Monthly Archives: October 2015

Intersections with John Brent Musgrave

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Intersections with John  Musgrave, on learning from his Colombian born wife Consuelo of his sudden death of a heart attack August 11, 2015 (by Richard Gordon)

I met John probably in my last (3rd) year of high school at the University of Chicago Laboratory School. He was then an undergraduate at the University of Chicago, and a member of the Astronomy Club (still in business). The president Tom was the older brother of a girl who was a year ahead of me in the Lab School. Tom made me recite some constellations (a difficult task for me, allergic to memorizations) to join the club. I learned them once and promptly forgot most, though Big and Little Dippers, Cassiopeia and Orion still stick. By the time I entered UC in 1959 as a 16 year old student, skipping the senior year in high school, John was President, I became Treasurer, and there were no other members and no membership fees. It was typical of John’s wry humor, which I went along with, that he gave me this null responsibility for all our money. I enjoyed the irony.

John lived in the crawl space between the roof and the ceiling, just high enough to sit up on the mattress he set up in there, above our club room atop the Ryerson Physics Building, accessed by a narrow helical staircase. John kept his personal belongings locked in the club room, explaining that the purpose of locks was to keep honest people honest. Above the club room, from which we could look east across the campus, was the observatory on the roof containing a 6 inch refracting telescope. Daytimes I would occasionally sketch projected images of the sun’s spots. At night I sometimes brought a date up there. I tried simultaneously photographing the same meteorites with my brother, with him at our home in southwest Chicago and me at UC. I had built a strobing device consisting of a fan blade on a motor that went in front of the camera, so that the images of meteorites would be a sequence of dashes, allowing calculation of their velocity But the film cracked in the cold of night when advanced in the camera, and I didn’t think about how to overcome that problem. Dan later became an excellent amateur astronomer with his own observatory, and a prize winning astronomy photographer. He still volunteers at McDonald Observatory in Texas.

Astronomy overnights with John meant we played with an ancient brass calculating machine we had, listened to classical music on WFMT (a radio station still on, now available on Internet), and browsed through negatives of galaxies photographed by previous members. That space became my second campus home, my first being my own lab over the central lecture theater in the Kent Chemistry Building, where I kept a cot and cooked canned spaghetti in a beaker. I prepared specimens for students to analyze for the quantitative chemistry course, after taking that course my first summer before I entered UC. Ed Anders taught it. I later worked with him on organic matter in meteors.

John majored in history of science, and via him I gained an appreciation for that history. I recall sitting in on a course on modelling in science, undoubtedly because of John. John questioned everything, especially having to do with authority, and I owe much of my professional and daily skepticism to discussions with him. He told me about Vulcan, the planet deduced from its perturbations of Mercury’s orbit, and that was sometimes observed, between Mercury and the sun. It was later explained away by relativistic effects on Mercury’s orbit. We discussed phenomena such as people seeing lights on the Moon. John told me that when he was a kid, in broad daylight he used his telescope to watch something in the sky that had parts twirling around and going in and out, unlike any aircraft with which he was familiar. He later wrote a short book on UFO sightings in Canada. Again, I learned from him open-mindedness about things, raising questions, but not jumping to conclusions based on scant evidence. He was not a believer in UFOs, just open to their possibility. After a visit 5 years ago that Natalie and I paid to the UFO museum in Roswell, New Mexico, I made sure they got a copy of his book into their extensive library.

John came to my home, where my parents Jack and Diana Gordon got to know and like him. This probably made it easier on them when at 17 I moved out and shared an apartment with John and one other fellow in Hyde Park, north of the University. He also got to know George and Susan Meschel. Susan was a grad student in Quantitative Chemistry, who along with Jim Dwyer looked after me. I was younger than everyone else in my class, so it was these people, along with Helmut Hirsch and later Victor Fried, a prodigy in Biophysics, also my age, who formed my world.

I went off to graduate school at age 19 to the Institute for Molecular Biology at the University of Oregon. John’s pacifism wore off on me: “Do you believe in the use of force? Well, I do use a can opener.” Always a wry point of view. At UO I was kept out of the army draft “in the national interest” and joined many of the discussions pro and con about the Vietnam War. But this is John’s story.

John visited me once in Oregon, driving up from California, where his parents lived. His father, a laborer as I recalled, in the San Diego area, had done a lot of reading on witchcraft, which influenced John. (My father, a home remodelling salesman, was likewise a collector of all books on Franklin D. Roosevelt.) On a visit to John down there, he made a remark about my moustache looking like Hitler’s. When I mentioned this to him 50 years later, he said it showed how cruel kids can be to one another. The bad memory was laid to rest. In retrospect his remark was just his observation of the incongruity of a Jew bearing such a moustache. Although not Jewish himself, he did observe that most of his friends were Jewish.

On one visit John and I drove to and stayed with an old friend of his, who lived on the coast of northern Oregon. We caught razor clams on the beach, overcoming their amazing speed through sand with a half meter long sheet metal pipe capped at one end to let air out, with thumb over the hole to pull out a core of sand with clam. His friend couldn’t pay the taxes on his tiny home, so it went up for auction, and he bought it. More wryness.

For a year or two I kept a diary of sorts in the form of long, handwritten letters to John. Unfortunately, in his wanderings he had to lighten his load, and they were gone.

John collected books, amassing over 3000 of them, for which Consuelo now needs a buyer. He had rare books of interest to historians of science, and an eclectic variety of others. When I sold mine to begin full time RVing with Natalie, I had only 2000 to my name, much the same in kind, but focussing on biology instead of physics and astronomy. He moved to Edmonton, was in graduate school at the University of Alberta for a while, and I visited him there with his newly wed Consuelo, our young sons Chason and Justin in tow. When later he was short of cash, I bought a shelf of books from him on religion and science.

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John’s beloved wife Consuelo Sanclemente Musgrave in a playful moment

Natalie and I visited John and Consuelo during our two stays in Osoyoos, British Columbia, winter 2013/14, seeing them at their home in Oliver and in restaurants. I attended a meeting of the local historical society with John. He was much the same, but had drifted far from science, the two of them having fostered many First Nations kids, and he getting involved in the history of local First Nations affairs. The last I saw him was when he came to our RV camp site (run by the Osoyoos Indian Band with whom John worked) to try to help me with a bolt on our trailer hitch, which would not budge with the tools we had between us.

John was one of those fine intellects who could never have made it in academia. I squeaked through, despite the attitudes I learned from John and concurred with. In retrospect, though I didn’t think of him that way, he was a fine, exemplary big brother. I’m off shortly to a conference on the origin of life, where I will be trying to tempt people to join me in a book on The Habitability of the Universe Before Earth, which if it comes to fruition will be dedicated to John’s memory.

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Some of John’s Publications:

Musgrave, J.B. (1979). UFO Occupants & Critters: The Patterns in Canada. New York, Global Communications.

Musgrave, J.B. & J. Houran (2000). Flight and abduction in witchcraft and UFO lore. Psychological Reports 86(2), 669-688

Musgrave, J.B. & J. Houran (2003). The Witches’ Sabbat in legend and literature. Lore and Language 17, 157

Musgrave, J.B. (2003). Smallpox as a weapon of genocide in the Okanagan and Similkameen? Report of the Okanagan Historical Society 67, 41-43.

Book Update

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Schrödinger’s Cat as conceived by Doug Hatfield

 We have had some very good people reviewing our chapters in Embryogenesis Explained as they enter final stages and get shipped to the publisher. The publisher now has 1-8, with 9 very close to going off. 10,11,12 have some comments to go in. We got the following back from our friend and support, physicist Jack A. Tuszynski at University of Alberta, Edmonton Canada, about Chapter 12.

Wholeness and the Implicate Embryo: Embryogenesis as Self-Construction of the Observer

This is the chapter where Dick shows how far science has come (or not come) at unifying embryogenesis and physics.

Hi Dick,

I read the chapter with great interest. No offense but I didn’t realize you are such a great story teller. Wow! This is a masterpiece of popular science literature. I like the combination of anecdotes and hard science facts. I thought you’d be unable to explain the Schoredinger equation for the lay audience but you pulled it off. The only  possible suggestion would be to expand a bit the last part when you discuss your hypothesis to achieve a better balance between introduction and conclusion of the chapter but feel free to ignore it. Congrats on a fantastic piece of work.

Best regards,

Jack

We have been aiming for a work that can explain embryogenesis at the level of the lay person who starts the book with nothing more than maybe high school biology. This gives me great hope that we have succeeded. (And we did add a conclusion summary as Jack suggested.) Many thanks to our readers/editors who have caught so many times where we made mistakes like assuming the reader knew this or that or where we missed some concept important to what we are trying to say. The book has been immeasurably improved.
(The orange cat in the featured image is our very own Klinger. Schrödinger notwithstanding, we actually like cats.)

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.

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Natalie circa 1990 with an old Mac of similar vintage.

Book Excerpt: Why Evolution is Progressive

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Image is from  University of California Museum of Paleontology’s Understanding Evolution

One of the outstanding recent scandals of biology has been the notion that evolution is not progressive, a concept that flaunts the evidence of our eyes. Any reading of the fossil record shows simpler starts followed by increasing sophistication, along many lines. Even where morphology doesn’t appear to change, competition between organisms can lead to an arms race, known as the Red Queen hypothesis from the children’s book Through the Looking-Glass, and What Alice Found There: “Now, here, you see, it takes all the running you can do, to keep in the same place”. Overall, there is indeed an increase in biodiversity over evolutionary time which we could delibately maintain. To be sure, there is some apparent backsliding, as when an independent organism, even a bacterium, becomes a parasite, or parts become vestigial or discarded, or features disappear and recur in closely related species, or a comet or an asteroid wipes out 95% of living species. But on the whole, some species in each branch of the tree of life tend to march on with richer diversity of structure and perhaps behavior. One caveat is that the total number of species, though perhaps not their complexity, may have peaked 530 million years ago, due to subsequent extinctions.

Those that stay behind may not progress, or at least not appear to do so in morphology. The most blatant example of the latter is that we are descended from bacteria, yet there are still plenty of our brethren bacteria around. And while we can’t be sure yet that modern bacteria are any more complex than the earliest ones, it is clear that the number of niches they live in has increased, and the corresponding biochemical and genetic diversity amongst bacteria has evolved. The diversity of minerals has increased with the evolution of life, so for example we can expect a parallel increase in the number of environments on minerals for bacteria, let alone environments in and on other organisms, in the evolution of bacterial film communities, symbioses and communities on and in eucaryotes that have been called symbiocosms. The heterogeneity and geographic separation of places that bacteria can live contributes to their diversity, and many have been classified as extremophiles or polyextremophiles for the extreme environments they live in. Therefore progress may be occurring at every level.

Some work on progressive evolution has been couched in the language of “increase in complexity”, and thus centers around the construction of measures of complexity and empirical data on whether complexity is increasing. For example, John Tyler Bonner counted the number of cell types in an organism as a measure of complexity. In our work, because of the direct link between the number of cell types and the number of differentiation waves, this count is clearly a measure of both differentiation and morphogenesis, i.e., it operates at widely different size scales. On the other hand, the differentiation tree is not a linear, but rather a branched structure, so it is not subject to simple, scalar measures of complexity. The problem of estimating the complexity of differentiation trees in a way that allows comparison is a subset of the problem of complexity of networks, which is under active investigation. Insofar as the differentiation tree is the genetic program of the organism, a bifurcating alternation of molecular events and physics (differentiation waves), it may be possible to calculate its algorithmic complexity, defined as the length of the shortest computer program that successfully mimics embryogenesis.

“Progress” became a dirty word in biology because it smacks of “purpose”, and the implication that the purpose of evolution was to produce us. The concept suggests that evolution indeed has a direction, which to many religious people (including many scientists), means “God did it”. Thus, for a biologist to speak of progress is said to play into the hands of the creationists and the Intellegent Designers (who distinguish themselves from other creationists by not uttering the word “God”). Rather than take this head in the sands approach, we will confront progress in evolution in this chapter.

On the question of the centuries old debate of the relationship between science and religion, we stand firmly in the belief that the universe is one, deserving one unified explanation that works, and do not opt for the so-called “Nonoverlapping magisteria” or “…lack of conflict between science and religion due to the lack of overlap between their respective domains” . That is an imaginary line in the sand. Attempts to draw it, or to claim the whole territory, from either side, are failing. Rather than propose a God of the gaps or science of the gaps, we prefer to push our investigations as far as we can with testable hypotheses, and leave the gaps of both kinds for later generations to work on.

Our plan in this chapter is, then, to delve into the evolutionary consequences of differentiation waves, ending with a plausible demonstration that they may be responsible for progress in evolution.

Introduction to Chapter 11, Why Evolution is Progressive, in Embyrogenesis Explained.

Snake Migration Season

Tumbleweeds Tumbling

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Manitoba is famous among snake admirers for the Narcisse Snake Pits. Each spring the snakes emerge from their dens in limestone caves that reach below the frost line. They are sluggish and slow and you can handle them. The ground will have so many snakes you have to watch where you go. The town of Narcisse has turned their snake problem into a tourist attraction.

Alonsa also has migrating snakes. A couple of decades back, in an effort to get the snakes out of the local school, the Conservation District created a snake pit like the one nature made in Narcisse on a smaller scale. Each year in spring, the snakes migrate out from the “hibernaculum” and for about three weeks the town of Alonsa is full of snakes. When the fall arrives, the snakes return and for about three weeks we have snakes everywhere again. Since the…

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Recurrent Dreams of Life in Meteorites

Meteorite in Aurora

This stunningly beautiful image of a meteorite falling through aurora borealis was taken at Patricia Beach, Manitoba by photographer Shannon Bileski of Signature Exposures in March 2013       and is used with her kind permission.

Humans have probably been looking for signs of life from the stars since we first looked up. The first claim for life in meteorites was for a meteorite that fell in 1682. The most famous claim is based on an examination of a carbonaceous chondrite meteorite that fell in Orgueil, France in 1864. There a no less than 440 papers on that meteorite alone. All told there have been eight rounds of claims of discovery of life in meteorites including the Orgueil one.

There are two approaches to deciding if life is in a meteorite: morphology and chemistry. When considering the possibility of morphological evidence in meteorites the friability, salinity, and porosity of the meteorite samples has to be considered. One problem is that primitive life consists of single cells, sometimes strung in filaments or in clusters. It is hard to tell a “real” fossil of such life from an inorganic growth or precipitate.

Some chemicals have been presumed to be unique to life. However, the development of organic chemistry soon showed it was possible to create organic compounds (including those found in meteorites) in the laboratory. Now we know that many of them abound in interstellar space. Therefore, organic compounds alone are no longer considered sufficient proof of life.

Another problem is that life is everywhere on Earth. Examining a meteorite found on the Earth means that if you do find life, it is far more likely to be contamination from life we already have here than any sort of novel panspermia sample. It has been argued that if a possible microfossil were found on the interior of a meteorite it could not be the result of contamination. However, a huge taxonomic diversity of prokaryotes colonized the Tatahouine meteorite in less than 70 years making such claims dubious. And when a meteorite lands on earth it comes from a vacuum and so will suck in air into its interior upon entry and cooling. Carbonaceous chondrites, the most likely kind of meteorite to contain life from space, are hygroscopic, i.e., drawing into them any moisture in the vicinity. And so it is possible for some eager microorganism to be drawn into or crawl into the interior of the meteorite. It is far more reasonable to assume that motile microorganisms, perhaps from spores in the air falling on the surface, invaded museum specimens at times of high humidity and subsequently fossilized. We give an example in Embryogenesis Explained of hot springs bacteria that get fossilized in 2 days. Earth rocks often contain live bacteria deep inside. Similarly, organic chemicals can seep into rocks and meteorites. It can even be assumed that anything that got close to Earth might get contaminated since Earth life, like diatoms, have been claimed to be found floating about on the outer reaches of our planet’s atmosphere. Since the 1960s, if a meteorite fell through our atmosphere, then any life found on or in it can be safely presumed to be Earth life contamination.

And then there are hoaxes. Dick was involved as an undergraduate in a 100-year reexamination of the Orgueil meteorite. Ed Anders and he uncovered a hoax in which some unknown person placed a piece of coal and the dried bud of a local plant into a sample of the meteorite. Dick showed, by analyzing it for the amino acid hydroxyproline, that the mass had been put back together with animal glue. The hoaxster placed the specimen on the local museum shelf, where it sat 100 years. They probably didn’t live to see their crafty work found, but it did make scientists extremely wary a century later.

We therefore agree with the decision of NASA to keep Rover far away from the place where NASA seems they have found water. No matter how carefully NASA cleaned up Rover before sending it off, there is always the possibility one of our more persistent and clever forms of Earth life hopped a ride and would immediately start colonizing the Red planet’s water. That would not only be bad science, it might also be a violation of the Prime Directive.

You can read the full article on this topic with references and additional information at: Recurrent Dreams of Life in Meteorites by Richard Gordon and Jesse C. McNichol (2012), a chapter in Genesis – In The Beginning Volume 22 of the series Cellular Origin, Life in Extreme Habitats and Astrobiology. Or ask Dick for a reprint: DickGordonCan@gmail.com

If you would like a hard copy of the gorgeous picture of the meteorite against the aurora, you can purchase it by contacting Signature Exposures.