[Via Dot Earth]
Al Gore’s new book finds the core of the climate challenge, and solutions, in the human brain.
[More]
I bought the book and have started reading it. Revkin provides a nice viewpoint but the comments are full of people who are spouting the same drivel that has been shown to be either wrong or misleading.
But it does appear that there are a lot more who agree with Gore’s perspective. Perhaps some day soon we will make some real progress.
Open Source Science? Or Distributed Science?:
[Via Common Knowledge]
I was asked in an interview recently about “open source science” and it got me thinking about the ways that, in the “open” communities of practice, we frequently over-simplify the realities of how software like GNU/Linux actually came to be. Open Source refers to a software worldview. It’s about software development, not a universal truth that can be easily exported. And it’s well worth unpacking the worldview to understand it, and then to look at the realities of open source software as they map – or more frequently do not map – to science.
The foundations of open source software are relatively easy to track. In the beginning, there was free software and Richard Stallman. RMS didn’t just invent the GPL as a legal, he wrote crucial foundational software for writing software, notably the GNU compiler collection, GNU Debugger, and the original Emacs. So from the beginning, there was not only a free legal tool, but tools for coding that were better than other systems at the time.
Simultaneously, we can see that the emergence of microcomputers and ubiquitous access to the internet expanded the number (and interconnectivity) of potential programmers. Suddenly there were tens of thousands of programmers with computers at home and at work. The explosion of the Web saw the creation of infrastructure like code repositories, version control systems, and coding communities. Thanks to object-orientation, software was also very amenable to being broken into defined, modular chunks and tasks. One coder could work on a kernel function, another on a user interface function, a third on an application, and they could be reasonably sure that as long as they all followed the standards, their work would snap together into the growing distribution. The phrase “open source” can sort of be a shorthand for this kind of innovation, which we also see in wikipedia and other community built projects.
Open source, if we view it through a different lens, is really more about a distributed methodology for software development. The burden of creation is widely distributed across a massive community with more-or-less equal access to tools and systems. In this context, the role of the legal tool is more akin to an enzyme. It was an essential piece of a puzzle, but it was not the only piece. In fact, without the rest of the infrastructure (connectivity, tools, and people) the legal tool on its own would not have led us to GNU/Linux.
[More]
A really nice discussion of the differences between Open Source approaches in high tech and the need for Distributed Sources in science. There have been an lot of overlap in the development of new high tech tools and those seen in biotech.
Open source has its place but the idea of making a network deal with the needs of science is something that needs to be given careful thought. But it should be possible.
After all, the Web was created at CERN to deal with distributed science.
The Hidden Economic Carnage in Science and Education
[Via The Scholarly Kitchen]
Economic statistics don’t measure science or training well. Our fields are being hurt inordinately, but the damage isn’t being measured. What will it mean long-term?
[More]
Anyone who thinks things are getting better needs to read this. Because it is often the best trained, most intelligent ones who are being forced to leave. We are beginning to provide much fewer rationales for people to spend so much time becoming well trained and very educated.
Especially if those people are let go because their expertise costs too much money. We already treat airline pilots as bus drivers with some working at regional carriers making $22,000 a year, the poverty line for a family of four.
Because our current system does do really want to pay for expertise.
I love the last paragraphs:
So, the next time you hear that perhaps the recession is lifting, that halcyon days are on the horizon, remember that the numbers being used for those rosy projections are based on items that are easy to measure, slower to grow, of decreasing value, and not vital for future growth.
This could be a lesson in how intangibles become tangible, I’m afraid.
It will be a long time before employment levels are back up to what they were, especially for those with the most training.
by dog ma
The Sea Change That’s Challenging Biology’s Central Dogma
[Via Discover Magazine | RSS]
For decades, RNA was seen as a simple slave to DNA. Newer research shows it has an active and critical role in every disease from Alzheimer’s to cancer.
[More]
This is a great story about how a small group of focussed people working on a seemingly obscure problem can sometimes provide incredible insight. The author provides some really great insight into the path the research took, including the fact that the researcher who first published on this work, who was one of the key instrumental scientists involved, did not initially get tenure.
His work was viewed as too obscure.
The article does an excellent job of portraying these researchers as flesh and blood humans, rather than Promethean geniuses or lone wolfs.
The only thing a little off is that this work’s challenge to the Central Dogma (i.e. DNA to RNA to Protein) is a little more subtle than simply overturning it. It is more like the effect of Relativity on Newtonian mechanics.
It provides a more sophisticated explanation while leaving much of the framework intact.
In the Central Dogma, proteins are the really important things. They determine just what a cell does. DNA is simply the memory and RNA the transmitter. But proteins are the key.
The big challenge this work provides, where it does some real overturning of paradigms, are to some of the hypotheses regarding so-called junk DNA. Many people have had a feeling that this supposedly unused DNA might actually have a use. It has just been hard to figure out what it is. Now we have an idea of what some of it does.
It is there for a reason.
And what it does is really important. One area where the Central Dogma is influential is with the idea of genomic sequencing as an insight into disease. ‘If we want to know what the protein sequence is, we can look at the DNA sequence.’
However, it is really hard to determine the sequence of a protein, while it is easy to get DNA sequences. So genomic sequencing has been a surrogate for having protein sequences. The Dogma suggests that there is a one-to-one mapping of DNA sequence and protein sequence. With some small exceptions, this remains true.
This makes sense since mutations in DNA often produce alterations in proteins. A change in quality of one is seen in a change in the quality of the other. So we have been hearing a lot about getting everyone’s DNA sequenced. Then we will know what diseases they are likely to be susceptible to. At least in a simple world.
This is a leftover of the Central Dogma’s proposal that changes in proteins are reflected in changes in DNA sequences. But I have already discussed how epigenetic factors (here, here, here, here, here ) can break this relationship, producing different disease states without changing the genetic sequences.
Proteins are still important. But simply knowing what their sequence is – indirectly from DNA – does not describe fully the complex nature of a cell. More than just protein sequence is used to determine what a cell does.
The work on microRNA demonstrates that simply knowing a person’s genomic sequences does not tell the whole story. These RNAs are critical for controlling the amount of different proteins found in each cell.
And the quantity may be just as important as the quality.
Along with epigenesis, microRNAs show us that disease can be caused by the wrong amount of a protein.
So, the dogma of DNA to RNA to Protein is still present. Things are just a little more complex. What a cell does is not just determined by the quality of protein, its sequence that then determines its structure and activity.
It is also determined by the quantity of the protein. Some cells may have a protein that can prevent disease. But if microRNAs prevent it from being produced, then we have disease. Knowing the DNA sequence might not really help us much in this case.
Having too much or too little of a particular protein in a specific cell may well be the cause for many of the diseases we see today. Sometimes it will be because the protein itself is ‘wrong’ and sometimes it will be because the amount of protein present is wrong.
Knowing the genomic sequence of a person will be really important and useful to have. But it will be critical to know how much protein is produced. Knowing how microRNAs work will be critical for understanding this.
by Hey Paul
Can a GOP walkout really stop the climate bill?
[Via Congress Matters]
No.
I’m posting from the road, on my phone, so this won’t be as comprehensive and link-rich as it should be, but here goes.
It’s been pointed out that there’s a rule in the Senate Environment and Public Works Committee that requires the presence of two minority side Senators for a markup to go forward. But like most such rules, it’s probably not “self-executing,” meaning that in order for it to have an effect, someone needs to show up to point out that there aren’t the requisite number of minority Senators in attendance. A majority side Senator could certainly do that, but why? The job of protecting minority rights belongs chiefly to the minority. Let them do it. And when they do, you politely point out that if you’re present enough to object, then you’re present enough to count towards a quorum.
Now, this particular rule requires two minority Senators, not just one. That sounds like a rule designed by someone who had been burned by the one-Senator rule before. So technically, one Republican can show up, point out that there aren’t two, and try to invoke the rule. And if that happens, what can the chair do about it?
Well, one way around it is the way the Judiciary Committee traditionally deals with a similar rule. They ignore it.
Another would be to bypass the formal use of the committee entirely, and use Rule XIV to move the bill to the floor when they’re ready. That is, Chairwoman Boxer could convene a meeting of anyone who’s on the committee and who wants to participate in the process, and in effect simply ask them, “If this were a committee markup, what amendments would you offer, and how would you vote on them?” Then she could alter her draft bill accordingly, and either try to move it to the floor under Rule XIV, pass the resulting document on to the next committee of jurisdiction for its consideration, or set it aside for whatever future merger process the leadership may have planned for it.
[More]
I wrote about this the other day.The Republican members of the committee were going to vanish, making it impossible to continue because 2 minority members were required for markup to continue.
But it requires someone to be present to ‘notice’ that the minority members are absent. If no one ‘notices’ then things are fine. What an perfectly diabolic way to get around a rule.
And then if someone from the GOP does show up to ‘notice’ well, the majority just says that this is not a real committee meeting. “We just happened to get together to talk about the bill. Want to join us?”
Parliamentary procedure at its best!
