Genetic Manipulation

European corn borer

Are you happy to eat genetically modified foods? What about your friends and colleagues? Do the GM pros outweigh the cons?

I asked a few contacts for some answers by way of building up to a more formal response to those kinds of questions that will be published soon in the International Journal of Biotechnology (IJBT, 2008, 10, 240-259).

Plant geneticist Dennis Lee, Director of Research at mAbGen, in Houston, Texas, suggests that GM crops have several significant advantages. “Total cost per acre can actually be significantly less for GM crops,” he says. This is particularly true for crop species, such as maize, that have been modified to produce natural toxins that fend off insect pests or protect the crop from the herbicides need to keep weed growth at a minimum. However, he points out that, “In practice, this is often not the case – farmers tend to err on the side of caution and continue to use significant amounts of pesticides and herbicides.”

That said, crops can also be modified to grow in substandard conditions, such as strains of tubers grown in Kenya that are capable of surviving both drought conditions and high-salt soils. “Obviously, this is beneficial to yield – you can actually get some food out of places where you previously could not,” adds Lee. In addition, it could be possible to modify some crops to have greater nutritional content, such as the so-called “golden rice” project by Ingo Potrykus then at the Institute of Plant Sciences of the ETH Zurich.

One of the biggest perceived problems regarding GM crops is the possible contamination of other species. What if herbicide-resistant genes could jump into weed species, for instance? Lee points out that this putative problem can be overcome by using terminator technology to jumping genes. “However, in doing so, it creates a different problem,” Lee adds, namely that farmers must buy seed from the agbiotech company each year rather than save seed for planting.” One might say that this is an exploitative industry focused purely on maximizing profits, but at the same time it solves a serious technical problem that has been seen as one of the biggest stumbling blocks to the acceptance of GM crops.

Jeff Chatterton, a Risk and Crisis Communications Consultant at Checkmate Public Affairs, in Ottawa, points out that the pros are well documented: increased yield per acre, ease of use and perhaps, some day, increased ‘consumer level’ benefits such as higher nutritional values. But, echoes others’ comments on the hidden con of farmers the world over potentially being locked into the agbiotech company’s seed and having no recourse to produce their own from one year to the next.

“As traditional family farms are increasingly moving towards “Roundup Ready” corn or soybeans, you’re increasingly seeing a change in the business model of farming,” he says. “Rather than ‘family farms’ using traditional farming practices, agricultural operations are increasingly becoming factory farms.” It might be said that the emergence of factory farms is occurring outside the realm of GM crops, but with pressure being applied to produce more and more crops for non-food purposes, including, biofuels, unique polymers, and other products, the notion of a factory farm that doesn’t even feed us could become an increasing reality.

Lee also mentions an intriguing irony regarding the public perception of risk-benefits concerning GM crops and that is that the toxins produced by modified Bt maize is exactly the same toxin produced by the natural soil microbe Bacillus thuringiensis (Bt) itself and this is same Bt toxin that so-called “organic” farmers are usually allowed to use instead of “synthetic” pesticides.

Information Technology and Services Professional Bill Nigh of Bluenog, based in New York, provides perspective as a lay person. “We’ve been engaged in genetic manipulation for a long time now,” he says, “but it was limited by the technology at hand. With recombinant DNA it’s a remarkably more vast field of play and a whole new ball game.” He stresses that his main concern regarding GM crops is that, “We seem to be just smart enough to make drastic breakthroughs and inventions, and are driven by the dynamics of the marketplace and ego to produce a lot of new things quickly. However our systems of governance, oversight and coordination are not mature enough to work through the implications of those new things in a timely fashion, especially the unforeseen synergies the breakthroughs can unleash.”

All that said, an international team has now investigated the various issues and has assessed the public’s Willingness to Accept (WTA) GM foods based on experimental auctions carried out in France, UK, and USA. Lead author of the IJBT paper Wallace Yee now at the University of Liverpool, worked, while at Reading University, with colleagues in various disciplines, from agricultural and food to business and economics in Italy, New Zealand, UK and US to explore perceptions of risk and benefits, moral concerns and attitudes to the environment and technology.

“Trust in information provided by industry proved to be the most important determinant of risk/benefit perceptions,” the researchers conclude, “willingness to accept followed general attitudes to the environment and technology.” They also found that educational level and age could also enhance perceived benefits and lower perceived risks of GM foods. “Our research suggests that trust-building by industry would be the most effective approach to enhancing the acceptance of GM foods,” the team says.

“If the industry could educate people that GM technology does not pose any threat to the environment, but provides benefits to society as a whole and consumers as individuals, the attitudes of the public towards GM in food production would be favourable, and in turn increase their willingness to accept,” they conclude.

Computing professional Paul Boddie of Oslo, Norway, coming at the issue of GM crops from an indirect angle provides an allusion to computer programming that seems quite pertinent and was originally attributed to Brian Kernighan, which Boddie suggests readily transfers to other disciplines including genetic engineering: “Everyone knows that debugging is twice as hard as writing a program in the first place. So if you are as clever as you can be when you write it, how will you ever debug it?”

Yee, W.M., Traill, W.B., Lusk, J.L., Jaeger, S.R., House, L.O., Moore, M., Morrow, J.’., Valli, C. (2008). Determinants of consumers’ willingness to accept GM foods. International Journal of Biotechnology, 10(2/3), 240. DOI: 10.1504/IJBT.2008.018356

Sciencebase Seedier Side

Censored elephant

Anyone would think Sciencebase resided in one of the seedier corners of the internet. Because of all the recent fuss about the new seven deadly sins, I was just checking out the visitor traffic using Google Webmaster Tools and found some quite worrying search queries that bring you, dear readers, to this cybershore.

Apparently, 4% of the searches on Google Images this week brought you looking for the periodic table of sex!

Well, I have to admit, there is a thumbnail graphic of said item on the site, mentioned in a post Periodic Post, from August 2006. And, Sciencebase ranks #7 in Google for that phrase, so it’s perhaps not surprising. Slightly more worrying is what people were searching for who reached my post Giving Good Headline, which was about the subject of press releases and the best approach to headline writing. Then there are the dozens of visitors looking for Girly Games who found my article on the psychology of video game addiction and how it apparently differs between males and females.

I’m loathe to list some of the other terms people are searching for on Google Images for that brings them to Sciencebase, oh go on then, you twisted my arm: erectile dysfunction, premature ejaculation, seven deadly sins, erotic, and several I’d blush even to type.

Sexy search queries

Now, Sciencebase, for one reason or another (and it’s not because, it’s that kind of site) somehow ranks quite highly for several of those terms. However, there are a few others that bring visitors to the site for which the site ranks way, way down the search engine results pages (SERPs), and I don’t just mean the bottom of page 1, or page 2 even, I mean bottom of page 73. Now, that reveals true search diligence, I’d suggest. Whoever works their way through 72 pages of results to get to that one item?

Most visitors are not after smut, thankfully, they’re after the site’s hard-hitting science news and views with a cynical bite. Unfortunately, as I was writing this post, I realised that posting it in its original form was unlikely to reduce the tide of filth, in fact it might simply encourage more of those seedier searches, so I’ve removed a few of the less choice keywords, just to make it safe for work and to prevent the site from getting slapped with an adult-filtering ban.

Afters I’d put the finishing touches to this piece, I checked the site’s top searches in GWMT again, just to see if there had been any additional phrases of interest. I discovered that Sciencebase is now ranking for “polar bears willie soon” in blog searching. Asa search phrase that has to be pretty unique. I assumed it was from someone in the UK urgently tracking down Arctic bestiality sites, or Inuit innuendo, until I realised it’s actually two phrases – Polar Bears (the Arctic beast in question) and Willie Soon (the climate change skeptic) – both of which I mentioned in my CO2 refusenik post recently. It seems that Sciencebase is not quite the quagmire of filth some of the site’s visitors had hoped after all.

Rubbing Up the Gene Genie

Gene Genie Logo by Ricardo Vidal at My Biotech LifeSciencebase is this week proud to play host to the Gene Genie Blog Carnival thanks to an offer from Bertalan “Berci” Meskó over on the excellent ScienceRoll. For those who don’t already know, a Blog Carnival doesn’t usually involve a lot of be-costumed revellers dancing through the streets to the sound of the samba band, but is a gathering of like-minded bloggers brought together through the power of the tubular Interwebs to share their latest posts on a given subject.

The Gene Genie carnival has an obvious theme. No, it’s not the songs of aging but outlandish popster David Bowie. No, it’s not the magical character of Arabian Nights entombed in a lamp, and no it’s nothing to do with quasi-sci-fi-retro-fit BBC cop show Ashes to Ashes. It’s about genes. See, I told you it was obvious.

Anyway, the carnival (from the Latin carnis, meaning meat, and levare, to put away) covers some of the hot topics in the world of genes, genetics, DNA and all things inherited.

So, here we go:

  • Gene Found for Ghosal Hematodiaphyseal Dysplasia Syndrome: A Rare Syndrome with Increased Bone Density (DNA And You)
  • Home DNA tests on the up, ‘safer’ clinic DNA tests on the down (Genetics and Health)
  • Gene Plays a Role in Hair Loss Identified (The Biotech Weblog)
  • Extinction Fears of the Red-Headed Homo Sapien (GNIF Brain Blogger)
  • Where are brown people short? and Shadows of the Past in Genes (Gene Expression)
  • Genetics Cause of Smell Perception (ArticleBiz.com)
  • Why do we have common risk variants for metabolic diseases? (Genetic Future)
  • Researchers Discuss MEGF10 Gene Assocation To Schizophrenia (Scientificblogging)
  • Differences of gene expression between human populations (Anthropology)
  • Brain scan reveals cultural differences (Sciencebase)
  • Scientists Link Gene That Promotes Long Lifespan to Cholesterol (Biosingularity)

In the realm of personalized genetics:

  • NY Times: Insurance Fears and DNA Testing (DNA Direct Talk)
  • Ann Turner on Personal Genomics Companies 23andMe vs deCODEme and deCODE Launches PrCa Prostate Cancer DNA Test (Eye on DNA)
  • One Fifth of GDP! (Gene Sherpas)
  • Why should you get a free 23andme test? (bbgm)
  • 23andMe Adds Paternal Ancestry and an Updated Gene Journal (Genetic Genealogist)
  • New York Times: Genetics and insurance (Tracing the Tribe)
  • SNPwatch: One SNP Makes Your Brown Eyes Blue (Spittoon)
  • Global Awakening in Genetic Counseling (Scienceroll)
  • Your Future IS Your Genes: Diagnosing Bipolar Disorder from a Blood Sample (Living the Scientific Life)

    Genetic Futre ThumbnailThe next edition of Gene Genie will be hosted by DNA Direct Talk, watch out for it! For more information about the Carnival here.

Don’t Poison Your Dog This Holiday

Theobromine structure

‘Twas the night before Christmas, when all through the house
Not a creature was stirring, not even a mouse

Well, that may not be quite true, do you know what your dog is doing right now? What about the cat? They’re not rummaging through the presents under the tree are they? You didn’t leave any luxury plain or dark chocolates under there did you? If you did, you could wake up to a quite horrible surprise when Christmas morning comes around. Chocolate makes pets ill! That’s the important seasonal warning being delivered by vets everywhere.

Poisonous chocolatesSo, what’s the problem? Surely a little chocolate snack in the night isn’t going to harm good-old Fido? Well, our vet begs to differ and so do the veterinary toxicology sheets for the chocoholics’ favourite fast-food. Man’s best friend, and several other animals, you see lack a particular liver enzyme that their owners do possess, that breaks down a toxin found naturally in chocolate – theobromine.

Theobromine has nothing to do with the element bromine, rather it is a bitter alkaloid from the seed of the cacao tree, known scientifically as Theobroma. The basic chemical skeleton is a xanthine unit, same one on which several other more well-known natural chemicals are based. The stimulant caffeine (from coffee beans) is a xanthine, for instance, so too is theophylline (found in tea and used in treating COPD and asthma).

Non-chocolate Labrador

Lacking the enzymes to metabolize theobromine leaves dogs exposed to the toxic action of the compound, which can cause vomiting, diarrhoea, hyperactivity, tremors, seizures, abnormal heart rhythms, and in extreme cases death.

So, what are the first signs of chocolate poisoning, what’s the lethal toxic dose, and what should you do if you think your dog has been at the chocolatier’s produce? Well, the first signs of chocolate poisoning are vomiting and diarrhoea, increased frequency of urination, and nausea. A toxic dose that will cause symptoms is about 100-150 milligrams of theobromine per kilogram of body weight, toxic dose could be approximately 250 and 500 mg/kg. A kilogram of milk chocolate will contain about 2 grams of theobromine. So a greedy, little dog is at greater risk of a serious digestive upset than a big gluttonous dog if he or she snaffles a 250 g bar of milk chocolate.

There is no direct way to treat chocolate poisoning in dogs, although inducing vomiting if the animal is caught “brown-pawed” (best left to the vet) is probably a good idea. A dog that has eaten a lot of chocolate will almost certainly require hospitalisation for at least the four days while the theobromine is naturally excreted (It takes about 17 hours for a dog to excrete half of the theobromine in its system, which means this toxin will reach vital organs repeatedly via the blood stream). But, who needs that, or worse, at Christmas? As they say: a gram of prevention is worth a kilo of cure.

For lovers of cats (small, domestic, big, wild) keep the aspirin out of reach. It’s deadly poisonous to felines.

Male Semen is Redundant

Male sperm

You’ve seen the kind of thing: “Warehouse Razed to the Ground in Fire”, as if razing didn’t already mean the building was levelled. Worse, “Balloon Ascends Up into the Air”, ascending down is very difficult, simultaneously, at the same time, if not impossible; so too is descending up.

However, the award for the most redundantly tautological headline of the year has to go to Scientific American for Male Semen Makes HIV More Potent, that’s male semen as opposed to the female variety, is it? It’s an important discovery, nevertheless that a chemical constituent of semen affects the immune system facilitating viral infection.

Scientific American is probably not the first and original nor the ultimate and last publication to use this phrase though. DoctorNDTV ran a story with the title: Male semen loss concerns and risky sexual behaviour. Then there’s a research paper in the Journal of Avian Biology that discusses bacteria found in the “male semen” of red-winged blackbirds. Even the venerable and well-respected New Scientist recently published an item on insect courtship and egg laying. Apparently, the trigger for egg laying “is a small protein called sex peptide (SP) in the male’s semen.” Again, the word male, while perhaps making the sentence smoother, is totally redundant and not needed.

A search for the phrase “male semen” on PubMed produced not hits, although “male sperm” came up several times in various journals. So as not to appear sexist, I also did the equivalent searches for “female semen” and “female sperm” and quite surprisingly got several PubMed hits. One paper on mythology mentions how at one time in human history a godly being or other supernatural entity was thought to intervene in the merging of male and female semen to bring about conception. Not quite a modern biomedical reference point, then. The phrase “female sperm” gave absolutely no hits, unsurprisingly.

Maybe the clue as to why these various publications qualify the word semen lies in those papers discussing the mythology of reproduction. A quick Google shows that there are many references to religious and proto-religious texts that discuss both male and female semen as if they were both real. Perhaps by qualifying semen as male in modern writing, rather than simply discussing semen, there is some referential nod to humanity’s misconstrued understanding of reproduction. But, modern understanding of reproductive biology defines semen as a product of the male reproductive organs that acts as a transport medium for sperm, so, like I said, it’s redundant.

I asked linguistic guru Steven Pinker of Harvard University, whose book The Stuff of Thought I reviewed on Sciencebase recently, about this apparent paradox. Pinker told me that he suspects that, “the cause is not a nod to the ancients, but a desire to call the reader’s attention to the fact that it’s
the naturally occurring fluid that encourages the potency of the virus, not some externally administered product.

“Semen Makes HIV More Potent implies to me,” he said, “that adding semen increases the potency, rather than that the HIV exploits the properties of the semen it finds itself in.” He adds that it is peculiar that this may be the case. “Odd that the redundancy should do that,” he told me, “but somehow I think it does.”

Intriguingly, after I contacted Pinker, I saw that the journal Nature, as opposed to the popular science magazine, Scientific American, had covered the same story. In Nature, however, their piece was entitled – Semen boosts HIV transmission. So, for some reason they felt semen does not need a masculine qualification of any kind. The tautology of the phrase “male semen” may seem trivial, but it is an important issue.

Googling for Genes

Those clever people at Harvard are using Google‘s API to allow users to search for gene sequence fragments on the Web in combination with a text query. You’re limited to 1000 searches per day and have to enter your own API key to get the maximum benefit. But. that’s probably enough to be going on with.

From the site: Query Gene is distinctive because it is not limited to a single database. Instead it captures genetic information across the net using Google. It works by taking a gene sequence in combination with other search terms, finds similar sequences using NCBI’s MegaBlast, retrieves the descriptions of those matching genes from NCBI’s Entrez Nucleotide database, and performs a series of Google searches using the combination of your original search terms and each gene description. The percent sequence identity is indicated alongside each match: this indicates how much of your queried sequence is contained in the sequence it matches.

You might want to find out what disease states are associated with a specific nucleotide sequence. No problem. Paste in the sequence and enter a text phrase, such as “genetic disease associated with” and up pop the results. Well, actually, they didn’t with the test I tried, but that could be down to my browser configuration. I got “Sorry, we are under maintenance: Please try again in a few weeks”.

A sample sequence is given here. If someone else could confirm or refute the maintanance outage for ChemSpy readers that would be very helpful.

Murine faeces

I’m not sure whether I should admit to the following, but this morning I found little scatterings of murine faeces and could detect a musky yet strong smell of ammonia in the storage area where we keep our dog and cat food. Not nice. In case you haven’t guessed, we got mice.

Odd that these little critters should be so brave as to venture into the part of the house in which the cat spends some of its time and although he is getting on in years, he does still have the legs for a chase (especially when the dog slips her lead and chases him out of the door. Anyway, traps have been bought and placed, droppings have been removed and traces of murine urine have been mopped up (with a cotton bud) and the whole area disinfected.

I got to thinking about that word I used just now. Murine. The “ine” suffix means just means “of”, “like”, or “referring to”, while the “mur” was derived from “mus” then “mur” for mouse in an originating Indo-European language and thence to Latin – “murinus” meaning of mice. The root gives rise to the scientific group name for both mice and rats Muridae or sub-family Murinae. Others words of similar structure include porcine (pigs), bovine (cattle), ursine (bears), ovine (sheep), equine (horses), and of course feline and canine, but not supine.

Shopping for Genes

Leaning strongly towards the bio today, I thought I’d mention a new database for biologists that works like a shopping mall. An international team has opened a virtual bazaar, called PAZAR, which allows biologists to share information about gene regulation through individually managed boutiques. Customers may draw data for free from any boutique or extract information from the “superstores” that aggregate data of similar types.

In deciphering the human genome sequence, researchers hope to understand the “when and where” of gene expression because it could underpin novel cancer therapies, stem cells treatments for degenerative disease, and explain complex diseases such as diabetes.

Male-Female Crabs Split their Difference

Male-Female Crab

David Johnson and Robert Watson thought they had seen all there was to see in the Chesapeake Bay in almost three decades until they pulled out a crab from the way that had a male left half and a female right half. Now, that crab, acquired by Romuald Lipcius of the Virginia Institute of Marine Science at the College of William & Mary, has moved sideways into the world of natural metabolites where its gynandromorphic peculiarities have helped scientists, for the first time, discover that some molecules can be made only by one sex and not the other.

The male-female crab is a unique example of the blue crabs. It turns out that the males of this species produce a natural metabolite that is absent in females. This suggests that some complex biochemistry is underway that is activated only in males. Robert Kleps of the University of Illinois at Chicago and colleagues have isolated this small molecule and identified it as 2-aminoethylphosphonic acid (AEP), an uncommon but well-documented natural metabolite.

We used low-field NMR using phosphorus-31, to observe the small molecule, explains Kleps. He points out that science tends to get lost in the rush for higher field NMR running hydrogen-1 and carbon-13 on 100 kilodalton proteins. However, he adds that, “Even low-field NMR spectroscopists can make interesting discoveries. I’m very happy to have stumbled over this metabolite, while doing basic research on invertebrate metabolism.”

So, why might the existence of a metabolite in the males of this blue crab species and not the females have any bearing on our everyday lives? Well, there are well known differences between the sexes in people, such as disease susceptibility, anatomy and drug metabolism. Kleps points out that these differences might in fact be due to the presence or absence of a crucial metabolite.

Now that the existence of a sex-specific metabolite has been found for one animal the search is on for others, including ones that might exist in people.

For more details on the NMR study check out my column on SpectroscopyNOW.com, the research paper itself is available in Plos One.

You can hear a description of the crab from Lipcius here and listen to Kleps’ podcast

MMR and Statistical Manipulation

Measles virus

When I was still at high school, way back in the late 1970s, there was a health scare that got a lot of media attention. Apparently, there was a perceived risk that the whooping cough vaccine could cause brain damage. The fall off in vaccination for this disease is claimed to have led to the widespread outbreaks of whooping cough in 1979 and 1982, there having previously been almost zero annual cases. At the peak there were some 60,000 cases.

Fast forward to the near present and you will recall similar scare stories about the combined measles-mumps-rubella vaccine, the MMR, and claims by researcher Andrew Wakefield (Lancet, 1998) that MMR could cause autism in some children. It’s a topic guest blogger Michael Marshall covered on Sciencebase in November 2004. It seemed that, at the time, the debate was pretty much over. However, despite repeated demonstrations of the apparent inadequacies of the original research into a link between MMR and autism, the issue is resurrected on a regular basis. Most recently in a cover story in The Observer, which drew much flack, but also left the chattering classes once more in a flap.

Right now, I’m looking at an article from the print edition of The Times offering an answer to the Question of the Week – “Measles or vaccine?” – the article talks of how measles has reappeared and it is apparently all down to many parents’ reluctance to have their children vaccinated with the MMR jab. The article talks of “herd immunity” and how enough children have had a double dose of MMR which should stave off an epidemic. The emergence of herd immunity, of course, will be little comfort for a parent whose child experience any of the potentially severe side-effects of vaccination.

In the article, pictured alongside a blow-up of the measles virus and an image of a nasty-looking hypodermic needle, are two charts, one showing the number of cases of measles in the UK from 1940 to the present day and the other showing the number of deaths over the same period. Incidence of the disease ebbed and flowed during the period up to the early 1970s whereupon cases began to fall rapidly from a peak of 800,000 a year in the early 1960s to just one or two hundred a year by the mid-1970s.

The MMR vaccine was introduced in the US in 1971 and later in the UK, thereafter incidence of measles has pretty much fallen to levels close to zero. It seems that the pre-vaccine drop had another cause, presumably reduced overcrowding, improved nutrition, better hygiene and healthcare. No one knows at what point this fall would have reached a plateau.

In contrast, the second chart of death rates shows an exponential decline in measles deaths since the 1940s, by about 1970 measles deaths were also close to zero. The risk of getting measles is about one in three, assuming no vaccination coverage at all. The risk of serious consequences to this disease, which personally I had in 1972 or thereabouts, is somewhere between 1 in 5000 and 1 in 15,000. Compare that to the risk of death in a road accident. According to Transport2000 , the UK’s national environmental transport body, each of us has a 1 in 17 chance of being killed or seriously injured in a road crash during our lives. Such figures damn the disease statistics somewhat. Of course, vaccination does come with some risks, but adverse reactions, such as seizures with an associated risk of brain damage, exist at the 1 in 10,000 level.

There has been one UK death from measles since 1992 (as opposed to the several hundred each year during the 1940s). The unfortunate victim was apparently suffering an underlying lung disease for which he required long-term immunosuppressant drugs. He was very unfortunate to be exposed to the measles virus, and when he contracted the disease he was very unlikely to have recovered. This is one fatal case. Even with near 100% vaccination, there would still be a finite risk of any random member of the population contracting the disease. Unfortunate, but true. The statistics would not lie surely?