Darwin’s first inkling (1837)

Charles Darwin had been back less than a year from his tour on the HMS Beagle and he had been thinking furiously about the paradoxical diversity and commonality of life when he had a flash of insight. He reached for his “B” notebook and scribbled this sketch showing species branching and sub-branching from each other. This is one of the most famous images in science and a popular tattoo among scientists. It does not, however, look a great deal like a tree; it looks like a leftover grape stalk. Darwin does not use the word “tree” or “branch” in his notebook; instead he refers to “gradation” and “greater distinction.” What is most important about this sketch is often edited out of images and tattoos. The large letters at the very top read, “I think”: simultaneously a recognition of his own uncertainty and an expression of his way of working through problems. Darwin was 28 years old.

The Origin of Species (1859)

By the time Darwin came to publish The Origin of Species, he had been thinking about evolution for a further 22 years. The concept of speciation was more than just a cluster of splitting lines, it was a fully grown Tree Metaphor. The image above is the only diagram in the first edition of Origin. Instead of being a map of branches, Darwin has now added time as an axis to his map so that the early life forms begin at the bottom and move through time towards the top, branching as they go. Each horizontal line represents “a thousand generations; but it would have been better if each had represented ten thousand generations.” The diagram has also expanded its ambition to include extinctions and evolutionary cul-de-sacs. The diagram still does not look much like a tree. River weeds, maybe.

In the text, though, Darwin waxes prolix on the concept of the Tree of Life: “The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth.” What follows is one of his most memorable passages.

From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.

Beautiful ramifications, indeed. Gorgeous writing, and also very precise. From the diagram and from the text Darwin was very careful to neither imply nor refute a universal common ancestor. The Tree of Life referred to “all the beings of the same class” and not to all life on Earth. There might be one Tree or several. Darwin could not know and does not proffer an answer. Darwin wanted the reader to be very, very clear that the Tree of Life is a metaphor. In one sentence he calls it a “representation” and in the next a “simile.”

Ernst Haeckel’s flamboyant Tree of Life (1866)

Darwin wrote Origin of Species for other naturalists. Popularising the theory of evolution fell to others, possibly because Darwin’s gentle disposition did not lend itself to the rough-and-tumble of public debate where more combative personalities such as Thomas Huxley were to shine. Among the great popularisers was Ernst Haeckel, a German biologist who is best remembered today for his artworks. Haeckel’s illustrations are still considered among the most beautiful scientific drawings in history. Wikipedia hosts a small sample of his prolific output. In 1866, Haeckel wrote the first great popular book explaining evolution, and it includes this image of the Tree of Life:

Unlike Darwin’s stremlined diagram, Haeckel created a work of art. In the process, Haeckel lost two important features of Darwin’s Tree. First, Haeckel implied a universal common ancestor. Today we have good reason to hypothesise a universal common ancestor or at least a set of universal common ancestors, but most of the evidence upon which this rests was unimaginable in Haeckel’s time. Haeckel guessed right, but it was still a guess that he should not have dressed up as a certainty. Second, Haeckel abandoned the depiction of extinctions. Where Darwin laid out a number of dead branches on his evolutionary Tree, Haeckel ignores them altogether. What appear to be dead ends are not extinctions at all — those dead ends include molluscs and lichens and amphibia, creatures very much alive today. In fact, the dead ends don’t represent anything at all, they are simply the artist’s way of squeezing a lot of branches inside a rectangular border.

Despite Haeckel’s great contributions to art and science, his legacy is controversial today. He is the creator of a famous illustration of embryological development that his detractors consider fraudulent and even his most admiring apologists consider sloppy. Even harder to swallow, Haeckel came to be one of the foremost exponents of polygenism, a particularly revolting pseudoscientific formulation of racism that was directly at odds with everything Darwin stood for.

Haeckel’s Grand Oak (1879)

Thirteen years later, Haeckel returned to the Tree of Life in a book called The Evolution of Man. The Tree, as you can see, has flourished. It has grown from a bush into a massive oak that could have come from the deepest glades of the great forests of Europe. As art it is more awe-inspiring than Haeckel’s straggly bush of 1866, but as science it is even more flawed. The extinctions are still missing from the picture and the unwarranted assumption of a universal common ancestor persists; compounding his errors Haeckel has implied a heirarchical structure to the tree with humans, sorry (CAPS-ON) “MAN,” at the top. We even get a box around us to remind us how important we are.

According to Haeckel, the mammalian section of the tree grew out of the trunk marked Amphibia while the reptiles branch off to the side. Actually, mammals and reptiles diverged from common ancestors called the mammal-like reptiles. Humans, snakes, ostriches, as well as the long-gone dinosauria: we are all amniota, but amphibians are not. As errors go this is forgiveable given the lack of information available to Haeckel at the time, but the way he has gone about his error shows his bias towards humanity. Amphibia get their own massive-girthed trunk while the reptiles and birds get a scrawny branch, all because Haeckel didn’t intuit the correct sequence of divergences that lead to nature’s crowning glory (Western European human males, in case you hadn’t guessed).

Against the Tree of Life

The problem with Darwin’s metaphorical Tree of Life is that he derived it from the small subset of living creatures that were available to his observations. For animals, plants, fungi, and other macroscopic creatures, the Tree of Life is a very good representation of the sequence of divergences and extinctions that make up their history. But life goes back a long way before animals and plants and fungi. The oldest fossils known in Darwin’s time came from the Cambrian era, so Darwin only had access to the last sixth of life’s history.

When we look at our smaller cousins, the ones we need microscopes to observe, we notice that they do not reproduce as we do. Bacteria freely swap clusters of genes between each other. Scientists call this sexual transmission, but it is nothing like sexual reproduction in the animal and plant kingdoms. Bacteria even swap these gene clusters between individuals of completely different orders. Unlike mammals, who can only spread their genes into the next generation and only by mating with mammals of the same species, bacteria live in a massive orgy of DNA-mixing that makes the 1970s look like a church fundraiser (unless, that is, your local church is a pentecostalist megachurch). Some biologists even question whether we should use the term “species” when describing bacteria.

As a result, the Tree of Life for micro-organisms such as bacteria and archeans is a swirl of interlocking pathways. In the more extreme cases, not only do organisms swap packets of DNA, but one organism colonises another and comes to live permanently in a state of symbiosis with its host. The early microbes that swalled chloroplasts and mitochondria became the true bacteria. Those that became nucleated and swallowed mitochondria became the eukaryotes — that’s us, by the way, along with plants and fungi and protists.

One of the most vocal advocates of this view if life is W. Ford Doolittle. His map of evolution looks more like a mesh than a tree. He calls it the web of life.

 

There is little doubt that Doolittle’s web is a much better representation of single-celled evolution than Haeckel’s oak. It is also very up-to-date. It really does represent the best current knowledge. I think he has overplayed his hand by assuming the deep roots of the web are a “Common Ancestral Community of Primitive Cells.” It’s not that I disagree with Doolittle. I think a community of primitive cells is a vastly more likely progenitor of life than a single species, but we know so little about that phase of life that I think it is presumptious to map it as factual.

Resurrecting the Tree

Given that Darwin’s Tree is an excellent metaphor for large multicellular life forms and Doolittle’s Web is an excellent metaphor for single-celled organisms, how can we choose between the two? Well actually, we don’t have to. There are many types of tree besides imposing oaks. Here are two common trees that can act as metaphors for both the webbiness and the branchiness of life’s history.

The banyan tree, as illustrated in Nature over 200 years ago.

 

The base of a strangler fig (personal photograph). The upper reaches of mature strangler figs branch just like other trees.

Darwin’s Tree of Life is not entirely outmoded; it still has utility provided one adapts it to meet new evidence and one recalls Darwin’s original intent. The Tree of Life is a metaphor.

[Follows from a previous post]

In one sense, and I am sure this is the sense that New Scientist will use in its defence, the headline is perfectly true. Darwin was wrong. He wrote The Origin of Species in 1859. A small selection of the things he didn’t know about at the time were genetics (Gregor Mendel, 1865/6 but obscure until 1900), germ theory (Robert Koch, 1876), and DNA (first isolated by Freidrich Miescher, 1869, shown to be the molecule of inheritance by Frederick Griffith, 1928, but not really grasped until Crick and Watson described its self-replicating structure, 1953).

Since Darwin did not understand genetics, he made the mistake of assuming that inheritance was mixed like paint rather than discretely like genes. In general, when one looks at the offspring of two adults, the offspring tends to have a mixture of traits from both parents. If a white-skinned person and a black-skinned person mate, their children tend to have light-brown skin. The problem this posed for Darwin was that organisms in a population should mix their heritable characteristics more and more over time. Eventually they should all have much the same heritable features and be virtual clones of each other.

Darwin himself never came up with a solution to this hole in his theory. We know now the answer is that organisms inherit discrete units of inheritance, not mixable traits. Skin colour appears to mix because there are so many genes involved. When traits are determined by very few genes, as in blood type or colour-blindness, then mixing is clearly not a satisfactory explanation. The most dramatic example is sex: if inheritance was mixed, then children of men and women would not be boys and girls but would be mix-gendered instead and after a few generations, we would all be pretty much exactly half-men/half-women. From this single example, it should have been clear for thousands of years that inheritance is not mixed, and yet this did not occur to Darwin nor to anyone else active in science or natural philosophy before him.

In the case of sex in humans, the discrete particles are the X and Y chromosomes. In the case of red-green colour blindness, the discrete particles are two genes on the X chromosome. With blood type, it’s a single gene on chromosome 9. And it’s not just genes that do the discrete inheriting. Eye colour is determined by an interplay of DNA sequences called SNPs (pron. “snips”).

Darwin’s other big problem was that he didn’t know where diversity came from. He would have been happy to push the problem back to Creation, but since he knew that the Earth was at least many millions of years old, he could not explain where new heritable characteristics came from. How could dinosaurs arise from their not-very-dinosaurian ancestors? The answer we now know is mutation. DNA is a very efficient self-replicator, but it is not perfect. Because DNA makes errors when it replicates, new heritable traits are constantly bubbling up in living species.

So did Darwin make mistakes? Of course he did. And these are just his two biggest mistakes; there are many others. But he was right, absolutely right, about what really matters in biology: life evolves, and it does so through descent with modification.

Had New Scientist run an article about Darwin’s errors and what we have learned in the last 150 years, there would be nothing to complain about. Darwin was, after all, trying to practise science and not prophecy, so he expected to make mistakes. But Graham Lawton wasn’t interested in anything as mundane as that. He wanted to create a stir. Unfortunately he did so by making errors of his own that are far more egregious than any Darwin made.

1. Error of fact: Graham Lawton writes, “For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree.” Let’s put this plainly: this is unadulterated bullshit. It would be a fair description of biology before Darwin, which was mostly an exercise in discovering new species on the one hand and trying to fit them into classification systems on the other. But after Darwin, biology exploded — and not just in evolutionary theory. Chemistry became biochemistry. Physics (especially electricity) drove the new science of neurology. Physics and chemistry combined to make physiology. Ecology became a new science. Paleontology boomed. Genetics didn’t even exist until 1900. This statement is about as truthful as saying nothing much happened in engineering between the the Second Industrial Revolution’s steam engines and the release of the iPhone. 

The idea that biology stood motionless under the baleful glare of Darwinism is an invention of Lawton’s intended to make his story appear more revolutionary. He’s not doing journalism, he’s doing side-show spruiking. Roll up! Roll up! Come see the amazing Wolfman! Only when you get into the tent, you find the Wolfman is an alcoholic layabout who hasn’t shaved for ten years and whose only remaining teeth are his canines.

2. Exaggeration and misdirection: Lawton writes as if he’s got hold of a stunning new development. In fact, what he is arguing is that the “Tree of Life” metaphor fails because life doesn’t just branch outwards. Sometimes genes are transferred not by direct descent but by swapping from one organism to another — often from completely different species. This is known as horizontal gene transfer (as opposed to “vertical” gene transfer when you inherit DNA from your parents). We now know that horizontal gene transfer has been a lot more important in evolution than we used to think. Where it was once considered to be a relatively uncommon process, we have now accumulated evidence that it may have been a major force behind evolution. As some writers have put it, the Tree of Life is really more of a web than a tree. But this is not especially controversial.

Despite Lawton’s best efforts to make this look like some internecine feud between scientists, the only ongoing debate is about the degree to which horizontal gene transfer has influenced evolution. HGT (to abbreviate) was first described back in 1959. Like Mendel’s work, this paper was not recognised until much later. It was not until 1984 that HGT became a big research field. But that’s still 25 years ago and Lawton is acting like it’s some extraordinary revelation.

3. Error of fact: “As early as 1993, some were proposing that for bacteria and archaea the tree of life was more like a web,” says Lawton. Rubbish again! The “webbiness” of life was understood a long time before 1993. Not only was HGT (and its ramifications) understood, there is a related concept called endosymbiosis, where one organism becomes symbiotic with another inside it, which was detailed by Lynn Margulis in 1970. She was very sharp in pointing out what this meant for evolution — it wasn’t just about competition; co-operation was just as important. “Life did not take over the globe by combat, but by networking.” She was certainly aware of the “webbiness” this implied, saying (admittedly later) “the tree of life often grows in on itself.” But even 1970 wasn’t the first mention of endosymbiosis — the idea was proposed, with good evidence, by Konstantin Mereschkowski back in 1905! Lawton could have found all this out by checking Wikipedia.

Does this matter? A little pizazz is always welcome in science journalism, but one has to draw the line when the pizazz distracts from important truths rather than drawing light to them. What really, really irks me about this story is that it covers exactly the same ground, and interviews exactly the same people, about exactly the same research paper as a much better article written nearly two years ago by Lisa Zyga.

Ms Zyga was capable of writing a fascinating article without misrepresenting anything and in about a fifth the word-length. Given the remarkable similarities, I wonder if Mr Lawton read Ms Zyga’s piece. I’m not suggesting plagiarism (Lawton might have written a decent article if he had) and in fact I’d suggest Lawton should have read Ms Zyga’s article prior to going to press. If he had done so, he would have been much better equipped to deal with the scientific concept he so clearly fails to understand.

4. Error of Fact: Lawton says,

The tree-of-life concept was absolutely central to Darwin’s thinking, equal in importance to natural selection, according to biologist W. Ford Doolittle of Dalhousie University in Halifax, Nova Scotia, Canada. Without it the theory of evolution would never have happened. The tree also helped carry the day for evolution. Darwin argued successfully that the tree of life was a fact of nature, plain for all to see though in need of explanation. The explanation he came up with was evolution by natural selection.

Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth. At its base is LUCA, the Last Universal Common Ancestor of all living things, and out of LUCA grows a trunk, which splits again and again to create a vast, bifurcating tree.

But this is completely wrong. For one thing, Lawton is confusing the Darwin with later biologists who expanded the Tree of Life metaphor into areas Darwin himself could not have contemplated. Darwin himself had nothing to say about a Last Universal Common Ancestor because he had no way of knowing anything about the subject. Darwin suggested that modern species had common ancestors, but he made no predictions about whether there was one or many common ancestors. It is also untrue that the theory of evolution would never have arisen without the Tree metaphor. There were many pillars of evidence that Darwin drew on. The common features of related species was only one of them. I understand that Lawton is quoting another scientist here, but to repeat such a quote uncritically does not indicate good research.

In comparison, here’s Zyga’s take:

While parts of evolution certainly are tree-like, other parts may be nets or webs or other complex models. Most importantly, however, there seems to be no “theory of everything” in evolution, no metanarrative to unify all life forms…

As for any blow to Darwin’s ego, the scientists [Doolittle and Baptestse, the same scientists interviewed by Lawton] point out that he never wrote about reconstructing the tree in an attempt to relate every living thing, but rather used the model as a general guide.

“I’d like to think he would adjust,” Doolittle said about Darwin. “After all, his theory was developed before there was any understanding of genetics and when bacteria were still believed to be spontaneously generated.”

Isn’t it amazing? If you actually know the history of Darwinism and you quote scientists in a more reasonable manner, you get a story that is just as interesting without all the puffed-up conflict and inflated sense of revolution. And what’s more, you can do it two years ago!

5. Pandering to the barbarians at the gate: It has been less than a week since New Scientist ran this story and already it has been quoted by creationists trying to push anti-evolutionary material into the Texas school curriculum. [More on this at Panda's Thumb.] You may note, as further evidence of New Scientist’s intransigence, that they reported on this development without mentioning that the creationists were referring to a New Scientist story.

Next: Not dead yet: the Tree of Life as an active metaphor

Observe the New Scientist cover above.

This is the final straw for me. I used to subscribe to New Scientist, but after reading a series of very poor articles I let the subscription lapse. Since then, I have bought a few issues from the newsstand and I see the occasional story referred on by email, and I am saddened by its descent from a truly grand science magazine into a venue for anti-scientific tripe. (See also this open letter written by Greg Egan criticising a cover article full of pseudo-physics.) At this point, I have gone beyond being disappointed in New Scientist. Dismayed and mistrustful would be better words now.

So what is wrong with this story? Well, in a nutshell, it is not the topic per se — the article by Graham Lawton explores several views on a concept that is well worth writing about: that is, one of the metaphors Darwin used to explain evolution is deficient as a total theory of biology. There are, however, a number of flaws in the article, not the least of which being that Darwin never intended the Tree of Life to be a total theory of biology and always presented it as a metaphor to aid understanding.

But the New Scientist editorial team has elevated the feature to utter irresponsibility by promoting it to the cover with a graphic that looks like it was designed to win the admiration of ID theorists and creationists. Indeed, in less than the two days since the issue came out, the cover has already been seized upon as a propaganda coup by the Discovery Institute and by anti-evolution Catholics.

There is no crime in being misrepresented by creationists. All the best scientists have been — but let’s be very clear, (i) the cover implies that Darwin was wrong fundamentally, and so is evolution — that’s exactly what readers would expect in stories similarly titled “Freud was wrong!” (and so is his psychoanalytic theory) or “Copernicus was wrong!” (and so is heliocentrism), and (ii) there is no way known that New Scientist ran that cover without knowing that it would give succour to creationists.

Even in the UK, around a third of people are either skeptical or outright hostile towards evolution, and even more appalling, a recent survey showed 29% of UK science teachers think it is a good idea to teach creationism alongside evolution in science classes. While New Scientist may not be aware of these particular poll results, it is certainly aware of the underlying trend because it has reported on it many times before. And so, in this environment, any story by New Scientist that appears to add weight to the anti-evolution argument will be seized upon by active creationist organisations, but even more critically, people who have simply drifted into creationism because of their parents’ beliefs or because they were exposed to anti-evolution propaganda in the more retrogressive faith schools, or simply because they keep reading news reports about overthrowing Darwin — after all, this story has already been picked up from New Scientist and repackaged by the Daily Telegraph and the Guardian. It’s not just the lay public who respond to these stories, it is also journalists under pressure to provide new stories, and if New Scientist runs it on its cover, then the majority of journalists (most of whom have no science training) will assume the story is sound and feel safe in repeating it uncritically.

But worst of all is the fact that the general public does not get many ideas from articles and fine-tuned argumentation. Life is too short to develop deep knowledge about everything. Instead, most people absorb the cultural messages around them. The only message most people will take in is from seeing the front cover of New Scientist as they walk past the newsstand; millions of people will brush past and take on board the message that one of the most respected science magazines has announced that Darwin was wrong. Very few will buy the magazine to read the article, which is the only way they will learn that the story is only about a metaphor that Darwin used and not a critique of the theory of evolution.

There is no defence for New Scientist on this one.

Next: A guide to the errors in the New Scientist article.
Next+1: Why Darwin made mistakes but the Tree of Life wasn’t one of them