Monthly Archives: November 2015

Musings on Alligators and Polar Bears

Polar_Bear_-_Alaska_(cropped)Alan Wilson’s Polar Bear Image (http://www.naturespicsonline.com/copyright)

We have arrived at Panacea Florida where we will stay for the next three months. This has me thinking of alligators and polar bears. Why this strange combination? Both alligators and polar bears will happily hunt and eat humans given a chance. Both alligators and polar bears are also being hunted by us. Polar bears are far north of us in our home in Canada and alligators live here in Florida in our winter retreat but have been much in the news lately due to our new government’s strong support of climate change mitigation in order to save polar bears from extinction among other fine goals.

Our host here, Jack Rudloe, lived through the terrifying experience of seeing his dog captured and eaten by an alligator. We are a short drive away from Otter Lake. He liked to start his day with a swim back then. The lake has alligators in it but he had a “I don’t bother them, they won’t bother me” attitude. One day the alligators proved they were the Master of the Lake. Jack came up from the water after his swim with his beloved dog Megan. He was ahead of her getting out of the water. She was just clear of the water when the alligator leaped out and up from the shallow water, powered by his back legs, steam roiling from his nostrils, and it snatched the poor dog and dragged it back into the water. Jack leapt onto the alligator and began a life and death struggle to save his dog. The dog lost.

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The rather innocuous cartoon style sign warning of the danger at Otter Lake

Jack wrote up the horrific tale and submitted it to Sports Illustrated. They sent it off for fact checking (something which I think rarely happens these days)  and chose an eminent scientist to review. This scientist rejected the entire article because alligators cannot rise on their hind legs or swell up or emit steam from their nostrils. Jack was fired from Sports Illustrated although he later published the article with Audubon and Reader’s Digest. As it turns out, the expert was wrong. Alligators do indeed rise up on their hind legs to leap and to grab prey. You can watch an alligator go up on its hind legs and leap in this Alligator Leap video and this Alligator hunting birds.. You can also read another expert describing this behaviour. Even the expert who originally trashed Jack would later (after he had presumably matured) wrote an article about how another expert should have been wary of making fast pedantic judgements on the observations of alligators by a non academic, nonscientist. In any case we remain fascinated by alligators and polar bears.

I do know we humans are fascinated by the idea of large predatory creatures that can and do occasionally eat us, including [warning both videos are graphic but the human is fine in the end] an alligator  biting scientist (and indicating how very smart some scientists are) and a polar bear attacking a woman.

I’ve never actually seen a wild polar bear since we are quite a bit south of their natural range. I have seen live wild alligators including ones in Otter Lake that were about 10-12 feet long. I intend to keep far far away from them.

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Ianaré Sévi‘s image of an alligator.

 

RE-CONCEPTUALIZING THE ORIGIN OF LIFE

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RE-CONCEPTUALIZING THE ORIGIN OF LIFE

A Meeting in Washington, DC, November 9-13, 2015.

To listen to people speaking at this conference, one would gather that there are three basic questions for which we have no answer:

  1. Why is there anything?
  2. How did life start?
  3. What is consciousness?

The problem we have been working on, embryogenesis, is regarded as basically solved by incanting “gene regulatory networks”, which to my surprise were invoked by two speakers talking on origin of life. They were both colleagues of Eric H. Davidson, who just died last September. The problem with the gene regulatory network approach to embryogenesis is that it does not account for the division of most organisms into cells, and cannot predict the spatial and time course of embryogenesis. The networks do exist within cells, but are components, the regulons, a term we coined in Embryogenesis Explained, rather than the whole show.

The idea that a cell is a well stirred bag of chemicals harkens back to the beginnings of biochemistry a century ago, which followed upon regular chemistry. We were always taught to thoroughly mix the contents of our beakers, to get chemical reactions to occur stoichiometrically. The teflon coated magnetic stirring bar became the icon of this approach. The very notion that chemical reactions in the real world occur in heterogeneous conditions was not taught. At best, one might get introduced in advanced stages of academic training to “surface chemistry” as an esoteric subject. Even here, the surfaces had to be chemically clean. The contrast could be seen in the fine lecture by Robert Hazen on the role of minerals in the origin (and evolution) of life. In his lab reactions are run on atomically clean, known surfaces of crystals. He did remark that such pristine crystals on an early Earth or exoplanet might be gunked up and thus have a problematic role to play. But we must start somewhere, control what we can, and hope that it is relevant to the larger problem.
So aside from mineral or membrane surfaces, there was no structure assumed at this meeting for the origin of life. The problem was posited as one of getting from a “tar” of materials produced in interstellar space and found in meteorites, with tens of thousands of organic compounds, down to the relatively few involved in living organisms. Even self-reproduction was phrased in terms of autocatalytic reaction schemes, more than in terms of the division mechanism(s) of protocells.
Our host, in whose driveway we parked and lived in our trailer, Stephen M. Levin, attended the conference for two days. Steve is a retired orthopedic surgeon who has pioneered the concept of biotensegrity as applying to all levels of structure in biology. To his disappointment there wasn’t a smidgen of biotensegrity offered there in any of the attempts to figure out the origin of life. I mulled it over, concluded he was right, and began discussing FtsZ, the chain molecule involved in prokaryote (bacterial) cell division with him and Natalie. Soon we started looking at the self-reproduction of centrioles, which contain microtubules, which were evolutionarily derived from FtsZ. Maybe we’re onto something.
The conference was organized by Sara Imari Walker who quite openly spoke about the need for new ideas on the origin of life, saying that 50% of the participants were different from those generally encountered at origin of life meetings. Indeed, I haven’t attended an origin of life meeting since about 1975. The Carnegie Institute of Washington hosted it, and kept us well fed with plenty of opportunities for interaction. George Cody of CWI gave a great opening talk and raised the money that paid for everything. It was a privilege to be there, get up to date, and meet enthusiastic scientists, many born after 1975.

Monday, November 9, 2015 – 8:00am to Friday, November 13, 2015 – 3:00pm

“Hosted by the Carnegie Institute of Washington in Washington D.C. from the 9th to the 11th of November 2015, this conference aims to explore ways to build a deeper understanding of the nature of biology, by focusing on modelling the origins of life on a sufficiently abstract level. The conference will cover a diverse range of topics bearing on the problem of solving life’s origins, starting from prebiotic conditions on Earth and possibly on other planets and moving up through the hierarchy of structure in biology all the way to social complexity. The focus is therefore on studying the origin of life as part of a larger concern with the origins of organization, including major transitions in the living state and structure formation in complex systems science.”

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Dick, Natalie and Stephen M. Levin who, with his wife Olga, kindly hosted us for the two weeks we were in DC. Olga took the picture. Steve is holding one of his tensegrity models.

Video of the Honouring of Jack Rudloe during the Joel Sartore opening.

We previously blogged about our visit to the National Geographic museum and how we were guests where our friend Jack was honoured.

Here is a wonderful video of Jack Rudloe and his being honoured at the Joel Sartore PhotoArk exhibition opening. Dick and I were privileged to appear and we made what I like to think of as a couple of cameo appearances. What a great day!

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CT brush and CancerZap!: two video games for computed tomography dose minimization

CT brush and CancerZap!: two video games for computed tomography dose minimization

Alvare and Gordon Theoretical Biology and Medical Modelling (2015) 12:7

As parents, we frequently despaired of ever getting our children, especially our boys, off video games and onto things we considered more important, like homework and eating. It was a constant war, one we have happily turned over to our daughters-in-law and we have smirked more than once when the obsessions of our grandson have our sons complaining.

Dick has been interested in improving imaging since early in his career. His most cited paper is

Gordon, R., R. Bender & G.T. Herman (1970). Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and x-ray photography. Journal of Theoretical Biology 29(3), 471-481.

It was an intersection of these two aspects of our life, video games and ART that inspired Dick to begin working with the very talented programmer Graham Alvare starting when he worked in the laboratory of Brian Fristensky and continuing after Graham was accepted into medical school at University of Manitoba. The concept is simple. X rays provide wonderful images doctors need. But our current 3D methods result in undesirable doses of X-rays. Imagine if we could get better images with less x rays? The human eye and brain is far better at spotting pattern and revealing it than any program. Efforts to replace radiologists with computers images simply don’t work. The best a computer can do is aid the radiologist to see better. So why not have the computer learn from the human? Combine the love of video games with finding images pertinent to physicians and humans will turn their brain to the problem of dose reduction. Data from the game is then used to find patterns that can be programmed into a computer. The resulting concept is CT Brush and CancerZap!

CancerZap

 The concept is a combination of video gaming, crowd sourcing and fun to improve imaging. The present game was not a “wow!” as far as our nine year old Alexander was concerned.  What would be really great is if some professional gamer types took the project on and ran with it. CT Brush is available online, with open code, permitting its further development and we hope to get feedback from readers and players.

Try it for yourself Here Cancer Zap!

Jack Rudloe Honoured at Joel Sartore’s Photo Ark Exhibit Opening

Dick & Natalie with Jack at Nat Geo

Today was one of those really nice days I will remember for a long time. Our friend and winter host Jack Rudloe was honored by National Geographic’s Joel Sartore in his Photo Ark Exhibit for Jack’s life long conservation and education efforts at Gulf Specimen Marine Laboratory. We were Jack’s guests for the event. We were even escorted in past crowds by a cheerful young woman who recognized us from Dick’s picture. Before the talks we wandered the halls and we found an image of the cover that Jack and his late wife Anne did on sea turtles, Race for Survival. We found out that their article on the grave state of sea turtles marked turning point for National Geographic. With that article National Geographic moved away from simply reporting on neat stuff around the world and started talking about the environment.

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Joel Sartore’s exhibit is called Photo Ark. We were very privileged to be part of the reopening exhibit ceremony. Sartore’s  goal is to create pictures of every species in captivity which is about 12,000 different kinds of animals. He does them all, birds, crabs, octopus, bud and elephants. The pictures he creates are stunningly lovely and intimate. The purpose to to raise awareness about the environment and to try to get people to stop doing the things that cause extinction. Among the causes are habitat loss, poaching, eating animals for bushmeat, and the nonspecific catchall of climate change. The solutions Sartore offered in his lecture was to reduce consumption, recycle, eat less meat, donate money to good organizations that work for preservation of animals like zoos and rescue organizations, and his own National Geographic, and be aware of what you buy and how it impacts on the natural world. He gave two specific examples of awareness, palm oil from farms created by the destruction of old growth forests in Indonesia and buying furniture made from the wood harvested from old growth forests world wide. He was also a truly engaging speaker. We laughed, we were sad, we were uplifted and inspired.

In some ways the talk about solution was simply pap. I don’t see how recycling cans in Washington DC can stop poaching and slash and burn practices in Indonesia. I also noted a strange irony in that the National Geographic headquarters proudly proclaims it is a carbon neutral building powered entirely by wind generated electricity. That is a trick because it is in downtown DC with no visible windmills. So I assume this means they produce/purchase the equivalent electricity elsewhere. And, of course, one of Sartore’s other heroes is trying to preserve prairie grouse that are being gravely impacted by several dangers including windmills. Given all the trouble Germany has had in its failed efforts to live entirely on wind electricity, and how the result is using more coal, not less, and all the other negative impacts of wind power generation which cannot survive without massive government subsidies using money we could arguably be better using elsewhere, National Geographic may well have simply traded one kind of environmental damage for another that might be even worse. Still, I really liked how Sartore’s talks emphasized what dedicated individuals can do and his uplifting success stories. He is very right that being positive makes people want to be participants in change whereas constant doom and gloom makes people give up trying.

I have spent many hours in the wilderness myself. I know that people who live in the city simply have no idea about what diversity in habitat is. In 2001 my husband and I found a 152 acre parcel of land for sale for $14,500. We had to borrow to buy it, but we did and we have never regretted it. This little bit of land is in prairie parkland, the transition zone between boreal forest and tall grass prairie and it has species from both zones. The land has never been broken and the abundance and diversity to be found there is nothing short of astounding. Because the land is used by breeding red headed woodpeckers (along with four other nonendangered species of woodpeckers) we were able to put it into a conservation agreement. Once the agreement was in place, the property was given a detailed species survey by scientists and among the species were three tiny bladderworts and two types of sundews considered “species at risk”. This makes a very important point. We were able to put the property in a conservation agreement only because the government regulations allow us to preserve habitat for red headed woodpeckers. We inadvertently ended up getting government to protect five other species of plants that were in far more trouble. All the other solutions, like recycling your drink cans and eating less meat are insignificant next to the benefits of setting aside tracts of land and preserving habitat. And this can be done by lobbying government and simply going out and buying a chuck of land yourself. I was slightly irritated that Jack’s well deserved honour for environmental education did not include any mention of Jack and his late wife Anne’s tireless efforts to preserve salt marshes and how they have been attributed personally for saving 35,000 acres of salt marsh in Florida’s Big Bend and Forgotten Coast region.

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All that being said, I still 100% support Joel Sartore’s work. There is a simple reason for it. Joel Sartore’s stunning images make all kinds of animals come alive. They make people care about the environment. While I may disagree with some of his emphasis on his proffered solutions and I might be willing to point out some of the inconsistencies of the National Geographic’s efforts, getting people to care is the most important things one can do. If people care, solutions will come even if we make a few mistakes (like windmills) along the way.

And I was delighted to discover that habitat preservation is one of National Geographic’s strongest positive aspects. In addition to the Sartore exhibit, they had an exhibit on the oceans and their effort to increase protected pristine ocean areas from 2% to 10% of the total. National Geographic “gets” it when it comes to habitat preservation. And so overall it was a wonderfully positive day being treated like a VIP,  seeing a dear friend get a well deserved honour, enjoying a chance to see how his work impacted a major organization and to be surrounded by people who care. And best of all was watching children, dozens of children, laughing and pointing and running around connecting with animals that came alive in their minds because of Sartore’s fabulous, intense, captivating images. You can see more, including many taken at or provided by Gulf Specimen Marine Laboratory, here.

Common octopus (Octopus vulgaris) at Gulf Specimen Marine Lab and Aquarium.

Common octopus (Octopus vulgaris) at Gulf Specimen Marine Lab and Aquarium. (with permission)