Craig Venter’s team has crossed another milestone in their quest to engineer artificial life – they have engineered a bacterium that can survive and reproduce with just 473 genes. This is the smallest genome of any free-living thing (so that does not include viruses).
The purpose of this is to create a minimal starting point for later genetic engineering. Venter says this minimal bacterium is like a frame onto which specific modules can be placed. He envisions a future in which you can have made-to-order genetically engineered bacteria in which you plug in specific functions.
The Basic Science
This research program is also interesting from a purely basic science perspective. The bacterium used in Venter’s research is Mycoplasma mycoides. The choice of a Mycoplasma bacterium was obvious, as the species in the wild with the smallest number of genes is the related Mycoplasma genitalium, which has 525 genes. The new bacterium has 52 fewer genes.
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What would happen if the US or the world banned the use of GMO (genetically modified organism) crops? A new study out of Purdue addresses that question.
The authors estimated the reduction in yields for corn, soybeans, and cotton if GM traits were abandoned. They then plugged the results into a well-established model of how much additional land would be needed to make up for that reduction in yield. They found:
Eliminating all GMOs in the United States, the model shows corn yield declines of 11.2 percent on average. Soybeans lose 5.2 percent of their yields and cotton 18.6 percent. To make up for that loss, about 102,000 hectares of U.S. forest and pasture would have to be converted to cropland and 1.1 million hectares globally for the average case.
The most significant environmental footprint of agriculture is land use. Every hectare (2.471 acres or 10,000 square meters) of forest or pasture that you convert to farmland increases carbon in the atmosphere contributing to global warming. Further, converting land to farmland reduces natural habitat or land for grazing.
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The farming systems we are putting in place now will need to feed the 9-10 billion people that will inhabit our planet in 2050. This is a huge challenge.
Many people speak about “sustainable farming,” which is a legitimate and important concept. Truly sustainable means that we need to track all of the inputs and outputs in the global food system and see that we can extrapolate that system indefinitely into the future.
One of the most, if not the most, important factor in sustainability is nitrogen. Plants need a lot of nitrogen to grow, and this is often the limiting factor in large-scale food production.
Thinking about where nitrogen ultimately comes from – the entire nitrogen cycle – is like thinking about where energy ultimately comes. It’s a very useful question to ask. For example, when people claim that they can run their car on water they are failing to ask this basic question. When you do you realize that the energy is not coming from burning the hydrogen and oxygen, but from whatever energy source you used the split the water into hydrogen and oxygen.
The same thought process applied to nitrogen is also illuminating. Continue Reading »
(Note: We have been having some website issues over the weekend, which is why there has not been a post in a couple of days. All seems to be working now, but we are monitoring closely.)
Science may have a replication problem.
One of the goals of scientific skepticism is to examine the process of science itself, often through the lens of pseudoscience. I find this remarkably helpful, and something that many mainstream scientists often do not understand.
By closely examining pseudoscience as a phenomenon, we can see clear examples of how science goes wrong, how the process of science is subverted, and all the different ways scientists can make mistakes or bias their results. We can then apply this knowledge to legitimate science, flushing out more subtle manifestations of the same problems.
Said another way – if we explore all the reasons that a scientist can come to the conclusion that homeopathy works (when it clearly doesn’t) we will learn much about all the possible ways to fail when people do science (or think they are doing science).
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I hadn’t planned on writing about GMOs again today, but I received an e-mail from a listener of the SGU which nicely represents common misconceptions that many people have about genetically modified organisms and farming in general. These are common anti-GMO talking points, which is why they are so widespread.
That even thoughtful skeptics have these concerns is testimony to the successful misinformation campaign waged by the anti-GMO movement, which is largely the organic lobby and some in the environmental movement, such as Greenpeace.
The strategy here is also clear – whenever you deal with one misconception about GMOs, opponents just slide over to another point which becomes the “real” reason they are against GMOs. The experience is identical to arguing with those who reject the claims of anthropogenic global warming, when forced to give ground on one factual claim (OK, maybe the Earth is warming), they just retreat to another (but do we know that this is bad?).
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The dating of phenomena in the past, such as the existence of a specific species of animal or the presence of humans, is always based upon the earliest and latest evidence discovered so far. When you think about it, it is obviously very unlikely that we will have discovered the absolute earliest or latest occurrence of anything in the past.
It it therefore very common for new discoveries of fossils or archaeological evidence to increase the range of a phenomenon. Date ranges are always tentative and changing, although new discoveries still often lead to headlines emphasizing how surprised scientists were at the find.
For example, when did humans first live in the Arctic circle? There are essentially three types of evidence for a human presence. The first is direct evidence – human fossils found in the location and dated to a specific time. The second is human artifacts, stone tools being the most common because they preserve well and are unambiguous human artifacts. The third is human activity, such as fire pits or butchered animals.
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Continued from Part I
5) How to Analyze a Scientific Study
I don’t expect a non-scientist, or even a scientist far outside their area of expertise, to be able to do a detailed analysis of the strengths and weaknesses of a study. That is what peer-review is for. However, there are some basic rules of thumb that could give even a lay person a rough idea how seriously they should take a study. Always ask at least the following questions:
Is the study controlled in some way? Was the treatment group compared to a control group, or was the alleged effect compared to some baseline?
Is the study blinded? Were the primary measurements or assessments performed by someone who was blinded to whether or not the alleged effect is supposed to be present?
Are the outcomes being measured subjective or objective? How are they being measured? What do they really mean?
How large is the study? Studies with small numbers of subjects or measurements (less than 50 per group is a good rule of thumb) are considered small and unreliable.
Is the study an observation or an experiment? Are they just looking for some correlation (in which it is difficult to make statements about cause and effect), or are they controlling for variables and isolating the one factor of interest?
What is the reaction of the scientific community to the study? Are experts generally critical or excited about the results? Continue Reading »
What does it mean to be scientifically literate? There is no completely objective answer to this question, it can be defined in multiple ways and the bar can be set anywhere along a spectrum.
Many tests of scientific literacy essentially ask a series of scientific facts – they are tests of factual knowledge, but not scientific thinking. This glaring deficit has been pointed out many times before, and was so again in a recent editorial by Danielle Teller. She writes:
There are a number of problems with teaching science as a collection of facts. First, facts change. Before oxygen was discovered, the theoretical existence of phlogiston made sense. For a brief, heady moment in 1989, it looked like cold fusion (paywall) was going to change the world.
I agree. A true measure of scientific literacy should be a combination of facts, concepts, and process. Facts are still important. Concepts without facts are hollow, and facts without concepts are meaningless. Both need to be understood in the context of the process that led us to our current conclusions.
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Campbell Soup has just announced that they are switching sides in the GMO labeling debate – they are now in favor of federal mandatory labeling for all products that contain genetically modified organisms. This has perhaps opened up a new chapter in the debate.
In response Mark Lynas, a journalist who, after researching the topic, is staunchly pro-GMO, has responded with an interesting essay agreeing with this move by Campbell.
Let me state up front that I think the answer to mandatory labeling is no, but let me also walk you through my thinking on this complex issue.
The Scientific Case Continue Reading »
I think we just have to face it – humans are cheaters. It’s in our nature.
We are also complex social creatures. The result, according to psychological research, is that most people will engage in small cheats if given the chance and they think they will get away with it. Various studies show, for example, that 75-98% of high-school and college students cheat at least once during their careers.
This makes sense given that we evolved in a resource-limited situation. There was an ever present real risk of starving to death, and so the willingness and ability to sneak a little extra food from the group would have had a distinct survival advantage.
At the same time there was a survival advantage to defending oneself against cheating, and living in groups meant that the group could defend against cheating using social pressure. Humans are therefore conflicted – we want to cheat but we feel bad about it because we also have a feeling of disgust toward cheating in order to pressure others into not cheating. We feel guilty and fear the shame of getting caught. When you balance all these things out, most people will cheat a little when they can get away with it. Those who cheat more are better at rationalizing their own cheating. Increased cheating may also result from greater pressure to perform, overcoming the social pressures against cheating. Continue Reading »