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.

Stem Cell Therapy in India

The 17 March, 2005, issue of Nature has a story titled, "Indian regulations fail to monitor grown stem-cell use in clinics", by K.S. Jayaraman.  The article explains that guidelines for research will be discussed soon, though stem cell are already being used in clinics.  It is yet another indication of how readily new biological technologies will be adopted as soon as they become available.  Like the clinical use of stem cells in Russia, the article notes there appears to be little central awareness of which studies are being performed where.  The "nation's premier medical institute" is pursuing clinical applications of stem cells for treating a variety of conditions without governmental knowledge or approval.  The article notes that, "The quality of cells being used in therapy is of major concern, as is the failure of clinicians to understand basic stem-cell biology."

If these treatments do show promise, I wonder how quickly US and European regulators will move to get clinical trials underway, or if they will insist that treatments on this side of the world be derived from a more basic understanding of mechanisms.  That will definitely slow things down.

"Stem-Cell Craze Spreads in Russia"

A tidbit from the AP today about quasi-legal stem cell treatments in Russia (via Wired News), "Stem-Cell Craze Spreads in Russia".  Evidently, treatments putatively consisting of adult and/or embryonic stem cells are being used as treatments for everything from cosmetic adjustments to MS.  The treatments are totally unregulated and at best skirt the edge of what is legal in Russia.  It is unclear where the cells are coming from, or whether those performing the injections have the skills and equipment to isolate stem cells in the first place.  No studies are being performed to follow the patients, or to find out if the treatments are causing harm.

This demonstrates the lengths people are willing to go in order to take advantage of new, unproven technologies.  It also suggests the extent of body modification we can expect when real treatments are demonstrated using stem cells, particularly those that have been genetically modified or coaxed to differentiate into particular tissue types.  Feather goatees will be passe.

Mining the Moleskine

I have carried lots of notebooks over the years, and I only recently found the Moleskine.  It is my favorite by far.  From time to time, I will delve into the pages of my Moleskine for a blog entry.

So, with no further ado...

1 December 2004 :: Tokyo

After getting lost once again in Shinjuku station, finally finding my way to the right subway line, and stumbling into the four story metal robot-ninjapuppet-goddessqueen, I am now sitting happily at Segafredo in the upper lobby of Mori Tower, Roppongi Hills.  There are vast numbers (relatively) of Westerners in suits here, as well as meandering the mall.  But for all their ex-pat spending power, they are out-yenned by the many Japanese patronizing all the Western shops and restaurants.  With equivalent lines at Segafredo and the Starbuck's just downstairs, I wonder how distinctly the concepts of "Western", "European", and "American" are differentiated in the Japanese (and more generally Asian) mind.  Does it make a difference?  Does the conception of the US as a place and culture distinct from Europe, perhaps as exemplified by foreign policy,  come into decisions about where to shop, or with which brands to self-identify?

2 December 2004 :: Approximately the Int'l Date Line

This I wonder -- as clocks (developed largely to assist with navigation) brought about a general  public concern for the precise passage of time, and a common means to accurately measure it, what other tools and concepts so momentously impact the zeitgeist and human condition?  Not relativity and quantum mechanics, I think, because these are neither commonly understood nor measured, and as yet neither find application in common technology.  Indeed, at least for the time being we avoid quantum mechanics in our computers and make little or no mention of the effects of relativity on travelers or satellites.

What will be the tool or concept that changes our conception of biology?  Will it have a polysyllabic name we already know; genomics, metabolomics, proteomics, transcriptomics?  We barely know how to define those terms, and are not yet proficient in measuring any of them.  Perhaps revolution will be found in "molecular medicine", the reduction of health care to understandable, describable interactions of compounds dispensed with a foreknowledge of their effects.

And how will the concept of "molecular medicine", with its reduction of biology to mechanistic interactions and its probable reliance upon stem cell therapies -- even those drawn from the patient -- be received in the context of an apparently resurgent Christian philosophy wherein every cell that possesses the capability of generating a new life, a new individual, is held to have a soul?  What happens when it is demonstrated that stem cells removed from an adult can be reprogrammed and used to generate a new human being?  Will opponents argue that the line is too easy to cross?  Or will the potential health care benefits overwhelm the desire for a self-consistent philosophy?

The Thousand Dollar Genome

I have once again been hearing noises about the "thousand dollar genome" (TDG).  That is, a human genome read de novo for a USD 1000 or less.  Here (REVOLUTIONARY GENOME SEQUENCING TECHNOLOGIES -- THE $1000 GENOME), for example, is a request for proposals from the National Human Genome Research Institute to develop technology that would enable the TDG.

Based on my early efforts to quantify how the productivity and cost of sequencing were changing, Steward Brand asked me back in 2002 when we would get the TGD. 

Here is the plot I generated in response (click on the figure thumbnail for a full-sized version).

The cost hasn't changed dramatically recently, and at the current pace we we won't get the TDG until sometime after 2020.  With 3 billion (3x10⁹) bases in the human genome, we need to hit USD .3x10^-6 per base (which is .3 microbucks, 300 nanobucks, 300 nanodollars per base -- nanoeconomics anyone?) to reach the Thousand Dollar Genome.  However, the numbers on the plot are primarily based on instruments that use slab gel electrophoresis and capillary electrophoresis.  Thus as new technologies emerge we could very well get to the TDG much more rapidly.

Recombination vs. Reassortment

Here is a story in today's Wired News about Henry Niman and his ideas about viral evolution in the Avian Flu (H5N1).  While the text of the story is a bit unclear about the difference between recombination and reassortment, one of the associated images is quite nice.  This is yet another take on the specific mechanisms of viral evolution.  The figure defines reassortment as the emergence of a new strain via the replacement of whole genes from another (related) virus, and defines recombination as the insertion of fragments of genes into a new viral strain from another genome, potentially from the host.

Ignoring what labels are used, it seems the important point is that there may be two mechanisms for introduction of new sequences into an influenza viral genome; 1) inclusion of whole genes into a segmented genome or 2) insertion of gene fragments from another strain or species within a given viral gene.

Niman seems to think that not only is there evidence that the current H5N1 strain is evolving via the second mechanism, but that this is also the origin of the Spanish Flu (see my post "The Spanish Flu Story"), despite the fact that there appears to be a historically low occurrence of homologous recombination in negative sense RNA viruses (see my post "A Confluence of Concerns").

Reverse Genetics for H5N1 Vaccine

Just as I was banishing my ignorance about how the forthcoming trial vaccine for H5N1 was produced, a trio of excellent articles from the Wall Street Journal and Fortune landed in my Inbox, facilitating my education.  The short story is that the virus grown in chicken eggs as the source of an attenuated vaccine is not actually H5N1.  The genes that cause the virus to be so fatal to eggs have been replaced with genes from less virulent strains, while the HA protein on the surface of the virus is modified so that it is more stable.

Alas, because the WSJ doesn't allow you to look at their list of stories in the print edition without a subscription, I can't even provide links to the stories.  Fortune, evidently, is more forthcoming.  Here are the titles, etc;

"A primer on the Threat of Avian Flu...", by Gautam Naik, and "Avian Flu Poses Challenge to Global Vaccine Industry...", by David Hamilton and Gautam Naik; both are from the 28 Feb, 2005 issue of the WSJ.  "The Coming War Against Bird Flu", by David Stipp, will appear in the 7 March, 2005 issue of Fortune.

The upshot of the three articles is that the vaccine is produced in sterile chicken eggs via a recombinant virus that is a modified version of H5N1.  This strategy requires a large number of those eggs, which are not easy to come by, and produces a vaccine that prompts the production of antibodies against a virus that may, or may not, be similar to the wild type H5N1.  That is what human trials will have to determine.

Thus my initial concerns (here and here) about this issue were not so far off target.  Stipp's article does an excellent job describing the production of the vaccine, and associated challenges.  It is pretty clear we need to come up with alternative means of producing vaccines, preferably rapid synthetic approaches that are deployable from a distributed infrastructure.

UPDATE (7 March 2005): I stumbled over this article in The Scientist, "H5N1 vaccine strain in a week", from 29 January 2004, which opens;

A prototype vaccine strain of the H5N1 flu virus causing havoc in Asia will probably be ready next week, John Wood of the UK National Institute for Biological Standards and Control (NIBSC) told The Scientist today (January 29). However, months of other hurdles remain before it may be ready for public health use.

The article describes several genetic manipulations of the H5N1 strain that will make it easier to produce in chicken eggs, beginning with the removal of, "a stretch of 4 or 5 basic amino acids at the hemagglutinin cleavage site that allows the virus to replicate in every organ of a chicken's body, rather than respiratory and gut tissue normally infected".

The article cites Klaus Stohr as saying, "The H5N1 virus kills chicken eggs, the normal medium for growing flu vaccine viruses, so the WHO laboratories are using reverse genetics to lower the pathogenicity of the virus to chickens and to get a high yield in the egg cultures", and describes the additional genetic manipulations; "Using other lab strain flu plasmids containing the other components of the viral genome, the team will then reassort the pieces into a nonpathogenic vaccine strain." 

Finally, the article suggests that, "Sufficient amounts of safety-tested prototype vaccine virus will probably be available for the necessary 1 to 2 months of clinical trials in the next 4 weeks".  The date of this article, again, was 29 January, 2004.

Looks like we are well on our way, circa January 2004, to producing a lovely vaccine against a bug that doesn't actually exist in nature.  We clearly need an alternative to attenuated (or killed) whole virus vaccines.  When I have time, I will post what I have been learning about DNA vaccines.