Author: Andrew Thaler

Marine science and conservation. Deep-sea ecology. Population genetics. Underwater robots. Open-source instrumentation. The deep sea is Earth's last great wilderness.

Bring the trench to the bench or bring the bench to the trench? The future of deep-sea exploration

Posted on By Andrew Thaler
Science

AndrewThumbNewsweek, in is new and impressive digital format, released a series of articles this week on deep-sea exploration, the challenges of human occupied and remotely-operated vehicles, and the decline in funding for ocean science, particularly in the deep sea. The main article, The Last Dive? Funding for Human Expeditions in the Ocean May Have Run Aground, is a deep, detailed look at the state of deep-sea science, seen through the eyes of Dr. Sylvia Earle and Dr. Robert Ballard, two giants in the ocean community. The follow-up, James Cameron Responds to Robert Ballard on Deep-Sea Exploration, provides insight into the mind of James Cameron, who last year successfully dove the Challenger Deep in his own deep-sea submersible.

Both the articles continue to perpetrate the canard that there is a deep chasm between the human-occupied submersible (HOV) and remotely-operated vehicle (ROV) communities. The reality is that deep-sea scientists use a variety of tools, from mechanical samplers to autonomous robots, to study and understand the deep. The choice comes down to which tool is most efficient, least expensive, and currently available. Absent a sea change, ROV’s will continue to be the workhorses of deep-sea research. And that is a good thing. I sang the praise of my robot underlings the last time this debate breached the public consciousness. I also discussed why basic deep-sea research and training highly skilled ROV pilots is a matter of national security.

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This Week in the Deep

Posted on By Andrew Thaler
Science

New and noteworthy publications in deep-sea science for the week of January 7, 2013.

Deep Sea Research Part 1: Oceanographic Research Papers: Discovery of a new hydrothermal vent based on an underwater, high-resolution geophysical survey

 

A new hydrothermal vent site in the Southern Mariana Trough has been discovered using acoustic and magnetic surveys conducted by the Japan Agency for Marine–Earth Science and Technology’s (JAMSTEC) autonomous underwater vehicle (AUV) Urashima. The high-resolution magnetic survey, part of near-bottom geophysical mapping around a previously known hydrothermal vent site, the Pika site, during YK09-08 cruise in June-July 2009, found that a clear magnetization low extends ~500 m north from the Pika site. Acoustic signals, suggesting hydrothermal plumes, and 10 m-scale chimney-like topographic highs were detected within this low magnetization zone by a 120 kHz side-scan sonar and a 400 kHz multibeam echo sounder. In order to confirm the seafloor sources of the geophysical signals, seafloor observations were carried out using the deep-sea manned submersible Shinkai 6500 during the YK 10-10 cruise in August 2010. These discovered a new hydrothermal vent site (12°55.30′N, 143°38.89′E; at a depth of 2922 m), which we have named the Urashima site. This hydrothermal vent site covers an area of approximately 300 m x 300 m and consists of black and clear smoker chimneys, brownish-colored shimmering chimneys, and inactive chimneys. All of the fluids sampled from the Urashima and Pika sites have chlorinity greater than local ambient seawater, suggesting subseafloor phase separation or leaching from rocks in the hydrothermal reaction zone. End-member compositions of the Urashima and Pika fluids suggest that fluids from two different sources feed the two sites, even though are located on the same knoll and separated by only ~500 m. We demonstrate that investigations on hydrothermal vent sites located in close proximity to one another can provide important insights into subseafloor hydrothermal fluid flow, and also that, while such hydrothermal sites are difficult to detect by conventional plume survey methods, high-resolution underwater geophysical surveys provide an effective means.

 

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Surviving Grad School: A Practical Guide to an Impractical Lifestyle

Posted on By Andrew Thaler 1 Comment on Surviving Grad School: A Practical Guide to an Impractical Lifestyle
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

Posted on By Andrew Thaler 2 Comments on Arduino Project Log: Getting Started with a Digital Compass
The Open CTD Project

Andrew ThumbAs 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

Posted on By Andrew Thaler 1 Comment on Bluefin Tuna and the Tsukiji Fish Auction: caution in drawing conclusions from record breaking prices
Uncategorized

Andrew ThumbToday 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.

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This Week in the Deep

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

Posted on By 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

Posted on By Andrew Thaler 6 Comments on Five organisms with real super powers that rival their comic book counterparts
Popular Culture, Science

Andrew ThumbThere 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
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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