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The Tree of Life Consolidates

kdawson posted more than 6 years ago | from the pruning-it dept.

Science 266

Roland Piquepaille writes "The Tree of Life is an expression first used by Charles Darwin to describe the diversity of organisms on Earth and their evolutionary history. There are only two life forms, — eukaryotes, which gather their genetic material in a nucleus, and prokaryotes, such as bacteria, which have their genetic material floating freely in the cell. Until recently, eukaryotes, which include humans, were divided into five groups. But now, based on work by European researchers, the Tree of Life has lost a branch. After doing the largest ever genetic comparison of life forms they concluded that there are only four groups of eukaryotes."

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Science is a moving target (5, Insightful)

davidwr (791652) | more than 6 years ago | (#22144588)

The more we know, the more we know that what we knew was wrong.

Or, as a coworker of mine used to say when we realized we didn't know what we were doing: "Everything you know is wrong."

New life forms found HERE. Yes, it is opinionated. (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22145068)

Look HERE [goatse.cx] . This portal was created by the repeated actions of an elephant over a number of decades and leads to another dimension much different than our own. Here, you will find new forms of flora, fauna, and various microbial life. Scientific discoveries beckon--this subject must be investigated with great reverence and gratitude to those who gave most endearingly for the creation of the wormhole to the next dimension. Behold. Excelsior!

MOD PARENT UP (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22145258)

I don't see why this is a troll. It makes no sense to be a troll. If you are the person who modded this down, you are a douche bag.

Re:Science is a moving target (2, Funny)

A beautiful mind (821714) | more than 6 years ago | (#22145124)

This is precisely why we believe in the guy up in the clouds who pulls the strings behind the curtains!

Oh wait...

Just hoopla over definitions (2, Informative)

chrisjbuck (950790) | more than 6 years ago | (#22145142)

I never heard of "PLoS ONE", it claims to be a peer reviewed journal at least. If this was ground breaking I'd expect it to be published in Nature though. The "PLoS ONE" website isn't loading for me at the moment, but hopefully I'll be able to read the actual article. This seems to be hoopla over definitions though, we can sort organisms into kingdoms and phyla any way we like, this seems identical to the tug-of-war over whether Pluto is a planet or a planetoid. Is it the size of the planet? Is it if an organism has x+2 mutations in a histone protein/gene it gets slotted into one kingdom or another?

Hey the journal finally loaded, here is a link to the actual paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000790 [plosone.org] , although its taking a long time to load for me, and it's not even slashdotted yet. :P

Re:Just hoopla over definitions (2, Interesting)

Angostura (703910) | more than 6 years ago | (#22145622)

It's a bit more than that. The question of whether Pluto belongs to the class 'Planet' is basically decide by one metric only: size. A phylogenomic study is rather more interesting than that since it casts light on the actual intrinsic interrelationships between different organisms and their likely evolution paths.

I've had a quick look at the paper you linked to, and frankly its over my head. My degree was genetics/molecular biology but that was 20 years ago and taxonomy used to bore me rigid.

Re:Just hoopla over definitions (3, Informative)

Seiruu (808321) | more than 6 years ago | (#22146462)

[quote]I never heard of "PLoS ONE"[/quote]

Then you have also never heard of Open Access, because then you would certainly know what PLoS ONE is. A shame you've never heard of it, because it is a very significant and rapidly growing movement within the scientific community. It puts the emphasis on opening up the access of scientific literature to everyone by switching from reader-pays to author-pays models. And with that said, it is very likely that scholars select PLoS ONE or other OA journals (peer reviewed of course) to show that they believe in the Open Access concept and let everyone with a digital connection have access to it.

Re:Science is a moving target (1)

Chris Mattern (191822) | more than 6 years ago | (#22145302)

Or, as a coworker of mine used to say when we realized we didn't know what we were doing: "Everything you know is wrong."


"Black is white, up is down and short is long."

Just forget the words and sing along!

Re:Science is a moving target (0)

Anonymous Coward | more than 6 years ago | (#22146020)

Or, as my middle-school science teacher used to say, "Science is a lie that keeps getting better."

  It's nice to admit that we're not taught the absolute truth -- and that when we grow up we can not teach the absolute truth to our children in a much clearer way.

Pretty good guess (1)

EmbeddedJanitor (597831) | more than 6 years ago | (#22146344)

5 instead of 4? Well that's a pretty good guess given that the previous generation of scientists did not have a lot of the tools that the new kids on the block have.

Science is a moving target which is one of the reasonse we should never use terms like "scientifically proven" and should never get ioverconfident.

Science is a process (2, Insightful)

2short (466733) | more than 6 years ago | (#22146394)


Our understanding of the world is, and will always be, approximate.

Science is a process by which we improve that approximation. Nothing we used to know is now wrong. Some things we used to roughly understand we now understand better.

It appears that the Eukaryotes emerged sometime over a billion years ago. As far back as we could figure out, it looked like there were five groups of them, but we didn't understand which of those groups were more closely related to each other. Further research has now refined our approximation, and it appears two of those groups are more closely related that the rest.

So, certain single-celled organisms are understood to be more closely related to certain other single celled organisms than previously thought. Compared to any of the organisms involved, you're still more closely related to certain other single celled organisms, as well as all animals and fungi. If that shakes your world view, you need to get out more. :)

Makes Sense (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22144602)

When you think about it, niggers and monkeys are basically the same species.

Re:Makes Sense (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22144682)

Speaking as a chimpanzee I find that remark personally offensive.

Re:Makes Sense (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22145346)

Agreed, chimps are far more intelligent than niggers.

Re:Makes Sense (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22145484)

They smell better too!

Oops, my bad (4, Funny)

sm62704 (957197) | more than 6 years ago | (#22144676)

I should be more careful with that chainsaw. Poor tree, only 5 branches , I hope it survives...

Re:Oops, my bad (2, Funny)

Bill, Shooter of Bul (629286) | more than 6 years ago | (#22145642)

Dude, just graft on a branch from the tree of insanity. Nobody will notice the difference.

First we lose pluto and now we lose this. (5, Funny)

Anonymous Coward | more than 6 years ago | (#22144722)

What else will science rob from us before we decide enough is enough?

At the risk of being called a Tao-rrorist... (5, Interesting)

KublaiKhan (522918) | more than 6 years ago | (#22144878)

In the pursuit of knowledge, every day something is added.
In the pursuit of understanding, every day something is removed.

Re:At the risk of being called a Tao-rrorist... (2)

andphi (899406) | more than 6 years ago | (#22144938)

The Tao that can be expressed . . .

Re:At the risk of being called a Tao-rrorist... (2, Funny)

KublaiKhan (522918) | more than 6 years ago | (#22144994)

Is only a second-order approximation, at best, for the real Tao.

What chance does that give me? (1)

Boronx (228853) | more than 6 years ago | (#22146246)

Only the true messiah would deny his divinity.

PLoS ONE: Phylogenomics Reshuffles the Eukaryotic (1, Redundant)

davidwr (791652) | more than 6 years ago | (#22144726)

Phylogenomics Reshuffles the Eukaryotic Supergroups [plosone.org]

Fabien Burki1*, Kamran Shalchian-Tabrizi3, Marianne Minge3, Åsmund Skjæveland3, Sergey I. Nikolaev2, Kjetill S. Jakobsen3, Jan Pawlowski1

1 Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland, 2 Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland, 3 Department of Biology, University of Oslo, Oslo, Norway
Abstract
Background

Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial.
Methodology/Principle Findings

Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history.
Conclusions

This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name 'SAR' (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes.

Citation: Burki F, Shalchian-Tabrizi K, Minge M, Skjæveland Å, Nikolaev SI, et al. (2007) Phylogenomics Reshuffles the Eukaryotic Supergroups. PLoS ONE 2(8): e790. doi:10.1371/journal.pone.0000790

Academic Editor: Geraldine Butler, University College Dublin, Ireland

Received: June 17, 2007; Accepted: July 26, 2007; Published: August 29, 2007

Copyright: © 2007 Burki et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This research was supported by the Swiss National Science Foundation grant 3100A0-100415 and 3100A0-112645 (JP); and by research grant (grant no 118894/431) from the Norwegian Research Council (KSJ).

Competing interests: The authors have declared that no competing interests exist.

* To whom correspondence should be addressed. E-mail: Fabien.Burki@zoo.unige.ch

First used by Darwin? (0, Offtopic)

Fyre2012 (762907) | more than 6 years ago | (#22144756)

"The Tree of Life is an expression first used by Charles Darwin"

So Charles Darwin, born in the 1809, predates the Kabbalah? [wikipedia.org]

Re:First used by Darwin? (2, Informative)

Scrameustache (459504) | more than 6 years ago | (#22144934)

"The Tree of Life is an expression first used by Charles Darwin"

So Charles Darwin, born in the 1809, predates the Kabbalah? [wikipedia.org]
That's cosmology, not biology [wikipedia.org] .

Re:First used by Darwin? (1)

Mark Gordon (14545) | more than 6 years ago | (#22145116)

So the Kabbalah predates the Torah [mechon-mamre.org] ?

Re:First used by Darwin? (1)

Afecks (899057) | more than 6 years ago | (#22145734)

So the Torah predates the Egyptian deity Saosis's tree of life [wikipedia.org] ?

Re:First used by Darwin? (1)

LordLucless (582312) | more than 6 years ago | (#22145618)

The Tree of Life is an expression first used by Charles Darwin to describe the diversity of organisms on Earth and their evolutionary history

I didn't know the Kabbalah involved discussion of evolutionary history. Or possibly you should quote entire sentences rather than out of context fragments which support your unjustified criticisms.

Re:First used by Darwin? (1)

Fyre2012 (762907) | more than 6 years ago | (#22146156)

well, it was more an attempt at a bad joke than a criticism.
But thanks for the response!

Re:First used by Darwin? (0)

Anonymous Coward | more than 6 years ago | (#22146426)

You beat me to it. Exactly, this has been a jewish metaphor for thousands of years.

Not really a tree... (5, Interesting)

myowntrueself (607117) | more than 6 years ago | (#22144770)

While a tree-structure is algorithmically convenient and very enticing... the "tree of life" is not a tree.

Ie it is not a "directed, acyclic graph".

Unfortunately it has 'cycles'.

Blame retroviruses; they can take genetic material from one species and insert it into the genome of another thereby creating cross-branches.

As I recall, from my genetics days, baboon retroviruses are a great example of this. Again, IIRC, domestic cats and humans both contain fragments of baboon retroviruses.

Its possible that the "Cambrian explosion" is a sign of the appearance of retroviruses on the scene.

The thing is that it is significantly harder to reason about graphs; trees are so much easier to deal with.

So its very tempting to see things like this as trees and to 'simplify out' the nasty cross-branches.

(I've studied genetics, computer science, logic and discrete math)

Re:Not really a tree... (2, Insightful)

MightyMartian (840721) | more than 6 years ago | (#22145042)

You're substantially exaggerating the effect that horizontal gene transfer has on the tree. ERVs are taken into account, and are in fact, quite useful in narrowing down where specific species and higher cladistic groupings sit in the tree.

Re:Not really a tree... (2, Informative)

Otter (3800) | more than 6 years ago | (#22145048)

Unfortunately it has 'cycles'.

Someone helpfully linked the paper [plosone.org] (and was modded down for his trouble); they address that concern extensively.

Re:Not really a tree... (1)

bar-agent (698856) | more than 6 years ago | (#22145060)

Wouldn't it be a directed, cyclic graph? All connections only go in one direction: forward through time.

So, what you are saying is..... (1)

StressGuy (472374) | more than 6 years ago | (#22145098)

Your "tree of life" has inter-connecting branches?

That sounds a little....incestuous....no?

Re:So, what you are saying is..... (4, Insightful)

MightyMartian (840721) | more than 6 years ago | (#22145316)

There's a small part of most organisms' genomes that are made up of ERVs. These are insertions of retroviral DNA into our genomes. For the most part, these viral sequences are in neutral or junk genome stretches, so they don't have any influence on the organism. Unlike what the poster is saying, these don't make producing the tree more difficult, but in fact are extremely useful in fine-tuning the tree.

The odd-man out here are some prokaryotes, such as bacteria, where a sort of pseudo-sexual reproduction can take place by direct genome transfers. Still, this does not stop the classification of bacteria, but it does probably mean that the root of the tree of life, those earliest primitive self-replicators, probably swapped genes a helluva lot, so there may be no common ancestor per se, but rather a nest of common ancestors who swapped chunks of their DNA, RNA or whatever the earliest genetic molecules were.

Oldest life forms: Whores or sluts? (0)

Anonymous Coward | more than 6 years ago | (#22145812)

"those earliest primitive self-replicators, probably swapped genes a helluva lot"

Are you saying the world's oldest profession really is the world's oldest profession, or are you just calling them sluts?

Re:So, what you are saying is..... (-1, Troll)

Anonymous Coward | more than 6 years ago | (#22146564)

It's like looking at a negro's family tree. Jungle bunnies will hump anything that moves due to the underdeveloped impulse control centers in their malfunctioning brains.

Re:Not really a tree... (1)

Kjella (173770) | more than 6 years ago | (#22145166)

Ie it is not a "directed, acyclic graph".

Unfortunately it has 'cycles'.
I'm sure that's a correct mathematical defintion, but it doesn't apply to common usage. If you take a large family tree you'll almost certainly find some common ancenstors like sharing a great grandfather from the time people found their spouses in small rural communities. That doesn't prevent us from calling it a family tree, as long as it has a direction in time that branches out to multiple individuals/species I don't think a anyone but a mathematician would object.

Re:Not really a tree... (1)

rucs_hack (784150) | more than 6 years ago | (#22145276)

While the tree of life does have cycles, those are similar adaptations to similar problems, and can occur in diverse species which have been seperate for many millions of years.

Take the saber tooth adaption. That's been recurring since the pre-dinosaur reptilian era. Always to solve the same basic problem.

Re:Not really a tree... (1)

phliar (87116) | more than 6 years ago | (#22145740)

Indeed. In fact some (e.g. Lynn Margulis) believe that this is the primary way species evolve, not through mutation. See her book Aquiring Genomes [amazon.com] .

omg (0)

Anonymous Coward | more than 6 years ago | (#22145774)

(I've studied genetics, computer science, logic and discrete math)

You sir are the biggest fucking nerd i've ever seen.

/me bows down and worships

Re:Not really a tree... (2, Informative)

Anonymous Coward | more than 6 years ago | (#22145984)

Tree != Directed, acyclic graph.

In a tree, each node has exactly one parent. Even if links are bidirectional, non-trivial cycles cannot exist. In a DAG, nodes can have multiple parents; making links bidirectional could create cycles. Every (unidirectional) tree is a DAG, but not every DAG is a tree.

The "tree of life" IS a directed acyclic graph - even when considering retroviruses, since "higher" organisims have more than one parent. Retroviruses allow gene transfer between individuals of different species, thus allowing organisms to have more than two parents. A cycle would mean that some individual received genetic material from one of its descendents. If you define an individual as a set of genes that is available to pass on to descendents, then a cycle, by definition, cannot exist.

Archaea (5, Informative)

virology-not for com (841426) | more than 6 years ago | (#22144774)

Let's not forget that many scientists think there are three domains (Prokaryotes, Eukaryotes and Archaea). Archaea are very similar to Prokaryotes in that they don't have a nucleus, but they also share many features with Eukaryotes, including several key enzymes. Due to their similarity to the two other lineages, it is thought that Archaea may in fact be the grand daddy of all life. http://en.wikipedia.org/wiki/Archaea [wikipedia.org]

Re:Archaea (1)

Lurker2288 (995635) | more than 6 years ago | (#22144978)

That was my big complaint about the summary; glad to see there are other folks here keeping the faith. ;)

Re:Archaea (1, Informative)

Anonymous Coward | more than 6 years ago | (#22145644)

Little Nit - Archaea are technically Prokayotes (meaning "before nucleus"). The distinction is not between Prokaryotes and Archaea, but between Archaea and Eubacteria [wikipedia.org] .

Although you can slice and dice as Eukaryotes/Prokaryotes, it's commonly accepted that Archaea are as different genetically from Eubacteria as Eubacteria are to Eukaryotes. In fact, it is usually said that Archaea are more closely related to Eukaryotes than they are to Eubacteria, so grouping Eubacteria and Archaea together as "Prokaryotes" because they lack a nucleus makes as much sense as grouping bats and birds together because they can fly.

Re:Archaea (3, Informative)

reverseengineer (580922) | more than 6 years ago | (#22146016)

The level of organization being discussed in the paper treats a subdivision of the eukaryotes into "superkingdoms." (There's actually not a completely agreed upon term for this level.) This would put these groups a level below the three domains (Eucarya, Eubacteria, Archaebacteria) proposed by Carl Woese. There's a high-level differentiation between the superkingdoms involved based on organization of flagella, with a high-level split between unikonts (one flagellum) and bikonts (two, naturally). This is of course based on evolutionary ancestry- humans are unikonts, but don't have many cells with flagella.

The unikonts contain the amoebae lineages in one grouping, and the animal and fungi together in another. The bikonts contain the plants and algaes in one grouping, and also a handful of other groupings which take care of the rest of the eukaryotes, most of which are unicellular organisms of various sort. It is the "various sort" that's being ironed out with this paper- the authors argue that on the basis of a common genetic heritage, a couple of the leftover groupings can be consolidated.

Ironically, this move would actually reunite groupings that were fairly recently separated by the argument that no firm evidence of relation existed. Back when the "five Kingdoms" (Animalia, Plantae, Fungi, Monera, Protista) were considered the top level of organization, Protista existed as a sort of "junk drawer" for simple organisms which did not clearly fit in the other categories. Now it looks as though some of these organisms really are related.

This does not answer the important question: (1)

jd (1658) | more than 6 years ago | (#22146598)

Why do biological names look like an explosion in an alphabet soup factory? At first, I thought this was because the classicist biologists had all learned Latin, but I think this vandalism, this hacking a branch off the tree of life reveals the true answer. The vandals ARE setting off explosions in an alphabet soup factory and writing down the words that form.

Proof? (4, Insightful)

Amorymeltzer (1213818) | more than 6 years ago | (#22144782)

Anyone who says "Evolution is taken as faith" or doesn't understand that the theory is based on the evidence, and that new evidence means changing the theory can look at this and shut up. A rather fundamental point was proposed to be rather fundamentally different based on new research and that's just fine. Whether it pans out or not, this is a beautiful example of the glory of science.

Three levels of truth (maybe more...) (3, Insightful)

gillbates (106458) | more than 6 years ago | (#22145028)

Yes, being able to correct mistakes is the glory of science. But being right the first time is the glory of religion.

When religion doesn't get it right, people abandon it completely. When science doesn't get it right, they say, "well, that's just part of the process..."

Each particular method has its strengths and weaknesses:

  • Religion reveals the truth of divine revelation. Which means that it is true by axiom, not proof. If the "revealed truth" isn't actually true, then it isn't of divine origin. Which does much to explain why religious institutions are very conservative when it comes to accepting new ideas.
  • Mathematics is provably correct. That is, apart from an error in the proof, what is true today will always be true.
  • Science is experimentally correct. That is, the hypotheses called true today may be shown false tomorrow with the discovery of additional data.

The key, I think, is not to confuse the various levels of truth. Those who take religion as if it were a scientifically-verifiable fact are just as confused as those who think scientific theorems are as reliable and trustworthy as the Gospel or mathematical proofs. There is a large difference between the three, and understanding the subtle limitations of each is just as important as understanding the ideas they espouse.

Re:Three levels of truth (maybe more...) (5, Insightful)

NIckGorton (974753) | more than 6 years ago | (#22145344)

When religion doesn't get it right, people abandon it completely.
No they don't. They just reinterpret the primary tenets of the religion to suit their current desired conclusions. Religious works and religious beliefs are interpreted in the light of the present society and its prejudices. Rather than being taken at face value, they are used to justify what people want to believe. For example, there is no real prohibition against abortion in the Christian Bible. For another example, the selective interpretation of Leviticus as condemnation of homosexuality while ignoring the condemnation of poly-cotton blends and Red Lobster.

Well, unless you are someone who strictly interprets the OT: http://www.godhatesshrimp.com/ [godhatesshrimp.com]

Re:Three levels of truth (maybe more...) (0)

Anonymous Coward | more than 6 years ago | (#22146078)

Aren't all those "you can't eat this or that" rules abolished in the New Testament?

Re:Three levels of truth (maybe more...) (2, Funny)

gardyloo (512791) | more than 6 years ago | (#22146274)

Aren't all those "you can't eat this or that" rules abolished in the New Testament?
I like to think of it as a slightly newer release candidate.

Re:Three levels of truth (maybe more...) (3, Insightful)

zulater (635326) | more than 6 years ago | (#22146096)

But many denominations do try to interpret in context and in light of the culture they were written in. Not to mention that the old law (old covenant/testament) was fulfilled after Christ's death and resurrection. That started the new covenant/testament which has no real limitations on what you eat. This isn't to say that there aren't valid teaching in the old testament but that the rules and regulations for ceremonial cleanliness don't apply anymore since there is no longer a need for sacrificing to cleanse sin. Abortion is murder in the eyes of the church because in most cases the church believes that life begins as conception or when the zygote attaches to the uterus. Many passages speak of God forming the child in the womb (Job 31:15, Psalm 139:15, Isaiah 44:2, Isaiah 49:5 etc). I agree that many do take the scriptures out of context and try to twist them into what they want to hear not what is actually meant. This is the folly of man trying to interpret scripture outside of other scripture.

Re:Three levels of truth (maybe more...) (3, Informative)

yali (209015) | more than 6 years ago | (#22146184)

When religion doesn't get it right, people abandon it completely.
No they don't. They just reinterpret the primary tenets of the religion to suit their current desired conclusions.

A good demonstration of this is in the classic study When Prophecy Fails [wikipedia.org] . A group of social psychologists studied a doomsday cult whose leader had predicted the end of the world. When the predicted date passed and the world didn't end, people did not leave the cult. Instead, they found reasons to explain it away (God was so impressed with their devotion that he put off the apocalypse on their behalf). The end result was that their beliefs were strengthened, not weakened, by disconfirmatory evidence.

(As a sidenote, the study was an important early test of Leon Festinger's theory of cognitive dissonance [skepdic.com] ; Festinger had predicted the cult's response based on his theory.)

Re:Three levels of truth (maybe more...) (1)

gillbates (106458) | more than 6 years ago | (#22146304)

As one who has had to endure the suffering of a polyester-cotton blend, I, for one, think Moses got that one right the first time. We'd all be much better off without polyester (well, except maybe baseball players, with apologies to George Costanza...)

But in all seriousness, there are some very good theological reasons why the civil parts of Mosaic law were discarded while the moral parts remained in force. It has to do with the coming of what had been promised by Moses, the fulfillment of prophecy, and the establishment of a New Covenant. Hopefully, I've given you enough to research for yourself, but this shift was not merely an arbitrary change in religion, but rather, the expected outcome. Even the Jews, who do not accept Jesus Christ as Messiah, still await the coming Messiah. So while the continued condemnation of homosexuality without the attendant adherence to the civil law of the Torah may appear completely arbitrary, it was the side effect of a long awaited event promised by scripture.

As for religion getting it wrong, I was referring to the various dead religions, such as the Greco-Roman gods, and to the various cults which spring up from time to time, only to splinter off and die later when people wake up and realize the truth.

Re:Three levels of truth (maybe more...) (4, Interesting)

JeanPaulBob (585149) | more than 6 years ago | (#22146380)

For example, there is no real prohibition against abortion in the Christian Bible.
There is also no real prohibition against shooting people in the Christian Bible.

For another example, the selective interpretation of Leviticus as condemnation of homosexuality while ignoring the condemnation of poly-cotton blends and Red Lobster.
Far be it from me to interrupt your game of "Bash the Fundies", but...

The "condemnations" of homosexuality [bible.org] on the one hand and shrimp [bible.org] on the other are not the same, using entirely different words. (Just because the 400 year-old language in the KJV uses the word "abomination" in both passages, doesn't mean the Hebrew is the same.)

That raises the question, why do you make the peculiar assumption that every command in the OT law is of the same type, for the same kind of reason? Do you allow no distinction between ceremonial rules, and rules involving inherent moral/ethical concerns? Do you think that ancient Hebrews viewed dietary laws (prohibition of shrimp) and the command about mixed fabric as moral issues, in the same sense as murder, adultery, theft, and injustice? If so, why? If not, why base your arguments on absurd equivocation?

Re:Three levels of truth (maybe more...) (0)

Anonymous Coward | more than 6 years ago | (#22145590)

Yes, being able to correct mistakes is the glory of science. But being right the first time is the glory of religion.

When religion doesn't get it right, people abandon it completely. When science doesn't get it right, they say, "well, that's just part of the process..."

So how do you explain the existence of people who believe in the Christian Bible, and yet do not believe that they should stone their children to death if such children show any sign of stubbornness or rebellion? From Deuteronomy 21:18-21

If a man have a stubborn and rebellious son, which will not obey the voice of his father, or the voice of his mother, and that, when they have chastened him, will not hearken unto them: Then shall his father and his mother lay hold on him, and bring him out unto the elders of his city, and unto the gate of his place; And they shall say unto the elders of his city, This our son is stubborn and rebellious, he will not obey our voice; he is a glutton, and a drunkard. And all the men of his city shall stone him with stones, that he die: so shalt thou put evil away from among you; and all Israel shall hear, and fear.

Re:Three levels of truth (maybe more...) (1)

mike2R (721965) | more than 6 years ago | (#22145694)

Religion reveals the truth of divine revelation. Which means that it is true by axiom, not proof. If the "revealed truth" isn't actually true, then it isn't of divine origin. Which does much to explain why religious institutions are very conservative when it comes to accepting new ideas.

I'm absolutely fine with that. As far as I'm concerned the big fat red line comes when religious "evidence" is fed back into the scientific process.

As long as this line isn't crossed religion is just religion, and can be treated as such. It's when it starts to intrude upon other areas that the problems start.

I wouldn't even bother to say this, but I'm terribly afraid that large parts of the American public do not agree.

Re:Three levels of truth (maybe more...) (1)

Angostura (703910) | more than 6 years ago | (#22145716)

When religion doesn't get it right, people abandon it completely.


So to be clear, are you saying that if any aspect of the Bible were shown to be erroneous, there would be no more Christians a week later?

Re:Three levels of truth (maybe more...) (1)

Belial6 (794905) | more than 6 years ago | (#22145800)

I would describe it differently. It is more an issue of claimed completeness of knowledge vs. margin of error in the information we do have.

Religion: Claimed Completeness = 70%, Margin of error = 100%

Mathematics: Claimed Completeness = 70%, margin of error = 20%

Science: Claimed Completeness = 5%, margin of error 50%

Re:Three levels of truth (maybe more...) (1)

ppanon (16583) | more than 6 years ago | (#22145886)

When religion doesn't get it right, people abandon it completely.
Sometimes. And sometimes those who try to abandon the religion are called heretics, leading to persecutions and wars that last decades or centuries and cost thousands or millions of lives.

With science, when somebody's wrong, they might lose their grant and need to investigate something else.

There's lots to learn from religions about how to be happy and live with others as a productive part of society, to everyone's mutual benefit. But the world would be a lot less dangerous if everyone realized that religions are no more a revelation of truth than science is.

Re:Three levels of truth (maybe more...) (1)

nagora (177841) | more than 6 years ago | (#22146098)

When religion doesn't get it right, people abandon it completely

Eh? On what planet? By that argument there would be no religion left.

Religion reveals the truth of divine revelation.

No it doesn't. It reveals the ideas of a small group of philosophers and their students.

Those who take religion as if it were a scientifically-verifiable fact are just as confused as those who think scientific theorems are as reliable and trustworthy as the Gospel or mathematical proofs.

While I agree with this, I would say that anyone who "takes religion as if it were a scientifically-verifiable fact" is some sort of headcase.

TWW

Re:Three levels of truth (maybe more...) (1)

jgoemat (565882) | more than 6 years ago | (#22146400)

Religion reveals the truth of divine revelation. Which means that it is true by axiom, not proof. If the "revealed truth" isn't actually true, then it isn't of divine origin. Which does much to explain why religious institutions are very conservative when it comes to accepting new ideas.

You cannot be talking about organized religion then. The only religious people then would be ones that have had divine revelations and the only religion would be based on those personal revelations. I haven't seen any burning bushes lately, have you? If you go off of divine revelations made to other people, then you have to look at their accounts, which means the bible for the most part, or people saying that God talks to them (i.e. David Koresh, Pat Robertson, Jerry Fallwell and Oral Robers, who had a "divine revelation" that God wanted people to send him $8 million or God would smite him).

When religion doesn't get it right, people abandon it completely.

When Martin Luther [wikipedia.org] thought that the Catholic church had it wrong, he changed Christianity completely. He believed that the only true word was the bible, which is ironic because it was the Catholic church that chose the four stories to make up the new testament out of the sixteen or so there were. When attitudes changed, even the Lutheran church denounced his hateful writings about Jews. If you look at the old testament then the Jews are the chosen people of God, how could you even denigrate them without raising God's ire? At least he broke away from the polytheism of the Catholic church with it's three main "gods" (Father, Son, and Holy Ghost) and the fourteen holy helpers [wikipedia.org] . If you're Catholic and wish a safe trip, you pray to the God of Travelling, "Saint" Christopher. There's also their goddess Mary, who Pope John Paul II credited with guiding the bullet that hit him so that it would not kill him (I wonder why she wouldn't make it miss altogether?)

When religion doesn't get it right, people abandon it completely. When science doesn't get it right, they say, "well, that's just part of the process..."

The difference is that science gives you a way to tell if something is true. Religious has someone telling you something or reading a 2,000 year old book written by people that are long dead and that contradicts itself in many places and says to assume that it is all true and go from there. If you go by that, then the Earth is 6,000 years old. We can count tree rings back to 13,000 years (rings from generations can be aligned by changes in size and gaps for instance). We know that light has a speed limit and that the theories of General and Special relativity fit all observable data (GPS wouldn't work if it didn't account for differing gravity at 22,000 miles up and the gravity of the Sun has been shown to warp the path of light from distant stars). You can prove the speed of light yourself by observing IO and Jupiter [colorado.edu] or by shining a laser on a mirror astronauts placed on the moon and seeing that it takes 2.5 seconds to get back. We also can calculate [newscientist.com] that the Andromeda Galaxy is 2.5 million light-years away. That means that the light we're seeing now left the galaxy 2.5 million years ago. Ergo the universe must be older than 6,000 years and anyone that truly believes that is simply incapable of understanding basic scientific concepts. Religion has therefore changed instead of being abandoned, as recent popes' concessions that evolution is not incompatible with religion and Pope Gregory XIII in 1580 saying that the earth was created in 5199 BCE. So religion must change in light of newly discovered facts to avoid having its followers choose between leaving or looking like an idiot.

Re:Three levels of truth (maybe more...) (0)

Anonymous Coward | more than 6 years ago | (#22146456)

Okay, first of all, I'm only posting as Anonymous Coward here because I've gotta leave the office and don't have time to register.

As probably one of the only ordained clergy people who reads Slashdot, I have to say that a bit of humility is called for in these "science vs. religion" conversations. I don't go weigh in much on genetics or string theory because I haven't studied them sufficiently to have an informed understanding. Well, religion is a major field of human endeavor, with thousands of years of history behind it and a staggering variety of forms. So sweeping generalizations about "religion" in general (Buddhism? Reform Judaism? Pentecostal Christianity?) tend to fail as most sweeping generalizations about complex phenomena tend to fail.

Two important points:

Not all religious people are textual fundamentalists/literalists.

When religion encounters new circumstances and new truths, it often finds ways to incorporate those truths and perspectives into its world view.

"We must accept the truth whatever its source."

Now, who said that....

Oh, yeah, it was Rabbi Moses Maimonides in the 12th century.

By the way, Darwin got the phrase Tree Of Life from the Bible. :-)

Over and out,

fstab

Re:Proof? (2, Informative)

LWATCDR (28044) | more than 6 years ago | (#22145102)

No but Evolution is still mostly theory but it is the best current theory. At least some evolution has been seen in the "wild". Drug resistant bacteria is a good example of evolution in action.

Re:Proof? (5, Insightful)

MightyMartian (840721) | more than 6 years ago | (#22145248)

Define "seen"? Because by your argument, electrons may or may not exist, Proto-Indo-European may or may not have existed and you may or may not have had great-great-grand-parents.

Evolution is confirmed not just by observing what goes on now, but by observing the fossil record, and just as importantly nowadays, by gathering molecular data. These two lines of evidence fit very well together into the so-called twin-nest hierarchy.

If you wish to wander down the road of epistemological nihilism, that's your affair, but be aware that everything, and I mean everything you think you know you can't actually know at all. Either you admit that inference is a legitimate means of gathering factual knowledge, or you render the whole show, including what you see, hear, touch, feel and taste irrelevant.

Re:Proof? (2, Insightful)

LWATCDR (28044) | more than 6 years ago | (#22145570)

"electrons may or may not exist", not exactly. A particle wave duality that carries a negative does exist. Some of the theory about what a electron really is still in the realm of theory.

Evolution is still a theory and as I said it is the theory that fits with all the current data the best. But the theory of Evolution is still just a theory. A lot of questions are still unanswered about how Evolution works. Being scientific means having an open mind about scientific theories. You should keep your mind open but not so open that your brain falls out.

Anyone that says that the current theory of evolution is fact isn't being scientific.

Re:Proof? (1)

KingSH4M4N (1210508) | more than 6 years ago | (#22146340)

I think part of the problem is the negative connotation that anti-evolution people give to the word 'theory.' The truth is, 'facts' don't exist (in sciece anyway [and that's all that really matters]). One can make 'observations' and from those, develop theories. I don't see anyone trying to claim that gravity doesn't exist, yet it also is "only" a theory. The difference between gravity and evolution that makes it hard for people to accept one while they plainly expect the other, is that gravity happens in a time scale that is easily perceived within a human lifetime and evolution usually takes a much longer span of time to be noticed. The exceptions include rapidly reproducing organisms such as prokaryotes and viruses in which the mutation rate is fast enough to make the observation that the mutations are subject to selective pressures. Unfortunately, not everyone is privey to experiencing that observation, and so doubt lingers, unlike gravity, where everyone knows it exists. I'm not saying that the theory of evolution will never be disproven, or the theory of gravity for that matter (yet to be detected graviton particles???), but the slide in it's acceptance is more related to timescale of observations rather than from it being unsound or wrong. Getting back to the article, I am glad to see other people have asked the question about lateral gene transfere. I am curious about that myself. It would seem like all the genes they are using to do the phylogenetic analysis could possibly have originated from a different species. For large, multicellular creatures it's more obvious. There are only a limited number of ways for new genes to be added (viruses, etc.), but for single celled organisms, like algae, it's conceivable that there are many very simple vectors for lateral gene transfere. Such simpler systems involving fewer cells could simply eat up genetic material and incorporate it into their genomes, so I wonder if these things are taken into account. In all honesty, I think they probably are. Sequence conservation, biological history, and geological history, and lots of other tools seem like they would make it possible. But I mean come on! Opisthokonts? OPISTHOKONTS??? "Animals" just had such a nice ring to it ;)

Re:Proof? (1)

MightyMartian (840721) | more than 6 years ago | (#22146556)

You seem on one hand to be pretty deeply confused about the nature of evidence in science, and seem to playing pretty fast and loose with the definition of the word "theory" on the other. Basically you're committing an etymological fallacy, and at the same time trying to create an artificial barrier by which a quantum mechanical explanation of the electron can pass muster, but the twin-nested hierarchy of common descent is somehow a lesser quality of observational science.

You cannot see an electron directly. You can only infer its existence from its effect on phenomona that can be directly viewed. In fact, you can't even do that, because what you "see" is in fact passed down the optic nerve and is heavily processed. Everything you know, whether through your senses or by the aid of instruments, is simply various levels and degrees of inference.

Evolution is a fact. We observe that the genetic makeup of populations changes over time. We can infer from this and the observations in the fossil and molecular DNA that this process has been ongoing for at least 3.5 billion years. All genomes thus far analyzed fit within the hierarchy. In short, evolutionary theory explains biology just as QM and GR explain physical properties of the universe.

Re:Proof? (1)

Tsiangkun (746511) | more than 6 years ago | (#22145264)

Evolution is a fact.
Evolution accounting for some of the diversity of life on this planet is also fact.

The theory is that evolution accounts for all of the diversity in life on this planet.

There may well be multiple instances of origins of life, thus evolution as the basis for all diversity would be false.

Re:Proof? (1)

LWATCDR (28044) | more than 6 years ago | (#22145762)

What part of the Theory of Evolution is fact? Is evolution gradual as Charles Darwin first stated or is punctuated? What is the mechanism of evolution? Is it limited to changes in DNA or can it us other mechanisms? What about the effects of retroviruses on evolution? What about mitochondrial DNA?
Or you talking about the simple fourth grade level "Theory of Evolution"? AKA life changes over time to fit the environment?

Re:Proof? (2, Insightful)

Tsiangkun (746511) | more than 6 years ago | (#22146132)

The aquisition or modification of gene function over time is fact.
The accumulation of DNA modifications over time is a fact.
The aquisition of gene function due to alteration of DNA sequence is a fact.
The modification of gene function due to alteration of DNA sequence is a fact.
The modification of gene function due to transposable element insertions, and remobilizations, is a fact.
The alteration of gene function due to chromosomal rearrangements is a fact.
The generation of neo-centromeres is a fact.
That neo-centromeres are stability propagated over time is a fact.

Evolution is not limited to changes in DNA, it is also caused via chromosomal rearragements that change the environment where the gene is expressed.

It is a fact that retrovirus change gene expression and function. We use them as mutagens all the time in screens for new mutations.

Evolution of mitochondrial sequences is one of the best known ways for mapping the history of the human race.

Re:Proof? (0)

Anonymous Coward | more than 6 years ago | (#22146626)

Or you talking about the simple fourth grade level "Theory of Evolution"?

How about employing a fourth grade level of reading comprehension? He didn't say that the Theory of Evolution is a fact. He said that evolution is a fact. The theory considers how and why that fact occurs.

Re:Proof? (0)

Anonymous Coward | more than 6 years ago | (#22146214)

Uhg, do we have to start this every time?

Bush (-1, Offtopic)

Anonymous Coward | more than 6 years ago | (#22144784)

This is all because Bush didn't sign onto Kyoto, causing mass extinction. 365 days to go. But this cannot be undone.

two? (1)

Geoffrey.landis (926948) | more than 6 years ago | (#22144812)

There are only two life forms, -- eukaryotes, which gather their genetic material in a nucleus, and prokaryotes, such as bacteria

Two? For several decades, I thought most biologists considered life as being divided into three main branches ("domains"): eukaryotes, prokaryotes, and archaea.

Re:two? (2, Informative)

wizardforce (1005805) | more than 6 years ago | (#22145408)

it depends on what you're going after in regard to categorization. three domainss: eucaryotes are cells with nuclei where as procaryotes are cells without nuclei with the third group being archea because of the large genetic and structural differences in comparison with bacteria [eubacteria]. although you could also classify them into archea+eubacteria [from the now defunct monera (5 kingdom classification)], protista, animalia, plantae, fungi under the 6 kingdom classification

Taxonomy especially is inexact. (4, Interesting)

verbalcontract (909922) | more than 6 years ago | (#22144850)

When I was in 9th grade (I guess about 10 years ago!), there were five "kingdoms": bacteria, protista, fungi, plantae, and animalia. Three years later, there were six: archaea, monera, protista, fungi, plantae, and animalia.

Now there are branches? And four of them? On a tree? That's news to me. But it's all a matter of naming and grouping, so I guess you say potato, I say tomato.

Re:Taxonomy especially is inexact. (2, Funny)

Tailsfan (1200615) | more than 6 years ago | (#22145286)

THis will really screw up my AP Bio.

Re:Taxonomy especially is inexact. (1, Interesting)

Anonymous Coward | more than 6 years ago | (#22145414)

Taxonomy is an extremely confused science. Our marine biology teacher used to amuse himself by showing us different new 'trees'. I got the distinct feeling that taxonomists has their own Religious Wars.

Oh, they used to sort by similarity but genetics changed that. Now they are sorting by heritage, which is saner, but the "official" tree is pretty fucked up. It being an unholy mix.

I missed that class.

Rather, you haven't been keeping up. (4, Informative)

IdahoEv (195056) | more than 6 years ago | (#22145608)

When I was in 9th grade (I guess about 10 years ago!), there were five "kingdoms": bacteria, protista, fungi, plantae, and animalia.


What's happened is that better information has rapidly come to the fore as genetic analysis have been done during the last 15 years. The tree has been revised several times.

The five kingdom model was already known to be wrong 10 years ago, but that information hadn't propagated to gradeschool and highschool textbooks yet. If you'd studied biology in college, your information would be more up to date.

These days there are three superkingdoms: Bacteria, Archaea, and Eukarya. (Bacteria and Archaea were formerly grouped together as "monera" or "bacteria" before it was realized that genetically they are as distinct from each other as they are from Eukarya.) Eukarya is broken into a number of kingdoms, and that number has just changed from 5 to 4. Even the 5 they were last year weren't exactly same ones that you learned in school.

Ummm.... (3, Insightful)

Otter (3800) | more than 6 years ago | (#22144944)

The Tree of Life must be re-drawn, textbooks need to be changed, and the discovery may also have significant impact on the development of medicines.

This is a bit over the top. It's not like there's a single canonical "Tree of Life" that's going to have to be changed across the board; there's endless (mostly self-promoting) squabbling over what should be considered fundamental branches, to which this is yet another entry.

Frankly, if this were as important as they make out, it would be in Nature, not the if-it's-not-objectively-wrong-it's-in PLoS ONE.

"...the largest ever genetic comparison of higher life forms on the planet"? Maybe, I guess it depends what dimension you measure "largest" on.

Re:Ummm.... (1)

ArsonSmith (13997) | more than 6 years ago | (#22146216)

The Tree of Life must be re-drawn, textbooks need to be changed, and the discovery may also have significant impact on the development of medicines.

This message brought to you by Learning Resources Publications(r) and the United Drug Association(tm).

Re:Ummm.... (1)

ArsonSmith (13997) | more than 6 years ago | (#22146298)

...Ohh, and The Artistic Tree Drawers Union.

Correction: "Tree of Life" is an old expression (1)

popo (107611) | more than 6 years ago | (#22145086)

Saying that the "Tree of Life" was first used by Darwin to describe evolutionary relationships should be taken with a grain of salt. The use of a "tree" to describe decendants and family relationships dates back to (at the very least) pre-Roman times. Paintings depicting lineage were long adorned with leaves and fruit. There is a reason that the Bible used a "tree" to signify life -- because the symbolism of a trunk, limbs, shoots and offshoots was well established by mankind long before the Bible was even written. Norse mythology also used the concept of a "Tree of Life" to describe the relationships of one generation to the next: The Gods at the trunk, the more recently 'evolved' mankind at the branch tips. (And the Runes at the roots). [ifate.com]

I'm a big fan of Darwin. But let's not give him credit for applying some of mankind's oldest and most widely used symbols to the very thing it typically symbolized.

But the circle of life... (4, Funny)

fahrbot-bot (874524) | more than 6 years ago | (#22145110)

...stays the same:
  • Born, Live, Read /., Die
Non-geeks, substitute "Read /." with "Move Out" and "Have Sex".

There are three lights... err, branches (1)

trainman (6872) | more than 6 years ago | (#22145324)

Submitter was close, but not quite right, there are three kingdoms. Eukaryotes, bacteria and archaea. While archaea may look a lot like bacteria, biologists recognize this group as a distinct kingdom in the tree of life.

Thanks for playing, please try again next time.

The Undiscovered (1, Funny)

Anonymous Coward | more than 6 years ago | (#22145340)

They haven't tested Cheney yet, we'll be back to 5 types if Congress does its job.

Re:The Undiscovered (0)

Anonymous Coward | more than 6 years ago | (#22145992)

Yeah, the 5th one will be "cyborg"
He's a terminator prototype.

A-ha! See! (1)

urcreepyneighbor (1171755) | more than 6 years ago | (#22145692)

<sarcasm>This is further proof that the Bible is the Word of God and vindicates Intelligent Design!</sarcasm>

No! (4, Funny)

waveformwafflehouse (1221950) | more than 6 years ago | (#22145702)

4 supergroups? [apollon.uio.no] Wait, did Journey break up? Who stopped believing!

Science Journalism is Neither (1)

blair1q (305137) | more than 6 years ago | (#22145858)

What a worthless article that is.

2,000 words, and they never listed the "Before" list. And in the text following the "After" list, they implied that there's still a group of organisms not in the list, meaning all these guys really did was move some entries between two branches.

Worthless. Come back when (a) it's done and (b) it's written-up clearly enough that the facts can be listed in two sentences.

Not a cut (0)

Anonymous Coward | more than 6 years ago | (#22146226)

The branch was not cut, it was merged!
Bet nature used GIT for that! :-)

What now? (1, Interesting)

glwtta (532858) | more than 6 years ago | (#22146272)

Both the summary and the article made no sense whatsoever (and I am not bored enough to read the paper), can someone clarify this for me?

The "branches" on the "tree" of life are pretty much arbitrary, you could draw a single node called "Life" or you could draw every single individual organism that ever existed - both would be valid.

Are they saying that they combined two groups on some taxonomic level because they are more closely related than previously thought?

I don't know what exactly they mean by "the five groups...", but I'm pretty sure their little unreadable graphic (which, by the way, wtf?) doesn't cover all of Eukarya - is this groundbreaking research transforming one mostly unknown pet classification into another?

Then there's this: "Previously, these species were thought to be completely unrelated."

Unless I slept through something fairly major, all currently living organisms on Earth are still considered to have arisen from a common origin (or created by the gods in a flash of omnipotence, etc, etc.), so all species are related.

And of course it explains that to arrive at these conclusion they have "studied" the genes - I'm sure anything more specific would make our poor little heads hurt.

Can someone summarize what they actually did?

Ah, the Irony (1)

TerminalOldFart (1196043) | more than 6 years ago | (#22146282)

Darwin didn't come up with the phrase "Tree of Life". It was first used in the Bible in the Book of Revelations describing Heaven. That Darwin lifted the phrase amuses me to no end. I wonder if God has enforced his IP rights on that?

fewer big ones (1)

epine (68316) | more than 6 years ago | (#22146372)

The Tree of Life tells the story of life on Earth, and our research can say something about how quickly life developed. Our discovery suggests that there were fewer big "events" than we have previously assumed in the development of higher life forms.
I really hate it when your average scientist tries to think. What we can determine (from what we know so far) of the history of life on earth is that there is a fairly large term representing a "winner take all" effect that determines how this tree is ultimately pruned. The insight this scientist was trying to express is that there are relatively few "split pots" on earth's evolutionary tree.

I've long suspected that a few twinges of our human predilection for genocide stems from a deeply rooted evolutionary belief that we are still seated at such a table. Do unto others before they do unto you.

Up until the Cambrian era, mother nature was doing quite the nice job of covering up her dirty work. Then she tried to hide the equatorial crime scene high atop a cliff face of a mountain range in desolate southern Alberta. She was just in the process of tuning up a rabid strain of stampeding bison to cover off the eastern approach, but then some upstart seafaring albino monkey got the notion that India lay due south of Newfoundland, and her reputation has never been quite the same since.

No worries (1)

Dachannien (617929) | more than 6 years ago | (#22146596)

Ultimately, this is all moot. In 2029, the Tree of Life will get what's coming to it, as administered by a giant hexapedal cloaking tank with miniguns for arms.

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