Evolution

T. gondii Continues

The previous post that a parasite triggers wolves to become courageous leaders may sound fantastic, but something difficult to accept as a fact. If you recall rule number one of statistics: “correlations are not causations”, you may realise that there could be other explanations to understand wolves’ the peculiar behaviour of some wolves who happened to have been infected.

What if the same behaviour, aggression, tendencies to walk out of the pack, and courage is the reason that caused the disease in the first place? The claim is not entirely without reason, as the animal gets the illness from cougars that share the same land space. After all, these are observational studies. Naturally, we would have liked to see results from a controlled study.

The researchers selected 64 laboratory rats and infected 32 of them (experimental group) with a cyst-forming strain of the parasite. The other 32 are given a placebo (control group). The rates were exposed to an area, and its corners contained distinct odours, representing four species – rat, cat, rabbit and neutral.

Now, a bit of evolution. Small mammals under heavy predation pressure evolved as species that could identify and avoid the presence of their predators. For rats, it is the ability to smell and avoid cats. You know already that it is not a rat that decided to build the capability to help itself; rather, as per the principle of survival of the fittest, only those rat species survived and had multitudes of offspring. Studies have shown that rats don’t lose the anti-predator behaviour (aversion to cat smell) even after hundreds of generations without having felt the presence of a cat.

And this is where our study got interesting. In the experiment, the status of the rats, infected or otherwise, did not change their movement towards the three non-cat selling areas. Whereas the uninfected rate disproportionally avoided cat-smelling spots compared to the infected.

References

T. gondii Continues Read More »

When a parasite can make you macho

What controls a person’s behaviour? Humans always seem to have some answers to this question. Historically, and still is the case for a large portion of humanity, it has been attributed to some types of divine power. At some stage, people, especially poets, thought it was the heart that controls humans; listen to your heart, they said! As science has progressed, the importance of the brain to our existence came in, and now the scientific community knows how the brain, and chemicals called hormones, can make a person. There is a new entrant to this list – parasites!

Parasite cheerleaders

The impact of Toxoplasma gondii, a protozoan parasite, on species has been the subject of several studies over the years. Past experimental studies have shown that infections can raise dopamine and testosterone production. All it requires for a parasite is to make a cyst at the right place, i.e. the brain. And can cause increased aggression and risk-taking behaviour, failure to avoid olfactory predator cues (i.e., seeking out instead of avoiding felid urine), and decreased neophobia (fear of novel food).

T. gondii in wolf’s clothing

A recent article by Meyer et al. in Communications Biology is another example, this time about the behaviour of wolves infected with the parasite. And they had 26 years of serological and observational data.

The researchers looked for three parameters of risk-taking: 1) leaving the pack, 2) getting dominant social status, and 3) approaching people and vehicles, and two causes of death: 1) death from other wolves and 2) death from humans.

The study has shown that the parasite has influenced the behaviour of wolves. The researchers identified an increase in the odds of dispersal and becoming a pack leader in wolves seropositive for T gondii.

References

Meyer et al., 5 (1180), 2022: Communications Biology
Parasite gives wolves what it takes to be pack leaders: Nature
Fatal attraction in rats infected with Toxoplasma gondii: Proc Biol Sci.

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Neanderthal mother and a Denisovan father

We have seen that the Neanderthals lived in Western Eurasia and Denisovans in Eastern Eurasia (basically, Denisova cave). The 2018 report by Slon et al. provides the DNA analysis of a bone, Denisova 11, that comes from an individual who had a Neanderthal mother and a Denisovan father!

The previous sequencing had established that the Neanderthals and Denosovals diverged from each other by about 390 kya. It is, therefore, fascinating to note what was found in the Denisova 11 sample. The mitochondrial (mt)DNA showed it was a Neanderthal type, and carbon dating said it was more than 50,000 years old. And what is more: 38.6% of its DNA fragments possessed alleles matching the Neanderthal genome, and 42.3% carried alleles matching the Denisovan genome!

Reference

The genome of the offspring of a Neanderthal mother and a Denisovan father, 2018, Nature, 113

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Post # 365: What Have We Learned in One Year?

We started with the equation of life, Bayes’ theorem, how it mimics the natural learning process, and how even experts can not escape the curse of the base rate fallacy.

We understood the law of large numbers but failed to notice that there was no law of small numbers and continued gambling, hoping to even out, leading to complete ruin.

We have learned mathematically that at the Roulette table, the house always wins, yet we spent countless minutes watching YouTube videos learning strategies to beat the wheel. We also watched financial analysts all day on TV, reasoning on hindsight and glorifying market-beating fund managers, forgetting they were just the survivors of Russian roulette. The same people continue to make us believe in momentum and hot hands.

People gamble and play the lottery, where they are guaranteed to lose, and fail to invest for their retirement, where they are guaranteed to win. Three-quarters of Americans believe in at least one phenomenon that defines the law of physics, including psychic healing (55 per cent), extrasensory perception (41 per cent), haunted houses (37 per cent), and ghosts (32 per cent).

Rationality, by Steven Pinker

We have seen how journalism can mesmerise readers by reporting an 86% increase in myocarditis for the vaccinated, a 300% increase in thrombosis over oral contraceptives, or an 18% risk of colorectal cancer by eating processed meat. We just became easy prey for our inability to make decisions based on risk-benefit trade-offs and the eternal confusion between absolute and relative risks.

We found how the world can make us believe in diseases with causes and designs with a purpose when events were nothing but random processes. We see how careless choice of words and phrases and incorrect teaching lead to myths about evolution.

Even in an era of open data, data science and data journalism, we still need basic statistical principles in order not to be misled by apparent patterns in the numbers.

The Art of Statistics: How to Learn from Data, by David Spiegelhalter

The author was referring to variabilities in the observed rates of events when the population is small, which is the concept behind funnel plots.

We understand that international trade is a win-win for both parties, yet we let free rein to populism and Brexit. We know that the Muslim community in India is on the fastest downhill in the fertility curve, yet we want to believe that the opposite is true and continue believing in one-child policies.

We also know that life is not a zero-sum game and that probability theory is not another useless thing you study in schools and forget later, but it is about how we make decisions and appreciate life. The understanding, or the lack of it, can be a choice between life and death, as we have just witnessed in the global pandemic.

Could everyone have a fact-based worldview one day? Big change is always difficult to imagine. But it is definitely possible, and I think it will happen, for two simple reasons. First: a fact-based worldview is more useful for navigating life, just like an accurate GPS is more useful for finding your way in the city. Second, and probably more important: a fact-based worldview is more comfortable.

Factfulness, by Hans Rosling with Anna Rosling Rönnlund and Ola Rosling

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The Denisovan Story

Another spectacle that emerged from Pääbo’s group was the discovery of Homo Denisovans from a bone sample excavated in Denisova Cave in southern Siberia. They possess the type of hominin mtDNA that shares a common ancestor with modern human and Neanderthal mtDNAs. And the stratigraphy of the location suggested the new samples lived at similar times to Neanderthals.

Where do they stand?

If we define the timelines as a function of pair-wise nucleotide differences of the complete mitochondrial DNA (mtDNA) from modern humans, Denisovans existed about 385 units away from humans. To put it in perspective: the modern humans are between 0 – 100, the Neanderthals at around 202 and the Chimpanzees at 1462.

Interbreeding

The researchers then searched for gene flow (interbreeding) similar to what was found with the Neanderthals using the five samples (San, Yoruba, Papua New Guinean, Han Chinese, and French) from modern humans. This time, there was no overlap between the French and the Han but found ca. 4% match with the Melanesian.

The new representation, combining the findings of the two studies (genome sequencing of Neanderthal and that of Denisovan), is presented below.

Reference: https://commons.wikimedia.org/w/index.php?curid=65505773

References

Krause et al., The complete mitochondrial DNA genome of an unknown hominin from southern Siberia, NATURE, 2010, 464, 894

Reich et al., Genetic history of an archaic hominin group from Denisova Cave in Siberia, NATURE, 2010, 468, 1053

The Denisovan Story Read More »

The Neandertal Affair

The contents of this post are based on Svante Pääbo’s 2010 paper titled “A Draft Sequence of the Neandertal Genome“, published in Science (Green et al., Science, 328, 710, 2010). The study reports genome sequencing of three samples collected from Neandertal bones from Vindija Cave in Croatia, and are carbon dated to be around 38,300 years old.

Based on the existing pieces of evidence, modern humans (Homo Sapiens) and Neandertals (Homo Neanderthalensis) diverged from the common ancestor (Homo Heidelbergensis) around 500,000 – 800,000 years ago. Here is a representation made by Dbachmann of the immediate ancestry of humans and taken from Wiki.

Reference: https://commons.wikimedia.org/w/index.php?curid=65505773#/media/File:Hominini_lineage.svg

The numbers on the Y-axis represent the past years in millions (mya). If you are wondering who appears on the two sub-branches of the branch, Pan, they are Chimpanzee (P. troglodytes) and Bonobo (P. paniscus)!

The earlier analysis of the mitochondrial DNA of Neanderthal, which was the subject of a publication in 1997, showed a lack of relationship between modern humans and Neandertals. That was insufficient to prove that interbreeding never happened, as other parts of genomes also need to be studied. If you are confused about what these are all about – a typical genome of a multicellular animal has two distinct parts: the nuclear genome and the mitochondrial genome. Most genomes (e.g., humans and other cellular life forms) are made of DNA (deoxyribonucleic acid).

The biggest challenge to confirming the interbreeding was the reason for similarities is the fact that these two have a common ancestor within the last million years. So a similarity between the two groups can be within the variability margins of homo sapiens themselves. To reemphasise the point: even if no interbreeding ever happened, the Neanderthals and Sapiens can still have similarities (e.g. humans and chimps have more than 90% similarities in their genomes).

The study compared the Neandertal genomes to five present-day humans: one each from San (Southern) Africa, Yoruba (West Africa), Papua New Guinean, Han Chinese, and French (Western Europe). To cut the long story, they found that the Neandertals are more closely related (by about 3-5%) to present-day non-Africans than to Africans, suggesting some form of interbreeding. The following graphic represents the findings.

Reference: https://commons.wikimedia.org/w/index.php?curid=65505773

Tailpiece

Most of the similarities and differences are academic. And society should not start equating them with friendship, relationships and identities. They are far more complex and, many times, socially constructed.

The Neandertal Affair Read More »

Svante Pääbo

The man who sequenced the first Neanderthal genome, the person who discovered a new type of human, the Denisovans, Svante Pääbo, is the winner of the Nobel prize in Physiology this year.

Let’s start with perhaps the most important one – the 1997 publication on the sequencing of mitochondrial DNA (mDNA). It established the presence of an extinct human, who was unlike the modern human. But in 2010, he sprung another surprise through genome sequencing and showed that there was, indeed, a gene flow from Neanderthal to modern non-African humans.

He’s not done yet! In the same year (2010), he published the mitochondrial DNA genome of an unknown hominin from southern Siberia, the Denisovans.

References

Krings et al., Cell, 90, 19–30, 1997
Green et al., Science, 328, 710, 2010
Krause et al., Nature, 464, 894, 2010

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The Nature in Natural Selection

We have seen before misconceptions about the theory of evolution still prevail due to generations of improper education. As a consequence, together with the existing cultural doctrines, the word nature got a superior stature as the ever-benevolent parent who can do nothing by love and care. So nature selects living organisms to something (perfection to some, purpose to another).

Let’s spend time and understand what is ‘nature’ in natural selection against the backdrop of evolution. What causes new species or the entities that survived?

Yes, nature is a killing machine. The species who endured it had differentiating features to accomplish the incredible. The species who prevailed can’t see the horror, but a hypothetical alien sitting outside the earth can vividly see the extinction of millions in favour of the hundreds.

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The Trouble with Evolution

With millions of pieces of evidence, the theory of evolution is as factual as, say, Newton’s laws of motion! Yet, how it’s taught in schools requires a reexamination before it can achieve its intended goals of education. Some items need attention before introducing the subject to the interested parties.

Lamarck’s theory

The theory that says evolution is the adaptation of organisms to their environment has only historical relevance. It is not how evolution works. People are stuck to Lamarck’s theory, partly because it was taught before Darwin’s and also because it fits our fantasy of conversion and purpose. We will address these two terms soon. To repeat: individual organisms don’t evolve or pass their aspirations to offspring through genes.

Metaphors taken literally

We already know that nature doesn’t select anybody. Also, physical strength and superiority have nothing to do with the survival probability of a species. Yet, we carry the burden of natural selection and survival of the fittest in their literal meaning. These terms are strictly metaphors to communicate, perhaps wrong choices from people who lived a hundred years ago!

Another common feature in science communication is to say genes want to copy and spread. It creates a false notion of purpose in listeners’ minds. Again, a gene has no brain to decide anything, unlike humans, who are involved in designing artefacts for their use. You know, this purpose is not that purpose!

It goes in branches

This one came from a cartoonist – the money to the man. It is not a conversion process that works linearly. Once a species passes the baton, it doesn’t exit the scene. Evolution steps are random branching processes. So monkeys may survive, and so do apes or the great apes. Some may perish as well.

In summary

The features we see in today’s organisms are not part of any plans for perfection but simply a collection of clues about our past.

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Darwin’s moth for Darwin’s Orchid

Remember the story of Tiktaalik, the missing piece in the evolution that connected fishes and four-legged animals? Here is another equally exciting example. And how Darwin predicted the existence of a species after seeing a flower!

In 1862, Charles Darwin received a box of orchids from a well-known grower of his time. Among them was Angraecum Sesquipedale. Check the link to see how it appears. Look at the long spur or nectary, the nectar-secreting organ in the flower. Seeing the extraordinarily long nectary, Darwin wondered about the existence of moths with long tongues. As nectar-liking moths are crucial agents for pollination, such an orchid would not have evolved without the help of a moth with fitting organs.

In 1907, years after Darwin’s death in 1892, the culprit was found – Xanthopan Morganii Praedicta, from Madagascar!

To conclude this story, in the 1990s, biologists made direct observations of the meeting of the two. See the cover page of the Botanica Acta of 1997.

Reference

Arditti et al., ‘Good Heavens what insect can suck it’– Charles Darwin, Angraecum sesquipedale and Xanthopan morganii praedicta, Botanical Journal of the Linnean Society, 2012, 169, 403–432.

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