Andrew Thaler

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” »

Arduino Project Log: Getting Started with a Digital Compass

January 7, 2013January 10, 2013 Andrew Thaler 2 Comments

The Open CTD Project

As I mentioned during the last Blue Pints episode, this year I’m going to be attempting to build a low-cost open source CTD for basic oceanographic measurements. This is in addition to my ongoing work with the OpenROV. I have a pretty solid electronics background, but in order to accomplish this goal, I also need to learn how to program microcontrollers, something that I’ve never done before. For the next several months I’m going to tackle various small Arduino project to get comfortable with the fundamentals. I’ll be working out of Environmental Monitoring with Arduino: Building Simple Devices to Collect Data About the World Around Us and Arduino Projects to Save the World, both of which feature beginner to advanced projects based around environmental monitoring and data collection, as well as Programming Arduino Getting Started with Sketches for as a basic programming primer.

For my first project, I wanted to start with something that could eventually be implemented with the OpenROV–a magnetometer to provide compass headings while navigating the robot. As a first step, I wanted to learn how to program the Arduino board to calculate compass headings from a magnetometer and develop some sort of rough visual readout of that heading.

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Bluefin Tuna and the Tsukiji Fish Auction: caution in drawing conclusions from record breaking prices

January 5, 2013January 6, 2013 Andrew Thaler 1 Comment

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Today marks the first Tsukiji fish market tuna auction of 2013, and, as in the previous two years, the first fish sold broke all previous records. In 2011, the record breaking tuna sold for $396,000. Last year, we tipped the scales at $736,000. Early this morning, the record breaking bluefin tuna blew the previous records out of the water, fetching a whopping $1,800,000 at the auction block, making this 488-lb tuna the most expensive fish ever purchased.

Over the next few weeks, I’m certain that we’ll see this number presented as an argument against bluefin tuna fishing, as an example of an industry out-of-control, and as a symbol of how ruthlessly we’ll hunt the last few members of a species to put on our dinner plates. These issues are reflected in the tuna market, but I want to urge caution in drawing too many conclusions from this record breaking number.

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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Watch Blue Pints Episode 5: 2012 in review, what’s in store for 2013

January 4, 2013October 27, 2013 Andrew Thaler

Uncategorized

httpv://www.youtube.com/watch?v=3vuOrHXkMuk&feature=plcp

Join us tonight at 7 for the first 2013 edition of Blue Pints!

January 3, 2013October 27, 2013 Andrew Thaler

Uncategorized

We’re kicking off the new year by reviving our popular Google+ Hangout — Blue Pints! Join us tonight (Thursday, January 3) at 7 for a casual conversation about marine science and conservation. On this episode, we’ll be reflecting on our favorite moments from 2012 and giving you a peak at what we have planned for … Read More “Join us tonight at 7 for the first 2013 edition of Blue Pints!” »

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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On Vacation

November 29, 2012December 27, 2012 Andrew Thaler

Uncategorized

Southern Fried Science is taking its annual December Blogcation. A few pre-scheduled posts will leak through over the next week, but we’ll resume regular service in January. In the meantime, please check the Best of SFS page for our favorite posts from the last 4 years. Feel free to use this comment thread to wish … Read More “On Vacation” »

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.