When Does Circular Reasoning Work?

When you are on the circle?

My Catholic roommate senior year in college was a little amused when I accepted an invitation from the Asian Christians who lived on our hall to attend an InterVarsity (IV) large group meeting. Our hallmates included a drawgroup of eight Asian Christian guys who made our hall very lively. There was a lot of running up and down the hall, mechanical engineering constructions regularly outside my door at 4am, and tea time in the hallway. There were also lively debates at dinnertime about Christianity, and the musically talented group also held weekly sessions next door with singing and guitar. A side benefit of all this activity was that we could leave our doors open at any hour of the day or in the middle of the night, fall asleep or leave the room, and not worry about safety or the unattended laptop in plain view. Though this is generally true all across Stanford.

Sometimes when eating with another drawmate, we would share a table with a bunch of the guys and end up being silenced by the lively debate about Christianity. We were unable to join in the discussion, and just didn't understand how they could be so passionate and discuss it in so much detail and all of the time.

Occasionally on Wednesday evenings, they would go down the hall inviting people to an IV meeting. The non-Christian Asians among us would refer to this as trying to "convert" people. I thought the Asian Christians in general had an awesome camaraderie, but I didn't understand what was the deal with Christianity, and why it seemed impossible for Christians and non-Christians to be friends. To me, it seemed like the non-Christians were willing to be friends with both Christians and non-Christians, but the Asian Christians could only be close friends with other Christians, so it ended up that non-Christians could only be friends with other non-Christians. (On a side note, I recently peeked at the Stanford IV Web site, and from the photo it looks like the group is much more racially diverse now.)

Anyway, I was interested in getting a glimpse of what it was like to believe in one God and a religion that says it is the only true religion. How do you know which of all the religions that claim to be the true religion is the real one? How do you know there is only one Truth? (And why is Truth capitalized?)

I don't remember what the speaker at the meeting said, nor the skit of a Bible story that was performed. I only remember walking behind the church back to the dorm from the Geo Corner with the Pui-Man and the guy who had recruited me, who was clearly eager to get me to see what he saw. In answer to my question on how does one know there is one Truth, his answer was something like, "because of the Bible," and "because of Jesus."

When you are not on the circle, this kind of answer just doesn't make sense. Because you have to believe in the Bible to believe in the Bible, and what it says about Jesus. Which is like saying Truth is Truth. Which sounds like circular reasoning. I was a bit confounded by this sort of answer.

The other circle of reasoning is the one which says that all religions are valid and all views could be true. Except that the one puzzling thing about this belief is that in order for all religions to be valid, you can't believe in religions that say that not all religions are valid. So you can only group with religious views that say that all religions are valid, and not the ones that say that not all religions are valid. Sort of a paradox. Figuring out this puzzle was probably one of my initial motivations to attend the IV meeting and learn a little about Christianity.

It takes a lot to knock a person from one circle of reasoning to another, and once you are going around in a circle, it's pretty difficult to go off. The being in midair state is even weirder, where sort of both circles are true and not true, like maybe in a fourth dimension.

Actually, from a logical standpoint, the paradox of all religions being true is probably an indicator that that sort of viewpoint doesn't work so well. The belief that not all things are true actually holds up.

The "it's true because it's true" type of statement started to make sense after dealing with doctors who can't believe that some illnesses exist. Then I was in the position of not having a more convincing argument than just saying that what I say is true, and it is because it is.

Some other things started to make sense to me too, like why Christians could only marry Christians, and only be close friends with each other. It would be like, if you had an illness and someone just didn't believe that you had it, it would be pretty difficult to marry or be friends with the person.

The guy that invited me to the meeting seemed disappointed that I just didn't get what he was trying to tell me about, and I didn't end up going to any more meetings. I guess I'm glad that during my Stanford experience, I did go to one event. And perhaps he didn't realize that a little moment might be a seed planted and remembered almost ten years later.

Blogging Exploration

For the last week or so, I think I've actually been up for the majority of the time between when I get up in the afternoon and when I go to bed. This is a pretty good improvement over spending almost the entire last year in bed. Being up mostly consists of sitting at the computer surfing the Web, but I think I can revive the going outside and walking around the yard for a few minutes every few days.

I've been totally distracted by Lara's new template so I started looking again at what is available for bloggers. There are not a lot of templates available for Blogger Layouts, so I actually played around with porting a WordPress theme to Blogger, which turns out to not be too difficult if you are a programmer. This also shows that my brain is working better. The first pass, though not completely done, has taken a few days (in the chronic fatigue measure of days). It would probably have been even faster if I had decided to read and look up things in a CSS manual and the Blogger help pages first, instead of figuring out how they work from the code.

This was more of a technical exercise since I don't know if I actually want to use the template. And then I contemplated using WordPress itself, since a lot of good things have been said about it, and it sounds interesting technically. However, I found that a lot of the customization features and the nifty features for a developer aren't accessible through the free hosted WordPress.com, only if you host the open source WordPress software elsewhere. Anyway, my biggest complaint about WordPress sites is that the pages load very slowly.

This seems to be a good time to try cleaning up my blog too. After a few years, it seems cluttered. And since becoming sick, it seems to have taken on multiple personalities and new subject categories. I've contemplated having separate blogs for different subjects. That would also be a hack for getting two dimensions of labeling. I started trying to clean up my labels, to reduce the number of labels and reduce labeling posts with multiple labels. From this effort, I have ended up with more instead of fewer labels. And found that my writing seems to have been better before.

Hrm.... hierarchical labels would be nice. Yeah, I don't understand one-dimensional labels and tags. Because, if they had the ability to be nested or hierarchical, you could still use them one-dimensionally if you wanted to, but if you wanted more dimensions, you could do that too. I have to try to adapt my labeling behavior to the available technology, rather than what should be the other way around.

During this process, I also visited some random blogs and found some very interesting stuff. The blog world is evolving. More photography, better templates, group blogs, and just a lot of people writing. Too many blogs to read. It's interesting, as we seek more reading material and art from sources that are less "official" or authoritative. There are fabulous writers, artists, and people with interesting stories everywhere.

Human-Plant-Fuel Hybrids

What would happen if computer technology became so sophisticated with artificial intelligence that software programs could do the work of human software engineers and create new programs? Or robots could create new robots? At one time I pondered what if reproducing robots took over the world...? I figured, with procreating computer programs, you could just unplug their source of electricity.

After spending a few minutes reading at some environmental news portals, I think that robots coming to life is much farther away than something like the opposite problem. We're turning life forms into machines.

One company, Agrivida, is developing "ethanol-optimized corn technology" by incorporating engineered enzymes into corn plant varieties to improve "liquefaction and saccharification". On one hand, we have organic food, and on the other hand, we now have techno-corn.

Think gas prices are high? Some dude from from another company said, "The big increase in the use of biodiesel in recent years has caused soy and canola prices to rise, increasing the need to develop crops dedicated to biodiesel use and not for human consumption." (Biodiesel Designer Genes, TreeHugger) Biofuels are going to compete for staple food crops and the land to grow them.

This company, EvoGene, is also developing a "protein farming platform for the pharmaceutical industry". Pharmaceuticals are also going to compete for and change our food.

The USDA has "given a preliminary green light for the first commercial production of a food crop engineered to contain human genes, reigniting fears that biomedically potent substances in high-tech plants could escape and turn up in other foods." The company, Ventria, wants to grow human immune system proteins in rice in Kansas, and put the harvested proteins into yogurt and snack bars so that kids will recover from diarrhea more quickly. Some dude from the company says that "plants are phenomenal factories."

With the strange growth of gluten-intolerance appearing in recent years, this seems to be a great way to introduce a worldwide allergy to rice as well. That would really suck for people who are already gluten-intolerant.

Vote with dollars: "A previous plan to grow the rice in southern Missouri was dropped when beermaker Anheuser-Busch -- the nation's largest rice buyer, which has expressed concern about the safety and consumer acceptance of gene-altered rice -- threatened to stop buying rice from the state if the deal went through."

At the same time as the company claims they can keep the rice plants and seeds from escaping into nearby fields, and the USDA claims there is no risk, the USDA revealed other engineered rice varieties that have already escaped and contaminated our rice. "A type of rice seed in Arkansas had become contaminated with a different variety of genetically engineered rice, LL62, that was never released for marketing. The error was discovered in the course of an ongoing investigation into the widespread contamination of U.S. rice by yet another gene-altered variety, LL601, which has seriously disrupted rice exports." (USDA Backs Production of Rice with Human Genes)

Oh, and there's also Codon Devices, the Constructive Biology Company, which develops the biological devices for the corn technology among other things. It sounds as though they can build and deliver any gene from scratch. I hope they do not accidentally or purposefully construct new viruses, bacteria and other pathogens. Not that that isn't already being done with older technology.

Well, I have thought before that it might be nice to be able to grow meat on plants so that we wouldn't have to kill animals to eat meat. Maybe that isn't such a far-fetched idea after all.

Bush Apparently Had Lyme Disease

I'm not kidding. Here's an article from Thursday:

Bush Apparently Had Lyme Disease, Washington Post

I like this quote from this random blog:

"While this doesn't explain the first 6 years of bad decision making, it might help with the past year."

Also, when I search for Bush Lyme, Google search wants to know if I mean Bush lame instead.

Interestingly, the doctors never tested him for it. Is that because they know that the lab tests are not very good? Or, maybe they did test him for it, and it was negative, so they don't want people to know.

Or how about the notorious Dr. Wormser being quoted as saying that "if he got it in Texas, it was undoubtedly STARI." How undoubtedly can it be, when no bugs were looked for, new bugs are discovered all the time, and the causative agent of STARI hasn't even been identified yet? Unless STARI is another name for "unidentified". It was undoubtedly unidentified.

Well, STARI is supposed to be milder than Lyme disease. In any case, the President is too old, and "lame", to notice if he ends up having long-term problems from the infection.

Witch Broker

It's probably good that we closed the sale of my condo right before all the news about credit crunch. With "For Sale By Owner", I think you can get about 5% less than a realtor can get, which makes it even. In any case, the cost of selling is figured in. I wasn't expecting on selling the condo after only two years, but I probably broke even with... renting a very expensive apartment over the same time period.

There are a bunch of businesses that market "Flat Fee FSBO" services which use a network of brokers around the country who will list properties on the MLS for a few hundred dollars. Apparently, sometimes you get a good one, and sometimes you get a bad one, assigned at random. My aunt and mother had used this company before and had a good experience. Looking at their Web site, I probably wouldn't purchase something from a Web site that looked like that. There are better-looking "Flat Fee FSBO" Web sites that I've found. I suppose younger people have better Web-sense.

Updating an MLS entry seems simple enough. The first time my mom spoke to the broker on the phone, she said she sensed something was wrong, like he was not a good person. Without going into details, after things weren't getting done and contacting a void, I ended up circumventing the broker by making friends with a data entry customer service person at the local MLS directly. The guy, who is probably paid not much more than $10/hr for data entry, was so nice over e-mail and phone, like he just wanted to help people and loved his job.

Anyway, on searching the broker's name on the Web, I found that the same name belongs to a big-time author and leader in Wicca, witchcraft, paganism, and that sort of thing. I tried searching to find out if they were the same person, but was unable to conclude anything.

Not too long ago, I thought all religions could be true, and that there was nothing wrong with religions such as Wicca. Lately, and these days, it really seems like there is deception and dark and evil spirits around.

¹¹ Put on the whole armor of God, that you may be able to stand against the schemes of the devil. ¹² For we do not wrestle against flesh and blood, but against the rulers, against the authorities, against the cosmic powers over this present darkness, against the spiritual forces of evil in the heavenly places. (Ephesians 6:11-12, English Standard Version)

Addendum to the Previous Two Posts

Apparently the name of the game show where the math puzzle comes from is "Let's Make A Deal", and that even professors and statisticians get it wrong. The "statistics" required to solve the problem is extremely simple, but people have a lot of trouble defining what the problem is and not making faulty assumptions, such as the two choices are independent of each other, or that the two choices are even similar.

These kinds of mistakes happen all the time in everything including the path to Nobel Prize-winning medical research, which is part of the reason why it took twenty years to convince the medical community. One interesting part of the story is that they were unable to culture the bacteria, until accidentally one weekend the lab was too busy with other things to do what they had been doing with the plates, which was to throw them out after two days. After this discovery, they stopped throwing away the plates before the bacteria could grow. Ta-dah!

Not only is there the problem that medical people incorrectly conclude that inability to culture a bacteria is "proof" that it is not the cause, or doesn't exist, but apparently the efforts to culture bacteria and probably any other scientific procedure have to be questioned due to high chances of them just being done wrong without knowing.

Another thing was they were looking for corkscrew-shaped spirochetes, but the bacteria presented differently on the plates and biopsy specimens. Important things can be passed over because of assumptions.

It was also interesting that the two researchers described some elements of their background and skills which enabled them to accomplish Nobel Prize-winning work, including general training rather than specialized training, a tendency of thinking off onto what might be considered inconsequential tangents, and hobbies in engineering, photography, and drawing. The latter helped to see detail.

Nobel Prize in Medicine 2005: Psychosomatic Until Proven Otherwise

The discovery and proof that bacteria instead of stress causes ulcers, which won the Nobel Prize in medicine in 2005, has been cited as an example of how prevailing medical knowledge gets turned on its head. I did not realize how interesting the story is until I read the Nobel lectures and the autobiographies. These Nobel lectures, and maybe this expensive book, Helicobacter Pioneers, should be required reading for medical students. Some of the more interesting quotes are below. The story has more relevance to chronic fatigue syndrome and Lyme disease than I thought.

I was actually searching the Web for diseases once thought to be psychosomatic but eventually proven otherwise. Most of the time, Google search finds answers for me in a few seconds. This one is not so easy. There are references to all sorts of diseases such as epilepsy, multiple sclerosis, tuberculosis, and diabetes having been thought to be psychosomatic in origin, but I wanted to find a more "reputable" reference. This type of information seems to be found only in lore and anecdotes. Perhaps the medical authorities don't want to mention the history on their Web sites.

The dictionary definition of psychosomatic is "Of or relating to a disorder having physical symptoms but originating from mental or emotional causes."

In actual usage, psychosomatic is used to mean, "We don't know a physical cause or mechanism, so that means that the cause is psychological stress and anxiety, because we don't understand what not knowing is."

Despite the discovery about H. pylori in the 1980s, and the researchers finally convincing the medical community about twenty years later, and the Nobel Prize being given for it in 2005, I have still heard at least one doctor in the last year reference ulcers as an example of illness induced by stress. And here is an encyclopedia definition of psychosomatic illness that prominently describes peptic ulcer as a classical psychosomatic disorder caused by stress.


Interesting quotes from the Nobel lectures:

Helicobacter Connections, Nobel Lecture by Barry J. Marshall

To quote historian Daniel Boorstin: “The greatest obstacle to knowledge is not ignorance; it is the illusion of knowledge”. The relevance of his quotation is that in 1982 the cause of peptic ulcer was “already known”. Ulcers were caused by excessive amounts of acid secondary to personality, stress, smoking, or an inherited tendency. The successful introduction of H2-receptor-antagonists (H2RA) five years earlier seemed to confirm this idea because nearly all ulcers could be healed by lowering stomach acid secretion with these drugs. Thus, when Helicobacter was revealed, doctors were not looking for a new cause of peptic ulcer, that territory had already been taken by the illusion of knowledge.

It was certainly a paradox and so everybody had ignored Magnus’s findings because they did not fit in with what people thought would be the norm. When I presented our data in October 1982 at a meeting in Perth, a local gastroenterologist said to me; “Barry you’ve got that wrong, people with duodenal ulcers don’t have gastritis. The stomach is usually normal.” From what I had seen of Warren’s biopsies, I could say “How do you know since nobody ever biopsies the stomach of duodenal ulcer patients?”

Interestingly, I saw many patients who had ulcer symptoms, but in whom no ulcer could be found. Many doctors believed that such patients had a psychosomatic illness. However, I soon collected many such “crazy people” in whom symptoms greatly improved during antibiotic treatment. I started to believe that it was not always necessary to have a visible ulcer in order to suffer from ulcer symptoms. Perhaps duodenal inflammation, a pre-ulcer condition, could cause pain.

I found the response to my presentations very illogical and rather irritating. One day, after I presented my histology data showing the healing of gastritis with bismuth, the senior hospital pathologist stated “Dr Marshall these changes seem very subtle.” Actually the changes were quite dramatic, and this was the first time anyone in the world had been able to heal gastritis! I bit my tongue to stop myself from saying “are you crazy?” Others suggested again that these commensal bacteria merely infected people who already had ulcers. But quite clearly I had presented data from patients with gastritis who did not have ulcers.

I realized then that the medical understanding of ulcer disease was akin to a religion. No amount of logical reasoning could budge what people knew in their hearts to be true. Ulcers were caused by stress, bad diet, smoking, alcohol and susceptible genes. A bacterial cause was preposterous.

I knew that most people continued to believe that ulcers were psychosomatic so it was important to ensure that patients were completely unaware of which treatment they received.
...
As part of the study I included a psychometric test called the Jung Scale, which approximately measures things such as sleep patterns, optimism, wellbeing etc. I wanted to see if the so-called ulcer personality had anything to do with the ulcer disease.
...
the Jung Scales showed that the patients’ mental status improved when I eradicated their Helicobacter. When patients were in remission from their ulcer, Helicobacter eradication correlated with significantly lower Jung scores. Thus it seemed likely that the “ulcer personality” merely reflected a diminished state of health related to chronic infection of the stomach.

Helicobacter - The Ease and Difficulty of a New Discovery, Nobel Lecture by J. Robin Warren

Since the early days of medical bacteriology, over one hundred years ago, it was taught that bacteria do not grow in the stomach. When I was a student, this was taken as so obvious as to barely rate a mention. It was a “known fact,” like “everyone knows that the earth is flat.” Known facts can be dangerous; to quote Sherlock Holmes (Conan Doyle, The Boscombe Valley Mystery) “There is nothing more deceptive than an obvious fact.”

I was unable to convince the clinicians of the importance of the organisms. Generally, they did not believe they were there at all. ‘Everybody knows the stomach is sterile’.... Another common question was ‘If they are there, why has not anyone described them before?’ At that stage I did not know why I had not seen them, let alone no one else.

It has become apparent over the years that gastric bacteria have been described many times over the last 100 years. However, these descriptions were not generally known.... The apparent absence of any previous report was given to me as one of the main reasons why they could not be there at all.

Math Puzzle: Do You Want To Change Your Mind?

My mom came across this math puzzle recently. I had already seen it and solved it as it was given as a homework assignment in high school senior year in our special math class. Nowadays, it would be difficult to give these kinds of problems as homework, with the Web and Google search.

You are on a game show. There are three doors. Behind one of the doors is the prize of a million dollars. There is nothing behind the other two doors. You get to choose one door to open. If the prize is behind that door, you win. After you choose a door but before it is opened, the game show host opens one of the other doors and shows that it is empty. He then gives you the option to change your mind. Do you go with your first choice, or change your mind?

In other words, what is the probability of winning if you stay with your first choice, and what is the probability of winning if you change your mind?

Any takers?