Let's talk about GMOs, series introduction.

Introduction

Over the past two weeks, I have seen the responses to my blog post and the posts of others. I see a lot of confusion on the techniques, results, safety, ethics and current application of GMOs. However, I am well aware that I do not know everything. Let's look at various aspects of GMOs and learn together.

What I want to do is to look at the entire process of GMOs. In this post, we will focus on what the concept is. What is DNA? How does it work? Can we use that for agriculture and other things? In the next post, we will look at the techniques necessary to realise that concept. This will introduce a striking difference, as a revolution towards a new and fancy technique called CRISPR/Cas9 has just taken place. 

When we know how they are made, we can look at what we are currently using them for. Can we see how the technique has been applied currently? Of course, after looking at the past and present we will move on to the future. What can we use them for? What are ideas are currently under consideration? 

Hold on, we also have to discuss whether or not they are safe. Isn't it dangerous to mess with DNA? This is an oft-discussed point, and I think it has merit to look at it clearly. There are some other issues surrounding GMOs that have a lot of people upset. I can imagine this, and we will have to discuss them. For this, we look at the application of GMOs in farming. Don't worry, we will spend some time talking about pesticides, seed saving, patent law and 'industry' as well. 

After we have discussed the concept, the techniques, the current application, the future application, their safety and the surrounding issues, we have the information to discuss the ethics of GMOs. I have to warn you, that means I will actually discuss ethics - not make a verdict, but discuss differing viewpoints of ethics on the issue.  At that point, we can discuss regulation. Not only how GMOs are currently regulated, but also how we ought to be regulating them.

That said, let's review some science. We will continue to use the rather sloppy label of "GMO". Both of us have some sense of what we mean; laboratory-bred varieties that have their DNA sequences deliberately altered by engineers.

Before I move on to the review we need to continue, I'd like to tell you who I am. I am a recent graduate of Delft University of Technology, specialised towards theoretical quantum condensed matter. I am now employed at the TU Delft as non-academic support for biophysical research (i.e. I do not do research, but help others with their setups, software and data analysis). This blog, my website and my Facebook page are mine, and mine alone. The content I write here is mine. There are no conflicts of interest. I write about issues I care deeply about. At the end of this series, I hope that you see why I care about this.

Science Review: What is DNA?

3D helix structure of DNA (source: Nature).
Schematic (left) and realistic (right) depictions.
A long time ago, Charles Darwin explained the variation in the natural world. He did this by positing one mechanism of inheritance and mutation. If this was present, as had been observed, it follows that (natural) selection should lead to change, accumulating to give us the transmutation of species.

He didn't know the mechanism, but we do. The genetic information of every living creature on this planet - and even some that are differently alive - is stored in the same base form. A long period of the 20th century was spent trying to discover the mechanism, leading to its discovery in 1953 and the award of the 1962 Nobel Prize in Medicine jointly to Crick, Watson and Wilkins.

At its simplest, DNA is a very long chain. DNA means Deoxyribonucleic acid. It describes a molecule that consists of a sugar backbone, to which nucleotides are connected. The sugar backbone is a long, stable skeleton. Each link has a nucleotide connected, which is often referred to with a letter. In most life, these letters are A, C, G and T. The nucleotides are Adenine, Cytosine, Guanine and Thymine. Often, we refer to a (small) strand by writing down its letters. For instance, we could speak of an ATCAGTCG strand, or refer to the letters as the code.

These are molecules, specific arrangements of atoms with shared electrons. Sharing electrons indicates a bond between two atoms and, depending on the specifics of the sharing, it can mean an almost unbreakable bond. The specific arrangements indicate a specific distribution of charge and thus electric field.

In that sense, each nucleotide connected to the DNA backbone can be seen as a weird magnet. It has two poles, but its north pole can only connect to a specific south pole. It turns out that these poles are such that A's pole connects to that of T, and C to G (we say that these nucleotides are complementary). Two strands of DNA that are complementary, meaning that each nucleotide in one strand is replaced by its complementary nucleotide in the other, will have an electrostatic connection. This is far weaker than sharing electrons, but it still binds the two strands together. Due to the specifics of the skeleton, such a double strand will turn into a double helix.

While this might seem miraculous, I must point out that different backbones and different nucleotides exist. In the first phase of life, it is supposed that it did try the alternatives. This primal form of genetics was already undergoing evolution by natural selection, and this made it settle on a specific backbone and specific nucleotide. What could it select for? Well, rate of self-replication, lifetime, measure of heritability and variability, and so forth.

How does this explain variation and heritability? Well, the molecular machines aren't 100% foolproof. Sometimes, they make mistakes - in the sense that they put the wrong nucleotide, the wrong letter, down. Sometimes, it is an outside source - say, radiation or a mutagen. It doesn't really matter; the change in the genetic information is there. If that is the genetic information involved in reproduction (for us, DNA in egg or sperm cells) then offspring inherit.

Science Review: The central dogma of molecular biology

DNA isn't a blueprint. It contains information, yes, but that information is used by the machinery of the cell. DNA is the stable molecule, storing most of the information. As such, it is unwieldy. How does it translate to the changes we see between animals?

Depiction of Eukaryota cell structure.
DNA resides in the nucleus, while
proteins are made in the Ribosome.
The central dogma of molecular biology explains how this happens. DNA typically codes for one of two things. First, it can code for controlling other parts of the code. Second, it can code for a protein. Proteins are very large molecules in a specific spatial confirmation. One or more proteins together can act as molecular machines of what seems impressive specific functions. In the group where I work, we do research into the way these molecular machines go about their business.

Coding for controlling other parts of the code means that a molecular machine 'reading'  the DNA gets instructions for what to do to other parts of the code. Coding proteins is harder; the DNA itself cannot do this. In Eukaryota, the domain of life to which animals and plants belong, the DNA is stored inside the nucleus of a cell. Another part of the cell, the Ribosome, is the molecular machine making proteins.

The molecular machines that read DNA encode parts of it - codes for a protein - into pieces of RNA. This RNA is less stable than DNA, and it doesn't always assume the double helix structure. The double helix structure allows for easy error-checking, which RNA doesn't need. The RNA pieces are brought into (or even float freely) the Ribosome, which then reads the RNA and synthesises the protein. This is the central dogma of Molecular Biology:
Central dogma of molecular biology. On the left, you see DNA. If it looks weird to you, that is because it is rolled up for storage by a molecular machine called a nucleosome. The machines reading the DNA send out messenger RNA, which is less stable but cheap to make. Finally, this RNA is read by the Ribosome which then synthesis a protein. (Embopress).

The concept of genetic engineering:

Engineering typically means a structured way of using science to some purpose, be it the building of machines, cities or spacecraft. With genetic engineering, we usually mean literally altering the genetic code.

As many people have pointed out, artificial selection is a form of genetic engineering in that sense. We know that most variation in life is heritable. Suppose we're breeding some crop. We want it to be drought resistant. We plant crops in a relatively dry environment, and only those with variations that resist that drought survive. We make it drier, and so on and so forth. Ultimately, we end up with a drought-resistant crop.

However, there are numerous questions associated. First, is there actually variation in this trait? It could be that all crops do badly, but reproduce without ever changing something. You do not know how large the variation is and whether it will continue to improve. Second, you do not know what exactly you are altering. With the variation for drought resistance might come the introduction of a mutagen, poison or delicious flavour. The point is that you do not know what else it does.

What we usually mean with genetic engineering is somewhat more specific and complicated. It is a process started somewhere in the second half of the latter century, and it continues to be used and improved. In principle, it means making use of molecular machines to make targeted changes to the DNA of an organism, usually a seed or bacteria.

I say targeted, and it is. First, you must assess what DNA to target. For drought resistance, there are numerous possible mechanisms. Such mechanisms are identified (i.e. in a cactus) and then introduced in different organisms by targeted genetic change or even genetic insertion (putting a whole new series of letters on the DNA). The process thus involves a long study of mechanisms, followed by targeted genetic change and extensive evaluation, made even longer by the stringent safety regulations that are present all over the world.

Conclusion

Traits such as drought-resistance, moisture-resistance, bug-resistance, disease-resistance, bigger fruit, more nutritious fruit, etc., all have clear applications in agriculture. Not all of them have been realised, and the current big crops are mostly either bug-resistant or pesticide resistant. Golden Rice, a non-profit initiative started on universities, wants to add the vitamin A precursor present in e.g. carrots to rice. This would allow an non-invasive change to the diets of regions of Asia where vitamin A deficiency is a large problem. Note that already, a large number of pharmaceuticals are produced by genetically modified bacteria (example).


This is the promise of genetic engineering; targeted change in everyday organisms. Can it fulfil this promise? Can it do so safely, both economically and in terms of health? That is what this series is about. The next post will be about the techniques.

















Rebuke: Climate Change in 12 minutes - The Skeptic's Case

Introduction

Over on The Chronicle Flask's page, a climate change "skeptic" responded to a share of a guardian article on Trump's "crackdown of politicized science".

He shared a youtube movie, which is relatively short. I'll reply to it here. It's called Climate Change in 12 Minutes - The Skeptic's Case. It is authored by a Dr. David Evans, who is not unknown.

Rebuke

The first claim is that they checked the climate models versus the latest data, and the climate models got all the major predictions wrong. Beyond the obvious request of a (peer-reviewed) citation, the claim opposes various papers. A few examples:
  • doi:10.1038/nclimate3079: "climate sensitivity estimates have now been reconciled and are consistent with the modelled range".
  • doi:10.1038/nclimate3066" Correcting for these biases and accounting for wider uncertainties in radiative forcing based on recent evidence, we infer an observation-based best estimate for TCR of 1.66 °C, with a 5–95% range of 1.0–3.3 °C, consistent with the climate models considered in the IPCC 5th Assessment Report."
Rather than continuing on that claim, they move on to a second one. They explain the common CO2-water vapour feedback (explanation), and then continue to note that water vapour basically means clouds which will reflect the sunlight back. As this changes the energy coming in from the sun, thereby cooling the earth and reducing warming effects.

However, it is not that simple. Clouds at low-levels mostly reflect sunlight, cooling the planet. High-level clouds, however, trap heat and thereby greatly increase the warming effects. It won't surprise you that this is taken into account in the models in use by e.g. the IPCC (explanationipcc). The IPCC reports, amusingly, that one common-bias found by observational tests is an over-prediction of optically thick clouds. Those are the clouds that reflect sunlight, thereby inducing cooling. Yes, the effect they claim is ignored has actually been over-estimated. Current knowledge is that when the temperature increases, the low-level clouds their presence is reduced, leading to reduced cooling (faster warming) (DOI: 10.1007/s00382-011-1279-7).

They then claim that, because the Earth has a "long-lived and stable". A few points to make. While the planet has never gone into runaway greenhouse effect like Venus has, that doesn't mean the turning point is suitable for H. sapiens or any other species living today. An additional point is that we probably can't call human activity a perturbation. It is true that one way to test the stability of a system is by perturbing it slightly and seeing how it responds. A system that can withstand a small perturbation is stable. It is not at all clear that human activity fits this description. Human activity simultaneously adds heat and skews the response in the wrong way. I must emphasise just how much CO2 is added by our species, and worse greenhouse gases too boot. We're not giving the system time to respond; we add 0.5% CO2 to the atmosphere yearly, which is our net contribution (Wiki). Typically responses to small perturbation are slow, because the system feedback slowly recovers its original state. We don't give it that time.

They now return to their claim that the models have it wrong. To back this up, they add the additional claim that the models haven't really changed in the last 30 years. That's just bollocks; with the increase of researchers, models have been increasing, new ones are devised (example) and so has accuracy (example).

At this point, I must admit I'm losing interest. Yelling that something is wrong won't help, and the data and conclusions used in this video would lead to several high-impact publications (if they pass peer-review). 

They ramble on, mentioning that the models predict an atmospheric hotspot which wasn't found (data error) and that earth radiation hasn't decreased (it has).

 Conclusion

As I might have mentioned before, I grew up in a Dutch Polder. Close to my parental home is a little sign stating "Welcome to sea bottom!". For the Netherlands, all of this is more real; a lot more of the local effects are already visible, with double the average temperature increase, the introduction of a summer, increase in precipitation and heavy rainfall occurrences (source)

I know that the mechanisms explained in the video sound relatively simple and accessible. They are, which is why the proper response to this sort of video is to see if the climate scientists have actually checked. Not surprisingly, usually you'll find that they did. Ultimately, the message is that you should check your sources. Not only to see if they're credible, but if there are better or equivalent sources available. 




















On the International Monsanto Tribunal

Introduction

These are the basics of Shiva's monologues.
In October 2016, the Monsanto Tribunal, to hold Monsanto accountable for human rights violations, crimes against humanity and ecocide, takes place in The Hague. That sounds scary and official, doesn't it?

The organic movement is organising a fake trial, set up deliberately so that people might take it seriously. For such weighty issues, it was announced early - more than a year before the event takes place. Even then, people got confused and needed to be explained that this was merely theatre

Their victims of course genuinely care for the future of humanity and the planet we inhabit. There is a rumour that the 'Modern Revolutionary' and 'Brilliant Scientist' Vandana Shiva is only asking for a first class flight and a 40 thousand speaking fee. A true bargain, and you can see how much she cares (source). The budget for the tribunal is 400 thousand euro (source) or 500 thousand euro (source), which makes you wonder what they want to use it for. Their budget is not at all transparent. 

A friend of mine, Anke Jaanen,  has compiled an analysis of the speakers for the fake tribunal. What I want to do here is to quickly discuss the speakers and rebuke their likely points. The fake tribunal is apparently split into four parts. These are the impact on human health, the impact on soil and plants, the impact on animal health and the impact on biodiversity.

I would like to point out that this is not an in-depth article. As such, in-depth discussion of claims is not going to happen. I am going to tell you why I do or do not deem a claim likely. I am not going to put down lists of individual studies.

Part I: Impact on Human Health

The first witness is Sabine Grataloup, who claims to be a victim of RoundUp/Glyphosate. Her son was born with esophageal atresia, a birth defect affecting the alimentary tract. The esophagus ends in a blind-ended pouch rather than connecting to the stomach. The defect occurs in approximately 1 of 2500 births (DOI: 10.1186/1750-1172-2-24). From what I can determine, the birth defect is caused by errors in embryonic development. It is rarely inherited, which seems to indicate that it is a mutation that happens during (pro-)embryonic development. Grataloup claims that she was spraying glyphosate-based herbicide in the third week of her pregnancy, without special protection because there was no indication she should have. 

The second witness, Maria Liz Robledo, has a similar claim. Her daughter was born with birth defects. Apparently, she had an agricultural chemical supply near her house during her pregnancy. 

A quick survey of the literature using Google Scholar shows that significant correlation between pesticide exposure and birth defects has not been found. I must also point out that Roundup interacts with the biochemistry found in plant life, not mammalian life. Given the lack of correlation and the lack of a mechanism, I must deem her claim unlikely.

The third witness is Christine Sheppard, who owned and operated a Hawaiian coffee farm. They applied RoundUp to their crops. Later, Sheppard was diagnosed with non-Hodgkin lymphoma, a cancer in the lymphocytes, a group of white blood cells part of the immune system.  

The fourth witness is Timothy Litzenburg. Litzenburg is a part of a law firm that sues on behalf of Roundup victims. Their website states very clearly that they do so, and they claim that glyphosate can cause non-Hodgkin's Lymphoma and multiple myeloma (i.e. blood cancers). Clearly, there are no conflicts of interest here.

Sheppard and Litzenburg's claims are easily deemed unlikely. Just recently, a bit of controversy happened when the IARC, the cancer branch of the WHO, said glyphosate was 'probably carcinogenic', despite the contrary scientific evidence and consensus. This was quickly rectified when the WHO, EPA and EFSA issued reports that state glyphosate is unlikely to be a carcinogen. The common preoccupation of the organic movement with Europe makes the EFSA statement the most pertinent:
"EFSA concluded that glyphosate is unlikely to pose a carcinogenic hazard to humans and the evidence does not support classification with regard to its carcinogenic potential".
The fifth witness is Klomon Saman, apparently a victim from Sri Lanka. While no more information could be found, we can take a guess. North Central Province in Sri Lanka has a pronounced form of chronic kidney disease. The cause is unknown, so that the literature refers to it as CKDu (Chronic Kidney Disease unknown). 

The sixth witness is Channa Jayasumana, a scientist from Sri Lanka that is investigating CKDu, so that we can feel confident in our guess that this is the topic of these two witnesses. Similarly, there is little doubt that the claim is that glyphosate is the culprit.

Looking at the scientific literature, little indication of a pesticide connection is found (DOI: 10.1186/1471-2369-15-125). It seems that pesticides, including glyphosate, can be ruled out as a causative factor (3.5% of 57 CKDu cases, 10.1186/1471-2369-14-180). Nevertheless, their witness is a scientist investigating this case. What does he have to say?
"Although glyphosate alone does not cause an epidemic of chronic kidney disease, ..." (doi:10.3390/ijerph110202125)
I've read parts of that study, and it seems to me that these authors are elevating a minor correlation to the level of a major factor by means of an extremely speculative and spurious hypothesis.  The ellipsis in the quote above makes this clear: "it seems to have acquired the ability to...". Indeed, he might add, "Although unicorns have never been confirmed to exist, they seem to have acquired the ability to be invisible to humans". 

The seventh witness is Damian Verzenassi, a medical doctor that is convinced agricultural chemicals cause everything, including cancer, birth defects and miscarriages. He is involved in the organic movement, seems to be a firm believer of the Big Pharma conspiracy and so forth. Really, there is little in his profile that supports credibility. He apparently was a part of the "Physicians in the Crop Sprayed Towns" group (read more), which I find sufficient to deem this unlikely.

Finally, the eighth witness is Marcelo Firpo de Souza Porto. He is a signatory to a letter calling for a ban on Highly Hazardous Pesticides (HHPs), a letter that uses glyphosate as an example of a HHP. However, Glyphosate has a LD50 of 4230 mg/kg (table 4, slightly hazardous) and is thus classified as slightly hazardous, which is the 2000-5000 range. This pronounced error is sufficient to deem his claims unlikely.

This concludes the Impact on human health segment. The summary is that bad things happen to people, so they blame Monsanto without evidence to support.

Part II: Impact on soil and plants

The first (part II) witness is Diego Fernandez, a GM farmer from Argentina. The only match we can find is a farmer visiting a conference where Verzenassi was present. In this article, Fernandez is only named because his back hurt. Given that Verzenassi is present, it is clear that this will be blamed on agricultural chemicals. 

The second witness is Don Huber, a former professor at Purdue University that now goes on publicity tours apparently sponsored by several anti-science groups. From a secondary source (Genetic Literacy Project) we find not only citations to establish his sponsors, but also several citations of severe criticism. One such criticism: "...  

He will not release it to the wider scientific community for further tests, even after eight years of no publications or any signs of progress. ..." (Dr. Kevin Folta's blog). It is apparently a DNA-lacking alien lifeform that he claims is a causal agent to many diseases and disorders in not only mammalian, but all earth-based life. Nevertheless, despite the claimed impact, importance and so forth he has not released it to the scientific community at large. It apparently thrives in agricultural chemicals and genetically modified life.

I'm going to keep referring to his life form as "alien". The reason for this is that all known lifeforms (at least to the scientific community at large) are DNA-based lifeforms. While other chemical backbones are possible (RNA, FANA, etc.) they are not used throughout Earth-based life. This indicates a singular proto-cell system evolving DNA and DNA-related cellular machinery before branching to the tree of life as we know it. There has been no evidence of any non-DNA lifeform presented to the scientific community. Thus, a non-DNA based lifeform is most likely alien. Additionally, origins of life research focusses almost exclusively on nucleic acids with some backbone (e.g. RNA hypothesis, but also FANA and other variants have been researched, as have hybrid backbones).


Surprisingly, this already concludes part II. The summary is that you cannot simply blame everything on GM and agricultural chemicals; extraordinary claims require extraordinary evidence. In this case, the evidence isn't extraordinary nor existent.


Part III: Impact on Animal Health

Which, for some reason, is seen as distinct from Human Health, even though we are mammals. This is often the case in policy, as most humans consider humans to matter more.

The first (Part III) witness is Art Dunham, an Iowa veterinarian. He believes that GMO crops are wreaking havoc with the health of animals. His daughter wrote a book on it, drawing on her father's notes and the work of 'scientists' like Don Huber. So we are back to the alien lifeform that is supposed to be the cause of nearly everything? Apparently (source), another claim is that glyphosate 'ties up' cobalt, manganese and other nutrients that should be present in animal feed. This claim is also propagated by Don Huber, so it appears Dunham and his daughter did not arrive at these conclusions independently. Either way, scientific literature does not back this claim (DOI: 10.1021/jf302436u): "... Our conclusions are that ... although there is conflicting literature on the effects of glyphosate on mineral nutrition on glyphosate-resistant (GR) crops, most of the literature indicates that mineral nutrition in GR crops is not affected by either the GR trait or by application of glyphosate ...".

The second witness is Monika Krüger, is a German scientist at the university of Leipzig. She apparently believes that glyphosate is responsible for so-called chronic botulism in cattle. It appears she is alone in this belief (secondary source, comment by schillipaeppa on May 29th). Looking at a study by Krüger in the Journal of Environmental & Analytical Toxicology, we see a citation of the now-famous Seralini Affair paper, retracted because they were reporting on the finding of hay in an oversized hay bale. The basic argument of the paper seems to be that glyphosate is bad and has been detected in cow urine (their experiment is measuring this). Well, glyphosate does not interact with mammalian enzymes; it interacts with a plant-specific enzyme. With the retraction of the Seralini Affair paper, their paper is reduced to the exciting message "stuff detected in cow urine". The German federal institute for Risk Assessment has declared glyphosate to be safe (source), as did the EFSA, WHO and others. Note that we return to Krüger's papers when discussing the third witness.

The third witness is Ib Borup Pedersen, another acolyte much like the first.  He wants to tell you what he has seen in his collaboration with Monika Krüger (source). He continues to refer to Don Huber and a number of other individuals that failed to present sufficient evidence to influence scientific consensus. When he read those individuals work, he saw the similarities with the pig-related problems on his farm, and sent them to Krüger. He then refers to their paper, in which they report finding glyphosate in all organs. He claims that they found a distinct correlation between glyphosate and rate of malformation. However, this is not a part of the study, which writes essentially that Pedersen reported these rates - that is not significant evidence. Honestly, I have sincere doubts with regards to the Journal of Environmental & Analytical Toxicology - this is not a paper. This is barely a first-year laboratory report. And upon further investigation, we find that "OMICS Publishing Group is a publisher of open access journals that is widely regarded as predatory." (Wiki, Beall's list).

In summary, we still can't blame random things on glyphosate.

Part IV: Impact on biodiversity

The first (part IV) witness is Feliciano Ucan Poot. He is joined by Angelica El Chanche, whom we can't find much information on. Additionally, he is joined by Maria Colin, Greenpeace Mexico's legal advisor. Poot is a member of the Beekeeper collective of Campeche, the region where he apparently lives. They protested against an governmental decision to introduce GE crops in state of Campeche, a region where indigenous communities (Maya) still live (source).

The judge ruled "The government secretariats of SAGARPA (Ministry of Agriculture) and SEMARNAT (Ministry of Environment) must guarantee that no genetically engineered (GE) soy will be grown in the state of Campeche starting from the 7th of March 2014". So, GM soy was not introduced despite the permit to introduce GM soy in Mexico. Despite that, reporting news sources go off on a tangent, discussing the impact of glyphosate (source). While some crops are indeed engineered to be resistant to RoundUp/glyphosate, this does not mean that you have to spray them. Indeed, it seems that they should've banned glyphosate if that is what you're concerned about. If you recall (old blog post), Monsanto also has a Lepidoptera resistant crop for sale; this does not involve glyphosate, but is just flat-out resistant to moths, butterflies and their larvae.

The beekeepers have a financial interest in honey exported to the European Union. The EU has ruled, in 2011, that honey containing GM derived pollen does constitute foodstuff containing ingredients (pollen) derived from GMOs within the meaning of the regulation. This is mostly a technical ruling whether or not pollen is regarded legally as an ingredient to honey, which would mean it falls under a regulation that requires foodstuff incorporating GM derived ingredients to be subject to an authorisation scheme before being allowed on the market. Allowing GM soybean to be grown throughout their farmland would certainly impede their export.

The final decision by the judge was not primarily influenced by all of the above, according to the rather biased story in the Guardian. The Mexican constitution includes an obligation to fully consult indigenous communities before making major decisions about what happens on their territory, which includes what crops are planted. As a result, the permit issued without any consultation of these communities was unconstitutional and immediately revoked.

The second witness is Steve Marsh, an Australian organic farmer. The story is quite interesting. Steven Marsh's farm had a neighbouring farm, owned by Michael Baxter. Marsh was a certified organic farmer, while Baxter grew GM canola. Marsh sued his neighbour, Baxter, for contaminating his organic crops with GM material. Marsh claimed that he lost his organic certification for more than half of his property for almost three years.

The judge ruled that the implementation of GM crops by Baxter was entirely conventional, as was his harvest methodology. Marsh did not grow canola, so there could be no contamination of end products. Marsh attempted to get more than 80 thousand dollars in compensation. The costs of the process were to be paid by the losing party, Marsh (source).

In an amusing response, Baxter said (source):
He's an organic farmer, he can't spray, he can't use chemicals, you know he's got red mite, he's got aphids, he's got rust, he's got all the diseases in the world, does he worry about that? They blow over the fence, I get them all the time. Do I whinge, do I complain? No, not at all.
Marsh attempted to appeal for compensation of court costs, but here too he was denied. The rather clear statement was that he had put his land to abnormally sensitive use and could not unilaterally enlarge his own rights. This seems fair; his decision for organic certification should not place limits on his neighbours decision to grow GM crops.

The stress induced by Marsh on Baxter resulted in the breakup of the latter's marriage. The actions taken by Marsh seem even more extreme when you consider the following (source):
Marsh had never grown canola so there was no risk of a genetic transfer from Baxter’s GM plants. The so-called contamination consisted of “eight GM canola plants found to have grown up as self-sown volunteer plants”. That’s right – just eight plants, easily removed.
So, the two cases are interesting in that neither actually fits the topic: Impact on biodiversity. The first was a legal ruling regarding the rights to consult of indigenous communities, the second was a ruling regarding two farms. Neither involves biodiversity.

Part V: Impact on Farmers and the right to food

The first (part V) witness is Ousmane Tiendrebeogo. Tiendrebeogo is apparently a cotton farmer (source), and claims not only that GMO cause adverse health and environmental effects but also that they accentuate the impoverishment of farmers. Tiendrebeogo claims that GMO varieties such as Bt Cotton have higher seed costs and actually yield less product. This claim is easily shown to be false (Journal of Agrobiotechnology management and economics):
On average, Bt-adopting farmers realize pesticide reductions of roughly 40%, and yield advantages of 30-40%. Profit gains are at a magnitude of US $60 per acre. These benefits have been sustainable over time. Farmers' satisfaction is reflected in a high willingness to pay for Bt seeds.
Looking into the story, it's pretty simple. The cotton variety that was used to produce the genetically enhanced variant has a different fibre length than the cotton variety previously used in the region. As a result, cotton fiber length is different than what the buyers, the cotton companies, expected. Therefore, a new biofortified cotton strain based on the original variety is under development. (source1source2).

The second witness is Kishan Bir Chaudhary, joined by Ashvani Mahajani. They claim that the change to Bt cotton was a total failure, causing severe losses for Indian cotton farmers. That the loss combined with a "debt trap" forced thousands of growers to commit suicide. However, Bt cotton has been very effective overall and there has been no resurgence of farmer suicides (doi: 10.1080/00220388.2010.492863). Yields have improved by 18% overall, while insecticide volume sprayed dropped by 55% (doi: 10.1016/j.worlddev.2010.09.008). The story was high-profile, and eventually turned up in Nature News:
... It can be hard to see where scientific evidence ends and dogma and speculation begin...During an interview in March, Vandana Shiva, an environmental and feminist activist from India, repeated an alarming statistic: “270,000 Indian farmers have committed suicide since Monsanto entered the Indian seed market,” she said. “It’s a genocide.” ... Although financial hardship is a driving factor in suicide among Indian farmers, there has been essentially no change in the suicide rate for farmers since the introduction of Bt cotton. ... In a study of 533 cotton-farming households in central and southern India, Qaim found that yields grew by 24% per acre between 2002 and 2008, owing to reduced losses from pest attacks. Farmers’ profits rose by an average of 50% over the same period, owing mainly to yield gains.
 The third witness is Farida Akther. Some Bangladeshi farmers are part of a pilot scheme by a research institute, testing a GM Eggplant that modified with the Bt gene, producing a protein (cry1Ac) against some pests. Akhter claims that, despite the utter lack of evidence for any health problems due to this protein, and despite the lack of any problematic findings in this particular Pilot, long term health problems cannot be ruled out. This is the common evasion tactic of the anti-GM movement, where they overuse the precautionary principle. In this case, the scientific evidence is long since clear; Bt and the produced protein are safe. The burden of proof lies firmly with the anti-GM movement.

The fourth and final witness for this part is Percy Schmeiser. Schmeiser apparently claims that he was just using conventional breeding for his Canola crop, attempting to grow a variety well-suited to the prairies environment. In 1998, he received a lawsuit notice from Monsanto. Monsanto claimed that they had been growing Roundup Ready Canola, without a Monsanto license. Schmeiser claims that the reason this happened is because in 1996, their neighbour started to grow these GM crops and that this contaminated their crop. In 2004, the Supreme Court for the Parliament of Canada ruled that, because Schmeiser had not used the GM-traits of the plants he had no monetary benefit. As such, he owed Monsanto no money. Both had to pay their own legal costs (source). Despite the monetary aspects, it remains a violation of patent law (source). The other claims are mostly against the current patent law systems implemented throughout the world.

Monsanto tells the story very, very differently (source). They did try to settle the matter out-of-court, but Schmeiser claimed they grew there by accident. Schmeiser might tell a nice story, but he is just a patent infringer. He saved Monsanto seed; he deliberately used Roundup to select those plants resistant in his fields, then saved these seeds. He also had the seeds treated, indicating that he was fully aware of the GM-traits. Tests revealed that 95-98% of Schmeisers plants were Roundup Ready plants, which means that "contamination" does not explain the utter dominance of the GM traits. The Supreme Court found that they actively cultivated Roundup Ready Canola (source). However, Monsanto sought accounting of profits. Because Schmeiser did not make more profit than he would have using non-GM Canola, there were no profits due to the patent infringement. This primarily tells you something about Schmeiser's qualities as a farmer. Additionally, the court ruled that the plant could not be patented itself; in my view, a failure of acknowledging genetic inheritance. Either way, a contractual obligation (prohibition on saving seeds) is sufficient to protect Monsanto's (or any companies) interest in their product.

To summarise Part V, GM plants promise improved yields and reduced pesticide applications (in a full growing cycle). 

Part VI: Pressures on stakeholders and institutions

The first (Part VI) witness is Pedro Pablo Mutumbajoy, who is apparently claiming to be a victim of Plan Colombia. Plan Colombia is a US military and diplomatic aid initiative aimed at combating Colombian drug cartels and insurgent groups in Colombian territory (source). Apparently, as a part of this initiative the US policymakers bought massive amounts of RoundUp Ultra to spray on drug crops.  I am not sure if Mutumbajoy is a part of the drug cartels. Given that they are "trying Monsanto for crimes against Humanity", it is clear that this story is not relevant. Selling pesticide to the US is hardly a crime; their questionable use of it is a question that US and Colombia voters should ask themselves. It seems likely that Mutumbajoy claims to be a victim of Plan Colombia in the sense that the Aerial Eradication initiative sprayed over his farmland. While this is conceivably possible, the program claims to target illicit crops. However, it seems that a variety of skin, respiratory and other ailments is present in spray zones. Some claim this is the result of the sprayed glyphosate, while the US claims it is the agricultural chemicals they themselves use. I find the second scenario more likely; we have already discussed how glyphosate works and that it is inert in humans.

The second witness is Paul Francois. He claims neurological damages after inhaling Lasso, a trademark pesticide owned by Monsanto (source). While the French courts did assign damages to Francois, the primary reason was not literally stating the need for a respiratory protection mask. The label did note the need for appropriate protective clothing, including gloves and protective equipment for the eyes and face (Monsanto). The decision is not yet final.  I must admit I find this surprising; protective equipment for eyes and face includes, in my view, respiratory protection. Either way, damages are assigned for a technical reason and not because of anything weird. The pesticide is not approved in the EU (source).

The third witness is Juan Ignacio Pereyra. Pereyra is another lawyer representing the "victims". The clearest document we can find is quite literally a local version of the Monsanto Tribunal (source). For instance, the first presentation is Verzenassi. Either way, we have already discussed the health impact of glyphosate (none), so it is hard to see how there can be any victims. Some pesticides, certainly, can have negative impacts if inhaled (as we saw just now). The larger question is whether if it constitutes inappropriate usage. If I misuse a product, then I am the one responsible - not the manufacturer. If you drive your car into another car, you ought not be able to sue and win the manufacturer of either car.

The fourth witness is Miguel Lovera. Lovera is from Paraguay, a country involved in quite extensive land right issues (source). Apparently, about 85% of Paraguay land is controlled by 2.6% of the population, while a third of the rural population lives in extreme poverty. This is a legacy of a 35-year dictatorship of General Alfredo Stroessner. During the past decade, Paraguay's soya land coverage and exports have doubled. It is clear that the 1.6% has a strong interest in agriculture. A previous president (Lugo) apparently tried to fight the wealth gap by tightening regulation of soybean production (source). This is where Miguel Lovera comes in; he was appointed as the head of the National Service for Quality and Health of Vegetables and Seeds (SENEVA). He was accused of incompetency and corruption, with several of the nation's media asking for his resignation (source), and the next president (Franco) replaced and persecuted all civil servants appointed by Lugo, including Lovera. It is not at all clear how Monsanto features in this story; I would surmise that Monsanto, as an agricultural company, is blamed for (part of) the conflict in this country. However, I must point out that selling GM seeds and pesticides is not a crime; in this context, it has little to do with anything. The Monsanto Tribunal has listed him as a health expert; there seems to be no support for this description.

The fifth witness is Gilles Eric Seralini. He is among the most well-known figures in the anti-GM movement. The Seralini affair has led to a situation where Seralini's name on a paper,or citing him in any context other than utterly rebuking him are sufficient reason for zero credibility. Rather than explaining the situation again,  I would refer you to other sources (examples: source1source2source3source4source5).

The sixth witness is Shiv Chopra. Chopra worked at Health Canada when he testified to the Canadian Senate that he was pressured by senior supervisors to approve multiple drugs of questionable safety, among which Bovine Growth Hormone and Baytril. Bovine Growth Hormone (BST) is a peptide hormone produced by cows. It was synthesised using recombinant DNA technology to create recombinant BST, developed by four large pharmaceutical companies. Monsanto was the first of these to receive approval in the US and other countries. The FDA, WHO and National Institutes of Health have independently stated that dairy products and meat from (r)BST-treated cows is safe for human consumption. However, the EU report states that its use often results in "suffering and distress" for cows (wiki). The EU and numerous other countries have (rightfully) banned both (r)BST treatment.

Chopra testified or became a whistleblower to the Canadian Senate (source), which concluded that the presented scientific evidence does not lead directly to the conclusion that rBST residues are unsafe. They recommend that the manufacturer submits the long-term studies identified as missing data from the submission for approval. Missing data, however, is not the same as unsafety. Recent studies still clearly state that rBST is safe (doi: 10.2527/jas2013-7383) - animal rights/welfare issues are a separate story. However, whistleblowing on a Monsanto chemical makes a nice story for the Tribunal. Despite the above and the publically available minutes of his testimony, Chopra is still telling people that the EU banned rBST because of questions regarding its safety and similar ill-sounding phrases (source).

The seventh witness is Claire Robinson. Robinson holds a Master's degree in Philosophy, and actually has papers to her name. The first is in Environmental Research, but the second I checked was in a journal by OMICS, which we discussed for Krüger - a predatory publisher. Robinson is an editor at GMWatch, a heavily criticised pseudoscientific organisation (example).  As a good example, her common anti-GM arguments have been wrecked by William Selatan (source). Robinson co-authored a book that, among things, claims that "conventional breeding continues to outstrip GM in developing crops that deliver high yields, better nutrition and tolerance to extreme weather conditions and poor soils(source). We've discussed a few examples of this before, and it is clear that these promises have been met by GM technology (secondary source).

The eighth and final witness is Peter Clausing. He was an expert in non-rodent toxicology at a research-driven pharmaceutical company (his linkedin), and is now at the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC). This is a private, non-profit organisation that accredits institutions for achieving their standards outlined in the Guide for Care and use of laboratory Animals. PETA disagrees with the effectiveness of this accreditation (source). Clausing is also associated with the Pesticide Action Network (PAN) in Germany. Clausing has called into question the EFSA verdict on glyphosate (source) and wants the world to farm organic (source). Clausing has also defended the Seralini Affair paper ((source). A quick survey of his published work (researchgate) - which came to a stop after 2001 - shows that he has nothing to do with pesticide safety evaluation and has no published work that supports opposition to positive pesticide safety assessments.

Clausing's critique of the EFSA safety assessment is essentially critique of the response written by EFSA's chief executive to the open letter by Portier. However, the critique is rather empty. The PAN's press release notes that Clausing says that the response arguments have no scientific basis and that EFSA takes refuge behind a requirement of methodology. The response by EFSA does not seem to do this in my opinion. For instance, in annex 2b of the response letter the EFSA responds to Portier's letter. Portier notes that you need to 'properly weigh studies' in an interpretation of findings, and states that the IARC did this but EFSA did not. However, IARC was widely regarded to give inappropriate weight to small-sample studies with weak methodology. EFSA gave these studies a more appropriate weight, and compared them to other studies with superior sample size. This is not hiding behind methodological concerns, but simply a proper weighting of large versus small sample size studies. Smaller studies are, amongst other concerns, more susceptible to sampling bias. Selecting 20 swans from Australia could lead one to the conclusion that all swans are black; however, in the rest of the world they are white. (Nobody would claim all swans are all white. This is an illustration of sampling bias.)

To summarise, the connections to their topic continues and increases to be very bad. Furthermore, the witnesses in this segment are relatively unknown characters with very tedious and tentative claims. The essence remains the same; blame everything on Monsanto with a complete and utter lack of science to back it up.

Conclusion

As expected, the entire Fake Tribunal is a theatre. This is not a scientific conference, nor a court of law. It is quite literally a gathering of people that use pseudo-science to promote "natural" and "organic" alternatives to conventional and contemporary agriculture. Their most important part is in no way their data, their science, or the interests they represent; rather, it is their ability to form incomprehensive gish gallop combined with fear-mongering.

By doing so, they cast doubt on the credibility of science and technology. Worse, they negatively influence public opinion on contemporary agricultural technology that has the potential to greatly improve upon agricultural practises, in ways that benefit health through nutrition (e.g. Golden Rice), reduce pesticide usage (e.g. Bt Crops, Lepidoptera-resistant crops) and improve farm life.

The intense negative feedback they generate is truly horrifying. This YouTube video illustrates it nicely; look, especially, at the scientist Dr. Kevin Folta responding to a tweet (around 4 min).


I would much rather be talking about the prospects of an exciting technology with the potential to adapt our agriculture to climate change, lessen environmental impact and improve yield. A technology that can improve the areas of the world living in poverty by the simple prospect of sustained yield.










Rebuke: "On the physics of high-rise building collapses".

Introduction

A while ago, I was alerted to an article by "four physicists" in a "scientific journal". Apparently, these authors had "shown" that the conspiracy is real. Behold:
A European scientific study has concluded that on September 11, 2001, the Twin Towers were brought down by a controlled demolition. The study, conducted by four physicists and published in Europhysics Magazine, says that “the evidence points overwhelmingly to the conclusion that all three buildings were destroyed by controlled demolition.”(your news wire)
 We discussed the article briefly, mostly dismissing it because it is not a scientific study, nor is it by four physicists, and its conclusions do not follow from the evidence.

However, the conspiracy crowd seems real happy with it. The Credible Hulk, for instance, had several `truthers' all over his page (here).

I decided that, as a physicist, it would perhaps be interesting to write a rebuke of this article. Now, I'd like to point out a few points before I start. First, this was published in the member magazine of a non-profit organisation for the promotion of physics and its practitioners. Second, it was not written by four physicists. Steven Jones was a physicist, apparently an outspoken Mormon and a truther. Robert Korol was a civil engineer. Anthony Szamboti is a mechanical engineer. Ted Walter is apparently only affiliated with Architects & Engineers for 9/11 Truth. So, to conclude, the study was by zero physicists. (By my long standing convention of not counting non-practitioners.)

It's also speculative and different from [the magazine]'s purely scientific articles:



On the Physics of high-rise building collapses

The authors start by noting that the (US) National Institute of Standards and Technology, NIST, launched its investigation in 2002. They claim that NIST stated its premise that the WTC towers were the only known cases of total structural collapse where fires played a significant role.

The authors continue to state that, "Indeed, neither before nor since 9/11 have fires caused the total collapse ...". That's interesting, but for a very different reason than you would suppose.  Their source [1], a NIST report conducting a survey of just such historical information, notes:
The results of the world-wide survey indicated that a total of 22 fire-induced collapses were identified spanning from 1970 to the present. The 2001 World Trade Center (WTC) collapses accounted for four of these events. Seven major multi-story fire events were also identified as having significant structural damage due to a fire, but did not exhibit collapse. (NIST)
The authors continue to explain why steel-framed high-rises have endured large fires. While interesting, they continue by re-stating that countless other steel-framed high-rises have not suffered total collapse due to fires, citing the above source. As you see, the source does not seem to back this up. The applied trick seems to be in the wording, as the above quote is about collapsing multi-story buildings, but the authors are only speaking of "steel-framed high-rise" buildings. Steel-framed seems to indicate a building technique (for e.g. skyscrapers) and high-rise is a tall building used as residential or office building.

However, this is not very strong. The reason being that the number of buildings that fit their criteria are about 30 in 1970, 60 in 1980 and about 280 in 2001. As they have just explained, fires typically are not hot enough or last long enough to heat structural members, fire-suppression systems are present, they have fireproofing materials and they are designed to be redundant. So, about 260 buildings existed for some time before 2001; the problem is data bias. You are selecting buildings that are both well-protected and rare. Of course you did not find collapses in this very small selection.

They banter on a bit about how strong the materials are, but then point out that the head structural engineer, John Skilling, explained that the towers had been designed specifically to withstand the impact of a jetliner. While he did state that his people did a calculation showing they could withstand the impact (Seattle Times), it is not clear that this was in the design phase. More importantly, that is the structural damage due to impact. The issue, as various investigations concluded, is that the long-lasting fire with jet fuel added to it caused the material properties of the structure to deteriorate.

And now, they attempt to make Skilling say things he did not. The authors state that "In other words, Skilling believed the only mechanism that could bring down the Twin Towers was controlled demolition.". That's false. Skilling stated that he did not think a 200-pound car bomb would cause major damage, because of design redundancy. However, he thought that properly applied explosives of that magnitude could do it, such as done by the top demolition expert. That does not  imply this is the only mechanism, merely that with a fixed amount (200 pound) of explosives, an expert could do it.

The authors continue to explain thermite demolition, where thermite charges are used to cut the support columns. You cut only on one floor, call it floor C. The floors above C collapse down onto C, crushing the columns that support floor C. The entire building thus collapses down, with each new floor taken up into the 'hammer' made of previously collapsed floors. A slightly more sophisticated method works from the inside-out, so that the collapse moves inward and downward, confining the debris.

While reading that explanation of thermite demolition, the first thing I thought is that a building with many support columns and a sufficiently hot fire would automatically collapse in the sophisticated manner. The reason being that a wide-spread fire is hotter near the centre, so those columns are the first to collapse. This puts more stress on slightly more outward columns, which thus collapse at a lower temperature, and so on.

NIST final report. Downward velocity of the north face
roofline as WTC 7 began to collapse.
Now, in addition to showing the badly made Figure 2, the authors refer to the NIST report (NIST final). They claim the building dropped in "absolute free fall for the first 2.25 seconds of its descent" and that the stasis-free fall transition was "sudden, occurring in approximately one-half second". The cited NIST report whose Figure is reproduced on the right, however, says that the stage I descent was slow and lasted about 1.75 seconds, followed by the free-fall stage 2 descent lasting about 2.25 seconds and the final stage lasted another 1.4 seconds. Clearly, they disagree with their cited source. What is also important is that this is a video measurement of the downward displacement of a point near the centre of the roofline. It is not about the entire collapse; videos taken from different angles show that the collapse started earlier, with the East penthouse collapsing, putting the total collapse at 16 seconds or so (TCH video). This video correlates with Table 3-1 in the final report of NIST.

The NIST report is really rather clear, with the leading hypothesis clearly attributing the collapse of WTC 7 to fires. The fires resulted in a loss of lateral support and the (critical) columns started buckling. The initial local failure progressed up to the east penthouse, as shown in the above video. The combined loss of lateral support and damage due to falling debris led to progression of the failure, ultimately resulting in the collapse of the entire structure.

What is actually quite interesting is that NIST expended considerable effort to compile evidence and determine whether intentionally set explosives might have caused the collapse. Numerous scenarios were investigated, but the lack of breaking windows and sound levels broadcasted by these explosions means this hypothesis lacks confirmation of any kind. Therefore, they concluded that there was no demolition-type blast that would have been intense enough to lead to the collapse.

Back to the authors, we meet the following. It is quite painful, so I'll quite the sentence verbatim:
"Given the nature of the collapse, any investigation adhering to the scientific method should have seriously considered the controlled demolition hypothesis, if not started with it. Instead, NIST (as well as the FEMA, which conducted a preliminary study prior to the NIST investigation), began with the predetermined conclusion that the collapse was caused by fires.
 I've described the developed Leading Hypothesis before. And, we've just discussed the hypothetical blast scenarios. Quite clearly, the investigation adhered to the scientific method and has seriously considered the controlled demolition hypothesis. They have neglected to read sources they cite. 

The authors then carry on about the 'predetermined conclusion'. The preliminary study by FEMA was, apparently, not clear on the specifics. I wonder if the authors know what preliminary means. The authors to continue to claim some things that someone else allegedly said, without citing any sources. They then claim NIST never acknowledged free-fall, until they acknowledged stage II. I'm going to guess that NIST answered the entire collapse took longer than free-fall. They move on to claim that NIST computer models does not show the period of free fall. However, the NIST computations focussed primarily on reproducing empirical features of the collapse. Table 3-1 gives an impression of this. The analysis times recorded there indicate that the observed events are well within the analysis. (If you're wondering why these are not exact matches, there are numerous input variables that determine the exact timing of the events. What is important is that the events are in the correct order and that the observed times are within the zero to extreme debris parameter range.)

The authors claim that the NIST final report provides "an elaborate scenario involving an unprecedented failure mechanism", meaning that the fires weakened the lateral support allowing for buckling. The authors claim that the NIST was able to arrive at this scenario only by omission or misrepresentation, citing a pseudo journal as support for this allegation. The authors then claim that the NIST computer model fails to replicate the collapse, showing a metal-frame model under a very odd angle. If you look at the video material for WTC 7 (e.g. here), you see that various fault lines are clear in the exterior of the structure when it collapses. The "large deformations to the exterior" are observable, especially if you show the video in slow motion. The thing is, the clearest deformations, buckling near the bottom of the structure, are not observed in the video because other buildings block the view.

The authors move on to consider the Twin towers. They claim that the definite report by NIST does not contain analysis of why the lower sections fail to slow the descent of the upper sections. They cite an engineering mechanics paper and the Questions and Answers (here) regarding WTC 1&2.  This strikes me as exceedingly odd, as the NIST NCSTAR 1-6 report concerned this topic. Here, "Insights gained from .. were used, in turn, to formulate and execute nonlinear, temperature-dependent finite element analyses of global structural systems to predict the collapse sequence of each tower. The structural analyses were guided, and where possible validated, by observations..". This quote is from the abstract. It seems that the authors are cherry picking a source that fits their story, rather than using the report concerning the topic under consideration. They also complain that NIST could not provide the full explanation because the computer models did not converge. What this means is that several models, each taking into account or detailing different aspects of a non-linear system, did not converge on a singular solution. What it does not mean is that they are all wrong; the combined systems provide you with a envelope inside which the observations fall. Non-linear systems are notoriously hard to work with, and often do not converge. A very limiting factor is the available computational power, which was far less when these investigations happened.

The authors then misrepresent partial sentences to make the NIST seem incapable. The authors make it seem that NIST cite a paper rather than not investigating the issue themselves. This condemnable misrepresentation by the authors is very revealing, in that they truly want to present a story despite the evidence. The quotes are found in section 9.4.4 "Comparison with other collapse hypotheses". It is in this setting that they cite the 2002 paper by Bazant and Zhou, and find it agrees with their hypothesis. They then cite the pseudo journal again, claiming "researchers" have found that the Bazant paper was wrong.

The authors wrap it up with overestimating the significance of "puffs of smoke", which sounds remarkably like dust expelled during the collapse from small structural fractures. They also wonder why the segment that fell into the interior of the building (e.g. the penthouse) is not visible within the rest of the videos. This is easily explained by their own explanation of how interior-first deterioration of support columns causes the building to fall inward. The authors continue their rant, for instance claiming that molten aluminum has a silvery appearance. While it is true that most metals in their liquid phase appear like metals, we also know of many metals that glow red hot at some point. The same is true for aluminum (e.g. video). As temperatures reached about a thousand degrees Celsius (NIST), an aluminum has a melting point of 660 degrees Celsius. At a thousand degrees, it will glow red hot - just like a light bulb. The mechanism is called black-body radiation (discovered by Planck, and part of a number of anomalies in 19th century physics that led to the discovery of quantum physics and the modern electronics of today).

The authors wrap it up with the following conclusion:
It bears repeating that fires have never caused the total collapse of a steel-framed high-rise before or since 9/11. Did we witness an unprecedented event three separate times on September 11, 2001? The NIST reports, which attempted to support that unlikely conclusion, fail to persuade a growing number of architects, engineers, and scientists. Instead, the evidence points overwhelmingly to the conclusion that all three buildings were destroyed by controlled demolition. Given the far-reaching implications, it is morally imperative that this hypothesis be the subject of a truly scientific and impartial investigation by responsible authorities. n
I would like to provide my own version:

It bears repeating that fires have caused the total collapse of multi-story buildings before and since 9/11. Did we witness an unprecedented event on september 11, 2001? Yes, planes flying into buildings. The NIST reports, which support the likely conclusion that fires burn and melt, persuade a growing number of experts and laymen. The evidence points overwhelmingly to the conclusion that all three buildings were destroyed because, turns out, fire is hot. Given the far-reaching implications, it is morally imperative by utility, categorical imperative and scientific values that hypotheses continue to be tested in truly scientific and impartial investigations, as the NIST has done.

More comments

The authors have quite clearly been shown to misrepresent and cherry pick the NIST report fragments they present, in order to cling to a preordained conclusion even after it has been considered and subsequently demonstrated to be unpalatable. Amusingly, this is exactly what the accuse the NIST of.

There are a number of things that the conspiracy theorist try to use as if it is an enchanted sword granted to them by a naked lady living in a lake. For instance, that multiple news channels reported the collapse of WTC 7 too early. This is rather simply explained; the NYFD explained to reporters that WTC 7 would collapse, they misinterpreted and thought it had already happened.

To the question of "what other buildings do you know that collapsed only by fire", I saw someone respond with this video. That's the Faculty building of Architecture of Delft University of Technology. It burned down about a year before I entered.  As you can see, the building also nicely falls towards the interior. Here, the collapse doesn't continue because the upper part of the building is not sufficiently heavy.


Sorry, conspiracists. You still have no evidence that the plot of Assassin's Creed (the part involving Abstergo) is real.















A tale of selection

Introduction

While reading my delightful new book - which I will name at the end - I realised how only a small part of people realises all implications of natural selection.

It was Charles Darwin, in the Origin of species (By means of natural selection) that first postulated an explanation of evolution by a one mechanism of heritability and another of variability. We know both mechanisms; they are in our DNA. DNA is the mechanism of heritability, and copying errors and sexual reshuffling are the mechanism of variation.

Not too long ago, breeding was invented. By this I do not mean merely the breeding of livestock, but the deliberate selection of offspring so as to produce some sort of phenotypical change. The result are the many 'races' of dogs and cats we are familiar with. 

The first chapter of the Origin is `variation under domestication', and is essentially about breeding or artificial selection. From there, Charles Darwin leaps onto 'variation under Nature' and natural selection as a mechanism. The rest of the book is essentially an extremely satisfying list of examples, by leading naturalist (expert in natural history) of the day. Anybody that claims there is no evidence for evolution should read the Origin.

Variation under Domestication

Leaf cutter Ants (source).

As pointed out in the new book I am reading, domestication isn't necessarily limited to humanity. Indeed, many species of ant practise agriculture and husbandry in their nests, with the prime example of the leaf-cutter ant. The leaf-cutter ant cuts leaves to feed to their fungi farms. The image to the right came with a description: "What a wonderful example of symbiotic relationships.". I disagree; this is a wonderful example of domestication, of farming in the wild. 

"Nevertheless", that author might say, "these ants have also radically changed their habits and are very dependent on the fungi farms. Truly, both species have adapted to their cooperation and the correct description is a symbiotic relationship." I might even grant that. Indeed, I would respond, we are in a symbiotic relationship with cattle and crops. 

"What nonsense is this", my imaginary friend says, "we have domesticated them, not the other way around". Perhaps, I might say. From their perspective, of course, they have a slave species that provides sustenance (fertiliser, animal feed), protection (pesticides, fences, pastures) and so forth. And what do you think of the evolution of lactose-tolerance? "Even so", she says, " we eat them; we take their young, we determine who reproduces. Clearly, we are dominant and I conclude they are domesticated by us". I agree, I add; that is how humans define domestication. And thus, I conclude leaf-cutter ants have domesticated fungi. "Oh, shut up", she adds, "and make me a sandwich". 

Seen in this light, many more examples of domestication suddenly pop into view. For instance, grass is domesticated by grazing animals. This might seem odd, until you realise that grass does better in the presence of these grazing animals. From the grass its point of view, cattle provide the service of killing off competitors, such as saplings. From the cattle's point of view, there is a plant that grows leaves sufficiently fast for grazing. And as time goes by, both reinforce this relationship. But, as we just states, the cows eat the grass and can eat the seeds of grass. The cows are dominant, so they have domesticated grass. Now, isn't that a thought?

Agricultural Revolution

We all should know how it works. From a herd of cows, we breed only the female cows that give a large amount of milk. From their offspring, we select the bulls and again the high-producing females. And so we continue; as the generations go by, our cows are better at giving milk than they were. This is a selection of natural variation in milk-producing capacity that is artificially selected.

Ever since we got a clear picture of that process, we've been breeding. But even before that, our species or genus was a selective pressure for many other species. Consider a nomadic tribe, in a landscape with several other nomadic tribes. Our nomadic tribe is peaceful, and they agree on their tribal lands with the other tribes. Over the years, the tribe develops habits. In the winter, it survives on the edge of a lake, spending the time with fishing and hunting animals coming for water. In the spring, it moves out to the plains, where herds of grazing animals are now breaking up and forming smaller, huntable packs. Then, as summer rises, the plain becomes too hot and the tribe moves up the mountains, past the mountain stream. Here, there is relatively easy hunting in comfort. As autumn comes, the tribe moves back to the plains, to catch the migration of the grazing animals, which move from fertile grounds to wherever they spend the winter.

As the tribe makes it rounds, they gather some plants in the area. A vine with berries is plucked, but the inedible seeds are deposited all around the camp. Certain roots are picked, the thickest grass seeds are eaten, berries plucked. Around the camp, the inedible parts and leftovers are deposited. The tribe moves on. In the cleared space that was the camp, the inedible seeds and leftover roots start to grow again.

The next year, the next cycle. The tribe comes into the area, and finds that the camp of their past year is now full of plants. So, they set up camp close by and set to gathering and hunting. As they walk into their previous camp, they find it is full of edible plants. They gather it, and inedible seeds and leftovers are once again spread around the camp. Each cycle signifies another round of unconscious selection for the lushest berries, the easily found root, full of nutrients and so forth. While otherwise not beneficial for the plant, the rewards are many. Their offspring grows without much competition, is sure to be spatially transported. The new grounds are usually full of nutrients - after all, a tribe of humans just left that area. 

And so, at one point, the previous camp is filled with grapes, potatoes, elderberry, cabbage and wheat. Not wholly the varieties we have today, but the first domesticated version. Who knows how the first farm started? Perhaps a young family is left behind because their expected birthing is during the moment the tribe must get to the grazing migration. The tribes leaves them, comes back and finds that the (now larger) family is still there, happily living off the plants of the past camps with a little hunting on the side. Soon, the entire tribe spends part of the cycle farming. And, as they accidentally select the crops, spend a larger part of the cycle farming. Until one day, one tribe of farmers throws a rock at another tribe of farmers and we call it civilisation.

Selection

I'm not sure, but I think the inception of agriculture was before that of animal husbandry. Perhaps a sickly horse or a lost foal hung around the easily-gathered foodstuffs of the early farms. Maybe a kindly disposed human, adult or not, nursed such a foundling to adulthood or healthiness. Either way, animals were domesticated as well.

The capacity of a farm is limited. Aas the animals multiply, you must at some point reduce the herd. Naturally, you choose those animals that are least productive. The skinny bulls, the cows that do not produce the least milk. And lo', you have practised artificial selection. As this continues, presumably simply because of herd size versus farm capacity, each farm prunes the weak and least productive. Sometimes, no doubt, farms traded or gifted part of their livestock. Even so, the domesticated cattle was unconsciously selected towards greater production of human foodstuffs. 

As time went on, humans became more and more dependent on agriculture and animal husbandry. The selection of the humans is that the bad farmers died out. So, the human species progressed towards better farmers. In that sense, we are domesticated by our livestock and crops.

I don't know how breeding came to be. I imagine it was something of a reward. This meek stallion that worked so well in my field, he must have time with the mare. For humankind, sex is usually seen as a reward. And with our anthropocentric thinking, the same must be true for our livestock. In this way we started to artificially select and breed our livestock. 

The results are out there. At some point, breeding made it into the halls of aristocracy.  Usually, this can be a bad influence at first. For instance, in 'Daughter of the Empire' by Raymond Feist, there is this amusing passage between the (new) Lady of the House and her highest clerk. The clerk expresses his confusion that many Houses choose their breeding bulls by looking at certain characteristics that reflect the masculinity of the Lord of the House. The Lady replies that, as she doesn't require reflections of her masculinity, but that he should just breed as he thinks is best. 

Even so, the reward-system still holds. And, as feudal strongholds grew, so did their kennels. And dog-breeding started. Eventually, breeding turned into a white-collar hobby. At some point, the question of the transmutation of species arose. And Charles Darwin, a young naturalist, went with the HMS Beagle - already called for an artificially selected breed of dog. And soon, most of the western world knew the principles behind breeding.

Directed Evolution

With that, far stronger breeding methods were developed. Eventually, in the early 20th century, we started to mess with the mechanism of variation. Various things can lead to mutation, and the breeding method called mutagenesis was born.

By whatever method, be it the addition of mutagens or ionizing radiation, scientists were able to directly affect the variation in offspring. Take a large amount of seeds, treat them and see what variation this led to. What improvement there is; the rates of mutation changed so very drastically. 

Mind you, it's a real lottery. You have little idea of what you're doing; you are just greatly increasing (perhaps by orders of magnitude) the variability of the resulting offspring and then add regular breeding to get those varieties you were looking for.

Nowadays, a strong movement exists that tells us to "Eat organic" and "Natural". Surely, they would disagree with this practise of radical variation? No, they don't. Instead, mutagenesis is a part of the accepted breeding methods for Organic Agriculture. 

Directed Mutation

Suppose you are a young scientist doing genetic research on plants. Specifically, you are looking at the problems surrounding caterpillar damage to soybean crops.

You know that, for example, a specific plant in Northern Europe is especially resistant to caterpillars. This, you find, is because it makes a specific protein that is inedible to caterpillars, and even detected by butterflies and makes them less eager to put their offspring on the plant. The gene sequence is quite simply, really. Let's call it the NOCATERPIE gene sequence. You also find that the NOCATERPIE protein acts through a mechanism that is not even present in humans, and is thus completely safe to eat.

After ten years of studying genetics and its mechanisms, you have learned that is in principle possible to insert a new gene sequence and have it synthesised by the cellular machinery. During your studies you have seen the methods (enzymes/proteases/nucleases) used by cells to cut, read and edit the DNA code. You devise a clever scheme to insert the NOCATERPIE gene sequence into the soybean genome.

In the lab, in a carefully quarantined room, you grow the new plant(s). You test if the protein is present, do PCR to confirm the changes made to the genome. You test the plants within quarantine for caterpillar damage. Forward a few years; after many tests, you have determined the plant is exactly what you aimed for. After passing an extensive review by not only your university, but also the country's ethical research committees, you are allowed to take the plant to the university greenhouse. Again, you test extensively and confirm your expectations. Finally, you are allowed to do a field test and find you've created a soybean variety that is resistant to caterpillars.

That's called genetic engineering. It is the most recent addition to our breeding efforts. The exceedingly clear name in the new book I am reading is: Genetically Engineered Mutations. The author is completely correct in that view; all that is done is genetically engineering a mutation. These mutations, however unlikely, can spontaneously happen in nature. 

Sure, it is a very direct and guided way of going about variation. Even so, there is nothing ethically wrong with it. The precautionary principle applies just as strongly as it does for 'mere' natural variation, mutagenesis, cross breeding/fertilisation, and so forth. Locations are not an ethical consideration; that it was done in a lab does not make a sufficient justification for ethical condemnation.

The book, by the way, is The Ancestor's Tale  and is written by Dr. Richard Dawkins.