Complex Systems - What Works Best?

METHOD 1

LOOP: [entities] compete 
      select best [entities] 
      increase best [entities]
      diversify best [entities]
      destroy remaining [entities] 
      go to LOOP


Observed Results


entities=
genes            success
organisms        success
species          success
businesses       success
ideas            success
schools          not tried


METHOD 2

experts design [entities] 
LOOP: [entities] operate 
      experts identify problems with [entities]
      experts make small changes to [entities] 
      go to LOOP



Observed Results


entities=
airplanes          success
cars               short-term success, long-term failure
businesses         failure
economies          failure
ideas              failure
schools            short-term success, long-term failure

Mike

Sanya usually went to sleep early. That night she wasn't feeling well so she was in bed by 9. I was still wide awake so I thought I may as well walk over to Freeburger. I was going through one of my phases, at least that's what Sanya said. I was drawing and sculpting and wondering how a lump of clay or an oil on canvas could generate emotions. I smoked and sculpted and drew, and never went to classes. Yeah, Sanya was right, it was a phase.

So I walked over to Freeburger. It was almost deserted. Went straight to the over-sized books. That's where they kept the art books, the ones filled with color reproductions. I was flipping through a book on Impressionism. A hundred years ago everything happened. Darwin, Freud, Marx, Cezanne, Monet. I was looking at Cezanne's Boy In a Red Vest. The library was very quiet, all the windows were dark. I felt like I was the only one in the place. Suddenly this little slimy guy in a security guard outfit was standing there. Hi, how are ya he said. Hi I answered. His face was frozen in an oily smile and he was extending his hand. When I shook it I felt the fag handshake. That's what people called it - the middle finger folded into the palm. What are you doing tonight? he said. Studying, exams ... I said. See ya around he said as he strolled away, that smile still hanging in the air. I took the book, walked through the library searching for a desk, a little fortress. Couldn't find one so I walked down the stairs and out into the night air. But I had started thinking about other times that guys had done that to me.

I used to hitchhike almost every day. But after a while getting picked up by fags started to bother me. Do you have a girlfriend? they would say. I didn't but after a few times I had learned to say yes. They would paste on a sickly sweet smile the whole time and answer Wherever you're going when I asked where they were heading. Straight guys gave me rides too. Once I got a ride from three black guys smoking up. The car was so thick with smoke you could barely see out the windshield. They were laughing and toking. I passed the joint but when I got out I had a buzz. I liked hitchhiking but people stopped doing it around 1972. Everybody was safer but we were all living in an even more hermetically sealed bubble. Why do people make themselves lonelier than they already are? But I did meet a good friend hitchhiking. His name was Mike.

Mike had graduated from the university a few years earlier and he had read nearly everything that I had. But at 25 he was delivering pizzas. One summer he got me a delivery job at the same place. After work, 2 am or so we would hang out, have a drink or smoke a joint. We were high one night listening to some tapes in his car. He popped one in and, damn if it wasn't my favorite at the time. Flute and Piano. Most guys would have called it faggy but I listened to it every day that summer. I said You like this? ... I love this album. He smiled and looked at me like he knew something about me that I didn't. I wondered about the feeling I had for him at that moment. Later that summer he told me that his father had died of Huntington's disease at 45 and that there was a 50% chance he had the gene. There was a test but he didn't want to know or at least he didn't have the courage to find out. I understood why he was delivering pizzas. I felt sad like I wanted to hug him. I guess I was confused because a straight guy couldn't love another guy.

I had walked a few blocks towards home with thoughts of hitchhiking bouncing around in my head. I thought Why not?, went to the side of the road and stuck out my thumb. A pair of headlights was approaching. The car slowed and I walked to the side to look inside. Shit! I thought. It was that same creepy little security guard. I fell right into a full sprint. In the opposite direction. After a quarter mile I slowed down and jogged the rest of the way home.

When I walked into the bedroom Sanya made a funny sound. What's wrong, kid? I said. Evan, my head ... I've got a splitting headache, she was almost in tears. I sat on the bed beside her, gathered back her hair, put two fingers softly on each temple and began to massage. You'll feel better soon I said.

Kristen

One night Sanya invited Kristen and her boyfriend over. Sanya was my girlfriend at the time and we lived together off-campus in an old apartment building. Kristen lived in the dorms and was an English major. Barry was in law school.The place was mildly depressing, kind of dark. Sanya kept sitting down and standing up, looking out the window, eating chips and cashews, adjusting pillows and such.

Finally there was a knock. When they came in Kristen looked great as usual. She was taller than Barry but he was somewhat stylish also in a shiny leather jacket. The three of them sat on the couch and I sat opposite on a chair. I hadn't meant to but I was lined up perfectly with Kristen. She was wearing jeans, not the tight kind but not baggy either. Sanya poured us some wine and put on some music. We talked, had more wine. Everyone seemed to relax. Barry had put his hand on Kristen's knee, his fingers touching the inside of her thigh. I thought I must have noticed too long so I glanced all around the room and out the window. When I looked back at Kristen her expression hadn't changed. I smiled at her and said Does anyone want a beer? We're out of wine. Barry said he would like one so I went into the kitchen which was only a few steps away because the apartment was so small.

I was standing at the counter opening a couple bottles and Kristen walked in. She kept walking, right up to me, pressed her body against mine, put her lips to mine. We kissed for a second or two, very wet, very open, not a slow well-planned kiss but an urgent kiss. She glanced into my eyes just long enough to hold them then she picked up a bottle and walked out. Now I need to tell you that I have never been good at picking up messages from women. That may be a cliche but I honestly didn't know what that kiss was. Sure we were friends so maybe it was just a friendly kiss. Or was it loving kiss, a sexy kiss, a goodbye kiss, a hello kiss? A joke of some sort? Did I imagine it? I grabbed my bottle and walked back in. We chatted for another hour. I found it hard to avoid noticing that Barry's hand had moved up a few notches on Kristen's thigh. Then Barry yawned and they said they had to get going.

I saw Kristen every now and then over the next few weeks. Sometimes Sanya and Kristen and I would have coffee or lunch or go to the library. We never mentioned the kiss. But I had been thinking about it. That was like me - wait weeks or months to formulate a response. So it was already nearly the end of the semester when I woke up one morning thinking about Kristen. OK, I thought, today is the day to do something. I had never actually called her before but that day I called her and asked if she'd like to get lunch downtown at a Chinese place called Bo Long. We rarely ate that far from campus. She sounded happy and said OK.

We took the train a few stops and then walked a few blocks to the restaurant. I can't recall what we ate or much of the conversation just that the kiss was never mentioned. We watched each other as if waiting for it to come up but it didn't. Lunch was pleasant enough, back on the train and to campus. We were walking up Murray Hill, it was late fall, damp, cloudy, good time for a nap or a jog, I thought. I was about to turn towards my place but she was talking about something. We slowed down and then stood on the sidewalk facing each other. Do you want me to walk you home? I said. No I have a class in an hour so I'll stay around till then. she said. But she didn't turn, she didn't even look in the direction of campus. A few moments passed and I said OK, well thanks it was fun. I guess I will see you ... and I touched her coat sleeve. She smiled and turned towards campus. I walked home, got under the blankets with a book and fell asleep on the second page.

We had exams a few weeks later then break. The next time I saw her was late January at the old Freeburger library. She was checking out a book. We chatted for a minute, How was your break? ... Good ... Yours? ... Same. Then she said I'll talk to you soon ... and pranced off. Freeburger was more a large overcrowded bookstore than a library. Like a warren of tunnels lined by books, just a few tables and desks at the periphery, very cozy and nothing like the new library building with its soaring interior that felt like an airport terminal. I almost randomly picked a few books, an English author on sociology, a French author on art, the Congressional Record from some day in 1965. Usually I could spend a blissful afternoon there, reading by a window for hours, seeing maybe one other person in that whole time because few came to this library anymore. But I felt strange that day, lonelier than usual.

She called me the next day. For the first time. Would you like to go back downtown to Bo Long for lunch? she asked. Sure I said. We sat in a half dark part of the restaurant at a table with a candle in the middle. We drank hot tea that felt warm and talked about school. Sometimes we just gazed at each other. Coming back to campus the same thing happened - we didn't want to separate. We got to about the same place as before but this time it was really cold, too cold to mill around in the Ohio winter. I wanted to walk one way or the other. So, how's Barry these days? I said. He's OK, how about Sanya? We hadn't mentioned Barry or Sanya up till then. Sanya is doing well as always I said. OK then Evan dear I will see you later. You look cold. That was the first time she had ever called me dear.

It was about a week after that. Sanya had just come back from class, she walked into the kitchen where I was looking for something to make for supper. Hey guess what! Kristen and Barry are getting married! she said. Wow really? Thats' great ... I said then How long have they been together? It hasn't been that long, has it? but I didn't really listen to the answer. While we were eating supper Kristen called and Sanya chatted with her for a few minutes. When she came back she said They're having a party to celebrate. This Friday, downtown at a place called Bo Long.

When we got to Bo Long that Friday I went straight to the bar and ordered a Scotch. What kind? said the bartender. Any kind I said. When I saw Kristen she was smiling and laughing with a group of friends. An hour into the party we were standing near each other and I turned towards her. She smiled but it wasn't her real smile I could tell. We found a few trivial things to say but we were mainly just watching each other fluster. There was a lot of noise, I couldn't hear what she was saying and I was starting to feel light-headed. Presently a friend came up to Kristen's ear and she began to turn away haltingly. I mumbled Good Luck or Congratulations and turned aside to look for Sanya.

Half an hour later we walked out into a beautiful clear night. The cold air felt like a caress. Sanya and I looked up into the sky. I think Kristen has gained some weight. What do you think? she said. You're right, definitely I said as we walked towards our car.

Obama

People of my age can vaguely remember John F. Kennedy. He was young and boyish for a president and had Irish charm. He smiled naturally. One day I found my mother weeping in front of our TV set. The president was shot. I couldn't understand why my mother had been in love with someone she had never met. I was scared that day. Months later my father was watching a talk show and I asked him what it was about. He said they were talking about the JFK assassination. I said, "What, after all this time?" In 1969 Neil Armstrong walked on the moon and people said we had met Kennedy's challenge to send a man to the moon and return him safely to Earth.

Some people inspire other people. The people feel good about themselves and their country. They think that they can do extravagant things like going to the moon.

Barack Obama is young and boyish for a president and has Kenyan charm. He has an unforced smile. He makes me feel good about myself and my country. And I long to feel the way it felt when Kennedy was president and our country had a hero.

Democracy

The candidates are black, white, and Hispanic, male and female, extremely wealthy and not wealthy, from all regions of the country, sons of CEOs and sons of firemen, former doctors, lawyers, business executives, and preachers, Harvard MBAs and state college graduates. They include advocates of immediate withdrawal from Iraq and no withdrawal, nationalized health care and private health care, tax boosts and tax cuts. These fourteen spent the last year wooing voters, courting contributors, selling their ideas and qualifications.

If you say there is no choice, the candidates are all the same, or this isn't real democracy that's your right. Complaining is the sound of democracy. But behold the contest. Does your favorite football team always win? And when they lose do you cry, "it's fixed!" The same is true in American elections.

The contest for power isn't a pretty minuet, it's a dance of sexual seduction: manipulation, flattery, coyness, and pleading. It appeals to insecurity, greed, and vanity, as well as love and generosity. For some, the result is ecstasy and for others, anger and humiliation. Do you blame the lover who isn't honest, patient, and gentle? Are you? Then why do you denounce politics?

Every four years Americans overthrow their government. We do it without riots, tanks and firing squads. We've taken the violence out of an inherently violent activity. So all of the other facets of our human nature become our weapons.

The Altruistic Immune System (Draft)

Immunity is a resource investment that benefits not only the host organism but also others in its community by preventing the transmission of infectious pathogens. Immunity presumably presents an energy cost to the host for system maintenance as wells as the risk of detrimental effects to the host organism during appropriate or inappropriate immune response. An individual organism living in a community faces a choice as to the quantity of resources (“QR”) to invest in its immune system. A self-interested individual may choose the QR necessary to optimize its own survival. However, if all or most individuals invest a super-optimal QR such that a primary infected individual more effectively fights infection, transmission rates may fall and thereby benefit the community as a whole. This raises the possibility that cooperative population dynamics (ref) may cause QR to evolve to a super-optimal level. As shown in (ref), unicellular organisms living in a spatially structured environment will in some cases cooperatively use a slow rate/high yield respiratory path for ATP production that confers community benefit although each individual organism has the option of exploiting its neighbors by shifting to a high rate/low yield pathway.

In humans, a large portion of the population is affected by allergies, asthma, rheumatoid arthritis and other conditions that may be caused by a ‘hyper-vigilant’ immune system. These conditions may be thought of as part of the cost or burden of the human immune system.

From an individual host's viewpoint, if QR is too low, infection is likely to kill the host but if QR is too high, resource depletion will likely kill the host. So the optimal QR for host survival lies between the two extremes and is influenced by the mix and virulence of pathogens in its environment as well as the probability of primary and secondary infection. In a community of interacting individuals, as QR rises, the probability of secondary infection decreases thus pressuring QR to fall. Similarly, as QR falls, the probability of secondary infection increases thus pressuring QR to rise. However if QR is uniformly high in a community, the decrease in individual survival from the higher QR may be more than offset by an increase in survival from lower secondary infection and thus lead to a net benefit to the community. This raises the following interesting questions: will QR in a community of evolving individuals tend toward the individually-optimized QR or some higher value based on an "altruism" effect? Will individuals increase their QR beyond that required to optimize their own survival so as to benefit other individuals and thereby the community? And will they do so in the face of the evolutionary situation embodied in game theory's "prisoner's dilemma", i.e., if all members of a community invest a high QR, an individual can "defect" by decreasing its own QR and thus enhance its own survival probability at the expense of the community.

In order to explore these ideas, I have created a simulation. Results will be discussed in the next iteration of this post.

Why We Haven't Encountered Intelligent Extraterrestrial Life

Life is a result of the process of evolution and, there being no reason to believe that the Earth is uniquely suited to hosting evolution, it seems reasonable to believe that life is common throughout the universe. The simplest hypothesis would suggest that, of the total star systems in the galaxy, some contain planets with the necessary ingredients and conditions to support life, and of those some have evolved life. Of those planets with life some have evolved forms highly organized into complex, technological cultures. By this logic something like the "Star Trek" universe (or galaxy) seems likely.

The puzzle is this: assuming that we live in a Star Trek universe, why haven't we been contacted or visited by other cultures?

Contrary to the Star Trek universe, the fastest feasible speed for interstellar travel may be limited to some small fraction of light speed. If this is the case then a typical journey between advanced cultures in different star systems might require times on the order of many lifetimes of the individuals.

Very long interstellar journeys would thus require the culture and the individuals comprising it to invest resources for the benefit of their descendants in the distant future, highly altruistic behavior. In fact, the existence of technology for interstellar travel implies a highly organized and highly cooperative culture, one in which a complex web of rules would be necessary to share benefits fairly thus ensuring cooperation. In our own history, as societies have become more complex and as individuals have become more specialized and therefore more dependent upon society, we have developed ever larger bodies of abstract rules embodied in religion, law, and ethics to provide incentives for cooperative behavior. The core and the source of this cultural system is our propensity towards altruism. Our culture is built upon and benefits from the philosophy of altruism and cooperation which is implemented by abstract rule systems. These rule systems seem to evolve towards increasing generality or 'universal-ness' so that our culture's altruistic impulse has even manifested itself as legal protection for other species and for the 'natural' environment.

As Earth culture is the only example we have at the moment, let us assume that other cultures would behave similarly to our own. Projecting our culture into the future or using these ideas to predict another advanced culture, it seems necessary that the achievement of interstellar travel would be accompanied by a high degree of altruistic behavior.

And this is where Star Trek-type ideas give us guidance. It may be that such advanced star-travelling cultures address other less-advanced cultures with a "do not interfere" or "do no harm" policy as in Star Trek. So it may be that other cultures are aware of the existence of our culture but have refrained from making contact out of a desire to protect us in some way.

PostScript: Apparently Daniel Dennett has advanced a similar idea about the development of what he calls "conscience" in humans. This excerpt from Wikipedia discusses his thinking:

In game theory terms, a free rider is an agent who draws benefits from a co-operative society without contributing. In a one-to-one situation, free riding can easily be discouraged by a tit-for-tat strategy. But in a larger-scale society, where contributions and benefits are pooled and shared, they can be incredibly difficult to shake off.

Imagine an elementary society of co-operative organisms. Co-operative agents interact with each other, each contributing resources and each drawing on the common good. Now imagine a rogue free rider, an agent who draws a favor ("you scratch my back") and later refuses to return it. The problem is that free riding is always going to be beneficial to individuals at cost to society. How can well-behaved co-operative agents avoid being cheated? Over many generations, one obvious solution is for co-operators to evolve the ability to spot potential free riders in advance and refuse to enter into reciprocal arrangements with them. Then, the canonical free rider response is to evolve a more convincing disguise, fooling co-operators into co-operating after all. This can lead to an evolutionary arms races, with ever-more-sophisticated disguises and ever-more-sophisticated detectors.

In this evolutionary arms race, how best might one convince comrades that one really is a genuine co-operator, not a free rider in disguise? One answer is by actually making oneself a genuine co-operator, by erecting psychological barriers to breaking promises, and by advertising this fact to everyone else. In other words, a good solution is for organisms to evolve things that everyone knows will force them to be co-operators - and to make it obvious that they've evolved these things. So evolution will produce organisms who are sincerely moral and who wear their hearts on their sleeves; in short, evolution will give rise to the phenomenon of conscience.

This theory, combined with ideas of kin selection and the one-to-one sharing of benefits, may explain how a blind and fundamentally selfish process can produce a genuinely non-cynical form of altruism that gives rise to the human conscience.

Brief Notes

Chromosome 8 Analysis (Nature 19-January-2006): Genomics is providing some interesting insights into human evolution. Analysis of chromosome 8 shows two regions that appear to be undergoing very rapid evolution as revealed by linkage disequilibrium (linkage among chromosome regions increases over time so disequilibrium indicates recent origin) and synonymous/non-synonymous substitution ratio, that is, the ratio of neutral/protein-changing mutations (the ratio is lower if a gene is undergoing positive selection.) Two genes in these regions are MCPH1, mutations in which cause microencephaly, and so is thought to influence brain size, and CSMD1 which is widely expressed in brain tissue.

Small Interfering RNAs (siRNAs) Successfully Protect Mice Against Herpes Simplex Virus 2 (HSV-2) (Nature 5-January-2006): SiRNA technology has been around for a while but (as far as I know) has not been very successful as a therapy. In this study, siRNAs were mixed with lipids and appear to have been taken up by epithelial cells and silenced the expression of several HSV-2 genes without inducing an immune system response.

Rational Strategies in a World with Irrational Agents

Traditional economic theory assumes that economic agents (individuals or firms) always act in a purely rational manner, that is, agents always have perfect knowledge of potential outcomes and always choose optimal strategies for satisfying their preferences. A large body of evidence contradicts these assumptions. So in general the world consists of a mixture of some rational and some irrational agents.

How can aggregate behavior be understood in this context? One way to think about the problem is to use the twin concepts of complementary and substitute strategies.

Strategies are substitutes when agents profit by doing the opposite of others' strategies. In this case, rational agents counteract or limit irrational strategies. With substitutes, evidence indicates that a minority of rational agents may generate aggregate outcomes predicted by the fully rational model. This type of market provides an opportunity for better-informed traders to profit from poorly-informed traders. An example is the case of prediction markets in which an asset is traded up until a precise time when the asset price is determined. For instance, orange juice futures prices, which are very sensitive to cold weather, have been found to predict freezes in Florida better than U.S. Weather Service forecasts.

Strategies are complements when agents profit by matching the strategies of others. In this case rational agents' strategies amplifies irrational strategies. In the case of the stock market, for instance, because there is no fixed future time when a firm's value is determined, well-informed traders cannot guarantee a profit even if they have perfect knowledge of the fundamental value of a firm.

Because of the large amount of volatility in the stock markets, even a well-informed, well-capitalized investor takes a substantial risk by betting against the 'momentum' of the market and can be forced into following the crowd, that is, trying to predict the strategies of others and get there first. As Keynes said, "Markets can stay irrational longer than you can stay liquid." Thus we have examples of large mispricings in the stock market including mutual funds whose underlying aggregate value does not match the fund's share price.

A well-known example of the difference in these two situations can be seen when a firm is put into 'play', that is, when it appears that the firm will be acquired. Rational traders suddenly have an opportunity to use their knowledge to make a profit and the share price often increases dramatically. Clearly the reason is not a sudden increase in the intrinsic value of the firm.

Gender Differences in Feelings of Empathy and Revenge

Empathy is the ability to share feelings with others. Current models of empathy state that the observation or imagination of another person in an emotional state automatically activates a representation of that state in the observer. Imaging studies show, for instance, that similar activations in the brain occur when a subject experiences pain or observes another person in pain. So it is thought that the same neuronal systems underlie both our own experience of pain and our ability to empathize.

In the present study (performed at University College of London and California Institute of Technology) empathic response was inferred from the measurement of increased activation in the 'pain network' of the brain when subjects observed another person receiving a painful stimulation (an electric shock.) As expected, subjects displayed empathic responses when they observed others in pain. And the level of response was correlated with subjects' scores on standard empathy scales.

In order to investigate whether empathic responses vary depending on the perceived fairness of others, subjects were induced to perceive another person as fair or unfair based on their play in a simple game. The subject and another person (an actor) played a version of the Prisoner's Dilemma game in which the actor was instructed to make either a 'fair' or 'unfair' response in the game.

Then the subject observed the actor receiving painful stimulation. Responses showed a marked difference in the sexes. Men subjects showed no empathy when viewing an unfair player in pain but a significant response when viewing a fair player in pain. Women subjects, however, showed significant levels of empathy when viewing either fair or unfair players in pain, with only a slight decrease for the unfair player.

The researchers then investigated activation in the 'reward' system of the brain looking for evidence of a desire for revenge. Again a marked difference in the sexes was observed. Men, but not women, showed a greater response in activation when perceiving the unfair player receiving pain compared to the fair player. And, for men, this response correlated with the expressed desire for revenge.

The authors conclude that a neurobiological foundation exists for our preferences to reward fairness and punish unfairness and the social dynamics that derive from these feelings. They also speculate that the observed gender differences may indicate a biological mechanism underpinning the predominant role of men in enforcing justice and punishment in society.

Ref: Science 26-Jan-2006 Pg 466

What I Like About the Internet

It's a great outlet for creative people. Here are three of my favorite videos from YouTube:

Tasha and Friends

Dancing Around the World

Supermarket Disco


If you live in or near Cleveland Heights: I think we need a Cafe Scientifique! Hey, there is a storefront for rent on Lee Road near Lopez that would be perfect!

The Threat of Real ID

If you live or work in the United States, you'll need a federally approved ID card to travel on an airplane, open a bank account, or take advantage of nearly any government service.

The Real ID Act hands the Department of Homeland Security (DHS), the department that was responsible for the Hurricane Katrina response, the power to set these federal standards and determine whether state drivers' licenses and other ID cards pass muster. Only ID cards approved by DHS can be accepted "for any official purpose" by the feds.

The card will contain name, birth date, sex, ID number, a digital photograph, address, and a machine-readable technology to read that data. DHS is permitted to add additional requirements--such as a fingerprint or retinal scan--on top of those. We won't know for a while what these additional requirements will be but DHS has indicated that it may require radio-frequency identification (RFID) chips which would allow your ID card to be read remotely without your knowledge. (The State Department is already going to be embedding RFID devices in passports.)

Real ID demands that all driver's licenses or ID cards have pictures that can be read by facial-recognition technology.

The Real ID Act also requires states to interconnect their databases to a national database.

The machine-readable technology embedded in your ID card will make it possible for banks, retailers, airlines, etc. to demand your ID card and to easily collect all your personal data into their systems. This will clearly make identity theft much easier. And the data collected could be sold to commercial companies such as CheckPoint which have had large amounts of data stolen by identity thieves.

Cleveland Clinic Part I

Last December the Wall Street Journal ran a series reporting on the relationship among the Cleveland Clinic, the Clinic's CEO Dr. Toby Cosgrove, and medical device companies. The Cleveland Plain Dealer also commented on the controversy. The articles looked at how these relationships create a conflict of interest between financial and patient care concerns at the Clinic.

While at the Clinic, Dr Cosgrove sat on the board of the medical device maker AtriCure, was an investor in the company, and continues to receive royalty payments from the company. The Clinic itself invested $25 million in the company which makes equipment used in an operation to correct atrial fibrillation or heart flutter. Doctors at the Clinic performed the procedure on over 1,200 patients without informing them about the financial ties among the Clinic, AtriCure, and Dr Cosgrove.

Our society has longed recognized the corrupting influence of financial inducements that may conflict with the primary responsibilities of politicians and other government officials as well as many others who are entrusted with providing vital services to the public. The Governor of the state was convicted and fined for accepting a round of golf without disclosing it. Financial services firms pay huge fines for conflict of interest violations that may mislead investors.

Medical professionals, especially, carry a huge responsibility to avoid flirting with the possible corrupting influence of financial ties that may influence patient care. As the Hippocratic Oath says, "I will remember that I remain a member of society, with special obligations to all my fellow human beings."

Personally, I am stunned that Dr Cosgrove and the Clinic allowed themselves to be put into this position, if for no other reason than that it damages the reputation of the Clinic and the trust that patients place in their Clinic physicians. I suppose that, with a board of trustees consisting of about 90 members, many of whom are retired CEOs, no individual member feels much responsibility for the hard job of enforcing ethical behavior.

But if I were one of the 1,2000 patients who have undergone the AtriCure procedure, I would be feeling quite betrayed.

Our Visit to the Zoo



Hi, guys! Came to see me right? Well I'll tell you all about what's going on ...


Hey, wait a minute! Come back, I'm not done yet ... Aww, gosh ...


Hey, human, make yourself useful, give me a back rub ...


Oh, yeah, that feels good ... a little lower please ...


Well, I gotta go hang out with my boys ...


Check it out, can you do this? ...


Yeah ... boring ... Anyway, I gotta fix this door ... now, let's see here
... looks like I'm gonna have to go to Home Depot for this one ...


Oy, there he goes again, always trying to fix stuff ... if his brain were
any smaller ...


Hey, sucker, who you talkin bout with a small brain? Don't dis me ... Bring
it on, fool ...


OK, here I come, Ostrich ...


I didn't mean it ... I didn't mean it ...


Are you two goin at it again ... Gorilla, if you wanna date me, you gotta
have some manners ...


But baby, feast your eyes, you know I'm fine ...


Hmmm, there he goes again, struttin like he's all that ... now if I could
just get Polar Bear to pay me some attention ...


I've been trying to tell you ... I'm already in a committed relationship ...


Oh, no, here we go again, the great Polar Bear romance ... gag me with a
spoon ...


But isn't love wonderful? Look how cute we are ...


Hey, are they arguing about who's the cutest again ...


Yeah, I think so ...


I prefer to be judged by my intellect rather than my appearance ...


Yes, Turtle, I fully agree ...


That reminds me ... I have some physics homework to do ...


Oh, Turtle, you are so smart, can we hang out sometime ...


I'm afraid not, I'm going for a swim ...


Oh, Turtle, why don't you care for me? ... boo hoo ...


If only someone would notice me ...


On my way, baby ... the gansta of love is comin ...


Are you guys leaving so soon, but wait I wanted to tell you about my day ...
Aww, gosh ...

Publicly Funded Research Not Available to U.S. Businesses

I am currently working on pattern recognition ideas and tried to download a face database for testing. The author did not respond to my emails so I sent this letter:



Victor L. Lechtenberg
Vice Provost for Engagement
Purdue University

John A. Schneider
Assistant Vice Provost for Industry Research
Purdue University

Dear Mr Lechtenberg and Mr Schneider,

I am writing to ask about the policy of Purdue University regarding resources generated by researchers at the University.

Specifically, the AR Face Database (see http://rvl1.ecn.purdue.edu/~aleix/aleix_face_DB.html) is a set of photographs of faces that was built at Purdue to test computer face-recognition algorithms. According to the web page above, it is totally free to "academics wishing to test their software" and has been downloaded by researchers in France Germany and Japan. However, according to the web page, it is apparently not available to any form of commercial entity engaged in similar research here in the United States. In fact, the faculty member who generated the database did not respond to two emails asking for access to the database.

It seems odd to me that resources generated, at least partially, with state and federal funds is freely available to academic researchers world-wide but not to businesses here in the U.S. working on similar research. I would be interested to know if Purdue University condones this practice of discrimination against business researchers and if any Purdue policies cover this situation.

Sincerely,

Where I have lived ...

This graphic shows all of the places that I have lived since 1975 starting at the red circle and going to my current home represented by the orange circle. So in thirty years, I have moved a total of about 10 miles. I wonder what that says about me? Anyway, your challenge is to identify the city in which I live.

Why Do Animals and Plants Reproduce Sexually?

Sexual reproduction is costly. Half of the individuals in a sexually reproducing species do not produce offspring and time and energy expenditures involved in searching for and selecting a mate are significant. Also, sexual reproduction may disrupt favorable gene combinations.

A hypothesis originally proposed more than 100 years ago asserts that sex allows natural selection to operate more effectively because it increases genetic variation. This hypothesis was recently put to the test by researchers at Imperial College London.

When supplied with sufficient nutrients and a benign environment, yeast cells reproduce asexually but when subjected to a harsh environment, cells produce haploid spores (spores containing only one copy of each chromosome) which can, when conditions improve, germinate and mate with spores of the opposite mating type.

To measure the benefits of sex, researchers engineered a yeast strain lacking certain genes necessary for meiosis so that the mutant yeast could not reproduce sexually but instead produced diploid spores (spores containing both copies of each chromosome) which were genetically identical to the parent and developed directly into new cells. They then subjected both the normal and mutant strains to repeated cycles of the benign environment (during which asexual reproduction occurred in both strains) followed by the harsh environment (to induce sporulation) simulating evolution over about 300 generations. The growth rates of the yeast cells were then assayed by comparing the growth rate of the new cells to that of the original ancestral strain. In the benign environment, no difference in growth rate was found between the sexual and asexual strains. In the harsh environment, both strains showed an increased growth rate, the asexual population showing an increase of 80% and the sexual strain 94%. The researchers conclude that the sexually reproducing strain's more efficient adaptation to the harsh environment was due to the beneficial effects of genetic recombination.

Ref: Nature 31-Mar-2005 Pg 638

Why Do Mice Have ADAMTS5?

Human osteoarthritis is a progressive disease of the joints characterized by degradation of the cartilage, a major component of which is aggrecan. Several groups of researchers have recently identified ADAMST5 as the primary enzyme responsible for the degradation of aggrecan and the resulting loss of cartilage in mice.

Adult mice lacking the active portion of the ADAMST5 gene (knockout mice) were found to have no gross abnormalities and 17 tissue types as well as blood and serum were examined and found to be normal. Knockout mice underwent surgery to simulate joint injury. A significant reduction in cartilage destruction was observed in these mice compared to wild-type mice.

Again (see the previous article), ADAMST5 appears to confer no benefit and actually exacerbate injury and yet has been conserved in the mouse genome.

Ref: Nature 31-Mar-2005 Pg 644

Why Do Mice Cells Have Cyclophilin D?

Several groups of researchers investigating the mechanisms of cell death have reported a puzzling result. Mice lacking the gene for Cyclophilin D appear to develop normally and additionally to be more resistant to cell necrosis.

Cells die in two ways. Apotosis is a controlled process in which the cell's contents are broken down before the cell membrane ruptures thereby avoiding inflammatory damage to nearby tissue. Necrosis is an uncontrolled process which occurs in response to injury such as lack of oxygen and causes further injury to nearby tissue.

When blood supply to a tissue is disrupted (ischaemia), cells begin to die by necrosis. If a long time elapses before blood flow is restored (reperfusion), additional cells undergo necrosis causing even further damage to the tissue. The recent research establishes that Cyclophilin D mediates the process of necrosis after reperfusion.

The puzzling finding is that mice lacking Cyclophilin D develop normally but also appear to be protected from reperfusion injury following ischaemia. Why would a gene that appears to confer no benefit and actually exacerbate injury be conserved in the mouse genome?

Ref: Nature 31-Mar-2005 Pg 658

Can Plants "Evolve Backwards"?

Researchers at Purdue may have discovered a revolutionary new ability of organisms to correct their DNA. Using a mutant variety of the plant Arabidopsis, they found plant offspring that had apparently corrected various mutations in their DNA.

The rate at which the corrected mutations occurred ruled out chance as the explanation. The possibility that the correction came from another similar DNA segment acting as a template was also considered and ruled out. The researchers scanned the entire genome for similar sequences without result. Also, the fact that the correction was to a single nucleotide and no flanking DNA was different from the wild-type gene makes it unlikely that a similar but not identical sequence was used as the basis for the correction.

The authors speculate that the correction mechanism is based on a cache of ancestral sequences in RNA carried in the gamete. If true this would be a powerful new evolutionary mechanism that could help to explain how organisms can evolve at observed rates. The authors further speculate that the phenomenon may be related to some type of stress-recognition system.

Assuming that gametes carry a cache of ancestral RNA templates, when an organism detects that is undergoing stress, the new mechanism may use the cached templates to "evolve backwards" by correcting recently mutated genes thereby passing to offspring the ancestral DNA sequence.

Because it is generally thought that the vast majority of DNA mutations are detrimental, such a mechanism would allow a mutation to be "tested" in one generation and corrected in the next generation if it were determined to cause stress to the organism. So the evolving organism could avoid some detrimental mutations becoming fixed in the genome. And thus the overall rate of beneficial mutation in a population would increase.

Ref: Nature 24-Mar-2005 Pg 505