Evolution

The Advanced One

Which is the most advanced form of life?

Before we reach the answer, we must know that evolution is not a linear process (like a ladder), unlike what Aristotle thought, but a branched (like a tree). Consider the family of Apes. The apes (Hominoidea) branches into two families – the ‘great apes’ and the ‘lesser apes’.

The lesser apes contain a bunch of gibbons. The great apes are further divided into two – Homininae and orangutans.

Does this picture mean the orangutans and homininae are higher than the gibbons? No, and the scheme can also be drawn in the following way.

Homininae goes to gorillas and hominini. In other words, the gorillas and the hominini have a common ancestor. Hominini then goes to pan (chimpanzees and bonobos) and humans.

You may conclude that an advanced species goes from left to right. That is also not true. The picture can also be like this.

All these living lineages have the same amount of time to evolve; therefore, they are equal!

Reference

Ape: Wiki

Understanding Evolution: Berkeley

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Genetic Drift

We have seen natural selection as one mechanism of evolution. To clarify the whole process, this way of evolution involves two steps: 1) a random (accidental) modification of genes (mutation), followed by 2) a proliferation of a certain kind because it somehow fits well with its environment (natural selection).

But natural selection is not the only mechanism for evolution. Another means of evolution is genetic drift. In such cases, there could be no features of the genetically different versions of the species that have advantages or disadvantages from the environment. Still, random fluctuation causes one of the gene types (allele) to reduce its frequency. This also suggests that this feature is especially significant in small, isolated populations.

To give a (silly) example to distinguish the two types of evolution, we have seen the story of A moth named Biston betularia earlier. The survival probability of the black-coloured moths was higher in the industrialised (coal-polluted!) England. This is an example of natural selection. Now, think about a small population of 20 moths – 15 white and five yellows in a bright, normal neighbourhood. Someone accidentally stepped over the group, perishing seven whites and all (5) yellows. We know neither species had a special trait to withstand the boots. Yet, in the end, only eight whites were the only survivors. They then increased to a large group of white moths.

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Turn of the knob

Came across one of the finest videos on YouTube about our past, present and future life, Yuval Noah Harari’s talk to youngsters and teachers, which triggered the idea of this post.

Turning the knob

Knowledge is like turning the knob. When it turns, you see things in a new light; until then, no matter how hard you try, you don’t get it out of ‘common knowledge’. Unfortunately, the common knowledge is almost always wrong!

The hyperpigmented on the equator

Take the favourite example of pigmentation of humans living in the equatorial region. For a moment, let’s ignore the people who believe that people of colour are of a separate species. We are dealing with more reasonable people here. If the narrative is that people in sunny regions have become dark-skinned because of heat and light, it’s an easier narrative to sell. It fits with the common knowledge – we all know what happens when we fry things; a little too much and it turns black.

Unfortunately, that’s not how things evolve. The theory of evolution switch needs to turn on. What about this: a group of people (perhaps dominated by the light-skinned) reach a sunny region. A few of them got skin cancer due to their lack of protective pigmentation and died maybe a few years earlier than their accidentally darker companions. That raised (by a small margin) the probability of darker parents, their children and their children having the advantage, and wow, after 10,000 years, there was a complete dominance of the dark. So, will that happen in Australia after 10,000 years? We’ll answer that in the end.

Humans of Flores

There used to be a pack of humans living in Flores, an island in Indonesia (until they were extinct about 50,000 years ago). They were humans as they shared the homo family. They were different humans because we are homo sapiens, and they were not. They were pretty short – about 1 m. tall – people. Not just them but the animals of that island as well. A simple convincing argument is that the animals got trapped on the island, became resource-constrained, and to survive, they had to consume less food. And they became smaller. It’s convincing because 1) it gives a feeling that one bunch of people after starvation has shrunk, or 2) they passed a genetic code to the children and made them shrink.

Turn the switch, and you get it: big humans reached the island. Once they got disconnected from the mainland due to sea level rise, the larger ones faced a more significant disadvantage due to food shortage, and the smaller ones survived better. In the next generation, there were disproportionally smaller kids from the surviving parents (the new group has larger ones too). Turn a few pages, centuries and generations: the island is full of smaller humans. This narrative is difficult to fathom without the switch as it is against the common knowledge. First, how can more miniature humans be fitter? That doesn’t conform very well with the stereotypes! Second, something forcing people (in one lifetime) to become smaller is easier to imagine than this chance game of smaller ones surviving (in a hundred lifetimes).

The future evolutions

That naturally begs the question. Will the Australians (the white Australians) turn back after 10,000 years? Even the broader question: What will be the next evolution of humans? The answer to the first question is a no, and the answer to the second question is impossible to predict.

The code lies in the knowledge paradox we are in. Australian whites won’t turn black because they know why it happens and what to do against death from skin cancer. It could be as simple as using sunscreen (or deciding not to venture out in the UV-intense part of the day). And this will translate to other things as well. If we know something gives us a disadvantage, we will engineer means to counter it. It has to be a disadvantage that gave the survivors the chance to survive, and we are closing those weaknesses!

Must watch video

Yuval Noah Harari Speaks to Young Readers & Teachers: Yuval Noah Harari

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The Science We Trust

People lament about the dominance of beliefs and the reduction of scientific temperament in society. Unfortunately, it is a fact and can only be worse in future. And I want to argue that it can only be like that. Let’s look at a few reasons why achieving scientific character is a mission impossible.

It’s another religion

Unfortunately, it has to be.

Take the example of the discovery of gravitational waves in 2015. The number of people involved in the observation, which includes the setting hypothesis, the detection, and the mathematical modelling, could be about 1000. The rest of the world (1000 short of 7 billion) only gets the publication, which is already a heavily cut-down, readable version of the actual data.

Imagine a million people downloaded the paper.

As per an old report in physics today, the percentage of physics graduates (minimum decent training level in this field) was about 0.01. It suggests the inconvenient truth that 99.99% of people are already at a considerable disadvantage.

I.e., half all physics graduates and the rest others!

The people who understand the model (the specific mathematics behind the event) are even fewer and could be in the hundreds at best.

All the others – 6999 million out of 7000 – get the news from the media. And they must trust the report. A belief system is created but is not going to last like a religion, as we shall see soon.

What is Science

Most people know science through technology, the application of the former into products. To define it in one word: science is hypothesis testing. And most people are alien to it. It is probabilistic, conditional, and will/must update with time. Each of these contradicts the doctrines of religion.

Probabilistic thinkers meet the real people

Back to the gravitational waves: Movements on the ground, temperature changes in the instruments or numerous other known or unknown errors can all lead to artificial signals or noises. The importance of the results led to keeping a significance level for the rejection of the null hypothesis (that the observed signal is a noise) to be extremely low – one in a billion. If you recall, most of our ordinary life experiments that is one in 20!

The team investigating the gravitational waves published the findings (as real) only when they found the probability that it could happen by chance is one in a billion. Yet, they would only use the words such as ‘likely’, ‘probably’ or ‘mostly’, to respond to the public, who want ‘yes’ or ‘no’ as answers.

And they change with time

Science updates with new information. Remember the chaos during covid time? The understanding of the illness changed daily during the pandemic. The use of masks (to use or not to use) and modes of contagion (airborne vs liquid-borne), to name a few. While the changes of advice were perfectly understandable and acceptable for those scientists, it was causing confusion and anger to the 99.99%.

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An Ocean Full of Bombay Duck

Here is a story of the survival of the fittest. It seems it is caused by global warming or some other confounding factor. A recent publication by Kang et al. in “Environmental Biology of Fishes” tells a curious – potentially scary – case of things to come.

The team noticed a sudden spike in a particular variety of fish off the coast of southeast China. This weirdly named fish, the Bombay Duck, has had a ten-fold population growth in the last decade. Bombay Duck (Harpadon nehereus) is fish that can survive a low Oxygen environment due to a high (about 90%) water content in its tissues.  

So scientists postulate that as the water temperature rises, thanks to global warming, the dissolved oxygen levels in the water drop, and makes the lives of the indigenous fish species in danger, leaving only those species that can thrive under these conditions to multiply in numbers. So a fish that did not exist in the national statistics as an independent species until recently suddenly becomes a dominant variety.

Increase of a hypoxia-tolerant fish: Environmental Biology of Fishes

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Three-parent baby

We have seen Mitochondrial DNA (mtDNA) as a valuable tracer to follow maternal ancestry. To take a step back: the majority of human DNAs reside inside the cell nucleus, and a few are inside another structure inside the cell, the mitochondrion. During reproduction (fusion of egg and sperm), nuclear DNA undergoes recombination with material from both parents participating, whereas mtDNA we possess entirely comes from the mother’s ovum. It happens due to the faster degradation of mitochondria from the sperm during fertilisation.

Leigh syndrome

Leigh syndrome is a fatal disorder, and its genes reside in the DNA of the mitochondria. If the mother has the disease, it’s sure to reach the offspring, jeopardising its health. In 2016 John Zhang’s team at the New Hope Fertility Center in New York City found a solution. They ‘swapped’ the mitochondria of the mother with a healthy donor.

The technique was to take a healthy donor egg, remove the (cell) nucleus and replace it with that from the mother. Scientists then fertilised the egg with the father’s sperm and implanted it into the mother’s womb. While the majority of the genetic material is from the mother and father, those from the mitochondria are from the donor, thus making her the ‘third parent’.

World’s first baby born with New “3-parent” Technique: New Scientist
The three-parent baby technique could create babies at risk of severe disease: MIT Technology Review

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What Asteroid Ryugu Tells Us

I’m sure you remember Miller–Urey experiments that, in the 1950s, generated molecules of life by passing electric discharge over a mixture of methane (CH3), ammonia (NH3), water (H2O) and hydrogen (H2). The molecules reported were amino acids such as aspartic acid, glycine, alanine and alpha-amino butyric acid.

Ferus et al. in 2017 went even further. They shone electric discharge (simulating lightning) and laser (simulating asteroid plasma) on a mixture of NH3, CO and H2O, producing RNA nucleobases – uracil, cytosine, adenine, and guanine.

Straight from space

While laboratory experiments such as these demonstrated the origin of fundamental molecules from simple gaseous species present in the universe, it can never replace evidence from space, the true cradle of these building blocks of life. And that’s what happened when scientists analysed samples from an asteroid.

The team led by Yasuhiro Oba analysed samples collected in 2018 from asteroid Ryugu and found uracil, one of the four bases of RNA.

Pristine sample

The beauty of this sample is that it was uncontaminated by anything from the earth as it was collected and sealed at the asteroid surface by the Hayabusa2 mission.

Studies like these suggest that foundations of life, such as the molecules of interest, might have been formed in carbonaceous asteroids and delivered to the early earth.

Reference

Yasuhiro Oba et al.; Nature Communications, 2023, 14:1292

Asteroid sample study: The conversation

Stanley L Miller, A production of Amino Acids Under Possible Primitive Earth Conditions, Science, 1953

Formation of nucleobases in a Miller–Urey reducing atmosphere, PNAS, 2017

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Natural Medicines and Fallacies

The terms nature and natural products invoke cult-like sentiments in society. They are usually used as opposites for synthetic products, chemicals, toxins, poisons, etc. Let’s look at some common irrationalities associated with ‘nature’.

Argumentum ad populum

Or appeal to the people. In simple language, it means since everybody thinks it’s true, it must be true! There are more reasons why something popular is likely wrong, especially in specialised fields of study, as the population of practitioners in topics such as medicine is negligible in society.

Post hoc ergo propter hoc

We have seen it before. It means Y happened after X; therefore, X caused Y. Almost all traditional medicines against what is now known as viral infections are examples of this fallacy. A famous example is Phyllanthus, as a cure for Hepatitis A, a water-borne viral infection (of the liver). The illness, if it’s caused by Hepatitis A or E, will go away in itself. But what happens if a person gets the same symptoms caused by Hepatitis B? Not something pleasant.

Argumentum ad antiquitatem

Appeal to tradition is often related to one’s cultural identity. It was written, so it must be true. A classical case is where people from the East think of modern medicines as Western medicines and take pride in ancient science that treated almost everything.

Absence of data as proof of absence

The presence of side effects is a common criticism directed against evidence-based, modern medicine. They consider the treatment of an ailment using a drug to be a trade-off between the risks and benefits. Naturally, this mandates the inventors to probe deep into the dangers and advantages of the given molecules used for treatment. Historically, similar scrutiny has never occurred in traditional medicines, thereby lacking data on their adverse effects.

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Peto’s Paradox

We saw possibilities of random errors during cell divisions leading to mutations. Despite all the corrective mechanisms that the body has, some of those can lead to genetic diseases such as cancer. Naturally, one would expect the probability of cancer to be proportional to the number of cell divisions. If you extrapolate the logic further, it is logical to conclude that the number of cells, the larger the animal, will lead to more occurrences of cancer.

In other words, an elephant has more probability than humans, which, in turn, has a lower chance than a blue whale. But that is never seen in real life. This lack of correlation between animal size with the propensity to get cancer is known as Peto’s Paradox.

Peto’s paradox: Wiki
What is Cancer: NIH

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Long-Term Evolution Experiments

The Long-term Experimental Evolution Project of Prof. Richard Lenski’s team at Michigan state university is a significant movement in our understanding of evolution. The team so far has achieved three decades of evolution of E.Coli bacteria in their laboratory. That corresponds to more than 76,000 generations of the organism starting from the common ancestor, noting that it goes through six or seven generations per day!

The experiments started with growing bacteria colonies in a petri dish and taking small sub-samples to 12 flasks containing a solution of glucose, potassium phosphate, and citrate at 37 oC. On the next day, 1% of the sample from the flask is transferred to a fresh sterile flask. And the process has been repeated every day for the last 34 years.

For humans, 76,000 generations could mean more than 1.5 million years. But does it mean the experiments are expected to see what changes animals or humans to accumulate in 1.5 million? Well, this is a question that ant-evolutionists ask. We will answer these questions in the coming days.

References

Long-Term Evolution Experiments: LTEE

LTEE: Wiki

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