Why Darwin was wrong about the tree of life

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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

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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?

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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
Fledgling science site at http://www.sciencefile.org/SF/content/view/54/98/ needs members and original articles. If you can help, please join.

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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!)

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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?
Fledgling science site at http://www.sciencefile.org/SF/content/view/54/98/ needs members and original articles. If you can help, please join.

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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.
If brains were made of dynamite, I wouldn't have enough to blow my nose.

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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)

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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=?

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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!

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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...

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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.

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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 »
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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?
If brains were made of dynamite, I wouldn't have enough to blow my nose.

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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.

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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.
If brains were made of dynamite, I wouldn't have enough to blow my nose.

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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...

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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.
Science is continually evolving. Nothing is set in stone. Question everything and everyone. Always consider vested interests as a reason for miss-direction. But most of all explore and find answers that you are comfortable with

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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.
Remember, the organ of thought is the brain, not the oesophagus!

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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 »
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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.
Please disregard all previous signatures.

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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.
Remember, the organ of thought is the brain, not the oesophagus!

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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 »
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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?

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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.
Stefan
"No testimony is sufficient to establish a miracle, unless the testimony be of such a kind, that its falsehood would be more miraculous than the fact which it endeavors to establish." -David Hume

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Offline Asyncritus

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Why Darwin was wrong about the tree of life
« Reply #25 on: 21/03/2009 01:55:03 »
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?

Try and get this Sophie. It's really not too difficult to follow.

Darwin's idea of the incompleteness of the fossil record was complete nonsense. There are so many fossils available today, that argument is a complete non-starter.

"Well, we are now about 120 years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn't changed much. The record of evolution is still surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than we had in Darwin's time. By this I mean that some of the classic cases of Darwinian change in the fossil record, such as the evolution of the horse in North America, have had to be discarded or modified as a result of more detailed information - what appeared to be a nice simple progression when relatively few data were available now appears to be much more complex and much less gradualistic. So Darwin's problem has not been alleviated in the last 120 years and we still have a record which does show change but one that can hardly be looked upon as the most reasonable consequence of natural selection."

David M. Raup, "Conflicts Between Darwin and Paleontology," Field Museum of Natural History Bulletin, Vol. 50, No. 1, January 1979, p. 25. (He says a similar thing on p. 50.)

http://evolution-facts.org/New-material/Cambrian%20Explosion.pdf

As Darwin himself wrote, before the different phyla appeared there must have been "vast periods" during which "the world swarmed with living creatures" (Excerpt A, p. 83). In the fossil record, however, most of the major animal phyla appear fully formed at the beginning of the geological period known as the Cambrian, with no fossil evidence that they branched off from a common ancestor. Darwin was aware of this, acknowledging in The Origin of Species that "several of the main divisions of the animal kingdom suddenly appear in the lowest known fossiliferous rocks." He called this a "serious" problem which "at present must remain inexplicable; and may be truly urged as a valid argument against the views
here entertained" (Excerpt A, pp. 82, 85).
(A) Charles Darwin, The Origin of Species, Sixth Edition (New York: D,
Appleton, 1890), Chapter X.

What significance does the Cambrian explosion have for evaluating Darwin's theory that all animals are modified descendants of a common ancestor? As we have seen, Darwin himself considered it a serious problem (Excerpt A). Although Darwin's theory predicts that animal evolution should proceed from the "bottom up," with the largest differences emerging last, James Valentine and his colleagues wrote in 1991 that
the pattern of the Cambrian explosion "creates the impression that metazoan evolution has by and large proceeded from the 'top down' " (Excerpt B, p. 294).

Harry Whittington,an expert on the Cambrian fossils from the Burgess shale, wrote in 1985:

"It may well be that metazoan animals arose independently in different areas. I look sceptically upon diagrams that show the branching diversity of animal life through time, and come down at the base to a single kind of animal" (Excerpt F, p. 131).

Evolutionary biologist Jeffrey Levinton, though convinced of the common ancestry of animals, acknowledged in 1992 that the Cambrian explosion -- "life's big bang," as he called it -- remains "evolutionary biology's deepest paradox" (Excerpt G, p. 84). Although "the body plans that evolved in the Cambrian by and large served as the blueprints for those seen today,"

Levinton saw "no reason to think that the rate of evolution was ever slower or faster than it is now. Yet that conclusion still leaves unanswered the paradox posed by the Cambrian explosion and the mysterious persistence of those ancient body plans" (Excerpt G, pp. 84, 90).

In 1999,University of California biologist Malcolm Gordon wrote: "Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes)" (Excerpt H, p. 331).

Gordon concluded: "The traditional version of the theory of common descent apparently does not apply to kingdoms [i.e., plants, animals, fungi, bacteria] as presently recognized.
It probably does not apply to many, if not all, phyla, and possibly also not to many classes within the phyla" (Excerpt H, p. 335).

References

(F) Harry B. Whittington, The Burgess Shale (New Haven, CT: Yale
University Press, 1985).
(G) Jeffrey S. Levinton, "The Big Bang of Animal Evolution," Scientific
American 267 (November, 1992): 84-91.
(H) Malcolm S. Gordon, "The Concept of Monophyly: A Speculative Essay,"
Biology and Philosophy 14 (1999): 331-348.

That enough, or do you really need more quotes to establish the point that the idea of a branching tree of life is a complete myth?
 
« Last Edit: 21/03/2009 02:07:18 by Asyncritus »
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lyner

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Why Darwin was wrong about the tree of life
« Reply #26 on: 21/03/2009 09:51:06 »
Quote
There are so many fossils available today, that argument is a complete non-starter.
There are millions and millions of fossils. But there will be very few fossils, if any, of creatures which died in the wrong circumstances for the formation of fossils.
Are you aware how difficult it is for a fossil to form?
« Last Edit: 21/03/2009 09:53:15 by sophiecentaur »

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Offline BenV

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Why Darwin was wrong about the tree of life
« Reply #27 on: 21/03/2009 11:18:46 »
There is not point contrinuing to argue with Asyncritus - he admitted that his problem is not with evolution but with the percieved attack on his beliefs in a different thread.  He is unwilling to accept any explanation for life on earth that does not involve his god.  Therefore, this discussion is not worth having.

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Offline sldunn01

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Why Darwin was wrong about the tree of life
« Reply #28 on: 24/11/2009 08:06:26 »
I was on reading another post and came across this one...basically im trolling...and i know the thread is "dead". To the point - the argument that darwin's theory is invalid because of an incomplete fossil record is bunk. darwin was extremely self conscious about his writing and was postulating about a possible theory as to why there was an insufficient amount of empirical data to "prove" his postulates. Today, this simply does not matter, evolution is supported by similarities between rRNA (ribosomal RNA)sequences. Basically the organisms genetic code, not "how it looks". Modern genomic "trees" base their classifications on similarities between genetic material in the rRNA. Organisms that are closely related have similar rRNA strands while dissimilar organisms have well....dissimilar rRNA code. Now phenotypic characteristics are often miss leading when classifying organisms but rRNA is not. Back to the point...it doesn't matter one HOOT if the fossil record does not support evolution. Genetic material does. Arguments based on "an incomplete fossil record" are simple outdated...by nearly 40 years. They are remnants of a time when science couldn't prove evolution one way or the other because there was only phenotypic data to observe. Today this is not the case -- evolution is a proven fact. If not on the macro scale, clearly on the mirco scale. Personally i don't think evolution removes god from the page at all. FYI- evolution is a basic fact, there is an incredible amounts of data which back it up. [O8)]
« Last Edit: 24/11/2009 08:09:09 by sldunn01 »