If you think I don't understand transcription and translation, please have a word with the academics marking my exams in a few weeks.

And Will, how do you know when something is a code?

Trust me, that's not the only possible criticism. I just have better things to do than debate confused metaphysics with someone who has demonstrated that they don't have the ability to properly engage the arguments of others, or to produce a coherent point of view.

Sorry, but I've got bigger fish to fry and more important battles to win.

Wow, Will, I think you just lost what tiny speck of credibility you still had by claiming that adenine, guanine, cytosine and thymine are amino acids, not nucleotides. Technically, the nucleobases in a DNA polymer aren't *strictly* nucleotides, but they're close enough. Definitely not amino acids.

A "nucleotide" in a DNA polymer is to a free nucleotide, as an "amino acid" residue in a protein/polypeptide is to a free amino acid.

If you don't know basic, basic, BASIC biochemistry, I'm afraid you're not at all qualified to make any sort of grand pronouncement about biology.

I'm not an IT-ist! Some of my best friends are IT professionals!

Will, I am writing a blog post to respond to your accusation of my being an ideologue. Just because, you know, it struck a chord with me.

The source of all the quotes in my banner (which is a rotating image, by the way, so it should change every time you visit the site) is my Twitter feed, but they were made so long ago (relatively) that I can't find the original tweets. Needless to say, I'd linked to an article about something or rather that had linked Islamic fundamentalists and evolutionary biology, and I needed to say something about it. You know me.

Will was not involved.

Carl Woese:" No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves." http://www.pnas.org/content/95/12/6854.full

Do orthologous gene phylogenies really support tree-thinking?
"We conclude that we simply cannot determine if a large portion of the genes have a common history.,,, Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading." http://www.ncbi.nlm.nih.gov/pubmed/15913459 - Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF.

Charles Darwin was wrong about the tree of life - 2009
"We have no evidence at all that the tree of life is a reality,"
Eric Bapteste, evolutionary biologist http://www.guardian.co.uk/science/2009/jan/21/cha...

Beyond the Tree of Life: a new thematic series from BioMedCentral, 12 Jul 2011.

Graham Lawton, "Why Darwin was wrong about the tree of life", NewScientist, 21 Jan 2009.

"Discovery of jumping gene cluster tangles tree of life" by David Salisbury, Vanderbilt University, 4 Feb 2011.

BMC Evolutionary Biology, 22 Sep 2010. "We find significant conflict between phylogenies constructed using molecular and morphological data."

Patrick J. Keeling, "Deep Questions in the Tree of Life", 10.1126/science.1149593, p 1875-1876 v 317, Science, 28 Sep 2007.

Laura Spinney, "Evolution: hacking back the tree of life" , "Back to their roots," p 48-51 v 194, New Scientist, 16-22 Jun 2007. "We have vastly underestimated evolution's fondness for pruning."

Geir Hestmark, "Temptations of the tree" p 911 v 408 Nature, 21/28 December 2000. "Phylogenetic trees are common in today's scientific journals, but there it is seldom realized how speculative they are because they look so real."

Francis S. Collins and Karin G. Jegalian, "Deciphering the Code of Life" p 86-91 v 281 n 6, Scientific American, December 1999. "A more apt analogy ...will be a net or a trellis ...rather than a tree...."

Will Provine, professor of Paleontology at Cornell University, states, “We’ve discovered that Darwin’s idea of evolution by descent from comment ancestors does not really work well as soon as you get behind multi-cellular organisms….and our methods phylogeny reconstruction are so poor, that we will never have a tree of life that goes back to the origin of life.”

Chris, the rest of these two comments are by Will - he was having trouble posting it normally for some reason, so he emailed it to me.

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Actually, here is no problem in providing many more references on a controversial topic that is well-known to practicing biologists. But because many ppl believe in evolution as an a priori default position, no matter how much evidence is presented against that ideological belief, they will continue to hold on to it because a priori beliefs are not based on evidence or science.

Other than the direct criticism of the Darwinian tree of life concept by E Koonin in his "Laws of Chance" book, it should not have to be noted that such claims are never made in a vacuum. Respected scientists make purely radical claims that cannot be supported only at their own risk. Here are just a few other references by evolution scientists:

Charles Darwin's tree of life is 'wrong and misleading', claim scientists
The Telegraph 22 Jan 2009
Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: "For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality."

"The tree of life is being politely buried," said Michael Rose, an evolutionary biologist at the University of California, Irvine. "What's less accepted is that our whole fundamental view of biology needs to change."

Dr John Dupré, a philosopher of biology at Exeter University said: "Having uprooted the tree of unicellular life biologists are now taking their axes to the remaining branches."

Harvard biologist and writer Stephen Jay Gould believes there is no prescribed hierarchy of life; evolution wanders aimlessly, and is as likely to go down as up. Therefore, he has said that the tree of life is a low bush.

Wikipedia "Tree of Life" --
.. the view is now emerging that the tree of life gives an incomplete picture of life's evolution. It was a useful tool in understanding the basic processes of evolution for prokaryotes, but cannot explain the full complexity of the situation.

Doolittle, W. Ford (February, 2000). Uprooting the tree of life. Scientific American 282 (6): 90–95

Doolittle, W. Ford, and Bapteste, Eric. Pattern pluralism and the Tree of Life hypothesis PNAS, February 13, 2007, vol. 104, no. 7, 2043-2049.

We have fossil evidence for such "branches" existing in the past. Even if we did not, they could be inferred from phylogenetic reconstruction.