Aquatic environments videos

1 09 2015

While developing and revising “ENVS 3450 – Aquatic Environments”, I’ve been discovering quite a few good aquatic environments videos, animated GIF files & interactive pages.  Inspired by Meghan Duffy’s Dynamic Ecology post on videos for teaching, I thought I’d compile a list of useful aquatic environments videos and share those here. Many thanks to Dr. Andrea Kirkwood who passed along great links!

The videos must illustrate an important scientific concept related to aquatic environments, and be useful for undergraduate and graduate classes. Beautiful photography and compelling storytelling also helps!

I’ve added another important criteria which is overlooked too often. The videos must be accessible through the use of subtitles and captions, published scripts or other visual cues within the video itself. This symbol (cc) indicates high quality captioning / subtitling already included in the video.

The list is far from complete. If you see missing videos or gaps below, please do let me know in the comments or send me a message via Twitter / email. I will continue updating this list. [New links will have a date next to them.]

Now, the videos and animated GIFs, loosely organized by category:

Water Science (physics, chemistry)

Limnology & oceanography (science & conservation)

Lakes & other aquatic habitats of the world

Plankton & microscopic organisms

Macroalgae (seaweed)


Macrophytes (aquatic plants)







How humans use & impact upon aquatic resources

Fisheries & overfishing:


Ecosystem impacts & manipulation

Series & Collections

Do you know of any other aquatic environment videos and animated GIFs which should be included in this list?

Project 52 No 7 – a plant bug on a dandelion

17 05 2011

For my birthday several weeks ago, Cosmoboy gave me a snap-on Raynox macroscopic lens converter for my 4/3 camera (Pansonic Lumix G2 HD). It is a nifty little tool which clips on to the end of a lens to enable macro pictures in a hurry.  I’ve been having some fun experimenting with this, and found that it creates lovely  bokeh when using a shallow depth of focus.

This image of a true bug (Hemiptera) on a dandelion was taken two weeks ago on a rare sunny evening in between rainstorms.  It was steadily making its way across the flowertop, then flew off into the sunset.  This tiny bug was one-third size of my fingernail, and I was pleased with how well the macro lens converter allowed me to capture its details so well.  Furthermore, the green grass provides a very nice painterly bokeh background for the little bug.

A true bug on a dandelion

Natural history note:  People who study insects only use the term “bug” (or true bugs) for the insects falling into the Hemiptera order.  Those insects, which are not beetles (Coleoptera), share certain characteristics including the way its wings fold and its proboscis mouthparts.  I think this little bug falls into the Lygus genus.

Great Lakes, Great Stakes! Part 2. Tilting at wind turbines.

11 05 2011

Lake Ontario is a beleaguered Great Lake. Millions of Americans and Canadians live around the lake and countless others depend on the Lake Ontario watershed for water, fish, transport and shipping. It is inevitable that harmful impacts will arise from all those people relying on the lake’s resources.  But, is it also possible to generate postive impacts?

TransAlta claims so.  They have built one of the largest wind farms in Ontario and are leading the forefront of the so-called, “green energy” industrial development in North America.  The wind farm is on the truly buccolic Wolfe Island, just a short ferry ride from the City of Kingston.

Wolfe Island wind turbines from air

Wolfe Island wind turbines from air

The area around Kingston is one of the windiest in Canada, making it a freshwater sailing mecca, and the host of many sailing  regattas and championships. As students at Queen’s University know, wind and kite surfers are a common sight along the shoreline. To take advantage of this energy bounty, TransAlta’s wind turbines, 86 of them, covers the entire island from head to foot, the description locals fondly use for the western and eastern tips. Every turbine, standing a gargantuan 80 meters tall (24 stories), is located on private land with TransAlta paying a generous fee to the land owner. Many farmers have found the turbines to be a significant boost, allowing them to expand their businesses and produce for local markets. However, many residents find the turbines to be ugly, noisy and harmful to the peace of their cherished island.

The IJNR fellows had happened to arrive on Wolfe Island on an important day.  Wednesday May 5 marked the beginning of  a tax-assessment hearing on the impact of wind turbines on property values.  As the Kingston Whig-Standard reported, Wolfe islanders were arguing that the wind turbines had lowered property values on the island.  Other opponents of wind farm developments elsewhere on Lake Ontario had come specifically to sit in the hearing.  As a result, the IJNR had to tread carefully and sensitively to avoid the impression of bias towards any group on the island.

An IJNR fellow photographing a wind turbine tower

An IJNR fellow photographing a wind turbine tower

We toured the island to see the wind turbines up close. They truly tower over the entire island which otherwise consists of farms and 2-story houses. The structures are so prominent in the landscape that local touring companies now have their boats go by the island specifically to view the turbines. Our lunch stop was  a church, which had been carefully selected because it represented neutral ground for all factions on the Island.  Farmers, TransAlta representatives and anti-wind community members then discussed issues with the journalists.  As a Queen’s professor and an observer, I did  not directly participate in those sessions but used this as an opportunity to listen and learn about the issues.

Green energy initiatives are simply not as clean-cut as one would like, or the press would have us believe. Wind power does produce minimal pollution when generating energy, a big advantage in a province that relies on dirty coal-powered generating plants and controversial nuclear plants.  However, having such dominant structures planted throughout one’s community really changes one’s relationship to the land and landscape.  Wolfe Island is now an important case study for all communities and corporations considering wind power developments.

After Wolfe Island, we travelled to Picton where we had a lovely evening meal at one of the local restaurants. Frank Allen spoke in detail and gave some intriguing perspectives on environmental reporting and communicating complex ideas to the public.

Frank speaking on environmental journalism at IJNR dinner in Picton

Frank speaking on environmental journalism at IJNR dinner in Picton

The next day, they joined a fishing trip led by my colleague Tim Johnson, a scientist with the Ontario Ministry of Natural Resources fisheries research station in Glenora. I said my good byes that evening, but I’ll definitely be following the work of all the journalists I met during this trip.  It was a wonderful opportunity, not only for the journalists, but also for this scientist, to discuss Lake Ontario environmental issues.

My thanks go to the Institute of Journalism and Natural Resources for their invitation and hosting.

[Part 1 of this two-part post on the rising & declining fish populations in Lake Ontario is linked here.]

Great Lakes, Great Stakes! Part 1. The rise and fall of fish species.

10 05 2011

Are the Great Lakes important? Should people outside of the region care about our Great Lakes?  The Institutes for Journalism and Natural Resources (IJNR) think so.

Last week, a group of American and Canadian journalists travelled around Lake Ontario on an IJNR fellowship.  Travelling on a bus rented from a Montreal hockey team, they started their journey canoeing down the Don River in Toronto. After the canoe trip, they continued along their route, stopping at various sites to meet experts and learn about environmental issues affecting Lake Ontario.

Frank Allen of IJNR invited me to join them halfway through their trip.  I met the journalists in Sackets Harbor in New York and spent a lovely evening talking about science communication and the journalist perspective.  The next day, inspired and energized by the discussions from the night before, I joined several journalists on a charter fishing boat captained by “Megabite”.  The goal for the day was to land some trout, but the heavens opened early.

IJNR Fellows fishing in the rain

IJNR Fellows fishing in the rain

Despite the downpour, it was a good trip. We went to a deep trench in Lake Ontario by an island where trout and salmon congregate at their preferred cold temperatures and caught many fish.  And throughout the day we talked extensively about the science and economics of the introduced fish.

IJNR fellows interviewing Captain "Megabite"

IJNR fellows interviewing Captain "Megabite"

Most trout and all salmon in Lake Ontario are not native. They have been stocked by state and provincial governments for several decades.  They are the cornerstone of a thriving multi-million dollar sportfish and recreational fishing industry around the lake.

Just as I wrote about Lake Erie, Lake Ontario is not the same lake it was 50 years ago.  Invasive species, especially round goby, now make up a high proportion of the trout and salmon diets. After meeting with the charter boat captains and New York biologists we discussed native, introduced and invasive species. The Sackets Harbor captains mentioned that the round goby had very probably revived their fishing businesses in a big way!

Trout caught by IJNR fellows for lunch!

We then drove over the Canadian border to meet with a group of people working on the endangered American eel.  The rain simply would not abate, and we had to huddle under a bridge by small river for shelter. This particular river is an important site for young eels and we were to see a demonstration of electro-fishing. My colleague, John Casselman and his graduate students spoke about their work with American eel, which has an amazingly intricate marine-freshwater lifecycle that is threatened by dams along the St. Lawrence Seaway.

In addition, John Rorabeck, an expert commercial fisherman, spoke about the historical importance of American eel to fishing industries. Unfortunately the boat was not working so we could not collect American eel, but the journalists got to listen to top-notch stories by two leading experts.  It was wonderful to listen to John R, especially as he truly has close ties to Lake Ontario and he had worked with one of my graduate students on the Rideau Lakes catching fish for our food web analyses.

Commercial fisherman John R speaking about American eel

Commercial fisherman John R speaking about American eel

By the end of the day the complexity of the lake was becoming very apparent. We had considered introduced fish species which were benefiting from an invasive fish species, the trout and the round goby. We also discussed a native species fast declining in the Great Lakes.  Lake Ontario is changing very rapidly… what will it be like in the future? Even the most knowledgeable scientists and fishermen are not sure.

Tomorrow:  Tilting at wind turbines.

The End of Astronomy?

9 05 2011

Astronomy as we know it…. Is it the beginning of the end?

The Monty Python foot from the skyWe are creatures that respond to change, to uncertainty, to excitement. In a society where either the media, or the filters we create around us, cater to our most basic desires, what is the role of awe, wonder and curiosity about the vast Universe around us?

Some would point to the immense interest in technology that today’s youth display as testament to them being the most scientific generation ever. But i-pads, fads and widgets are the mothers of necessity rather than invention. When you strip away the social aspects of technology, just how motivated by science are they? Is there an urge to piece together the building blocks of reality? Unweaving the tapestry of creation in which our lives are woven, if you will.

So perhaps my title should be The End of Interest in Astronomy?, but that isn’t quite as catchy.

yawningAn EU survey highlights that the majority of the younger population (15-25) doesn’t see the sky above them as something really worth knowing about. Only 1 in 5 note significant interest in astronomy. The interest in technology and the environment is 200% higher. Even more disturbingly, while only 11% are disinterested in environmental issues, almost four times as many are disinterested in astronomy.

wrestlingFor those of us that work in astronomy these numbers are a punch in the stomach. Have we overestimated public interest arising from inspiring words by Carl Sagan years ago? Or, taking a positive view, perhaps the youth of North America are fundamentally more interested in the heavens above than our European cousins? While a N. American survey is sadly lacking, some countries, Latvia for example, show an interest in astronomy that is four times the European average.

But in my darkest moments, I wonder, could astronomers themselves be partly to blame for these interest levels? Have we just not engaged people the way we should?

The true measure of astronomy’s value is how it contributes to our society. While there is plenty of data to suggest it has many economic benefits, astronomy has given us a cultural legacy of immense proportions – it has taught humankind its true place in the universe. As some have said, to understand the Earth’s value, we actually had to leave it.

Bad analogiesSo is the lack of interest apparent in the youth of Europe just a matter of communication? Have astronomers failed to explain themselves and their work in ways that the public can easily understand? Are the analogies we use failing to inspire? The following xkcd strip beautifully explains the challenges we face.

For many years I saw research in very black and white fashion. I subscribed to the idea that if I couldn’t explain the value of what I was doing in a paragraph, I wasn’t doing anything useful. It’s a deceptively appealing concept that makes things sound like they have their place. No arguing, no dilly-dallying, you can explain why it’s useful or it simply isn’t.

grandparentsBut just try explaining General Relativity in a paragraph, or Quantum Theory. You can’t just sit granny/grandpa (assuming they aren’t physicists of course) and walk them through the details in 30 seconds – there are entire books that try to explain those concepts. Yet, these complex ideas underpin some of the most critical technologies we have today – think GPS or semiconductors. And don’t cop-out by saying the technological & economic applications mean those are important.  Newton’s Law of Universal Gravitation, developed in the 1600’s, was separated by centuries from commercial applications in communications satellites.

So communicating ideas has always been a problem. Are the portents of doom perhaps then more driven by the idea that astronomy research is somehow becoming less relevant?

A number of prominent astronomers (e.g. Andy Lawrence) have written about how the questions of astronomy are becoming progressively tougher to answer. And how, as we push back the boundaries of our knowledge, and delve into the immensity of details underlying the universe, the questions we can truly answer are becoming more specialist.

It’s true that we’ve answered the easy questions. We’ve figured out the geometry of the Universe, how galaxies cluster and some of the more simple aspects of galaxy formation and stellar structure. Many of these things could be explained quickly and succinctly.

GaiaBut there are a great many challenges ahead. The Gaia mission to develop a 3-d map of a billion stars in our galaxy, will revolutionize our knowledge of stellar motions, and despite decades of study we still don’t have a comprehensive understanding of how stars interact with spiral structure. This is an immense challenge.

jwstHubble Telescope’s long talked-about replacement, the James Webb Space Telescope is also coming in 2015. We’ll see the first galaxies in our Universe and uncover evidence of the earliest giant black holes. Complemented by 30m class ground-based telescopes, such as the TMT or E-ELT, the light-capturing power of telescopes will rise by an order of magnitude. The SKA radio telescope, will reveal the Universe at radio wavelengths in ways we can only imagine today. And tantalizingly, evidence of alien life might possibly be found with these instruments.

So when I was asked, “What will Canada lose if we don’t invest in astronomy?” I responded: “It’s simple. When scientists announce another planetary system with life has been found, and answer one of the most profound questions humanity has asked, do you want a Canadian to have any chance of making that announcement?”

But aside from answering amazing science questions, our challenge as professional astronomers is to reach out and communicate about the incredible science we get to do. And in turn, to pass on our awe at how amazing the Universe around us really is.

We aren’t even close to the end of astronomy. The Universe has more up its sleeve than we’ve yet to imagine.

World Water Day 2011

22 03 2011

Spring ice break-up in riverIt is now Spring Ice Break-up time in southern Ontario, a time of great interest to “lake ice phenologists“. As I write this, I am looking out of the window at a very wet scene in the back garden.  There was an early Spring snowfall yesterday, which is now melting away.  The snowmelt is flowing towards the street where it is going down the drains which will eventually lead to Lake Ontario.  While I look outside, I take a sip of my tea, which was made with treated Lake Ontario water from the tap.  Lake Ontario, one of the world’s largest lakes, is interconnected with my life and that of my neighbours in numerous intimate ways. Yet we hardly ever take the time to think about the waterbodies flowing around our city.

Today, we get this opportunity.  Today is the Global World Water DayWorld Water Day 2011 Logo (English) (March 22), spearheaded by several United Nations agencies.  It is a day of global celebration and learning with events in thousands of cities, towns and villages around the world, including many across Canada and United States.

The focus of World Water Day is on clean drinkable water for people.  Water is essential, not only for our survival, but also for our health by ensuring sanitary habitats.  Clean water is also essential for the stability of human societies.  There is no way around it — access to clean water is a fundamental human right.  Without it, there will be death, suffering and widespread chaos.

City of Toronto from airMany Canadians are very fortunate to have access to cheap clean drinkable water from lakes, rivers and groundwater — we even use it to flush our toilets! However, Canada is not except from water access issues.  Many communities in the north struggle with access to clean water with severe consequences. Even in the south, there has been occasional outbreaks of water-borne diseases due to improper monitoring and oversight.   We all must work together to ensure we have access to safe water at all times.

Water is also essential for healthy ecosystems.  Pollution is wide spread. We all are connected through air and through water.  Due to atmospheric Hazard Waste awaiting pick up for proper disposaltransportation, there is chemical contaminants in water bodies world-wide, even in remote sites.  Temperature and nutrient pollution are widespread in large lakes where people live.  Physical pollution such as garbage, plastics and unwanted objects can create havoc for both aquatic and terrestrial biota.

Lucky for us all, there are success stories and we can still share the beauty of our lakes and rivers with the world.  Take a moment to appreciate your neighbouring lakes and rivers, oceans and estuaries.  Whether it is snowing, raining or dry where you live, think about the water you use and where you get the water from.   Water is amazing, and connects us all.  Celebrate World Water Day by drinking a glass of clean water!

Rideau River at Sunrise

Agent Orange and the challenge of assessing toxicity – Part 3

17 03 2011

This is the third part of the Agent Orange series.  Part 1 discussed the make-up of the two herbicides that go into Agent Orange, and Part 2 covered the  chemistry that led the formation of toxic dioxins in Agent Orange during manufacture.  This part will cover the toxicity of the 2,3,7,8-TCDD in Agent Orange and why it is still of concern.

Before we get into the toxicity of 2,3,7,8-TCDD and Agent Orange, let’s go into the basics of risk assessment. Just because something is known to be toxic does not mean we need to worry.  Assessing the risk means we need to assess several key factors first.

For example,  as we all know, we depend on water for our health and functioning such that we cannot survive for long without water.  However, if drunk in sufficiently large amounts, water can be toxic because sodium in your body becomes diluted to the point where you cannot function.  Obviously, drinking such large quantities of water is not a concern for most of us, so we know that drinking water has low risk most of time, and is in fact highly recommended.

So when assessing risk of potentially toxic substances, scientists and medical workers tend to take into account three important and connected concepts:

  • Hazard – what are the hazards of this substance? For example, would it result in allergic reactions, illness or burns on exposure?
  • Exposure – What are the routes of exposure? Would it be inhaled, eaten, or absorbed through the skin? How much of this substance is being would be transferred through exposure?
  • Toxicity – what is the mechanism of toxicity after exposure?  How does the toxicity response show up?

So drinking freshwater water has low risk, due to its low hazard and toxicity only incurred to very high exposure through drinking.  Of course, water can be very risky in other settings, such as slipping on a puddle on a marble floor and breaking your hip, or drowning in the bathtub.

In terms of toxicity, 2,3,7,8-TCDD is quite the opposite of drinking water, and avoidance of this substance is highly recommended by all experts.  So how is it so toxic?

We’ll be delving into biochemistry in this posting this time! In brief, the toxicity of 2,3,7,8-TCDD is due to its ability to bind with a key receptor in our cells, which leads to a cascade of effects. As a part of our healthy cell functioning, there are thousands of receptors in our cells throughout our bodies which act as our messenger system.

The receptors bind to key chemical molecules. Usually, they are made of proteins with certain structures that enable chemical bonding on its surfaces in a manner often described as “a lock and a key”. Once a receptor is paired with its “chemical key”, it then can influence the DNA expression within a cell.  This helps to organize useful chemicals to enable healthy cell functioning.

In the case of 2,3,7,8-TCDD, scientists are the most concerned with Ahr, or the Aryl hydrocarbon receptor. It has been speculated that the Ah receptor may be a relic of from our long-past evolutionary history, with its “key” being a growth-regulating hormone which we no longer use. The Ah receptor is not only found in humans but also in numerous animal species. The Ah receptor in modern organisms now binds naturally occurring organic contaminants such as those produced by combustion of wood. In fact, dioxins are only toxic when the Ah receptor is involved!

The Ah receptor will bind with organic contaminants containing a 6-carbon hexagon ring. Once the Ah receptor binds with an organic contaminant, the Ahr-contaminant complex moves to the cell nucleus where DNA genes are activated. Enzymes are produced to break down the unwanted contaminant and remove it from the cell.   In this case, this involves a group of enzymes called the cytochrome P-450. If all goes well, those enzymes activate a reaction to break down the contaminant in the cell, and therefore helping to remove the toxic substances from the cell and the body.

In this case, 2,3,7,8-TCDD has been found to bind with the Ah receptor extremely well. In fact, 2,3,7,8-TCDD has the best binding constant with the Ah receptor among the various organic contaminants, explaining its extreme toxicity.  It has been hypothesized that the 2,3,7,8-TCDD may be very similar in structure to the original hormone partner of the Ah receptor before we lost this hormone a long time ago in our evolutionary history.

After exposure and uptake, the 2,3,7,8-TCDD-Ahr complex will then proceed to the DNA in the cell nucleus, where activated genes will result in (1) production of the P450 enzymes; and (2) regulatory chemicals important for growth and division of cells.  In some ways, the dioxin mimics the behaviour of hormones regulating important cell functions. Also , it is thought that by binding with the Ah receptor for too long, it could result in the wrong signals being sent out during development, resulting in birth defects and developmental delays after birth.

Those two actions will lead to a cascade of effects throughout the cell and the affected organ.  First, due to the high affinity of 2,3,7,8-TCDD for the Ah receptor, sometimes the dioxin is not broken down. Therefore, P-450 enzymes are produced in the cell for an extra long time.   All those extra enzymes does not break down the dioxin immediately, but it can lead to the breakdown of other hormones.   The breakdown of regulatory hormones can lead to dysfunctional cells and promote cancer.  Down below is a figure that illustrates the pathways within a cell:


Dioxin and Ah receptor cascade in cell

Dioxin and Ah receptor cascade from Mandal (2005)

Second, the Ah receptor has other functions beyond enzyme induction. It can control certain genes and cell functions particularly those governing rowth and differentation. As an example, 2,3,7,8-TCDD is somewhat similar to an important thryoid hormone, the thryoxine, as shown below:

2,3,7,8-TCDD and Throxine

As a result, 2,3,7,8-TCDD may mimic certain hormones after binding with the Ah receptor.  Since hormones to not act alone, this interaction of dioxin hormone mimics with hormones can result in a cascade of effects throughout the body.

There has been many studies showing that certain cancers and diseases respond with increasing exposure to dioxins. But it has been difficult to precisely pin down the association due to the complex biochemistry and the cascading domino effect whenever hormonal systems in cells are affected.

So what?  The discovery of dioxins in Agent Orange and the subsequent explosion of biochemical and environmental research into dioxins world-wide has led to our much improved understanding of organic contaminants, their toxicity and the need to better regulate and monitor those contaminants.

Should we be worried?  Yes.  2,3,7,8-TCDD is one of the most toxic compounds people have ever produced due to its ability to bind so strongly to the Ar receptor found in numerous organisms.  But there are good news.

Over past 50 years, as our awareness of environmental contaminants and management of sources improved, the release of dioxins to the environment and the accumulation of dioxins in wildlife has been steadily decreasing.  As a population, our overall environmental exposure is decreasing on average.

However, dioxins are persistent in the environment, often present for decades. Scientists can still measure dioxins in lake sediments from the 1950’s!  Dioxins also can accumulate in fatty tissues and in soil, where they can be transferred up the food chain.  As a result, exposure to dioxins can include both immediate exposure to the chemicals such as Agent Orange, and long-term exposure through food and skin contact from accumulated dioxins in the environment.  This further adds to the complexity of understanding dioxin toxicity and relating heath concerns with environmental exposure over a long period.

However, remember that risk assessment of a chemical depends on three things, hazard, toxicity and exposure. The extent of toxicity and health impacts depends on the length of exposure and how people were exposed. As a result, the occasional driver who drove by Ontario’s highways during spraying have far less to worry about compared to the highway workers who sprayed Agent Orange on unwanted foliage.  However, showing causation and relationship between current heath issues to past dioxin exposure is exceedingly difficult even for exposed workers.  We are exposed to so many organic contaminants which also trigger the Ah receptor cascade, and each of us respond differently depending on our genetic make-up.   Despite over 50 years of research, there is still much that needs to be unravelled.


References & Resources:

Birnbaum (1994). The Mechanism of dioxin toxicity: relationship to risk assessment Environmental Health Perspectives, 102, 157-167 [Subscription required]

Mandal, P. (2005). Dioxin: a review of its environmental effects and its aryl hydrocarbon receptor biology Journal of Comparative Physiology B, 175 (4), 221-230 DOI: 10.1007/s00360-005-0483-3 [Subscription required]

Schecter, A., Birnbaum, L., Ryan, J., & Constable, J. (2006). Dioxins: An overview Environmental Research, 101 (3), 419-428 DOI: 10.1016/j.envres.2005.12.003 [Subscription required; another link to the PDF here.]

Health Canada. 2005. Dioxins and Furans – It’s Your Health. Healthy Living Series. [website] (Last accessed March 14, 2011).  [Free access]

Images of 2,3,7,8-TCDD and thryoxine are from the  Wikipedia Commons image library.

Thank you to Nathan Ackyrod, Rob Thacker and anonymous reviewers for their comments.

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