The Tangled Tree by David Quammen (Book Summary)

The way the world’s top scientists view evolution transformed greatly from 1859 – the time Charles Darwin released his groundbreaking book – to now. As a matter of fact, a lot has occurred since that time that this may look overwhelming to attempt and be up-to-date.

Fortunately, there is David Quammen, the writer who focuses on making challenging matters accessible and fascinating. In this book, Quammen directs perusers in the obscurity of biochemistry and explains the main advancements that have shown the past of existence to be a little complicated network of bacteria and genes.

When you thought that the ancestry of any type of species has been straight, consider that again. Reading these chapters, you can even begin to be uncertain if the vocabulary “organism” possesses any actual sense at all!

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

There has been a probability that one time, you have an image of a “life tree”. That is a drawing that has a tree shape that signifies the transformation of a form of life, following progression starting with the primordial amoeba root then continuing with a fish, and ending with an amphibian, it goes on. At different times in the process, branches deviate from the main trunk, signifying rodents, reptiles, worms, and further animals.

Those drawings have for a long time functioned as a beneficial instrument, a basic pictorial prototype of a complicated subject.

Similar to a lot of many aspects of science, the idea after the life tree diagram may be founded in Aristotle. Aristotle inside the Animals’ History book that was written in the 4th hundredth year BCE made mention of the progressional development of animals. But, Aristotle proposes that progression in the natural environment is similar to climbing stairs; living entities begin as elements like fire, earth, and water, and slowly develop into herbs, animals, finally humans. Humans become heavenly beings at the peak of this evolution stairway. The entire life is the piece of a “ladder to heaven”, in other words.

That structure was well known for hundreds of years, with the “ascent ladder” even mentioned in 16th-hundredth year woodwork. However, in 1745, Enlightenment-time philosophers had begun making use of further tree-like structures.

During that point, explorers started seeing the world more. Knowledge and Evidence were being disseminated, and scholars required more than just a one-way stairway to categorize the whole various novel animals and plants. The tree was not really a good illustration of advancement as an apt means to classify biological knowledge.

Similar to how it was written in 1801 by Augustin Augier, a botanist from France, a demonstrated “tree looks to appear the most accurate method to understand the rank and staging” of a plant’s life.

The life tree may reach its peak with the talented biologist and illustrator Ernst Haeckel. During the last 50 years of 1800, Haeckel released various volumes of books full of extraordinarily comprehensive drawings of captivating minuscule life forms and further little life trees.

However, different from Augier’s, Haeckel illustrated progressive trees which showed the exact ancestry of living beings. He created vertebrates’ trees, mollusks’ trees, plants’ trees, and mammals’ trees, among others.

Haeckel was creating clear assertions, however, his output was actually an addition of someone else’s ideas which are from Charles Darwin.

Chapter 2 – The evolution theory of Darwin is still very significant.

Beginning around 1831, Darwin used almost five years on the ship of HMS Beagle, traveling from the Islands in Canary throughout South America’s coasts until reaching the Archipelago of Galapagos. That had been a transformative journey that produced adequate resources for several books, with Darwin’s revolutionary Regarding Species’ Origins, which was released around 1859.

That is important to state that Charles Darwin had mainly organized his concepts about evolution not too long after he got back from the trip. Records inside his journals in 1837-1838 display him solving the information of the way species alter according to the environment they are in and transferring these desirable characters to descendants.

The focus of that hypothesis has been “natural selection,” the hypothesis that Darwin assumed was the cause of trait inheritance and adaptation. Natural selection has mostly been regarded as “the fittest’s survival” which signifies that just the species having traits useful to survival in their surroundings can survive to transfer their attributes to the following generation.

However, when it was time to publicly state his ideas, Darwin took time. What seems to have eventually helped him had been a guy called A. R. Wallace. He also traveled around the globe; he had spent a lot of years around the Archipelago of Malay, and what he saw made him have the exact assumptions regarding inheritance and evolutionary adaptation similar to Darwin.

February of 1858, Wallace had felt hopeful to release a paper regarding his evolutionary thoughts, and with a common 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, offering a speech at a science organization of the UK – the Society Linnean. But it was scorching and the speech was really boring that their entire presentation was disregarded. Almost one year and a half after, Darwin’s book got a lot of public attention that his speech with Wallace was unsuccessful to generate. That time around, the hypothesis was clearly written in language that is relatable to, and immediately became the bestseller.

Even up till now, Darwin’s hypotheses are being talked about even today, both in good and in bad aspects. The writer has performed extreme scrutiny regarding his effort, most of those for the former book, and the writer thinks Darwin is worth his location in history. While we are getting to know in the following chapters, his key thought – which natural selection has been the cause of evolution – might be inaccurate, however, this does not mean his entire inspections need to be ignored.

Chapter 3 – Our knowledge of evolution has greatly transformed at the time scientists started observing molecules for understanding.

At the finish of the 19th hundredth year, microscopes have been offering scientists a spectacular new view of this world. Instantly, novel inquiries and ground-breaking answers started to accumulate.

Of specific significance had been the discrete findings of Constantin Merezhkowsky, a zoologist from Russia, and Ivan Wallin, a biologist from America.

Merezhkowsky has been a debatable figure of science, all partly owing to the track of kid molestation accusations he had in the past. However, at the end of the hundredth year, he had been an initial person to propose that cells might have developed through symbiosis –meaning, that a cell might have absorbed something such as a bacteria, starting to utilize that like its limb.

As a matter of fact, Merezhkowsky suggested that the cells of plants acquired chloroplasts – the exclusive organelles which allow photosynthesis – by engrossing and taking up a bacterium. That turned out obvious to Merezhkowsky following studying their diatoms, which look like algae that have one cell. A lot of diatoms obtain energy by photosynthesis, at the time Merezhkowsky studied them utilizing a microscope, saw that chloroplasts appeared more terrible similar to bacteria.

That made him have even a bigger knowledge, which Merezhkowsky said in his paper around 1905 that chloroplasts aren’t “homegrown organs” which evolved inside the cells of plants in time, like what was assumed before. Rather, the cells of plants were one time the exact thing as animal cells; however, afterward, they took up photosynthetic bacteria, which turned them into the cells of plants. Merezhkowsky further created a word for the formation of new types of life with the combination of two different organisms: symbiogenesis.

Around 1905, his notion was so excellent, however, over 50 years after, this hypothesis on the way chloroplasts occurred inside the cells of plants might be proven by advancements in biochemistry.

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

During the middle of the 1920s, Wallin created different prescient papers claiming that the reciprocal intercourse that occurs between organisms and bacteria has been the cause of main developments in the life of our planet.

Chapter 4 – Following the findings of DNA, more comprehensive knowledge might be revealed regarding this life’s history.

During the 1960s, some scientists had the notion that, in a time in the past, cells seized and absorbed bacteria. This began with mitochondria and chloroplasts, however, around 1966, Lynn Margulis – a biologist from America – proposed that the wavy things of cells, such as the cilia or flagella which enabled them to move, also developed from absorbed bacteria.

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

As fascinating as these notions might look, at that era, opinions similar to Margulis’s have been outnumbered. The common notion as of then was that life forms do not take up and consolidate with other life forms. In agreement with the Darwinist idea, an organism evolves gradually over the course of time, maybe with the assistance of the mutation of genes.

But, our knowledge of the way animal and plant cells evolved changed intensely as the molecular phylogenetics field started to change. This field makes use of molecules for working on evolution, therefore, this was essentially created by Francis Crick during the 1950s ends, an intelligent person that found DNA’s real nature.

Crick and James Watson – a peer biologist – released a publication describing the way the 2-helix form functions in DNAs in 1953. Initially, it was assumed that it was an irrelevant molecule, however, DNA was explained as the possible contender for the “machinery” which allows our genetic material’s reproduction.

With this first finding, Crick kept finding DNA’s nature, at the same time focusing on RNA, the entity that forms proteins according to the blueprints of DNA. That was during the year 1957, at the time Crick was hypothesizing on the way proteins could be formed using information from DNA, that was also when he hypothesized that those proteins, filled with extensive ropes of 100s of different amino acids, may have important data regarding their genetic ancestry. Because there was no technology to read the whole genome, this looked like the perfect method to reach the data.

Crick’s ordinary idea is the way molecular phylogenetics started, but the area did not have a name then until later. Carl Woese was a very notable scientist in the area, a man keen to observe the extent he might reach by checking the “inherent fossil record” of a cell. Woese named this “DNA”, amino acids, and RNA which he could check as a type of a “fingerprint” for proteins.

The findings of these fingerprints could transform the life of science afterward 10s years.

Chapter 5 – “Fingerprinting” of bacteria transformed our perception of evolution even more.

All through the majority of the 20th hundredth year, people thought that life forms have been steady – meaning when a species spreads from the life tree, this branch stays single and doesn’t combine with further branches. However, this understanding was challenged in the 1970s.

Then, Carl Woese a microbiologist had a laboratory at Illinois University, the place he worked on innovative work on ordering microorganisms’ RNAs. At the time he began doing this, scientists had a habit of separating the world of living things into 2 groups known as “eukaryotes” and “prokaryotes”.

The latter is the short form for prokaryotic – mainly the word for cells without nuclei. “Eukaryotes” means eukaryotic and those are cells with nuclei. Momentarily, all the things could be precisely fit into any of those groups.

Then, there was the 1977 publication of Carl Woese, explaining what he did by “fingerprinting” methanogen, unusual organisms, having a tendency to appear in swamps and very extreme surroundings such as those in thermic vents of underwater. He discovered that those life forms could not be categorized as “prokaryotes” or “eukaryotes” – they were entirely different, a group that would ultimately become archaea.

The “fingerprinting” of Woese would keep revealing major things. Ford Doolittle, a molecular biologist, while working with Linda Bonen, a specialist lab technician, was determined to go after Lynn Margulis’s previous notion regarding the bacterial roots of chloroplasts. Also, with a closer look, Bonen and Doolittle established that chloroplasts had actually caught bacteria, having been absorbed by the cells of plants.

Shortly, that same group verified that mitochondria were also bacteria in the beginning, which, at a moment, was assimilated by a different life form by symbiosis. After, around 1985, Woese discovered this exact bacteria was proteobacteria, like that is known as now – a kind of purple bacteria, parasitic which has still been very present now.

 Nevertheless, conventional science had not been prepared to admit these unbelievable advances, for it proposed that life’s past is dependent on a thing that was not meant to occur: gene transfer horizontally.

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

Chapter 6 – Around 1990, opposing life trees existed, and these didn’t look like trees whatsoever.

During the initial times of the 80s, scientists encountered concrete proof that life had been much like a patchwork or an amalgamation of merging elements than formerly assumed. Due to that, novel prototypes of evolution – novel trees – started to appear in an effort to show this novel comprehension.

Carl Woese, as well as his colleague named George Fox, showed what they termed the “Great Tree,” in 1980 and this was a result of a lot of effort for years in proving archaea as having a distinct dominion – e.g. “domain”, what Woese chose to name it.

In 1987 and 1990 Woese restructured the Great Tree, however, it began with three key branches known as Bacteria, Eukarya, and Archaea, each of them originating from the peculiar part named “Joint hereditary place”.

Since there are no nuclei in Bacteria and Archaea, 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” needs to be dismissed totally. How significant would it become when it used 2 domains which have been “completely different from one another”?

The thing that was actually provoking had been that the 1990 tree of Woese also claimed that both Eukarya and Archaea have the same lineage. Additionally, this signified that the entire animals and plants, as well as humans, have ancestry that contains the archaea he found just some years prior.

But the thing Woese did not expect had been that the 90s might experience a storm of evidence that backs up gene transfer horizontally (HGT). On that point, more rapid, and more accurate instruments for sequencing DNAs were utilized and during the middle of the 90s, the whole genome of humans – the complete sequence of the human genetic compound – could be discovered. It was becoming very easy to identify complete pieces of archaeal or bacterial genes inside the genomes of other organisms. 

That could be understood as proof of symbiosis in addition to external genetic substances being amalgamated at some specific time in the history of an organism.

Due to that, a lot of scientists identified that the “life tree” was not a tree whatsoever, and new diagrams started to develop to mirror that. Some scientists proposed that this tree had really been related to the web, or maybe coral reefs, having stages of intertwined sections.

Doolittle released his form of life tree in 1999, and it still had Woese’s Eukarya, Bacteria, and Archaea domains. However, funnily and  straight starting from the beginning, all branches were tangled, incorporating and separating from each other to create what he named “a reticular tree.”

For tens of years, a lot of scientists disregarded anything that seemed very different from the previous Darwinian idea of evolution. However, through the finish of the 20th hundredth year, there had been a lot of evidence to disregard.

Chapter 7 – Proof of HGT has transformed the manner in which we reason about evolution.

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

Think of the extended past of evidence related to HGT. Around 1928, a civil servant from the UK called Fred Griffith found that a form of expired bacteria might be resurrected when combined with the 2nd kind of bacteria. Currently, zombie bacteria are really shocking. However, think about: at the time the bacteria were brought back to life, it resurrected as that 2nd kind of bacteria! The conversion similar to that was not meant to be probable.

Or what about bacteria unexpectedly developing unaffected by drugs? That occurrence has been known for decades, however, it lately just got extensive notice, a threat for people, and a case of HGT.

A very important additional record of drug-proof bacteria happened in Japan after WWII. Situations around the nation were ugly; dysentery was disseminating very fast. Not just that alone; however the bacterium that caused dysentery, Shigella dysentery, had been rapidly evolving and forming tolerance to cure – initially to just a drug, and afterward to 2 drugs. They were facing a microorganism, being durable against 4 distinct kinds of antibiotics during the late 1950s

This durability had been growing rapidly so that this might not be described by mutations explained by Darwin, and usual inheritance. Presently, it’s more commonly known that bacteria may have something called the transmissible resistance elements, which have the ability to quickly move from 1 species to 1 other species, inheritance of Darwin is not required.

The case of dysentery illustrates to us the drive behind HGT and that after evolution itself as well. For quite some time currently, that has been turning out obvious that the actual survival agents have been the genes instead of the hosting organism of the genes.

Nevertheless, there are specific proteins, for instance, tRNA synthetase, which could be seen in humans, cows, and bacteria. Around 1997, Doolittle, alongside his coworker Jim Brown, created 66 distinct trees for finding 66 proteins just like that one; they displayed how that type of genes possess their ancestry, an ancestry independent of certain species or certain organisms. Occasionally genes proceed horizontally since, as Doolittle said, genes possess “their selfish benefits.”

With these realities, that is virtually become smart to criticize and disrepute Darwin; however, the author as well as other people in science, recommends against this. There was possibly no way that Darwin could have been aware that HGT existed. Therefore, he is still worthy of recognition for putting science in the accurate direction with advancement; he only didn’t realize the machinery after evolution accurately – neither did he!

Most dangerously, efforts to disrepute Darwin mostly fall to creationists’ hands, and that is the reason Richard Dawkins, even a well-known atheist, the writer of “Selfish Genes”, recommends not to condemn Darwin.

Chapter 8 – There are still a lot of questions; however, it is obvious that our perceptions of individuality and species have been less steady compared to what 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 existed microbes, living in the body of humans. When you combine the entire gut microbes, including the ones found in eyelashes, armpits, and skin, it shows that you have further microbe cells compared to “human” cells. Also, amid all these tiny life forms, HGT has been present.

However, these aren’t intruders – they’re vital to people’s health, welfare, and other crucial purposes, like food digestion. Therefore, are we individuals or a group of life forms? A group of scientists goes really further to ask if the notion of the “organism” still remains valid.

Although some perceptions might be lower than valid, it is obvious that HGT had not only been a chance 4000000000 years previously in assisting in the creation of further complicated cells. This had a huge role in forming every life form we are aware of.

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

Many things have occurred since Charles Darwin’s publication is released around 1859. Since that time, it’s been confirmed that the substance of genes does not need reproduction to be able to be transferred onto another organism. For the last tens of years, gene transfer horizontally (HGT) which is the procedure of genetic substance that is being transferred and engrossed via symbiosis, is established to become a key element in life’s evolution in our world.

 Due to the reality that it has even happened among distantly connected species, that is obvious that the entire existence in this world is much more closely intertwined than we’d formerly assumed.

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