A New Review of Embryogenesis Explained

The review is by:

Dr. Palmiro Poltronieri
Editor-in-Chief, Challenges
National Research Council of Italy,
AgroFood Department,
Institute of Sciences of Food Productions
via Monteroni km 7
73100 Lecce, Italy

“The model discussed by the authors is based on a simple, unifying idea that differentiation waves, based on cell cytoskeleton, i.e., contraction and expansion of the network of microfilaments and microtubules, is at the basis of mechano-transduction signalling, that brings transcription factors to regulate chromatin into specific cell-stage differentiation states, based on regulons, i.e., the wholeness of opened DNA regions and inaccessible DNA regions. Thus, from determination of a cell’s fate, i.e., signaling to advancement of process, to differentiation state, i.e., new transcriptional program and reprogramming of active regulons, clusters of cells thus divide, mature and form the various cell type component tissues of the developing embryo.”

And my favourite part:

“Overall, the book is a great book, documenting with images, schematic reproductions and drawings the embryo development, showing parallelisms, universal processes and the peculiarities of various vertebrates and invertebrates.”

You can read the full open access review here:

The Science Police

The Science Police

by

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.

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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!

 

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.

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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!

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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.