Technology transfer to middle school students

The upcoming 86th ANNUAL MEETING of the AAAS Pacific Division will be in Ashland, OR, June 12-16, 2005.  There will be a couple of workshops put on by Bio-Rad to help teachers understand how to use various kits within the classroom.  From the looks of it, some fairly sophisticated technology is now being introduced to students as early as middle school.  No genetic modification, but the workshops cover tools everyone uses in the lab to understand the systems they are working on, or systems they are building.

From the Meeting Schedule:

Bio-Rad Corporation of Hercules, CA, is presenting the following five hands-on workshops to give middle school, high school and university instructors the opportunity to try out some of the molecular biology kits they offer to educators. There is no charge for these workshops. However, participants must be registered for the meeting. Be sure to wear your meeting badge to each session. Space is on an “as available ” basis and preregistration is not required. Bio-Rad representatives will provide certificates of attendance for those desiring to utilize these workshops for professional development credits.

Wednesday, June 15

8:30 a.m.Genes in a Bottle. Extract and bottle your own DNA. Introduce your students to molecular biology with their own DNA! In this activity, you will extract and bottle the DNA from your own cheek cells to make a necklace. This real-world laboratory procedure is used to extract DNA from many different organisms for a variety of applications and integrates multiple life science standards in a single lesson. Seeing DNA makes it real. Be the first at your school to wear your DNA!

10:30 a.m. ELISA Immuno Explorer. Biology's magic bullet. Explore immunology with this topical, new hands-on classroom lab.ELISA (enzyme-linked immunosorbent assay) is a powerful antibody-based test used to detect diseases such as HIV/AIDS and SARS, and to trace pathogenic agents in water, food, and the air whether these emerge naturally or through acts of aggression. You will simulate the spreading of a disease, perform ELISA, and learn how this assay is used to identify and track agents of disease , or to detect molecular markers of cancer, pregnancy, and drug use. This kit integrates multiple standards in a single lesson, including antigen-antibody interactions and the role antibodies play in medicine, epidemiology, and biotechnology.

1:30 p.m. PV92 PCR. What pair of genes are you wearing? PCR is central to forensic science and many medical, archaeological, and ecological procedures. You will extract DNA from your own hair samples, then amplify and fingerprint a pair of alleles, an Alu repeat within PV92, a real forensic marker. This activity integrates multiple life science standards in a single lesson and covers a range of core content areas, from DNA replication to evolution to Hardy-Weinberg equilibrium theory.

Thursday, June 16

9:00 a.m. GMO Investigator/Analysis. Have your favorite foods been genetically modified (GM)? Currently, genetically modified organisms (GMOs) in foods do not have to be labeled in the US. Regardless of where you stand in the GM debate, wouldn't it be fun to know if the corn or soy-based foods you eat are GMO foods? This kit uses DNA extraction techniques, PCR, and gel electrophoresis to test common grocery store food products for the presence of GMO foods. This activity integrates and reinforces multiple life science standards in a single lesson.

1:00 p.m. Protein Fingerprinting. Can molecular evidence support evolution? DNA gets a lot of attention but proteins do all the work. Proteins give organisms their form and function and are the raw material for evolution because natural selection acts on phenotypes. Over time, accumulated changes in DNA (genotypes) lead to variation and ultimately, speciation. You will extract muscle proteins from both closely and distantly related species of fish and use protein electrophoresis to generate protein fingerprints to look for variations. This activity integrates multiple life science education standards in a single lesson from physiology to the theory of evolution to exploring the molecular framework of biology. DNA>RNA>Protein>Trait.

1957 Flu Redux (...almost...)

The AP carried a story today that announced a recomendation (order?) from the WHO to destroy shipments of flu strains sent to labs around the world as part of an ongoing testing program.

The problem, it seems, is that the test kit contained the 1957 pandemic flu strain, which no one has been vaccinated against since 1968.  The story reports that, "It was not immediately clear why the 1957 pandemic strain, which killed between 1 million and 4 million people -- was in the proficiency test kits routinely sent to labs."  The story continues;

Most of the samples were sent starting last year at the request of the College of American Pathologists, which helps labs do proficiency testing. The last shipments were sent out in February.

Dr. Jared Schwartz, an official with the pathology college, said a private company, Meridian Bioscience Inc. of Cincinnati, Ohio, is paid to prepare the samples. The firm was told to pick an influenza A sample and chose from its stockpile the deadly 1957 H2N2 strain.

Regardless of the wisdom of this choice, it is interesting that it was caught at all -- one of the labs correctly identified the 1957 strain.  That bodes well for infectious disease surveillance, but note that this was a test kit sent to the labs, not an environmental sample that they had to test completely blind.

Note also that the strain is now out in the world again, and could thus be kept as a potential weapon.  Most of the kits were shipped to labs in the US, and the College of American Pathologists has requested confirmation in writing that all the test kits have been incinerated.  Which is great.  Except that the bug is still now out in the world.  Even if this was an accident -- especially if this was an accident -- the incident highlights how ill prepared the global community is for biological surprises.

UPDATE (14 April 05): Effect Measure has nice coverage of this incident.

Space Elevator Conference Update

Here are Blaise Gassend's notes from Space Exploration 2005 about progress towards building the Space Elevator.  Also a Slashdot thread, full of the typical penetrating discourse.

It's the end of the world as we know it!

The editorial in Science last week (8 April '05), "Twilight for the Enlightenment" (subscription required), laments the challenge to our "confidence in science and in rational methods of thought" by a trend for "some school boards [to] eliminate the teaching of evolution or require that religious versions of creation be represented as 'scientific' alternatives".  Donald Kennedy, the Editor in Chief, is also perturbed that, "In several school districts, geology materials are being rewritten because their dates for Earth's age are inconsistent with scripture (too old)."  This challenge obviously comes from the right.

Interestingly, there is a commentary in last week's Nature by Dick Taverne, a member of the UK House of Lords, entitled, "The new fundamentalism" (again, subscription required).  Lord(?) Taverne (never thought I would type that particular appellation) is concerned about, "The growing influence of 'green' activists who approach environmental issues with a semi-religious zeal and seemingly little regard for evidence".  Taverne suggests that these viewpoints, "Imperil not only the future of the biotech enterprise but also the health of society as a whole".  Thus science is getting it from the left, too.

So it seems the problem is a bit more general than "evangelical Christianity" pushing to smudge the boundary between church and state (Kennedy), or Greens engaging in "scaremongering" that might "allow new technology to be summarily dismissed on the basis of unsubstantiated claims...technologies on which our future health and wealth depends" (Taverne).  Across a broad swath of the political and social landscape, from the right and the left, there is a fundamental turn away from the mindset that has brought us profound increases in our standard of living and profound decreases in human suffering.  Though we have lots of work to do on both points on a global scale, we aren't going to get there by turning away from the Enlightenment.

Then again, perhaps it is just our turn to watch the empire pass.  India, China, Islam in the middle ages; these cultures all had their day in the sun and made choices that let the mantle pass to others.  But with the passion for science and technology throughout Central and East Asia, coupled with education and an excellent work ethic, the wheel may be coming back around.  At least progress will happen somewhere.  We get to choose whether they have all the fun.

Bio-ERA: Thinking Ahead

Bio Economic Research Associates has now published its first report examining possible outcomes of a flu pandemic, Thinking Ahead: Anticipating Early Impacts of an Avian Influenza Pandemic.  The report, and the associated research service, are designed to help answer the following questions:

• What key indicators and signposts should the business community be watching with respect to pandemic influenza?
• If human transmissible H5N1 broke out in Asia, what specific actions (travel advisories, quarantines, travel restrictions, etc.) should we expect to be implemented by governments and public health authorities?
• How would these actions impact regional and global economies, and businesses operating within and/or interconnected with, affected regions?
• How would these developments affect investors and financial markets?

ProMED-mail

If you want up to the minute information about emerging diseases, ProMED-mail is a service run by the International Society for Infectious Diseases and the Federation of Americal Scientists (FAS).  The FAS also runs ahead/ILIAD, which specifically tracks infectious animal and zoonotic diseases.

There is also link in the "Navigation" bar of the ProMED-mail site to recent medical product and food recalls and medical alerts.

This is good stuff.  But don't read it just before going to bed.

Geographical Distribution of Biological Technologies

I just stumbled over William Hoffman's World Stem Cell Policy Map, which shows the geographical distribution of policy about stem cells and major genome sequencing centers.  It is part of a larger project to create Global Maps of Human Technological Development, including Global Biotechnology Clusters and Global Biotech Crops.

With the amount of cutting edge research and development taking place in China, India, Taiwan -- the list goes on -- it is interesting to see things laid out this way.  I have concentrated mostly on how technologies are changing in time, and on constructing analogies to help understand what sorts of technologies we need to do better biology.

But the geographical perspective is instructive.  There are obvious clusters of research, some of which lie in countries that are dramatically more permissive about clinical trials than is the US.  It wouldn't take that much in the way of resources to plunk down a cutting edge center in most of the blank areas of the map.  I hope Mr. Hoffman keeps things updated so we can see how the maps develop.

Nanobacteria in the News

When I showed Sydney Brenner the first paper claiming a physiological role for nanobacteria ("Nanobacteria: an alternative mechanism for pathogenic intra- and extracellular calcification and stone formation", Kajander and Ciftcioglu, PNAS, 95 (8274-8279), 1998), he just chuckled.  And rightly so, given the expansive claims of that and succeeding papers.  Early claims that 30 nanometer particles visible in electron microscopy experiments contained DNA were challenged when the resulting sequences were shown to be identical to those found in common bacterial laboratory contaminants.  That is, while the original work pointed to some interesting evidence, there wasn't enough meat on the bone to convince people who have been watching biology since its modern beginnings.

Work has continued, however, and now careful studies have demonstrated nano sized objects at the core of structures from human bodies, where those nano objects definitely contain DNA.  In "Evidence of nanobacterial-like structures in calcified human arteries and cardiac valves" (Am J Physiol Heart Circ Physiol 287: H1115-H1124, 2004), Miller et al examine a variety of human tissues removed during surgery and conclude that "nanometer-scale particles similar to those described as nanobacteria isolated from geological specimens and human kidney stones can be visualized in and cultured from calcified human cardiovascular tissue."

The paper describes using light and scanning electron microscopy, immunostaining, and DNA staining to characterize objects 30-150 nm in size that appear in physiological samples.  Interestingly, there is already a commercial antibody available, "8D10", that appears to recognize a ~50-kDa protein only found in tissues and cultures that were observed to contain the nanobacteria.  Moreover, simultaneous immunostaining using 8D10 and DNA staining using PicoGreen revealed that structures cultured from filtered homogenates of human aneurysm contained both protein and DNA.  The most compelling evidence from a traditional biology perspective is that the nanobacteria can be propagated in culture media.  That is, the structures are self-replicating.  Decalcified particles contained structures that appear akin to cell membranes.

By way of acknowledging alternative explanations for their data, the authors note that;

Although a unique nucleic acid sequence remains to be identified from the nanosized particles identified within human arterial tissue in the present report, it is possible that these structures may represent either a variant form of microorganisms or an unrecognized bacterial growth stage such as L-forms, cell wall-deficient bacteria, and/or defective bacteria that have been hypothesized to represent either pleuropneumonic-like organisms or Mycoplasma species, which have been detected in serum of patients with long histories of chronic diseases. They may also represent an Archaea symbiont that requires cell contact or lipids from other cells for growth.

They go to observe their data are consistent with nanobacteria as a cause of disease;

Nanobacteria derived from bovine serum are internalized by human cells and appear to be cytotoxic. Similar internalization of nanolike particles in arterial smooth muscle would be consistent with induction of apoptosis, formation of matrix vesicles, and the inflammatory basis of atherogenesis. An infectious etiology of arterial calcification is consistent with increased lesion formation in experimental models of atherosclerosis.

Note that this text implies nanobacteria may be infectious agents.  Miller et al lay out the test of this hypothesis;

...A definitive cause and effect relationship needs to be established between these nanoparticles and [pathogenesis]. For example, it will be necessary to evaluate severity of calcification and disease progression in the absence, presence and titer of nanoparticles in humans. In the experimental setting, it will require infection of a naïve animal with cultured nanoparticles and subsequent identification of the particles within arterial calcification. Definitive characterization of these unique particles will require isolation and sequencing of genetic material (DNA or RNA).

No doubt the debate over nanobacteria will continue until the above criteria are met, but the Miller paper definitely contributes significantly to the discussion.

In the end, this sort of report illustrates how naive we are about what organisms inhabit the human ecosystem.  We haven't even isolated all the viruses and "normal" bacteria that live in and on humans.  And then something strange like nanobacteria come along.  We have lots of work to do.

Science is the only news.

Because I keep misplacing the quotation, I thought this blog would be a good place to drop a bit of graffiti.  It is one of the most profound things I have ever read.

"Science is the only news. When you scan through a newspaper or magazine, all the human interest stuff is the same old he-said-she-said, the politics and economics the same sorry cyclic dramas, the fashions a pathetic illusion of newness, and even the technology is predictable if you know the science. Human nature doesn't change much; science does, and the change accrues, altering the world irreversibly."

- Stewart Brand, Cofounder of GBN and the Long Now Foundation. Founder and editor of the Whole Earth Catalog and the Whole Earth Review; founder of The WELL computer teleconferencing system; author of The Clock of the Long Now, How Buildings Learn, and The Media Lab.

That's quite a resume.

Somewhat more obscure, but perhaps just as profound, is a bit of graffiti from an overpass in Portland, OR, once accompanied by a doodle of Kilroy peeking over a wall, but now long painted over: "God licked my brain, Ho-Ha!"  Something to ponder.

As long as I am at it, I will throw down another bit of brilliant, profound graffiti, this one from the blackboard in Richard Feynman's office; "What I cannot create I do not understand."  He probably meant this in terms of theory and calculation.  Feyman made it a point to be able to reproduce calculations from first principles.  But for me it holds a somewhat different significance, quite well captured in Oliver Morton's recent Wired article on Synthetic Biology as;

"In a nutshell...the scientific case for synthetic biology. To many scientists, the field's real appeal is that it provides a new way to unlock the mysteries of biology. Trying to do the things that nature does - say, orchestrating the interactions of genes and proteins triggered by some external event - is a way to discover fundamental principles that govern living systems."

There is a certain tension for me between "science is the only news" and "understanding through creation".  I suppose it is primarily a cultural thing, having been "brought up" professionally in academic physics departments, where engineering is a dirty word.  But there is some truth in the observation that many engineers aren't so concerned with fundamental principles; they prefer to build cool stuff.  And don't get me wrong -- without that cool stuff we would still be living in caves.  In the end, I suppose, the test of understanding as the ability to create something that behaves the way you expect is a difficult one, and much more stringent than simply telling a story consistent with the data.  Creation the only way to go if you want to change the world.

Ah, the Symphony...

Thanks to good friends, I was able to sit in fine seats last weekend and listen to the Seattle Symphony.  This is the first time I've had a chance to go to Benaroya Hall, and the acoustics there are marvelous.  It's been years since I attended the symphony.  Thinking back, the last time I heard an orchestra perform live might have been 1992 or 1993, perhaps also the last time I was on stage performing.  Abraham Kaplan conducted Mozart's Requiem -- as soon as the last note sounded I wanted to sing the whole thing over.  Couldn't have done it physically -- the first time through took everything out of me -- but the experience was so powerful I wanted to dive back in.

Anyway, the sight of the conductor this weekend engaged in his own little performance, a sort of parallel solo modern dance set to strings, cymbals, and brass, elicited from me the following haiku:

Prokofiev's Three Orange March (20 March 05)

conductor's hair flies
flung with studied abandon
full springtime bluster

And he had the perfect hair for it, too.