Friday, August 27, 2010

Seeing the future in the light of the past...

I have always been fascinated by history. Somehow, viewing the present and the future in the light of the past always makes more sense and it makes one appreciate things a lot more.

Long ago I had come across this fascinating story of Coley's toxin and the development of his work into a burgeoning field of scientific study. A brief discussion with an acquaintance who is planning a presentation on immunotherapy and the recent interest in the use of bacterial DNA for cancer immunotherapy, made me revisit the article where I had first read about Coley's work. And I must say, the article by Frances Balkwill in Nature Reviews Cancer, tiled as "Tumor necrosis factor and cancer" manages to do a wonderful job at tracing the history of TNF (which is a ubiquitous factor in immunology jargon these days) and our present understanding of the same. It is a fascinating story that makes one really appreciate the hidden lessons in history and the sheer brilliance of scientific methodology. This story is also a great example for how serendipity knocks on our doors ever so often and then it is completely in our hands to make something out of the opportunity. William Coley did that and his life’s work is remembered long after he is gone as a landmark phenomenon we are still trying to understand. Such is the wonder of science and history plays a vital role in our understanding of science.

William Coley, a New York surgeon in the late 1800's was an expert surgeon and a very observant man. His fascinating work in 1890, at the start of his career laid the foundations of cancer immunotherapy and the role of bacterial toxins in the same. History says that in 1890, Coley was called in to treat a 17 year old woman who had a nagging pain in her right hand. However, in spite of Coley's expert surgical intervention, Elizabeth Dashiell died a few months later of an aggressive round cell sarcoma that disseminated at an alarming speed through out her body.

As an interesting footnote, Elizabeth Dashiell was a close friend of J D Rockefeller Jr and her death was an inspiration for the philanthropic work of his family which continues to this day in the form of the Rockefeller institute for medical research or the now Rockefeller University. It is amazing how much influence one pers
on's death can sometimes indirectly have on history. Other than the extremely moving effects of Elizabeth's death on Rockefeller, its effect on Coley was also remarkable and this death heralded the beginning of our story. Dashiell's death had a profound effect on Coley as he immersed himself in pouring through hospital records to learn more about this rare but devastating malignancy.In his studies of the sarcoma induced deaths, Coley found an intriguing anecdote: the case of a German immigrant who 6 years previously had been dying of a large facial tumour. Fred Stein’s fate seemed to be sealed when a post-operative bacterial infection took hold but, as the fever subsided, the sarcoma has regressed. With dogged determination at this point, Coley searched the lower east side tenements for a man with a scar, and he found Stein alive and well 6 years after the surgery. Coley did not give up now. He began a line of enquiry which he pursued for is entire lifetime. Going by the case history of that one man, Coley first infected cancer patients with bacterial isolates, and then he made “Coley’s mixed toxins”, slightly less dangerous filtrates from cultures if Streptococcus pyogenes (the bacteria that causes Erysipelas) and Gram-negative endotoxin-producing Serratia marcasens. The work was controversial (not unexpected!) and few were able to reproduce the beneficial effects that Coley obtained but, if the published case histories are to be believed, Coley was able to obtain a rapid and sustained response in patients who would present a major challenge to the medical oncologists’ in the 21st Century.











With the developments in radiotherapy and chemotherapy, the interest in Coley’s toxins waned over time but some scientists were still attempting to reproduce his results in animal models of cancer and under the principle underneath. One of the earliest studies was in 1931, when Gratia and Linz showed that bacterial extracts caused tumour necrosis in guinea pig model of Sarcoma. In 1944, another report by Shear et al, isolated lipopolysaccharides from bacterial extracts and showed them to be responsible for the tumour regression seen in a mouse model of cancer. Work by O’Malley showed that the serum from endotoxin-treated animals was also capable of causing tumour necrosis, thus leading to the conclusion that it contained a “tumour necrotizing factor”. The entire field made a leap in understanding when in 1975 Carswell et al, reported that it was a factor made by host cells in response to endotoxin and not the bacterial endotoxin itself that destroyed the tumours. Thus, the term “tumor necrosis factor” was coined to describe this activity, reportedly produced by macrophages, which led to the necrosis of both mouse and human tumours.

The next two decades marked the identification of this elusive tumour necrosis factor and it was soon realised that this protein belonged to a family of related cytotoxic proteins. By the 1990s, in addition to the TNF, the genes for the two receptors which bind to TNF were also cloned. By mid 1990s, it was becoming clear that neutralizing antibodies and soluble receptor fusion proteins targeting this cytokine TNF would be successful treatments for a range of human inflammatory diseases and the cytokine itself was under investigation as a cancer therapeutic. In good agreement with the research done for the previous 40 years, recombinant TNF induced necrosis of both syngeneic and xenografted tumours. TNF was injected locally and repeatedly and it managed to cause a regression except in the periphery where there was a risk of regrowth. The tumour necrosis caused by TNF was found to be haemorrhagic in nature with major destruction of the vascular bed which was believed to lead to increased tissue concentrations of the administered chemotherapy.

However, the course of scientific research never really runs smooth and by around 1987, intriguing reports started to emerge which demonstrated increased presence of TNF mRNA and protein in cancer biopsies and blood plasma of the patients. There were also these paradoxical observations that suggested that TNF might actually stimulate tumour growth. By the early 1990s however the entire TNF saga was one giant cauldron of confusion as reports found TNF to contribute to oncogene activation and DNA damage. Long term TNF treatment was found to result in transformation of immortalized cells. These studies thus raised the possibility that TNF might actually be a target instead of a treatment and that it might be beneficial to neutralize TNF activity in cancer patients. This was tried in Phase I and II clinical cancer trials with TNF antagonists as single agents, with some evidence of clinical activity. Even today the role of TNF antagonists in cancer prevention is not clear as some of the studies suggest a role for TNF in the promotion of early cancers, but then given our current understanding of the role of TNF in regulating innate immunity, the increased risk of infection precludes the wider use of the current TNF antagonists. However, TNF antagonists are being used for the treatment of chronic inflammatory diseases like rheumatoid arthritis and the incidence of cancer under these conditions is being monitored closely.

Our current understanding of TNF is quite a mixed bag and as the TNF timeline moves into the future a number if questions remain to be answered. How can we explain the apparent efficacy of Coley’s missed toxins and the long but anecdotal history of cancer regression associated with acute bacterial infection? Can the tumour necrosis ability of TNF be harnessed without promoting cancer or inducing a cytokine storm? Will TNF antagonists have a more important role in cancer therapy and if so then under what conditions must it be administered?

Our understanding of Coley’s work although still not completely clear has had some significant strides. We now realise that Coley’s mixed toxins must have been powerful stimulants of TLRs thereby inducing a range of inflammatory mediators, not just TNF. As a closest recent approximation to Coley’s work, bladder cancer was reportedly successfully treated with Bacillus-Calmette-Guerin. The current thinking is that probably both the BCG and the Coley’s toxins trigger an inflammatory response through the TLRs which not only stimulates macrophages to kill the tumour cells but also promotes the development of sustained and effective adaptive immunity to the tumour. This type of a response may also contribute to a more successful chemo or radiotherapy as dying tumour cells were able to cross-present the antigen to the dendritic cells in a TLR4 the efficacy of chemotherapy and radiotherapy was reduced.

Interestingly, in 1949, Coley’s daughter, Helen Colet-Nauts reviewed the case histories of the 484 patients who were treated with the toxin preparations an recorded that approximately 50% of his patients were alive 5 years after the treatment began. The toxins were given both locally and systemically for maximum effectiveness and the treatment was continued for long periods ranging from months to even years.

The history of TNF is interesting in many ways. It began with a serendipitous discovery and with the dogged determination of one man. TNF shows us how inflammation can have both positive and negative effects on cancer and how its effects will have to be controlled and manipulated to attain the desired effects (In an anthropomorphic explanation, TNF like us has a good and bad side and it depends on the situations and the context as to where which instinct dominates!). The kind of work done by Coley is certainly no longer possible in a world dictated by social rules and norms (as it is today) but despite all the legal and ethical obligations, one must remember the preliminary insight which was provided by Coley which has laid the foundations of an entire field of cancer immunotherapy. It was his preparedness to observe and analyze, his dogged determination and his ingenuity that has opened new vistas and no matter in what time scale we live, these are the qualities that propel science forward.

Saturday, August 21, 2010

Its not all about the mean....

Biology as we understand today is a result of the study of averages. We attempt to study the life and fate of the individuals by studying the properties of the population. The assumption has always been that the properties of the mean is a good representation of the individual. The outliers were ignored as a minor population whose fate may not change things much. However, it is increasingly clear that the study of the outliers could largely determine more phenomena. For example, imagine treating a population of bacteria with a particular antibiotic... while most would succumb, it is the few outliers who are resistant to the drug who will determine the next outbreak. Imagine the case of chemotherapy... while resecting a tumor and chemotherapy will take care of the bulk of the tumor, the few resistant cells are sufficient to repopulate a tumor. This has increasingly shifted the focus towards measuring the properties of individual cells and not the mean or the median of the population. The conventional outlook was of course largely adopted due to technological limitations and not just as a matter of choice. The sensitivity of our imaging systems and the size of our cells make population measurements the only option left. Of late however, technology has evolved to permit the study of individual cells but the availability and the accessibility have been other limitations still preventing their widespread usage.

I have however remained a skeptic about these fancy single cell imaging systems till I came across a recent paper in the reputed journal "Cell" by Loewer et al, detailing the novel dynamics of an important tumor suppressor protein- p53, in individual cells. p53 is one of the most widely studied tumor suppressor (proteins which suppress tumor growth) which is lost in more than 50% of the cancers and is inactivated in most of the others. Since its discovery in 1979, p53 has emerged at the center stage of cancer biology as a possible therapeutic target whose restoration and reactivation in cancer cells could hold the key to successful therapy. Thus, a comprehensive understanding of this protein and its cellular functions is essential. What is presently understood is that the p53 protein, having a short half life, gets activated in cells upon conditions of cellular stress. Upon activation, p53 activates a set of downstream targets which subsequently determine cell fate. The activation of p53 was known to be mediated through post-translational modifications which alter its stability and activity.


Through imaging p53 dynamics in live cells, this paper shows that the p53 protein exhibits pulsatile dynamics in both stressed and unstressed cells spanning over a few hours. The difference under the two conditions only being in the synchorinicity and the frequency of the pulses. This however could not have been detected earlier since the occurrence of sporadic increases in the p53 protein would not have been detected by the earlier population averages.


In a very elegant way, this study causes a paradigm shift in our current understanding of p53 biology. They show that instead of being absent under stress-free conditions and active upon conditions of DNA damage, the p53 protein is actually pulsing in the cells showing a cyclical increase and decrease. The activation seen upon stress by conventional studies is only a result of the increased frequency and duration of these pulses arising out of post translational modifications of the p53 protein.


Thus, this paper by Galit Lahav from the Harvard Medical school, has managed to convince the skeptic in me that the mean, no matter how informative can still be misleading in biology. And it is thus wiser to focus on the single cell dynamics of the various proteins and signal transduction cascades towards garnering a more comprehensive understanding.

And if SJ Gould came to the conclusion that the "median isn't the message", it seems true that the mean too, is not always the message !!

Here's to a new wave in biology focusing on the individuals and not just the population...

Tuesday, August 17, 2010

Of bugs, superbugs and the buggers galore !!

The last week in the Indian media has been raging with reports about a new superbug, a new plasmid which confers resistance to all beta-lactam antibiotics which are of course our primary mode of treatment for gram negative bacterial infections. More than the concern for the antibiotic resistance, the media and the Indian politics is going gung-ho about the 'assumed' implications for medical tourism in India and the supposed attack on national pride!


It is appalling that the media is blowing an issue completely out of proportion without a clear understanding of the science behind it. There have been accusations to the tune of a conspiracy by the western powers to destroy the burgeoning medical tourism in India. The involvement of Wellcome trust and the Wyeth pharmaceuticals as funding sources for the study is also used as insinuations against the Western powers. The fact of the matter is that the media is trying to blow up a story without an accurate understanding and this is only diverting the public focus from the more important issue of the development of resistance in microbes to the other peripheral issues of private funding, national pride etc etc.


I am trying to present here the issue as i see it with my limited perspectives... based on a reading of the research paper and some of the more rational and balanced news reports...


Firstly, one must realize that bacteria from clinical and non-clinical settings are fast becoming resistant to conventional antibiotics. This is not a new phenomenon and has been a potential problem that was known for a long time. Since the bacterial life spans are short, the development of resistance in bacteria was always well anticipated and this has spurred the search for newer and newer antibiotics for a very long time. The possibility of horizontal gene transfer in bacteria only hastens the process of acquisition of resistance several fold and this has also been know for long!


Ten years ago, concern was focused on gram positive bacteria, particularly the meticillin-resistant Staphylococcus aureus (MRSA) and the Vancomycin-resistant Enterococcus spp. The current concern arises because clinical microbiologists are increasingly agreeing that multi-drug gram negative bacteria pose the greatest threat to public health particularly since there are fewer new and developmental antibiotics active against gram-negative bacteria. The increase in the resistance of Gram-negative bacteria is mainly due to mobile genes on plasmids that can readily spread through bacterial populations. Human air travel and migration, which are happening at unprecedented levels now, are also reasons for the spread of such resistance markers.


So what's the latest hue and cry all about ?


The latest in line of acquired resistance among bacteria is the new so-called super bug... This drug resistance bacterial gene, the so called super-bug was named as NDM-1 or New Delhi Metallo-beta-lactamase-1... Why NDM-1? Well, because, as is customary in the naming of a new pathogen or organism or species or chemical, NDM-1 was first identified in 2009 in a Swedish national who was admitted in New Delhi.


But for some reason this nomenclature for the plasmid is being perceived as a national insult especially in the way it is being projected in the media by the politicians... No one raised a question when Nasikabatrachus sahyadrensis, a new frog species found in Sahyadari was named so... There is even a Mycobacterium lineage named after Beijing... I don't remember Beijing raising a storm over that !! This is not a question of national pride... it is just a tradition of scientific nomenclature. How can we want to claim our name on anything complimentary (however distantly related it might be - from V Ramakrishnan's Nobel to the identification of N. sahyadrensis !!) and shun anything which might be remotely incriminating ? Why is the Indian media not putting forth the facts as they are and instead feeding the public frenzy ?


The entire controversy however began when Lancet Infectious Diseases published a study by Kumaraswamy et al in august 2010 ("Emergence of a new antibiotic resistant mechanism in India, Pakistan and the UK: a molecular, biological and epidemiological study"). The study reports the identification of gram negative enterobacteriaceae strains which are found to be resistant to Carbapenem, which is a powerful antibiotic and one of the last lines of treatment for infections caused by gram negative bacteria. The present report, has carried out a large scale sampling of enterobacteriaceae from different cities in India and the UK and has identified a good proportion of the bacteria to be resistant to Carbepenem. Interestingly, a previous study published by Journal of association of Physicians of India (JAPI) in March, around 22 cases of Carbapenem-resistant NDM-1 were collected within three months from a Mumbai hospital. Thus, the entire issue is not necessarily new although it has come to public light only relatively recently.


Magnitude of the problem ?


While i am saying that there is a needless media created hype surrounding the issue, the fact of the matter is that the issue is indeed important. The rise of resistance species is of critical importance and a recent editorial by Dr Ghafur highlights the major issues associated with this "super bug" in the Indian context in sharp, punishing tones !


The situation is critical especially in India since resistance to extended-spectrum beta-lactamases (ESBL) drugs like the third-generation Cephalosporins is between 60 to 70% on average, compared to the less than 15% seen in the developed countries. Thus, a more common way of treating the severe form of ESBL infections is through the use of Carbepenem - which becomes the drug of choice as it has the lowest resistance and the broadest action against gram negative infections. The emergence of resistance against Carbepenem is bad news undoubtedly but for the patients and physicians in India who now have to look for new antibiotics but this is a self created nuisance too. The spread of resistance is not surprising keeping in view the fact that the drug is over used by the physicians. The easy over-the counter availability of these drugs also makes the problem more acute as patients end up self medicating in sub-lethal doses (For the bacteria of course), thus, leading to the acquisition of resistance. These are problems which have been known to the medical community for a very long time but have not been addressed by the government, the media or the Public...


It took a report such as this where the introduction of NDM-1 to the UK was attributed to the emergent practice of medical tourism (where a number of patients in UK were coming to India for medical treatment, esp for things like cosmetic surgery, dental treatment etc as a cost effective measure which could aid the NHS in saving money). The Indian politicians of course do not want to let go of this easy source of foreign exchange and are over zealously contradicting the problem. The fact of the matter is that medical tourism is only part of the reason for the spread of the disease. In fact, typing the plasmid did not even identify common strains of E. coli of K. pneumoniae between the indian subcontinent and the UK or between the north and south India, suggesting disparate origins. The Indian subcontinent has always been a rich source of many infectious diseases - HIV, TB, Enterobacterial infections, malaria, dengue etc etc. There never was a hue and cry about any of these diseases ever affecting medical tourism. The western countries are also battling with their share of health concerns - emergent resistant strains like MRSA, VRSA; increasing health care costs etc etc. No one is going to stop traveling there !! Also the spread of the NDM-1 plasmid can occur because of routine travel of people... and there is no way that travel across the world is going to come down because of this "superbug"!!


It is thus pragmatic that the Indian media focus on the more important issues such as educating people against self medication and the government focus on increasing its efforts towards R&D for newer more effective treatments and towards getting a more accurate picture of the actual spread of the superbug; instead of raising a hue and cry about something which is frivolous and a completely fruitless exercise !!


The Indian government, public, medical community and the media need to work in close synchrony to understand the real severity of the problem and to counter the same - if not for the foreign currency but for the future health of this country where epidemics spread faster than wild fire and where health is already a major challenge. Thus, instead of creating a storm in the tea cup, the Indian media, the public and the politicians should focus on the threatening storm on the horizon and be prepared for that !!!




Monday, August 9, 2010

Subjective objectivity.... and the pitfalls therein...

"Science is rooted in creative interpretation. Numbers suggest, constrain and refute; they do not, by themselves, specify the content of scientific theories. Theories are built upon the interpretation of numbers, and interpreters are often trapped by their own rhetoric. They believe in their own objectivity and, and fail to discern the prejudice that leads them to one interpretation among the many consistent with their numbers."

- SJ Gould

A wonderfully true statement which not many can appreciate !

The subjectivity involved in being objective... :-)

It is the true understanding of our inherent biases and conditioning that can make science truly objective. This is where lessons from history become invaluable in our understanding and appreciating the magnitude of bias that we introduce in science. Hindsight is often the best form of sight that can make things appear in new light !! :-)


Friday, August 6, 2010

The Panglossian Paradigm in evolution

"All this is a manifestation of the rightness of things, since if there is a volcano at Lisbon it could not be anywhere else. For it is impossible for things not to be where they are, because everything is for the best...."

Dr Pangloss in "Candide" on the great Lisbon earthquake of 1755 in which up to 50,000 people lost their lives.

Voltaire heaped ridicule on Dr Pangloss in "Candide":

"Things cannot be other than they are.... everything is made for the best purpose. Our noses were meant to carry spectacles, so we have spectacles. Legs were clearly intended for breeches, and we wear them."


Point being made :

Evolutionary biologists tend to focus exclusively on the immediate adaptation to local conditions, and tend to ignore architectural constraints and preform just such an inversion of explanation.

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Courtesy: The Spandrels of San Marco, An essay by SJ Gould.



Evolution and beyond ?

The following is the mail from a physicist expressing his concerns about the widespread acceptance of the evolutionary theory. I was asked by a friend to respond to the same and what followed was a letter attempting to address some of the issues raised here...



The following analogy from physics might help clarify what I am referring to. In the late 1600's when Newton discovered patterns in planetary motion and proposed his laws, everyone thought we had discovered how the universe functions. In fact by the mid 1800's, armed with many physicists had assumed we understood almost everything about the laws governing nature. But they were all shocked in the late 1800's and early 1900's that they had not appreciated a completely new approach to physics described by quantum mechanics where classical mechanics was merely an "effective" approach. Of course quantum effects are rather subtle and Newton's ideas are still valid almost in all daily experiences. So Newton certainly deserves a lot of credit.


In the same way, I feel the theory of evolution of Darwin, could be a very useful first step in our understanding of life. But there may be many surprises on the way! And as scientists we should be ready for it. In my opinion there are already many questions that evolutionary theorists should be asking. Hopefully, they are building more realistic models and testing the theory of evolution rigorously. Trying to poke holes into the theory. would be surprised if they are not!


For example, some of the subtler questions could be related to the quantum mechanical effects that govern the probabilities in the evolutionary mechanism. I have heard that the physics of protein folding is an open problem in biochemistry and I some people believe quantum mechanics is playing an important role there.


Finally, I am sure you will agree that human emotions and feelings are "observed facts". At some point of time we should address them. How do they arise? We cannot just say "these arise from "complex" connections in the human brain"! You can almost explain anything away through the use of word "complexity" these days and you are not allowed to ask any more questions! Why? "Because it is complex"! Sounds very much like religion to me!


Why did evolution create a human brain that is capable of "sacrifice" for the sake of others that by very nature goes against preserving the "gene"? Why did evolution create many human brains that thinks that "sacrifice" for others is an admirable trait in a human being and respect those people rather than "kill" them at first site! These are some questions I wonder about. I hope scientists just dont use "complexity" to explain away these observed facts and shut me up!


The bottom line is that some people become happy with an explanation about the observed phenomena. Others do not. People who accept an explanation easily are always happy. The question always is where do you draw the line? We scientists have developed some bit of arrogance as compared to non-scientists. We think we understand something better. That may be! Unfortunately, we too have to draw the line somewhere else and say, I am happy with the current explanation since I cannot go beyond this. It is too complex!



My response :


Well, I appreciate the sentiments behind the mail and the spirit behind the questions raised but as someone who has been in a closer association with the field, I do think that some of these thoughts are a result of lack of in-depth study of the field.

Let me clarify, while as scientists, it is right to be a little skeptical about any fact till it is completely proven, Darwin's evolutionary theory is pretty much at that stage in biology. However, the questions that you raised are valid and have been the subject of several studies. Our current understanding is progressing and has still not been able to refute the fundamental principles of evolution. However, yes, we still do not have explanations for all such conundrums in biology. The origin of altruism (sacrificing oneself for others) is one such problem, there are others such as the origin of handicap principle (the male peacock has huge tail feathers which completely incapacitate its flight movements - why it would evolve something like this is another problem which has puzzled evolutionary biologists for long), the evolution of consciousness, the evolution of our mental faculties, emotions etc, the origin of antlers in a stag etc etc… there are numerous such examples for which we do not have proper explanations but the hypotheses that are available are all based on the framework of evolution.

However, there is a caveat here. Evolution as is understood today is of a very different form from that which is commonly understood. In fact, a greater understanding of the subject can be obtained from Stephen J Gould's essays.

There are few things that we need to remember when looking at things from an evolutionary perspective -


  1. What exists today is a result of a large number of random events operating at different levels (natural cataclysms to random mutations at the gene level)… but the outcome of these random events is shaped by the process of natural selection (as was proposed by Darwin).


  1. Also, one must be careful when ascribing an evolutionarily selective benefit to every trait or character we see. Some of these characters may actually be a case of "spandrels" (as was written by SJ Gould in his essay on the Spandrels of San Marco) i.e. they may not have a selective advantage and may just be a by product of the constraints of life and evolution. Like the spandrels which just exist because of the nature of the construction of the building and not because of the purpose they serve, in this case too, a lot of features in biology are not advantageous all the time.

  1. Also, some of the features we see in life today are actually natural consequences or by products of certain other constraints and may not in themselves be subject to the forces of natural selection.

  1. Addressing some of your questions specifically,

  • The origin of altruism has been a subject of scrutiny in several societies, not just the human. It is seen in other insect societies as well. The "kin selection theory" tries to explain this by speculating that sacrificing oneself still could be advantageous in an evolutionary perspective if one tries to save one's closest kins (because your genes still survive… ). In fact, the genetic relatedness between individuals has been seen as a measure of the tendency to give up one's life. Man, however, is the part of a more complex social structure where the social structure is based on cooperation and coexistence. (I speculate that humans lack the physical strength/skills necessary to subsist as solitary creatures and therefore had to resort a more social living where interdependencies are mandatory).

  • In fact, the fields of evolutionary psychology and sociobiology have been attempting to address these and other such questions which are of relevance to explaining human social behavior and psychology in the light of evolution.

  • The question of peacock feathers, antlers is another intriguing phenomenon - the handicap principle has come up with another hypotheses to explain the same. It is believed that the bearing of such handicaps could indeed be a symbol of greater ability as individuals (males) surviving despite such handicaps (very evidently responsible for the name of theory) are actually perceived as more attractive for their ability to survive despite such handicaps. There are other theories to explain the same and studies are attempting to prove one as against the other.

  • The origin of human consciousness, mental faculties, emotions etc are also areas of intense investigation in evolutionary light. One other aspect which needs to be remembered is that, some traits and features are exaptations - i.e structures which arise for a certain purpose but then gradually evolve for a different purpose all together. That is some of these structures may actually be a consequence of some other evolutionary features. The evolution of human consciousness for example is something which is often explained as a natural end product of a highly developed brain with a very "complex" neural network underneath. A lot of our mental faculties also may not have a natural selective advantage - they may be a natural consequence of certain other features for eg, the evolutionary increase in brain size may have as a consequence developed our faculties for language, social structure, arts etc. These areas still remain in the arena of speculation and are branded as "complexities" not with the intention of evading the problem but because they are genuinely not understood. The human brain remains one of the biggest "black boxes" in life sciences and efforts are underway to try and understand the molecular processes underlying the complexities of memory, perception, thought etc etc.


Lastly, while biologists are working at trying to understand life and the underlying complexities, they are all only trying to do it in the light of evolution because honestly there has not been a better alternative for our understanding of the same. However, the definition of evolution has been expanding ever since the term was coined and newer perspectives are being added with each passing year.


I hope I have managed to shed at least some light on the questions that have been raised by you. I do not claim to be an expert but as an occupational hazard, if not anything else, I have been more acquainted with the evolutionary principles. And, as time goes by I only realize that there is a lot more I need to know. Some things make intuitive sense while some are more difficult to understand and appreciate. It only requires deeper study of the views and counter views to arrive at a clearer picture of the complexities of evolution.


I am sure you will find many more questions and answers to many of your already existing questions if you go through the existing literature in the field. References in case you are interested further -

The selfish gene

The essays of Stephen J Gould

The greatest show on earth

The blind watchmaker

The moral animal

Rise and fall of the third Chimpanzee


Finally, I would like to say that I do agree with you when you say that we should not be blind to other possibilities and as scientists be open and skeptical… but, it just necessitates a more open approach where evidence is interpreted unbiased by prejudices. And that holds true for every subject and field not just with evolution and biology.