Archive for the 'General Science' Category

Dec 05 2017

Plastic Waste

Published by under General Science

I know, there are already so many things to worry about. It’s almost painful to hear about one more way in which we may be harming the world. Such reports are also often couched in emotional and dramatic terms.

However, it’s important to sift through the rhetoric and evaluate what the science says about what is actually going on. There is increasing reporting about the coming plastic apocalypse. We are dumping massive amounts of plastic into the environment, and some of that plastic is winding up in the world’s oceans. The world produced 343 million tons of plastic in 2014. Only 10% of that plastic was recycled. In total we have produced 8.3 billion metric tons of plastic, which does not biodegrade for hundreds of years.

The fact is, human civilization is big enough that we have to think about the effects of our massive industry. Producing that much plastic will likely have an impact on the environment. The biggest impact may be the percentage that winds up in the oceans – about 10%. Once there is just breaks down into smaller and smaller bits. Many animals accidentally eat the plastic, which can be fatal.

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Nov 30 2017

Semi-Synthetic Life With Expanded Genetic Code

Published by under General Science

It’s interesting to follow truly cutting edge research that has the potential to significantly change our world. I include in this category research into brain-machine interfaces, regeneration through stem cells, genetic engineering, and fusion energy. I would also add research into creating synthetic life.

Synthetic life research views living organisms like a technology. It is, in a way, the original nanotechnology, using complex tiny machines to manufacture chemicals, collect and store energy, degrade toxins, and other functions. Scientists have been very successful in tweaking existing organisms to harness them as tiny factories. Many modern drugs are now made in this way, making drugs like insulin widely available.

Some researchers, however, want to go beyond tweaking existing organisms. What if we could create synthetic organisms, even just single cells, entirely from scratch? That is Craig Venter’s dream – to strip down cells to their bare essentials, and then use that as a template to create a completely artificial minimal generic cell. That basic artificial cell, which we understand well because we built it from the ground up, can then be modified to perform endless functions – designer cells.

There is more to this vision, however. Once we free ourselves from the constraints of existing organisms we can explore novel properties that did not happen to evolve. Evolution is powerful, and it has had several billion years to experiment with life, but evolution is also constrained by its own history. For example, all life on earth uses the same genetic code, based upon two pairs of bases in the DNA – cytosine bonds with guanine and thymine bonds with adenine. This produces a 4-letter alphabet for the genetic code (CTAG), and also gives DNA the double-stranded structure and its ability to make copies of itself. The code consists of 64 3-letter words.

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Nov 13 2017

Raccoons Are Smart But Not Good Pets

Published by under General Science

raccoon-AesopsAnimal intelligence is fascinating for a number of reasons, not the least of which is that it forces researchers to think carefully about what intelligence is. The comparison might also provide a window into what constitutes human intelligence in particular.

There is no question that humans have intellectual capabilities that no other species has. However, some animals are smarter in certain ways than you may imagine. Certain birds, like corvids (jays and crows) have demonstrated significant problem-solving capability, for example. Researchers are also finding that raccoons may be even smarter than we suspected.

One paradigm of animal intelligence research is known as the Aesop’s Fable test, based on the the story of the thirsty crow. In this tale a thirsty crow came upon a tall pitcher with water at the bottom, but it could not reach down the long neck to the water. So it dropped stones in the pitcher to raise the water level until it could reach. This behavior demonstrates creative problem-solving and some basic understanding of cause and effect. Corvids have the ability to pass this test – they can figure out how to use objects to raise the water level to gain access to water or food.

A recent study performed the same test on raccoons. They were given access to a long tube with marshmallows floating lower down, too low for them to reach. First they were shown how dropping stones would raise the water level. Two of eight raccoons tests were then able to use this effect to gain access to the marshmallows. Statistically this is not as good a performance as corvids, but at least some raccoons are smart enough to pass the test. Continue Reading »

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Nov 10 2017

Glyphosate Not Associated with Cancer

Published by under General Science

IARC-Headquarters_ExteriorIn March of 2015 the International Agency for Research on Cancer (IARC), part of the World Health Organization (WHO), published their assessment on glyphosate, Monsanto’s popular weedkiller, classifying it as 2a – a probable carcinogen. This was like red meat to the anti-GMO crowd, and even sparked class action suits against Monsanto and may lead to banning use of the chemical in the EU.

There were significant problems with the IARC report, however. First – it is at odds with every other expert review of the scientific literature on glyphosate. I review the evidence here, citing many expert panel reviews, all conclude that the evidence does not support a link between glyphosate and risk of cancer. The IARC conclusion is a clear outlier, which reasonably prompts questions as to why their designation stands out.

We also need to put the IARC classification of 2a – probable carcinogen, into context. This is the same classification that the IARC gave to drinking hot beverages or eating red meat. Overall they tend to err on the side of caution when making their classification.

But there were problems that go beyond where the IARC sets their threshold for “probable.” Two main criticisms have emerged. The first is the lack of transparency. Reuters has published a series of articles on the issue, outlining, for example, that when the EPA reviewed the safety of glyphosate they also published a 1300 + page document that outlines the entire deliberative process. The IARC produced no such document.

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32 responses so far

Nov 06 2017

US Government Report Affirms Climate Change

climate changeThe U.S. Global Change Research Program Climate Science Special Report was recently published, and its conclusions are crystal clear:

 This assessment concludes, based on extensive evidence, that it is extremely likely that human activities, especially emissions of greenhouse gases, are the dominant cause of the observed warming since the mid-20th century. For the warming over the last century, there is no convincing alternative explanation supported by the extent of the observational evidence.

That conclusion is nothing new to those following the science of climate change for the last couple decades or so. The more this question is studied, the more data is gathered, the firmer the conclusion becomes – the planet is warming due to human release of greenhouse gases, such as CO2. There are error bars on how much warming, and the exact effects are hard to predict, but that’s it. The probable range of warming and effects are not good, however. It will be bad, the only real debate is about how bad and how fast.

The conclusions of the report, therefore, at least scientifically, are not surprising. It was, however, politically surprising. The special report began in 2015, under Obama. Because of Trump’s stated position that global warming is a Chinese hoax, and his appointment of many global warming deniers to key positions, it was feared that his administration would slow or frustrate the publication of this report.

However, according to the NYT, Trump himself was simply unaware of the report. Further, the fate of the report was largely in the hands of those amenable to following the science, rather than putting a huge political thumb on the scale. As a result the report was not hampered or altered. It was approved by 13 agencies who reviewed its findings.

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Nov 02 2017

The Long Winter That Killed the Dinosaurs

Published by under General Science

ChixulubThere is still a bit of a debate about what, exactly, was responsible for the extinction of the non-avian dinosaurs and 75% of all species on Earth about 65 million years ago (the K-Pg extinction event). There is no question that a large meteor impacted near Chicxulub crater in the Gulf of Mexico at precisely that time, and was certainly responsible for at least some of the extinction. However, volcanism near the Deccan traps in India was also stressing the environment and may have contributed to some degree to the extinction. The debate is really about the relative contribution of these two factors, plus a potential third factor, marine regression.

As a non-expert enthusiast my reading of the consensus of scientific opinion is that the meteor impact was the main cause, perhaps made a bit worse by the pre-existing stressors which were already causing a minor extinction of their own. But the K-Pg event would not have been a mass extinction without the meteor strike.

Adding to this view is a recent analysis that indicates the impact would have caused a devastating continuous subfreezing “winter” from 3-16 years long, enough to make the Starks shiver (sorry for the gratuitous GOT reference). Scientists have been drilling in the Chicxulub crater to learn more about the specific effects of the impact.

I wrote in May of this year that scientists have discovered that the impact threw up large amount of gypsum (calcium sulfate dihydrate). The sulphur this would have thrown up into the atmosphere would have effectively blocked out the sun, reducing photosynthesis and breaking the food chain. The researchers even speculated that the impact was in the worst possible location, because the shallow seas have a lot of gypsum, which would not have been present on land or in deep ocean.

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Oct 03 2017

Nobel in Medicine for Circadian Rhythm

Published by under General Science

Nobel 2017-MedicineRemember that time Sarah Palin said:

“[tax] dollars go to projects that have little or nothing to do with the public good — things like fruit fly research in Paris, France. I kid you not.”

OK, she was actually referring to the olive fruit fly, Bactrocera oleae, not the staple of genetics research, Drosophila melanogaster. The comment is still a legitimate target for criticism because it is not clear that Palin understands the difference (or she wouldn’t have said it that way), her statement seems to imply that scientific research into the humble “fruit fly” is a waste, and she is generally anti-science (when it conflicts with her ideology).

At the time of her statement many scientists and reporters delighted in pointing out how central fruit fly research has been to scientific advancements. Well, we can add another example from this year’s Nobel Prize in Physiology or Medicine. The prize goes to three American scientists, Jeffrey C. Hall, Michael Rosbash and Michael W. Young, for their work on the circadian rhythm.  Continue Reading »

5 responses so far

Sep 29 2017

GM Wheat for the Gluten Sensitive

Published by under General Science

gluten (1)Celiac disease is a serious disorder that affects about 1% of the population worldwide. The disease results from an immune reaction to gliadin, which is part of the gluten protein found in wheat, rye, and barely. Glutens are stretchy proteins that give breads their sponginess and allow breads to rise.

Those with celiac disease make antibodies to gliadin, which causes inflammation of the lining of the small intestine and a number of painful and harmful symptoms. It can now be accurately diagnosed with blood tests for the anti-gliadin antibodies, but the only treatment is a life-long diet free of any gluten.

Gluten has also caught the attention of the clean-eating food fad crowd, who have convinced many people they have non-celiac gluten sensitivity. As I discussed previously, this entity is controversial at best and probably doesn’t exist. However, it is always important to point out that many people who end up falling into an ultimately false diagnosis may have a different real disease. Some people who now get labeled as gluten sensitive may actually have wheat allergies. There are other possible culprits as well, such as FODMAPs (fermentable, oligo-, di-, monosaccharides, and polyols).

Regardless, life for those with celiac disease can be challenging. The diet is rigorous, and even the smallest amount of gluten can trigger a reaction in those truly sensitive.  Continue Reading »

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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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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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