Until recently, the central tenets of Darwin’s theory of evolution, from how heredity works to the gradual variation in species, had been regarded as settled and beyond challenge. But as David Quammen, a National Geographic contributing writer, explains in his new book The Tangled Tree, new discoveries in human biology in the last few decades have led scientists to radically alter the story of the origins of life, with powerful implications for our health—and even our very nature.

When National Geographic caught up with the author at his home in Montana, he explained how the discovery of a new “third kingdom” of life changed our understanding of evolution, how so-called kissing bugs can move DNA from one species to another, and why the gene-editing tool CRISPR presents exciting new possibilities, as well as ethical challenges.

Your book opens with Charles Darwin making a little sketch in a notebook. Put us inside that moment and explain how the image of the tree of life has altered over the centuries.

Darwin is home from the voyage of The Beagle, a young man living in London, and thinks that perhaps species have evolved over time. But he doesn’t have a theory for how it occurred. He makes this little sketch in his B Notebook, one of his secret transmutations notebooks, which was his term for evolution, draws a little stick figure of a tree, and writes above it in his scrawly hand, “I think.”

The tree of life is an old image, going back to the Book of Revelations. But that tree drawn by Darwin was the first evolutionary tree of life. My book is about the history of that but more importantly about the way that image has been radically revised as a result of the discoveries we have made from genome sequencing in the last 40 years.

One of the most arresting statements in your book is that “we humans probably came from creatures that, as recently as 40 years ago, were unknown to exist.” Introduce us to archaea.

The archaea are a third domain of life that was unknown to exist before 1977. It was a group of organisms thought to have been bacteria. Through a microscope, they looked like bacteria, little bugs with no complex anatomy. But with genome sequencing they were revealed to be not only not bacteria, but more different from bacteria than they are from us in terms of their genomes.

Your book is as much about scientists as it is about science, and casting a huge shadow over the story is the biologist Carl Woese, whom you call “a brilliant crank.” Explain why he is so important to this story.

He was a microbiologist at the University of Illinois, in Urbana, in the middle of the American prairie, working away during the late 1960s and early 1970s. He was deeply interested in the early history of life on Earth, going way back to the beginning of cellular and pre-cellular life close to 4 billion years ago. He thought, “How in the world can I learn about that?”

He decided the way to do it would be to go inside living cells, find a single molecule common to all forms of life, pull that molecule out, sequence its genomic letters, and then collect paragraphs of those letters for one organism and another and compare them to see who was related to whom, how distantly, how closely, and the way life had diverged over billions of years. He then made the discovery that some of these creatures that looked like bacteria, were, in fact, not bacteria at all but the archaea, this third kingdom of life. That discovery got him on the front page of the New York Times on November 3, 1977.

The British research lab at Porton Down has been much in the news recently because of the Skripal affair. Take us inside this top-secret facility and talk about the strange case of NCTC#1.

I wrote a previous book about emerging diseases, like Ebola, and much work has been done on that at Porton Down. I then discovered it’s also the home of the NCTC, a library of frozen microbes that have been preserved over time for scientific and medical purposes. I thought, “Well, I’d better go look at some bacteria.”

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It’s not an easy place to get into but after applying I was warmly welcomed and shown some of these freeze-dried microbes, including one called NCTC #1. It’s called that because it was the very first acquisition of the collection: a sample of a form of pathogenic bacteria that causes the disease shigella, which is a sort of dysentery. The particular bug is called shigella flexneri, and was isolated from a British soldier named Ernest Cable in 1915 during WWI, when he died in a hospital in France from dysentery, which killed a lot of soldiers.

This specimen was tucked away at Porton Down until about a decade ago when one tube of the samples was pulled out, thawed, regrown in a laboratory by a team of scientists led by one Kate Baker, and its genome examined. Lo and behold! One of the things they found out about this 1915 sample of bacteria was that it was already resistant to penicillin. People said, “Woah, wait a minute! Penicillin hadn’t even been discovered yet!” Its use against bacteria was not discovered until the late 1930s and not put into medical use until the early 1940s. But here was a bug killing a British soldier back in 1915 that already had resistance to that anti-bacterial substance, penicillium.

One of the key concepts you explore is “horizontal gene transfer.” Give us a layman’s explanation of what this is, with reference to the strange phenomenon of “kissing bugs.”

Horizontal gene transfer is essentially sideways heredity. It’s the passage of genetic material sideways, from one creature into another, from one species into another. It can even go from one kingdom of life into another, sideways, across great barriers. That was thought to be undoable. I first read about it back in 2013 and my reaction was, “Wait, what? No! That doesn’t happen! That can’t happen!”

In fact, genes can go sideways across vast species boundaries. For instance, a gene for resistance to one kind of antibiotic in one form of bacteria, like staphylococcus, can move sideways into another, completely different form of bacteria, say, E.coli. This can happen not just in bacteria but also in animals, plants, and higher organisms, generally as a result of infection or parasitism.

One example is a form of transposon. Big, complicated word. [laughs] What’s a transposon? It’s a stretch of DNA that transposes from one part of a genome within a creature to another part. But scientists have discovered that these things can also jump from one creature to another, and even from one species to another.

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One transposon has been given the name space invaders. It’s a long stretch of DNA that invades lots of different organisms. It seems able to pass, for instance, from a reptile into an insect or from a possum into a rat, by way of something called a kissing bug, an insect that, when sucking blood, sucks in some of this transposon. The transposon then moves from one species to another and becomes part of the heritable genome of that new species.

A 2009 headline in the British magazine New Scientist said “Darwin was wrong” and was immediately seized upon by creationists. Explain the issues and how the latest science is rewriting the idea of natural selection.

It’s not rewriting the idea of natural selection. Rather, it’s rewriting our understanding of evolution, of which natural selection is still a very important part. There are two phases in classic Darwinian evolution. First, there is the arising of variations from one creature to another or one individual population to another. That was thought to occur incrementally, in very slow stages, by mutations in the genome. Once there are variations among individuals, natural selection, the survival of the fittest, acts upon those variations.

What is new, and caused New Scientist to run that over-stated and provocative headline, “Darwin Was Wrong,” is that we now understand there is another, hugely significant form of variation. It’s not just incremental mutation, but horizontal gene transfer, bringing entirely new packages of DNA into genomes.

One of the axioms in Darwin’s day, natura non facit saltus, which your good Latin training [laughs] will tell you means nature does not make leaps; things happen incrementally. But horizontal gene transfer has revealed that nature does sometimes make leaps, whereby huge lumps of DNA can appear in an individual or population quite suddenly and then natural selection acts on them. That can be a very important mechanism in the evolution of new species.

Most of us are unaware of just how many bacteria are swarming in our gut or armpits. Take us inside our microbiome and explain how it is crucial for human health.

We now realize, because we can sequence genomes, that we have great populations of bacteria living within us. People think if you’ve got a bacteria you’re sick. In fact, there are hundreds, if not thousands, of different kinds of bacteria that live benignly within our guts, armpits, ears, noses, pores, or on our skin. This is known as the human microbiome. It’s the ecosystem of microscopic critters, mostly bacteria, which live on and in our bodies. The maintenance of that ecosystem of microbes is essential to human health, which is one reason why the over-use of antibiotics can be a bad thing. Most antibiotics tend to be broad range. When you take them to kill off a particular bacteria that may be causing you a sore throat, you’re going to also be killing other bacteria, many of which are beneficial or even necessary to your good health and the balance of microbes within you.

One of the questions you pose is, “What implications do these discoveries carry for the concept of human identity?” What’s the answer, David?

We now understand that we humans, along with most other creatures, are composites of other creatures. Not just the microbiome living in our bellies and intestines, but creatures that have over time become inserted in our very cells. Every cell in the human body contains, for instance, little mechanisms that help package energy. Those are called mitochondria. We now realize that those mitochondria are the descendants of captured bacteria that were either swallowed by, or infected, the cells that became complex cells of all animals and plants. Likewise, 8 percent of the human genome, we now know, is viral DNA, which has come into our lineage by infection over the last 100 million years or so. Some of that viral DNA is still functioning as genes that are important for human life and reproduction.

You end your book in the present, with the advent of the gene-splicing tool CRISPR. Tell us about it and how it is revolutionizing biology and genetics.

CRISPR is an acronym for a gene-editing tool discovered in the last 10-15 years that is very powerful and inexpensive. With it, scientists can now edit genomes, delete mutations or insert sections of new genes. It promises a lot of wonderful medical possibilities and a lot of really troubling moral and societal choices.

It’s wonderful if scientists can correct a genetic defect in a fertilized human egg, and prevent a child from having a congenital disease by editing its genome. But how far does it go? Does it go to the point where wealthy people will be able to choose designer children, whose genomes have been edited to make them smarter or stronger? These are, to put it mildly, really difficult ethical propositions. So, there will be a lot of discussion about CRISPR in coming years.

But it is something that has always existed in nature. Microbes were using CRISPR to protect themselves and to edit their own genomes before it was ever discovered and put to use in a laboratory by some really brainy humans. [laughs]

This interview was edited for length and clarity.