Wonderful science writing

NYT et al: Rumors of a gene’s death have been greatly exaggerated
[Via Knight Science Journalism Tracker]

It was always a good bet that all the so-called junk DNA in our genomes wasn’t nonfunctional trash. Gradually functions are being found for some of it. Now comes word, via Science Online, that a form of muscular dystrophy is caused by a supposedly dead gene in the junk mutating into an active form.

It causes progressive weakening of muscles in the forearms, shoulders and face. It is a dominant trait with a 50-50 chance of being inherited by children of those with the disease. It afflicts about 1 in 20,000 people.

From the new finding, we now know that the gene that causes it is in all our genomes but normally disabled by the lack of something known as a poly (A) tail. This is a stretch of repeated adenine bases needed for any gene’s messenger RNA to get out of the nucleus and be translated into a protein. In this case, the defunct gene somehow has reacquired the ability to have the “tail” attached to its messenger RNA.

It’s a fascinating discovery, and the New York Times put Gina Kolata’s very good story on A1. She backs into the news, much as this post does, writing of fossil genes that “rise from the dead like zombies.” The Boston Globe picked up her story but rewrote the top with a straight lede that gets right to naming the disease in question. Over at Vanity Fair’s Web site, Alexandria Symonds needlessly whips up anxiety with a lede that says the finding is “something new and terrifying to worry about.” Symonds appears to have done no reporting herself, relying purely on Kolata’s story.

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Kolata’s article provides some nice insight into the work. Science has so many great stories and it is nice to see some good writers using them. The idea that ‘dead’ genes could become reactivated is a compelling one.

Life and disease are so magically complicated, yet so wonderfully simple. Understanding the simple cause of a disease explains so many complex ramifications.

Of course, science, while often generating simplicity, always seems to generate more complex questions. This disease is only seen in people with less than 10 repeated copies of the gene and where some copies have become active.

What was the original purpose of the gene to begin with? At one time there must have been only one copy and it was active. What did it do and why has it become something deleterious unless inactivated?

I imagine some fun research will go into figuring it all out.

But let’s talk about the mosque instead

A climate change tipping point: Plant growth, once boosted by warming and increased CO2, may now be declining
[Via Knight Science Journalism Tracker]

Satellite measurements of plant productivity in 2003. Green shows increased productivity, red decreased. (NASA)

Global climate change, as many have observed, is a story that does not break; it oozes. Yet in today’s Science comes a climate change story that does, in a sense, break. To wit: the increased plant productivity caused by warming temperature, increased carbon dioxide and shifting rainfall pattterns has run out and the curve has reversed slope. Whereas plant productivity–the amount of atmospheric carbon taken up by plants–increased by about 6 percent during the 1980s and ’90s, it has since fallen by about 1 percent.

The implications for food production are obvious. If the small decline grows and population increases, malnutrition and outright starvation are likely to get worse.

And yet, as of mid-day on Friday, hardly any news organizations had picked up the story. The only major U.S. source to have it was AP’s Randolph E. Schmid. International Business Times in the UK also has a story by Balasubramanyam Seshan.

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Plant productivity is down due to climate change and no one notices because few in the media discuss it. A search of Google News for “plant productivity” yields about 1100 hits the past week. “Ground Zero Mosque” yielded about 13,000 hits over the last week in News. There are as many news stories discussing “Obama is a muslim” – those exact words in that order appear in the text as discuss this Science article, whose abstract ends with this:

A continued decline in NPP [net plant productivity] would not only weaken the terrestrial carbon sink, but it would also intensify future competition between food demand and proposed biofuel production.

Nice scientific way of saying famine and energy needs may be severely impacted worldwide.

Ten times more media attention on the Internet for a prayer room in a community center in New York city than for a sign of possible famine worldwide. As much attention on the idiotic discussion of the President’s religion.

Managed ignorance seems to be pretty rampant. Who does that really benefit?

It is the innovator’s dilemma

Going Hollywood
[Via In the Pipeline]

A reader at one of the big pharma companies sends along this note: . . .Over my 10 years or so of experience, I have seen a severe decline in risk tolerance at my company, and other large companies as…

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The Innovator’s Dilemma, written by Clayton Christensen, mentions the real problem – to a small company, $50 million is the jackpot. To a large one, it is an afterthought. Where do you think smart people will really have to bring forth their best creativity: for the jackpot or for the afterthought?

What happens as companies get successful and expand? The laws of large numbers means that they have to have greater and greater blockbusters just to stay level.

Real creativity in a large company costs billions, which is why they are so risk averse. Real creativity in a small company costs thousands.

The problem is that it is really hard for large companies to act like small ones. Their size means that there is a lot of overhead so the base costs are already large. Getting rid of all of that removes any advantage that they have.

Avatar may have cost $300 million to make but that $300 million supported thousands of people, providing them with a well-paying livelihood and some stability. No small independent could have done that.

Independents are important; they provide an important niche for some people. But they really do not provide the stability that larger companies can nor the sheer number of jobs.

There is a place for large companies. What needs to happen is to find ways to lessen some of the costs. That is, Avatar would have simply cost billions to do a few years ago. Technology greatly reduced the costs.

Big Pharma simply must find ways to lessen some costs by perhaps coming up with some more creative business models – perhaps moving much of its creative risks such as drug development, off to smaller independents that it creates while it maintains the huge advantage in production and marketing that it maintains.

I expect one or more will figure out a way since I think that is the only way they will survive. Me too blockbusters will be harder and harder to find.

Another example of how science works

by DaveFayram

Setting the record straight
[Via Genomes Unzipped]

The current issue of Cell has some important correspondence in response to an essay published by Jon McClellan and Mary Claire King in April. Daniel covered the original piece and hosted a guest post from Kai Wang which detailed some of the more obvious flaws in their argument. Now, Wang and his colleagues from Philadelphia have published an official response in Cell, in parallel with a similar letter from Robert Klein and colleagues from New York. Accompanying these is a further reply from McClellan and King. Read on for an overview of three contentious statements made in the original piece, and the rebuttals to each.

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A paper comes out that has some controversial conclusions. Other scientists examine the paper, uncover data that provide alternative explanations and write their own paper. A huge amount of very human arguing about things goes on, each trying to disprove the other.

Eventually, controversy dies down because the data that were generated along the way cause one idea to fall away.

This current controversy – what genome wide sequencing can really tell us about disease – is mainly if interest to relevant scientists but even bystanders can follow what is happening because of blogging scientists. And interested bystanders can comment and ask questions about the process.

In particular, examine the comment by Stephen, where he makes the point that summarizing someone else’s viewpoints often uses simplifications that alter the original views. The response by the blogger was to not only agree but to locate and print the views that most closely matched the summaries.

Now everyone has a better idea of what is being said and being discussed.

And perhaps gain some understanding of how science works.

When cynical world views meet cynical politics

I [Heart] Ankh-Morpork New Yorkers
[Via Balloon Juice]

FSM bless the cynical inhabitants of the city of my birth, who know that every political scandal is just a question of who’s gunning for which benefits. The gated-community HOA fiefdoms and small-town Baptist baronies of Heartland America™ may pose atop their whited sepulchres, but the teeming hordes of the metropolis are forever at war with the propriety of convenient public memory, or the lack thereof. Frank Rich indulges himself on the topic of “How Fox Betrayed Petraeus”:

So virulent is the Islamophobic hysteria of the neocon and Fox News right — abetted by the useful idiocy of the Anti-Defamation League, Harry Reid and other cowed Democrats — that it has also rendered Gen. David Petraeus’s last-ditch counterinsurgency strategy for fighting the war inoperative. How do you win Muslim hearts and minds in Kandahar when you are calling Muslims every filthy name in the book in New York?
[...]

Their sudden concern for ground zero is suspect to those of us who actually live in New York. All but 12 Republicans in the House voted against health benefits for 9/11 responders just last month. Though many of these ground-zero watchdogs partied at the 2004 G.O.P. convention in New York exploiting 9/11, none of them protested that a fellow Republican, the former New York governor George Pataki, so bollixed up the management of the World Trade Center site that nine years on it still lacks any finished buildings, let alone a permanent memorial.

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The dueling demonstrations today in New York should be interesting.

Of course, how come none of the rhetoric from pundits, politicians etc. to gin up emotional responses is actually directed to the spot where most of us might have some real interest – Ground Zero. We are almost 9 years past 9/11 and there is no discussion about the memorial that will be open in just a year or so..

The most controversial memorial in the US – the Vietnam Veterans Memorial – was completed only 3 years after the idea was developed.

The winning design for the memorial was chosen in 2004. Yet here we are 6 years on and still some time from completion. And no real national discussion about this.

I expect that next year at this time, there will be some sort of ginned up controversy about the memorial – some noises are already being heard but the politicians and pundits are not really engaged yet. They will be by next year.

Will it be a museum or a shrine?” asks David Simpson, a professor at the University of California-Davis who wrote 9/11: The Culture of Commemoration. “Sometimes you have to wait 20 or 30 years to tell a story. It’s not a great time for an open discussion of 9/11.”

If we have a hard time having an open discussion about a community center being built blocks from Ground Zero by the ‘wrong’ folks, what sort of discussion will we have about the site itself.

I wish all the energy swirling around a business development project blocks away from Ground Zero had been used to actually do something that would have real meaning for all of us. Instead, politicians and pundits play word games to divide us. I expect they will do so next year also.

Now who does that serve? Who wins win Americans are divided? Certainly not Americans.

Oh No. We are like Europe.

by Olof S

EU-US convergence ?
[Via Crooked Timber]

The NYT ran yet another round in the long-running EU vs US series a week or so ago. Although it’s not covered explicitly in the NYT, there is actually some news to report here, in addition to rehearsal of the same old themes.

For quite some time, the US and the leading EU countries have been fairly comparable in terms of output per hour worked. The US has had higher output per person for two reasons: a relatively high employment/population ratio and very high average hours worked per person. The first of these is important because it raises the possibility that EU countries performing well on productivity measures are benefiting from the “Thatcher effect” . If low-skilled workers are excluded from employment, for example by restrictive macro policy, as in Thatcher’s case, or by labor market sclerosis, as claimed by critics of European institutions, then productivity measures are artificially boosted.

This issue is now moot. As a result of the crisis, the US employment/population ratio has dropped sharply, to the point where the US is now little different from the EU. The difference in GDP per person between the US and leading European countries is driven primarily by differences in average hours worked by employed people.

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Things have changed a lot recently between Europe and the US. The differences between GDP of the US and major European countries has historically been due to higher employment, productivity and hours worked.

Now data shows that almost all the difference in GDP can be found in hours worked. And that difference is within the error bars of the data, making it no real error at all.

Not the best thing to base the superiority of our economy on. We work more hours in the day is just not the same as saying we get more done in an hour than you or our economy is so strong we hire more people than you.

Another way this current economic mode has humbled us. There is now less separating our economy from Europe’s.