First impression review: The Tangled Tree: A Radical New History of Life, by David Quammen
This book focuses on scientists' quest to categorize bacteria and understand their evolution, the discovery of horizontal gene transfer, and what it means for evolution and our understanding of ourselves. As a quick summary:
Bacteria were always hard to fit into traditional taxonomy of organisms because A) they are very small with fewer distinguishing features to help sort them, and B) they don't reproduce sexually, so the biological species concept - the dominant species concept used for animals that says a species is a group organisms that interbreed with each other but not members of other groups - doesn't work for them at all. As DNA sequencing became a thing, scientists began to realize several things. First, there were two very distinct types of "bacteria" or, rather, some of the things we had lumped in with bacteria were different from the others in their DNA and lifestyle. These organisms are now known as archaea, and they may even be more closely related to us and all other eukaryotes (organisms with a cell nucleus) than to bacteria. Collectively, we call bacteria and archaea "prokaryotes". Second, prokaryotes swap DNA with each other pretty frequently, which means that, say, a gene lending antibiotic resistance can hop between otherwise distantly related prokaryote "species". Third, eukaryotes can also pick up new genes via this "horizontal gene transfer" (HGT).
Things I liked:
The writing is very engaging and easy to understand. When a big "science word" is unavoidable, Quammen often humorously highlights it to make it memorable. There are details about the lives of the scientists involved in this story that humanize them, and illustrate how our personalities and beliefs - for better or for worse - influence what questions we find interesting, how we engage with critics and collaborators, and so on. Carl Woese and Lynn Margulis are two larger-than-life figures that are give a special feature in this tale. In some ways, these profiles are a good cautionary tale, as they illustrate that just because someone has one big, important, transformative idea doesn't mean they are right about everything! It is also very cool to reflect that not only are each of us an ecosystem, with many of the cells in our body belonging to microbes, but that our genome has bits and pieces that we picked up along the way from these tiny companions.
Things I didn't like:
The book isn't very clear about what it means by "Darwinism", even though it points out that unclear communication on this issue can erroneously give fuel to the anti-evolution crowd. See, Darwin had a TON of ideas, some of which have held up better than others. The ones that are still at the center of evolutionary biology are:
1. The process of natural selection. Because individuals in
a population vary in their traits, and some of those traits give an advantage
in survival and reproduction, any advantageous traits will increase in
frequency in the population from one generation to the next, while
disadvantageous traits will be weeded out. This can be directly observed by,
say, putting bacteria on a big plate with different levels of antibiotics andwatching them for two weeks as mutations arise and those that give more resistance spread.
2. Lineages of organisms change and branch over time, giving
rise to the diversity of organisms we see today. Lineages that split more
recently tend to be more similar to each other, having accumulated fewer
changes, than those that split a long time ago. This is a little less directly
observable, and there are ongoing debates over whether the phenotypic changes
happen all the time or mostly at the point that lineages split, but DNA
analyses have supported the branching-relationships idea overall.
Although early studies of inheritance were being carried out by Gregor Mendel during Darwin's lifetime, Darwin did not read his writings and had no idea how inheritance worked. He was going purely off of basic physical observations - for example, that children tend to resemble their parents. Certainly no one had any idea about DNA, and so to say that having variation contributed by horizontal transfer of DNA between lineages is "non-Darwinian" is nonsensical. Natural selection still applies, whether the variant arose internally via mutation, or whether it was inserted by a virus or a genetic engineer; it will only spread if it provides a fitness advantage.
The other claim of how horizontal gene transfer challenges
Darwinian thinking comes from the branching tree metaphor for how evolutionary
diversification happens. The author points out several times that tree branches
don't normally merge. But merging branches isn't the correct metaphor for HGT1.
It isn't two branches melding together, erasing their distinctions - rather, a
tiny piece of branch 1 (like a little hair-sized vine, perhaps) hops over and merges with
branch 2. But most of branch 2 is the stuff that was there before. That is why,
even though we have known about HGT for decades, we still use trees to
represent evolutionary relationships. If you look at a species' whole genome,
it still shares most of its sequences with phenotypically similar relatives
that branched off recently. For instance, suppose a bacterial gene hopped into
the genome of the common ancestor of humans and chimps. The genome of that
organism would still be 99.9999% what it inherited "vertically" from
its ape parents and grandparents and great-grandparents. If that bacterial gene
is advantageous, perhaps it spreads throughout the ape population. Then, when
that population splits, resulting in the two lineages that ultimately gave rise
to humans on one side and chimps on the other, both those lineages would
inherit the bacterial gene...which is now, practically speaking, an ape gene.
If you sequenced that gene in different organisms, the sequences found in
humans and chimps would probably be much more similar to each other than to the
sequence found in the original bacterium, because the copies of the gene in the
ape and bacterial lineages will have accumulated different mutations in the
millennia since the transfer. So tree thinking is still useful, so long as we A) use the whole genome or at least many
different genes to reconstruct that family tree and B) bear in mind that
vertical inheritance is not the only
way to acquire a trait.
1. It is almost right for hybrid speciation, but that is another story!
Recommendation: This is an enjoyable read if you want to learn more about microbial evolution and horizontal gene transfer, or if you enjoy history of science stories about connections between different lines or research...or crotchety scientists arguing with one another about stuff everyone else finds weirdly arcane.
