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Why Darwin was wrong about the tree of life

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IN JULY 1837, Charles Darwin had a flash of inspiration. In his study at his house in London, he turned to a new page in his red leather notebook and wrote, "I think". Then he drew a spindly sketch of a tree.

As far as we know, this was the first time Darwin toyed with the concept of a "tree of life" to explain the evolutionary relationships between different species. It was to prove a fruitful idea: by the time he published On The Origin of Species 22 years later, Darwin's spindly tree had grown into a mighty oak. The book contains numerous references to the tree and its only diagram is of a branching structure showing how one species can evolve into many.

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...

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. Each branch represents a single species; branching points are where one species becomes two. Most branches eventually come to a dead end as species go extinct, but some reach right to the top - these are living species. The tree is thus a record of how every species that ever lived is related to all others right back to the origin of life.

...The green and budding twigs may represent existing species, and those produced during each former year may represent the long succession of extinct species

For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

So what happened? In a nutshell, DNA. The discovery of the structure of DNA in 1953 opened up new vistas for evolutionary biology. Here, at last, was the very stuff of inheritance into which was surely written the history of life, if only we knew how to decode it. Thus was born the field of molecular evolution, and as techniques became available to read DNA sequences and those of other biomolecules such as RNA and proteins, its pioneers came to believe that it would provide proof positive of Darwin's tree of life. The basic idea was simple: the more closely related two species are (or the more recently their branches on the tree split), the more alike their DNA, RNA and protein sequences ought to be.

It started well. The first molecules to be sequenced were RNAs found in ribosomes, the cell's protein-making machines. In the 1970s, by comparing RNA sequences from various plants, animals and microorganisms, molecular biologists began to sketch the outlines of a tree. This led to, among other successes, the unexpected discovery of a previously unknown major branch of the tree of life, the unicellular archaea, which were previously thought to be bacteria.

By the mid-1980s there was great optimism that molecular techniques would finally reveal the universal tree of life in all its glory. Ironically, the opposite happened.

The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.

Which was correct? Paradoxically, both - but only if the main premise underpinning Darwin's tree was incorrect. Darwin assumed that descent was exclusively "vertical", with organisms passing traits down to their offspring. But what if species also routinely swapped genetic material with other species, or hybridised with them? Then that neat branching pattern would quickly degenerate into an impenetrable thicket of interrelatedness, with species being closely related in some respects but not others.

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Have your say
Comments 1 | 2 | 3 | 4

Science Is Dead

Wed Jan 21 18:21:59 GMT 2009 by Polemos

Darwin was wrong in all respects. The universal time itself is nonlinear and forms a closed loop. The effect influences the cause and thus eliminates determinism.

Science is dead. Intuitive pattern recognition is the only valid way of studying the universe.

Science Is Dead

Wed Jan 21 18:34:07 GMT 2009 by Earth to Polemos

Hurfa durfa huuuuuur. Hurfa huuuuuuur. Duuuuuuuuuuuuuuuur. You're not very good at thinking are you?

Science Is Dead

Wed Jan 21 18:53:51 GMT 2009 by Dr Braun

http://en.wikipedia.org/wiki/Asperger_syndrome

I believe this link summarizes Polemos's condition.

"It is characterized by qualitative impairment in social interaction, by stereotyped and restricted patterns of behavior, activities and interests"

and

"People with Asperger syndrome often display behavior, interests, and activities that are restricted and repetitive and are sometimes abnormally intense or focused"

Oh, and my favourite quote: "Speech may convey a sense of incoherence; the conversational style often includes monologues about topics that bore the listener"

Science Is Dead

Wed Jan 21 19:08:05 GMT 2009 by Tyler

I've got Asperger's, and I have to say that I'm not pleased that you are using it to negatively characterize the author. To me it's comes across the same as calling him a 'stinking Arab' or a 'dirty Jew'.

Science Is Dead

Wed Jan 21 19:11:33 GMT 2009 by Polemos

"abnormally intense or focused" = abnormally coherent. Like laser light.

I like it. Thanks, Emmett.

Science Is Dead

Wed Jan 21 21:33:41 GMT 2009 by PM

I have Asperger's, and while it's possible that Polemos has the condition, it wouldn't be the primary contributer to his 'creative' way of thinking and I see no evidence that he has it. He strikes me as suffering from schizophrenia; he exhibits a marked dysfunction in his ability to assimilate information and draw rational conclusions from it, which is a form of psychosis that's fairly common in schizophrenics.

People with Asperger's often have uncommon opinions, but we're also usually quite excellent at and enthusiastic about defending our opinions through reasoned debate, while Polemos has, to my knowledge, made no attempt at a reasoned defense of his position, preferring instead to simply reiterate it at every opportunity and without regard to it's relevance to the subject at hand.

If you look up the writings of Francis E. Dec, you may notice the similarities, and there are some very amusing audio renditions of his rants. Francis Dec in all likelyhood suffered from a particularly severe case of schizophrenia and he became increasingly psychotic with time as his condition deteriorated, as evidenced by his personal writings/ravings and his public dealings.

Science Is Dead

Wed Jan 21 18:39:01 GMT 2009 by Polemos

One feature of a closed time-loke curve (CTC) is that it opens the possibility of a worldline which is not connected to earlier times, and so the existence of events that cannot be traced to an earlier cause. Ordinarily, causality demands that each event in spacetime is preceded by its cause in every rest frame. This principle is critical in determinism, which in the language of general relativity states complete knowledge of the universe on a spacelike Cauchy surface can be used to calculate the complete state of the rest of spacetime. However, in a CTC, causality breaks down, because an event can be "simultaneous" with its cause--in some sense an event may be able to cause itself. It is impossible to determine based only on knowledge of the past whether or not something exists in the CTC that can interfere with other objects in spacetime. A CTC therefore results in a Cauchy horizon, and a region of spacetime that cannot be predicted from perfect knowledge of some past time. (http://en.wikipedia.org/wiki/Closed_timelike_curve#Consequences )

Science Is Dead

Wed Jan 21 19:06:19 GMT 2009 by Polemos

Time = gravity.

Space (history, the collection of all moments of time) = gravity looped back upon itself.

Thus, history (=evolution) is noncausal and indeterministic.

***

"This is where Amos Ori from Technion, the Israel Institute of Technology in Haifa, comes in. He says that according to Einstein's theories, space can be twisted enough to create a local gravity field that looks like a doughnut of some arbitrary size. The gravitational field lines circle around the outside of this doughnut, so that space and time are both tightly curved back on themselves. Crucially, this does away with the need for any hypothetical exotic matter.

Although it is difficult to describe what this would look or be like in real life, Ori says the mathematics reveal that every period of time between when the doughnut was created and the present moment would be somewhere in the vacuum inside the doughnut."

(http://www.nature.com/news/2005/050711/full/news050711-4.html )

Science Is Dead

Wed Jan 21 19:37:12 GMT 2009 by BostonEddie

You do know that brane theory depends on continuous matrices? These theories don't work if space is shaped like a doughnut hole. Try making a doughnut shape out of an infinitely long and wide flat sheet without puncturing. Can't do it.

Show me the math otherwise, not just hot air.

Science Is Dead

Wed Jan 21 19:55:17 GMT 2009 by bostonEddie

I ran down the reference. The Nature paper is only available by subscription. OTOH, Ori's paper on his time machine says:

http://arxiv.org/abs/gr-qc/0503077

"...Stability is the only question."

So Ori's time machine is not a device that is as yet even theoretically possible in the physical universe.

Science Is Dead

Wed Jan 21 22:48:45 GMT 2009 by Jason

I like chocolate doughnuts with chocolate sprinkes. Yuuuummmyyy!

Science Is Dead

Wed Jan 21 22:06:08 GMT 2009 by Joker

Polemos, this article's about Darwin. It's Biology not Physics.

Can I point this out without getting ranted or insulted?

Science Is Dead

Wed Jan 21 23:21:35 GMT 2009 by Mike Gale

The curse of the commons the curse of the commons.

Somebody who goes completely of any target you wouls recognise steals your time and eliminates your desire to debate.

Now to my point.

The article is framed as cutting down, eliminating, taking the axe to "the tree". What a load of baloney.

The tree is valuable. It's a first approximate it now needs decorating, refining and improving. It has always evolved.

In my mind that evolution is a tree that then grows "lianas" from one twig to another resulting in a much more interesting structure.

Lets get away from sensationalist Darwin is Wrong headlines. Please give us careful thought. Hopefully this is still science and not journalism (which is often a fact free pursuit).

Otherwise the writers are not much different from Polemon.

Science Is Dead

Thu Jan 22 00:16:33 GMT 2009 by Heath

It's probably a fuzzy tree.

Science Is Dead

Thu Jan 22 03:01:12 GMT 2009 by N. Roberts

Oh dear...

While this is an excellent article, perhaps downplaying the central twig of the web of life (or the thicket of life) a little, it invites creationist lobbies to lampoon evolution (and science in general) as well as misrepresenting science. When a scientist is wrong about a detail of his theory (by the sounds of it, the tree was the inferred form of interrelations between species, based on all available evidence), it does not call for a triumphant 'HA!' at the person's grave. Personally, I think he would respond with 'thank you and congratulations.'



N.B. You know that wall of Science articles (mostly NS) at the Creationist Museum NewScientist published an article about? This cover will probably be the A1 sized, gilt and framed centerpiece before the week is out.

Science Is Dead

Thu Jan 22 02:21:28 GMT 2009 by Ron

I reakon we all get together and grab a few Planck's and beat the Brane's out of Polemos.

Science Is Dead

Thu Jan 22 03:20:36 GMT 2009 by Ron

Reakon,reckon,wrecken,sh-t,maybe I am getting wrrecked to often.

Oh, Pass My Salts!

Wed Jan 21 18:41:39 GMT 2009 by bostonEddie

What? Some details of Darwin's theory were wrong? You mean science has made new discoveries in the last 150 years and new data has led to modifications of a minor detail of a well established scientific theory? How unthinkable!

Why, science should never change any of it's theories! Every detail of every scientific theory must be unchangable, true and immutable in every way for all time if it is to be valid! Science should be just like religion!

Geez, I swear, every time things get dull around the NS offices they dredge out some half-assed half-understood article about evolution or science in general and hype it up.

Oh, Pass My Salts!

Wed Jan 21 19:01:01 GMT 2009 by Russell

Amen to that :)

Oh, Pass My Salts!

Wed Jan 21 19:18:15 GMT 2009 by Eric M. Jones

Double amen to that :)

Oh, Pass My Salts!

Wed Jan 21 20:38:41 GMT 2009 by Jeremy

I tend to agree. And they hype up everything.

The notion of a traditional tree does not easily allow for backbreeding or successful breeding between two closely-related species.

Still, the tree concept was once revolutionary and inspirational. It still basically works. But horizontal gene transfer (HGT) is something new to many people who never went beyond more basic biology, and as the article says there is still a lot to find out: how much has occurred, how it makes us what we are, and its mechanisms of action.

Perhaps the concept of a trailing vine that periodically re-roots itself into the soil (to get HGT from bacteria) and sequentially dies off at its old roots is more apt.

Various models could be visualized and simulated with computer graphics nowadays.

The part about the larvae was particularly interesting.

Oh, Pass My Salts!

Wed Jan 21 21:17:51 GMT 2009 by Anonymous

Triple amen to that, even! :)

Oh, Pass My Salts!

Thu Jan 22 08:12:13 GMT 2009 by SDee

You miss the point.

The "tree view" or vertical gene transfer is what most people intuitively see and regard as normal.

Although many people understand the science, this view of normality causes a back lash against the ideas genetic engineering because people feel it is "not normal" and so in some way not moral.

What the article is challenging is the residual belief in the model we have been using and noting the surprising resistance to change despite the plethora of evidence pointing towards a different model

The web view, with horizontal gene transfer as being almost as important as vertical, challenges most lay peoples current way of thinking about life.

This is of relavance to the scientific community because horizontal gene transfer is in parts more akin to genetic engineering.

Getting people to switch their mental modal and understanding the ubiquity of horizontal gene transfer, then getting them to accept it as their world view is really a paradigm shift and worth of the comment that Darwins model was wrong give or take a bit of journalistic license.

How Do We Define "species"?

Wed Jan 21 19:09:30 GMT 2009 by Maquiavelo

Which is the defining criterion for a species? Is it not that two individuals that belong to the same species (and are not hampered by unilateral health issues that cause infertitlity) are able to produce fertile offspring? Whereas two individuals that can produce fertile offspring with others, but not with one another, due to their genetic divergence, are separated by the genetic boundary between two different species?

Should the genetic ability to produce fertile offspring not count as the (combining and isolating) criterion for a species, rather than some anatomic similarities?

Which is the criterion used to distinguish between different "species" of sea urchins, although they arise from "near-identical" larvae? Can the adult larvae still interbreed? Then their differentiation in several species seems superficial - aren't they subspecies rather than species that are separated by a genetic boundary?

Can they not interbreed, or only in 1-in-a million random event, when biochemical circumstances provide an exceptional fit? Then the observed similarity between their larvae seems superficial.

The lateral gene transfer between monocellular organisms makes the definition of "offspring" more difficult, though. Should the term "species" be applied to organisms that swap chunks of their genetic material in routine fly-bys? Some kind of genetic core must remain stable between generations, though, or else there would be no such characteristics as make certain archaea identifiable and distinguishable from others. Since most monocellular organisms are not dependent on a partner to procreate, it seems to find another criterion for them, which is more fuzzy than the ability to procreate with a partner organism: something like "replication stability"? This means that organisms that can replicate without having to merge gene material with a partner organism would morph into a different "species", once they accumulate too many genetic differences from their ancestor(s). The question of what defines "too many" would be a matter of degree and open to case-by-case assessments. So instead of the word "species", we should perhaps use something like "geniton", borrowed from soliton (for waves that remain stable for a time, but can interact with other solitons and emerge from "collisions" unchanged but for phase shifts).

For organisms that cannot swap packages of genetic material other than by mating, though - why should we not apply the sharp criterion "ability to produce fertile offspring"with one another to group individuals within one species and separate them from other species?

How Do We Define "species"?

Wed Jan 21 19:26:58 GMT 2009 by bostonCharlie

"For organisms that cannot swap packages of genetic material other than by mating, though - why should we not apply the sharp criterion "ability to produce fertile offspring"with one another to group individuals within one species and separate them from other species?"

(Despite Dr Asimov) There are fertile mules. The definition of species, as with many Aristotelian definitions, is not as hard and fast and all encompassing as is commonly imagined.

And how would you prove a Neanderthal and a modern H. sap is or is not a similar species?

How Do We Define "species"?

Wed Jan 21 23:31:17 GMT 2009 by Jason

We could use Poleman's doughnut theory to throw him back in time, ask him to mate with a neanderthal, return to the present and give us the facts.

How Do We Define "species"?

Thu Jan 22 00:04:45 GMT 2009 by Polemos

I have no desire to ameliorate your lineage, Jason. Stay purebred

Comments 1 | 2 | 3 | 4

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This "Tree of Life" sketch is seen in Darwin's "B" notebook, at a press preview of the new "Darwin" exhibition at the American Museum of Natural History November 15, 2005 in New York City (Image: Mario Tama / Getty)

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