Lazy cat

Yesterday I had to defend my internship report; everything went better than I could’ve expected. I almost couldn’t stop talking, and my presentation was between 45-50 minutes (while 20 minutes was sufficient). Anyway, the questions afterwards were not that difficult, and all in all they were happy with the way I had worked during my internship.

Now I’m at my parents for a few days, and when I was goofing around with one of our cats, I had the chance to stare right into the belly of the beast:

Straight into the belly of the beast

Cosmic background radiation

I finally finished my course on Quantum Optics; in the book we used was a question about the “number of photons per unit volume excited in a cavity at temperature T” (Loudon, Quantum Theory of Light). After deriving a formula for this, you can show that the cosmic background radiation contains about 4-5*10^5 photons per litre.
I always got stuck at the same point, but now I finally know how to solve this.

Read the attached pdf if you want to know the solution.

Hurricanes and global warming

There’s an article in Scientific American (July 2007) about the relation between global warming and hurricanes. I learned a few things from this:
A cyclone, typhoon and hurricane are the same thing; they only differ in the region where they are observed.

How do hurricanes form?

• The sun raises the Sea Surface Temperature (SST)
• Water is evaporated to release the excess heat
• The moisture raises and condenses into rain
• When raindrops are formed, latent energy is released
• The heat goes up and creates ‘updrafts and thunderclouds’
• Beneath this area, a low pressure zone is created which ’sucks up’ moist air
• Due to Coriolis forces due to the earth’s rotation a vortex is created
• “The eye” is a low pressure area at the bottom of this vortex
• Due to the circling hot air, the rising air dries and gains energy
• Some of this air is absorbed again in the eye, and some of the air ’spirals out’ over a large area (many kilometres)

The different seasons play a role as well:
The energy released when raindrops form heats the atmosphere

• In winter, the heat goes up and radiates into space
• In summer, the heat rises to higher altitudes in tropical areas

Further ingredients needed to start a hurricane:

• high SST (>26 degrees Celsius); SST may rise due to the greenhouse effect
• plentiful water vapour
• low pressure at the ocean’s surface
• weak wind shear between low and high altitudes (strong winds destroy emerging vortices)

The rising SST may (partly) originate from the greenhouse effect. However, in 2004 and 2005 we saw a lot of hurricanes, but 2006 was a quiet year.

Some scientists believe this is due to the “Atlantic Multidecadal Oscillation” (AMO), which is basically a cycle in which temperatures rise and fall. But simulation shows that this can’t be the whole story (the temperature difference is only 0.5 degrees Celsius). The models do show (as far as they are correct; which is difficult to assess) that human action is likely a cause of the rising SST. Approximately 0.6 degrees Celsius can be attributed to human action (probably without the AMO) since 1970. It is noted that this may sound small, but only one degree can change the storm’s intensity to a higher category. This may well explain the rise in the number of ‘high’ category hurricanes.

The fact that 2006 was a quiet year (in stark contrast to 2004 and 2005) is due to a different factor. In 2004/2005, El Nino warmed the ocean. La Nina cooled the ocean the subsequent year. This is explained in the remainder of the article.

The article concludes that the hurricane threats are likely to get more severe.

An argument against tax increase on alcohol (in Russia)

Now an article from New Scientist about alternatives to alcohol used in Russia. The article opens with the following:

“A shocking 43% of deaths in working-age Russian men result from drinking alcohol not meant for human consumption, such as cologne and cleaning agents, according to a new study.“, which helps explaining why Russian men have the lowest life expectancy at just 59 years!

The alternatives to alcohol are cheaper and have a higher alcohol content. On the positive side, when drinking eau the cologne, burping may give a more pleasant smell… This must be an attractive feature to the women ;).

Not surprisingly, the people that drink the ‘alternatives’ to alcohol, have a much higher risk of alcohol related death.

Finally some shocking figures:

• “Russian men who drink non-beverage alcohol have a five-times greater risk of alcohol-related death (such as liver cirrhosis and alcohol poisoning) than those who do not consume these products“
• “Men who drank only non-beverage alcohols had up to a 20-times greater risk of death“
• These figures are probably higher, as the research didn’t include men who lived alone, or men who lived on the streets
• “Alcohol is linked to 72% of murders and 42% of suicides in Russia, according to 2005 figures“

Bring on the Soviet-Russia jokes ;).

Antibacterial soaps

In the category ‘Weird Science’ an article appeared on the site of Scientific American about antibacterial products. More and more antibacterial products are used, but to what avail?
Normal soaps wash away ‘nonspecifically’, “meaning they wipe out almost every type of microbe in sight—fungi, bacteria and some viruses—rather than singling out a particular variety.“
On the other hand, after applying antibacterial products, conditions may arise which may actually help the resistent bacteria, because not all bacteria may be killed. In fact, “a small subpopulation armed with special defense mechanisms can develop“, so that these bacteria develop a tolerance and reproduce. This, in turn, may help the bacteria in growing resistant to certain antibiotics.
A problem that arises is that, at least in America, certain antibacterial compounds are found in “60 percent of America’s streams and rivers“, and may eventually end up in crops.
In the end, the advise is to wash your hands 3 times a day with regular soaps, and leave the antibacterial soaps at hospitals.

Ringfinger response

From one “research“:

Kids with longer ring fingers compared to index fingers are likely to have higher math scores than literacy or verbal scores on the college entrance exam, while children with the reverse finger-length ratio are likely to have higher reading and writing, or verbal, scores versus math scores.

From different “research“:

The research, done at the University of Alberta and announced Wednesday, found a connection between the length of the male index finger relative to the ring finger and the tendency to be aggressive.
No such connection was found in women.

Testosterone promotes development of mathematical and spatial skills. On the other hand, more estrogen promotes development of verbal skills, which lengthens the index finger.

On the same page it is mentioned that the longer the ringfinger is, the larger the amount of testosteron during the pregnancy. More testosteron results in more agression (at least, it makes it more likely; nothing can be said about individuals, only about groups). So this perfectly explains why you see all the agressive bald mathematicians, with those leather jackets, tattoos with hearts of “Mama”, scars and such at the G8 demonstrations.

Remember though, that other things like “flawed brain chemistry, brain damage, genetic defects, an unhealthy psychological environment” all contribute to the behaviour, so one needs to be careful about deducing characteristics from future lovers.

Oh yeah, my ringfinger is approximately 13 mm longer than my indexfinger. Nothing unexpected, as people know me as a highly agressive vegetarian listening to 60s music, enjoying math.

(The reason the word “research” is between quotes, is because I’m not too confident in these types of research. There may be a correlation, but that doesn’t mean  there’s a connection (in the form of causation) between the two. I have to admit I didn’t read the original articles (which were published), but my expectations are too low to be bothered with it. Also, the amount of test-subjects in both “researches” is pretty low; add some statistics, and you can easily produce true lies.)

Think more, get less

There’s an article in the June 2007 episode of Scientific American, also published on their site.It is written by Kaushik Basu.
It’s about the curse of rational choices when playing the “Traveler’s Dillemma” game:

“Lucy and Pete, returning from a remote Pacific island, find that the airline has damaged the identical antiques that each had purchased. An airline manager says that he is happy to compensate them but is handicapped by being clueless about the value of these strange objects. Simply asking the travelers for the price is hopeless, he figures, for they will inflate it.Instead he devises a more complicated scheme. He asks each of them to write down the price of the antique as any dollar integer between 2 and 100 without conferring together. If both write the same number, he will take that to be the true price, and he will pay each of them that amount. But if they write different numbers, he will assume that the lower one is the actual price and that the person writing the higher number is cheating. In that case, he will pay both of them the lower number along with a bonus and a penalty–the person who wrote the lower number will get $2 more as a reward for honesty and the one who wrote the higher number will get $2 less as a punishment. For instance, if Lucy writes 46 and Pete writes 100, Lucy will get $48 and Pete will get $44.

What numbers will Lucy and Pete write? What number would you write?”The point is, when you don’t think much about it, you’d choose $100. However, when you start thinking more, you’d write down $99: because if you write down $99, and the other person will write down $100, you will get $101, while the other only gets $99. Then you start wondering if the other person thinks the same… and you obviously don’t want the other person to have more money. So you reduce your amount to $98 (thinking the other person will write down $99), so you’ll get $100, and the other person only $96. And so on. In the end, you’ll arrive at $2. In this way, you earn a lot less then the naively chosen $100.

This problem is the same, the article explains, as the Prisoner’s Dilemma: “… in which two suspects who have been arrested for a serious crime are interrogated separately and each has the choice of incriminating the other (in return for leniency by the authorities) or maintaining silence (which will leave the police with inadequate evidence for a case, if the other prisoner also stays silent).”

A Nash equilibrium, is when there’s no benefit (put simply) to change your strategy: in this case the equilibrium is at $2 (the absolute minimum of choices). This is what Game theory predicts; but it conflicts with our intuition.

In experiments, the choice people make depends on the reward: when the reward is low, the choice will on average be higher. On the other hand, when the reward is high, the choice will be lower. This makes sense, because when the reward is high relative to the choice, it’s more advantageous to lower your choice. For example, if the reward is not $2, but $50, you wouldn’t want your choice to be too high: the penalty you’d get would severely impact your profits.

Then why do we make these choices, based on our expectations that the other person will choose a high number? The article suggests:
“Perhaps altruism is hardwired into our psyches alongside selfishness, and our behavior results from a tussle between the two. We know that the airline manager will pay out the largest amount of money if we both choose 100. Many of us do not feel like “letting down our fellow traveler to try to earn only an additional dollar, and so we choose 100 even though we fully understand that, rationally, 99 is a better choice for us as individuals.”

The moral: sometimes it’s good not to think too extensively about seemingly simple questions.

Calculating Pi for fun and profit

This one is for my grandchildren :P. I found a nice intuitive way of calculating Pi. The only thing you need to understand is the Pythagoras Theorem. Consider the figure below:

To calculate the area of the circle, we take small steps.

• First we calculate the area of the grey part. It’s simple to see that this area is 0.5(1×1).
• Then the area of the red part. This is a little more tricky. To calculate the area, we first want to know the length of S. We see that the length from A to B equals 2S. With the use of Pythagoras, we find that 2S equals the square root of 2. So we know S: 0.5*sqrt(2). If we would also know T (and hence 1-T), then we could find the red area. But T is equal to S. A different way of finding T, is using Pythagoras again; we know OA=1, and we know S, hence we know T: the square root of 0.5. Thus the area of the red part equals: 0.5*0.5*sqrt(2)*(1-sqrt(0.5))=0.104.
• Now the green area. Well, we know (1-T) and S. So we know V. And W is 0.5*V. Now we only need to know the small side of the green triangle. This is where it gets tricky. (And messy). If we know O-fi then we’re all set. But OA=1, and we know Afi=W! Using Pythagoras (remember him?) we find filambda=1-fiO=1-sqrt(OA^2-Afi^2)=0.0439. So the area is approximately 0.0439*W=0.0439*0.29289=0.01286.

Note: wordpress doesn’t allow Greek symbols. So that explains “fi” and “lambda”
The only thing that needs to be mentioned, is that we have to multiply the grey are with 4 for a complete circle (we only considered 1 quadrant), the red area with 8, the green area with 16, etc.

Of course it’s possible to make a small script for this. I did all the fun for you, and coded it in Matlab. The code is a mess, but it’s posted here as a reference. If you understood the above (or if you came to this point without weeping), the code shouldn’t be hard to follow.

The real Pi is 3.1415926535897932384626433832795
# of iterations             found value

1                                    2.0000000000000000000000000000000
2                                    2.4142135623730949234300169337075
3                                   3.0614674589207182551770244842800
4                                   3.1214451522580524351896677430859
5                                   3.1365484905459392823695871570607
10                                 3.1415877252771597505203060598746
25                                 3.1415926535897902256560013790759
30                                 3.1415926535897951086718985911613
50                                 3.1415926535897951086718985911613

This means there’s a difference of 1.7764e-015=0.0000000000000017764, or a percentage of 0.5953e-13%=0.0000000000005953%. Not bad.

After about 30 iterations, we don’t see any change in the calculated Pi anymore. This is due to my coding skills, and the precision of the script. But I think it’s clear it does what it needs to do; the method works.

Huntington’s disease

In the April/May 2006 (Yes, it’s an oldie, but I’m just catching up) edition of Scientific American Mind, there’s an interesting article written by Juergen Andrich and Joerg T. Epplen about Huntington’s disease.

It starts with simple incidents, such as forgetting a familiar address, or dropping a cup. But they are not incidents. Not clumsiness, forgetfulness or overreaction either. At least, when you have Huntington’s disease, an inherited disease of which the mutating gene was discovered in 1993. It leads to “progressive destruction of the brain, crippling muscles and mental function“. This mutation wreaks havoc inside the brain.

A single gene on chromosome 4 (the huntingtin gene (no misspelling)) is the cause. DNA consists of 4 bases: Cytosine, Adenine, Guanine and Thymine. If the CAG sequence on this gene occurs more than 35 to 40 times (instead of the regular 28 times), this chain becomes too long and causes trouble. The longer the chain of CAG-sequences, the earlier the disease starts showing, and the more severe it gets.

The symptoms usually show up when at age 35-45, but this also depends on the length of the chain.

Saint Vitus dance, an “involuntary movement disorder“, is characterized by “brief, irregular contractions that are not repetitive or rhythmic, but appear to flow from one muscle to the next. These ‘dance-like’ movements of chorea (from the same root word as “choreography”) often occur with athetosis, which adds twisting and writhing movements.” This is also seen in Huntington’s disease. But mental symptoms often occur before the physical problems, which also leads to social problems (relatives, friends, etc.), and even suicide. Before 1993 (when the responsible gene was discovered) people were often misdiagnosed as “mentally ill or alcoholic”.

What follows is something I don’t fully understand and therefore may not be very clear, but I’ve included it nonetheless:
When the elongated protein starts binding with other proteins, the function of those proteins is in danger.
Glutamate is a neurotransmitter, a chemical which helps a neuron “talk” with another cell. Synapses allow the neurons to form a network and communicate, and function as a system.
Via some complex process, some neurotransmitters won’t be removed “such as glutamate from the synapses“, resulting in “adjacent neurons continually excited” which will damage the cell.
Because of some other difficult process, it’s inpossible for the huntingtin protein to bind to the HIP-1 protein: “the neurons are driven to kill themselves.”

Science and Law – Part 3

-Read part 0 here -
-Read part 1 here -
-Read part 2 here -

Genetic Science and Truth
As with fingerprinting the uniqueness of a profile, be it a DNA profile or a fingerprint, is an important component in the legal inquiry. However, this should not be confused with the ‘attribution question’. Jasanoff argues that the attribution question molds into the unniqueness question, indicating “how faith in science’s truth-telling capability can distort both the logic and the normative function of legal inquiry.”

Especially with the amount of information gained from genetic science, overreliance on the implications of genetic studies can be troublesome. As more and more genes are mapped by the Human Genome Project, the focus on predictors of physical traits (eye / hair color, diseases, mental conditions) shifts to behavioral characteristics (agression, thrill-seeking), paving the way for eugenetics (leading to the racial rationale in the Nazi regime). This mapping of genes doesn’t eliminate the ‘nature vs. nurture’ -debate, as behavioral characteristics are heavily influenced by surroundings. However, as is noted by the author, money is still spent on research for finding “biological solutions to deep social problems“, as a faster solution for the various (slow) social policies to solve poverty and inequality (e.g. just let the intelligent people survive, to create a more balanced society. Or is there a genetic marker only existent in violent people?).

Science is used as a tool to repair human behaviour and mental conditions. But, as results from the Human Genome Project indicate, because the relative low amount of genes in the human species (only about twice as much as a fruit fly), the explanation of human behaviour doesn’t come from the genes alone.

Extreme care should be taken in explaining human behaviour on the basis of genetic information, or in extending results beyond what the research question.

Jasanoff ends with the article with:
“In a court of law, science cannot hold itself out as simply science, the source of transcendental truths; more modestly, and with appropriate caveats, it can be the source of just evidence.“

Science and Law – Part 2

-Read part 0 here -

-Read part 1 here -

Law Enforcement Science
It’s impossible to completely dismiss the possibility of human error. Some mistakes are easy to detect and correct, others are almost impossible to find. Mistakes can result from pressure, insufficient quality control mechanisms, fraud, etc.

Through the act of “normalization of deviance“, people anticipate on common problems and compensate them without starting all over again, which would be costly and time-consuming. Visibility of a high profile case can lead to cover-ups because of fear of public opinion (e.g., a mistake is made, but due to high public pressure the mistake is never admitted).
Also, even in the scientific community, researchers “seduced by the lure of success” are able to make up results, and it may take quite some time before the “organized skepticism” works as it should have. Examples are the various claims that AIDS can be cured, cloning embryonic stemcells, cold fusion, etc. But this fraud is not limited to the scientific community; fabricating evidence (e.g. by law officers) is something that can be done easily, even subconsciously. For example, when comparing two fingerprints, it’s easy to say that the two prints match even if they don’t, just because the need for a suspect. The need for “organized skepticism” is enormous, especially when someone’s life is at stake.
Jasanoff expresses it beautifully: “When the purpose is to free a presumably innocent, wrongfully convicted prisoner, forensic scientists have every incentive to produce the most reliable and persuasive results within their power. By contrast, when the purpose is to convict the guilty, extraordinary pressures may exist to produce results that will satisfy the prosecutor’s and the public’s desire for speedy convictions.“

Science and Law – Part 1

-Read part 0 here -

Truth in Science and Law

Science as a independent research topic, and science used in the aid of convicting both look for truth. The difference between the two activities is the context:
“For the most part, facts produced to serve the aims of litigation do not grow out of, nor play a part in, the same kinds of social interactions as do the facts produced in basic research science or even in regulatory science.“
Because of the different contexts, there’s also a difference in what is regarded as “truth”. A simple illustration is in the judiciary: to convict a suspect, facts have to be “proved” beyond reasonable doubt. In a strict sense this is not a proof, as doubt may always exist. It’s not a mathematical formula that can be proven. So, in short, what is true for the law, doesn’t need to be true for science.
There are four differences between Truths in science and law:

• A truth in science should be valid in a general case, whereas truths in the law is only of interest in specific cases. With this notion, it immediately becomes clear that the way the scientific community eastablished facts doesn’t work in law: in most cases there’s no peer review, hence no replications of the fact. Also, the purpose of science is to advance the knowledge, so that that knowledge of today can be used tomorrow. In contrast, the purpose of science in the law is to use the knowledge of today for things that happened in the past. This leads to enormous costs in order to reduce any doubt, needed for a just process. Those resources could be used more efficiently.
• Delay. Among with the enormous cost comes a long delay to iron out all the doubts. But it is necessary; otherwise the defense can easily punch a hole in the argument: “In civil cases, plaintiffs need only demonstrate by a perponderance of the evidence that their version of the case is more likely than not to be true. In criminal cases, the defendant needs the quantum of evidence that produces a reasonable doubt in the jury’s mind in order to be acquitted. Legal evidence, in other words, need not and should not be held to scientific standards of robustness.“
• It’s “ethically and practically questionable” that foolproof science can be used to remove any doubt, as it’s mostly “the poor, the disadvantaged, and the racially makred who are actually executed.” Especially in an adversarial system like the US, the judge doesn’t have an active role in finding the truth. He / she listens to both parties, and hopefully tries to distill the truth from that. A good (expensive) defense lawyer is essential in the creation of doubt; in this way the poor aren’t likely to be acquitted.
• Law has the final word in the conviction (situation in the US). This is illustrated by a 1993 Suppreme Court decision, “which held that a claim of actual innocence is not enough to reopen a criminal conviction based on a fair trial; the prisoner, who is no longer entitled to a presumption of innocence, must also show constitutional error.” Or, to put it differently, science can be used to convict someone, but it can’t be used to free an already convicted prisoner (unless there’s a constitutional error). In the Netherlands this is a little different, but comparable (Puttense moordzaak). Therefore, a scientific truth and a legal truth aren’t the same.

Science Daily – I

inspired by  γιδω’s blag I copied some headlines from Sciencedaily:

Ceiling Height Can Affect How A Person Thinks, Feels And Acts
Science Daily — For years contractors, real estate agents and event planners have said that whether building, buying or planning an event, a higher or vaulted ceiling is always better. Are they right? Until now there has been no real evidence that ceiling height has any influence or advantage with consumers. But recent research by Joan Meyers-Levy, a professor of marketing at the University of Minnesota Carlson School of Management, suggests that the way people think and act is affected by ceiling height.

A Woman’s Age At First Menstruation Influences Risk Of Obesity For Her Children
Science Daily — A new study published in PLoS Medicine suggests that the age when a woman’s periods start may affect her children’s growth rate during childhood, final height and risk of obesity in later life. Researchers from the Medical Research Council and University of Cambridge, led by Dr Ken Ong, studied the association between mother’s age at first menstruation, mother’s adult body size and obesity risk, and children’s growth and obesity risk in 6,009 children from the UK Avon Longitudinal Study of Parents and Children (ALSPAC) in Bristol.

Sleep Strengthens Your Memory
Science Daily — Sleep not only protects memories from outside interferences, but also helps strengthen them, according to research presented at the American Academy of Neurology’s 59th Annual Meeting in Boston.

Science and Law – Part 0

In the Journal of Law, Medicine & Ethics, Volume 34, Number 2, there’s an article titled “Just evidence: The Limits of Science in the Legal Process”, written by Sheila Jasanoff. It talks about the reliance on science in the legal process. What follows is a summary, with some short notes added.

It starts with an introduction about the Massachusetts governor, who tried to reintroduce the death penalty, mainly because science would produce failsafe/infallible results. Science produces a lot of facts, and with the help of the self-corrective nature of science, the reliance on those facts is high. Peer reviews are important in this respect. Organized skepticism, communalism, universalism and disinterestedness are important notions in the science community, as noted by the sociologist of science Robert K. Merton.

The law and science have different frameworks, different contexts, for producing facts. Therefore, the law shouldn’t always defer to “science’s overriding commitment to self-correction”. Trial judges should act as “surrogates for the scientific community in determining admissibility”. This isn’t a perfect solution, however. For example, in the post about the Monty Hall problem, there were a lot of math professors who didn’t agree with the solution. When science ultimately decides about someone’s life or death, these failures can’t be tolerated.

Science can’t proceed the same way in the courtroom, as it would outside it. It simply can’t remove the uncertainty that the law itself would have when convicting/judging a suspect.

DNA and Truth-Telling

“Science may be a social activity, but when executed correctly, the results are viewed as no longer bearing traces of human subjectivity.” Because of the removal of human elements, the facts that are produced by scientists, are very reliable kinds of evidence. The transition from the subjective legal definitions to more objective scientific notions, through the removal of fallible human interpretations in criminal law through diagnostic instruments, is a process we already see happening with the advance of DNA technology. “The hope is that technology, through its mechanical reproducibility, will be impervious to context and will provide unbiased and reliable evidence about the facts of the matter.” Again, DNA technology is a good example. The enormous discrimination possible with DNA (random match probabilities of 1 in a billion for a complete profile) are negligible with respect to the chance a mistake is made by a human factor: problems with taking samples, mixed up profiles, contamination, holes in the chain of custody, etc. Those factors are far more likely to occur, and illustrate that an overreliance of DNA profiles is dangerous. Also, the human element in the law, and the urge of the public prosecutor to convict somebody (e.g. bias), are noteworthy components that shouldn’t be forgotten. The ability of DNA to establish identity is not questioned; it’s the interpretation of the results that should be questioned. Alternative explanations, no matter how unlikely, should all be removed before there’s a certainty for a rightful conviction.

Three more propositions will be investigated:

• “Truth-seeking in science is equivalent to truth-seeking in the law” (See part 1)
• “Law enforcement (or forensic) science establishes the truth as reliably as science in pure research contexts” (See part 2)
• “Genetic science is a particularly dependable source of truth, especially in disputes concerning human identity” (See part 3)

Vegetables

In the May edition of Scientific American, there’s an article about consciousness of coma / vegetable patients. It’s titled “Eyes Open, Brain Shut”, and written by Steven Laureys.

When people slip into a coma, they don’t open their eyes, but some of them may show some reflex movements of the limbs. If people come out of their coma, they can enter a vegetative state, in which they remain unconscious; they are awake, but not aware. For instance, they have sleep/wake cycles, and some form of movement which is not purposeful but only reflexive.

How do you measure the awareness of a patient? How do you diagnose a vegetative state? This may be helpful to distinguish between patients who may recover or not. A MRI or CT scan can show how damaged the brain is, but it’s impossible to see if the patient has some level of consciousness. An EEG (ElectroEncephaloGram) measures the brain’s electrical activity which is able to show the state of wakefulness, but not a reliable change in awareness.

With the use of a PET (Positron Emission Tomography) scanner, the metabolic activity can be viewed (measured by its consumption of glucose). In the vegetative state this metabolism is lower. When the patient is at rest, it can’t successfully distinguish between the vegetative and minimally conscious state. This changes when external stimuli like pain and spoken words are added to the equation. This makes sense, because the awareness in a vegetative state is lower then in a minimally conscious state.
Persons in a vegetative state may very well understand commands: there is a “conscious linguistic processing in the vegetative patient”. Furthermore, in some “mental imagery tasks”, the patient understood the tasks (tasks like: imagine walking through the rooms of your house). These responses were indistinguishable from that seen in the healthy subjects. However, there may be a possibility that the patient was transitioning to a minimally conscious state, in which the awareness is raised.

It’s a well written article; so if you have access to it, I’d recommend reading it.

Monty Hall problem

I was thinking about the Monty Hall problem, a problem my statistics teacher once told me about. In short it’s about the following:

You appear on a game show. There are three doors, behind one there is a prize. The other two are empty.
Assuming you want to win the prize, you guess which door holds the prize: A,B or C. The gamehost subsequently shows one door behind which the prize doesn’t reside. The question is, should you alter your choice or not?

The counterintuitive but correct answer is: Yes.
It’s sufficient to look at the two situations: either you alter your choice, or you don’t.

If you don’t swap:
Two things can happen:

• You choose a door. You have a chance of 1/3 to choose the right door immediately.
• Hence you have a chance of 2/3 to choose the wrong door.

Chance of failing: 2/3
Chance of winning: 1/3

If you do swap:
Two things can happen:

• You choose the door behind which the prize is (chance is 1/3). The gamehost then shows you a door behind which the prize doesn’t reside. Two closed doors remain. You change your choice to the other door, so that your final choice will be the wrong one (you fail).
• You choose a door behind which the prize doesn’t reside (chance is 2/3). The gamehost then shows you a door behind which the prize doesn’t reside. Again two closed doors remain. You change your choice to the other door, and hence your final choice will be the right one (you win).

Chance of failing: 1/3
Chance of winning: 2/3

You see it’s better to change your choice in such a situation.

Small matlab code:
(Note: ceil(3.*rand(1,1)) means that a random number is generated, not higher than 3, rand(1,1) is a random 1×1 matrix).
Sorry for the fucked up code; blogger doesn’t like tabs :\.

function findprize=findprize(repeat, swap)

WIN=0;
FAIL=0;
if swap==1;
for i=1:1:repeat
prizenumber=ceil(3.*rand(1,1));
choosenumber=ceil(3.*rand(1,1));

if prizenumber==choosenumber;
FAIL=FAIL+1;
else
WIN=WIN+1;
end
end
end

if swap==0;
for i=1:1:repeat
prizenumber=ceil(3.*rand(1,1));
choosenumber=ceil(3.*rand(1,1));

if prizenumber==choosenumber;
WIN=WIN+1;
else
FAIL=FAIL+1;
end
end
end

FAIL, WIN

This gives:
no swap:
findprize(100000,0) gives: 66625 failures, 33375 wins

swap:
findprize(100000,1) gives: 33438 failures, 66562 wins

There ya go.

PER3 Polymorphism Predicts Sleep Structure and Waking Performance

The latest edition of current biology holds an article about the connection of VNTRs on genes and sleep behaviour. (Current Biology 17, 1–6, April 3, 2007)
The genetic background about sleep and waking patterns is largely unknown. This paper writes something about it; not everything is understandable for me, as I have a limited background in biology (actually, no background in biology), but with the use of wikipedia I could draw some conclusions.
Individuals were monitored in their sleep-wake cycles, after which some intensive physiological tests were done. This was done in normal conditions, and in conditions of sleep loss. The persons, selected on basis of their genotype and homozygosity for the PER3 -gene, showed no significant differences in bed time, wake time or sleep duration.

Note: PER3[4/4] means that the person is a homozygote, with 4 repeats of the characteristic amino acid.

In their normal patterns, there was no significant difference in the different stages of sleep (REM sleep, stage 1 sleep, stage 2 sleep, total sleep time), but

“PER3[5/5] subjects fell asleep more readily than PER3[4/4] subjects”

When the PER3[5/5] were kept awake for a long time, the subjects performed worse than PER3[4/4] persons on spatial, reaction-time, and logic tests, especially in the late night and early morning hours:

“Most strikingly, PER3[5/5] homozygotes performed very poorly during the hours after the melatonin midpoint. The decrement in waking performance in the PER3[4/4] homozygotes was far less. These major differences in performance between the two genotypes occurred during the late-night and early-morning hours, a time known from both laboratory and field studies as the nadir of the circadian timing system and during which performance is poorest and sleep propensity at its peak. “

“The PER3 5-repeat allele, which is the less frequent one in most ethnic groups, has been associated with extreme morning preference, while the 4-repeat allele has been linked with DSPS in our previous study.”

DSPS is a delayed sleep phase syndrome; people with this syndrome tend to fall asleep late at night, and have difficulty waking up in the morning. Furthermore, for a lot of these persons it doesn’t matter at what time they go to bed, because they fall asleep at approximately the same time anyway. DSPS is a syndrome from the bigger family of Circadian rhytm sleep disorders; a well known member from this Circadian rhytm sleep syndrome is the jet lag. This may mean that there’s a problem with a part of the brain that produces melatonin, which receives information from the eyes about light and dark.

These results, among others,

” (…) led us to consider it as a candidate for mediating some of the marked individual differences in sleep-wake regulation. These individual differences include the preferred timing of sleep-wake cycles, the structure of sleep, EEG patterns during sleep and wakefulness, and their response to sleep loss and circadian-phase misalignment.”
“Our results indicate that the PER3 polymorphism may contribute to the marked individual differences in performance decrement during sleep loss.”

All in all, this may signify that there’s a relation between day- and nightpeople.

“Conclusions
The effects of the PER3 polymorphism on SWS (slow wave sleep), SWA (slow wave activity), and the decrements of waking performance during the biological night, as observed in this study, are significant and substantial. This implies that this polymorphism may be an important marker for individual differences in sleep and susceptibility to sleep loss and circadianphase misalignment, which are major causes of health problems and accidents in our society.”

Of course, there are still a lot of open questions: what happens for example with heterozygotes? Or with a smaller number of VNTRs on the PER3 gene? Is there a connection, or is it just a correlation? I’m not in the position to answer these questions, as I could barely understand the article ;).

From: Viola et al., PER3 Polymorphism Predicts Sleep Structure and Waking Performance, Current Biology (2007), doi:10.1016/j.cub.2007.01.073

Why is ice slippery?

There’s an article in the December 2005 episode of Physics Today written by Robert Rosenberg, titled ‘Why is ice slippery?’
A simple question, but the answer is however not so simple. The first part of the solution is the following: for example, when you’re on ice skates the pressure (force per unit area) is very high (the blades of the skates occupy a small area, whereas the weight on them is large). This increase in pressure results in a lower melting temperature of the ice below the skates: -3.5 degrees Celsius. Thus, the ice melts, and you skate over the water. Simple. Or not?
However, what happens when the outside temperature is below -3.5 degrees? Can’t you skate below that temperature? Nonsense. Also, the pressure on the snow exerted by a skier is not enough to make it melt (larger area). What happens when you slide over the snow or ice, is frictional heating. The author then mentions an experiment, with the following brilliant remark:

“The increase in temperature with velocity, they observed, was consistent with frictional, localized heating of the ice underfoot to create a thin water layer. Were pressure melting -an endothermic process- the dominant contribution, the researchers would have expected a decrease in temperature.”

The heat created due to friction causes the temperature to rise, so a waterlayer is created, and you can skate over the ice.
There, problem solved. Not quite.
But why can ice be slippery when you’re standing still on it? This question is analyzed in the remaining pages, where he shows what evidence there is for the existence of a liquid-like film at the surface, even at temperatures below zero. He concludes with a discussion of experiments about the thickness of the film and temperature-range of the effect.

Omega-3 Fatty Acids and Mood Disorders

Another interesting article from the American Journal of Psychiatry, titled

“Omega-3 Fatty Acids and Mood Disorders”

Here are the main points; below that there’s a summary of the article.

Objective: This article is an overview of epidemiological and treatment studies suggesting that deficits in dietary-based omega-3 polyunsaturated fatty acids may make an etiological contribution to mood disorders and that supplementation with omega-3 fatty acids may provide a therapeutic strategy.

Method: Relevant published studies are detailed and considered.

Results: Several epidemiological studies suggest covariation between seafood consumption and rates of mood disorders. Biological marker studies indicate deficits in omega-3 fatty acids in people with depressive disorders, while several treatment studies indicate therapeutic benefits from omega-3 supplementation. A similar contribution of omega-3 fatty acids to coronary artery disease may explain the well-described links between coronary artery disease and depression.

Conclusions: Deficits in omega-3 fatty acids have been identified as a contributing factor to mood disorders and offer a potential rational treatment approach. This review identifies a number of hypotheses and studies for consideration. In particular, the authors argue for studies clarifying the efficacy of omega-3 supplementation for unipolar and bipolar depressive disorders, both as individual and augmentation treatment strategies, and for studies pursuing which omega-3 fatty acid, eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA), is likely to provide the greatest benefit.
(Am J Psychiatry 163:6, June 2006)

I learned a few things from this paper: first, the omega-3 fatty acids can be either marine-based or from plants.
The rapid growth in population has been associated with a change in diet, resulting in a decrease in omega-3 while the uptake of omega-6 (e.g. from vegetable oils) has increased. Some authors suggest that there’s a connection between the depression-rate and other neurological disorders and the increase of the omega-6 fatty acids; there’s a possible link between fish consumption and mood disorders. Both Iceland and Japan, which both have high consumption rates of fish, have low rates of “seasonal affective disorders”. As the consumption rate of fish declines (and the consumption of ‘Western’ food rises), the rates of seasonal affective disorders increases, even when they receive more winter sunlight. Furthermore, the “likelihood of having depressive symptoms was significantly higher among infrequent fish consumers than among frequent consumers.” Some research also opposes these findings, but there’s a general tendency to support the previously mentioned claims. Other research state that this is especially so with women. But in short, 5 out of 6 researches find that there’s a correlation between fish consumption (omega-3 intake) and mood disorders.
During pregnancy the fetus accumulates more DHA (primary component of omega-3) than the intake of the mother, and after the birth the depletion of the omega-3 acids continues by breast-feeding. This contributes to the risk for depression around the time of birth. So feed your wife some fish during pregnancy (finally a reason to be happy someone eats dead animals);

• it’s safe
• it may have “additional benefits for the infant’s neurodevelopment”

Then there’s a lot of biological mumbo-jumbo, which I don’t fully understand, but which still support the previous claims. Some possible mechanisms are presented, to continue to the treatment studies. Bipolar/depressed/borderline patients which took omega-3 had in general greater symptom reduction. On the other hand, there are some experiments which don’t reproduce this effect, but again, in general, the results support the previous idea.

Interesting stuff.

Spatial memory and depression

In my first post I already mentioned that this blag is mostly for myself, and that I’d add notes for myself about things I like or want to remember. This is such a piece.
In the American Journal of Psychiatry I found an interesting article titled:

Performance on a Virtual Reality Spatial Memory Navigation Task in Depressed Patients

The title doesn’t leave much for the imagination on what it’s about, but the findings are interesting nonetheless:

Method: Performance on a novel virtual reality navigation task and a traditional measure of spatial memory was assessed in 30 depressed patients (unipolar and bipolar) and 19 normal comparison subjects.

Results: Depressed patients performed significantly worse than comparison subjects on the virtual reality task, as assessed by the number of locations found in the virtual town. Betweengroup differences were not detected on the traditional measure. The navigation task showed high test-retest reliability.

Conclusions: Depressed patients performed worse than healthy subjects on a novel spatial memory task. Virtual reality navigation may provide a consistent, sensitive measure of cognitive deficits in patients with affective disorders, representing a mechanism to study a putative endophenotype for hippocampal function.
(Am J Psychiatry 2007; 164:516–519, link )

Well, there you go. I think this was interesting, and I want to remember it.
(The only question I have that the article didn’t answer is, if there existed a correlation between the familiarity with the game and the people who were depressed. I.e. whether the depressed people could be more familiar with the game)

Common sense?

Scientific American: Fact or Fiction?: Living People Outnumber the Dead
Booming population growth among the living, according to one rumor, outpaces the dead.

I read in the above article about the question whether the living people outnumber the dead. From the article:
“The human population has swelled so much that people alive today outnumber all those who have ever lived, says a factoid whose roots stretch back to the 1970s. Some versions of this widely circulating rumor claim that 75 percent of all people ever born are currently alive.”

Unless you believe the world started populating around the time Jesus supposedly died on the cross, this can’t be true.
A highly simplified model could be the following:
If we start with 1 couple (2 people), which produce slightly more than 2 children who (when their time comes) produces more than 2 children … and so on, we can ask the following:

When is the sum of all the people produced equal to 6 billion (current population)?
If we take as an exponent 1.025 (so that 1000 couples produce 1025 new couples), it takes less than 800 generations. Of course, we didn’t take anything in account (plagues, food shortage, wars, infertile men/women, gay couples, abortions, women who are never in the mood, ugly/stupid people who couldn’t get a date, etc), but the exponent is very low.
Even if we take as an exponent 1.002 (1000 couples produce 1002 new couples), we need less than 8200 generations to accomplish the total amount of 6 billion people who are dead. The first homo sapiens originated from about 200.000 years ago from Africa (Wiki).

Estimations for the year 2050 range between 7.3 and 10.7 billion people, giving a much larger exponent than we took.
I think we can safely say it’s bullshit to say that more people are alive now than that ever lived.
(The article comes to the same conclusion; it just surprises me that people could ever believe such a statement)