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Ranking your Google searches, plus search tools for science sites

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Way back in the day — say, a year or two ago — using search engines to research science topics was rather a crapshoot. I was an active Wikipedia writer back then, and the majority of my work was on science-related articles. And finding reliable web-based information was always challenging.

Take the article on the beautiful, endangered freshwater fish known as Asian arowanas, which is mostly my work (and I can't say I'm not proud of it). Google searches for Asian arowanas turn up mostly commercial sites and fan sites. Neither of these is a reliable source of science information: the commercial sites mix bona fide science with marketing information, while fan sites are prone to misinformation. This problem was a major hindrance to my work on the article.

Google search ranking

Now Google Search has a new feature for users signed in to their Google accounts: search ranking. (Try it.) Google says the ranking will help teach the search engine how to customize searches for you. Perhaps after some training, Google search will be less likely to turn up commercial sites and more likely to turn up useful research information.

But that will take time. In the meanwhile, two other search engines are available for people interested in finding real information on the web: hakia (still in beta) and Scirus.

Hakia, er, hakia

Hakia (whose name officially is not capitalized, but my inner English teacher just won't let me start a sentence that way) uses a new technology called semantic searching to help higher-quality, more credible sites show up higher in the search results, regardless of popularity. Other search engines, including Google, use popularity as a major criterion for search rankings; this is why SEO (search engine optimization) strategies include techniques like obtaining incoming links.

A script on the homepage allows a user to compare hakia and Google searches. I ran it for "Asian arowana." Hakia's top two sites were a fan site and a blog, while Google performed a bit better with the Wikipedia article and a commercial breeder's site. But a very significant difference between the two was visible on each page's right side: Google displayed an Adwords advertisement, while hakia showed a "hakia credible site": a journal article from the National Institutes of Health on the fish's mitochondrial genome. Hakia credible sites are those recommended by librarians, who know a thing or two about finding reliable information. Getting results like that "above the fold" is a huge advantage for the Web researcher.


Scirus is billed as being "for scientific information only." It indexes journals, scientists' web sites, and other relatively reliable sources. In this regard, it is fundamentally different from both Google and hakia, which both cover the whole Web. So I compared it to Google Scholar, which searches academic journals.

My search for "Asian arowana" on Google Scholar turned up an unadorned list of various articles. The Scirus results, on the other hand, used logos to show each result's source at a glance. It also included a tool for refining the search. Scirus makes it easier to evaluate and filter search results. Its developers obviously understand the needs of a person looking for credible science information better than Google Scholar's designers do.


The First Images of Exoplanets

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Visible-Light Composite Photo/Image: Planet (Exoplanet) orbiting Fomalhaut from Hubble Space TelescopeThe first photographic images of exoplanets (planets orbiting stars other than our Sun) have recently been reported in sources including Scientific American, Space.com, and NASA. Exoplanets are typically discovered through indirect observation. Direct observation and photography of these worlds is notoriously difficult for a host of reasons: their tiny size (by definition, a planet must be smaller than even a dwarf star), their dimness, and their relatively close proximity to their parent stars, whose bright light drowns them out.

The image pictured comes from the University of California at Berkeley and depicts a planet orbiting a star called Fomalhaut. This composite image from the Hubble Space Telescope shows the planet's position in 2004 (bottom) and 2006 (top); from these data astronomers have calculated and graphed the planet's orbital path. Fomalhaut and its planet are relatively nearby, about 25 light years away.

Infrared Image of Family (System) of 3 planets (exoplanets) orbiting HR 8799: Keck ObservatoryAnother amazing image consists of a system of three exoplanets, pictured at left, which have been detected orbiting a star with the unassuming name HR 8799. The Keck Observatory, which sits at the summit of Mauna Kea in Hawaii, claims the honor of creating these images.

There is a catch in calling these "the first" images, though. The devil is in the details, which not even many of the science writers reporting these images seem to have caught. As a matter of fact, at least two direct images of exoplanets already exist! I should know, because I wrote an article about them last month. One was taken as far back as 2004, and the other was reported (again, incorrectly as "the first") earlier this year. Oh, how quickly these science writers forget!

Neither the Fomalhaut nor the HR 8799 images are the first direct images of exoplanets.

As nearly as I can tell, the "firsts" for these images are this: the Fomalhaut images seem to be the first planet discovered through direct observation of visible light. The HR 8799 system images seem to be the first family of exoplanets discovered through direct observation of infrared light. The previously existing images I mentioned above, on the other hand, were discovered through the indirect methods that so far have been the main way of detecting exoplanets; the images were created only later.

All of these images are exciting. Planets outside our solar system intrigue the imagination! But please, I wish the science reporters would do a little fact checking and get their stories straight.


Caption Contest #1 Winner

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The winner of the first Leave the lights on caption contest is:

"So you see, because I'm more important to the ecosystem, that's why the government had to bail ME out."

Congratulations to Rev. Eric Brown! Since he does not use Entrecard, he wins the dubious distinction of displaying this banner wherever he chooses (his blog, his desktop, his toilet seat, etc.*)

*I do apologize to any readers offended, as some are in Britain, by my use of a Latin abbreviation. This is a Catholic blog, and we like Latin here.


Gardasil, poison, and vaccine reactions

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I had the misfortune finding an article by one Cynthia A. Janak on Gardasil, the vaccine against human papillomavirus. Though I would like to merely dismiss this article (oh, I so, so wish I could merely dismiss it), I am just too horrified by the heinous abuse of science. I cannot resist picking up poor Science, brushing her off, and patching her wounds a little.

I won't even address Janak's heavy use of anecdotal evidence. Instead, I'll focus on her attempt, starting about a third of the way down the page, to condemn Gardasil based on its "toxic" ingredients. She goes through the list one by one, quoting the horrible toxic effects of each ingredient:

  • Gardasil contains 225 mcg of aluminum. Do you know how little that is? That's about 1/4000 gram, or less than 1/100,000 ounce. You get more aluminum eating out of aluminum cooking pots.
  • Histadine is a substance found widely throughout the body. It can safely be taken daily in supplement form in amounts 2000 times greater than what is found in Gardasil.
  • Polysorbate 80 is a type of compound commonly called a "wetting agent" and is found in ice cream and milk.
  • Sodium borate is used to keep the pH balanced. Wikipedia flat out states that it "is not acutely toxic." You have to deal with very large quantities before you need to worry about safety precautions.
  • Sodium chloride is table salt.
Did you notice that Gardasil also contains dihydrogen monoxide? You might like to read more about it here. I should warn you, though, that dihydrogen monoxide is just another name for water.

Janak's blog, Truthspace, is a manifestation of a mind deeply troubled by paranoia. The truth is that the first rule of toxicology is that the dose makes the poison. Cyanide, arsenic, and lead are all harmless in tiny enough quantities, while necessary substances like vitamin A, iron, and even water can be toxic in high doses.

Time may show that Gardasil is not a completely safe vaccine. I see no reason to make that assumption at this time. Gardasil may be a controversial vaccine, but not because it contains substances like table salt.

Poor Science. I hope she feels a little better now.


Caption Contest

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We like the occasional Friday contest around here. Today is a caption contest. This cartoon is from the New Yorke, and the caption is cute, but I'm sure my readers can do better than that!

There is a real prize available this time, too! The winner will get 100 Entrecard credits. Or you can have the lovely Leave the lights on contest-winner banner, if you don't use Entrecard. But if you have a blog, you really should look into Entrecard — especially now that you have the opportunity to get started with 100 free credits. (See the widget on the sidebar to find out how it works.) Deadline is next Friday, November 14.


The science of evil

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"Good" and "evil" are moral values that are defined in a metaphysical context of faith. In Christianity, "good" means that which is of God, and "evil" is that which is opposed to him; in fact, the words "good" and "god" have the same etymological root.

"Good" and "evil" are things we know not just with our minds or even our hearts, but with our spirits. A Christian would say that since they are spiritual concepts, they can never be defined scientifically.

What makes something evil?

What if you are a secular scientist who is nevertheless aware of the idea and existence of evil? You might do what artificial intelligence researcher Selmer Bringsjord, of Rensselaer Polytechnic Institute, did: try to define this non-scientific concept in scientific terms. Here are the criteria he came up with to define an evil person:
  • The person must have planned or attempted (with or without success) to do something with the explicit intention of causing harm or pain to others.
  • He or she must have done it without prompting, that is, independent of peer pressure.
  • The person's reason for doing the morally bad thing must be either "incoherent," or the person must regard the harm caused as something good.
Compare these criteria to the three criteria that, according to Catholic moral reasoning, are necessary to make a mortal sin, that is, a grave evil that kills the life of Christ in one's soul:
  • The act must be a grave matter — i.e., a serious wrong — or considered by the person to be a grave matter.
  • The person must be aware that it is a grave matter — ignorance is an affirmative defense with mortal sins.
  • The person must give full consent to the act without being coerced against his or her will.
These three criteria match Bringsjord's first two criteria rather well. Bringsjord's third criterion, though, seems superfluous or possibly even exonerating: if your reason for doing something bad is "incoherent," then you may not be sane and therefore not fully culpable for your actions; if you regard your evil act as good, you may fall into the category of people who are not aware they are committing a serious wrong.

Evil deeds v. evil people

One major discrepancy between Bringsjord's criteria and Christian views of evil stands out: Bringsjord is defining an evil person, while Christians talk only about evil acts. Traditional Christianity holds that all of us suffer from a fallen nature, so we are all inclined toward evil deeds; but because we were created in God's image to be with him, and because any sin can be forgiven, no human can be essentially evil. Thus the Church speaks of sins, not of evil people.

Why define evil with a secular world view?

What is Bringsjord's purpose behind defining evil people? He even created a computer model of a perfectly evil person — but to what end?

His model is part of a larger program of developing simulations for human behavior. If you have a wholly secular, materialistic worldview, and regard human behavior as the result of scientifically definable brain activities, perfect simulations are theoretically possible.

I would argue that Bringsjord is barking up the wrong tree. Moral decision making is dependent on the spirit, not just the organic brain. Computerized copies can never be more than approximations based on outward appearance; they will never capture the free will of the soul, which is involved in all choices having to do with good and evil.


Look out, Australia: Down syndrome cooties!

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In the United States, about 1 in 800 live births is that of a child who has an extra copy of chromosome 21, a condition which results in a cluster of symptoms known as Down syndrome. The rate is much lower than it could be because the medical community is very good at preventing Down syndrome births. They cannot prevent this defect from occurring, but they can detect it before birth and kill affected children in utero. In the U.S., at least 80% to 90% of children with Down syndrome are killed in this way. In the United Kingdom, over 90% of babies with Down syndrome are killed before birth.2

The practice of aborting affected babies is euphemistically called "the result of a termination decision" rather than "eugenic abortion."

Down syndrome is not contagious. You can't get any Down syndrome on you by touching someone with the condition, nor by letting them into your community.

Nevertheless, the Australian immigration department seems frightened of letting Down syndrome in.3 A doctor from Germany, whose services are desperately needed to serve the health care needs of a rural part of Australia, has been denied permanent residency because his 13-year-old son has Down syndrome.

Fear of chromosome 21 cooties is not the official reason for the decision. The official reason is that the boy would be a burden to the Australian community. But this excuse is laughable because letting the family stay would plainly be a net gain for Australia; they need this doctor's services, as he is the only internist in the region.

To his nation's credit, the premier of Victoria, John Brumby, supports the family's cause for permanent residency status, as does the health minister. They can see what is clear and obvious: the doctor's son requires far less in terms of services than his father provides to the community.

People with Down syndrome have a higher incidence of health problems and generally have mental retardation to varying degrees. Yet they are cheerful, happy folks, some of whom are able to earn university degrees despite their disabilities. Like other children, Down syndrome kids are gifts, and Australia should welcome this family, not slam the door in their face.


  1. Comarow, Avery, 1995. "An earlier test for Down syndrome." U.S. News & World Report.
  2. Mansfield, Hopfer, and Marteau, 1999. "Termination rates after prenatal diagnosis of Down syndrome, spina bifida, anencephaly, and Turner and Klinefelter syndromes: a systematic literature review." Prenatal Diagnosis 19(9): pp. 808-812.
  3. Associated Press, November 1, 2008. "Australia denies residency for dad of boy with Down syndrome."


All Souls Day prayer for the forgotten

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Today is the Commemoration of All the Faithful Departed, also known as All Souls Day. The church consists of all baptized people who have ever existed except for those now in hell; the rest of us are here on earth (the Church Militant), in heaven (the Church Triumphant), or in Purgatory (the Church Penitent).

"All baptized people" includes most Protestants, of course, but Protestants generally do not believe in Purgatory. And as a result, they don't pray for their dead. I find it poignant to consider people in the Church Penitent whose loved ones on earth do not pray for their purification to be complete. Here is a prayer for the forgotten souls in Purgatory:

Lord, hear the forgotten souls in Purgatory. Purify them and bring them to your side to sing your praises forever. Amen.