservation experience at Ocean Conservancy. She is Deputy Chair of the IUCN Shark Specialist Group and Conservation Committee Chair for the American Elasmobranch Society, has co-authored numerous publications on shark fisheries management, and serves on most of the U.S. federal and state government advisory panels relevant to sharks and rays. Her awards include the U.S. Department of Commerce Environmental Hero Award, the Peter Benchley Shark Conservation Award, and the IUCN Harry Messel Award for Conservation Leadership.

The last twelve months added up to another exciting year in shark and ray conservation policy. We certainly saw and should herald a lot of great progress in 2012. I think it’s also important to acknowledge what went wrong so we know where we stand and how best to move forward. I’ve taken a look back and compiled a top ten list of what I see as the best and worst events in shark fisheries management for 2012, based on my work at Shark Advocates International. I’m starting with the low points, but keep reading! It ends on a high note.

Five organisms with real super powers that rival their comic book counterparts

January 2, 2013September 19, 2013 Andrew Thaler 6 Comments

Popular Culture, Science

There is no force more creative than the painstakingly slow process of evolution. Ever wanted to walk through walls? Naked mole rats can physically bore through concrete. How about fly? There are a couple dozen different ways to accomplish that goal, even if you’re a squid. Incredible power of regeneration? Flatworms, roundworms, and echinoderms have us beat. Among the vertebrates, species like the axolotl can regrow limbs, organs, and parts of their brain. For practically every super power we can imagine, something on the tree of life has come up with a real-world analog.

Some real super power are more super than others:

1. The immortal rotifer that absorbs the abilities of anything it touches.

Bdelloid Rotifers. photo by Diego Fontaneto

Around 80 million years ago, a small, unassuming group of metazoa decided that sex just wasn’t for them. Instead of going through the effort of recombining their genetic material with a mate every generation to produce a viable offspring with a roughly 50% contribution from each parent, Bdelloid Rotifers started reproducing asexually. Males completely disappeared from class bdelloidea, leaving females to generate genetic duplicates through parthenogenesis. This is not their super power.

Bdelloid rotifers are incredibly tough. When environmental conditions are less than favorable, they can enter a dormant state. In this dormant state,they can survive the worst unscathed. Dehydrated, they can endure extreme temperatures, drought, even ionizing radiation. A bdelloid rotifer in its dormant state can even survive in space. If that isn’t enough, while dormant, these rotifers continue to produce offspring, which also remain dormant. This is not their super power.

Bdelloid rotifers’ super power appears when they recover from their dormant state. As they rehydrate and repair whatever damage their cells incurred, they incorporate DNA fragments from their environment. This includes partially digested food and any DNA in close proximity to them, even bacterial and archael DNA. It is this ability that allows bdelloid rotifers to overcome the limitations of asexual reproduction and survive for 80 million years without mates. They can literally absorb the attributes of those around them.

Their incredible toughness, celibate lifestyle, and ability to absorb the powers of anything they touch, put Bdelloid Rotifers firmly on par with X-Men perennial favorite: Rogue.

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13 wrong things about sharks that conservation advocates should stop saying in 2013 (and what they should say instead)

December 27, 2012December 27, 2012 David Shiffman 64 Comments

Conservation, Science

davesquare

While the rest of the scientific and management community and I are grateful for the passionate support of many shark conservation advocates, passion is no substitute for knowledge and accuracy. Some conservation issues are a matter of opinion and can (and should) be reasonably be discussed by people with different views, but many others are a matter of fact. Presented here, in no particular order, are 13 incorrect statements and arguments commonly made by well-intentioned but uninformed shark conservation advocates, along with the reality of the situation.

1) “Shark finning” is synonymous and interchangeable with “the global shark fin trade.” Shark finning is a specific fishing method. It is not the only way to catch sharks, and it is not the only way to provide shark fins for the global fin trade. Stopping shark finning is a worthy goal (that has largely been accomplished already *) because it is a wasteful and brutal fishing method that complicates management, but stopping shark finning does not stop the global shark fin trade. Many people calling for a ban on finning really seem to want no shark fishing and no fin trade of any kind (a viewpoint I disagree with, but regardless, proper terminology matters). For more on the difference between shark fishing and shark finning, see this post from June 2012.

2) 100 million sharks a year are killed for their fins. The origin of this number is still debated, but it was popularized by Sharkwater. While we will likely never know exactly how many sharks are “killed for their fins”, the best scientific estimate of the scope of the fin trade we have comes from a 2006 paper by Dr. Shelley Clarke. She found that the fins of between 26 and 73 million sharks end up in the fin trade each year, with a simulation average of 38 million. Dr. Clarke wrote an essay for SeaWeb on the misuse of her work, which is worth a read.

3) 1 in 3 species of sharks face extinction. This one is actually relatively close to accurate, and can be fixed with the addition of just two words. An IUCN Shark Specialist Group report found that 1 in 3 species of “open ocean” sharks are Threatened with extinction (Threatened means Vulnerable, Endangered or Critically Endangered according to IUCN Red List standards). 1 in 6 species of shark, skate, ray, or chimera are Threatened- while still a troubling number indicative of a very bad situation, it’s half as bad as claimed by many advocates. Also, please note that I included skates and rays, which are similarly threatened but often ignored by conservation advocates (with one notable exception from 2012).

PolitiFact calls claims of menhaden declines “Mostly False”, is completely wrong

December 17, 2012 David Shiffman 3 Comments

Conservation, Science

A menhaden, image courtesy Pew Environment Group

Despite their small size and plain appearance, menhaden have been called “the most important fish in the sea” because numerous coastal fish species rely on them for food. Although they aren’t typically eaten by humans, there is still a huge fishery for them for bait, aquaculture food, and oil. That fishery has been essentially unregulated, allowing fishermen to take as many as they want. Recently, there’s been a campaign among certain environmental groups to fix this problem and put catch limits in place for menhaden.

I was surprised to see PolitiFact, a non-partisan political fact-checking website, address this issue. I’ve checked PolitiFact pretty regularly for years, and I’ve never seen them cover a topic like this before. They focused on a claim by the Pew Environment Group that “In recent years, menhaden numbers along our coast have plummeted by 90 percent.” While I admit I am not familiar with specific details of menhaden population trends, anyone who has paid any attention at all to the ocean knows that we’re overfishing at alarming rates. According to the UN Food and Agriculture Organization, approximately 1/3 of all global fisheries are depleted or overexploited, many by more than the 90% referenced for menhaden. Shockingly, PolitiFact called the claim by Pew “mostly false”. Their reasoning for this ruling is even more ridiculous than the ruling itself:

Meet WormCam

December 5, 2012December 3, 2012 Guest Writer

Science

Technology in water? That seems a bit counter-intuitive doesn’t it? Well, Dr. Kersey Sturdivant, during his undergraduate and graduate years, denied the golden rule of electronics and submerged a video camera under water. But this is not your typical Canon Powershot D10. This is WormCam. As much as I love thumbing through magazines and flipping page … Read More “Meet WormCam” »

Math is hard: the use of complex equations decreases the chance a paper will be cited

November 16, 2012 David Shiffman 17 Comments

Science

How many of you asked “when am I ever going to need to know this” in math class? While basic mathematical literacy is essential for life in the modern world, most people can achieve success in their careers if they can’t remember the difference between pi and apple pie.

One of the exceptions to this comes from my own career path- scientists absolutely, positively need to have strong quantitative skills in order to perform research. However, many scientists struggle with math. I can’t even count how many conference presentations I’ve attended that included a statement along the lines of “don’t worry about all the complicated equations here”, or how many students or journal club attendees have told me that they just skipped over the section of a paper focusing on models and equations. See what I did there? Can’t even count? Anyway, while math may be more directly relevant to our jobs than it is to some of yours, we still find it hard.

What does a day of discarded plastic from a molecular lab look like?

November 14, 2012 Andrew Thaler

Science

To complement my post earlier today on the need for best practice guidelines to minimize plastic waste in a conservation genetics lab, I asked my labmates to save all of their consumables from a day of molecular benchwork. The above picture (Sharpie for scale) is the result. All told, we produced about 1/2 kilogram of plastic … Read More “What does a day of discarded plastic from a molecular lab look like?” »

Establishing Best Practices to Minimize Waste in a Conservation Genetics Lab

November 14, 2012 Andrew Thaler

Conservation, Science

I am, among other things, a conservation geneticist. What that means is that I use the tools of molecular ecology and population genetics to make observations about species and populations in at-risk ecosystems, assess the status of anthropogenically disturbed populations, and generate data that has direct applications to conservation and management issues. Essentially, the only difference between what I do and what a population geneticist or molecular ecologist does is the motivation—I select systems to work in that have a high conservation priority.

This motivation leads to a constant intellectual conflict at the bench. The tools of molecular ecology—PCR, gene sequencing, and, more frequently, high-throughput sequencing—are waste intensive. In order to avoid cross-contamination and practice precise, clean, technique, we use thousands of tiny plastic consumables every day. These come in the form of pipette tips, sterile packaging material, micro-centrifuge tubes, and numerous other plastic widgets. Often, because of the biohazard potential, these consumable cannot be recycled.

So we have a problem. As a conservation geneticist, we need these tools to produce the data necessary to make wise conservation and management decisions. As a sustainability minded individual, I find the massive daily accumulation of plastic waste inexcusable. Do we just accept this waste as the cost of conservation genetics? I believe that the answer is no. I think we can and should develop best practices to minimize the amount of plastic waste produced by a molecular lab while maintaining good, sterile technique. I would like to propose four guidelines, based off the principles of Reduce, Reuse, and Recycle, for minimizing waste in a conservation genetics lab.