Microscopy

 I took up a new hobby. I bought microscopes from ShopGoodwill.com and some prepared slides from Amazon. I was happy to be able to take some pictures with my cellphone using my Celestron NexYZ adapter. The first foray was easier and more rewarding than my attempts at astrophotography. In both fields, my primary interest is in verifying for myself what I read in books. I also benefit from the discovery or revelation of facts not perceived in daily life.

Based on my experience in astronomy, I sought to avoid early mistakes by finding a discussion board that I could rely on and participate in. The astronomy board Cloudy Nights has a forum for microscopy, "Cloudy Days." There, I found a recommendation for Oliver Kim's Microbe Hunter website (here), YouTube videos, and discussion board (forum). 

Kim has an MSc in microbiology and teaches high school biology. I found his narratives interesting, informative, and objective. Some others have complained that he is salesman for his favorite brands. I have not found that so. He does insist that quality and price are on curves and that the average person can find a good-enough microscope for a few hundred dollars or less. I found these two for under $75 each with shipping and handling. (I searched for 1-cent shipping and Buy Now versus bidding.) I still hold to my longterm goal of buying a Zeiss university classroom instrument for about $1000 when the time comes for me to upgrade. That will depend on my learning curve.

I also bought books, of course. I have an instructor's edition for a survey class in microbiology, a couple of lab manuals, and two handbooks on microscopes. 

Onion rind

Picking up where I left off 60 years ago, I found vegetables a lot easier to work with. The sets of prepared slides were not expensive and for that reason were also not carefully prepared. I am not big on bugs, but I could do (and have done) a better job. The specimens are mashed and tangled. So, the next step will be to buy slides, slips, and mounting fluid. (I confess to being a little shakier now than I was at 12 years of age and I think that I can focus past the intentional tremor.) 

Ultimately, I will be exploring histology for anatomy and physiology. As attractive as plants are, they do not tell me much about myself. 

I do appreciate the unity of life. One of the prepared slides is "Lily Ovary." Miss Lily's ovary speaks to the astounding multifarious expressions in complicated matter since the invention of sexual dimorphism. A science fiction story could consider a watery world in which all of the single cells share communication and thereby constitute a self-aware intelligence. The extent to which the cloned daughters would vary could be a plot element if not the story line. How is difference perceived--and is it accepted--when just about everyone is almost exactly alike? 

BAMBOO

Be that as it may, in the mean time, my new toys need cleaning. I have Zeiss fluid and other tools. However, I hesitate to disassemble the oculars and objectives. When I started in astronomy, I had a Celestron 130-mm (4.25-inch) Newtonian reflector. It came with a 20-mm and a 10-mm oculars. A little later, I bought the Celestron Lens-and-Filter Kit that I saw several others with at my first star party. I could not get a filter to screw into the bottom of the 20-mm, so I unscrewed the top--and was rewarded with a handful of small glass lenses. Fortunately, it is a known problem and Celestron has a page on their website on how to put it back together. But it was never the same. I got the faces right, but the axial rotation was off. They are supposed to be circles, of course, but at that level, they are not perfect circles and a little bit makes a difference. So, I have to decide whether and to what extend I want to pay for the lessons being presented here. 

That also impacts another toy, truly a toy, an Educsope. It cost less than $15 from Goodwill and came with a kit of tools and slides. But the stage will not stay up. From an old Tasco microscope set that a neighbor gave me some years ago, I already know this to be a problem with cheap microscopes that kids use. I can take it apart easily. Whether I can clean and tighten the rack and pinion is another question entirely. I actually did that with the Tasco. It works better now. The Eduscope is all plastic and does not hold much promise.

Previously on Necessary Facts

Epigenetics

Bob Swanson and Genentech

Biohackers

Biobash: Chamber Replicates Success

THE UNWISE SAPIENS OF YUVAL NOAH HARARI

Harper, 2014, 443 pages

I was on a long waiting list despite the many copies at the Austin Public Library. When I was done, I could not renew the checkout because other people were waiting. Gratefully, I did not pay for the book. Despite (or perhaps indicative of) its runway popularity, it is shallow and facile, drawn from second-hand sources and not well integrated in its presentations.

Harari failed to correctly explain the origin of writing, the origin of counting, the origin of money, and the origin of coinage.  They are all tightly bound. In every case, his supporting citations point to other popularizers, rather than validated peer-reviewed academic publications. So, he gets a lot of the details wrong. From those he builds his attractive and erroneous narrative. Finally, like me and other bloggers, he is a synthesizer, collecting and republishing ideas that he likes without actually challenging any of those claims for their want of proof. 

One such assertion is that the agricultural revolution was not worth the price. Domestication of wheat brought longer working hours and slavery. It actually brought malnutrition, and set the stage for periodic starvation never known to hunter-gatherers. I reviewed Against the Grain: How Agriculture Has Hijacked Civilization by Richard Manning (North Point Press,  2004 ISBN: 0865476225) for the Objectivist discussion site, Rebirth of Reason, here  in 2006 and later in 2010 here.  I wrote: "Among Manning's many points is that the "surplus" usually went to a handful of unproductive people, priests and nobles."  

Moreover, as I pointed out in my original review, the nobles themselves hunted -- which they denied to those who were bound to the cultivating fields.  Nobles did not suffer a steady diet of grain.  When times were good, they ate well, a variety -- another point Jacobs made about city life -- with lots of fresh meat." It is an interesting fact to consider. But Harari just stops there. He does not see strawberries in January. Cutting off our food supply is integral to his thesis, which includes disdain for liberal humanism. Harari advocates for the postmodern anti-industrial revolution. 

PREVIOUSLY ON NECESSARY FACTS

Not Conned by Seghal’s “Coined” 

Debt: the Seed of Civilization 

Accounting for Civilization 

Art as Ordered Narrative

Money as Speech 

Of Watches and Beaches and Atheists

I patronize the local atheist boutique to buy bumper stickers, pens, pencils, lapel pins, and badges. This one sat on my desk for a couple of weeks. Then, I had a reply. 

Watches only prove that beaches were not designed to be watches. And in fact, as variable as the tides seem to be to us land lubbers, for people who depend on the sea, the tides are more meaningful than an arbitrary clock, no matter how precise and accurate. You go out when the tide is right, not when the clock strikes an hour. 

Do watches prove that trees were not designed? Anything can be used to mark time. If we see a child after some months, we might say, "How you have grown!" Do watches prove that children were not designed?  In the near future, children might very well be more carefully designed than the best watch.

Our clocks are arbitrary. And we are always re-setting them. Timekeeping based on the rotation of the Earth is corrected against atomic clocks based on the vibration of Cesium-133 when excited by a specific wavelength of microwave radiation.  

Cesium Atomic Clock

http://tycho.usno.navy.mil/cesium.html

Leap Second

https://en.wikipedia.org/wiki/Leap_second

https://www.sciencedaily.com/releases/2016/12/161228213356.htm

https://www.nasa.gov/feature/goddard/2016/space-timekeeping-nasas-sdo-adds-leap-second-to-master-clock

The fallacy goes to the root of arguments for atheism.  You cannot prove a negative assertion. When you try, you run into non-sequiturs.

When something is true, it is provable many ways. (Over 300 proofs are known for the Pythagorean Theorem.) True statements are supported by other truths, and in turn lead to still other truths.  Truths do not come from falsehoods or lead to fallacies. That is the nature of truth.  Furthermore, when a statement is false, it fails in several contexts, not just one. So, attempting to prove that beaches were not created leads to nonsense statements.

The burden of proof for the creation of the universe, the Earth, or us is with anyone who makes the assertion.  Atheism holds only that, so far, no proof has passed the tests of objectivity, i.e., of empirical evidence explained by a logically consistent theory.

It may remain that the universe, the Earth, and we humans are anomalies: objects or events that are observably real (empirically real), but which lack a logically consistent, rational  explanation.  Quasars and tachyons are in that class.  We discover more facts about them as we observe them more often, but we have no consistent theory to explain them.

Also, while it is true that the universe had no creator, the Earth might have.  After all, we build houses, and cities. So, those are two separate questions. The creation of humans might be a third event, not directly related to the origin of the Earth, which was just here with its evolved animals until “someone” tweaked the chromosomes of apes, merging two and making us. 

 

https://www.mun.ca/biology/scarr/Human_Ape_chromosomes.htm

Be all that as it may – and I have no answers, even for myself – the fact remains that time and tide wait for no man because TIME and TIDE derive from the same root word. In the theoretical construct language “Indo-European” (spoken by our Caucasian ancestors about 6000 years ago),  dã-(i) meant “to part” or “divide.”  In modern German, the word for TIME is ZEIT, which is obviously close to TIDE. And in modern English, we still have archaic words such as Yuletide and eventide. 

PREVIOUSLY ON NECESSARY FACTS

Imaginary Numbers are Real - but Pegasus is not
Atheists in Foxholes
god is not great
Kicking Nuns for Fun and Profit

The Unremarkable Origin of Species

The most surprising facts are (1) Darwin’s Origin of Species is still a lightning rod for religious fundamentalists and (2) in various locales those fanatics actually gain control of publicly-funded education. 

Unlike Galileo’s Two New Sciences and William Gilbert’s De Magnete (both reviewed on this blog), Darwin’s work stood on a generation of similar explorations and discoveries.  Darwin was only in the right place and time to earn 150 years of rebuke.  Moreover, The Origin of Species by Natural Selection, or: the Preservation of Favored Races in the Struggle for Life took the uniformitarian side against catastrophism in what we now regard as a false dichotomy.  Nonetheless, his theory is surprisingly robust despite the fact that he had no way to know the actual mechanisms of inheritance. 

World's Largest Dinosaur.
Cleveland Museum of Natural History here.

Darwin acknowledged George Leclerc Comte de Buffon, George Cuvier, Jean-Baptiste Lamarck, Geoffrey Saint-Hillaire, and ten others, before concluding with Herbert Spencer, Alfred Russell Wallace, and (“Darwin’s bulldog”) Thomas Henry Huxley.  All of them asserted with various evidences and arguments that the species we know today did not always exist.  That roster began with Aristotle who pointed out that the forms of our teeth—incisors in front, molars in back—developed by adaptation.

Darwin apparently did not know the work of William Smith who mapped the geological strata of England.  Smith sought to predict the presence of coal deposits, in part, by noting that simpler forms of prehistoric animals never appear above more complex forms of the same type.  (On NecessaryFacts here.) 

In 649 pages (Modern Library paperback, 1998), Darwin laboriously details the small facts of variation, and the consequences of them for survival and reproduction.  Accepting Charles Lyell’s estimate that the Earth is more than 300 million years old, Darwin sought to demonstrate that over spans of geological time, many small changes accumulate into large and permanent differences among both plants and animals. It seems hard to argue against that.

ALSO ON NECESSARY FACTS

Great Scientific Experiments

Teaching Science with Science Fiction

Science in the Middle Ages

Misconduct in Scientific Research

Fossils and Behaviors

Sub-adult American alligator 

in Pearl River Delta, Mississippi. 

Photo by Kristine Gingras 

from the journal artlcle.

Crocodiles can climb trees.  "If crocodiles were extinct and you only knew them from fossils, you wouldn't be able to guess they climb trees because they don't have any physical adaptations," University of Tennessee researcher Vladimir Dinets told Reuters. "Assumptions based on fossils," he said, "can be far less correct than people think."
The article "Climbing behaviour in extant crocodilians" by Vladimir Dinets, Adam Britton, and Matthew Shirley appeared in Herpetology Notes (Vol 7:3-7; 2013), an online journal of Societas Europaea Herpetologica. 

"Extant crocodilians are generally considered to be predominantly or semi-aquatic. And, although the role of terrestrial activity in their natural history is increasingly recognized (see, for example, an overview of terrestrial hunting in crocodilians in Dinets, 2011), they are virtually never thought of as animals capable of climbing. Their non-arboreality is often taken for granted in various analyses of tetrapod limb evolution and behaviour of extinct Archosauria (see Birn, Jeffery et al., 2012, for a discussion of the subject and a bibliography)."

Reuters news story here.  

Original journal article here.

The article and the news story both state that this is not a discovery.  Crocodiles have been reported in trees by locals as well as by scientists in the field. The authors gleaned much of their data by convenience, surfing the Web for pictures. The climbers are overwhelmingly juveniles because they have high ratios of strength to body weight: strong claws and limbs; not much to lift. Fearsome as they appear and can be - death by crocodile is a reality for rural women in Africa - like most animals, they avoid conflict, dropping into the water to escape humans in boats who come within ten feet (three meters) or so.  The thesis of the article is that we admit some ignorance before speculating on the behaviors of dinosaurs.

  

Note that the primary investigator, Vladimir Dinets, has a broad range of interests (Wikipedia here; his own blog here).  He completed his doctorate at the University of Miami in 2011 studying crocodile behaviors, including coordinated hunting, and the use of tools. His publication in an online journal (with an essentially non-academic co-worker) also marks a kind of evolution.  The traditional peer review process of print journals has always been a trade-off between the screening out of crackpots and the exclusion of originality. Also, the long lead times were acceptable in the steam age.  Cyberspace is a new environment. We can share more, faster.  Of course, survival of the fittest in science still depends on empirical validation and falsifiable testing of rationally consistent claims. More subtly, we may well be living in a Renaissance time of broad personal achievements.  Scientists take cameo roles on television shows; and Hollywood actors have degrees in science. The co-authors of the article cited here footnote their marketing interests beyond the university. 

ALSO ON NECESSARY FACTS

Epigenetics and Evolution

The Origin of What?

Epigenetics

Biohackers

Epigenetics and Evolution

The mechanism of evolution has not been discovered.  No consistent theory exists. Random mutations adapting to changing environments was the first suggestion.  When subatomic radiation was discovered, that became a proposal.  Now, epigenetics may indicate another, more powerful, model.  

Darwinian evolution does not explain the lack of intermediate forms. Scientists have bombarded fruit flies and mice with every radiation known and produced no new species.

Jason Head, assistant professor of Earth and Atmospheric Sciences,
at the University of Nebraska Lincoln
holds a fossil and fossil cast from the jawbone of
Barbaturex morrisoni, a large ((2 meters; 30 kgs) lizard
that coexisted with mammals in southeast Asia
40 million years ago. (Press release here.)

Epigenetics is the study of how environmental factors affect the expressions of genes.  We know that we share something like 90% of our DNA with yeasts - and yet we are very different from them. We know that strawberries have not a double helix, but a quadruple helix - yet they are not "superior" to us double helix lifeforms.  
  

A series of prehistoric creature illustrations demonstrates
the evolution of mammals through the ages.
More fact than fiction, these wild characters followed transitional Jurassic period animals
that sported mammalian skull traits and reptilian teeth.
A more familiar design, humans, mark the present.
- National Geographic, "The Rise of Mammals"

Random mutations adapting to changing environments is a (partial) explanation. Radiation seems to create such mutations, also. Epigenetics offers another aspect of understanding. It seems that the mechanisms of process are inherent in all life, but the millions of components are active or inactive according to causes we may now be coming to understand -- given that in 50 or 100 years some other engine will be discovered. 

Also on Necessary Facts
Epigenetics 
The Origin of What?
Biohackers 
Bob Swanson and Genentech 

The Origin of ... (What?)

Fertile hybrids demonstrate the limitations of strict Darwinian taxonomy.  According to the easy definitions, a species is a genetically distinct group of plants or animals.  In fact, fertile hybrids are common. And they seem fundamental to evolution.

Dozens of Hybrid Sharks Found Off Australia
January 2nd, 2012 - 10:59 AM ET
The world's first hybrid sharks have been discovered in substantial numbers off the coast of Australia, and scientists say it may be an indication the creatures are adapting to climate change.
Australian researchers say they've found 57 animals that are a cross between the Australian blacktip shark and the common blacktip shark, two closely related but genetically distinct species.  (More here.)

Since 1874, at Halle, a series of successful matings of polar bears and brown bears were made. Some of the hybrid offspring were exhibited by the London Zoological Society. The Halle hybrid bears proved to be fertile, both with one of the parent species and with one another. Polar bear/Brown bear hybrids are white at birth but later turn blue-brown or yellow-white.   DNA studies indicate that some brown bears are more closely related to polar bears than they are to other brown bears. All the Ursinae species (i.e., all bears except the giant panda and the spectacled bear) appear able to crossbreed. (Wikipedia on Ursid hybrids here.)

Granting that hybrids are possible between species of the same genus, such as donkeys and horses, it is too easy to expect them all to be "mules", i.e., sterile.  Macroevolution.net is a blog by biologist Eugene M. McCarthy, PhD.  His site includes biographies of biologists, helpful glossaries of Greek and Latin for science, and much more.  He also provides an authoritative explanation of the prevalence of fertile animal hybrids.  Read here.

ALSO ON NECESSARY FACTS
Biopunk: DIY Scientists Hack the Software of Life
Epigenetics
Disruptive Diagnostics and the Business of Science
Austin Biobash November 2012
Bob Swanson and Genentech
Mayim Bialik