ISIS Report 29/11/04

ISIS Lecture

Fluid Genome & Beyond

Invited lecture presented at The Precautionary Principle in Science and Politics, Federation of German Scientist Conference, 22-23 October 2004, Marie-Elisabeth-Luders Haus & Magnus Haus, Berlin

References for this lecture are posted on ISIS members’ website. Details here.

Mae-Wan Ho Institute of Science in Society, PO Box 32097, London NW1 0XR, UK, www.i-sis.org.uk

A time and a place for gene transfer

These two butterflies, poised so delicately on a flower, are engaged in rampant gene transfer of the natural kind. And they stay like that for hours, quite remarkable considering their short lifespan.

Those butterflies know that there is a proper time and place for gene transfer, and they only do it with soul mates.

Life began some 3.8 billion years ago. The geological epochs are marked by origins of major groups, big transitions, radiations and extinctions. There is a time and place for every group and every species to come on the evolutionary stage. The species did not all evolve at once, or all in the same place, so gene transfer was naturally limited by space and time; except at the dawn of life, when the ancestors of the three major life-domains - Archaea, Bacteria and Eukaryotes – were not yet distinct. As a rule, organisms, including bacteria, have many ways to prevent foreign DNA getting into their genomes.

In contrast, genetic modification involves recombining or joining together new combinations of DNA from widely different sources, and deliberately inserting the artificial constructs into the genomes of organisms [1].

Genetic modification is breaking all the rules of evolution. Genetically modified organisms are unnatural, not just because they have been produced in the laboratory, but because many of them can only be made in the laboratory, quite unlike what nature has produced in the course of billions of years of evolution. It is short-circuiting the evolutionary process.

Thus, it is possible to introduce new genes and gene products, from bacteria, viruses and other species, or genes made entirely in the laboratory, into crops, including food crops, that we have never eaten; that have never even been part of our food chain.

That’s important, particularly in view of discoveries that geneticists have been making since the mid 1970s, which tell us there is really no holding the genome still. Francis Crick and James Watson were largely right about the structure of DNA, but they are woefully wrong on how genes are supposed to determine the characteristics of organisms.

Francis Crick’s Central Dogma of molecular biology decrees that genetic information flows strictly one way, from DNA to RNA to protein, and by implication, to the characteristic determined by that protein. That must have been the inspiration for genetic modification. And if it were really that simple, genetic modification would work just fine.

The scientific myth that launched and sank a thousand companies

But even as biotech companies were set up, genetic engineering as a research tool was making momentous discoveries that would overturn every single assumption of genetic determinism and eventually sink the industry, as explained in detail in my book [2]. A more representative picture is what geneticists in the early 1980s were already calling, "the fluid genome", although it is only within the past two years that it has become respectable to question the Central Dogma [3]:

"It will take years, perhaps decades, to construct a detailed theory that explains how DNA, RNA and the epigenetic machinery all fit into an interlocking, self-regulatory system. But there is no longer any doubt that a new theory is needed to replace the central dogma that has been the foundation of molecular genetics and biotechnology since the 1950s."

Gabriel Dover and Dick Flavell, two geneticists who played key roles in defining the new genetics, put it succinctly in 1982 [4]:

"The application of new molecular techniques reveals that, beneath the level of the chromosome, the genome is a continuously changing population of sequences. Mobility, amplification, deletion, inversion, exchange and conversion of sequences create this unexpected fluidity on both an evolutionary and developmental timescale."

The ‘fluid genome’ is in constant conversation with the environment, which changes not only the patterns of gene expression in each and every cell, but also the structure of the genome and the genes. You can read more about the latest developments in successive issues of our magazine, Science in Society.

Natural versus artificial genetic engineering

James Shapiro [5], whose specialty is in jumping genes, referred to the processes of the fluid genome as the "natural genetic engineering" that the organism has to do to survive. This natural genetic engineering has all the appearance of being quite precise, and to be regulated by the organism as a whole. It is part of the ‘dance of life’ in which every part of the organism – down to individual molecules - is intercommunicating and hence working together in a perfectly coordinated way. In contrast, artificial genetic engineering is crude and uncontrollable, basically because the human genetic engineer does not know how to intercommunicate with the whole organism, and can only gain force-entry into the genome, using aggressive means to make the organism express the foreign genes (see below).

A typical unit-construct for artificial genetic engineering consists of a promoter, a gene-switch that says to the cell, "copy the following message (the gene or coding sequence) for making a protein", and another signal, the terminator, to say, "stop here, end of message". All three parts are often from different sources. The gene itself could also be a composite of different DNA, made artificially in the laboratory, and with substantial changes in the coding sequence as well [6].

So far, the only way to get foreign genes expressed reliably in the organism is to use very aggressive promoters belonging to viruses. The cauliflower mosaic virus (CaMV) 35S promoter is the most widely used.

The artificial constructs are further spliced into gene carriers or vectors, and introduced into cells by invasive methods that result in random integration into the genome, giving rise to unpredictable effects, including gross abnormalities in animals and unexpected toxins and allergens in food crops. One recent publication characterises the GM insert as follows [7]:

"… scrambling of transgene sequences through recombination of both large and small non-contiguous fragments of the delivered DNA, frequent incorporation of genomic DNA sequences into the transgene loci and rearrangement in the genome DNA flanking the transgene locus."

A transgenic line is essentially regenerated from a single cell in which specific events of transgenic DNA integration occurred. Each event will give rise to a different line. In other words, there is no possibility for quality control. This problem is compounded by the overwhelming instability of transgenic lines, because the artificial constructs cobbled together from DNA of different sources tend to have weak joints.

I have referred to the instability of transgenic lines as the "best kept open secret", because everybody has known about it for years, but agree to say nothing, while regulators turned a blind eye. I have been pressing for "event specific" molecular characterisation of the structure of the insert(s) and their position(s) in the genome in successive generations, as proof that the transgenic line is stable [8]. This requirement was finally written into the 2001 European Directive (2001/18/EC) for deliberate release.

But it was not until last year that French government scientists checked the transgenic inserts of five transgenic lines: Monsanto’s MON810 maize, Roundup Ready soya, GA21 Maize, Bayer’s T15 maize and Syngenta’s Bt 176 maize; and in every case, the transgenic insert(s) had rearranged, not just from the construct used, but since characterised by the company [9, 10]. Moreover, many breakpoints involved the CaMV 35S promoter, there is scrambling of host genome at the site of insertion, and the inserts appear to show a preference for retrotransposons, which is bad news, because that means they could easily transfer again, and spread.

The French scientists reported their results in a poster at a conference in Barcelona in June 2003 with the title, "Characterization of commercial GMO inserts: a source of useful material to study genome fluidity" [9]. It is indeed genomic fluidity that makes genetic modification both futile and dangerous [2].

Belgian scientists confirmed the instability of the transgenic lines analysed by the French [11,12]. But there were small and large discrepancies between the two studies, which suggest that the transgenic lines were also non-uniform. Either one of those aspects would make the transgenic lines illegal for Europe under the current deliberate release directive. I communicated the findings to the European authorities and other governments.

Genetic instability is a serious safety issue, as the GM varieties are now different from earlier generations that were assessed and licensed as safe for cropping or for food and feed.

Major uncertainties over safety

Indeed, there are major uncertainties over the safety of GM food and feed that have yet to be addressed. I give a list below.

• The European Food Safety Authority (EFSA) gave Monsanto’s GM maize Mon863, containing the biopesticide Cry3Bb1 a positive assessment, despite "very disturbing" results of feeding trials showing kidney malformations and increased white blood cells in male rats and high blood sugar and reduced immature red blood cells in female rats [13].
• Last year, up to 100 villagers in the south of the Philippines living near GM maize plots became ill when the GM maize came into flower [14]. Terje Traavik of the Norwegian Institute of Gene Ecology in Tromsø found antibodies to Cry1Ab produced by the GM maize in the blood of 39 villagers [15]. The same illnesses recurred this year [16].
• Between 2001 and 2002, twelve dairy cows died on a farm in Hesse, Germany, after eating Syngenta’s Bt176 GM maize, and others in the herd had to be slaughtered on account of mysterious illnesses [17]. The Spanish Food Safety Authority has withdrawn authorisation for Bt176 cultivation [18].
• Arpad Pusztai and colleagues found that GM potatoes with snowdrop lectin adversely affected every organ system of young rats, and the stomach and small intestine lining grew up to twice the thickness of controls [19].
• Scientists in Egypt found similar results in the gastrointestinal tract of mice fed GM potato with Bt toxin [20].
• US Food and Drug Administration had data since the early 1990s showing that rats fed GM tomatoes with antisense gene to delay ripening developed small holes in their stomach [19].
• Aventis (now Bayer) found 100% increase in deaths of broiler chickens fed glufosinate-tolerant GM maize T25 compared to controls [21].
• Numerous anecdotes from farmers and others indicate that livestock, wildlife and lab animals avoid GM feed, and fail to thrive or die when forced to eat it [21, 22].

Different species of GM food or feed with different GM genes have caused problems in many species of animals. You don’t have to be a scientific genius to suspect that there is something wrong with the GM process itself or the GM insert common to them. One of these is the CaMV 35S promoter.

The CaMV 35S promoter

In 1999, two laboratories [23, 24] independently confirmed earlier suspicion that the CaMV 35S promoter has a recombination hotspot, which resulted in frequent breaks and rearrangements of the transgenic DNA and other signs of increased transgenic instability.

My colleague Prof. Joe Cummins was the first to warn against using the CaMV 35S promoter or any viral genes in plants because it had been shown that such viral transgenes in plants could recombine with naturally occurring viruses to generate, in some cases, super-infectious viruses. Subsequently, the CaMV 35S promoter has been found to substitute for the promoter of many plant and animal viruses to produce infectious viruses.

We wrote a review [25] drawing attention to the hazards of the promoter, calling for all GM crops containing it to be withdrawn. We were viciously attacked and vilified. We replied to all the scientific criticisms in a paper [26] that was much longer than the original, and our critics never acknowledged it. In the course of debating with our critics we uncovered even more damning evidence: the CaMV 35S promoter is active in species across the living world: bacteria, fungi, algae, plants, animal and human cells included [27]. Again, our critics never acknowledged this to themselves or to the public.

Because the CaMV 35S promoter is very aggressive and active in animal and human cells, there is a possibility that it could trigger cancer by making certain oncogenes over-express. The problem is worse, because in some cases, the CaMV 35S promoter contains extra ‘enhancer’ and booster sequences; and none of these constructs has been tested for safety.

For example, the AGBIOS Database describes Mon 863 maize as follows [28]:

"The introduced DNA contained the modified cry3Bb1 gene from B. thuringiensis subsp. kumamotoensis under the control of the 4-AS1 promoter (CaMV 35S promoter with 4 repeats of an activating sequence), plus the 5’ untranslated leader sequence of the wheat chlorophyll a/b binding protein (wt CAB leader) and the rice actin intron. The transcription termination sequence was provided from the 3’ untranslated region of the wheat 17.3 kD heat shock protein (tahsp17). The modified cry3Bb1 gene encodes a protein of 653 amino acids whose amino acid sequence differs from that of the wild-type protein by the addition of an alanine residue at position 2 and by seven amino acid changes."

Some of you may recall the headlines in 2000 on the first success of gene therapy after some 12 years trying. Gene therapy is the genetic modification of human cells, and use methods and constructs very similar to those employed for genetic modification of animals and plants.

Bone-marrow cells from infants suffering from an X-linked Severe Combined Immune Deficiency were genetically modified in a petri-dish, and the transformed cells re-implanted into the patient.

Eleven infants were treated and nine were apparently successful. However, among the nine successes, two developed leukaemia in 2002. It turns out that the transgenic DNA jumped into a gene, that when over-expressed, triggers cancer [29-32].

Box 1 summarises why GM is inherently hazardous. These concerns have never really been properly addressed.

Yesterday, the representative of your research minister asked, "Which science do we need for a precautionary politics?"

My answer is that we need a different kind of science, and the fluid genome is pointing the way to it.

Beyond the fluid genome

IBM has been building a new supercomputer, Blue Gene, projected to be complete in two years time, which will be the most powerful supercomputer on earth [33]. It will perform one quadrillion (10 to power 15) operations per second. Even then, it will take a year to simulate an average protein folding into shape.

Our body contains some 100 trillion (10 to the power 14) cells, each expressing a unique repertoire of the millions of proteins that could be made. Not only do the proteins fold simultaneously to perfection in split seconds, they also carry out millions of catalytic reactions at the rate of thousands to hundreds of thousands cycles per second. And all the diverse activities are orchestrated, from the molecular and microscopic through to the macroscopic domain, from trillionths of a second to hours, days and years.

The organic whole is quintessentially diverse and pluralistic. The organism is the antithesis to uniformity and homogeneity. It is truly remarkable that we should habitually think of ourselves as "I" in the singular. So what makes such a vast conglomerate of diverse molecules and cells a whole?

One way to think of the tens of thousands of genes and millions of proteins that must work together as a whole, is that they constitute a ‘molecular democracy of distributed control’, a phrase first introduced by Henrik Kacser [34], who was in Edinburgh University.

Conventional biochemistry still tends to see enzymes and their substrates bumping into each other as they wander about haphazardly and randomly in a solution of water inside the cell. But since the early part of the last century, evidence has been accumulating that the cell is intricately organised, perhaps down to the level of individual molecules; much of that evidence was reviewed by Joseph Needham, distinguished Cambridge biochemist later turned historian of Chinese science, in his book, Order and Life, first published in 1936 [35].

Not just enzymes and substrates, but even the water molecules are organised in a liquid crystalline continuum, as Needham had predicted in his remarkably prescient book, and as we discovered in my laboratory in 1992, when we half stumbled upon a novel, non-destructive imaging technique that enabled us to see the insides of live organisms in pure, vivid colours. It inspired me to write a book [36] around what the colours mean, entitled, The Rainbow and the Worm, The Physics of Organisms. This book also explains why organisms are so sensitive to low doses of toxic agents, by the way.

In this new vision of the organism as a liquid crystalline continuum, electric and electromagnetic energies of all kinds enable the molecules to intercommunicate and coordinate their activities. When intercommunication and coordination are perfect, we get to a state of coherence or wholeness. The living organism is so coherent that it looks like a dynamic liquid crystal display, because all its molecules are moving coherently together.

I have referred to this dance of life as ‘quantum jazz’, where every single player, however small, is improvising freely from moment to moment, and yet keeping in beat and in sync with the whole.

Organisms are not controlled from the outside, that much is clear. They are not even controlled from the inside. There is no ‘master-gene’ turning development on, nor armies of ‘control’ genes that are not themselves also ‘controlled’.

The ideal organic whole, quintessentially pluralistic and diverse, works by total participation and intercommunication, and is at once most coherent and most free, for the parts as for the whole.

In contrast, the dominant mechanistic culture reduces all to uniformity and homogeneity, it operates in rigid hierarchies of controller versus the controlled, and sees only inevitable opposition between the individual and the collective, the public and the private. This failure to see nature as organic, entangled wholes is the ultimate source of all wars and conflicts, and of the lack of precaution. Science with precaution is also science with social responsibility.

Taking the ideal organic whole seriously involves entirely new programmes of scientific research in sustainable agriculture, holistic health and sustainable energy use, with equal partnerships between scientists and traditional health practitioners and farmers in the field. We have initiated a discussion paper Towards a Convention on Knowledge [36], which has been widely adopted by scientists and indigenous peoples organisations.

And to turn our words into deeds, we launched an Independent Science Panel (ISP) to produce our own report [37], The Case for a GM-Free Sustainable World, calling for a ban on GM crops and a comprehensive shift to non-GM sustainable agriculture.

The ISP had a very successful briefing to the European Parliament on 20 October 2004, where we put this message across loud and clear [37, 38].

To live with the fluid genome is to leave behind the mechanistic culture of death and destruction for a thoroughly organic paradigm that regenerates life and creativity; that would truly nurture individual freedom and diversity with universal love.

So let us work freely, creatively and coherently together, like the dance of life that I am going to show you now.

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