But one more year until the end of century 20.1?

End Century by kevindooley

A little decadence
[ViaBad Astronomy ]

Quite by accident, just the other day I found myself embroiled in a controversy on Twitter of my own making. I made an offhand mention that the decade would be ending in a few short days. That seemed obvious enough to me, but apparently not so to many others. What ensued was something of a firestorm of people, many of whom disagreed with me. However, I maintain that I was right all along. Here’s the scoop.

My claim is that December 31, 2009 — today, as this is posted — is not just the last day of the year, but the last day of a decade. Now, I don’t mean that in the trivial sense that any moment is the last moment of the past ten year period — you can always talk about the last ten years that end at any time.

I meant, and still mean, specifically the first decade of the 2000s. That does in deed and in fact end today.

What people were arguing over were things like centuries and millennia, and how there was no year 0, and therefore the last day of the decade is actually December 31, 2010. But that’s not relevant because we don’t measure decades the same way we do centuries.

Certainly, the last day of the 20th century was December 31, 2000. In that case, there was no year 0, so the first year of the 1st century ended on December 31, 1 A.D. Doing the math, it’s easy to see that 1999 more years needed to elapse to end the 20th century, and so its demise was on that last calendar day of 2000. January 1, 2001 marked the first day of the 21st century.

But we don’t reckon decades like that. We refer to them by the tens place in the year’s numerals: the 70s, the 80s, the 90s. And since we do, clearly, today is the last day of the decade we will call the aughts or zeroes or whatever

[More]

I just had this exact same discussion. It is almost as if we did too good a job 10 years ago explaining that 2000 was not the beginning of a new century but that 2001 was (thus the name of the book/movie). I was on one of those Y2K committees charged with preventing Armageddon by making sure all sorts of paperwork was completed. I spent many times explaining all of this to people.

A decade has a year 0, thus ten years pass after the end of a year ending in 9. Thus today is the last day of the decade. But since we do centuries differently, I guess we can call next year the end of century 20.1!

Making leaves better for energy

by ellievanhoutte
Engineered tobacco plants have more potential as a biofuel:
[Via EurekAlert! - Biology]

(Thomas Jefferson University) Researchers from the Biotechnology Foundation Laboratories at Thomas Jefferson University have identified a way to increase the oil in tobacco plant leaves, which may be the next step in using the plants for biofuel. Their paper was published online in Plant Biotechnology Journal.

[More]

I wrote a bit ago about using tobacco seeds for fuel. Here, they make the leaves a better source. They doubled the amount of oils that are in the leaves, making the plats much more suitable as a source for biofuels.

It would be pretty ironic if the tobacco industry came to our energy rescue.

Technorati Tags: Environment, Science

Still rely on snowpack as a reservoir

Hood by nosha

Yakima water plan moves forward
[Via All Today's News - Sightline Daily]

It’s full speed ahead on developing a plan to supply water for fish, farmers and cities in the Yakima River Basin in the decades to come. Three Central Washington counties – Yakima, Kittitas and Benton – have all now committed to continue the planning process after six months of work appeared on the verge of being scuttled.

[More]

My previous post discussed changing rainfall patterns in the US over the next 80 years or so, with the Pacific NW getting large amounts in our mountains. Well, eastern Washington is already looking to manage water by filling reservoirs, etc. But I thought the last paragraph of the article was off somehow:

The three-county basin relies on snowpack — commonly referred to as the sixth reservoir — to supply early-season irrigation water. The five existing reservoirs hold less than half of what is needed annually.

Snowpack provides more than half the water needed annually. So they had better hope the snowpack does not disappear or that the glaciers on all the mountains remain. Otherwise that 6th reservoir will not be available.

I would imagine that they will simply build more reservoirs to hold the water. We may not be able to rely on cold weather holding our water for us but we can probably figure out ways to retain what we need.

[Listening to: Help Me Girl from the album "The Animals - Retrospective" by The Animals]

I got here first

The Wizard turns on…
[Via Hot Topic]

Catching up with some of the stuff that got lost in the Copenhagen hubbub, this morning I stumbled on a major new effort to provide interactive climate data and visualisations — the Climate Wizard. This amazing tool is the web front end to a collection of temperature and precipitation data and model projections, and allows the user to create custom maps of climate change over the last fifty years, and projections for the 2050s and 2080s for three IPCC scenarios across 16 models. It provides state-level detail for the USA, but coarser regional and global maps for the rest of the world. It can also create ensembles of model projections on the fly:
[More]

The wizard is a lot of fun to play with. The picture above shows what the models indicate the rainfall will be in the US in as this century ends. You can see 2 very dark blue bands indicating the areas of greatest precipitation in the US. They correspond with the Olympic and Coastal Ranges along the coast of Washington and the Cascade Range in the interior of Washington and Oregon. In fact, these models indicate that the precipitation in these areas will be greater than it was during the last 50 years.

Seattle, Portland and the Willamette valley are nestled between these two large sources of water. The Pacific Northwest could be in as important a position with regards to water usages in the US as Texas and California were with regards to oil in the 20th Century. Some parts of the Southeast also see some increase but the total number of inches is no where near what these two ranges get. And most of the Southwest would get much less water.

Only parts of the tropics will get this much rain.

One reason I moved to the Pacific Northwest 25 years ago was that I figured that it would be the only place along the West Coast that would not have to worry about water. Looks like the same could be true by the end of the century. Perhaps Washington state should be discussing its immigrant policy now.

Of course, this is based on the average of several models. That is it shows what things look like where half the models are better and half are worse. If we look at the ‘worst’ case model we get this picture of 2080:

Still lots of rain out here. Not much elsewhere. I hope this model is way off because otherwise everyone will be moving here.

And don’t even look at the temperature changes. Eastern Washington in summer will be as hot as Houston is now. The Seattle to Portland area, though, still remains mild.

[Listening to: Who Will You Run To from the album "The Essential Heart [Disc 2]” by Heart]

New image search site

Mount Everest from base camp one by Rupert Taylor-Price via Flickr.
Search Engine for Creative Commons and Public Domain Images
[Via ResearchBuzz]

After watching major search engines develop way to search for Creative Commons images, it’s no surprise to discover that there’s a search engine dedicated exclusively to Creative Commons and public domain images. It’s called Sprixi and it’s available at http://www.sprixi.com/. What it finds is rather limited (at the moment it finds only items from Flickr and OpenClipArt as well as any images that are uploaded to Sprixi) its presentation is excellent.

The site has a basic keyword search; just enter a couple of words that describe what you’re looking for. I did a search for snow. Sprixi divides its search results into two panels: the first has thumbnails of the results and the second has a larger version of a chosen image, with even more data if you hold your mouse over the image.

Along with viewing the image, you have the option of specifying whether you think the option is a good result for your keyword search, which will help Sprixi give better results over time. If you click on the larger image in the right panel, you won’t get anything. But if you look at the bottom of the second panel, you’ll see there are direct links both to the image and to the Flickr user who uploaded the image. Beneath that you’ll see a notice of public domain or the picture’s Creative Commons license, as well as the original dimensions of the image.

[More]

This is kind of cool. A nice interface to the site. And it is still in the process of learning so the best photos have a real chance. It will be interesting to see what comes out, compared to flicker. It is kind of nice to automatically have the creator info put IN the picture.

[Listening to: Down To The River To Pray from the album "O Brother, Where Art Thou?" by Alison Krauss]

Now that would be a great movie!

Anniversary of a cosmic blast
[Via Bad Astronomy]

Five years ago today — on December 27, 2004 — the Earth was attacked by a cosmic blast.

The scale of this onslaught is nearly impossible to exaggerate. The flood of gamma and X-rays that washed over the Earth was detected by several satellites designed to observe the high-energy skies. RHESSI, which observes the Sun, saw this blast. INTEGRAL, used to look for gamma rays from monster black holes, saw this blast. The newly-launched Swift satellite, built to detect gamma-ray bursts from across the Universe, not only saw this blast, but its detectors were completely saturated by the assault of energy… even though Swift wasn’t pointed anywhere near the direction of the burst! In other words, this flood of photons saturated Swift even though they had to pass through the walls of the satellite itself first!

It gets worse. This enormous wave of fierce energy was so powerful it actually partially ionized the Earth’s upper atmosphere, and it made the Earth’s magnetic field ring like a bell. Several satellites were actually blinded by the event.

So what was this thing? What could do this kind of damage?

Astronomers discovered quickly just what this was, though when they figured it out they could scarcely believe it. On that day, half a decade ago, the wrath of the magnetar SGR 1806-20 was visited upon the Earth.

[More]

Read the entire post. It is an amazing story and really shows just how powerful some of the forces are in the galaxy. Thank goodness it was not any closer.

But think of the movie we could have, with all our satellites fried. Or worse. Lots of potential for some very interesting stories. It would just depend on whether Michael Bay or James Cameron directed. In one, Bruce Willis or Nike Cage could be the resolute hero, leading a group of survivors to a safe haven, with lots of huge explosions as the vestiges of military organizations try to save (destroy) civilization. In the other, Sigourney Weaver tells someone to get of out the f@#king way as she leads a group of survivors to a safe haven, with lots of huge explosions as the vestiges of military organizations try to save (destroy) civilization.

In one, the explosions would be the highlights while in the other the surround environment would. Neither would have much narrative depth but either would be a visual spectacle.

[Listening to: Baby Hold On from the album "Taking The Long Way" by Dixie Chicks]

Central Asia and the long view of innovation

by Gusjer
Central Asia and the long view of innovation
[Via Andrew Hargadon]

Frederick Starr wrote a brilliant essay, Rediscovering Central Asia, which provides a perspective on the current quagmire in Afghanistan that predates, by several millenia, the post-9/11 version currently guiding public opinion (and policy). Starr has impeccable credentials as an expert in this region and its history, and I leave any policy disagreements to him and others equally qualified. This was one of those essays, however, that has as many implications for innovation and innovation policy as it does for statesmanship and central asian policy.

Central Asia is, in Starr’s words, the “vast region of irrigated deserts, mountains, and steppes between China, Pakistan, Iran, Russia, and the Caspian Sea,” with Afghanistan traditionally considered the heart of the region. Despite its backwards appearance in the press, with war correspondents standing in front of deserted plains or smoldering cities, Central Asia was once one of the most intellectually vibrant communities in world history.

<>From this region came “mathematics, astronomy, medicine, geology, linguistics, political science, poetry, architecture, and practical technology” that influenced the west and the east alike in both its logic, empiricism, aesthetics, and faith. As Starr argues,

Between 800 and 1100, this pleiad of Central Asian scientists, artists, and thinkers made their region the intellectual epicenter of the world. Their influence was felt from East Asia and India to Europe and the Middle East.

What makes this essay on Central Asian culture so vital to understanding innovation lies in Starr’s reasons for both why such an intellectual wellspring emerged and flourished and why it dried up.

[More]

New ideas that arise due to the ‘friction’ of different cultures has been a hallmark of innovation throughout history. Perhaps one reason the US has been a leader in innovation is because it is the first culture that is purely made up of immigrants. We may have more cultures represented than at any other time in history.

But, the rise of static, rigid, authoritarian orthodoxies is what destroys innovation. I=t has in the past and could happen here. The signs are there, at least for certain parts of our culture. central asia declined as an innovative center in large part to the loss of tolerance for other cultures, to the rise of conservative Islam: the religions that flourished in their early stages hardened into orthodoxy. The intellectual and cultural exploration that led growth becomes threatening to the stasis of orthodoxy: “the demands of a steadily rigidifying Muslim orthodoxy gradually narrowed the sphere in which free thought and humanism could be exercised.“

We are not immune to these pressures. America has tried to stifle the flow of new cultures and ideas before. If these approaches harden into dogma, then our ability to find solutions will become tremendously hampered. As this article ends:

Have we tapped out the confluence of ideas, technologies, and aesthetics that came from Europe and Asia over the prior centuries? Will the modern-day “trade routes” that placed us at the confluence (now most prominently financial) sustain further growth or are they in decay. Has the nexus of cultural growth shifted again? Finally, has our own orthodoxies hardened to the extent that the benefits of intellectual and cultural exploration are outweighed by their perceived threats to the stasis of orthodoxy?

We can talk all we want about corporate cultures, garage start-ups, and our legacy of innovation but if history tells us anything, it’s that nothing endures. Moving forward, our ability to innovate hinges on how we choose to tolerate, assimilate, and build on the ideas of others—and how we manage the intolerance of others threatened by this process.

[Listening to: Me and Bobby McGee from the album "Those Were the Days" by Dolly Parton with Kris Kristofferson]

Avatar redux

Well, I took my wife to see Avatar yesterday. Twice in two days for me. It was an interesting experience to see it in 3-D again. It reminded me of something – the original Star Wars. Not only in its general aspects (incredible visuals, simple plot) but in its historic sense. Just as Star Wars was the first movie of the computer era that touched deep emotional feelings through its images, I think Avatar will be seen as the first movie that utilizes 3D CGI imagery to produce a more immersive emotional response.

I saw Star Wars on the Friday it opened at Mann’s Chinese Theater in LA. I had several friends who ad worked on some of the special effects and they wanted to see ow they came out. I still remember the first scene with the huge imperial ship that seemed to go on forever chasing the small transport. I knew we were in for a very different film than I had seen before.

Avatar lets us know right off that it will be a different type of movie.

Avatar starts on a much smaller scale but with a sense of playfulness and awe that really needs to be seen in 3D to feel. I knew I was in a much more immersive movie experience. It has been discussed many times that seeing a movie is like a cream – it gets quiet and dark; then images appear for us to watch. The original Star Wars was such a wonderful dream.

I’ve seen several 3D movies before but this was the first one that took the immersive qualities to a higher level. In some ways, my brain was fooled and instead of seeing this as a dream, it seemed to react as though what it saw and heard was real, at least on an emotional level. Even a second time, when I knew what to expect, I reacted. In fact, the emotions were deeper and stronger because they were not just visceral, reacting to the moment.

Even a second time, my emotional responses were much more amped up than usual. I think that this is one of the real benefits of a well-made 3D movie. It can hit at a deeper emotional level than regular movies because that is how some part of our brain is ‘tricked’ to feel.

What separates movies from other media are the visuals and the sound. Nothing else can impact our senses tis way, which is really a direct line to our emotions. Books can sometimes ‘fool’ our brain into very strong emotional responses but nothing like a movie. And a 3D movie such as Avatar hits a deeper and stronger emotional spot than few other movies have.

Before seeing the movie, I had been worried about its apparent simple, even rehashed, plot. But now I am convinced that it needed to be relatively simple. If we had been concentrating too much on the plot, the incredible visual experience would have been lessened. In fact, seeing it a second time actually increased some of my emotional responses. I was aware of what was going to happen and actually responded strongly before it happened. Some of the scenes, which were so visceral the first time, were just heart-breaking the second.

People forget that Star Wars had a very simple derivative plot but its visuals, which had not been possible before, produced incredible emotional responses. Avatar is as much a line in the sand as Star Wars. It is the first movie since Star Wars where I want to see it again (I saw Star Wars 11 times in the theaters), as often and as soon as possible. Maybe on Christmas.

Technorati Tags: General

But was he clutching his pearls when he lied

The Rachel Maddow Show Finds Old McCain C-SPAN Footage
[Via Crooks and Liars]

DOWNLOADS: (348)
PLAYS: (3001)

Oh lookie here. Apparently Rachel Maddow loves the C-SPAN. As a part time C-SPAN junkie and fellow geek myself I can relate. Apparently after her show contacted them about the missing footage of John McCain cutting off Sen. Mark Dayton and objecting to him having another thirty seconds to debate the Iraq war, they went back to their original analog tapes and reposted the footage on their web site.

Maddow: Either Sen. McCain cannot remember that he objected to a Senator getting an extra thirty seconds to finish his remarks during the Iraq war debate or Sen. McCain knows perfectly well that this stuff happens in the Senate. It happens. And he just said it was unprecedented out of sheer hackitude.

Good for Rachel and her staff for following up on this. John McCain, thy name is hypocrite. Hackitude indeed. Hackitude and anger management problems. My apologies again for thinking Tweety had this and Rachel missed it.

[More]

So, when McCain accused Franken of destroying the comity of the Senate, he was purposefully forgetting that he had done the same thing, that this sort of thing happens. To paraphrase ‘I’ve never seen this before, except I did the same thing 7 years ago.’ Wow! Fake outrage, thy name is McCain.

What is so cool about this story is the way the facts came out. Maddow had found the transcript of the 2002 exchange but the video available ended, just ended, before that happened. She mentioned it on one show and the guys at C-SPAN heard that, went to their old analog tapes and found the missing footage.

For those who care, the internet can fact-check your ass. At least they know that previous records are producible to demonstrate when a politician is lying or not.

And for a bipartisan example of that, look how the left wing sites are demonstrating that Obama did include the public option in his campaign, although he now denies that. While we know that politicians lie all the time, it is so much easier to catch them at it now. It makes life much more fun for those of us living in the reality-based world.

[Listening to: Young Lust from the album "Pink Box: Songs of Pink Floyd" by Elliot Easton (The Cars) & Glenn Hughes (DEEP PURPLE)]

Visual over truth

by kekremsi

The Mighty Power of Blogosaurus?
[Via The Loom]

Over the past few days, I’ve been following a tale of paleontological woe with a surprisingly happy ending.

Matt Wedel, a paleontologist, has been blogging about his experience with a television show on the Discovery Channel called Clash of the Dinosaurs. It didn’t go well. The producers edited Wedel’s interviews to turn his words around 180 degrees. For example, remember that old notion of big dinosaurs having a second brain along their spinal column? Not true! Wedel explained this, but if you tune into the show, you see Wedel essenitally saying, True!

Wedel understandably flipped out. He complained to the producers and got back a non-apology that just made him angrier. He was transformed into the terrible Blogosaurus, and with his resonant nasal cavity he let out a clarion call for his fellow blogosaurs to stampede the production company

I’ve heard this sort of story many times before, and this is where it usually ends. Blogosaurus slinks back to his office and sulks.

But today the story has another ending. Wedel now reports that someone from the Discovery Channel called him up and is going to make things right. I can only guess that blogs do actually make a difference some of the time. Or maybe just this once.

[More]

A very nice discussion about the clash of science programs and science. In many cases, the video producers goal is to produce great visuals. That is what the medium requires. So far so good. But excellent programs require good narratives also, in order to capture people’s interest.

The problem often arises when a really nice visual narrative, loved by the producers, runs up against the facts. Does the producer drop the wonderful narrative or find some way to keep it in, even if it requires twisting some of the words of the scientists.

As long as producers have no real pressure to get the facts right (and things like Nostradamus 2012 indicate that this is obviously true) misrepresentation will be a worry. This does present a conundrum. Many researchers want to get the science out to a lay audience. But the wrong science can be really to take back.

Perhaps the researchers should ask for some sort of final vetting of the program for reality. But I have real doubts about this actually working. I have a hard time seeing producers letting go of great visuals simply because the narrative is weak. All you have to do is look at Avatar to see this.

[Listening to: Mystery from the album "Tyranny" by Shadow Gallery]

Explosive duck penises

Kinkiness Beyond Kinky

[Via The Loom]

There comes a time in every science writer’s career when one must write about glass duck vaginas and explosive duck penises.

That time is now.

[More]

I had read about the weirdness of duck penises before. But the title of the paper Zimmer discusses really caught my eye :

Reference: Patricia L. R. Brennan et al, “Explosive eversion and functional morphology of the duck penis supports sexual conflict in waterfowl genitalia,” Proceedings of the Royal Society of London, doi: 10.1098/rspb.2009.2139

They tried to use a model female oviduct made out of silicone. The ‘explosive eversion’ broke it. The duck penis enlarges at a rate of 1.6 meters per second. Wow. There is even a video for those really kinky types.

Can a failed state be fixed?

by Bernt Rostad

Fixing California
[Via Cosmic Variance]

This past year has been a long, slow downward spiral for California into one of the worst financial crises in state history. Revised revenue projections in February led to huge slashes in funding for an array of programs from higher education to state parks, and a $25 billion budget shortfall looms next year. State employes and university (both Cal State and UC) employees have been furloughed, and UC tuition has gone up dramatically – 32% within a year. Protests at Berkeley, UCLA, and my own institution, UC Davis, led to dozens of arrests in November.

[I was amazed, the night of November 19, to see a helicopter with a powerful searchlight circling over the main administration building at UC Davis. The police, many from jurisdictions 20 miles away, had created a perimeter about 100 yards from the building, which was still occupied by students who were later arrested for trespass (and the campus police returned to find their tires slashed). The next week saw another protest, resulting in amnesty for those previously arrested...]

People are angry, and justifiably so. There are over 400,000 parents in the state who are getting a giant kick in the pants (myself among them – my daughter is at Berkeley). But who should we be angry at? Faculty? UC administration? The government in Sacramento? The global economy? What can we change that will truly fix the problems California faces?

One simple and direct idea has emerged, from a professor of linguistics at Berkeley, George Lakoff. He proposes the following 14-word amendment to the state constitution for the Nov. 2010 state ballot:

All legislative actions on revenue and budget must be determined by a majority vote.

With a million signatures, this proposition will be on the ballot next fall, and I am going to predict at this point that this will very likely be the case. If adopted, this would put an end to the 2/3 majority of the legislature required in California to enact any tax increase, and thereby end the present tyranny of the minority that hamstrings the state that I wrote about before.

[More]

Anyone who has been following California politics knows about the tyranny of the minority. And, as is often the case, what happens in California often is then seen on a national scale. Thus the tyranny of the minority in Washington.

Perhaps California will pull back from the ledge by passing this amendment. But I would not hold my breath. A very large group of people there apparently do want a failed state, one whose tax revenues can never meet its social obligations. They have been relying on cheap tax dodges for a long, long time.

I was in California when Proposition 13 passed. This not only lowered property taxes tremendously but also inserted the requirement for a 2/3rd majority on tax issues, not only at the state level but also at the level of local government. Not too surprisingly, many of the property tax provisions have greatly benefited corporations, which continue to pay a smaller percentage of the overall tax. Funny how the companies always make out well and the average citizen can not afford to send their child to state college.

The increases in tuition at its Universities may provide some financial relief for the poorer students in the form of financial aid, but it will do little to provide for middle class students. Instate tuition will rise from about $7000 in 2009 to about $10,000 in the fall of 2010. That is enough to wake up some people but what it really indicates is the increasing problem of attending college for middle-class families.

Perhaps letting the majority determine tax policy would be a good thing and this experimentation with minority control will fade away.

[Listening to: Hopelessly Human from the album "Point of Know Return" by Kansas]

My avatar thoughts

Saw Avatar today. In 3D. Yes, it does have a pretty simple, straightforward narrative. But, that is fine because it gives us more of a chance to just really enjoy the visuals. There has never been a movie that created a foreign world in such an immersive way.

He does have lots of things inspired by others. I saw stuff from Poul Anderson, Ursula LeQuin, Anne McCaffrey and others. But no one else has created visuals of what the authors produced. The attention to detail is just awe-inspiring. And there are some images whose beauty brought me to tears.

In addition, this is the first 3D movie that I really enjoyed. Others often gave me a headache, with changing depths of field that caused eye strain. But Cameron used the third dimension to give a real sense of motion. When things attacked, you got a real sense of their movement through space in ways that a normal movie does not. If others can copy this approach, 3D could become even more popular.

So, the simple story allows us to concentrate more on the sheer beauty of the movie, which is really what Cameron wanted us to do. Movies are, after all, a visual medium and Cameron pushes the envelope here.

Well, my next goal is to see it on an IMAX screen. That should be awesome.

Technorati Tags: General

Another paper on CO2 and ice sheets

by skycaptaintwo

Coupling of CO_2 and Ice Sheet Stability Over Major Climate Transitions of the Last 20 Million Years
[Via CaltechAUTHORS: No conditions]

Tripati, Aradhna K. and Roberts, Christopher D. and Eagle, Robert A. (2009) Coupling of CO_2 and Ice Sheet Stability Over Major Climate Transitions of the Last 20 Million Years. Science, 326 (5958). pp. 1394-1397. ISSN 0036-8075 http://resolver.caltech.edu/CaltechAUTHORS:20091216-121815722

[More]

Examining fossil foraminifera the authors were able to determine what the carbon dioxide levels were over the last 20 million years. They also determined the acidity of the oceans (which should become more acid as carbon dioxide levels rise). Both were increased during periods of high temperature and reduced during periods of low temperature.

This conclusions tells it all:

These results show that changes in pCO₂ and climate have been coupled during major glacial transitions of the past 20 My, just as they have been over the last 0.8 My, supporting the hypothesis that greenhouse gas forcing was an important modulator of climate over this interval via direct and indirect effects. Variations in pCO₂ affect the radiative budget and energy balance of the planet. Such changes will inevitably have consequences for temperature, the hydrologic cycle, heat transport, and the accumulation and ablation of sea ice and glacial ice. The data presented here do not preclude alternative mechanisms for driving climate change over the past 20 Ma. However, they do indicate that changes in pCO₂ were closely tied to the evolution of climate during the Middle and Late Miocene and the Late Pliocene glacial intensification, and therefore, it is logical to deduce that pCO₂ played an important role in driving these transitions. High-resolution records of pCO₂ and other climate parameters should help to resolve whether pCO₂ was a trigger and/or feedback (or both).

Carbon dioxide levels are closely tied to global temperatures. IN addition, the authors have this to say about glacial ice depending on carbon dioxide levels:

By comparing our reconstruction to the published data sets described above, we are able to estimate past thresholds for the buildup of ice in different regions. When pCO₂ levels were last similar to modern values (that is, greater than 350 to 400 ppmv), there was little glacial ice on land or sea ice in the Arctic, and a marine-based ice mass on Antarctica was not viable. A sea ice cap on the Arctic Ocean and a large permanent ice sheet were maintained on East Antarctica when pCO₂ values fell below this threshold. Lower levels were necessary for the growth of large ice masses on West Antarctica (~250 to 300 ppmv) and Greenland (~220 to 260 ppmv).

Carbon dioxide levels have gone up over the last century to levels that have been closely correlated with loss of glacial and sea ice in the Arctic. And that is just what we are seeing. We are also above the concentration associated with the increase of Greenland glaciers. And we continue to see loss of these also.

So, historic data using another approach indicates that carbon dioxide levels are tightly correlated with temperature and pH changes, as have so many other approaches. The physics indicates that this should be true and it is nice to see that fossil data confirms this.

Glaciers represent a tremendous resource used by mankind to store the fresh water it needs. What will happen when these are gone?

[Listening to: Song for America from the album "The Ultimate Kansas" by Kansas]

The new basic biology

by Cushing Memorial Library and Archives, Texas A&M
I’ve collected my data, now what do I do with it?:
[Via Bench Marks]

4-dimensional live cell imaging has gone from being a rare technique used only by cutting-edge laboratories to a mainstream method in use everywhere. While more and more labs are becoming comfortable with the equipment and protocols needed to collect imaging data, performing detailed analyses is often problematic. The application of computational image processing is still far from routine. Researchers need to determine which measurements are necessary and sufficient to characterize a system and they need to find the appropriate tools to extract these data. In Computational Image Analysis of Cellular Dynamics: A Case Study Based on Particle Tracking, Gaudenz Danuser and Khuloud Jaqaman introduce the basic concepts that make the application of computational image processing to live cell imaging data successful. As one of the featured articles in December’s issue of Cold Spring Harbor Protocols, it is freely accessible for subscribers and non-subscribers alike.

The article is adapted from the new edition of Live Cell Imaging: A Laboratory Manual, now available from CSHL Press.

[More]

My first year as a biochemistry graduate student, one of the classes simply dealt with the analytical technologies we would be using. Things like NMR, UV spectroscopy, circular dichroism, fluorescence and X-ray crystallography. They would help us understand the properties of isolated biological molecules

This paper gives a great view of some of the new analytical approaches that examine entire living cells, not just isolated molecules. Now it looks like students will also have to get some firm understanding of image analysis. There will be some really interesting results from these sorts of technologies. The conclusions provide insights into the promise and the problems:

Computational image analysis is a complex yet increasingly central component of live cell imaging experiments. Much has to be done to make these techniques useful for cell biological investigation. First, algorithms must be transparent, not necessarily at the level of the code but in terms of their sensitivity to changing image quality and the effect that control parameters have on the output. Second, the design of imaging experiments must be tightly coupled to the design of the analysis software. All too often, images are taken without careful consideration of the subsequent analysis and are forwarded to the computer scientist to retrieve information from the images. To avoid these problems, communication must be initiated early on, and experiments must be designed with the appreciation that data acquisition and analysis are equivalent components. Third, software development and application require careful controls, as is customary for molecular cell biology experiments. This article provides a brief introduction to the ideas useful for implementing such controls. Hopefully, the cell biological literature will include a more extensive discussion of the measures taken to substantiate the validity of results from image analysis. On the other hand, manual image analysis should no longer be an option. As discussed in this article, manual analyses fall short in consistency and completeness, two essential criteria underlying the validity of a scientific model derived from image data.

While the results can be amazing, there needs to be close collaboration between the different researchers involved. Because very few people will have all the expertise necessary for success. This tight coupling of researchers with vastly different backgrounds and focus (i.e. cell biology and bioinformatics) is a relative new aspect of modern biological research.

There may be slowing of this coupling in some labs but the successful results by those that can accomplish this type of collaboration will rapidly overtake those who take a slower course. As I mentioned below, large collaborations may be a big part of the published record as we move forward.

Technorati Tags: Science, Social media