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]

Which you have yet to define precisely.

Which is no different than "evolution" or "species".

[Nebullis]

So, is a termite mound designed or not? And why?

[Trickyguy]

Since we share 25% of our DNA with plants, I bet the Tree of Life looks like a dandelion!

[AndrewC]

So, is a termite mound designed or not? And why?

Does a termite have a mind?

[Jeremiah Jr]

Revelation 2:7

"He who has an ear, let him hear what the Spirit says to the churches. To him who overcomes I will give to eat from the tree of life, which is in the midst of the Paradise of G-d."

THE RIVER OF EDEN AND TREE OF LIFE - PART 1

Habakkuk 2:14
For the earth will be filled With the knowledge of the glory of the LORD, As the waters cover the seabed.

Come on in, the well is fine!

[Nebullis]

You can't answer. Perhaps you don't have defined criteria for determining design.

[AndrewC]

Perhaps you don't have defined criteria for determining design.

Is that kinda like a species?

[AndrewC]

[RightWhale]

You know, you can try to make that figure out of dowels or wire and styrofoam or whatever, and it isn't hard. When you do that, though, you realize the structure isn't stable unless you put in those extra links like this diagram.

[forsnax5]

Perhaps you don't have defined criteria for determining design.

I just spent about an hour googling "Recognizing Intelligent Design" (and a number of variations thereof), and this appears to be one of those "I know it when I see it" things.

The most interesting thing that I found was the difference between the published (Nature, Science, etc.) discussions and the underground (I suppose I can include FreeRepublic in that category, but there are LOTS of sites on the internet discussing this topic).

In the published articles, Dembski, Behe, and other proponents of ID harp on complexity, (either irreducible or specified) as the key indicator of design, and the (published) opponents of ID nitpick the concepts of irreducibilty and specificity.

In the underground category, examples of design focus on simplicity rather than complexity. A good example of that category is the picture of the Nazca spider that AndrewC posted -- very simple and obviously produced by an intelligence (and derived from a very complex design from nature).

Even seemingly complex designs by humans (an automobile, for example) are less complex than what they serve to replace (a horse). An airplane is less complex than a bird. A computer is less complex than a brain.

Complexity would seem to be a contra-indication of design...

[LogicWings]

It was these circumstances, and this intellectual milieu, that led philosopher Friedrich Nietzsche to declare that "God is dead" and to predict the rise of new and terrible manifestations of barbarism in the century that was to come. As he put it, "For ... we shall have upheavals, a convulsion of earthquakes, a moving of mountains and valleys, the like of which has never been dreamed of ... there will be wars the like of which have never yet been seen on earth." The non-believer Nietzsche would agree wholly with the Christian believer Dostoyevsky about one thing: Without faith in God, all horrors, all of man's worst nightmares, would become possible. And so they did."

I had heard this charge against Nietzsche so many times I just assumed it to be true. When I actually read what he wrote I was surprised to find this not to be the case. What Nietzsche was actually talking about was that religion was ceasing to have any cultural influence over the conduct of human beings. The moral power of belief in God was falling away, even when people still believed. Like an appendix the church was a fading appendage that still existed but had no real influence anymore. People still believed, it just had no power over them anymore. He wasn't declaring a metaphysical fact, but a social one.

When I look at history, any part of it, I see relatively brief periods of civilization between eras of barbarism and savagery. A gander at the Inquisition, where they did things that I don't even like to think about, the Crusades, or the fact that somewhere between 3 to 8 million mostly women and children were burned at the stake, and other delightful punishments for being accused of being witches in Europe during the Christian era of the previous 2 millenia are just minor examples.

There weren't the same number of people, so the numbers aren't anywhere near close, but as percentage of the population things were just as bad. And the actual tortures were many times worse. In the inquisition they used to heat up an iron chair until it glowed red hot and . . . never mind.

More people are alive than all those born before about 1900 or so. I could make the same prediction and it will be true, because there are more people to die. But in reality it is no different. It has always been so. Every culture I've ever studied, no matter where, at times, practiced the most despicable things, no matter what they believed.

The Commies just have the pleasure of holding the numbers record. As for the quality of torture, I would say the Phonecians win the prize there. Why they used to take a person and put him in a . . . well, I don't want to give you nightmares. But it took 3 weeks to die.

[stanz]

I recall Clifford Jolly stating that, rather than looking at Darwinian prediction as a tree, it could be suggested that it resembles the rings of an onion with phyla radiating outward. Interesting construct, but I never saw any chart.

[general_re]

I had heard this charge against Nietzsche so many times I just assumed it to be true. When I actually read what he wrote I was surprised to find this not to be the case.

That quote is extremely popular with people who haven't actually read Nietzsche, as you've discovered. I long ago despaired at trying to correct anyone on it, though. Life is too short to try and bring sight to those who refuse to see.

[Alamo-Girl]

Thank you so much for your post!

Evidently the naturalist side is already considering a response to discoveries in support of intelligent design: Metaphysical Naturalism and Intelligent Design

[Doctor Stochastic]

Simple. The rate is independent of the total number. There are systematic biases such as one only looks at psecies that are easy to observe. If .01% of the observed species disappear each century, this is an estimate of the disappearance rate of all species. There is a large variance in these types of computations however. There are relevant papers in Biometrica, Biometrics, PNAS, and other publications.

[Doctor Stochastic]

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.

A statistically meaningless question. That's like saying that uncorrelated two binary sequences match at half their locations. The guy's article is just nonsense mathematical ly.

More relevant would be the correlation between sequences.

[Sabertooth]

If .01% of the observed species disappear each century, this is an estimate of the disappearance rate of all species.

Based on the assumption that unobserved species disappear at the same rate, for which we have zero evidence. That strikes me as a shot in the dark, whereas an estimate ought to be an educated guess.

[PatrickHenry]

Bump in the night.

[Doctor Stochastic]

No, the fossil date look like trees. One can easily see the structures. One (unfortunately now deceased, at 90+) palenologist friend of mine showed me his work from the late 1940s and early 1950s showing the family structures of trees on both sides of the South Atlantic. The oldest fossils were exactly the same. Later fossils showed a binary divergence along the Atlantic. The orignal structure split into two structues, one in Africa and one in South America. The structures continued to evolve independently. One could trace family trees back to a common ancestor from before the split. This was before the mechanism of continental drift was discovered.

[Doctor Stochastic]

...godless bayesean priors...

(With your permission) I hope to use this quote some day during a statistical discussion. Sometimes I do indulge in ein bischen Schadenfreud (spelling?) watching the Bayseans, Frequentists, and Fiducialists, argue.