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.

I dug out the name and story

I mentioned in the post the other day about California loyalty oaths that I remembered reading about someone who was able to get around it. Many professors had fought this loyalty oath since 1949 when the Regents imposed it. Even graduate students had to sign this oath.

I’m not sure if this is the one I remember but one was James Endres Howell , a molecular biologists at Berkeley. He explains the story here. As he states, it is hard to take it ‘freely’ when it is a condition of employment and could result in termination if not taken.

Another biologist discusses his run-in with he oath here. He got around the oath by finding a novel route to fund his graduate work.

And, you have to sign a new oath if you are re-employed after one year. It is like in that one year, you went and became disloyal but now retaking the oath will turn you loyal again.

The ironic thing is that to actually support and defend the Constitution would also mean fighting against the use of loyalty oaths as a requirement for employment. We fought a Revolution and created the Constitution partly so that Americans did not have to prove their loyalty to the State.

I just wonder what in the world they expect to do with someone who really is disloyal but signs the oath? What determines disloyalty? Has anyone ever been sent to prison for signing this oath and then being found disloyal? Would you get into trouble if you said “I think the 14th Amendment is garbage and needs to be changed?”

Do they really think that a real Communist infiltrator is going to see this oath and simply turn around? The only people this oath seems to trap are people of real conviction about its meaning, like Quakers.

Now if more courts just made sane rulings

Court Says It’s Okay To Secretly Record Conversation If Done For Legitimate Reasons
[Via Techdirt]

While there have been a lot of concerns lately about efforts to misuse “wiretapping” laws that forbid any recordings of people without their knowledge, it appears at least a few courts are recognizing how silly that is. Yet another court has now said that secretly recording a conversation — in this case with an iPhone — is okay, assuming there was no crime committed with the recording, and the recording was for a legitimate purpose. As the court noted:

“The defendant must have the intent to use the illicit recording to commit a tort of crime beyond the act of recording itself.”

That makes sense. The act of recording alone, shouldn’t be a criminal act, as it really depends on what is being done with the recording. And, in an age where not only is recording everything easier, but for some becoming standard, requiring permission to record all audio seems like an outdated concept.

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Making a recording should not be a crime. Doing something unlawful with it should be. But if you have a legitimate purpose, it should be okay.

It is trivial now to use an iHone or iPad to record a business meeting. Under some states, anyone at the meeting could get the DA to charge the owner of the mobile device with a felony, resulting in large prison sentence. All for recording a meeting instead of taking hand notes.

Perhaps the courts will eventually catch up.

Using the iPad to help victims of Gulf Oil Spill

by southerntabitha

Apple’s revolutionary iPad assists poison control for BP oil spill victims
[Via MacDailyNews]

“The director of the Louisiana Poison Center is using an iPad to help manage patients poisoned by the BP oil spill in the Gulf of Mexico,” Mitch Wagner reports for Computerworld.

“Mark Ryan, director of the Louisiana Poison Center, uses the $29.99 LogMeIn Ignition application on the iPad to log in remotely to his office PC, so he can use the center’s data collection application to coordinate planning with the U.S. Health Department,” Wagner reports. “The Poison Center forwards every report of oil-related poisoning to the Health Department, to help coordinate reacting to geographic clusters, and get early warning of emerging trends.”

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Sometimes government employees can use new technology to speed things along. Here a state employee forwards information on to a Federal department, forwarding the report to the Feds within 15 minutes.

Using his 3G iPad, he can log into his desk from anywhere and download the information, using a $30 app called LogMein Ignition. ANd his eyes are doing so much better using the iPad rather than his iPhone.

See, the government can help, especially when Apple devices are used.

Wow, what a day

So I spent most of today getting my son a nice bed and all the little things that make living in a group house so much fun.

Then I get back to the hotel and find out that this post on study groups that I posted at 10 PM last night has one of my highest 24 hour hit counts.

I can see why for-profit sites want to discuss anything about Apple – the more controversial the better– if their hit rates increase like that.

One of those things

by rizobreaker

California’s Loyalty Oath
[Via Big Think]

I just had to sign a loyalty oath as a condition of my employment at a California state university. The California constitution requires all state employees to sign the oath. And I frankly find it offensive.

It’s not that I have any reservations about bearing “true faith and allegiance to the Constitution of the United States and the Constitution of the United States of America” or supporting and defending them “against all enemies, foreign and domestic”—although as a lecturer in a freshman class I won’t exactly be called upon to defend the state against its enemies or execute its laws. But I love my country and its Constitution as much as anyone. It’s rather that I object to being required to prove my loyalty to state simply to teach a class. I feel the same way about the Pledge of Allegiance—do children really need to swear not betray their country every morning before school starts? Is treason really a big problem among elementary school children?

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One of the things to remind you that California is not just a place of wild-eyed hippies but also has a strong legacy of red-baiting that still lingers today. You can get fired for not signing the loyalty oath in California, although I do remember reading about someone who was big enough to get away with it. The average professor does not have that option.

Study groups in the cloud using an iPad – the way of the future for textbooks?

by thms.nl

Former Apple employee’s Inkling adapts bestselling college textbooks for Apple’s revolutionary iPad
[Via MacDailyNews]

“Maybe the iPad will move digital college textbooks out of theory and into practice,” Jeffrey A. Trachtenberg reports for The Wall Street Journal. “Although electronic book sales have exploded, digital college textbooks have been slow to get off the ground, in part because of high prices and hardware concerns. Now, a former Apple Inc. employee, Matt Mac Innis, is trying to shake up the market with a new approach that taps into the iPad’s strengths.”

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Textbooks are going to change rapidly and if the major publishers do not get on top of the wave quickly, it will crash over them. Putting multimedia content on an iPad is so obvious that someone will figure out how to do it right.

Perhaps Inkling has. Because if you watch the video at their site you find out something the WSJ article missed that will make Inkling a big deal.

About halfway through, they show a student bringing up a note on a page and asking a question. Then all their friends also using the textbook see a little thumbnail of him on the same page he put his question. They can then tap and see what his question is and answer it.

Study groups in the cloud!! No longer to you have to be in the same room at the same time with others in the class for a recitation session or to ask others questions about areas you do not understand. Now, asking questions can just happen and relevant people from your social network can help you answer it.

Turning your notebook into a social tool is a great idea and could change how learning is done at a University. If this plays out, schools will be giving iPads to their students already preloaded with important stuff linking them to incipient social networks for any entering Freshman – bookstore, library, etc. Textbooks can be purchased and downloaded to the iPad without having to stand in ine at the boostore.

I hope so – upgrade for iPhone 3G performance coming

Steve Jobs email: iOS 4 update to address performance issues on iPhone 3G ‘coming soon’
[Via MacDailyNews]

“A new email from Apple CEO Steve Jobs appears to confirm that the company will soon be issuing a software update to address issues with the iPhone 3G’s performance under iOS 4. Late last month, the company acknowledged that it was “looking into” user reports of the issue,” Eric Slivka reports for MacRumors.

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I have not upgraded my iPhone 3G because of the performance issues. If this takes care of some of them, I’m on board.

Traveling

I spent most of today helping my son move into the house he is sharing with 5 friends at college. Long drive across the state. And he has a ton of things he needs to get but that is the fun of having your own place, even if you share it with 5 others.

So, I’ll spend a little time catching up and write some in a little bit.

Come and join in

We are having quite a nice discussion in the comments of the post about Republican Muslims if you would like to join in.

Nooooo!!

Customers Warm to Coffee Shops That Ban Wi-Fi Access
[Via Age of Engagement | Big Think]

More signs of a shift in society towards time and space that is unplugged: Cafes are attracting customers by banning Wi-Fi access. “People come here because we don’t offer it. They know they can get their work done and not get distracted,” Los Angeles cafe owner Dan Drozdenko tells the blog Where the Locals Eat.

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Why would I go to a coffee shop if I simply wanted to sit?

I go to coffee shops to get work done, work that often requires an internet connection. Am I going to be forced into WarDiving to find my wifi connections? Will free Wifi only be found at dingy little parlors found on the bad side of the tracks while the upscale people, who all have offices of their own to access the Internet, get the nice places?

Truthfully, I often sit in a cafe drinking something with no wifi for hours. I have had 2 hour discussions with people in a cafe. Nobody tries to run me out because I am preventing the table from being turned over. Why only stopwatch police for laptops?

How about this – use congestion charging. WiFi is free when the place is empty. When occupancy reaches a threshold, charge for the Wifi. SImply give people 5 minutes to complete there work and make the WiFi password protected. To get the password, buy a drink.

Best of both worlds. Then I will not have to get work done in some rat-invested dump with barred windows.

I will have to be very, very careful reading this article

by inju

Vanity Fair’s Broken Washington: A Few Solutions
[Via Age of Engagement | Big Think]

Todd Purdum has a feature in Vanity Fair this month that is so rich with insight, color, and analysis regarding the communication challenges facing the Obama administration that I immediately plugged the article into my graduate course syllabus for the semester.

“The sheer growth of the federal government, the paralysis of Congress, the systemic corruption brought on by lobbying, the trivialization of the ‘news’ by the media, the willful disregard for facts and truth, these forces have made today’s Washington a depressing and dysfunctional place,” writes Purdum in the subscription protected article. “They have shaped and at times hobbled the presidency itself.”

Purdum describes what’s historically different today about Washington even in comparison to the Clinton era. He relates the loss of civil discourse, the structural dysfunction of redistricting that enables House members to be ever more hyper-partisan, and the roadblock of the filibuster. He also focuses on the loss of bi-partisan socializing among Congressional members, as Republicans sleep in their offices rather than maintain a home and social ties in Washington, DC , avoiding the risk of being “polluted” by the Capital’s “cozy culture.” And of course, there is the ever stronger influence and financial might of lobbyists.

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I agree with everything said in the second paragraph. Every clause is correct.

At least to what I already think. I will have to be very careful reading it, then, to make sure it is not a case of confirmation bias. It will have to have some facts that really do demonstrate that there is a quantitative difference in discourse today in Washington than before and that the media is really a big cause of the problem, rather than simply an effect.

I will have take some time reading the article and digesting it. What? It is behind a pay wall and can not be accessed. Of course, I forgot it is being published by the same media that it is railing against. While it may be correct – it is a logical fallacy to belive someone’s job description means that they can not possibly be correct – it does serve as a reminder that contemplating one’s navel like this is part of the media.

What would be important is not just ‘recognizing’ there is a problem but to also suggest pathways to: 1) verify that the model is correct , and 2) find solutions.

Mimicking ALS

by Monica’s Dad

Study Says Brain Trauma Can Mimic A.L.S.
[Via NYT > Health]

A study suggests that head trauma can cause degenerative diseases similar to A.L.S. and that Lou Gehrig may not have had Lou Gehrig’s disease.

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I have written about Dr.McKee’s work before. Concussions can have lifelong effects on some people. It appears that the brain reacts to the trauma by depositing some proteins in cells in the brain that eventually result in a degenerative brain disease, one that may mimic Lou Gehrig’s Disease according to her recent paper. The brain is affected throughout, even into the brain stem.

This paper, entitled TDP-43 Proteinopathy and Motor Neuron Disease in Chronic Traumatic Encephalopathy, is freely available – I love Open Access. She looked at 12 people that had developed a neural disease called chronic traumatic encephalopathy (CTE). The hallmark of this disease is a lot of a protein called tau deposited in the brain.

In 10 of the 12 people they also found a preponderance of another protein, called TDP-43. Three of the cases were former athletes who had been diagnosed with ALS. Examination showed that they probably did not suffer from ALS but from CTE, suggesting that many patients diagnosed with ALS might be suffering a different disease, one with a different disease course.

It may be that many cases of sporadic ALS, in contrast to familial, are due to traumatic brain injury. That is, it may be that CTE and sporadic ALS are the same thing. In fact, a lot of people diagnosed with ALS had a traumatic head injury within 10 years of onset. And onset happens later in these cases.

Reading about all the severe concussions Gehrig sustained – being knocked unconscious for over 5 minutes and then playing the next day, for example – really suggests that his disease may not have been ALS.

I expect that because of the severe head traumas seen with the current military actions in the world, that we will be seeing a lot more of this disease.