Daily Archives: November 29, 2012

Major weather in the American West?

There are these things called “Atmospheric rivers.” They are big long things up in the air that are loaded with water vapor, and much of the rain and other precipitation we experience comes out of them. This is notable when one of these rivers is extra wet, and there is an extra wet one out West in the US.

The Sierra Nevada range will be accumulating something like 16-20 inches of rain, but where that translates into snow, it will be up there in the 12 foot range, maybe more. There will be a very significant risk of flash flooding north of Sacremento and places in northern California and Oregon are going to get very very wet. The Bay Area will see lots of rain but mostly to the north, in Marin County.


A significant rainfall event is underway across portions of the West Coast as unrelenting Pacific moisture slams into the region. Northern California and southern Oregon will see the greatest rainfall totals of 10 to 20 inches by early next week. Strong winds and mountain snow will also impact the area.

The reason I mention this at all (those of you who live there, I’m sure, are totally up on this) is the following: This sort of excess rain is exactly what we expect to see more often because of global warming. This is the effect that global warming has on the hydrological cycle. It fills the Atmospheric Rivers with more moisture than would otherwise develop in them.

Wear knickers.

First close up of DNA ever

When Bill O’Reilly said that you “can’t explain tides” I laughed. Why did I laugh? Because if he wasn’t such a dumb-ass he could have EASILY named a dozen thing that science claims to “know” that a reasonably good rhetorician could convince the average Tea Bagger that science really can’t “know” because it can’t really “see” them. The tides have been understood not only by science by by a lot of regular working class potential Republicans (though many are not) who eek out their living on the shores of the briny sea. Bill O’Reilly must have looked like a complete idiot to them. Meanwhile, almost everything we know about the details of what happens inside a cell is either invisible or so close to invisible that it would qualify as “If we can’t even see it, how can we now that?” material.

Of course, we DO KNOW that stuff. It just isn’t easy to know. I’ve discussed that at some length here.

But now, one of the interesting inferences that science has made about something very tiny inside (usually) cells has been confirmed by direct observation, back in the early 1950s in a paper by these guys named Watson and Crick, has been confirmed by sight. A research team in Italy has produced a snapshot, a photograph, of the DNA Double Helix. Sort of.

It looks like this:

From the paper's Abstract: Direct imaging becomes important when the knowledge at few/single molecule level is requested and where the diffraction does not allow to get structural and functional information. Here we report on the direct imaging of double stranded (ds) ?-DNA in the A conformation, obtained by combining a novel sample preparation method based on super hydrophobic DNA molecules self-aggregation process with transmission electron microscopy (TEM). The experimental breakthrough is the production of robust and highly ordered paired DNA nanofibers that allowed its direct TEM imaging and the double helix structure revealing.

Pretty cool, huh? What you are actually looking at is a set of DNA strands wrapped in a very orderly fashion around a single strand that forms a core for the others. You’d have to squint really hard to see the actual double helix, but it is in there somewhere.

In order to get this picture, a strand of DNA was stretched between two pillars of nanoscopic cilicone. The surface that included the nano-pillars was designed to be hydrophobic, which caused the DNA to be left stranded (ha ha) at the super microscopic level so instead of getting all bunched up a single strand could be located. The photograph is sort of an electron microscopic image, but with technology made just for this setup. This technique is a whole new way of visualizing tiny stuff. Keep an eye on the nano silica pillar technique.

There is an article here in the New Scientist as well.

…at present, the method only works with “cords” of DNA made up of six molecules wrapped around an seventh acting as a core. That’s because the electron energies are high enough to break up a single DNA molecule.

Using more sensitive detectors that can respond to lower-energy electrons should soon allow the team to see individual double helices, and even unwound single strands of DNA. “With improved sample preparation and better imaging resolution, we could directly observe DNA at the level of single bases,” says di Fabrizio.

Watson, J. D., & Crick, F. H. C. A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953)

Gentile, F., Moretti, M., Limongi, T., Falqui, A., Bertoni, G., Scarpellini, A., Santoriello, S., Maragliano, L., Proietti Zaccaria, R., & di Fabrizio, E. (2012). Direct Imaging of DNA Fibers: The Visage of Double Helix Nano Letters DOI: 10.1021/nl3039162

Ice Loss at Poles Is Increasing, Mainly in Greenland

From NASA:

PASADENA, Calif. – An international team of experts supported by NASA and the European Space Agency (ESA) has combined data from multiple satellites and aircraft to produce the most comprehensive and accurate assessment to date of ice sheet losses in Greenland and Antarctica and their contributions to sea level rise.

In a landmark study published Thursday in the journal Science, 47 researchers from 26 laboratories report the combined rate of melting for the ice sheets covering Greenland and Antarctica has increased during the last 20 years. Together, these ice sheets are losing more than three times as much ice each year (equivalent to sea level rise of 0.04 inches or 0.95 millimeters) as they were in the 1990s (equivalent to 0.01 inches or 0.27 millimeters). About two-thirds of the loss is coming from Greenland, with the rest from Antarctica.


From the abstract of the paper:

We combined an ensemble of satellite altimetry, interferometry, and gravimetry data sets using common geographical regions, time intervals, and models of surface mass balance and glacial isostatic adjustment to estimate the mass balance of Earth’s polar ice sheets. We find that there is good agreement between different satellite methods—especially in Greenland and West Antarctica—and that combining satellite data sets leads to greater certainty. Between 1992 and 2011, the ice sheets of Greenland, East Antarctica, West Antarctica, and the Antarctic Peninsula changed in mass by –142 ± 49, +14 ± 43, –65 ± 26, and –20 ± 14 gigatonnes year?1, respectively. Since 1992, the polar ice sheets have contributed, on average, 0.59 ± 0.20 millimeter year?1 to the rate of global sea-level rise.

The melting since about 1992 to the present has contributed to about 0.44 inches of sea level rise (about a fifth of the sea level rise over that period, and there was sea level rise prior to 1992 as well). The main outcome of this study is to clean up the predictions from previous models with much better data and to narrow down the best predictions for future melting. Also, the pace of ice loss now is greater than it was at the beginning of the study period, 20 years ago. Greenland is losing ice about 500% faster now than it was in the early 1990s, while Antarctica is losing ice at about the same rate now as it was then.

UPDATE: See also this post from the LA Times

Shepherd, A., Ivins, E., A, G., Barletta, V., Bentley, M., Bettadpur, S., Briggs, K., Bromwich, D., Forsberg, R., Galin, N., Horwath, M., Jacobs, S., Joughin, I., King, M., Lenaerts, J., Li, J., Ligtenberg, S., Luckman, A., Luthcke, S., McMillan, M., Meister, R., Milne, G., Mouginot, J., Muir, A., Nicolas, J., Paden, J., Payne, A., Pritchard, H., Rignot, E., Rott, H., Sorensen, L., Scambos, T., Scheuchl, B., Schrama, E., Smith, B., Sundal, A., van Angelen, J., van de Berg, W., van den Broeke, M., Vaughan, D., Velicogna, I., Wahr, J., Whitehouse, P., Wingham, D., Yi, D., Young, D., & Zwally, H. (2012). A Reconciled Estimate of Ice-Sheet Mass Balance Science, 338 (6111), 1183-1189 DOI: 10.1126/science.1228102

Photo of icebergs in Disko Bay, Greenland from NASA

Using ScreenFlow and the Reverse Classroom

Next Fall, I will probably try something new in teaching an intro Biological Anthropology course: The Reverse Classroom. This is an idea that is being increasingly applied in High School settings. The simplest version of this idea is that classroom lectures are converted to an on line resource that the students access on their own time, and what would have been study or homework time is done in the classroom. In reality it is a bit more complex than this, because a “lecture” converted to an on line resource may, and probably should, be very different than an in-class lecture, and the activities that are done in the classroom would not consist of students sitting by themselves reading or doing some sort of work. The on line “lecture” would be broken into smaller-than-lecture bits, and involve more interactive tools, and the in-class activities would involve more group activities and tutorials. Also, I don’t intend to create a fully reversed classroom; I’ll use this technique for parts of the course, distributed across the semester.

Pursuant to this, I’ve been looking at tools to help make this work, and on the advice of Peter Sinclair, famous for his most excellent climate science related videos, I’ve obtained a demo copy of ScreenFlow
icon. ScreenFlow works on an iMac. It allows one to specify a window or screen to capture, while at the same time (optionally) to record video and audio off of the hardware built into the computer. So, for example, one can make a Libra Office Impress or Keynote
icon presentation, then “film” oneself giving the presentation. Your head, talking, and your voice are then joined with the presentation you are running through. Your talking head can be in a little box in the corner, the box can be moved, or it can be made invisible. Aside from the presentation itself, one can add text box overlays or other graphic elements. There is even a facility to have a text-to-speech insertion, so I can have a computerized voice read off part of the presentation, though I’m not entirely sure yet why I would do that. Maybe I can make a virtual heckler.

One can also get entirely out of the “presentation” (read “PowerPoint”) mode as well, by simply recording the display of graphics via a file viewer, or for that matter, PDF’s. I’ve done this sort of thing as a lecture tool to some effect. Using this method, instead of showing a presentation on screen in a lecture context, you show your computer’s desktop on which there are various files, perhaps even folders of files. Then, as part of the lecture presentation one opens web browser pages, graphics using a file viewer, sections of spread sheets, etc. etc. Incorporating a window with Google Earth, especially including a pre-programmed fly-over is a nice touch as well. So, you show a web page with a recent news report on some site, use Google Earth to fly from the site of the campus you are on to the location of the site, zoom in, discuss terrain and geographical context, then using the file viewer show a handful of photographs of the site, then open a spreadsheet page with some data, pull up a few graphs, and finally display a PDF file of a published report on that site for a detailed discussion.

Then, ideally, engage in a live Google Hangout with the site’s excavator and one or two other scientists who want to complain about the excavator’s findings for a steal cage death match showdown.

That method … the desktop based meta-presentation … would also be ideal for capture with ScreenFlow. And my head can be there in a box down in the corner being amazed at it all. Though it would probably be better to get someone else’s head.

ScreenFlow allows for quite a bit of editing of the captured screen activity, combining of different sessions, etc. And, I just discovered (but have not yet tested) ScreenFlow’s ability to use a Green Screen. So, not only can my talking head be down there in the corner talking, but I can make myself appear to be somewhere I’m not. A few hominids tooling around in the background, a fancy laboratory setting, the Library of Alexandria for my Carl Sagan imitation…. the possibilities are endless!

Have you used any sort of screen capture software to record lectures or other presentations? Are you familiar with ScreenFlow? Want to take my class and see how it goes?

The Great Transition: Triassic Life on Land

Let’s see … The Triassic is about here:


(You can also look it up in this PDF file supplied by the USGS.

It is situated between two major extinction events, and is especially interesting because it is during this period that modern day ecological systems and major animal groups took a recognizable form. The preceding Permian, if contrasted with modern day, would form a very stark contrast while the Triassic would be at least somewhat more recognizable.

But of course the Triassic was in many ways distinct, different, and fascinating. Dinosaurs arose during the Triassic. The Triassic is also famous for its enormously large insects. It was also the time of Pangaea, where most of the Earth’s land was concentrated instead of being more or less spread out as it is now. Mammals, or at least the progenitors of what we now know of as mammals, arose then as well.

The Triassic was hot compared to today, and dry. Lots of sandy, arid-land deposits visible today date from this period. The poles were temperate, and the middle regions of the one giant continent was probably … very continental (mainly, dry).

So, all this adds up to the simple fact that the Triassic was a very interesting time period, and I assume that you would like to know a lot more about it. That would be where the new book, Triassic Life on Land: The Great Transition, comes in. This new volume in a series on “Critical Moments and Perspectives in Earth History and Paleobiology” (of which there are several other interesting must-have installments) comes in.

Sues and Fraser’s accessibly priced volume is neither a popularization of palaeontology nor a monotonous monograph of esoterica. It is a scholarly but readable detailed yet succinct description of this incredibly interesting time period. This is the kind of book that you will sit down to relax with, but do so with a pack of post-it notes handy just in case you need to mark something. Triassic Life .. is sufficiently detailed and well documented (excellent references and index) to be used as a textbook in a middle level palaeontology course, and sufficiently engaging for you to use as a source book for your next cocktail party.

The authors are widely recognized and respected experts in their field. The publisher did an excellent job with the book, which is very heavily illustrated and well laid out. Yet, most of the illustration are very nicely done line drawings and black and white photos, which keeps the price of this volume down despite the nice paper and excellent binding.

The book has eleven chapters, seven of which serve as mini-monographs of specific Triassic sub periods in specific geographical locations (such as “Late Middle and Late Triassic of Gondwana” and “Late Triassic of the Western United States”). Each of these chapters gives the basic information on where, when, and what for that particular subset of paleontological phenomena. Chapter 9, “Two Extraordinary Windows into Triassic Life” focus on two cases of Konzentrat-Lagerstätten (places of especially good preservation or richness): Solite Quarry in the eastern US and Madygen in Central Asia. Triassic insects. Very nice.

Chapter 10 is an overview of the large scale pattern of biological change during the period, and Chapter 11 examines the Triassic end-times, exploring the possibility of an end-Triassic impact, and other issues.

If you have an evolution-oriented relative or friend who’s birthday is coming up, now’s your chance: The book is new enough and specialized enough that there is no way they’d have it already. And, it looks enough like a coffee table book that others looking on will see it as a great gift even if it is a bit over the top in geek points.