Tag Archives: theoretical biology

Embryogenesis Explained Feedback 1

220px-quinzy

We sent out a message to everyone of of the 1900+ scientists we referenced in our book. Some of the answers we have gotten back have been fun to read.

Dear Richard,

I can’t imagine why you might have cited my work in ecology in Embryogenesis Explained.  You’ve certainly piqued my curiosity, though. Can you give me a hint?  :o)
Congratulations on your achievement.  I look forward to hearing back from you.
All the best,
Peter

Dear Peter,

Well, I’ve lived in Canada long enough to know how to build a quinzhee. Here’s the paragraph in Chapter 12 ending with a reference to:

Marchand, P.J. (2014). Life in the Cold: An Introduction to Winter Ecology. Hanover,  University Press of New England, 4th.

In biology, the atom is generally the level at which we start our studies.

The energies involved in splitting atoms or fusing atomic nuclei releases

ionizing radiation which damages living organisms. So we think of

organisms as made up of stable atoms, and usually do not have to trouble

our thoughts with what is going on at lower, subatomic levels. Exceptions

are when we have to think about the key role of natural background

radiation in generating mutations, and thus in evolution23. This energy

also keeps the ground warm in winter (ref 24), permitting life to go on under

the snow (ref 25).

This is part of the background setting up reductionism vs holism in solving embryogenesis. The rub is that quantum mechanics is holistic, as I show. Had this checked by a friend who writes books on quantum mechanics.

While it’s not my forte, I have taught Pollution Biology, and learned some ecology in the process. There seems to be a nice overlapping field of ecoembryology waiting to be developed. I coined the word while writing a grant application:

Rudloe, J., N.K. Björklund-Gordon, R. Gordon, A. Hodges, M. Hodges, K. Lu, E.W. Cake & C. Rudloe (2013). A Vision for Sustainable Farming of Oysters Along Florida’s Forgotten Coast: A Restore Act Proposal. Panacea, Florida,  Gulf Specimen Marine Laboratory.

which didn’t get funded. I suspect that oyster embryos differ in salinity tolerance depending on the salinity in which their mothers existed, and that seeding with spat would be more successful if this were understood.
So that’s the tale, and you might enjoy our book. Thanks.
Yours, -Dick Gordon

Embryogenesis Explained is printed!

We got an email message today from someone who had preordered their copy of our book Embryogenesis Explained. His copy has arrived and he was reading it and enjoying it! How exciting is that? Our own personal copies are somewhere in transit. Hopefully they will arrive in Alonsa shortly.

We are also sending out a personal email to every single one of the over 1900 scientists whose work is cited in the book. This assumes that they are still with us, as some have gone on to that great laboratory in the sky. And it also assumes that we can find a correct email. Some of these scientists are retired and some have vanished from academia, or are students who have graduated and gone on to other careers.

We are also sending out emails inviting book reviewers. If you are a scientist or someone interested in science written at a popular level and would like do a review for publication, we can arrange for you to have a free copy for review purposes. Just contact us and we can start the ball rolling.

If you use the code WSGSML20 you will get a 20% discount. The code is good until December 31.

 

Biocommunication Sign-Mediated Interactions between Cells and Organisms

Gordon&Seckbach2016 Biocommunication Table of Contents

Dick’s latest book published by World Scientific as coeditor with Joseph Seckbach is now off to the printers. It includes a chapter on the Cybernetic Embryo which is an expansion of the idea in the final chapter of our book Embryogenesis Explained. The book will be out about December 2016.

Table of Contents:

Part I Theoretical Approaches

1. Molecular Biocommunication by Alexei A. Sharov

2. Key Levels of Biocommunication by Guenther Witzany

3. Zoosemiotics, Typologies of Signs and Continuity Between Humans and Other Animals by Dario Martinelli

4. Communication as an Artificial Process by Massimo Negrotti

 

5. Cybernetic Embryo by Richard Gordon and Robert Stone

6. Superfast Evolution via Trans and Interspecies Biocommunication by Ille C. Gebeshuber and Mark O. Macqueen

7. Channel Capacity and Rate Distortion in Amino Acid Networks by Boaz Tamir and Avner Priel

8. Communication Languages and Agents in Biological Systems by Subhash Kak

Part II Experimental Approaches

 

9. Chemical Communication by Ally R. Harari and R. Sharon

10. Paenibacillus vortex — A Bacterial Guide to the Wisdom of the Crowd by Alin Finkelshtein, Alexandra Sirota-Madi, Dalit Roth, Colin J. Ingham, and Eshel Ben Jacob

11. The Crosstalk Between Plants and Their Arbuscular Mycorrhizal Symbionts: A Mycocentric View by Cristiana Sbrana, Alessandra Turrini, and Manuela Giovannetti

12. Attraction of Preferred Prey by Carnivorous Plants by Douglas W. Darnowski

13. Animal Communication: Competition for Acoustic Space in Birds and Fish by Hans Slabbekoorn

14. The Contribution of Biocommunication (BICO) to Biomedical and Tissue Engineering: A Tech Mining Study by Angela Machado Rocha, Fernando Palop, Maria Clara Melro, and Marcelo Santana Silva

15. Communication Languages and Agents in Biological Systems by Noga Gershoni-Emek, Eitan Erez Zahavi, Shani Gluska, Yulia Slobodskoy, and Eran Perlson

16. Ethical Methods of Investigation with Pan/Homo Bonobos and Chimpanzees by E. Sue Rumbaugh, Itai Roffman, Elizabeth Pugh, and Duane M. Rumbaugh

17. Conversing with Dolphins: The Holy Grail of Interspecies Communication? by Toni Frohoff and Elizabeth Oriel

It’s done! Galley Proofs are off to the publisher.

At about 5:00am this morning Dick finished up the final touches and the book is now back with the publisher. This final round of proofing went very quickly. We found a few typos but there were no substantial changes. Three figures have to be reformatted because their size was changed in this round so they got either all stretched out of squashed short. The thing that took so long was the index.

Indexes are pretty much a thing of the past given electronic books, but this book is going out first in hard cover and so it needed a proper index. The publisher prepared a simple one but we weren’t satisfied. We ended up buying an indexing program for PDFs called PDF Index Generator. It worked quite well so I can recommend it. We were able to set the program to find every unique word, combine plurals and skip pages that were reference pages. We still ended up with a very long list of words of unique words. (42 pages in a word document) We then spent two days each combing put this list. We had to remove the words like “if”, “and”, “but”, “for”. We also found some words like “blastoceole/blastocele” with two, both correct, spelling versions to deal with.  We had to pick one and stick to it consistently. The indexing program is also unable to do phrases like “Robertsonian translocation”. So we had to go through our key phrase list and add those manually. For some words, like “gene” there were so many entries we simply removed the word and created a half a dozen key phrases which included the word gene.

There was a surprising  bonus to taking the time to do this indexing step, frustrating as it was. We ended up confronted with about a dozen more typos to fix.  For example, one of the words that turned up in the list was “microfilamet”. That should have been “microfilament”, of course, but somehow in all our readings and even with many spell checks, we missed that one. It is now fixed. This last four days of effort getting the index right was worth it, even if just for finding typos.

It has been a long long journey getting to this point with the book. The next step should be a hardcover book in our hands in a few months. The kindle version will follow. The reality of finally being done with this book is hitting me in waves and I suppose will continue to do so for the next few days.

Of course we have a few other projects going. We can now turn to some of the other work we have going, like “origin of life” and “diatom morphogenesis”. I have a published short story in science fiction I have halfway expanded into a full novel. Now I can finally start working on that.

And after some reluctance I gave in to the Amazon prodding and I now have my own Author Central page. Dick has had his for a long time.

Galley Proofs

If you have published a book you know there is one last peek before it goes out generally known as galley proofs. This is a set of proofs that are in the final form where you get one last chance to cross an ‘i’ or dot a ‘t’ and make sure all the previous corrections from the proofs have been added correctly. You can’t make any major changes, even one as small as adding a sentence or moving a paragraph without causing a major problem for the publisher and adding weeks to months before the book is published. Today those galley proofs arrived for us to look at. One last chance to make sure it is all perfect and then you have to let it go and let it stand as it is.

So exciting!

Near Misses: Paths not Crossed with Richard Bellman

World Scientific Publishing recently had a sale of electronic books, in which I came across and downloaded:

Bellman, Richard (1984). Eye of the Hurricane: An Autobiography,  World Scientific. Web:  https://books.google.com/books?id=6rN7QgAACAAJ; http://www.worldscientific.com/worldscibooks/10.1142/0076

for US$9.90. I had heard that Bellman had a reputation of meeting someone, having a chat, and sending them a manuscript to co-author the next day. In this way he was the applied math complement to Paul Erdös, about whom I wrote:

Gordon, R. (2011). Cosmic Embryo #1: My Erdös Number Is 2i.  http://www.science20.com/cosmic_embryo/cosmic_embryo_1_my_erd%C3%B6s_number_2i

While Bellman doesn’t discuss this story, he did love to travel, and much of the book is about the places he has been, even including in some cases the addresses of hotels he liked. He was indeed prolific: “Over the course of his career he published 619 papers and 39 books. During the last 11 years of his life [1920-1984] he published over 100 papers despite suffering from crippling complications of brain surgery” (https://en.wikipedia.org/wiki/Richard_E._Bellman). Whoever added his CV to the end of the autobiography upped it to 620 papers and 40 books. While it was written in 1978, his autobiography seems to have been published after his death in 1984. He doesn’t even mention his medical condition in the book.

What what I found uncanny about his autobiography is how many people he names who I also knew, and one he didn’t name, but undoubtedly knew: my own father, Jack Gordon. I deduce this because both played handball at Brighton Beach near the boardwalk to Coney Island, New York, on one-wall courts. Bellman, born in 1920, was 7 months older than my father, who I recall was winning at handball at age 13, on those courts. Maybe he trounced Bellman. While my father focussed on handball all his life and became a USA national champion (Singer, Stuffy (1994). Gordon honored with Kendler Award. Handball 44(1), 18.), Bellman was an all-round jock, claiming to excel at other sports: tennis, table tennis, track, football, basketball, baseball, swimming. He even did some ballet. I can recall those courts, the boardwalk, the hot summer beach on which one could hard boil an egg, building sand castles, the lines of rocks with oysters perpendicular to the beach, out into the water, and Nathan’s hotdog stand. It was there my mother, then Diana Lazaroff, met my father. This book rang of childhood nostalgia for me. I was raised nearby until age 5, when my parents moved to Chicago about 1948.

But our lives were further intertwined. I postdoced with Stanislaw Ulam; he reviewed Ulam’s “A Collection of Mathematical Problems”, and knew him well. Three more misses: “Nixon announced that two billion dollars would be available for cancer research. The experts in the field were to gather in Warrentown, Virginia, a suburb of Washington, to divide up the pie. I was chairman of a committee on the use of mathematical methods. The other members of the committee were, John Jacques, Fred Grodins, Bob Rosen, Monas Berman, and John Hearon…. At Warrentown, we had a good time deciding how we would spend the money. Alas, it was a typical Nixon trick. He posed for TV cameras and gave away pens, but not a penny ever appeared.” I had postdoced with Bob Rosen at the Center for Theoretical Biology at SUNY/Buffalo, worked under John Hearon at the Mathematical Research Branch at NIH, and knew Monas Berman while there. Natalie and I had a strange encounter with Bellman’s former student John Casti at the Third International Workshop, Open Problems of Computational Molecular Biology, Telluride, Colorado, July 11-25, 1993, albeit after Bellman’s death. Casti, guest of honor, left the conference the first evening, when (not knowing who he was) I said to him “we can explain that” in reference to a remark about embryology by the host. Beyond that, the book is full of names of mathematicians and scientists whose work I knew, a slice in time through that culture, written by someone one generation ahead of me, but overlapping. It was quite a journey, watching Bellman’s parallel life.

It was from a couple of Bellman’s math books that I learned about concepts such as differential-delay equations and invariant embedding. The former helped me understand the 30 year cycle in academic hiring, reported going back to the 1800’s in:

Nyhart, L.K. (1995). Biology Takes Form: Animal Morphology and the German Universities, 1800-1900. Chicago,  University of Chicago Press.

Let’s say jobs are available for would-be professors. Lots of students decide to go into the open disciplines. By the time they are trained (the delay), the jobs are being snarfed up. So the next generation of students seek other disciplines. And so it goes, with no one doing long-range, 30 or more year planning, to equalize supply and demand. I suppose we could call the oscillating academic job market an emergent phenomenon! I actually hit one of those peaks, at age 33 in 1977, when I applied for 100 jobs, got a couple of interviews, and no offers. Out of luck, with 300 to 500 younger applicants per job opening at that time, I answered a phone call from Winnipeg asking me to recommend someone for a job there with “How about me?”. And so I ended up at the University of Manitoba.

Like Ulam (who is discussed in my blog on Erdös), Bellman was a mathematician first. For instance, he had a moral compunction to work on the H-bomb, but when his math didn’t prove useful to the project, he dropped out, rather than solve the problem with whatever it took. As with Ulam, we would not have seen eye to eye: “There is a subtle difference between mathematical biologists and theoretical biologists. Mathematical biologists tend to be employed in mathematical departments and to be a bit more interested in math inspired by biology than in the biological problems themselves, and vice versa” (Gordon, R. (1993). Careers in theoretical biology. Carolina Tips 56(3), 9-11, http://life.biology.mcmaster.ca/~brian/biomath/careers.theo.biol.html).

I was about to wind up this blog by adding a photo of Bellman, but came across something even better, a movie by his grandson:

Bellman, G.L. (2011). The Bellman Equation [movie].  http://www.bellmanequation.com; http://www.amazon.com/Equation-Goldstein-Betty-Jo-Dreyfuss-Landauer/dp/B00C6WHRM4

So rather than color my blog by the movie, I’ll post this first, and enjoy the movie tonight with Natalie.

20% off our book thanks to GSML

Thank you Gulf Specimen Marine Lab!

Big news at Gulf Specimen     
“Embryogenesis Explained”
Now available for pre-order!!
Announcing the newest book by co-authors Dick and Natalie Gordon, about embryology; that Gulf Specimen fully recommends to anyone interested in conception of life and the development of cells.
Here’s a video directly from the author herself, explaining the purpose behind their book, “Embryogenesis Explained”

For years, these Canadian scientists have been involved as volunteers and advisors on a wide variety of technical subjects.  Such as digitizing all of Jack & Anne Rudloe’s book to be available on Kindle, applying for government grants to improve the facility, helping  with the success of our online fundraising campaigns and studying the behavior of octopuses and their human interactions.

They also have decades of experience of raising aquatic life in captivity, including disease control and nutrition. Over the past few months, Dick and Natalie have spent their evenings finalizing their book, ” Embryogenesis Explained” right here in Panacea, FL.

Now is your chance to get in on the ground floor of this unique and easy to understand book.  Pre-order your copy today and use the code “WSGSML20” and receive an extra 20% off.
Click the link below to find out more:

http://www.worldscientific.com/worldscibooks/10.1142/8152

Our latest publication!

Gordon, N.K. & R. Gordon (2016). The organelle of differentiation in embryos: the cell state splitter [invited review]. Theoretical Biology and Medical Modelling 13(Special issue: Biophysical Models of Cell Behavior, Guest Editor: Jack A. Tuszynski), #11. (The publication is open source, no fee to read.)

Abstract

The cell state splitter is a membraneless organelle at the apical end of each epithelial cell in a developing embryo. It consists of a microfilament ring and an intermediate filament ring subtending a microtubule mat. The microtubules and microfilament ring are in mechanical opposition as in a tensegrity structure. The cell state splitter is bistable, perturbations causing it to contract or expand radially. The intermediate filament ring provides metastability against small perturbations. Once this snap-through organelle is triggered, it initiates signal transduction to the nucleus, which changes gene expression in one of two readied manners, causing its cell to undergo a step of determination and subsequent differentiation. The cell state splitter also triggers the cell state splitters of adjacent cells to respond, resulting in a differentiation wave. Embryogenesis may be represented then as a bifurcating differentiation tree, each edge representing one cell type. In combination with the differentiation waves they propagate, cell state splitters explain the spatiotemporal course of differentiation in the developing embryo. This review is excerpted from and elaborates on “Embryogenesis Explained” (World Scientific Publishing, Singapore, 2016).

Book Excerpt – Literature Reviews Before Search Engines.

In May of 1990 we got our first hints of the presence of a physical wave in the ectoderm. By the end of 1991 we had the entire trajectory of that first wave well documented. There were also long stretches of time between, waiting for the embryos to reach the correct stage for filming. We had classes and teaching duties and grants to write at the laboratory. At home, we had children who needed things from us like school lunches, stories before bed, hugs and clean clothing. Still, the differentiation waves occupied our thoughts in every spare moment.

We scoured the literature over several months collecting every related paper we could find. Google did not exist in those days and there were no online journals to download articles in a PDF form. Finding papers meant hours of searching physical indexes or the limited, mostly keyword, computer searches that existed in those days. PubMed was a brand new tool. Using it was like being the proverbial kid let loose in the candy store. Once a reference was located, we had to walk to the library and pull out physical copies of journals, carry them to a photocopier, and make a paper copy to work from. We would read that copy carefully, underlining or highlighting critical components. Each paper had multiple references to follow up on which meant more trips to the library. If the journal was not available in our library, and it often wasn’t, we could try ordering it through interlibrary loan and it would arrive after a few weeks or months. (We would often find ourselves wondering why we ordered a particular paper once it finally came.) We would also contact the author and ask for a reprint. Most scientists were using email by that time and so our requests were acknowledged in a day or two with a promise to drop a reprint in the mail. Some of the scientists, especially those in key papers by senior members of the field, had to be petitioned in formal politely worded paper letters. Each workday, one of us would run to check the mail to see what eagerly awaited gems had arrived by “snail mail”. We would also trek to the library to see what precious items may have arrived via interlibrary loans. Our desks were soon piled high with towers of papers covered with notes. After six months of hard work, we found enough clues from the literature to create a plausible pathway between microfilament contraction and changes in gene expression. Still we were left with a lot of unlabeled arrows in our original nuclear state splitter model. Molecular biology of eukaryotic cells was in its infancy back then. Like genetics, the field was exploding. We published the collected ideas as a working model in our paper, “Nuclear state splitting: a working model for the mechanochemical coupling of differentiation waves to master genes”, in 1993.

While theoretical papers are easy to publish in fields like physics, and it is quite respectable to do so, in biology theoretical papers are generally viewed with disdain. More than one colleague advised us to not publish the idea until we had more data. We knew we would have a very difficult time finding any standard journal to publish a mere idea. We did find a welcoming colleague in Russia, Lev Beloussov, who has a long history of investigating the physics of amphibian embryos. We therefore published our idea, in Russian first, in the journal Ontogenez. Our English version appeared in their “translation” version of the journal a few months later, the Russian Journal of Developmental Biology, though of course that was the original and the Russian version was the translation. We took the opportunity of the delay to prepare an Addendum to the English version.

As the years passed, and biochemical, molecular biological and genetic knowledge grew in great leaps and bounds, more new pathways and interactions and proteins were collected and catalogued. It was not unusual to have a student spend their entire PhD characterizing a single protein within a complex pathway. Once the knowledge of the proteins was combined with the genetic sequence producing the proteins, families of biochemical components were discovered and their evolution and relationships across species were explored. Not surprisingly, the protein carefully studied in one organism often turned up in another organism in a closely related form. All too frequently this homologous protein would have an entirely different name or function ascribed to it by some other PhD student or postdoctoral fellow and his or her supervisor. Since the early days of the field, the general amount of knowledge of scientists studying these processes has doubled about every five years. We have tried to follow all of these developments as they came out and, while we found a lot of new detail, we never found anything contradicting the general layout of our first nuclear state splitter model. In fact, the more the scientific community learned, the more correct our original working model appeared to be and the more blank arrows in our model acquired names. Today, there are no blanks. There was very little interest from anyone else in our early model. It is so easy to not see the forest for the trees, especially when you are trained to focus on leaves. Those were exciting and giddy days full of new discovery and heady wonder. It doesn’t matter if no one else listens to us. There is only one test the counts. Every idea or theory must be tested against nature and in the end nature will prove us right or wrong.

Natalie 1990

Natalie circa 1990 with an old Mac of similar vintage.