Plants and Real Estate

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.

Chicken for Protein, Egg for DNA

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?

Are We Humans Special?

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.

Classifying Life

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”.

Reverse Swing of Societal Norms

The other day in a near empty car park, I carelessly parked my car across the marked lines covering a few parking spots. I knew that my daughter was waiting to be picked up and that it was only a matter of a few minutes. That might have been a good excuse for a parking officer. Not for my teenage daughter though. She vehemently disapproved of my action.

Stunned by her rebuttal, I remembered another “rule of the road” issue that bothers me often. My experience on roads tells me that most drivers tend to go a bit over the legal speed limits. That ‘a bit’ was a bit too much when I drove in Spain earlier this year with most cars speeding past my car at well over 130 kmph on a 120 road. I have this dilemma. Should I be legally legitimate and drive within the prescribed speed limits? Or be legitimate by societal norm and speed up that little bit? To me the latter option feels safer as I have to negotiate less traffic.

These matters might be trivial but the news I heard on car radio was a bombshell. Steve Smith had admitted to a ball-tampering ploy. The cricketing world was shaken. I went on news hunt overdrive to check the reactions from all over the world.

A news item in a leading Indian newspaper carried this line: “Where Smith and the ‘senior’ group slipped up was that they did it so blatantly with so many cameras in place. And Smith’s admission made things worse.” It then went on listing leading cricketers from many countries who had performed the act of ball-tampering at times and admitted to it later in their lives.

People are tempted to take advantage of a situation to the level of unfairness permitted by the rules. Not justified by any means, but it’s in human nature perhaps. We see all the time soccer players fouling others and feigning injury to gain advantage.

Morally-wrong-yet-politically-correct ways have been accepted by our society for a while now. This had to burst and it’s only a start. The results are not going to be pleasant. Strange political leaders are gaining prominence all over the world. They are mostly by-products of people’s gradual rejection of mainstream politicians’ political correctness – a system where we all know something is part of our lives and yet twist it to suit our game at a time appropriate for us.

By inadvertently being part of this course correction, Steve Smith has unwillingly done us some favour. For there lies a criminal in all of us and this regime of political correctness encourages us to go ahead with the crime. It tells us that the whole problem is only when you get caught. Until that moment, you are perfectly fine in the eyes of the law as well as of people in that business.

Somewhere sometime our inner voice prompts us: In this age of competition, everyone does it. The trick is to fool the system a little bit more than others and yet a bit less than the point where you can be caught. It is that point and not the legal word, which in reality defines the line everyone says you should not cross. Your correct judgement of that line at the appropriate time is a measure of your smartness. If you do a Steve Smith, you are an idiot. If you do a Steve Smith minus one, you are a genius.

We may be leaning towards organic food, but are losing out on the organic ways of life. We are letting marketing drive our values and lifestyles a lot. We need a marketing campaign (#MeToo) endorsed by celebrities to destroy a well-marketed celebrity image. We ingest television shows, media headlines, brand promotions knowing fully well that it is money and only money that is driving these. We ridicule the concept of arranged marriage yet enjoy Married At First Sight. Money matters may well determine the outcome of this entire ball-tampering saga too. The problem will remain and build up further… till someone gets caught again.

Let’s not fool ourselves. Let’s not pretend adult celebrities are role models for our kids. Kids who are yet to grow up to the twisted ways of us adults are the real role models. It’s time we seek a better way of life by looking down to them. Let’s kid ourselves, literally. And yes, I did take my daughter’s disapproval seriously and have decided to not park car illegally even for a moment.

Bone of Contention

It’s all quiet after the storm. The storm that could have grown bigger had it not been time to drop Nick to his tennis class. The kind of storm that usually eventuated in them not talking to each other for days. He is relieved that it didn’t go that far this time.

It began with a small issue when he forgot to switch off the bathroom fan after use. What followed was a series of generalisations — about him… ‘forgetting is no excuse’, ‘always leave a dirty basin after morning brush’, ‘never pack lunch for kids’, ‘always buy more alcohol for guests than required’, and so on; and about her… ‘never put lid on containers’, ‘usually leave dress on the bed’, ‘can’t do multi-tasking’, ‘spend freely but never log on to internet banking to check finances’, and so on.

She will be away for the next couple of hours doing weekly grocery shopping after dropping Nick. It’s time he did something. Something to ease the situation.

He loves to cook and thinks that’s the best way he could take some pressure off her. He’ll cook as much as he can in two hours so she need not worry about food for the first few weekdays at least. This would let her devote more time towards writing, something she likes to do but never gets enough time for.

He opens the fridge to see what key ingredients he can use and is immediately repelled by the stink of rotten flesh. He shuts the door back. What was that? Ah it was the lamb bone that was left from last weekend. He had kept the bone after removing flesh from a portion of lamb leg. He thought they could use that to make lamb stock. Making stock out of residual bony pieces of meat was in fact her idea. He had thought he would implement that during the week. That never happened. And she was complaining already, “It will ruin everything in the fridge in a few days. What’s the point of leaving something for future that you can’t do?”

Nah, that’s the first thing he needs to fix. Holding his breath, he takes out the bowl containing the bone and empties into rubbish bin. He then washes the bowl thoroughly with extra soap to get rid of the stench.

It’s time to have another look at the fridge. His eyes brighten on seeing a fresh portion of lamb leg tightly wrapped in clear plastic. His cheeks balloon as the jaws manufacture a big smile.

He prepares a mixture of spices and yoghurt in the bowl he had just washed. Then carves lamb leg into small bite-size pieces ideal for curry. He stirs the lamb pieces into the marinate mixture and when ready puts the bowl back in the same spot in the fridge. This time he discards the leg bone in the rubbish, collects all the daily rubbish and throws them in the council bin outside the home.

He goes on to prepare two vegetarian dishes. But he knows his trump card is that lamb marinate. Relieved, he takes a shower when it’s nearly two hours since she left. He is chuckling to himself imagining how she would be pleasantly surprised to see the marinated lamb in place of that rotten lamb bone. He even starts dreaming about night time reward he will get for this act.

Loud noises emanating from the kitchen breaks his dream sequence. She has arrived. But what is she yelling at? He quickly wipes his body, covers his bottom half with bath towel and gets out of bathroom.

Her yelling is amplified at the sight of him, “Don’t you think you need to tell me what you were going to do while I am out? I mean how stupid you could be! You cut the lamb, marinated it and then placed it in the same bowl and at the same exact spot? How am I supposed to know that? When I was putting vegies in the fridge, I didn’t find much space and then saw that bowl. I thought it still had that goddamn bone. I was so annoyed I didn’t look inside and threw everything into the bin.”