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.

The social replicators

I have been planning to write over this topic for a long time now. Ever since I read this book by Sir Richard Dawkins (British ethologist), named “The selfish gene” (my favourite), I was fascinated by the idea that “Ideas” evolve. To talk about this book in brief, it puts forth how evolution of organism is gene centered (rather than organism as a basic unit of its action). This is the basis of neo-Darwinism. This book also introduces to a term, “meme”. Most importantly the book calls the gene 'selfish', itself is a big topic of discussion (as this statement imparts a charateristic of consiousness onto genes, which are till date only known to replicate as a result of “so called” simple process of Replication).

Coming back to the original topic, if we define 'gene' as a structural unit of life, then 'meme' has to be defined as 'the cultural unit of life'.

Web definition of meme: a cultural unit (an idea or value or pattern of behavior) that is passed from one person to another by non-genetic means (as by imitation); "memes are the cultural counterpart of genes"

(Source: wordnetweb.princeton.edu/perl/webwn).

It has been more than 3.5 billion years that life is evolving. From its original state of some basic chemical reactions guided by some catalysts (enzymes) to very complex mechanisms of K+/Na+ nerve impulse transmissions and reaction to stimulus, it has achieved a great degree of organisation. Throughout this course all the forces of nature, which caused evolution (i.e. Natural selection, mutation, variation), acted upon the basic units, 'genes'. Approximately 15000 years ago man began its journey of becoming the highest evolved organism on earth and today he has reached its peak, using tools like techology, innovation and imagination. But what led to this extraordinary process of we the humans (Homo sapiens) reaching such greater heights? What boosted such a rapid change in the normal organismal behaviour? What would you bet on, genes? Or something else?

Initially may be yes, since we do not have an answer even to the sudden cranial expansion, that resulted into intellectuals like us ;-)

But there was something else that was moving through the generations and through the populations, faster than genes could: “MEMES”.

These ideological units could transfer faster, since the breakthrough of scripts, languages etc. That was a better medium of passing them, than other biological mediums, like learning by experience. The theory of evolution tells us that rate of evolution is proportional to the variations available in the population. More the variation, better is the selection process and faster is the adaptation (from nature's point of view). As we can see that memes take less time to pass down from person to person and are easily mutable. It is quite clear that a gene will take a complete generation to show its effect of mutation, but a meme can mutate 'N' number of times during a generation and that results into a group of people with variable ideas at the same time, such that selection process can act on such a varied/distict forms of memes in such a short span. This helps building better concepts and ideologies in very short period. This is how I believe that man could come to this state. Well I am going to comment on the other aspects of this issue in my forthcuming articles (as and when possible, as this was just an introduction to the concept).

So we can conclude that, till the time humans came into this big picture of evolution 'genes evolved', then 'memes took over' (offcourse this doesn't mean that genetic mode of evolution is on hold).

I would like to end this article with few of the best lines I have read in any biological books which make me think deeper into this vast expanse of biological world (but they might not be related to the current article): I quote #

“Our genes made us. We animals exist for their preservation and are nothing more than their throwaway survival machines. The world of the selfish gene is one of savage competition, ruthless exploitation, and deceit. But what of the acts of apparent altruism found in nature-the bees who commit suicide when they sting to protect the hive, or the birds who risk their lives to warn the flock of an approaching hawk? Do they contravene the fundamental law of gene selfishness?”

# Introduction to the book 'The selfish gene - Richard Dawkins' by Jeffrey R. Baylis.

Parallel strategies

The new series recently shown on discovery channel, 'Life' is an amazing picturisation of what life is actually about. The show tells us that its all about survival. The episode on Mammals ended on a very interesting note that struck a chord in my brain. The last sentence of that episode, as narrated by David Attenborrogh said that Mammals could survive very well and diversified on this beautiful planet because of passing of wisdom from one generation to another in a family structure (i.e. Grouping together) and emotional attachment among individuals. (# Apologies for not quoting the exact words. #)

Taking advantage of 'not being alone' is not a strategy developed by Mammals, not even by insects (ex. Ants, termites etc.) but it goes beyond that. It was discovered by the first multicellular organism which came into existance on this earth millions of years ago. Life as we know originated in the water bodies or pools or 'soup'(as called by many theorists). First coecervates and then prokaryotes came, which were solitary. Then came eukaryotes where for the first time, advantage of 'not being alone' was exploited. Multicellularity came into picture. I would love to say that, cells understood that sticking together made their chances of being alive greater than usual. Factually speaking, those who could do it were given a green signal by nature, in other words 'naturally selected'. They continued doing so and thus we see all the giant structures formed as a result of that ability. Here I would also like to remind the readers about those who are not existing today and the ones of whom we just hear stories of, “The Dinasours”.

Multicellularity is not just about being together in numbers, its also about sharing work. With the process of differenciation the whole unit (organism) was able to utilise the resources well and also the components of the unit became inter dependent. This was a stage of division of labour. And this is indeed a good survival strategy, proved by the expanse of multicellular organisms on this planet.

In animal world, Mammals have used this strategy exceptionally well to become the dominant class of organisms on earth. Our globe was ones ruled by some other class of animals, named Reptiles. They so much represented this planet that there is a whole era (Jurassic) named over them. Mammals co-existed but just to live in small holes and hide from massive strong predators. Suddently Mammals came to power. Offcourse there are other reasons of upwelling of this class like extinction of the Dino's, higher adaptation capabilities (being warm blodded animals), high brain weight to body weight ratio (shows greater use of intellect than insticts), but the one that cannot be forgotten is sticting together. Family structure, sharing, caring, dependence is prominently seen in Mammals. In a different way but the strategy of grouping together is being used by these creatures. May it be the herds grazing in Savannas, Meer cats standing tall & watching over each others backs, a group of elephants in Africa, bunch of Lions hunting together with tactics, a group of dolphins fishing in deep sea and so on.... (not to forget humans being social animals).

This shows the use of same old strategy, 'NOT TO BE ALONE', in a parallel way at different instances of evolution of life.

NOTE# All these things bring forward a point raised by Sir Richard Dawkins, that individuality should not be given to the organism but to the genes, because ultimately its a fierce battle amongst them and everything starts with it.