Slashdot Mirror

For reasons you can see by looking at the tree of life entry for Eukaryotes: fungi it turns out are much more closely related to animals than plants are, and of course plants are vastly more closely related to animals than bacteria or viruses. That makes it hard to find antifungals that have a high therapeutic index: the ratio of the quantity needed to produce toxicity over the quantity needed for therapeutic effect.

http://tolweb.org/
Is also a Tree Of Life project, but unlike OpenTree, it have pictures and descriptions and it also contains extinct species.
For examples for Aves:
https://tree.opentreeoflife.or...
http://tolweb.org/Aves

http://tolweb.org/
Is also a Tree Of Life project, but unlike OpenTree, it have pictures and descriptions and it also contains extinct species.
For examples for Aves:
https://tree.opentreeoflife.or...
http://tolweb.org/Aves

Wonderful - now all the scientific feuding over whether Amborella is the basal angiosperm can spill over into wiki edit wars.

(Amborella trichopoda is a New Caledonian flowering plant (angiosperm) with no close relatives. The deepest split in the angiosperm phylogeny may be Amborella splitting from everything else. Much ink and enmity has been spent on whether or not this is so. Here is a summary I found, although on a skim read I suspect it was written by a partisan.)

> Primarily because the school boards aren't in the business of
> writing textbooks or funding the creation of the same.

Classical English literature
===================
you can get Shakespeare's works *FREE* from project Gutenberg http://www.gutenberg.org/ebook...

Astronomy
========
http://nineplanets.org/ (yeah, the website name is an anachronism) *FREE* and since it's a website, you don't need to order and pay for a new edition each time new discoveries are made

Evolution
=======
Tree of Life Project http://tolweb.org/tree/

Dinosaur Specific http://www.ucmp.berkeley.edu/d... *FREE* and since it's a website, you don't need to order and pay for a new edition each time new discoveries are made

For those fundamentalist schools who don't believe in evolution Project Gutenberg has the King James Bible and the Douay-Rheims version

A school district should be able to get a good chunk of its needs free off the web. Most of these sites will easily give permission to download and duplicate. Instead of handing out 16 KG of books to each student, hand out 16-gigabyte USB keys to each student with the necessary e-books and/or mirrored websites.

Because you have no clue how anatomy works?
We have thousands of fossils and skeletons of dinosaurs so we do know how the skeletons of those animals looks like. And it's not like every species is different, all Tetrapods following the same basic skeleton plan. Palaeontologist have enough knowledge and expertise to identify the species of a single bone correctly and if you can find some teeth you already know if it's a carnivore or herbivore.

It's basically Tetrapods>Reptiliomorpha>Amniota>Diapsida>Archosauromorpha>Archosauria>Dinosauria
http://tolweb.org/Dinosauria/14883

"creationism" is not a theory. You can call it a "hypothesis" in a sense that there is a flying teapot somewhere in the Universe. But at least the teapot "hypothesis" is a theory if you assume that we live in a limited universe.

The one difference between a scientific theory and nonsense is very simple: a scientific theory can be falsified.
You cannot falsify "creationism", or "God".

How would you try to falsify "creationism"? You need a time machine to go back to whatever time the "creationism" claims that "God" created everything. You can't use evidence because you don't know what "God" is so you can't say: it is because the evidence shows that that was God. You need to define and prove "God" first. Since anything can be "God".

Let me put it this way. If I say: God blessed me with my good wife and my good children. Can you _disprove_ that is was not God? If it is not possible to _disprove_ something, it is not a theory, it's faith.

Let me ask now. If I say: my genes shows that we share at least 90% similarity with hominidae, and Hominidae share genes with Catarrhini, and they share genes with Primates, and they share genes with Placental Mammals and further with Mammals. Of course you can disprove that, it's easy: just analyse the genes and get evidence that I'm wrong.
See Tree of life Project

You see now the difference between a "scientific theory" and faith?

Eh, evolution is proven beyond any doubt. If anything the theory of evolution is the best proven theory. I think, even the Theory of Relativity is not as good proven as the theory of evolution.

Actually, in classical taxonomy Mammals are a class that originates from the clade Amniotes, as are birds and reptiles. That method of classification was recently abandoned because it was too complex. Especially for this topic: the term "reptile" never had a sound definition (it used to be "all amniotes that are not birds or mammals"). Phylogeny attempts to be the less ambiguous replacement.

See also the lower right corner here. As for Wikipedia, I prefer to use this one.

But fungi are closer to animals than plants! It should be easier to cross a dog with a champignon. Or a fly with a fly agaric.

http://tolweb.org/Eukaryotes/3

http://live.tolweb.org/Octopoteuthidae/19834

http://tolweb.org/Priapulida/2476

Yes, they're called priapulidae.

From skeptic anoted bible :

In Genesis, the earth is created (1:1) before light (1:3), sun and stars (1:16); birds and whales (1:21) before reptiles and insects (1:24); and flowering plants (1:11) before any animals (1:20). The order of events known from science is in each case just the opposite.

A few clarification why it is not the correct order :
1) Bird were certainly late at the party after the reptile were created.
2) Sun and star were certainly created before planet and earth (heavy element were created in novae IIRC)
3) Whales are mammalians, a late addition to the animal worlds. Certainly came after the reptilians and insects.
4) more damning as said above angiosperm are a late addition only 130+ million year old roughly

Quote : " 2. Go throgh a textbook on evolution with the list you wrote in step one and you will discover something very odd. Same order."
Only if you don't know when flower came into the evolutionary tree, ignore that whale are mammals, ignore that byrd are late addition too, ignore basic astronomy. Oh well anyway let us ignore science altogether , and you are right

Let's try that again with the link this time.
From this page here at ToL, you can see that there is a collaboration between efforts as to not overlap in data. It also states that the goals of each are slightly different in that EOL focuses more on specific species, whereas the ToL is more about phylogenetic classifications and evolutionary branches. I've been looking into the National Science Foundation's AToL program recently because of an offer for grad school which is due to a grant from that specific program and I'm curious what, if any, connection there is between the two.

So where can we download this data and what is the license?

The data from tolweb.org are downloadable under a Creative Commons license.

Only 30000?
There are Tens of millions of different species on earth - Flowering plants ALONE are numbering 250000!
there is another similar project called tree of life

Not the story - the project. What I mean is: how is this new project related to this one: http://tolweb.org/ if at all?

I could not, would not, on a boat.
I will not, will not, with a goat.
I will not eat them in the rain.
I will not eat them on a train.
Not in the dark! Not in a tree!
Not in a car! You let me be!
I do not like them in a box.
I do not like them with a fox.
I will not eat them in a house.
I do not like them with a mouse.
I do not like them here or there.
I do not like them ANYWHERE!

A deathly fear of squid and octopus?

Well, I hate to mention this, but if you're serious, don't look up Vampyroteuthis infernalis . Like this one from Hawaii, which looks somewhat similar, it is a deep red color and lives in the deep sea. Vampyroteuthis is also known as the "vampire squid", it shares traits of both squid and octopods (another similarity), and its body is (wait for it) described as having "the consistency of a jellyfish". So, it sounds rather close to the "jellysquidfishapus" you imagine in your nightmares. Sorry. It looks like it exists already. If it's any consolation, it's small (max. 13cm long).

There have been 8 armed squid described before including the Taningia danae species by the same scientists, though our understanding of these animals is poor at best. Though I have to say I am puzzled as to why the Octosquid was assigned to the Mastigoteuthidae genus other than it seems to be a catchall genus for weird squid species that we do not know much about...

Oh and hey Otter! What's up dude? I actually had no idea these guys were in Kona. Had that been known, I would have visited last time I was there.

You might want to hip yourself to isochron dating before you suggest that there's any rationally perceptible chance that the age is off by six orders of magnitude.

And yet again, you force words in my mouth that were not spoken. WHEN did I suggest that there is a serious chance that the age is off by six orders of magnitude? Quote me. Specifically, where did I say it?

It seems to me that you are simply hearing what you want to hear. And THAT is how you are forcing a confrontation when none exists.

Ah, and here's the real meat - you don't want that to be true. Your use of the term 'macroevolution' is a revealing code word.

Oooo. A "codeword". Explains everything, doesn't it? (Excuse me while I roll my eyes.)

But as to evolution after the origin of life - Why is it that the genomes of all life, when compared, form a nested tree where branches and mutations can be traced in detail and with quite rare ambiguity, and by remarkable coincidence that tree matches up essentially perfectly with the independently generated (indeed, generated before genetics) "tree of life" based on physical classification?

And here we see that you have no idea what you're really talking about, but you're going to defend it to the end, anyway. From the tree of life website:

The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of Life. We hope to provide a comprehensive discussion of these issues on this page soon. For the time being, please refer to the papers listed in the References section.

Darwin's "Tree of life" is not useful to the modern evolutionary scientist, as a variety of new research into the factors that change life (such as recombination, gene loss, duplication, and gene creation are a few of the processes whereby genes can be transferred within and between species) make the concept of the Tree of Life outmoded. More info: http://www.physorg.com/news92912140.html

And even that's silly. Look at cheetahs. They apparently went through a genetic 'pinch point' about 10,000 years ago. Their genetic diversity is so low that they can accept skin grafts from each other without rejection - only one other species is known to be able to do that. If humans went through a similar 'pinch point' anywhere in the last 100,000 years, how come transplant rejection is such a problem?

And again, you demonstrate that you know enough to be dangerous, but not enough to actually know what the hell you're talking about. Here:

Humans have remarkably little genetic diversity, especially in comparison to our closest living relative, the chimpanzee. Indeed, there is substantially more genetic difference among individuals within chimpanzee troops in West Africa than among all living humans on earth. As shown in Figure 1, this is due to a series of bottlenecks in human evolutionary history. Geneticists studying many different parts of the human genome have concluded that the past effective population size (that is, the number of reproducing females) averaged only 10,000 individuals over the last one million years, and was as low as 5,000 around 70,000 years ago. Compare this to the approximately one billion reproducing females alive today, and it becomes clear just how narrow these bottlenecks were.

Hey, I'm not the one forcing the confrontation.

If you'll pardon my crassness, bullshit. You're intentionally forcing an argument because you belive you already understand both sides of the argument, and y

I hope there's not too much duplication with the Tree of Life.

the tree of life project: http://tolweb.org/tree/phylogeny.html

...and also this http://www.tolweb.org/tree/

That's not surprising i think, we are talking about millions of species (that's even if we are only talking about creatures > 0.1mm) And for many of those it's sometimes not easy to see whether 2 instances are from the same species or not. See the http://www.tolweb.org/tree/tree of life for an overview.

"I find the lack of 'intermediate' species, (like fish who are starting to grow legs, or whatever) difficult for me to accept."

"Lack"? What, like, until discoveries in the late 19th century or something?

There's Eusthenopteron , Panderichthys , and the very recently-discovered Tiktaalik , which was even the subject of a previous /. article. There's also Acanthostega , which is a very "fishy" tetrapod (vertebrate with 4 limbs).

Or do you mean why aren't there any now? There are mudskippers, I suppose, but the reality is, the land already has many leg-bearing vertebrates, so there isn't the same incentive for fish to expand into that environment as there was back in the Devonian, when the first tetrapods evolved from lobe-finned fish.

Well, here's the "thumbnail":

http://www.nature.com/news/2006/060403/full/060403 -7.html

The cited article does mention that the paper is in Nature. If you subscribe to it, or the institution where you work does, you can get the full paper.

Dang, even from the thumbnail-sized picture it is a rather fishy-looking tetrapod, or a tetrapod-looking fish. Either way, it is a beautiful fossil specimen that looks as "transitional" as fossils already known, such as Acanthostega .

I don't think you want to play as a Fungi. Unless you don't mind being someone else's dinner or lab experiment.

Here is an example of marketing the Tree of Life to our kids.

Evolution is not a fact, it is a testable, refutable scientific theory that thus far has been an accurate predictor of the observed biological world.

...ptero"saurs" - they were warm-blooded furry and laid eggs. That is a monotreme, like the spiny echidna and duck-bill platypus.

Not really. You've picked two of the defining features of monotremes, but it takes much more than that to group creatures together. And the "fur" from pterosaurs is almost certainly very different from mammalian hair.

Pterosaurs are a group related to dinosaurs. They're both part of the Archosaurs - a group that contains modern crocodiles and birds and their extinct relatives. Archosaurs in turn are part of the Diapsids, which brings in modern lizards.

Monotremes are a subset of Mammals, which are Synapsids. You can look this stuff up at the Tree of Life web page.

I don't mean to be rude here, but your statement is a bit like saying that two people at a family reunion must be brother and sister because they're both of medium build with blond hair.

birds in general have their origins traced back to dinosaur-era reptiles. That's a pretty huge developmental shift between humanity and bird.

1. For viable species, selection favours those most efficient at doing what they do, which is unlikely to favour innovation except in times of stress.
2. While there are well known examples of convergent evolution, there are a lot more examples of the loss of ancestral function in descendant clades.
3. Of the millions of species descended from the last common ancestor (LCA) of birds and mammals, homo sapiens sapiens is but one and thus clearly atypical.*

Cockatoos ... develop intelligence of many sorts, though of a more social nature.

it also seems to make the possibility of intelligent life outside our known observed environments seem less unlikely too - especially if it can develop in so seemingly independant circumstances, despite a somewhat shared environment.

But I'm more inclined to think that these guys probably have a lot more interesting robotics applications than octopusii do.

Unless they think that making robots taste delicious is the secret to robot movement. Mmm... octopod

"i wonder which specific DNA sequence they use, since it should be present in all species and sufficiently divergent to discriminate between species."

True if they actually want to infer a phylogeny of all those species (the so-called Tree of Life). Choosing the adequate data is only one of the problems for those seeking to do this, among other you have huge computational problems (give use faster computers please!) as well as biological problems such as: is the history of life adequatly represented by a tree ? (if the answer is no, the computanional problems get worse since networks are much more complex than trees).

Also, incongruence can arise not only because different data sets are used, but also because different optimality criteria are used in phylogenetic reconstruction. Evolutionnary biologists have used and still use today a plethora of different such criteria as implemented in the many distance methods (clustering and least-squares), maximum parsimony methods, maximum likelihood methods and now bayesian methods (check out Joe Felsenstein's page to see some of the software available to phylogeneticists).

However the authors seems to only want to identify species. From their web site : "DNA-based systems promise to revolutionize the task of identification by providing reliable, inexpensive, and rapid diagnoses of species identiy".

Finally, remember that classification (puting organisms in russian dolls that are called species, genus, family, order, class and phylum) and phylogeny (infering the phyletic relationship between groups of living organisms, usually in the form of a branching diagram - i.e. what you refer to in your comment) are not the same thing. Classification tend to be based on phylogeny, but they need no be.

What struck me first about the schematic was the sexual reproduction or lateral gene transfer between languages in the '70s and '80s compared with the speciation into distinct languages by the late 1990s. In the past, it seems, ideas were often combined into new languages (Scheme = Lisp + Algol), while now they've stratified into identifiable species (Python, Ruby, Java, Perl, PHP, etc, where a recent exception would be C#).

However, further inspection shows that the timeline is distorted, making recent changes look more significant. Unlike more complete evolutionary records, this phylogeney shows languages that are important enough to remember (read: ancestors of currently used languages). A more complete tree would probably show that new languages are still being created that are amalgamations of ideas implemented in current languages. Some of these new languages we'll all be using in 15 years, but right now no one would think to include them in such a diagram.

A more interesting study would track language features, and show features transferring into languages, e.g., the addition of OO to Perl.

"Also, if the first animal hatched then why do bird fossils - even proper dinosaur fossils - appear so late in the piece?"

If the the first car had wheels, why did the quad cam v8 turbo 4WD appear so late in the piece?

'Hatching' is the general rule right up until mammals, and even then monotremes still lay eggs.

"The fossil sorting we do see seems to be based more on environment and density than on any systematic idea of age."

Yeah, sure it does. Take your creationist tripe elsewhere, this is the *science* section, not the fundamentalist christian religion section.

So, it would be reasonable to conclude that most had this super muscle. But birds and mammals both evolved from these things... why give up such a big advantage? Evolutionarily speaking, it just wouldn't happen. You don't select for weak muscle, especially to such a degree that absolutely zero examples exist today.

Mammals did not evolve from dinosaurs and, I'm guessing, birds could have evolved from small dinosaurs. Not all dinosaurs were huge. Also, evolution will select for whatever is better at making babies. It only favors bigger muscles if bigger muscles have a significant reproductive advantage. But apparently they were all wiped out my an asteroid so the point is moot.

Perhaps this research will allow to make some adjustments to the tree. However, there are already interesting facts in the current version. For example, bats are closer to primates than most other mammals. On the other hand, armadillos must have branched very early, although they did it after opossums.

Perhaps this research will allow to make some adjustments to the tree. However, there are already interesting facts in the current version. For example, bats are closer to primates than most other mammals. On the other hand, armadillos must have branched very early, although they did it after opossums.

Perhaps this research will allow to make some adjustments to the tree. However, there are already interesting facts in the current version. For example, bats are closer to primates than most other mammals. On the other hand, armadillos must have branched very early, although they did it after opossums.

According to the Tree of Life Web Project, all the animals mentioned (rodents, felines, humans) belong to the infraclass Eutheria (placental mammals).

If you look closely at the tree, you will see that the Tree of Life does indeed have order Rodentia closer to the order Primates. I recall learning this in high-school biology, also.

Yes this does seem to be a bit of old news.

According to the Tree of Life Web Project, all the animals mentioned (rodents, felines, humans) belong to the infraclass Eutheria (placental mammals).

If you look closely at the tree, you will see that the Tree of Life does indeed have order Rodentia closer to the order Primates. I recall learning this in high-school biology, also.

Yes this does seem to be a bit of old news.

ISTR hearing that one of the most commonly shared, and least mutated, genes known has something to do with how DNA gets coiled up into chromosomes. little wonder something like that would be common! wish i could find a reference for the quote, though...

Google for phylogeny, or just check out this page for a relatively good introduction. Comparative geneticists use sequence comparisons between species to determine relative evolutionary separation, much like the subject of the article. We haven't gotten rid of the kingdom-phylum-order-class-family-genus-species thing yet, but we're working on it.

Here's a few sites that'll be maybe at the very limits of the kids' grasp and understanding. But that's good. They should be challenged to learn "the next step up", rather than being fed dumbed-down Barney crud. There's nothing in these pages that a parent can object to (unless they happen to be diehard creationists).

http://tolweb.org/tree/phylogeny.html

The Tree of Life is a collaborative web project, produced by biologists from around the world. On more than 2600 World Wide Web pages, the Tree of Life provides information about the diversity of organisms on Earth, their history, and characteristics.

http://whyfiles.org/

"Science behind the news"

http://www.seds.org/billa/tnp/

The Nine Planets is an overview of the history, mythology, and current scientific knowledge of each of the planets and moons in our solar system. Each page has text and images, some have sounds and movies, most provide references to additional related information.


http://parallel.park.org/Canada/Museum/extinctio n/ tablecont.html
Extinctions: Cycles of Life and Death Through Time (more than just the dinosaurs 65 million years ago)

As an April's fool joke on April 2nd...
I was getting ready to jab at Michael for posting a joke as real, but it appears that I'm the fool here. This thing exists, and it does have hooks. Google led me to the " Tree of Life Web project"
1. Tentacles
1. Club with hooks.
...
Comments
Hooks are also present on the arms. This is the only genus in the Cranchiidae with arm hooks.

as well as several other articles. Bummer of a dateline, though.

The full name of THIS
squid is Mesonychoteuthis hamiltoni Robson. It's the
only species in it's genus, and it barely gets 2m
long. This doesn't even begin to touch Architeuthis
Clarkei (the giant squid). This is perhaps a really
lame attempt at an april fools joke?

• A focus. While they couldn't give us a mother and cubs, they could've given us the evolutionary equivalent. Take a couple of classes or orders and get us to care what happens to them over then next 200 million years. Introduce the squids early on. The only continuity TFIW had was "location of former cities"
• Drama- rather than suddenly show the last mammal, they should've shown 100 million years of decreasing diversity.
• Digressions. TFIW had few animals per time zone. If TFIW didn't have the computational budget to animate more they at least could have had more still shots. Documentaries tend to be filled with side loops, constantly showing local diversity- while the predator waits, we take five minutes to check out a cute symbiotic relationship, or a flock of colorful birds, or the prey's prey, or a dung beetle (which also is part of my next point...)
• Humor. Let's see some baby spiders falling off the web before going into the extinction of mammals next time.

• Flying fish- yes, they do exist, flapping their tiny pectoral fins: check out some of the Amazonian Hatchetfish species.
• The unlikeliness of X (giant land squid, silver spiders, etc): who'd have predicted what Pikaia-like creatures could lead to over the next 500 million years
• the diversity of life over the past 500 million years: spend a few hours exploring the Tree of Life Project: after that, none of TFIW speculations seem too weird (although they made some physiological mistakes- as pointed out by others, the giant tortoises's legs don't make sense)
• Extinct mammals: well, out of all of these all we have left are the birds.
• Missing signs of humans: I've seen estimates (can't find them right away- one was in Sci-Am I think) that suggest most large-scale signs of humans (buildings, satellites, canals) would be gone within 500,000 years. Even the longest-lasting signs (large concentrations of radioactive elements, space probes, AOL CDs) won't last more than 100-200 million years given subduction, etc).

• A focus. While they couldn't give us a mother and cubs, they could've given us the evolutionary equivalent. Take a couple of classes or orders and get us to care what happens to them over then next 200 million years. Introduce the squids early on. The only continuity TFIW had was "location of former cities"
• Drama- rather than suddenly show the last mammal, they should've shown 100 million years of decreasing diversity.
• Digressions. TFIW had few animals per time zone. If TFIW didn't have the computational budget to animate more they at least could have had more still shots. Documentaries tend to be filled with side loops, constantly showing local diversity- while the predator waits, we take five minutes to check out a cute symbiotic relationship, or a flock of colorful birds, or the prey's prey, or a dung beetle (which also is part of my next point...)
• Humor. Let's see some baby spiders falling off the web before going into the extinction of mammals next time.

• Flying fish- yes, they do exist, flapping their tiny pectoral fins: check out some of the Amazonian Hatchetfish species.
• The unlikeliness of X (giant land squid, silver spiders, etc): who'd have predicted what Pikaia-like creatures could lead to over the next 500 million years
• the diversity of life over the past 500 million years: spend a few hours exploring the Tree of Life Project: after that, none of TFIW speculations seem too weird (although they made some physiological mistakes- as pointed out by others, the giant tortoises's legs don't make sense)
• Extinct mammals: well, out of all of these all we have left are the birds.
• Missing signs of humans: I've seen estimates (can't find them right away- one was in Sci-Am I think) that suggest most large-scale signs of humans (buildings, satellites, canals) would be gone within 500,000 years. Even the longest-lasting signs (large concentrations of radioactive elements, space probes, AOL CDs) won't last more than 100-200 million years given subduction, etc).

For instance, we're doing an open source phylogenetic project called The Tree of Life, which promotes both the open access to phylogenetic information, and open source software through the code itself. Many biologists are using open source software to further their research - case in point in O'Reilly's recent Bioinformatics conference.