Sunday, June 30, 2013

Cloud Atlas (DVD 2012): a sort of review

I just watched Cloud Atlas.

"An exploration of how the actions of individual lives impact one another in the past, present and future, as one soul is shaped from a killer into a hero, and an act of kindness ripples across centuries to inspire a revolution."

What a bunch of crap. What codswallop. If you piled an Ossa of bollocks upon a Pelion of bollocks, you would not overtop this pile of bollocks.  A quick check around the net shows that it's supposedly six related  stories that show the interconnectedness of lives as souls reincarnated in new generations. Previous acts have far reaching consequences. The depths of evil and the heights of humanity in each person ebb and flow across lives.

The movie sketches this out by having the same distractingly few famous actors play all the major roles.  Unfortunately the movie is also composed of a patchwork of about four thousand already-existing scenes, and in many cases clichés, stitched together like Frankenstein's Monster to lumber across our view for almost three hours of screen time.  I don't mean to say the film-makers (including the famous Wachowski Siblings of The Matrix fame) used previous film footage, like a demented fan-montage - no, each scene was lovingly created by hand, and each ended up somehow resembling an iconic scene from a previous movie.

My overall feeling is that literary types shouldn't essay science fiction - for some reason they always assume they are breaking new ground. They aren't. Some dyspeptic whisky-drinking genre writer most likely got there in 1939. There's no shame in that, but don't come over shouting about you made a breakthrough.

Here are the homages, or clichés, or familiar-looking-scenes, however you want to characterize them, that I remembered afterwards.  We did hoot at a few more during the actual viewing.  If you have any to add, let me know and I'll put them in.

  1. Death star bridge extension scene with the hero leading the heroine across a chasm pursued by blaster fire.
  2. Someone with no imagination must have suggested they use the made-up dialect from Mad Max 3, only to be countered with "Wait, can't we use the made-up dialect from Waterworld?" And so the decision was made to use both.
  3. The concept of Soylent Green – so great they used it three times – as a reference in the old folks home, as in Fabricants eating Fabricants and in the far future, and where the scary guys from the 13th Warrior eat the nice jungle dwellers.  The Fabricants also "use a lot of energy" – suggesting the Matrix human batteries, as well.
  4. The Tron Lightcycle chase.
  5. The Logan's Run early termination with nice trappings scenario.
  6. Blade Runner's Asian city street decor in New Seoul.
  7. The mountains from Lord of the Rings. (Maybe these are hard to disguise, though...)
  8. The happy-primitive paradise people's clothing resembling the net-covered post-apocalypse people of Waterworld.
  9. The maudlin old guy telling the kids around the fire what happened in the old days from about 20 different movies including at least one Mad Max.
  10. Meronys dressed as Senator Amidala in the arena, firing her blaster with pinpoint accuracy as during her raid on the palace.
  11. The Jason Isaacs role of the Irish bruiser throwing someone off a building from Divorcing Jack – except, even though the person thus jettisoned is a book critic, the pseudo-Isaacs does not have the wit to crack, "Fastest reader I ever met – 15 storeys in 20 seconds."
  12. A scene of the devastation of the homestead when the adventurers come home from the mount – so familiar-looking I actually said out loud, "Look at these blast points – only Imperial Stormtroopers could be so precise."
  13. The Star Wars scene where Princess Leia is dragged out of her cell on the Death Star – including a chin-pinch, but not from Wilhuf Tarkin – instead from a guy who looks just like Mr. Spock.
  14. Sending a message from a dish as in that one where they do that (Contact?). Powering up the blue power beam from the dish from about five different movies.
  15. Computer interfaces that are all "twiddle your fingers in mid-air" to operate. I sometimes think that if I lived in that future, if I lost my balance while carrying a tray of drinks or something, my free arm's gyrations would start World War III.
  16. A hunted pair – a native and an outsider – go to ground in The Zone (My name for the crowded working-class or high-immigrant color-filled place where you happen across things like carts selling rat-on-a-stick, prostitutes with a heart of gold and people buying your urine for dye mordants. Every other science fiction movie and a third of historical thrillers have a Zone scene.)
  17. The ruling class of Neo Seoul are called Purebloods for no reason whatsoever that I can see.  (I think there's a Neo Seoul simply so someone can say "Old Soul" at one point, which is the only time that the supposed big themes of love and death, reincarnation and the possibility of change over lifetimes is ever really expressed.)
  18. The rest of Neo Seoul being, of course,  Coruscant from Star Wars.
  19. The opal-button deal, from the similar time-hopping movie Velvet Goldmine, that symbolizes a life transferred to the next body in both movies.
  20. The Spirit of Jazz from The Mighty Boosh (actually, the original stereotype is from Baron Samedi) (Also Riddley Walker's Drop John.)
  21. Phrase "off world colonies" from Blade Runner.
  22. Sonmi-451's name from Fahrenheit 451 (and the concept from THX 1138 and Ralph 124c 41+)
  23. Use of exotic artificial slave-girls who are Asian - they're always Asian these days as in The Windup Girl.  (Sigh.)

Thursday, June 27, 2013

Roundup of the interwebz and more

I've always been a sucker for reading the comments sections on the interwebs. I don't know why - it's rarely rewarding. But I always have.

This commenter on a Paris Jackson news item appears to have a fear of the Scunthorpe Effect:

DEMI    Due to those cir***stances FB should shut their trap, and erase her page.

From the Grauniad, a response from whistleblower Edward Snowden about Beijing:

12.04pm ET Question: Guardian staff Spencer Ackerman17 June 2013 4:16pm  
Edward, there is rampant speculation, outpacing facts, that you have or will provide classified US information to the Chinese or other governments in exchange for asylum. Have/will you? 
Answer:This is a predictable smear that I anticipated before going public, as the US media has a knee-jerk "RED CHINA!" reaction to anything involving HK or the PRC, and is intended to distract from the issue of US government misconduct. Ask yourself: if I were a Chinese spy, why wouldn't I have flown directly into Beijing? I could be living in a palace petting a phoenix by now.
I can't help thinking Snowden actually believes in phoenixes. I think he really imagines they live in Beijing palaces. I'd turn whistleblower in an instant if I could live in a palace with phoenixes, so I know how he felt.

Disinfo has an article on hallucinogens:
In Oliver Sacks‘ book The Mind’s Eye, the neurologist included an interesting footnote in a chapter about losing vision in one eye because of cancer that said: “In the ’60s, during a period of experimenting with large doses of amphetamines, I experienced a different sort of vivid mental imagery.”

That's a really odd thing for cancer to say. 

Once, many years ago, I got into an argument on Usenet because I said that saying you were "American" if you came from the US wasn't fair to other Americans, like Canadians and South Americans.  Usenet retorted, "Only an American would say that!" which was funny because I wasn't American at the time. Anyway, I sort of lost the argument, but now, only 18 or so years later, The Atlantic writes an article saying a similar thing to me. I WIN! USA USA USA!!! 

Unfortunately, the Canadians still don't seem to care either way. 
I was sitting with an Argentine friend, well educated and well traveled, who was reading The Atlantic online. A headline used the term "America" as a synonym for the United States of America. "That's incorrect," he said, sounding shocked that an esteemed publication would make such a junior mistake. "America is a region, not a country."

Many years ago,  when I was a kid I was fascinated with one story in a Porky and Petunia Pig comic book, where the two pigs were caught by the giant leafy hands of a Patagonian Pork Eater plant and hoisted into the air. I really wanted that plant – being a kid I hadn't really thought through how I was going to obtain a supply of pork for it.

I was fascinated, therefore, to learn that the British Royal Horticultural Society's  Chilean Sheep Eater Plant was in bloom. There's no mention in the article of any Patagonian relatives, but it's nice when life imitates art.

The Royal Horticultural Society (RHS) at Wisley said the Puya chilensis, a native of Chile, would bloom in the next few days and last about a week.In the Andes it uses its sharp spines to snare and trap sheep and other animals, which slowly starve to death.The animals then decay at the base of the plant, acting as a fertiliser.
No mention of how a new world plant evolves to eat old world sheep – presumably it practiced on guanaco or llamas or whatever in the region.  Also, rather disappointingly, it doesn't have big leafy hands. It looks like a particularly unwell yucca. 

In a newspaper article about a boy who decided she was a girl, and so was to be dressed as a girl, the comments section included these two:

chodd  Sarah Bostock  3 days ago are you serious? do you have an education? Do you have children. My son thinks hes hulk Hogan right now but im not going to paint him green everyday.
Jacqueline Miller  chodd  3 days ago Hulk Hogan is a real wrestler who is white with blonde hair. THE HULK is a green supper hero.

I love the idea of a supper hero.

Monday, June 24, 2013

The political aspects of genetic engineering (1979)

See earlier post for preamble and reasons why I'm posting an old essay.




Restriction enzymes are a class of proteins produced by organisms in order to attack and render harmless invading or foreign DNA. Each type has a recognition site at which it attaches, and then subsequently breaks each strand of DNA, either at a specific sequence or merely close to the recognition site, depending on the enzyme. The recognition sequence is generally a palindrome. The cuts do not occur straight across the DNA and generally leave single—stranded tails, half of which are identical and half of which are the complementary sequence. (See diagram A) Depending on the frequency of this sequence in a given DNA molecule, the restricted fragments may be long or short.

Once work began in earnest on Restriction Enzymes, it was recognised that fragments restricted by one enzyme would form loose associations by hydrogen bonding of the single—stranded tails. This gave rise to the possibility of finding a plasmid with one restriction site, opening it to a linear molecule by the restriction enzyme, and joining the plasmid to a restricted piece of DNA from a different 4 source. This would form a plasmid containing a piece of foreign DNA, a Hybrid Plasmid. Using the self—replicating capability of the original plasmid, the piece of foreign DNA would be propagated in a bacterial cell or ‘cloned’.

It was later discovered how to covalently link the two kinds of DNA, making a more stable hybrid, but a problem was encountered in getting high yields. The hybridising process was forming plasmid—plasmid hybrids, foreign-foreign hybrids and the wanted plasmid-foreign hybrids. Eventually a method was discovered to increase the yield by adding to the single—stranded tail a series of identical bases using poly(dT) and tailing the other species of DNA. with poly(dA). This meant that the different species preferentially joined with each other, and also obviated the need for covalently joining the hybrid molecule as the long complementary sequence gave the molecule sufficient integrity.

Both prokaryotic and histone—deprived eukaryotic DNA can be cloned, in this manner, although eukaryotic gene regulation is different and a gene placed into a bacterium may not be expressed unless supplied with a prokaryotic promoter.


The most common method of preparing DNA for insertion is ‘Shotgunning’, involving extraction of the DNA of whole cells, which is then restricted, prepared and inserted into the plasmid. With this method there is no check on the content of the plasmid —  it may contain a whole gene or one restricted in the centre, or it may merely contain a random piece of repetitive DNA.

The plasmid generally contains an antibiotic—resistance factor so that cells taking up an hybrid plasmid can be distinguished from the rest on growth in a medium containing the antibiotic. The remaining cells are diluted and spread on agar. Each cell grows into a colony, and all the colonies hopefully form a ‘library’ of the total genome of the donor cell. These can be kept for future sequencing and analysis.

Secondly, the DNA may be partly characterized after restriction by its molecular weight as determined by gel electrophoresis.

Thirdly, a specific gene may be identified with a hybridization of its mRNA, after melting the DNA into single strands. Alternatively, also in a situation where the mRNA can be purified, a system can be set up using reverse transcriptase to make DNA complementary to the messenger. However, this cDNA does not contain any spacers or ‘punctuation marks’ present in the original gene, and therefore may not be expressible in a bacterium.

Finally, if the amino—acid sequence of the desired protein is known, using biochemical techniques developed by Khorana and co—workers, it is possible to synthesize DNA molecules base by base. This has been successful in producing Somatostatin, a commercially important brain protein only 14 amino-acids long. Although the initial expenditure is enormous, once the gene is functioning it costs only as much as maintaining an ordinary culture of E. Coli.

Although of necessity oversimplified, this short review covers techniques generally used in the formation of hybrid plasmids. The possibilities for this technique are endless, from cheap insulin (which is now being produced in the lab), to a whole range of antibiotics. It will be possible in the future to cure defective genes in Man, but it is impossible to discuss the morals of this move here.

However with the growing recognition of the ability of DNA molecules to ‘jump’


from site to site, to be taken up as a naked molecule and recombined inside a cell, it became necessary to ask the question: “Is it dangerous to transfer genes of unknown ability to the ubiquitous E. coli, whose natural habitat is inside the human gut?”

A yearly conference of molecular biologists takes place in America, known as the Gordon Conference on Nucleic Acids. In 1973 this took place at New Hampton, Hampshire, where advances in recombinant DNA technology were discussed. From this discussion conferees voted to send a letter to Philip Handler, President of the National Academy of Sciences, about the possible consequences of the new technology. The letter stated:

“We are writing to you on behalf on a number of scientists, to communicate a matter of deep concern...(description of the capabilities of the science)... new kinds of hybrid plasmids or viruses, with biological activity of unpredictable nature may eventually be created. These experiments offer exciting and. interesting potential both for advancing knowledge of fundamental biological processes and for alleviation of human suffering. 

Certain such hybrid molecules may prove hazardous to lab workers and to the Public. Although no hazard has yet been established, prudence suggests that the potential hazard be seriously considered.”
The letter was printed in Science 181 1114, 1973.

The signatories to the letter were Maxine Singer and Dieter Soll. Singer knew more than was presented at the conference. In 1972 she had been in contact with Paul Berg, a researcher at Stanford University. Berg was currently working with SV40, a monkey tumour virus. This virus had been accidentally injected into millions of young Americans in the late 1950’ s in contaminated Polio vaccinations; although no ill effects seemed to ensue, this had caused an interest in SV40 leading to it becoming a lab favourite.

Berg was working with SV40 in order to carry animal genes into other cells, much as a ‘phage is used to transfer bacterial genes. As animal genes were not available at that time, Berg was using Lambdadv for transference into animal cells. It was subsequently realised that if gene transference could occur one way, then perhaps Lambda could transfer the oncogenic SV40 DNA into bacterial cells. There was no evidence for or against this possibility, and work was shut down while Berg talked about the ethics of his work to various people, one of whom was Singer. (Biohazard pp34-38)

Although outwardly little notice seemed to be taken of the letter, much discussion must have taken place, and on the 26th of July 1974, a letter appeared in Science signed by 11 leading scientists of the field calling themselves The Committee on Recombinant DNA. They included Paul Berg, David Baltimore, Stanley Cohen, and James Watson. The letter called for “scientists of the world (to) join with this


committee in voluntarily deferring the following types of experiments, which were the construction of hybrid plasmids containing drug resistance or bacterial toxin that would be used with bacteria not already carrying these genes and in combinations not already found in nature, and secondly the linkage of whole or restricted DNA from oncogenic or other animal viruses to plasmids. The letter also included information on a recent success: Goodman et al’s insertion of the Xenopus laevis DNA coding for ribosomal RNA into a bacterial plasmid, after which RNA complementary to the original DNA had been produced in an E. coli cell.

The letter also called to the Director of the National Institutes of Health (NIH) to set up an advisory committee, and promised an international meeting of scientists to work out guidelines with a view to ending the ‘moratorium’ as the deferral came to be called. Part of the letter was also reproduced in Nature, July 19th 1974 (vol 175) with the headline “NAS ban on plasmid engineering.”

In Nature, July 26th, a reply from the NIH was reported. A letter had been sent to NAS president Philip Handler by the director, indicating that he would set up a committee to look into the possible hazards of the research, and that he would support a meeting of scientists. Asked if the moratorium was established, Baltimore replied that peer pressure meant that no scientist would now undertake such experiments. This later proved to be correct as two researchers destroyed several years work on realising it to be outside the guidelines at that time in force. Peer pressure also involved various Journals refusing to publish the work of these who undertook ‘forbidden’ experiments, and this may well have been a stronger factor in discontinuation than respect for another’s opinion. In this article the first personal opinions began to appear. Ken Murray wrote “The wisdom of using a normal enteric bacterium as host organism in these experiments might be questioned...(others might be used but this)...would be to forsake the wealth of information and experience with E. coli and its viruses accumulated from decades of research.” An article by Prof. Anderson of Colindale appears headed by a quote “The indiscriminate use of antibiotics has exerted more pressure on the bacterial population than could be wielded by all research workers in the field put together.” He also believed that care in using Physical Containment techniques would be sufficient, following the rules laid down for the handling of dangerous pathogens. “The average microbial geneticist or molecular biologist, (their) manipulation chills the blood of anyone accustomed to handling pathogens.” However with the two English laboratory—started outbreaks of Smallpox, among other things, this is no longer a popular view.

In Britain, the subject was taken very seriously. By January 1975, the Government working party set up to investigate had produced a document, The Ashby Report on


the Experimental Manipulation of the Genetic Composition of Micro—organisms. (Cmnd 5880 HMSO Jan 1975.) The report discussed the capabilities of the science, and recommended that in order to encourage research, a second working party should be set up to lay down guidelines in the handling of recombinant DNA. In the meantime the moratorium appears not to have been totally voluntary. There are hints in the literature that directives were handed down to researchers asking them to refrain from the two classes of experiments in the Berg letter.

In the United States, the promised international meeting of scientists took place in February at Asilomar. In attendance ‘were over 150 workers in the field. Many had been briefed before the meeting to form into groups and work out documents to present to the meeting in their own specialist areas. These documents were read and discussed. he idea was to classify experiments according to possible danger and work out a containment system for each level of hazard. The first task was to explain the techniques involved to the laymen reporters and lawyers present, and then to try to explain them to the other groups, as the field was so new that the ‘phage group, say, had very little in common with the eukaryotic group.

At one point James Watson rose to ask “Why, according to the panel, is Xenopus DNA safer to work with than say, cow DNA?” A1thouh this phylogenetic distance principle is now firmly established, no one at the time wanted to answer Watson. The principle assumes that DNA from a source far removed from humans is less likely to be pharmacologically active, and also less likely to carry viral DNA sequences harmful to man than, say, simian DNA. As discussions grew more heated, the scientists discovered the limitation of their own fields (one talked about the possibility of getting malaria from mosquito genes in E. coli, to the derision of others) and the difficulty of coming to an overall agreement on relative dangers which had not been demonstrated and had no parallels up to the present. What is the danger to the relatively unexplored E. coli ecology of a strain carrying a random eukaryotic DNA sequence? Would the ‘coddled’ lab strain, E. coli Kl2, survive outside the lab in competition with wild—type? Is working with a live virus more or less dangerous than cloned viral DNA? Many scientists felt that the classification of risk presented to them was somewhat arbitrary. Some were totally against all controls on research, but these wore in a minority as most realised that if biologists did not limit themselves, then the government, having now been alerted, would legislate quickly and probably harshly. This view was mainly American, the Eng1ish being conditioned to intervention from above in the form of the Science Research Council.

Gradually the leadership of Paul Berg began to take effect, and votes were taken on parts of the statements submitted to and altered by the conference. A classi-


fication system was evolved and sent to NIH for review and an account of the conference sent to Science (published in vol 107, pp991—995, June 1975).

The statement said in part, “the evaluation of potential biohazards has proved to be extremely difficult. It is this ignorance that has compelled us to conclude that it would be wise to exercise considerable caution in performing this research ... most of the work on construction of recombinant DNA molecules should proceed, provided that appropriate safeguards, principally biological and physical barriers adequate to contain the newly created organisms, are employed.” It stated that safeguards should be over—protective initially and reduced as necessary when the true risk should be known. The level of containment should match the estimated risks, as far as that could be determined. As risks were higher with larger volumes small scale experiments should be encouraged. (This section effectively blocking industrial exploitation of gene products.)

The containment system involved a twofold classification: That of physical containment, ranging from a standard microbiological laboratory (class P1) to a laboratory of the type originally equipped for biological warfare (P4), such as Fort Detrick in the USA and Porton Down in England. The second type was of biological containment, involving the production of crippled bacteria and plasmids (host/vector systems) which if left outside a lab environment would not replicate or survive long enough to pass on their DNA. This system was at that time purely hypothetical. Each possible experiment was to be assigned a place in these systems, running from minimal risk (P1 + EK1 where EK1 is the use of standard E. coli K12) to very high risk (P3 + EK3, a severely crippled strain proven to be unable to survive outside the lab), which was at that time an impossible experiment.

Since this self regulation was a purely unselfish act it was not surprising that a politician would misunderstand the motive. Senator Edward Kennedy, a man of great influence in Congress, was Chairman of the Senate Subcommittee on Health. In April 1975, he convened a meeting at which he questioned a panel of four people about the Asilomar Guidelines and how they were arrived at. After Stanley Cohen had explained the basics of the subject to the Senator, Kennedy asked him about possible theft of hybrid plasmids. He was obviously thinking about the theft of fissionables, now a major worry in the other Nuclear Debate; it took some explaining that plasmids could not be counted or weighed and the only possible check was to limit the number of labs working with the plasmid. He then abruptly changed the subject. (Biohazard p149)

Kennedy later delivered an address at the Harvard School of Public Health and delivered an attack on the Asilomar Conference, calling it "inadequate" and saying


that “scientists alone decided to impose the moratorium and scientists alone decided to lift it.” David Baltimore said of the speech, “We weren't arguing that Asilomar was the last word - but at that time we were the only ones that knew what was going on, and our whole point was to alert the public. (Biohazard p156)

Kennedy later signed a Bill to restrict the research.

After Asilomar, the NIH held meetings in San Francisco and Woods Hole to assign categories to experiments. After the latter, a storm of protest arose. The guidelines produced were less strict that those of Asilomar. They were described as “Quite likely to draw the charge of self—serving tokenism.” A petition of 50 bacteriophage workers was sent to DeWitt Stetten, the committee chairman, beginning; “We are concerned that the present draft appears to lower substantially the safety standards set and accepted by the scientific Asilomar.” (Playing God, p125) The media took up the outcry and a further meeting was planned at La Jolla, California, in December.

By the time the La Jolla meeting, took place, American recombinant DNA research was suffering badly. The moratorium was still in force except where the Asilomar Guidelines were considered detailed enough, and this was rarely. Most work still continued was the drive to produce disabled vectors and hosts and was proving more difficult to accomplish than the Asilomar Group had believed. Overall was the fear that if acceptable rules were not produced soon then legislation - by such Antis as Senator Kennedy - was inevitable. The British situation was not any better. The Williams committee was still considering the evidence, and until the report was published very little work could proceed. The rest of Europe, in the main, waited for the European Molecular Biology Organisation (EMB0) to form a decision making committee, and as far as can be determined, kept to the moratorium.

At La Jolla, three sets of guidelines were to be discussed. and synthesised into a document satisfying everyone. Once again, points of disagreement arose immediately. Does a regulation forbidding release of recombinant DNA into the environment include new nitrogen fixing plants? How pure is “highly purified”
DNA? What is an acceptable demonstration of "characterised" DNA? To imagine part of their deliberations - Reptilian DA will not have a high likelihood of containing proteins affecting humans. However what about other animals coming into contact with expressed reptilian DNA in E. coli? If the DNA is from a snake, how can it be purified in order to exclude venom genes? Perhaps it will be useful to clone venom genes, and in this case, to what higher category should the experiment be assigned? If it proves impossible to clone in E. coli due to a weakness, say of the cell wall, and a more vigorous or  pathogenic bacterium must be used, could this experiment still be allowed?


For every DNA discussed a similar set of considerations must be taken into account.

A few days before the La Jolla meeting, a workshop was held at Torrey Pines, Calif. called the Design and Testing of Safer Prokaryotic Vehicles and Bacterial Hosts For Research on Recombinant DNA Molecules". As an example of the success of physical—only containment, Fort Detrick (the highest containment facility in the States) had had 423 hospitalizations and 3 deaths during its period as a biological warfare centre - about 30 years. (Biohazard p 116) This was while working with strains of known pathogenicity. How much more lax were workers going to be when working with E. coli differing from the norm in only a short strand of DNA? At the meeting Berg stated “I’m convinced that physical containment is overrated.” Discussions took place on the possibility of using other organisms besides E. coli, the possibility of building temperature sensitive bacteria which would die if introduced into the human gut, and the like. The only positive advance discussed at the workshop was made by Dr. Roy Curtiss who had crippled an E. coli K12 which; required many nutrients, could not transfer its DNA, and was unable to survive at mammalian body temperatures. This was to be discussed at the next meeting of an NIH committee, in order to determine if it was suitable for EK2 status. Here Sydney Brenner made one succinct point; would NIH be able to afford the time and money to assess every new host/vector system as they began to be presented to them?

Almost simultaneously, the final versions of the Eng1ish and American guidelines were prepared and published. In the middle of 1976, the Williams Report was published. The report called for legislation to be prepared along the lines which it recommends. The main features of the report are: That a body to be known as the Genetic Manipulation Advisory Group (GMAG) should be set up, comprising a committee to advise and monitor each research project. Instead of drafting inflexible guidelines, GMAG would consider each case on its own merits, gradually building up a body of case law. However, guidelines are included in the report, classifying experiments phylogenetically, into a series of 4 categories. The categories are based mainly on physical containment, each experiment being lowered 1 category if a disabled host/vector system is used. There is another subdivision into random or purified DNA, and if the DNA used in purified non—pathogenic, then the system is lowered one category.

The guidelines are, however, not at all exclusive, and discussion with GMAG and local safety officers and committees are an integral part of them. The actual report is 32 pages long, mainly consisting of what comprises the lab containment of each category. (CMND 6600 HMSO August 1976)


The report was incorporated into legislation in force by the end of 1976, and although GMAG did not become a legal entity until 1978, it began operation before then.

On June 23rd, 1976, Dr. Frederickson of the NIH issued the finalized guidelines, somewhat stricter than the Asilomar conference and the following meetings had required. Dr. DeWitt Stetten described them as “in no way opening the floodgates - rather a closing of leaks (in the Asilomar guidelines)” The guidelines are much more detailed that those of the Williams Committee, running to over 200 pages and including sections on the requirements of containment levels, training of lab workers, the constitution of the NIH committee, and appendices on the use of Bacillus subtilis in recombinant DNA research, a report on safety practices in the lab, rules for the care of experimental animals, and the quantity of proprietary bleach needed to sterilise a spill.

As to the administration, the regulations state that the institution to which the NIH grant is made is responsible, via the principal investigator, for determining the level of containment and training the staff to that level. A Biohazard Committee should be set up in each institution, composed of sufficiently qualified people. (NIH Guidelines for Research Involving Recombinant DNA Molecules, June 23rd 1976, US Government Printing Office.)

While the predictable furor (in either camp) over these guidelines was still continuing, the NIH committee met to consider the various hosts and vectors  developed for EK2 status. Dr. Curtiss’ E. coli phi 1776 was passed as EK2 , when used with two plasmids, PSC1O1 and ColE1 Kan. A strain of Lambda developed by Phil Leder was also passed for use with 1776 in this system. (Nature, 262, p2.)

In the City of Cambridge, Mass., a new type of incident occurred, when Mark Ptashne of Harvard submitted a request to his superiors to have several rooms converted to a P3 facility. The buildings are old, infested with cockroaches and ants able to chew their way into labs and feed on any material left on the lab benches. Although many of the staff at Harvard were in disagreement, the local biohazard committee approved the move. This prompted some people to go and see the Mayor, Alfred E. Vellucci, who misunderstood and went away with the idea that the researchers were going to create “things that crawl and things that creep” - which must have been a reference to the cockroaches - and further fueled by a newspaper report, he called a council meeting on June 23rd. Vellucci was not noted for his pride in having two such establishments as Harvard and the Massachusetts Institute of Technology within his city. He accused the head of the biohazards committee of not consulting him or the people (which was denied) and demanded a shutdown on all recombinant DNA research in the city, including that which was


already going on. To cut the story short he allowed a cooling off period  of 3 months during which there would be a “good faith” moratorium, and spent his time collecting facts. On July 7th a council meeting limited the moratorium to P3 and P4 research. In a subsequent vote a “Cambridge Laboratory Experimentation Board” was set up, following the NIH rules but with certain extra powers. He later took his grievances to a meeting of Mayors, and urged them to do likewise. (Nature 262 p163 ). Vellucci’s attitude is understandable had this been a small southern town, but is surprising at Cambridge. The real danger was that other cities would take up his witch—hunt against scientists, leading to a welter of city, State and Federal laws enclosing scientific research.

By February, 1977 this situation had almost come to pass. The State Assembly of California had drawn up a set of guidelines for use in the State which had had 4 readings before it heard that the State Dept. of Health had its own and was preparing to implement them. There was a bitter exchange over the 'ownership' of scientists. Senate and Congress had several bills before them, one by Carter, and one by Kennedy, and others. (New Scientist, l7th Feb, 374 and 17th Mar, 640) However, some of the Bills did not make it by the end, of the session, and in September, they received a severe setback. Senator Kennedy changed his position after receiving evidence from a risk assessment meeting at Falmouth, Mass.. Although the evidence convinced Kennedy, the cautious statement that perhaps the risks were not as high as had been at one time believed, was described as a “scandal” and “misleading and incomplete” by Jonathan King of Science For the People. Kennedy then went on to suggest a commission be set up, including himself, The Assistant Secretary for Health, and the Chairman of the Institute of Medicine. (New Scientist, 6th Oct 1977, p 219)

Reported later that month (New Scientist 27th Oct p219), was a report that ‘natural’ gene engineering occurs in sewage. An outbreak of porcine diarrhoea occurred which proved to be due to the linkage of an enterotoxin gene with a multiple drug - resistance plasmid. This event added weight to the growing feeling that most recombinant DNA molecules have been tried by nature at some time and in most cases discarded.

Since by late 1977 the issue of experimental regulation had been settled (except in the eyes of a vociferous minority), the emphasis shifted to the administration of the bodies formed. Much of the debate centered on secrecy. In December 1977 GMAG held a meeting to discuss confidentiality. The Chairman, Sir Gordon Wolstenholme, had drawn up a document as the matter of patents arose. Since any work had to be reported to the GMAG, any ‘leak’ through the group could lead to a loss of patentability. The legal aspect - whether a bacterium producing a protein was a patentable device - was a secondary though hotly contested argument.


When GMAG became a legal entity in 1978 each member would have to sign the Official Secrets Act, although by the Health and Safety at Work Act 1974 information could be disclosed if anyone's health was at risk. Wolstenholme furthermore had a list of business interests of the members of GMAG,  and saw to it that only disinterested people attended a given meeting. (NS 76 1977 p397)

In late 1978 in America, the debate centered upon excessive secrecy.  Joseph Califano, the Secretary of Health, Education and Welfare, emphasised the need for public participation. “The decision making process must be done democratically  not by special debates.” However, when a proposal for the revision of the NIH guidelines was discussed, it was confined to those in “biomedical circles”. All who testified in support of the proposed revisions were of the field. The lawyer, Professor Boreano, accused the NIH committee of being an “old boys' network” and a report by Nancy Pfund showed that 70% of the members of the Institutional Biohazard committees were in microbiology, biochemistry and molecular genetics. Frederikson’s  proposals to “broaden (the committee) modestly as needed for expertise” and to “include, perhaps, a dissenter from NIH policies” were described as inadequate. To a certain extent, this was taking place in Britain, where ASTMS member Donna Haber declared “even cleaning ladies have a part to play”. (Nature 12th Oct, 1978 p468).

In August 1978 a substantial revision to the NIH guidelines was proposed.  After public and private discussion the new guidelines came into force just before Christmas. The new system meant that almost every kind of experiment was downgraded one step, and several kinds were exempted altogether. The exemptions included:

Work with naked DNA, which is considered unlikely to be harmful
Recombinant DA from a single non—chromosomal or viral source
Recombinant DNA from one organism when propagated only in that organism
Recombinant DNA from species within the following list:
Escherischia Spp.
Serratia Spp.
Edwardiella Spp.
Enterobacter Spp.
 Erwinia Spp.
Citrobacter  Spp.
Pseudomonas Spp.
Salmonella Spp.
Rhizobium Spp.
Klebsiella Spp.
Shigella Spp.
Acinobacter calcoaceticus
Agrobacteriim tumifaciens
Rhodopseudomonas spharoides
Also Local Biohazard Committees were renamed "Biosafety" committees. Dr. Prederickson.


finally stated: “While it is true that other techniques in genetic research, such as cell fusion and chromosome transfer, may result in the formation of recombinant molecules, I don't believe at this time we should mandate or extend the guidelines to research in these areas.’ (Nature 10th Aug 1978 p411)

When the guidelines were released Califano stated that they were a reflection of decreased concern within the scientific community, and also partly because research in America was being held up compared with that in laxer countries. On the implementation of the guidelines, new systems of organisations for the various governing bodies were announced giving a much larger share of the decision making to laymen with other skills, such as lawyers. This was due to a review presented by the DHEW’s General Council, Mr. Peter Libassi. (Nature2l/28 Dec. p 744 & NS 4th Jan 1979) At the same time, Califano found a way to bring industry within the guidelines. He instructed the Food and Drug Administration and the Environmental Protection Agency to use their statutory authority “to require that recombinant DNA research conducted by the private sector complies with the NIH guidelines.”

This change left Britain in a position of repression compared with the USA, a situation still found at the conclusion of reading for this review. The situation is so awry that GMAG were on the point of instructing researchers to notify them if performing a self—cloning (coli—coli) experiment, whereas in the States a lab may clone shotgunned genes of a plant—tumour forming bacterium in coli without any restrictions.
However, a completely new system of classification has been proposed, entirely different from the old phylogenetic approach. This risk assessment analysis involves a mathematical consideration of the possibility of escape or danger at every step - eg, Escape from containment, persistence in the environment, access to risk and the reduction of risk factors. The unveiling of this system caused some disquiet, as many believe that more must be known about the risks before we can start multiplying them together. However, GMAG have agreed to institute the system for a trial period of one year. (Nature 276, 104-7)

This then, is the situation up to April 1979 in Britain and America.



Little can be found in the standard literature about the controls of communist countries, and not much more on the European communities.

A review in New Scientist gave the following information on the European situation. Despite their relative inactivity in the field the leaders were invited to Asilomar. On returning, what research was being done continued under the Asilomar guidelines. By 1975, the French authority, the DGRST, set up two committees, one to look into the ethical side of the work and one to regulate experiments. In Germany, the DFG met in June 1975 to discuss the situation, by which time Holland and Sweden had formed their own committees. By March 1977 official action had. been taken in Belgium, Denmark, Norway, Switzerland, Israel, Italy and some others. The Soviet Union was expected to draft guidelines by June, but no report of this has subsequently been found.

Most European countries accepted the provisional NIH guidelines while waiting for the Williams Report. After both were available, they were faced with a choice of one or a synthesis of the two. As the two are by no means identical, this led to a situation where a researcher would telephone colleagues in another country and ask if a particular experiment may be performed there. There are several international bodies, the European Molecular Biology Organisation (EBO), the EMB laboratory, and the European Science Foundation (ESF). The EtBO committtee recommended a synthesis of the two, and it and the ESF agreed that each country should establish a national committee. Following the issuing of the new laxer American guidelines, most European countries followed, leaving Britain with the harshest legislation in the west. (NS 10th March 1977 p592-4)

In January 1979, the EEC was left considering a suggestion from its commission that genetic engineering be considered hazardous and that each practitioner be registered and approved by the appropriate national authority in each member state. “To request,” says the report, “statutory controls and legislation does not constitute an aggression to progress, but, on the contrary, a recognition of the need to adapt society to new scientific developments. (NS 4th Jan 1979)

—14 —



From the time of the Asilomar Conference, it has been suggested that the best way to asses the risk is to perform the “ultimate experiment” that is, to obtain a newborn germ—free mouse, and to infect it with bacteria, or phage, containing DNA from the tumour—producing mouse polyoma virus, and finding of tumours subsequently would prove the risk of working with recombinant DNA from viruses.

Both Porton Down and Fort Detrick instituted experiments in their P4 labs, but only one result has been announced. The National Institute of Allergy and Infectious Diseases inserted Mouse Polyoma Virus into a phage and injected it into mice. It was found that if only one copy of the viral genome was present, no tumour would develop, but if two were present in tandem, then two out of five of the mice developed tumours. (Nature l5th Feb, 1979) This result would seem to show that the shotgun method of preparing DNA may in fact be less dangerous than purifying genes before insertion.

According to Jonathan King, very many infections are caused by E. coli, usually in people weakened by a previous illness. Blood infections and meningitis are among the diseases aggravated, and King estimates that 10,000 deaths a year are partly caused by E. coli complications. His point is that if a coli carrying the gene for insulin or oestrogen should get into the body, what would the consequences be? (Nature 276 ., Nov 1978) However, E. coli seems to pose little threat to healthy people. Dr. Charles Weissman swallowed a considerable amount of Kanamycin—resistant E. coli containing a marked plasmid. Three days later there was no sign of the plasmid, although the Kanamycin resistant strain of E. coli lasted until an attack of diarrhoea flushed it out of his system. (Playing God, p118—9)

In early 1977, there was an explosion in a biology lab at the university in Pittsburgh. David Baltimore suggested that the explosion was too severe to allow any organisms to survive, but as Friends of the Earth pointed out, there no provisions for this in the guidelines, beyond a stipulation that no lab should be adjacent to a store of inflammable materials. (NS Jan 26th, 1977)

Chargaff and Sinsheimer take the view that planting eukaryote genes in bacteria is “betraying state secrets at the molecular level” and may lead to prokaryotes with dangerously increased infectivity. This poses “incalculable evolutionary dangers”. However, this not a popular view, as many people believe that most combinations of genes have been tried by nature in the past, and if they do not exist now, it is because they have no advantage.


I personally believe that the dangers are overrated and remain undemonstrated. The research is not only a race to keep up with the Russians, but also a tremendous possibility for good. Unlike James Watson, who underwent a change of heart since his signing of the Berg letter, I do not favour a removal of all controls from the research, though I do feel that genetic engineering is an area unfairly singled out by people overawed by a technological society and looking for someone to blame.

One can only hope that further work will be done on finding a host/vector system not so closely associated with man, if possible one with a severely restricted environment. Crippled E. coli, such as phi 1776, may have little chance of surviving outside the lab, but by all accounts it is difficult to keep it alive inside.

Some are inclined to believe that eukaryotic cells provide the answer. Yeast, Saccharomyces cerevisiae, would be an ideal system. Reports on the possibility of using yeast are beginning to filter in. Hennan, Hicks and Fink succeeded in transforming yeast sphaeroplasts using a ColE1 plasmid, and reported that the plasmid integrated on the yeast chromosome, though the latter is in some doubt. While yeast is easy to culture and does not inhabit people and animals, there is still a tremendous amount of work to be done before it could ever be as useful as E. coli.



Biohazard by Michae1 Rogers, Knopf, New York 1977
Playing God by June Goodfield, Hutchinson and Co, London 1977
The Recombinant DNA Debate, Scientific American 22—34 1977
Letter, Science 181 1114, 1973
Letter, Science July 26th 1974
Letter, Nature 174 July 1974
Letter, Science June 1975, pD99l—995.
Nature, 262 p2 1976
Nature, 262 p163 1976
New Scientist 17th Feb 1977 p374
New Scientist 17th Mar 1977 p640
New Scientist 6th Oct 1977 P219
New Scientist 76, p397 1977
Nature 12th Oct p468 1978
Nature 10th Aug 411 1978
Nature 21/28 Dec p744 1978
New Scientist 4th Jan 1979
Nature 276, 104—107 1979
New Scientist 10th Mar 1977 p592—594
New Scientist 4th Jan 1979
Nature 15th Feb 1979
Nature 276, Nov 1978
New Scientist Jan 26th 1977
Clarke and Carbon, Proc. Nat. Acad. Sci.  72 4361—4365 1975.

NIH Guidelines for Research Involving
Recombinant DNA Molecules, June 1976
US Government Printing Office.

The Ashby Report on the Experimental
Manipulation of the Genetic Composition
of Micro—organisms, CMND 5880 HMSO 1975
Report of the Working Party on the Practice of Genetic Manipulation, CMND 6600, HMSO Aug 1976

Background material mainly from the two books, Molecular Genetics lectures,
Editorials in the Weeklies. Acknowledgements for help and advice from Charles
Weiner of Massachusetts Institute of Technology and from Jon Beckwith of Harvard Medical School.

(Cleared up some scanpos, removed university name - Queen Mary College -  as article was not run by school's legal before posting 06/25)

Genetic Engineering is forty years old this year

Genetic Engineering is 40 years old this year.

It was discovered (or invented) in 1973, when researchers found that some organisms deployed "restriction enzymes" to fight off attackers.  These were enzymes that snipped DNA into bits, rendering the invading organism unable to replicate. But each class of restriction enzyme cut DNA at a certain sequence of bases, and since they didn't cut straight across the DNA but above and below that sequence, they left a sticky tail of single stranded DNA wherever they cut. Since single-stranded DNA prefers to be double-stranded, these short tails each continued to look for its complementary cut half to make itself whole.  Scientists quickly realized that if you cut up one piece of DNA with a restriction enzyme,  for instance a plasmid, the short circle of DNA that bacteria use to swap useful genes between themselves, together with another piece of DNA, such as the piece for human insulin, and mixed them together, as they found their apparent partners, some of the products were going to form plasmids with the gene for insulin inside them. And you could then introduce that 'recombinant' plasmid to a bunch of bacteria – such as the well-studied gut bacterium E. coli  – and some of the bacteria would accept it 'thinking' it was a useful gene. They'd then produce insulin.

This breakthrough occurred, as I say, in 1973, just 40 short years ago. Since then we have seen all kinds of developments in molecular biology that rival computing and Moore's Law with ease.  Forty years ago, biologists spent two or three days at a time in the lab trying to add one or two base pairs to something. Today, gene replicators are commonplace and you can get your ENTIRE genome sequenced for less than your life savings (down from $3 billion).

I was at college in 1979, studying Molecular Biology, this 6 year old science, and it eventually occurred to me to ask: How did it come about that scientists get to cut up genes and put them into gut bacteria? isn't it dangerous? Doesn't anyone give a shit?

I wrote an undergraduate essay on the subject. The bottom line: the people who decided it could be dangerous were the scientists themselves, and they put in place a moratorium until they could figure out the dangers. Once the politicians caught up, this was not regarded as adequate, and thundering was heard from city to state to congress. 

Other tidbits included learning that mayors of big college towns are not scientifically literate and will interpret your request to upgrade a cockroach-ridden facility to a sterile one will be seen as something to do with things that crawl and things that creep  - and therefore be vetoed, but on the other hand, as rules evolve you'll see "Biohazard" committees officially renamed to "Biosafety" committees as if Orwell was personally in charge.

What follows is the undergraduate essay itself, from1979.  There are a lot of Britishisms – because I was British – and a great deal of undergraduate earnestness that might be off-putting. The quoting and the referencing style is not-very-good 1970s, and so might not reach the standards of today, but I'm not going to change it.  The discussion section was pure sucking up to my professors, so you can totally discount it.

All in all, if you want to know more about the era, I'd still recommend the major reference in it, Playing God, by June Goodfield.  It's out of date, but that's the point.

The essay follows. 

Thursday, June 20, 2013

Redstar Lokomotiv gigs this week

Redstar Lokomotiv bassist Rob Newby writes to tell me they have a gig tomorrow (or today, as you Brits would call it - Friday) at Forest Gap, in London followed by one on Saturday in Stoke Newington.

I'd go if I could but it would take me a while to get to London from CA. (Although I understand you can now fly in to a London Docklands airport and miss out on all the Heathrow circuses...still probably not enough time.)

Tuesday, June 18, 2013

Redstar Lokomotiv

Redstar Lokomotiv: Nameless

Even more nameless, I guess as I can't see what its name is anywhere.

Yuri Gagarin

Redstar Lokomotive are Space Rock - a kind of Hawkwind for the 2010s.  The music is driving, and the overall effect is transcendentalist. Recommended.

Miniature car chase


Better than most things on TV. How do people find the time to do these things?

Friday, June 07, 2013

What species?

I was having a text conversation with someone who asked whether something I'd typoed was Gungan or Yodaish, and he said, "Who is what species?"

So I asked Google. I typed as far as "what species" and it auto-completed "What species is Yoda?"

So the majority of people asking Google "what species" are asking about Yoda? Whoah.

For those of you in suspense, it said that Yoda's species is unknown. But that's not really the point of this post, which is: Really, Google?

Wednesday, June 05, 2013

Public Service Broadcasting - Spitfire


And I'm sorry that people like Vivian Stanshall and Bob Calvert are not around to see the culmination of Britishness on display here.

Mind you it's the only track of theirs I've ever heard. I'm told they are fabulous live, though.

Monday, June 03, 2013


A couple weeks ago, Charlie Stross asked his followers about headlines that wouldn't have made sense ten years ago.

"The language of alienation."

I thought of half a dozen or so but didn't post. Ever since then, I've been noticing things that really aren't comprehensible unless you've had a dose of the moderns. Here's one:

Facebook: Hey, Your Grandma wants more virtual sheep.

(From reddit's jbpear)


Blog Widget by LinkWithin
I sometimes mention a product on this blog, and I give a URL to Amazon or similar sites. Just to reassure you, I don't get paid to advertise anything here and I don't get any money from your clicks. Everything I say here is because I feel like saying it.