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.
-NSF-
For a list of the Assembling the Tree of Life grants, see: http://www.nsf.gov/bio/pubs/awards/atol_02.htm
Nope. You can analyse the data without the assumption of a tree and a tree will emerge. It's a tangled mess at the root, (a root ball, really), the trunk is very wide (lots of slush) but the branches are well defined. If you look for a lawn, you find a tree.
No, it is most definitely not garbage. You don't always know what your total population is. You don't need to. This is part of everyday science and experimental design.
Do yourself a favour and read up on statistics.
Except in the case of photosynthesis.
More lawyering tricks counselor? Yes it has a conventional meaning. Is that your meaning? You won't tell us. Why not?
You see counselor, the question at hand is not whether I think this or that is designed, but do you and why? You are the one making grand claims about detecting design, not I. I think the jury knows this. They know that you've been repeatedly challenged to give a definition of design and detection method and you have not done so. It'd be so easy for you to go to dictionary and pick your definition from the list, supposing your definition is indeed conventional. The jury wonders why you won't do that.
For the record, my definition of design is the conventional one I think. To be designed a supposed artifact must be the intended result of an action. For example, I think that the Nazca lines are the result of intentional human action and therefore constitute design. Any inference of design must use an argument about origin and intent. The reliability of the inference directly flows from the quality of evidence regarding origin and intent. With good evidence it is possible to reliably infer "designed" or "not designed" (although the latter requires additional assumptions). Without evidence about origin and intent then the most one can say about the design of a supposed artifact is "unknown."
For some specific examples, I think the sand castles are designed - I happen to know people do that intentionally. The termite mound is not designed - I don't think termites are capable of intention (but perhaps I'm wrong about that). The chimp nut-crushing station? Designed to the extent that chimps are capable of intention.
According to my definition, arguments from the supposed artifact alone back to origin and intent are not allowed. It appears to me that you think your definition of design does allow this backward inference. In fact I understand that to be central to the ID argument. It's this difference of opinion that's kept this dialog going so long.
Now counselor, I think I've been pretty explicit explanation of what I think about design. Why don't you present for the jury an similarly explicit explanation of what you think? Then we can subject it to analysis and let the jury decide if it corresponds to what they think.
It always helps to have a definite case to consider. I assume you're familiar with constellations. To me Orion is the most recognizable, in fact I can't look at it without seeing in my mind's eye shoulders, ankles and a belt and sword. After you tell us what you mean by design, tell us whether the Orion constellation is designed and why or why not. If you have some additional informative cases please present them too.
And it does.
However, this has proved false. It has given some very different results and now evolutionists have thrown out mtDNA as proving their theory:
You are mistaken. You are misunderstanding the point of the article you cite.
It in no way says that mtDNA analysis is being "thrown out" as you falsely assert. It simply points out that it's not free from ambiguous results, which is another thing entirely.
Is it so hard to just answer the question? Would you or wouldn't you expect to see a correlation between the trees? Why or why not?
if the information is real then any analysis is meaningful and could lead to discovery
Again, you're begging the question. If the big tree emerged by pasting together the small ones, would it be meaningful to you? Would you think it called for an explanation?
I really don't want to get into a philosophical debate about the meaning of real. I suggest we stick to simpler territory.
Bottom line to me is that 99.98% of the Darwin tree (which is vertically by time) will remain hypothesis.
Bottom line to me is that if the small trees correlated (which I do expect) and if pasted together they made a big tree (which I think they will) then it is meaningful and requires an explanation. Absent other knowledge I'd propose as the simplest explanation that living species are related in a tree-like fashion by common descent. Further, again absent other knowledge, I'd say that living species are a random sampling of all (living and extinct) species and would feel justified in supposing that all (living and extinct) species are so related.
A "par for the course" placemarker.
Right off the bat, the website confirmed what I believed to be true (emphasis mine):
I didn't find anything at the Berkley site to answer my question, so I clicked on a link they provided to the "Natural History of Genes."
That took me to a Utah website. Genetic Science Learning Center- University of Utah
The home page was generalized, so I searched on "evolution" and found some information:
Homeotic Gene Organization Is Conserved Through Evolution
Mutations In Mammalian Homeotic Genes
Homeotic Mutations Could Be Involved In Evolutionary Change
Both of these articles are very interesting hypotheses that homeotic gene mutations could be the cause for change in body shape (and presumably, new body plans or phyla.)
So far, all the information is quite interesting but has not elevated the value of 99.98% of the evolutionary tree from being a hypotheses, nor has it shown "in detail how genetic information for long extinct species can be deduced using genetic information from living species".
So again I am left with an evolutionary tree where 99.98% of it is hypothetical and only the very top .02% can be confirmed by genetics. It still looks like a "lawn" or "periwinkle" or "onion skin" to me.
It seems to me if the geneticists can project the DNA of a long extinct creature, they could also actualize it to see if they were correct. Of course, that still doesn't "connect the dots" to the next one, but given enough time and a controlled environment perhaps they could provoke a natural mutation.
The investigation did however raise another question in my mind. If homeotic gene mutuations are responsible for the body plans and diversification --- then why haven't there been any new animal phyla (body plans) since the Cambrian explosion which began about 530 million years and last only, what, 50 million years? It seems presumptuous that the surviving 30 or so body plans exhausts the entire universe of viable body plans.
Do you have any more links that would help with my original question?
Photosynthesis is not an organism, even less a species. The phylogenetic tree under discussion is not for individual genes or processes coded for by individual genes.
I don't really enjoy this flitting about from subject to subject when we haven't yet progressed beyond some very simple ideas.
The 25% match quote you pasted earlier refers to individual bases, not sequence. Dr. Stochastic and I both pointed this out to you independently on this thread. Living organisms share individual nucleotides or carbon or water. We are all related. Just for analogy, suppose you call a claim of mine only a hypothesis. You then do a web search on the word 'hypothesis' and return with a number of hits, all of them unrelated to my claim and say "Just as I thought, your claim is only a hypothesis!".
To get an idea of the relationship between organisms or species, we look at sequence not at individual bases or atoms. Does that make sense?
My question was not a trick question. It was clear. You took six paragraphs and did not answer "Are the Nazca lines designed?" in an unequivocal manner as I pointed out. That manner was with a single word answer, yes or no. Alone those words are unequivocal. Now as I pointed out, the reason I answered your question in another thread with you as the design detector was due to your insistence upon something above and beyond the normal definition of design. You expected an algorithm and a testing procedure("Give me the algorithm. " morphed to "can you provide an unambigous definition of design and a testable method for detecting it?" morphed to "how you will go from my answer to an unambiguous definition of design and a general method of detecting it from first principles"). I do not see that in any definition of the word design. It is you doing the lawyering. In each case of these discussions, it was you that questioned something I had posted. You don't like my answer, fine. But we have now determined at least two things. The first was a direct statement "Design can be inferred". This came as a result of you posting a ridiculous question "To you a cell looks and acts like a Rolex watch?". After about 2 days by the record you concurred by posting "I absolutely agree that design can be inferred reliably when there is reliable historical knowledge."(A lawerly answer, I add)
The second point now established is not as clear. It is rather a negation of your assertion --- We need that precise definition of design and an algorithm to detect it.. It is apparent that you have not given an algorithm nor a precise definition of design. Yet you have, as I have, determined that the Nazca lines are designed. The people that "first" saw them also concluded that they were designed. Some used backwards inference to impel them to search for the designers. That is what often happens in archeology. An artifact is discovered then the designer is sought. Your argument does not convince me.
The grand claims I made about detecting design have been what? "Design can be inferred." Now I add to that "the dictionary definition of design is sufficient to allow the inference". You have now brought up the red herring lawyer charge in this discussion. Red herring are a sign of people fishing about.
They may be capable about intention regarding some matters, but none regarding the design of the mound. The termites respond to chemical and visual signals from the environment. Each termite follows a set of very simple rules and knows not what the other termites are doing. The mound is an emergent structure.
Gratuitous "Gasp!" and "No kidding!"
The tree sequence is this
"We did a kind of tree analysis of all 188 genes to determine what the best evolutionary tree was. We found that a fraction of the genes supported each of the different possible arrangements of the tree. It's clear that the genes themselves have different evolutionary histories," Maybe alamo-girl's lawn is not so far-fetched after all. And this also demonstrates that when you seek a tree, you find a tree, at least as far as it pertains to tree analysis. 239 posted on 11/24/2002 7:44 PM CST by AndrewC To: AndrewC And this also demonstrates that when you seek a tree, you find a tree, at least as far as it pertains to tree analysis. Nope. You can analyse the data without the assumption of a tree and a tree will emerge. It's a tangled mess at the root, (a root ball, really), the trunk is very wide (lots of slush) but the branches are well defined. If you look for a lawn, you find a tree. 341 posted on 11/25/2002 10:12 AM CST by Nebullis To: Nebullis If you look for a lawn, you find a tree. Except in the case of photosynthesis. 344 posted on 11/25/2002 12:39 PM CST by AndrewC Then your 351 which this is answering |
If you have an objection to the article I excerpted earlier, I suggest you ought to take it up with the author, Jonathan Marks, Department of Anthropology, University of California, Berkely. He claims to be both a geneticist and an anthropologist.
For lurkers, the article is What It Really Means To Be 99% Chimpanzee
As to the point you and Doctor Stochastic raised, I can only say "Jeepers, of course we are talking about gene sequences!" I could have accurately remarked that every creature that every was or now is - is made of fields and thus 100% of the same stuff. That has nothing to do with a biological evolution tree though it would have a great deal to do with Cosmology.
Can we please skip the didactic and find an answer to this: "in detail how genetic information for long extinct species can be deduced using genetic information from living species"
Do you have any more links that would help?
It's hardly a red herring. Lawyers have a side. They argue for it using a variety of rhetorical methods irrespective of the evidence. I'm just pointing out that your behavior is like that. You don't have a scientific attitude.
To take an example, I asked you point-blank if you were a lawyer. You could have said yes, you could have said no, you could have said it's immaterial. Instead you didn't answer but said the question should be asked of me instead. Bravo!
For the record, I'm not a lawyer.
My question was not a trick question. It was clear.
Yes, it is a trick question and no it isn't clear. For example, you think my robot drawing a picture of a spider is design. I trust you think this based on your definition of design. Based on my definition I don't think it is design. The robot is designed. The fact that it draws is by design. The fact that it drew a spider is not by design.
Now I even gave you a link to a dictionary entry for the word design. What conclusion should the jury draw from the fact that you didn't simply go there and copy your supposedly conventional definition out? Lazy, contrary or lawyerly?
You took six paragraphs and did not answer "Are the Nazca lines designed?" in an unequivocal manner...
I've been as unequivocal as I can. To reiterate, based on my definition and inference procedure they are an instance of design. I think I've given a more satisfactory answer to your question than you have of mine.
You expected an algorithm and a testing procedure... I do not see that in any definition of the word design.
We're also talking about inference of same, correct? Inference to me imples a procedure for performing the inference. An algorithm is one way of being explicit about procedure. Feel free to provide it any way you like.
The grand claims I made about detecting design have been what? "Design can be inferred."
I've assumed all along you are arguing for Dembski's position, that from examination of a supposed artifact alone one is able to say reliably "designed" or "not designed." Is that not your view?
Now, about Orion. Is it design or not? Why or why not?
I guess YOU were.
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