http://initforthegold.blogspot.com/2010/10/mashey-gem.html
http://www.realclimate.org/index.php/archives/2009/02/on-replication/langswitch_lang/in/
People are making an error common to those comparing science to commercial software engineering.
Research: *insight* is the primary product.
Commercial software development: the *software* is the product.
Of course, sometimes a piece of research software becomes so useful that it gets turned into a commercial product, and then the rules change.
===
It is fairly likely that any “advanced version control system” people use has an early ancestor or at least inspiration in PWB/UNIX Source Code Control System (1974-), which was developed by Marc Rochkind (next office) and Alan Glasser (my office-mate) with a lot of kibitzing from me and a few others.
Likewise, much of modern software engineering’s practice of using high-level scripting languages for software process automation has a 1975 root in PWB/UNIX.
It was worth a lot of money in Bell labs to pay good computer scientists to build tools like this, because we had to:
- build mission-critical systems
- support multiple versions in the field at multiple sites
- regenerate specific configurations, sometimes with site-specific patches
- run huge sets of automated tests, often with elaborate test harnesses, database loads, etc.
This is more akin to doing missile-control or avionics software, although those are somewhat worse, given that “system crash” means “crash”. However, having the US telephone system “down”, in whole or in part, was not viewed with favor either.
We (in our case, a tools department of about 30 people within a software organization of about 1000) were supporting software product engineers, not researchers. The resulting *software* was the product, and errors could of course damage databases in ways that weren’t immediately obvious, but could cause $Ms worth of direct costs.
It is easier these days, because many useful tools are widely available, whereas we had to invent many of them as we went along.
By late 1970s, most Bell Labs software product developers used such tools.
But, Bell Labs researchers? Certainly no the physicists/ chemists, etc, an usually not computing research (home of Ritchie & Thompson). That’s because people knew the difference between R & D and had decent perspective on where money should be spent and where not.
The original UNIX research guys did a terrific job making their code available [but "use at your own risk"], but they’d never add the overhead of running a large software engineering development shop. If they got a bunch of extra budget, they would *not* have spent it on people to do a lot of configuration management, they would have hired a few more PhDs to do research, and they’d have been right.
The original UNIX guys had their own priorities, and would respond far less politely than Gavin does to outsiders crashing in telling them how to do things, and their track record was good enough to let them do that, just as GISS’s is. They did listen to moderate numbers of people who convinced them that we understood what they were doing, and could actually contribute to progress.
Had some Executive Director in another division proposed to them that he send a horde of new hires over to check through every line of code in UNIX and ask them questions … that ED would have faced some hard questions from the BTL President shortly thereafter for having lost his mind.
As I’ve said before, if people want GISS to do more, help get them more budget … but I suspect they’d make the same decisions our researchers did, and spend the money the same way, and they’d likely be right. Having rummaged a bit on GISS’s website, and looked at some code, I’d say they do pretty well for an R group.
Finally, for all of those who think random “auditing” is doing useful science, one really, really should read Chris Mooney’s “The Republican War on Science”, especially Chapter 8 ‘Wine, Jazz, and “Data Quality”‘, i.e., Jim Tozzi, the Data Quality Act, and “paralysis-by-analysis.”
When you don’t like what science says, this shows how you can slow scientists down by demanding utter perfection. Likewise, you *could* insist there never be another release of UNIX, Linux, MacOS, or Windows until *every* bug is fixed, and the code thoroughly reviewed by hordes of people with one programming course.
Note the distinction between normal scientific processes (with builtin skepticism), and the deliberate efforts to waste scientists’ time as much as possible if one fears the likely results. Cigarette companies were early leaders at this, but others learned to do it as well.
Wednesday, October 28, 2020
Monday, October 26, 2020
Breakthrough Narrative and Time Machines, and Carbon Eating Trees
http://thingsbreak.wordpress.com/2010/10/26/stop-the-presses-climate-journos-think-the-emissions-reduction-issue-looks-an-awful-lot-like-a-narrative-problem-no-word-yet-on-just-how-nail-shaped-people-wielding-hammers-see-it/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+ThingsBreak+(The+Way+Things+Break)
Wow. Not to put too fine a point on it: """
Did I mention that this New Narrative meme is being pushed by the same people who are arguing against any sort of meaningful emissions pricing? They wouldn’t have a vested interested in framing emissions legislation as a dead, would they?
...
It’s nice that you have a meme. It’s nice that some journalists bit. When you feel like getting around to actually hooking some grassroots support, give us a reason to support your Narrative besides an appeal to novelty.
"""
This Breakthrough meme is exactly like a call for more time-machine funding. The only reason they are pushing for stratospheric saline geysers and carbon-eating mega-trees is that they would seem more plausible to the uninformed than a time-machine. Their plausibility is the foremost attraction, their actual viability is a far distant concern -- and that is morally noxious.
Wow. Not to put too fine a point on it: """
Did I mention that this New Narrative meme is being pushed by the same people who are arguing against any sort of meaningful emissions pricing? They wouldn’t have a vested interested in framing emissions legislation as a dead, would they?
...
It’s nice that you have a meme. It’s nice that some journalists bit. When you feel like getting around to actually hooking some grassroots support, give us a reason to support your Narrative besides an appeal to novelty.
"""
This Breakthrough meme is exactly like a call for more time-machine funding. The only reason they are pushing for stratospheric saline geysers and carbon-eating mega-trees is that they would seem more plausible to the uninformed than a time-machine. Their plausibility is the foremost attraction, their actual viability is a far distant concern -- and that is morally noxious.
Wednesday, October 7, 2020
Education: "Waiting for Superman", Union Busting, and Obscuring the role of Parental Responsiblity
http://www.democracynow.org/2010/10/1/waiting_for_superman_critics_say_much
I agree that the teachers' union get hit with cheap shots in the school debate. I agree that the teachers' union is full of professionals dedicated to providing excellent education in the "really existing" world, and the construction of alternative scenarios (maybe fanciful) for education that blink the teachers' union out of existence has less to do with delivering quality education in the real world and have more to do with crude union busting.
But it silly to pretend that there is no conflict whatsoever between the education needs of the students and the political convenience of the teachers' union. Those are two distinct entities, and they have different political needs. For example: the mechanism that prevents capricious termination of union employees is in conflict with the discretion a school principal would wish to assert to fire a lacking teacher to replace with a potentially better suited teacher. For example: the mechanism that prevents threat of pay reduction being used to punish a union employee is in conflict with the discretion a school principal would want be able to better compensate superior teachers working from a constrained budget for teacher compensation.
The key point as I see it: the *existence* of teaching as a professional discipline is obscuring the primary role of *the responsibility of parents* for America's education of children. The parents are all too happy to shed responsibility, and push the responsibility to teaching professionals. If parents appropriately shouldered the responsibility for the quality of education of children, the primary role of teaching professionals would diminish, plainly.
Taking responsibility does not necessarily mean home schooling. It DOES mean attending PTA meetings and supervising children's homework every school night and being aware of trends of grades and children's enthusiasm or frustration in coursework -- parents taking every and all opportunity to take a full role in their children's education, paid for in *time*. If that time is then not available for television and amusement or if that time is then not available for working to support a certain level of consumerism, so be it.
In America, teaching professionals take the primary role, for praise and for blame, fair and unfair, because of the sloughing off of responsibility by America's parents.
I agree that the teachers' union get hit with cheap shots in the school debate. I agree that the teachers' union is full of professionals dedicated to providing excellent education in the "really existing" world, and the construction of alternative scenarios (maybe fanciful) for education that blink the teachers' union out of existence has less to do with delivering quality education in the real world and have more to do with crude union busting.
But it silly to pretend that there is no conflict whatsoever between the education needs of the students and the political convenience of the teachers' union. Those are two distinct entities, and they have different political needs. For example: the mechanism that prevents capricious termination of union employees is in conflict with the discretion a school principal would wish to assert to fire a lacking teacher to replace with a potentially better suited teacher. For example: the mechanism that prevents threat of pay reduction being used to punish a union employee is in conflict with the discretion a school principal would want be able to better compensate superior teachers working from a constrained budget for teacher compensation.
The key point as I see it: the *existence* of teaching as a professional discipline is obscuring the primary role of *the responsibility of parents* for America's education of children. The parents are all too happy to shed responsibility, and push the responsibility to teaching professionals. If parents appropriately shouldered the responsibility for the quality of education of children, the primary role of teaching professionals would diminish, plainly.
Taking responsibility does not necessarily mean home schooling. It DOES mean attending PTA meetings and supervising children's homework every school night and being aware of trends of grades and children's enthusiasm or frustration in coursework -- parents taking every and all opportunity to take a full role in their children's education, paid for in *time*. If that time is then not available for television and amusement or if that time is then not available for working to support a certain level of consumerism, so be it.
In America, teaching professionals take the primary role, for praise and for blame, fair and unfair, because of the sloughing off of responsibility by America's parents.
Monday, October 5, 2020
race on the brain
http://www.stat.columbia.edu/~cook/movabletype/archives/2010/10/racism.html
I would much rather deal with racists than people who have "race on the brain".
I am not interested in searching the world for people free of racism, because it is hard to imagine people who *really* don't allow race to inform *any* judgement whatsoever. I have met some children and adults who I would guess come very close, but so very very few to make the effort not worthwhile.
So I would much rather deal with racists, because, honestly, I must judge myself a racist.
I *do* have a problem with people who have "race on the brain" -- when the topic of race comes up they are reduced to blithering idiocy and vile reactionary tribalism. White males haven't cornered the market on this particular form of idiocy -- it is embarrassing when Latino candidates win office on nothing more than their publicized ethnicity (such as the insubstantial Los Angeles mayor Antonio Villaraigosa, aka Tony Villar).
Political correctness makes physical and verbal violence against traditionally disadvantaged groups less likely, and that is good, but it cannot do much to lesson "race on the brain" on both sides of the racial divide. Only the self-imposed discipline of critical thinking can do that, and people get too much pleasure from their vile reactionary tribalism to self constrain their thought.
I would much rather deal with racists than people who have "race on the brain".
I am not interested in searching the world for people free of racism, because it is hard to imagine people who *really* don't allow race to inform *any* judgement whatsoever. I have met some children and adults who I would guess come very close, but so very very few to make the effort not worthwhile.
So I would much rather deal with racists, because, honestly, I must judge myself a racist.
I *do* have a problem with people who have "race on the brain" -- when the topic of race comes up they are reduced to blithering idiocy and vile reactionary tribalism. White males haven't cornered the market on this particular form of idiocy -- it is embarrassing when Latino candidates win office on nothing more than their publicized ethnicity (such as the insubstantial Los Angeles mayor Antonio Villaraigosa, aka Tony Villar).
Political correctness makes physical and verbal violence against traditionally disadvantaged groups less likely, and that is good, but it cannot do much to lesson "race on the brain" on both sides of the racial divide. Only the self-imposed discipline of critical thinking can do that, and people get too much pleasure from their vile reactionary tribalism to self constrain their thought.
Wednesday, April 15, 2020
good summary gelman philosophy of Bayesian statistics
Bayesian statistical pragmatism
Thank you for writing this. This is the clearest and quite comprehensive (even though short and to the point) support for your philosophical views, and I am inclined to agree on all counts.
I read Gelman and Shalizi 2010, and enjoyed it a lot, what my novice brain could understand. But the summary above hits and handles all the difficulties, and is easy to read.
I would recommend people read Gelman and Shalizi 2010 "Philosophy and the practice of Bayesian statistics" [ http://www.stat.columbia.edu/~gelman/research/unpublished/philosophy.pdf ] for the section on Mayo's "severe" testing of models, Section 4 "Model checking" - the only lack of the summary above that I can see.
Tuesday, April 14, 2020
size of genome
[Part 1 of 2]
Forgive my ignorance, but I am trying to make sense of different descriptions of the human genome, and different descriptions of the information needed to fully specify a large mammal, like a man.
You talk about 3.5 Gb for the genome, and, giving Ray Kurzweil the benefit of the doubt, 50 million bytes after loss-less compression.
If someone made extravagant claims about a computer program that runs on some unknown hardware and unknown OS, I would be unamused if they handed me a thumb-drive containing the compressed binary executable, and nothing more. This single file would demonstrate nothing.
I would demand the original source code, the specification for the code (including the business decisions the code is meant to automate, at the very least), some documentation demonstrating that I can move back and forth between points in the specification and the source code lines encoding that part of the specification, and the code for the automated tests (so an automated test can demonstrate what changes to the code will still keep it within specification, at the very least).
And maybe the same for some of the libraries and hardware - maybe needing the full specification if the libraries, OS, and hardware if they all are very novel, quite unlike any I have worked with before.
So there would be a dramatic explosion of information needed, moving from the binary executable to a bare minimum specification of a computer program as defined above.
Forgive my ignorance, but I am trying to make sense of different descriptions of the human genome, and different descriptions of the information needed to fully specify a large mammal, like a man.
You talk about 3.5 Gb for the genome, and, giving Ray Kurzweil the benefit of the doubt, 50 million bytes after loss-less compression.
If someone made extravagant claims about a computer program that runs on some unknown hardware and unknown OS, I would be unamused if they handed me a thumb-drive containing the compressed binary executable, and nothing more. This single file would demonstrate nothing.
I would demand the original source code, the specification for the code (including the business decisions the code is meant to automate, at the very least), some documentation demonstrating that I can move back and forth between points in the specification and the source code lines encoding that part of the specification, and the code for the automated tests (so an automated test can demonstrate what changes to the code will still keep it within specification, at the very least).
And maybe the same for some of the libraries and hardware - maybe needing the full specification if the libraries, OS, and hardware if they all are very novel, quite unlike any I have worked with before.
So there would be a dramatic explosion of information needed, moving from the binary executable to a bare minimum specification of a computer program as defined above.
[Part 2 of 2]
In the debate between PZ and Kurzweil, PZ makes this point:
http://scienceblogs.com/pharyngula/2010/08/ray_kurzweil_does_not_understa.php
"""
Let me give you a few specific examples of just how wrong Kurzweil's calculations are. Here are a few proteins that I plucked at random from the NIH database; all play a role in the human brain.
First up is RHEB (Ras Homolog Enriched in Brain). It's a small protein, only 184 amino acids, which Kurzweil pretends can be reduced to about 12 bytes of code in his simulation. Here's the short description.
MTOR (FRAP1; 601231) integrates protein translation with cellular nutrient status and growth signals through its participation in 2 biochemically and functionally distinct protein complexes, MTORC1 and MTORC2. MTORC1 is sensitive to rapamycin and signals downstream to activate protein translation, whereas MTORC2 is resistant to rapamycin and signals upstream to activate AKT (see 164730). The GTPase RHEB is a proximal activator of MTORC1 and translation initiation. It has the opposite effect on MTORC2, producing inhibition of the upstream AKT pathway (Mavrakis et al., 2008).
Got that? You can't understand RHEB until you understand how it interacts with three other proteins, and how it fits into a complex regulatory pathway.
"""
I am inclined to grant PZ the point, and say his understanding of the immensity of the task outstrips Kurzweil's understanding.
Would the explosion of information needed to move from the complete genome to the complete specification of a large mammal be on the same order of the explosion of information needed to move from the binary executable to a bare minimum specification of a computer program as defined above? Did I capture the gist of it, or am I hopelessly mistaken?
In the debate between PZ and Kurzweil, PZ makes this point:
http://scienceblogs.com/pharyngula/2010/08/ray_kurzweil_does_not_understa.php
"""
Let me give you a few specific examples of just how wrong Kurzweil's calculations are. Here are a few proteins that I plucked at random from the NIH database; all play a role in the human brain.
First up is RHEB (Ras Homolog Enriched in Brain). It's a small protein, only 184 amino acids, which Kurzweil pretends can be reduced to about 12 bytes of code in his simulation. Here's the short description.
MTOR (FRAP1; 601231) integrates protein translation with cellular nutrient status and growth signals through its participation in 2 biochemically and functionally distinct protein complexes, MTORC1 and MTORC2. MTORC1 is sensitive to rapamycin and signals downstream to activate protein translation, whereas MTORC2 is resistant to rapamycin and signals upstream to activate AKT (see 164730). The GTPase RHEB is a proximal activator of MTORC1 and translation initiation. It has the opposite effect on MTORC2, producing inhibition of the upstream AKT pathway (Mavrakis et al., 2008).
Got that? You can't understand RHEB until you understand how it interacts with three other proteins, and how it fits into a complex regulatory pathway.
"""
I am inclined to grant PZ the point, and say his understanding of the immensity of the task outstrips Kurzweil's understanding.
Would the explosion of information needed to move from the complete genome to the complete specification of a large mammal be on the same order of the explosion of information needed to move from the binary executable to a bare minimum specification of a computer program as defined above? Did I capture the gist of it, or am I hopelessly mistaken?
Wednesday, March 21, 2012
Monday, February 27, 2012
Nice sarcastic invite for blog comments
Image via WikipediaWhile reading Reddit Politics, I spotted this comment pointing out the solicitation for comments on the site "The Big Picture":http://www.reddit.com/r/politics/comments/ftpis/president_of_fox_news_will_be_indictedmaybe_even/c1ijv3p
The Big Picture - http://www.ritholtz.com/blog/
"Please use the comments to demonstrate your own ignorance, unfamiliarity with empirical data, ability to repeat discredited memes, and lack of respect for scientific knowledge. Also, be sure to create straw men and argue against things I have neither said nor even implied. Any irrelevancies you can mention will also be appreciated. Lastly, kindly forgo all civility in your discourse . . . you are, after all, anonymous."
Friday, March 4, 2011
The importance of stupidity in scientific research
Image via WikipediaFrom a comment toHere's Feynman on the 'terrible uncomfortable feeling called confusion'. And here's a great little paper on 'the importance of stupidity in scientific research' - "actively seek out new opportunities to feel stupid."
The importance of stupidity in scientific research
Excerpt:
I recently saw an old friend for the first time in many years. We had been Ph.D. students at the same time, both studying science, although in different areas. She later dropped out of graduate school, went to Harvard Law School and is now a senior lawyer for a major environmental organization. At some point, the conversation turned to why she had left graduate school. To my utter astonishment, she said it was because it made her feel stupid. After a couple of years of feeling stupid every day, she was ready to do something else.
I had thought of her as one of the brightest people I knew and her subsequent career supports that view. What she said bothered me. I kept thinking about it; sometime the next day, it hit me. Science makes me feel stupid too. It's just that I've gotten used to it. So used to it, in fact, that I actively seek out new opportunities to feel stupid. I wouldn't know what to do without that feeling. I even think it's supposed to be this way. Let me explain.
For almost all of us, one of the reasons that we liked science in high school and college is that we were good at it. That can't be the only reason – fascination with understanding the physical world and an emotional need to discover new things has to enter into it too. But high-school and college science means taking courses, and doing well in courses means getting the right answers on tests. If you know those answers, you do well and get to feel smart.
A Ph.D., in which you have to do a research project, is a whole different thing. For me, it was a daunting task. How could I possibly frame the questions that would lead to significant discoveries; design and interpret an experiment so that the conclusions were absolutely convincing; foresee difficulties and see ways around them, or, failing that, solve them when they occurred? My Ph.D. project was somewhat interdisciplinary and, for a while, whenever I ran into a problem, I pestered the faculty in my department who were experts in the various disciplines that I needed. I remember the day when Henry Taube (who won the Nobel Prize two years later) told me he didn't know how to solve the problem I was having in his area. I was a third-year graduate student and I figured that Taube knew about 1000 times more than I did (conservative estimate). If he didn't have the answer, nobody did.
That's when it hit me: nobody did. That's why it was a research problem. And being my research problem, it was up to me to solve. Once I faced that fact, I solved the problem in a couple of days. (It wasn't really very hard; I just had to try a few things.) The crucial lesson was that the scope of things I didn't know wasn't merely vast; it was, for all practical purposes, infinite. That realization, instead of being discouraging, was liberating. If our ignorance is infinite, the only possible course of action is to muddle through as best we can.
Monday, January 3, 2011
Links on Rational Discussion
Image via WikipediaCurrently, I see that Rationality is all about a very high standard for yourself and for your allies. Worrying about the standard of rationality of enemies and opponents should be a very small part. There is a finite amount of energy, and that energy is best used to keep the self from deluding the self with comfortable ideas.
It is interesting that nobody wants to be seen as irrational, but very few happy assume the burden of a very high standard for rationality for their own thoughts.
John Wilkins - Evolving Thoughts - A Code of Conduct for Effective Rational Discussion
- The Fallibility Principle
- The Truth-Seeking Principle
- The Clarity Principle
- The Burden of Proof Principle
- The Principle of Charity
- The Relevance Principle
- The Acceptability Principle
- The Sufficiency Principle
- The Rebuttal Principle
- The Resolution Principle
- The Suspension of Judgement Principle
- The Reconsideration Principle
- Fleck’s Addendum
- The next tack in Climate Disruption denialism - Scientists must be Nihilists
- The difference between Skeptics and Deniers
- Shifting between the genial general and the hard-nosed specific as a form of the "Shell and Pea game" - A juicy example of The Art of Controversy
- Uncertainty is not an argument for the status quo
Subscribe to:
Posts (Atom)