Category Archives: Nerdy Tumbleweeds

The Science Police

The Science Police


On highly charged issues, such as climate change and endangered species, peer review literature and public discourse are aggressively patrolled by self-appointed sheriffs in the scientific community.

A profoundly important article that describes how peer review is really done. In most fields it is not important enough to have cables denying funding because of what the public might misperceive. Still, the science police exist. People inclined to be science police tend to gravitate to positions of power such as grants committees and senior academic administrative chairs.

I wish I had a nickel for every time we wrote a grant on our waves and got back an answer that basically said, “It’s an interesting result but it goes against the prevailing wisdom and so we won’t fund you to test it”

Our system of peer review is made up of deeply sincere individuals who are so convinced they are right and others are wrong that research progress is slowed and huge amounts of money are wasted,

I once had a fellowship application for a grant turned down with the following:

“You have written an excellent application, clearly showing your methodology and goals. Your references, publication record and previous accomplishments prove you are well qualified to do this research and you have a high probability of success. The project itself is completely novel and potentially ground breaking. However because you have never published about this topic in a reputable high impact journal we cannot fund you.”

My husband has the same committee tell him in one year he was brilliant and if the work held up it was likely time for another nobel prize in embryology. In the following year the same committee rejected him saying it is a wonder he ever graduated from high school. The only thing that changed was who the chair of the committee was.

This article is long but it very clearly illustrates a phenomena first described to me by writer and naturalist Jack Rudloe (though he says he heard it from someone else.)

“You can always tell an academic by the number of knives in his or her back.”

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.


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.


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.


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


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.


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.



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.


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.


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.


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


Staying on the road with bungee cords.

Richard Gordon

March 17, 2017, Cedar Lake, Ouachita National Forest, Oklahoma, USA

In the race to see who ages faster, we or our now 7 year old travel trailer, the trailer seems to be winning, held together indefinitely by duct tape. We buy the everyman version known as Duck tape because it comes in many colors which show less when we tape something. Duck tape is marvelous to hold together the cover of our air conditioner or a bandage on Fred. (Duct tape, unlike the regular bandage tape meant for use on humans, doesn’t pull out fur when removed, and he can’t bite through it.)

Unlike duck tape however, bungee cords not only come in brighter colors and pleasing patterns, but don’t leave marks when replaced. So we keep a good supply of all sizes on hand, much like our bandage supply for us and the pets.Bungee

Actually, it was our escape artist cat, Klinger (who should have been named Houdini), who taught us the value of bungee cords. He outwitted us for years with his charges through the open door underfoot, flying from the bar counter, sneaking from under my computer lab bench or an exiting dog, opening the screen door slider (just another cat door to him), and when we put on a latch, throwing his body against the door to transiently warp it enough to fly out. But one bungee cord, knotted to sufficient tension, finally defeated him. Now Klinger is a well travelled and very expensive cat, having stayed at the Toronto Feline Hilton en route to rejoin us in Disneyland after one deft escape into the talons of an eagle. Bungee cords are cheaper.

Klinger of course has nothing more to do all day than plot his escapes, awake or in his dreams (he sleeps a lot, except when we do). His latest success was learning how to open a window screen. Being hairless apes, we scratched our heads but finally recalled The Bungee Solution. The metal prairie rose (by our friend Steve McGrew) anchors a bungee cord to the screen now. Enough about our cat. This was supposed to be about our trailer. Anything not secured manages to meander to the opposite end of our trailer unless it’s tied down – via bungee cords. The metal stair, needed on those ungraded hilltop RV sites, and our portable microscope, are battened down.

One essential bungee cord keeps our red, white and blue towels from plunging into the toilet, which must be kept open for, you guessed it: the cat, who is toilet trained. Leaving and returning to Canada is a cold experience due to our government’s 6 month and a day bed check rule, so we keep the trailer bathroom warm for Klinger with a vent pad, held in place by – a bungee cord.

Of course, on rough roads our kitchen drawers always fling open, now kept closed by a cleverly placed bungee cord. Note the counter balance on the sink door, so that the knobs aren’t pulled out. But au contraire, when we’re parked, especially on one of those sites tilting us port, the drawer won’t stay out while we put away the silverware, so another bungee cord comes to the rescue. The tall Sodastream bottles in the door leave us with a narrow shelf, good for cheese and sausage.

The other crash, into the bathroom sink, is now also a fond event from our past.

Medicine cabinet

One bungee cord keeps the computer lock away from the mouse, and doubles to restrain the battery backup from scooting to the floor while en route.

That takes care of the interior of the trailer, for now. Outside a bungee cord holds the power cord up away from wandering ants, though a ring of Vaseline is still sometimes needed. On our roof are four solar panels, protected, when needed, from hailstones by Styrofoam panels, held in place by bungee cords. A too sharp turn once severed the power cord from the trailer to our workhorse pickup truck. The replacement didn’t quite match, and is held in place by bungee cords. Inside the truck’s cap, our travelling garage, bungee cords keep the spare propane tank, bikes and lawn chair from rattling around. On the side of the cap, two bungee cords suspend our pick axe, so it doesn’t crash to our toes. A bungee cord also helps secure our canoe.

The original bungee cord was a 1930s elastic cord for launching a glider. If we outlast our trailer, our earthbound spaceship, perhaps someday it will be replaced it by an airborne trailer towed by an aircar. Undoubtedly it, too, will be held together with bungee cords (and duck tape).


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!


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


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



“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.”

Embryogenesis and the G-d Factor.

Many years ago Dick and I reached am impasse on our research on the waves. We had the image of the wave on the top part of the ectoderm but we couldn’t actually see the bottom half. Our engineer collaborator said the wave must cover all the ectoderm and therefore could not be THE differentiation and organizing signal. I said our engineer was wrong. I had observed enough embryos that I just knew the wave did not go all the way around the embryo. I was absolutely certain I was right.

We had an argument over it. It started at work and it continued after we got home and the kids were in bed. Now normally we never argue. We have these very rational easy going discussions about everything from laundry to dishes. This time we ended up shouting at each other into the wee hours of the morning. Neither one would back down. In the end we concluded that the only thing to do was more research. We  did top and bottom pictures simultaneously and it turned out I was right. End of story.

There was one tiny issue. The next morning after our huge argument our neighbour came over for coffee with the wife of the newly wed couple who had just moved in next door. As soon as Dick left and she asked me if I was all right. Was I injured? Had he hit me? We had been yelling so loudly we had awakened her. She was so worried about me! How embarrassing. I had to assure her we were only arguing over data interpretation and we had concluded the way to settle the argument was to do more experimental work. She left, somewhat reassured but still dubious, and we made a decision to be certain the windows were closed if we ever needed to fight over data interpretation like that again. We never did have such an argument because we both learned an important lesson. The embryo is always right and when you have a disagreement you must always go back to the embryo to settle it. (I only occasionally rub it in that I was right.)


From our giddy newlywed days and our only really ferocious argument.

The second worst debate we ever had was over the G-d factor in our book. Dick is an avowed atheist although he does occasionally stray off that stance and exhibits more of an agnostic position. Although I am no biblical literalist,  I am a religious person and I deeply and absolutely accept the idea of a higher power I call ‘The Master of the Universe’ according to my beliefs. In preparing our book I really wanted to make sure we acknowledged the Master of the Universe.

I wrote the first draft of Chapter 1 and every time Dick did his round and he removed the G-d factor. I would review his work and put the G-d factor back in. This went round and round quite a few times. He argued there is no place for a G-d factor in a purely scientific book. He is right but this is also MY book and we were going to have that G-d factor. One reason I was so intent on having it in there is I am not alone in being both a scientist and being a religious person and I often feel the lack of acknowledgement of the Master of the Universe in science. It’s like one can’t be both religious and scientific which is obviously untrue. I have a lot of company.

My first mentor in embryology was Hans Laale and he was also a deeply religious man. On his desk was a picture of his parents and a rosary bead hung on that. He kept his religious beliefs out of the classroom but he did acknowledge them once. About half way through his course, when I was having  deep philosophical discussion, he complained how hard the problem of embryology was and he said he wondered if the problem would ever be solved. Maybe there were just some things that we weren’t meant to know.

I disagree. G-d has created this universe with a set of rules and regulations, constants and laws. They may be hard for us to understand but as we grow and learn as a species I see absolutely no reason we should not be able to figure out exactly how the Master of Universe did it. Nor would figuring it out in any way diminish the glory of His creation. In fact I think greater understanding will only serve to increase our appreciation for Him.

We talked a lot about the problem over the years together. I like to think that at least in part, Dick agreed to co-edit a book where creationists and scientists debated the origin of life because of my influence. There is an interesting story he references there which we first heard from a rabbi. It is about a scientist who has been climbing the mountain of ignorance seeking answers to how the universe works. He arrives on the mountain top to find a lovely flat spot. And there, sitting around a fire discussing the problem, is a group of theologians (Jastrow, 1992). Dick’s book ended up creating more questions than answers but at least they got to questioning.


From this process Dick acquired enough respect for theology that although he maintains his personal firm stance as an atheist, he was nonetheless ready to compromise with me and eventually allow me to keep the G-d factor in the book.

Dick and I added the following paragraph we could both agree on;

“The religious among us who nonetheless embrace the overwhelming evidence for evolution often see the finger of G-d as stirring that primordial goo: yes, life did start out as goo somewhere in the universe, maybe more than once, but it could only have done so because G-d did it. … And if one must invoke G-d, then we can at the very least, expect to figure out exactly how He does it.”

And that is the how and why of the brief appearance of the G-d factor in Embryogenesis Explained.

Stadium Waves and Embryogenesis.


I (Natalie) was at a southern barbecue eating good food and enjoying good company when our book came up in conversation. With it came a request to explain the waves in simple terms. Being surrounded by a bunch of really keen American football fans I invoked the stadium wave.

The stadium wave (also called the Mexican wave) is great fun phenomena where someone starts a “wave” that is made by people in the stands leaping up and putting their arms in air. The wave will travel around the stadium. The differentiation waves are much the same. A sheet of cells is ready to participate in the wave but each cell doesn’t actually stand up and wave its arms until the cell next to it does it first. If you look at the stadium way, the people can watch what other people are doing. A cell has no eyes and no brain. So instead of watching for the wave and watching it as it passes, the cell has its bistable organelle on top to sense if a wave is coming its way. When the cell next to it “waves” it gets its signal to do its thing.

When I was a little girl in Brownies we attended a huge event in honour of Canada’s 100th birthday in 1967. The Montreal Arena was absolutely packed full of little Brownies all in uniform and we each had a cushion. My cushion was yellow on one side and brown on the other. All those in my pack had the same cushion. All the packs sitting in my section had the same colour. Other packs in other sections had other cushions, with different pairs of colours but always light and dark. I recall being absolutely fascinated by how the person directing from the floor was able to make incredible patterns across the stadium by the simple act of saying things like “Everyone on the south side hold up their cushion with the dark side out.” The arena became a brown sea. “Now everyone turn your cushion over!” and suddenly the area erupted in gigantic patches of bright colours.

Imagine a bunch of little girls in their cute little Brownie uniforms but instead of one cushion each Brownie has five cushions. The cushions are numbered 1 through 5. The Brownies are all in their seat and they follow instructions to take out cushion number one and be ready. Cushion number 1 is red on one side and white on the other. Now the leader gives instructions. Everyone on this row, turn your cushions to white. In the row beside them everyone turn their cushions to red. Now “go”.  In embryonic terms, the cell is ready with a “cushion” that is the bistable organelle, the cell state splitter. The cell state splitter can either expand or contract in response to an outside mechanical signal or to what the cell next to it can do. Red cushion is analogous to contraction, white to expansion.

The result would be a moving wave of white in one direction and red in the other other that would move around the stadium until the red and white meet on the opposite side and then the wave would stop. We would now have the stadium neatly divided into half red and half white. This is exactly what happens during the embryonic stage in mammals known as compaction. A ball of cells is neatly divided into two parts, the inner cells mass and the outer trophoblast. Instead of red and white we have contraction of the inner cell mass and expansion of the outer trophoblast. The contraction action actually moves the contracted cells into the inside. The expansion results in an outer sphere of cells. The balls of cells of the recently fertilized egg undergoes it first differentiation. The inner cell mass will become the future mammal. The outer sphere will come the placenta, and amniotic sack and other supportive tissue which is later discarded at birth.

What part do “genes” play? Go back to our little Brownies. Now once the first wave has gone by the leader says to the Brownies “Check your cushion for instructions!” The white side of the cushion has printed on it “Put the red and white cushion away and put cushion number 2 (brown and orange) away with it and take out cushion number 3 (green and yellow). The red side of the cushion has the instructions “Put the red and white cushion away and take out cushion number 2 (brown and orange) and put cushion number 3 (green and yellow) aside with the red and white cushion. Now repeat the entire event but this time the two start rows are not at one end of the stadium but instead are started in the middle. Two rows in the middle of the white section are instructed to have one row wave green and the other row wave yellow. Meantime in red section the two rows are to use their brown or orange side respectively. The result of triggering the waves again is the division of the stadium into four sections, brown, orange, green and yellow.

The only “outside” information required to do this division of Brownies in a stadium is to watch the girl next to you and do what she does except for the ones in the start row. This is how the differentiation waves work. The only information a cell has is what the cell next to it does. The response is inherent in the colour of the cushions the child is carrying and the directions on those cushions which is analogous to the genetic code each cell carries. The code includes instructions of which part of the code (cushion) each girl is to use next. The code also contains instructions for which genes (cushions) to put away and not use.

This response to the wave, reading the cushion instructions, is the embryonic process of “determination”. If we wanted to carry the analogy even further, imagine that each little girl has brought a suitcase of clothing along, separated in five numbered bags that match the cushion colors. After she participates in the red wave, the instruction on the cushion include the directive to take out and change into the clothing in one of the bags. Eventually all the girls are wearing a new outfit corresponding to which waves she participated in. This changing of clothing would be analogous to “differentiation” where cells stop producing one set of proteins and change to another set of proteins and in doing so become a new type of cell. The genetic code carries not just the instruction on the cushion (which are signal transduction to the nucleus i.e. determination) but the instructions for how to make the clothing in the suitcases (differentiation). Each different cell uses some of the code but not everything in the code (some cushions nut not others) depending on where the cell is and what sequence of waves it has participated in.

In our cell sheets, the start of the wave is signalled by some mechanical force in the cell sheet instead an announcer/leader. If we take the ectoderm contraction wave as an example, the underlying invagination of mesoderm touching the underside of the sheet of cells is the signal. This mechanical signal is passed from cell to cell the pushing and tugging of neighbours.

The ectoderm contraction wave actually goes through more than one tissue. It starts in tissue that will eventually become notochord then passes through tissue that will become tailbud mesoderm and then finally through to the ectoderm. In early embryogenesis, many of the waves go through more than one tissue. However, if the cell in that tissue has been previously subdivided by earlier waves, the result is simply that the wave passing through more than one tissue type will create a pattern duet each cell having a different set of instructions (or a different cushion). If you look at the “Best Wave” sequence, the audience has previously been divided by being given different cushions. The wave in the stadium simply exposes a preexisting difference in a spectacular fashion. Note how once the wave has created the beer glass pattern, there is another wave inside just the beer glass that empties it visually. A second wave (or third or fourth or fifth) on one section of an embryo but not another allows refinements of the pattern of embryogenesis.  In our model, the people who make the beer glass drain would be a tissue type that once triggered is primed to be trigger again even though the people around it stay quiet. Repeat waves are also very common in embryogenesis in development of the early brain, for example.

One other little bit of embryological jargon. A cell can only participate in a wave if it is “competent” as in ready to go. In the case of the beer commercial below, it is like the people waiting, cushions ready, like the people at the beginning to the video.



It is hard to explain the waves of embryogenesis in few sentences in a break between barbecued steak and key lime pie to a group of people whose sole common interest, aside from being related, is that we have all watch football. But the stadium wave, and my experience as a Brown back in 1967, served as an excellent analogy where everyone seemed to “get it”. Yes, “the genes” do it but waves explain why genes only “do it” in the right place at the right time.


Lil Girl Released to the Sea.

Yesterday we attended the release of a loggerhead sea turtle named Lil Girl. Lil Girl had been a resident of Gulf Specimen Marine Lab since she failed as a test subject on a turtle exclusion device. She was one of several hatchlings who were taken from Florida, transferred to Galveston Texas where she was raised by NOAA until she was the perfect age and size to stand in as a Kemp’s Ridley sea turtle in experiments on mandatory equipment used by shrimp fishermen that allow turtles to be excluded instead of drowned.

Turtle exclusion devices are, in my opinion, the very best of humanity in action. Instead of simply railing at the evil of humans who accidentally kill turtles as by-catch a constructive solution was researched, developed and then tested. The problem is solved in a rational and practical way that still allows humans to eat shrimp. This wonderful and incredibly valuable work is still on going at NOAA’s Fisheries Service Sea Turtle Facility which Dick got a tour of during our Galvaston trip.

Lil Girl was originally raised in this facility. After she flunked the TED test she got sent to Gulf Specimen Marine Lab to be used as a teaching animal until she reached adult size. As a young adult capable of breeding, and therefore extremely valuable to the wild loggerhead population, Lil Girl was deemed ready to go this December.

Lil Girl was a long time favourite at GSML. She arrived as a tiny turtle in 2008 at 13.6 inches long (32cm) and weighing 12.5 lbs (5.7kg) and at the time of her release she had gown to an astonishing 27.7 inches  (70.4cm) and 81.6 lb (37kg). Every year when we arrived back at GSML we looked forward to seeing Lil Girl again and see how much she had grown. An estimated 180,000 people have come to GSML and have seen Lil Girl. She has been a wonderful Ambassador for her species. The picture above is Lil Girl in 2014 and then two years later in 2016 and you can see how her shell is not only bigger but grew longer as she grew. Dr. Robbin N. Trindell of the Florida Wildlife Services decided it was time for Lil Girl to have her chance to make it on her own out in the big wild ocean. Dr. Trindell was on hand for the release and to reassure the public this was the right thing to do.

Lil Girl arrived in the GSML truck and staff gathered to say goodbye. More than one was in tears because Lil Girl had become something of everyone’s favourite pet at GSML. The guest of honour seemed to be very nonchalant and relaxed about the entire thing.

There was a thunderstorm in the area at release time and the big moment was delayed while this small twister passed by and eventually formed a small water spout over the bay before the weather cleared and the sun came out. To everyone’s delight a group of three dolphins swam by, coming close to shore to check out the fuss as the water spout moved out of sight.

Members of the public took advantage of the delay to get one last close up look at Lil Girl.


Very special guest of honour was little Kai Rudloe with his Mom April. Will Kai Rudloe grow up to come the third generation of Rudloes to work in a third generation at Gulf Specimen Marine Laboratory? Only time will tell but he did get a great start today.

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So Lil Girl was removed from the vehicle and loaded up into the transfer sling for her walk down to the beach. More than one staff member was fighting tears.

It was hard to let her go. And she didn’t seem all that keen to be off herself. Unlike Allie who was straining to be free again at her release, Lil Girl looked all around and blinked her eyes obviously very puzzled about what was going on. She has always been in the care of humans and she trusts us completely and something was up she didn’t understand. In the end, she needed some shoving by Cypress Rudloe before she finally headed off into the great ocean she had never seen or swam in before.



This fabulous picture was taken by Nic Christie, a professional photographer who does a lot of great work for GSML. It is not our picture though I sure wish it was! A great place to see more of his work is on the GSML Facebook Page.

When the waves began hitting her in the face, her bewilderment passed and she seemed to know what to do. She finally moved into the water and swam off. She paused briefly to lift up her head and take a breath and then she was gone.

As she swam off I found myself humming the old Cat Stevens song

Oh baby baby it’s a wild world
It’s hard to get by just upon a smile
Oh baby baby it’s a wild world
And I’ll always remember you like a child, girl

I’ll always remember you like a child, girl
You know I’ve seen a lot of what the world can do
And it’s breaking my heart in two
‘Cause I never want to see you sad girl
Don’t be a bad girl
But if you want to leave take good care
Hope you make a lot of nice friends out there
But just remember there’s a lot of bad and beware

Part of me is afraid you got only a few miles from shore and some shark, a creature you never knew, swam up and ate you or you’ll go seeking people you knew who fed you and get hurt by a boat or hooked on a fishing dock. Being a reptile, and therefore mostly programmed by instinct and not so much by learning, you should be all right. There are records of turtles like you turning up, healthy and fine, years after release and having adapted well. I take the presence of dolphins as good sign. Good luck Lil Girl. I hope you get to make baby loggerheads and swim the sea for many years.