Category Archives: Uncategorized

Can you patent DNA?

No. Not if it is natural.

In a decision that could have broad-reaching effects on the future of science and medicine, the Supreme Court on Thursday ruled that:

— “A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated.”

— But, synthetically created “strands of nucleotides known as composite DNA (cDNA)” are “patent eligible” because they do not occur naturally.

SOURCE

Our system of patents is badly broken, I think. About the only people I’ve ever heard say otherwise are … wait for it … patent lawyers.

At least this one little part of it is fixed now.


Photo Credit: Josh*m via Compfight cc

Growing Up as a Zealous Jehovah’s Witness

My friend James wrote this book:

Deliverance at Hand!: The Redemption of a Devout Jehovah’s Witness is James Zimmerman’s fascinating story of growing up as a zealous Jehovah’s Witness. It is a gripping account of the unique difficulties and all-consuming nature of belonging to an insulated, apocalyptic community. James is held up as a shining example for other youths in the religion, is given unprecedented privileges, and spends his youth proselytizing. He may very well have knocked on your door.

But as he matures, fissures begin to form in the bedrock of his fundamentalist Jehovah’s Witness belief system. Is the bible the literal, infallible word of God? Can the story of Noah’s ark really be true? Are these the final days before Armageddon? Will the Witnesses soon inherit paradise while the nonbelievers are destroyed? Is the day of deliverance truly at hand?

As James’ doubts grow, so does his predicament: Leaving a religious community that teaches its members to shun former members would have deep and painful ramifications. He must make the decision between intellectual honesty and his way of life.

At this point I think you can only PRE ORDER it but go ahead and do that!

Bob Alberti. Would you look at that face!?!?

Bob Alberti is a friend of mine in Minneapolis (actually, he was even my student for a few weeks). I was rather startled to see is very scary face staring at me from the Internet this morning (see above). All I can say, is if you run into this guy, watch out! His snark is very, very sharp.

From the Star Tribune article featuring Bob:

A recent study declared Minneapolis parks the best in the nation. We also have another fine natural resource: technology pioneers/comedians who go on the Internet and smack down snooty New Yorkers. Which brings us to Bob Alberti.

“When I was a kid, I went from living in Queens, where my mother was cruel and wouldn’t let me swim in the overflowed sewers in the streets, to living on a lake in Minnesota, and I knew what I liked better.”

“I am a professional insult comedian.”

Bob invented two things before he started his career as a Vilification Tennis master: He invented gaming and he invented the internet!

Check out the story.

Speaking of Cold Fusion …

I’ve noticed a lot of Internet chatter about the Mantis Shrimp lately, and I don’t know what that is about. But it could be this:

How would you design an experiment to test each of the hypotheses suggested here?

(Also, I note that I do not endorse the contents of this video. Spiffy music and a smart sounding voice tells our brains this must all be true and accurate but most YouTube videos like this in areas I now about are full of mistakes. If you are an expert on this stuff feel free to make comments or corrections below. Also, my reference to “cold fusion” is snark, in case that was not obvious.)

Are you fat? You can’t earn a PhD, according to one Evolutionary Psychologist

Geoffrey Miller, author of The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature, has made a goof.

Miller is an evolutionary psychologist with an interested in IQ, the usual sex related things Evolutionary Psychologists are interested in, etc. etc.

On June 2nd he wrote this tweet:

Dear obese PhD applicants: if you didn’t have the willpower to stop eating carbsk, you won’t have the willpower to do a dissertation #truth

The number of way in which this is wrong is myriad.

Anyway, he’s in a heap of trouble. Here is a video from his university, the University of New Mexico, showing his department chair trying to do some damage control.

Good luck with that.

I’m guessing this … that if you are fat you are not PhD material … is not really a scientific assertion on the part of Professor Miller. Rather, it looks more like a bone-headed remark he made because of something personal that happened to him. Professor Miller may have demonstrated something useful, though. If you are X stay away from Twitter because you are a jerk. I’m not sure what X is. Maybe it is just being a jerk. If you are a jerk stay away from Twitter because you are a jerk. Hard to say.

Anyway, Professor Geoffrey Miller is digging in and/or backpedaling. As you can see in the video, and indicated on this UNM web page, Miller now claims that he is carrying out a research project in which he produces inflammatory tweets.

Do you think he’s telling the truth? What would you do if you were his department chair?

The Power of The Sea

On June 6th, 1944, some 160,000 soldiers aboard about 5,000 boats of diverse design crossed the English Channel and carried out the Invasion of Normandy, one of the more important events in recent history. Many of the soldiers were so sick from choppy seas that leaving the boats and walking or running into German gunfire seemed like a good idea. The invasion was originally planned for the 45h of June, but a very precise weather forecast told the Supreme Commander, General Eisenhower, to wait until the next day. The forecast for the 6th of June, integrated with the logistical features of the operation, had the landing craft arriving on the German-held beaches just as wave heights were reducing from a level unacceptable for this operation to something that could be managed by most (but not all) vessels.

[a timely repost]

If you’ve seen “The Longest Day” or any of the other classic semi-documentary dramatizations of D-Day, you may recognize the name Captain James Stagg. Stagg was the meteorologist on Eisenhower’s staff, and as such he was the conduit and translator for the information that came from the meteorology group. That, in turn, was a combination of American and British scientists with very different methods and backgrounds, but both using data and analyses that involves a large number of individuals making observations and crunching numbers, from teams at Scripts Institute in California who developed the primary predictive models in use to British Coast Guard observers making observations at sea several times a day.

The Power of the Sea: Tsunamis, Storm Surges, Rogue Waves, and Our Quest to Predict Disasters by Bruce Parker elucidates the science behind this historic moment in great detail in one of several riveting chapters about the ocean, and stuff the ocean does. Parker is a former chief scientist of the National Ocean Service so he knows something about waves, storms, tides, tsunamis, storm surges, and the like. This book is a nice combination of primer on meteorology ala the ocean and weather-related adventure stories. Throughout the book I kept running into things that I had always wanted to know about … like how exactly did that one huge ship I’ve seen so many times off the Cape Peninsula in South Africa sink? (The ocean did it!), what really was the story behind Stagg’s predictions (as discussed) and what is a future with greater storm surges and rising sea going to look like?

I recommend this book for non-experts who need to know all about ocean related science, who need to better understand the effects and dynamics of storms like Sandy, Tsunamis, and similar events. Parker does not hold back on the science and the detail. This is a very enjoyable way to elevate one’s self to the level of armchair oceanic meteorologist in a few evenings of enjoyable reading!

Dr. Donald R. Prothero has been awarded the 2013 James Shea Award by the National Association of Geoscience Teachers

Hey, check this out:

Dr. Donald R. Prothero recently retired from his professorship at Occidental College in Los Angeles, CA after 27 years of teaching in order to concentrate on his writing and consulting. Dr. Prothero is an indefatigable advocate for geology and paleontology, which he combines with a passion for communicating science to the public. Notably, he has served as a consultant for Discovery Channel, History Channel and National Geographic specials. He frequently gives public talks and presentations to groups interested in Earth science, including presentations to the NYC Skeptics, The Bone Room in Berkeley, CA, Bay Area Skeptics, and the Natural History Museum of L.A. County. Dr. Prothero is a prolific writer; he posts a weekly blog at “Skepticblog” and has published over 30 books. His talks and blogs focus on debunking pseudoscience and defending the science of evolution and climate change. He has made numerous contributions to advancing his fields of expertise by publishing in technical journals. He has authored and co-authored 259 papers, including papers in the following peer-reviewed journals: Nature, Paleobiology, Geology, Palaeogeography, Palaeoclimatology, Palaeoecology, Journal of Paleontology, Journal of Geology, Science, Journal of Geological Education, Palaios, Paleoceanography, and Geotimes to name a few. Prothero has served as a reviewer and editor throughout his career. He served as adjunct editor for Paleobiology and he has also served on the editorial boards of Skeptic magazine and for Geology. In addition, he has served as technical editor for Journal of Paleontology and as a consulting editor for the McGraw-Hill Yearbook of Science and Technology. In recognition of Dr. Prothero’s exceptional contributions in the form of writing and editing of Earth science materials, NAGT is proud to award him with the 2013 James Shea Award.

See also: Greenhouse of the Dinosaurs and Donald Prothero Radio Interview.

And, some of Donald Prothero’s other books:

Evolution: What the Fossils Say and Why It Matters

Rhinoceros Giants: The Paleobiology of Indricotheres (Life of the Past)

Abominable Science!: Origins of the Yeti, Nessie, and Other Famous Cryptids

Reality Check: How Science Deniers Threaten Our Future

After the Dinosaurs: The Age of Mammals (Life of the Past)

Catastrophes!: Earthquakes, Tsunamis, Tornadoes, and Other Earth-Shattering Disasters

Bringing Fossils To Life: An Introduction To Paleobiology

Sedimentary Geology

The Evolution of Artiodactyls

The Terrestrial Eocene-Oligocene Transition in North America

The 1970s Ice Age Myth and Time Magazine Covers – by David Kirtley

This is a guest post by David Kirtley. David originally posted this as a Google Doc, and I’m reproducing his work here with his permission. Just the other day I was speaking to a climate change skeptic who made mention of an old Time or Newsweek (he was not sure) article that talked about fears of a coming ice age. There were in fact a number of articles back in the 1970s that discussed the whole Ice Age problem, and I’m not sure what my friend was referring to. But here, David Kirtley places a recent meme that seems to be an attempt to diffuse concern about global warming because we used to be worried about global cooling. The meme, however, is not what it seems to be. And, David places the argument that Ice Age Fears were important and somehow obviate the science in context.

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h3>The 1970s Ice Age Myth and Time Magazine Covers
– by David Kirtley

A few days ago a facebook friend of mine posted the following image:

From the 1977 cover we can see that apparently a new ice age was supposed to arrive. Only 30 years later, according to the 2006 cover, global warming is supposed to be the problem. But the cover on the left isn’t from 1977. It actually is this Time cover from April 9, 2007:

As you can see, the cover title has nothing to do with an imminent ice age, it’s about global warming, as we might expect from a 2007 Time magazine.

The faked image illustrates one of the fake-skeptics’ favorite myths: The 1970s Ice Age Scare. It goes something like this:

  • In the 1970s the scientists were all predicting global cooling and a future ice age.
  • The media served as the scientists’ lapdog parroting the alarming news.
  • The ice age never came—the scientists were dead wrong.
  • Now those same scientists are predicting global warming (or is it “climate change” now?)

The entire purpose of this myth is to suggest that scientists can’t be trusted, that they will say/claim/predict whatever to get their names in the newspapers, and that the media falls for it all the time. They were wrong about ice ages in the 1970s, they are wrong now about global warming.

But why fake the 1977 cover? Since, according to the fake-skeptics, there was so much news coverage of the imminent ice age why not just use a real 1970s cover?

I searched around on Time’s website and looked through all of the covers from the 1970s. I was shocked (shocked!) to find not a single cover with the promise of an in-depth, special report on the Coming Ice Age. What about this cover from December 1973 with Archie Bunker shivering in his chair entitled “The Big Freeze”? Nope, that’s about the Energy Crisis. Maybe this cover from January 1977, again entitled “The Big Freeze”? Nope, that’s about the weather. How about this one from December 1979, “The Cooling of America”? Again with the Energy Crisis.


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Now, there really were news articles in the 1970s about scientists predicting a coming ice age. Time had a piece called “Another Ice Age?” in 1974. Time’s competition, Newsweek, joined in with “The Cooling World” in 1975. People have collected lists and lists of “Coming Ice Age” stories from newspapers, magazines, books, tv shows, etc. throughout the 1970s.

But if it was such a big news story why did it never make the cover of America’s flagship news magazine like the faked image implies? Perhaps there is more to the story.

In the 1970s there were a few developments in climate science:

  • Scientists were finding answers to the puzzle of what caused ice ages in the past: variations in earth’s orbit.
  • Scientists were gathering data from around the world to come up with global average temperatures, and they found that temperatures had been cooling since about the 1940s.
  • Scientists were realizing that some of this cooling was due to increasing air pollution (soot and aerosols, tiny particles suspended in the air) which was decreasing the amount of solar energy entering the atmosphere.
  • Scientists were also quantifying the “greenhouse effect” of another part of our increasing pollution: carbon dioxide (CO2), which should cause the climate to warm.

The realization that very long cycles in earth’s orbit could cause the waxing and waning of ice ages, coupled with the fact that our soot and aerosols were already causing cooling, led some scientists to conclude that we may be headed for another ice age. Exactly when was still a little unclear. However, the warming effects of CO2 had been known for over a century, and new research in the 1970s was showing that CO2 warming would more than compensate for the cooling caused by aerosols, resulting in net warming.


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This, in a very brief nutshell, was the state of climate science in the 1970s. And so the media of the time published many stories about a coming ice age, which made for timely reading during some very cold winters. But many news stories also mentioned that other important detail about CO2: that our climate might soon change due to global warming. In 1976 Time published “The World’s Climate: Unpredictable” which is a very good summary of the then current scientific thinking: some scientists emphasized aerosols and cooling, some scientists emphasized CO2 and warming. There was no consensus either way. Many other 1970s articles which mention a Coming Ice Age also mention the possibility of increased warming due to CO2. For instance, here, here and here.

Fake-skeptics read these stories and only focus on the Coming Ice Age angle, and they enlarge the importance of those scientists who focused on that angle. They totally ignore the rest of the picture of 1970s climate science: that increasing CO2 would cause global warming.

The purpose of the image of the two Time magazine covers, and of the Coming Ice Age Myth, is not to show the real history of climate science, but to obscure that history and to cause confusion. It seems to be working. Because today, when there really is a consensus about climate science and 97% of climatologists agree that adding CO2 to the atmosphere is leading to climate change, only 45% of the public know about that consensus. The other 55% must think we’re still in the 1970s when scientists were still debating the issue. Seems newsworthy to me, maybe Time will run another cover story on it.

To learn more see:

Linking Weather Extremes to Global Warming

Global Warming is the increase in the Earth’s temperature owing to the greenhouse effects of the release of CO2 and other gasses into the atmosphere, mainly by humans burning fossil fuel, but also by the release of Methane from oil wells and melting of Arctic permafrost, natural gas from leaky pipes, and so on. This increase in temperature occurs in both the atmosphere and the oceans, as well as the land surface itself. During some periods of time most of the increase seems to happen in the atmosphere, while during other times it seems to occur more in the oceans. (As an aside: when you use passive geothermal technology to heat and cool your home, the heat in the ground around your house is actually from the sun warming the Earth’s surface.)

ResearchBlogging.org“Weather” as we generally think of it consists partly of storms, perturbations in the atmosphere, and we would expect more of at least some kinds of storms, or more severe ones, if the atmosphere has more energy, which it does because of global warming. But “weather” is also temperature, and we recognize that severe heat waves and cold waves, long periods of heavy flooding rains, and droughts are very important, and it is hard to miss the fact that these phenomena have been occurring with increasing frequency in recent years.

We know that global warming changes the way air currents in the atmosphere work, and we know that atmospheric air currents can determine both the distribution and severity of storms and the occurrence of long periods of extreme heat or cold and wet or dry. One of the ways this seems to happen is what is known as “high amplitude waves” in the jet stream. One of the Northern Hemisphere Jet Streams, which emerges as the boundary between temperate air masses and polar air masses, is a fast moving high altitude stream of air. There is a large difference in temperature of the Troposphere north and south of any Jet Stream, and it can be thought of as the boundary between cooler and warmer conditions. Often, the northern Jet Stream encircles the planet as a more or less circular stream of fast moving air, moving in a straight line around the globe. However, under certain conditions the Jet Stream can be wavy, curving north then south then north and so on around the planet. These waves can themselves be either stationary (not moving around the planet) or they can move from west to east. A “high amplitude” Jet Stream is a wavy jet stream, and the waves can be very dramatic. When the jet stream is wavy and the waves themselves are relatively stationary, the curves are said to be “blocking” … meaning that they are keeping masses of either cold (to the north) or warm (to the south) air in place. Also, the turning points of the waves set up large rotating systems of circulation that can control the formation of storms.

So, a major heat wave in a given region can be caused by the northern Jet Stream being both wavy (high amplitude) with a big wave curving north across the region, bringing very warm air with it, at the same time the Jet Stream’s waves are relatively stationary, causing that lobe of southerly warm air to stay in place for many days. Conversely, a lobe of cool air from the north can be spread across a region and kept in place for a while.

Here is a cross section of the Jet Streams in the Norther Hemisphere showing their relationship with major circulating air masses:

Jet Stream Cross Section
Cross section of the atmosphere of the Northern Hemisphere. The Jet Streams form at the highly energetic boundary between major circulating cells, near the top of the Troposphere.

Here is a cartoon of the Earth showing jet streams moving around the planet:

The Jet Streams moving around the planet.  Not indicated is the Intertropical Convergence Zone (ITCA) around the equator which is both not a Jet Stream and the Mother of All Jet Streams.  This post mainly concerns the "Polar Jet."  Note that the wind in the Jet Streams moves from west to east, and the Jet Streams can be either pretty straight or pretty curvy.  Curvy = "high amplitude." This figure and the one above are from NOAA.
The Jet Streams moving around the planet. Not indicated is the Intertropical Convergence Zone (ITCA) around the equator which is both not a Jet Stream and the Mother of All Jet Streams. This post mainly concerns the “Polar Jet.” Note that the wind in the Jet Streams moves from west to east, and the Jet Streams can be either pretty straight or pretty curvy. Curvy = “high amplitude.” This figure and the one above are from NOAA.

Here is a depiction of the Jet Stream being very curvy. The waves in the Jet Stream are called Rossby waves.

The Jet Stream in a particularly wavy state.
The Jet Stream in a particularly wavy state.

(See also this animation on Wikicommons, which will open in a new window.)

Research published in the Proceedings of the National Academies of Science last February, in a paper titled “Quasiresonant amplification of planetary waves and recent Northern Hemisphere weather extremes,” links global warming to the setup of high amplitude waves in the Jet Stream, as well as relatively stationary, blocking, waves that cause extreme warm or cold conditions to persist for weeks rather than just a few days. According to lead author Vladimir Petoukhov, “An important part of the global air motion in the mid-latitudes of the Earth normally takes the form of waves wandering around the planet, oscillating between the tropical and the Arctic regions. So when they swing up, these waves suck warm air from the tropics to Europe, Russia, or the US, and when they swing down, they do the same thing with cold air from the Arctic…What we found is that during several recent extreme weather events these planetary waves almost freeze in their tracks for weeks. So instead of bringing in cool air after having brought warm air in before, the heat just stays.”

So how does global warming cause the northern Jet Stream to become wavy, with those waves being relatively stationary? It’s complicated. One way to think about it is to observe waves elsewhere in day to day life. On the highway, if there is enough traffic, waves of cars form, as clusters of several cars moving together with relatively few cars to be found in the gaps between these clusters. Change the number of cars, or the speed limit, or other factors, and you may see the size and distribution of these clusters (waves) of cars change as well. If you run the water from your sink faucet at just the right rate, you can see waves moving up and down on the stream of water. If you adjust the flow of water the size and behavior of these “standing waves” changes. In a baseball or football field, when people do “the wave” their hand motions collectively form a wave of silliness that moves around the park, and the width and speed of that wave is a function of how quickly individuals react to their fellow sports fan’s waving activity. Waves form in a medium (of cars, water molecules, people, etc.) following a number of physical principles that determine the size, shape, speed, and stability of the waves.

The authors of this paper use math that is far beyond the scope of a mere blog post to link together all the relevant atmospheric factors and the shape of the northern Jet Stream. They found that when the effects of Global Warming are added in, the Jet Stream becomes less linear, and the deep meanders (sometimes called Rossby waves) that are set up tend to occur with a certain frequency (6, 7, or 8 major waves encircling the planet) and that these waves tend to not move for many days once they get going. They tested their mathematical model using actual weather data over a period of 32 years and found a good fit between atmospheric conditions, predicted wave patterns, and actual observed wave patterns.

The northern Jet Stream originates as a function of the gradient of heat from the Equatorial regions to the Polar regions. If air temperature was very high at the equator and very low at the poles, the Jet Stream would look one way. If air temperatures were (and this is impossible) the same at the Equator and the poles, there would probably be no Jet Stream at all. At various different plausible gradients of temperature from Equator to the poles, various different possible configurations of Jet Streams emerge.

One of the major effects of global warming has been the warming of the Arctic. This happens for at least two reasons. First, the atmosphere and oceans are simply warmer, so everything gets warmer. In addition, these warmer conditions cause the melting of Arctic ice to be much more extreme each summer, so that there is more exposed water in the Arctic Ocean, for a longer period of time. This means that less sunlight is reflected directly back into space (because there is less shiny ice) and the surface of the ice-free northern sea absorbs sunlight and converts it into heat. For these reasons, the Arctic region is warming at a higher rate than other regions farther to the south in the Northern Hemisphere. This, in turn, makes for a reduced gradient in the atmospheric temperature from tropical to temperate to polar regions.

Changing the gradient of the atmospheric temperature in a north-south axis is like adjusting the rate of water flowing from your faucet, or changing the number of cars on the highway, or replacing all the usual sports fans at the stadium with stoned people with arthritis. The nature of the waves changes.


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In the case of the atmosphere of Earth’s Northern Hemisphere, global warming has changed the dynamic of the northern Jet Stream, and this has resulted in changes in weather extremes. This would apply to heat waves, cold snaps, and the distribution of precipitation. The phenomenon that is increasingly being called “Weather Whiplash” … more extremes in all directions, heat vs cold and wet vs. dry, is largely caused by this effect, it would seem.

This study is somewhat limited because it covers only a 32 year period, but the findings of the study are in accord with expectations based on what we know about how the Earth’s climate system works, and the modeling matches empirical reality quite well.


See also: Killer Heat Waves and Floods Linked to Climate Change by Stephen Leahy and Slowing Rossby Waves Leading to Extreme Weather? by Stuart Staniford.

More about Climate Change HERE

Petoukhov, V., Rahmstorf, S., Petri, S., & Schellnhuber, H. (2013). Quasiresonant amplification of planetary waves and recent Northern Hemisphere weather extremes Proceedings of the National Academy of Sciences, 110 (14), 5336-5341 DOI: 10.1073/pnas.1222000110