The Naturalists: Hilbrandt Boschma and Niko Tinbergen

 

 

Hilbrandt Boschma's work revising the taxonomy of the Milleporids is a monument to his painstaking study of the morphological species specific characters.  

 

The link above directs to a wikipedia page that presents a general biographical picture of his career.   As one may see from a casual reading of this Wikipedia entry, Boschma's career went far beyond the painstaking work of revision of the taxonomy of Millepora spp.   

 

Lu Eldredge, a professor of mine at the University of Guam,  told of Boschma hiding in between shelves at the Rijksmuseum at Leiden, from the Nazi's during the occupation of  The Netherlands.  Due to my interest in the Holocaust---born during my formative years, as I read Mein Kampf and the stories of the exodus from Germany to Israel---this story of Boschma's trials and tribulations has remained with.  I recently Googled for more information about his life, and ultimately stumbled upon the accounts in Wikipedia.

 His role at the Rijksmuseum  was far more crucial than his zoological work might suggest.  He was, at some point during the occupation, director of the museum.  Important in my mind was to learn he had saved the scientific instruments in the institution, concealing them---apparently in a manner similar to the way, as I had I heard from Professor Eldredge, he hid his person from the Nazis.  

 I wonder how, as director of the Museum he could have kept himself concealed during those years.   

A PDF of his Eulogy is located here, in Dutch:

 https://dwc.knaw.nl/DL/levensberichten/PE00004104.pdf

  

I ran this pdf through Google Translate, by way of a convoluted sequence of processes: running an OCR on the dutch pdf via gscan2pdf, saving the German text file, opening this on Google Docs,  and finally using Google Translate.  The next step would be to use LaTeX to clean up the translation, format and typset; however, I skipped it in this instance.    It would probably be faster and easier on Apple Infrastructure, but freedom from the numerous encumbrances of that approach is worth the learning curve and effort, using the wonderful tools of GNU/Linux.  

The English machine translated version is long.  It is appended temporarily at the end of this post.  (Perhaps I will link to a pdf at some point, depending on space available, should I finally clean it up).  

 

Niko Tinbergen

 

An excerpt from a paper about Tinbergen is of great interest; it provides context, as well as insight into Niko Tinbergen, his work, and his trials and tribulations.  Freedom fighting scientists: perhaps a lesson for our time.

 

World War II. In May 1940 the Netherlands were overrun by the German forces. In 1941 most of the teaching staff of Leiden University resigned in protest against the treatment of their Jewish colleagues, and in 1942 many of them, including Tinbergen as well as many other of the most prominent figures in Dutch society (professors, cabinet ministers), were taken hostage by the Germans. They were to be the subject for reprisals after actions by the Dutch underground; in the end, some twenty of them were shot. The hostages were interned in a former training college for priests in Sint-Michielsgestel in the south of Holland.

Tinbergen was to spend two years in the hostage camp, in reasonable comfort but with the threat hanging over him. The inmates organized lectures, plays, and concerts, and there was considerable intellectual activity as well as political discussion. Tinbergen was able to write. One product of that time was a text in Dutch, Inleiding tot de diersociologre (Introduction to Animal sociology), published as a 184-page paperback after the war, in 1946. It was visually appealing, with many of his drawings, but it was never much of a success, having been written in a rather schoolmasterly style. There was a kaleidoscope of social behavior, with several arguments about behavior organization as in his previous publications. As an interesting kind of throwback, in places Tinbergen insisted that animals behave for the good of the species. Given the context in which it was written, it was not surprising that the author was not in top form. Another result of his hostage camp efforts was a series of handwritten and richly illustrated booklets about animals, for his children at home. Two of these were later published in English: Kleew (1947), about gulls, and The Tale of John Stickle(1954), about the behavior of sticklebacks.

After Tinbergen was finally released from the hostage camp in September 1944, he would spend seven more months under the German occupation, living with his family close to his field study sites near Hulshorst. Life in Leiden was too difficult in that period, known as the “hunger winter,” with serious shortages. 

 

The Naturalists: Sidney Hickson, a bold (and often wrong) authority

 [Here will be an account of some of Hickson's errors of interpretation.  He was an authority, often cited, often wrong.  A WORK IN :PROGRESS]

 

The Fantastical Life Cycle of Millepora was wrong 

Hickson was wrong about the nature of the life cycle of Millepora.  He presented a figure of insipient stages of male and female gametes, with absolute certainty...and absolute falsity.  Later, he admitted to the error.

 

 

The Ultimate Lumper

 Hickson argued that all species of genus Millepora were ecomorphs, and synonymized every one with Millepora alcicornis, a caribbean species.  Later, during WWII, Hulbrandt Boschma hid from the Nazis in Holland, in the archives of the Reichsmuseum in Leiden, while he painstakingly split this mass into substantially the same complex of species we know today.

 

 

The Naturalists: John Ellis, an eclectic naturalist and microscopist

[I starting writing this post several years ago in a separate blog.  Ellis is a favorite of the naturalists.  This deserves to be re-written.  For now, just some editing changes.] 

John Ellis was a student of Zoophytes, literally "animal plants."  Why did he consider Halimeda spp., calcifying green algae to be animals? This deserves some investigation. John Ellis deserves to be taken seriously on several accounts.  He is memorialized in the  "Ellis-type microscope" bearing his name.  This kind of microscope---also known as a "simple microscope"---is considered a botanical microscope, as well as an aquatic microscope.   The aquatic microscope figures prominently in early marine (and freshwater) zoological studies.  The glass stage can be either a concave shallow dish similar to a watch glass, or a flat glass plate, appropriate to whatever specimen is under observation.  Minute hydroids or bryozoans, for example, were investigated in this manner.   The clip can hold a specimen apart from the stage.  

 

These microscopes were important to many early zoologists. . Ellis was a Zoophytologist.  We now understand that the hybrid nature of zoophytes derives from it's existence as a "holobiont," a single organism that is a fusion of two symbiotic species that live in a cooperative arrangement, each benefiting from the other.  Another example, perhaps more familiar to some, is the lichen.  This organism exists as an obligatory fusion of an alga and a fungus; neither can live in isolation from the other.   

 

Zoophytes behaved like plants, in that they were attached and immovable, in many cases.   Corals, one of the most important groups of these, live only in shallow water, where sunlight can support photosynthesis.  Yet they exhibit intentional movement, like the animals they are.  Such organisms we now call  "holobionts,"  partnerships living a mutually beneficial relationship.  Often, such as in the case of corals, this partnership is "obligate: neither partner can carry out all functions to support life.   On coral reefs such relationships are common.   

 Zooxanthellae are dinoflagellates that live within corals, sea anemones, and upside-down jellyfishes.  These dinoflagellates employ subsidiary pigments, Xanthophylls in partnership with Chlorophyll.   

 Back to Ellis.  As I have recently learned, it was Ellis who originally described and named Halimeda spp. as Corallina.  Corallina opuntia, one of those species, is now called Halimeda opuntia, a common algae around coral reefs in Micronesia.    Wikimedia exhibits a copy of a plate from Ellis and Solander's publication in which Corallina spp. are described:

 

From Ellis and Solander ...

The Ellis-Type Aquatic Microscope

At https://microscope-antiques.com/ellis.html this scope is dated c.1765,  identified as a "Trembley-Ellis Type Aquatic Microscope."  Trembley is remembered for his extensive studies of Hydra.  It may well be that this aquatic microscope was designed by him, at least in part, for study of  Hydra.  One species of hydra is a holobiont, living in partnership with a single celled green algae.   

 

Such microscopes as these are "simple microscopes."   A concave glass---similar to a watchglass, serves as a stage, when viewing minute aquatic organisms.  

Image from https://microscope-antiques.com/ellis.html

 

Unlike our "compound microscopes," which have two or more lenses, simple microscopes have a single lens organized on a mechanism enabling the focusing of moving organisms on the stage, or in the watchglass.  The lens can be focused vertically, and swung from side to side to follow movement or search for interesting features.   

Protein diagrams

[Work in progress] 

 

 I am an aficionado of proteins.  I am made of proteins.  An undergraduate course in Biochemistry opened my eyes to the simplicity and wonder of the grand "central dogma" of biology: proteins do all the work; DNA is the blueprints for proteins.   Four classes of "macro molecules" (giant molecules, made of smaller modules that are, in most cases, molecules themselves) are the building materials (so to speak) from which living organisms are constructed.  The pattern is the same for every kingdom (or domain) of life: plants, bacteria, protozoa, animals, fungi---all are systems of these four kinds of macromolecules operating through similar or identical principles.  Early on, it occurred to me at the time that macromolecules are pretty easy to understand; I wonder whether my students have found this to be the case.  Did my approach succeed?   Did it fail miserably?    

 

Macromolecules of three of the four kinds are chain polymers, snapped together like "pop-beads" or perhaps one-dimensional legos.  Wonder of wonders!   Proteins and Nucleic Acids (DNA and RNA) are never branched; some carbohydrates are branched, or form interconnected chains and sheets.  The  entirety of living  existence and functions is based upon the motif of linear sequences.  

 Atoms 

Many of my students did not come pre-supplied with the knowledge of   existence of atoms as the building blocks of molecules.  This foundational perspective must be explained.  I told the story of how, one day, my mother told me to look around me: everything my eyes could see, she told me, was made of a small number of kinds of atoms.  This made a big impression on me.  I now had this background knowledge; but most of my students had not.  

The organization of a living thing begins with atoms.  We can think of them as particles.  (Greek philosophers proposed that all matter is made of particles; they used the word "atom" without understanding what they are.  

 Molecules

Molecules are bunches of atoms organized in a particular way.  

 

The Water Molecule 

Water is H2O.  Two hydrogen and one oxygen atoms in a precise structure. This structure may be represented in various ways, or "models" including the three represented here:

Labelled Diagram

 

Ball and Stick Model

 

 

 

 

 

Space Filling Model

 

 

 

 

 

 

 

 

Macromolecules 

Macromolecules are groups of molecules.  For Proteins, Carbohydrates, and Nucleic Acids, we may refer to Subunits, the molecules that connect together to form supermolecules.  

 Think of a string of beads without a string.  Biological macromolecules are organized in the same way, especially Proteins and Nucleic Acids (DNA and RNA).  Carbohydrates are as well, but the strings can cross link.   Lipids, the remaining type of Macromolecule---fats, oils, and waxes---are not organized in this way.  I think it is remarkable that life itself demonstrates this kind of organization at the core.  

 Individual molecules, the subunits, can bond into chains.  Subunits of carbohydrates are sugars.  Strings of these sugars---mainly starches---are assembled without regard to order.  We will not concern here with carbohydrates.  Their main function is as energy sources, or for energy storage.  

In both Proteins and Nucleic Acids, particular subunits are assembled in a particular order.  Critically, the order of these subunits defines the functions.  

 Nucleic Acids primarily function as strings of coded messages.  The messages are blueprints for the order of subunits in proteins.  The blueprint for a protein is a gene.

The Subunits of proteins are Amino Acids. 

Proteins of humans and most other organisms are assembled from 20 different amino acids.  The order of these amino acids determines the function of the protein, for a particular reason: in almost every instance the function of a protein is determined by the shape into which the completed chain is folded.   A crude example is shown, from Wikipedia:

 

In this diagram, the filled black amino acids have hydrophobic natures---they run from water, because oil-like side chains of the amino acids flee from water.  On the right hand side, we see that this effect has helped organize the shape, into a clump.  This and other effects are responsible for the final shape of a protein, which ultimately determines the activity of the protein.     

We  begin to construct a conceptual model of a living organism as---not a mechanism, but understandable as a system, at some level---of macromolecules.  I am amazed that four general types of macromolecules make it all happen.  It had to start from the beginning,   I dare say that a few  of my students received these pieces of the puzzle enthusiastically.  

Proteins are central.  

 Life is, at some level, a system of Proteins interacting among themselves and Nucleic Acids (which carry the blueprint for their production), fueled by Carbohydrates, constrained within membranes made of Lipids (fats and oils, which also store energy and serve other functions.).  Life is, of course,  far more complicated than this; but this is the core idea.

Proteins are the prime actors.  Proteins DO everything, with few exceptions.  They are the most important structural components, and the most important actuators in all living things.   Every living organism (with a few interesting exception) is made of cells.  Proteins are the essential components of the functioning cell.  

 The following is a short list of some kinds of proteins in a living organism, from the simplest to the most complex.

• Enzymes: catalysts of chemical reactions.  Digestive enzymes like Amylase, which breaks starch---bundles of sugars that cells cannot use as fuel---apart into into sugars, which are small, and easily imported by the cell.  Other enzymes build proteins from Amino Acid (under direction by DNA).  Enzymes repair damaged components of cells; other enzymes break down proteins that are no longer useful.  Enzymes regulate chemistry in the cell.
• Action proteins: muscle, flagella, cilia all operate through the agency of proteins.  
• Transport: Motor proteins carry packets of other molecules (many of them proteins) around in the cell.  Hemoglobin carries Oxygen. 
• Antibodies function to defend cells from invasion.
• Structural protein: hair, keratin, nails, claws, barbs and arrowheads, protective spines, the "cytoskeleton" that provides structural support to cells.  .
• Venoms and toxins are, in many cases, proteins.
• Proteins in cell membranes regulate the movement of materials in and out of the cell.  Some of these are critical to the operation of the nervous system.
• Signalling proteins: 
• Hormones (insulin, for example) secreted from cells in one organ of an organism act as messages to other organs. 
• Neurotransmitters are proteins that, when secreted by one neuron, trigger an impulse in the next neuron.
•  Pheromones are similar to hormones; however, these are chemical messages that, when secreted by one organism, are understand by other indivisuals.  For example,  cats mark territories (and their humans) with scents.  Female moths secrete sex pheromones, mating signals, that are recognized by males even miles away; female dogs famously signal they are in "heat" through scents that draw males in a neigborhood.  Alarm pheromones are secreted by organisms to warn of danger.  Ants mark their trails with trail pheromones.    

 

Protein structure determines protein function 

A protein  is a chain of one of about 20 Amino Acids in a very specific order determined by the DNA that codes for it.  Each of these Amino Acid has unique properties.  Some are charged, either + or -.  Some love water (are hydrophilic),  and others abhor water (are hydrophobic).  These and other properties of Amino Acids cause the chain to fold upon itself in certain ways.  Imagine a giant spaghetti monster made up of one extremely long strand of spaghetti, a chain of Amino Acids with different properties that cause certain links in this chain to attract or repel one another, or fold away from the water inside the cell, or to embrace it.  In the end, the strand of spaghetti folds into a precisely determined shape, it's structure.  The shape of this blob of spaghetti determines it's function.  Structure determines  function.   Imagine, perhaps, this strand of spaghetti has tiny magnets at precise locations along its length.  Some magnets are negative, and others positive.  When the spaghetti folds into a blog, the magnets help to direct specific parts of the strand to pair, or repel one another.  Some parts of the spaghetti may have tiny bits of fat precisely located along the strand, that cause the spaghetti to fold (in a water medium, like the cell) inward, away from water.  These are other forces determine the shape of a protein.   If the position of one of the magnets is changed by a tiny amount, this can alter the structure---the shape---of the resulting blob.  Such a protein would fail to function efficiently.

 Remarkably, this is exactly how it all works.  Thousands of blobs of spaghetti shaped each in it's own unique way, interact with one another.  A digestive enzyme may break starch---chains of sugars---by breaking these sugars apart.  The enzyme to break the starch chain has a pocket that precisely fits a starch molecule in a specific configuration, between two sugars, the sub-molecules of that starch chain.  The bond between these two sugars is now placed under stress and weakened, and caused to break.   If even one of the Amino Acids making up this chain were changed, say from positively charged to neutral, the shape would lose its integrity; the enzyme (amylase, in this instance) would not operate at peak efficiency., or perhaps fail to work at all.   

Each protein achieves its function through the precise ordering of its Amino Acid components, which determines the manner in which the chain folds into it's 3-dimensional structure.  DNA is a chain 4 sub-molecules, Nucleotides, in a specific order.  This order providing  the code for the Amino Acid sequence in a proteins is a gene.  

 

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Today I want to look at diagrams that have been devised to help us see and understand the structures of proteins.  Structure Diagrams, .   protein is a straight chain of amino acids. 

Proteins, after all, attain every aspect of their functions from their shapes.  Their shapes are written in a linear code.  

On a visit to Lawrence Berkeley National Laboratory (LBNL) I observed a poster wrapped around a column,  touting that the shapes of over 8,000 proteins had been characterized at that facility.  

 

8,714 Proteins.  A Poster in the Advanced Light Source of LBNL.

 

 

 

Close up showing protein structure diagrams.  

The double helices are proteins!

Today I decided to dive into the  dark waters of these diagrams, that I have never understood.    I discovered something wonderful: A Wikipedia guide to proteins structure diagrams!  Put a pin in that.  I also stumbled upon an article about the LBNL Advanced Light Source, written in April 2025:

 Today, the nine structural biology beamlines at the ALS passed a major milestone of collectively depositing over 10,000 protein structures into the Protein Data Bank (PDB), a worldwide, open-access repository of protein structures. 

 

WOW!

Here, then, is a link to the Wikipedia Page about Ribbon Diagrams.

On this page I learned about early ribbon diagrams, hand drawn by Jane Richardson, who drew the first such diagrams by hand in 1980.   Two reproductions of her work:   

Triose P isomerase monomer

 

 

 

A Prealbumin Dimer:

As marked, a Prealbumin dimer draw by Jane Richardson.

 

 

 

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The following is different kind of model, a space filling model: an animation of Salivary Amylase breaking the bond between sugars in a starch chain.  Shown is  it's active pocket.  Starch nestles into the pocket, is broken apart by the enzyme, and is spit out in two parts.  Click in the lower right hand corner to enlarge it.  It can then be rotated using a mouse.  This is a different form of model, a space filling model.  Note the attribution.  My profound gratitude for the enormous amount of work that went into this.

 

`

Starch hydrolysis by amylase by svt4ever on Sketchfab

 

Salivary amylase is secreted by our salivary glands as seen as it detects the presence of starch, for example after eating a donut in the morning.  Right away the starch---which is a chain of sugars, albeit not a simple linear chain---begins breaking the starch down.  This process continues as the donut moves through our digestive system, by other forms of amylase.  

 

Proteins do it all. 

 

 

The Horror Story of the Ocean SUV EV: a story with a heart-warming outcome. Or, why we need more regulation.

 The company Fisker sold an SUV, the Ocean.  When they went bankrupt, they left the owners high and dry.   Owners, in can-do manner, formed a partnership and reverse engineered the code and the keyfobs, and wrote an open source replacement.  This is a great story.  It also is a terrible story.  What happened to the criminal who were let off the hook through bankruptcy.  

 The Stooges (not the three stooges) abhor regulation.  But would regulations protect the little guys from corporate outlaws like Fisker?  Here's a link to the story on Slashdot:

 

https://tech.slashdot.org/story/26/05/16/2318249/how-owners-of-evs-from-bankrupt-fisker-saved-their-cars-with-an-open-source-nonprofit 

 

 

Chaos is unfolding at warp speed: profit drives us over the cliff.

 Radical new technologies assaulting the senses.  Promises of profit and even better life styles.  

 As a reminder, technologies like self-driving cars, automation, and robots, as mere examples, were designed by humans.  We do not have a good track record.  

 Unforeseen consequences are inevitable.  The human brain evolved to solve problems.  These problems were solved incrementally.  An example of incremental "progress' is science; another one is technology.  The nuclear reactor was not designed in one step.  Accidents have resulted in improvements.  But the assertion by those in Japan who say that the lessons of Fukushima have been learned fails to recognize the inability of the human brain to see the whole picture.  Other errors will inevitably creep in.  

Waymo has had to reprogram self-driving  vehicles after a power outage in San Francisco, because humans who wrote the programs did not foresee this inevitability.

 AI?  AI was designed by humans.  Is it possible for us to design something more perfect than ourselves?  

  

Rolling out small scale solar in Africa. Encouraging.

 https://climatedrift.substack.com/p/why-solarpunk-is-already-happening