Where did the magic go? (Asian Scientist, 23rd September 2013)

Every undergraduate dreams of winning the Nobel Prize. A PhD student, however, dreams of getting a clone or converging a simulation, or perhaps today, of scooping competitors. This difference in ambition is not merely a transition from the starry eyed to the practical, but a reflection of something deeper, a loss of a sense of magic. Students as diverse as Bertie Bott's every flavour beans are taken into PhD programmes. Mix well and condition for five years under an unrelenting competitive atmosphere, and they emerge as specialized agents, as wary of sharing new knowledge as a Gringotts goblin. What is responsible for this? In my view, competition and specialisation. Specialisation taken to an extreme has become an accepted way of doing science. The number of academic job positions are increasingly fewer than the number of PhDs being trained yearly, putting both students and post docs under pressure to generate more data. Laboratories work on a tiny detail of a problem, often communicating only with other labs also engaged in the same sub-field and, therefore, convey their findings to only a select and already primed audience. I did a cursory search on the Pubmed website to see how many paper titles I as a trained biologist could understand. The very first one stumped me- 'A Role of Kindlin-3 in Integrin αMβ2 Outside-In Signaling and the Syk-Vav1-Rac1/Cdc42Signaling Axis'. The emphasis on publishing as many papers as possible and the increasing demands on the amount of work in each paper means that professors hiring new post docs routinely ask for people with prior experience in the field: they do not want to waste time training ‘inexperienced’ scientists. The fallouts of this are many; increased stress, increased reports of data manipulation and a gradual stifling of the happiness and creative freedom that people who opt to do science hope for. This corporate outlook that has seeped into doing science (without corporate-style pay) means that every aspiring scientist is busy trying to do experiments before his competitors do them and then couching the results in a manner likely to please the reviewers of specific journals. There is little time or inclination left to think outside one’s own area of sub-specialisation, let alone time to indulge in hobbies, traditionally supposed to stimulate creativity. As an undergraduate I attended a series of science lectures at a summer camp, and was thrilled by a talk about how microbes sense their environment. I remember a colleague asking the speaker afterwards ‘If I join your lab, can I find out how they move?’ The answer was prompt 'Maybe. But you must work hard'. The answer struck me as chilling, in hindsight perhaps unfairly so coming from a speaker tired after a long talk. But it was an abrupt bump down to earth from the magic of the visuals in the talk to the apparently disciplinary and confined real world laboratory. Perhaps it is unrealistic to talk of a Leeuwenhoek (a janitor) or a Spallanzani (a priest who did experiments in his spare time) who did all their work in a world where science was not yet institutionalised. The survivors of our system certainly include a subset of people who manage to work creatively and enjoy the process, but what about those we have left behind? Have we forced other leisurely and creative Spallanzanis to fall behind simply because our current system of science does not cater to them? Can we estimate the loss incurred to creative science? Certainly, institutes would be hard put to departmentalise Louis Pasteur . Very likely he would be refused funding for jumping so skittishly from the stereochemistry of tartarates to disproving spontaneous generation, and from wine making to silkworms. Perhaps all we need is a change in the way we view science. The question remains, can we bring back the wonder?

A cryptic gene converts prey to predator (Deccan Herald, 17th September 2013)

'Cryptic genes' are genes that appear perfectly functional but are not expressed, that is, they do not seem to make any RNA or protein. They look just like regular genes and can only be told apart when one checks to see whether or not they are actively being used by the cell. Their presence in bacterial genomes which mutate rapidly has been particularly puzzling. This is because genes that are no longer functional are extra baggage for the cell to carry, and usually tend to accumulate mutations and get weeded out. Recent work has suggested that several such genes annotated as 'cryptic' may in fact be expressed readily under natural conditions; it is just that the laboratory conditions in which bacteria are studied are often unsuitable for them to be expressed. Robert Sonowal and co-workers from the Indian Institute of Science and National Centre for Biological Sciences, Bangalore, have carried out a study1 that provides a unique role for one such cryptic gene system using laboratory bacteria as well as bacteria isolated from the soil and belonging to Enterobacteriaceae (intestinal bacteria). Their model system of study was a gene system consisting of many genes in a stretch (operon) called the beta glucoside (bgl) operon. This operon encodes enzymes that act upon complex sugars released into the soil by plants. Plants release several compounds that are by products of their own metabolism into the soil, and many of these are used as food by other soil inhabitants, such as bacteria. They break down sugars called 'aromatic beta glucosides', such as for example the sugar salicin, and in doing so release glucose, which is a source of food and therefore energy for the bacteria. Standard laboratory bacteria, perhaps from lack of exposure to the substrate (which is present in soil but not in standard laboratory media where bacteria are cultured) are unable to break down salicin unless their operons are 'activated' by mutation. That is, their genetic material needs to be changed before they can utilise salicin as a food source. The authors found that in contrast to this, several soil bacteria possess functional bgl operons and use it not only to obtain energy but also in another survival strategy: to ward off predators. The study used simple experiments to uncover this novel phenomenon: bacteria that could break down salicin (Bgl+) and bacteria that were incapable of the break down (Bgl-) were grown separately with two predators, in each case in the presence and absence of the sugar. The predators used were a soil amoeba called D. discoideum and a nematode or round worm called C. elegans. Both are well studied laboratory organisms routinely used in biological studies, and are known to prey on bacteria as their food. It was found that only Bgl+ bacteria proved toxic to the predators in the presence of the substrate salicin. The Bgl- bacteria along with the sugar salicin had no impact on predator viability, and nor did the Bgl+ bacteria in the presence of a different sugar- for instance glucose. This indicated that the Bgl+ bacteria were making something using salicin, which was proving toxic to the predators. To identify what substance this might be, the authors used the medium in which the bacteria were grown and subjected it to analysis using chromatography and NMR (Nuclear Magnetic Resonance). By this they were able to identify the toxic breakdown product as the chemical saligenin (2- hydroxyl benzyl alcohol). The C. elegans worms used as predators were then subjected to what is called an 'occupancy assay' where they were placed at an equal distance from both kinds of bacteria, Bgl+ and Bgl- , on a petri dish. Salicin was supplied as the food source. The authors found that the worms actually moved towards the Bgl+ set. In other words, not only was saligenin toxic to the worms, but it actually lured them to their death. The authors also showed that bacteria in turn can use dead worms as the sole source of nutrition, closing the cycle of attract-kill-eat, and morphing from prey to predator. Bacteria take up chemicals using surface receptors on their cells. Many of these are now well characterized, and one can use mutant bacteria or mutant worms which are unable to take up one or the other chemical to understand more about how the signalling works. In order to investigate how saligenin is taken up by the worms, the authors tested mutant worms defective in various receptors, choosing them on the basis of previous studies2. Worms with a defective receptor for taking up the chemical dopamine (dop1) showed decreased migration towards Bgl+ bacteria, indicating that saligenin could act through this receptor. This was with laboratory worms. Examination of natural soil nematodes showed that some species of worms avoided saligenin rather than moving towards it, suggesting that they could have evolved to recognize the toxin in their environment. The authors argue that in addition to sugar breakdown, the ability to 'repel or lure predators and thereby gain a nutritional advantage' could be a major reason why the 'cryptic' bgl genes have been retained. They also suggest that aromatic sugars made and released by plants could be used in controlling crop pests such as parasitic worms and amoebae. Future research might further demystify the role of 'cryptic genes' and lead to greater surprises. References 1 Sonowal, R. et al. Hydrolysis of aromatic beta-glucosides by non-pathogenic bacteria confers a chemical weapon against predators. Proc Biol Sci 280, 20130721,(2013). 2 Collin, D. T. et al. Saligenin analogs of sympathomimetic catecholamines. J Med Chem 13, 674-680 (1970).

What it means to be 98% chimpanzee (Deccan herald, 6th August 2013)

'What it means to be 98% chimpanzee' is the title of a book by biologist Jonathan Marks. His aim is to make people aware of the fact that what we can learn from gene sequences is limited. The limitation is mostly to knowing what proteins can be made by an organism, and to some extent in estimating how genes are ‘networked’. In short, he exposes the fallacy of giving exaggerated importance to gene sequence information. No wonder that lay people are unaware of the fallacy: even the scientific community keeps falling into the trap.  It is important to pause and reflect on what people like Jonathan Marks are saying.

As taught in school - and perhaps more effectively by films like Jurrassic Park - DNA is made up of sugars, phosphates and four different nitrogenous bases that are abbreviated as A,T, G and C. The sugars and phosphates provide a backbone to hold the bases. They are irrelevant for understanding how DNA encodes information. It is the arrangement of the four bases in various combinations that decides what protein (if any) corresponds to a sequence of DNA. In the 1970's a scientist by name Frederick Sanger developed a technique by which DNA could be 'read', meaning that the precise sequence in which A, T, G and C occurred in a given sample could be determined. Today we have available a host of techniques to sequence all of the DNA in an organism, which is known as its 'genome'. The ability to do so and to manipulate DNA has certainly expanded our understanding of the nature of living organisms. However, does this mean that until DNA sequencing came on the scene we knew nothing about how living systems work at the molecular level? The answer is a clear no. In fact the foundation for what is known as molecular biology today was largely laid by meticulous genetics done in the 1940's to 60's, when there was no way of inferring the exact sequence of long stretches of DNA (and for much of the time without a clear appreciation of the central role of DNA). However, in recent times the hype surrounding gene sequencing has exaggerated the information one gets from it and the value of such information when we do have it at hand. Let us look at the facts.

A DNA sequence that is called a gene is said to be a ‘coding sequence’ because the sequence of bases carry coded information to make a protein or an RNA molecule that performs a specific function (All proteins are made from RNA molecules called 'messenger' RNAs, but other kinds of RNAs perform functions on their own, and do not need to be converted to protein). The sequence can be compared to a meaningful sentence in a language. With some degree of success, biologists can identify where (i.e. with what base) a sentence begins and where it ends. The rest of the DNA that does not make up readable sentences is said to be 'non-coding'. As far as we know it does not code for a protein or RNA molecule. But most of the time we have no idea what it DOES do. Some such sequences previously thought of as 'non coding' have led to the discovery of several new kinds of RNA molecules a that participate in regulation or co-ordinating the functions of genes. However, non-coding DNA can be quite a lot. For example, a staggering 95 % of the human genome belongs to this non-coding category. Just 5 % of our DNA seems to be making protein or RNA. Further investigations may raise the figure. But unless our ideas are fundamentally flawed (and as of today we do not see how that could be), it appears unlikely that more than 10% of our genome could code for proteins or RNA. Additionally, in multicellular organisms (like humans), the coding sequences themselves are frequently rearranged in a process called 'splicing', which means that the same stretch of DNA could be combined in many ways to make the final protein. Some genes are present across most life forms, and are referred to as 'conserved'. They can then be used to look at how organisms have changed over time in that specific respect- for instance a gene that helps in respiration called 'cytochrome C' is a popular choice. Because the genome sequences of so many organisms are now available, it is possible to compare specific sections across genomes and use this as one estimate of how close to each other the two organisms are. However, when we compare two DNA sequences, it is important to compare the right bits, and to be conservative in drawing conclusions about similarity.

For example, if you wanted to compare a human genome with the genome of an insect, say a fruit fly, the information is now available. A fruit fly genome is 60% similar to that of a human. Does that mean a human being is 60% fruit fly? It is clear that this is an absurd conclusion to draw. However, as the similarity draws closer, as for instance with the great apes (which includes chimpanzees) people quite frequently use the argument that 'chimpanzees are 98% human' in fighting for animal rights or even trying to get across a scientific point. It did not take gene sequencing to see that gorillas, chimpanzees and orang-utans look more like human beings than any other animal. In fact the common name of the orang-utan itself translates to 'old man of the forest'. This is not to say that we must not protect the great apes or place appropriate restrictions on their use in experiments where one would not use humans. Indeed everything we have learnt about them suggests that they display an emotional and intellectual sensitivity well above most other animals. However, it is scientifically inaccurate to translate genetic similarity to an all encompassing overall similarity. When two stretches of DNA are compared, they are lined up next to each other and the base at every position is compared. Two short sequences can be 0% similar, for instance CCGAT is completely different from GACTA. However, as there are only four bases in DNA, for large sequences, there is a 25% chance that the same base will occur at the same position in both stretches of DNA. In other words, a 0% similarity is really a 25% similarity. This means that at the lower end differences are over-estimated, and as the numbers climb higher, differences are under-estimated.

As Marks points out, humans are not 98% chimpanzees. We might add, nor are they 60% fruit flies or 30% daffodils. While data from gene sequences is undeniably useful, we are yet to fully understand HOW best to interpret or use it. More so, many of the promises held out by the knowledge of sequence information has not materialized. Ten years after the human genome was sequenced, at this point it remains more an impressive technical achievement than a scientific advance in knowledge. Two major expectations have been disproved. The number of human genes expected was far more than the number actually found to exist (~25,000 vs ~100,000), already indicating that gene numbers alone were unlikely to define a unique identity. Secondly, the expectation that knowing the sequences could lead to quick diagnosis and prevention of several diseases has not materialized. We now have a lot of information. The trouble is sorting and understanding it. Even if (as the current field of 'proteomics' replaces the older one of 'genomics') we knew the function of every gene there is, it wouldn’t lead us to an instant understanding of how the organism is made or operates. The idea that breaking down things to their most fundamental parts will reveal how the whole works (often called 'reductionism' in biology) does not necessarily work with complex systems, and living organisms are as complex as things can get. Their function depends on an intricate interplay between genes, the physical environment, social inputs and so on. Knowledge of DNA sequences remains useful and important. But because of the pitfalls listed above in sequence comparisons and in going from sequence to function, it is only one part of what we need to understand how life works. Even if it held true to all available comparison methods, the statement ‘Human DNA and chimpanzee DNA are 98% similar’ would tell us very little about what it means to be a human or a chimpanzee.

The Coelacanth- a 'missing link' (Deccan Herald, 23rd July 2013)

The term 'missing link' is often used in the popular press, and equally often deplored by biologists as a rather glamorous over simplification. It refers to an organism with features intermediate between two existing classes of living organisms, and is thought of as a bridge between them during the course of evolution. In actual fact, the existence of organisms with features of two different classes of animals is both exciting and important to our understanding of organic evolution, but rarely has it been reduced to the level of a single animal. Rather, several animals with features transitional between two currently existing classes of animals have been discovered from the study of fossils found all over the world. Sometimes, these represented paths that explored a novel form which did not evolve further into anything else, what is referred to as an 'evolutionary dead end'. In other cases, some features have evolved many times over evolutionary time (for instance the ability to fly, instinctively linked with birds by a layperson, has evolved many times, among insects, birds and mammals as well) and so cannot be used as sole evidence to speak of 'the' missing link.
The theory of evolution by natural selection put forth by Charles Darwin and Alfred Russel Wallace speaks of a gradual transition from one living form to another over the four billion years or so that life has existed and diversified on earth. This would mean that there must be animals that look partly like amphibians and partly like reptiles, and so on for all closely related classes of living beings. However, from our own experience, the living world is composed of distinct species and types of animals and plants. On encountering an unfamiliar creature, we are unlikely to be confused about whether it is a bird or a monkey. Where then are these intermediate creatures that show the transitional forms between existing and clearly defined species? The place to look for organisms that once existed but are no longer represented in the current world, is among fossils. The fossil evidence shows that several intermediate species were not as successful in establishing themselves as the two species 'flanking' them and went extinct. Darwin himself was the first to lament the incomplete nature of the fossil record. A chapter of his famous book 'On the Origin of Species' is in fact entitled 'Absence or rarity of transitional varieties'. In this he says "If my theory be true, numberless intermediate varieties, linking closely together all the species of the same group, must assuredly have existed; but the very process of natural selection constantly tends, as has been so often remarked, to exterminate the parent-forms and the intermediate links. Consequently evidence of their former existence could be found only amongst fossil remains which are preserved".

However, although the fossil record is by no means complete, over the years palaeontologists have discovered several interesting and amazing creatures as fossils. Perhaps among the most popular examples is the flying dinosaur, the archaeopteryx, with the feathered wings of a bird but carrying a tail and teeth that were like those of dinosaurs. It was hailed as the oldest bird and the possible link between reptiles and birds. This with particular fervour, as it was discovered in 1861, just two years after Darwin published “The Origin of Species”. After this however other bird-like dinosaurs and dinosaur-like bird fossils have been unearthed, blurring the special status of archaeopteryx.

Another fascinating organism that has been hailed as a missing link is the coelacanth. Interest in the coelacanth has recently resurfaced as its genome sequence was worked out and made public just two months ago. The coelacanth is special among all those fossils hailed as 'missing links' because it suddenly emerged as a live specimen off the coast of East Africa in 1938. Samantha Weinberg in her book "A fish caught in time" describes the events leading up to and following its discovery. The story reads like a thriller. In 1839, the Swiss scientist Louis Agassiz described the fossil of an unusual fish tail found in the north of England. He named it Coelacanthus granulatus, because the fin rays were hollow (Coelacanthus is Greek for hollow spine) and the scales appeared to be decorated with tubercles (granulatus). After this, several Coelacanth-like fossils were discovered all over the world, from China to Brazil to Madagascar. All of them had the same features but were vastly different in size, ranging from a few centimetres to as much as three metres. The oldest fossil dated back to about 400 million years (the Devonian period), while the most recent was about 70 million years old (the Cretaceous period). It was generally assumed that the creatures had become extinct around 70 million years ago along with the dinosaurs. It was known that sometime in the end of the Devonian period, a species of freshwater fish evolved limb like structures and moved on to ‘conquer’ land. There were three main candidates for such 'Ichthyostega' or 'walking fish': the lungfish, the rhipidistian and the coelacanth. But poring over fossils it was hard to determine which was the best bet, as the search was both for limb-like structures as well as the ability to breathe on land, that is the presence of lung like structures. It appeared that a study of the soft parts was necessary. In December of 1938, Marjorie Courtenay Latimer, working as a curator in the East London Museum in South Africa, was brought a pile of fish to sort for the museum. This was part of the routine specimen collection for mounting and display. She discovered a blue green fish of five feet with an iridescent sheen and a 'funny puppy dog tail'. Although she didn’t know what it was, its appearance was sufficiently unusual to contact an expert. This first live specimen of a coelacanth survived many near disasters: Marjorie Latimer's near rejection of the fish pile, the lack of a cold storage facility, the scarcity of formalin to preserve it and the delay in response from the expert, J.L.B Smith. As a result the soft parts could not be saved, and there was another hunt for a living coelacanth. Finally one was found off the Comoro islands between Mozambique and Madagascar after nearly 15 years. This species of coelacanth was named 'Latimeria chalumnae' in honour of the discoverer.

Was this then a great-great..great grandparent of the first land vertebrate? Studies comparing lungfish and coelacanths tended to support the lungfish as closer than the coelacanths to the first vertebrate on land. However, because similarities between genes are believed to be clues to relatedness between groups of animals (phylogeny), the Coelacanth genome sequence was eagerly awaited. Lungfish genomes are very large, and unwieldy to deal with. They contain about 100 billion base pairs of DNA. The Coelacanth genome is about the same size as the human genome, about 3 billion base pairs. The complete sequence of the African coelacanth (today we have another species, the Indonesian Coelacanth) was worked out two months ago and the study published in the journal Nature. The study compared sequences of genes involved in limb development (as this was an important element of living on land) as well as regulation of genes involved in building a body plan compatible with life on land. It also compared several gene sets across lungfish from the limited amount of sequence data that is available, tetrapods (representative four legged vertebrates) and coelacanths. The result of this comparison showed that indeed the lungfish are more closely related to early land animals than are coelacanths. In order to assess the rate at which the coelacanth genome has evolved, the authors calculated a 'substitution rate' which estimates how frequently the coelacanth genome has undergone mutations over evolutionary time. The conclusion was that the coelacanth genome has been evolving at a significantly slower rate than the genes of lungfish and tetrapods. In fact the authors suggest that the strange prehistoric appearance of the current day coelacanth is because of the slow rate of evolution of its genome. This is a somewhat surprising result, because in other aspects the coelacanth genome appears to be similar to its lungfish or tetrapod counterparts. Critics argue that because all genomes contain regions that change more frequently than others, the choice of gene sets that have been compared could have biased the findings . Without knowledge of how the coelacanth genome is regulated, it is not easy to determine which genes should be compared with which between lungfish and tetrapods. However, it does appear clear that coelacanths are not the immediate ancestors of the first land vertebrates. Lungfish are the closest we have to such a link today; future fossils may lead to an even closer link. Be that as it may, by existing today coelacanths have enriched our knowledge of our own past and the world around us by their dramatic appearance and prehistoric looks. As yet there remain precariously few - about 400 individuals- in their African hideout. It is up to us to ensure that they remain safe.

Prions- the selfish proteins (Deccan Herald, 26th September 2006)

“DNA is the basis of life.” This sentence is drilled into every school child today. However, in the days when biologists could only dream of discovering the genetic material, the advent of DNA (deoxy-ribonucleic acid) as a candidate was greeted with scepticism. This was because, as a chemical, the DNA molecule seemed too simple. Proteins were then the most prominent and complex bio-molecules known. DNA was a long chain made up of 4 different subunits whereas proteins had 20. It seemed logical that proteins being the more intricate molecules would be better for encoding the complexities of heredity. Gradually, however, overwhelming evidence accumulated in favour of DNA, leaving little room for doubt.

In the 1960‟s, shortly after the structure of DNA was described, a medical doctor by name Gajdusek travelled to New Guinea to investigate a strange disease characterized by wasting away of the muscles; leading to paralysis and finally, death. It was called „Kuru‟ which meant „trembling‟ in the language of the local Fore tribe. The disease symptoms suggested that the nervous system was gradually being destroyed, suggesting an abnormality in the brain. The strange thing about the disease was this: it appeared to be spread by cannibalism. Fascinatingly, Gajdusek‟s investigations revealed that the Fore tribespeople practiced cannibalism as a ritual, where the bodies of dead people, often relatives, were routinely consumed. The most prestigious members of the tribe got to eat the brain, considered the prize portion. Kuru was found predominantly among the tribal chiefs and occasionally in very young children. It turned out that women prepared the meal with their youngest children in tow, often handing out titbits while cooking and thereby transmitting the infectious agent to them. Having traced the infectious agent to the brain, Gajdusek spent many years attempting to purify it. Finally, he came out with the startling announcement that the agent was a pure protein. It contained neither DNA nor RNA (Ribonucleic acid, also known to be the genetic material in some viruses by then). In other words, it appeared that a protein by itself could be transmitted like a virus; it appeared to be alive.

Ironically, the tide had changed. Scientific belief had turned against the possibility that proteins could be infective (that is, that they could multiply without any DNA or RNA).

Practically the entire scientific community discredited his claim. They insisted that there must be traces of DNA or at least RNA in the infective agent which he‟d evidently missed. Gajdusek went on to win the Nobel prize for his work on Kuru, but the infectious agent remained a mysterious entity. The mystery was finally solved after many years of work and many hurdles. Another medical researcher, Stanley Prusiner, was awarded the Nobel prize for the „Discovery of Prions- a new biological principle of infection‟ in 1997.

„Prions‟ stands for „Proteinaceous infectious particles‟. These unique „protein-only‟ particles do indeed make copies of themselves without the aid of any nucleic acid. Thus, they shake the belief that life must be based on DNA or RNA. Today they are best known to us as the causative agents of BSE or the Mad Cow disease. There are several more prion diseases. All are fatal, but they are so rare that they do not attract attention from the general public. So how do prions make copies of themselves? To see this, we have to look at protein „folding‟.

The accurate folding of a protein molecule is critical for its functioning. Under normal circumstances, the cell identifies and degrades misfolded proteins. Prions are accidentally misfolded forms of normal cellular proteins which escape degradation. They have the special ability to make copies of themselves using their normal cellular counterpart as a seed. In other words, they can catalyze their own formation. Therefore, once an accidental misfolding of the normal form occurs, the prion form keeps increasing in quantity. In addition, being highly resistant to degradation, they form clumps within the cell. Just as an isolated rotting apple does no damage, whereas in a fruit basket it spoils all other fruits, prions keep increasing in number in the presence of the normal copy.

The earliest known record of a prion disease is in sheep from Scotland. It was termed „Scrapie‟ because the sheep would be seized by uncontrollable itching and scrape themselves on the nearest fence, so much so that they finally bled to death. Prusiner named the human prion „PrPSc‟ with „Sc‟ standing for Scrapie. All of us carry a prion-gene whose protein is made only in the brain. It has been named „PrPC‟ with „C‟ standing for „cellular‟. We still do not know what its function is. What we do know is that a single misfolding event that produces the specifically misfolded prion form (PrPSc ) is sufficient to trigger the beginning of disease. Once formed, prions clump and in effect, strangle the neuronal cells in the brain. The hype around the Mad Cow disease and its human

counterpart focused attention on prions in mammals. What is not as well known, however, is the presence of prions in a much studied microbe, the budding yeast. At least four kinds of prions have been identified in yeast. All are misfolded forms of normal cellular proteins. They are unable to serve the normal function and therefore cause the cell harbouring them to behave abnormally. This helps in distinguishing between cells that contain prions and cells that do not. In yeast, however, it seems that prions neither help nor harm the cell. In a fungus called Podospora, a prion has been discovered which in fact helps normal cellular functioning. In other words, a misfolded protein has been selected in addition to the normal cellular form; it functions like an alternate form of the original protein. In addition, since yeasts are single celled creatures, prions are automatically transmitted from one cell to its daughter. What is special about this?

Darwin‟s theory of natural selection tells us that characters acquired during the lifetime of an individual cannot be transmitted to the progeny. Lamarck‟s theory, on the other hand, claimed exactly this. Yeast prions confer novel properties to the cell harbouring them, but they do so in the absence of any change in the yeast DNA. They can be retained in daughter cells and transmitted over many generations. In other words, they represent a case of the inheritance of characters acquired during the lifetime of an individual.

So the fact that prions exist, goes against what was believed to be a general rule in biology. Today there are two main schools of thought concerning prions. One argues that prions benefit their hosts in special conditions. If a cell has an alternate form of a normal cellular protein, and if that form can copy itself, the cell can acquire different properties without committing itself to a permanent, i.e, genetic, change. When cells have to live in changing environments, this ability could be of advantage. The other school of thought claims that prions indicate an abnormality. If the first is true, we need to understand exactly what these „special conditions‟ are that are needed for prions to be beneficial. If the second is correct, then we need to study the spread of prions and their effects in nature. Are prions „selfish‟ proteins that employ the cell for their propagation? Or are they willfully maintained by the cell for some purpose unknown? The field of prion biology remains an exciting one with much scope for investigation. With a little bit of license, the reason can be summarized in the following haiku-"DNA was prime, Till prions came, Challenging the monopoly".

The Handicap principle (May 2010, Resonance, published by the Indian Academy of Sciences and Springer publications jointly, http://www.springerlink.com/content/h767m3tg2653gp42/)

Charles Darwin, in his path-breaking book, On the Origin of Species, proposed a mechanism known as ‘natural selection’ to explain how the diverse living creatures on earth possibly evolved. Being both very meticulous and by nature diffident (it took years to consolidate the book) he also simultaneously put before the public several natural phenomena he had observed that he felt could not be adequately explained by his theory of natural selection. Prominent among such puzzles was the tail of the peacock.

 Why does the peacock possess an apparently cumbersome and huge tail? To most of us it may even seem a stupid question on the face of it. ‘Because it is attractive’ would seem to be the obvious answer, exposed as we are to tales of rain dances and maybe the occasional lucky sighting of a peacock displaying its gorgeous tail feathers to the peahen during the mating season. But in the animal world as we understand it, it is not enough to be beautiful; for a phenotype to be selected, it must be ‘fit’ or have a higher ability to transmit the trait to the next generation. But the heavy tail seems to almost impede the movement of the peacock and surely it must make it a disadvantage in the face of predators and when it wants to take flight. Why, then, is the long tail ‘selected for’ over evolutionary time? Why does the peacock have a cumbersome tail? This question has been tackled extensively by behavioural biologists over the years, with Fisher’s ‘runaway sexual selection’ being perhaps the most innovative idea. Fisher suggested that the reason for males of certain species to carry extravagantly developed secondary sexual characters could indeed have started with a slight female preference when the trait first appeared. Initially the slightly exaggerated feature was perhaps linked with stronger or biologically fitter males. However as selection favoured these slightly more ornamented males, the trait itself got out of hand and extravagantly decorative males evolved, individuals who no longer were the fittest since the trait, so to speak, overwhelmed the organism and became ridiculous and cumbersome. In other words, Fisher proposed that the peacock’s tail was indeed once upon a time associated with the strongest males but is not so linked any longer and in fact has apparently become a burden.

 After Fisher, the subject of sexual selection received its share of interest but there was no major breakthroughs to offer in understanding this puzzle, not least because experimental evidence was insufficient if not absent. It was only in the mid 1970’s that the husband and wife scientist couple of Amotz and Avishag Zahavi published a book titled ‘The Handicap Principle’. In the book, they put forward a novel idea to explain several previously baffling aspects of animal behaviour, including the famous tail of the peacock. The principle relies on three chief tenets - a) Animals communicate with each other through signals; b) These signals, in order to be effective, must be honest and c) Honest signals are expensive, i. e, the animal producing an honest signal incurs a cost in doing so. The peacock carries its tail as an advertisement of its fitness. They suggested that the elaborate tail is a means of saying that “in spite of carrying the handicap of a cumbersome tail, I am able to carry on my daily activities as well as a peacock which has a lesser tail”. The Zahavis argue that a signal is liable to be effective when it is honest, that is, when it conveys a true measure of how fit the signaller is. An honest signal, however, must be expensive. Why? Because signals do not come for free. They cost something (e.g., energy) to produce. The stronger you are, the more easily you can bear this cost. A strong individual can afford to incur a larger cost than a weak individual can. The upshot is this; if you convey the impression that you are handicapping yourself, and if the nature of the handicap is such that a weak individual could not afford it, you are signalling that you are strong. Assuming that you are not a fool (and fools do not survive long), if you go out to bat against Shoaib Akhtar without a helmet, you are signalling your genuine ability to deal with short-pitched balls. This is the essence of the Handicap Principle The Handicap Principle was a startling concept when the Zahavis first applied it to animal behaviour. But in some ways it is an old idea. We have an instinctive appreciation for what success in the face of an impediment. Where a good violinist is applauded, a good violinist who is blind is given a standing ovation. In his book “The theory of the leisure classes” the nineteenth century economist Thorstein Veblen attempted to explain the squandering of resources by the wealthy. He called it conspicuous consumption. Veblen’s explanation anticipated a form of the handicap principle. He claimed that the wealthy indulge in waste in order to advertise their wealth. Coming back to the peacock, do females in fact prefer males with ‘more beautiful’ tails? This was answered by a series of experiments carried out by Marion Petrie and her colleagues at the Whipsnade park in the U.K, and the brief answer is yes, they do. Marion Petrie et al used several parameters to define what ‘beauty’ might constitute, for example they used the weight of the tail (clearly a handicap), the number of feathers and the length of the tail as some parameters. Interestingly they found that the number of eyespots on the peacock’s tail is a measure used by the female in choosing a mate! We do not know yet whether in fact the female has some way of counting these spots or whether having more spots simply makes for a more impressive display, for example. The Handicap principle- an honest signal: The handicap principle can be used to account for mating preferences in animals. The key idea here is that no female would choose a truly handicapped male to father her children. A desirable male is one who is fit in spite of the handicap he carries. The handicap works like a badge that announces quality. Only a confident individual can afford it. Consider a human parallel. Both popular cinema and common perception proclaim that when in danger, a confident individual adopts a frozen stance, with hands folded across the chest and the chin pointing upwards, in fact the worst kind of posture with which to prepare for a fight. A handicap cannot be faked. This is what makes it honest, and reliable as a signal. This is because flaunting the handicap requires a genuine investment on the part of the animal. If an individual cannot afford to make that investment, it cannot afford to cheat. The courting peacock’s eye-catching but heavy tail, the threatened gazelle’s spectacular but attention-drawing jumps, the gullible crow’s feeding of baby cuckoos - all find an explanation in terms of the handicap principle. Let us look at two of these situations in more detail. An example of the handicap principle in operation: Hunter and hunted would seem to us to have conflicting interests. After all, one is looking for food and the other does not want to be eaten. However, it is in the interests of both to avoid a conflict that is going to result in the prey getting away. If such an encounter is predictable before hand, the predator would save time and effort and look elsewhere for weaker or easier prey, while the potential prey can save the energy used in running away. The authors use the behaviour of ‘stotting’ as an example here. Stotting refers to the up and down jumps exhibited by gazelles upon spotting a wolf or other predators, prior to their running away. The authors argue that this is illogical behaviour for a gazelle that is keen on escaping, it should just run; and not apparently “waste time” with such jumps. They suggest that a gazelle that indulges in such a dangerous practice must be signaling its physically fit status to the predator. By doing so, it is communicating to the predator that it has seen it (therefore the advantage of surprise is lost), and it is strong enough to outrun the predator in a chase. Based on many field observations, it is known that very often predators faced with stotting gazelles leave and look for other prey. The authors propose this as an example of an honest signal that has evolved as a means of communication between predator and prey. It involves an investment of energy on the part of the gazelle, and so cannot be faked. It would be suicidal for an unfit gazelle to attempt such jumps; it would only expose its inability sooner and fall an easy prey. Mating displays are good hunting ground to observe the handicap principle in operation: Like in the case of the peacock, other mating displays also are an oft quoted example by the authors. 
  Typically, females invest more in their offspring than males do. Also they are receptive only at certain times in the year, and once they conceive will be unable to conceive again for the period of the pregnancy and for some time after. So they need to be choosy in picking a mate. Males however, mate with several females in the short period of time when they are receptive, thereby aiming to maximize the chance that their genes are passed on. In the mating season, therefore, each male must do his best to attract, and mate with, as many females as possible.The peacock, as already discussed, holds his tail upright - in itself a process that would seem to need strength -and shakes it vigorously from time to time. By doing so he appears to prove his physical fitness to the watching female. Also, his tail feathers are developed at a time of year when there is a scarcity of food. A male who has developed a fine tail plumage, therefore, is offering proof of his ability to successfully look for and find food even under conditions of stress, and hence is advertisings his desirability as a mate. In the mating season, the spectacularly coloured male bird of paradise hangs upside down on a tree, spreads his feathers and flaps the wings. He is dancing with a handicap. During the mating season white pelicans develop bulges at the base of the beak (just ahead of the eyes). A bulge is a handicap. It makes it hard for the pelican to see and impairs its ability to fish. A successful fisher proves to potential mates that it can fish well in spite of the impairment. These mating display observations however, have been made for several years and as observations are nothing new to naturalists. However, when they discuss single celled fungi, the yeasts, the authors put forth both a novel observation and a new hypothesis to explain it. Yeast cells reproduce both asexually (by budding or fission) as well as sexually. There are two distinct mating types in yeast, referred to as ‘a’ and ‘α’. Both use a peptide molecule on the cell surface as a mating ‘signal’ as the authors term it. These peptides are seldom bare, and usually carry oligosaccharide moieties and occasionally even lipids attached to them. The authors suggest that yeast cells advertise their desirability as mating partners by ‘decorating’ the peptide molecule that is their mating signal. To make the modification, they need to use expensive chemical resources (such as lipids and sugars). The modified signal works like a handicap. Most importantly, the hypothesis is testable, and indeed a ‘decorated’ peptide appears to be preferred to an ‘undecorated’ one, suggesting that the handicap principle could be one innovative way of looking at signals even at the single cell level. In Darwin’s own words: As these examples show, there is what looks like wastefulness behind many sexual displays, and the handicap principle tries to explain why this is so. But this theme has been a subject of discussion among naturalists for many years. Indeed, Darwin himself proposed something reminiscent of the handicap principle when he wrote “The females are most excited by, or prefer pairing with, the more ornamented males, or those which are the best songsters, or play the best antics; but it is obviously probable, as has been actually observed in some cases, that they would at the same time prefer the more vigorous and lively males” (The Descent of Man and Selection in Relation to Sex). However exciting and plausible the handicap principle, however, the authors appear to be carried away by enthusiasm unsubstantiated by data when they bring up human analogies. Topics ranging from the colour of cheeks and lips to cave-paintings are discussed as examples of the handicap principle in operation. Even beards are not spared. In many instances, they appear to have picked something that could qualify as a signal and then constructed an explanation around it. Having said that, the idea still remains innovative, unique, and above all, provides ample scope for clever experimental design and hypothesis-verification. 

  When the handicap principle was first proposed in 1975, it met with wide scepticism. Mathematical models seemed to show that it could not work. It appeared destined to share the fate of other ideas in the history of science that were appealing but incorrect. After 1990, however, scientific opinion turned around. This is because of increasing support from observations and due to sophisticated mathematical modelling by Alan Grafen that showed that this is a workable theory. It has come to be accepted as a novel concept, with wide application in understanding animal behavioural strategies. In speaking of the fifteen-year gap, Zahavi says “Biologists remained unimpressed by the logic of the verbal model, and accepted the handicap principle only when expressed in a complex mathematical model, which I and probably many other ethologists (behavioural biologists) do not understand”. Budding biologists might well support this rueful statement.