Why we need genetically modified crops October 22, 2006
Posted by Hegemony in Science, Science Rants.18 comments
I don’t usually post in such quick succession but my recent post about cloned animals got me thinking. Why is there so much opposition to genetically modified crops? I believe people that are against it fall into one of three categories: health concerns, concerns for the “sanctity” of nature, or environmental concerns. I’ll address these as scientifically as I can first before I rant about my personal feelings.
Some people feel that genetically modified (GM) food is not safe. Up front I’ll say that’s not true. I can’t for the life of me figure out how they think that. I’ve heard them talking about “toxic” DNA. Of course there’s no such thing. So what does DNA do? DNA codes for proteins. Each set of three DNA base pairs (called a codon) code for one amino acid. A chain of amino acids becomes a protein. All that is being changed in GM crops is the proteins they express. Can these proteins hurt you? No, in no way are regular plant proteins dangerous. Now prions on the other hand are dangerous, but that’s a different issue. Most of the proteins you eat are broken down and the amino acids absorbed so you can make your own proteins. There just isn’t any rational theory as to how this could be dangerous to anyone. In fact millions of dollars are spent by the FDA to test GM crops before they are used.
For others they have some notion that we shouldn’t be messing with nature. This seems to be a more abstract complaint and thus I’m even less sure what they are talking about. But I’ll say this, humans have been selectively breeding crops for millennia as the basis of agriculture. Cross pollinating the plants that did well and grafting plants together has been a common practice long before we even knew what DNA was. The main difference is that GM crops are doing the same thing faster. If you look at a codon from wheat it’s identical to the same codon from tomatoes. It’s all nucleic acid… ribose, phosphate, nitrogenous bases, that’s it!
Still others claim that protecting the environment from GM crops is necessary. They tell us that organic farming is the best way to feed the world. If all current farm land were converted to organic farms we would only produce 2/3 of the food we do now. And what’s so environmentally unsound about GM crops? They can produce massive yields with out the need for pesticides. It’s a fact of growing food that insects are pests and they’ve been doing just fine despite the fact we’ve been killing them for many years now. And I’ll be the first one to admit that the pesticides we use now are nasty. So how could we avoid the use of pesticides? Hmm… oh yeah, genetic modification! Here’s an example: some plants have proteases (proteins that destroy other proteins) that operate only at alkaline pH. All vertebrates have acidic digestive tracts. Insects however, have alkaline digestive tracts. By adding the gene for this protease to GM crops the plants have a natural defense against insects. Testing in this arena is the responsibility of the EPA, and they spend quite a bit of money to do it.
Now for the rant. Opposing GM crops is without a doubt one of the most idiotic things that a person can do. These foods can feed the world safely and cheaply. With over 20,000 people dying of starvation every day who are we to ignore the advancement that could save these people from suffering? People that are proponents of raw foods and the like seem to forget that most people don’t have the luxury of deciding what to eat. It’s selfish to oppose GM crops and everyone that does should think about the 20,000 lives lost every day. I bet starving people could care less if that bread was made from grain with a few transgenic genes.
In 2002 at the Environmental summit in Africa the US tried to give several tons of GM food to poor nations. Several groups including Greenpeace convinced the leaders of these nations that the food was poisonous. Can you fucking believe that? On this poor advice these nation turned down the offer. Of course there was nothing wrong with the food and those same crops have been grown elsewhere with success. In Zambia, where people are starving to death, Greenpeace unleashed their political agenda and probably killed many people. It wasn’t about the food really being dangerous (as I’ve outlined above) it’s about Greenpeace having an ulterior motive… politics. The world cannot be at peace when so many go hungry.
Helicobacter pylori: the bacterium you should know more about October 20, 2006
Posted by Hegemony in Health, Science.add a comment
Helicobacter pylori has been living with humans for a long time. But it was first characterized in 1875 as strange spiral bacteria in the stomach. However, it could not be grown in culture so it was disregarded. In 1982 two Australian doctors Barry J. Marshall and J. Robin Warren isolated the bacteria. It was eventually discovered that H. pylori plays a major role in the development of peptic ulcers and stomach cancer. Not long after research began to work out the role of H. pylori in humans, evidence indicated that the bacterium was disappearing. It seems that in developed nations antibiotics and better sanitation have decreased the incidence of H. pylori colonization. As it turns out, that’s not as good a development as one might think.
H. pylori is made up of 1.7 million base pairs comprising about 1550 genes. Remarkably, 6% of this bacteria’s genome is not shared by other strains of H. pylori. Humans share over 99% of our genome with chimpanzees, which are a completely different species. This tells us that H. pylori has many distinct yet functional forms that have developed over a very long time in humans.
One notable variant of this organism is the presence or lack of a protein called CagA. CagA is protein whose genes reside near those for a type IV secretion system. This seems to indicate that CagA utilizes this system to enter host cells. Once in the cell it causes the cell to signal to the immune system resulting in an inflammatory response. Those carrying strains of H. pylori expressing the CagA are more likely to develop gastric cancer.
Another variant of interest is the production of VacA. This is a toxin secreted by H. pylori that caused the formation of vacuoles in endothelial cells and (more importantly) turns off leukocytes in the area. Several different versions of this gene have been noted. The first were S1, S2 and M1, M2. The S1 variant had been divided into 3 distinct sub classes: s1a, s1b and s1c. It seems that the S1 and M1 forms produce the most potent version of the VacA toxin. Thus organisms with both CagA and VacA are the most likely to cause disease. The subtypes of the S1 gene have been used to track human movement in the past.
Different populations have different proportions of these genes. For example, s1b is prevalent in Spain and Portugal as it is in areas of Latin America settled by Spain and Portugal. The s1c variant was found in high numbers in some Amazonian areas as it is in the far east. This seems to show that H. pylori was with humans when they crossed the Bering Straight over 11,000 years ago. Genetic evidence from H. pylori can place it in the human population as far back as 60,000 years.
In developed nations only about 10% of people are colonized with H. pylori; whereas 70-100% of people are in developing nations. Humans have been carrying this organism for thousands of years and now the microenvironment is changing. The drop in H. pylori has corresponded with a drop in the incidences of certain types of stomach cancer as one would expect. However, we are seeing a massive jump in esophageal adenocarcinoma, rising 7-9% each year. This is a cancer of the esophagus just above the stomach with a 5 year survival rate of 10%. The primary risk factor gastroesophageal reflux disease (GERD) has gone up; it was completely unknown before the 1930’s. The correlation is hard to miss, When H. pylori colonization decreased these diseases increased.
The key is a negative feedback loop with the host. Humans and H. pylori have been coexisting for so long that there are certain adaptations involved on both sides. The bacteria use various signals to protect themselves as well as the host. An example is pH; if the stomach is too acidic the bacteria die, if it’s not acidic enough opportunistic pathogens can invade. When the acidity is high H. pylori will secrete large amounts of CagA. The resulting inflammatory response will lower acidity. The opposite is also true, low acidity slows production of CagA allowing the acidity to rise. Carrying H. pylori without the CagA gene results in weaker pH control and in people without H. pylori this regulation does not happen at all. If there is no control it is more likely that the esophagus will be exposed to highly acidic stomach contents as in GERD.
In the not too distant future could H. pylori be used as a probiotic? It is certainly not outside the realm of possibility. It is certainly more likely than using species of lactobacillus that are not so intertwined with humans. As we learn more about H. pylori it may become possible to give an individual the right bacterial load of Helicobacter to result in the lowest likelihood of stomach and esophageal cancers.
Food from clones coming to a store near you! October 18, 2006
Posted by Hegemony in Science, Science Rants.1 comment so far
So I hear tell that the FDA plans to allow milk and meat from cloned animals to be sold to people. “But wait,” you think “isn’t that dangerous?” Well, no it isn’t. Cloned animals have been around for many years now. You may think that Dolly the sheep was the first, she wasn’t. Dolly was just the first mammal to be cloned. The risks of cloned animals have been fully explored. A recent study of cloned animals has shown that there is no difference in their fatty acid content, proteins, or even hormone levels in their milk. I’m not trying to convince you of whether or not it’s right to eat meat. Just that not every advance in science is potentially hazardous to your health.
A cloned animal is just that, a clone. It is identical to the original animal. There is no genetic engineering (not that I’m against transgenics) of any kind involved. If you would eat the original you should have no problem eating the clone. Think of the benefits of having herds of the most efficient cattle. You would have fewer animals to feed, producing more food in the long run.
I find myself wondering what problem people could have with cloned animals. People often seem so scared of technological advancement, and as far as I can tell they don’t usually have a reason. Does anyone remember irradiated meat? I do, and it was a great idea. Delivering safer products to consumers… what could go wrong? The name, apparently. People just refused to buy something that said “irradiated” on it. You don’t hear so much about it any more because it was basically a loss. But you’d be surprised how much irradiated food you eat these days without noticing it. Treating food with bacteriophages may not get off the ground at all. People find out that a bacteriophage is a virus and refuse to listen to reason. Yes it’s a virus, a bacterial virus. There has been a move to label food treated with phages in the face of public pressure. I believe this would surely doom the practice. If there’s anything that scares people more than radiation it’s viruses.
There are a lot of people on Earth. The numbers aren’t getting any smaller. We need to embrace new methods of food production. Without these applications of biotechnology more nations will suffer from mass starvation as the population continues to climb. Adopting practices like cloning animals could even help bring some nations back from the brink. People must let go of their preconceived notions and step in to the 21st century.
Intelligent Design: A Threat to Science Education October 12, 2006
Posted by Hegemony in Science Rants.5 comments
Ok, lets talk about intelligent design (ID). It’s crap… to put it more effectively it’s stupid crap. It is a concept so flawed in its basic premise that I’m surprised it has gained support in the mainstream. The premise of course, is that divine creation is a valid scientific theory. It’s just an effect of intentional ignorance. Some people simply refuse to believe that humans evolved from lesser forms of life. But how do they come to ignore science and believe such a farce?
Often they come to this decision because evolution conflicts with their religious beliefs. This often happens when they are young and these ideas are indoctrinated in them by a parent. Of course this is common, parents teach their children what they believe. The hitch comes when they refuse to consider science a reputable source. Sticking firmly to their beliefs, many people do not even listen to the accepted theories of human origin. Instead they choose ignorance, or worse do not understand the scientific concepts that are so poorly introduced in the classroom. They hear that people evolved from apes and think, “Why are there still apes?” or “Why can’t I see an animal evolving?” This is of course a ridiculous misinterpretation of evolution, but they are not told any different by teachers that simply glaze over evolution in an effort to avoid the controversy.
But indeed it is their prerogative to be morons all their life. However, implying that a dressed up form of creationism should be taught in schools is absolutely ridiculous. This is really what seperates creationism from ID. Supporters of ID say it’s science, it’s not. You see dear reader; they come to believe this intelligent design business so firmly that it becomes a basis for their world view. They must only assume that those who believe the evolutionists must not have happened upon that pearl of wisdom they had that proved evolution wrong… probably that business about the apes (or something equally as incorrect). And of course, that means people must be made to see the truth. What better way to convince a populace that evolution is untrue than to provide an alternative, easier to understand version of human origins in their science curriculum? It’s easy to chalk up the complexity we see in the world to a supreme being… too easy if you ask me. Still, many simply can’t (or don’t want to) understand evolutionary concepts and buy into this bunk.
This is when it leaves the realm of personal choice (to be a moron) and becomes a social problem. ID is not science, it’s religion. There is no evidence to support it, just “evidence” to cast doubt on evolution. Though, I must say that most of the propaganda passed off as evidence is pure crap. ID is in no way testable or observable. A responsible society cannot allow what limited science education they have to be tainted by it. As far as I’m concerned there isn’t enough science education in schools.
Most people don’t realize it, but the US is one of the most fundamentalist nations in the world. By fundamentalist I’m referring to how closely social policy parallels the religious policy in a country. We are, in fact about on par with India in this department. The few who out rank us include Iran, Saudi Arabia, and Syria. Do we really only want to be a little bit less fundamentalist than Iran? I hope not but it seems like it’s getting worse. It’s been a slow decline over past years that is taking us farther away from the reason of science.
Even when I was in high school biology (in 1999) there was little or no discussion of evolution. I recall the chapter on Darwinian evolution was just skipped over. One of the most historically important discoveries in biology just skipped over. The subsequent chapters about the work that has been done since were also cut. If I didn’t have the initiative to learn about it on my own I wouldn’t have understood it myself. I don’t mind telling you I was pissed. When it became clear that they were not going to cover evolution I asked the teacher about it. She said she was given a lesson plan by school administrators and those chapters weren’t on it. Is this how we want science education in our country to go? I know I sure don’t.
Transmission of Human Pathogens Via Transfusion October 6, 2006
Posted by Hegemony in Health, Science.add a comment
Those with bleeding disorders like hemophilia have long felt the brunt of the unknown in medical transfusions. Despite recent advances in this area of care the risk posed by emerging pathogens is great. The emergence of HIV is an example of what can occur if we are not vigilant in the search for new human pathogens. Coagulation-factor Concentrates (CFC) have been beneficial in that they are treated more thoroughly, but the threat remains.
When a virus enters the human population it goes through three main steps. The first is introduction. This means a new virus come into contact with humans or an existing human virus adapts in some way. An example of this is how SARS was originally introduced by zoonotic transmission from birds, or HIV from chimpanzees.
The next phase is adaptation. At this stage a pathogen establishes itself and spreads in the species. This often occurs after an alteration in the environment; it can be related to expansion of industry, new medical technology, or a change in public health practices. For example the construction of Aswan dam caused 200,000 deaths from Rift Valley fever which was originally spread via an arthropod vector.
In the final stage a pathogen becomes actively dangerous in a population. This is called emergence. This can occur one of two ways: abruptly with a shorter outbreak (like Ebola) or more gradually and thus more wide spread (like HIV).
There are many viruses that blood products are screened for but the question remains if an emerging pathogen will be caught in time. Part of the problem is that some diseases present no clinical symptoms for a time even though the plasma may be highly infective. One such pathogen is West Nile Virus, a flavivirus. At the peak of the epidemic in New York West Nile infection through transfusion was thought to be about 1.5 in 1000. CFC is usually treated in such a way that West Nile is inactivated. West Nile and other lipid envelope viruses are relatively easy to inactivate compared to the non-enveloped viruses.
The non-enveloped, or naked viruses, may cause a greater risk to CFC as some methods will be ineffective at eliminating them. Many different serotypes of enteroviruses have been isolated from human donations. Some of these are potential pathogens. Enterovirus 70 is a known cause of acute hemorrhagic conjunctivitis and Enterovirus 71 seems to cause various encephalitis diseases. Circoviruses are even smaller and resist nanofiltration. There are no known human diseases associated with Circoviruses but it has show the ability to jump species.
Prions are also of particular interest here. The emergence of variant Creutzfeldt – Jakob disease showed that spongiform encephalopathies can be easily transmitted. The normal prion protein (PrPc) is present in the plasma meaning that there is potential for PrPsc to be present as well. The altered prion protein (PrPsc) has been shown to be transmissible 10-20% of the time in sheep. While it is possible to transmit this disease in blood products it is only a theoretical threat at this point.
Those with coagulation disorders like hemophilia have a special risk of contracting these diseases. Receiving transfusions of blood products for their entire life increases the odds dramatically. After the AIDS epidemic got into full swing the life expectancy for a patient with hemophilia went from 57 years to only 35 years by 1995. These patients also tend to be infected with hepatitis B and C, which complicate their care. Recent advancements in clotting factor replacement therapy have shown promise though. While plasma derived clotting factors could carry disease, new recombinant technologies may put an end to this threat.
Clotting factors can be made by immortal cell cultures with less chance of viral contamination. So called first generation cell cultures contain human proteins and thus have the capability to carry prions. In second generation cultures the stabilizing animal proteins are replaced with carbohydrates reducing the risk of prion transmission. Finally, in third generation no human or animal proteins are added. This is believed to be the safest source of human clotting factors.
Hemophilic patients are exposed to the sum of human disease and often pay dearly for it. Recent advances may provide safer sources of the clotting factors they need. But it will never come soon enough for some.
What’s wrong with the Jehovah’s Witnesses? October 5, 2006
Posted by Hegemony in Uncategorized.18 comments
This is a departure from my usual science writing but I couldn’t help myself. I got a handwritten note from someone I had never met. It had my name (as it appeared on my mailbox) and address. In addition to the note (God, blah blah blah) there was a pamphlet. And oh goodness, you’ve never seen such a thing. Inside there was a ton of biblical verses but the cover was great, here it is:
How’s that for weird? Such a strong claim, “all suffering soon to end”. So we can assume that this image is the Jehovah’s Witnesses’ idea of a world without suffering.
So in their ideal world the following are true: there will be pumpkins… lots of pumpkins. Because, you know, pumpkins are useful for so many things… like pumpkin pie… and other things I’m sure. Also there will be apples (for when you’re sick of munching on pumpkins). After a day of harvesting pumpkins and apples will be placed in a garden of ambiguous looking flowers.
In the ideal Jehovah’s Witness paradise the moose will have lost its desire to protect its territory. In fact, here they will graze quietly near humans that have apparently just
harvested some pumpkins and apples. And it seems that black people do the harvesting. I’m not saying that Jehovah’s Witnesses are in favor of slavery… I mean there’s no suffering there. But maybe the artist should have thought that through better.
Oh, and log cabins, you bet there’ll be log cabins. Who needs modern building technology anyway? But don’t fear, we can still use horses for transport. So I guess everyone is happy and free… except for horses.
How malaria’s effects on the brain kill millions October 1, 2006
Posted by Hegemony in Science.3 comments
Malaria is one of the most prevalent diseases in the tropical and sub tropical world. It is caused by infection with parasites of the genus Plasmodium. In addition to the common symptoms there is also the possibility of developing Cerebral Malaria. This is a rare occurrence but accounts for over two million deaths a year in children under 5 years of age. Examination of the brain tissue of diseased individuals shows blockage of brain microvessicles. These blockages are composed primarily of host platelets and Plasmodium infected red blood cells, sometimes with the presence of leukocytes. The damage to the brain can only be studied in deceased human patients. However, the use of a Murine (mouse) model illustrates the course the disease is likely to take in humans.
The breakdown of the blood brain barrier is key to the pathogenesis of the disease. The mouse model implicates the host platelets as having a key role in this. There are three possible ways that platelets can alter the blood-brain barrier (endothelial cells). They can secrete inflammatory mediators like IL-1, affect leukocytes directly, and congregate with infected red blood cells forming clumps. To study this interaction more thoroughly the authors developed an in vitro model of a cerebral malaria endothelial lesion. The findings corresponded with what was known about the pathogenesis in humans. Platelets were found in higher levels in the brain microvessicles of those that died of cerebral malaria. Platelets express large amounts of CD36 on their surface. This protein is known to assist in the binding of the platelet-infected RBC aggregate to endothelial cells. These observations indicate a definite role for platelets in the pathogenesis of cerebral malaria. The accumulation of these cells in brain micovessicles may contribute directly to the microvascular damage.
Microparticles have also been implicated in the disease process. Microparticles are phospholipid micro vesicles containing cell surface proteins from their parent cell. These are released during membrane rearrangement and vesiculation in eukaryotic cells. Plasma samples from individuals with acute cerebral malaria indicated far higher levels of endothelial microparticles than are present in a standard malaria infection. These levels also correlated to increased levels of TNF, which is known to increase the release of endothelial microparticles.
In a mouse model using knockout mice deficient in ABCA1 (a protein relating to erythrocyte vesiculation) the disease process was tracked. The mice lacking ABCA1 had no legions and did not contract cerebral malaria. Levels of TNF and microparticles were also much lower in the experimental mice as compared to the control group. This seems to indicate that microparticles are involved as with decreased vesiculation comes less microparticle production. While it can not yet be proposed that microparticles have a definite role it seems possible as we know they can act as effector molecules. Additional tests show that microparticles from the control animals caused more clotting than the microparticles from the knockout mice.
These discoveries could result in new therapies for cerebral malaria. If the cell to cell interactions of platelets and infected red blood cells could be lessened it would likely result in resistance to the breakdown of the blood-brain barrier. In addition microparticles may also be targeted. The decrease in microparticles in knockout animals seemed to protect them from the neurological symptoms.
