Shoreline Features

One of my favorite chapters to teach is the one covering shoreline features.  I'm especially fascinated by depositional shores.  Long Island, NY, is a great place to study them.

Here's a linked photo-essay on impressive shoreline features from around the world.
Shoreline Feature article - World Geography.com

A 'Hot' Topic

Image Credit - NASA

During our discussions of the world ocean and its myriad aspects and characteristics, we don't often discuss what the earth would be like without it.  Scary thought!

Read on to the linked Scientific American article about the results of a new study about climate change/the greenhouse effect.

Scientific American - Greenhouse Effect article

Color-Changers

Sorry for the lack of posts during July, but I was travelling for over half the month.

Just this morning I was catching up on my reading; this article from Science Daily.com caught my eye.  Check out this video from National Geographic, too...National Geographic - Color Changing Ocotpus
And another article here...BBC Nature - Octopus & Squid

Mechanism Behind Squids' and Octopuses' Ability to Change Color Revealed

July 25, 2013 — Color in living organisms can be formed two ways: pigmentation or anatomical structure. Structural colors arise from the physical interaction of light with biological nanostructures. A wide range of organisms possess this ability, but the biological mechanisms underlying the process have been poorly understood.

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Two years ago, an interdisciplinary team from UC Santa Barbara discovered the mechanism by which a neurotransmitter dramatically changes color in the common market squid, Doryteuthis opalescens. That neurotransmitter, acetylcholine, sets in motion a cascade of events that culminate in the addition of phosphate groups to a family of unique proteins called reflectins. This process allows the proteins to condense, driving the animal's color-changing process.

Now the researchers have delved deeper to uncover the mechanism responsible for the dramatic changes in color used by such creatures as squids and octopuses. The findings -- published in the Proceedings of the National Academy of Science, in a paper by molecular biology graduate student and lead author Daniel DeMartini and co-authors Daniel V. Krogstad and Daniel E. Morse -- are featured in the current issue of The Scientist.

Structural colors rely exclusively on the density and shape of the material rather than its chemical properties. The latest research from the UCSB team shows that specialized cells in the squid skin called iridocytes contain deep pleats or invaginations of the cell membrane extending deep into the body of the cell. This creates layers or lamellae that operate as a tunable Bragg reflector. Bragg reflectors are named after the British father and son team who more than a century ago discovered how periodic structures reflect light in a very regular and predicable manner.

"We know cephalopods use their tunable iridescence for camouflage so that they can control their transparency or in some cases match the background," said co-author Daniel E. Morse, Wilcox Professor of Biotechnology in the Department of Molecular, Cellular and Developmental Biology and director of the Marine Biotechnology Center/Marine Science Institute at UCSB.

"They also use it to create confusing patterns that disrupt visual recognition by a predator and to coordinate interactions, especially mating, where they change from one appearance to another," he added. "Some of the cuttlefish, for example, can go from bright red, which means stay away, to zebra-striped, which is an invitation for mating."

The researchers created antibodies to bind specifically to the reflectin proteins, which revealed that the reflectins are located exclusively inside the lamellae formed by the folds in the cell membrane. They showed that the cascade of events culminating in the condensation of the reflectins causes the osmotic pressure inside the lamellae to change drastically due to the expulsion of water, which shrinks and dehydrates the lamellae and reduces their thickness and spacing. The movement of water was demonstrated directly using deuterium-labeled heavy water.

When the acetylcholine neurotransmitter is washed away and the cell can recover, the lamellae imbibe water, rehydrating and allowing them to swell to their original thickness. This reversible dehydration and rehydration, shrinking and swelling, changes the thickness and spacing, which, in turn, changes the wavelength of the light that's reflected, thus "tuning" the color change over the entire visible spectrum.

"This effect of the condensation on the reflectins simultaneously increases the refractive index inside the lamellae," explained Morse. "Initially, before the proteins are consolidated, the refractive index -- you can think of it as the density -- inside the lamellae and outside, which is really the outside water environment, is the same. There's no optical difference so there's no reflection. But when the proteins consolidate, this increases the refractive index so the contrast between the inside and outside suddenly increases, causing the stack of lamellae to become reflective, while at the same time they dehydrate and shrink, which causes color changes. The animal can control the extent to which this happens -- it can pick the color -- and it's also reversible. The precision of this tuning by regulating the nanoscale dimensions of the lamellae is amazing."

Another paper by the same team of researchers, published in Journal of the Royal Society Interface, with optical physicist Amitabh Ghoshal as the lead author, conducted a mathematical analysis of the color change and confirmed that the changes in refractive index perfectly correspond to the measurements made with live cells.

A third paper, in press at Journal of Experimental Biology, reports the team's discovery that female market squid show a set of stripes that can be brightly activated and may function during mating to allow the female to mimic the appearance of the male, thereby reducing the number of mating encounters and aggressive contacts from males. The most significant finding in this study is the discovery of a pair of stripes that switch from being completely transparent to bright white.

"This is the first time that switchable white cells based on the reflectin proteins have been discovered," Morse noted. "The facts that these cells are switchable by the neurotransmitter acetylcholine, that they contain some of the same reflectin proteins, and that the reflectins are induced to condense to increase the refractive index and trigger the change in reflectance all suggest that they operate by a molecular mechanism fundamentally related to that controlling the tunable color."

Could these findings one day have practical applications? "In telecommunications we're moving to more rapid communication carried by light," said Morse. "We already use optical cables and photonic switches in some of our telecommunications devices. The question is -- and it's a question at this point -- can we learn from these novel biophotonic mechanisms that have evolved over millions of years of natural selection new approaches to making tunable and switchable photonic materials to more efficiently encode, transmit, and decode information via light?"

In fact, the UCSB researchers are collaborating with Raytheon Vision Systems in Goleta to investigate applications of their discoveries in the development of tunable filters and switchable shutters for infrared cameras. Down the road, there may also be possible applications for synthetic camouflage.

Other members of the UCSB interdisciplinary research team involved in these discoveries include Elizabeth Eck, Erica Pandolfi, Aaron T. Weaver, and Mary Baum.

This research was supported by the Office of Naval Research via a Multidisciplinary University Research Initiative award and an Army Research Office grant through UCSB's Institute for Collaborative Biotechnologies. As well, use was made of UCSB Materials Research Laboratory central facilities and equipment, which are supported by a grant from the National Science Foundation.

Our Visit to Woods Hole Oceanographic Institution

Here's a recent "image of the day" from WHOI's website.  The researcher who snapped this picture spoke to us regarding her work with marine mammals.


Image of the Day



JULY 2, 2013
Shadowing Whales

MIT-WHOI Joint Program graduate student Julie van der Hoop snapped this quick self-portrait as she prepared to locate a whale tag with a VHF antenna in the spring of 2013. Van der Hoop was part of anexpedition led by Michael Moore, a WHOI marine biologist and director of the Marine Mammal Center, to study the physiology and behavior of whales that feed in and around the Kaikoura Canyon, a deep, productive part of the ocean just off the coast of New Zealand's North Island. (Photo by Julie van der Hoop,Woods Hole Oceanographic Institution)

Summer Schedule

Sorry for the delay between posts; it was an intense finish to the school year.  I will be away at times this summer, however I will continue to post updates to the blog.  Thanks for following the blog this year and I hope you keep checking back this summer.

I was thinking of what to post today.  As I indicated, it was a particularly intense finish to this school year.  As a result I'm behind on all of my reading, not just for science.  I was contacting my state senator when I noticed this short video on the NYS Senate website.  What better way to begin the summer by giving thanks to our gracious God and for being fortunate enough (blessed enough) to be born and live in our great nation. But of course, how could we not give thanks to the many men and women of our armed forces who have had such an indelible effect on our comfortable lives: freedom to worship (although that is under attack by our President Obama), freedom to vote, freedom to move about as we wish, and so on - there are far too many to list here.

So as we begin this summer, let us all give thanks to our veterans, living and deceased.  Without their sacrifices, we would not be able to enjoy our lives as we do.  If you know a veteran, say, "Thank you for your service and sacrifice."  If you knew a deceased veteran, say a grandfather who fought in "The Great War," pay your respects at his grave.  Give thanks, give thanks, give thanks.

If this short video below from State Senator Dean Skelos doesn't arouse your pride in being a citizen of this great nation and bring a tear to your eye, I don't know what will.

Prayers and blessings for a safe and restful summer vacation.
- - Bro. Benjamin

Oyster Restoration in the Chesapeake Bay

Check out this fascinating article from NOAA fisheries regarding oyster reef restoration in the Chesapeake.

Largest Oyster Restoration Project in the Chesapeake Bay

View slideshowStephanie Reynolds Westby, NOAA's Chesapeake Bay oyster restoration coordinator, at the Harris Creek restoration site. Credit: NOAA

How Oysters Improve Water Quality Parts of six states and Washington, D.C., drain into the Chesapeake Bay—an area that’s home to 17 million people. One of the biggest threats to water quality in the Bay is stormwater runoff, and with increasing urban and suburban development in that watershed, the threat is increasing. Stormwater runoff from developed areas carries a lot of nitrogen into the Bay. Nitrogen is not toxic, but it is a potent fertilizer, and it causes algal blooms. When the algae die, they sink to the bottom and decompose. That robs the water of oxygen and can cause dead zones in the Bay. Filter-feeding oysters consume algae, and if there were enough of them, they would help control algal blooms. Oysters aren’t a panacea, and they wouldn’t keep the Bay healthy on their own—managing runoff at the source is also important. But a restored oyster population would mean billions of tiny water filters doing their part to keep the water clear and oxygen levels high in the Chesapeake Bay.

Restoration Collaboration Many partners are collaborating on the Harris Creek oyster restoration project, and each brings their particular expertise. The partners include: NOAA Fisheries, which maps the seabed using sonar and assesses habitat. U.S. Army Corps of Engineers, Baltimore District, which provides engineering support and funds reef construction. Maryland Department of Natural Resources, which regulates the oyster sanctuary, works with local communities in support of the project, and funds reef construction and seeding. University of Maryland, which produces the oyster seed. Oyster Recovery Project, a non-profit that plants the seed and monitors oyster growth.

It was a clear and unseasonably cold spring morning as the 30-foot aluminum survey boat Potawaugh skimmed along the surface of the Chesapeake Bay. Outfitted with sidescan and sub-bottom sonar, it can reveal the composition and three-dimensional structure of the seafloor and even peer through it to see the next layer down. With the sleek, gray vessel’s multiple sonar systems clicking away, the boat seemed perfectly named. Potawaugh is a native Algonquin word for dolphin.

Steve Giordano, a biologist with the NOAA Chesapeake Bay Office’s Habitat Assessment Team, piloted Potawaugh to Harris Creek, a tributary of the Chesapeake on Maryland’s eastern shore that is the site of the largest oyster restoration project in the Bay. Biologists hope that the 377 acre site will soon be home to a self-sustaining population of Crassostrea virginica, the species of oyster that once filled the Chesapeake with vast, layered reefs so great that their peaks emerged from the water at low tide like small Pacific volcanoes.

Only about 1 percent of that historic oyster population remains, the rest having succumbed to centuries of overharvesting, pollution, and disease. Today, the bottom of the Chesapeake is mostly mud, and this presents a challenge to restoration ecologists. You build an artificial reef by dropping millions of cubic yards of hard substrate into the water. But put that material down in mud and it will settle into the bottom and disappear.

Acoustic Seabed Mapping

Reef-building material, like all construction material, is expensive. “Any resources that we’re putting in the water out here,” Giordano said, “we have to be sure to put it in the right place.”

And that’s where the Potawaugh and the Habitat Assessment Team come in. Acoustic seabed mapping is their specialty, and they’re here to identify sites that are suitable for reef construction.

Giordano lowered the sidescan sonar unit into the water. It was a meter-long, bright yellow torpedo tethered by a cable, and it ran in the wake of the boat. Inside the cabin, a series of wall-mounted computer screens displayed a live sonar image. Different bottom types showed up in different colors—orange for sand, red for rock, and blue for oyster shell—that together formed a complex pattern of bands and ripples superimposed on a map.

We were looking for shoals of hard sand in water deep enough that a constructed reef wouldn’t present a hazard to navigation. The next phase of reef construction would happen at those sites.

Oysters Clean the Water and Provide Habitat

After mapping a section of bottom, we checked on a reef that was constructed two years before. Stephanie Reynolds Westby, NOAA’s Chesapeake Bay oyster restoration coordinator, hooked a small dredge to a winch. She dropped it in the water, let it drag for a bit, then brought it onboard. Up came the two-year-old oysters, and they didn’t look like what you’d find at your local seafood market. They were cemented together in a heap, the sharp ends of their shells pointing outward like serrated blades.

Westby liked what she saw. “See these spaces?” she said, poking a muddy finger into the gaps between the bound-together oysters. “These provide habitat for all types of creatures we care about.” Blue crabs and striped bass are just two of the species that spend their juvenile phase on the oyster beds, where the nooks and crevices offer shelter from predators.

In addition to providing habitat, filter-feeding oysters also clean the water. “There used to be so many oysters here that they filtered the entire volume of the Bay about every three days,” Westby said. Today, the same volume is filtered about once a year—not nearly fast enough to keep the water clear.

The Largest Oyster Restoration Project Yet

At the start of their lives, oysters spend two weeks as floating larvae. Then they need to find a hard surface to settle down and grow into adult oysters. But because most of the Chesapeake’s historic reefs are gone, and the bottom is mostly mud, many larvae never find a place to set.

By constructing reefs and then seeding them with young oysters, ecologists are attempting to kickstart the population. With time, new generations of oysters will settle on older ones and, as the layers accumulate, the reef will expand and eventually resemble a natural reef.

That’s the hope, anyway. But Harris Creek does have one thing going for it that earlier restoration projects did not. It’s big. When complete, the project will sport 377 acres of reef within a 4,400-acre sanctuary. Until a few years ago, a twenty-acre project would have been considered large. And size matters. A high-density network of reefs like the ones being built on Harris Creek increases the chances that oyster larvae find a good place to settle down.

Westby tossed the two-year-old oysters she was examining back into the water, then she hosed down the deck. “We’re trying to do restoration at a scale that matches the scale of the problem,” she said. 

Gill Nets

From ScientificAmerican.com...

Terrible Toll of Fishing Nets on Seabirds Revealed

A fisheries closure backs up suspicions that nets drive down diving-bird populations

By Daniel Cressey and Nature magazine

 

Hundreds of thousands of seabirds are thought to perish in gillnets every year.Image: Brandon Cole Marine Photography / Alamy

Evidence for the horrific impact of fishing gear on seabirds has been revealed by the closure of Canadian fisheries after fish stocks collapsed in the early 1990s.

Biologists have long worried that diving birds can become entangled in gillnets, which are anchored in fixed positions at sea. Designed to snare fish by the gills, these nets can also trap and drown birds.
This has been graphically demonstrated by finds of birds enmeshed in nets, but a quantitative assessment of the effects of such ‘by-catch’ on seabird populations has been hard to come by.
Now, that hard evidence has come from a careful study of seabird populations off the eastern coast of Canada, where cod and salmon fisheries were closed and gillnets removed in 1992. This work comes just weeks after another report estimated that hundreds of thousands of birds die each year in gillnets around the world.
Ecologists Paul Regular and William Montevecchi of the Memorial University of Newfoundland in St John’s and their colleagues examined data on various marine birds at five major Canadian seabird reserves in Newfoundland and Labrador between 1968 and 2012. They then compared bird population trends with data on gillnet use between 1987 and 2009.
The team found that populations of diving birds such as murres and gannets, which are vulnerable to entanglement in nets, increased after the ban. But in the same period, the numbers of gulls and other surface-feeding scavengers that benefit from unwanted fish thrown away by fisheries decreased, the researchers report in Biology Letters. Although the gull populations declined, these species are not at risk of extinction and it is likely their numbers are returning to more natural levels with the reduced influence of human activity.
Hard numbers
“Based on previous estimates of tens of thousands of murres killed each year in regional gillnet fishes, clearly significant numbers of breeding murres have survived that wouldn’t have otherwise,” say Regular and Montevecchi. The data ”support the widely held but rarely documented contention that by-catch mortality affects seabird populations”.
The authors say that fishing pressure off Canada's Atlantic coast is much lower now than it was before the closure of the fisheries, but bird deaths from by-catch are still an issue as some fisheries are still open. They suggest a move to alternative methods of capturing fish, such as pot traps that allow fish to swim in but not out, and which pose little threat to diving birds. They also recommend the creation of reserves called marine protected areas, in which Canada is currently “very sorely lacking”, they say.
Cleo Small, who works on seabird issues for the Royal Society for the Protection of Birds in Sandy, UK, notes that data on by-catch in gillnet fisheries are scarce, so Regular and Montevecchi's paper will be “a very important reference for future work”.
Earlier this month, Small and her colleagues reported a global review of seabirds caught in gillnets in Biological Conservation. Looking at all the published estimates they could find, they concluded that 400,000 birds were killed in this manner every year.
“I was taken aback by the scale of the numbers once we added them up,” says Small. “I hope that this Canadian review and the global review will help stimulate research and policy action that will help find some solutions.”
This article is reproduced with permission from the magazine Nature. The article was first published on May 29, 2013.