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Author Topic: Why Darwin was wrong about the tree of life  (Read 11901 times)

paul.fr

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Why Darwin was wrong about the tree of life
« on: 23/01/2009 19:10:06 »
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 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.

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.

We now know that this is exactly what happens. As more and more genes were sequenced, it became clear that the patterns of relatedness could only be explained if bacteria and archaea were routinely swapping genetic material with other species - often across huge taxonomic distances - in a process called horizontal gene transfer (HGT).

At first HGT was assumed to be a minor player, transferring only "optional extra" functions such as antibiotic resistance. Core biological functions such as DNA replication and protein synthesis were still thought to be passed on vertically. For a while, this allowed evolutionary biologists to accept HGT without jeopardising their precious tree of life; HGT was merely noise blurring its edges. We now know that view is wrong. "There's promiscuous exchange of genetic information across diverse groups," says Michael Rose, an evolutionary biologist at the University of California, Irvine..........

http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html?full=true


 

lyner

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Why Darwin was wrong about the tree of life
« Reply #1 on: 23/01/2009 22:25:33 »
Bearing in mind that Science advances as knowledge increases, what's your beef with poor old Charles? Didn't he, in fact, do quite well?
 

Offline DoctorBeaver

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Why Darwin was wrong about the tree of life
« Reply #2 on: 23/01/2009 23:06:34 »


Didn't he do well
 

paul.fr

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Why Darwin was wrong about the tree of life
« Reply #3 on: 24/01/2009 13:30:40 »
Bearing in mind that Science advances as knowledge increases, what's your beef with poor old Charles? Didn't he, in fact, do quite well?

"Sophie", I was merely posting an interesting article "higher". No comment "lower".

(ermmmmm, dolly dealers!)
 

Offline DoctorBeaver

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Why Darwin was wrong about the tree of life
« Reply #4 on: 24/01/2009 13:34:37 »
Does that make me a member of the STB?
 

Offline Don_1

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Why Darwin was wrong about the tree of life
« Reply #5 on: 24/01/2009 13:49:32 »
Does that make me a member of the STB?

I think you already were a member. I also think I could do with a snack.
 

lyner

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Why Darwin was wrong about the tree of life
« Reply #6 on: 25/01/2009 20:23:55 »
SDB = ?
(sorry)
 

paul.fr

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Why Darwin was wrong about the tree of life
« Reply #7 on: 26/01/2009 15:02:22 »
STB=?
 

Offline dentstudent

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paul.fr

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Why Darwin was wrong about the tree of life
« Reply #9 on: 26/01/2009 15:20:19 »
Yes I saw that, but the topic title asks the question "Do you have STB syndrome?", but fails to tell you what the syndrome is!
 

Offline dentstudent

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Why Darwin was wrong about the tree of life
« Reply #10 on: 26/01/2009 15:23:21 »
Yes I saw that, but the topic title asks the question "Do you have STB syndrome?", but fails to tell you what the syndrome is!

I'm SURE it says it at the beginning...
 

lyner

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Why Darwin was wrong about the tree of life
« Reply #11 on: 26/01/2009 19:25:50 »
Paul
Let's ignore the diversions. (Adopts po face)
This is interesting as it could account for some very radical changes taking place in just one generation, and could account for the lack of fossil evidence of intermediate versions.
It brings into doubt the 'school' definition of a species, based on ability to reproduce successfully.
 

Offline Asyncritus

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Why Darwin was wrong about the tree of life
« Reply #12 on: 18/03/2009 14:07:20 »
Alas, Darwin, and his followers are all up a tree with no way down.

How come?

Because there are zillions of new species, families, phyla right there in the Cambrian, the lowest stratum with any really significant amounts of fossils.

Darwin's tree should be lying on its side, not growing up!

Here's a nice reference for you all:

Then, between about 570 and 530 million years ago, another burst of diversification occurred, with the eventual appearance of the lineages of almost all animals living today. This stunning and unique evolutionary flowering is termed the "Cambrian explosion," taking the name of the geological age in whose early part it occurred. But it was not as rapid as an explosion: the changes seems to have happened in a range of about 30 million years, and some stages took 5 to 10 million years.
http://www.pbs.org/wgbh/evolution/library/03/4/l_034_02.html

Note the word 'explosion'! Right up the evolutionist's trouserlegs. ::)
« Last Edit: 18/03/2009 14:21:29 by Asyncritus »
 

Offline Don_1

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Why Darwin was wrong about the tree of life
« Reply #13 on: 18/03/2009 16:46:36 »
OK, fine, I give up. I am now a convert to creationism. We were all created by God, as the Bible tells us, around 6000 years ago.

I have no idea how those damned Egyptians managed to formulate society 7000 years ago and what the devil were dinosaurs doing 100 million years ago? But of course, how silly of me, it was a miracle!!!

Do you detect an air of sarcasm here?
 

Offline dentstudent

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Why Darwin was wrong about the tree of life
« Reply #14 on: 18/03/2009 16:50:04 »
Go on, ask me a question.

Answer: God did it.

Go on, ask me another question.

Answer: God did it.

Another?

Answer: God did it.

God did it.

God did it.

God did it.

God did it.

God did it.

God did it.

It's a safe life, but Jesus it must be boring.
 

Offline Don_1

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Why Darwin was wrong about the tree of life
« Reply #15 on: 18/03/2009 16:57:46 »
Good grief!!!!

You have answered all the questions correctly. Go to the top of the class, collect £200 as you pass 'GO'.

I'm afraid I got one answer wrong:-
Q) If x is equal to D(42 + y) explain R.
A) God did it.

I gave the answer 'My Mum did it'. Silly me.
 

Offline dentstudent

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Why Darwin was wrong about the tree of life
« Reply #16 on: 19/03/2009 07:54:18 »
Good grief!!!!

You have answered all the questions correctly. Go to the top of the class, collect £200 as you pass 'GO'.

I'm afraid I got one answer wrong:-
Q) If x is equal to D(42 + y) explain R.
A) God did it.

I gave the answer 'My Mum did it'. Silly me.

My answer here was "My dog ate it". Naughty step time...
 

Offline Andrew K Fletcher

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Why Darwin was wrong about the tree of life
« Reply #17 on: 19/03/2009 09:23:05 »
Good post Paul, Enjoyed reading it very much. Evolution has many branches. Gravity plays a vital roll in evolution, yet has been ignored. Only recently have NASA and other space based programmes began to understand the rapid cellular changes apparent in micro gravity environment.

Our own physiology is altered in space through rapid degeneration. Sperm motility for example is totally confused by the reduction in gravity, so why not investigate how gravity drives the fluids to begin to understand how evolutionary processes work? After all we are all here on Earth under itís influence, so it would be folly to ignore this powerful force.
 

Offline Asyncritus

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Why Darwin was wrong about the tree of life
« Reply #18 on: 19/03/2009 19:47:28 »
OK, fine, I give up. I am now a convert to creationism. We were all created by God, as the Bible tells us, around 6000 years ago.

I have no idea how those damned Egyptians managed to formulate society 7000 years ago and what the devil were dinosaurs doing 100 million years ago? But of course, how silly of me, it was a miracle!!!

Do you detect an air of sarcasm here?

Yeh, I do.

What I DON'T detect is any semblance of an answer to the point.
 

Offline Asyncritus

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Why Darwin was wrong about the tree of life
« Reply #19 on: 19/03/2009 19:49:52 »
Go on, ask me a question.

Answer: God did it.

Go on, ask me another question.

Answer: God did it.

Another?

Answer: God did it.

God did it.

God did it.

God did it.

God did it.

God did it.

God did it.

It's a safe life, but Jesus it must be boring.

Um, what's your comment/ answer to the palaeontology quote I made?

I know - anything but God did it!

I got that right?
« Last Edit: 19/03/2009 20:00:12 by Asyncritus »
 

Offline Bored chemist

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Why Darwin was wrong about the tree of life
« Reply #20 on: 19/03/2009 19:50:21 »
"What I DON'T detect is any semblance of an answer to the point."
Allow me to reiterate it for you
"Bearing in mind that Science advances as knowledge increases, what's your beef with poor old Charles? Didn't he, in fact, do quite well?".

The reason he got it "wrong" was that he was working with a rather incomplete data set.
 

Offline Asyncritus

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Why Darwin was wrong about the tree of life
« Reply #21 on: 19/03/2009 19:52:00 »
OK, fine, I give up. I am now a convert to creationism. We were all created by God, as the Bible tells us, around 6000 years ago.

The Bible says nothing of the sort. Usher said so, but as far as I'm concerned that's tripe.
 

Offline Asyncritus

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Why Darwin was wrong about the tree of life
« Reply #22 on: 19/03/2009 19:58:29 »
"What I DON'T detect is any semblance of an answer to the point."
Allow me to reiterate it for you
"Bearing in mind that Science advances as knowledge increases, what's your beef with poor old Charles? Didn't he, in fact, do quite well?".

The reason he got it "wrong" was that he was working with a rather incomplete data set.


Well, the data is now pretty complete, in fact it is embarrassingly so, because zillions of specimens are waiting to be catalogued. Here's Olsen:

After a century of further searching and examination of the fossil record, many paleontologists are beginning to believe that the fossil record is complete since none of the gaps in the fossil record that existed in Darwin's time has been filled by subsequent study. E.C. Olson observes,

"A third fundamental aspect of the record is somewhat different. Many new groups of plants and animals suddenly appear, apparently without any close ancestors .... This aspect of the record is real, not merely the result of faulty or biased collecting. A satisfactory theory of evolution must take it into consideration and provide an explanation."

I've yet to see an 'explanation'! Got one? Or two, or....?
« Last Edit: 19/03/2009 20:01:29 by Asyncritus »
 

lyner

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Why Darwin was wrong about the tree of life
« Reply #23 on: 20/03/2009 15:34:51 »
I think you've got it wrong about fossils. They are formed under fairly special conditions and not be some zealous zoologist collector. The data is far from complete, as you might expect.
Btw, what data do you have for your theory?
 

Offline _Stefan_

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Why Darwin was wrong about the tree of life
« Reply #24 on: 21/03/2009 01:27:19 »
Even if there were no fossils, comparative DNA analysis, developmental biology and several other areas of research all confirm evolution by producing fairly detailed and accurate information. Fossils are really just a bonus.

Oh, but Asyncritus doesn't even accept that DNA analysis is valid.
 

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Why Darwin was wrong about the tree of life
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