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

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

Before Darwin

John Leonard Riddell (1807-1865) completed a bachelor's degree at Rensellaer Academy and was later granted a master's for his field work in botany. He earned doctorates in medicine from the Ohio Reformed Medical College (1834) and from the Medical College of Ohio (1836). He taught chemistry at the University of Louisiana (1839-1865) while at the same time he served as chief melter at the New Orleans Mint (1839-1848). Though loyal to the Union, he was the postmaster at New Orleans during the Confederacy.

“Marine and lacustrine beds of marly earth, formed unknown ages ago, are often met with, which, under the microscope, prove to consist, sometimes, wholly of the sileceous shells of diatomaceous animalcules, frequently bearing a precise resemblance to the living forms which now abound in all our stagnant waters.  But in the more conspicuous fossil remains occurring in the geological strata of different ages, important modifications of structure are apparent; certain species of animals and plants prevailing for a while, becoming extinct, and being succeeded by others of a modified type.

“Without unduly dwelling upon this subject, it is worthy to be remarked, that at least one great lesson may be learned from the study of these organic remains; especially from contemplating those of the more highly organized types, namely: That as we, in the brief day of our actual observation, have seen organic individuals begin and end their respective lives; organic varieties, as of fruit, &c., appear, flourish, and decay; and even organic species to become extinct, as the Dodo and the Irish Elk; so may we infer, from the inspection of the remains of successive extinct races of beings, that all species or kinds, as such, have begun their career, will flourish for, we know not how long, and will ultimately decay and disappear; their places to be supplied by modified species and kinds.

"The observed average duration of individual beings varies, from a few hours, as is exemplified in the minute world of life revealed by the microscope,--as in the Vorticella ramose, different species of Mucor, &c.,--to a few centuries, as is inferred to be exemplified in whales, elephants and forest trees. What naturalists call varieties, possess a duration extending, more or less well marked, through, perhaps four or five generations of individuals. Species, so called, have a much longer life. Concerning the average duration of species, nothing very reliable is known; perhaps a thousand successive individual generations might retain to the last, the essential specific characteristics. To pursue this subject further, by attempting to conjecture the duration of organic races and natural orders, would be profitless, inasmuch as mere conjecture would alone provide  us foundation to build upon. Nevertheless, a careful study of the organic remains which geological researches have brought to light, give strong color of truth to the general conclusion, that all organic matter is in a state of continued change; the progress of which, though often too slow for our direct appreciation, is, in the limitless flight of long successive ages, not the less certain.”

J. L. Riddell, M.D., Professor of Chemistry, Introductory Lecture, Delivered on November 18^th, 1851, Before the Medical Class, University of Louisiana, New Orleans, “On Our Knowledge of Nature, the Natural Sciences, and certain Truths revealed by the Microscope.”

PREVIOUSLY ON NECESSARY FACTS

From Texas to the Moon with John Leonard Riddell

The Map that Changed the World

The Unremarkable Origin of Species

Epigenetics

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

Evolution vs. God

The premise is that Darwinian evolution is unproved and unprovable. It is accepted on faith, passed to students on the authority of professors.   Darwinian evolution has its problems, but this video does not address any of them.  It is a religious tract.

I got the video on the UT campus where they were being handed out.  Packaged as a bait and switch,  Evolution vs. God is a one-sided argument with an assortment of college students and professors. They are neatly boxed in by their own ignorance of Darwinian evolution and their personal failings as moral philosophers.  And, of course, we never see the ones who were not defeated.

Scientists have bombarded fruit flies with radiation for over 100 years, and never created a new species.  However the monsters turn out, they remain fruit flies, apparently still able to breed with others of their kind.  (Institute for Creation Research.)  On the other hand, the Archaeopteryx of the late Jurassic remains factually among several transitional animals between reptiles and birds. Gratefully, we can go swimming without meeting any of the creatures of the Devonian.  What survived is fearsome enough. 

William Smith’s geological map of England was possible only because he relied on the facts of evolution. Simpler forms of the same kind never appear in rock strata higher than more complex forms.  Smith died 20 years before Charles Darwin published The Origin of Species.  

None of that is discussed in this video.  Nor did anyone ask the interviewer what happened to the dinosaurs.  And why do we not find fossil dogs and cats in rocks 150 million years old?

In the nineteenth century, geologists debated catastrophism versus uniformitarianism, and volcanism versus neptunism.  In other words, did the world we know now come about by sudden changes or gradual processes?  Were the primary forces violent explosions or accreting deposits?  Today, we regard those as false dichotomies. 

The debate between Darwinian evolution and Lamarckism may be another false dichotomy.  Epigenetics is the relatively new study of how the environment affects heredity.  The evidence seems compelling – and it seems unlikely that the environment would have no affect, leaving all evolutionary processes at the level of quantum physics.  The easy answer is: “I don’t know.” 

In science we live with our limits.  Science is self-correcting as we work to discover more about the world around us, and put that knowledge into an order that allows predictions.  Religion has no such limits.  They all claim absolute knowledge and – obviously and tragically – disagree about what that absolute truth may be.  Several times near the end, the interviewer (Ray Comfort, the producer) quoted an English translation of the Bible.  Which translation is right?  What happens when they disagree?  And, for that matter, the Qu’ran mentions Jesus about 25 times calling him Messiah and the Son of God.  And the Qu’ran acknowledges Mary as the Virgin and Mother of God.  Yet, somehow Muslims and Christians seem not to get along well. 

Evolution vs. God offers a second thesis: Darwinian evolution allows (even encourages and advocates) immorality.  According to this video, survival of the fittest excuses the harms, crimes, and horrors we perpetrate.  People embrace evolution to avoid following God’s Commandments.  “Are you a good person?” the interviewer asks.  Of course the subjects think well of themselves.  “Have you ever told a lie?”  “Have you ever stolen anything?” "Have you ever had lust in  your heart?" “Have you ever taken God’s name in vain?”  If you stop and think about it, the interviewer is also a sinner, but having accepted Christ’s sacrifice, he does not need to worry about that – or even mention it.  That being as it may, it is not a divine revelation that a selected handful of university undergraduates and professors have no idea what morality is.

All in all, the presentation was no better or worse than Reason TV productions where university students who say they voted for President Obama are happy to sign a petition based on the 1931 Nazi Party election platform. 

ALSO ON NECESSARY FACTS

The Map that Changed the World

The Origin of What?

Epigenetics and Evolution

God is Not Great

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

THE MAP THAT CHANGED THE WORLD

William Smith (1769 – 1839) drew the first geological maps of England. He was born into a culture that was certain that the world had been created at 9:00 AM on Monday, October 23, 4004 BC.  He died twenty years before The Origin of Species was published.  Yet, he invented the predictive science of geology by marking time with fossils.  In the hour of his success, his work was stolen shamelessly by the gentlemen of the Geological Society.  He was forced into debtor’s prison and spent 20 years homeless, working as best he could in the rural countrysides and counties far from London.

William Smith’s father was a blacksmith and so his formal education was minimal. But he was determined to make something of himself; and by 1794, he worked as a surveyor for the construction of canals.  Eventually and soon he was recognized as the man who could solve practical problems in draining farm fields and predicting where profitable coal fields were to be found.  He recorded his daily work in a continuous multi-volume journal. 

Those notes let him create a series of huge colored maps showing the rocks and strata of England.  (He eventually included more of Britain.)  The keys to his work are two interlocking discoveries.  First, the rock strata are uniform.  Everywhere the strata are the same. Even if some (unknown) process or force (apparently) has displaced or tilted the layers, they can be logically reconstructed into a continuity.  Second, while sandstones and marls and limestones and all the others are to be found repetitively layer upon layer in succession they can be differentiated one from another by the fossils within them. No identical fossil forms ever appear in two different layers of the same kind of rock.  Simpler forms of the same animals are found lower down. 

We know now that cycles running millions of years repeatedly created land, drowned it, and then lifted it up, separating some plates as others collided.  Smith knew nothing of that; and neither did anyone else.  The dilettante gentlemen who robbed Smith of his creation debated whether all rocks precipitated from the ocean or whether all rocks were born of volcanoes.  Anything more complex was beyond their range.  Smith, however, was not at all a British Empiricist.  The men who stole his work were.  Their chief, George Bellas Greenough, denied the validity of theory.  But Smith’s work depended on it. The gentlemen of the Geologic Society attempted to produce their own map (from Smith’s work) without theory, and failed.  They had to admit to the correctness of Smith’s method, as well as to the value of his labors.

Simon Winchester’s biography of William Smith takes you into the fields of England.  He stops to explore and explain.  His college degree from St. Catherine’s Oxford is in geology.  However, after exploring Greenland, among other adventures, most of his career has been in journalism.  (His website here.) Winchester has several popular books to his credit. I read The Professor and the Madman about the Oxford English Dictionary over a decade ago.  His most recent book is The Men who United the States: America's Explorers, Inventors, Eccentrics and Mavericks, and the Creation of One Nation, Indivisible.

ALSO ON NECESSARY FACTS

Great Scientific Experiments

Claude M. Watson

Seeing in the Dark: Amateurs and Astronomy

Fantastic Voyages: Teaching Science with Science Fiction

Misconduct in Science and Research

Epigenetics

It is not surprising that we share 98.9% of our genome with chimpanzees.  It is challenging to consider that we have about the same number of genes as mice and fish; but we have far fewer genes than plants.  It is a high school science experiment to extract DNA from strawberries. Rather than a double helix, their DNA is wrapped in a quadruple helix. Obviously, the chromosomes and genes are only part of the picture.

“Every time we see two things which are genetically identical, but which aren't the same, we're seeing epigenetics in action.” – Nessa Carey.

Epigenetics is often presented as a new frontier in biology. In fact, the word originated in the 1940s; and the first book came out a decade later. Following Crick and Watson, science was focused on the chromosomes, and then on the genes.  The Human Genome Project was declared to be successful and the equivalent of Project Apollo, both for the complexity of the task and for its promise for our future.  Enter into your Web browser the phrase “scientists find gene for” and it would seem that we are living on the Moon.

• The Epigenetics of Birds by C. H. Waddington (Cambridge University Press, 1952), reviewed by: J. T. Marshall in Bios, Vol. 24, No. 1 (Mar., 1953), p. 59.
• Epigenetics. A Treatise on Theoretical Biology by Soren Lovtrup (Wiley, 1974), reviewed by Clifford Grobstein in The Quarterly Review of Biology, Vol. 50, No. 4 (Dec., 1975), p. 439.

Ghost in Your Genes: PBS Nova (BBC 2006; WGBH 2007, 2008) delivers graphic evidence that genetics is not heredity.  Identical twins raised in the same home diverge, one developing autism.  Twin sisters discover that one has cancer, but the other does not.  The town of Överkalix in northern Sweden provided a paradigmatic story of the effects of environment on heredity as grandparents who had suffered starvation passed the consequences not to their children, but to their grandchildren – depending on the sex of the ancestor and the sex of the descendant. 

The same differentiation was shown in the twins Jenna and Bridget. Bridget’s autism is associated with a genetic deletion in Chromosome 15 - the ubiquitin-protein ligase E3A (UBE3A) gene (Mayo Clinic here).  It is called Angelman Syndrome. However, the same deletion is also associated with Prader-Willi Syndrome, a form of obesity.  The outcome depends on whether the X-chromosome carrying it is inherited from the mother or from the father.  The chromosomes and genes themselves are identical in both cases; the expressions are markedly different.

“The route from genes to morphological characters is convoluted and, in many aspects, still escapes us. This is the reason why we have no hypothesis or model yet of the sequential steps of the development of an organ. There is no evidence that any part of the genome (a gene or a number of genes) codes or determines steps for developing a brain, a heart, or even a strand of hair. It is true that genes or genetic networks are involved or responsible for developing such characters, but their involvement is not linear: a number of different types of cells have to be differentiated and arranged in specific spatial patterns in order to form the organ. But both cell differentiation (Christopher and Helin, 2010) and dedifferentiation (return of cells to pluripotency) (Takahashi and Yamanaka, 2006), as well as activation of gene regulatory networks (Cabej, 2010, pp. 23-24, 39-80), are epigenetically rather than genetically determined. -  Building the Most Complex Structure on Earth: An Epigenetic Narrative of Development and Evolution of Animals by Nelson R. Cabej (Elsevier, 2013, pg 67.)

As depicted in the PBS Nova production, the Överkalix study revealed an array of distinctions laid over the chromosomal inheritances.  Diabetes, early death, or longer life in the descendants depended on whether the affected ancestor was male or female. Whether the ancestor was within the womb or out also effected contrasting outcomes. Exactly when during gestation the event occurred also effected a different result.  

Wikipedia has a bit more to say. “The Överkalix study was a study conducted on the physiological effects of various environmental factors on transgenerational epigenetic inheritance. The study was conducted utilizing historical records, including harvests and food prices, in Överkalix, a small isolated municipality in northeast Sweden. The study was of 303 probands, 164 men and 139 women, born in 1890, 1905, or 1920, and their 1,818 parents and grandparents. 44 were still alive in 1995 when mortality follow-up stopped. Mortality risk ratios (RR) on children and grandchildren were determined based on available food supply, as indicated by historical data. Among the sex-specific effects noted; a greater body mass index (BMI) at 9 years in sons, but not daughters, of fathers who began smoking early. The paternal grandfather's food supply was only linked to the mortality RR of grandsons and not granddaughters. The paternal grandmother's food supply was only associated with the granddaughters' mortality risk ratio.  … The father's poor food supply and the mother's good food supply were associated with a lower risk of cardiovascular death.”

In The Epigenetics Revolution (Columbia University Press, 2012), virologist Nessa Carey tells a similar story from the Dutch Hunger Winter of 1945.  “If a mother was well-fed around the time of conception and malnourished only for the last few months of the pregnancy, her baby was likely to be born small. If, on the other hand, the mother suffered malnutrition for the first three months of the pregnancy only (because the baby was conceived towards the end of this terrible episode), but then was well-fed, she was likely to have a baby with normal body weight. … The babies who were born small stayed small all their lives, with lower obesity rates than the general population. For forty or more years, these people had access to as much food as they wanted, and yet their bodies never got over the early period of malnutrition. …  Even more unexpectedly, the children whose mothers had been malnourished only early in the pregnancy had higher obesity rates than normal.” (pp 3-4). And this tendency to overweight was inherited in the grandchildren (pg. 102).

Nessa Carey has a virology PhD from the University of Edinburgh. She worked for five years at the Metropolitan Police Forensic Science Lab in London. (Her website is here.) In this book, she carries the analogy of a Shakespeare play. The text of Romeo and Juliet is the same for everyone. Almost every cell of your body has exactly the same chromosomes. (Red blood cells and sex cells are exceptions.)  But you do not grow teeth in your eyes. The director’s comments, distributed with the script, provide more information. Methylation and histone deacetylations change the expressions of genes. Moreover, actors write notes in pencil or attach Post-its.  We smoke cigarettes, drink alcohol, and ingest insecticides and herbicides. They affect us, of course, but it seems likely that they also affect our grandchildren.

These facts, should have been the clues to scientists that the chromosomes, the genes, DNA and RNA must be directed by other agents. Otherwise, as Carey says several times, you would grow teeth in your eyes.  By analogy to the exploration of space, a series of giant steps over centuries allowed us to plot the orbits of the planets correctly.  The work of Darwin, Mendel, Crick and Watson, the human genome project, all provided the shoulders of giants for today's research. Epigenetic medicine may be the equivalent of the Lunar colony.

ALSO ON NECESSARY FACTS.

Biopunks Hack the Software of Life

Austin Biobash 2012

Austin Biobash 2013

Fertile Hybrids Challenge Darwin

Bob Swanson and Genentech

Disruptive Diagnostics and the Business of Science

Biohackers

For most of the history of life sciences, major discoveries were made in labs less sophisticated than today’s kitchens … Laser meat thermometers. Handheld blenders. Microwave ovens. Ziploc bags. A steady supply of electricity, clean water, and refrigeration.

Biopunk: DIY Scientists Hack the Software of Life by Marcus Wohlsen (Current Penguin, 2011) does for the next generation of homebrew science what Steven Levy’s Hacker’s Heroes of the Computer Revolution did for the previous transformation from a world based on industrial manufacturing to one dependent on information services.  The next revolution will transform our inherited legacies into self-made potentials.

Each of us is an individual.  Individualism is not an abstract political idea.  It is a biological fact.  

"In his apologia for chemistry, The Same and Not the Same, (Columbia University Press, 1995) Nobel laureate Roald Hoffmann asserts that no two hemoglobin molecules are identical. So-called “identical twins” are not. Individualism is objectively real: both empirically knowable and rationally explainable." (From this blog post.)

The consequences of genetic individualism serve as one large motivator for many of the innovators and inventors spotlighted in this book.  Many of the biohackers who build labs in kitchens, closets, and garages, seek to get beyond the medicines for mass populations, to discover the origins of individual problems and find the one exactly right solution for that person. 

A point not made explicitly by Wohsen or Levy but fundamental to them both – and in reply to Pres. Barack Obama and Prof. Elizabeth Warren on the question of who built what: invention comes from individuals. Even with Wikipedia and Google, we do not share a collective mind.  Someone had to invent the shovel before “we” could build roads.  Not everyone employed in a government laboratory – or for a pharmaceutical firm – innovates, invents, creates, or discovers.  As both Wohlsen and Levy demonstrate, those new ideas and processes come from outside the norm, beyond the expected, without approval or permission – or even funding. 

Biohacker Kay Aull’s father was found to have hemochromatosis: his body absorbs too much iron. It is a genetic defect. She carries the gene, also.  Kay Aull verified this by building her own laboratory test in her kitchen for under $100. 

Like the replication and mutation of DNA itself, Wohlsen tells essentially the same story about very different people working in their own ways on problems they find interesting.  They hack processes on the cheap to replicate that for which industry and government laboratories pay catalog prices in the hundreds of thousands of dollars. Meredith Patterson built her own “LavaAmp” thermocycler for polymerase chain reactions. J. Chris Anderson, Raymond McCauley, Anne Wojcicki, Linda Avery, Aubrey deGrey, Guido Nuñez-Mujica, and a dozen others have their own hacks, their own missions.

And they rely on commercial labs as needed. In fact, the wet lab as a marketable service is one aspect of this new revolution. In addition, the biohackers have conferences and meet-ups of their own, while they also attend mainstream events. Many have advanced university degrees; some dropped out of college to pursue biohacking. Many of them know each other, just as Bill Gates and Steve Jobs crossed paths in Albuquerque. 

This is a global phenomenon. Wohlsen tells of the cotton farmers of the Gujarat state of India who arguably captured and then remarketed a Monsanto product, Bt Cotton, now known variously as BesT Cotton, Navbharat 151, etc. Moore’s Law for computers found a generation every 18 months. Biology trims a few months off of that. 

Biohackers also eschew the secrecy that surrounds genetics research. Billions of dollars are at stake. Competition is fierce. Corporations have every incentive to keep their knowledge base proprietary, secret, and then when announced, locked in patents. But this retards progress.  Despite the claim that patents “promote the Progress of Science and the useful Arts” (Art. I. sec. 8. of the Constitution), the historical evidence is that openness works much better.  Biohackers share information.

You cannot have heroes without villains. The bad guys hang out in the halls of Congress. Bart Stupak represented northern Michigan which is still Paul Bunyan country; he is now retired and working as a lobbyist. Stupak called frontline genetic research "snake oil."  Henry Waxman still speaks for Beverely Hills. They led and lead the gang that would crush biohacking with new federal laws. Those laws would prevent you from resequencing your own DNA to fix your own problems. 

Unfortunately – something of modern trend in books like this – the notes are in the back; and lack direct references such as numbers or asterisks in text, but are listed by page number and key phrase. 

This book is an excellent introduction to the open community of biopunks and gene hackers.  Wohlsen provides websites, citations, and other supporting documentation. If you are looking for a biohacker conference or website, or want to join a meet-up, this is a good overview of the culture, its arts and industries.

ALSO ON NECESSARY FACTS
Epigenetics
Disruptive Diagnostics and the Business of Science
Austin Biobash November 2012
Austin Biobash February 2013
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Fertile Hybrids Challenge Darwin

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.

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Epigenetics
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Austin Biobash November 2012
Bob Swanson and Genentech
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