Tag Archives: biology

Our Pond and Wet Meadow

Our little house on the northern prairie is in a place with a high water table. We live in the aspen parkland zone near the 51st parallel. Aspen parkland is a narrow strip of transition between boreal forest and the three prairie zones, tall grass, mixed grass and short grass. Because it is a transition zone it, we have many plants from both boreal forest and prairie. In our specific area, we have mostly boreal and tall grass prairie plants but we are also blessed with some medium grass plants. The parkland is an area rich in diversity. We have so many different birds nesting right around our yard that I can’t name them all. I will try. The types of birds I see in my yard every single day are ruby throated hummingbirds, robins, mourning doves, Baltimore orioles, cedar wax wings, American goldfinch, purple martins, wood, barn and cliff/mud swallows, nuthatches, juncos, chickadees, three kinds of kinglets, common red polls, pine siskins, yellow bellied sap suckers, northern flickers, downy woodpeckers, blue jays, marsh and house wrens, about 15 different little brown sparrow types birds I can’t identify, and often overhead, riding the thermals, sandhill cranes and pelicans. They arrive to enjoy the vast abundance of insects, seeds and nectar our nearby wetlands and wildflowers produce. Many of these birds are featured in this delightful blog.

When we first moved into our little house, we were confronted with a real eye sore. Our sump pump drains at least once a day, and in spring or periods of heavy rain it can kick in as often as once an hour. It pumps out about 20 litres of water each time. The result was an ugly brown bare place where nothing grew. It showed up as a sunken, slimy pest hole beyond our deck. I went looking for pictures of it and I found I have very few pictures because it was so ugly and embarrassing that I mostly took pictures around it. In addition to this bare ugly eyesore is a low ditch that drains rainwater from our typical three day prairie monsoon rains. Years ago someone tried to plant cypress trees but they are long dead, drowned, and one sickly potentilla bush struggles to survive in the muck.

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The ugly bare spot and the ditch that is perpetually wet are visible in the background  of this picture where I am showing off garden produce.

With so much to be done getting the neglected old house in proper shape, I just ignored that ugly spot as much as I could. One day, my husband noticed life in the muck. We had a stroke of inspiration. You can’t beat nature. She is far too powerful and she always wins. You can take advantage of her though, if you are willing to work cooperatively. And so we decided to create a pond.

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In this view you can see potentilla in the foreground, a dead cypress tree and the bare ground eroded out by constant flooding from the sump pump hose coming out of the house at the front of the deck.

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My husband noticed life in the small temporary pond created by the sump pump drain.

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Our first step was to try to disguise the ugly drain pipes with something useful and so we planted a raspberry cane near the deck. This is our raspberry starter cane in the first year.

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By the second season the raspberry cane was taking off and spreading just as hoped it would. It was obvious mere raspberries would never hide the yuck.

The water did not hang around if the input was low. It would drain off, soaking the gravel/sand in the scouring area. The grass would start to creep in only to be washed away as soon as the next heavy rain took place. While we were out shopping for other things, we found a pond liner under-pad on sale for next to nothing so we grabbed it. We ordered a proper pond liner of the correct size from Amazon. It would precisely fit and go over the scoured out area.

It was lot of digging. Anyone who visited ended up doing some digging. Over the course of the second summer we got the pond dug out to our satisfaction. We made many trips to collect suitable pretty local rocks to prevent the liner from moving. We felt like we were getting somewhere by the end of the summer. The pond liner stopped the scouring. The water from the sump pump is ground water and therefore hard, but rainwater from the roof is collected and sent via another pipe into the same area.  The pond has an overflow channel that directs water into the low ditch. This keeps the water level in the pond constant. The pond is maintained by the sump pump drainage and is regularly flushed out by rainfall off the roof. We had a stable pond! On our regular walks we began searching for native plants with appealing shapes and forms.

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We soon found ourselves with a lush growth of algae. Yuck! We began bringing home buckets of local pond denizens, snails, beetles, water striders and the like to try to control the algae. We soon had a marvellous flourishing of pond life. We worried about mosquito larvae but a few passing dragon flies ended that issue and we now grow dragon fly larvae  in abundance. These ferocious hunters live as the apex predators of our pond ecosystem. We simply never see moquette larvae. Several of the water plants ‘took’ and we soon had lily pads, bullrushes and sedges in pots.

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The drainage from the overflow channel ended up creating a constant wet zone in the nearby ditch. We decided to extend the pond area to have a wet meadow in the ditch. A wet meadow would be a lot easier to maintain than a wet soggy ditch that is often impossible to mow. We began looking for plants that inhabit areas that are soaking wet in spring and subject to flooding in heavy rains, but dry up in late summer or between rains. We transplanted individual plants and collected and spread seeds. It has been a labour of love. Each year we have seen small improvements in our pond and wet meadow garden as lawn is replaced by local native plants. Because they are native plants, once established they need no care. This spring we were positively delighted and astounded to discover native orchids like our wet meadow. I moved the grass around and found these lovely late yellow lady slippers (Cypripedium parviflorum). Though common in our area they are as lovely as any orchid you can find anywhere else.

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We have stopped trying to mow the drainage ditch/wet meadow. It’s pretty messy yet but you can see a flash of yellow among the dandelions going to seed marking our lovely orchid. And we found this. I think it might be a showy lady slipper orchid. If it is, we will have two spectacular native wild orchids growing in our wet meadow. It will be years of tending before our pond and wet meadow look exactly like the ponds and wet meadows of the surrounding area. It will take time and persistence to get rid of the lawn grass and the other nonnative plants. But the lawn grasses really have no chance to compete when people aren’t helping them. And so we are hopeful. And we will have less lawn to mow.

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The slender green shoot with branches looks a lot like a Showy Lady Slipper. Time will tell!

 

Our Fourth Positive Review

Miller, D. (2017). The cell state splitter: Embryogenesis Explained: A review. Systems Biology in Reproductive Medicine, doi: 10.1080/19396368.19392017.11290160.

“What I was not expecting was a whole new and potentially paradigm shifting concept in our understanding of what drives cell determination and fate in the developing embryo, in the form of the cell state splitter and differentiation trees. I am not alone in being (up till now at any rate) ignorant of these fascinating ideas.”

 

David Miller

from Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK

A Third Positive Review

We are running three for three now.

“The entire work is richly illustrated and the authors’ passion for their subject is evident in every page, making for an enjoyable and informative read. The coverage of experimental works and the authors’ almost conversational style of writing are effective in breaking up a topic which is traditionally mired in abstruse theory and terminology.” Richard Mayne, University of the West of England

This review is in press and and will be published in International Journal of Unconventional Computing and will appear on line soon.

“You Did Not Use the Standard Nomenclature and Terminology of Embryology!”

When I was an undergraduate there were two things I hated more than anything else. First I hated being forced to memorize and regurgitate. The best example of this was Intermediate Biochemistry 101 in my second year as a biochemistry major. I was essentially handed a huge book as thick as telephone book and told to memorize it. It was one of the most boring courses I ever had to take. Lectures consisted of writing out all the steps of the Kreb’s cycle, glycolysis, glycogenesis and other pathways. I don’t ever recall being taught what these pathways were for. Our professor wrote out all the steps of the pathways and talked about carbon backbones and proton transfer. Our exams required we precisely regurgitated the complex diagrams and pathways. Marks were deducted for every letter and sign we did not put on the paper. No matter how hard I tried I could not regurgitate those diagrams without mixing things up. I literally cried over the pages I practiced on as I wrote it out again and again and again. I always failed.

If I had not gotten lucky about something else I probably would have given up biochemistry. I had to juggle day care needs of my children with my class schedule so I asked for permission to take a third year biochemistry course as a co-requisite that same year. This course was taught in totally different fashion. It was called Nitrogen Fixation. I loved this course! It was so fascinating! The professor gave us the diagram about nitrogen fixation and we learned about the role of fixation in the life cycle of plants. We studied where and how nitrogen fixation takes place. We learned wonderful things such as how farmers cultivate floating plants that can fix nitrogen in rice paddies to increase yield. We also studied how the system worked as whole including what the effect of specific mutations of genes for enzymes. My final exam had a two sentence questions.

“The enzyme GlnA in a specific legume is mutated so the efficiency drops to 15% of normal. What happens to the plant?”

Even more amazing, we actually had a diagram of the cycle to consult!

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I ended with the term two things that were stunning and depressing. I got an A in Nitrogen Fixation and I got a C in Intermediate Biochemistry. My kindly nitrogen fixation professor saw me struggling to regurgitate those diagrams for Intermediate Biochemistry and he told me that he thought I had a learning disability similar to his daughter’s. She had dyslexia. He referred me to student services. After testing, it turned out I did indeed have a genuine, measurable, real, learning disability so that I flipped groups of atoms at random on the carbon backbones of those diagrams. it wasn’t my fault. I was not stupid, sloppy or lazy!

For the rest of my undergraduate career I would have to go to the department head at registration time and ask for an exemption. All the subsequent biochemistry courses I took required a C+ in Intermediate Biochemistry and I only had a C. I would pull out my official diagnosis of a learning disability with my proof of a need to be accommodated.  Each and every time the department head would look at me and shake his head in wonder and ask me “How could you get a C in Intermediate Biochemistry and an A in Nitrogen Fixation? Everyone knows that the Nitrogen Fixation is a much harder course and hardly anyone ever gets an A.” Then he would sign the waiver for me.

How indeed. It was many years until I figured it out. It was partly my learning disability. The Intermediate Biochemistry course was based entirely on the ability to memorize and regurgitate a set of diagrams and I just couldn’t do it. No understanding was required to pass that course. No ability to think was needed. You just needed an ability to reproduce diagrams which I did not have. You don’t even have to be able to speak English. You just needed to be able to draw the pathway precisely as laid out in the textbook. After you have completed that “essential” learning step, then and only then can you, as a student, move on to learning real stuff.

Nitrogen fixation was taught in a manner that required I really understand how the whole thing worked. The professor who taught it complained (and warned us) that many of the student who took the course would write out the diagrams for him in the exam but they would fail. He was not interested in having us write out the diagrams. He was interested in knowing we understood the content he was teaching in the context it operated in. No wonder it was such a fascinating course!

My Introduction to Embryology course was much the same though not as bad (for me) as Intermediate Biochemistry. I was required to memorize and regurgitate all the proper labels of diagrams on stages of embryogenesis. This included correct spelling of terms like coelom, archenteron, and blastocoel. If you had a single letter wrong you got a zero score. This did nothing to increase my understanding of embryology. There was a really great lab with three dimensional models and time lapse movies. We also got to study carefully prepared serial section slides of stages of development over time. I learned the anatomy of the embryo from those labs, not the lectures. I got almost nothing out of the lectures. For the exams I got lucky because I have always been fascinated by Latin and Greek elements in words. I even took an optional course in it simply because I liked the topic. That made it much easier for me to reproduce that arcane language correctly because I knew the roots all the horrid words came from. My fellow students without such a background struggled terribly and most left the course with a C for poor spelling and hating embryology as a topic.

So why do we make students go through the pain and suffering of memorizing and regurgitating in the first courses they take in a topic? It can’t be because it helps students learn. It does the opposite. It bores them and drives them away. It can’t be because it helps understanding. There is no understanding required. It can’t be to give them “a solid grounding in the basics” because I have never encountered a need to have the entire Kreb’s cycle memorized or the correct spelling of “gastroceol” in any work I ever did. Active researchers use databases and computer programs of such things and always check their memory against real data. Memory is unreliable and not something to be trusted. The greatest metabolic geneticist I ever knew, Dr. Cheryl Rockman-Greenberg, had the pathways she encountered most often in the clinic memorized but I still saw her consulting a text book more than once. We would be working on something and she would get telephone calls from clinicians from all over the world. We would pause while she took the calls and I would sit and listen. She would often pull out a textbook and consult it in her conversations. it was fascinating to watch her really using biochemistry but she did not count on her memory. I kept asking my question about why we do this to students but no one had a good answer. When I got a little more senior in my studies, when I was closer to being ‘one of us’ as a PhD student, I still kept asking. Why do we make students memorise and regurgitate diagrams?

Finally one professor literally snarled at me and said “I had to do when I was an undergraduate and they are all damn well are going to suffer through it too!”

That’s when I finally understood. This is a form of hazing. We make students do this horrible useless exercise in order to make them prove they really want to be “one of us”. We force students to learn and then adopt the special language we use. This special language keeps “us” as an exclusive group that outsiders can’t join easily because they can’t understand our private conversations. You want to be an embryologist? You have to first prove you deserve to become one of us by proving you will let us make you spell every arcane, old fashioned word there is in our special secret language. You want to be a biochemist? You have to memorize a textbook of stupid diagrams to show you really want to belong to our special club no matter what we do to you. This hazing creates a nice camaraderie within the profession. It also drives away some of the best and brightest at their first exposure. Worse, it stifles those who think independently and who might therefore challenge the current consensus of whatever is considered the great truth scientific of the day. it helps explain why scientific breakthroughs resulting from paradigm shifts take so long to occur and meet so much resistance before they are accepted.

When I taught engineers and mathematicians embryology, I did not use diagrams with all those arcane names and labels. I used models with clay, and pictures and movies and live embryos. I explained how the embryo changed over developmental time giving them only a few key terms. I never mistreated them for a misspelling. I did not make them memorize anything. I allowed as many questions as they wanted to ask. I noticed these students learned much more quickly and understood much more thoroughly than the poor biology student who is forced to memorize and regurgitate diagrams. And my students never got bored with either biochemistry or embryology. And I don’t see why an engineer should be prevented from applying his skills to development because he hasn’t been forced to prove he can correctly spell “syncytiotrophoblast” or “integumentary”.

This is also why I am not bothered by the criticism that I did not use the standard nomenclature and terminology of embryology in our book. We wanted a book that was accessible to as broad an audience as possible, and one that reveals the miraculous beauty of embryogenesis without the stultifying jargon. We don’t want embryology to be a closed society with a secret language. We want everyone to love embryology as much as we do.

Another Review!

“Embryologenesis Explained is a pleasure to read, presenting difficult concepts clearly and effectively. It carries deep biological thought, and whether one agrees with the differentiation waves theory or not, it is inspiring and stimulating.”

Biol Theory
DOI 10.1007/s13752-017-0260-z

BOOK REVIEW

Mechanistic Development

Natalie K. Gordon and Richard Gordon: Embryogenesis Explained; World Scienti c, Singapore, 2016, 784 pp., £164 hbk, ISBN 978-981-4350-48-8

Jean-Jacques Kupiec1

© Konrad Lorenz Institute for Evolution and Cognition Research 2017

 

Excerpts:

“Overall, Embryogenesis Explained is a very interesting book. Although it is primarily intended to be theoreti- cal, it provides a large overview of the data collected on various subjects of developmental biology and could thus also be used as a complementary textbook. Of course, it raises a number of questions. The main question concerns the di erentiation waves theory itself. I am typically one of those biologists referred to by the authors who usually does not put the cytoskeleton and mechanical forces at the forefront for understanding development. So, was I con- vinced that the cell state splitter is the driver of develop- ment? The theory is certainly coherent. It is based on data and it suggests testable hypotheses. In this regard it should be accepted, and its research program should be developed. Natalie and Richard Gordon undoubtedly point to some- thing very important, and molecular biologists focused on gene expression will bene t from reading this book.”

“Am I entirely convinced, however? When reading this book, a question will inevitably arise in the mind of any reader: could it be that simple? In the preface, the authors argue that a theory of embryogenesis has to be simple. But, I am perplexed. Although I agree that the physics of biology has not been su ciently taken into account, and this is why Embryogenesis Explained is valuable, I have some reservations about the purely mechanical theory proposed here and the broader holistic philosophy in which it is inserted. First, the di erentiation waves theory is totally deterministic, whereas the stochastic aspects of cellular physiology, notably in gene expression, are amply docu- mented now. Integrating the randomness of cells into the picture will produce a radical change. Because of this inherent stochasticity in cellular behavior, cell fate cannot be determined exclusively by the cell state splitter as described here in a purely deterministic way. I would rather see the physics of biology as imposing constraints that give a direction to cells but not as acting as their rst causal mover. Second, I am not at ease either with the holistic philosophy the authors wrap their theory in. I even nd it to be paradoxical. Mechanism is philosophically associated with reductionism. There is no doubt that if Descartes were alive today he would enthusiastically approve and applaud the authors’ mechanistic theory. But, I think there is a widespread confusion among a number of biologists today. Because they reject genetic reduction- ism they tend to reject reductionism in general and adopt a holistic perspective. However, there are different forms of reductionism. Natalie and Richard Gordon’s theory is physicalist, and physicalism is an even more radical form of reductionism than genetic reductionism. In my mind this is not an infamy. Historically reductionism has been (and still is) the prima philosophy and methodology of science. It is beyond the scope of this review to analyze these issues in depth. I mention them only to show possible further discussions. It does not diminish the merit of Natalie and Richard Gordon. Clearly, they are successful writers, and I enthusiastically recommend their book. Embryology Explained is a pleasure to read, presenting difficult concepts clearly and effectively. It carries deep biological thought, and whether one agrees with the differentiation waves theory or not, it is inspiring and stimulating.”

Our First Review Now Available Online!

Igamberdiev, A.U. (2016). Book Review: Morphomechanics of Development. Lev V. Beloussov, Andrei Lipchinsky. Springer International Publ. BioSystems, In press. Web:  http://www.sciencedirect.com/science/article/pii/S0303264716302532

The article is now available on line (though behind a paywall if you don’t have a university or similar library access. Here are our two favourite excerpts!

The title of the book is based on the belief of the authors that the fundamental phenomenon first described by them forms the basis for a profound explanation of the phenomenon of embryogenesis and represents a “right theory” of individual development of biological organisms. Thus the book provides an expanded explanation of this new theory of how embryos build themselves using the phenomenon of generation of differentiation waves. The background given for the theory combines simple physical principles with the most recent breakthroughs in genet- ics, biochemistry, and biophysics. Despite a huge amount of detail and experimental data, the book is accessible to a broad audience includ- ing not only embryologists but also biologists of different profiles, researchers working in many fields of science, teachers and students.

This book by Natalie and Richard Gordon represents an important development in the field of developmental biology and in the foundations of theoretical biology. Its clear presentation and style makes it a perfect complementary textbook for teaching embryogenesis and re- lated courses. It is strongly recommended to everybody who is interested in the problems of embryogenesis and, in general, in foundations of biological organization. In the end, after reading this book, we are convinced that the concept of differentiation waves explains the mystery of embryogenesis. Further elaboration and strengthening of the experimental basis of research related to the phenomenon of differentiation waves may provide new further evidence in support of this great concept.