3 Myths about Genetically Modified Crops

Genetically modified oilseed rape, one of the four main commercial GM crops. Photograph: David Levene

Genetically modified oilseed rape, one of the four main commercial GM crops. Photograph: David Levene

The debate about GM crops has reached a new level with many countries deciding on its fate. Among all this shrill and cacophony about it, we indeed have been fed many myths about it. Scientific American published a nice article on it some days ago, tiled – 3 Myths about Genetically Modified Crops . It looked into some detail about the 3 most important myths.

Lets have a look, shall we ?

Myth 1: GM crops have bred superweeds

Verdict: FALSE

This issue has been quite a contentious issue for more than a decade now.

US farmers had widely adopted GM cotton engineered to tolerate the herbicide glyphosate, which is marketed as Roundup by Monsanto in St Louis, Missouri. The herbicide–crop combination worked spectacularly well — until it didn’t. In 2004, herbicide-resistant amaranth was found in one county in Georgia; by 2011, it had spread to 76. 

Many scientists, and even some of my colleagues have argued that use of GM crops which are herbicide resistant are responsible for the evolution of herbicide resistance in many weeds.

Twenty-four glyphosate-resistant weed species have been identified since Roundup-tolerant crops were introduced in 1996.

However, herbicide resistance has been a problem for farmers regardless of whether they plant GM crops or not. For more see this chart on the rise of super-weeds:

‘The rise of superweeds’  Source: Scientific American

‘The rise of superweeds’
Source: Scientific American

So, blaming just the increased use of GM crops wont solve the problem of these super-weeds.

Myth 2. GM cotton has driven farmers to suicide

Verdict: FALSE

Now this has been a big news item in India recently when a leading rights activist and environmental campaigner Vandana Shiva alleged that some 270,000 farmers have committed suicide ever since GM crops have been used. Bt cotton which has a gene from the bacterium Bacillus thuringiensis has been planted in India and has been the major bone of contention in India.

Seeds initially cost five times more than local hybrid varieties, spurring local traders to sell packets containing a mix of Bt and conventional cotton at lower prices. The sham seeds and misinformation about how to use the product resulted in crop and financial losses. This no doubt added strain to rural farmers, who had long been under the pressures of a tight credit system that forced them to borrow from local lenders.

This claim was however refuted by researchers at the International Food Policy Research Institute in Washington DC, who scoured government data, academic articles and media reports about Bt cotton and suicide in India. Their findings, published in 2008 and updated in 2011, show that the total number of suicides per year in the Indian population rose from just under 100,000 in 1997 to more than 120,000 in 2007. But the number of suicides among farmers hovered at around 20,000 per year over the same period.

Suicide Rates and GM crops Source: Scientific American

Suicide Rates and GM crops
Source: Scientific American

The important thing to note here, is that the focus of argument in India has shifted from a balanced discussion on the various ways technology can benefit us to calls for outright bans on using it. This would never solve the issue but aggravate it.

Myth 3: Transgenes spread to wild crops in Mexico

Verdict: UNKNOWN

We finally come to another issue about how transgenes have spread to far-off maize fields in Mexico. What started all of it was:

In 2000, some rural farmers in the mountains of Oaxaca, Mexico, wanted to gain organic certification for the maize (corn) they grew and sold in the hope of generating extra income. David Quist, then a microbial ecologist at the University of California, Berkeley, agreed to help in exchange for access to their lands for a research project. But Quist’s genetic analyses uncovered a surprise: the locally produced maize contained a segment of the DNA used to spur expression of transgenes in Monsanto’s glyphosate-tolerant and insect-resistant maize.

Now, as GM crops are not approved in Mexico, the only possible source of such transgenes could only have come from GM crops imported from the United States for consumption and planted by local farmers who probably didn’t know that the seeds were transgenic. When the results were published it brought a furore in Mexico with people arguing for and against the issue. Ever since, few detailed studies have been done on the spread of transgenes via GM crops.

In 2003–04, Allison Snow, a plant ecologist at Ohio State University in Columbus, sampled 870 plants taken from 125 fields in Oaxaca and found no transgenic sequences in maize seeds.

But in 2009, a study led by Elena Alvarez-Buylla, a molecular ecologist at the National Autonomous University of Mexico in Mexico City, and Alma Piñeyro-Nelson, a plant molecular geneticist now at the University of California, Berkeley, found the same transgenes as Quist in three samples taken from 23 sites in Oaxaca in 2001, and in two samples taken from those sites in 2004.

In another study, Alvarez-Buylla and her co-authors found evidence of transgenes in a small percentage of seeds from 1,765 households across Mexico.

However, some scientists argue that transgene spread could in effect have a neutral or even a positive effect on local crops.

In 2003, Snow and her colleagues showed that when Btsunflowers (Helianthus annuus) were bred with their wild counterparts, transgenic offspring still required the same kind of close care as its cultivated parent but were less vulnerable to insects and produced more seeds than non-transgenic plants.

In the end, i would quote something from the article here:

Tidy stories, in favor of or against GM crops, will always miss the bigger picture, which is nuanced, equivocal and undeniably messy. Transgenic crops will not solve all the agricultural challenges facing the developing or developed world, says Qaim: “It is not a silver bullet.” But vilification is not appropriate either. The truth is somewhere in the middle.

What in fact, would be beneficial for ending the food insufficiency problems would be develop GM crops which would have more protein content, or even essential animal proteins or could produce various other required molecules in our body. These would benefit us in more ways than by simply developing GM crops for resistance to insecticides/ herbicides. The industry needs to look at developing a holistic view of GM crops and instead of creating shrill noise, detractors should sit together with the scientists from academia/industry,policy makers and industry honchos to use technology for our benefit.

For further reading:

1). Bt Cotton and Farmer Suicides in India: An Evidence-based Assessment, Guillaume Gruèrea & Debdatta Senguptaa,The Journal of Development Studies,Volume 47, Issue 2, 2011.

2). Field versus Farm in Warangal: Bt Cotton, Higher Yields, and Larger Questions, Glenn Davis Stone, World Development,Volume 39, Issue 3, March 2011.

3). Economic impacts and impact dynamics of Bt (Bacillus thuringiensis) cotton in India, Jonas Kathage and Matin Qaim, PNAS, 2012.

4). Are GM Seeds to Blame for Indian Farmer Suicides?, Adam Pugen, Feb 2013, The International.

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Beer Lovers Rejoice: A new study says a mere sip of beer triggers chemical pleasure in the brain !!

English: Taken in an Irish Pub located in Madr...

English: Taken in an Irish Pub located in Madrid, Spain on January 3rd, 2007. (Photo credit: Wikipedia)

To start off, let me begin by saying that i love drinking beer especially an Irish stout. Now, whenever i take a couple of sips, moments later there is always  a distinct sensation of pleasure. Now urban legend would have it that the beer exudes a blend of aromas due to a  blend of malt, hops and yeast which produces that sensation in us. Just take a look at the Beer Flavour Wheel below from Mark Dredge‘s upcoming book – Craft Beer World

CBWFlavourWheelMarkDredge908

Now scientists have known for a long time that the pleasurable sensation which alcohol produces in us is because of the release of a particular class of neurotransmitter called dopamineThis molecule is known is to act as reward for the brain and is associated with other tasks like sleeping, sex etc. So, now you might reasonably ask if we already know that then what’s new?? Well, what’s new here is a paper published in Neuropsychopharmacology titled – Beer Flavor Provokes Striatal Dopamine Release in Male Drinkers: Mediation by Family History of Alcoholism. 

This paper published by  David Kareken and other researchers of Indiana University tries to answer this question – As intoxication via alcohol leads to the release of dopamine, does the same thing happens when you take a sip of alcohol? Or the release of such reward molecules subject to intoxication alone? Now, answering this question would lead us towards a more complete explanation of the process of addiction towards alcohol and lead us to develop deterrents in the process.

So, what they did was to strap 49 men to a  Positron emission tomography (PET) scanner   after giving them a sip of beer to drink. The key idea here was to track the levels of various molecules in the brain which are released in response to the alcohol intake. To make the study more scientifically more sound and interesting, they chose the participants in varying levels of alcohol tolerance from, almost teetotalers to heavy drinkers. The delivery mechanism for the beer was completely automated to spray 15 millimeters only which ensured that any difference in levels of molecules observed wouldn’t be a by-product of intoxication.

Surprisingly, what they observed was when men tasted beer there was a significant release of dopamine when compared to tasting a mixture of gatorade + water. Incidentally the researchers also asked the participants whether they had any cravings for the drink they had been given and they were generally much higher after tasting beer than Gatorade or water. However, the amount of dopamine release was not random but was seen in higher levels in people with a history of alcoholism. The researchers believe that this could be a clue as to why some people are predisposed towards alcoholism—and why it’s more difficult for them to quit. The immediate release of dopamine from just a taste of beer would likely serve as a powerful mechanism that would drive their cravings, and this tendency towards experiencing a burst of pleasure might also be genetically inheritable. This could be part of the reason that people with a family history of alcoholism are twice as likely to experience alcoholism themselves.

This experiment shows that for a few unlucky people all it takes for alcoholism to develop is a sip of beer !!

For the rest, i say PROST !!

Additional Readings-

1). Neural response to alcohol stimuli in adolescents with alcohol use disorder, Tapert SF, Arch Gen Psychiatry, 2003.

2). Influence of cue exposure on inhibitory control and brain activation in patients with alcohol dependence, Mainz V, Front Hum Neurosci, 2012.

Genomic Evidence for Adaptation to Global Warming??

The "burning embers" diagram above w...

The “burning embers” diagram above was produced by the IPCC in 2001. (Photo credit: Wikipedia)

Global Warming – The ultimate quibble of this century !! Or should i say the “haute” of this century. Why? Now, common ask yourselves, which single topic apart from the religion/atheism debate, you always hear in any gathering or book reading circles or conferences or on social platforms which is ready to divide people into two opposing camps. Books are being written, movies made, debates fought and what for – “The legitimacy of Global warming”. Despite numerous evidences detractors still love to question it. However, a new paper published this month in PNAS provides genomic evidence for phenotypic responses to climatic warming.

What’s it all about?

Ongoing changes in regional climates, especially the trend of warming winters and blazing summers are pushing many species (both plants and animals) to shift their distribution toward higher latitudes and altitudes. Such a change in the species distribution, with an expansion in previously hostile areas and contraction in their own habitats which are becoming less favorable, can occur rapidly both in plants and animals. However, not all species can migrate to lesser hostile areas, and there are many reasons proposed for it. Primarily among them is the increasing trend of Habitat Fragmentation. Habitat fragmentation can result from human expansion into wilder areas resulting in few phenomena:

  • Reduction in the total area of the habitat
  • Isolation of one habitat fragment from other areas of habitat
  • Breaking up of one patch of habitat into several smaller patches
  • Decrease in the average size of each patch of habitat

As, a result of such human activity many species especially plants can’t migrate into other areas resulting into their dwindling numbers. But some species do survive in such increasingly fragmented habitats and hence have adapted to the climatic warming. Though some previous studies in Drosophila melanogaster have shown adaptive trait variation in relation to climate change in both natural and experimental population, however in some cases, the evolutionary response to climate change may be slow due to genetic constraints causing a time lag between the environmental change and an observed evolutionary response. Hence,understanding how various species track climate warming by genetically based adaptive trait variation and which traits facilitate the evolution of such adaption is important.

What is the new evidence?

Thymus vulgaris

The authors decided to look at Mediterranean wild thyme (Thymus vulgaris), a low growing herbaceous plant which is native to Southern Europe and is often used as a culinary herb. The plant contains many oils and the chemical composition(phenolic or non-phenolic) of it varies in different regions based on the temperature. These oils make a plant adaptable to freezing and hence different climatic areas have plants with varying composition of oils (chemotypes). So it would be worthwhile to see if the recent trend of gradual warming of extreme winter freezing events, has brought about an evolutionary response in plants i.e, has their chemical composition changed over time? Interestingly, any such change in the respective oil compositions in different climactic areas with different temperatures would have a genetic basis. And this is what the authors looked about.

The study area had a Mediterranean climate with summer drought but also severe winter freezing temperatures within the basin as a result of a dramatic temperature inversion In this area, there are six different chemotypes that are the expression of a genetically controlled polymorphism in T. vulgaris. Two phenolic chemotypes (carvacrol and thymol) are largely dominant on the slopes above 250-m elevation and four nonphenolic chemotypes (linalool, thuyanol-4, α-terpineol, and geraniol) below 200m elevation, where they experience the winter temperature inversion. Hence, phenolic chemotypes are predominantly winter non-tolerant whereas non-phenolic types are winter tolerant.

There is thus a sharp gradient in the chemotype frequency over only 3–5 km that goes from 100%of either phenolic or nonphenolic chemotypes to 100% of the other form, with a narrow transitional zone. In short, nonphenolic chemotypes show adaptation to habitats, which in the past have experienced extreme freezing temperatures in early winter, whereas phenolic chemotypes are sensitive to intense early-winter freezing and occur in habitats where extreme summer drought can exclude nonphenolic chemotypes.

Coldest annual temperature from 1955 to 2010 at the weather station of SaintMartin-de-Londres (filled squares), which occurs in the zone dominated by freezing-tolerant nonphenolic chemotypes, and from1970 to 2010 at the Centre d’Ecologie Fonctionnelle et Evolutive–Centre National de la Recherche Scientifique experimental gardens on the northern periphery of Montpellier (open circles), where natural thyme populations are dominated by freezing-sensitive phenolic chemotypes.

Hypothesis: Phenolic chemotypes (thymol and carvacrol) now occur in sites where they were previously absent or have increased their frequency in the transitional sites due to a relaxation of selection pressure normally associated with extreme early winter freezing temperatures due to climatic warming.

To do so, they compared the chemotype composition of populations observed in the early 1970s  to that in 2009–2010 for 36 populations sampled along six transects. Each transect was <10 km long, each containing six populations, with two “phenolic,” “mixed,” and “nonphenolic” populations.

They found that the mean percentage of phenolic chemotypes in a population was significantly (df = 35, S = 68.5, P < 0.01) higher in the contemporary samples (overall value of 53.1%) than in those of the initial study (47.7%) of 1970’s. The changes in composition of the initial nonphenolic populations were associated with the appearance of the thymol chemotype in all eight of the populations whose composition changed and the carvacrol chemotype in three of them.

The changes reported involved a reduced intensity of freezing events and changes in frequency of freezing tolerant and nontolerant phenotypes in natural populations of the Mediterranean aromatic plant, Thymus vulgaris. A significant appearance of freezing-sensitive phenolic chemotypes in sites where they were historically absent and an increase in their frequency in previously mixed populations was observed. Such changes have occurred in 17 of the 24 populations where they could potentially occur.

Such studies, illustrate that a rapid evolutionary response to temperature modifications can occur where genetic variation is combined with a change in a previously strong selection pressure, even for a perennial woody plant. Hence, this provides quite a neat example of genetic changes brought about by climatic warming.  I guess, the detractors of global warming would be feeling quite uneasy now !!

More on this:

  1. Genetic consequences of climate change for northern plants, Alson, Proceedings of Royal Society B, 2012.
  2. Climate extremes: Observations, modeling, and impacts, Easterling DR, Science, 2000.
  3. Ecological and evolutionary responses to recent climate change, Parmesan C, Annu Rev Ecol Syst Evol, 2006.
  4. Ecological responses to recent climate change, Walther GR, Nature, 2002.
  5. Rapid shifts in plant distribution with recent climate change, Kelly AE, Goulden ML, Proceedings of National Academy of Sciences, 2008.

  6. The distributions of a wide range of taxonomic groups are expanding polewards, Hickling R,Global Change Biology, 2006.
  7. A globally coherent fingerprint of climate change impacts across natural systems, Parmesan C, Nature, 2003.

  8. Running to stand still: Adaptation and the response of plants to rapid climate change, Jump AS, Ecology Letters, 2005.
  9. Genetic response to rapid climate change: It’s seasonal timing that matters, Bradshaw WE, Molecular Ecology, 2008.

  10. Climate change and evolutionary adaptation, Hoffmann AA, Nature, 2011.

The human brain simulation project (Blue Brain) wins a billion euros!!

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In one of the biggest funding exercises ever, European Commission has selected Prof. Henry Markrams (pictured above) dream project – The Human Brain Simulation Project for a mammoth grant of € 1 billion over a period of ten years.

The Human Brain Simulation Project or the Blue Brain project has been a center of quite a controversy ever since it started in 2005 at the  École Polytechnique Fédérale de Lausanne (Switzerland). It aims to create a synthetic brain by reverse engineering a human brain down to its molecular details. It uses the famed Blue GENE supercomputer  and uses Michael Hine’s NEURON software to recreate neural connections not just by using Artificial Neural Networks but by a closer approximate model of neurons.

What is it all about?

Neuroscientists have been trying to understand the inner workings of our human brain for some centuries now. First came, the detailed anatomical drawings by Rufus of Ephesus, Galen and Leonardo da VinciThen English physician Thomas Willis published his Anatomy of the Brain which assimilated all its inner structures. The goal of understanding what brain is and how it does work started from these anatomical drawings and has continued on to constructing detailed mathematical models of how each of the cells within it work. Of course, i am talking about the famous Hodgkin-Huxley model which for the first time describes how action potentials in neurons are initiated and propagated.

The quest for understanding how billions of neurons come together in a complex network with millions of feedback loops and yet function so harmoniously without any hint of chaos is considered to be one of the Holy Grails of Science. In this picture comes Prof Markram’s Human Brain Simulation project. With advanced supercomputer at one side, and brilliant electrophysiologists at the other the aim has been to model not just the neural circuits involved in, say, the sense of smell, but to model everything,

“from the genetic level, the molecular level, the neurons and synapses, how microcircuits are formed, macrocircuits, mesocircuits, brain areas — until we get to understand how to link these levels, all the way up to behaviour and cognition”

 

Progress until now?

Obviously to even start off this mammoth task, one has to first demonstrate this so-called unified approach on a smaller scale. And that was indeed what he started off with. From 1995 to 2006 he collected data on the simulation of a rat neocortical column, which can be considered the smallest functional unit of the neocortex (the part of the brain thought to be responsible for higher functions such as conscious thought). Such a column is about 2 mm tall, has a diameter of 0.5 mm and contains about 60,000 neurons in humans; rat neocortical columns are very similar in structure but contain only 10,000 neurons (and 108 synapses). By December 2006, Markram was able to map all the types of neurons and their connections in that column.

By 2008, the researchers had linked about 10,000 such models into a simulation of a tube-shaped piece of cortex known as a cortical column. Now, using a more advanced version of Blue Gene, they have simulated 100 interconnected columns.This has indeed proven that  such unifying models can, as promised, serve as repositories for data on cortical structure and function.

Source: Human Brain Project

All of this has only been possible due to the large-scale advances in supercomputing technology and data storage facilities. The computer power required to run such a grand unified theory of the brain would be roughly an exaflop, or 1018 operations per second, which were quite hopeless in the 1990’s when Markram started off the project. But as available computer power doubles roughly every 18 months, so exascale computers might be available by the 2020’s.

Source:

Source: Human Brain Project

There has been some criticisms to this project, and that has to do with the media hype generated by Markram. His critics argue that he has been making his case through talks, media interviews, well-placed ads, and through the traditional means of publishing articles, reviews etc. The detractors also argue that the Markram’s bottom-up approach might yield such a model  which could be so detailed that it is no easier to understand than the real brain. Also, the progress till now has not been daunting either, as the rat neocortex has no inputs from sensory organs or outputs to other parts of the brain, and produces almost no interesting behaviour.

But despite all the criticism, one hopes that this gargantuan project with its lofty aim would yield interesting results, even if not a complete replica of human brain but at least a shadow simulacrum would be enough. For all the critics, who are too afraid of Markram’s bold new ideas I would reiterate James Russell Lowell:

 “Creativity is not the finding of a thing, but the making something out of it after it is found.”

More on this:

  1. Turing at 100: Legacy of a universal mind, Nature News, 2012.
  2. European researchers chase billion-euro technology prize, Nature News, 2011.
  3. Bioinformatics: Industrializing neuroscience, Markram, Nature, 2007.
  4. The Blue Brain Project, Markram H, Nature, 2006.
  5. Human Brain Project, EU Initiative.
  6. The Blue Brain Project @ EPFL

Researchers find a hidden genetic code

Source: Stephanie Mitchell/Harvard Staff Photographer

Source: Stephanie Mitchell/Harvard Staff Photographer

A recent paper published by Arvind Subramaniam (pictured above) and co-authors in Proceedings of National Academy of Sciences have attempted to provide a solution to a decades old problem in genetics.

Though the genetic code, the rules by which DNA gets transcribed to RNA and then translated to proteins, is quite well understood, but what has remained puzzling is the degeneracy of the genetic code underlying protein synthesis. Now before understanding more about what they did, let me give you a brief primer on the problem itself.

What is it all about ?

Decoding of DNA is accomplished by the ribosome, which links amino acids in an order specified by mRNA (messenger RNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time.  So mathematically we can calculate that, with four different nucleotides (in RNA), a three nucleotide code  could code for a maximum of 43 or 64 amino acids. However, in the process of translation (RNA to proteins) only 20 kinds of standard amino acids are produced. So, many of these groups of nucleotides, called codons  produce same amino acids i.e, code synonymously.  For example, the amino acid can be produced in six different ways. A cool figure below shows all the 64 codons and the different amino acids they code for.

figure-09-08

This apparent degeneracy has been a core problem in genetics, i.e, whether those seemingly synonymous codons truly produced the same amino acids, or whether they represented a second, hidden genetic code. Now Harvard researchers have published a possible solution to this problem, and they hope the solution would lead to developing new methods to fight resistant bacteria.

How did they solve it?

To try and decipher this synonymous coding problem, they decide to use a simple bacterium Escherichia coli. First they considered the synonymous codons for seven amino acids: Leucine, Arginine, Serine, Proline, Isoleucine, Glutamine, and Phenylalanine. This set of seven amino acids is representative of the degeneracy of the genetic code,as it includes six-, four-, three-, and twofold degenerate codon families. Then they constructed a library of 29 yellow fluorescent protein (YFP) gene variants, in such a way that each version of the gene could code for a specific amino acid. Then all these genes were inserted into E.coli. To test whether the codons function similarly or not, they applied environmental perturbations on E.coli. This perturbation was in the form of amino acid availability. They monitored growth and YFP synthesis in these strains during amino acid-rich growth as well as during limitation for each of the seven amino acids.

What they found, was quite startling that under different environmental conditions (amino acid availability) the codons produced proteins at a different rate.  If the bacteria are in an environment where they can grow and thrive (amino acid rich), each synonymous codon produces the same amount of protein, but if they are starved of an amino acid, some codons produce a hundredfold more proteins than others.

The reason for such differences in protein production lie in the nature of tRNA, the Transport RNA which ferries the amino acids to the cellular machinery that manufactures proteins. The authors managed to rule out the usual rules associated with tRNA abundance and codon usage. Rather,it was the competition among tRNA isoacceptors for aminoacylation which was the underlying reason for the robustness of protein synthesis. In plain-speak, what this means that different tRNA molecules have different levels of amino acid carrying efficiency. So, if some tRNA molecules are not able to deliver the amino acid to where it needs to be, the cell would not be able to manufacture the proteins it needs. In an environment where amino acids are in short supply, that ability to hold onto them becomes very important.While the system helps cells to make certain proteins efficiently under stressful conditions, it also acts as a biological fail-safe  allowing the near-complete shutdown in the production of other proteins as a way to preserve limited resources.

What now?

Given the universality of the genetic code, it would very interesting to explore what role (if any) differences in the seemingly synonymous portions of the genetic code may have in other organisms. Also, in diseases like cancer, the cancerous cells deplete amino acids faster than normal cells, so given that environmental perturbations lead to different protein production efficiencies, would it be possible to devise any interventions or treatments to combat them!!

More on this:

  1.  Degeneracy and complexity in biological systems, Edelman GM, Gally JA, Proceedings of National Academy of Sciences, 2001
  2. Cooperation between translating ribosomes and RNA polymerase in transcription elongationProshkin S, Rahmouni AR, Mironov A, Nudler E, Science, 2010
  3. The GCN2-ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivation, Ye J, et al., EMBO J, 2010
  4. High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma, Zhou Y, Goodenbour JM, Godley LA, Wickrema A, Pan T, Biochem Biophys Res Commun, 2009