What Darwin Never Knew

butterflies on top of flowes

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What Darwin Never Knew – Documentary Notes

Reading time: ~11min.

The Trip to the Galapagos

The documentary starts off by summarizing Darwin’s childhood and explaining how he went on a 5-year boat trip when he was 26. In this trip he passed through the Galapagos Islands, where he collected lots of birds and where the local people told him they could identify on which island a turtle lived based on their shell. When he came back to Britain, he started organizing the collection and thinking about all that he saw and about what he had collected. Darwin would jot down the thoughts on paper as they were coming through him. Then he reached one of the first important conclusions which was that somehow, species changed. This was partly because of the turtles and also because he noticed how there were several variations of the same species of bird (e.g. the finch). He also noticed how some species were extinct but others similar to those were still alive, further strengthening of species changing. This was a dangerous opinion at the time, when everyone believed god created things, which were of course immutable since they were perfect from the get-go. But he argued, what’s the point of creating so many different types of finches that look so similar?

Animals’ Connectedness and a First Glimpse Into Evolution

At the time, 19th century, scientists fiercely studied the development of embryos and so did Darwin. One interesting thing he noticed was how baby snakes, near their conception, seemed to have things resembling legs, which wouldn’t develop any further. Moreover, whales, when embryos have teeth which disappear before they are born. For him this meant that whales descended from creatures with teeth. He also found similarities between fish embryos and humans’. So later on he came to think that all species were somehow connected. It was the concept of the tree of life taking shape. If we went further back in the tree of humans, we would find fish. So species were mutable, through generations, he then thought. But what was making them change? One of the things that gave him a clue was dog breeding. At the time, in Victorian England, people loved dogs. And dog breeders were known to selectively mix species to purposefully get different results. They would mix a great sniffer dog with a fast runner to get a fast good sniffer dog, good for hunting. Darwin thought whether it was possible that there was something like this going on in nature without human intervention. Contrary to most people’s views of a peaceful nature, his voyages showed him a different picture. Nature was brutal, and death was everywhere. It was a constant struggle for survival where only the most adapted to their specific environments survived. But what was the relationship of this and the Galapagos finches? For example, each specie had different beaks. It turns out, it varied depending on their main food source on that island. For example, in islands with lots of seeds, beaks were shorter and stronger. For islands with lots of flowers, beaks were longer and narrower. But how come this differences appeared from a supposed single ancestor? Looking at home, and people, he could see that despite having the same parents he and his brother were slightly different. No two people are exactly equal. The same must be true for other animals. And so in a natural environment, with its harsh conditions, and over several generations, tiny variations that are better for that environment make those individuals more likely to survive, and in the long run accumulate and result in totally visible characteristics from the original — the theory of evolution by natural selection. So in 1859 Darwin finally published his master work on the origin of species. But he acknowledged there were holes in his theory. How exactly did it work? What were the physical changes inside of animals’ bodies that enabled this to happen? Now scientists can look inside animals’ DNA and answer that.

Enter the DNA

DNA, which all living things on Earth have, with just 4 “letters”, contains all the information to make living things grow. Mutations, which happen when cells divide, are responsible for differences between genes (a gene is a certain combination of those 4 letters, e.g. ACGAGGA), which are then responsible for, for example, someone having blue or brown eyes. If it wasn’t for mutations, species wouldn’t evolve. There’s a species of mice that live in a desert area. A part of that area has become volcanic, so the main color of the ground became dark. So, there are now a white and a black furred mice of the same species which live very close to each other, but in these 2 different areas. So scientists started comparing all genes of those mice to try to pinpoint exactly what gene was responsible for fur color. They all looked identical… except for 3 places where the sequence of those letters were different. They discovered that all dark-haired mice had those 3 places with different sequences that the white-haired ones. This was just one of many examples of genetic mutations being responsible for differences and thus evolution. Scientists can now pinpoint to many more examples.

The Human Genome Project was born to sequence all the genes in human DNA (called genome). At the same time, they were doing the same for other animals. How big is our genome compared to other animals’? In 2003 we got to know the answer. We have ~23 000 genes — as many as a chicken and less than corn and many other plants. It seems it doesn’t take as many genes to make a human as we once thought. Not only that, but many of our key genes are identical to other animals such as chimpanzees and fish. With this scientists concluded that it’s not how many there are that matters but how you use them. To further investigate this idea, some started studying fast reproducing cheap animals — the fruit flies. They noticed that some had black shades on the wings and others didn’t, and that the gene responsible for this was the same in both. Which meant that the same gene was being used in different ways. In trying to find more answers, some scientists started researching what was previously known as “junk”. This junk comprises about 98% of the genome and was thought to be made of genes that didn’t do anything. The other 2% is what actually makes proteins, the main building blocks of living beings. Even now, no one knows what this non-coding area actually does. They found another gene that differed. So they picked up a gene that makes jellyfish glow in the dark, and put it in the fruit fly without shades in its wings, in the same spots where the shades would be. It developed glow in the dark shades. It meant that the gene from the jellyfish had somehow turned on the gene to show shades. This meant that some of those non-coding genes were switches. They aren’t to create proteins, but to switch on and off genes that do. It allows animals to chose where and when to display a certain gene. For example there might be a gene for blue color, and then another gene that specifies the place.

The Tree of Life and the Types of Genes

A number of members of a species that originally lived in the ocean got stuck in a lake so through evolution they lost some spikes that they had to protect from ocean predators. However they still have the genes for the spikes, but the  they are simply switched off. Scientists then wondered if it was a similar process that was responsible for the losing of legs of mammals that became water dwellers (e.g. whales).

But then again… what is making those switches turn on and off? So they went back to analyze the pinches (those Galapagos’ birds that have different beaks). They focused on studying genes that were known to alter birds faces, and discovered that there was only 1 gene responsible for the beak appearance, what changed was when it was turned on and off and by how much during the embryo’s development. The gene of the pinches with stronger beaks was turned on 1 day earlier. This gene for stronger beaks also was the boss of other genes. When turned on, it ordered the cartilage and fat genes for the beak to be turned on too.

The narration now talks about the tree of life again, and how all 4-legged animals descend from fish. Our embryos have gill slits, just like fish, but in us it results in ear bones whereas in fish, the gills. Darwin had no idea how that happened. However, he still theorized that if this was true, then somewhere there must be a fossil of a transition animal, which was neither fish nor 4-legged animal, but something in between. Some scientists tried to find it. It seemed that such transition should have started to occur about ~350M years ago. So they found a fossil in a place where rocks of that age were exposed. The fossil had a typical head of a fish that puts its head out of the water (eyes on top of its head, kinda like a crocodile). Its body had scales, and it was very fish-like. But it had strong fins (or weak arms, however you prefer to think about it). That structure had the same bone structure that is seen in arms and legs that all 4 limbed animals have. A big bone at the top, then 2 in the middle, ending in a cluster of bones in the wrist and hands/feet. But why? Turns out that fish lived in a place with big predators. With those fin-like arms it could drag out of water for a while. But scientists wanted to study the DNA that enabled that transition. From a fossil that old, there’s no DNA that survived to be studied so they needed a similar fish. They found a fish that is even more primitive (but still alive) that is from a similar place in the tree of life, which means that it should have the same genes as the fish that evolved limbs. They found that that the genes of the inside structure of fish’s fins are the same as the bone structure of 4-limbed animals. There’s a gene for the top fin = top bone, another gene for the middle bones/fins, and so on. What happened were just tiny changes in when and where it turned on and off, and a fin could become a limb.

So far our understanding is that there are at least 3 kinds of genes:

  • Type 1: code the materials and structure (and resulting properties) of the things in our body;
  • Type 2: switch on and off type 1 genes;
  • Type 3: control type 2 telling them when and where to turn on/off the types 1 and with how much strength.

Human Similarities With Other Primates

When thinking about what species we descended from, Darwin started by saying that we descended from fish. But it was when observing the first captive chimp and how human-child-like it was, that he started thinking that our closest relatives might be the monkeys. Later when he then proposed the theory that we directly descended from the monkey (chimp) family, which resulted in him getting totally ridiculed! It may have been so because it attacked the belief that humans were special, a creation of god. To say that we, these perfect superior beings, descended from monkeys was seen as an insult. To make fun of Darwin and his theory, people draw pictures of him with fur, and other mockeries of him. Today it is totally accepted in biology.

We now analyze how only 1% of difference between our genome and monkeys’ is responsible for so many differences. One of the key differences is that we have thumbs that are able to touch each of the other fingers, and therefore, grip things easily and with force (called opposable thumbs). Some scientists then focused on studying that tiny 1% difference between us and other primates. They noticed that there was one sequence that was different in 13 places, but they didn’t know what it did. So they put the gene, with another gene attached for it to glow (so they could know where it was active) into the embryo of a mouse. It seemed to be active in various places. And it did became active in the thumb and big toe.

Another important difference between us and other primates is, of course, the brain. Some diseases are caused when genes are faulty. But then again, they might be turned on or off. Some people are born with smaller brains, which tend to result in mental problems such as lower intelligence/retardation. Scientists looking to understand that condition look for genes involved in it. One promising gene is one that is responsible for cell division in the brain. They first looked for it in smaller animals, then in families of people with that disease and found it — it was defective in those families. The mutations/errors can be many. A missing letter, a misplaced letter. They also compared that same gene in healthy families with chimps, and saw that it was very different. In order to better understand our difference and of chimps, another scientist put a supercomputer to look for human genes that are different from chimps, but that chimps share with other animals. She found that half the differences were on the brain. One of the most striking differences was on the cortex (the rugged outer layer of the brain) embryo development gene. Monkeys differed only 2 letters to chickens but 18 letters to humans.

Great documentary, not only the topic but the images and the narration. 5/5

What other great documentaries like this one do you know? This was a pleasure to watch.

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