Archive for the 'General Science' Category

Feb 08 2018

Did a Comet Kill the Mammoths

Published by under General Science

Between 12,800 to 11,500 bp (before present) there was a cold period in North America called the Younger Dryas – named after the dryas flower whose pollen is a good marker for such cold periods. During this time the megafauna of North America, including the Mammoth, largely died out. Along with them went the Clovis culture – a big game hunting culture with distinctive stone points.

What caused this period of climate change and mass extinction?

This is a genuine scientific controversy. One group of scientists believe that the melting glaciers dumped fresh water into the northern Atlantic, temporarily shutting down the ocean currents that bring warm water to North America. Another group think that a comet impact is to blame.

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Jan 30 2018


Published by under General Science

The Human Genome Project was started in 1990 and completed in 2003. It took 13 years, multiple labs around the world, and hundreds of millions of dollars to sequence the human genome – this was more than two years ahead of schedule and millions of dollars under budget.

The reason for exceeding expectations is that the technology for sequence the genome was not static – it progressed throughout the project. DNA contains a code of four letters, the nucleotides indicated by the letters G, T, A, and C. This four-letter alphabet creates 64 different three-letter words, which code for different amino acids or operations that control the conversion of the code into proteins. Sequencing the genome essentially consists of discovering the order of these four letters in the string of a DNA molecule.

In 1997 the movie Gattaca, right in the middle of the genome project, portrayed the near future in which a cheek swab would rapidly yield an individual’s genome. It turns out this is not far fetched at all – we are almost living in Gattaca’s near future, at least in terms of sequencing technology. Scientists have just published a report of the nanopore device, which is a hand-held device capable of sequencing an individual’s genome.

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Jan 29 2018

Shameless Organic Fearmongering

Published by under General Science

I and others have long pointed out that anti-GMO fearmongering was largely created by the organic food lobby as a way of smearing their competitors. The strategy is simple – scare people way from genetically modified organisms (GMOs) and offer organic products as a non-GMO alternative. This is nothing new in advertising, create a fear and then offer your product as a safe haven.

A recent video posted by Stonyfield Organic makes the connection between anti-GMO fearmongering and buying organic explicit, as the screen capture shows.

There are many problems with this short video, not the least of which is that they use young girls to parrot their anti-science. Clearly not aiming for subtlety, the first girl declares that GMOs are “monstrous.” To apparently explain what she means, the second girl says that, “They take a gene from a fish and put it into a tomato.”

No, “they” don’t.

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Jan 18 2018

The Dangers of Celebrity Culture

Zooey Deschanel has a Facebook page where she gives advice on complex scientific topics. I love Deschanel as an actress and enjoy much of her work (particularly the otherwise mediocre movie version of the Hitchhiker’s Guide), but that does not mean I want to take advice from her on which foods I should eat.

Celebrity culture, in one form or another, has always been part of human society. Even chimpanzees will follow a charismatic leader, and it seems likely that humans are wired also to follow those we admire, and elevate them perhaps a bit too much. There is even research that shows that when we listen to a charismatic speaker the executive function part of our frontal lobes shuts down. We literally turn off our critical thinking when basking in the glow of our glorious leader.

Recognizing that this is part of the human condition is important. First, we need to be vigilant about surrendering our thinking to others. It’s also important to remind ourselves that everyone is a flawed human, and so constantly give those pedestals a reality check.

But that does not meant we should not admire and respect those who deserve it, or even look up to them for wisdom (as long as we maintain our critical eye). It does mean we need to choose carefully those we respect and follow.

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Dec 22 2017

Science in 2017

Published by under General Science

Science continues to kick ass in 2017, despite the fact that it often feels as if our species can’t get out of our own way. Obviously we need to keep our eye on important social and political issues, but it is reassuring to realize that there are many scientists quietly working away in their labs, clinics, observatories, or wherever to nudge our collective knowledge forward.

Here are some of the science news stories from 2017 that I think deserve notice and give us a good indication of what is to come.

The Age of Genetic Engineering

Genetic engineering is nothing new, but we seem to be on the upswing of an exponential curve with this technology. In recent years CRISPR has provided cheap and fast genetic manipulation, resulting in an explosion of research and potential applications. The technology borrows a system from bacteria used in their immune defense against viruses. It allows for the specific targeting of sequences of DNA which can then be clipped out and even replaced.

CRISPR technology continues to advance on two main fronts – improving the technology itself, and finding applications for it. This year researchers discovered how to adjust the specificity of CRISPR targeting – making it slower but more precise as desired. As powerful as this tech is, we are still on the steep part of the curve and it continues to improve. Continue Reading »

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Dec 14 2017

Antarctic Ice

Published by under General Science

Perhaps one of the most underrated science stories of 2017 was the separation of a massive iceberg the size of Delaware from the Larsen C Ice Shelf in Antarctica. That is because this is not an isolated event, but just a dramatic part of a larger story – the melting of Antarctica.

Antarctica contains most of the ice on Earth (90%). Much of that ice sits on top of land, unlike Arctic ice which is floating. When floating ice melts it just fills the space that it had displaced. There is a little bit a sea rise due to rising temperatures – water expands as it warms. But this amount of sea rise is small overall. When ice that was sitting on land flows into the ocean, it raises the sea level more significantly.

Antarctica is comprised of glaciers sitting on top of the continent, which itself is mostly below sea level. These glaciers are as thick as three miles. They are divided into a western glacier system and an eastern glacier system. West Antarctica, which is melting faster, contains enough ice to raise the sea level by 14 feet. East Antarctica is more stable but still showing some early signs of melting. All the ice here could raise the sea level by 175 feet.

As the glaciers melt during the warmer months they follow channels out to the ocean. These channels, however, are blocked by ice shelves, which act like a cork, keeping back the ice and helping to maintain the stability of the glaciers.

The ice shelves themselves have a certain structure – they rest on the sea floor but as they extend out from the continent eventually the ice lifts off the sea floor (called the grounding point) and as the ice extends out further it is floating on top of the water. The breakup of these ice shelves is a concern, because that would essentially remove the stopper and greatly accelerate the rate at which glacier melt finds its way to the ocean.

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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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