The Tangled Tree by David Quammen (Book Summary)

The way the world’s top scientists view evolution has changed greatly since 1859 when Charles Darwin published his groundbreaking book, On the Origin of Species. As a matter of fact, a lot has occurred since that time that it can look overwhelming to attempt and get up to speed.

Fortunately, there is David Quammen, an author who focuses on making challenging matters accessible and fascinating. In this book, Quammen directs readers through the obscurity of molecular biology and explains the main developments that have shown the history of life to be a little complicated web of genes and bacteria.

If you thought that the ancestry of any type of species is a straight line, well think again. After these chapters, you may even begin to be uncertain if the word “organism” has any actual meaning at all!

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1 – The idea of a tree of life has been in existence for long amongst scientists and naturalists.

There’s a probability that at a point, you’ve seen an image of “the tree of life.” It’s a drawing that has a tree shape that signifies the evolution of one form of life, following progress from its “roots” as a primordial amoeba then to a fish to an amphibian and it goes on. At different points along the way, branches deviate from the main trunk, signifying worms, reptiles, rodents, and other animals.

These drawings have for a long time functioned as a beneficial tool, a simple pictorial model of a complicated subject.

Similar to a lot of other things in science, the idea behind the tree of life diagram can be traced back to Aristotle. Aristotle in his book History of Animals that was written in the fourth century BCE made mention of the progressional development of animals. But, Aristotle proposes that progress in nature is similar to climbing a ladder; living organisms begin as elements like earth, water, and fire, and slowly develop into plants, animals and then humans. At the peak of the evolutionary ladder, humans become heavenly beings. The entire life is part of one “stairway to heaven,” so to say.

This model was well known for a lot of centuries, with the “ladder of ascent” even mentioned in sixteenth-century woodwork. However, by 1745, Enlightenment-era thinkers had begun making use of more tree-like models.

During that point, explorers started seeing the world more. Knowledge and Evidence were being disseminated, and scholars required more than just one-way ladder to categorize the whole various new plants and animals. A tree wasn’t really a good illustration of evolution as an apt means to classify biological information.

As it was written in 1801 by the French botanist Augustin Augier, a demonstrated “tree looks to be the most accurate method to understand the rank and gradation” of plant life.

The tree of life may have gotten to its peak with the talented illustrator and biologist Ernst Haeckel. During the last half of the 1800s, Haeckel published various volumes of books full of extraordinarily comprehensive drawings of captivating microscopic creatures and more than little trees of life.

However, different from Augier’s tree, Haeckel illustrated evolutionary trees that showed the exact lineage of living things. He created a tree of vertebrates, mollusks, plants, and mammals, and so on.

Haeckel was creating clear assertions, however, his work was actually an addition of someone else’s ideas which is that of Charles Darwin.

2 – Darwin’s theory of evolution is still very significant.

Beginning in 1831, Charles Darwin used almost five years on the ship of HMS Beagle, traveling down past the Canary Islands and along the coast of South America to the Galapagos Archipelago. It was a life-changing journey that produced adequate resources for several books, with Darwin’s revolutionary On the Origin of Species, that was published in 1859.

It’s important to state that Darwin had mainly organized his concepts about evolution not too long after he got back from his trip. Records in his notebooks between the years 1837 and 1838 display him solving the information of how species adapt to their environment and transfer these desirable characters to their offspring.

The focus of this theory is “natural selection,” which Darwin assumed to be the cause of adaptation and the inheritance of traits. Natural selection is mostly regarded as “survival of the fittest,” which signifies that just the species with traits useful to survival in their surroundings will live to transfer those traits to the following generation.

However, when it was time publicly state his ideas, Darwin took time. What seems to have finally helped him was a man called Alfred Russel Wallace. Wallace also traveled around the world; he’d spent years in the Malay Archipelago, and what he saw made him have the exact assumptions about evolutionary adaptation and inheritance as Darwin.

February of 1858, Wallace was hopeful to publish a paper on his own evolutionary thoughts, and through a mutual friend, the paper eventually got to Darwin’s hands. Instantly, Darwin was in misery; Wallace’s notions were very similar to his.

However, in the summer of that year, Darwin accepted to merge with Wallace and offer a presentation at the Linnean Society, a British science organization. But, the weather was scorching and their presentation was really boring that their entire presentation was disregarded. Almost a year and a half after, Darwin’s book got a lot of public attention that his presentation with Wallace was unsuccessful to create. This time around, the ideas were clearly written in language that is relatable to, and immediately became a best seller.

Even up till now, Darwin’s ideas are still being talked about both good and bad terms. The author has performed extreme research on his work, most of it for a former book, and he believes Darwin is worth his place in history. As we’ll get to know in the following chapters, his key idea – that natural selection is the cause of evolution – may be inaccurate, however, that doesn’t mean his entire observations should be ignored.

3 – Our knowledge of evolution has greatly changed when scientists started observing molecules for understanding.

At the end of the nineteenth century, microscopes were offering scientists a spectacular new view on the world. Instantly, new questions and ground-breaking answers started to pile up.

Of specific significance were the separate findings made by Russian zoologist Constantin Merezhkowsky and American biologist Ivan E. Wallin.

Merezhkowsky is a debatable figure in science, all thanks in part to the track of child molestation charges he left behind him. However, at the end of the century, he was part of the first people to propose that cells could have developed through symbiosis –meaning, that a cell could absorb something such as a bacteria and start to use it as its own organ.

As a matter of fact, Merezhkowsky suggested that plant cells acquired their chloroplasts – specialized organelles that allow photosynthesis – by engrossing and internalizing a bacterium. This became obvious to Merezhkowsky after studying their diatoms, which look like single-celled algae. A lot of diatoms obtain their energy through photosynthesis, and when Merezhkowsky studied them under a microscope, he saw that their chloroplasts appeared more terrible like bacteria.

This made him have even a bigger knowledge, which Merezhkowsky said in a 1905 paper that chloroplasts are not “homegrown organs” that evolved in plant cells over time, as was assumed then. Rather, plant cells were one time the exact thing as animal cells; however, then they absorbed photosynthetic bacteria and turn into plant cells. Merezhkowsky even created a word for the formation of new types of life through the combination of two different organisms: symbiogenesis.

In 1905, Merezhkowsky’s notion was so excellent, however, over 50 years after, this theory on how chloroplasts came to occur in plant cells would be proven by advancements in molecular biology.

Although, before this occurred, there was a scientist who didn’t only like Merezhkowsky’s theory; he didn’t know it would go far enough. Also, the American biologist Ivan E. Wallin was checking the microscope and noticing what seemed like bacteria. However, instead of chloroplasts, Wallin was seeing mitochondria, which is the organelle, or little organ, that provides energy to cells through the burning of nutrients and oxygen. Obviously, Wallin assumed, this signified another situation of symbiosis. He would also be ultimately proven to be right.

During the mid-1920s, Ivan E. Wallin created different prescient papers claiming that the symbiotic relationship that occurs between bacteria and other organisms has been the cause of main developments in the life of our planet.

4 – Following the findings of DNA, more comprehensive information could be revealed about the history of life.

During the 1960s, a few scientists were maintaining the notion that, at some time in history, cells had captured and incorporated bacteria. It began with chloroplasts and mitochondria, however, in 1966, American biologist Lynn Margulis proposed that even the wavy things on cells, such as the flagella or cilia that enabled them to move, also developed from captured bacteria.

Margulis published a book a year after, stating that the entire eukaryotic cells –meaning, cells with just one nucleus –are caused by symbiosis with bacteria.

As fascinating as these notions might sound, at the time, opinions like Margulis’s were in the minority. The common notion as at then was that organisms didn’t absorb and incorporate with other organisms. According to the Darwinist idea, an organism evolves gradually over the course of time, maybe with the assistance of a genetic mutation.

But, our knowledge of how plant and animal cells evolved changed intensely as the field of molecular phylogenetics started to change. This field makes use of molecules to study evolution, and it was essentially created by Francis Crick during the late 1950s, one of the intelligent people that found the real nature of DNA.

Crick and fellow biologist James Watson published a paper describing how the double-helix structure of DNA functions in 1953. Initially, it was assumed to be an irrelevant molecule, DNA was explained to be the possible contender for the “mechanism” that allows the reproduction of genetic material.

After this first finding, Crick kept finding the nature of DNA, while also focusing on RNA, the molecule that forms proteins based on DNA’s blueprint. It was during the year 1957 when Crick was hypothesizing on how proteins are formed from DNA information, that was also when he hypothesized that these proteins, filled with long lines of hundreds of different amino acids, might have important information about their genetic lineage. Because the technology for reading the whole genome was still far away, this looked like the perfect method to access the information.

Crick’s casual idea is how molecular phylogenetics started, but the field didn’t have a name then until later. Carl Woese  was one of the most notable scientists in this area, a man keen to see how far back he could go by checking the cell’s “internal fossil record.” Woese named this the DNA, RNA and amino acids that he would check as a type of protein “fingerprint.”

The findings of these fingerprints would change the life of science in the decades after.

5 – Bacterial “fingerprinting” transformed our perception of evolution even more.

All through the majority of the twentieth century, people thought that organisms are steady –meaning once a species branches from the tree of life, that branch stays single and doesn’t combine with other branches. However, this understanding was challenged in the 1970s.

Then, Carl Woese a microbiologist had a laboratory at the University of Illinois, where he was doing innovative work on sequencing the RNA of microorganisms. When he began doing this, scientists had a habit of separating the living world into two groups known as proks and euks.

“Proks” is the short form for prokaryotic, which is mainly the word for cells without nuclei. “Euks” means eukaryotic and those are cells with nuclei. For a while, all the things could be precisely fit into any of those groups.

Then, there was Carl Woese’s 1977 paper, which explained what he’d been doing in “fingerprinting” methanogens, peculiar organisms that had a tendency to appear in swamps and very extreme surroundings such as those in thermal underwater vents. He discovered that these organisms cannot be categorized as euks or proks – they are entirely different, a group that would ultimately become archaea.

Woese’s fingerprinting would keep revealing major things. Molecular biologist Ford Doolittle, while working with Linda Bonen a Woese’s expert lab technician was determined to follow up on Lynn Margulis’s previous notion about the bacterial roots of chloroplasts. Also, with a closer look, Doolittle and Bonen established that chloroplasts were actually captured bacteria that’d been incorporated into plant cells.

Shortly, that same group verified that mitochondria had also begun as bacteria, which, at some point, had been internalized by a different organism through symbiosis. After, in 1985, Carl Woese discovered this exact bacteria to be proteobacteria, as it is known as now– a kind of parasitic purple bacteria that is still very present now.

 Nevertheless, mainstream science was not prepared to admit these unbelievable advances, for it proposed that the history of life is dependent on something that isn’t meant to occur: horizontal gene transfer.

The prevalent belief was that genetic information was a one-way street –transferred to the offspring through reproduction. If Woese, Bonen, and Doolittle were right, genetic material had been normally consumed from one species by another species with no reproduction needed. The tree had started to get twisted.

6 – During the 1990s, there were opposing trees of life, and they no didn’t look like trees whatsoever.

During the early eighties, scientists encountered concrete evidence that life was much like a mosaic or a compound of merging elements than formerly assumed. Due to that, new models of evolution – new trees –started to appear in an effort to show this new understanding.

Carl Woese, as well as his colleague named George Fox, showed what they termed the “Big Tree,” in 1980 and this was a result of years of work in proving archaea as having a separate kingdom– or “domain,” as Woese chose to name it.

In 1987 and 1990 Woese restructured the Big Tree, however, it began with three key branches known as Eukarya, Bacteria, and Archaea, all originating from a mysterious part named “Common ancestral state.”

Since there are no nuclei in Archaea and Bacteria, the scientific group was still seeing this as a prokaryote, a difference that got Woese furious even till the point of his death. He proposed that the term “prokaryote” should be dismissed totally. How significant could it be if it used two domains that are “completely different from each other”?

The thing that was actually provoking was that Woese’s 1990 tree also claimed that both Archaea and Eukarya have the same lineage. Additionally, this signified that the entire plants and animals, as well as humans, have ancestry that contains the archaea Woese found just a few years before.

But what Woese didn’t expect was that the nineties would experience a storm of evidence that backs up horizontal gene transfer (HGT). At that point, faster and more accurate tools for DNA sequencing were being utilized and during the mid-90s, the whole human genome – the complete set of our genetic material – would be discovered. It was becoming very easy to identify complete pieces of bacterial or archaeal genes within another organism’s genome. 

This would be understood as proof of symbiosis and outside genetic materials been incorporated at some specific time in the history of an organism.

Due to that, a lot of scientists identified that the tree of life wasn’t a tree whatsoever, and new diagrams started to develop to reflect this. Some scientists proposed that the tree was really related to the web, or maybe a coral reef, with layers of intertwined sections.

Ford Doolittle published his own form of the tree of life in 1999, and it still had Woese’s domains of Bacteria, Eukarya, and Archaea. However, funnily and right from the beginning, all the branches are tangled, incorporating and separating from one another to create what he named “a reticulated tree.”

For decades, a lot of scientists disregarded anything that seemed very different from the old Darwinian idea of evolution. However, by the end of the twentieth century, there was a lot of evidence to disregard.

7 – Proof of horizontal gene transfer has transformed the manner in which we reason about evolution.

A few times, findings can be overlooked. Or perhaps it’s importance only turns out to be clear later on.

Think of the long history of evidence about horizontal gene transfer (HGT). In 1928, an English civil servant called Fred Griffith found that a form of dead bacteria could be resurrected when combined with the second type of bacteria. Now, zombie bacteria are really shocking. However, think about: when the bacteria were brought back to life, it resurrected as that second form of bacteria! A conversion like this wasn’t meant to be possible.

Or what about bacteria unexpectedly developing resistant to drugs? This occurrence has been known for decades, however, it lately just got extensive attention, both as a threat to humans and as a case of HGT.

One of the additional important records of antibiotic-resistant bacteria happened in Japan after World War II. Situations in the country were ugly, and dysentery was spreading very fast. Not just that alone; however the bacterium that caused dysentery, Shigella dysenteriae, was rapidly evolving and forming resistance to treatment – initially to just a drug and then to two drugs. They were facing a microorganism that was resistant to four different kinds of antibiotics during the late 1950s

This resistance was growing rapidly that it couldn’t be described by Darwinian mutations and usual inheritance. Presently, it’s more commonly known that bacteria can have something called the transferable resistance factors, which have the ability of quickly moving from one species to another, no Darwinian inheritance is required.

The case of Shigella dysenteriae also illustrates to us the drive behind HGT and that behind evolution itself. For quite some time now, it’s been becoming obvious that the actual agents of survival are the genes instead of the organism hosting the genes.

Nevertheless, there are specific proteins, for instance, tryptophanyl-tRNA synthetase, which is seen in humans, cows, and bacteria. In 1997, Ford Doolittle, alongside his colleague Jim Brown, created 66 different trees to find 66 proteins just like that one; they displayed how that type of genes have their own ancestry, an ancestry independent of certain species or specific organisms. Sometimes genes move horizontally since, as Doolittle said, genes possess “their own selfish benefits.”

With these facts, it’s virtually become smart to criticize and disrepute Darwin; however, the author as well as others in the scientific society, recommends against this. There was possibly no way that Darwin could have been aware that HGT was even there. Therefore, he still worthy of the recognition for putting science on the accurate direction with evolution; he only didn’t realize the mechanism behind evolution accurately– neither could he have!

At its most risky, efforts to disrepute Darwin mostly fall into the hands of creationists, and that is why even Richard Dawkins, a well-known atheist and the author of The Selfish Gene, recommends not to condemn Darwin.

8 – There are still a lot of questions; however, it is obvious that our perceptions of species and individuality are less stable than we assumed.

Therefore, what do understand by all this?

Even with a lot of evidence for HGT activity in bacteria, there were uncertainties about the influence it would have on animals as well as humans. Another strong conviction was that animals’ germ positions –which are, the eggs, sperm, and reproductive cells – are very safeguarded from the effects of bacteria.

Unfortunately, this isn’t the situation. Experiments conducted at the University of Rochester revealed that Wolbachia bacteria which is a group of parasitic bacteria, displayed in the genomes of a variety of insects and invertebrate animals for instance head lice and crustaceans. Therefore, it was deduced that the bacteria’s target was ovaries and testes and was transferred to the offspring through infected eggs. Perhaps the most astonishing was its effect on flies: nearly the whole genome of the bacteria was seen in the insect’s own genome.

The idea of HGT became normal during the 2000s. However, there is still a lot of question on how intensely this type of gene transfer has affected the history of life. Part of the very recent evidence recommends that, over millions of years, the genes of “alien” have been fused into “the deepest cellular individuality of plants, fungi, and animals.” They’ve migrated from chloroplasts and mitochondria and now can be seen in the important genomes of complicated creatures.

Also, there are all the microbes that live in the body of humans. When you combine the entire gut microbes, not to say the ones found in your armpits, skin, and eyelashes, it shows that you have more microbe cells than “human” cells. Also, amid all these tiny creatures, HGT is present.

However, these aren’t intruders – they’re vital to your health, well-being and other crucial purposes, like food digestion. Therefore, are you an individual or really a network of organisms? Some scientists go really far as to ask if the idea of an “organism” still remains valid.

Although some perceptions may be less than valid, it is obvious that HGT wasn’t only a fluke four billion years ago in assisting in the creation of more complex cells. It had a huge role in forming all life as we are aware.

The Tangled Tree: A Radical New History of Life by David Quammen Book Review

Many things have occurred since the publication of Charles Darwin’s book “On the Origin of Species” in 1859. Since that time, it’s been confirmed that genetic material doesn’t need reproduction to be able to be passed onto another organism. For the last few decades, horizontal gene transfer which is the process of genetic material that is being transferred and engrossed through symbiosis has been established to be a key element in the evolution of life in our world.

 Due to the fact that it has even happened among distantly connected species, it is obvious that the entire life on Earth is much more closely intertwined than we’d formerly assumed.

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