Sunday, September 23, 2012

Lost Rebuttal from Dr. Ena

Dr. Ena Valikov is a Veterinarian from Huntington Beach, CA.  She frequently comments on posts, usually those regarding transgenic technologies, and presents coherent arguments that elevate the discussion.  She has a background in biochemistry so she speaks science well and can discuss the literature.

Yesterday morning my gmail account posted several responses to my September 21 post. There were two there from Dr. Ena.  I was excited to read them and prepare my responses. Yet when I looked at the comment section of the article one of her comments was not there.  Instead, there was an appropriately cynical comment from Dr. Ena about censoring the comments.

I have no idea what happened or where her comment disappeared to.  However, I was disappointed and upset for several reasons.  First, I appreciate an informed rebuttal because I am the first to admit, I might be wrong.  I'm glad to consider all evidence in my synthesis.  Second, I would never, and have never censored a comment. On one of my YouTube posts someone made rude and offensive comments about one of my student's foreign accents.  I left it, and pointed out its ignorance. This is a marketplace of ideas and to be a censoring or dismissive gatekeeper is the stuff of activism, not science.

I'm posting here Dr. Ena's lost comment.  I can't seem to find her as I don't have her actual email address, so I hope this is acceptable (I'll take this down if you don't want it posted, Ena).  I just feel awful, I don't like how it taints the perception of communication in this forum.

So here I post Dr. Ena's points in response to my Sept 21 post, and her arguments supporting Seralini's recent work.  My comments will appear below in the Comments section.

Ena Valikov has left a new comment on your post "Rats, Tumors and Critical Assessment of Science": 

(KF) Ena, a replicated study would be great, unfortunately Seralini's stuff never is replicated.
Meaning that you don't have a single LONG TERM STUDY examining laboratory animals for Long Term Chronic effects.

No, I don't think this study is trash, because I know mammary tumors to be estrogen sensitive. The study demonstrated elevated estradiol levels in both males and females and even proposed a mechanism of action by which EPSPS can alter estradiol levels. 

As to the control groups and experimental group : why is there a study on biofortified composed of 15 rats, which none of you objected to?
Prima facie evidence that a phytocystatin for transgenic plant resistance to nematodes is not a toxic risk in the human diet.http://www.ncbi.nlm.nih.gov/pubmed/14747684

It is a study on 15 rats fed purified extract rather then the genetically modified rice… and the only biochemical/ hematological patient data actually published is

TABLE 1
Summary of results from the toxicological study of male Sprague-Dawley rats administered the cystatin OcIΔD861

OcIΔD86 [mg/(kg · d)]
0 0.1 1 10
Food intake, g
    d 3–7 25.04 ± 0.94 25.80 ± 0.90 26.82 ± 1.48a 25.36 ± 1.42
    d 7–10 26.06 ± 0.40 25.68 ± 1.32 27.74 ± 1.43a 25.82 ± 0.98
Organ weight
    Cecum (empty), g 0.305 ± 0.033 0.334 ± 0.057 0.32 ± 0.013 0.35 ± 0.041a
    Liver, g 3.12 ± 0.16 3.00 ± 0.072a 3.02 ± 0.090a 3.04 ± 0.12
Serum analysis
    Potassium, mmol/L 4.51 ± 0.27 4.78 ± 0.318 4.66 ± 0.251 4.95 ± 0.82a
    Urea, mmol/L 6.58 ± 0.82 5.61 ± 0.67b 6.09 ± 0.616 6.24 ± 0.887
    Creatinine, μmol/L 39.0 ± 2.83 39.7 ± 3.02 41.0 ± 1.66 41.5 ± 3.21a
    γ-Glutamyl transferase, U/L 0.07 ± 0.067 0.42 ± 0.67a 0.13 ± 0.11 0.18 ± 0.13

——————————————————————————————
Here is what a blood panel should actually look like:
Test Result Reference Range
ALK. PHOSPHATASE 294 10 – 150 U/L HIGH
ALT (SGPT) 57 5 – 107 U/L
AST (SGOT) 25 5 – 55 U/L
CK 171 10 – 200 U/L
GGT 4 0 – 14 U/L
AMYLASE 344 450 – 1240 U/L LOW
LIPASE 397 100 – 750 U/L
ALBUMIN 3.9 2.5 – 4.0 g/dL
TOTAL PROTEIN 8.4 5.1 – 7.8 g/dL HIGH
GLOBULIN 4.5 2.1 – 4.5 g/dL
TOTAL BILIRUBIN 0.2 0.0 – 0.4 mg/dL
DIRECT BILIRUBIN 0.1 0.0 – 0.2 mg/dL
BUN 34 7 – 27 mg/dL HIGH
CREATININE 1.2 0.4 – 1.8 mg/dL
CHOLESTEROL 336 112 – 328 mg/dL HIGH
GLUCOSE 131 60 – 125 mg/dL HIGH
CALCIUM 11.0 8.2 – 12.4 mg/dL
PHOSPHORUS 8.3 2.1 – 6.3 mg/dL HIGH
TCO2 (BICARBONATE) 25 17 – 24 mEq/L HIGH
CHLORIDE 87 105 – 115 mEq/L LOW
POTASSIUM 4.3 4.0 – 5.6 mEq/L
SODIUM 144 141 – 156 mEq/L
A/G RATIO 0.9 0.6 – 1.6
B/C RATIO 28.3
INDIRECT BILIRUBIN 0.1 0 – 0.3 mg/dL
TRIGLYCERIDE 98 20 – 150 mg/dL
NA/K RATIO 33 27 – 40
HEMOLYSIS INDEX (1) N
LIPEMIA INDEX (2) N
ANION GAP 36 12 – 24 mEq/L HIGH

WBC 26.7 5.7 – 16.3 K/uL HIGH
RBC 8.03 5.5 – 8.5 M/uL
HGB 19.1 12 – 18 g/dL HIGH
HCT 52.0 37 – 55 %
MCV 65 60 – 77 fL
MCH 23.8 19.5 – 26.0 pg
MCHC 36.7 32 – 36 g/dL HIGH
NEUTROPHIL SEG 80 60 – 77 % HIGH
NEUTROPHIL BANDS 5 0 – 3 % HIGH
LYMPHOCYTES 4 12 – 30 % LOW
MONOCYTES 11 3 – 10 % HIGH
EOSINOPHIL 0 2 – 10 % LOW
BASOPHIL 0 0 – 1 %
AUTO PLATELET 725 164 – 510 K/uL HIGH
PLATELET COMMENTS
PLATELETS APPEAR INCREASED.

ABSOLUTE NEUTROPHIL SEG 21360 3000 – 11500 /uL
ABSOLUTE NEUTROPHIL BAND 1335 0 – 300 /uL
ABSOLUTE LYMPHOCYTE 1068 1000 – 4800 /uL
ABSOLUTE MONOCYTE 2937 150 – 1350 /uL
ABSOLUTE EOSINOPHIL 0 100 – 1250 /uL
ABSOLUTE BASOPHIL 0 0 – 100 /uL

SENIOR PROFILE W/ TRIG : T4
Test Result Reference Range
T4 (1) 2.5 1.0 – 4.0 ug/dL


The study’s limitations are quite obvious: its duration is 21 days and N=15, not to mention that the rats weren’t fed the genetically engineered rice, but rather the isolated protein (which is not equivalent to the whole food).

Can you please explain how findings in 15 rats fed this GMO for 21 days imply safety in millions of people, eating the stuff for decades?

Because from my vantage point, the only time you really care about control group size, or statistics--is when a study comes out suggestive of long term harm. You know ... the kind you would never catch, if you only study the GMO for the required 90 days. 



Posted by Ena Valikov to Illumination at September 21, 2012 10:47 PM


Friday, September 21, 2012

Rats, Tumors and Critical Assessment of Science



My email box exploded with new messages.  A flurry of notes contained a link to a new peer-reviewed paper, a work showing that rats fed “GMO” corn developed massive tumors and died early, compared to controls.  Immediately I smelled a Seralini paper.

A click on the link did not disappoint-- it's Seralini again.  I was electronically whisked to a PDF of the whole text and began to read.  Within minutes I was blown away by the lack of rigor, poor experimental design, attention to controls and loose statistics.  Most of all, I was blown away by the conclusions drawn by a study with tiny numbers of subjects in a rat line known to grow endochrine tumors.

The anti-GMO interests were quick to anoint this new work as a rigorous pillar of exceptional science, a hard-science detailing of the danger of transgenic food.  They want this to influence public policy.

I was really impressed by how the scientific media and the science blogosphere pounced.  The best names in the business, Terwavas, Leyser, Goldberg and many others were interviewed and provided detailed analysis of the work, pointing out its many flaws.  Those reviews can be foundthroughout the internet, and they are awesome. Like this one! I don’t need to reiterate them here.

What I will do, which is highly uncharacteristic and but consistent with the post hoc analysis done all the time, is provide a level of analysis that was not explored.  There are features of this paper that hint at a motive, an intent.  I do not believe this was a hypothesis tested.  I believe that this was an experiment designed to frighten.  I believe that this is blatant mis-use of science to forward an agenda.

Those are strong words and I never thought I’d cast such allegations at someone else’s peer-reviewed research.  That’s usually pretty low.  However, there are facets of this work that are clearly indicate the intent of the authors is to provide shock, not a good test of a hypothesis.  In fact, the word “hypothesis” does not appear once.  

This is why the report is in Food and Chemical Toxicology and not in Nature, where it would be if it was a properly conducted study.

Here are some red flags the others have not mentioned.  I’m reading between the lines here. I will describe what a good scientific report should not do and then give you some strong inferences from what the paper does not show, as well as how data are presented.

1. The first line of the paper claims an “international debate”, yet he cites himself and nobody else.  Easy to claim a debate when nobody else is participating in it.

2.  Figure 3.  This one really makes me see red.  Look at tumors.  Look at massively deformed rats.  Shocking, isn’t it?   The authors tell us in Table 2 that control rats also develop tumors.  Why not show them?  Why are the controls not shown in that figure?  It is because if they are identical to the experimental treatment rats then the fear factor is gone.   This is inexcusable and the authors, reviewers and editors should be ashamed.

Sometimes the way data are presented can expose the relative objectivity and hidden intent of a study. Left-rat that ate GMO corn.  Center- rat eating GMO corn and roundup. Right- rat fed roundup. Their associated tumors shown on the right. Wait!  What about the control rats, the ones that also got tumors?  How convenient to leave them out!   

3.  The labeling on the figure is “GMO” or “GMO+R” (R stands for Roundup).  GMO is not a product. It is not a genetic line of corn.  It is a technique.  There are many kinds of GMOs, plant lines bearing different transgenes.  Even if these results linked rat tumors to the food (which they don’t in my assessment) they would  link it to one kind of transgenic crop, not any transgenic crop.  This again shows the authors’ intent to overstep the data in a manner that will inflame the reader and further vilify a technology. To be fair, they do state it properly in the conclusion, but few are reading past the sensational photos.

4.  They show comparable effects of Roundup treatment and the transgene.  This should be a tip-off as well.  What is the likelihood of both inducing identical problems?

5.  Low numbers of subjects are a sign of poor design.  When tumor incidence is 30%, vs 50% or 70% that means three rats vs. five or seven.  The incidence of endocrine tumors in Sprague-Dawley rats is 70-80%.  Imagine you roll a die and numbers 1-4 mean develop tumors, 5 and 6 mean tumor free.  Now roll it ten times and log the result.  You’ll find that there will be times when you consistently roll 5 or 6, maybe 5 times out of ten.  Other times you’ll roll 5 or 6 only 2 times out of ten.  That’s natural random variation, and if you roll it 100 times, 1000 times, then the real probabilities will even out. 

6.  Low numbers + a line known to get tumors = some frequency of data that will prove the authors’ beliefs.

7.  A prediction-- the larger study will never be done and these results will not replicated by other labs.

8.  The Discussion.  Lots of guesses on how to link the food or Roundup to the symptoms. Quite a bit of speculation and hand waving, with no likely mechanisms discussed.

I could go on all day. For fun reading review the press conference. It was a bigger joke.  

The bottom line is that if we look at the report and what it says, and compare it to what the data really say, there is limited concordance.  To the trained eye the data say that these rats get endocrine tumors at high incidence and that what is being observed is the natural variation of the tumors in small numbers of rats, where the authors'  “significance” is found in statistically meaningless samples.

Alas, it is now part of the true-believers' war chest of crap information that now will be used to steer the unsophisticated and influence public policy. 

Monday, July 16, 2012

The “Arctic Grape” Sneaks Through Public Approval

We are currently witnessing the USDA public commentary period on the Arctic Apple, a transgenic apple that does not exhibit browning upon injury or cutting.  The anti-browning trait was installed by scientists at Okanagan Specialty Fruits. A copy of the apple gene for polyphenol oxidase (PPO) was overexpressed, which triggers a plant response to silence the over-expressed gene.  The same process also suppresses the apple’s endogenous PPO genes.

Trees have been growing for ten years and are poised for widespread adoption.  But as expected, the critics have now emerged against this non-browning apple.  They say that the apples are untested in humans, that the pollen will contaminate other plants.  They say that it is unnatural and will need more pesticide. 

But the same criticisms were strangely silent against what was essentially the Arctic Grape.  A major genetic alteration affected the PPO gene of the ‘Sultana’ grape, a genetic change that was unknown, uncharacterized and uninvestigated. All the scientists knew is that they didn't brown. The resulting grape exhibited the same anti-browning properties as the current Arctic Apple, and gained rapid favor for the production of light-colored raisins and low-oxidation wines.  Unlabeled and untested, this genetic aberration spread quickly throughout the dried-grape industry, as consumers and farmers realized great gains from the sweet, white and golden raisins.  

Worse, it turns out that scientists later deciphered the molecular basis for the disorder. The normal PPO protein was unprocessed, a new protein created!  Just like the anti-GMO folks warn us about all the time, the new protein, untested for allergenicity and long-term feeding consequences, accumulated in the modified Franken-fruit background.  This new freakish protein was the unnatural reason that the grapes did not brown, and the raisins remained white or golden.

The Punchline.  You’ve likely eaten them.  You might have even bought them at an organic market.  You never cared.

In fact, the PPO mutant occurred spontaneously in 1962 in a grape line called “Sultana”.  A mutation in the grapevine changed a gene so that the PPO oxidase protein (the one suppressed in Arctic Apple) could not be processed and made functional.  The fruits were largely white and did not show PPO activity. 

Why?  The active enzyme is about 40 kilodaltons in size, but in ‘Bruce’s Sport’, the ppo mutant, the protein was not processed.  The modified protein was not a functional PPO.  A new protein was formed and caused the lack of browning. How did this mutant atrocity ever escape regulation?  Surely Monsanto ram-rodded this through the FDA and USDA!

Not so much.

In fact, not at all. 

The PPO mutant was found in 1962.  Nobody cared about why the grapes didn’t brown, they just knew was a great trait.  In 1992 scientists finally figured out that the non-browning trait was caused by the fact that a new protein was formed in the plant, an unprocessed form of PPO that could not complete the browning process.

The year 1962.  The year 1992.  Changes in genes, new proteins formed.  All untested, unlabeled, and accepted as perfectly fine; happy golden raisins to go with your granola.  De-lish.

Turn ahead to 2012.  The same gene is suppressed in apples with great precision.  A group of people object to the process. They worry about allergies, cross-pollination and GMO Franken-dangers.

Questions.

Why is this process completely acceptable when unknown, unpredictable and untested back in the 1960's? 

Why is the process decried when it is understood, documented and tested now?

These two questions frame an intellectual inconsistency of the anti-GMO movement that I cannot understand, and show that it is not the product, but the process that activists find objectionable.



References

Rathjen and Robinson (1992)  Aberrant Processing of Polyphenol Oxidase in a Variegated Grapevine Mutant Plant Physiol. 99(4): 1619–1625.

Dry and Robinson (1994) Molecular cloning and characterisation of grape berry polyphenol oxidase Plant Molec. Biol. 26: 495-502

 

Antcliff (1962)  Bruce’s Sport:  A Mutant of the Sultana.