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

[Youngblood]

Of course it’s a sampling question. Even if your sample represents only 1% of the group of interest your findings are relevent, so long as your sample is randomly chosen from across the board. All you have to do is take your known group, put them all in a hat, pull a bunch of them out, do your number crunching, then repeat. If there is an underlying pattern to the data, it will show up. National opinion polls are regularly based on samples of 1000-1500 people. If you interview 1500 people across the US, chosen totally at random, and 70% say they love GW Bush, then it’s pretty clear that the majority people are happy with the President’s performance. You don’t need to know the total population, unless you want to give the exact figure (70% of 280 million, whatever that is) who like Bush. It’s the proportions that we’re normally interested in.

Take the good Doctor’s advice and read up on stats. And just because I disagree with you does not mean I’m dishonest.

[AndrewC]

Wasn't I unequivocal?

No. you were not unequivocal. My definition has nothing to do with it. Design has a conventional meaning. The word was around before I was born. People used that word to communicate. The lines at Nazca are older than you or I. The lines did not exist at a certain point in time. Now the simple question stated in "Are the Nazca lines designed?" does not mention me or any esoteric definition of design. It should not be difficult to answer for the normal person. I answer, yes. You see, my answer is not equivocal. I did not say "yes, but it depends on what you mean by design". Now, last time we had a discussion, my answer was contingent on you. The reason I did that was due to your request of something not inherent in the word "design". In order to keep confusion to a minimum, I used what I considered a fairly reliable "device" with a capacity to detect design, you. After about a day we did reach an answer to your satisfaction, namely that "Design can be inferred". Thus, I was correct in my assessment of the design detector. At this point it appears as if the detector has developed a malfunction. Please prove me wrong and state the answer to "Are the Nazca lines designed?" in an unequivocal manner as I did. Let me repeat my answer. Yes.

[Junior]

BEFORE PHOTOSYNTHESIS LIFE WAS IMPOSSIBLE BECAUSE THERE WAS NOTHING TO EAT

Somenone should tell that to the chemosynthetic life around the black smokers...

[AndrewC]

Somenone should tell that to the chemosynthetic life around the black smokers... [sic]

[PatrickHenry]

Placemarker to start another day

[js1138]

There are lots of features in the mars photos besides the "face". there are, for example, the "glass worms".

Unless you can demonstrate how your "criteria" can be applied to a specific instance, you are just blowing smoke. So lead us through a step by step analysis.

[gore3000]

It's garbage, whether you realize it or not. ,P> You still cannot refute my statement. There is no problem with the scope. All parts of an organism interact with each other. Also because you did not see that your example disproves evolution does not mean that it does not.

[gore3000]

Somenone should tell that to the chemosynthetic life around the black smokers...

I mentioned that and chemosynthesis is an even bigger impossibility to have arisen by chance than photosynthesis. So as I said, the whole 'research' is shamefully dishonest because before that there was nothing to eat.

[gore3000]

There are lots of features in the mars photos besides the "face". there are, for example, the "glass worms".

Well, I have not seen those and unlike evolutionists I do not like to speak about things without the facts before me.

However, take abiogenesis, we know life was intelligently designed because:

1. there are no chemical reactions specifying the order we find in DNA.
2. DNA is highly complex, it would take a minimum of half a million bases in the correct order to produce a living, reproducing organism. The odds are greater than astronomical no matter how you slice it.

So there you have it - specified complexity not attributable to any possible natural mechanism.

[gore3000]

Even if your sample represents only 1% of the group of interest your findings are relevent,

In sampling you know the total population being examined, here you do not. You cannot solve for x (total species known and unknown) when all you know is y (known species). You have insufficient data to make a valid determination - as I have been saying from the beginning. There is no criteria to prove that the existing species comprise 1%, 5%, 10%, 20% or even 50% of the total amount of species ever. Such a ration could only be arrived at if we know the total number of unknown species in the first place which by definition we do not know. It's garbage.

[artios]

You start with the government program you want to start and the freedom you want to erode, then work backwords. Very simple really. If you have sufficient anger toward God and hatred for freedom it is a piece of cake.

[Junior]

So as I said, the whole 'research' is shamefully dishonest because before that there was nothing to eat.

So, how do you explain the microbes that "eat" minerals?

[general_re]

All parts of an organism interact with each other. Also because you did not see that your example disproves evolution does not mean that it does not.L

And there's the fallacy, right there in a nutshell. Just because one part of the cascade depend on another part, that doesn't mean that all parts of an organism are dependent on that cascade, or that they're dependent on anything at all. You've gone way out on the deep end and defined irreducible complexity so broadly that even Dembski and Behe wouldn't follow you. Your heroes had the brains to pull up and stop going, whereas you just sailed right off the cliff. Better luck next thread - I'm done with you on this one.

[MEGoody]

"The real "Tree of Life" is the one on which Jesus loved us."

Amen!

[MEGoody]

By golly, if you turn it on its side, it does kind of look like a lawn.

[MEGoody]

"Tree (connected), lawn (disconnected)."

Not completely true. In a lawn, there are plants that are not connected to one another. However, there are also blades of grass that have 'runners' (e.g. roots that travel along under the ground) off which other blades of grass have grown.

[MEGoody]

How can extinction rates be estimated by way of an estimated 10% sample of an unknown (but estimated) survey population? Easy. Because we "know" that humans are a rainforest burning, species killing, blight on holy mother Earth.

That was merely a rant, not an answer. If you take 10% times a number you don't know, you aren't going to know what the resulting number is. Pretty simple.

[js1138]

However, take abiogenesis, we know life was intelligently designed because:

1. there are no chemical reactions specifying the order we find in DNA.
2. DNA is highly complex, it would take a minimum of half a million bases in the correct order to produce a living, reproducing organism. The odds are greater than astronomical no matter how you slice it.

Point one simply restates the assumption that bases are like letters of an alphabet.

Point two is genuinely interesting, but it is more compatible with a bottom up design approach rather than a top down approach. There is no way to know (in advance) the effect of a change without running the program, particularly when the environment can change between conception and adulthood.

In fact, the more complex the "design" and the more complex the interaction between competing designs, the more impossible it becomes to envoke top down design principles. One is left with trial and error.

[Right Wing Professor]

It's a great idea. There hasn't been nearly enough support for vertical integration of the ever-increasing volume of genome information. The only downside is $17 million isn't a whole lot of money. It's a lot for NSF to commit - NSF is chronically underfunded - but if NIH were to take something like this on, they could throw $$$ at it.

BTW, whoever came up with the ping list, thanks!

[Nebullis]

It would be very helpful if you could provide a link to a university or government website which describes in detail how genetic information for long extinct species can be deduced using genetic information from living species.

Here's a start. The Museum of Paleontology at Berkely has an informative website here.