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Researchers Show How Cellular Complexity Can Evolve

Unknown Lamer posted more than 2 years ago | from the cellular-reverse-engineering dept.

Biotech 140

ananyo writes with an excerpt from a Nature news release: "By bringing long-dead proteins back to life, researchers have worked out the process by which evolution added a component to a cellular machine. ... In a paper published in Nature, researchers recreated an 'ancestral' version of a cellular machine called the V-ATPase proton pump, which channels protons across membranes and is vital for keeping cell compartments at the right acidity. Part of this machine is a ring of six proteins that threads through the membrane. Animals and most other eukaryotes have a ring composed of two types of protein component; fungi are alone in having a ring with three. The researchers used computational methods to work backwards and find the most likely sequences of these proteins hundreds of millions of years ago. The team inserted the DNA into yeast and found that just two mutations can turn the simple 2-protein ring into the more complex 3-protein ring."

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140 comments

So this is not... (-1, Offtopic)

unitron (5733) | more than 2 years ago | (#38639404)

So this is not about cell phone networks?

Re:So this is not... (1, Insightful)

ColdWetDog (752185) | more than 2 years ago | (#38639620)

So this is not about cell phone networks?

Nope, it's biology. Biology manages to make lemonade out of lemons. Cell phone networks make vinegar out of cider.

How do like them apples for a mixed metaphor?

Re:So this is not... (2)

ColdWetDog (752185) | more than 2 years ago | (#38639668)

But back to reality ...

tl;dr - you can make complex machines out of simple ones. Even with biologic 'machines'. Not something anyone who has thought about molecular evolution would find surprising, but it's nice to see some reasonable experimental evidence to show that it's real.

Thorton's lab has done some interesting work in the past. Nice to see he is getting some exposure. It does bother me a bit that Nature (the journal, not the mom) is continuing to take a very politically polarized editorial stance. They're really egging on the creationists (pun intended, I guess).

Re:So this is not... (1)

Anonymous Coward | more than 2 years ago | (#38639982)

That's the Nature blog ... it's definitely not the part of Nature that publishes peer-reviewed articles nor is it even Nature News. I highly doubt there is much if any editorial control at that level, and think that egging on creationists (especially because it's a quote from one of the authors) at that level is fine.

Re:So this is not... (3, Informative)

Genda (560240) | more than 2 years ago | (#38641106)

We need to have a nice sit down talk with all the folks involved. Sort of explain the basic rules for playing the game. The guys on the left. What you do is not science. It has no basis in science. Its belief... faith... it needs no foundation in science, because its about your mythos and the stories you tell about the creator. You absolutely have a right to that, and in this country the freedom to celebrated and express that faith any way you see fit, save acts that harm or risk harm to others. Stop trying to crib you faith into some psuedo-scientific theoretical framework. When you try to force facts to fit theory, you end up with something contrary to the very nature of science and anyway, its klugie, smells like feet and you've gone and dressed it funny.

You, yes, all y'all on the right. Stop poking at the folks on the left. They aren't stupid. They are practicing a perfectly natural human behavior and if it doesn't pass the muster of your process for validating truth and reality, tough, it isn't meant to, they have the right engage in magical thinking, and in some very interesting conversations, may well have things to say a human beings and metaphysics that will take the scientists among us a very long time to determine one way or the other. I mean its nonsense to mess with intangibles that way, would you try to quantify the elements of your healthy emotional life? There are parts of the human experience and behavior that are illogical, and presuppose completely unprovable assertions. Trying to logic your way through them will only irritate the natives and undermine your ability to communicate or demonstrate the amazing power of your rigorous intellectual process for determining reality when the general populace will some day most need that bright thinking.

Please, play nice and stop trying to break each others toys. Its irritating. I know some of you get your hackles up when you see Cavemen riding on the backs of Apatosaurs at the Christian Museum in Kansas City (a la Flintstones.) It wasn't so long ago you believed in St. Nick. Stop trying to screw up the others kids Christmas morning, its not your place. Maybe some day soon, somebody will squish something big at the LHC and what quirts out displays a message that says "Jesus is here too!", until then, cut each other a little slack and try to enjoy the toys you have.

Re:So this is not... (0)

Anonymous Coward | more than 2 years ago | (#38641374)

This kind of thing needs to be said more often. I often feel when reading scientific criticism of religion, or religious criticism of science, that I can see where both sides are coming from and what they fail to grasp (or acknowledge) about the other side. You pretty much nailed it.

Re:So this is not... (1)

jedidiah (1196) | more than 2 years ago | (#38642522)

Except scientists aren't usually trying to invade churches.

This is quite commonplace for "the other side".

It's hard to achieve "peaceful coexistence" with Ghengis Khan. Temujin just won't let you.

They like to play the victim but they aren't really.

Re:So this is not... (1)

Raenex (947668) | more than 2 years ago | (#38644822)

they have the right engage in magical thinking

And others have the right to try and dispel that magical thinking. If people want to go around preaching that crap, I find it completely justified to counter it.

inb4 (-1, Offtopic)

DC2088 (2343764) | more than 2 years ago | (#38639414)

inb4 anyone mentions Creationism. But seriously, this is incredibly fascinating and I'm looking forward to how this knowledge can/will be applied.

Re:inb4 (1, Insightful)

rufty_tufty (888596) | more than 2 years ago | (#38639606)

What could a creationist do with this?
Would not an intelligent designer re-use the most efficient design in all the lifeforms? Unless someone can demonstrate that the 3 ringed design is better for fungi but only for fungi; but even in that case that just shows limited random mutation combined with selection of the fittest works. I just don't get how this can be used for ignorance.
Although arguing against creationism is kind of like arguments against flat Earth...

Re:inb4 (5, Insightful)

ColdWetDog (752185) | more than 2 years ago | (#38639722)

This is just an example why you can't really 'argue' with a creationist. Anything you come up with, they can make a magic-fairy-dust argument that it's because God wanted it that way.

It isn't science.

Re:inb4 (4, Insightful)

Kenja (541830) | more than 2 years ago | (#38639764)

I'm fine with people saying evolution is the method, with a deity being the driving force. The issue is when they say that god created everything from nothing in six days around 6,000 years ago and any evidence to the contrary was put here by the devil to lure us away from the truth.

Re:inb4 (4, Funny)

ColdWetDog (752185) | more than 2 years ago | (#38639798)

I'm fine with people saying evolution is the method, with a deity being the driving force. The issue is when they say that god created everything from nothing in six days around 6,000 years ago and any evidence to the contrary was put here by the devil to lure us away from the truth.

So, you're saying, really that the Devil is in the details?

(sorry)

Re:inb4 (1, Interesting)

tgd (2822) | more than 2 years ago | (#38640038)

I'm fine with people saying evolution is the method, with a deity being the driving force. The issue is when they say that god created everything from nothing in six days around 6,000 years ago and any evidence to the contrary was put here by the devil to lure us away from the truth.

Then your position is no more supportable or rational than the people you claim to have a problem with. Both of you are wrong. Degrees of wrong is interesting from an academic standpoint, or when you want to mock someone, but wrong is, in fact, black or white. But you're drawing a line in a non-rationally-supportable position, so you're already on the wrong side of it.

Re:inb4 (4, Insightful)

blueg3 (192743) | more than 2 years ago | (#38640258)

Nonsense. Most models are wrong. They're still enormously useful compared to something that's more wrong. Newtonian mechanics is wrong, but it was -- and still is -- very useful for the overwhelming majority of situations.

It is very wrong to say the earth is flat. There are many, many ways of demonstrating its wrongness and assuming the earth is flat will lead you to wildly incorrect conclusions for many problems.
It is less wrong to say the earth is a sphere. However, it's harder to demonstrate that it's wrong, and you can do many useful calculations assuming a sphere for simplicity.
It's also wrong, but not very much, to say the earth is a slightly squashed sphere. It requires very careful measurement to demonstrate this, and it's such an accurate approximation to make that it's rare to see someone actually model the earth's correct shape.

Re:inb4 (1)

houghi (78078) | more than 2 years ago | (#38641024)

Some say the earth is flat. Others say the earth is around and those two groups are against each other.
Why don't you all play along and see that the earth is both flat AND round. Just like a pizza.

Re:inb4 (1)

OG (15008) | more than 2 years ago | (#38640288)

I'm not sure I follow what you're saying. Is your point that it's just as rational to constantly change views of superhuman beings in order to hold on to religious beliefs (I've never seen Satan described as more than a tempter -- there's certainly no indication that God gave him such power of creation to physically affect physics, geology, biology, etc in such a way to make the universe appear much older than 6000 years old) than to accept such evidence as face value? If so, I think we have different views of rationality.

Re:inb4 (1)

tgd (2822) | more than 2 years ago | (#38640790)

"I'm fine with people saying evolution is the method, with a deity being the driving force."

That is an rationally unsupportable stance.

Re:inb4 (3, Insightful)

RoccamOccam (953524) | more than 2 years ago | (#38641624)

Is it functionally different than the "Are You Living In a Computer Simulation?" argument? Is that rationally unsupportable?

Re:inb4 (1)

Kenja (541830) | more than 2 years ago | (#38643160)

I never said I agree with their stance, just that it at least is not in denial of what our senses tell us.

Re:inb4 (1, Insightful)

AJH16 (940784) | more than 2 years ago | (#38640082)

As a Christian, I have to say the biggest frustration I find is the fact that so many Christians are so insistent on 6 24 hour days when there wasn't even the concept of a modern day for the first several days. Even more direct, Jesus said he would come again "soon". I'm pretty sure that rules out the idea of our idea of time being anything like what God considers time so I have no idea why someone would insist it MUST be 6 24 hour days. Could God have made things look like they do and do it in 6 days if he's all powerful? Sure, but why would he. It doesn't make sense and there isn't anything Biblical that says that it is 6 24 hour days either.

Re:inb4 (1)

LunaticTippy (872397) | more than 2 years ago | (#38640638)

Genesis 1 explicitly states "...and the evening and the morning were the first day" and so on for each of the 6 days. It's pretty clear, although it makes it obvious that the author was unaware of how night and day work. I think some Christians become uncomfortable about glossing over things like this as poetic license because if the Bible is something that can't be taken literally the whole thing becomes suspect.

All of the people I've spoken with that are biblical literalists have to perform bizarre mental contortions in order to continue to believe that every word of the bible is absolutely true.

Re:inb4 (1)

AJH16 (940784) | more than 2 years ago | (#38641644)

Yeah, but the actual Greek words aren't so clear. The word for day also can translate as age. The word for morning can translate as soon or dawn and the word for evening can translate as twilight. Roughly they mean start and stop to an age. It's still a somewhat poetic read, sure, but Jesus himself spoke in parables that clearly were not literal events.

And don't get me wrong, personally, I still am fairly convinced that the Biblical creation story can be accurate as recorded, but I don't think that evening and morning have the same meaning prior to the existence of conventional evenings and mornings. It really doesn't fail to match up with our current understanding of how we think things happened, particularly if you consider it as a poetic recording of a vision given to whoever actually wrote it down (since obviously they weren't there themselves at the time).

I don't actually run in to a problem with taking everything as actual historical description until Noah, which I have trouble explaining the resultant movement of land masses and the rising of mountains necessary to have had it be possible to flood the entire Earth within what would appear to have to be the geologic time scale. Continental drift presents a far larger problem to solve than the big bang theory or evolution ever dreamed of presenting, but it unfortunately gets overlooked and has almost no discussion in any circles I've come across.

Re:inb4 (1)

Anonymous Coward | more than 2 years ago | (#38641770)

Greek? Genesis was written in Hebrew. The word often translated as "day" is yom, which is indeed pretty vague.

Re:inb4 (1)

LunaticTippy (872397) | more than 2 years ago | (#38643978)

I disagree. Genesis 2 states that after 6 days of work God rested on the 7th day and sanctified it. That pretty clearly indicates that we're talking about actual days.

I think of the creation story as written from a naive perspective that was plausible at the time but is not very believable with current scientific knowledge. The flood is baldly impossible, probably based on verbal tales of a large regional flood that was exaggerated over time. People then didn't understand how large the world was, or even the shape. I've heard it discussed numerous times as one of the more problematic areas of scripture.

Re:inb4 (3, Funny)

bloobamator (939353) | more than 2 years ago | (#38641138)

Let's say a "day" is the time it takes for the earth to rotate 360 degrees. (Interesting all by itself since such a concrete measurement was unavailable before the earth was created, but whatever.) And then let's say that it took 6 such days for God to create a proto-earth, i.e., the earth the way it was 3.5 billion years ago or whatever.

And then let's say, at the end of day 6, God popped this proto-earth into his cosmic-sized Time Accelerator Machine, closed the lid, programmed the machine such that the relativity factor inside the box yields a 3.5-billion year speedup, set the timer for 1 "day", and then kicked back and cracked open a cold one, or the godly equivalent of a cold one, His work being done.

Re:inb4 (1)

frank_adrian314159 (469671) | more than 2 years ago | (#38641828)

Let's say...

Let's say a giant bird had indigestion and threw up a planet-sized rock from it's gizzard! It then took a crap on the planet, making it ready for life. The bird took a seed from a neighboring planet and dropped it in its own dung and then flapped it's wings causing a tachyon inversion that sped up time 1,000,000,000-fold and caused the plant to evolve into the plants, creatures, and people we know today.

Wow! Anyone can play this game and this "theory" sounds just as likely!

Re:inb4 (1)

Petron (1771156) | more than 2 years ago | (#38641260)

Just quote the verse that states (paraphrased): to God, a 1,000 years is but a day, and a day is a 1,000 years. Aka, God exists outside of time. That supports my believe that such a Creator would exist in some other dimension, and can view the 4th dimension (and perhaps travel) the same way we do in 3.

Re:inb4 (1)

AJH16 (940784) | more than 2 years ago | (#38641342)

Yeah, this also makes it far more clear how the concepts of eternity or God being all knowing could make sense. If you could see time as we see things in three dimensions, then it becomes trivial to see the "future". A lot of the Bible makes far more sense if you assume that God isn't bound by time. (And really, I don't think it is much of an assumption to make.)

Re:inb4 (1)

gtall (79522) | more than 2 years ago | (#38642794)

Matthew chapter 16: "Verily I say unto you, There be some standing here, which shall not taste of death, till they see the Son of man coming in his kingdom."

So you've been contradicted by Jesus as reported via Mathew.

Re:inb4 (1)

mcgrew (92797) | more than 2 years ago | (#38640858)

The issue is when they say that god created everything from nothing in six days around 6,000 years ago

What I think is hilarious is that I've never, not once, heard anyone actually say that "six days" was exact (and in the original Hebrew "period of time" is translated to "day" in the modern texts) and nothing existed more than 6000 years ago -- except at slashdot.

Re:inb4 (1)

Dog-Cow (21281) | more than 2 years ago | (#38641548)

and in the original Hebrew "period of time" is translated to "day" in the modern texts

The term used in the creation story (Genesis), Yom, is the Hebrew word for day. Translating it as "day" is perfectly accurate.

Re:inb4 (1)

jedidiah (1196) | more than 2 years ago | (#38642692)

Except it doesn't just mean day. It can also mean epoch. It's not quite that cut and dried. It's not like "day".

The Darmok problem occurs far more often than not.

Re:inb4 (1)

OG (15008) | more than 2 years ago | (#38642694)

Then I'd love to trade lives with you. That's exactly the religious mindset I was inundated with growing up, and it's what my sister's teaching her kids.

Re:inb4 (1)

steppedleader (2490064) | more than 2 years ago | (#38644762)

I'm fine with people saying evolution is the method, with a deity being the driving force.

I've never found that position to be compatible with the evidence, either. Here is why: If God is the driving force behind evolution, then why can humans control evolution in the laboratory? Anyone who has had a college genetics course has probably done the experiment where you force E. Coli to develop ampicillin resistance, for example. If an E. Coli culture is placed under a UV light for a limited amount of time, samples from the UV-exposed culture will be found to have the ability to grow on ampicillin-amended media, while samples from a control culture will not (or, at least, there will be fewer colonies arising from the control -- the function of the UV light is to speed mutations; they will occur at lower rate naturally).

The point is, simply placing mutating bacteria in a given environment can lead to it adapting to that environment. If a UV photon strikes the bacteria's DNA in the right spot to activate the ampicillin-resistance gene (and the mutation goes un-repaired), it becomes ampicillin resistant; otherwise, it doesn't. The mutations are random when a single bacterium is considered, but the bulk result is always the same. What role is there for God in that? Was God controlling our choice to attempt to grow the bacteria on ampicillin amended media? Does God always step in and force the ampicllin-resistance mutation to occur just to trick us into thinking it was natural (or is Satan doing that part)?

That example is a microcosm of how all evolution occurs -- for God to be involved he would have to be either directly controlling the environment or directly controlling the mutations. All evidence that I know of appears to show he isn't guiding the mutations (unless he is trying to trick us), so that leaves the environment. In that case, the "deity drives evolution" argument would either have to be limited to events where humans are not involved or God would have to usurp our free will.

God controlling the environment to achieve a certain evolutionary end while still being consistent with current evidence seems to be problematic, too (even when humans aren't involved). God could have set the initial conditions of the universe in such a way that life would arise in environments that would push it toward the development of humans, but that would either require a deterministic interpretation of quantum mechanics or God personally manipulating random quantum processes in a deceptive manner, just like with the ampicillin-resistance mutations mentioned above. That again seems improbable, for the same reason as with the mutations -- quantum processes are random in isolation, but give consistent results when considered in bulk.

I've wondered about this ever since I had my college genetics lab -- if anyone can knock down this argument I'd be interested in hearing it.

Re:inb4 (2)

tgd (2822) | more than 2 years ago | (#38640010)

This is just an example why you can't really 'argue' with a creationist. Anything you come up with, they can make a magic-fairy-dust argument that it's because God wanted it that way.

It isn't science.

And more importantly, it isn't rational.

But its just an arbitrary bar. Once you've stepped off the rational, any opinion is suspect. It doesn't matter if you pray to "god" when you're having a shitty day, believe in "intelligent design" or live in a compound having incestuous relations with 9 year old girls ... its all a matter of degree. The path of rationality is very narrow, and once you step off it, and aren't willing to step back onto it, the rest is just haggling over price, as they say.

Re:inb4 (2)

Dcnjoe60 (682885) | more than 2 years ago | (#38640180)

This is just an example why you can't really 'argue' with a creationist. Anything you come up with, they can make a magic-fairy-dust argument that it's because God wanted it that way.

It isn't science.

And more importantly, it isn't rational.

But its just an arbitrary bar. Once you've stepped off the rational, any opinion is suspect. It doesn't matter if you pray to "god" when you're having a shitty day, believe in "intelligent design" or live in a compound having incestuous relations with 9 year old girls ... its all a matter of degree. The path of rationality is very narrow, and once you step off it, and aren't willing to step back onto it, the rest is just haggling over price, as they say.

Of course the square root of -1 isn't rational either, but we couldn't do a lot of physics without it.

Re:inb4 (1)

JoeMerchant (803320) | more than 2 years ago | (#38640122)

This is just an example why you can't really 'argue' with a creationist. Anything you come up with, they can make a magic-fairy-dust argument that it's because God wanted it that way.

It isn't science.

You, too, would have lost the Scopes Monkey trial. You forget the initial premise that neither "God" nor "Science" have intrinsic value.

pro- and anti- camps both demonstrate biases (1)

perpenso (1613749) | more than 2 years ago | (#38640438)

This is just an example why you can't really 'argue' with a creationist. Anything you come up with, they can make a magic-fairy-dust argument that it's because God wanted it that way. It isn't science.

"Scientists" don't always follow science either. With respect to religion the pro- and anti- camps have both let personal biases interfere with the scientific process. For example leading scientists of the day dismissed the big bang theory because it "smelled like creationism". These eminent scientists were biased because the big bang theory was introduced by catholic priest.

"Monsignor Georges Henri Joseph Édouard Lemaître ( lemaitre.ogg (helpinfo) 17 July 1894 – 20 June 1966) was a Belgian priest, astronomer and professor of physics at the Catholic University of Louvain. He was the first person to propose the theory of the expansion of the Universe, widely misattributed to Edwin Hubble. He was also the first to derive what is now known as the Hubble's law and made the first estimation of what is now called the Hubble constant which he published in 1927, two years before Hubble's article. Lemaître also proposed what became known as the Big Bang theory of the origin of the Universe, which he called his 'hypothesis of the primeval atom'."
http://en.wikipedia.org/wiki/Georges_Lemaitre [wikipedia.org] .

Re:pro- and anti- camps both demonstrate biases (1)

Black Parrot (19622) | more than 2 years ago | (#38643518)

"Scientists" don't always follow science either. With respect to religion the pro- and anti- camps have both let personal biases interfere with the scientific process. For example leading scientists of the day dismissed the big bang theory because it "smelled like creationism". These eminent scientists were biased because the big bang theory was introduced by catholic priest.

And yet it's accepted by almost every scientist today.

That's what makes science difference from other "ways of knowing" - evidence always wins the argument in the end.

Also, I'm curious about how many scientists rejected it because it was introduced by a priest. Almost all of them? A lot of them? A few? One?

Re:pro- and anti- camps both demonstrate biases (1)

perpenso (1613749) | more than 2 years ago | (#38644430)

"Scientists" don't always follow science either. With respect to religion the pro- and anti- camps have both let personal biases interfere with the scientific process. For example leading scientists of the day dismissed the big bang theory because it "smelled like creationism". These eminent scientists were biased because the big bang theory was introduced by catholic priest.

And yet it's accepted by almost every scientist today.

And various Christian churches accept the Copernican model (the sun, not the earth, is the center of the solar system), that the earth is billions of years old, etc. Scientists are not the only ones able to change their view based upon scientific study and observation.

That's what makes science difference from other "ways of knowing" - evidence always wins the argument in the end.

I believe the catholic church has explicitly stated that scientific observations are not in conflict in faith, including those observations related to evolution. Also the scientific "way of knowing" - observe, hypothesize, predict, test - was largely established in the west by members of the clergy in the middle ages.

It is a myth to believe that science and the scientific process are inherently in conflict with christianity.

Re:inb4 (2, Insightful)

mcgrew (92797) | more than 2 years ago | (#38640476)

It isn't science.

No, it isn't. It's philosophy, and it shouldn't be in a science story, but somehow the athiests on this board insist on bringing it up anyway.

Logic won't convince a a religious person that there's no god any more than you can convince me that my computer doesn't exist, but no argument can sway anyone into believing, either. The religious person has percieved his god, so he doesn't need faith to believe any more than I need faith to know that this computer is real (although I could be locked in a rubber room dreaming this nonexixtant computer up). The athiest needs faith.

The only logical position is agnosticism. It's a pointless argument, why do you guys keep insisting on the argument? It['s tedious and tiresome and I wish you'd stop. It's completely offtopic.

Re:inb4 (2, Insightful)

ph0rk (118461) | more than 2 years ago | (#38640714)

To re-hash the point for the millionth time:

The athiest needs faith.

Technically, no, he does not. There are gnostic and agnostic atheists, just as there are gnostic and agnostic theists.

A gnostic atheist "knows" there is no god(s), an agnostic atheist does not believe in the existence of a god(s), but will claim they cannot know for certain.

Admitting the lack of certain knowledge -and- the lack of a belief in what are essentially unsubstantiated rumors don't require much faith in anything other than one's own powers of observation.

Re:inb4 (1)

Suddenly_Dead (656421) | more than 2 years ago | (#38641842)

Hey, you say don't want this debate, and then you bring in this like you're just asking for one:

. The athiest needs faith.

The only logical position is agnosticism.

Atheism means that you don't have a belief in a god. It doesn't mean anything more, it doesn't mean that you "believe a god doesn't exist".

Faith means that you believe in something without any evidence. Most religious people even say that they have faith, it's an important part of some religions that you believe even though God doesn't physically reveal himself to you, and you very often hear the word bandied about in churches. Atheism doesn't require this, per the earlier definition.

Agnosticism means that you don't claim knowledge of god's existence or non-existence, or ("strong" agnosticism, a later creation) that you think this knowledge is impossible to determine. You can be an agnostic theist (I believe in God, but I don't know if He exists), but that's not necessarily a rational or logically-consistent position.

Re:inb4 (2)

Black Parrot (19622) | more than 2 years ago | (#38643622)

The only logical position is agnosticism.

I disagree.

The world is full of religions, none of which can offer any better supporting evidence than any of the others. Therefore the only logical positions are to set a low standard of evidence and accept them all, or set a high standard of evidence and reject them all.

However, most of them make claims that contradict the others, so accepting them all isn't logical unless you're willing to accept that reality is inherently contradictory.

Ergo, the only logical position is to reject them all... sometimes known as atheism.

Re:inb4 (2)

Ihmhi (1206036) | more than 2 years ago | (#38640534)

I try to find a short, concise rebuttal that utterly defeats that argument.

The best I've found is, "Science is about the ability to test a claim. You cannot test the claim that God did it, therefore it is irrelevant to science and as such irrelevant to my life." If anyone wants a shot at wording this more succinctly or effectively, go for it - I'd love to hear it. (I'd also love to hear any potential counterarguments).

It is an unfortunate byproduct of being an Atheist that people generally challenge my beliefs (or rather, lack thereof) and I've had to come up with a few defense mechanisms over the years.

Re:inb4 (0)

Anonymous Coward | more than 2 years ago | (#38641356)

So, anything which is untestable given the current state of technology is inherently irrelevant to your life?

I'll give the folks at CERN a call and tell them to stop looking for the Higgs boson. Since we can't test for it successfully right at this moment, any claims about it are irrelevant.

Next week, we might be able to successfully prove of disprove it, but its irrelevant because its untestable now, so we should just stop trying.

Re:inb4 (1)

jedidiah (1196) | more than 2 years ago | (#38642814)

> So, anything which is untestable given the current state of technology is inherently irrelevant to your life?

I will up the ante.

It doesn't matter if each and every scientific "truth" is contradicted tomorrow. It simply doesn't matter.

Science does not exist to give you some sort of warm fuzzy or a sense of continuity.

Re:inb4 (0)

Anonymous Coward | more than 2 years ago | (#38642288)

"Science is about the ability to test a claim. You cannot test the claim that God did it, therefore it is irrelevant to science and as such irrelevant to my life."

I think your statement is clear and concise and I support everything except the last part "and as such irrelevant to my life". I hold a great respect for science and what it can teach us about the world. However, your statement precludes anything outside science (ie: religion) having any relevance to your life.

That may work for you. I would however propose that the following statement is just as valid as yours above:

"Religion is about having faith in something transcendent to one's self. Science cannot prove or disprove God exists, therefore it is irrelevant to religion."

Science and religion look at two completely separate things. Neither has anything to say that informs the other. One is the careful examination of the physical world, the other involves a choice to believe in something metaphysical. Any attempt by either side to bridge that gap and "win" the argument is a foolish mix of ignorance and arrogance that I find incomprehensible.

Re:inb4 (1)

Ihmhi (1206036) | more than 2 years ago | (#38643750)

I should rephrase that last bit. Rather, it's not relevant to my day-to-day life.

Philosophical ventures aside, whether or not God exists doesn't affect what video card I purchase or whether I end up going for a walk in the park or just down the block.

Re:inb4 (1)

mapkinase (958129) | more than 2 years ago | (#38640746)

Exactly. Religion is not science, but so is any unverifiable theory, including theory of origin of different things.

The paper gives you an idea how things _might_ have happen.

Re:inb4 (0)

Anonymous Coward | more than 2 years ago | (#38640928)

This is just an example why you can't really 'argue' with a creationist. Anything you come up with, they can make a magic-fairy-dust argument that it's because God wanted it that way.

It isn't science.

Strawman. Educate yourself:

http://www.newadvent.org/cathen/04475a.htm
http://www.newadvent.org/cathen/05654a.htm
http://www.newadvent.org/cathen/05655a.htm

Re:inb4 (1)

jedidiah (1196) | more than 2 years ago | (#38642870)

It's not an argument if it's meant to be an open philosophical discussion, especially if creationism is being portrayed as some sort of quasi science.

It's all good until religiously motivated busy bodies try to distort public policy.

Re:inb4 (0)

Anonymous Coward | more than 2 years ago | (#38639784)

"What could a creationist do with this?"

Didn't you RTFS?

It has a mention of 'hundreds of million years ago'. A good creationist begins to 'Can't year you!' at that point.

Re:inb4 (2, Interesting)

s0litaire (1205168) | more than 2 years ago | (#38640012)

Their "battle cry" against Evolution is "Irreducible Complexity" meaning some biological systems are so complex that if a single part is removed the system fails.

It's the equivalent of saying "if i remove the cam shaft from a vehicle it can't function, therefore GOD must have created vehicles"
(Crap car analogy but can't be arsed thinking like a "new earth Creationist")

Re:inb4 (1)

Dcnjoe60 (682885) | more than 2 years ago | (#38640224)

Their "battle cry" against Evolution is "Irreducible Complexity" meaning some biological systems are so complex that if a single part is removed the system fails.

It's the equivalent of saying "if i remove the cam shaft from a vehicle it can't function, therefore GOD must have created vehicles"
(Crap car analogy but can't be arsed thinking like a "new earth Creationist")

No, it is not. But then again, somebody or something did create vehicles.

Re:inb4 (0)

Anonymous Coward | more than 2 years ago | (#38640332)

Don't be silly, the car evolved from horses. Everybody knows that! /me removes tongue from cheek

Re:inb4 (1)

omnichad (1198475) | more than 2 years ago | (#38640350)

Not quite. You'd conclude that vehicles were created by intelligence, which would be true (for some manufacturers).

Re:inb4 (1)

Empiric (675968) | more than 2 years ago | (#38640678)

Add in the notion that if the car can't drive 5 miles without the camshaft, we'll never get to the point of adding the radiator, and you're... closer.

Re:inb4 (0)

Anonymous Coward | more than 2 years ago | (#38641320)

"Irreducible Complexity" does no really apply to all cellular organisms, the human cell has many redundant systems in place, there is for example not a single cancer regulating system, there are many (more than 1 at least) pathways to activate celular apoptosis, cancer tends to occour when several of those systems are affected.

Re:inb4 (0, Insightful)

Anonymous Coward | more than 2 years ago | (#38640210)

A creationist with any sense would acknowledge adaptation. Only fools refuse such inter species evolution exists.

As a creationist I beleive in the vast majority of modern science with the caveat that it was all created by Someone/thing (in my case God) with vast complexity built-in. We don't see the big picture, which is why it is important to explore these avenues of how things came to be, how they adapted and why. We don't know why the 3 ring is better for fungi, but that is the very reason why it must be explored.

I give you 4 words (1)

RobertLTux (260313) | more than 2 years ago | (#38641540)

the camps are split by 4 words

In The Beginning ? (GOD|BANG)

You can't say that SOMEONE didn't create everything since you can't prove that a Supreme Someone does not exist.

AIG and ICR are 2 sites that gather the details of things that should make Macro-Evolutionists go Oh Really?? (simple stuff that is not simple and problems with dating and the order of fossils are 2 examples)

did you know that there are Fossils with BioMatter included??

also the non-wackadoodle Creationists attribute The Great Flood with making most of the fossils.

Re:inb4 (1)

omnichad (1198475) | more than 2 years ago | (#38640296)

A creationist would probably argue about this being proof against macroevolution, since such increasing complexity violates the 2nd law of thermodynamics. The fact that the most efficient design is seen across multiple species would be turned into an argument that the Maker's mark is on all creation, and not an argument for divergent evolution.
 
Oh, wait. You wanted this to be a rhetorical question. The fact is, that many forms of creationism are still based on a rational mind trying to apply logic science - with the exception of allowing for supernatural intervention. And of course that alone is reason enough for many to ridicule the conclusions AND the thought process.

Re:inb4 (1)

Fallingcow (213461) | more than 2 years ago | (#38640408)

A creationist would probably argue about this being proof against macroevolution, since such increasing complexity violates the 2nd law of thermodynamics.

Which--as I hope you know but I feel should be pointed out for others who might read this and think it has some merit--is complete nonsense.

Second Law of Thermodynamics [wikipedia.org]

The key word in the first sentence is "isolated".

Re:inb4 (1)

omnichad (1198475) | more than 2 years ago | (#38640450)

Right, but it's still a baffling thought to imagine increasing orders of complexity with no intelligent input. Still baffles me.

Re:inb4 (2)

Fallingcow (213461) | more than 2 years ago | (#38640654)

Agreed, though I find the complexity and mystery that unavoidably surrounds a hypothetical creator-intelligence to be significantly more baffling.

Re:inb4 (1)

Alsee (515537) | more than 2 years ago | (#38642844)

increasing complexity violates the 2nd law of thermodynamics.

Lets start with a simple block of ice. The sun shines on it, melting it into chaotic water which flows into the ocean. The sun shines on the ocean evaporating the water into even more highly random water vapor. In the winter the water vapor cools in a cloud, and falls as highly ordered and complex snowflakes.

You are completely misapplying the 2nd law of thermo. It does not prohibit things from becoming more complex or more ordered. In fact, as noted above with snowflakes, when there is an energy flow it is normal and common for order and complexity to spontaneously arise.

When the sun shines on the water, when the sun shines on the earth in general, that sunlight is a source of flowing energy, and that energy can and does do work. It can and does do work forming order and complexity within the system.

The second law of thermo is not violated because the second law says that on average disorder increases, and under the second law the sun is burning a gigantic amount of energy and experiencing a vast increase in entropy. It is normal and permitted to have a small and continual increase in order in one place (the earth) along with a large and continual increase in entropy in the sun. The sun pays for the energy and work needed to continually increase order and complexity on the earth.

a baffling thought to imagine increasing orders of complexity with no intelligent input. Still baffles me.

One key is that there is energy input. Energy can do work.

The other key is that selectively deletion is all it takes to convert random noise into directed information.

If you flip two hundred coins, all it takes is selectively killing off the one hundred tails to end up with perfectly directed perfectly ordered one hundred heads.

Lets say we have a hundred dice all with 2's on top. We put in energy and they reproduce to 200 dice. Normally they reproduce keeping the same number on top. But lets say there's a 10% chance that each "child" die is born flipped one-number-lower. And lets say there's a one-in-a-million chance for each "child" die to be born flipped one-number-higher. So basically we have 180 dice born with 2's, and 20 dice born with 1's. Now we kill off half the dice, starting with the weakest (lowest number). So we wind up with 100 dice all with 2's again. We keep doing that for many generations, many dice mutate to lower numbers and get selectively killed off, and eventually one die will be born with a 3 on top. The 3 survives and multiplies while the 1's and 2's start getting killed off. Pretty soon you have a hundred 3's. As they reproduce you get lots of mutants with 2's, and they are all selectively killed off. Eventually a 4 is born, survives and multiplies. The 3's start ding off. Then a 5 is born, and eventually a 6 is born.

Even though there's a huge 10% chance of a random bad mutation, and a tiny one-in-a-million chance of a random good mutation, all it takes is reproduction + natural selective death to convert that randomness into perfectly a directed continual increase. There is a 100% chance that you will eventually turn a population of all 2's into a population of all 6's.

Now lets get to a powerful illustration of how "zero information" mutations can almost magically create useful new information and valuable increases in complexity.

Lets consider an animal that has black-and-white vision, such as dogs. They have a gene for the eye protein that detects light. A mutation to that gene with typically destroy the ability to detect light, it will render the animal blind. Any time that happens we can assume the animal will die out, so we can just ignore that case. However some mutations will only make a very minor change to the vision protein - some mutations will merely re-turn the protein to detect a different frequency of light. The animal would still see in black-and-white, but it's vision would be based on a different color of light. Lets say the animal's original gene was already tuned to see based on the "best" or "brightest" frequency of light. An animal with a mutant vision gene tuned to a different frequency would be either neutral or slightly negative. It could still see, but with equal or lesser vision. That sort of mostly-harmless mutation may linger around for a while, but over time it too will tend to die out.

So what he have so far is a mutation that is at best "zero information" or a "minor decrease in information value".

Now lets consider a different kind of simple common mutation. Sometimes a cell can accidentally make an extra copy of a gene. The new copy is identical to the original gene, so it clearly has zero new information. The animal is simply born with two identical genes for detecting light.

Now consider what happens when we combine those two "zero information" mutations. We wind up with an animal born with two genes for vision, and they are tuned to see two different colors of light. In fact lets duplicate one of the genes again, and one copy gets randomly mutated to detect yet a different frequency of light. One gene tuned to detect red light, one gene tuned to detect green light, and one gene tuned to detect blue light. Guess what? That is exactly human full-color vision.

Even with nothing more than "zero information" mutations, they can obviously and easily combine to create increases in complexity. They can evolve black-and-white vision into human-level full-color vision. You have an increase in information, you have the information for red-vision plus the information for green vision plus the information for blue vision. That is clearly an increase in valuable information, compared to the original animal that could only see in black-and-white.

I've only begun to scratch the surface explaining how evolution works, but hopefully it's enough to establish the basic point that information and complexity can easily increase. And once it's established that information and complexity can and do increase, and that the increase can stack up more and more over time, then hopefully it basically resolves your "bafflement" how evolution can work.

Most fields of science seem baffling before you've learned how they work. How airplanes can stay up is baffling if you haven't learned anything about aerodynamics.

Once you fully understand it, evolution makes perfect sense. Once you understand it then evolution is not merely possible, but obviously inevitable. Once an initial living reproducing cell exists, the evolution of increasing diversity and increasing complexity is obvious and inevitable.

-

Re:inb4 (1)

Black Parrot (19622) | more than 2 years ago | (#38643700)

Right, but it's still a baffling thought to imagine increasing orders of complexity with no intelligent input. Still baffles me.

Why?

What is the link between complexity and intelligence?

Re:inb4 (1)

omnichad (1198475) | more than 2 years ago | (#38643918)

We make complex things. We are intelligent (to varying degrees). Our own ego says that nature can't do better than us by blind guessing.

Re:inb4 (1)

Black Parrot (19622) | more than 2 years ago | (#38644402)

We make complex things. We are intelligent (to varying degrees). Our own ego says that nature can't do better than us by blind guessing.

We also make simple things. In fact, we deem simplicity as one of the hallmarks of good design.

Re:inb4 (2)

Cyberblah (140887) | more than 2 years ago | (#38640442)

What could a creationist do with this?

I once pointed out to a creationist that an intelligent designer probably could have done a better job with the human sinus cavity, and he attributed the problems with it to the imperfections in creation introduced after Adam and Eve's fall (that is, eating of the tree of knowledge of good and evil).

Re:inb4 (1)

gtall (79522) | more than 2 years ago | (#38642868)

Hell, I'm still looking for a better Eve. Look at their problems, two chesticles that have a tendency to get cancer, a plumbing system that is in constant need of vigilance. And if that's an easy way to give birth, try pulling your upper lip over your head (Carol Burnett's response to an audience member asking her what giving birth is like).

inb4 (-1)

Anonymous Coward | more than 2 years ago | (#38639426)

inb4 creationist jokes

Re:inb4 (-1)

Anonymous Coward | more than 2 years ago | (#38639486)

Creationism is a joke!

Actually it not evolution but degeneration... (1)

Anonymous Coward | more than 2 years ago | (#38639658)

From the article:

"The work, published online in Nature, reveals the pathway by which the two-component ancestral protein (let’s call the components A and B) became a three-component one. The gene encoding protein A duplicated, and two identical copies of the gene started making proteins A1 and A2. Then, A1 and A2 started to accumulate mutations so that they could no longer substitute for each other in the ring."

"In this case, the more complex version doesn’t seem to work better or have any other obvious advantage compared with the simpler one; it is more likely that A1 and A2 proteins were just corrupted by random mutation. (The yeast didn’t seem worse off when they were stripped of their own three-protein ring and instead used one built of two ancestral proteins.) “What’s surprising to me is the idea that greater complexity doesn’t require acquisition of new functions. It can come from partial degeneration of the ancestor,” Thornton says."

Re:Actually it not evolution but degeneration... (4, Informative)

ByOhTek (1181381) | more than 2 years ago | (#38639794)

It may have had an advantage at one time (such as viral resistance).

However it could also be a no-benefit/no-cost change, which can also happen, it isn't degeneration (a weakening of the creature), and even degeneration would be a subset of evolution, since it would involve changes over time which are influenced by natural selection, genetic drift, etc.

There's no such thing as degeneration (1)

LanMan04 (790429) | more than 2 years ago | (#38641812)

Evolution does not *necessarily* imply an increase in complexity.

If complexity is expensive and is not providing an advantage to the organism, the mechanism in question may mutate "back" to a state that an ancestor of that organism already expressed/had. But you're still "evolving" because you're better able to compete *now*.

Error in post (3, Informative)

Anonymous Coward | more than 2 years ago | (#38639728)

The research was published in PLoS Biology, not in Nature.

Wrong paper? (3, Informative)

Anonymous Coward | more than 2 years ago | (#38639822)

Second link points to wrong paper, Nature paper is here. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10724.html

Its quite easy (-1)

Anonymous Coward | more than 2 years ago | (#38639840)

Verizon sneaks in a new charge, they see who complains. If no one they leave it, if people do they remove or reduce it.

This process is repeated as often as possible.

Cellular complexity is the result

Old News? (3, Funny)

arun84h (1454607) | more than 2 years ago | (#38639860)

"The researchers used computational methods to work backwards and find the most likely sequences of these proteins hundreds of millions of years ago."

So why are we just hearing about it now?

Re:Old News? (0)

Anonymous Coward | more than 2 years ago | (#38642296)

We just haven't figured out what the cave paintings mean yet.

Wait for it... (4, Insightful)

Kamiza Ikioi (893310) | more than 2 years ago | (#38639974)

Pat Robertson: "Science perverting resurrection is an abomination, and God's wrath will strike us most likely in the form of a random earthquake or hurricane or tornado sometime within the 12 months."

I'd add the /sarcasm tag just to show I'm just making fun of him, but I actually think my prediction of what will show up on YouTube from him next is pretty accurate.

Re:Wait for it... (1)

mcgrew (92797) | more than 2 years ago | (#38640616)

Richard Dawkins should be jealous of Robertson, who has converted far more Christians to athiesm than Dawkins ever dreamed of. But what, exactly, does Pat Robertson have to do with researchers working out the process by which evolution added a component to a cellular machine?

Re:Wait for it... (1)

Kamiza Ikioi (893310) | more than 2 years ago | (#38641362)

Richard Dawkins should be jealous of Robertson, who has converted far more Christians to athiesm than Dawkins ever dreamed of. But what, exactly, does Pat Robertson have to do with researchers working out the process by which evolution added a component to a cellular machine?

Pat Robertson's involvement with protein goes back a long time: http://www.cbn.com/communitypublic/shake.aspx [cbn.com]

Error in summary (5, Interesting)

damn_registrars (1103043) | more than 2 years ago | (#38640160)

The V-ATPase generally has more than 6 proteins that cross the membrane. Depending on the species, it is usually more around 10-12 individual subunits that work together to form a ring for useful transport.

From a biochemical perspective, it is also worthwhile to point out that the enzyme is powered by ATP hydrolysis - hence the name V-ATPase. It is a motor, and ATP is the fuel. Without ATP you get no useful work.

Link to the Nature Article (2)

damn_registrars (1103043) | more than 2 years ago | (#38640270)

Here is the Nature Article mentioned in the summary [nature.com] - the link in the summary goes to a PLoS Biology article.

It was just published online today, I don't see any other copies available yet. However, the primary author of the paper is supported by an NIH grant, so the paper should be released in its entirety as a non-paywalled article fairly soon to comply with the NIH funding rules.

obliggetry (0)

Anonymous Coward | more than 2 years ago | (#38640488)

in b4 6000 year's

No, they did not. (1)

mapkinase (958129) | more than 2 years ago | (#38640710)

"researchers have worked out the process by which evolution added a component to a cellular machine"

No, they did not.

Intelligent Design Disproves Intelligent Design (0)

Anonymous Coward | more than 2 years ago | (#38640826)

Let me get this straight...

1)We start with a system which has a valid, functioning two-protein arrangement, and a valid, functioning three-protein arrangement. Therefore, even according to the creationists, the three-protein design is not irreducibly complex, and its "design," even according to them, proves nothing for creationism. We should have started with the two-protein ring and worked out how it was created from a one-protein design. THAT would throw them for a loop. No pun intended.

2)We engineer an "ancestral" protein using our human intelligence. All we can derive is a working protein which has only components of the two shared proteins we have - there's no way to presume that this is in any way ancestral to what we see today, because portions of the genome which have changed may have changed in only one fork, and portions which are ancestral may have been removed from, or changed in, both modern genomes.

This is akin to looking at the latest Linux mainline kernel, and the latest Android kernel, and deriving an actual copy of Linux 2.2.0. If someone can tell me how this can be done, I'm all ears, because it would eliminate the need for source control and diffs and make my job much easier. In reality, all we've done is engineered a third, artificial, sequence which has the desired functionality. Is it ancestral? No, we just made it up, and have no idea if it reflects a previous version of the genes any more than we can recreate Linux 2.2.0 without anything but two forks of the newest kernel version.

3) To make this hypothetical protein, we use a custom-built lab, and computational methods.

4) We determine which "ancestral" (hypothetical) sequences are valid by only selecting for those which work, by intelligently determining which work and which don't.

5) We define a pathway by which this ancestral genome could have forked into what we see, and work out a way to make that happen.

6) We then engineer the mutations to make our predicted path to mutation happen, from our intelligent study of genetics.

7) We observe no evolutionary advantage from the new, mutation-engineered protein over the engineered hypothetical ancestral protein. Therefore, were it to arise in the wild, it would not have been actively preserved by natural selection, yet the real three-protein ring has been preserved. If the two-protein system evolved in fungi to the three-protein system, then at some point there were two-protein fungi and three-protein fungi. There are no two-protein fungi any longer, which means that the three-protein ring produced an evolutionary advantage, which preserved its hosts while the two-protein-ring-containing fungi were all eliminated. This should be a red flag that there's a problem with our hypothetical ancestral reconstruction.

So basically, we created an artificial system, call it ancestral, and work out a way to engineer it to become the system which we see today. We use intelligent design (by humans) to disprove intelligent design (by a god).

Guys, I'm all for disproving these wackos, but if we're going to do it we're going to have to do better than setting up a house of straw which someone who doesn't even agree with them can knock down with five minutes of thought. This is really just making us all look stupid. The fact that Nature would publish it and say it is evidence against the creationists, in any medium, and stand by its claims just makes me a bit sad for the kinds of straws we'll grasp at to try and shut these guys up. Aren't we supposed to be the ones with the critical thinking and rationality?

Re:Intelligent Design Disproves Intelligent Design (1)

robmarms (1249924) | more than 2 years ago | (#38642044)

I would like to address the idea of working backwards in biology. I can see how ridiculous this methodology would seem to the lay person. However, it is a bit similar than say the linux kernel. Biology is a three letter code of chemical components. These three letters have known translations and the chemistry of mutations is very well understood. In addition, at some point, multiple species arise from a common ancestor. These lineages of speciation are fairly well understood. Basically, you work backwards so that you get to a common ancestor via the most probable mutation path. I would be like if you took the kernel example, except that we know pretty well the probability of programmers to use certain formatting/variables and there were many many more kernels that arose from a common kernel. That way predicting the order of past events could be estimated fairly well. In addition, with biology, the translations are known so it would be like compiling and running the code with each backwards guess to make sure that there wouldn’t be an endless loop or crash. Hopefully that somewhat makes sense.

Re:Intelligent Design Disproves Intelligent Design (1)

InterArmaEnimSil (2549238) | more than 2 years ago | (#38643590)

Biology is a three letter code of chemical components.

Yes. Genes have three bases - adenine, thymine, guanine, and nothing. Cytosine is a silly myth. Also, all of "biology" is this simple.

The rest of the example, while decent, neglects the fact that we are ignorant of any information which has been completely removed from both genomes, and thus is ignored in our comparisons, or which has been modified in both to different outcomes, so that it appears to be new in each, but is not. We can devise a new similar genome using the methods you describe - however, it is merely a probable recombination of the two modern original genomes - an engineered third. It is a shot in the dark whether the proportions and pathways which we observe today were equally distributed millions of years ago. This is a major operative assumption which must be absolutely true to recreate a previously extant genome, and it is not guaranteed to hold true.

Moreover, we're dealing with random mutations. Randomness inherently implies that it cannot be reliably re-created - nature is not a seeded pRNG. We may observe variation across species, but we cannot know the precise mutations which occurred - only the "diff" across each species. Any changes not evidenced by these diffs are lost by virtue of the fact that they were randomly created and then randomly modified - if we had the original, we could only compare step A to step C - B is effectively obscured. Similarly, we can only create a possible "ancestral step A" from the data which we have in our various C0...Cn descendants. Even if we understand probable pathways as they stand today, there is substantial lost data through the mutation process, and it cannot be recreated.

We might be able to guess at it by our observations of modern mutations, but this is folly. Presuming the "most probable mutation path" to be stable and static over millions of years is just as silly as presuming the species of animals to be equally static over such a timescale.

Extrapolation is a b---h, in statistics or in science.

Also, I love the arrogance inherent in labeling others as "lay person[s]" while having no idea what their background may or may not be, while assuming oneself relatively more qualified and able to educate the original poster. As much as I hate to do it, I have to agree with the grandparent here - we're not going to make any headway getting fanatics to shut up as long as we're as condescending as they are.

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