Is Bioinformatics--and Open-Source Software--in ABI[base ']s Future? [GenomeWeb]

ABI is on the right track. It could become the world leader if it can make software that scientists really understand. The problem is not just making it easier for scientists to find information; they must be able to disperse it also. No one person can know what fact could have an explosive effect on another's thought patterns. We publish papers with this hope (Well, it does help our own careers a little ;-). Putting one of my ideas into the hands of someone who can take it even further is really appealing. Technology not only makes this more likely, but it also allows us the ability to verify how the information passed, making it progressively easier to allow more information to flow. I may just have to give Lee a call.  11:13:28 PM    

Molecular machine could develop drugs for bioweapons victims [EurekAlert!]

I am getting to where I trust no press release if it mentions bioweapons or bioterrorism. It has nothing to do with why this work was originated and is simply a post hoc attempt to hype the work. NOw, a complete structure of the ribosome is nince, although there have been pretty good glimpses published before. It is an amazing effort. It would have been nice to see if there are any novel developments in how it works, etc. I guess I'll have to figure out a way to read the article.  11:07:05 PM    

Scientists discover genetic defect responsible for microcephaly [EurekAlert!]

A very nice study. Using a small, non-outbred group like the Amish, they have found a single gene defect that has a devastaing effect on the development of the fetal brain. And, it appears that all the families affected descend from a single Amish couple. The lack of gene flow in the Amish, as in other small, isolated populations, makes finding these mutations easier, simply becuase they are more likely to be seen. What is nice about this study is that everything originated from doctors that wanted to help families deal with this mutation. If they had not leapt in to help, there might be a large number of Amish families dealing with tragedy. Nice work.  11:02:37 PM    

U.S.-Russian team announces breakthrough in fight against tuberculosis [EurekAlert!]

Not a very in-depth release but it is always nice to add a new weapon to the arsenal agaist this very tough disease.  10:55:57 PM    

Wasting intellectual effort through bad knowledge management.

K. Eric Drexler, in the lucid 1987 article Hypertext Publishing and the Evolution of Knowledge, illustrates familiar patterns of communication problems in science through the history of the rise and fall of the (fictitious) square-wheel research program. Most of these issues arise because subcommunities either communicate poorly with one another or distrust one another:

• Bad ideas adopted through ignorance of refutations - Transportation researchers, concerned with bumpy wheels, pursue work on the square wheel. They reason that it is superior to higher polygons, since it has fewer bumps; further, since its fewer corners probe the height of the ground at fewer points, it is less sensitive to typical bumps on a road. Bearing researchers are familiar with arguments that the decisive issue is bump magnitude rather than number, but the transportation research community remains ignorant of them. Work on the square wheel goes forward under a major defense contract, and major intellectual effort is misinvested.
• Bad ideas maintained despite outsider's refutations [...]
• New thinking twisted by misinformation [...]
• New ideas generated but not pursued [...]
• Good ideas neglected through ignorance [...]
• Good ideas neglected because refutations are suspected [...]
• New thinking undermined by ignorance [...]
• Old ideas redundantly pursued out of ignorance [...]
• Effort consumed by research and publication - All of the above ways of squandering intellectual effort could be avoided, given thorough-enough searches of a complete-enough literature. But in reality, the costs of search (which may be fruitless) are high enough that it often makes more sense to risk wasting effort on bad or redundant work. 

Alas, these problems are all too relevant even now that we have more than enough telecommunication and information technology available to largely suppress them. What's missing is the proper culture to exploit that technology. One of yesterday's posts proposed simple ways of fostering inter-group communication.

[Seb's Open Research]

Written in 1987 and it anticipates so much of what we are doing today. A very nice article and one I will have to read at my leisure.  10:43:11 PM    

"Can Global Warming Trigger a "Little Ice Age"?" [Daypop Top 40]

I've mentioned this before but it is still quite interesting. Global warming has been envisioned as creating some kind of hell on Earth. But the Earth is a chaotic system and very small changes can have huge effects. It would be ironic if global warming resulted in colder temperatures in the temperate regions. What is amazing is the information indicating that these sorts of changes can happen very quickly (less than 10 years) and last 1000 years. Because one of the main arguments from environmentalists is that plants and animals can not possibly adapt rapidly enough to the global warming we are generating. Yet, this is taking a century. Little Ice Ages take 10 years and have to be just as devastating to some forms of life. How have they adapted in the past to these sorts of rapid climate changes, ones that we DID not cause? That would be a fun research project.  10:41:27 PM    

VCs Flee Genomics Shops in Q3; Bioinformatics Providers Hardest Hit [GenomeWeb]

Not many pure plays in bioinformatics or proteomics anymore. Everyone is a Drug Discovery Company now. Of course, veryone prety much has access to the same information regarding human proteins, right. So how do you create a competitive advantage? If 500 are looking at the same thing, then blind luck might be better than actively searching. My bias: use modern tools to help create knowledge from the information. This will require not only changes in the way software is used, but active training of the scientists involved. The companies that succeed in this will reach decision points faster, increasing the probability that 'luck' will happen.  10:19:23 PM    

BusinessWeek: "If you try to print or copy sections of Middlemarch on an Adobe eBook Reader, you'll be informed that Adobe allows users to copy only 10 sections every 10 days. Readers of Aristotle's Politics, which as far as anyone knows was never copyrighted, aren't permitted to copy or print any text." [Scripting News]

I love adding copyright restrictions to public domain material. Isn't this supposed to protect original works? Making a living coping other people's creative works and then preventiung others from copying it. Some sort of ethical dissonance should be occurring, at least in rational human beings. How much money has been made on 'It's a WonderfulLife'? This movie only got popular because its copyright protection ran out and it got a lot of air play on TV. If it had still retained its copy right, hardly anyone would know of it. And it has generated a lot of money for some people along the way. I am just about to the point of refusing to visit Disney World, one of my favorite places, because of my disenchantment with Disney. Their next big cartoon rips off Robert Louis Stevenson. What is Disney going to do when it can only rip off authors from before 1900? They will have mined them all by then. They are going to be hampering their own 'creativity'. The Lion King is the only recent one that was created entirely in-house rather than using a well known literary character to start. They simply make money from licensing old characters like Mickey Mouse and ripping off old characters that are in the public domain.   10:19:23 PM    

FOR GOD'S SAKE, PEOPLE, USE GOOGLE!!!. What good are modern information-management tools if people won't use them? One of the most frustrating things about being an optimistic "computer revolution" guru is that over and over again I run into people who could use the magnificent information management tools we have at our disposal, have every incentive to use them (so as not to look stupid), and yet do not use them. Today's example: I read Slate and find Eric Umansky bashing the New York Times for... [Semi-Daily Journal]

This will happen more and more. It is just too easy to check facts online and get the original numbers. Bradford-delong took 2 mouse clicks to answer the rhetorical question posed in the article. Becuase it was just that easy to show that the rhetorical question was simply false and not so full of rhetoric as it was of hot air. Lazy writers will lose credibility, at least among anyone who is not a rabid, unthinking follower of a particular pundit.  1:27:36 AM    

More Sleazy New York Times-Bashing From Slate. Another example of sleazy New York Times bashing from yesterday's Slate: Mickey Kaus's claim to report "some things the NYT didn't tell you about those new Census stats,"--including that during the recession of 2001 "the child poverty rate for [B]lacks actually continued to fall." Did the Black child poverty rate continue to fall between 2000 and 2001. The right answer is that we cannot tell. The Black child poverty rate is not a very precisely estimated number. If I remember... [Semi-Daily Journal]

Sleazy because it completely ignores simple statistics to make a rhetorical point. When dealing with a lot of these Census Numbers, there is a margin of error. In this case, the margin of error for the Black child poverty rate in those two years overlaps the number given. This means that there is likely no significant difference between the two rate. This may not allow the writer to make a nice point but it is the truth as far as we know it. Some people still care about that.  1:24:49 AM    

Bobcat Goldthwaite. "America's one of the finest countries anyone ever stole." [Quotes of the Day]

I love the Bobcat!!

Charles Kuralt. "Thanks to the Interstate Highway System, it is now possible to travel from coast to coast without seeing anything." [Quotes of the Day]

Of course, we all know that Charles was busy seeing something, or someone in all his travels;-)

Margaret Millar. "Most conversations are simply monologues delivered in the presence of witnesses." [Quotes of the Day]

Hey, none of my monologues are conversa.. I mean. Oh, never mind!!

Flip Wilson. "The cost of living is going up and the chance of living is going down." [Quotes of the Day]

Ain't it the truth, Honey. Basketball Jones. I got the Basketball Jones.

Tom Lehrer. "I know that there are people who do not love their fellow man, and I hate people like that!" [Quotes of the Day]

Tom Lehrer is God. Rhino has all his stuff out now.

Indira Gandhi. "You can't shake hands with a clenched fist." [Quotes of the Day]

Yeah but can you hit them with an open hand? Something to think about ;-)

Will Rogers. "The income tax has made liars out of more Americans than golf." [Quotes of the Day]

Someone who was way ahead of his time. We need him more than ever.

Steven Wright. "If you shoot at mimes, should you use a silencer?" [Quotes of the Day]

The man who asks the questions that MUST be asked!!

George Burns. "I can remember when the air was clean and sex was dirty." [Quotes of the Day]

Rim shot, please, although George never needed to stoop to that. I wonder when he said this. I'd guess after Gracie died but he always had such a nicely cynical view of life to contrast with her naive zaniness.

John Andrew Holmes. "It is well to remember that the entire universe, with one trifling exception, is composed of others." [Quotes of the Day]

I try to remember this at least once a day. While I am incredibly important to myself, a little less so to my family, slightly less to my friends and not at all to 4.5 billion people, I know that 10,000 years from now that I will ... still be important. Yeah, I AM egotistical!!

Wernher von Braun. "I have learned to use the word 'impossible' with the greatest caution." [Quotes of the Day]

Now this is true but so should the word 'possible' be used. That is what makes life so neat. We spend our lives figuring out what us impossible and what is possible, and possibilities, or impossibilities, often change from day to day, minute to minute.

Bismarck. "When a man says he approves of something in principle, it means he hasn't the slightest intention of putting it into practice." [Quotes of the Day]

You have to picture Oliver Reed saying this.

A. H. Weiler. "Nothing is impossible for the man who doesn't have to do it himself." [Quotes of the Day]

Unless you are Werner von Braun. Remember Tom Lehrer.'That's not my department, said Werner von Braun.'

Mark Twain. "Part of the secret of success in life is to eat what you like and let the food fight it out inside." [Quotes of the Day]

This can be taken in so many ways. Or maybe it is just so late at night I am having waking dreams. 'In Xanadu, did Kublai Khan/ A stately whirlpool order' I think I will finish this in the morning.  12:56:19 AM    

HoustonChronicle.com - Stepfather uses stun gun to discipline boy [Daypop Top 40]

I particularly loved the step father's response.

I felt I did the right thing,' he said. 'The belt didn't work; this did. It hurts less than the belt. 'I've whipped his ass so hard that it left marks. That just didn't send the message and this did.'

12:56:00 AM    

A new study from KPMG argues that the content indu .... A new study from KPMG argues that the content industry should focus on developing new business models rather than locking up intellectual property. While it is fighting (and losing) the wrong battle, it is losing billions in revenue. "Rather than embracing the Internet as an inexpensive means of delivering top-quality creative content to the consumer in a highly customized format, industry executives remain mesmerized by the destructive potential of online piracy." KPMG is a pro-business tax and financial consulting firm. (Thanks to Terry Foreman.) [FOS News]

A very nice read and right on target. Media powerhouses will not give up there markets and they have the government in their pockets. It could get ugly.  12:13:56 AM    

Dude, don't get all invady on me The Onion asks those ordinary people on the street about the dance between the Bushies and Iraq. [RatcliffeBlog: Business, technology & political comment]

Sometimes I wish the Onion had a newsfeed. This 'WHat do you think?' page only needed Tom Poston or Don Knotts or Louis Nye to make it complete.  12:04:03 AM