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Featured Scientific Evidence for Universal Common Descent

Discussion in 'Evolution Vs. Creationism' started by usfan, Jul 4, 2019.

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  1. Subduction Zone

    Subduction Zone Veteran Member

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    It may not be evidence, it may be merely confirmation bias.
     
  2. shunyadragon

    shunyadragon Veteran Member
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    Based on our previous dialogue you have not been inclined to accept scientific research and publications a=based on objective verifiable evidence.

    First, 'common origins' crosses the nine with abiogenesis. Second if we go back to the earliest known life forms and begin there there is an argument for common ancestry through the research of DNA and RNA ancestry The evidence is in the progressive changes in DNA over time in small increments. This rate of change is compared to the known rate of change of DNA in recent history. Of course, not all questions have been answered in the sciences of abiogenesis and evolution, but the evidence is vaste from different sources but . . .

    As before you will likely deny this is evidence by the Fundamentalist Creationist standard.

    From: The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All Life

    The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All Life

    One researcher put the basic biological assumption of a single common ancestor to the test--and found that advanced genetic analysis and sophisticated statistics back up Darwin's age-old proposition


    In the 19th century, Charles Darwin went beyond others, who had proposed that there might be a common ancestor for all mammals or animals, and suggested that there was likely a common ancestor for all life on the planet—plant, animal and bacterial.

    A new statistical analysis takes this assumption to the bench and finds that it not only holds water but indeed is overwhelmingly sound.

    Was it not already obvious, from the discovery and deciphering of DNA, that all life forms are descended from a single common organism—or at least a basal species? No, says Douglas Theobald, an assistant professor of biochemistry of Brandeis University and author of the new study, detailed in the May 13 issue of Nature. (Scientific American is part of Nature Publishing Group.) In fact, he says, "When I went into it, I really didn't know what the answer would be."

    Despite the difficulties of formally testing evolution—especially back across the eons to the emergence of life itself—Theobald was able to run rigorous statistical analyses on the amino acid sequences in 23 universally conserved proteins across the three major divisions of life (eukaryotes, bacteria and archaea). By plugging these sequences into various relational and evolutionary models, he found that a universal common ancestor is at least 10^2,860 more likely to have produced the modern-day protein sequence variances than even the next most probable scenario (involving multiple separate ancestors).*

    "Evolution does well where it can be tested," says David Penny, a professor of theoretical biology at the Institute of Molecular BioSciences at Massey University in New Zealand and co-author of an accompanying editorial. Yet, he notes that evolution can make "testable predictions about the past (especially quantitative ones)" tricky at best. "That Theobald could devise a formal test," he says, "was excellent…. It will probably lead to a jump in what is expected of the formal evaluation of hypotheses, and that would help everybody."

    Common ancestor acrimony

    The mid-20th-century discoveries about the universality of DNA "really nailed it for people" in terms of establishing in popular—and academic—culture that there was a single universal common ancestor for all known life on Earth, Theobald says. And since then, "it's been widely assumed as true," he notes.

    But in the past couple decades, new doubt has emerged in some circles. Microbiologists have gained a better understanding of genetic behavior of simple life forms, which can be much more amorphous than the typical, vertical transfer of genes from one generation to the next. The ability of microbes such as bacteria and viruses to exchange genes laterally among individuals—and even among species—changes some of the basic structural understanding of the map of evolution. With horizontal gene transfers, genetic signatures can move swiftly between branches, quickly turning a traditional tree into a tangled web. This dynamic "throws doubt on this tree of life model," Theobald says. And "once you throw doubt on that, it kind of throws doubt on common ancestry as well."

    With the discovery of archaea as the third major domain of life—in addition to bacteria and eukaryotes—many microbiologists became more dubious of a single common ancestor across the board.

    A test for evolution

    Other researchers had put certain sections of life to the test, including a similar 1982 statistical analysis by Penny testing the relation of several vertebrate species. Theobald describes the paper as "cool, but the problem there is that they aren't testing universal ancestry." With advances in genetic analysis and statistical power, however, Theobald saw a way to create a more comprehensive test for all life.

    In the course of his research, Theobald had been bumping against a common but "almost intractable evolutionary problem" in molecular biology. Many macromolecules, such as proteins, have similar three-dimensional structures but vastly different genetic sequences. The question that plagued him was: Were these similar structures examples of convergent evolution or evidence of common ancestry?

    "All the classic evidence for common ancestry is qualitative and is based on shared similarities," Theobald says. He wanted to figure out whether focusing on those similarities was leading scientists astray.

    Abandoned assumptions
    Most people and even scientists operate under the premise that genetic similarities imply a common relation or ancestor. But as with similarities in physical appearance or structure, these assumptions "can be criticized," Theobald notes. Natural selection has provided numerous examples of convergent physical evolution, such as the prehensile tales of possums and spider monkeys or the long sticky insect-eating tongues of anteaters and armadillos. And with horizontal gene transfer on top of that, similar arguments could be made for genetic sequences.

    "I really took a step back and tried to assume as little as possible in doing this analysis," Theobald says. He ran various statistical evolutionary models, including ones that took horizontal gene transfer into consideration and others that did not. And the models that accounted for horizontal gene transfer ended up providing the most statistical support for a universal common ancestor.

    Murky origins
    Theobald says his most surprising results were "how strongly they support common ancestry." Rather than being disappointed about simply backing up a long-held assumption, he says that at least, "it's always nice to know that we're on the right track."

    These findings do not mean that a universal common ancestor establishes the "tree of life" pattern for early evolutionary dynamics. Nor, however, do they infer a "web of life" structure. The tree versus web debate remains "very controversial right now in evolutionary biology," Theobald says, reluctant to pick a side himself.

    One of the other big unknowns remaining is just when this universal common ancestor lived and what it might have looked like—a question that will take more than Theobald's statistical models to answer. Theobald also notes that the support for a universal common ancestor does not rule out the idea that life emerged independently more than once. If other, fully distinct lineages did emerge, however, they either went extinct or remain as yet undiscovered.

    Research will likely push on into these dusky corners of early evolution, Penny notes, as "scientists are never satisfied." He expects that researchers will try to sort back even earlier, before DNA took over, and assess the early stages of evolution during the RNA days.

    On a more foundational level, Penny says, the paper should not put an end to the assessment of ancestral assumptions. Instead it should be a reminder that "we have never thought of all possible hypotheses," he says. "So we should never stop considering some new approach we haven't thought of yet."
     
  3. Dan From Smithville

    Dan From Smithville Well-Known Member
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    My personal belief is that too, but the story in Genesis is an allegory and not what actually took place.
     
  4. Dan From Smithville

    Dan From Smithville Well-Known Member
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    All this scientific evidence and explanation in support of common descent. Surely you will get a cogent, rational and well thought out response. Of course not. If past performance reflects future results it is going to be more diversion, ad hominem attacks, logical fallacies and deceit from the anti-science, anti-evolution, anti-common ancestry supporter.
     
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  5. usfan

    usfan Well-Known Member

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    Well, all the disclaimers and premptive strikes are not necessary, but the ad hom is mild so I'll look at your argument.
    1. Common descent, is the debate, not common origins. A fine point, since OUR origins is the Big Question. But, abiogenesis is not the debate. I see no reason for your 'correction', here.
    2. The 'progressive changes in DNA over time in small increments', is EXACTLY the debate. That is believed and assumed, with no evidence. It is hypothesized, and has no scientific basis.
    3. The article you quoted seems to be about statistical analysis, written by a journalist, from studies she quotes. I will look at them in more detail and reply later. So little science has been offered, I'm desperate for a scientific analysis.

    But i suspect it will be the typical 'conclusions', based on assumptions, conjecture, and plausibility. Is it ok for me to make premptive conclusions, too? ;) ..and shall i suspect the usual outrage.. the 'Thou Fool!!' kinds of responses, before the pixels are dry? ;)
     
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  6. Dan From Smithville

    Dan From Smithville Well-Known Member
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    As usual, no ad hominems, but there will be a claim that there are. Plenty of science that will not be understood. I predict it will be dismissed with a wave of the hand. Snowflakes cannot last under the heat of science.

    I have been reading Theobalds work. On the very, very, very minute chance that you get a response attempting to address it rationally, will it look like anything I have seen in the literature about this work? Probably not. Who am I kidding, you will not get a rational response. It will be more about imaginary ad hominems than anything.
     
  7. metis

    metis aged ecumenical anthropologist

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    That's what none of us in reality know.
     
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  8. shunyadragon

    shunyadragon Veteran Member
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    Again, this is the response I expected, and will be the response on every scientific research article posted. The article did reference scientific research articles that support the conclusions. If you read the specific research cited the conclusions would b the same.

    The progressive changes are observed by objective verifiable evidence, and they are related to contemporary evolutionary changes in populations it is a vague 'argument from ignorance.' You believe that unless the genetic progressive changes in the past are not directly observed it is not evidence,

    All this is a given taken into consideration that you reject all science that does not support your agenda, and which you have no basic knowledge of. You could simply search and read the scientific evidence available. Why do you not do this?
     
  9. usfan

    usfan Well-Known Member

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    Ok, as promised, i will examine this article, based on statistical analysis.

    From the article:

    In the 19th century, Charles Darwin went beyond others, who had proposed that there might be a common ancestor for all mammals or animals, and suggested that there was likely a common ancestor for all life on the planet—plant, animal and bacterial.
    A new statistical analysis takes this assumption to the bench and finds that it not only holds water but indeed is overwhelmingly sound.

    This is an article in a magazine about a statistical study of dna. It is a computer analysis, set up to measure probability based on assumptions of common descent.

    Theobald was able to run rigorous statistical analyses on the amino acid sequences in 23 universally conserved proteins across the three major divisions of life (eukaryotes, bacteria and archaea). By plugging these sequences into various relational and evolutionary models,

    What is being done here, is entering data from amino acid sequences into a computer model.. a program based on the assumption of descent. They project evolutionary sequences, to draw a conclusion of probability.

    he found that a universal common ancestor is at least 10^2,860 more likely to have produced the modern-day protein sequence variances

    Probability cannot be measured, statistically, unless you have assumptions about the data. By assuming common descent, and projecting from the simplest sequences (assumed to be the earliest in the tree of life) to the later, more complex ones, a figure can be calculated, to project probability. Details about the data and calculations are omitted.

    He ran various statistical evolutionary models, including ones that took horizontal gene transfer into consideration and others that did not. And the models that accounted for horizontal gene transfer ended up providing the most statistical support for a universal common ancestor
    .

    Points about this article:
    1. The data, parameters, and assumptions for each computer model are not revealed or defined.

    2. Conclusions ABOUT the study are trumpeted, but not the actual data and methods of calculations.

    3. Flawed assumptions, that apply circular reasoning, using the premise to prove the conclusion, are present.
    From the journalist:

    Microbiologists have gained a better understanding of genetic behavior of simple life forms, which can be much more amorphous than the typical, vertical transfer of genes from one generation to the next

    This is asserted, but is an assumption that contradicts itself.. the vagaries of 'amorphous transfer of genes', is not established, is unevidenced, and assumed.

    With horizontal gene transfers, genetic signatures can move swiftly between branches, quickly turning a traditional tree into a tangled web.

    This is assumed and unevidenced. It is a conjecture based on the assumption of common descent. No actual data or studies have DEMONSTRATED the belief in 'horizontal gene transfer', which insinuates the 'tangled web', i.e., that genes flow easily between phylogenetic types, plugging into any organism equally. Attempts have been made for over a century, to show, by experimentation, that organisms can move from one genotype to another, without sucess.

    4. The flawed conclusions by journalists, and those promoting the belief in common descent override any scrutiny as to what this study actually shows.

    5. Computer models can be programmed to generate a desired outcome, and are not empirical, especially when dealing with something as vague as 'probability!'

    6. The article is a cheerleading piece, singing the praises for common descent, and glossing over what was actually done, leaving it to the imagination and wishful thinking of True Believers to see, 'Evidence!', in a contrived computer model that shows probability, if you assume common descent.

    7. The desperation of the True Believers, to see this as 'Evidence!', is a tragic commentary on the decline of critical thinking and skepticism. This is not evidence of anything, except the creative ability of man to deceive himself, with smoke and mirrors. There is NO EVIDENCE of 'new!' genes, chromosomes, genomic structures, or anything resembling common descent. It is conjecture and assumptions, trumpeted as 'proof!'

    How is this evidence of common descent? Did anyone actually read it, with scientific scrutiny? Is confirmation bias the only thing needed to see 'proof!', in these studies?
     
    #669 usfan, Jul 22, 2019
    Last edited: Jul 22, 2019
  10. usfan

    usfan Well-Known Member

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    No, they are assumed, and entered into a computer model. Nothing was 'observed!'

    Railing about my motives is an ad hom deflection. Examine the study, and the article. Then show me where any genetic evidence of common descent takes place.

    This is desperation from True Believers, frantically trying to find empirical evidence for their beliefs.
     
  11. usfan

    usfan Well-Known Member

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    This is not true. I have carefully read and critiqued any and all studies and references given.

    Besides, this is a journalistic fluff piece, targeting laypersons. The references to the actual study are poor, and fantastic conclusions and declarations are given with no credible basis.

    Dancing around with fist pumps and high fives over this journalistic extrapolation is not very scientific. Scrutiny and skepticism is woefully lacking, just eager confirmation of belief..
     
  12. Skreeper

    Skreeper Member

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    I'm sorry that I have to be the one to tell you that no one here cares about your critique of scientific studies.

    Don't pretend that you're here to learn about the theory of evolution. If you really wanted to learn you would have gone to the experts who could have given you all the information you want. But somehow you ended up here because you, just like the rest of us, are here because you like to argue.
     
  13. usfan

    usfan Well-Known Member

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    :shrug:
    I have never pretended or suggested that..

    I'm here for rational discussion, about SCIENCE. I am very familiar with the topic, and have vaid insights and perspective.

    Other than bickering with the hecklers, every now and then, i keep it on a scientific, rational vein.

    If some here do not know WHY they believe in common descent, i can't help that. I can expose fallavies, and address science, but thos is just a discussion forum. To think i come here to 'learn!', about science is pretty absurd.
     
  14. shunyadragon

    shunyadragon Veteran Member
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    If you have 'carefully read and critiqued any and all studies and references given, why other with the thread? You have already read the material and reject the science. You can easily do your own research and read the volumes of research on the subject, but nonetheless reject all this too.

    Still not answered . . . Why bother with the thread if you have rejected the literature on the science of abiogenesis and evolution?

    Looks more like an intensive 'Hand waving exercise.'

    . . . and you are a layman as far as the science of abiogenesis and evolution goes.
     
    #674 shunyadragon, Jul 22, 2019
    Last edited: Jul 22, 2019
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  15. Neutral Name

    Neutral Name Active Member

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    I don't think many people know the difference between the allegories, the histories and anything God might have actually given as knowledge to people.
     
  16. tas8831

    tas8831 Well-Known Member

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    One will note that the creationist could not address this:

    You have yet to explain, or provide a rationale, or give examples regarding this 'requirement' for "new genes, traits, or structural changes in the genome " in order for 'macroevolution' (which you also have not defined) to have occurred.

    Why are "new genes" required for macroevolution (as you define it)? And what is your evidence for this?

    What are "structural changes in the genome" required? I have provided evidence that major structural differences in genome architecture can produce creatures with strikingly similar morphology that are interfertile - where is your evidence that such changes would be required?

    New traits are a given, but that is easy - unless you have a unique definition for 'trait' as well?
     
  17. tas8831

    tas8831 Well-Known Member

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    He has avoided addressing these strawmen of his several times now, each time whining about being 'belittled' and the like:

    You have yet to explain, or provide a rationale, or give examples regarding this 'requirement' for "new genes, traits, or structural changes in the genome " in order for 'macroevolution' (which you also have not defined) to have occurred.

    Why are "new genes" required for macroevolution (as you define it)? And what is your evidence for this?

    What are "structural changes in the genome" required? I have provided evidence that major structural differences in genome architecture can produce creatures with strikingly similar morphology that are interfertile - where is your evidence that such changes would be required?

    New traits are a given, but that is easy - unless you have a unique definition for 'trait' as well?​
     
  18. tas8831

    tas8831 Well-Known Member

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    And he ignored and dodged again - almost as if he knows he's got nothing, and just whines as an excuse.:

    You have yet to explain, or provide a rationale, or give examples regarding this 'requirement' for "new genes, traits, or structural changes in the genome " in order for 'macroevolution' (which you also have not defined) to have occurred.

    Why are "new genes" required for macroevolution (as you define it)? And what is your evidence for this?

    What are "structural changes in the genome" required? I have provided evidence that major structural differences in genome architecture can produce creatures with strikingly similar morphology that are interfertile - where is your evidence that such changes would be required?

    New traits are a given, but that is easy - unless you have a unique definition for 'trait' as well?
     
  19. tas8831

    tas8831 Well-Known Member

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    So is this one:

    [​IMG]
    "And btw, this phylogenetic tree has evidence to support it. The genetic lines can be traced, not just presumed."
    How do you propose that one could use mtGenomic data or nuclear genomic data to assess "molecules to man" anything?

    The above is a "genetically evidenced descendancy chart" (aka "phylogeneitc tree") , with clear evidence of mtDNA progression of the lesser and great apes.

    That is, it is evidence for macroevolution.

    Perhaps you could provide some examples of anyone claiming that a "genetically evidenced descendancy chart" (aka "phylogenetic tree") such as the one above was intended to support the UCD?

    I'm thinking that you cannot do so.

    I have never said so. Nobody I know of has said so. I have never read in any literature wherein the phylogeny of a specific group was portrayed as evidence for UCD.

    There are rRNA phylogenies that have analyzed reps of all living things back to prokaryotes, but that is not 'molecules to man.' And it is logical to conclude that given the overwhelming concordance of all individual phylogenetic trees with one another (where applicable), there is good reason to tentatively conclude that these relationships can go back much further. But you place arbitrary limits on it all.

    No, because I am unaware that anyone had made such a leap - it seems to me to be made-up accusation.

    Now, had you limited this thread SOLELY to UCD, I probably would never have made an appearance in it.

    But you wrote in the OP:

    "I propose a discussion about the evidence for this theory of origins. AKA, 'the theory of evolution',"

    The theory of Evolution is NOT about "origins" as such - no "molecules to man" anything in 'On the Origin of SPECIES...' Evolution is not about the original life, whatever it was. So when you expanded the topic of the thread in your OP, I chimed in. I did not present my "wall of text" that was "too long" for you to address to support UCD, but to demonstrate the veracity and validity of the techniques employed in analyzing phylogeny - techniques which you have made it clear that you accept up to the point that you stop accepting for no reason at all.

    Contrary to your frequent refrains and assertions, the very same sorts of analyses that you wholeheartedly accept and endorse for Canids (which are not a haplogroup, by the way) demonstrate larger-scale phylogenies such as for the primates in the study from which the "genetically evidenced descendancy chart" (aka "phylogenetic tree") above was taken. There are larger scale studies looking at all vertebrates, even some looking at representatives from all major groups of eukaryotes (including things like yeast), and even others looking at reps of all living groups.

    Why will you reject those out of hand, yet continue to endorse the Canid paper?

    It is true that the techniques have been tested on knowns and shown to be accurate - and you very clearly accept the results of such analyses, but you seem to arbitrarily stop accepting them at some un-specified point for reasons that you will not explain - and thus larger-scale phylogenetic analyses should be accepted as tentatively valid until we see clear reasons not to do so.
    Yes - because in this thread on this forum, you boasted of decades of study, to be a science geek, and to understand the material, yet still write things like "genetically evidenced descendancy chart", and wrote things like what I presented in the 'pretender' thread. You dismissed it, claiming they were somehow 'out of context' and the like, but they are not - and no context will rescue these statements of yours:


    "Analysis of DNA" shows very little similarity, in the actual genes

    "But if there is no genetic proof of descendancy, it is mere speculation to suggest it happened. How? What mechanism overcame the high genetic walls? It cannot happen, it did not happen, & it will not happen, with what we know of genetic science. Unless a force or mechanism can be defined & demonstrated, the leaps between genome pairs & genetic parameters is impossible. It is a myth based on children's drawings trying to indoctrinate naturalistic origins."

    "The haplogroup is all the haplotypes together."

    "Also, to clarify terms, 'haplotype' is the specific clade or branch in this tree, like dogs, coyotes, etc."

    "Because you can put together a graphical 'tree', showing plausibility of descent, does not provide evidence for descent. The conjectured graphic does not prove itself."​

    ... as being anything other than the words of someone not very familiar with the science being discussed.
    All YOUR words. NONE out of context. NO 'gotchas'. NO caricatures - just you engaging in being you.

    And you expect anyone to take you seriously?
    Yes - for the clear reasons outlined above and elsewhere.
    So you keep writing - if that were the case, it seems that the easiest thing for you to do to shut me down would be to demonstrate your actual superior understanding that 4 decades of study should have produced. But you seem content to instead complain and hurl false accusations.

    In my first year in graduate school, I found scientific papers in my future field to be filled with "technobabble" that I could barely pronounce, much less understand. But through study, I was able to pretty much master the field-relevant technical language within a few months, and because I found that understanding the terminology was so helpful, I produced a scientific terminology class for our majors and have been teaching it for about 9 years. It seems to help. Maybe you should enroll in such a class.

    So....Why is it that in your 4 decades of study, you've never progressed beyond calling it all "technobabble" and continue to mis-define common terms and misinterpret the science?

    How is it that you did not know the actual definition of "haplogroup"? You've apparently been using the term for some time, and you were so confident in your proclamation about it, yet you were completely wrong.

    Not a single propaganda meme, caricature, cherry picked 'gotcha!' quote, or fallacy.

    Just you letting us all know about your supposed grand study.
    I do expect excessive projection and obfuscation from you.

    And I keep getting it.


    ADDED IN EDIT:
    The "Tree of Life" is not about "molecules to man" or "dust of the ground to Adam", but about the evolution of living things FROM the first successful life, whatever it was.

    The very premise for this thread is founded on a misinterpretation/misrepresentation of the concept of the 'Tree of Life' .
     
    #679 tas8831, Jul 22, 2019
    Last edited: Jul 23, 2019
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  20. tas8831

    tas8831 Well-Known Member

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    Well... I was asked if he was supposed to take me seriously....
     
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