Archive for the 'General Science' Category

Jun 13 2017

The CRISPR Controversy

Published by under General Science

CRISPR-mechanismI suspect that CRISPR is rapidly following the path of DNA in that many people know the abbreviation and what it refers to but not what the letters stand for. Clustered regularly interspaced short palindromic repeats (CRISPR) is a recently developed technology for making precise gene edits. Such technology carries a great deal of promise for treating or even curing disease, for accelerating research, and for genetic modification technology.

However a recent study has thrown some water on the enthusiasm for CRISPR and sparked a mini-controversy. The authors looked at two mice that were treated for blindness with CRISPR-cas9, sequencing their entire genome. They found over 1,500 unintended mutations. That would be bad news for the technology, which is revolutionary partly because it is supposed to be so precise.

For a little background, CRISPR was discovered in bacteria and archea. It is essentially part of their immune system – locating inserted bits of DNA from viruses and clipping them out. Researchers realized they could use this system to target specific sections of a genome to insert or remove a genetic information. The technique is fast, cheap, and convenient.

What this has meant is that genetic modification can now be cheaply available to even small labs. Further, since the technique can be used in living organisms, it could theoretically be used to cure genetic diseases.

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20 responses so far

Jun 02 2017

The Sixth Extinction

Published by under General Science

ExtinctThere have been five major extinctions since the evolution of multicellular life on earth. These are events marked by a geologically rapid loss of biodiversity, the most dramatic of which was the end Permian extinction 245 million years ago with 90% species lost. The other four events had between 19-30% species loss. It is interesting and scary to think how close we came to total extinction in the end-Permian event.

The causes of these extinctions vary. Events 1 and 4 were due to volcanic activity. Events 2 and 3 are uncertain but perhaps causes by climate change due to tectonic plate activity. The fifth extinction, the one that wiped out the non-avian dinosaurs 65 million years ago, was mostly due to an asteroid impact.

Many scientists believe we are in the midst of a sixth great extinction event, caused by human activity. It is always difficult to tell when you are in the middle of such an event – it is easier to discern from a perspective after the event is completed. But it’s pretty clear humans are having a dramatic effect on the ecosystems of the world and other species are paying the price.

There have actually been several books titled: The Sixth Extinction. The first, which I read many years ago, is by Niles Eldridge.  Most recently, in 2014, Elizabeth Kolbert published a book: The Sixth Extinction, An Unnatural History.

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38 responses so far

May 30 2017

Superantibiotic for Superbug

Published by under General Science

enterococcus_faecalis-splImagine a day where you get a bacterial infection, and the doctors tell you that there is no antibiotic which is effective against this bug. It is resistant to everything we have. They can give you supportive care, but the infection just has to run its course and may be fatal. For this reason hospitals have to take extreme measures to prevent the spread of infection – disinfecting and wearing disposable protective garments each time they enter a patient’s room. This is already the case for patients with certain kinds of exposures and infections.

This is a serious concern, not hype like most of the doomsday scenarios the press likes to scare you with. Bacteria are slowly (or sometimes not that slowly) evolving resistance to our antibiotics. Even worse, bacteria have loops of DNA called plasmids which they can share with each other. Those plasmids might contain the code for resistance to one or more antibiotics. The more we use antibiotics, the more selective pressure there is for resistance.

The two main things we need to do to avoid a “post-antibiotic era” includes first uses antibiotics as smartly as possible. Use them only when necessary, use narrow-spectrum antibiotics when possible, and complete all courses of antibiotics so all the bacteria are killed.

The second thing we need to do is develop more and better antibiotics. Attacking bacteria using new mechanisms is especially useful. Ideally these antibiotics would be resistant to resistance – they would attack a vulnerability in the bacteria that they cannot easily evolve a defense against.

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May 26 2017

Pyramid Homology vs Analogy

Pyramid nonsenseI saw this post on the Credible Hulk Facebook page today. It refers to an old claim by proponents of ancient astronaut theories that the fact that there are similar looking pyramids from different locations on Earth proves cultural contamination from an extraterrestrial source.

While this is a silly argument, it is interesting to explore exactly why it is silly. The underlying principles have to do with homology and analogy, and are exactly the same as they are applied in evolutionary theory. The displayed meme implies that because there are step pyramids in Mexico, Egypt, and Indonesia – countries too far removed to have had direct contact with each other – the idea of a step pyramid therefore had a common source.

This is similar to the evolutionary argument that because two structures look similar or serve a similar function, they must have had a common source, which means the feature was derived from a common ancestor. But we know that this is not always true. The wings of bats, birds, and pterydactyls have similar features, but not a common evolutionary origin. The eyes of vertebrates and cephalopods also have features in common, but evolved independently. But giraffes and humans both have seven cervical vertebrae.

So how do evolutionary biologists tell the difference? They try to determine if the features are homologous (derive from a common ancestor) or analogous (independent origins but similar structure). They can do this in a number of ways, either based on direct evidence or inference. Direct evidence would be finding a fossil of a common ancestor with the feature.

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15 responses so far

May 25 2017

Organic Farming is Bad for the Environment

Published by under General Science

land useMarketing sometimes involves the science of making you believe something that is not true, with the specific goal of selling you something (a product, service, or even ideology). The organic lobby, for example, has done a great job of creating a health halo and environmentally friendly halo for organic produce, while simultaneously demonizing their competition (recently focusing on GMOs).

These claims are all demonstrably wrong, however. Organic food is no more healthful or nutritious than conventional food. Further, GMO technology is safe and there are no health concerns with the GMO products currently on the market.

There is an even more stark difference, however, between beliefs about the effects of organic farming on the environment and reality.  In fact organic farming is worse for the environment than conventional farming in terms of the impact vs the amount of food produced.

First, organic farming may use pesticides. They just have to be “natural” pesticides, which means the ones they use are not chosen based upon their properties. Ideally choice of pesticide and the strategy in using them would be evidence-based and optimized for best effect, minimal impact on health and the environment, cost effectiveness, and convenience.   Organic farming, however, does not make evidence-based outcome choices. Their primary criterion is that the pesticides must be “natural”, even if they are worse in every material aspect. This represents ideology trumping evidence. It is based on the “appeal to nature” fallacy, an unwarranted assumption that something “natural” will be magically better than anything manufactured.

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75 responses so far

May 16 2017

The Impact That Killed the Dinosaurs

Published by under General Science

asteroid impactI have loved science as long as I can remember, partly because scientists have the best stories to tell. The stuff that actually happened is usually far more interesting than any fantasy, and has the added bonus of being real. Reality is complex, dramatic, and interesting. Reality is also endlessly surprising.

Lucas wanted to evolve Star Wars. I always thought that was an interesting idea, adding a new layer to the film medium. It would love to see a great director do that well, not only updating special effects, but evolving the story as the culture evolves. Unfortunately, most of the changes Lucas made were crap, watering down character arcs and adding blandness. Some of the extra CG was OK.

Science stories, however, seem to always just get more interesting. That is because the universe has already written the entire script from the beginning, and we are just peeling back the narrative layers one by one. As the story gets deeper, it all makes sense because it has to. Plot twists are never contrived, because they were baked in from the beginning.  Continue Reading »

21 responses so far

Apr 28 2017

Shaky Evidence for Humans In Americas 130,000 Years Ago

Published by under General Science

mastodon bonesScientists like to be really sure. That is pretty much what the scientific method is all about – systematically controlling for all possibilities, all confounding factors, all variables and all alternative interpretations. We feel more confident when multiple lines of evidence converge on one explanation, and when rigorous attempts to disprove that explanation fail.

I like seeing that process in action over specific claims, especially when the claim itself is interesting.

One such interesting question is, what was the earliest human presence in the Americas? Any question about first or earliest is always tentative in paleontology. It simply refers to our current evidence, but it is statistically unlikely that we will have found the literal earliest example of a species or an occupation. So conclusions about “earliest” are always changing, moving back as more evidence is found.

There is solid archaeological evidence for human occupation near the  Bering Strait 14,000 years ago. There is strong but not universally accepted evidence for this occupation going back 24,000 years. So that is the current range of possible dates for the earliest presence of humans in North America.

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25 responses so far

Apr 20 2017

Retreat of the Cryosphere

glacier-retreatPatrick Burkhart and his colleagues recently published a review of their research on the cryosphere, which is a collective term for all the ice on the surface of the Earth. In addition to their review of the science, the new information they add is a photographic project documenting the retreat of glaciers around the globe.

The retreat of the cryosphere is one of the many lines of evidence supporting the idea that the earth has been warming over the last half-century. There are several different ways to look at this. You can look at each pole to see the extent of ice coverage at their peak in winter and minimum in summer. You can look at specific ice sheets, like Greenland. You can look at glaciers. And you can look at total global ice, the cryosphere, which of course is the best single measure.

With regard to glaciers, the authors point out that there are many variables affecting the current size of any individual glacier. It is possible but difficult to account for all these variables and isolate one as a primary cause of melting. However, you can survey glaciers from around the world, which is a good way to control for local variables. When we do this we find there is a significant trend toward glacial retreat.

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179 responses so far

Mar 20 2017

The Need for Publicly Funded Science

Trump-ScienceThe American scientific community is in a bit of a panic over Trump’s first proposed budget. The budget calls for an 18% decrease ($5.8 billion) for the National Institutes of Health (NIH). There are deep cuts in energy research and Earth science as well.

The reaction of the scientific community has been consistent – such cuts would be disastrous.

It probably comes as no surprise that science is expensive. This is despite the fact that scientists are generally paid very little, especially when compared to their years of training. Science is a career of passion. But maintaining a lab or conductive field research can be very expensive. Research often requires expensive equipment and materials, lab space, support staff, and lots of time.

Research is not just something that scientists do – it requires extensive infrastructure. That infrastructure needs to be maintained mostly with one-off grants. The vast majority of scientific research will not directly generate profits for the researchers, the lab, or the supporting institution. Keeping a lab going is like keeping plates spinning, the researchers are constantly applying for grants and weaving together the funding they need.

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46 responses so far

Mar 16 2017

Does Glyphosate Cause Cancer?

Published by under General Science

glyphosate-effects-fbGlyphosate, the active ingredient in Roundup, is the most popular herbicide used in the world. It has gained particular attention because several of the more commonly used GMOs are glyphosate tolerant, and therefore are intended to be used with the herbicide. Glyphosate is also manufactured by Monsanto (although it is off patent and there are generic versions available).

The question of the safety of glyphosate is in the news again after the New York Times did an article about a recent court case against Monsanto and the documents revealed through discovery and made public by the judge. Unfortunately, in my opinion the NYTs article is poorly done, and reveals significant bias – anti biotech bias is nothing new for the NYTs or the author of this article, Danny Hakim.

Last year I wrote about another article that Hakim wrote in the NYTs about GMOs, concluding:

In my opinion Hakim’s article in the Times was a hack piece with a biased narrative that is nothing more than a rehash of tired anti-GMO tropes that have already been widely deconstructed. He is entering this conversation late, and isn’t up to speed.

There are essentially two questions raised by Hakim’s latest article. The first concerns the behavior of Monsanto. Hakim alleges that they ghostwrote scientific articles for academics and used political pressure to shut down EPA reviews of glyphosate’s safety. I would not assume this assessment is true, and certainly don’t trust Hakim’s journalism given his history. The academics in question deny the allegations, and Monsanto claims these e-mails are taken out of context. We have certainly seen that before.

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31 responses so far

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