Discovering the Tree of Life

National Science Foundation Office of Legislative and Public Affairs ^ | November 18, 2002 | NSF Press Release

[forsnax5]

NSF awards grants to discover the relationships of 1.75 million species

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.

-NSF-

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

[AndrewC]

I would agree. As I said before, we can try to make some educated guesses about the relationship by using the degrees of difference to try and place them in a relative taxonomy. That's not conclusive, of course, but it can point us in a productive direction. And we can compare our results to morphological/cladistic taxonomies, to give us another factor in deciding the relationship.

Yes, some judgement can be made by taking other information into consideration. COGS has little cladistic trees for each COG.

This must be viewed in light of the photosynthesis experience.

As for the materialism, been there, done that.

Mat 4:4 But he answered and said, It is written, Man shall not live by bread alone, but by every word that proceedeth out of the mouth of God.

[forsnax5]

A great example of total dishonesty. Dembski is listing the explanations of evolutionists, not saying that they are correct. In fact he is explicitly saying that they are not correct. Let's look at the 'quote' in context:

Thank you for posting the entire section. It makes it easier to respond.

In the introductory paragraph that you included, Dembski sets the stage to discuss the gaps in the evolutionary record. Here is the only line that Dembski offers to explain the evolutionist point of view:

Evolutionary biology attempts to explain the absence of intermediates from an evolutionary path on the assumption that the intermediates did once exist.

Then he switches to his own voice, and proceeds with the setup:

But now let’s turn the question around. Suppose that discontinuity is a fact not just about the history of life as we know it but about the history of life itself -- in other words, the intermediates never existed. In that case, how did biological forms in all their vast complexity and diversity come about? In asking this question, let's hold off asking for the underlying cause or causes of biological complexity and diversity. Rather, let's merely ask what a video camera would see if it were scouring the past and recording key events in life’s history. There are exactly four possibilities:

Note that he's not talking about what causes the discontinuities (the gaps in the fossil record), only how those discontinuities would appear to an observer who was actually there.

The possibilities listed below are Dembski's proposals of what would be seen by his video camera, NOT proposals by evolutionists of what actually happened:

1. Nonbiogenic emergence. Organisms emerge without the direct causal agency of other organisms. In place of life begetting life, here we have nonlife begetting life.
2. Generative transmutation. Organisms, in reproducing, produce offspring that are vastly different from themselves.
3. Biogenic reinvention. Organisms reinvent themselves in midstream. At one moment they have certain morphological and genetic features, at the next they have a vastly different set of such features.
4. Symbiogenic reorganization. Organisms emerge when different organisms from different species get together and reorganize themselves into a new organism.

These four points are the ways that Dembski offers to close the gaps in the fossil record. He then goes on to say:

None of these possibilities is out to lunch.

By which he means any or all of the four could have been seen by his video camera. Then he goes on to give the reasons why he thinks each is plausible:

Nonbiogenic emergence had to happen at least once, namely, at the origin of life.

The above is the line that I quoted. Taken in context, it is clearly spoken by Dembski. It is direct and to the point, and completely unambiguous.

After discussing the other three possibilities he makes the general statement:

With regard to these four possibilities, the crucial question now is this:

Then he makes the statements you emphasized:

How does one make sense of these possibilities in light of intelligent design? Clearly, none of these possibilities makes sense without some directed coordination.

Here, he's referring back to his original point -- that these are all possibilities for the way the gaps in the fossil record were filled, and IN THAT CONTEXT, they required "directed coordination." If you have not recognized this context, then you have assumed that Dembski thinks that the designer (who is not necessarily God) created the first life, and that leaves you with a paradox.

With your dishonesty you have again given proof of much that I said - that the interest of evolutionists is not truth or science, that they are motivated by atheism and are willing to go to any extent to win against opponents including obvious lies. What this shows to me is a totally unChristian disregard for the truth. It also shows that evolutionists themselves are quite aware that their theory is a lie and therefore feel compelled to use lies to defend it.

Where is the obvious lie?

[general_re]

Materialism explains some things very well, and other things not at all. The trick is knowing which is which...

[AndrewC]

The trick is knowing which is which...

That is the question.

[Nebullis]

Does the genome support conditional operations and recursives?

Most gene transcription and RNA splicing works on a conditional type operator.
Replication is recursive. Clonal expansion of single traits or single cells is recursive.

[Alamo-Girl]

Thank you for the information!

[gore3000]

NAME THE EVOLUTIONIST







Note: In this contest there are no winners, only losers!

[PatrickHenry]

Placemarker.

[Heartlander]

Me: It could logically be self evident to some that natural causes do not explain even the most obvious thing in ones life, i.e. consciousness.

You: That sounds contradictory or maybe I just don't take your meaning. How can something be logical and self-evident? Self evidence requires no argument but logic does.

It is a given even for a child that he/she is a conscious individual and logically so. But beyond this, should truth be logical as well? If not, it seems logic should dismiss it as truth. (as you pointed out)

"We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable rights, that among these are life, liberty, and the pursuit of happiness.”
-Preamble to the Declaration of Independence
(although self-evident was originally “sacred and undeniable”)

Oh, but I seem to have digressed once again. Western science and thought were based on the theory of design. In science, sure they observed natural causation but from an engineering standpoint. In thought, it was believed that free-will is part of a plan and choice should not be imposed. (Now exceptions can be presented but I believe they can be distinguished from an individual belief and the entire philosophy or theology)

Now back to ‘how do we detect design?’ We use our consciousness to detect design and IMHO our consciousness cannot be explained by naturalistic causes and definitely not by material causes.

I read your text, detect design, transcription takes place, I respond. This is intelligent design from man (not to mention the means by which this is taking place). Now, no one denies that DNA contains information but beyond this; transcription takes place, it responds, and builds in a precise sequence based on inside stimuli and outside stimuli. IMHO this is design. Again, I do this with my consciousness but within your self-consciousness you can deny this and attempt to explain it another way.

Let’s do a little ‘Zen thing’ here – I know you are familiar with ‘If a tree falls in the forest and nobody is around, does it make any noise?’ Let’s take it to a different level, ‘If a universe exists without life or intelligent life, does information exist?’ Regardless if you believe information exists in that universe, the information would be meaningless for that universe (and you must use your consciousness to determine this one way or another for a universe without consciousness). Take this random, meaningless universe; ‘just add humans’, and why does or should this change the universe? Consciousness? So now we are able to view this universe… This expanded reality doesn’t sound like a boon, more like a boondoggle. (But it seems that I have digressed again)

So we use our consciousness to give us an acceptable explanation and meaning to the universe and our existence. Our explanations are thoughts and for the materialist, these thoughts must also be material processes. This takes away the “I” or “self” in our own consciousness and shifts it to matter or nature. For the materialist, since human consciousness exists, nature somehow has formed individual ‘ I’s ‘ to observe all random events.

I see everything as designed, planned, and for purpose. It is self-evident and logical IMHO.

[Doctor Stochastic]

You mean that OJ's blood wasn't created ex nihilo at the scene? Or perhaps it was just transubstantuated from Philip Vannatter's butt of malmsy?

[gore3000]

You are correct. That honor belongs to theism.

ID is not religion, it is science. It is meeting evolution in its supposed field and showing that it is not science at all. Evolution has never been science. That is why it keeps getting refuted by science constantly. That's why it is always behind the eight ball with each scientific discovery.

[general_re]

That was the alternate alternate defense theory, to be used in case the glove presented problems for them, and the Colombian-necktie thing proved to be too ludicrous for the jury.

[gore3000]

Think of an example like this: suppose you have two segments, one that reads AGVLUR, and a second that reads LRGVAU (which I just made up out of thin air). Both those segments are composed of exactly the same parts, just as your algebraic expressions have the same numbers and the same operations, just in a different order. And just like your expressions, the order matters - they have the same parts, but the products are likely going to be completely different because the order of operations is different in either case. So even though they're made up of the same parts, position and order are critical, and the two segments will not match each other at all for comparative purposes. That's why scientists try very hard to align the segments they want to compare, to insure that they get the best comparison possible.

This is where your whole theory goes to pot and you do not see it. Yes indeed the sequence of amino acids does indeed have bearing on the protein produced. However a protein like anything else is more than the sum of its parts and these 'scientists' should be ashamed to claim otherwise. Proteins are very specific, that is why the human body needs 100,000 of them to function. Every single amino acid in a protein contributes to how the protein folds and what shape it takes. This is very important since the shape is often the function of the protein. In attacking viruses and bacteria the shape enables the destruction of invaders. Shape is so important that the mere changing of the shape of a protein can result in death. That is what happens with mad cow disease.

[gore3000]

Again, the fact that bats, flies, and birds have wings and they flap them to fly does not establish a common ancestry. The point established by the photosynthesis result is that common features and common solutions do not indicate the ancestry of the process. The pieces and parts could indicate "plagiarism" or common solutions.

That's the problem with evo-science. It is not science at all. It is just a set of assumptions based on ignorance and a complete arrogance towards both the public and nature. That is why evolutionists are proved wrong by real science so often. How arrogant could they be to postulate that 95% of DNA, which is replicated in just about all of the 100 trillion cells of the human body is junk? How arrogant could they be to propose that mytochondrial DNA was infinitely changeable just so they could trace species lineages? They seem to keep proposing that nature is like bones, just there to help prove their theory. Just as the evolutionist non-sensical assumptions were wrong with junk DNA and mtDNA they are absolutely wrong in this example.

In the case of these genes having similar sequences, the reason is that each amino acid has certain specific properties. The amino acids are not interchangeable at will and for this reason biologists attempting to modify genes in the lab need special programs that will take into consideration these properties in attempting to change them. One important property for example is solubility in water. Amino acids which are soluble in water will seldom be found on the outside of a protein since this would destroy the protein. Amino acids also have chemical properties which enable them to react chemically to perform their functions. It is therefore not to be wondered that in proteins where chemical actions are required to perform a function, similar sets of amino acids will be required. Here's a diagram of the properties of the 20 amino acids used in life. Since there are only 20 each one is named after a letter of the alphabet:

Figure 1. A Venn diagram showing the relationship of the 20 naturally occurring amino acids to a selection of physio-chemical properties thought to be important in the determination of protein structure [2].
From: PROWL

The following gives the common names of the amino acids as well as the side chains which help them chemically react with other substances:

Name	Symbol	Mass (-H2O)	Side Chain	Occurence (%)
Alanine	A, Ala	71.079	CH3-	7.49
Arginine	R, Arg	156.188	HN=C(NH2)-NH-(CH2)3-	5.22
Asparagine	N, Asn	114.104	H2N-CO-CH2-	4.53
Aspartic acid	D, Asp	115.089	HOOC-CH2-	5.22
Cysteine	C, Cys	103.145	HS-CH2-	1.82
Glutamine	Q, Gln	128.131	H2N-CO-(CH2)2-	4.11
Glutamic acid	E, Glu	129.116	HOOC-(CH2)2-	6.26
Glycine	G, Gly	57.052	H-	7.10
Histidine	H, His	137.141	N=CH-NH-CH=C-CH2- |__________|	2.23
Isoleucine	I, Ile	113.160	CH3-CH2-CH(CH3)-	5.45
Leucine	L, Leu	113.160	(CH3)2-CH-CH2-	9.06
Lysine	K, Lys	128.17	H2N-(CH2)4-	5.82
Methionine	M, Met	131.199	CH3-S-(CH2)2-	2.27
Phenylalanine	F, Phe	147.177	Phenyl-CH2-	3.91
Proline	P, Pro	97.117	-N-(CH2)3-CH- |_________|	5.12
Serine	S, Ser	87.078	HO-CH2-	7.34
Threonine	T, Thr	101.105	CH3-CH(OH)-	5.96
Tryptophan	W, Trp	186.213	Phenyl-NH-CH=C-CH2- |___________|	1.32
Tyrosine	Y, Tyr	163.176	4-OH-Phenyl-CH2-	3.25
Valine	V, Val	99.133	CH3-CH(CH2)-	6.48

From: Amino Acid Side Chain Structure .

For more information on amino acid properties see Amino Acid Information .

[gore3000]

The only "number" that was put on the conjecture that OJ killed his wife was the sequence comparison of his DNA to the blood recovered at the scene.

If the comparison had shown 55% concordance would he have been guilty or innocent?

[gore3000]

Where is the obvious lie?

You have unmitigated nerve. Dembski in no way considers any of those possibilities achievable without an intelligent designer having accomplished them. It is his conclusion and I underlined it for you and for the lurkers:

How does one make sense of these possibilities in light of intelligent design? Clearly, none of these possibilities makes sense without some directed coordination.

So not only did you dishonestly try to imply that Dembski believed that abiogenesis is possible but you have the nerve to continue making the assertion after it has been pointed out to you. There is only one word for you and what you are doing.

[gore3000]

Western science and thought were based on the theory of design.

It still is. Science is based on discovering the relationships in nature and formulating the rules by which those relationships are accomplished. From chemistry to physics to biology it is all about relationships and the conditions by which those relationships are accomplished. In a sense therefore science is about finding the algorithms in nature. This is how the equations in science have been found, how experiments are made and how the theories and laws of nature have been and continue to be formulated. Saying that something occurs randomly is not science, it is non-science. That is why with each scientific discovery we are able to understand and predict more closely what will happen in given circumstances. With increased knowledge randomness dissappears and design becomes more obvious. That is why evolution and materialism, which propose randomness as the organizing principles of nature keep losing ground on a daily basis.

[general_re]

If the comparison had shown 55% concordance would he have been guilty or innocent?

You question makes no sense. None of your posts do, but this one makes even less sense than usual. If you compare a particular sequence of OJ's DNA to a corresponding sequence of unknown sample DNA, and you only get a 55% correspondence, that's a pretty clear indicator that your unknown sample is from a non-human species.

motA, ExbB, and MTH1022 are all similar, with correspondences in the 30-50% range, but they're not identical because they come from different organisms, representing different genera and species. And the whole idea behind exploring the similarities is to explore how closely related different organisms are to each other. Once again, you've discovered that things that are different are not identical to each other. Congratulations.

[Nebullis]

The only "number" that was put on the conjecture that OJ killed his wife was the sequence comparison of his DNA to the blood recovered at the scene.

That number was a match of 1 in 720 million. The jury, like a bunch of creationists, rejected that evidence because it was still probability obtained by a scientific method they did not understand.

[Nebullis]

motA, ExbB, and MTH1022 are all similar, with correspondences in the 30-50% range, but they're not identical because they come from different organisms, representing different genera and species.

I find it highly suspect that AndrewC readily accepts numbers in that range for evidence of horizontal transfer, but spends pages and pages arguing about similar numbers for that more parsimonious assumption of vertical transfer.