The precision, complexity, and all-pervasiveness of natural genetic modification leave organisms and ecosystems particularly vulnerable to artificial genetic modification.
by Dr Mae-Wan Ho
Invited lecture at 1st Forum of Development and Environmental Safety, under the theme “Food Safety and Sustainable Agriculture 2014”, 25 – 26 July 2014, Beijing, China.
A fully referenced version of this article is posted on ISIS members website and is otherwise available for download here, or with the accompanying powerpoint presentation here.
The new genetics and natural genetic modification
Genetics has been turned upside down beginning the mid-1970s and especially since the human genome was announced in 2000. The tools of genetic manipulation have been advancing and improving in leaps and bounds. Today, geneticists can dissect and analyse the structure and function of genes and genomes in minute detail down to the base sequence of a nucleic acid in one single cell using ‘next generation deep sequencing’ (see Box 1 reproduced from [1]).
Box 1 Next generation deep sequencing Next generation sequencing (NGS) extends sequencing across millions of reactions taking place in parallel. This enables rapid sequencing of large stretches of DNA base pairs spanning entire genomes, with instruments capable of producing hundreds of gigabase (Gb) data in a single sequencing run. To sequence a single genome, the genome is first fragmented into a library of small segments that can be uniformly and accurately sequenced in millions of parallel reactions. The newly identified strings of bases, called reads (of a defined length) are then reassembled using a known reference genome as a scaffold (re-sequencing), or in the absence of a reference genome (de novo sequencing), assembled by overlaps. The full set of aligned reads reveals the entire sequence of each chromosome in the genome. NGS data output has been rising steeply since its invention in 2007, when a single sequencing run could produce a maximum of about one Gb data. By 2011, the rate has reached nearly a terabase (Tb, 1012b), a thousand fold increase. By 2012, researchers can sequence more than 5 human genomes in a single run, producing data in roughly one week at a cost of less than $5 000 per genome. The $1 000 genome is now within our grasp. NGS high throughput capacity has enabled ‘deep sequencing’ of genomes and transcriptomes to look for rare DNA variants or rare species of RNA transcripts. Deep sequencing means that the total number of reads is many times larger than the length of the sequence under study. ‘Depth’ (coverage) is the average number of times a nucleotide is read. |
Back in the mid-1970s to 1980s, the primary motivation for both artificial genetic modification and the human genome project was classical Watson-Crick molecular genetics based largely on the Central Dogma that genes control the characteristics of organisms in linear causal chains. That picture has been overwhelmingly contradicted by empirical findings that began to trickle, then stream, and pour out of laboratories. The new genetics is telling us in no uncertain terms that the genome is fluid and dynamic. It is constantly conversing with the environment in circular networks that mark and change genomic DNA in myriad ways, with both DNA and RNA taking part in transmitting genetic information and in executing and altering genetic information in real time. I use the term ‘natural genetic modification’ for the totality of changes made by organisms in the genetic information of cells and tissues as part of their survival strategy, and some of the changes are passed on to the next generation(s) [2]. Artificial genetic modification invariably interferes with the natural process, and I suggested that is [3] Why GMOs Can Never be Safe (SiS 59).
Natural genetic modification employs the same copy, cut and splice tools as artificial genetic modification, but with much greater finesse and precision. (Artificial genetic modification is possible only by usurping the tools of the natural process.) It enables organisms to express genes in different parts of the genome at the appropriate levels, or mark and modify them, as and when required in specific cells and tissues.
To produce even one protein – originally thought to be single continuous message – requires elaborate cut and splice operations. The international research consortium project ENCODE (Encyclopedia of DNA Elements) data have revealed that the vast majority of genomic DNA include ‘non-coding’ segments [4, 5]. The ‘gene’, a theoretical construct that has never been possible to define rigorously, is now known to be scattered in bits across the genome, overlapping with bits of multiple genes that have to be spliced together before translating into a protein. The term used for the bits is ‘coding sequences’ or exons.
The expression of each gene already requires the assembly of a small army of special molecular engineers. The human genome contains about 20 000 protein-coding genes, most of which would be active in one cell or other of the body at any one time.
That’s not all. Humans contain practically the same number of protein-coding genes as nematodes that have only 1 000 cells compared to humans’ 1014 cells. In contrast, non-protein-coding DNA, largely absent from bacteria, increases with increasing complexity of organisms [6] (see [7] Non-Coding RNA and Evolution of Complexity, SiS 63), reaching 98.8 % of the human genome. Much of that was considered ‘junk DNA’ until geneticists discovered to their surprise that most of the sequences (latest estimate > 85 % [8]) are dynamically and differentially transcribed in tissues and cells, into many families of short and long non-coding (nc)RNAs. These ncRNAs regulate gene expression and genome architecture by interacting with DNA, RNAs, proteins, and other cofactors.
Cells and tissues also respond to their environments by recruiting different contingents of molecular engineers for marking and modifying, cutting and splicing specific RNA or DNA, or remodelling chromatin (complex of DNA and histone proteins) at specific genome locations. We know only a small fraction of the vast amount of details involved. But it is already so remarkable that leading molecular geneticist James Shapiro at University of Chicago is saying that practically nothing happens at random [9, 10]. Cells and their genomes are not [9] “passive victims of replication errors or DNA damage” (see [11] Evolution by Natural Genetic Engineering, SiS 63). Instead, just about everything, including so-called random mutations happens by “natural genetic engineering” (almost the same as what I call natural genetic modification).
Indeed, cells have special proof-reading and error correcting functions to eliminate and repair damaged/mutated bases in the genetic material, getting errors down to below 1 in a billion bases under normal conditions. But during starvation, bacteria can also target precise mutations to specific sites in the genome to generate new metabolic functions [9, 10]. Such ‘directed’ or ‘adaptive’ mutations are now well-documented in bacteria as well as human cells (see [9] Non-Random Directed Mutations Confirmed, SiS 60). The human immune system executes accurate cut and splice genome rearrangements to create a large variety of immunoglobulin chains and also targets hypermutations to specific immunoglobulin variable sites to generate huge diversities of antibodies for defence against invading pathogens.
I have only given you a tiny sampling of the organisms’ remarkable feats of natural genetic modification, which are precisely targeted, context dependent, complex, and negotiated by the organism as a whole. It is a well-known paradox that both plant and animal cells maintained in culture undergo uncontrollable mutations and chromosomal rearrangements (somaclonal variations) [13], in contrast to cells within the healthy organism, which show extremely low levels of ‘random’ mutations.
Artificial genetic modification acts against and undermines the natural process
The targeted precision and complexity of natural genetic engineering/ modification makes clear that genetically modified organisms (GMOs) created by the crude methods generally used until very recently can only be highly unsafe [2, 3]. Much current effort is dedicated to ‘genome editing’ using guided or otherwise specific DNA cutting enzymes to alter DNA sequence at target locations in the genome. But off-target, cytotoxic effects continue to dog the latest attempts [14-16]. Artificial genetic modification invariably interferes with natural genetic modification, and it is well-nigh impossible to avoid doing so. It depends on disrupting and overriding the organism’s own minutely choreographed process, the result is uncontrollable and unpredictable off-target effects.
To override the natural system, the synthetic GM DNA molecules are forced into the cells in large numbers with stressful methods such as gene gun [17] or electric shock [18], carried by vectors (such as the Agrobacterium binary vector) designed to invade genomes. Further, the transgenes are equipped with aggressive promoters such as the cauliflower mosaic virus (CaMV) 35s and similar viral promoters in order to force the cells to express the foreign genes (see [2]). These and other stresses (as Shapiro points out) are well-known to mobilize endogenous transposons (jumping genes) that scramble and destabilize genomes. Consequently, transgenic lines are unstable, both from silencing and loss of transgenes, which makes horizontal transfer of transgenic DNA more likely than non-transgenic DNA. For the same reasons, transgenic lines often suffer yield drag; while complete crop failures have been reported in India [19-22] (GM Crops Failed, SiS 13/14, Transgenic Cotton Offers No Advantage, SiS 38) and during the recent drought in the United States [23] (GM Crops Destroyed by US Drought but non-GM Varieties Flourish, SiS 56). The same transgene instability may have been responsible for the latest failure in the pilot commercial planting of Bt brinjal in Bangladesh [24] (Bangladeshi Bt Brinjal Pilot Scheme Failed, SiS 63).
Natural genetic modification is not something that happens only occasionally, it is constant and all-pervasive in the life of the organism; interconnecting millions of molecular players in a cell at any one time. That is why artificial genetic modification has failed to produce any ecologically beneficial or complex traits, while even the ‘single gene’ traits are unstable. Artificial and natural genetic modification is contrasted in Table 1.
Table 1 Artificial vs natural genetic modification |
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| Artificial | Natural |
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Context-inappropriate, hence uncontrollable & unpredictable hazards: scrambled |
Context-dependent |
|
Depends on disrupting the natural process, hence adverse & hazardous interference Stressful methodology – gene guns, electric shocks, invasive vectors (Agrobacterium), aggressive virus promoters (CaMV 35S) – multiply hazards and destabilize genomes, resulting in transgene instability, yield drag, and horizontal transfer of transgenes. |
Always appropriate to context and hence no adverse interference |
|
Reductionist aims, without regard to the whole organism (uncontrollable somaclonal variations of cells in culture) |
Negotiated by the organism as a whole (very low random mutation rates in cells unless targeted) |
Artificial GM imperils the biosphere by hijacking the natural process
Despite its failures and inefficacy, artificial genetic modification can nevertheless endanger organisms exposed to its sphere of influence. There is abundant reliable evidence that GM feed and other exposures to GMOs invariably cause harm, regardless of the species of animal, GM crop, or the genes and constructs involved. The health impacts of GMOs are independent of those caused by glyphosate herbicides, the world’s top herbicide used with glyphosate/Roundup tolerant GM crops and for other purposes, which fill volumes on their own. Laboratory findings obtained by scientists independent of the biotech industry have fully backed up the real life experience of farmers in the field: liver and kidney damage, infertility, excess deaths, birth defects, tumours, cancers. Since our last comprehensive review in 2013 [25] Ban GMOs Now (ISIS special report), further corroborating evidence have become available.
Male rats fed Bt corn MON 810 showed a wide range of organ and tissue abnormalities [26, 27], these effects were replicated in male and female rats and their offspring during a three month feeding trial [28].The changes were attributed to the Cry1 AB toxin engineered into the Bt corn. Certainly, the transgene product itself is a conspicuous source of harm, as is the toxicity of the herbicides used with herbicide tolerant GM crops. There are two other major categories of harm arising from GMOs: the uncontrollable, unpredictable effects of artificial genetic modification and the GM insert and its instability, which I have dealt with at some length previously (see [2, 3, 25]).
Here, I shall highlight aspects that are increasingly important in the ‘new generation’ GMOs being pushed onto the market. New nucleic acids and other unintended artificial modifications of the genome can act like a Trojan horse to harm organisms and ecosystems by hijacking the natural process; especially via nucleic acids in food, horizontal gene transfer, and trans-generational inheritance.
New nucleic acids enter the human food chain to alter gene expression & worse
A research team from China first reported in 2011 that short regulatory micro (mi)RNAs (~ 22 nt) originating from plants eaten can resist digestion, enter the bloodstream, and get into cells to change the expression of specific genes [29]. It raised serious concerns over the safety of GMOs, for they introduce entirely new nucleic acids into the human food chain [30] (How Food Affects Genes, SiS 53), both intentionally created and unintended within the GMOs. Monsanto orchestrated an attempt to discredit this finding (see [31]). But it has been abundantly confirmed and extended.
A survey of human plasma for miRNAs using next generation sequencing (NGS) carried out by Kai Wang and David Galas at the Institute for Systems Biology and Paul Wiles at University of Luxembourg found extensive and widespread presence of miRNAs originating from grains and other food items including soybean, tomato and grape. Some of the miRNAs or miRNA-like molecules were synthesized and transfected into mouse fibroblasts, and found to alter the expression profiles of a number of genes [32].
Researchers at Moringga Milk Industry Zama Kanagawa, Japan, using more conventional microarray and quantitative PCR analyses, identified 102 miRNA in cow’s milk, 100 in colostrum and 53 in mature milk, with 51 common to both [33]. In addition, some messenger(m)RNAs were found in the milk. These miRNAs and mRNAs were wrapped inside lipoprotein vesicles rather like the exosomes identified in the bloodstream of animals (as well as in cell culture medium) that are believed to be part of the nucleic acid intercommunication system of the body (see below). Both miRNAs and mRNAs were also present in infant formulas bought from Japanese supermarket.
A team at University of Louisville Kentucky USA succeeded in isolating exosome-like nanoparticles from the edible plants ginger root, grape, grapefruit and carrot, which contain proteins, lipids and miRNA. These were taken up by intestinal macrophages and stem cells of mice and preferentially induced the expression of antioxidant genes and genes involved in the maintenance of intestinal homeostasis [34] that protect against all kinds of chronic diseases including cancer. This serves to remind us that epigenetic effects can be beneficial or harmful, and why it is important to eat good wholesome food.
Not only RNA, but also DNA from meals eaten could be identified. A study led by Sándor Spisák at Hungarian Academy of Sciences in Budapest and Harvard Medical School Boston, Massachusetts in the USA analysed over 1 000 human adult samples from four independent studies using NGS and NGS databases, and found DNA fragments derived from food in all plasma samples, some large enough to code for complete genes [35]. The team found DNA from dozens of plant species differing between individuals, mostly likely reflecting their diet, including grains, beans and vegetables. There was also meat DNA, but because animal DNA is more similar to human DNA, it is more difficult to ascertain.
There is increasing evidence that cells in the body intercommunicate via circulating nucleic acids actively secreted into the bloodstream [2, 36] (Intercommunication via Circulating Nucleic Acids, SiS 42). These circulating nucleic acids are able to influence gene expression in other cells and to transform other cells by horizontal gene transfer. Cancer cells use the system to spread cancer around the body. Thus, nucleic acids from meals eaten including those containing GMOs may also enter the bloodstream to influence gene expression and to transfer horizontally into the cell’s genome with potentially harmful consequences associated with insertion mutagenesis, including cancer development and genome instability. The cauliflower mosaic virus (CaMV) 35S promoter, used to drive the expression of transgenes in almost all commercially grown GM crops, is known to contain a recombination hotspot (hence prone to horizontal gene transfer), is promiscuously active in all kingdoms of organisms including human cells, and specifically induces transcription factors required for CaMV and HIV replication [37] (New Evidence Links CaMV 35S Promoter to HIV Transcription, SiS 43); and after it has been widely used in commercially grown GM crops for 20 years, regulators ‘discovered’ it overlaps with another dangerous virus gene involved in RNA silencing [38] (Hazardous Virus Gene Discovered in GM Crops after 20 Years, SiS 57), and most likely involved in host defence against virus attacks.
The new GM crops based on RNA interference (RNAi) are obviously hazardous in this regard, as RNAi – based on sequence-specific interactions between regulatory RNA and target(s) (see [39] New GM Nightmares with RNA, SiS 58), are known to tolerate numerous mismatches, changing in different cells at different times, and certainly beyond control [40, 41] RNA Interference "Complex and Flexible", SiS 59). The potential off-target effects are huge.
Horizontal transfer of GM nucleic acids
Horizontal gene transfer is part and parcel of natural genetic modification. In its simplest form, horizontal gene transfer involves uptake of foreign nucleic acids into cells and incorporation into the cell’s genome. For this very reason, GMOs carrying bacterial and viral genes and other synthetic genetic elements can readily exploit this natural avenue to spread antibiotic resistance and to create new pathogens as some of us have been warning since the late 1990s [42]. All the more so, as GM constructs are designed to overcome natural barriers and to invade genomes [2, 3]. There is already evidence that widespread unintended horizontal transfer of GM DNA has probably occurred. The most decisive evidence was provided in 2012 by Li Jun Wen, Jin Min and colleagues at Sichuan University in China [43]. (It appears that scientists in China are taking the lead in biosafety research.) The team set out to look for horizontal transfer of the ampicillin antibiotic resistance marker (arm) gene blá, which has been extensively deployed in artificial genetic modification. By using the appropriate molecular probes (primers), sufficiently sensitive polymerase chain reaction (PCR) for detection, and constructing a metagenomics plasmid library, they detected the GM arm gene in all of China’s rivers, despite the fact that the country has not been growing any GM crops commercially, but field trials of GM crops containing the arm gene have been carried out [44] (GM Antibiotic Resistance in China’s Rivers, SiS 57). This is the first study of its kind in the world. The researchers concluded that horizontal transfer of GM antibiotic resistance gene may be linked to the rise in antibiotic resistance in livestock and humans in China. The possibility that genetic engineering biotechnology may have contributed to the increase in antibiotic resistance and the emergence of new viral and bacterial pathogens was raised by some of us since the 1990s [42], but it has never been admitted by the World Health Organisation or any other agency monitoring the spread of antibiotic resistance and infectious diseases.
New findings suggest that even very short (~20 bp) and damaged pieces of DNA can be taken up and incorporated in the bacterial genome [45], making it clear that GM nucleic acids can indeed spread antibiotic resistance and create new viruses and bacteria that cause diseases by horizontal gene transfer and recombination (see [46] Horizontal Transfer of GM DNA Widespread, SiS 63). But regulatory agencies in the US, Europe, and elsewhere are still denying that horizontal transfer of GM DNA has taken place, based on unfounded assumptions and the failure to use sufficiently sensitive up-to-date detection methods with the correct molecular probes. It is a case of “don’t look, don’t find.”
Transgenerational inheritance
Finally, the effects of GMOs are perpetrated and amplified across generations, because they can be inherited. As mentioned earlier, the scope of genetic information passed onto the next generation of cells and organisms has greatly expanded to include besides genomic DNA, DNA marks (such as methylation), histone marks, chromatin structure (whether inactive heterochromatin or active), plus a host of small RNA regulators of gene expression. It appears that different RNAs not only register so-called epigenetic change as the organism responds to the environment, they also transmit acquired genetic information to subsequent generations independently of DNA (reviewed in [47] RNA Inheritance of Acquired Characters, SiS 63). Once again, this highlights the potential perils of using RNA interference in GMOs (see above). The exposure of organisms to regulatory RNA molecules (without transgenesis) could already result in the transmission of effects to subsequent generations [48].
Certain small regulatory RNAs can be independently replicated by RNA-dependent RNA polymerase, an enzyme present in RNA viruses that do not go through a DNA intermediate, while another form of this enzyme is present in all eukaryote genomes [49], and is suspected to be involved in the maintenance of transcriptional silencing.
Regulatory RNAs are passed on via germ cells from one generation to the next, and they may be stabilized by RNA methylation to survive the maternal-to-zygote transition during early embryogenesis to influence gene expression in the development of the offspring.
RNA also operates in a RNA-memory system to distinguish ‘self’ and ‘non-self’ via viral and other sequences integrated into the genome that can defend the host from viral infections and animal predators. This memory system is centrally involved in maintaining active as well as silenced genes across generations.
Female germ cells carry maternal RNAs, and maternal effects are well-known and generally accepted. Much less known is that male germ cells are particularly adept at picking up somatic RNA and DNA and carrying the cargo into the egg at fertilization in a process that has come to be known as ‘sperm mediated gene transfer’ [50, 51] (Sperm-Mediated Inheritance of Acquired Characters, SiS 63) . While most of the extraneous nucleic acids added to mature sperm in vitro are taken in and transmitted as extra-chromosomal DNA in mosaic fashion (present in some cells), integration into the genome can also occur. The inheritance of acquired characters via the male germ cells has been demonstrated in all species examined.
The first hint that fathers can pass on acquired characters was the discovery that the experience of young boys could affect not just their health in later life, but also the health of their sons and grandsons. That was the beginning of the epigenetic revolution [52] (Epigenetic Inheritance – What Genes Remember, SiS 41). All kinds of life experiences, good and bad, from caring mothers to environmental toxins, leave epigenetic imprints that are passed on for generations afterwards (see [53, 54] Caring Mothers Strike Fatal Blow against Genetic Determinism, and Epigenetic Toxicology, SiS 41). In the case of environmental toxins, Michael Skinner’s reproductive biology lab at Washington State University Pullman in the United States first reported in 2005 that injecting pregnant rats with endocrine disruptor fungicide vinclozolin caused sperm abnormalities that persisted in the male progeny for at least 4 generations [55]. The effects on reproduction correlate with altered DNA methylation pattern in the germ line (though the methylation differences vary widely among the animals, and failed to satisfy his critics [56]). Subsequently, they found that insecticides DDT and permethrin, jet fuel, plastic additives phthalates and bisphenol A, and dioxin can all trigger trans-generational health effects in rats such as obesity and ovarian disease, and each resulted in a different pattern of methylation in sperm DNA.
In the context of epigenetic toxicology, we should also highlight the abundant evidence on the toxicity of glyphosate, the top herbicide used worldwide. It is an endocrine disruptor at very low concentrations, implicated in male infertility, birth defects and cancers [57-59] (Ban GMOs Now, ISIS Report, Glyphosate/Roundup and Human Male Infertility and Glyphosate and Cancer, SiS 63). A new study [60] shows that acute exposure of male rats to Roundup herbicide at 0.5 % (typical of agricultural waters after Roundup application) for 8 days was sufficient to increase aromatase enzyme that alters testosterone/oestrogen balance in the testis and to increase abnormal sperm up to 54 days afterwards, as consistent with the herbicide’s endocrine disrupting action.
The processes and agents responsible for transmitting transgenerational effects are summarized in Box 2 (see [47, 51-54]).
Transgenerational effects transmitted by
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The importance of natural genetic modification and the numerous molecular mechanisms for the inheritance of acquired characters have large implications for social policy (see [11]). A pioneer of modern genetics Joshua Lederberg (1925-2008) invented the term euphenics [60], practices intended to improve phenotypes as opposed to eugenics, practices intended to improve genotypes. He was remarkably prescient. In the light of the fluid genome, optimising the environment for euphenics will automatically guarantee the good genes desired in eugenics, on account of circular causation in the fluid genome. For the same reasons, no amount of eugenics or good genes will protect you from a hostile adverse environment, gene therapy and genetic modification notwithstanding.
Is euphenics so idealistic that it is just a fantasy? Not at all! They are the things most if not all people have always wanted: social equality – the benefits of which are backed up by a lot of serious data – (see [61-63] Global Inequality and Its Ills, Capitalism and the Inexorable Rise of Inequality, and Equality is Good for You, SiS 63), non-stressful work places, creative collaborative atmosphere at schools and universities as well as in society, good wholesome non-GM food produced ecologically while safeguarding natural biodiversity, renewable energies and a circular non-polluting green economy [64] (Living, Green and Circular, SiS 53) just around the corner.
What’s notably missing so far is any investigation on the trans-generational epigenetic effects of GMOs and glyphosate herbicides; and this glaring omission in risk assessment can no longer be ignored and swept aside.
But don’t wait for it. Take it upon yourselves to ban GMOs now, at individual and local community levels. It has failed and will fail again, being based on a reductionist, obsolete science. It is an agronomic disaster, and bad for climate change. Most of all, it is standing in the way of sustainable, biodiverse, climate friendly, non-GM agriculture that’s productive, resilient and health-promoting (see [65] Food Futures Now: *Organic *Sustainable *Fossil Fuel Free (ISIS publication).
