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Dr.GH



Posts: 2324
Joined: May 2002

(Permalink) Posted: Mar. 16 2009,15:41   

"Astonishing DNA complexity demolishes neo-Darwinism"

is the title of a recent "opus" by YEC botanist Alex Williams.

Post here, and I'll splice together a responce.

My first observation is that he merely makes the "its too complex- it cannot have evolved" argument we have heard since Palley. Bull shit then, bull shit now.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
JLT



Posts: 740
Joined: Jan. 2008

(Permalink) Posted: Mar. 16 2009,17:44   

WHY? Why did you make me read that drivel?

The most obvious blunder is that he equates "RNA transcripts present" with "has function". To be fair, this misconception was widespread in the press when the ENCODE articles were published. But it's wrong nonetheless.
Larry Moran wrote about some of the limitations of the study here.
Something not directly related to ENCODE but exactly to the point:
Larry Moran  
Quote
There are a lot of studies suggesting that a substantial percentage of the genome is transcribed even though less than 5% is known to be functional. This leads to the idea that it encodes some unknown function. The argument is that these regions would not be transcribed unless they were doing something useful.

One objection to these studies is that the workers are looking at artifacts. The so-called transcripts are just noise from accidental transcription. This ties in with the idea that the EST database is full of examples of "transcripts" that don't make any biological sense.

There's another possibility. The regions of junk DNA could be transcribed regularly but the transcripts are rapidly degraded. They do not have a biological function. They are junk RNA.

Arthur Hunt has just posted an article on Panda's Thinb that supports this idea [Junk to the second power]. He describes the work of Wyers et al. (2005) in yeast cells. They show that there is a large class of junk RNA. The take-home lesson here is that you can't assume that some region of genomic DNA is functional just because it's transcribed. It's a lesson that many people need to keep in mind.

And he's not alone with this view.
T. Ryan Gregory:
 
Quote
- A large fraction of the sequences analyzed, both in introns and intergenic regions, appears to be transcribed. However, most of this DNA is not conserved and there is no clear indication of function. It could be that the transcripts themselves play a functional role or that the process of transcription but not the transcripts per se contributes an important effect. It could be that the regions they examined, which were typically gene-dense, included transcribed introns (no surprise) plus longer-than-expected regulatory regions such as promoters near but outside of genes (e.g., Cooper et al. 2007), but that on the whole the long stretches of non-coding DNA in between genes are not actually transcribed. Or, it could be that transcription in the human genome simply is very inefficient. For example, the data in this study suggest that 19% of pseudogenes in their sample are transcribed, even though by definition they cannot encode a protein and are unlikely to play a regulatory role. It also appears that in other groups, e.g., plants (Wong et al. 2000), there is lots of intergenic DNA that is not transcribed, which may indicate that this is a process unique to mammals and is not typical of eukaryotic genomes.

- Looking at a broader scale, we must bear in mind that about half the human genome consists of transposable elements. Some of these clearly do have functions (e.g., in gene regulation), but others persist as disease-causing mutagens. It could be that a large portion of these have taken on functions, but this remains to be shown. We are also left with the question of why a pufferfish would require only 10% as much non-coding DNA as a human whereas an average salamander needs 10 times more than we do. The well known patterns of genome size diversity make it difficult to explain the presence of all non-coding DNA in functional terms, even as there is growing evidence that a significant portion of non-coding DNA is indeed functionally important.

Also interesting: Ultra-conserved non-coding regions must be functional ... right?

We KNOW that e. g. the human genome contains long stretches of non-functional DNA e. g. transposons, repetitive elements, pseudogenes etc. (Larry Moran again). So, the whole premise of the YEC article is bogus.

The next annoying thing was this:
 
Quote
Let’s now put this information together with Haldane’s dilemma.17 Famous geneticist J.B.S. Haldane calculated that it would take about 300 generations for a favourable mutation to become fixed in a population (every member having a double copy of it). He calculated that in the approximately 6 million years since our supposed hominid ancestor split from the chimpanzee line, only about 1000 (<2000 according to ReMine18) such mutations could become fixed. This is certainly not nearly enough to turn an ape into a human. But most importantly, we now know that there are about 125 million single nucleotide differences between humans and chimps, resulting from about 40 million mutational events. This means that somewhere between 39,998,000 and 124,998,000 deleterious changes have occurred since the split with our common ancestor.
That means we have degenerated from chimps, which
makes a mockery of the whole mutation/selection theory
of origin.


First of all, Haldane's dilemma doesn't exist anymore (in the stated form). Second, the author falsly equates "doesn't get fixed" with "is deleterious".
And the rest is also either wrong, stupid, or both.

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
JLT



Posts: 740
Joined: Jan. 2008

(Permalink) Posted: Mar. 16 2009,17:46   

Oh, and the ENCODE article in Nature is open access, just in case someone wants to read it.

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
Henry J



Posts: 5760
Joined: Mar. 2005

(Permalink) Posted: Mar. 16 2009,22:10   

Quote
This leads to the idea that it encodes some unknown function. The argument is that these regions would not be transcribed unless they were doing something useful.

An alternate hypothesis: regulation to prevent such transcription either never was or got broken at some point, and might not have been significantly detrimental at that time. (Secondary hypothesis: It might have broken before there was a whole lot of junk to be suppressed.)

Quote
He calculated that in the approximately 6 million years since our supposed hominid ancestor split from the chimpanzee line, only about 1000 (<2000 according to ReMine18) such mutations could become fixed.

Unless I'm confused, that argument was assuming that each fixation had to finish before the next one started. I don't think that's a valid assumption.

Henry

  
Dr.GH



Posts: 2324
Joined: May 2002

(Permalink) Posted: Mar. 16 2009,22:39   

Thanks. Keep going.

I might have to be away for a few days. But, I will return.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Mar. 16 2009,22:55   

wrong damn thread.

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You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Mar. 17 2009,04:31   

Don't know if relevant but I seem to remember a report about perfectly healthy mice being born even after portions of junk DNA being removed.

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Rocks have no biology.
              Robert Byers.

  
JLT



Posts: 740
Joined: Jan. 2008

(Permalink) Posted: Mar. 17 2009,05:49   

Quote (Quack @ Mar. 17 2009,10:31)
Don't know if relevant but I seem to remember a report about perfectly healthy mice being born even after portions of junk DNA being removed.

T. Ryan Gregory talks about it in this post:
Also interesting: Ultra-conserved non-coding regions must be functional ... right?

Very funny, the Disco'tute just blathers about an article in Nature that found a possible function for some ultra-conserved transcribed but not translated RNAs.
The title of the Nature article isChromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.

First, T. Ryan Gregory from the above link:
   
Quote
It is important to note that elements exhibiting signs of selective constraint make up a small fraction of the total genome of organisms like mammals, on the order of 5%. Ultraconserved elements in particular represent a very tiny portion of the total DNA. It would therefore be a major exaggeration to assume that the demonstration of such sequences implies that all non-coding DNA is functional. Most or all of it might serve a function, but there is no evidence to support this notion at present. It is also inaccurate to suggest that the discovery of some function in non-coding DNA is a total surprise.


Now the DI (Casey Luskin, who else):
   
Quote
The Nature article, titled, "Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals," finds that rather than being "transcriptional noise," over 95% of the non-coding RNAs studied in the paper show "clear evolutionary conservation." That's another way of saying that their sequences are more similar than would be expected if they were functionless and their encoding DNA was accumulating neutral mutations at a constant rate. After all, if such RNA has no function, you can mutate their encoding DNA with no negative consequences to the organism. But if they have function, then mutations in their encoding DNA would tend to be highly deleterious. By finding that they have highly similar sequences, we find evidence of stabilizing selection, which is strong evidence of function.

I highlighted the important part. The authors of that paper looked for highly conserved and transcribed sequences to find functional non-coding RNA. These highly conserved sequences are included in the 5 % T. Ryan Gregory talks about. They make up a tiny fraction of the genome.

More Luskin:
   
Quote
The article makes an extremely important point: "Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function." This is important because in his book, The Language of God, theistic evolutionist Francis Collins argues that a greater level of differences among species’ non-coding DNA than among their protein-coding DNA serves as evidence that the non-coding DNA is "junk." The alternative, of course, is that the large differences within non-coding DNA serve important functions that may actually help determine the differences between species themselves. In other words, the genetic holy grail — the differences in DNA that determine differences between species — was staring Collins in the face and he dismissed it as genetic junk. This shows how the "junk" DNA paradigm is deeply embedded within Darwinian thinking, and can serve to stifle scientific advance.


It boggles my mind how Luskin can say the "Darwinian thinking" about "junk" DNA stifles scientific advances if he just hypes an article WHICH FOUND FUNCTIONAL NON-CODING RNA BY APPLYING EXACTLY THAT KIND OF "DARWINIAN THINKING" AS HE HIMSELF DESCRIBES in the first quote.
And btw, the quote from the Nature article Luskin cites in context:
   
Quote
The main concern was raised by the observation that most of the intergenic transcripts show little to no evolutionary conservation5, 13. Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function. But, the markedly low rate of conservation seen in the current catalogues of large non-coding transcripts (<5% of cases) is unprecedented and would require that each mammalian clade evolves its own distinct repertoire of non-coding transcripts. Instead, the data suggest that the current catalogues may consist largely of transcriptional noise, with a minority of bona fide functional lincRNAs hidden amid this background.


That's why we call them IDiots (and lying scumbags).


[edit]Larry Moran has read it, too!:
Quote
In other words, most of the transcripts are probably transcriptional noise, or junk, just as I said. This is the consensus opinion among molecular biologists.

Guttman et al. wanted to identify the small subset that might be functional. They identified 1,675 transcripts that show evidence of conservation. The average transcript has six exons averaging 250 bp. Thus, each transcript has about 1500 bp. of conserved exon sequence.

Even if every single one of these lincRNAs have a biological function they will only account for 1675 × 1500 = 2.5 million bp. This represents less than 0.1% of the genome. Casey Luskin ain't gonna disprove junk DNA using this paper.
[/edit]

--------------
"Random mutations, if they are truly random, will affect, and potentially damage, any aspect of the organism, [...]
Thus, a realistic [computer] simulation [of evolution] would allow the program, OS, and hardware to be affected in a random fashion." GilDodgen, Frilly shirt owner

  
Art



Posts: 69
Joined: Dec. 2002

(Permalink) Posted: Mar. 18 2009,22:29   

A comprehensive list isn't worth compiling - this paper teems with stupidity.  But some items just scream out:

 
Quote
Copying (transcription) of the gene began at a specially
marked START position, and ended at a special STOP
sign.


Mr. Williams confuses transcription with translation, thereby reducing his credibility to the level of, say, Ken Ham.  (For any fans of Williams who are reading this, please post the STOP sign for transcription in eukaryotes.  Lots of people are interested.)

 
Quote
Genes were scattered throughout the chromosomes,
somewhat like beads on a string, although some areas
were gene-rich and others gene-poor.


Beads on a string describes the appearance of nucleosomes, not genes.

 
Quote
About 93% of the genome is transcribed (not 3%, as expected). Further study with more wide-ranging
methods may raise this figure to 100%. Because much
energy and coordination is required for transcription
this means that probably the whole genome is used by
the cell and there is no such thing as ‘junk DNA’.


Utter garbage.  (Pun intended - I have posted some essays that put this particular ID delusion to rest.)

 
Quote
Transcription proceeds not just one way but both
backwards and forwards.


Um, transcription proceeds in one and only one direction - 5' -> 3'.  The "backwards" direction (3' -> 5') doesn't happen.

 
Quote
The non-protein-coding regions (previously thought
to be junk) are now called untranslated regions (UTRs)
because while they are transcribed into RNA, they are
not translated into protein. Not only has the ENCODE
project elevated UTRs out of the ‘junk’ category, but it now
appears that they are far more active than the translated
regions (the genes), as measured by the number of DNA
bases appearing in RNA transcripts. Genic regions are
transcribed on average in five different overlapping and
interleaved ways, while UTRs are transcribed on average
in seven different overlapping and interleaved ways. Since
there are about 33 times as many bases in UTRs than in
genic regions, that makes the ‘junk’ about 50 times more
active than the genes.


UTRs are parts of protein-coding genes, not the non-coding RNA genes that so fascinate ID antievolutionists.  The business about interleaving is incomprehensible garbling of the two studies Williams is misrepresenting.

One final note - Williams should consider that a better term than code for the various properties he is so taken with is language.  And then he might reflect on the implications of the existence of multiple languages in the cell (in a manner of speaking).  Specifically, multiple languages -> multiple designers -> polytheism, etc., etc....  

Don't Christian IDists ever stop and think about what they write?

   
Henry J



Posts: 5760
Joined: Mar. 2005

(Permalink) Posted: Mar. 19 2009,12:46   

Quote
Don't Christian IDists ever stop and think about what they write?


A Creationists who stops to think is called an evolutionist. ;)

  
Dr.GH



Posts: 2324
Joined: May 2002

(Permalink) Posted: Mar. 21 2009,19:01   

I just got back in town. Thanks for the remarks. I'll try to get something in a draft shape soon.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Perfectly Candide



Posts: 2
Joined: Mar. 2009

(Permalink) Posted: July 26 2009,12:44   

Speaking of young earthers and genes, there is a type of calculations that I have not really seen done against those who think we we are descended that humans were created less than ten-thousand years ago.

The following is very rough draft.  Geneticists certainly can propose better numbers and assumptions but the following certainly gets the point across.  I will generally try to error in favor of being generous to the young earthers.

I have seen it claimed that humans are born on average with 175 mutations.  Our genome (diploid) is about 6E9 nucleotides long.   This gives any particular nucleotide base about 2.9E-8 chance per generation of being mutated.

For a 1000 base gene lets say the odds of a mutation is 1000 times higher: 2.9E-5.  (I know we should be more sophisticated but that should at least give us an crude estimate.)

Now we can look from Adam to you (and just Adam to you).  Lets say the Earth is 10,000 years old (high end of "mainstream" YEC estimates) and a short 16 years average generation time.  That gives about 625 generations.  

Ignoring diploidy, the odds of any particular gene mutating in 625 generations is 1 - (1 - 2.9E-5)^625=0.02 (rounding up).
Explanation: 1-2.9E-5 is the probability of no mutation in a generation. (1-2.9E-5)^625 is the probability of no mutation in 625 generations.  Subtract the last from 1 and we have the probability of a mutation in the gene in 625 generations.

We could try to take into account diploidy by giving 5.8E-5 as the chance of two 1000-base gene sites getting mutated per generation and redo the last calculation. With some rounding up that gives us 0.04 as the chance of a mutation in 625 generations.

Clearly young-earth creationism implies that the vast majority of your genes should NOT ever received a mutation in their entire history.   Given that each human can have only two version of a gene: Adam and Eve would have had at most 4 possible variants of any particular gene with only 625 generations at most to get all the mutations that exist.   (That an extreme bottleneck would have happened because of the Noah's Ark incident would have weeded many changes.  We would all be descended from Noah, his wife, and three wives of Noah's sons -- Noah's sons obviously already counted by Noah and his wife.  Only ten variants at most per allele could have survived. )  Genetics has clearly revealed we are far more genetically diverse than what all this implies.

Lets look at Olfactory receptors (ORs).  These are genes that allow us to smell things.  Many of these are broken.  That is one reason why we can't smell certain things that other animals can.  For this argument we will ignore that humans and other apes have many of these ORs broke in the exact same way implying common descent.  

I will use the following article that I found some time back via Google:
Niimura Y, Nei M (2007) Extensive Gains and Losses of Olfactory Receptor Genes in Mammalian Evolution. PLoS ONE 2(8): e708. doi:10.1371/journal.pone.0000708

From that article, the authors found that humans have 387 functional ORs and 415 non-functional ORs.  These non-functional ORs are pseudogenes which are ORs which have been mutated at least once in such a way to make them nonfunctional.

So what is the probability  that at least 415 our of 387+415=802 ORs will be mutated?

This obviously the same as the probability  of 415 mutations plus probability  of 416 mutations plus the probability  of 417 mutations plus ... plus the probability of every single gene being mutated.  That is the same as one minus the sum of the probability of no mutations plus the probability of 1 mutation plus ... plus 414 mutations.  Looking at a statistics textbook followed by looking at what functions Microsoft Excel 97 has, I get the following:
1-BINOMDIST(414,802,0.04,TRUE) as the probability.
The answer Excel returns is zero: odds are so small that the program can't numbers so small.  

So lets flip the problem around:
BINOMDIST(x,802,0.04,TRUE) is the probability of x or less OR genes getting mutated.  

The probability of
Zero of your ORs being mutated is 6.04685E-15
10 or less is 3.85599E-06
20 or less is 0.013900639
30 or less is 0.39781607
31 or less is 0.469316024
32 or less is 0.541095275
40 or less is 0.931403353
50 or less is 0.999020943
60 or less is 0.999997942
70 or less is 0.999999999
71 or less is 1 (obviously Excel is rounding)

As a reminder that at least 415 of them have been mutated in humans.  But lets point out just how generous I have been to the YECs.  I have falsely assumed it only took one mutation to turn those 415 ORs to pseudogenes.  While that might be true in some cases, it might always be true.  I have assumed that the 387 functional genes have never gotten mutated at all which is a really a bad assumption.  I have ignored for both functional and nonfunctional ORs the possibility of neutral mutation that make no functional change.  Thus instead of assuming a 0.04 chance of mutation since Adam and Eve, I should have really assumed a much lower chance of a mutation capable of destroying gene function.  

What is even worse for the YECs is that I look just from Adam and Eve to you.  We ignored over six billion people literally.  Most of these OR genes that have been mutated into nonfunctional status have also been mutated to nonfunctionality in the exact same way for the entire human population.  To account for any OR pseudogene shared by all of humanity then you have to estimate when the last common ancestor of all humans lived (say some generations after Adam) and redo the calculation for far fewer number of generations.  In any event these calculation imply that humans could not have more than 50 pseudogenes and that different populations should have a dramatically different distribution of which OR genes will be included in the 50 or less figure.  This is not the case.  The calculations also ignore that we usually have both copies of an OR gene mutated and not just one: clearly we need to adjust the probability even more against the YECs to be realistic.  

And it gets even worse for YECs.  We have totally ignored natural selection.  Surely some of the 802 OR gene will be protected by natural selection.  If losing functionality of any of the 802 OR genes results in the resulting person being more likely to die or less likely to reproduce then the probability calculations need to shifted even more against the young earthers.  And we have good reason to suppose that this is the case.  Smelling certain things make it less likely that you will eat food that is rotten in some way.  Smelling certain bad smells make it likely that someone will avoid certain harmful things.  Thus we again really should, to be realistic, drastically adjust our calculated probabilities against the YECs.

I encourage people to suggest more appropriate calculations and/or figures if they feel it is necessary. If someone thinks they can redo this whole essay in better form: feel free.  Obviously some simplifying was done.  Any YECs want to suggest how the calculations can be changed to make your "science" believable?  Bear in mind that it should not contradict any other aspect of reality.

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: July 26 2009,15:33   

Adam and Eve aren't the most recent Biblical bottleneck. Try Noah and his family.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Perfectly Candide



Posts: 2
Joined: Mar. 2009

(Permalink) Posted: July 26 2009,15:56   

Quote (midwifetoad @ July 26 2009,15:33)
Adam and Eve aren't the most recent Biblical bottleneck. Try Noah and his family.

Actually I did discuss Noah and his family in my post.

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: July 26 2009,16:29   

Quote (Perfectly Candide @ July 26 2009,15:56)
Quote (midwifetoad @ July 26 2009,15:33)
Adam and Eve aren't the most recent Biblical bottleneck. Try Noah and his family.

Actually I did discuss Noah and his family in my post.

The general response to this kind of argument is that all the bad mutations happened after the Fall. AIG and the like would claim a period of super fast evolution after the Flood.

Once you go ad hoc, anything is possible.

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: July 28 2009,20:49   

Quote (Perfectly Candide @ July 26 2009,12:44)
I have seen it claimed that humans are born on average with 175 mutations.

I agree with midwifetoad that this sort of argument isn't going to persuade the typical YEC. Many of them won't be able to follow the probability calculations anyway.

But as to the number of mutations per generation, this came up in a recent discussion over on the xkcd forums, where I posted some supporting references. See here.

Bottom line is that current data apparently suggests a slightly lower number, around 130 new mutations per zygote. Which means it would take even longer to accumulate all the mutations we have.

But that's all moot, 'cause God zapped 'em there after Eve made Adam eat that apple, so mutation don't have nuthin to do with it.  :p

  
MichaelJ



Posts: 462
Joined: June 2009

(Permalink) Posted: July 28 2009,21:45   

Even starting Noah it would be less generations because didn't people live for hundreds of years in those days?

But I agree that the response that there was superfast evolution in those days as they had to diversify from the few animals on the ark to all of the diversity we see now.

  
Wesley R. Elsberry



Posts: 4966
Joined: May 2002

(Permalink) Posted: Aug. 10 2009,09:22   

Today only, David DeWitt of AiG will be taking questions on the Human-nonmoderated YahooGroup.

Sign up and ask some questions...

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Dr.GH



Posts: 2324
Joined: May 2002

(Permalink) Posted: Aug. 10 2009,12:50   

Quote (Wesley R. Elsberry @ Aug. 10 2009,07:22)
Today only, David DeWitt of AiG will be taking questions on the Human-nonmoderated YahooGroup.

Sign up and ask some questions...

Sorry, I am going fishing.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Henry J



Posts: 5760
Joined: Mar. 2005

(Permalink) Posted: Aug. 10 2009,22:41   

Quote
Sorry, I am going fishing.

Just for the halibut?

Henry

  
Dr.GH



Posts: 2324
Joined: May 2002

(Permalink) Posted: Aug. 11 2009,09:32   

Quote (Henry J @ Aug. 10 2009,20:41)
Quote
Sorry, I am going fishing.

Just for the halibut?

Henry

No, but we did catch one.

:D


I caught a few nice sized bass, but I got bored with bass. So instead of fishing I wandered around the boat and taught tourists how to fish. It was more fun to watch them catch their first fish than to catch any more myself.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
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