Showing posts with label biohackers. Show all posts
Showing posts with label biohackers. Show all posts

Saturday, April 11, 2020

No One Needs a Computer in Their Home

“No one needs a computer in their home.” -- Ken Olsen, 1977.
What is really funny about that is the way Snopes debunked it back in 2004.  
Quote: “What Olsen was addressing in 1977 was the concept of powerful central computers that controlled every aspect of home life: turning lights on and off, regulating temperature, choosing entertainments, monitoring food supplies and preparing meals, etc. The subject of his remark was not the personal use computer that is now so much a part of the American home, but the environment-regulating behemoth of science fiction. Digital historian Edgar H. Schein described it thusly:‘What Olsen [was focusing on was] that in the 1950s and 1960s there existed the notion that the computer not only could but would control all aspects of our lives. Images of the fully computerized home that automatically turned lights on and off and that prepared meals and controlled daily diets were popular. And the fear that computers might, as in the movie 2001: A Space Odyssey, even try to take charge altogether was widely experienced.’ ”  -- https://www.snopes.com/fact-check/ken-olsen/
 On the eve of the Hall Process, Napoleon III served his most important state guests on aluminum dinnerware while dignitaries of lesser status ate from gold or silver. Our best hobby telescopes today in the $10,000 range would have been the envy of an observatory. Our dobsonian "light buckets" ten to 16 inches costing between $500 and $1000 would have been unthinkable to amateurs whose 3-inch refractors would be considered toys ($50 to $100) today. 

Your kitchen has appliances that would have been found only in laboratories of 1950, among them the variable high speed blender, microwave, and coffee filters.

If no one needs a computer in their home, do they need one in their pocket, to stream video chats, play music and movies, bring the news, and (functions I actually use) be a map accurate to ten feet, a directional compass, and a carpenter's level? 

Pundits of science tell us that the universe is beyond our imagination. I find it more compelling that our own civilization challenges our easy assumptions about what is possible--and what is helpful, useful, and ultimately necessary in common daily life.

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Thursday, July 10, 2014

Cell Repair and Tissue Sales


Back in the 1980s, the "cyberpunk" science fiction genre touted personal technologies in the early 21st century.  Here we are.   In the stories of William Gibson, in particular, but also Pat Cadigan, Lewis Shiner, John Shirley, and others, biotech takes the down-front stage position, even as computering of all kinds provides a rich array of characters (maybe even the chorus).  After I took the picture here - and I am sure that it meant cellular telephone repair - I saw a sign at a Walgreen that said " $$ Tissue Sale $$".  Soon… soon…

Previously on Necessary Facts

Sunday, December 1, 2013

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.
Disruptive Diagnostics and the Business of Science

Thursday, November 29, 2012

BioBash Austin Winter 2012

Dr. Matt Winkler
Dr. Paul Lammers
The Austin Chamber’s BioAustin Winter BioBash was held on November 28 at the Driskill Hotel.  About 150 of us celebrated the history of life sciences here in Central Texas with a keynote address from Dr. Matt Winkler, the chairman and CEO of Asuragen.  He was followed by Dr. Paul Lammers chairman and CEO at Mirna Therapeutics.  Mirna (from “micro RNA”), founded by Winkler, is a third-generation daughter of Ambion which Winkler created in 1989 while at the University of Texas and sold in 2005 to the Applied Biosystems Group of Applera and is now a Life Technologies label.



I first met Kyle Schulz of the Round Rock Chamber. He was there on behalf of Austin Community College, seeking to place their biotechnology students in internships with companies.  He found Maggie Bishop for me.  Maggie is with the Austin Chamber and is active on the Austin Biotech group on LinkedIn. She was the emcee for the event. (She is also on the committee to coordinate the creation of the new medical center here.)

UT researcher Scott Rynbrandt with Dr. Simona Perra.
Perra's expertise is the legal regulation of medical devices.
Standing together at a table, were Gail Darling of Gail Darling Staffing who brought her experience in federal contracting, and Nancy Goedeke whose MedMarComm provides marketing and communication services, Jason Choyce of DPR Construction, which specializes in complex projects for advanced technologies, and Kevin Fincher, a tax partner with Padgett Strateman.

Later, Gail introduced me to Stephen Frayser, the new executive director of Texas State University’s STAR Park. The 38-acre Science Technology and Advanced Research Park opened officially on November 9 to provide secure wet labs, clean rooms, and office space.

Not everyone we met had business cards.  (I ran out quickly.  After the Technical Writer cards, I was down to the Criminologist introductions.  I even gave out my Capital City Coin Club Vice President cards.)  And we met a lot of graduate and post graduate students working in university and private labs. 

Our last contacts were a trio from the Austin Technology Incubutor: Mike A. Sandoval of the IC2 Institute, Dr. Lydia V. McClure, an Accenture Venture Partner with Texas Venture Labs at the McCombs School of Business, and Michael R. Pierce also an Accenture Venture Partner.  Earlier this year, the ATI announced the launch of two companies, Savara Pharmaceuticals, and Terapio, which markets the RPLI76 protein as a countermeasure to radiation exposure and chemical threats.  About 30 companies are now in the incubator, including Alafair Bioscience, Integrated Medical Systems, Inc., Admittance Technologies, and Xeris which makes ultra-low volume biopharmaceuticals in auto-injection pens.


ALSO ON NECESSARY FACTS

Saturday, October 27, 2012

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.
Book cover showing schematics of microscopic particles

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
Bob Swanson and Genentech
Fertile Hybrids Challenge Darwin