Sunday, November 23, 2008

Five things about me meme

Glendon has tagged me

The 5 Things Meme

5 things I was doing 10 years ago:
1. Studying economics. Not a great success, as people might have gathered from the fact that I don't do it any more.
2. Living around the corner from where I am living now. In the intervening time, I've lived in six other places, not of them around here.
3. Spending way too much time on the internet. The amount of time I spend these days is nothing compared to back then.
4. Worked in a ware house.
5. Partied too much, as 23 year olds earning money are wont to do.

5 things on my to do list today:
1. Clean up my kitchen - it's a mess.
2. Visit a friend and watch a DVD (already done).
3. Finish a book or two. I'm currently reading too many books.
4. Send of a few emails, that I should have sent off earlier this week.
5. Catch up on my sleep.

5 snacks I love:
[I don't really do snacks, but I'll give it a shot]
1. Does grapes count? I guess they do.
2. As must figs - dried or fresh.
3. Prawn flavored chips.
4. Brownies.
5. Cashew nuts

5 things I would do if I was a millionaire:
1. Travel.
2. Take some time off, and finish my degree.
3. Buy a bigger place.
4. Fill it with books, CDs and DVDs.
5. Continue with my life in general.

5 places I've lived:
1. Copenhagen
2. In a boat, in Copenhagen's harbor.
3. On a friend's couch, for several months.
4. In a two roomed apartment en-suit with my brother. The fact that we still talk is a wonder.
5. Rented rooms, all over Copenhagen.

5 jobs I've had:
1. Cleaning
2. Ware house worker
3. Bouncer at parties
4. Weekend caretaker at a badminton club
5. Systems developer

5 people I'll tag: I'll skip this time, but any reader feeling up to doing this, please go ahead.

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The 100th Skeptics' Circle is up

It's amazing to think of, but there has been 100 editions of the Skeptics' Circle since St. Nate started it back in the days. I've been included in it a couple of times, and even had the honor of hosting it once.

Go read it over at Respectful Insolence

The 100th Meeting of the Skeptics' Circle: The trouble with Orac

Note: Yes I know I am a few days late, but I am unfortunately ever behind my blog- and mail-reading these days.


On the Shoulders of Giants

While talking about his work, Isaac Newton famously said "Pigmaei gigantum humeris impositi plusquam ipsi gigantes vident" [If I have seen a little further it is by standing on the shoulders of Giants.] By this he meant that his work built upon the work on other, often earlier, scientists.

This is a remark that's both banal and profound. Banal in the sense that we all depend on work done before by others to do our own work. Profound because it would be impossible to advance science without building on, and incorporating, earlier work. Science is a truly collaborate effort, both in time and space.

What I mean by this, is that advancements in science isn't done by disregarding earlier knowledge, but rather by new knowledge, or different understanding of existing knowledge.

This doesn't mean that old science doesn't get disregarded, as our understanding of how things work get better. What it means, is that even if we know a theory is imperfect, we don't disregard it, before we have a new theory that not only explains the parts the old theory had problems with, but also explains the parts that the old theory could explain just as well as the old theory.

Albert Einstein didn't overturn Isaac Newton's theories, he expanded them.

Charles Darwin did overturn earlier ideas, but that was because the older ideas didn't fit the facts. Darwin's theory of evolution did. Later biologists have expanded on Darwin's ideas, and incorporated Mendel's findings.

Every discovery in science strengthens our understanding of how things work, and allows us to modify our theories and hypothesis, so they get more accurate.

This is how science works.

This is what tells a scientists apart from a crank.

Yes, there are some times scientists who will make findings that are so groundbreaking, that we need to disregard our earlier theories, but this is a rare occurrence, and only happens as a result of a long hard process, where it's not only demonstrated that the facts don't fit the old theory, but that the facts fit a new theory instead. It doesn't happen by someone pointing at minor points where the mechanism is not entirely understood, and claim that this show the entire theory is flawed, as e.g. the neo-Creationist crowd tries to do with the Theory of Evolution.

Science adapt, but it also builds upon the existing knowledge. It doesn't accept the existing knowledge as the truth, and it continuously challenges the assumptions, but it doesn't disregard everything, just because there is something that's unclear. We know that there are flaws in some of theories, but as long as they are the best explanation, we keep them, fully expecting to expand on them in the future, modify them as needed, or even disregard them, if it turns out that they are too flawed to be of any use.

Scientists don't fear change - they embrace it.

People who do science, don't just stand on the shoulders of the giants in the past, they are also supported by a whole scaffold of other scientists on whose work and observations they base their own work and observations. This scaffold is strong, strong enough to continue to bear the weight of the scientists, even if one of the giants should collapse (as unlikely an event that might seem).

The giants are important to make the big steps in science, but all the other scientists are just as important. They are the ones that flesh out the theories, modify them to fit the data etc. They are the ones who take the work of the giants, and apply them.

This is why attacking the work of the giants won't help you overturn a scientific theory that you don't like. The giants, and their work, doesn't stand alone. When Theodosius Dobzhansky said "Nothing in Biology Makes Sense Except in the Light of Evolution", he didn't embrace just the work of Charles Darwin, he embraced the work of the countless biologist who went both before him and after him. Dobzhansky looked at the whole body of work and observations inside the field, and simply stated something that should be obvious to anyone looking at it. Our understanding of evolution got started with the giant Charles Darwin, but we know so much more now, and understand it so much better, that while some of the foundations he laid are still there, much of it has been modified over the time, to a point where it bears little resemblance to what he came up with. This is not surprising - Darwin did not have the knowledge that has accumulated in the intervening years.

This is why scientists have little patience with people who just attacks the ideas of one scientist - as important as he might be - to advance their own agendas. Science doesn't work that way. If a scientist is wrong, it can be demonstrated through the facts, but it doesn't mean that you can insert your own ideas instead. Those ideas have to go through the same process as the original ideas, and survive the same scrutiny, to see if they fit the facts better.

They rarely do.


Saturday, November 22, 2008

Book Review: Release It!

Release It! - Design and Deploy Production Ready Software by Michael T. Nygard

If you are in the business of making software systems, odds are that you might have heard about Nygard's book. People have raved about it since it was published in 2007.

That being the case, it had been on my to-read list for a while, but without any urgency. Then I went to the JAOO conference last month, and heard two sessions with Michael Nygard presenting his ideas. After that, I knew I had to get hold of the book straight away.

Release It! is something as rare as a book which is groundbreaking while stating the obvious.

First of all, Nygard makes the simple point that we (meaning the people in the business) are all too focused on making our systems ready to pass QA's tests and not on making ready to go into production. This is hardly news, but it's the dirty little secret of the business. It's not something you're supposed to say out loud. Yet Nygard does that. And not only that, he dares to demand that we do better.

Having committed this heresy, he goes on to explain how we can go around doing that.

He does that in two ways. First he present us for the anti-patterns which will stop us from having a running system in production, and then he present us for the patterns which will make it possible to avoid them. Or, if it's not possible to avoid them, to minimize the damage caused by them.

That's another theme of Nygard's book. The insistence that the system will break, and the focus on implementing ways to do damage control and recovery.

The book is not only aimed at programmers, though they should certainly read it, it's also aimed at anyone else involved in the development, testing, configuration and deployment of the system at a technical level, including people involved in the planning of those tasks.

As people might have figured by now, I think the hype around the book has been highly warranted, and I think that any person involved in the field would do well to read the book.

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Friday, November 21, 2008

God clarifies rules

Via Jill at Feministe

God Angrily Clarifies 'Don't Kill' Rule

Responding to recent events on Earth, God, the omniscient creator-deity worshipped by billions of followers of various faiths for more than 6,000 years, angrily clarified His longtime stance against humans killing each other Monday.

"Look, I don't know, maybe I haven't made myself completely clear, so for the record, here it is again," said the Lord, His divine face betraying visible emotion during a press conference near the site of the fallen Twin Towers. "Somehow, people keep coming up with the idea that I want them to kill their neighbor. Well, I don't. And to be honest, I'm really getting sick and tired of it. Get it straight. Not only do I not want anybody to kill anyone, but I specifically commanded you not to, in really simple terms that anybody ought to be able to understand."

Brilliant, just brilliant.

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Saturday, November 15, 2008

Why vaccinations matter

It's barely a week since Barack Obama was elected in the historical 2008 Presidential election, and there has been some rumors going around about which people he would pick for his administration. One of the names that has been mentioned, was Robert F. Kennedy, Jr. (RFK) as head of the U.S. Environmental Protection Agency (EPA).

RFK has a solid record on defending the environment, and some progressives where quite happy about this possibility. There was one group of people who were vehemently against this choice, however, the science bloggers (who are largely progressive). This might surprise people, but with a little background knowledge, it makes perfect sense.

Scientists, and science in general, have been among those most negatively affected by the Bush administrations, which were actively anti-science and anti-scientist. It would take too long to go into all of the ways this happened, but for more on this subject I recommend Chris Mooney's excellent book The Republican War on Science.

While not all scientists and science bloggers where overwhelmed by Obama, there was a clear sense that if Obama won, this would change. Politics would stop interfering in sound science, and scientists would not face political pressure to confirm with political stances. In other words, an Obama administration, would result in a, if not pro-science, then at least neutral attitude towards science from the politicians.

This is why the suggestion of RFK as head of the EPA dismayed many scientists and science bloggers. RFK as it happens, is not the sort of person that gives confidence of an pro-science atmosphere. As a matter of fact, RFK is considered not only ignorant of science, but actively against sound science by many of us.

Why do we feel this way? It all goes back to June 2005, where RFK wrote an article that appeared in both Rolling Stones and The article was titled "Deadly immunity" and was the shocking tale about how the scientific and medical community were covering up on how vaccinations causes autism. Or rather, how the component thimerosal, which degrades to ethylmercury, were the culprit of the rising number of autistic children.

This was indeed a shocking article, but not for the reasons RFK claimed. The shocking part of the article was the fact that anyone would publish it. Anyone spending more than five minutes on fact checking it, would have found numerous problems with it. The primary one being that there is absolutely no evidence of there being any kind of connection between vaccinations and autism. And it's not like there hadn't been any research into it at the time where RFK wrote the article. There had been large epistemological studies in several countries, including my own native country, Denmark, that couldn't find any causation between vaccinations and autism. While scientists and people in medicine, are cautionary in nature, there were an overwhelming consensus of rejecting any autism-vaccination link.

Another major problem with the article, is that RFK demonstrated rather impressively the difference between how scientists and lawyers debate. In science, it is regarded as a cardinal sin to leave out contrary evidence, to quote out of context (often referred to as "quote-mining"), and to pick just the data that suits your (called "cherry picking"). Among lawyers, this is not only acceptable, but actually good practice - they are trying to win a case after all. One of the things RFK did in the article, was to quote parts of the transcript from the Simpsonwood conference, where a possible autism-vaccination link was debated. The quotes RFK presented gave a clear indication of a conspiracy to hush up a autism-vaccination link, demonstrating to the readers that the scientists had something to hide. The problem was of course, that the quotes were taken out of context, as a skeptic blogger, Skeptico, demonstrated by finding the quotes in the transcript, and including the context (Robert F. Kennedy Junior’s completely dishonest thimerosal article). So, not only were the transcript of the conspiracy easily available on the internet, but a quick browse through it, would demonstrate that there were actually no conspiracy at all.

Still, RFK's articles did their job, making the readers believe that there were something dangerous about giving their kids vaccinations, thus increasing the number of people who didn't give their kids any.

That's unforgivable.

It's without any type of hyperbole that I would claim that vaccinations are among the most important contributors to the increased standard of living in the last 100 years. It's practically impossible to overstate the impact the availability of cheap, easily obtainable vaccinations have had on our societies today.

20 years ago, when I had English in my primary school, I had a teacher who could not use one of her arms, due to the polio she had as a child. Polio used to cripple, and even kill, children every year until the vaccinations made by Stalk in 1952 and Sabin in 1962 made it possible to vaccinate against it. Now polio is extremely rare in the Western World.

Smallpox used to be a major thread all over the world. According to the WHO fact sheet on smallpox: "As late as the 18th century, smallpox killed every 10th child born in Sweden and France. During the same century, every 7th child born in Russia died from smallpox." Now Smallpox is considered eradicated, due to a worldwide vaccination campaign.

Less serious diseases like Rubella, Mumps and Measles, are covered by the MMR vaccinations given in childhood. Rubella can cause brain damage to the child, if caught by a pregnant woman. Rubella and Mumps can cause hospitalization, but are rarely fatal. Measles, on the other hand, causes deaths. According to the WHO fact sheet on Measles:

# Measles remains a leading cause of death among young children, despite the availability of a safe and effective vaccine for the past 40 years.
# In 2006, it was estimated that there were 242 000 measles deaths globally: this translates to about 663 deaths every day or 27 deaths every hour.

In other words, Measles are not just a minor issue, and people who allow their children to get effected with Measles, are risking their lives. Even if the child survives, there is a real risk of brain damage from complications due to Measles.

And then there is the problem of herd immunity.

Some people who are vaccinated, are not actually immunized. This means that if there is an outbreak of the disease, they are at risk catching it. Others are not able to get the vaccination for medical reasons (problems with their immune system could be one reason). Again they are at risk during an outbreak. These people are dependent on "herd immunity", where enough people are immunized to keep the diseases from spreading. Due to the increased number of children not getting vaccinated, these people are at increased risk of getting the diseases. So, it's not just the health of their children the parents are risking, it's also the health of other peoples' children.

As it stands right now, it doesn't look like Robert F. Kennedy, Jr. is going to be appointed as head of the EPA, but the dark legacy of his fear mongering lives on. He has never retracted any of his statements in the article, and he is actively supporting the "Green Our Vaccines" campaign lead by Jenny McCarthy - another campaign aimed at getting people scared of vaccines. The war against science lives on, in another legacy. Let's hope it never gets officially sanctioned by the Obama administration.

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Thursday, November 13, 2008

PZ is getting slow

In the old days, PZ would not have let someone else scoop this story, but I guess he is getting slow now where he is king of the mountain.

ScienceDaily reports

Octopus Family Tree Traced Using New Molecular Evidence

Octopuses started migrating to new ocean basins more than 30 million years ago as Antarctica cooled and large ice-sheets grew.

I don't really have anything to add to this story, though I suggest people go read it. I just wanted to scoop PZ.

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Sunday, November 09, 2008

Be careful when working with computers in Pakistan

Via Wired, I became aware of a new cyber crime law in Pakistan.

The Wired article focuses on the death penalty part of the law, which I consider barbaric (as I do all death penalty), but which will require the death of others to be effectuated. In other words, those crimes would normally be covered by manslaughter or murder charges.

No, the big issue with the law is that it's overly broad. Teeth Maestro explains more: Draconian Cyber Crime Law in Pakistan

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Water, water, every where, Nor any drop to drink.

I found this new finding interesting. ScienceDaily reports on a new study that shows that sea snakes drink fresh water.

Sea Snakes Seek Out Freshwater To Slake Thirst

Sea snakes may slither in saltwater, but they sip the sweet stuff. So concludes a University of Florida zoologist in a paper appearing this month in the online edition of the November/December issue of the journal Physiological and Biochemical Zoology.

Harvey Lillywhite says it has been the “long-standing dogma” that the roughly 60 species of venomous sea snakes worldwide satisfy their drinking needs by drinking seawater, with internal salt glands filtering and excreting the salt. Experiments with three species of captive sea kraits captured near Taiwan, however, found that the snakes refused to drink saltwater even if thirsty — and then would drink only freshwater or heavily diluted saltwater.

So, saltwater sea snakes can literately dehydrate while swimming in their natural environment. That means that they need to live fairly close to fresh water, which limits their possible habitat.

This is why I love the scientific process. It was thought that we knew how sea snakes slake their thirst, but someone still make sure to investigate the subject, and thus proved the common assumption wrong.

The study can be found here (unfortunately behind a pay-wall)

For more information about the sea snakes, I recommend the wikipedia entry on the subject

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Saturday, November 08, 2008

Warming of polar regions attributed to human activity

The current issue of Nature Geoscience has a letter which contains some pretty interesting stuff, and luckily, they are nice enough to make it freely available on the internet.

Attribution of polar warming to human influence

The polar regions have long been expected to warm strongly as a result of anthropogenic climate change, because of the positive feedbacks associated with melting ice and snow. Several studies have noted a rise in Arctic temperatures over recent decades, but have not formally attributed the changes to human influence, owing to sparse observations and large natural variability. Both warming and cooling trends have been observed in Antarctica, which the Intergovernmental Panel on Climate Change Fourth Assessment Report concludes is the only continent where anthropogenic temperature changes have not been detected so far, possibly as a result of insufficient observational coverage. Here we use an up-to-date gridded data set of land surface temperatures and simulations from four coupled climate models to assess the causes of the observed polar temperature changes. We find that the observed changes in Arctic and Antarctic temperatures are not consistent with internal climate variability or natural climate drivers alone, and are directly attributable to human influence. Our results demonstrate that human activities have already caused significant warming in both polar regions, with likely impacts on polar biology, indigenous communities, ice-sheet mass balance and global sea level.

Basically, what the letter says, is that the scientists looked at the observed temperatures, and found that the only way they could be explained, was through anthropogenic temperature changes (i.e. through humans).

The fact that it's a letter, might make people think that it carries little weight, but letters in Nature Geoscience are actually papers which has passed peer-review, and not just the opinion of the writers (as they are in e.g. newspapers). So, in other words, this is a scientific study, like any other study published in Nature Geoscience.

The melting of the polar areas have long been a major example of how anthropogenic temperature changes affect the world, but until now, it has been hard to attribute the changes there directly to anthropogenic temperature changes. This paper goes a long way towards that.

Not that this conclusion was really in doubt among climate scientists, however, there has always been some uncertainty about whether part of the changes, in those parts of the world, might have had other causes. According to this study, it appears that they didn't.

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Aggressive people might get pleasure from the pain of others

ScienceDaily reports on a new study that indicates that aggressive youth get a kick out of seeing other people in pain.

Bullies May Enjoy Seeing Others In Pain

Scans of the aggressive youth's brains showed that an area that is associated with rewards was highlighted when the youth watched a video clip of someone inflicting pain on another person. Youth without the unusually aggressive behavior did not have that response, the study showed.

The youth were picked because they had a record of aggressive behavior, while the control group didn't have such records.

The study is interesting because it indicates that aggressive people don't just lack empathy, they actually enjoy seeing other people in pain. In other words, they are sadists (though not necessarily with the sexual connotations that word sometimes contains).

There is more about the study at the website of the University of Chicago, which also links to a pdf version of the paper which is published in Biological Psychology.

So, what does this mean? Well, I guess it will be easier to determine whether aggressive behavior by someone is an one-time occurrence, or it might be symptoms of a general tendency towards aggression. In the later case, it might be important to work with the aggressive person, so they can try to behave in a socially acceptable manner. It cannot be stressed enough that just because someone get pleasure from something, it doesn't mean that they cannot avoid doing that thing. So, in other words, this knowledge must never become a tool for judging people, though it could perhaps be used as migrating circumstances in first-time juvenile cases.

BBC also writes of the study, and they bring up an important point.

Dr Michael Eslea, senior lecturer in psychology at the University of Central Lancashire said the research was interesting but needed to be repeated in a larger sample.

"A better understanding of the biological basis of these things is good to have but the danger is it causes people to leap to biological solutions - drugs - rather than other behavioural solutions."

Yes, just going for drugs is not a good long-term solution, but in some cases it could perhaps be a short-term solution.

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Wednesday, November 05, 2008

Morning in America

As most of people in the world, I've waited for the US election result with excitement, mixed with fear. As the title of this blog shows, I am unapologetic pro-science, and as my posts show, I am a progressive. As such, there could only be one desired result of the US election. Thankfully, that's the one we got.

Obama is a little too religious for my taste, but he has good instincts about not making political decisions based on his religion. He is also very intelligent, and appears to understand that politics and diplomacy involves working together with others. All in all, he is not just "the lesser of two evils", but rather a good candidate in his own right.

Congratulations America, you made the right choice.

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