Left or Right?

I am up early morning and before I realize ‘am awake’… I have my sports shoes on. I am half asleep when I start jogging, but soon all the senses come alive. I try to go the distance till my muscles feel exhaustion. When I stop, I try controlling my breath. Sometimes while returning, there is a paper vender, whom I chat with. I ask for a specific paper on Saturdays’, as my wife likes to read the supplement which comes along with the main newspaper. Sometimes they are over before I reach the paper stall. Then I have to walk some extra distance to get a copy. Finally I come back home. All this happens in not more than 30 minutes of a day.

If we look at small instances of our lives (like an hour or two), we find that our body/brain is taking decisions continuously. Sometimes we are conscious of it, some are intuitive. Some decisions are important (as they influence our future) others have a short term effect. We opt for options provided to us by external conditions. That is a response towards stimuli. Other way round sometimes we drive the situations. Some decision making is at a level of biochemistry, which does not always involve conscious. In other words, our neurons do not participate in it. The physiological decisions have definite constrains within which each organism as a system has to function. As in my case, the sprint should end when a tiring feeling comes. This is a pure biochemical decision. I have to stop when the oxygen supply is not adequate in comparison to what my body is burning in that rigorous activity. Cells have to metabolize anaerobically producing loads of lactic acid in my muscles. So I stop for a breath.

The other level (tier) of decision making system involves brain. Concepts such as ‘right/ wrong’ come into play at this level. This comes under the domain of behavioral psychology. An old friend passes by, judging the affection that you two share, goes out the response; a handshake, just hello, a scream or a hug. Human decisions either follow a rationale or are based on emotional grounds. The later is true in most of the cases though. Again when it comes to logic, how much rational is our rationality is a subject of debate. It seems we cannot overcome the hard-wired errors we are predisposed to. But ignoring this aspect, momentarily let us focus on the two types of decision making systems one can follow; 1) rational 2) emotional.

The emotional intelligence humans possess can be looked at from two very different angles. The usual way of looking at it is the social view. Bonding between individuals of a species, empathy, development and maintenance of culture is the part of it. Second is the biological view. It depicts that the traits (like trust, empathy, altruism) we possess, do not exist because they represent the ‘righteous’ path, but simply because we are programmed to. These traits will find their roots in the urge for survival. We can observe that our emotions are greatly based upon intuition, which we can hardly explain. Hence, when intuition is relied upon, we take decisions first and then justify them with reasoning, which is acceptable to the society. Acceptance by society, group or community has a major influence on our judgments. If one tends to go against the consensus, the person is either called a ‘rebel’ or the person himself will experience guilt and take back the decision.

The other side, i.e. rational or logical, is relatively easy to understand. There lies a simple logic, limited parameters and mostly calculable consequences when it comes to rational decision systems. Even if we are convinced that logic driven systems are more accurate, you will see that humans believe what their ‘heart’ says. Why is it so? Why is it that we mostly go by our intuition rather than taking a learned decision? Is it that our brain already knows that its ‘heuristics’ are far better than the calculations it can perform (in other words does it prefer speed over accuracy)? Or are we simply lazy? The answers must be lying deep hidden in cognitive neurology and behavioral psychology. But as biologists (students of natural sciences), it’s our job to decipher reason behind the choices we make. So next time when your brain decides to go ‘Left’ ask it why not ‘Right’?

Determinism

This post has been brewing in the brain for some time, but the recipe was not clear. Finally I decided to chalk it down, irrespective of the ingredients I am adding here (because recently I learned from my colleague that cooking is more about confidence than the quantity of ingredients added ;) ).

Chapter 4 of the book ‘Genome - An autobiography of a species’ by Matt Ridley, is dedicated to the concept of ‘Fate’, i.e. organisms are destined to reach a state due to their predisposition towards certain conditions (disease/aging/other traits). The example discussed is about Huntington disease, caused due to ‘CAG’ repeats in the gene found on short arm of Chromosome 4. It has been observed that when the number of repeats is more than 39, the individual shows symptoms like loss of memory, hallucination, loss of primary body maintenance functions etc. Diseases like these and other conditions (like cancer) are major evidences of genetic determinism in living world. We display so many phenotypes; all of them are being governed directly or indirectly by various clusters of genes. How/ where/ when/ which genes control which phenotypes are the questions which have been the center of attraction for biology since Sir Gregor Mendel’s discovery of gene-phenotype correlation. Everyday there is more and more data pumped into the knowledge pool which helps to identify the mechanisms of each and every component affecting the phenotypes. All this summed up shows positive prospects towards answering the question; ‘How exactly Genes determine physiology of an organism?’

This cannot be called as an end of it. We cannot refrain ourselves from asking the broader questions of course. When we focus ourselves on ‘Gene-Phenotype’ as experiment systems, we are bound to relate these two as ‘cause-effect’ components, respectively. I would like to make a statement here; gene expression is a symptom, an effect, rather than a cause. Well, most of the biologists, who have moved beyond the reductionist approach, will not disagree to this statement. As even in Chapter 5 of Matt Ridley’s book (mentioned earlier); he discusses the influence of ‘Environment’ on cells. So there is another ‘cause-effect’ system which (‘environment-gene expression’) should be investigated in detail. Finally, we may end up saying that it is chains of such ‘cause-effect’ systems with which universe moves forward in time.

But the idea behind this post is not to conclude about the materialistic nature of Universe. That would be a digression right now. I would like to keep my thoughts (hence this post) around the effect of genes on behavior or nature of organisms. Since we call ourselves conscious about our own existence, studying genetic determinism with respect to behavior might get interesting. Definitely, this is not a novel thought. It has been explored earlier by many biochemists, behaviorists and psychiatrists (relatively less number of psychologists too). Since, humans are concerned about the safety of our own kind rather than the absolute knowledge; most of our efforts have been around the patho-psychological disorders and their genetic causes. In addition, if we logically think about it, we do find the correlation of both, environment as well as genes on the psychological states that we tend to get in. With this background in mind when I say; ‘I felt like doing a particular activity, so I did it’, sounds stupid. Naturally the thought arising at any given moment in the brain is based on 1) one of the previous states brain has experienced, 2) the environment/situation to which we are logically responding, 3) the emotional state (reaction) that is governed by hormones (ultimately gene expression) {NOTE: It would be an exciting area of research to build an automaton (response prediction system) based on the above mentioned prior data. Although, please excuse me for talking about such fictional system so casually. I do not wish to underestimate the complexity of a multi-parametric system that it is}. Hence, if we say ‘I wish to…’ and are not clear about why, then certainly we are unable to isolate and understand the objective behind our own actions. This reminds me of a great quote (apt to this discussion) by a great biologist;

‘Free will is a delusion caused by inability to analyze our own motives’ – Sir Charles Darwin on ‘Genetic Determinism’.

That leaves us with a rather discouraging thought that if we are predisposed to certain traits (physiological/psychological) then we have no choices to make but to follow the same determined path. Being an optimist, I have to negate the conclusion coming out of this discussion. Humans have another capability which can be applied in this case. If environment->genes->behavior is the working control structure in case of our thought process then we may work towards a better environment to ultimately reveal the true potential (knowledge) we possess (here better environment does not mean comfort, social or financial status).

A wrap up thought: Chaos theory talks about patterns existing in random processes in the universe. But I believe there is more to this universe than randomness. Motive exists (even to an individual thought); we need to introspect more, by asking the right questions.

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.