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

That number was a match of 1 in 720 million.

Well, in that case, on a planet of six billion, it's likely that about eight people match that genetic profile. Undoubtedly all eight of them lived in LA, had access to the crime scene, and had a motive for killing OJ's ex-wife.... </Johnny Cochran mode>

:^)

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.

Even if we assume the likelihood of horizontal transfers in all or most of these cases, it seems to me that this fails to address the ultimate source of those genes - they had to originate somewhere before they started getting swapped around by organisms. Or perhaps it does address the question of where they come from, in a roundabout sort of way.

In any case, it seems to me that the best way to differentiate horizontal transfers from vertical transfer is to compare multiple functional domains. If we find a relatively high degree of correspondence in only one domain, that domain seems a likely candidate for horizontal transfer. OTOH, if we find relatively high degrees of correspondence across many domains, then the likelihood of horizontal transfer would seem to drop precipitously.

In any case, it seems to me that the best way to differentiate horizontal transfers from vertical transfer is to compare multiple functional domains.

Precisely. Or compare one gene to other genes in the organism. There are sufficient problems with orthology or lateral gene transfer that will show up in incongruencies and call for a different explanation than vertical transfer. A large number of sophisticated statistical models are used in systematics. Calls for "put up the numbers" are hopelessly naive; they are meaningless without extensive background and context.

Creationists should take comfort from the fact that such effects are suspected, investigated, and discovered, instead of waxing insane about evolutionists finding only what they hope for with preconceived notions.

A large number of sophisticated statistical models are used in systematics.

That would partly explain the massive sums of money that I watched being spent on a rather large computing cluster here, along with the various other computational complexities of genome research. With the addition of the bioinformatics cluster, my little podunk state-U undergrad alma mater is suddenly listed in the top-ten supercomputing sites in the world ;)

This is where your whole theory goes to pot and you do not see it.

That has been bothering me also but for a different reason.

It appears the genetics functionally go beyond physical operators (1129) and include conditional operations and recursives (1165.) Therefore, I surmise that on this most elementary level, and evidently independent of its host, the genetics have a form of intelligence which at times could be counterindicative to the host's intelligence, e.g. best interest.

For this to fit the theory of evolution, it appears they must show that genetic intelligence is physical. Indeed, for materialists, all intelligence must be physical.

There is an implication of information in processing, because conditionals act on information. There is an implication of data base also where processes are learned. At this level, the genome could be its own database (hence the junk) - but there must be cognizance of information to effect conditional operations.

To effect replication of cognizance, remember how to do it again, that information must be indexed, or symbolized. Furthermore - logically, the operators, conditionals and recursives are collected and ordered to achieve purpose.

How could all of that actualize by random chance? Are evolutionists attributing survival instinct to information process? What physical process could conjure symbolism at the genetic level?

In my view, this genetic information processing phenomenon screams intelligent design. This may be "old hat" to you guys, but it's news to me. I had not contemplated the genetic discussion under information theory.

I was accused of "ignoring" numbers I don't recall seeing. I guess they are not there. Anyway HT as a mechanism seems to be readily and frequently used. This process involves not just fragments of genes or whole genes, but is possible with groups of genes.

Evolution of coenzyme B12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex.

Lawrence JG, Roth JR.

Department of Biology, University of Utah, Salt Lake City 84112, USA.

We have examined the distribution of cobalamin (coenzyme B12) synthetic ability and cobalamin-dependent metabolism among enteric bacteria. Most species of enteric bacteria tested synthesize cobalamin under both aerobic and anaerobic conditions and ferment glycerol in a cobalamin-dependent fashion. The group of species including Escherichia coli and Salmonella typhimurium cannot ferment glycerol. E. coli strains cannot synthesize cobalamin de novo, and Salmonella spp. synthesize cobalamin only under anaerobic conditions. In addition, the cobalamin synthetic genes of Salmonella spp. (cob) show a regulatory pattern different from that of other enteric taxa tested. We propose that the cobalamin synthetic genes, as well as genes providing cobalamin-dependent diol dehydratase, were lost by a common ancestor of E. coli and Salmonella spp. and were reintroduced as a single fragment into the Salmonella lineage from an exogenous source. Consistent with this hypothesis, the S. typhimurium cob genes do not hybridize with the genomes of other enteric species. The Salmonella cob operon may represent a class of genes characterized by periodic loss and reacquisition by host genomes. This process may be an important aspect of bacterial population genetics and evolution.

You have unmitigated nerve. Dembski in no way considers any of those possibilities achievable without an intelligent designer having accomplished them.

You're reading Dembski's mind, I'm only reading his words.

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.

Well, I'm expressing my opinion (which is, of course, more than one word), but that's probably not what you had in mind. :)

So, while you're in a good mood, why don't you explain the relationship between ID and God? Dembski seems to have to deal with the beginning of life in the same manner that some of the evolutionists do -- that is, God started it, then ID (or evolution) took over.

So, with ID, if God started it, then ID is simply creationism with a cadre of assistants.

This is a discussion, by the way. Feel free to discuss.

Anyway HT as a mechanism seems to be readily and frequently used. This process involves not just fragments of genes or whole genes, but is possible with groups of genes.

I don't think anyone would argue that it doesn't happen - the evidence seems clear that it does. However, "frequently" is a relative term that may or may not turn out to be appropriate as we learn more about the genomes of various organisms.

For example, human beta-hemoglobin shows a high degree of correspondence with beta-hemoglobin in chimps, a somewhat lower degree with beta-hemoglobin in llamas, and a still-lower degree of correspondence with beta-hemoglobin in chickens (guess what I was doing this morning). Horizontal transfers seem unlikely to have sufficient explanatory power to resolve this, particularly when those relationships dovetail nicely with what we already know from cladistic studies.

You have unmitigated nerve. Dembski in no way considers any of those possibilities achievable without an intelligent designer having accomplished them. -me-

You're reading Dembski's mind, I'm only reading his words.

Well, let the lurkers deside from Post# 1121 which was underlined for you:

With regard to these four possibilities, the crucial question now is this: How does one make sense of these possibilities in light of intelligent design? Clearly, none of these possibilities makes sense without some directed coordination.

If the comparison had shown 55% concordance would he have been guilty or innocent? -me- You question makes no sense.

Of course it does that is why you have to insult. You (and evo 'scientists') are saying that a 55% concordance in a specially selected area of a protein (selected for concordance) proves anything. It does not. Horses have legs, men have legs that does not mean that they descended from each other, all it means is that for certain functions (such as walking or motion in the case of the proteins discussed) a certain structure is needed. As pointed out in Post #1174 (which you carefully ignore) amino acids have certain properties and you cannot achieve a function by random combinations of them. Your whole proposition is anti-science. The combinations have a reason, the proteins have a purpose and are constructed to achieve that purpose.

That number was a match of 1 in 720 million. The jury, like a bunch of creationists, rejected that evidence

You really are twisting the facts! It is ID which says that something which has one chance in an almost infinite amount of tries cannot be true. It is evolutionists which say we should wait for a 'hopeful monster' to make the odds better. The problem is though that with each advance in science, the odds for evolutionists and atheists keep getting worse so there is no reason to expect such an event. The sole 'refutation' that evo/atheists have for ID is that perhaps, possibly, maybe, someday, something which they do not have the vaguest idea of what it could be will be found to support their theory. Hate to tell you that is not science, that is an inveterate refusal to acknowledge reality.

This is where to me the whole materialist structure falls apart - on information. Information has no material basis. Yes, we do need to transmit it by material means such as paper. However, the information itself has no material basis for it. For example take the following:

diNz eaetsh cheid.

Nietzsche is dead.

They both have the same material basis yet the first is nonsense (at least in English) but the second has information. It is the order that allows the letters to have meaning. The same information which was given in the second sentence could have been given on paper, by voice, by radio, by telegraph or whatever, the information would have been the same regardless of the material medium. The same with DNA or anything else, it is the order expressed, not the materials from which it is made which provide the functionality. One can have all the pieces to build an automobile, but if one does not know or have available the information on how to assemble it one will not be able to put it together.

Me: That number was a match of 1 in 720 million. The jury, like a bunch of creationists, rejected that evidence

You really are twisting the facts!

This goes to show how meaningless it is to put up numbers. Dolts haven't a clue what they mean. For lurkers: The DNA samples were such a close match that the chance of finding a random RFLP match in the general population would be 1 in 720 million.

You (and evo 'scientists') are saying that a 55% concordance in a specially selected area of a protein (selected for concordance) proves anything.-me-

Nobody is saying any such thing. Stop lying.

You can call me a liar, but your own words from the post I responded to prove who is the liar::

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.
1178 posted on 12/07/2002 6:58 AM PST by general_re

Also the so called evo 'scientists' which you quoted also make the same (by your own admission) ridiculous statement:

Together, these facts make a reasonable case for an evolutionary connection between the Mot proteins of the flagellar motor and the Exb proteins of outer-membrane transport (and by extension the TolQ/TolR proteins, which are related to ExbB/ExbD but whose functions are less understood).
1076 posted on 12/04/2002 10:26 PM PST by general_re

How you can deny something you have been arguing about for over 100 posts is beyond credulity. Clearly like other evolutionists you do not have much regard for honesty or even for your own credibility.

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