4 Sec.

Oct

25

Amazing DNA Folding

By Nader

Whenever I carry a wire earphone in my pocket, the next time I want to use it I find it tangled so badly that I have to spend 5 min detangling it! There are a lot of similar examples around us. Every string has a tendency to get tangled. Look at the wires behind your computer or TV. It is a mess. Now, think of the DNA chain with 3 billion base pairs and total length of 2 meter. This long and thin (2.5nm) chain is packed inside the incredibly small nucleus with diameter of 0.01mm (about 1/10 of the size of dot at the end of this sentence.). This is approximately 1000 times denser than the density of common silicon memory on computers today. The amazing thing is that the packing is dynamically done in such a way that the DNA chain never gets tangled. DNA is also packed in each organ differently (called fractal globule) so that the appropriate part of DNA which is used for making the related protein for that organ, i.e. active DNA, is available to the cell readily while the inactive part is hidden! Courtesy of www.physorg.com

This spatial organization of genome inside the nucleus has been under study for quite a while and last week some cool results where published on the 3D imaging of this process.

What is even more fascinating, is to think about the evolutionary path that the eukaryotes took to get to such an efficient and elegant folding mechanism. What were the deriving forces and advantages of developing such complex mechanisms from point of view of evolution? There is no universal theory about the original of nucleus. Some scientists believe that nucleus was an independent bacteria which started a symbiotic relationship with some other archaebacteria and they gradually formed eukaryotes. There have probably been other forms of symbiotic relationships among early bacteria as well but it is not clear exactly why the one that has such a complex DNA folding mechanism thrived. Bacteria and archaea have also dense supercoiled DNA structure called nucleoid but their density is not close to the density of DNA inside the nucleus of eukaryotes. Why the bisexual organisms did not develop from a prokaryote-like chromosome? What is the advantage of having such a dense nucleus? 

Sep

16

Save Your Child’s Treasures

By Nader

Good childhood memories usually coincide with the times we used to spend with our toys, books, and favorite TV programs/animations. But when we grow up, we gradually forget about those wonderful feelings. The memories and experiences fade away pretty fast. We remember having good times but we can barely replicate the feelings in our mind. It seems that our mind needs some clues for searching in the archive and reconstructing those feelings. How great it would be to save the childhood toys and use them later like a time machine to revive the childhood memories. Just hold one of your childhood books or toys and it will immediately take you to an amazing time travel! Everybody has experienced these wonderful feelings at least once.

It is so important that parents save all their children’s toys and books until they grow up. It is like saving part of person’s memory. Don’t think that this toy is junk or broken. That broken toy or worn-out book is part of your child’s memory. Think of it as a map to the key that will unlock a treasure box in your child’s brain when he/she grows up. Don’t deprive them from finding that treasure. Save it for them.

I know that there are so many treasures in my mind from my childhood. Sometimes they want to come to surface. I can feel their ripples but I have lost many of those maps that I need to find my lost treasures. Last year I found in my parents home several science magazines that I used to read every month when I was a teenager. They really took me back to a journey. As I was browsing over the lightly discolored pages, I could almost feel my surrounding changing to those days. That was a wonderful experience.

Sep

12

Failure of Psychological Thriller Genre

By Nader

Above warning is captured from the trailer of new movie “Sorority Row”. I understand that there is a big genre of psycho thriller in movie industry but what we are seeing these days in this genre is a total disaster. First of all, I do not understand how a person younger than 17 should even be allowed to watch these kinds of movies. The level of violence in most psycho thriller movies have gone up so high that it is psychologically damaging even for adults let alone kids. It is unbelievable to hear the warnings that are given on the trailers of these movies: “Strong bloody violence; Torture; Pervasive terror; Grizzly images, etc.” Yes, these are actual words. Why some people feel entertained by watching someone torturing another person or chopping their body parts by electric chain saw? I think there is something seriously wrong about this. Society should prevent this because it directly affects mental wellbeing of viewers and eventually safety and security of other people. These kinds of movies leave severe psychological impact on individuals and even more so on youngsters.

Aug

21

By Nader

A lovely conversation between piano and setar*:

Aug

12

Look up into the sky

By Nader

When I look up into the night sky and see a bunch of shinny stars and just think for a second about the possible civilizations that are living in these systems at this very moment, I feel how small we are and how small our problems and issues are compared to the vastness of this universe. When I am down, nothing enhances my mood more than going outside and staring at a star. I immediately feel better.

I need to go look up into the sky now. Maybe I also catch a few shooting stars from Perseid meteor shower while I am out.

Mar

17

Leaning against the wrong wall

By Nader

It’s incredibly easy to get caught up in an activity trap, in the busy-ness of life, to work harder and harder at climbing the ladder of success only to discover it’s leaning against the wrong wall. It is possible to be busy — very busy — without being very effective.

People often find themselves achieving victories that are empty, successes that have come at the expense of things they suddenly realize were far more valuable to them. People from every walk of life — doctors, academicians, actors, politicians, business professionals, athletes, and plumbers – often struggle to achieve a higher income, more recognition or a certain degree of professional competence, only to find that their drive to achieve their goal blinded them to the things that really mattered most and now are gone.*

*Quoted from the book “The Seven Habits of Highly Effective People” by Stephen Covey.

Feb

26

Stocks are worthless unless they pay dividend

By Nader

The recent collapse of stock market and wave of scandals in Wall street has shown the true nature of stock market. The system commonly known as “stock exchange” is a scam created and kept alive so executives and big shareholders of corporations collect people’s money and in return give them an empty hope called “common stock”.

What do you exactly get in return for your money when you buy stock? You may think that you will own this company, even though if it is very tiny piece of it. But does this ownership give you any real power? By most corporate bylaws, you can vote, and be nominated for directing the company but the truth is that it will not happen unless you are a majority shareholder. Usually the decisions in corporations are made by board of directors, who are also major direct share holders. It is these folks who decide how much bonuses they will give to themselves from the money that was generated by the public investment that helped the company to do their business in the first place. So, it doesn’t really matter if the Earning per Share (EPS) of a company is $10 or $1000 or $0.01. At the end of the day, whatever money the company makes will not go to your pocket unless the company pays you dividend. Now, how many companies are there that pay a decent dividend? Do you know who decides and approve the amount of dividend payouts? Yes, the majority share holders and board of directors. Not you, not me and not anybody who has a mutual fund contribution either. Even though %80 or %90 of share of a publically traded company belongs to financial institutions and Mutual Fund owners, they don’t have any say in the way company runs its business. It is always the CEO, and the board of director who run the business and make the decisions. So, ordinary shareholders have practically no control over the decisions and profit sharing of company. They only have some useless rights written on paper.

In a lot of midsize companies (with market cap of $0.5M to $5B), the major shareholders are usually a couple of venture capitals and two or three top executives. What happens is that when a company has a good quarter, the executives take these profits and give themselves huge bonuses, salaries, stock options, etc, instead of sharing these profits with common shareholders as dividend. If you don’t believe it, just read what happened in case of Merrill Lynch. They were not even midsize yet they managed to give $3.6B bonuses to top executives and 1 month after that they were broke.

If that is the case, why the stock should go higher when a company announces a good quarter? Does any of that nice profit go into shareholder’s pocket? The answer is NO. The stock goes higher becasue of manipulations. If I buy this stock $10 or $1 or even $1000, I still will not see a penny from the actual profits of the business activity that I invested. So I have to sit and ride along with a wave of manipulation of stock market crated by Wall street and observe the ridiculous show of market analysis and balance sheet performance review etc, while none of them really matter to an ordinary shareholder as long as the profit is not divided among every shareholder.

This is a fundamental flaw in stock market. I believe that buying any kind of stocks is as good as gambling and should not be considered as a long term investment options. The funny thing is that even companies that pay dividend are not required to do so and can stop or adjust it any time they like. So, here goes down the drain any hope for long term investment in companies which pay dividend as well. There should be regulations that make the dividend payouts mandatory so everybody can get a piece of the pie and corporations cannot take all the profits and give bonuses and perks to their selected few executives.

Apr

30

The Best Time of Our Lives

By Nader

When is the sweetest time of one’s life? Can we even point to a certain period and have such a preference? Is the answer a matter of personal preference or there will be an overlap between people’s answers to this question?

I think one of the best periods of life is between the ages of around 10 to 17 (with a couple of years variation). Before 10, one is too young to contemplate the world around himself/herself seriously. After 17, a new stage of life begins and a lot of distractions, and responsibilities that are usually accompanied by stress. After this period, life becomes too complicated with so many things. There are always unfinished businesses to bug the mind, unfulfilled dreams, worrying about loosing what you have, mourning about what you have already lost, etc. But between 10 and 17 you are on the top of the world. There are no responsibilities and no worries about the future. There are no serious sexual distractions either. Almost everything you do in life is fun and full of pure enjoyment.

This is the comfort window which we can never find again once lost. Try to see if you can feel as happy as you felt when you were 13. We may feel happy on different occasions when we are older but none of these come close to the general sense of freedom and happiness that exist in teenage years.

Apr

26

A Late Note on Earth Day

By Nader

Last Tuesday was the Earth Day and everybody talked about the importance of taking care of our planet. It is strange that we have to consciously think and act about this issue. Other animals take care of Earth by their nature. However, we humans have to consciously follow some rules to make sure that our home planet can keep up with our ever increasing demands due to huge increase in population and waste that we generate.

In nature, there is always a delicate balance between the population of different species in the food chain and also the environment. When the number of creatures which use certain resources (food, water, air, territory, etc.) increase, it provides a shortage of those resources gradually and this feedback mechanism control the growth of population. Human race, however, is the only creature that has used its scientific and technological advancement to its advantage and has escaped dramatic correction in the growth of its population in the last several hundred years.

In addition to resources that control the population, natural disasters also play as a control mechanism. Every once a while, nature brings a catastrophic event such as the Earthquake, storms, flood, fire, famine, epidemic diseases, etc. Although these disasters still kill humans in large numbers, we have been very good at protecting ourselves from them during the last century or so.

We practically do not have any creature above us in the food chain. We are sitting on the top of pyramid and consuming the resources of this planet like crazy. We have become very good at developing methods and means to increase the efficiency of the way we extract our foods and resources from nature but unfortunately we are not doing it in a sustainable fashion.

There is also a smaller pyramid on top of bigger pyramid that we occupy. On top of this smaller pyramid, are the residents of developed nations, who consume more and produce more waste compared to other nations. As a nation moves toward economic prosperity, its citizens gradually feel secure enough to spend some part of their income on things that are considered luxury. Wealthy nations consume more and create more waste. Not only that, they don’t clean up their mess hence creating huge environmental problems for themselves and for others.

Look at U.S. for example. There is no serious recycling program at residential levels. When I was living in Canada, every apartment building had 4 different boxes for recycling papers, glass, plastic, and card boards. Here in U.S. there is hardly any serious recycling done at the residential level. There is usually only one big box for card boards which usually nobody cares about them. I am sure that even if the waste management companies do some processing, it will not be as efficient as when the individuals do the recycling manually.

Another example is the type of vehicle we drive. I don’t get it when a single person drives a Humvee or an 8 cylinder full size SUV or an 8 cylinder sport car in the middle of a small city everyday. This shows about the existing attitude that should change among rich nations.

We should remember that economy and finance does not provide a true control mechanism. There may be ups and downs in the economy that temporarily reduce the consumption but economy is driven by demand and as long as demand is high, manufacturers will find a way to produce more and keep the price to the levels that they can sell their goods. At the end, it is the planet that will feel the pressure.

So far, we have been able to escape the consequences of our ignorance but sooner or later the limited useful resources of this planet will be exhausted and we will pay the price with a dramatic correction in the human population. We individually care a lot about our survival but when we gather around each other in form of societies, we loose the ability to control the situation.

It is said that a picture is worth a thousand words. This eye opening graphic made by Science Photo Library speaks volumes about the limited resources of water and air we have on Earth.


*Photo credit: ADAM NIEMAN/Science Photo Library

All the waters in the world (including oceans, seas, rivers, etc) are shown in the that small green sphere in the left and all the air in the atmosphere are shown in the small sphere in the right at see level pressure on the same scale as Earth. Look how small they are! More info on this photo and some calculations can be found here and here.

Mar

23

White Matter

By Nader

Summary of the main points in the recent article published in this month issue of Scientific American called “White Matter Matters“.

  • White matter in brain basically consists of the collection of interconnections (axons) between neurons in different regions of brain.
  • Most of these interconnecting axons are coated by several (10 to 150) layers of cells called Myelin, which has the white color hence the name white matter.
  • Myelin thickness varies on different axons in the brain. The optimal ratio of bare axon diameter to total fiber diameter (including myelin) is 0.6. 
  • Along each myelinated axon there are nodes called “node of Ranvier”. These nodes act as relay stations that generate, regulate and rapidly propagate electrical signals along an axon.
  • The thickness of the myelin number of these nodes along each axon affects the speed of electrical communication between two connected neurons.
  • It is believed that when several neurons in different regions of brain are interconnected together, this mechanism adjust the timing of the information traveling between neurons through interconnecting axons. If it was not for this mechanism, the electrical signals from different neurons would not arrive at the destination neuron at the same time since the length of axons is not the same for all neurons.
  • The myelination of axons starts at birth and continues through adolescence,
  • When we practice and learn new skills at young age, we form these myelin and the network of interconnects form gradually.
  • It takes almost 25 years to form myelin in the frontal lobe of the brain, which is responsible for reasoning and rational thinking.
  • It is difficult to form new Myelin in the older age, except a small region in the frontal lobe.
  • Some skills such as language or music, etc. if not learned during the young age, it may be impossible to be acquired with the same quality again in the old age since the relevant cells have already been myelinated.
  • From the evolutionary point of view, we have never needed to learn the skill sets such as new language in our adulthood hence it may explain why our brain lacks the capability to learn these skills with the same quality as a child does.
  • The brain plasticity (the phenomenon that shows our brain has the ability to change and learn new skills well into our old age by practicing) may be in contrast with this theory. This is under study.

Mar

3

The Inner Life of A Cell

By Nader

Animator John Liebler shows the world a beautiful ballet of molecules inside a cell.

This was only a glimpse of a tiny portion of the inner workings of a single cell. The complexity of our multi-billion cellular structure is even more amazing and beyond words. This hugely complex machine works beautifully and we usually fail to realize that. Sometimes I wonder if we are acting responsibly enough to be worthy of such a gift? Mankind is the only creature who abuses his own body despite all the knowledge that we have gained about the fragility of this complex machine.The full length narrated version of this educational video is available on Harvard University Multimedia Production Site. The video actually shows a phenomenon called “Leukocyte extravasation” which is the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection.

Feb

4

Stopping the cold

By Nader

I recently found a pill called “Cold MD” that is great for boosting the immune system to fight against the common cold virus and speed up the recovery. Its ingredients are mostly natural. It has worked for me every single time so far. Two pills at the first sign of sickness and you will not see the cold. I have recommended it to several of my friends and all of them have seen the same positive response.

Today, I was thinking, if a simple pill with some herbal/natural formula can stop cold at the early stage so easily, then why this pill is not popular? The answer suddenly became very clear. Just look at the huge revenue of pharmaceutical companies from marketing and selling cold remedy products. Tylenol cold, NyQuil, TheraFlu, Robitussin,… you name it. It is a multi million dollar industry. Are they really going to campaign for a pill that fixes the cold but cut all their revenues? Of course not. That is why the maker of Cold MD, “Iomedix Development International” is still a poor and unknown Canadian company, which doesn’t even have a website.

Look at these sales statistics of cold related products in 2001 to get some idea about the huge market for these products.

Jan

27

Is aging a result of evolution?

By Nader

This week, it was announced that scientists at USC have been able to extend the age of a strain of yeast fungus 10 folds by blocking two genes, which promote aging. This is pretty amazing achievement and if is linearly applicable to humans, it will lead to ages of 800 or more for humans. There is an interesting article on the Independent newspaper about this.

DNA3 We don’t really know why we age and why living beings have to die. The fundamental building blocks of living beings are cells that are made of chemical molecules whose arrangement is determined by the molecules in DNA chain. There are cells in body that regenerate, such as skins or blood cells and some cells that do not regenerate such as nerve cells and heart muscles. It is obvious that the longer an organism live, the greater will be the chance of damage to its cells due to different harmful interaction with environment such as radiation, exposure to toxic chemicals, physical damages, etc. The damages to the cells that don’t regenerate will be a big factor in aging. On the other hand, we know that even those groups of cells that regenerate gradually loose their ability to function properly as we age. It is hypothesized that this may be linked to the shortening of telomeres at the end of chromosomes during each cell divisions.

One of the issues that is raised in the article is a theory that is put forward by Valter Longo from the same research team at USC.

Longo is convinced that his experiments on manipulating the genes of yeast show that ageing is not a mere side-effect of life, but a deliberate, genetically programmed process honed by natural selection. “Basically, it is the first demonstration, to our knowledge, that ageing is programmed and altruistic,” Longo says. “The organisms we have studied die long before they have to in order to provide nutrients for ‘mutants’ generated within their own population. Thus, billions of organisms die early so that a few better-adapted individuals can grow.”

This is what I don’t understand about this statement: Living beings usually have an average life span of approximately 5 times the age of their maturity. Natural selection automatically corrects any defects that the organisms have during the age window that the individual can breed. This means that if there is any bad gene in the DNA that causes some defect during the old age, when the individual is incapable of breeding, the natural selection simply does not have any way to correct that defect because its effect appears too late. Hence, comes the question as how our genes can be preprogrammed to do the opposite. Any orders in DNA is result of natural selection, which is in contrast with this theory unless we believe that somebody other than natural selection put those genes there.

It seems that aging and dying are simply flaws in the design of our genes, which by chance or by intelligent design turned out to be beneficial to the whole evolution of species. Otherwise, the Earth would have been filled with microorganisms in the first million years of life and we would not have had the chance of walking on Earth after all. But now that we are here, it is possible to fix this flaw. Who knows, maybe this will bring an end to the traditional way of biological evolution. In fact, I have to write another post about this topic.

Jan

20

Why the physical laws are considered universal?

By Nader

This is a very interesting question, which one of my friends brought up:

why the physical laws are considered universal?
What I mean is that why do we believe that, say, Maxwell’s laws of electromagnetism is the same in a far away star as it is in our solar system?
It is true that we see their effect (e.g. in the form of light) the same as we predict them to behave, but isn’t it possible to observe the same thing from a far away, but the underlying mechanism that generates those ways be completely different? (so, in other words, their far-field effect is the same, but the near-field effect is different).
Is there any reason other than something like Occam’s razor principle?

I think the answer is that we can never be sure in a pure and abstract sense about this universality! The whole idea that “the physical laws are universal” is only a theory and not a law. However, it is a theory that makes a lot of sense and goes very well with the rationality and logic that we see in the physics so we never doubt it. Indeed, this is what we do in scientific method, which starts by observing (usually remotely), hypothesizing, and then testing. Of course, in this process Occam’s Razor principle also plays important role in the hypothesizing stage since it has been shown to be a logical choice empirically.

Let’s say we have tested 99% of the universe and have found that indeed the laws of universe were the same in these regions. We still cannot give verdict about the universality of physical laws until we test the remaining 1%. But what do we mean by testing? Do we actually need to go there and perform some measurement to make sure? Remember how David Scott replicated the Galileo experiment with a hammer and feather on the surface of the moon during Apollo 15 mission? But even before that experiment we already had a lot of data to be sure that indeed the gravitation law is valid on the moon too. In practice we rely on remote measurement to validate the models that we build for the universe around us. When we perform several complementary measurements and the outcome of these tests are in agreement with our theory, we will have higher confidence about the validity of our theory.

There is also the “principle of sufficient reason” as stated by Liebniz, which may be applicable to this question. If we assume that any of the fundamental physical laws in a remote region of universe is different from our own, there should be a sufficient reason for that. However, at the fundamental level of physical laws, the space is a relative parameter meaning that there won’t be a sufficient reason for one region of space to have a difference from another region in having a different underlying physical laws. Of course, this is true only if we assume that the physical laws themselves are not changed or altered by the local matter and energy.

I remember watching a documentary about the life of Newton. At one point, Netwon was telling how at very young age he believed that the stars were the lights of sun passing through holes that exist in the night sky! When you think about it, this cannot be disproved immediately but it leads to a lot of new questions that are even more difficult to answer than the original question. This is exactly where Occum’s razor principle enters the scene and we see the other picture and structure we assume for the night sky are more rational and have a simpler explanation. So we trust this picture until a new and better theory come along.

Now, the idea that the laws of physics have been universally constant at all time, is totally separate issue, which Smolin questions it in his book where he speaks of evolution of universal laws along with the evolution of universe.

* Picture courtesy of International Association of Astronomical Artists

Jan

16

Time May Not Exist

By Nader

  1. There is a very interesting article on Discover Magazine titled “Time May Not Exist“. Based on one of the theories that tries to unify theory of relativity and quantum mechanics, it seems that the fundamental description of the universe must be timeless.
  2. How does a brain floating in empty space, called Boltzmann’s Brain, perceives time? To learn about the answer, read the article on yesterday’s edition of New York Times titled “Big Brain Theory: Have Cosmologists Lost Theirs?“. The answer may surprise you.

Jan

12

Easy Philosophy

By Nader

Is the term “easy philosophy” an oxymoron? I personally don’t think so. I believe although philosophy touches on some difficult topics, it can still be presented with a much simpler and understandable fashion. I have always been interested in philosophy and every once a while have thought about taking some formal education in philosophy. However, when I review the philosophy programs, their curriculum, and the texts used in these programs, I change my mind. Philosophy can be both boring or extremely enjoyable depending on the way it is presented and discussed. Perhaps that is why I have always liked Socrates and his style of approaching the philosophical questions. He asks the students a series of questions and by trying to analyze and debate about different possible answers, he will arrive at the best conclusion. This keeps the whole discussion very lively and interesting. I would have left my job to attend the Socrates school if he was alive today!

Dec

22

What rhymes with 2008?

By Nader

Do you know what rhymes with 2008? “Procrastinate!”

Dec

22

Wired Science on PBS

By Nader

I really like the Wired Science on PBS. TV should have more programs like this. 

Dec

16

The Life of the Cosmos - Note # 2

By Nader

  Entanglement is one of the strangest phenomenon in the quantum theory. According to this property, any two quantum systems will be entangled after initial interaction. It means that they form a new system and their full quantum state description will be correlated independent of their physical distance. Observing properties of one of them will influence the outcome of the observation on the other one even if they are physically located on two different galaxies!

Thinking about the extension of this phenomena, Smolin in his book goes on to say this:

Given any one electron, its properties are entangled with those of every particle it has interacted with, from the moment of its creation. … there are atoms in my body that are entangled inextricably with atoms in the bodies of every person I have ever touched.

This makes me think about some of the strange feelings that we experience,  when something bad happens to one of our family members or loved ones. Many people sometimes experience a weird gut feeling of anxiousness and worry only to later find out that there has been indeed some real danger or trouble in the life of their loved ones even if they were physically very far from them. Are these just coincidences or they can be actually explained using the quantum entanglement principle? This can be a nice research project for a PhD student in physics and psychology assuming the student is bold enough to enter the realm of uncertainties!


Picture: La Despedida by Remedios Varo 1958

Sep

16

After Move

By Nader

I just passed an eventful and extremely busy month. Any relocation and change of job is stressful and requires a lot of planning. Many things went smoothly and some other things did not. For instance, in the middle of these hectic schedules and move, my car, which I always pamper and maintain regularly, broke down and left me stranded. I was so upset at that time because it had happened in the worst period. It created a lot of hassle not to mention the financial burden. However, when I look at everything now, I can imagine even the worse things that could have happened so I do not curse the damn car anymore!!

Sometimes when you calculate the probability of the things that can go wrong, the result will be extremely small but it is amazing how many times that minuscule possibility still happens despite all odds at the worst time and the worst place. This is what Murphy’s law is all about. As far as I know, there is no mathematical proof or explanation. It is only empirically justified. Yet, the folks who believe in The Secret and parallel reality claim that these unfortunate outcomes in the external world are the manifestation of the way we think and behave in the world within. Either way, I have found that the best way to cope with unexpected and unfortunate events is to surrender and by only focusing on the current moment rather than regretting about past or worrying about the future. Of course it is impossible, and perhaps unhealthy, to completely get rid of thoughts about past or future. We are biological creatures after all and some mechanisms such as anger or mourning is a natural response to different situations that arises everyday. The trick is to not loose the control and get completely overwhelmed by them.

I am still extremely busy with all the heavy workload at the new job so blogging will be probably lightly in the next few weeks.