More and more iPhones for us all

Verizon to push Apple’s iPhone with major ‘marketing muscle’ – report
[Via AppleInsider]

Following this week’s announcement that the iPhone is finally coming to Verizon, a new report claims that the largest wireless provider in the U.S. plans to advertise Apple’s handset heavily over competing Android phones.

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I hope that we are not inundated with so many iPhone ads as to make us sick of them. I wonder if Apple has any say in the tone of the ads?

Science does its job with regard to XMRV

wrong way by Johnny Jet

Searching for the cause of chronic fatigue syndrome: XMRV turns out to be another blind alley
[Via Field of Science Combined Feed]

Chronic fatigue syndrome (CFS) causes severe fatigue that can last for months at a time. CFS is difficult to diagnose and even more difficult to treat, and its cause has long been a mystery. In 2009, in an apparent breakthrough, scientists reported that a virus found in mice, called XMRV, might be the long-sought cause of chronic fatigue. Their results were reported, with great fanfare, by Judy Mikovits and colleagues in the journal Science (Lombardi et al., Science 2009;326:585), with reports in respected outlets such as the New York Times making it seem that the answer had been found.

Now it turns out that, like many initially exciting reports, this one has a much more mundane explanation: contamination.
As happens all too often when a “surprising” discovery is announced, the result turns out to be an experimental error. Contamination is a common type of error in modern molecular genetics, because nothing is actually visible to the naked eye, and we have to rely on very sensitive methods (such as PCR) to detect what is present. In this case, the experimenters had a common mouse cell line in their lab (not unusual), and it turns out these mouse cells were contaminated with a virus called MLV, which looks a lot like XMRV.
The new study by Hue et al. from University College London (Retrovirology 2010, 7:111) is titled “Disease-associated XMRV sequences are consistent with laboratory contamination.” The title pretty much tells the story, but here’s a brief synopsis.
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The first report that a retrovirus might be the cause of Chronic Fatigue Syndrome came out about a year and a half ago. But very quickly came conflicting reports that the retrovirus was not involved.

Now comes what appears to be the definitive answer – the supposedly specific tags used to identify the retrovirus actually cross reacted with another similar virus. And this other virus was found to contaminate cells in the labs doing the work.

The original paper presented some data that they interpreted as signifying that XMRV could be a cause of disease. Others then went out to verify this and showed that the original interpretation was wrong.

This is how science works. The thing that Feynman talked about was that scientists need to be aware of how easily they can be fooled and to strive to make sure that all controls have been done.

Here, we have a case of a lab that did not seem to fully perform this self-examination. They should have been the ones to find the contamination, rather than have others do it.

But whether done by the original scientists or by others, science works towards finding out what is really happening.

Now if only the media would realize the tentative nature of most science.

Got the OS X updates done

And I am clicking the Mac App Store Icon Now.

Wow, opened quite fast. And I saw that Delicious Library 2 was on the store so I clicked it. And am told it is already installed. Cool.

And I am downloading Pixelmator now. My evening is shot.

Problems in higher science education

photosynthesis by epSos.de

College upperclassmen still fail at scientific reasoning
[Via Ars Technica]

Most of us develop a sort of intuitive logic about how the natural world works. Unfortunately, a lot of that informal reasoning turns out to be wrong, which complicates scientific education. But as students make their way through the science education pipeline, they should gradually start moving beyond the informal reasoning of their earlier years. Or at least that’s what we’d like to think; instead, a new survey of college students, some in advanced biology classes, indicates that most end up with a confused mix of formal and informal reasoning.

The clearest example of the chasm between a typical intuition and scientific reasoning comes from the world of physics. Imagine a marble rolling around a curved track that comes to a sudden end. Physics tells us that, as soon as the marble is off the track, it’ll continue moving in a straight line until it runs into something else. But many people use informal reasoning and conclude that the marble will continue to follow a circular path even after it escapes the track. In other contexts, it involves an interventionist view of the world. As the people behind the survey put it, “When using informal reasoning, students look for ‘actors’ that drive ‘events’ and are aided by ‘enablers.'”

Scientific education, then, needs to convince people to move past their intuitions (at least if they want a more accurate picture of how the world operates).

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The article is not out yet apparently (January BioScience is not there yet. Only December.) The write ups seem to indicate even students quizzed in their specialties have ‘intuitive’ answers that are wrong.

This follows up on some of their previous work that indicated that incoming students had serious problems with what they ‘knew’ versus what was real.

I think science education requires a different approach to pedagogy than other fields. In other areas, our intuitive, heuristic approaches to things serve us well. But in science, even educated people can become fooled, especially when not thinking logically, rationally and deeply.

A fun example can be found in the comments regarding one of the questions:

Maple Mass

A mature maple tree can have a mass of 1 ton or more (dry biomass, after removing the water), yet it starts from a seed that weighs less than 1 gram. Which of the following processes contributes the most to this huge increase in biomass? Circle the correct answer.
A) absorption of mineral substances from the soil via the roots
B) absorption of organic substances from the soil via the roots
C) incorporation of CO2 gas from the atmosphere into molecules by green leaves
D) incorporation of H2O from the soil into molecules by green leaves
E) absorption of solar radiation into the leaf

Now, these questions are given to people who have had classes in botany or biology and so are well versed in the principles involved, if they have learned to think scientifically.

There was a discussion about the ambiguity of answers C and E. Several commenters though E would be a right answer, since without photosynthesis, there could be no growth. But E does not mention photosynthesis. It simply mentions absorption of solar radiation. There are many processes of absorption, such as thermal, that have nothing to do with photosynthesis. And even photosynthesis uses just a small amount of the total radiation.

E only ‘seems’ like a right answer if you take it to mean photosynthesis. But that ‘intuitive’ answer requires a leap to conclusions. Photosynthesis is not explicitly mentioned. Trying to use it for an answer is a leap not based on real data. Those that answer this question were guilty of making a leap to a conclusion that is not supported by the data provided– a very common error in non-scientific thinking.

Then there was a discussion about C and D. Someone found that photosynthesis performs the following reaction:

Hmm, unless the Wikipedia article on photosynthesis is wrong (6CO2 + 6H2O -> photosynthesis -> C6H12O6 + 6O2), it seems to me that the students are right to suggest that most of a tree’s mass is brought up from the soil (in the form of water). Six atoms of oxygen plus twelve of hydrogen definitely out-mass six atoms of carbon.

Or am I missing something?

There ensued some discussion about the atomic weights of carbon dioxide and water in order to determine whether the water from the soil is more responsible for the biomass or the carbon dioxide from the air. This is a much more productive and scientific discussion, one that actually really occurred in the scientific examination of photosynthesis and biomass.

Looking at the mass equation – which is greatly simplified but useful for discussion – one sees that oxygen is released at the end. Where does the oxygen come from – the carbon dioxide or the water? Even Wikipedia tells us – the released oxygen comes from the water. The only mass water contributes is its hydrogens.

This is one of the key discoveries regarding the process of photosynthesis. Anyone learning about this should remember that bit of data. I remembered this and the last class I took on photosynthesis was 30 years ago.

Biology students should remember this. Water is simply used as an electron donor. Other molecules can substitute for water in photochemical reactions using carbon dioxide.

And the experiments that were designed to show this is true – work that any student should have been taught – demonstrate wonderfully how the scientific method works and the underlying principles for discovery. How do we determine where the oxygen comes from? We use radioactively labeled oxygen in the carbon dioxide or in the water. When the radioactive oxygen is in the carbon dioxide, radioactivity stays in the plant. When the radioactive oxygen is in the water, radioactivity is released into the surround air.

So, to anyone who is taking science courses in biology and who is learning to think in a ‘scientific’ way should have been able to answer the question properly. The largest portion of the biomass comes from the incorporation of both carbon and oxygen from carbon dioxide.

Unfortunately, very few students were able to think these questions through in a way that brought their scientific reasoning to bear. They simply answered with what seemed like the best answer – the ‘obvious’ one, the ‘intuitive’ one – without engaging the parts of the brains most important for scientific thinking. They made a leap to the conclusion without fully analyzing the data provided.

Or they did look at the data provided but forgot the data they had learned and were unable to combine them in a way to discern whether C or D was most correct.

Thus the need to do better with scientific education. Scientific thinking require a rigor and attention to the systems details that is very different from the sorts of thinking we do to live our daily lives. Now we need to do a better job achieving that.

Eventually the truth catches up with denialists

barnum by FontShop

: BMJ calls Andrew Wakefield a fraud

[Via Bad Astronomy]

This is HUGE: The BMJ, an online medical journal, has accused Andrew Wakefield — the hero of the modern antivaccination movement — of being “a fraud”.

The skeptic and medical community have been hammering Wakefield for years; his study linking vaccines and autism was shaky from the start, and he suffered a series of humiliating defeats last year: the Lancet medical journal withdrew his paper, he was struck off the UK General Medical Council’s register, and was found to have acted unethically.

Of course, the word “fraud” implies intent; when writing about Wakefield I had my suspicions, but always wrote as if he were just wrong, and not deliberately lying to vulnerable parents.

But deliberate fraud is what he’s now accused of. Brian Deer, an investigative journalist, has written a multi-part series on the BMJ site which slams Wakefield. Fiona Godlee, BMJ’s editor-in-chief, also writes about this… and just to be clear, she uses the word “fraud” nine times in her editorial. Not surprisingly, it’s been picked up by several news outlets like CNN, MSNBC, and ABC.

Deer has been on Wakefield’s case a long time, and has been critical in exposing Wakefield’s shenanigans. Wakefield and the antivaxxers have attacked Deer many times, but their accusations are as hollow as the claims of links of autism to vaccinations. And let’s be clear: vaccines don’t cause autism.

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The anti-vaccine movement gained a lot of momentum from Wakefield work, now described as fraudulent. How much money was wasted on work trying to debunk his unethical work? He received over $600,000 by lawyers for producing these results.

But I expect him to still make quite a bit of money off of the anti-vaccine movement. I guess Barnum was correct.


Tablets, phones and computers live in a complex ecosystem now

CES: Analysts grow skeptical of iPad competitors due to iTunes
[Via AppleInsider]

Two analysts monitoring the tablet extravaganza at CES have issued reports indicating that euphoria about new tablets outside of Apple’s iPad may fall short of expectations because those products lack the iPad’s extensive App Store software library and access to the wide range of media in the “digital ecosystem” of iTunes.



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Apple has created a single ecosystem that can support devices from phones to tablets to laptops to desktops. There are app stores for each, with developers able to write to each. No other tablet manufacturer has anything similar. Nor a phone maker. Nor a PC maker.

This is the added bonus to what Apple has created. If some great new app is developed for an iPhone, it can easily be moved to every other type of mobile device as well as laptops with minimal effort. We cab play Angry Birds on iPods, iPhones, iPads and Macs.

No other ‘environment’ can accomplish this.

Someone else discusses Microsoft’s difficulties

steve ballmer by Microsoft Sweden

Microsoft’s tablet could take years, stirring doubts about Windows tablets beating out Apple’s iPad
[Via MacDailyNews]

“Instead of unveiling an elegant response to the iPad, Microsoft came to the tech industry’s premier gadget show with a collection of exposed computer guts,” Jessica Mintz reports for The Associated Press.

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And they weren’t very nice about it either. As I mentioned earlier, MS is doing great in the gaming world. Not so well elsewhere. This analyst does not seem impressed by the virtual demo of a tablet which may still be years away. Their phone strategy is a mess and the duopoly of Wintel may be at an end.

But here is why a lot of analysts are pretty stinging int heir criticisms:

Mintz continues, “It’s hard for anyone to applaud Microsoft without noting the threats posed by the growing popularity of Apple Inc.’s iPad. It’s also hard to see Windows as a tablet contender amid an onslaught of new tablets running Google Inc.’s Android software… Those concerns have been weighing on Microsoft stock, which has hovered around the $20 to $30 range for the past decade. Apple, on the other hand, has seen its share price more than triple since the first iPhone was announced in early 2007. Last year, Apple’s market capitalization surpassed Microsoft’s, making Apple the second-largest U.S. public company after Exxon Mobil Corp.”

It always comes down to stock price. Since 2007, MS is down almost 3% and Apple is up 255%. Since Ballmer took over in 2000, MS stock has lost half its value while Apple’s has gone up 10-fold.

I wonder who they will get to replace him, as if that would really make any difference.

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