Discovering the Tree of Life

One of the most profound ideas to emerge in modern science is Charles Darwin's concept that all of life, from the smallest microorganism to the largest vertebrate, is connected through genetic relatedness in a vast genealogy. This "Tree of Life" summarizes all we know about biological diversity and underpins much of modern biology, yet many of its branches remain poorly known and unresolved.

To help scientists discover what Darwin described as the tree's "everbranching and beautiful ramifications," the National Science Foundation (NSF) has awarded $17 million in "Assembling the Tree of Life" grants to researchers at more than 25 institutions. Their studies range from investigations of entire pieces of DNA to assemble the bacterial branches; to the study of the origins of land plants from algae; to understanding the most diverse group of terrestrial predators, the spiders; to the diversity of fungi and parasitic roundworms; to the relationships of birds and dinosaurs.

"Despite the enormity of the task," said Quentin Wheeler, director of NSF's division of environmental biology, which funded the awards, "now is the time to reconstruct the tree of life. The conceptual, computational and technological tools are available to rapidly resolve most, if not all, major branches of the tree of life. At the same time, progress in many research areas from genomics to evolution and development is currently encumbered by the lack of a rigorous historical framework to guide research."

Scientists estimate that the 1.75 million known species are only 10 percent of the total species on earth, and that many of those species will disappear in the decades ahead. Learning about these species and their evolutionary history is epic in its scope, spanning all the life forms of an entire planet over its several billion year history, said Wheeler.

Why is assembling the tree of life so important? The tree is a picture of historical relationships that explains all similarities and differences among plants, animals and microorganisms. Because it explains biological diversity, the Tree of Life has proven useful in many fields, such as choosing experimental systems for biological research, determining which genes are common to many kinds of organisms and which are unique, tracking the origin and spread of emerging diseases and their vectors, bio-prospecting for pharmaceutical and agrochemical products, developing data bases for genetic information, and evaluating risk factors for species conservation and ecosystem restoration.

The Assembling the Tree of Life grants provide support for large multi-investigator, multi-institutional, international teams of scientists who can combine expertise and data sources, from paleontology to morphology, developmental biology, and molecular biology, says Wheeler. The awards will also involve developing software for improved visualization and analysis of extremely large data sets, and outreach and education programs in comparative phylogenetic biology and paleontology, emphasizing new training activities, informal science education, and Internet resources and dissemination.

For a list of the Assembling the Tree of Life grants, see: http://www.nsf.gov/bio/pubs/awards/atol_02.htm

You set junk DNA up to be the breaking point of evolution -- biologists didn't. You're contentions about Pasteur have been shown to be invalid (he simply proved that microbes did not spontaneously generate, not that life from non-life is impossible -- there is a difference, but you're too narrow-minded to actually see it). All your points above fall into "this is what I claim evolution says, and I can therefore prove it's wrong." It's a whole lot easier to take down strawmen than it is to actually tackle the science involved. Of course, this has been shown to you time and again on these threads for the past two years and you still soldier on, immune to reality. You are not the end-all and be all of science -- hell, from your postings it's obvious you've never taken a college-level science course in your life and most of your science comes from Jack Chick pamphlets, otherwise you'd not use terms like "I proved" all the time. Your theology is as narrow as your understanding of science. You insult people who do not agree with you (calling them liars when they obviously haven't uttered a lie). You are a child, and little boy, if you don't start showing that you are actually learning something from these threads (i.e., you don't keep coming back with the same arguments shot down three threads ago) and treating people with some civility (take a page from Alamo-Girl -- I don't agree with thing one she's said, but she's civil about it and we treat her the same way) you are back on my virtual ignore list.

Note please, lurkers, I will not respond to him not because his arguments hold any validity -- they don't and haven't for centuries. I won't respond to him because he is a mentally-limited, thoroughly brutish holy warrior with whom actual conversations are impossible.

You set junk DNA up to be the breaking point of evolution

My point is much stronger. Evolution has been consistently refuted by science. Its predictions have been shown to be false consistently. Junk DNA is in a sense the final straw in evolution's back for several reasons. As I showed, evolution, when faced with the problems created for it by DNA needed to back up its theory with facts. It proposed two ways to do it: mitochondrial DNA as a 'molecular clock' of evolution and this one was proved false. Junk DNA sought to accomplish a similar function of showing the connections between species being shown by a sort of 'fossilized' DNA. Both failed and for very good reason - they assumed that the DNA in question was just there for the purpose of proving evolution. Now such a ridiculous assumption shows quite well the arrogance of evolutionists and their unscientific attitude. I say unscientific because a scientist looks for causes, for purpose not for purposelessness. To make the totally moronic assumption that 95% of DNA copied in the vast majority of the 100 trillion cells in the human body is purposeless is totally moronic and shows the desperation of evolutionists. It also shows that evolution is a hindrance to scientific progress. It would have had scientists looking for similarities amongst DNA rather than how it worked. It would have had them looking backwards instead of looking forward. It would have closed scientific inquiry of DNA instead of encouraging it. Instead, it is ID which encourages scientific inquiry. It seeks to answer the questions which science is supposed to ask: how, why.

What makes the dismissal of Junk DNA the final straw is what has been found in that 'junk'. The junk turns out to be the program of life, what runs the genes, what causes the organism to function. As science has shown, the genes are just factories of proteins and enzymes, they are run and controlled by the DNA which is non-coding. The genes do not do anything by themselves, they must wait for instructions on what, when and how much to produce. This makes evolution impossible because it makes new functions dependent on numerous factors arising and working together to accomplish it. One can postulate a single change arising at random, one cannot postulate an entire integrated system arising at random.

I must thank you yet again. By following those two key words and your author, I was able to locate exactly what I was looking for. He and other notable researchers have also underlined the importance of symbolization in genetics.

Here are some of the articles I found thanks to you!!!

The Physics and Evolution of Symbols and Codes:Reflections on the Work of Howard Pattee There are many links on the page with wonderful detail, but the heart of the discussion is summarized by Howard H. Pattee

"The two great scientific disciplines of physics and evolution theory have traditionally been taught as disjoint subjects. Yet some billions of years ago, certain collections of physical molecules reached a level of complexity that began open-ended evolution by heritable (symbolic memory-based) variation and natural selection.

Von Neumann was the first to propose explicitly why this "threshold" of complexity requires description-based reproduction (taken for granted by biologists), but his argument was focused on the logical, not the physical requirements. He did not discuss the organizational requirements that would allow normal physical molecules to function as descriptions, nor was he clear about his logical distinction between "active" physical dynamics and "quiescent" symbolic descriptions. He did not mention the origin problem except to say it was "a miracle of the first magnitude."

Even if we still do not have a clear picture of the origin of life, the significance of this fundamental distinction between descriptions and constructions, that is, between semiotic processes (rules, codes, languages, information, control) and physical systems (laws, dynamics, energy, forces, matter) reaches to all levels of evolution. This is an essential distinction from the earliest genetic control of the synthesis of proteins, to the codes and languages of the brain, to the distinction between the mind and the brain (the knower and the known, the epistemic cut), and even to physical theory itself that requires a clear distinction between universal physical laws and the local semiotic process of measurement - an area in which there is still no consensus. This distinction between laws and semiosis, as well as how they are related, needs to be made more clearly at all levels if we are to fully understand evolution, physical laws, and the languages of the brain.

In biology, the basic physics and chemistry of elementary life processes as they exist on earth is well-developed. However, our knowledge of the semiotic controls and interactions within and between organisms and in some cases even in single cells is far from complete. In evolution theory it is still not clear that blind variation in a virtually infinite semiotic search space is adequate to explain so many successful species.

And from Rocha's introduction on the webpage (emphasis mine):

Pattee notes that the questions physicists and biologists ask about life are quite distinct, and have lead many to think of living systems as paradoxical. Pattee chose to work on the boundary between these two branches of science, and pursue a theoretical biophysics. From this interface position, it became clear to him that to study life and its origin one needs to study the origin of the genotype-phenotype distinction, which he observes, is an instance of the origin of symbol systems from material components. This symbol-matter or subject-object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code, and instantiates an epistemic cut, a concept he thoroughly develops here. I'm pinging nebullis, gore3000 and junior because they might also be interested in these finds!

For a long time now I’ve been suggesting that the evolutionists should be malleable on the randomness tenet. I said that because it seemed like a good way to forge peace between that side and intelligent design with regard to teaching children in public schools.

However, after this research on information theory, algorithms and mathematics in genetics – in particular, the symbolization – I’m even more convinced that evolutionists insist on randomness to their own peril.

I realize the evolutionist position is that randomness does not mean the same thing as ‘roll of the dice’ – because random mutations are culled by natural selection. Nevertheless, the initiating event is a random mutation.

The presence of algorithmic information even within junk DNA (Complexity International – Brief Comments on Junk DNA [pdf]) is counter-indicative of randomness per se. The Chaitin papers [ps] explain why:

We now turn to Kolmogorov's and Chaitin's proposed definition of randomness or patternlessness. Let us consider once more the scientist confronted by experimental data, a long binary sequence. This time he in not interested in predicting future observations, but only in determining if there is a pattern in his observations, if there is a simple theory that explains them. If he found a way of compressing his observations into a short computer program which makes the computer calculate them, he would say that the sequence follows a law, that it has pattern. But if there is no short program, then the sequence has no pattern--it is random. That is to say, the complexity C(S) of a finite binary sequence S is the size of the smallest program which makes the computer calculate it. Those binary sequences S of a given length n for which C(S) is greatest are the most complex binary sequences of length n, the random or patternless ones. This is a general formulation of the definition…

In other words - to sustain the pillar, one would have to presume that random information content can be algorithmic (which is, by definition, not random.)

Even more to the point, the physics of symbols (H.H. Pattee) and the current state of the art (Rocha and Language-like features in junk DNA) strongly suggest that new research will show that mutations were opportunistic.

This would cause no violence to the theory of evolution or metaphysical naturalism were it not for the insistence on randomness in mutations. For one thing, they might have suggested that the mutations were either random or were opportunistic self-mutations - where the genetic language-like processes read an opportunity in the environment and mutated to gain advantage.

The intelligent design response to that could have been two-fold. First, that the capability itself is evidence of a designer. Second, that opportunistic mutations were additionally guided by external design, showing by information theory that symbolism and language could not have evolved sufficiently to account for the evidence, e.g. Cambrian Explosion. In response, the evolutionists and metaphysical naturalists would write both off to the anthropic principle.

In any case, I predict that intelligent design at first cause will be underscored since there is no origin for the minimal necessary information content whether or not opportunistic (Yockey seventh message).

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