Are we rational?

Every scientific enquiry needs an unbiased observation system to decipher the real meaning or understand the principles behind any phenomenon. This is the basis of science, which has its roots in rationalism. Every concept/ idea in science is first hypothesized, tested upon and then proved. We also see proved ideas challenged at later date. This is hence an iterative process. After these iterations, finally when we call the proven facts as laws, which lay foundation for the further works to be carried out, in the form of their applications. Although this is true in disciplines like physics and chemistry, we see very few laws in the field of biology. Even if the possibilities are not infinite, the decision making system becomes more complex with higher degrees of organization in the living world. Its one of the toughest challenges to deduce/ guess the final outcome of any process in the biological systems. Moreover these systems are highly influenced by the environment. Slightest changes in the extracellular concentration of few ions and/or biomolecules can even determine the fate of the cell (as observed in stem cells). While observing and analysing such complex processes we cannot have any biases or preconceived notions. These notions, if present can affect the conclusions derived from such experiments.

Probing into human psychology lets us see the deepest corners of human thought process. There is a very peculiar property which we possess. We tend to observe things in-line with their beliefs. We sometimes go to an extent that we ignore outliers, which might be of greater significance in biology, since we observe exceptions in biological experiments more frequently as compared to other fields. When it comes to scientific observations, in most of the cases its either we ourselves or the technologies developed by us are the observation systems. But if our minds in reality inherit the properties I mentioned here, that this tendency of humans is deleterious for the growth of science. Rather it can take us away from the actual truth and make us follow the ideologies of few people who are leading/ directing the process of development of science.

Further, one of the most prominent weakness, among the many that we possess, is fear of failure. This was highlighted nicely in a book named Crimes, Criminals & Cops, written by Ex-deputy Commissioner of Police, Mr. R. S. Kulkarni. He is well known for his expertise in criminology. In this book he shares five famous and successful criminal investigations carried out by his team. While describing the first case, he states that solving criminal cases is much like answering scientific enquiries. Further he mentions about times when police personnel tend to catch the suspect which appears to be guilty and/ or one, who can be charged with certain available evidences. This system of conviction (seems to work almost every time but) needs rechecking the facts and restating and proving the evidences to be more concrete and fact based, rather than just circumstantial. He has also stated, that due to time, media, failure and related pressures we follow the practices which need not search for the truth, but fit the scenario into available framework of observations (evidences). This insight into human psychology is really interesting learn. Having said all this, I really wish to answer to a very simple and basic question about human brain, “How much influence does our brain/ mind have on the observations we make?”

Economics of "Life"

The concept of Currency evolved around 2000 BC. Its form, shape & size have been changing ever since. It gained importance into the society as a medium of exchange and trade, taking over the earlier practices such as barter system. It helped nations bring their economies on a common platform. It boosted trade and built relations among different countries. Today, the same money seems to be influencing our daily lives. As we see, changes in the US dollar price having big impact on the decisions taken by different financial organizations all over the globe. Even the natural resources a country has are being calibrated using the same medium of exchange. Today it has become one of the most important concepts in the history of social development of humans.
 

Moreover when we zoom into the lives of the individuals in our society today, we see the major driving force or motivation to work is Money itself. This is true to the extent that most of us participating in this “rat race” never try to understand or question the basic need for running in the direction we are going. Turning to the classic evolution theories, fight amongst individuals/ species for the available resource has been the decision factor for survivability of an organism in a given population. The “rat race” can be a result of the same. Keeping aside the greed aspect, it is very important and interesting to know, from where we acquired the knowledge of “economics”? Or how this concept was discovered? Or was it a necessity based invention as in most of the cases? I believe the knowledge is already embedded within us, as life has its own economics.

The way we manage our income-expenditure equations and the noteworthy common Indian mentality to economize every aspect of daily life is amusing. If we zoom into “LIFE” itself, we may find many answers for this behavior. Every organism has a genome (the Blueprint), having genes, coding/non-coding regions, accessory elements (regulatory elements) etc. In all the aspects of organization, growth & reproduction of cell we see precision in the usage of all the above mentioned components. The size of genomes/ genes/ proteins, number of genes, percentage of non-coding regions in genomes, expression of particular genes at particular time points, their amounts, re-usability of particular proteins for different functions/ reactions/ interactions (hub proteins, having flexible structures), the way these elements fit into a series of reactions forming networks (may it be gene regulatory networks, biochemical network or signalling networks), all this is following certain thermodynamic constrains. In all this, the complexity is huge. But using all the above mentioned information in a genome, still following the constraints, cell tries to survive adjusting to given environmental factors. Ones a cell is born (as in after division), its internal machinery starts transacting with the environment using the currency of energy. It gains energy from exterior (in different forms). According to the availability of resources (and signals in case of multicellular organisms) it prioritizes its actions to either go into dormant (sustain), growth or reproduction/ division state. From the whole organism’s point of view, the maintenance charges also matter. The bigger the entity or component more energy is spent on taking care of it. Having more genes/ bigger sized genome (more information) is not always advisable for a cell. Bigger the genome, more energy is spent on its thermodynamic stability, repair mechanism etc. Same is the case with, cell as a system. All the proportions of its contents and overall size have to be maintained. Hence the rules seem to be universal. Although the evolution can be seen from two different dimensions (thermodynamic constraint based or adaptation based), both of which are leading to the same conclusion that the genome has prior information about the economics it is dealing with.

Likewise, most of rules seem to be embedded within us, which when explored result into progress in our thought process. The concept of language (grammar), programmability of a system (coding the machines), abstracts (mathematics), music etc, are derivatives of the same universal rule book nature follows (or may be have created). We need more unbiased observation systems and theories to learn more about the same. Interestingly one lifetime may not be enough to reach this state of understanding and knowledge about nature, we can merely try.

Chemicals to Conscious

A stretch of 200-400 ribonucleic acids moving in and around some of the organisms on earth, sometimes integrating into their genomes, otherwise just creating copies of themselves, in many cases controlling the fate of the host cells and at times killing them by turning lethal – we humans have named them The VIROIDS. It’s the simplest and most mysterious living structure known, which replicates itself and has no cell like structure or a layer/ coating covering the RNA. It is made of just a naked strand of RNA (also suggested to be showing activity like ribozyme), with very little known about its mechanism of replication in the host cell. In the last post I wrote about viruses, they being amazing creatures showing us a different lifestyle or a new way of living. Ever since I read about viroids in more details, I am much more mystified about the purpose of life. What is it that organisms like viroids heading to? What is their purpose in nature? Is it just to sustain/replicate? Or maybe there is none and we can rely on physics and chemistry to give us more details about these aspects of life (biological entities)? Only time can tell…!!

All these properties suggest us a lot to call it a selfish genetic material as suggested by selfish gene theory. Another important point to be noticed in the lifestyle of viroids being the acceptance of genes/genetic material to be integrated in each other’s (host/parasite) genomes, of course with specificity (needs to be explored more extensively), which suggests a single source of universal information. This cross compatibility is again a unique feature to life. There is one theory which states that life originated on earth only when the genetic material reached earth from outer space. This theory is supported by some ancient meteorite samples showing traces of nucleic acids. It seems the entire puzzle pieces may fit together some day to give us an answer to the ultimate quest of the origin of life. The field of synthetic biology is trying to answer the same above mentioned "HOW" class of issues. Consider, even if this question is answered in a few decades from now, the next will be; “WHY” set of questions which will pose more difficult challenges to all the human kind.
 

Genomes of all the organisms exhibit the same behaviour of maintaining their own identity. We can assume a cell (as a basic unit) to have the consciousness to replicate itself and propagate the genetic material. But how can we think of a single RNA strand to be embedded with such information to carry out all these activities (as in the case of viroids)? This indeed is difficult to digest. The plausible way to think about this phenomenon is that may be the genetic material has a characteristic to divide itself, managing the surrounding chemical components given optimal chemical conditions. To think over this or any such wild hypotheses we need to broaden our spectrum of thoughts. Since our perception of the universe is limited by our senses and different technologies we have developed to observe different phenomenon occurring in it. What if, the truth lies somewhere beyond our horizon and is inconceivable to us? We never know.
 

Simple components coming together to form a higher order structure, is a very common phenomenon seen in the universe. Living systems are an example of the same. They have a very high degree of organization, still following the laws of the universe (importantly the entropy law).  We would not be thinking so much; rather personally I would not be writing this blog if it was not for the consciousness that we exist in this universe. Does that mean that any entity in this universe above certain threshold of degree of organization, achieves a consciousness, such as to distinguish between itself and the surrounding universe? Secondly is it that a certain class of elements (nucleic material or so) is responsible to bestow the power to do such differentiation? Answers to these would be the points where the Chemicals will meet the Conscious. I really do not know the answer (or even have a philosophical opinion yet) and to find out I wish that the theory of reincarnation would be true. But at least for this moment, all these thoughts leave me astound and more curious about everything.

Finally I also want to put forth an interesting concluding thought, I thought about:
If God really exists as a being (meaning an entity with a materialistic body), then he designed biological systems only to understand the amount of complexity he can create and which can sustain.

The "Virus" way of living...

Interestingly, I am writing about an organism which always amazed me and I took so long to write some words about it. I studied it in detail, during my graduation. Introduction to these creatures during my curriculum made me more curious about them. It also imbibed another fact on to my brain, that biology is fascinating.

Recently I had a fever for a week or so, not something usual (since generally common cold and fever is seen for 2-3 days). It was a viral infection, as I was told. I was actually spending a lot of time with somebody of other species (unwanted although). It was a wait and watch. I could only wait for him to leave my body, as he was using my own cells to replicate his genetic material. There was nothing anybody could do, except for suppressing the symptoms he creates (fever). This is the smallest demonstration of power by these creatures. Pandemic Flu of 1918 (~ 50 million people died) and many such attacks show the real power (potential) of the one of the tiniest species on earth.

The theory put by Urey-Miller explaining chemical origin of life and generation of organic molecules including all 20 amino acids by a simple chemical reaction under reducing environment and available high electrical energy seems to be an explanation for what was the starting point from where life originated on earth. Lets believe for a moment that it was an accident (really hard to believe, but I will put my vote onto it), but since then life has never given up. Since its formation, it has been struggling to survive and has adapted to even the extremes. That is simply a diverse and dynamic behavior, which we can only appreciate (yet hardly understand). Why suddenly I am thinking about the origin and evolution process? One part of the answer is, I most of the times do that. The other part of the answer is, parasitism is the peak of all the survival strategies developed by organisms with simple but precise design which could not have appeared at first (as seen to be a resultant in Miller-Urey experiment) but it came as a living style later in the process of evolution when life started establishing itself on this planet. Life evolved, forming clumps, grouping together for protection, gaining higher degree of organization, specializing according to the environment... so on and so forth. But some of the forms did not care to achieve all these things. They were smart and cunning. This goes to all the parasites, although I hate your kind of living but have to admire your adaptive capabilities. The parasite class has many species on the list. Worms, bugs, many plant parasites, but smallest of all "THE VIRUSES". They sneak through everything, unseen, unheard and without anybody's knowledge they just make replicates (best example is some strains of Ebola virus, who do not even show any symptoms after infecting). Theory behind any parasite doing what he is doing is just that those genes wish to survive. We in general tend to think that, "Huh, a parasite must be enjoying his life, without really working hard, as seen against somebody like plant". Plants not only create food for themselves but even for other life forms (that is really a noble job). But this is not a case. Parasites do struggle and they really struggle hard. For us, host parasite interactions are difficult to understand. But by simple logic it is quite clear that a parasite has to adapt if a host tries to change. And he has to do it every time, if he needs to survive.

Let’s think about viruses’ way of living for a moment. He is precise to its host, because it needs a lot many personality changes for him to enter a new species. Like in case of portability of Avian-Swine-Human host of the flu viruses. These three hosts, must be having different protein signature (receptors), but they found a way in which they can bind to both forms or get transmitted from one species to another. This is an amazing capacity. Viruses are simple coat proteins with some specific structures to attach to host cells, and inside the capsid lies a simple strand of DNA/RNA which needs to replicate. So he knows, that change in which protein (attachment coat proteins) will make him species portable, and here is the natural selection acting, which selects the one whose genome has changed in such a way that only that protein has changed. Another thing with viruses is that they have no machinery to do all the activities like carry out replication on its own & carry out pathways which generally a normal cell can carry out. It needs a lot of complexity in the system and energy regulation techniques. Virus never seems to be concentrating on all those aspects. He rather chooses to use somebody else's machinery for all such activities. Does this ensure survival in a better way? Definitely yes, in case he is sure that life will anyways exist on this planet, which will help him to propagate. But if not, then what is he up to? Interesting...

Some time back when I questioned in philosophical terms, what viruses are trying to do on earth, I instantly replied saying that they are nature’s creation to make us aware that there are tiny species out there that can halt us and nature is the decision maker. On the other hand biologically speaking, Nature actually has nothing to prove here (this is a common human trait), it need not rather. So it looks like, “LIFE” just shows us that "there is another way it can propagate!”

Existance.

Human brain thinks of anything and everything it sees and observes in and around its own universe. The other day I was thinking, I exist in this beautiful, physics law bound place called universe. Well the next thought came was, I do not think that there is much of a choice for any organism to live, but this universe... hence we have to accept that whatever is there is beautiful. So my comment that 'universe is so beautiful' is justified. (I have to accept one fact that this universe is beautiful indeed, just for discussion purpose I tried answering my own question).

"I exist"... But does this mean anything to the universe I live in? Well, here I become a bit of Socrates. I really respect that guy for a simple reason, since he tried answering the toughest questions like, what is confidence? what are morals?... Somethings which humans invented but now are not sure of what these terms actually mean. Coming back to the question I posed just now, "what is existence?", I see it as a probability p(e). Here 'e' is whatever events that lead to the the formation and evolution universe till this state and then a little me in it. Talking about genes, it was 1/4 possibility that I become 'me' as far as the pairing of alleles is concerned. Also I have searched for uniqueness in all the organisms on this earth, as in humans we claim that each one of us is unique. 'The one' as best portrayed in the film 'The Matrix' -- I believe each one of us is The one. Here I am not only talking about the the unique genomes we possess, but also about the the universe that revolves around each one of us, and we are the centre of it. The thought that results into this kind of perception of universe, also makes each one of us, owner of ones own universe. Again I feel like saying, enough praising ourselves here. Universe is more that what it seems like.

I still strongly believe in Big Bang theory for universe origin and then Darwin's theory of evolution, that accounts for the current state of life on this earth. So considering all this, don't you believe that we are very miniature part of this mega structure. Although why we are, what we are is a myth... It is an ultimate question that haunts most of us putting forth universal questions about origin and stuff.

Our brains shouldn't have either reached such a level that we question and think about everything, i.e. something more than current survival and propagation, or else, if we have reached a level that we are thinking more that what I mentioned just now, then we should be able to answer these fundamental questions. Everything in this universe has a purpose (I don't know who said it, but I strongly believe in this). Hence evolution of human race and our possession of such a level of intellect is for a purpose. The purpose of solving this mystery of universe.

Selfish Morality

When we look at animal world from outside, it looks ruthless and cruel for anybody who watches animal planet. Just day before yesterday, I was at my friends place. All of us (me and his family) were watching animal world in the eve. We saw back to back two programs. One covered fight between two lion groups for terretory and second was about hunting sharks. All the eyes were stuck to the TV screen. Suddently my friends son shouted out "mom why did all those sharks target that small baby peguin? they were never bothered about the baby getting hurt by their teeth!!!". It was an innocent query. For sharks its was a feast, nice meal for the day, but for us, attacking animals or hunting them and getting them down to earth to eat it live is an immoral behaviour. Even after killing that small baby penguin, it was torn into pieces by other sharks and they literally fought for it (may be that is the way they share ;-)). This violent behaviour of animals can be justified by hunger and need of survival. Everybody wants to survive, and there's no exception.

The point that knocked my brain's door was, we also used to hunt in groups, we also killed smaller mammals to get food and shelter (by using their skin). But then, we developed farming and animal cultivation as an alternative for this field job. We changed with time and along came ethics and religion. We decided the code of conduct, some rules, laws and protocols to govern our society. Those who did not follow these, were punished by the tribe (sticking together as group is already discussed in "Parallel strategies" post earlier).

Our raw animal behavioural part is now masked by decent protocols decided by society, which was not the case earlier. Why suddenly did our species decide what is right and wrong?why some behaviour was considered as a shameful act for individuals in the society? How this behaviour fit into selfish gene theory?

First lets see what is morality.

Web definition of morality: Source Wikipedia;

"Morality can be defined as a system of ideas about right and wrong conduct."

Morals make individuals respect each other and as a resultant, creates a secured place for living. When we look at morals biologically, it is never an extra part of emotional intelligence that was imparted from somewhere outside, it is something which should have only helped better survival of the species in some or the other way. It did that as we can see today in case of humans. Morals are something which set constrains to individuals and make them act true. As being or acting right is always beneficial, this increases trust in the community. These are the set of ideas which seperate us from other organisms. It makes stable living possible as it reduces chaos. This social chaos can cause splitting of groups and individuals. As of now the dependancy of humans over each other has increased to such an extend that this splitting can be quite expensive for individuals (in terms of being alive). So on the whole morality increases the chance of survival of species.

From this we can conclude that morality helps humans in many ways and we followed it with a simple selfish motive of survival.

#Note: I want all the readers to take a note of this, that calling ourselves selfish need not be considered as depressive (again these are morals which make us rebound away from the idea of selfishness). This is the reason we exist in the universe, just to make our genes to propagate in future (rather they themselves make it happen). #

Memetic linkages

This post is an extention of the earlier one ("The social replicators"). I call it extention because this thought came to me while writing that post. Although this writing took a long time to get posted, since I decided to keep the scope of my earlier article to introduction to this topic. Now I believe I can go ahead with another related concept.

Memes have tremendous power (by this I do not mean any supernatural power :-P). They can control masses. Memes can be constructive or distructive (as in case of genes; can be lethal too [Web definition of lethal gene: A gene which brings about the death of the organism carrying it]). Let us consider ideas (memes to be precise) as an object. Something having physical representation, just like genes. They are a part of this evolutionary process and playing a major role in human evolution (about which I have already mentioned in my earlier post “The Social Replicators”). Here I am trying to put forth an analogy between genetic and memetic linkage.

Genetic linkage is an interesting concept. The best and most simple example that we come across in the biology textbooks is in fruit flies. The genes affecting eye color and wing length are inherited together because they appear on the same chromosome. [Web definition of genetic linkages: Genetic linkage is the tendency of certain loci or alleles to be inherited together. Genetic loci that are physically close to one another on the same chromosome tend to stay together during meiosis, and are thus genetically linked]. Appearance of two genes on same chromosome is not a sufficient criterion for considering those two genes to be linked. Their loci’s have to be so close, that there is a very rare probability that they are separated during the process of crossing over. To find out how much two genes are linked generally we need to calculate relative distances between two loci where the genes reside. Even simply by observing the phenotypic traits of a group of organism (in a population) we can assume the linked genes.

Now let us look at memes by taking an example. Consider a theist; any person who believes in God. He will also have a belief in satan/evil powers. Reason is obvious. His conscience tells him that, if something as pure or good as God exists (whom he may not see or experience) then something opposite of him may also exist. These are actually two seperate ideas. But still they exist together in a population. If these two ideas are considered as concrete objects and if we assume that they govern actions in our society by some means (analogous to phenotypic expression of genes), that shows that these are linked ideas; i.e. linked memes. The only difficulty is, placing these two object together (since they are not concrete in practicle world) so that they are not seperated during the process of crossing over. It is asumed in this case that, both these ideas (belief in God and evil) will be inherited together (explicitly talking about memetic inheritance).

If we look around we will find many examples in this context. The point I want to make here is, we inherit memes, they travel across generations as well as individuals, they may mutate (change) or may be conserved in certain environments, but some of them always travel hand in hand. This ideological linkage is difficult to explain, when we consider them as matter. But I strongly stand by this point that they show linkage in society.