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Stirring the Soup

Scientists say this time the soup is good here.

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49 Responses to Stirring the Soup

  1. Does anyone know:
    1) What the primitive soup was made of and where to find it (I mean, at least in which part of the world can we find residues of it or strate)?
    2) What was the earth condition on earth (temperature, atmosphere, soil composition, etc..)?
    and last but not least:
    3) who was the guy making sure that the phosphate doesnt react with the mixture at the early stage ,getting the right amount of UV at the right time, twist the molecules to get them left-handed and then make them form a cells that ran into a cave to escape the same UV radiation (and occasionally the different meteorites bombarding the earth at the time)?
    Good to know that my taxes are being well spent…

  2. 2

    Looks like very nice work (original paper here).

  3. 3

    Kyrilluk, just like every transitional form creates two new gaps, every discovery about the chemical origin of life creates new reasons to doubt the chemical origin of life.

  4. 4

    Correction: just as (not just like).

  5. This is the comment I posted on their forum, trying to keep this discovery in proper perspective…

    Yes, progress has been made but we are still light-years away from explaining OOL. The scientists were able to facilitate the quasi-spontaneous creation of ribonucleotides, similarly to the famous Urey-Miller experiment so many years ago. Granted, a ribonucleotide is a more complex molecule than an amino acid, but, essentially, the scientists have succeeded in creating a couple of letters of the biological alphabet.

    What they need to do now is create the remaining letters, and then show how these letters were able to attach themselves together to form long chains of RNA, and arrange themselves in a specific order to encode information for creating specific proteins, and instructions to assemble the proteins into cells, tissues, organs, systems, and finally, complete phenotypes.

    “It suggests that RNA would be forming it lots of pools, continuously, … meaning the probably of life forming spontaneously seems really high.”

    Gotta love the unbridled optimism, but no, what it suggests is that *ribonucleotides* *could* have formed in many pools continuously, but ribonucleotides are not RNA, and the conclusion, “the probably of life forming spontaneously seems really high”, is extremely premature.

  6. 6

    The paper shows clearly how RNA could have arisen purely chemically. Time to move the goalposts (a good start C Bass).

  7. David Kellogg,

    The goalposts are still in the same place about 10 universes down the field. There are a lot of first downs between where they are and any hope of ever seeing the goalposts. They discovered letters, not even a small English sentence. “See Spot Run” is still millions of light years away in the future.

    The fact that this is hyped is just another indication of how strong the ID threat is to them.

  8. 8

    jerry, I’m sure the world’s evolutionary biolgists are quaking in their boots.

  9. “I’m sure the world’s evolutionary biolgists are quaking in their boots.”

    Why the false hype? Why the continued attacks and denunciation of ID if it is a nothing idea. Why the worry when someone publishes a study that could be considered to be ID friendly. Can you think of another reason.

    Actually I can. They are nowhere on this topic so just getting announced in the batter’s box is a huge deal. Actually they haven’t made it as far as the batter’s box, they are scouting little league games for anything that breathes.

  10. How long would the RNA — assuming they someday actually do manage to synthesize RNA as opposed two ribonucleotides — have to survive before it manages to produce proteins able to create DNA code?

  11. David Kellogg,

    There was never a goalpost saying that RNA cannot form purely chemically.

    There is a goalpost saying that living organisms are not reducible to matter, energy, chance and necessity- ie purely chemically.

    And this stuff is a good start to seeing how reducible it is.

  12. I’ve never read where anyone claimed that ribonucleotide was a product of intelligent design and couldn’t be made naturally even though “RNA world” scientist has trouble with this. Yet in the article I read phrases like “new recipe” and “this time the cooks seem to have got it right” So it took this long for “the cooks” to find just the right condition (combination) just to be two of the basic building blocks?

    I do believe if given enough time man will be able to produce “life” from RNA and DNA yet it will be by “cooks” following a very complex “recipe” in the exact order.

  13. 13

    Joseph,

    “there is no natural route to RNA.” Dembski and Wells, The Design of Life (quoted at Evolution News and Views).

    That would seem to be a claim worth revising if not withdrawing.

  14. 14

    Smidlee, terms like “cooking” are not in the Nature paper but in the popular account. The paper itself simulates likely natural conditions and is very careful about its claims. I’ll quote the last paragraph:

    Our findings suggest that the prebiotic synthesis of activated pyrimidine nucleotides should be viewed as predisposed. This predisposition would have allowed the synthesis to operate on the early Earth under geochemical conditions suitable for the assembly sequence. Although the issue of temporally separated supplies of glycolaldehyde and glyceraldehyde remains a problem, a number of situations could have arisen that would result in the conditions of heating and progressive dehydration followed by cooling, rehydration and ultraviolet irradiation. Comparative assessment of these models is beyond the scope of this work, but it is hoped that the chemistry described here will contribute to such an assessment.

    That will be behind a firewall if you don’t have a personal or institutional subscription to Nature.

  15. The paper shows clearly how RNA could have arisen purely chemically. Time to move the goalposts (a good start C Bass).

    This is categorically incorrect. As I stated in my first response, ribonucleotides are not RNA. Ribonucleotides represent individual letters, but RNA also embodies such concepts as “words”, “spelling”, and “grammar”, all of which imply intelligent agency. By way of illustration, certain English letters, such as I, O, even W, can be observed in nature, but we have yet to observe the rules of English grammer in nature

  16. I can see what C Bass is saying here. Along the lines of pointing out that, if you demonstrate the existence of silicon on earth 4 billion years ago, you have not therefore demonstrated (or even come close to demonstrating) that RAM cards are prone to developing without guidance and/or foresight. So keep things in perspective.

    (Though I’d take a different tact compared to ID proponents and critics, and point out that there’s no way to scientifically demonstrate ‘with’ or ‘without’ guidance and/or foresight even if the event certainly came to pass. Those questions aren’t scientifically fruitful. They key for critics to understand is that the ‘without’ part isn’t fruitful either.)

  17. David Kellogg,

    “there is no natural route to RNA.” Dembski and Wells, The Design of Life (quoted at Evolution News and Views).

    That would seem to be a claim worth revising if not withdrawing.

    Again, nucleotides are not RNA. Dembski’s and Wells’ claim stands, until a natural route to grammar and/or spelling is discovered.

    Hell, we haven’t actually witnessed these lone ribonucleotides naturally linking up to form long chains, yet, but even if that does come to pass, it still wouldn’t represent RNA, not until and unless it contained specified information.

    It’s interesting how this aspect of the problem eludes the materialist mindset.

  18. 18

    C Bass, the problem of how RNA forms from its parts has been more or less addressed: activated ribonucleotides can form RNA. This paper provides a new route to understanding how those ribonucleotides formed in the first place.

    although there has been some success demonstrating that ‘activated’ ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases.

    This paper gets us to the chemical formation of ribonucleotides. We already have mechanisms for getting from ribonucleotides to RNA, and we already have good reason to believe that RNA molecules could produce the first proteins.

  19. Some additional perspective here, gents.

    Insight into RNA origins.

    A short article, but some selected quotes:

    However, Robert Shapiro, professor emeritus of chemistry at New York University disagrees. ‘Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever,’ he says. According to Shapiro, it is hard to imagine RNA forming in a prebiotic world along the lines of Sutherland’s synthesis.

    And..

    But Sutherland acknowledges the implications of his research in this debate. ‘The RNA world is a very restrictive, hypothetical arrangement and one shouldn’t necessarily interpret our results as just supporting an RNA world,’ explains Sutherland. ‘Our work doesn’t preclude metabolism being important, but it suggests that nucleic acids would be central to any early origin of life idea.’

  20. 20

    Of course, a great deal of Shapiro’s career has been built around opposition to the RNA World. So he’s got some self-interest in opposing Sutherland.

  21. 21

    Good of you to admit that anyone whose career is built around evolution has self-interest as a motivation in defending it.

    But anyway, it’s amazing what intelligence can do. Give chemists a problem and they solve it. I stand in awe of the power of intelligence.

  22. Of course I knew the words “recipe” and “cooks” were not scientific words but to put it in layman terms. Yet it stills give the general idea of what Shapiro wrote above
    “‘The chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely,’ ”

    The more we learn seems to ever increases the number of tight ropes blind nature has to walk cross.

  23. Also of note:

    ‘Of course, it is referring to an event of the past and therefore conclusions will never achieve a level of certainty as in other scientific fields,’ says renowned synthetic organic chemist Albert Eschenmoser. ‘But Sutherland’s work is a fundamental study referring to the problem of the origin of life. It is an exemplary piece of how to do synthetic organic chemistry research under very serious constraints of prebiotic chemistry,’ Eschenmoser adds.

    Let me guess: By downplaying the certainty, Eschenmoser is just reflecting that he too has self-interest in opposing Sutherland’s theory?

    And, tragic mishap does bring up a good point. Do these experiments, since they’re conducted by intelligent agents, add credibility to the ID perspective by demonstrating the power of planning and foresight? A little? A lot?

  24. 24

    Do these experiments, since they’re conducted by intelligent agents, add credibility to the ID perspective by demonstrating the power of planning and foresight?

    Oy.

  25. What ‘oy’? It’s a simple question. If it’s too awkward to give a straight answer to, well, I suppose I understand.

  26. 26

    I think it’s an absurd question. It’s one step from saying that nothing done in a laboratory can say anything about what happens in nature. That debate, I believe, was resolved with the invention of the air-pump.

  27. I didn’t say you had to choose between ID or nature here. Hell, I’m on record as arguing that science cannot rule on ultimate design questions one way or the other. The most (in this case) OoL research can ever hope to show is potential pathways for OoL, speculations about conditions, etc. Important stuff, but these experiments can’t falsify philosophical positions like naturalism, materialism, panentheism, theism, or broader ID categories.

    And who said that ‘nothing done in a laboratory can say anything about what happens in nature’ or anything close to it? I asked if these experiments demonstrate something about the capabilities of intelligent agents. Are -you- saying that such capabilities aren’t subject to scientific investigation or corroboration?

  28. Nice. Human intelligence manages to piece together a billionth of the puzzel needed for the great accident.

    methinks it is like a weasel…

    Intelligent designers seem to show up more often in materialist circles than they do in ID ones.

  29. 29

    nullasallas, I should have been clearer. I don’t think the capabilities of intelligent agents are in question. By the logic of your suggestion, one could take anything involving planning and foresight as supporting ID.

  30. If by ‘supporting ID’ you mean ‘demonstrating the power of intelligent agents’, perhaps. I already told you that I personally don’t think ID is a scientific proposition (ask most regulars here, I’m a routine pain in the ass on this.) I also don’t think no-ID is a scientific proposition. Science has little to say on such questions.

    But wait, what are you saying? That it’s clear and obvious that intelligent agents are capable of producing the OoL? Or guiding evolution either via front-loading or intervention? You can’t possibly be telling me that, say… “An intelligent agent is not capable of designing synthetic life” is not a falsifiable statement, after all.

  31. @David Kellogg “Kyrilluk, just like every transitional form creates two new gaps, every discovery about the chemical origin of life creates new reasons to doubt the chemical origin of life.”
    Actually, it raises more questions that it solved. It’s not because someone has found a way to produce RNA or even DNA that it means that they came into existence by random chimicals reactions. Actually, the higher the number involved into producing such molecules and the unlikely this make an early earth scenario plausible. In other word: the more we know about how to produce such complex molecules and the more unlikely it becomes.
    Thanks to this experiment, we can appreciate further the unlikelyness of such an event (even though, we still don’t know where and how exactly the primordial soup would have emerged). I mean, not only the scientist choose the “primitive earth conditions” the most likely to produce this particular molecule (out of all the different models for a primitive earth) but he had to make sure that at each step, its composition doesn’t get destroyed by the other components of its mixture (we spoke about the UV earlier on but your extract exposed others shortcomings).
    In other word, a good progress in the origin of life issue would be in making likely, feasible a certain process. We are not there yet.

  32. Tee Hee

    They’ve been trying this experiment for 55 years and still nothing happens. A bit like alchemy, n’est ce pas?

    You evolutionists are a hopeful, gullible lot.

  33. David Kellogg,

    Page 240 in “The Design of Life”:

    But suppose some as-yet-unknown materialistic scenario could have produced such a molecule. What would this molecule look like? And what would it be capable of evolving into? Would it be a single self-replicating RNA?

    They ask more questions about it.

    I am still looking into more passages from the book. So far I cannot find the quote you posted but that doesn’t mean anything.

    That said I would say if that quote is in the book they were referring to functional RNAs…

    (I’ll keep looking)

  34. Folks:

    A few notes:

    1 –> The research, though interesting in itself misses the gap between what is causally necessary and what is sufficient. (We do need nucleic acids as materials to create cell based life, but we need a lot more and we need to see how they become organised; especially if one is adopting a chance + necessity only model. Lucky noise of that degree of complexity — DNA, RNA, ribosomes, enzymes, transport networks, onward machines and operations of the cell — is simply not credible.)

    2 –> Also, can someone inform us on reactants and products: racemic vs homochiral, concentrations, etc. In particular, is Cytosine one of the products, in what proportion? [Note, as stereo-isomers are energetically equivalent, one would have to separately justify use of homochiral molecules of the "right" chirality.]

    3 –> In short, the assembly and organisation of the cell’s hardware, and the origination of the algorithms, data structures, codes and programs that use them, as well as how these are regulated, are all serious questions to be addressed. (For the cell contains a sophisticated, flexible, information processing system, in effect a digital computer based on the 4-state D/RNA code.)

    4 –> And so, we get to Shapiro’s complaint in Sci Am of a few years ago, which seems to be very much still on the cards:

    RNA’s building blocks, nucleotides, are complex substances as organic molecules go. They each contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides . . . .

    In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . . more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

    A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

    To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . .

    GEM of TKI

  35. 35

    nullasalus [30], in a sense I agree with you. Certainly science can say nothing against a possible ultimate designer.

  36. 36

    Joseph, I found the quote here, where it is attributed to page 59.

  37. What’s sad is how desperately Darwinists cling to slender results like these. Look at the rhetoric used to describe the study. Is it seemly for scientists to gush? We thought they were too dignified for that.

    It is not only Darwinism that hangs by a silver thread but scientism itself.

  38. Somebody developed a lego, actually two, in a very precise and clever way in the laboratory and with some new insight. The experiment apparently mimicked what could have happened on the early earth in some very controlled ways.

    Two things:

    Can this process stand up to conditions that would allow for a normal biotic soup, that is the presence of possibly thousands of other molecules in the soup that could also interact.

    and

    Nobody has built anything yet with these legos though I assume that will be a future step. The empire state building (ribosome etc.) awaits the self assembly of these legos though I assume they will be happy to just build a couple small walls first.

    This is somewhat equivalent to Stanley Miller’s experiments which showed the formation of amino acids from certain types of conditions. Miller never got the Nobel prize. It will be interesting to see if these people get nominated.

  39. 39

    David Kellogg:

    “I think it’s an absurd question. It’s one step from saying that nothing done in a laboratory can say anything about what happens in nature.”

    Only for a materialist would that be true David. Those of us who believe that intelligence was involved in both nature as well as the laboratory see only similarities.

  40. #20 David Kellog:

    Of course, a great deal of Shapiro’s career has been built around opposition to the RNA World. So he’s got some self-interest in opposing Sutherland.

    #21 tragic mishap:

    Good of you to admit that anyone whose career is built around evolution has self-interest as a motivation in defending it.

    Precisely. As if the materialist scientists would give up their 6-figure salaries and years or research (not to mention a cozy “there’s nothing there” worldview) without a fight, or straight up denial. Scientists whose entire careers are built upon an unconfirmed historical science would be left in professional ruins if they admitted that it was wrong. Not only would much of their work be rendered useless, where would they go from there? Militant materialist scientists aren’t defending the “truth”, they’re defending their careers

  41. Jerry,

    This is somewhat equivalent to Stanley Miller’s experiments which showed the formation of amino acids from certain types of conditions. Miller never got the Nobel prize. It will be interesting to see if these people get nominated.

    Dangit! You beat me to the analogy =P. I was actually going to make the same point. Is anyone able to quantify the potential of this method compared to the Miller-Urey experiment? After all, everyone knows that actually quantifying the realistic potential of such experiments is the materialists worst nightmare. In fact, in most cases any attempts at suggesting any possible physical/chemical limits whatsoever gets thoroughly scorned. I mean, it IS their world view and entire methodological framework on the line =P

    I’ll put it this way, when you’re talking about natural forces and the chance for them to produce meaningful, complex systems, the chance itself obviously cannot be limitless. Chance itself has a critical limit in empirical reality that is defined by the laws of physics and real world observation. An analogy is often used by Darwinists to support their view on the possibilities of chance by illustrating an infinite number of monkeys walking across an infinite number of typewriters, ergo at some point some advanced piece of literature MUST be produced. I wholeheartedly disagree with this scenario given the actual constraints in reality that would render such an occurrence impossible even given an infinite amount of time.

    If you were to consider the specific shape and size of a monkey foot, and superimpose it over the keys on a typewriter, also taking into account the length of the stride in each step, you can quickly and realistically assess that you’d never get anything intelligible over any period of time, and instead observe an eternal repetition of letters/numbers that follow the pattern of the group of keys pressed by each step in the shape of monkey feet.

    Are these limitations ever quantified, or even entertained in OOL scenarios?

  42. Oh, you can actually dismiss that question, I must have inadvertently skipped over Kairos’ post before I posted. That’s some good information KoF.

  43. The next step, I would think, is to see if these ribonucleotides can combine. They may have already done this since I assume they can isolate ribonucleotides now, just not in this supposed naturalistic way. And if they can combine to form a polymer, are any of the polymers useful?

    This should run into the same limitations on protein formation, namely there are so many possible combinations and so few useful ones. So how does the random combination of ribonucleotides lead to anything useful.

  44. David Kellogg,

    You were quote-mining. And then twisting the context.

    In SELEX experiments, large pools of randomized RNA molecules are formed by intelligent synthesis and not by chance—there is no natural route to RNA (in fact, the chemical processes in nature that facilitate the formation of nucleotide bases undercut the formation of RNA’s sugar-phosphate backbone and vice versa).

    The phrase “there is no natural route to RNA” pertains to the RNA used in the experiments discussed.

    IOW the RNAs used were artficially synthesized.

    That is all that part of the quote pertains to.

  45. C Bass, the problem of how RNA forms from its parts has been more or less addressed: activated ribonucleotides can form RNA.

    Well, perhaps, kinda sorta.

    When I stated, “Hell, we haven’t actually witnessed these lone ribonucleotides naturally linking up to form long chains, yet”, I was referring specifically to the ones produced in the experiment being discussed currently. I apologize for not being clear on that point, but there is no reason to conclude that the ribonucleotides produced in this experiment are “active” ones, yes? Is the process to “activate” a ribonucleotide a trivial one? What environmental conditions are necessary? Are they the same conditions required for their initial production/creation?

    According to articles such as this one (emphasis added):

    Solutions of such monomers in the prebiotic environment were likely to be very dilute, but in experimental simulations of polymerization reactions dilute solutions of activated mononucleotides in the millimolar range hydrolyze extensively, and only trace amounts of dimers and trimers are formed.

    What this paper goes on to describle is how freezing the solution can yield enhanced results:

    We report here that random medium-size RNA analogues with mixed sequences (5- to 17-mers with traces of longer products) can be synthesized in ice eutectic phases that are produced when dilute solutions of activated monomers and catalysts (Mg(II) and Pb(II)) are frozen and maintained at -18 °C for periods up to 38 days. Under these conditions, the monomers are concentrated as eutectics in an ice matrix. Hydrolysis of the activated mononucleotides was suppressed at low-temperature ranges, and polymerization was enhanced with yields up to 90%. Analysis of the mixed oligomers established that incorporation of both purine and pyrimidine bases proceeded at comparable rates and yields. These results suggest that ice deposits on the early Earth could have facilitated the synthesis of short- and medium-size random sequence RNA analogues and thereby provided a microenvironment suitable for the formation of biopolymers or their precursors.

    Of course, these conditions aren’t necessarily the same conditions Sutherland used to create the (active?) ribonucleotides in the first place. I don’t recall ice being used in Sutherland’s experiments.

    Reproducing individual steps in an alleged naturalistic process for creating life do not amount to much unless we can explain the apparent discrepencies in environmental conditions required at each step.

    And, at the end of the day, we still haven’t even begun to address information content (or lack thereof).

  46. Am I the only one thinking that those day, the louder the Darwinist trumpet a discovery the less this discovery is proving anything? On the other hand, other significant finding get swept under the carpet such as the definitive refutation of all selection naturelle and sexual selection hypothesis for the neck of the giraffe.. BBC:http://news.bbc.co.uk/earth/hi.....050298.stm
    and in zoology: http://www3.interscience.wiley.....8;SRETRY=0
    It remind me the latest refutation of this kind with the peackock tail..

  47. I think that, as an argument against ID, it shows a common misunderstanding of non-reductionistic positions. I certainly don’t expect the glucose in my strands of DNA to react “magically”–not like sugars at all. If they are identified chemically as sugars, then I expect that they react as sugars do.

    I’m actually glad for that, I think that various parts our bodies react chemically means that medicine can work with some amount of confidence. But, if we admit that our codes are made of “sugars”, and we accept that sugar is a natural substance, then producing a sugar does not explain where DNA comes from.

    In the same way, carbon, oxygen, hydrogen, iron, … all occur in nature, so my origin is just a matter of them all getting together in the way that formed me, right?

    When I smash a radio, I fully expect the music to stop, whether or not it was “created” by the radio.

    I agree with the poster above that this is not a even a first down, it’s more like the fraction of a second when the guard contracts his quads and starts opening the hole.

  48. David @ 6

    The paper shows clearly how RNA could have arisen purely chemically. Time to move the goalposts (a good start C Bass).

    You’re not the only one using the term “purely chemically”. Both the authors of the original paper and ID proponents are using the term in this discussion, but your comment stuck out.

    I think I understnad…but still I must ask what everyone means or think they mean when they say purely chemical….so…

    What is “purely chemically?

    Does that neccessarily exclude the chemist and his/her control of concentrations, sequences and dosing/timing?

    Should it neccessarily exclude any particular labware?

    A thought regarding this, for example, was how much UV was required. Was it sustained UV or specifically dosed? How might this relate to the real world (sans chemist & lab)?

  49. 49

    Hi Kyrilluk,

    It remind me the latest refutation of this kind with the peackock tail..

    That study had methodological and other problems, making its conclusions suspect.

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