Goggle Wave could be really cool

wavesby Duncan Rawlinson

One step towards writing papers in Google Wave:
[Via bioCS]

Google Wave’s underlying technology will not only enable collaboration with other people, it also make it possible for bots to interact with what you’ve written. I think this is going to change the way we work. E.g., all applications which require a significant amount of typing will benefit from the statistical auto-correction provided by the Wave app Spelly. In effect, Spelly goes over the text as you’re typing it and correcting the obvious mistakes, just as you would do a bit later.

In a similar vein, the proof-of-concept bot Igor is watching out for inserted references and automagically converts them to a citation and a reference list. When writing papers, I usually insert reminders: “REF Imming review”, “REF PMID 16007907“. If I adjust this convention a bit and provide a bit more detail, Igor can figure out by itself which paper is meant and fetch the citation. Google Wave and Igor save me the tiresome going back-and-forth between a reference manager and the editor to insert all the citation, and they remove distractions from the process of writing and editing the paper.

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I’ve been having a hard time getting my head around Google Wave. Perhaps if I actually watched the 80 minute video I’d have a better idea.

Anyway, this is pretty neat since dealing with citations in a scientific paper is such a pain. Here, the friendly bot goes out and does it for you. It is still pretty simple so far but a great start. collaborative documents are, I think, going to be a big part of how people create really rich, synthetic works that will be incredibly useful.

Now if schools will just move towards collaborative work, they might be able to enter the new era of learning.

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Systems thinking circa 2012

Systems Thinking: Ancient Maya’s Evolution of Consciousness and Contemporary Thinking:
[Via Ackoff Center Weblog]

Posted by Assistant Professor Tadeja Jere Lazanski, University of Primorska, Portoroz, Slovenia on his blog: “Systems thinking is a framework that is based on the belief that the component parts of a system can best be understood in the context of relationships with each other and with other systems, rather than in isolation. The only way to fully understand why a problem or element occurs and persists is to understand the part in relation to the whole. (Capra, 1997)

There are some historical facts regarding systems and systems thinking. Systems thinking as a modern approach for problem solving was revived after WWII even though it had been an ancient philosophy. We can track systems thinking back to antiquity. Differentiated from Western rationalist traditions of philosophy, C. West Churchman often identified with the I Ching as a systems approach sharing a frame of reference similar to pre-Socratic philosophy and Heraclitus. (Hammond, 2003)

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This is actually a link to this article by Dr. Lazanski. It is an interesting approach. While I do not think that things happen in exact cycles like that, with well-defined edges, the impact systems thinking can have could be formidable.

I just think that there are too many people who just can not bring a systems approach. There is still too much to be gained by being purely analytical and only looking out for oneself. There are some problems which just can not be solved with that approach, thus the Tragedy of the Commons.

The Mayans may not have had a direct metaphysical line to Galactic consciousness (I guess we will find out in 3 years) but I certainly think that only by focussing on synthetic approaches to problem solving will be be successful dealing with our troubles..

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Jet Propulsion Labs and Mt Wilson Observatory in harm’s way

mount wilson telescope by FlyingSinger
JPL threatened by fires:
[Via Bad Astronomy]

[Update (19:40 MT): On Twitter right now, several friends are saying Mt. Wilson -- a very famous and historic observatory -- may get hit by these fires. As of this moment, news is unclear. Yikes.]

[Update II (20:40 MT): Clifford Johnson has heard that the authorities may have to let the ...
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What is amazing to me is that these fires in Southern California are apparently NOT being driven by the normal Santa Ana winds. These occur in the late fall, closer to the end of October. As someone said, getting fire without a Santa Ana wind is like getting snow on a cloudless day. It just should not happen.

Maybe they will be ‘lucky’ then and a lot of the possible fuel will have burnt off before the Santa Ana winds come in October. I guess one can hope.

Having spent time at JPL, and considering it lies right at the base of the San Gabriel mountains, I can imagine it might be under some stress. And the Mt. Wilson observatory is an important icon to those of us who went to CalTech.

If you’d like to stay on top of things, you can follow the Google maps page and watch updated photos from the Mt. Wilson Observatory camera (although this is getting so many hits that is sometimes does not load).

UPDATE: When I was a student at CalTech in the 70s, you could still see an area on the closet hills of the San Gabriels where CalTech students had cleared out a very large ‘C’ years before. I wonder if this is still there or whether it have disappeared over the years?

UPDATE II: Here is another good maplink with more info.

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E pluribus unum

Renewed Faith By digby I have,sadly, become something of…:
[Via Hullabaloo]

Renewed Faith

By digby

I have,sadly, become something of a cynic in my old age and it’s not a happy thing to be. The world is darker, inspiration harder to find and humans are constantly disappointing me. But today, my faith in the goodness of human nature was renewed.

Howie Klein asked John Amato and I to an event last night at the Grammy Museum, which is in downtown LA near the Staples center and the convention center. It was a fabulous Q&A and concert with the great Jazz trumpet player Terrance Blanchard and his band. Unfortunately, when I got back in my car after the event I found that my wallet was missing. This venue is huge, tens of thousands of people are there at any given time from all over the area and all over the world. Whether stolen or lost, I had no hope that I would ever see it again. Just another night in the Naked City. I felt very down.

This morning I got a call from the Santa Monica Police telling me that a good Samaritan had found my wallet and they had called the police to tell them they would like to return it. (My phone number wasn’t in it.) I was stunned. And I also felt a little bit elated. It’s been a while since something surprised me in quite this way. (That cynicism again.) So I happily took the Good Samaritan’s number and called him.

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There are reasons that politicians, media moguls, plutocrats, union leaders, news readers etc. try to keep us apart, seek to divide us. Never trust someone who only seeks to divide, who attempts to create hatred of the other. They are concerned about gaining power, not helping.

As this story tells us, and each of us have our own stories to confirm it, individual people can be extremely kind. (Not everyone but enough can be to make it meaningful.) People often just want to help other people.

The problems we have arise from the people who do not really want to help other people, who abuse the inclinations of others in order to gain power solely for themselves.

That is why it is good to remember that there are some people out there who simply do the right thing, without real need to gain power. There are more of us than we think and if we could come together, actually create one out of many, we could kick the bums out.

That is why they really try to keep us at each others throats. Not only to keep power but to prevent us from taking it away from them. Perhaps someday soon enough of us will accomplish that.

America has done it in the past so why not?

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Nice try, I guess

I swear I haven’t been drinking, Officer. It was my gut flora!:
[Via NCBI ROFL]
Endogenous ethanol ‘auto-brewery syndrome’ as a drunk-driving defence challenge.

“For various reasons, the reliability of the results of forensic alcohol analysis are often challenged by the defence. One such argument for acquittal concerns the notion that alcohol could be produced naturally in the body, hence the term ‘auto-brewery’ syndrome. Although yeasts such as Candida albicans readily produce ethanol in-vitro, whether this happens to any measurable extent in healthy ambulatory subjects is an open question. Over the years, many determinations of endogenous ethanol have been made, and in a few rare instances (Japanese subjects with very serious yeast infections) an abnormally high ethanol concentration (> 80 mg/dl) has been reported… …With reliable gas chromatographic methods of analysis, the concentrations of endogenous ethanol in peripheral venous blood of healthy individuals, as well as those suffering from various metabolic disorders (diabetes, hepatitis, cirrhosis) ranged from 0-0.08 mg/dl. These concentrations are far too low to have any forensic or medical significance. The notion that a motorist’s state of intoxication was caused by endogenously produced ethanol lacks merit.”

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I had never thought of this excuse. So the driver is really drunk because of his intestinal bacteria. Right.

Of course, the law is driving while intoxicated. It never states HOW one became intoxicated. I would think that the judge would not care whether the high alcohol level came from drinking or from bacteria. The driver is still impaired and should not be driving.

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Complex applications often require significant testing

There’s many a slip ‘twixt spit and SNP: errors in personal genomics data:
[Via Genetic Future]

train-wreck.jpgPeter Aldhous has a great piece of detective work in New Scientist, which has revealed a bizarre and sporadic glitch in the online software provided by personal genomics company deCODEme to allow customers to view their genetic data.

The glitch appears to be restricted to the display of data from the mitochondrial genome (a piece of DNA with a special fascination for genetic genealogists, since it is inherited almost exclusively along the maternal line). On several separate occasions the deCODEme browser presented Aldhous with a mitochondrial profile that was spectacularly wrong, differing from the profile in his raw data at 44 out of 93 positions.

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It looks like the software glitch may have been fixed but it required some very astute observations by a knowledgeable user. And this case was pretty obvious with so many errors present.

What would happen with errors that are more subtle? Particularly when the data may be used to make medical decisions? I figure that these things will be worked out eventually but in the meantime, there will be a very strong need to carefully vet the results from applications such as this.

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The Wild West for sequencing

Complete Genomics back in action after 6 month funding delay:
[Via Genetic Future]

Complete Genomics is finally back on the road towards fulfilling its promises of $5000 human genome sequences, after delays in obtaining funding for a massive new facility pushed back its plans by six months. The $45 million in funding it announced this week will be sufficient to build the new Silicon Valley facility, which the company claims will have the capacity to sequence a staggering 10,000 genomes over the course of 2010.

Complete Genomics is an unusual creature in the second-generation sequencing menagerie: instead of aiming to generate revenue by selling machines to researchers and biotech, Complete has an entirely service-driven business model. Basically, it aims to create a series of extremely automated sequence factories with a single input (human DNA) and a single output (an accurate and comprehensive list of all of the variants present in that sample’s genome), operating on a massive scale. All of the steps in between will be performed using in-house sequencing technology and analytical software.

It’s an audacious plan – but clearly it’s a plan with sufficient plausibility to convince investors to cough up $45 million in the middle of a major venture capital drought. If Complete can meet their ambitious goals for 2010 they stand to gain pole position in a field where the pay-offs are potentially massive, as the preferred providers of the raw genomic material for the new field of personalised medicine.

So, will it work? I spoke on the phone to Complete Genomics CEO Clifford Reid and company director Alex Barkas about their plans over the next 18 months.

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$5000 for accurate, whole genome sequences really changes the ball game. This makes it very easy to envision this process becoming very common. There are a lot of big ifs here that have to be overcome.

My worry with some of this is that we are talking about having great accuracy calling over 3 billion bases. In a commercial setting there are going to be pressures to take some short cuts . These companies will need careful vetting of their procedures and have strong quality control to assure accuracy. It would be a shame if someone makes medical decisions based on inaccurate information.

but if they can do this, we are entering a new era for human genomics.

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Not good news if you like bananas

Banana diseases hit African crops:
[Via BBC News | Science/Nature | World Edition]

Two banana diseases have hit crops in Africa, putting supplies of the staple food at risk, experts tell the BBC.

Crops are being damaged from Angola through to Uganda – including many areas where bananas are a staple food.

Experts are urging farmers to use pesticides or change to a resistant variety of banana where possible.

Scientists have been meeting in Tanzania to decide how to tackle the diseases, which are spread by insects.

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When things like this are spread by insects usually the only thing to do is massive amounts of pesticides. But these often only work for a while until pesticide-resistant varieties of insects develop. Hard to know just what will happen but it might be harder to find bananas in a few years.

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The science of editing science

words by Boa-sorte&Careca
The Index of Banned Words:
[Via The Loom]

Over the past week I held my first real class, teaching a roomful of students writing about science on Appledore Island (along with a few ornithological auditors, shown in this picture of my classroom). They put up with a relentless schedule of researching and writing and ended up with some …

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Jargon explains science. Any scientist doing their job is full of words to describe what they do.

But these words can be used to put a wall between the researcher and anyone else. Immunology almost requires an education in a foreign language, using terms not found in any other field.

This can make it very hard to write for other audiences. While using the jargon can be distancing, using the wrong word can be confusing. witness the debacle over the word theory, which has almost opposite meanings in science and in general usage.

However, many times jargon is simply used because it is jargon and makes the author feel superior to their readers. “What, you don’t know what apoptosis means? well, I do.”

So, the words Carl choses are mainly ones where clarity as accessibility are key. Many are so over used that they almost no longer have much meaning: paradigm shift, breakthrough, utilize. These are words any editor would go after because of their cliche nature.

And there are better words to use that actually impart information to the reader. As Carl recognizes with his update, again demonstrating that the Web is a conversation, one that informed him about his writing:


Update, 6/18 11:20 am: Thanks for all the conversation, both in the comments and on Twitter. It’s made me realize that I should divide my banned words into a couple categories. Some of them, like utilize, are science words that should not be allowed to escape scientific journals. But others, like breakthrough, are words that both scientists and non-scientists alike may be tempted to use like steroids, to artificially boost their writing. These words often end up being just wrong, and in some cases–like referring to a preliminary experiment in mice as a miraculous cure–they can be cruel by raising hopes in the sick that may later be dashed.

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Who are they empowering?

They kept the Asian dude but lost the Black guy. And they actually look like they obviously put a White guy’s head on top since the hands are still black!

What a bad Photoshop job. And let’s not even talk about the color scheme. MS marketing needs some real help.

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Card sharks are like scientists

poker chips by Plutor
In which Orac defends Chris Mooney and Sheril Kirshenbaum…:
[Via Respectful Insolence]

I realize that I’m possibly stepping into proverbial lion’s den with this one, but a man’s got to do what a man’s got to do. As you may recall, former ScienceBlogs bloggers Chris Mooney and Sheril Kirshenbaum (and current Discover Magazine bloggers) recently released a book called Unscientific America: How Scientific Illiteracy Threatens Our Future. As you may also recall, the arguments and assertions that Chris and Sheril made in their book ruffled more than a few feathers around ScienceBlogs, chief among them the big macher of atheism around here, P.Z. Myers, who really, really didn’t like what Chris and Sheril had to say and has spent considerable verbiage trashing them (in particular Chris) wherever they’ve appeared promoting the book and getting in flame wars with Chris, who (foolishly, in my opinion)responded in kind. It became personal. Or maybe it was personal before the book was ever released. Of course, P.Z. wasn’t the only one who really, really didn’t like what Chris and Sheril had to say; almost overnight the science blogosphere in general and the science blogosphere in general appeared to become divided along the lines of those who agreed with Chris and Sheril’s thesis and those who were really, really hostile to it.

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Yes, Orac pulls a head-fake but provides a very good dissection of how denialists just do not seem to understand how science works and appear to hold onto myths long after they have been disproven.

When the myth is a supposed fake moon walk, no one is really hurt. When it is a vaccine, many in society can pay the price.

I guess this shows that denialism of science, of reality, when it is inconvenient for one’s personal beliefs is a human trait and not a conservative/liberal one.

A scientist actually likes being wrong (because we are so often!) because it often leads to the truth about Nature much more rapidly. Eliminating the possible means the real is arrived at faster. They are reality-based.

Denialists react to being wrong by hugging their myths even closer, by creating conspiracy theories of ever increasing complexity. As each theory is shown to be incorrect, they launch theories that are harder and harder to falsify.

As Orac mentions:


Yet, as I have explained time and time again, personal experience and anecdotes are inherently misleading. As Richard P. Feynman so famously said, “The first principle is that you must not fool yourself – and you are the easiest person to fool.” That’s lesson number one in the scientific method, but those who are not steeped in doing science often find this warning hard to accept, even though the ease with which all humans–you, Ginger, and, yes, I–are fooled is the very reason science is necessary.


Humans often deal with the world by so-called ‘rules of thumb’ or
heuristcs. It is often easier and safer to follow some of these than to actually think. Unfortunately, in a complex world, some of these rules of thumb are flat out wrong because our brains did not evolve to really deal with that problem. Math is one area where many rules of thumb are incorrect and higher orders of thought and reason need to be used.

A successful lottery is based on the inability of most people to understand the math of probability. No one makes consistent money at roulette, because it is an individual against a machine, and the odds favor the machine. But one can make a living playing cards. Professional poker players make money based on the inability of most people without significant training to properly understand the odds.

Scientific training provides us with similar advantages that untrained people do not have. It helps us learn how to more accurately identify our own bias and determine real evidence, not just what we hope to find. It provides us with a process to remove ourselves from the heuristics that can mislead us. It gives us reason, not feelings, in order to understand the world around us.

Few would go up against a card shark head-to-head without a lot of practice and training in order to understand the task at hand. Because they would lose a lot of money.

But denialists do this all the time with science. It can be, in fact, a lucrative field, one where people can parlay their views into book deals, think-tank positions, etc. There really is little negative payback for people who cater to denialist thought, who feed the incorrect heuristics used by many, many people

Remember, heuristics may be based upon hardwired connections. It can be tremendously difficult to alter them without a huge, directed effort. Logic, or other higher ordered thought processes, just do now easily work.

Using a more primitive, deeper hardwired approach can. Social pressures have been know to be effective. Ridicule could be used. It has reduced the Flat Earthers to a negligible group, as well as the Moon Walk deniers.

But it is a multiple-edged sword and one that can push back in harmful ways. Spending significant time and effort providing real training for each of these individuals might be useful for some but many would rebel against what they saw as ‘brainwashing.’

Denialists may just be a part of the landscape. Their thinking may be based on hardwired processes so altering the frame could just be impossible.

As a scientist, I can only believe that continuing to provide real facts that accurately describe the real world will eventually alter things for the better. Because I know for sure that denialists will never accomplish that.

Ultimately, denial of reality is a failure heuristic. It may not be as maladaptive as before (‘There is no lion there.’) but eventually its negative aspects will cause it to fail. It just may take a long, long time.

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A great time waster

Huge Database of Pro and College Athletes Launched:
[Via ResearchBuzz]

Fanbase has announced its official launch out of beta. This site contains information on over 1.7 million athletes and over 20,000 teams across 23 sports. The site’s full URL is http://www.fanbase.com/.

From the front page you can do a team search or an athelete search. I did a search for Cubs and to my surprise got over 17,000 results, including teams, people, games, and discussions. However the team I was searching for — the Chicago Cubs — was first on the list of the results.

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Combine this with Wikipedia and a fan can find out everything about any team or player. It provides connections and links to a load more information. It is like a media guide but just for fans instead of the media.

It will be interesting to see how well it deals with fan’s comments and dialogues. It could become a great place for fans to chat. And it appears to have some real integration with social networks like Facebook.

ANd, chatting with other fans is never REALLY a waste of time, right?

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We are number one! (Updated)

Washington students top nation in SAT scores – Puget Sound Business Journal (Seattle)::
[Via ]

Washington high-school students bested the nation in SAT scores for the seventh straight year, state school officials said Tuesday.

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Seven years in a row! Yet our state spending is 42th. Now if we could only run our healthcare system as well.

[UPDATE}: Okay, I actually spent some time looking at the numbers and this was a misleading little quote. We bested the national average, not the nation. My error.

As I expected, when the actual numbers are looked at, there really is little difference between states, since the standard deviation is well over 100. So, WA has an average math score of 531 ± 104 while TX has a score of 506 ± 108. And the national average is 515 ± 116. I would be very hard-pressed to say any of those numbers are significantly different.

I have not looked though every state but I would expect that there really is no significant difference in state test scores. The averages might differ somewhat but the errors are so large that it really becomes meaningless to compare them.

As the College Board itself says:


Media and others often rank states, districts and schools on the basis of SAT scores despite repeated warnings that such rankings are invalid.


Sage words for us all.

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A harbringer of the end?

This Week’s Sci-Fi Worthy Parasite: Leishmania spp.:
[Via Observations of a Nerd]

Ah, the joys of a tropical getaway. There’s warm, clear waters, soft, sandy beaches, and of course, a whole ton of amazing parasites waiting to gorge on your delicious flesh.

Anyone who has traveled out of the US has been told horror stories of the disgusting creatures that await them. Take a nice trip to Brazil for some sightseeing, for example, and you might find yourself at the mercy of a small, intracellular protozoan parasite of the genus Leishmania.

There are many species of Leishmania living all over the world, from Saudi Arabia to Texas. No one’s entirely sure how the parasites ended up in such diverse locations, or where they originated, but wherever there are sand flies, there is Leishmania. Like many parasites, it has a fairly complicated life, full of developmental stages and alternate hosts. Here’s a good explanatory figure:

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Leishmania is a very interesting organism. It has a complex life cycle and it causes one of the world’s deadliest infectious diseases. But the really cool fact, as delineated in this post, is that it has been doing this for a long, long time:


As for science fiction-worthiness, how’s this: some suggest that Leishmania might have did in the dinosaurs. Researchers have successfully found ancient parasites in amber-preserved insects. There are even books on dino parasites.

How could these little creatures have wreaked so much havoc? Well, some argue, they were new and invasive back then, and the reptiles didn’t have the opportunity to evolve immune defenses. Massive outbreaks causing devastating population decreases and even localized extinctions could have seriously hindered dinosaur species. So it’s possible that parasitic overrun might just have contributed to the fall of the great reptiles. Of course, other factors were also in play, but perhaps the parasites gave the final blow which kept dinosaurs from adapting to changing environments.

So, maybe Leishmania is responsible for major extinction events. At least indirectly.

Well, unless they find dinosaur skins with lesions on them, this is all just conjecture. The fact that the parasite can be found in the guts of ancient insects does not mean that they were able to find safe harbor in dinosaurs. Mammals make good hosts but dinosaurs?

I’m a little skeptical.

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Par for the MSM course

sea ice by Niko Herlin
Shoddy journalism from Stephen Sackur:
[Via Deltoid]

Read this passage (from a Greenpeace news story):

A recent NASA study has shown that the ice cap is not only getting smaller, it’s getting thinner and younger. Sea ice has dramatically thinned between 2004 and 2008. Old ice (over 2 years old) takes longer to melt, and is also much harder to replace. As permanent ice decreases, we are looking at ice-free summers in the Arctic as early as 2030.

They say you can’t be too thin or too young, but this unfortunately doesn’t apply to the Arctic sea ice. Polar bears are the first to suffer from it, but many other species could be affected as well.

Is this passage about:

A: the Greenland ice sheet

or

B: Arctic sea ice

If you answered “A”, then you may be Stephen Sackur, presenter of the BBC’s HARDtalk, who, despite the repeated references to “sea ice”, decided that Greenpeace was saying that the Greenland ice sheet would melt by 2030. He then ambushed Greenpeace’s Gerd Leipold in an interview, claiming that the passage was “plainly misleading” (See Youtube video). Sackur compounded his error by only reading out one sentence from the passage: “As permanent ice decreases, we are looking at ice-free summers in the Arctic as early as 2030.”, thus not giving Leipold a chance to explain what the passage was about. Leipold agreed that Greenland wasn’t going to melt by 2030 and that if that is what the Greenpeace story had said, then it was a mistake.

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Greenpeace is not one of my favorite organizations and some of their tactics may not be the best strategically, but to take them to task over this? I hate ambushes, because the only real purpose is to make someone LOOK bad on video. There is not real attempt at informing the viewers.

It is all gotcha media, something that tabloid TV does. I’m sorry to see that the BBC is using these approaches. I guess they have to make a buck but if so, there are so many other places where I can get real information and not ‘reality TV.’

Don’t they realize they lessen their brand with crap like this? Maybe not, since they have not made any sort of correction yet.

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