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.

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)

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)