Monday, October 1, 2012

Irreproducible Results

In my BBS days (probably in 1992) I stumbled upon an interesting text file. It claimed to contain the instructions to build a nuclear bomb! It was formatted in a sensible manner and written in good English. The content was highly entertaining, though I wasn't sure if smoke detectors' americium is really fissible material.

Alright, the text was from The Journal of Irreproducible Results - I think the text was titled "Let's Build a Nuclear Bomb". At the end of the file, there were teasers of other articles, such as "Let's Build a Solar System" or "Let's Make Contact With an Extra-Terrestrial Civilization" (if I recall correctly). Sounds entertaining but not really reproducible.

Is research supposed to be reproducible? If you read a research paper and take a look at its fancy charts and other visualizations, can you actually reproduce the results? If the paper claims a discovery that enables you to build an atomic bomb out of smoke detectors, can you prove it right or wrong? (Sure, a paper like that would probably not pass peer review phase, but hypothetically...)

Today - 20 years after I found the text about building a nuclear bomb - research often involves huge amounts of data. Often, that data is actually proprietary. The results may be entirely based on secret data that is not available to anyone, and cannot be (easily) generated by anyone else than its owner and generator. Still, the research can be held in great value - actually, that is how different products are certified for use.

As astonished I am about the fact that reproducing results is difficult, I am also about the fact that some have actually acknowledged the problem within the scientific community and developed tools and approaches to alleviate it. Lately, I have been looking at knitr which is an R module for dynamic report generation. Using knitr, there can be a direct link between the document and the original data set(!). Another interesting approach is lightweight markup languages such as Markdown which I evaluated in my bachelor's thesis some years ago. In a way, this is "open source research", where you open up the methods and data to anyone who is interested in them.

As a sidenote: Some years ago, the Finnish-language Master's thesis Kotileikkej√§ ja lastenkasvatuspuuhia was written by Juhapekka Tolvanen. An important aspect - though in no way related to the topic of this thesis in the field of sociology - was that it was released with the GNU Free Documentation License and the LaTeX source code was (and is) downloadable from the author's homepage, thus making the thesis printable and publishable in different formats. However, plain LaTeX source code is not very readable (though Mr. Tolvanen might disagree) - and most of the formatting of the actual text content could have been done with Markdown.

For smaller projects it is maybe easier to incorporate transparency, distribution of data sets used in the research and demonstrating exactly how the results were produced, but can this approach be more widely adopted by peer-reviewed journals? For that, I don't know the answer, I just know the direction where I would like them to go and where I will go.

Tuesday, June 19, 2012

My problems with Prometheus

Everyone wants to complain about Ridley Scott's Prometheus. Everyone has their reasons and so do I. I have a blog, so I must write something, right?


The problems start with the trailer. What do we know after seeing this?

  • Scientists go to find their creator, or ancient humans.
  • They find a deserted temple of some kind.
  • It turns out that it isn't deserted after all - it is Space Jockeys' base! Space Jockeys are human and they created us for some purpose!
  • There are alien eggs (or something) around there.
  • Chaos ensues and people (presumably) die one by one.
  • Humans' spaceship is destroyed in a collision with some other object (presumably trapping humans on the planet that they found).
  • A circular object drops from the sky or is otherwise falling on the ground.
Even before any trailers, the director gave hints that the events in this movie happen in the Alien universe before the time of the first Alien movie, but there are no Xenomorphs in this one. Instead, this movie shall in some way explore what the Space Jockeys are.

It would be disappointing if those observations from the trailer would appear correct, wouldn't it?


I think the movie was pretty enjoyable with some suspense, though no humor or horror elements. Special effects were relatively entertaining, but they were also quite generic CGI.

Spoiler: All of the above observations from the trailer ended up being totally correct.

I'll list my principal problems with the movie here.
  • General lack of motivation or sense of purpose. Things happen but there is no real reason for them to be happening. What triggered them? Ghost in the machine or some real mechanism that is supposed to be contained in the scenario?
  • Talk about the lack of aliens. Of course there are aliens here, it was revealed right in the trailer. Maybe there were not exactly the same type of adult Xenomorphs that we saw in the previous movies but aliens anyway.
  • Where do the baby aliens get all the biomass? How can they grow to fill a room in a day without eating anything?
  • Why do the scientists remove the helmets? It should be in the basic training of field work that you shall not contaminate the place. Also, if the alien planet has the same kind of atmosphere (including pressure) that Earth has, same kind of bacteria can also live there. Why did they not think about this? (Granted, Shaw is pretty cute.)
  • Shaw & co. went pretty far before seriously suspecting that there was something sinister in the company's motives behind funding this trip.
  • Even though the human entourage is full of scientists, there is no scientific discussion about what is happening. Things are just noted and accepted without questions.
  • When the captain notices that the cave forms a circle, he immediately knows that it is a spaceship and announces it. Everyone believes him. Why? In the Alien universe, spaceships do not look like circles. There is no apparent propulsion, crew areas, antigravitation, fuel, sophisticated control surfaces or other mechanisms that a spaceship would probably have.
  • Even when this spaceship started to levitate, it should not have been apparent that it was a spaceship. In the Alien universe, spaceships do not levitate - they have motors. 
    • When they arrive at this planet, why does the ship accelerate towards the planet? Shouldn't they be decelerating at that point?
  • It is difficult to conceive why the crew of Prometheus were so happy to kill themselves.
  • Why does David think that he could fly one of those ships? Are they made for children to fly?
  • Umm, why was the old guy on the ship?
  • Why was this movie released in 3D?!
That's it. A clever science fiction flick that plays with mystery, cool effects and aliens. Extremely predictable, especially after seeing the trailer. Why?

Monday, February 6, 2012

Error messages and invalid error messages

Error messages are necessary evil. If something goes really wrong, the user must know. However, they should always be useful - otherwise they should not be displayed, right? They should also be correct.

I use Foursquare on my Android phone. Every once in a while, in the maze of different Wi-Fi hotspots at University of Michigan Central Campus, the phone switches from mobile data to Wi-Fi and back. And does something, I couldn't care less. Foursquare apparently has a problem with this and it complains.

"Foursquare connection invalid", it says. Well, I can clearly see that at the moment there is no Internet connection at all, so how can Foursquare have a connection in the first place? How can I fix Foursquare's connection if there is no connection? Even if there was, what should I do?

"No Internet connection" is also a bad error message, especially when I am connected to Internet. If Foursquare has trouble connecting to its own servers, it should not give error messages about my phone's connection in general.

I know that switching between mobile data and Wi-Fi hotspots can be challenging connection-wise. However, shouldn't Wi-Fi connections make connectivity better, faster and more convenient? Actually, at the campus, the phone tries to connect Wi-Fi hotspots here and there, thus immediately abandoning the mobile data, even before actually establishing connection. The result may be that there is no network connection for long periods of time. This can be fixed by not using Wi-Fi at all, or "forgetting" all networks that the phone tries to connect. There is no "Disconnect" - they must be forgotten, at least on Samsung Galaxy S II.

Monday, January 23, 2012

Why I would not vote for Ron Paul for President

Ron Paul is one the four most prominent candidates in the race to be nominated as the Republican Party's presidential candidate, to run against Democrats' Barack Obama in 2012. Newspapers and social media websites are full of quotes from GOP debates - making it pretty obvious to me that most of the well-known Republican candidates are idiots.

I am (kind of) sorry for that expression, but I cannot avoid the impression I have got from the remarks they have made. Bachmann, Perry and Santorum are just way out of line and Cain did not seem to be smart enough to understand what's wrong with his message. Newt Ginrich is somehow just a boring, repulsive professional politican (with lots of experience) and Mitt Romney a less repulsive but just as boring politician. If I have counted correctly, that leaves out Ron Paul. Because I know many smart people who share (some part of) libertarian ideals, I thought I should write this blog post to explain why I (even though I am smart!) would not vote for him.

Many of the Republican stereotypes do not apply to Ron Paul; he does not seem to want to have a system that pushes his personal (religious or political) beliefs down everyone's throat. He is undeniably bold and intelligent and is not afraid of being at odds with even fellow Republicans. But of course, he is not a Republican at heart, he is libertarian and happens to be playing with Republicans out of necessity, as in United States you must be with the Democrats or Republicans in order to achieve any political offices.

I sincerely hope that Ron Paul wins the Republican nomination, for many reasons. It would be a shock to Republicans and may force them to rethink many policies, interventionist doctrines and so on. It would also make the future debates with Barack Obama much more interesting. He is very much "electable" but not probable to win. Against Obama, I think Paul would be the wrong choice (but I think Paul will try to get nominated every four years as long as he is alive). I am happy not to be writing about this as a U.S. citizen, so I do not have to make a choice and vote, because I do not like the U.S. political system in general.

The Ron Paul Newsletters - or different publications that were published under Ron Paul's name but him apparently not being aware what was being published - are a difficult matter. I know that Paul has said it was stupid not to have any knowledge of the stuff that the publications contained. They had a lot of text that would be considered racist, bigotry, conspiracy theories and so on. I find it very difficult to understand how a prominent businessman and politician could be so ignorant of what is published under his name, how can he screw up so badly?

As a politician, Ron Paul does not really have a track record of cooperation and going by the general opinion of his partymates or the government's. As a president, who leads the whole country, that is a major problem. Obama is criticized as being "too negotiating" and not taking enough stance on matters,  but I fear that Paul would be far too independent and constantly at odds with Congress and Senate. As a result, it would be difficult for him to push through any new policies, and as everybody knows, he has plenty of them. I am not convinced of his ability in making compromises in matters that he has declared as critically important.

I think many of the libertarian ideals that Paul upholds make a lot of sense. However, I do not think it is the best way to advance them to have a libertarian president who must fight the Senate and the Congress who very much disagree with those ideals. I know that libertarians believe that having no (or very little) taxes, no mandatory or state-provided health insurance etc. would contribute to a better world, more liberty, more jobs and less poverty. I do not believe that. Like communism, libertarianism would not work. Instead, both of them are useful and many of their ideals can be used in real world.

I am also worried about Paul's stance towards abortion. He regards an embryo a "person". This would mean that abortion is for some purposes, among other things, a murder. I dislike the American polarized discourse about abortion, but I do not think that abortion should be classified as murder (intentional killing of a person).

Even though I generally support Paul's ideals about not interfering other countries' matter so much, not waging war and not spending so many trillions of dollars into military (especially with budget deficit), I think his proposals are a too unrealistic again. The operations in Iraq and Afghanistan have left United States with obligations that it cannot just abandon like that.

I also don't like Paul getting money from a Ku Klux Klan leader and being satisfied with the donations. However, this might not be as big an issue as it has been advertised to be.

So, is Ron Paul, or would he be, a good leader? Caring yet strong, understanding of issues both domestic and foreign? Does he have friends, does he make friends? Is his view of the world correct? I think not.