Do we really inherit acquired traits?

Parenting is full of paradoxical situations. There are times when you hate to see your kids doing things that you also do, or at least did, oftentimes. When it first dawned upon me that my child has developed a habit of sucking her lower lip, I couldn’t decide if I should be concerned or happy. I was aware that my dental structure was ruined because of that very habit during my childhood. I have always been casual about looks, but the habit also affected my jaw function in the long run. Now, like most parents, I do not want my child to repeat my mistakes.

The sort of “happy” side to it was that I saw in this a potential living proof of Lamarck’s theory of evolution. The theory roughly goes like this: an individual acquires some traits during its lifetime and thus adapts to changes in environment; the traits then get passed on to the next generation and become evolutionary changes. Giraffes evolving longer necks and front legs is often cited in books as a likely example of Lamarckism. In my case the lip-sucking habit was acquired purely by my actions in my lifetime. I didn’t inherit it from my parents. No big deal, one might say, many babies suck lower lip. True, some babies do this as a natural reflex of sucking nipple for feeding. However, seldom do babies continue with this habit for months. I was doing that even after I started earning. My daughter at least stopped the habit when she had braces.

Proposed at the beginning of the nineteenth century, Lamarck’s theory has been out of favour for over a century now. Another theory, one by Weismann which caught the fancy of scientific world, killed it. Almost. Let me explain.

Let’s start with the development of an embryo inside mother’s body. Very early during the process, a specialised group of cells of the foetus is kept aside safely to be used later exclusively for sexual fusion after puberty. These forbidden cells are known as germ cells. All other bodily cells (jargon: somatic cells) eventually develop into organs which perform day-to-day activities. As far as exchange of genetic material is concerned, these two types of cells don’t talk to each other. Weismann argues that ongoing life characteristics can at best affect the somatic cells which are involved in the activities. Such changes cannot be transferred to the germ cells. And unless the changes affect the germ cells they cannot be passed on through heredity. This is called Weismann barrier which, most scientists agree, forbids inheritance of acquired characteristics. Lamarck therefore failed to become a legendary figure of evolutionary biology.

The new millennium however saw reemergence of Lamarck’s ideas. Certain acquired characteristics of brain were found to be inherited in rodents (Singer, 2009). The mechanism of transfer of such traits does not involve genome. Rather it’s attributed to things that affect how genes of the DNA are expressed for protein making (jargon: epigenetics). The “things” are chemical molecules acting like tags that tell a gene to be active or inactive. Even though the recipe for a particular protein is written in a gene, whether it will be made or not is determined by such tags. The tags are modified throughout the lifetime as the environment we live in changes. Note that the genome doesn’t change. In that sense it does not break the Weismann barrier. Yet the net effect is one of transfer of acquired traits.

When male and female germ cells fuse after mating to create the new fused cell (jargon: zygote), it was believed that the new formed DNA does not inherit the epigenetic tags. They are meant to be erased to provide the new cell with an “epigenetic blank slate”. It has been discovered recently that the erasure of tags is not complete. Some tags indeed pass through from parent cells to the next generation. Thus two generations are exposed to an environmental change such as smoking, and three generations in case of direct exposure of a pregnant mother. This is because a developing foetus has germ cells ready for contributing to the next generation. So before your baby comes out of your body, the seeds of your grandchild are already there.

Weismann barrier is thus no longer a valid objection to Lamarckian inheritance. There is another problem with Weismann’s theory which stems from lack of clear distinction between germ cells and somatic cells during embryo development. In fact the zygote initially divides into many cells which at that phase are like somatic cells, some of which go on to become germ cells for the next generation. Thus germ cells have a brief period of “somatic” life before they are assigned their role.

With the Weismann barrier gone and evidences of transgenerational epigenetic inheritance emerging, acceptance of Lamarckism is definitely on the rise. That may not necessarily mean however that I have passed on my lip sucking habit to my daughter. Though tempting to the scientist in me, until someone clearly explains the mechanism from end to end as a case study, I am not pleading guilty.

References:

Koonin, EV. (2014) Calorie restriction ? Lamarck. Cell 158, 237-238.

Singer, Emily (2009) A comeback for Lamarckian evolution. MIT Technology Review. https://www.technologyreview.com/2009/02/04/216134/a-comeback-for-lamarckian-evolution/amp/

The pandemic’s catastrophic effects have made a generation aware of the power of microbes. Our anthropocentric perspective usually ignores other powerful forces of nature. We might feel vulnerable against some natural calamities and acknowledge the might of inanimate forces such as earthquakes and cyclones. But we fail to admit that there are more dominating biological forces than us humans. Until of course the time a pandemic strikes. Like now.

Yet the fact remains that bacterial cells outnumber cells of our type (eukaryotes) by some orders of magnitude and viruses are even more widespread. Forget biosphere, our own bodies contain more bacteria than our own cells. If nature at all has concerns about survival of life, it makes more sense to think that she will worry more about bacteria than us.

As we have seen during the second wave in India, oxygen shortage affects us. What about bacteria?

The earliest bacteria lived deep in the ocean floor. The Earth’s oceans and atmosphere were practically free from oxygen molecules back then. It was all peaceful some three billion years ago. The earth had settled from the turbulent times of its formation.

Then some adventurous bacteria invented a machinery to harness sunlight for making energy that can be stockpiled. We know the process by the name of photosynthesis. Cyanobacteria were the pioneers of the technique long before plants came about. In fact, plants acquired photosynthesis from the cyanobacteria via a sort of technology transfer.

Photosynthesis was quite an invention. It splits water with the help of sunlight and uses hydrogen for energy generation and storage. With the help of this technological revolution cyanobacteria flourished and began to dominate the near-surface ocean. And the world had to deal with a new element – oxygen – the byproduct of the process of photosynthesis. Oxygen rose substantially in the atmosphere as a result of waste removal by cyanobacteria. That was some 2.5 billion years ago. It may sound contradictory or even weird to our perspective, but the arrival of oxygen wasn’t good news for life. Oxygen easily gives rise to some chemical entities collectively known as reactive oxygen species that are toxic to life. They damage DNA – the very core of life.

Life had this dilemma. Either face the wrath of the deleterious oxygen or shut down the photosynthesis factories. Gaining extra energy from the free Sun was too attractive a proposition to forego. And it did not make sense to not use a technology for which life had invested millions of years in R&D. Executive decision was made – photosynthesis will continue. Let’s find a solution to the problem created by oxygen. A group of bacteria took up the challenge.

While that group was working on the solution, photosynthesis was gaining popularity among microorganisms and some bigger organisms that arose 650 million years ago. This pumped more waste oxygen into the atmosphere and even oxygenated near surface ocean waters. Now there was no escape. The oxygen problem had become too big to ignore.

Fortunately just about that time the solution was ready. Life has this knack for turning threats into opportunities. It made use of one special virtue of oxygen, its hunger for electrons.

The earlier energy generation processes that life had at its disposal were all dependent on maintaining a pool of hydrogen ions (protons) on the other side of a membrane dam. Like a hydroelectric dam, release of protons is regulated via a channel which rotates a mechanical ATP generator to produce the life’s currency of energy. This pretty much is the fundamental process of energy generation in organisms.

Now all that a cell needs to do is maintain the proton concentration in the reservoir behind the membrane. This is where a series of electron acceptors come into play. They serially accept high-energy electrons to a lower energy regime and the energy thus made available is used to pump protons across the membrane.

Oxygen, because of its strong affinity for electrons, does this job more efficiently than other electron acceptors. Therefore when added to the series of electron acceptors, it makes a big difference to the cell’s ability to pump protons. Presence of oxygen enables organisms to make 15 times more ATP than primitive cells. One such energy generating entity is mitochondrion which lives inside our cells.

Relegated to the status of an organelle inside cell, mitochondria are now universally regarded as progeny of once free living bacteria. We know them as the power house of the cell. That is precisely because of their role in respiration via consumption of oxygen as per the method described above. Our body then can be considered as a colony of bacteria. The same applies to an ocean dwelling animal or any animal for that matter.

Oceans have a much less amount of dissolved oxygen compared to atmosphere. Remember, fundamentally life does not require oxygen. And it is toxic too as we have seen above. Yet once life had tasted the blood of oxygen via respiration, it didn’t look back. When animals came out of water onto the land, they were faced with extraordinary quantity of oxygen in the atmosphere.

Too much oxygen is like a flammable gas. You cannot have a flammable gas in a quantity that would set your house on fire. Yet you need gas regularly at a lower pressure to be able to sustain the flame for cooking food. Think of the supply of natural gas from producing region to your home. As it flows down the chain from processing plant through distribution mains and finally to your home, there is a cascading drop in pressure of the gas. Life does a similar balancing act to handle atmospheric oxygen. From atmosphere-body interface through lungs, blood and cell membrane, there is a cascading drop of oxygen pressure at every interface. When the oxygen finally enters the mitochondria, its pressure has dropped significantly to the level that a free living aerobic bacterium can handle.

Our entire body then seems like an infrastructure that helps make oxygen available at the right pressure to each of the mitochondria inside trillions of cells. The cumulative surface area of skins of all land animals thus becomes a defence wall against the toxicity of oxygen with nasal and mouth openings being the permissible channels for controlled entry of oxygen inside for further distribution.

So effectively by breathing in air we are allowing oxygen inside in a calculated manner for mitochondria to generate energy required for life activities. But more importantly, we are protecting mitochondria from “burning” by presenting several barriers in the path of oxygen – first by humidifying air after intake, then by mixing with carbon dioxide inside lung sacs, then mixing with blood and finally by diffusion into tissue cells and diffusion into mitochondria. See, we are letting our cells avoid oxygen rush. As does a fish which presents the first barrier in the form of gills.

At the heart of the architecture of such multicellular organisms lies a special material called sterol which imparts special properties to the cell membrane. In yet another example of how life turns threat into opportunity, sterols are made using oxygen and they in turn protect cells from oxygen toxicity.

Deep inside some big organisms including humans, the infrastructure is so designed that there are few chambers where oxygen is completely shut off. These protected chambers allow some bacteria to thrive using the “old technology” of fermentation in the absence of oxygen. Which is what some deep ocean bacteria do too. So what such animals like cow are effectively doing is creating the deep ocean like environment on land for bacteria to do their cooking the primitive way. That we oxygen breathing creatures do not like the waste methane – generated in the process and ejected from their mouth and anus – is another matter.

In our journey since we left the resourceful oceans and began conquering land areas, we animals have made progress working hand in glove with plants. Interdependence of plants and animals goes beyond the obvious oxygen-carbon dioxide exchange. We rely on plants to provide us with the essential amino acids. The stationary plants on the other hand rely on us for a number of functions such as reproduction. Together our march continues – away from the oceans and deep inside the continents. While cyanobacteria produce most of the oxygen in the atmosphere, plants chip in with their contribution. We in turn help with proliferation of plant life. By aiding in pollination, providing water, dispersing seeds and, more recently, by creating suitable environments for plants in unfavourable conditions. Have we been doing enough lately? Or merely consuming what the plants offer? Something to ponder over once the harshness of the pandemic wanes off.

We animals are, in a way, freeloaders. Plants do primary production and we consume. However we owe plants some favour in return. Here in my interdisciplinary take on animal-plant interactions and the water scenario I try to explain the give-and-take relationship. A bit of philosophy too is thrown in the mix. I find the overlapping boundaries of different scientific disciplines most interesting. 5 minutes read…

It’s natural to think of viruses as enemies of mankind. More so when we are in the middle of a pandemic. But things aren’t quite that bad when we extrapolate the impact to all living beings throughout the history of life. I wrote this short article where I tried to explain one benefit of viruses which has had a huge impact on who we are. There is also a high level overview of how viruses operate. Please read if you are interested. If the topic fires your curiosity, Carl Zimmer’s ‘A Planet of Viruses’ is a good beginners level book and the book referenced in the article is a pretty detailed take on the science of viruses.

Right now I am aware that my mobile is just about 30% charged. The battery icon at the top right corner is staring at me. The phone will prompt me as soon as the charge goes down below 20%. If I don’t plug it in, it will shut itself down when it is fully discharged. Thankfully, the risk is limited to me not being able to use the phone. It cannot cause much harm to me or to the device. I can afford to be lazy for now. It’s an altogether different story however when something similar happens inside my body.

When I am running out of energy, my body tells me to go and get some food. Or drink. Its alerting mechanism comprises of, among other things, the feelings of hunger and thirst. I cannot ignore these prompts for long. These are bodily sensations that belong to a particular type of feelings. Some other feelings are purely mental. Being happy or feeling disgust for example. There is a whole heap of feelings that are generated by our central nervous system which prompt us to do something. Researchers in Finland have mapped our 100 core feelings by analysing how pleasant and how prominent these feelings are. A much simplified view loosely based on their work is presented here.

Sex is expensive. At a minimum, it requires persons of opposite gender to come together. It may superficially seem to be a non-issue because for every female, there is a male around (well almost). But it does take quite a lot for a person from Venus and another from Mars to come to a meeting place on Earth. Yet getting together is just the beginning. They must then like each other to begin a meaningful conversation that could lead them further. Thereafter they need to love each other. It demands a lot of effort to impress one another. Too much energy goes in singing, dancing, feeding, eating, gift buying, villain-bashing, showing off beauty and strength, chatting (love letters in the past), and so on. All done. Then each of the lovers need to shun the competition. Because signalling does not discriminate between individuals of the opposite gender. Ask a plant which spends so much energy producing flowers with all their visual beauty and fragrance and then gets a bunch of freeloader insects who would not assist with pollination. Is it all worth it?

The above para was intended for fun. But there is a huge scientific cost too to this whole business of sex. Finding mates is a huge biological/ecological problem. Then there are costs associated with the fundamental sexual process of cell division – meiosis. Unlike mitosis (cloning) which finishes in under 2 hours usually, the sexual cell division of meiosis takes much longer to finish. If a female were to self-reproduce, she could pass all of her genetic material to the offspring and not just half. And then, ecologically speaking, half of the progeny in the form of males would not need to be produced at all. Why even bring these un(re)productive beings to life just to eat up resources?

What on Earth then are the benefits of sexual reproduction that the nature has preferred this mode over cloning? Well, that is one of the trickiest questions which the scientific world is yet to find a satisfactory answer to.

Cloning would produce the same individual every generation with the exception of cases affected by mutation. Does sexual reproduction enable life to stay ahead in the arms race with the villain who wants to disrupt life? By disturbing the pattern of life form just a little every generation? Making every eukaryotic individual unique? So that the villain cannot come up with a strategy based on its understanding of the earlier generation? And under this ever changing guise, life quietly goes a step further? But who is this ‘villain’? Even harder question is: who or what is this ‘life’?

With science, every answer leads to further questions, no?

Our body parts are all quite different – in form as well as function. The roughly triangular shaped dark-brown coloured liver processes blood to make it nutrient-rich and also produces bile – a fluid vital for digestion. The skin on the other hand takes the form of the animal itself and acts as an interface between the animal and the environment. Each of the diverse body organs grows by multiplication of cells of specific type. It is therefore weird to even think that they all originate from one single cell. It is true however that we all started as a single cell – the zygote.

As if that was not weird enough, the zygotes of different vertebrate animals are not different at all if one ignores the genes inside. Even during the early development stages, it is difficult to distinguish between a human embryo and a fish embryo.

Like the zygote, sex is another common denominator of most animals and many plants. If all sexually reproducing organisms had feelings (and money) like humans, they would buy erotic stories more readily than science fiction. That’s the benefit of appealing to the lowest common denominator that many storytellers aspire to draw.

For marine life, ocean – specifically the top part which receives light from the Sun – is where it’s all happening. The equivalent of ocean on land is the soil. Plants directly grow on soil whereas animals roam around and eventually merge themselves with soil. Plants and animals, and also a few other allied life forms grouped under Eukaryotes, have a basic unit – cell – which is the building block of their entire structure. Scientists have come up with the concept of LECA – last eukaryotic common ancestor – to represent life that could potentially have been at the junction where the plant, animal and other eukaryotic branches meet down the evolutionary tree of life.

LECA however is not the lowest common denominator of cellular life because it does not represent bacteria and archaea which also are made of cells, albeit lacking a nucleus. So encompassing them all is another imaginary ancient life form christened last universal common ancestor or LUCA. LUCA is sometimes also expanded as the last universal cellular ancestor. If, leaving the functions aside, we deem the information as the real ‘life’ thing, we can arguably consider as the lowest common denominator the genetic code or even the molecules that make up the genes. Beware though, any such move will immediately bring the viruses within the scope of life.

Whatever is the real lowest common denominator of life, cell is still the universally agreed basic unit. Just a casual look at cell structure presented in a text book makes one marvel at the level of organisation inside. No wonder then that life forms are called organisms, a term etymologically related to ‘organisation’.

It may seem too obvious to even start wondering about. Still, why do we wake up fresh at sunrise and feel tired by the night in the course of a normal day? Why do soft leaves and flowers open up fully with Sun and wilt down at dusk? Do they follow some sort of clock?

There are processes internal to plants and animals too – in fact many – that work in a near 24 hour cycle. We sleep, wake up, sense the surroundings and feed ourselves as guided by the day night cycle of planet earth. Our heartbeat, blood pressure, renal functions and digestive processes are regulated by the circadian clock. The circadian clock in plants controls processes like leaf movement, growth, photosynthesis, emission of fragrance and germination.

Numerous circadian clocks are at work inside living beings every moment they are alive. For ages we have studied how the circadian rhythm impacts the functioning of various organs and how disruption to the rhythm could lead to health concerns. It’s only in recent decades however that scientists have begun to realize how the circadian clock works at the cell level. American scientists Jeffrey C. Hall, Michael Rosbash and Michael W. Young received the 2017 Nobel Prize for Physiology or Medicine for their pioneering work that began to unravel the cell level intricacies of mechanisms governing the functioning of the circadian rhythm. They used the fruit fly Drosophila as their guinea pig.

The circadian rhythm at its smallest form operates within individual cells. Clocks operating at various organ levels are called peripheral circadian clocks. Imagine all the peripheral clocks operating independent of each other and the resulting chaos. Don’t worry. Nature is much better at foreseeing and handling problems than us humans. All mammals possess a central circadian pacemaker located at the hypothalamus of the brain. This “master” clock, called suprachiasmatic nucleus (SCN), ensures that all biological processes kick off at proper times. SCN forms the centre of a tightly coupled circadian system in the body.

Besides controlling other circadian clocks in the body, SCN performs an important role of entrainment of the clock in response to day-night cycle the body is exposed to. The jet lag we experience as we travel across time zones is a popular case that demonstrates this phenomenon of entrainment of circadian clock. Jet lag usually expresses itself with symptoms like fatigue, loss of appetite, insomnia and headaches and is usually cured in a few days. It is caused by the body being exposed to a new day-night cycle thus upsetting the circadian clock it was used to. And the cure comes from the clock’s entrainment in the new ambience with time. The retina normally receives light via rods and cones to make us see things. There is a third kind of receptor – photosensitive retinal ganglion cells – which is responsible for training the “master” clock to the light conditions of the ambience.

In order to understand the mechanism of circadian at the cell level, a recap of basics of genetics is helpful. A gene consists of DNA in the sense that words are made of alphabets. Genes reside inside the nucleus of a cell. Genes carry codes for specific purpose that are copied into messenger RNA (mRNA) via a process called transcription. It’s like duplicating the instructions of a blueprint onto a trusted object. The mRNA then crosses the nuclear boundary and hands over the code to ribosomes in the cell cytoplasm where using the instructions in the code protein is synthesised. The process is called translation. Proteins are the substances that make us and our organs grow. Specific genes are responsible for production of specific proteins.

A gene called Period gene causes production of Period protein. Note that Period is just a name given to the protein and the gene that causes it. The levels of both Period mRNA and Period protein are found to fluctuate periodically every ~24 hours in the fruit fly Drosophila. The Period protein level in the cytoplasm indirectly influences the process of transcription via a negative feedback to control the Period mRNA levels which in turn produces less Period protein. Less protein level then kicks off a positive feedback. The entire process of negative and positive feedback runs on a loop. The process of feedback in higher animals is a complex one. But it suffices to say that similar feedback loops work in humans and other living organisms and are responsible for the universal circadian rhythm of life. In photosynthetic cyanobacteria, circadian rhythms have been observed which do not rely on the transcription-translation feedback loop but rather on the redox state of the cell.

Cell cycle determines when a body cell undergoes division. Strong correlation between circadian clock and cell cycle operation has been observed in unicellular organisms such as cyanobacteria. Extrapolation of these results to multicellular organisms in general and to mammals/humans in particular is an area of active research. Many favour that circadian clock has at least “gating” affect on the cell cycle. Some even point to the reverse process of entrainment of circadian clock by the cell cycle processes. In particular, disruption of circadian rhythm because of external factors has been found to promote cancer development and proliferation of cancer cells. Further, forced entrainment of circadian rhythm though meal timing has been found to slow down tumour progression. Intake of caffeine via drinking of coffee – late in the day in particular – has been shown to disrupt the sleep cycle too. The circadian rhythm thus plays a vital role in our well being.

My city looks most beautiful in autumn. Credit goes to the trees lining the streets – Maples, Ginkgo, Claret Ash, Red Oak, Japanese Pagoda, American Sweet Gum, Chinese Pistachio, English Elm, and many more – and the shades of yellow, orange, brown and red their leaves transform into.

These temperate deciduous trees shed their leaves after changing colour from the normal green. This annual fanfare rekindles in me a line from Tagore’s song “jharaa paata go”:

“jharaa paata go basanti rang diye
shesher beshe sejechho tumi ki e”
[Fallen leaves, what colourful parting dress you have adorned yourselves with!]

Science has figured out the what and how of autumn colours and is still trying to make sense of why.

Autumn colouration doesn’t happen to all deciduous trees everywhere. It happens in temperate regions only. In other regions deciduous tree leaves usually just turn brown and fall off. Brown merely indicates dead cells.

Yellow and red and their various shades make autumn a visual feast. And they do represent two different mechanisms of colouration. Interestingly, their geographical distribution is also different. Yellow dominates the European autumn whereas North American deciduous trees usually go red.

Colours in plants are associated with pigments. The universal chlorophyll imparts green colour to normal foliage by absorbing other wavelengths. Shades of yellow and orange come from another type of pigment – carotenoids. These pigments are present all the time but the dominating chlorophyll masks their colour. Chlorophyll decays faster during autumn. This process unmasks the yellow-orange of the carotenoids.

The red colour comes from an entirely different mechanism. The pigment anthocyanin, responsible for the red colour, is produced during autumn as chlorophyll levels are falling. Anthocyanins also give red colour to fruits, but they are produced in the leaves of only certain species.

The reason for yellow colour is pretty obvious from the above. Winter is a period where temperate life switches to maintenance mode. Metabolism is at an all time low. Animals prefer to stay quiet. Invertebrates find relatively warm areas under the ground surface or beneath the fallen leaves. Most mammals hibernate. Life practically comes to a standstill. Plants in such regions also go through their own hibernation though scientists use the term dormancy for them. The idea is to somehow just survive the winter. Autumn is the time to prepare for that.

If you have enough food stored for survival, why spend energy making food? The fuel supply (sunlight) is also not encouraging. Let’s shut down photosynthesis factories and eventually dismantle them. But the leaves possess many useful nutrients. Though eventually everything goes into the soil and enriches the earth’s life system, the tree wants to retain some of the nutrients for itself – notably the precious nitrogen. Chlorophyll content of the leaves decrease for this reason in the autumn. The shades of yellow and orange of carotenoids – masked hitherto – show up.

The red colour is puzzling because the pigment responsible – anthocyanin – is actually produced in autumn. Why would the tree spend energy producing something when there is actually a need to conserve energy?

There are many theories. Some say that their antioxidant behaviour and/or absorption of harmful high energy rays prevent destruction of photosynthetic plant tissues. But why would plants want to protect photosynthetic structures in leaves that are about to fall? Carotenoids attract aphids that suck sap from leaves. Red colours in evolved species could help repel such insects, says one theory. Another reason given is that anthocyanin in leaves helps trees resorb more nitrogen in the trunks and less in the decaying leaves thus conserving the valuable resource.

They may be serving to warn the animals to prepare for the winter. The red colour could dissuade herbivore predators from eating the leaves, but this ecological reason appears to be more valid for young red leaves especially in the tropics than for the senescing autumn leaves of the temperate regions.

It could be a signal for animals to start preparing for the winter. Birds migrate to warmer parts of the globe. Animals such as squirrels store acorns and nuts for the winter. Bats breed during winter hibernation. Early autumn is mating time for them. The males show off their singing skills. Many other animals too have a last hurrah in the autumn before going quiet. The appearance of red, as per one theory, could simply be a warning for animals to go look somewhere else for survival. ‘Beware! We are about to fall.’

Whatever the motive, as the life’s sun goes down, o falling leaves, you brighten up my remaining soul just as Tagore wishes:

“ostorobi laagak poroshmoni
praaner momo shesher sombole
jharaa paata”

Fire destructs. Not always though. Ask the scientists who suggested that invention of cooking was a watershed moment in human evolution. They attribute increase in human brain size to fire – the use of fire. Good on those ancestors then who first chose to play with fire. We wouldn’t be us without them.

Devastating forces are all around us. The key lies in control. We have learned to control fire and make use of it. This risk taking has brought dividends to us. Did life come out of similar such risk taking in the first place?

What do we really mean by fire? Two substances – oxygen and fuel – cause fire when they come together in presence of heat. When the heat reaches a threshold, it triggers the first oxidation reaction. The fuel breaks down into simpler chemicals. The reaction is exothermic meaning it gives out energy. The energy in the form of heat triggers the next fuel molecule to ‘burn’ and a chain reaction begins. It ends with exhaustion of either oxygen or the fuel or when some external factor draws energy out of the system. The ‘light’ part of the energy makes us see the fire as flames. The end products of the chain reaction are water and carbon dioxide that go up in the atmosphere.

Do the two substances remind us of something close to our hearts? Our cells run a similar process with sugar as fuel and oxygen. We consume sugar as food and breathe in oxygen as air. The end products are water and carbon dioxide and a whole heap of energy in the form of ATP molecules. You got it right. The process is cellular respiration.

Alright, so you’ve noticed my clever omission of the role of heat in the above cellular process. The energy part is the real trick here that makes ‘life’ so interesting. Here is how.

We take in the sugar and the oxygen. Both are produced by the plants. In that sense we animals are parasites though science does not label us as such. The plant, via another outstanding life process photosynthesis, binds the light energy into sugar molecules. If we see the life in totality, the energy consumption part of the process happens in the plants. The strong chemical bonds of sugar molecules store the energy. During respiration, that stored bond energy is released which drives us to ‘burn’ more sugars.

The fire at the cell level is that photon which life has learned to control and capture and make use of to produce food for its processes. Life’s evolution, if not the origin, is thus fuelled by fire in the form of sunlight – the only regular external input into the earth system. Some primitive form of life – perhaps some microbe – first dared to play with that fire and here we are today, alive and kicking.

Plants arrange their leaves in patterns. Scientists call these arrangements phyllotaxy. Looking at a variety of such arrangements one wonders at nature’s designs. But could there be some compulsion on plants to grow the way they do?

470 million years ago, plants first appeared on land. They spread quickly to cover vast areas. The ensuing drop in CO₂ allegedly cooled the earth so much so that an Ice Age followed.

Their landward march began along the coastline. They kept moving up the continents as much as water allowed them to or as much water they could take along with them. We still have deserts in many interior land areas. It is quite clear then that water bearing land areas formed the real estate for plants to encroach upon. That real estate was much scarce early in the earth’s history.

Plants are good at harvesting solar energy. They have this urge to grab every photon falling near the earth’s surface. To be able to achieve that they need to install their version of PV cells – the leaves – more and more. And in patterns that allow sunlight to fall on each one of them. Necessity is the mother of invention is an old saying and plants knew it millions of years ago. So they invented phyllotaxy and grew taller.

Unlike animals, plants lack the ability to move which is a big handicap in self-defence. Their defence weaponry is limited to use of spines, hairs and visual and olfactory signals. Even these tools need to perform the delicate balancing act of repelling herbivorous animals yet attracting pollinators. And then there is the grand manipulator – human being. In spite of all this, the land is still mainly green. This is no mean feat. Plants didn’t just survive. They have had phenomenal growth. All the leaves’ surfaces together can cover 100 continents of the size of Australia! Such is the expanse of what is called the phyllosphere. Naturally they couldn’t have achieved this without looking upwards in the Z-direction for space.

What do you do when you don’t have much real estate? You build high-rises.

I see my backyard chickens pecking for food all the time. What could possibly be their purpose in life, I ask myself. Just feed their guts to process food and absorb the valuable and reject the unwanted? And produce eggs to make offspring who in turn will do the same? Is that all?

But why just chickens? Why on earth do we humans exist? At some point we ask ourselves: Do we eat to live or live to eat? Does the God or nature or whoever the supreme power is, if you believe in one, want us to protect our ‘selves’ or contribute something to the nature?

Let’s state this conundrum of life’s purpose in biological terms. All the work/activities that we do boils down to metabolism inside the body. We eat food which fuels metabolism. Of course it also helps us survive. But survival goes beyond that. Our genes want us to reproduce so that they get passed on to the next generation. It’s more about survival of our genes. Our fundamental question of activity-vs-survival thus translates to metabolism-vs-reproduction. What is the cause and effect relationship here? Does reproduction facilitate metabolism or benefit from it? Such chicken-and-egg problems refuse to go away whether you look at life at organism level or cell level or molecule level.

Inside the cell, genes containing information as special set of DNAs reside in the nucleus. However, all the action is outside of the nucleus – in the cytoplasm. That’s where protein synthesis happens and proteins make us do everything. The manufacture of protein however is directed by the code written in the DNAs.

Superfast reactions inside the cell materialise metabolic actions. The extraordinary operation of these reactions require a special type of proteins – enzymes – to speed things up. This process of catalysis is one of the fundamental requirements for life to exist. Even the DNAs require enzymes for replication.

Let’s go one level deeper. Life stores information as molecules. One may argue that inanimate objects also contain information. So what’s special about life? Where life differs is that it works on the information stored inside. For instance, an organism’s unique information is stored in the DNAs as code. Life then uses this information and produces proteins for various functions. One ‘special’ function replicates the information so that it can be passed on.

DNAs and proteins have strong mutual dependence. The proteins need DNAs to get created. The DNAs need proteins to get replicated. Another chicken-and-egg!

In spite of this mutualism, metabolic proteins and DNAs do not coexist in the same physical space. Proteins are chains of amino acids manufactured in the cytoplasm of the cell which faces the external environment. DNAs made of nucleotides, on the other hand, are tucked safely as single source of truth inside the nucleus. They are too precious – not to be messed up with – and hence are far removed from the external environment. Yet the DNAs must communicate with the cytoplasmic world to be able to guide the mechanism of protein synthesis. Enter RNA.

RNA, in fact a special type called messenger RNA or mRNA, is a working copy of the DNA. The copy gets made inside the nucleus and it crosses the membrane and enters cytoplasm with the code handy. The mRNA hands over the code to ribosomes in the cell cytoplasm. That is the building site where using the instructions in the code protein is synthesised.

RNA is capable of storing information and it can act as enzyme for catalysis. It can self-replicate too. Voila! You’ve got it. Here is the thing that can do it all. And a new theory of ancient life gets proposed – the RNA World. So, ladies and gentlemen, the first real ‘life’ was when it was all RNAs around! The specialised worlds of DNAs and proteins came later. The most fundamental of the chicken-and-egg problems is resolved.

You wish. If RNAs came first, how did they get converted to DNAs? Was reverse transcriptase available then? How? And also making RNAs out of inorganic raw materials is extremely difficult if not impossible.

If you are still hungry for more, here is another chicken-and-egg food for thought. What came first – virus or cell?

We do think of us as a special type of animal. So much so that when we say ‘animals’, we subconsciously exclude ourselves. Perhaps so does every species within its community. There is a difference though. We humans do not witness around us, mythological worlds aside, any species superior to us. So yes, in that sense we deserve to be called special. But are we really exceptional or merely the most evolved of the animals?

We have achieved a lot mainly because of our collective intelligence. Throughout human history, we have extended the extremes of our perception – to the far away stars and to the tiniest subatomic particles. That’s not the point though. The question that is bothering me at the moment is how we differ biologically from other animals in a significant way.

Not sure if we discovered fire first, but we are definitely the only ones who cook our food before consuming. In metabolic terms, we use external energy to initiate the breaking down of raw food outside of the body. For other animals, the process starts inside the body when their teeth commence the chewing operation. That surely gives us a huge advantage over them as we get more energy for less.

The other unique feature, unique among land animals anyway, is the fact that our females have a substantially long life post-menopause. For most animals, the main purpose of adult life seems to be giving birth to and raising offspring. Not for humans. The other species who share this trait are the ocean creatures killer whales and short-finned pilot whales.

It may appear so to the uninitiated, but we cannot lay claim to our exclusivity of cognition and social behaviour. It doesn’t take much to notice social behaviours in everyday animals. As regards cognition in animals, we humans often take one of the two extreme views: outright rejection and over-interpretation. Animals do have cognitive capabilities of acquiring, storing, retrieving and processing information to a level of complexity they can handle.

So what sets us humans apart from the other great ape lineages or even the Neanderthals? Why are we so successful? According to philosopher Kim Sterelny, humans evolved as a result of positive feedback loops because of ‘cooperative foraging’. In brief, it’s the simultaneous evolution of cognitive capacities of individuals, maintenance across generations of cultural information and cumulative innovation, niche construction and information-guided foraging – all feeding into each other.

Biologists Richard Wrangham, Suzana Herculano-Houzel and Karina Fonseca-Azevedo however think that invention of cooking played a big role in the evolution of human brain to its present size.

Why do we need to classify things? I guess the human mind needs it to put things in perspective.

Imagine if there was no concept of centuries and half-centuries in cricket. Strictly speaking, there isn’t much difference whether one scores 100 runs or 99 or even 90. A batsman does not require any special ability to score those few extra runs. Worse, the 30-40 runs he scores after the century are not perceived as valuable enough as the previous 10 runs. Strange, but that’s what classification does. Still it’s a necessity. It’s hard for people to remember every individual score of a player, but it’s easy to remember the number of centuries in his career. So in a way classification is a tool to help us humans overcome our limitation of not being able to comprehend and assess randomness in a continuum.

Biology is no different. We have a fancy jargon here – taxonomy – which further creates fancier jargons. There is classification everywhere – vertebrates vs invertebrates, eukaryotes vs prokaryotes, aerobic vs anaerobic, and so on.

Classroom Biology has taught us a classification system which is represented as the Tree of Life. It follows from the Darwinian model of evolution. So we have species grouped as genera grouped as families grouped as orders grouped as classes grouped as phyla grouped as kingdoms grouped as domains. Phew! And then there are subgroups as and when required.

For instance, the domestic cat has this taxonomic signature: F. silvestris -> Felis -> Felidae -> Feliformia -> Carnivora -> Mammalia -> Chordata -> Animalia -> Eukaryota. So starting with Eukaryota, you keep on adding a distinct property to move up a level in the Tree of Life to finally arrive at your species. Thus a cat can be thought of as a living object containing nuclear cells (Eukaryota) lacking a cell wall (Animalia), which has a notochord (Chordata), with female secreting milk (Mammalia), and which feeds on other animals (Carnivora), has double-chambered bones covering middle and inner ear (Feliformia) and hunts alone (Felidae) without roaring (Felis) and is a wildcat. Of course taxonomy is not so simple and not free from debates and disputes either. For instance, not all Carnivores eat meat all the time.

Notwithstanding the opinion of an Indian junior minister, Darwin was a genius because his model of evolution withstood the onslaught of extensive genetic studies carried out more than a century later.

Darwin’s Tree of Life, however, does not cover the entire gamut of life as we now know. It leaves out microbes – bacteria and archaea. Archaea is a newly discovered domain of life consisting of microbes with appearance similar to bacteria but which differ in genetic processes. Bacteria and archaea are together referred to as prokaryotes to distinguish them from eukaryotes. Unlike eukaryotes, they do not possess nucleus in the cell.

The concept of ‘tree’ reaches its limits with eukaryotes and cannot be extended to include bacteria and archaea types. These types – defined mostly using their genetic characteristics – are related to one another more like a network rather than hierarchical branches. Even the notion of ‘species’ is nearly impossible to apply to microbes let alone the “Origin of the Species”.

One may want to dismiss these ‘invisible’ forms of life for their tiny size, but their quantity is mind-boggling (estimated microbes in the order of 10³⁰). There are as many, if not more, bacterial cells in our body as human cells.

If that does not give an indication of the power of microbes, consider this: They are in a state of continuous evolution at a rate much higher than us eukaryotes because they can transfer genes among themselves laterally without having to wait for the arrival of offspring. The process is called horizontal gene transfer which dwarfs the vertical gene transfer we are capable of.

But wait, we haven’t finished with life yet. You haven’t seen anything until you consider viruses – the tiniest of all. Unfortunately, the dogma that viruses do not constitute life persisted in academic Biology for far too long. They were relegated to ‘particles’. That ostracizing was mainly on account of the fact that they cannot reproduce without entering a host cell. What was conveniently overlooked was that they carry the most important ingredient of life – genetic material – packaged inside a protein coating. And they outnumber all other life forms by a huge margin. There is a fresh drive now to include them within the scope of life. Some scientists call this “viral life” an empire, distinct from the other, our own, empire – “cellular life”.