[WORK IN PROGRESS]
Boschma's work revising the taxonomy of the Milleporids is a monument to his painstaking study of the morphological species specific characters.
Friday, September 4, 2026
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:
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| 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.
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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. |
Wednesday, July 22, 2026
Protein diagrams
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 processes according to 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.
Many of my students did not come pre-supplied with the knowledge of existence of atoms as the building blocks of molecules; now had they heard the news that all things are made of atoms and molecules. New foundations must be provided: I told the story of how my mother told me one day 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. This and Natural Selection formed the foundation of everything. Do I think it thesel concepts held an equal weight in the lives of my student? The jury is still out. I'll be happy to learn that they did, even for a few. I know of a very small number. (What then of everyone else? I can and do hope they picked up the important threads, even some of them, along this journey.)
We (I, I mean) then started constructing a model of a living organism as---not a mechanism, but---understandable as a system, at some level, of macromolecules. 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 truly is the core idea of life; it serves as an important way of understanding of living processes, of functioning organisms. Proteins are the prime actors; important structural components; and the most important actuating principles 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.
At 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.
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8,714 Proteins. A Poster in the Advanced Light Source of LBNL.
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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, such as this one.
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| Triose P isomerase monomer |
Here is another one: A Prealbumin Dimer:
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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. 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.
Tuesday, May 19, 2026
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:
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