2007-06-26

The Seashell on the Mountaintop

I just finished reading The Seashell on the Mountaintop, the Swedish version. Picked it up as a cheap pocket book and I was pleasantly surprised. The book was a fascinating read and showed many of the troubles scientists faced during 17th century, both political and religious.

The story involves
Nicholas Steno, born in Denmark as Niels Stensen and starts when he has just finished his anatomy studies. Being exceptionally skilled with the scalpel, Steno is the first to discover the saliva glands and the tear canal and his public dissections are quickly becoming famous events. He travels all over Europe, through Amsterdam, Paris, Florence and Hannover, spending most of his time working at the then famous Accademia del Cimento in Florence. The academy was funded by the brothers Ferdinando II and Leopoldo de Medici and was the first one focusing solely on "experimental philosophy".

After years of thinking about the problem of seashells being found inside rocks and mountains everywhere Steno figured out the final piece in the puzzle. By carefully studying layers of rocks in hills of Tuscany he realized that sediments in water were deposited at the bottom with the largest particles first and then smaller and smaller particles on top. Steno concluded that the layers and strata in the cliffs and mountains had been deposited in the same way with the newest layers in the direction of the smaller particles above the bigger ones. He also suggested that the seashells inside were real seashells from the sea, not growing inside the rock. He realized the significance of being able to tell the age of the layers of rock apart and opened the way to study the ancient history of Earth.

In 1669 he published his findings in a short booklet called De solido intra solidum naturaliter contento dissertationis prodromus, that translated means Preliminary discourse to a dissertation on a solid body naturally contained within a solid. This was the first published study of geology performed in a completely scientific way that included the
previously ignored time dimension that's so clearly embedded in the rock layers.

The rest of the book describes how Steno continues his studies of sediments and mountains, but also his increasing devotion to Catholicism eventually earning him the title of bishop. The book is well written and I could not put it down until I finished reading the last page.

Something that surprises me with the book is the amount of famous scientists and philosophers that Steno meets. He becomes friends or colleagues with such celebrities as Baruch Spinoza, Giovanni Borelli, the contemporary members of The Royal Society of London, Gottfried Leibniz and many more. Opinions and observations concerning Stenos interests in anatomy and geology made by thinkers like Descartes, Da Vinci and even earlier Aristotle is also included in the book.

Even if the world feels a lot smaller now with easy communication and quick traveling across the globe, it's still inspiring to see how people have always liked to travel and exchange ideas.
The Seashell on the Mountaintop made history feel more vibrant to me than it has in a long time.

2007-06-01

Altruism, empathy and morality

Recent research shows that when you do something totally unselfish, the same regions in the brain that responds to food or sex lights up. The study, originally published in October 2006 by Jorge Moll and Jordan Grafman, got a lot of publicity in the press lately. Some good summaries could be found in the Washington Post and Science Daily, and also in some blogs from people interested in this topic.

My personal uneducated take on altruism is that I know it feels good. My brain rewards me when I help someone, when I make someone else happy. The evolutionary benefit from this is a bit harder to pinpoint, but the articles mentioned above has some good theories. Scott Huettel draws the following conclusions from his study:
"Our findings are consistent with a theory that some aspects of altruism arose out of a system for perceiving the intentions and goals of others."
and
"To be altruistic, you need to see that the people you’re helping have goals, and that your actions will have consequences for them."
The also studies show that people with damage to a specific part of the frontal lobe lacked empathy and would solve tricky emotional problems in a cold "the-end-justifies-the-means" way. This sounds a lot like Asperger's syndrome to me. Now every other kid with a slight communication problem seems to get this diagnose, but I wouldn't be surprised if this condition has something to do with them having a slight error in parts of their frontal lobe.

Marc Hauser has done psychological experiments showing that people all over the world process moral questions in the same way, suggesting that moral thinking is intrinsic to the human brain, rather than a product of culture. That morality is comparable to language in the way that they are both intrinsic in humans. He suggests that people reach moral conclusions in the same way they construct a sentence without having been trained in linguistics. A quote from this excellent summary of a Nature article:
Thus, the findings confirm the notion that there are at least two neural systems involved in making moral decisions: one in which emotions are involved, and one which performs a cost-benefit analysis. [... ...] It is believed that the emotion-based system for making moral decisions evolved first, perhaps in a situation where small numbers of people lived in kin groups. [Antonio] Damasio says, “A nice way to think about it is that we have this emotional system built in, and over the years culture has worked on it to make it even better”.
A consequence of this kind of study is that we might have to rethink what is immoral and not. If morality is automatic and unconscious process, why are we so quick to differ on what's right or wrong in a moral dilemma? The Washington Posts article says:
U.S. law distinguishes between a physician who removes a feeding tube from a terminally ill patient and a physician who administers a drug to kill the patient. Hauser said the only difference is that the second scenario is more emotionally charged -- and therefore feels like a different moral problem, when it really is not: "In the end, the doctor's intent is to reduce suffering, and that is as true in active as in passive euthanasia, and either way the patient is dead."
The difference sounds clear at first thought since it feels like an active choice to administer a lethal drug. But removing a feeding tube is equally active and the two situations should defintely be equal before the law.

Anyway, I guess we should try to think more about the end results instead of moral. A good comment on this from an interesting blog called Atheist's Wager:
"Morality is about doing the right thing when no one is watching."
Let's all do the right thing.

2007-05-23

Classifying species

There's been a lot of articles, blog posts and news about the 300 year anniversary of Carl von Linné (Carolus Linnaeus) lately. He was born today, May 23:rd 1707 in Älmhult, Småland in southern Sweden as the son of a preacher.

In 1735 he published the first version of his now world famous Systema Naturae. It was 11 large pages that classified the natural world and humans were for the first time grouped together with other primates. The eleven pages in the first edition grew to three thousand pages in the final and thirteenth edition, published in 1770.

The system that made him famous was a simple two part naming system based on the physical attributes of the organisms. The two terms are the genus name and the specific descriptor.
The so called Linnaean taxonomy is the base for the system of scientific classification used in modern biology. Linnaeus hierarchy started with the division into three kingdoms, Animals, Plants and Minerals. The Kingdoms were divided into Classes and the Classes into Orders, which were divided into Genera, which were divided into Species. The classifications have changed a lot since Linnaeus' first version and only the groups in the Animal kingdom remain to this day, although heavily updated.

There have been some discussions about improving this centuries old classification style to something more modern, like a tree based nomenclature based on the recent discoveries from DNA studies. It's quite clear that even if animals or plants look the same, they can come from families very far apart. A classic example is the Hyrax that looks like a big guinea pig, but the closest relative is actually the Manatee. (It's also closely related to the Elephant but that's not the closest relative, even if they share the same ancestor.)

A system called PhyloCode grew out of a workshop at Harvard University in 1998 and it's still in the draft stage. Maybe the simplicity of the Linnaean system will prevail anyway. It seems to have worked quite well for the last 272 years...

2007-05-03

Longer life

Researchers in US have found that there's a gene that has the same kind of life-lengthening property as severe calorie restriction. Cutting calorie intake by about 60% have increased the lives of everything from yeast and flies up to mice and dogs. But constantly being on the verge of starving sounds like a nightmare to me, so I'd rather wait for some pill that mimics the effects the pha-4 gene has on nematode worms.

2007-05-02

Busy busy..

Been on a 2-week vacation to the Philippines with Justine and we just got back, hence the lack of updates to this blog.

Also, bought a new apartment yesterday so I'll be spending all my non-work time for the next few weeks fixing it. Already have one wall taken down!

I expect to do regular updates again in a few weeks. :-)

2007-04-03

Parasites

Parasites are scary and fascinating at the same time. It's disgusting to have a creature living and breeding inside another living animal, but the tricks they have to control their hosts can be surprising, weird and most of all scary.

There's been some talk about Toxoplasma gondii again because of this soon to be published paper. The paper describes how Toxoplasma gondii removes all fear of cats from rats infected with it. The reason for this is that the parasite only reproduces in cat bellies and of course the way to get there from the rat is to make it's host get eaten by one. The rats still had their normal anxiety and could learn to get frightened of other things.

It's strange how the the tiny parasite can control something so very specific. It's a common parasite too, about half of all people on earth are carrying it. It's not dangerous to humans unless you have a very weak immune system, like people with AIDS. Pregnant women should avoid getting it too. People get it the same way rats or other animals does, contact with cat litter.

Studies of humans infected with Toxoplasma have shown some subtle changes in personality. Quoting from this article:
Those infected, he found, show a small, but statistically significant, tendency to be more self-reproaching and insecure. Paradoxically, infected women, on average, tend to be more outgoing and warmhearted than controls, while infected men tend to be more jealous and suspicious.
There's not total consensus on this yet and it seems like only a few of all infected people have any notable issues with it. Toxoplasma infection has also been linked to schizophrenia, and medicine against schizophrenia made infected rats afraid of cats again. Why and how is not clear yet.

I would not be the slightest surprised if all of the truly cat-obsessed people are carrying Toxoplasma gondii.

Another classic example of a parasite controlling it's hosts is the Lancet Fluke. It has a complex three host cycle involving cattle, snails and ants. They live in sheep or cow livers where they mate and then leave their eggs out in the host’s feces. Snails eating that gets infected and to protect themselves they make slimy balls filled with parasites that they leave behind. Ants finding these slime balls eat them and get infected. Every night the fluke takes control over the and and makes it climb to the tip of a grass straw, hold onto it with it's mandibles and stay like that until the morning. Then it goes back to looking for food as normally, until the sun goes down. Finally, once some grazing animal accidentally eat the ant with the grass, the fluke is back in a host where it can reproduce.

There's more examples like this too. One fluke reproducing in wading birds makes infected fish shimmy and jump to make it easier for the birds to find and catch them. A certain hairworm who infect grasshoppers takes control of it's host when it is ready to leave it and makes the poor grasshopper suicide by jumping into some nearby water. The worm will be back in the water where it wants to be. (More hairworm here(pdf). Mind controlling parasites at LiveScience.)

I hope I'll never get a parasite infection. Especially not some slimy, crawling animal. Wikipedia has more information and links about this than you ever want to know...

2007-03-28

Geotagging

GPS tagging photos on Flickr has been done for a long time, but I had not seen it on regular blogs yet. Why not? You could do a lot of fun with that! At least I hadn't heard any noise about it so I thought it hadn't really taken off. But of course some clever people had started working on this long ago and things are well on the way.

The first thoughts around this I got from reading an article on O'Reilly radar about Google supporting GeoRSS. That led me to the GeoRSS homepage which links straight to geotagthings.com. In geotagthings (still in beta) you can subscribe to a feed that's an aggregation of many geotagged feeds that are limited to be within a certain area of your choice. I think it would be really fun to see what other bloggers in the block are saying and what pictures they are posting.

Then of course there's the question of how to easily add geotags to all blog posts. It should of course happen automatically if possible, but good support for adding it manually should be built into all blogging software. There should be the possibility to save some default locations where you do most posts from and a row with free editing, just to enter latitude and longitude.

There's a newly started GNOME project called GeoClue, which is about making a DBus service for geographic information. They have a great list on the homepage with suggestions of how this information could be used and I really hope this to takes off. The more this is integrated into the desktop the better.

One of many cool things mentioned on the GeoClue page is Placeopedia. Placeopedia is an effort to connect Wikipedia articles with the location they are talking about. This is exactly what I want to have in my Neo1973 when I'm out traveling somewhere. "Is there something interesting around here?" - One look on the map and I can click and read the article about it.

Of course some clever minds at Google have also been looking at this stuff. There's been some rumors that maybe Google was making a phone, but of course they were not going build any hardware. The proof for this is this patent for quicker search results when using a mobile device was dug up by Mad4MobilePhones. It shows that Google was, as usually, looking for a way to get better and faster search results. Jacqui Cheng at Ars Technica took a closer look on this new mobile search and really liked it. The last piece of the puzzle is how to add the positioning automatically. (Google's mobile search currently needs you to enter your current Zip code to tell where you are.)

GPS receivers are getting built into more and more things and now we have to make it possible to get the geographic information to all programs that can make use of it.

Population, Coriolis and more myths

There's a common rumor that there's more people alive now on Earth than have ever lived. I've always found this to be unlikely, but haven't really done any calculations on it. Luckily, some guy has already done the calculations. (See here)

Counting with very low estimates, starting with two homo sapiens 50,000 years ago and using the lower limit of estimated growth and populations, Carl Haub still got the estimation that slightly over 106 billion people had ever been born. The current 6.5 billion is not even close.

Another common rumor is that water running down a drain spins in different directions on the northern and southern hemispheres, but that's not true either. The Coriolis force is just too weak on smaller scales. (See here)

More interesting facts about urban myths and legends can be found at snopes.com

2007-03-23

Metal

I'm amused by this recent study by Stuart Cadwallader and Jim Campbell at the University of Warwick. They conclude that gifted students use heavy metal music to unwind. There's a nice write up at the Telegraph about it. The best quote is:
"Participants said they appreciated the complex and sometimes political themes of heavy metal music more than perhaps the average pop song. It has a tendency to worry adults a bit but I think it is just a cathartic thing. It does not indicate problems."
I'm not saying I was a "stressed gifted social outsider" as student, but I have always preferred fast and noisy music over easy listening. I don't really get why most "pop" have to be so boring. The majority of the songs I hear on the radio has melodies that are slow and repetitive and lyrics that are uninspired and boring, repeating some short and stupid sentence over and over again.

I'm convinced that fast music makes the brain work harder to decipher what is going on. I think it took over 10 times of listening before I could hear the whole lyrics to 88 Finger Louie's "I've Won". Great song, nice melodies and very very fast. Adam Goren's (Atom And His Package) music is not that fast but the lyrics are probably the best ever. Very funny and because of the rhymes and word plays it's not always obvious what he's joking about.

That is the kind of music that grows on you. A song or album where you hear every twist of the melody and every word of text the first time you hear it will bore you very quickly. The brain is a pattern matching machine and to keep it happy we have to feed it tricky enough patterns to solve. I think different people have different limits, and I think mine is somewhere at The Dillinger Escape Plan. (Calculating infinity is an amazing album).

Some of my favourites:
88 Fingers Louie, Abhinanda, Atom And His Package, Bad Religion, Beatsteaks, Billy Talent, Blindside, Boy Sets Fire, Children Of Bodom, Coheed And Cambria, Down By Law, Goldie Lookin' Chain, In Flames, Incubus, Jr Ewing, Looking Forward, Mighty Mighty Bosstones, Nine, Nirvana, NOFX, Q.O.T.S.A, R.A.T.M, Raised Fist, Rancid, S.O.A.D, Shai Hulud, Snapcase, Social Distortion, Spineshank, Stabb, Sublime, Sugar Ray, The Black Keys, The Bronx, The Hives, The White Stripes, The Who, Tiger Army, Tool and Zeke.

Also, always support your favorite band and go to their show if they're playing in town!

2007-03-20

The bottom of the sea

I have a feeling we don't know as much as we should about the life at the bottom of the oceans. About 70.8% of the surface of the Earth is covered by water and even if we know the topology of the bottom and the currents quite good from all satellites and sonar scans, most of it is still unchartered when it comes to creatures and plants. The discovery of the black smokers in 1977 near the Galápagos Islands showed that there are some very odd echo systems down there.

The problem deep down under water, like at 2000m - 2500m down where most black smokers have been found, is the lack of energy. No sunshine reaches these depths so the plants and creatures needs to use other sources to get their energy from. The strange environment with the darkness and high pressure gives rise to truly weird lifeforms.

A good example is a snail found in 2001 around some black smokers in the Indian Ocean. It uses Pyrite (aka Fools Gold) and Greigite to build a metallic shell. Covered with an iron plate mail it's like a miniature knight in armor. National Geographic did a nice article on this gastropod and Anders Warén, the lead researcher on this metal wearing snail, says they have found several thousand more new species around this kind of hydrothermal vents, and that's just counting mollusks.

The deepest dive ever made was done in 1960 by Jacques Piccard and Don Walsh with the bathyscaphe Trieste. They reached the bottom of the Challenger Deep in the Mariana Trench spending 20 minutes at the bottom. At the depth of 10916 m the pressure is extreme, about 1250kg per square centimeter, and currently no vessel exists that can withstand it.

The Japanese DSV Shinkai 6500 is currently the deepest-diving manned submersible in the world with a maximum depth of 6500m. It was put into service in 1989, 18 years ago, but it's still new compared the next best one, United States Alvin (the one used to find the black smokers). Alvin was commissioned in 1964, but has been updated several times, last time in 2001. It can stay at a depth of 4500m for 9 hours with three people on board.

Good to see that the National Science Foundation is well on the way to a new improved 6,500m capable deep diving vehicle that can reach more than 99% of the sea floor. I'm sure it will find plenty of interesting things.