Skip to comments.Discovering the Tree of Life
Posted on 11/22/2002 9:09:10 PM PST by 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.
For a list of the Assembling the Tree of Life grants, see: http://www.nsf.gov/bio/pubs/awards/atol_02.htm
A little something for a quiet weekend's musings.
"What men... believe---really does matter."
From Dr. Fuz Rana: "...the hominid fossil record is not a family "tree" but a "lawn."
("Toumai Man Offers Evolutionists No Hope," Connections, 3rd & 4th Quarter 2002, Quarterly Newsletter of Reasons to Believe.)
Crayola stock took a big bump!
No it does not. Evolutionists claimed that mitochondrial DNA would verify the classifications that had been made by phenotype. However, this has proved false. It has given some very different results and now evolutionists have thrown out mtDNA as proving their theory:
1. Ying Cao, Axel Janke, Peter J. Waddell, Michael Westerman, Osamu Takenaka, Shigenori Murata, Norihiro Okada, Svante Pääbo, and Masami Hasegawa, Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders, Journal of Molecular Evolution 47 (1998): 307-322.
It is widely believed that molecular data confirm morphological data when the history of groups such as the mammals is being reconstructed. Many cases exist, however, where molecules (such as proteins) give false or erroneous phylogenies. This paper, by a team of researchers from Japan, Germany, and Australia, demonstrates that different mitochondrial proteins can give different, and contradictory, groupings. In particular, the protein NADH dehydrogenase (ND1) places primates and rodents together as closest relatives, with ferungulates (artiodactyls + cetaceans + perisodactyls + carnivores) as more distantly related to primates -- in contradiction to most other data, which places primates and ferungulates together as closest relatives. The authors conclude that this anomalous phylogenetic grouping is not due to a stochastic error, but is due to convergent or parallel evolution (p. 321), suggesting that molecular evidence is not free from the confounding (historically misleading) effects known to plague other types of systematic data, such as anatomical patterns.
From: Bibliography presented to Ohio BD of Ed .
Your expectation has already been contradicted even without completely mapping the living genome. How will you revise your thinking?
My guess is slime mold is next. It can morph. Makes it easy for just-so stories
As edsheppa and Dr. Stochastic have said, this has already been thoroughly falsified. If you only listen to the selective lawyering from your side about the places where the data conflict, you could easily miss this. (Especially on this forum.) Nevertheless the overall picture is very plain.
Figure 4.4.1. Human endogenous retrovirus K (HERV-K) insertions in identical chromosomal locations in various primates (Reprinted from Lebedev et al. 2000, © 2000, with permission from Elsevier Science).
[This ping list for the evolution side of evolution threads, and sometimes for other science topics too. If you want to be included, let me know. This is not a ping list for the creationism side of the debate. If you've been getting unwanted pings, please tell me and I'll drop you.]
How can extinction rates be estimated by way of an estimated 10% sample of an unknown (but estimated) survey population?
Probably the environmentalists are using the same incredibly refined techniques as those used to estimate that there are 3 million homeless in the US. The numbers seem to come from the Seventh Planet.
Or perhaps the sixth, making it a stastical analysis by attenuation?
I had no idea using the term "lawn" would generate such a lively discussion. Jeepers!
I am aware that a device known as "the Tree of Life" is used in the Kabala (new age version) and Tarot reading. My understanding is the Kabala originally was rooted from the Torah (Spanish) and of course the Tree of Life is mentioned in Genesis and Revelation as being in the center of Eden and Paradise respectively. That's one reason why I believe Eden is in the spiritual realm - but I digress...
Several of you seem to believe my "lawn" choice has already been disputed. But I'm not convinced by your assertions. I visualized a "lawn" when I saw this article:
What it really means to be 99% chimpanzee (excerpts:)
But in fact, DNA similarity is not structured in quite that way. There are, as everyone knows, only 4 bases in DNA. And this places an odd statistical constraint on the comparison of sequences. No DNA similarity at all that is to say, two random sequences that share no common ancestry are still going to match at one out of four sites. In other words, the zero mark of a DNA comparison is not zero percent similar, but 25% similar.
Once again, the DNA comparison requires context to be meaningful. Granted that a human and ape are over 98% genetically identical, a human and any earthly DNA-based life form must be at least 25% identical. A human and a daffodil share common ancestry and their DNA is thus obliged to match more than 25% of the time. For the sake of argument lets say 33%.
The point is that to say we are one-third daffodils because our DNA matches that of a daffodil 33% of the time, is not profound, its ridiculous. There is hardly any biological comparison you can make which will find us to be one-third daffodil, except perhaps the DNA.
In other words, just as Simpson argued in the 1960s, the genetic comparison is exceptional, not at all transcendent. DNA comparisons overestimate biological similarity at the low end and underestimate it at the high end in context, humans are biologically less than 25% daffodils and more than 98% chimpanzees.
The focus on base-pair mismatch itself is misleading, for it encodes a number of archaic assumptions about genetics and evolution. In fact, it ignores what is quite possibly the most significant development in biology in the last quarter-century namely, the complexity of genome structure.
If humans and chimpanzees are over 98% identical base-for-base, how do you make sense of the fact that chimpanzees have 10% more DNA than humans? That they have more alpha-hemoglobin genes and more Rh bloodgroup genes, and fewer Alu repeats, in their genome than humans? Or that the tips of their chromosomes contain DNA not present at the tips of human chromosomes?
Obviously there is a lot more to genomic evolution than just nucleotide substitution. But the percentage comparison renders that fact invisible, and thus obscures some of the most interesting evolutionary genetic questions.
Once you recognize that there are easily identifiable differences genetically between humans and chimpanzees the presence of terminal heterochromatin is 100% diagnostic you can begin to see that the pattern of relationships between the species is actually the same genetically as anatomically. Humans and chimps are simply very similar to, yet diagnosably different from, one another.
You also visualize a lawn when you see the fossil record represented as vertical parallel lines. (You have posted such pictures.) That's a question-begging reconstruction which assumes what it tries to show, that nothing is related to anything else.
The scale of similarities appears non-linear, yes, but that's because nothing is a zero. Common descent and all that. The daffodil is not totally unrelated to you. Nevertheless, nothing is as related to you as the chimp.
So, in your opinion, no species is related to any other species, and any similarities are purely coincidental?
Just the opposite! I see 25% hard genetic similarities among every living thing, like soil. Actually, I suspect on the animal side of the lawn the similarities will be greater, more like 50% but that's just a guess. It would look like a rise in the soil.
The "grass blade" for a daffodil is on the same lawn as the chimpanzee and the human. The chimpanzee is a tad longer than the human. And there might be a blade with a fork or two where creatures have differentiated to adapt to their environment (like the finches.)
If all the sequences are maintained in drawing it, then to me, the end result will look like a "lawn."
It's certainly possible to look out at the world of living things and to see only discrete, stand-alone creatures, utterly unrelated. That's exactly what we do see the very first time we open our eyes and look around. But one of the glories of the human mind is that when we look long enough and hard enough, we have the capacity to see similarities and patterns. Ultimately we learn to use the highly refined technique of inductive reasoning, which can lead us to useful theories about the world in which we live -- such as evolution. That's when the Tree of Life takes shape. And then, goodbye lawn.
Deductive and Inductive Thinking.
I do recall that chart, it shows Time one way and morphological distance the other. The Darwin prediction looks like a tree, the fossil evidence looks like a lawn.
For lurkers, you can see the pictures here.
When did we crack the soil genome?
He had 10 bad years but recovered. He died a little young anyway. Too much cheese in the diet.
If conditions were just right for the formation of one living organism, couldn't billions of unrelated living organisms have started up at the same time? It is a large planet, lots of room for lots of organisms.
Then some organisms might have had offspring and some might not, and there is the lawn, with many of the individual grass plants being similar but not identical.
Eventually one family line will dominate in an area. We see this clearly in the fall when leaves change in the forest. All the leaves of one kind of tree in one area of the forest will change at the same time, yet the leaves of the same kind of tree in a different part of the forest will change at a different time. You can see this, it is clusters of autumn color separated by clusters of green. Each cluster of autumn color is of related individuals.
So the descendents of one aboriginal organism will carry on, and descendents of another aboriginal organism will disappear. Of the billions or trillions or zentillions of aboriginal unrelated organisms, only a few billion family lines survive to this day.
Can DNA be traced back to a single aboriginal strand of DNA? Consider that some DNA sequences are favored and will appear in many different, unrelated family lines out of the zentillions of aboriginal unrelated family lines.
Mere chance? No, not chance. Some DNA sequences favor survival.
LOL! It's just that I see all creatures being made up of pretty much the same stuff, genetically speaking about 25%. When I visualize that on a chart, I happen to think it'll look like soil. Just my two cents...
Yes, the daffodil and the chimpanzee are 25% the same. Likewise, the daffodil and the human are 25% the same. If that article is right, the first 25% (or more) is a given.
As to the lawn model: Is it likely that there was first a living organism and that everything living descended from it?
My understanding is that fossils generally cannot provide tissue to map DNA information. If that is the case, and if this research project stays away from making projections based on evolution theory, what they'll end up with is a huge database with specific genetic information (which is also huge) on each and every known type of creature - plus a few that are now extinct.
Therefore, I do not see where this can project will have the database to graph a "tree" which has time vertically and morphology horizontally. It would be based on available genetic information.
But using that information, I can see them sorting, parsing and matching the database to look for genetic matches. If the resulting chart is genetic information vertically and morphology horizontally - I personally think it'll look like a "lawn."
Just my two cents...
Therefore, I do not see where this project will have the database to graph a "tree" which has time vertically and morphology horizontally - because the graph would be based on available genetic information as opposed to fossils.
Except when it comes to detecting design.... so say the Darwininians.
Which you have yet to define precisely.