Our pests tell us about our history, by advanced data mining

lice by otisarchives4

Lice DNA Reveals When Humans First Clothed Their Nakedness
[Via Discover Magazine | RSS]

Putting on clothing to protect our woefully hair-deficient bodies is one of the key moments in the history of becoming human. Just when our species took this step, however, is open to a fair amount of guesswork—scientists can’t exactly dig up fossilized parkas and trousers. But what scientists can do is determine roughly when two species diverged, and that has made all the difference: Using the lice that have traveled with people for thousands of years, a team has tracked the time that humans first became dedicated followers of fashion—perhaps as long as 170,000 years ago.

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Very nice work (and you can look at the whole paper) based on a cool idea – when did head lice and body lice diverge. Since body lice require clothing for survival, this might give us some information regarding when we started to use clothing.

The dates have a large range, between 83,000 and 170,000 years ago, probably due to the fact that only four genes were looked at. This fits very well into the need for Ice Age protection and also with the Out of Africa time line.

But the really cool thing is that this work was done by using what was already in public databases. That means that actually anyone could have done a similar analysis. Of course, you would have to know the ‘right’ way to do this and be comfortable throwing around phrases like “Bayesian coalescent modeling approach” but even the programs they used for analysis were ones available for use.

They very smartly used databases to mine for information based on a hypothesis they had. No new experiments were needed.

So, in one sense, this work could have been done by anyone from home. It requires insight and deep understanding and maybe access to the right programs but it is not something that would require a huge research grant and lots of expensive equipment.

Of course, I would expect that if you had been doing this work based on a PC at home, you’s still be watching it run the Markov simulations. You might be able to do this at home but having access to fast computers is a large plus.

And now, we need to have the genomes of each species completely sequenced in order to narrow down the time range. We have done that for the body louse. It has the smallest genome of any insect – only 108 million bases pairs of DNA (for comparison, the human genome has about 3 billion base pairs). Let’s get the head louse – and perhaps the pubic ouse for good measure.

When denialists try to do math

bolt by James Bowe

Andrew Bolt vs percentages
[Via Deltoid]

Andrew Bolt may have the worst case of confirmation bias ever seen. To Bolt, whether something is true or not has nothing to do with its accuracy and everything to do with whether it suits him or not. Here in it’s entirety

If the evidence were so strong, there’d be no need for such untruths

Dennis Ambler checks the statistics behind recently claims that 97 per cent of climate scientists believe man is heating the planet and finds evidence of some exaggeration:

However a headline of “0.73% of climate scientists think that humans are affecting the climate” doesn’t quite have the same ring as 97% does it?

Er, no.

He’s referring to Doran and Zimmerman’s survey of 3146 Earth Scientists. The graph below shows their results for this question:

Do you think human activity is a significant contributing factor in changing mean global temperatures?

DoranAndZimmerman2009.png

So what’s Ambler’s argument that proves that the 97% is really 0.73%?

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Now I recognize that many scientists may not do well with some types of math – proper statistics is one area. But most would be able to properly figure out the correct percentages.

Especially if one were going to publicly display one’s work.

As one commenter stated, using Bolt’s argument since only 2 of the climatologists out of 10,157 don’t think humans are causing climate change, the percentage of denialists is 0.019%.

No matter how you calculate it, even by Bolt’s twisted logic, the data show that about 38 times as many climatologists say humans are involved as say humans are not involved. That’s a lot.

If I was making the point that few scientists disagree with AGW and that the more they know, the more certain they are, then the graph demonstrates I am correct. These numbers certainly do not support the argument that there is much dissent in the ranks of climatologists, or even of most scientists.

And even Bolt’s misguided attempt to redo the numbers does not hold up to any sort of examination. At least by anyone who can do division and think rationally.

How do we regain civility in our discousre?

To Regain Civility in American Politics, We Need to Rethink Media, Education, and How We Participate
[Via Big Think]

Whether it is climate change, immigration, or income inequality, America seems incapable of making progress on solving complex problems. In fact, it seems that the country is locked in a downward cycle of incivility and polarization. In an interview I did last year with Big Think, I discussed three specific areas where institutional changes can occur that could increase active public participation on what seem to be eternally gridlocked issues.

[More]

Well worth watching. Better idea dissemination, doing a better job with education and better participatory processes would go a long way.

Of course, perhaps higher employment levels would do so also.

Makes me wonder about Facebook

Iceland Officials Ask US To Explain Why It’s Trying To Get Lawmaker’s Twitter Info
[Via Techdirt]

On Friday, we noted that US officials had sent a court order (not a subpoena, apparently) to Twitter, asking for info from a few accounts that had some association with Wikileaks, including that of Icelandic lawmaker Birgitta Jonsdottir. Apparently, Icelandic officials are not too happy about this. They’ve asked the US ambassador to Iceland to explain the reasoning for this:

“(It is) very serious that a foreign state, the United States, demands such personal information of an Icelandic person, an elected official,” Interior Minister Ogmundur Jonasson told Icelandic broadcaster RUV.

“This is even more serious when put (in) perspective and concerns freedom of speech and people’s freedom in general,” he added.

Of course, we might not find out what was said until Wikileaks (or some other operation) leaks a new batch of State Department cables a few years down the road…

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We only know about this because Twitter pushed back against the court order and publicized it. I wonder if Facebook received such an order and just followed it without letting its users know?

The Mistakes The Government Made In Trying To Get Info From Twitter

The Mistakes The Government Made In Trying To Get Info From Twitter
[Via Techdirt]

Over the last month or so, we spent a lot of time going over the huge number of mistakes that the US government made in seizing a variety of domain names, supposedly for copyright infringement. Now, with the government seeking all sorts of info to build their legal case against Julian Assange and Wikileaks, it’s time to look at the mistakes the government is making there as well. Following up on the news that came out late last week of the government seeking info from Twitter, Christopher Soghoian has done a nice job highlighting some of the details and problems with the court order, some of which seem reminiscent of the problems with the domain seizures — meaning technical and legal errors, and a filing prepared by a rather surprisingly inexperienced government representative.

The 2703(d) order misspelled the names of one of the targets, Rop Gonggrijp. It also requested credit card and bank account numbers of several Twitter users, even though Twitter is a free service and so doesn’t have such information (presumably someone at DOJ knows a little about Twitter, since the agency has 350,000 followers of its official Twitter account).

The Department of Justice prosecutor named in the order, Tracy Doherty-McCormick, was prosecuting online child exploitation cases just five months before the Twitter order was issued. Given that the wikileaks investigation is the most high-profile national security investigation of the decade, and that the court order seeks records associated with an Icelandic member of parliament, you would think that DOJ would assign this case to someone more senior.

He also notes that the government must realize that three of the individuals named are computer security experts who probably used pretty strong encryption, so it’s unlikely this info will turn up much. Soghoian also points out the oddity of using this process to try to get info, as it would seem that there are much more reasonable ways that the government could request and get the same info.

I do wonder how much of these errors and sloppiness are due to basic rushing to try to get stuff done, or due to incompetence. Perhaps the government knows that it will get these kinds of things approved almost no matter what, so it doesn’t even try.

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Perhaps there is another reason. Perhaps it is all pro forma and they really aren’t trying very hard.

No. More likely incompetence. But the scary thing is that these sorts of mistakes in legal documents apparently happens all the time.

I’ve learned my lesson

I made the mistake of writing a post yesterday on a controversial subject while watching a football game. So I may not have been as clear as I would have hoped. Mea culpa. I hope I am clearer today.

I have friends who have Chronic Fatigue Syndrome and I know about the problems trying to get the medical community to even recognize it as a real disease and not a mental illness. That is why I was quite excited by the original report when it came out. It seemed like a very nice model to help explain the disease, as well as possibly implicate a retrovirus in other diseases.

However, subsequent work has muddied the waters and, in my opinion, weakened this model. The recent paper I talked about yesterday seems to provide strong, definitive evidence that contamination is a real problem. This along with the inability of other labs to replicate the work, appears to substantially weaken the model.

All this indicates is that the situation is quite complex – something we all knew anyway. Also, that much more and careful work will have to be done. It is as easy to get too positive about a model and fall in love with it. Researchers and others do this all the time.

And it is easy to be too negative about a model and hate it. Researchers and others do this all the time also. Perhaps I let my initial excitement turn too far to disappointment. I don’t think so but I am human. Perhaps that bled a little over yesterday. Damn football!

What I was trying to state yesterday was that the recent paper did its job – helping us understand why some of the results show XMRV and other results do not. They have now presented a model suggesting that cross-reacting PCR primers could give PCR artifacts from a contaminating virus.

If XMRV is actually involved, then researchers will to take the current results into consideration.

That is what I meant by science doing its job. The new report pretty definitively examined the problem of contamination and demonstrated that previous work may not have properly controlled the correct variables. Others will respond. This is the back and forth of cutting edge research where we have little understanding of all the things going on. I am sure this is not the end of the road.

We will get to the bottom of this. It may be XMRV. It might be another unknown gamma retrovirus. It might be something else entirely. When science does its job right, we eventually discover what it is. Feynman was right when he said that Nature always wins in the end, no matter what we want to believe.

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