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  Topic: Official Uncommonly Dense Discussion Thread< Next Oldest | Next Newest >  

Posts: 69
Joined: Dec. 2002

(Permalink) Posted: April 05 2008,11:58   

Quote (Bob O'H @ April 05 2008,08:33)
At the start of his post on Fisher's Fundamental Theorem, Sal quotemines four people: Walter ReMine, Mae Wan Ho, Stan Salthe and Mike Lynch.  ReMine is a creationist, Salthe is an oddball philosopher who dislikes evolutionary biology because of its moral implications.  Mike Lynch is a proper biologist, one of the big names in evolutionary biology (I really should buy his book!).  But who is Mae Wan Ho?

Well, Wiki helps.  Apparently she is a "noted and controversial holistic scientist" who believes that living creatures do not obey the second law of thermodynamics. She also signed the Disco Institute's Dissent From Darwin list.  So, not looking good as far as main-stream science.

Then I googled a bit, and found this little snippet in an interview:
ACRES U.S.A. So, what actually happens when we eat these foods?

HO. As I already mentioned, these modified genetic materials were designed to overcome the natural barriers between species. What happens when we eat ordinary vegetables and animal protein is that the DNA is broken down by our enzymes. Then, our cells also have enzymes for breaking them down further, and ultimately they will be nutrition for the cell. Unfortunately, if you design genetically modified DNA to jump into genomes and to overcome species barriers, then there is a chance that this DNA can avoid enzymatic breakdown and get into other unrelated species. For example, one of the dangers of these organisms is that, as I said previously, they are mainly made up of genetic material belonging to viruses and bacteria. So if these genetic materials meet other viruses and bacteria, they can join up to make new combinations — new viruses and bacteria that cause diseases and resist medical treatment.

Apparently she used to be a lecturer in genetics.  But she still believes in magic.  I'm rather more sceptical that sticking a strand of DNA to a gold particle, and then  shooting it at a plant will give the sequence the ability to avoid degredation later.

Where I shred one of Ho's more ludicrous claims:
On the cauliflower mosaic virus 35S promoter

Much has been made by anti-GMO zealots about alleged potential risks involved in using the CaMV 35S promoter in transgenic crops. These supposed risks are three-fold: it has been claimed that the 35S promoter might activate silent viruses in crops and humans, that this promoter could possibly activate potential oncogenes in humans cells, and that recombination in the 35S promoter (resident in human cells) could lead to chromosome breaks, cancer, etc. All of these claims are not only hypothetical to the point of absurdity (no anti-GMO zealot has ever documented any such adverse event associated with the 35S promoter), they are contrary to the actual science that underlies the activity of this promoter and its use in transgenic crops. The following is an attempt to explain the truth of the matter.

The first claim is often associated with assertions that the 35S promoter, as used in trangenes, is a “super-promoter”, a virulent, virus-specific agent that is capable of wreaking all manner of havoc, including massive activation of silent autonomous genetic elements in plants and humans. The fact of the matter is that the 35S promoter, while more active than many, is non-descript in both its overall activity and the tissue distribution of this activity. A list of references at the end of this post should be consulted for more information; for now, it suffices to point out that this promoter is relatively simple (two elements, or small DNA sequences that mediate interactions with transcription factors, with as many as perhaps five subelements amongst these) and is recognized by two or three host transcription factors. There are no viral factors involved, nor is the 35S promoter even close to the most active one that can be found in eukaryotic cells. Thus, it is no more likely to disrupt molecular homeostasis in plants than any of a large number of other promoters, or, when introduced into human cells (via, for example, consumption of plants), any of a number of “natural” plant promoters. (This latter possibility is, as we will see later, absurd.)

[As an aside, Ho claims that naked CaMV DNA is much more likely to be taken up by cells than packaged DNA. From the response to the criticisms raised by Futterer et al:

The intact, encapsidated CaMV, consisting of the CaMV genome wrapped in its protein coat, is not infectious for human beings nor for other non-susceptible animals and plants, as is well-known, for it is the coat that determines host specificity in the first instance. However, the naked or free viral genomes may be more
infectious and have a wider host-range than the intact virus.
This assertion is grounded in a comparison with studies showing that, with animal viruses, DNA is able to establish infections in non-hosts. This is but one of many shameless deceptions that can be found in Ho’s writings. Beyond the fact that the comparison is scientifically wrong, Ho’s implication vis-à-vis the relative infectivities of CaMV particles and DNA is also incorrect. Plant viruses do not enter cells via receptor-mediated processes, but rather are introduced mechanically. Because of this, intact virus particles are invariably more infectious than naked nucleic acid, owing to the greater stability of nucleoproteins. Ho claims that the 35S promoter has been converted to a form that is better at moving from cell to cell that an intact virus, but the fact is that just the opposite is true.

While we’re on the subject of Ho’s shameless deceptiveness, the next sentence in the passage is:

Human T-cell leukemia viral genomes formed complete viruses when injected into the bloodstream of rabbits (1).
The abstract from reference 1 shows us that the cited study involves , not HTLV-1 itself, but clones that had previously been adapted for rabbit cells. This abstract is at the end of the post.

I haven’t checked all of Ho’s references, but with each of the ones I did track down, I found that Ho had completely misrepresented the claims and findings of the cited studies. I am not impressed by her scholarship.]

The second claim arises, at least in part, from a claim by Ho that, because caulimoviruses share genomic features with retroviruses, the 35S promoter will, like retroelements, inadvertently activate genes by insertion into them. This claim is, IMO, a piece of willfull deception. Retroviruses act in the described manner owing to a unique feature of their genomes: they are terminally redundant, and the redundancy includes the promoter used to make RNA copies of the genome. In ascii art format, they are like:


with > denoting the promoter and its orientation. If the element inserts in the proper orientation, the terminal > will activate expression of otherwise silent genes.

The CaMV 35S promoter, as used in transgenic crops, does not have this property. Rather (and Ho herself illustrates this in her literature), it is used in the form:

>------- T

where T is a terminator of transcription. This means that any transcription starting from > will never get into adjacent host DNA, thus eliminating the chances of inadvertent activation of plant, or human, DNA at the insertion site. (There is a possibility that an enhancer element in the 35S promoter might act at some distance to disrupt normal gene expression, but this possibility can be estimated by empiral examination of transgenic collections to be small, and unrelated to the wild and inaccurate claim made by Ho.)

The third claim, that the recombination hotspot in the 35S promoter can cause wide-spread genetic havoc in those who eat GMO crops, can be seen to be absurd by doing nothing more than some simple math. First, recall that, in order for this to occur, the 35S promoter has to find its way, stably, into the genome of a human cell. Such an occurrence, through ingestion of GMO crops, has never been demonstrated (nor, as the numbers that follow indicate, will it). Consider, for example, the uptake of DNA by human cells. In the lab, if given optimal (very large) quantities of DNA, human cells must be specially treated in order to take up DNA. Typically, 10-100% of a sample of 1 million cells will take up a purified plasmid if treated with co-precipitating agents or powerful electrical impulses. However, leave out these agents, and none of the cells take up the DNA. Conservatively, it is safe to say that less than 1 cell in 10^4, when given very large quantities of DNA, will take any up. Translated to a human scale, if a typical human body has 10^12 cells, and if each and every one of them is bathed in large quantities of DNA, at the very most 10^8 will take any up (and likely many orders of magnitude less than this - but we’ll be generous for now).

But that’s just uptake. In order for the imagined adverse events to occur, this DNA must integrate into the human genome. This will have to be via non-homologous recombination, and will occur in 1 in 10^4 to 1 in 10^6 cells (typically - I’m probably overstating this as well, but we’re being generous). Using the higher number, this means that, in a typical human body, at most 10^4 cells, if bathed in very large concentrations of DNA, would ever end up with a copy in their genome.

But we’re not done yet. Remember, we’re talking about transgenic crops as the source of DNA. That proportion of a typical plant genome that could be 35S promoter is vanishingly tiny - 350/5,000,000,000 (350 being Ho’s size of the 35S promoter, and 5x10^9 a typical haploid genome size of a crop plant). Rounding things to make the typing easy, this is about 10^-7. Adding this consideration to the above, we now find that, if 1000 people had all of their cells bathed in very high concentrations of crop plant DNA, only 1 cell in all of these people might end up with the 35S promoter in its genome. That’s 1 cell in 1000 people.

But there’s more. In most of the body, very small quantities (if any) of crop plant DNA will be seen. Since DNA uptake is directly affected by DNA quantity, this means that the actual frequency would be much less than described above. It’s hard to say just how much, since it’s hard to know what fraction of plant DNA survives intact into the bloodstream, but it’s safe to say that the actual rates of uptake would be, very generously, 1% of those seen in optimized lab experiments. 1% of the cells in a body might see more DNA than this, but the uptake in even these cells would be less than seen in lab settings. But we’ll say, for now, that these cells (I am thinking of the cells in the digestive tract) are for some reason spectacularly efficient. (This helps in the math, so I’ll be generous here.) All of these considerations mean that 1 cell in 100,000 people might actually end up with the 35S promoter in its genome. (This is an incredibly generous estimate, but, as we will see, even this generosity cannot save the zealots.)

Now we can turn to the frequency of occurrence of adverse events involving the 35S promoter. Not every promoter recombined or causes chromosome breaks - if this were true, it could not be used as a tool. A lot of empirical observation tells us that such events are not common - while I don’t have a number at hand, it’s safe to say that fewer than 1 in 1000 such elements would ever undergo such an event once resident in a eukaryotic genome. (This number is too generous, as well. But I’m lazy.) This means that, if 100 million people were to be eating GMO crops, 1 cell in this population (at the very most) might undergo some sort of damage or breakage as a result of the presence of the 35S promoter. That’s far, far lower than the natural rate of chromosome alteration - which makes Ho’s objections completely irrelevant.

But it’s even worse for Ho and her cohort. DNA damage and chromosome breakage in and of itself will not cause cancer (which is Ho’s assertion in much of this). Many different events need to occur for cancer to develop. For one thing, the breakage must be in a “strategic” location in the genome. I don’t know how many there are - common sense says they are few, otherwise cancer would be rampant in all people. But let’s say that there are 3 million such places. That’s 0.1% of the genome. This means that, in a population of 100 billion people (20 earths, roughly), 1 cancer might be attributable to the 35S promoter. (The impact on overall cancer rates would, I daresay, be infinitesimally small.)

Then there’s the matter of coupling - just because a strategic site has been “hit” doesn’t mean that cancer will ensue. Many other events must also occur - such that, very “optimistically”, only 1 in a thousand or so of such events would actually contribute directly to the development of cancer.

Which brings us the bottom line, for now - in Ho’s worse-case scenario, if 100 trillion people consumed GMO crops that included 35S promoter-containing constructs, 1 person might develop cancer as a direct result of activities associated with this promoter. IMO, that’s not much of a risk - certainly, much, much, much lower than the risk that consumers of organically-grown foods face from, say, contamination by E. coli.

A bibliography pertaining to the transcriptional properties of the 35S promoter:

EMBO J 1989 Dec 20;8(13):4197-204, The ocs-element is a component of the promoters of several T-DNA and plant viral genes. Bouchez D, Tokuhisa JG, Llewellyn DJ, Dennis ES, Ellis JG.

Plant Cell 1989 Dec;1(12):1147-56, ASF-2: a factor that binds to the cauliflower mosaic virus 35S promoter and a conserved GATA motif in Cab promoters. Lam E, Chua NH.

Plant Mol Biol 1994 May;25(2):323-8, The plant transcription factor TGA1 stimulates expression of the CaMV 35S promoter in Saccharomyces cerevisiae. Ruth J, Schweyen RJ, Hirt H.

Proc Natl Acad Sci U S A 1989 Oct;86(20):7890-4, Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants. Lam E, Benfey PN, Gilmartin PM, Fang RX, Chua NH.

EMBO J 1990 Jun;9(6):1685-96, Combinatorial and synergistic properties of CaMV 35S enhancer subdomains. Benfey PN, Ren L, Chua NH.

EMBO J 1990 Jun;9(6):1677-84, Tissue-specific expression from CaMV 35S enhancer subdomains in early stages of plant development., Benfey PN, Ren L, Chua NH.

Finally, the abstract I promised:

Proc Natl Acad Sci U S A 1996 Jun 25;93(13):6653-8

Infectivity of chimeric human T-cell leukemia virus type I molecular clones
assessed by naked DNA inoculation.

Zhao TM, Robinson MA, Bowers FS, Kindt TJ.

Laboratory of Immunogenetics, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Rockville, MD 20852, USA.

Two human T-cell leukemia virus type I (HTLV-I) molecular clones, K30p and K34p were derived from HTLV-I-infected rabbit cell lines. K30p and K34p differ by 18 bp with changes in the long terminal repeats (LTRs) as well as in the gag, pol, and rex but not tax or env gene products. Cells transfected with clone K30p were infectious in vitro and injection of the K30p transfectants or naked K30p DNA into rabbits leads to chronic infection. In contrast, K34p did not mediate infection in vitro or in vivo, although the cell line from which it was derived is fully infectious and K34p transfectants produce intact virus particles. To localize differences involved in the ability of the clones to cause infection, six chimeric HTLV-I clones were constructed by shuffling corresponding fragments containing the substitutions in the LTRs, the gag/pol region and the rex region between K30p and K34p. Cells transfected with any of the six chimeras produced virus, but higher levels of virus were produced by cells transfected with those constructs containing the K30p rex region. Virus production was transient except in cells transfected with K30p or with a chimera consisting of the entire protein coding region of K30p flanked by K34p LTRs; only the transfectants showing persistent virus production mediated in vitro infection. In vivo infection in rabbits following intramuscular DNA injection was mediated by K30p as well as by a chimera of K30p containing the K34p rex gene. Comparisons revealed that virus production was greater and appeared earlier in rabbits injected with K30p. These data suggest that several defects in the K34p clone preclude infectivity and furthermore, provide systems to explore functions of HTLV-I genes.

Edited by Art on April 05 2008,11:59

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