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Believing is seeing

Our sense of sight mimics the mechanism of camera or maybe actually it’s the other way around. But that’s only half the story. Lights reflected by the dog’s face enter via lens and excite sensors at retina – the photographic film of the eye. That’s where the analogy ends I am afraid. The camera doesn’t interpret the image for us. We fall back on the eyes – rather the brain behind the eyes – for that, which is what you are doing right now if you are looking at the picture.

What is happening inside the brain is nothing short of miracle. Let alone the mechanisms we are yet to fathom, what we understand now is extremely complex processing. The retina map in the form of electrical signals are processed in many layers. The first layer deciphers the edges of the dog’s face and passes on that outcome to the next layer for a bit more detailed processing. And it goes on until we know it’s a dog’s face. But it needs to compare the outcome with something it knows. That aspect is taken care of thanks to our past experiences. We have seen many dogs before. This sums up how we experience seeing, most books say. The image analysis part of artificial intelligence is based on this processing. The ‘comparison with past experiences’ part is mimicked in deep learning. Recent success of AI then means that the above mechanism of ‘outside in’ processing really reflects how the conscious brain works. Right? Wrong – according to Anil Seth.

Seth in his book Being You says it all starts with our predictions based on our experiences. Sensory signals merely assist with error correction. In the end what we see is our best guess after all corrections. So it is ‘inside out’ processing and not ‘outside in’ that gives us our consciousness. The world our conscious mind sees is hallucination indeed, albeit a controlled one. That also explains why sometimes we only see what we want to see (the dog’s face in this picture for instance). The extra focus added by the camera kind of mimics the ‘precision weighting’ aspect of the brain’s mechanism.

Building Myself from Scratch

I was watching a sixties movie last week. Halfway through the black-and-white classic I remembered having heard from my father’s mouth that this was an outstanding movie. I was surprised that I had that insignificant and meaningless (to me then) one sentence film review in my memory because I must have been under 10 then. The movie really was very well made. It wasn’t a popular movie then and isn’t remembered much now either. It suited my taste and style though. I asked myself if I had acquired that taste from my father. This could be my wishful thinking. Yet it always amazes me to think how that half set of genes of each of my parents eventually shaped me to this day. How this 60+ kilos of my body with all its fully functioning organs emerged from that single tiny cell formed about 38 weeks before my birth? Read on …

Lovelock Writes at 100

We are the “highest” species on the Earth, at least in our anthropocentric view. Would we continue to dominate in future? No, says the visionary James Lovelock. Who then is going to take over? When? Are we going to continue or become extinct? Read on… only 3 minutes long…

Game, set, match Mother, by design

Almost like a ritual before preparing to serve, a tennis player picks up three balls, looks at them once and rejects one. How efficiently could one reject a bad ball out of three with just a casual glance? Yet statistically this process makes sense. If not for one’s inability to grab more than three, the player has a better chance of ending up with the best two balls if there are more balls to reject. Anyway, this act passes off as a trivial routine – too mundane to register in our minds focussed on what is going to happen when the ball is in play. But this is exactly the process that mitochondria follow at a crucial stage in our lives and this has a huge impact on who we are.

A mitochondrion is technically an organelle – a tiny organ inside a cell. One of the curious features of mitochondrion is that, like a cell, it has its own DNA. This sure sets it apart from other functional organelles inside the cell and raises its status as something that might have its own life. Indeed it is now widely recognized that mitochondria were once free living bacteria that an ancient cell had engulfed. It has been living inside and producing offspring ever since. Mitochondria multiply and so do mitochondrial DNA. Cells too multiply and divide the mitochondrial population among themselves.

So far so good. But then something happens to certain cells as a result of organisms performing sex which disturbs this usual peaceful settlement process. These ‘sex-related’ cells are called germ cells. When an organism performs the act of sex, a germ cell from outside (sperm) fuses with the resident germ cell (egg) along with its genetic content. The two DNAs recombine and become DNA of the fused cell. Now think of the mitochondria inside each of the fusing cells. There are two sets of populations – one from Mars (sperm) and the other from Venus (egg). Too many individuals to accommodate in a restricted space. Some primitive form of sex had the two parties settle the score among themselves by trying to kill each other. Things are much streamlined in higher organisms like us humans. Not sure if this was a peaceful solution but one set of mitochondria completely vanishes from the scene and the individuals belonging to the other set occupy the newly formed cell. No prize for guessing which group sacrifices itself. The intruders – the mitochondria that previously belonged to the sperm cell – of course.

The offspring of mitochondria that belong to the mother organism’s germ cell occupy the newborn fused cell which eventually develops into a new individual organism. And life goes on. In all animals and most plants and other eukaryotes, only mother’s mitochondria are passed on to the next generation. The male’s only contribution is in providing sperm for sex. Everything else is a dead end for male. So much for the patriarchal society we are proud of!

Besides nurturing the egg and, in mammals, the pre-birth baby, the female body carries out some amazing processes inside the egg cell before and after sexual fusion that are beneficial to the offspring and to the living world in general. To be precise, to the mitochondria. One such process of great significance is called mitochondrial bottleneck. Let me explain.

The single biggest threat to life is damage to its DNA. Back in the times of early Earth, ultraviolet radiation from the Sun would do most of DNA damage. These days, a slow process of damage happens in the form of mutation during the process of creating copies. A few random mutations here and there are non-life-threatening. However, in bacteria such mutations tend to accumulate in the cells and over a period of time could potentially cause extinction of the species. The phenomenon has a popular scientific name – Muller’s ratchet. Mitochondrial bottleneck during the process of fertilization is a mechanism to mitigate the risk posed by accumulating mutations. Just like that tennis player, the egg cell sorts its mitochondrial DNA in clusters and then selects only a few to be passed along while rejecting the rest. Statistically, this process leads to reduced mutations in the mitochondrial DNA that is eventually passed on to the offspring thus ensuring a safer mitochondrial genome for the next generation.

You may be thinking, but that ‘purifies’ the mitochondrial DNA and not the DNA of the cell that in reality is the blueprint of an individual. How important are mitochondria to the overall functioning of the cell and eventually to the organism is a topic in itself – too big to cover here. From the obvious respiration which provides energy, to control of almost every aspect of the cell including sex, ageing and death, mitochondria have a critical role in our well-being. And in a yet another clever design by nature, a mother will pass on more mutational load to her male offspring (that cannot pass on the deleterious mutations further) than to her female progeny. This phenomenon – often referred to as mother’s curse – has been studied in the fly Drosophila – the most common guinea pig for genetics studies (Innocenti et al., 2011) and is likely to be present in all animals. If you are a male reading this, bad luck, but it’s just nature’s design to ensure the protection of what matters most – mitochondrial DNA!

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Innocenti et al. (2011) Experimental Evidence Supports a Sex-Specific Selective Sieve in Mitochondrial Genome Evolution. Science, 332, 6031.