Scholarly integrity


Homer Jacobson wrote a paper 52 years ago in which he speculated about the chemical conditions underlying the origin of life. After discovering that the paper is frequently cited by creationists, and after reviewing the work and finding multiple errors, he has retracted the paper. Good for him. It won’t matter to the creationists, though; this paper will continue to get cited and mangled and misused.

The writeup makes an excellent point.

It is not unusual for scientists to publish papers and, if they discover evidence that challenges them, to announce they were wrong. The idea that all scientific knowledge is provisional, able to be challenged and overturned, is one thing that separates matters of science from matters of faith.

Yes. Science has an integrity and dedication to the honest evaluation of the evidence that religion lacks.

Comments

  1. Bruce Anderson says

    You mean science can be wrong? Or that ideas can change over time? That’s terribly disturbing.
    I will, along with Stephen Colbert, wait until “all the science is in” before I hitch my wagon to it.
    /end snark

  2. says

    What exactly does retracting a paper entail?

    All of my papers have things that I would change if I could go back in time and do the work again. But that doesn’t matter, the papers stay in the journals.

    Being accepted for publication is the first stage of peer review, not the last.

  3. negentropyeater says

    Yes, but this is also a double edge sword :

    Scientist : science shows that the earth is 4.5 bill y old, the galaxy, the universe, etc…

    Creationist : yes but science also says that “scientific knowledge is provisional, able to be challenged and overturned”. So, I’ll stick with the Bible.

    Scientist : but you don’t understand, bla bla bla

    Creationist : are you insinuating that I am ignorant ? bla bla bla

    Pointless discussion again.

  4. Pablo says

    I agree that retracting the paper seems odd. Shoot, most of the papers in the old literature are wrong in some way. It’s the way science works. As new information is learned, old conclusions are revised.

    Instead of retracting the paper (which won’t take it from the literature), the better solution is to write a paper that corrects the mistakes of the previous one. Either the original authors can do it, or others can do it for them.

    It happens all the time.

    Citing a 1960 paper when there are papers in the 80s showing that the original paper was flawed is the sign of bad scholarship. Call them on it.

  5. Pablo says

    “Creationist : yes but science also says that “scientific knowledge is provisional, able to be challenged and overturned”. So, I’ll stick with the Bible.”

    “Sorry, the Bible was challenged and overturned 150 years ago, at least.”

    This is a point I always like to make: It’s not like creationism is a new hypothesis that has never been considered. Shoot, for so many years, it WAS the prevailing paradigm. The problem was that it had to be abandoned because it didn’t agree with physical observation. See my post above – the Bible is part of that old literature that is wrong.

    The question you have posed above takes that full circle. Since the current scientific view will eventually be shown to be incorrect, we should adopt this other description, which was shown to be incorrect 150 years ago.

  6. dogmeatib says

    It is a nifty little catch-22 the ID/creationist folks have, isn’t it:

    1) Science has integrity, it is about provisional ideas changing as new evidence gives us a better understanding of the world.

    2) The evidence is there, Evolution is fact, it is correct, it is the most challenged theory in all of science and has withstood all of those challenges, there is no debate within the field.

    Now in the first case ID/creationists can say, “see, you admit you can be wrong, therefore our “theory” should be included. In the second case they can (and do) claim that evolution is nothing more than a dogmatic religion.

    Must be nice to be that cynically opportunistic to turn two strengths of your opponent into weaknesses. (That and a multimillion dollar PR firm … oh yeah, and toss in a few lies)

  7. says

    Bully for Professor Jacobson! Scientists need not be perfect, but we need be honest.

    As to the question of what it means to “retract” a paper: that would seem to mean that the person who published it no longer stands by it, and discourages future researchers from relying on it in any way.

    I would say that a retraction indicates something stronger than saying that a paper makes conclusions that are no longer tenable. I think it means that something about the paper is fundamentally flawed.

  8. Dave S. says

    The paper will of course stay in the Journal. But so will the retraction. Anyone citing the paper without citing the retraction (whether they agree or not) is now plainly dealing in dishonesty, easily proven.

  9. vox nihili says

    Good for Jacobson. I think the only reason this was “retracted” instead of just updated/replaced was the very fact that it had became so loved by the creationists.

    On an unrelated note, I would like to remind my fellow viewers that if they wanted to donate to the Pharyngula Freethinkers for an Effulgent Future at Donorschoose – you have not missed out. The bar on this blog shows 100% funded (because we met our goal of $20,000) but there are 3 projects left partially unfunded.

  10. Ron says

    Glycene? What’s that? :-) (I’m now doomed to make a stupid spelling mistake in this post)

    I can understand Dr. Jacobson’s feelings about his work being highjacked by people pushing an anti-science platform, however, I would have been happier if he had handled the problem a little differently. He could have written a letter pointing out the errors in the paper, but he shouldn’t have retracted the paper unless the errors were central to his conclusions based on the knowledge at the time. He could have then gone on to indicate that anyone relying on a paper from 52 years ago in an area of active scientific inquiry doesn’t understand science. Adding a list of current work that has something to say about the topic would be a bonus. Send the letter to Sigma Xi, but also send copies to PZ, Panda’s Thumb, and a few other websites to help spread the word.

  11. NC Paul says

    He could have then gone on to indicate that anyone relying on a paper from 52 years ago in an area of active scientific inquiry doesn’t understand science.

    Considering many creationists cite a source that was written centuries ago, a 52 year old paper is like Current Contents to these people.

  12. Jim Thomerson says

    I don’t know about this business of ignoring older work; probably because most of mine is moving into that category. At a meeting last year, I very much enjoyed listening to a cutting edge person cite data from one of my 1966 papers. But then I’m a systematist and have the Law of Priority to perpetuate some of my work forever.

  13. Lago says

    From the story:

    Vance Ferrell, who said he put together the material posted on Evolution-facts.org, said if the paper had been retracted he would remove the reference to it. Mr. Ferrell said he had no way of knowing what motivated Dr. Jacobson, but said that if scientists “look like they are pro-creationist they can get into trouble.”

    “There is an embarrassment,” Mr. Ferrell said.”

    No one seems to catch this BS that the scientist is suggested to have been frightened by being caught saying something anti-Darwinian? The story even goes on and tries to establish this as the case by responding:

    “Dr. Jacobson conceded that was the case. He wrote in his retraction letter, “I am deeply embarrassed to have been the originator of such misstatements.””

    He was not saying that he conceded to a, “fear of getting in trouble” or any such BS. He realized his work was being used to state crap, and this simply embarrassed the guy.

  14. Lana says

    He’s 84 and has been retired for 20 years, so I don’t think it’s reasonable to expect him to write another paper now. I’m pleased he did what he did when he found out his work is being misused. As for “who will know?” I read it this morning in the front section of the NYT and I’m nothing like a scientist.
    And as Dave S noted, anyone who tries to use his paper now would be dishonest not to note the retraction. What’s that? Some of those guys are dishonest? Oh.

  15. says

    Jacobson didn’t actually retract the entire paper, only a couple of sentences. Looking at them after he found the quote mines, he thought he had been wrong at the time and not just been overtaken by later discoveries.

    There was an editorial that accompanied Jacobson’s letter that apparently isn’t on line but I quote from it here.

  16. MikeM says

    Somewhat related, perhaps: SF Bay Area teachers report that students spend less than one hour per week studying science…

    It’s almost as though people like us (mostly over 30 at this blog, I’d guess) are the last people in America with any scientific curiosity.

    I also ran across Mark Morford’s column yesterday, which I found unnecessarily bleak.

    Maybe my kids aren’t typical, but my daughter is doing far more than an hour per week of science. More like 10 hours; that class has a lot of homework.

    What Jacobson is doing here shows a great amount of integrity; I hope our science teachers are paying attention and use it as an example.

  17. Valhar2000 says

    Scientist: Science shows that the earth is 4.5 bill y old, the galaxy, the universe, etc…

    Creationist : Yes but science also says that “scientific knowledge is provisional, able to be challenged and overturned”. So, I’ll stick with the Bible.

    Scientist: You’re right, Science was wrong before, and then scientists changed it, so that it was less wrong. The Bible was wrong before, and they haven’t changed it, so it is still wrong!

    Now, what would the creationist answer to that?

  18. fardels bear says

    How usual is an individual scientist retracting her/his own work? To be sure, the entire system of science tends to correct past mistakes but do individual scientists? I would think this is much rarer.

    One well-known example I can think of is psychologist Carl Brigham retracting his own racial interpretation of intelligence scores of the Army Alpha and Beta tests of WWI. He published a book in the early 1920s endorsing the racial interpretation and then published a paper retracting that interpretation in the 1930s.

  19. windy says

    …he shouldn’t have retracted the paper unless the errors were central to his conclusions based on the knowledge at the time.

    Exactly, and that’s what he did:

    Things grew worse when he reread his paper, he said, because he discovered errors. One related to what he called a “conjecture” about whether amino acids, the basic building blocks of protein and a crucial component of living things, could form naturally.
    “Under the circumstances I mention, just a bunch of chemicals sitting together, no,” he said. “Because it takes energy to go from the things that make glycine to glycine, glycine being the simplest amino acid.”
    There were potential sources of energy, he said. So to say that nothing much would happen in its absence “is totally beside the point.” “And that is a point I did not make,” he added.
    Another assertion in the paper, about what would have had to occur simultaneously for living matter to arise, is just plain wrong, he said, adding, “It was a dumb mistake, but nobody ever caught me on it.”

    It seems that the errors aren’t something that only the latest research revealed, more like neglecting to mention the obvious (of course all scientific authors do that, but in this case it looks like it really affected the conclusions. Otherwise he could have published a correction – or maybe SA doesn’t accept corrections after 50 years? ;)

  20. Rey Fox says

    “It’s almost as though people like us (mostly over 30 at this blog, I’d guess) are the last people in America with any scientific curiosity.”

    The age thing might be an interesting poll to run. I know I’m still on the south side of 30.

  21. says

    I use the older research literature all the time. Good science is timeless, or rather good data is timeless. Not having looked at his paper, I can’t say if it should have been retracted or not. I consider that papers in the scientific literature are communications from one scientist to other scientists, and there is an expectation on both sides (writer and reader) that it will be looked at skeptically and with an appreciation of the whole literature on the topic (with a strong emphasis on the most current literature). No “scientist” would quote a 50 year old hypothesis paper to refute current papers which contain data.

  22. jen_m says

    Rey Fox asked, “Is anyone going to even hear of this retraction other than us?”

    You mean is anyone who knows of this article going to know of the retraction, absent reading the NYT article? Probably not, given that American Scientist is only indexed in MEDLINE from 1965 onwards. If the article was indexed, then the retraction would be linked to it whenever the article citation was called, but if no one can call the article through MEDLINE then practically speaking no one will see the retraction. Unless, of course, the people citing the article also cite the retraction. Improbable, given the blow to their integrity dealt by citing a 1955 article as current evidence.

  23. says

    after reviewing the work and finding multiple errors, he has retracted the paper. Good for him.

    Good for him?

    Now what does he expect to do about the hundreds, if not thousands of papers that have been published since 1955 that have confirmed his conclusions that it is not possible, by any known mechanism, for life to have emerged from the primordal soup by accident?
    A much more likely explanation is that organic compounds and indeed, life itself came to earth from elsewhere.
    I think that Dr. Jacobson is just pissed off that his own words are being used to support a point of view which he does not presently hold, a common reaction by scientists whose work is believed to endorse creationist ideas.

    The Rise of Atmospheric Oxygen
    James F. Kasting
    Science 3 August 2001 293: 819-820

  24. Josh says

    I don’t know as good data are timeless. Observations have shelf lives. Or, at least some do. Ever try to find a quarry based on 75 year old locality data?

  25. raven says

    Jacobson should have published a correction or update.

    It would have been a stronger move for him to show where he was wrong and why. More interesting to see how the science has evolved and superceded his original work. Retraction is a more drastic step taken when something is completely wrong or false.

    As a few pointed out, at 84 maybe he isn’t able to or doesn’t care enough to bother.

    But really it won’t make much difference. The creos quote mine, misrepresent, and just flat out make stuff up all the time. The only way to support a pack of lies is with more lies.

  26. Pablo says

    “Jacobson should have published a correction or update.”

    Nah, he didn’t need to. The corrections and updates have already been published by others.

    This is the way science works. Someone reports a study, others take it and run with it and, if mistakes are found, they get corrected.

    The problem comes when (dishonest) people focus on the original work and ignore what has been said after it and about it.

    Science citation index is your friend!

  27. says

    I use the older research literature all the time. Good science is timeless, or rather good data is timeless.

    That’s certainly true in general; in extreme cases, it can even be life-critical:

    Black holes in the medical literature? The Johns Hopkins literature search

    A Johns Hopkins panel investigating the June 2001 death of a [healthy] volunteer in a Johns Hopkins University asthma study concluded that the principal researcher may have neglected to do a thorough search of the literature on the drug hexamethonium before the drug was used in a clinical investigation. The researcher searched PubMed, which indexes articles back to 1966, as well as a limited number of other resources, but missed earlier reports of the drug’s toxicity. Medical journal articles published in the 1950s apparently warned of lung damage caused by hexamethonium.

    The article goes on to make recommendations about how to do a thorough literature search, not just doing a PubMed search and calling it done. Although it’s focused on safety in clinical research, the underlying principle that science doesn’t begin and end with what’s indexed in PubMed is very important–“timeless”, as you describe it.

  28. AlanWCan says

    Valhar2000: Now, what would the creationist answer to that?

    First, they’d call you arrogant. Then they’d stick their fingers in their ears and go ‘lalalalala I can’t hear you.’

  29. says

    Observations have shelf lives. Or, at least some do. Ever try to find a quarry based on 75 year old locality data?

    Thanks, Josh–you reminded me that I was being somewhat parochial and looking at everything through a biology lens.

    I appreciate the gentle reminder that other sciences have other data needs, and I was overgeneralizing.

  30. Josh says

    Actually, I really liked your comment. I thought for a while before I wrote my reply, contemplating the various kinds of data I look at and how frequently I refer to old papers versus more current ones. In very general terms though, yeah, for us it seems that the older an observation is, the larger the error bars on it are likely to be (many reasons for this, including the evolution of the discipline itself).

  31. Carlie says

    I thought it was very good of him to do that. I read the retraction just last week, in fact, when I got the issue. Sure, it would have been nice for him to cite a few of the papers that prove him wrong in the letter, but again he’s 84 and didn’t need to do this in the first place. Now it’s in print, in the same publication, that he personally admits that his prior conclusions were wrong (and he even mentions that it was one of his first papers that he wrote before he really knew what he was doing). The importance of it is that it’s now on permanent record that even he disagrees with what he wrote.

  32. David Marjanović says

    Glycene? What’s that? :-) (I’m now doomed to make a stupid spelling mistake in this post)
    I can understand Dr. Jacobson’s feelings about his work being highjacked

    (emphasis added)

    Gotcha. The Bierce-Hartman-McKean-Skitt Law of Prescriptivist Retaliation knows no mercy.

    How usual is an individual scientist retracting her/his own work? To be sure, the entire system of science tends to correct past mistakes but do individual scientists? I would think this is much rarer.

    It is very rare, but I’ve seen a few cases.

    Ever try to find a quarry based on 75 year old locality data?

    Has been done once, right in the middle of the badlands of Alberta. I don’t know how many other attempts have failed…

  33. David Marjanović says

    Glycene? What’s that? :-) (I’m now doomed to make a stupid spelling mistake in this post)
    I can understand Dr. Jacobson’s feelings about his work being highjacked

    (emphasis added)

    Gotcha. The Bierce-Hartman-McKean-Skitt Law of Prescriptivist Retaliation knows no mercy.

    How usual is an individual scientist retracting her/his own work? To be sure, the entire system of science tends to correct past mistakes but do individual scientists? I would think this is much rarer.

    It is very rare, but I’ve seen a few cases.

    Ever try to find a quarry based on 75 year old locality data?

    Has been done once, right in the middle of the badlands of Alberta. I don’t know how many other attempts have failed…

  34. Mooser says

    Good point made above. Don’t let those creationist bastards pretend that evolution is somehow the codifying of baseless folk wisdom or is a “traditional” view which is now being overturned by creationism.

    Creationism was the prevailing theory for thousands of years and almost every religion in the world has one or another form of the creation legend.

    So Darwin was not simply accepted as dogma cause it fit in with prevailing beliefs, no, not at all. Creationism wass the universal belief, so Darwin’s was the most challenged theory in history, I submit.

  35. Owlmirror says

    Now what does he expect to do about the hundreds, if not thousands of papers that have been published since 1955 that have confirmed his conclusions that it is not possible, by any known mechanism, for life to have emerged from the primordal soup by accident?

    What? Cite one.

    A much more likely explanation is that organic compounds and indeed, life itself came to earth from elsewhere.

    Eh. This just pushes the problem of abiogenesis further out. Given powerful ionizing radiation and no liquid water, I think panspermia/cosmic origin is far less likely than earth-bound abiogenesis.

    Are there any comparison studies out there?

    Hm.

    “Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations”
    http://www.talkorigins.org/faqs/abioprob/abioprob.html

    “Protection of Bacterial Spores in Space, a Contribution to the Discussion on Panspermia”
    http://www.springerlink.com/content/h171534701359381/

  36. Josh says

    Has been done once, right in the middle of the badlands of Alberta. I don’t know how many other attempts have failed…

    Yeah, and I figure you probably know how much hell D went through to pull it off.

  37. Ben M says

    From a science perspective, there’s no point in Jacobsen writing a new paper correcting the old one—the relevant corrections have been in the literature for decades, and everyone interested knows.

    From an anti-ID perspective, there’s no point in Jacobsen writing a new paper—the IDers aren’t going through the literature looking for valid, unrefuted results, they’re looking for quotes to mine. They would ignore Jacobsen’s new paper the same way they ignore the rest of modern biology.

    The retraction, then, is beautiful. Missing a relevant piece of literature is merely sloppy. Citing a retracted paper is getting towards fraudulent.

  38. says

    What? Cite one.

    I did.

    The notion that the primordal atmosphere contained mostly ammonia, methane and hydrogen has been soundly debunked. More likely it contained large amounts of carbon dioxide, nitrogen and water vapor. All of these compounds have fairly high heats of formation precluding any possibility that they could spontaneously break their bonds and rearrange themselves.

    This just pushes the problem of abiogenesis further out.

    So what?
    “By any mathematical analysis, life is unlikely to have arisen by chance from nonliving chemicals here on Earth. The likelihood is so tiny that it does not improve significantly if we expand the range of possible origination sites to the whole universe. It seems unlikely that it would happen in any universe. It requires fewer miracles to believe that life has always existed. Alternating between long quiescent periods of waiting in space as mere wispy potential, and eventual emergence on planets everywhere, life may have always been.”

    http://panspermia.com/thebegin.htm

    “A noiseless patient spider,
    I mark’d where on a little promontory it stood isolated,
    Mark’d how to explore the vacant vast surrounding,
    It launch’d forth filament, filament, filament out of itself,
    Ever unreeling them, ever tirelessly speeding them.

    And you O my soul where you stand,
    Surrounded, detached, in measureless oceans of space,
    Ceaselessly musing, venturing, throwing, seeking the spheres to connect them,
    Till the bridge you will need be form’d, till the ductile anchor hold,
    Till the gossamer thread you fling catch somewhere, O my soul.”

  39. says

    Have you actually read the Kasting paper you cited? It doesn’t support your creationist views at all.

    Your panspermia quote is crap, too. Go ahead, give me “any mathematical analysis” that shows what you claim, and that isn’t some clueless git pulling bogus numbers out of his butt.

  40. John B says

    I don’t want to defend a creationist viewpoint here, but just on the rhetorical strategy pointed at in comment #19:

    Scientist: You’re right, Science was wrong before, and then scientists changed it, so that it was less wrong. The Bible was wrong before, and they haven’t changed it, so it is still wrong!

    Now, what would the creationist answer to that?

    Once you’ve conceded that you were wrong then and you are still wrong now (though less wrong, by your measurements), the creationist would just reply that the Bible is right.

    Then you’ll find yourself describing what you mean by ‘less wrong’, and watch the creationist hold onto the fact that you’re wrong like a bulldog on a bone.

  41. Owlmirror says

    The notion that the primordal atmosphere contained mostly ammonia, methane and hydrogen has been soundly debunked.

    By whom? As PZ points out, the paper you pointed at does not support this at all.

    More likely it contained large amounts of carbon dioxide, nitrogen and water vapor.

    According to whom? Who are these famous geochemists who have calculated the exact probabilities of the composition of primitive atmosphere?

    It requires fewer miracles to believe that life has always existed.

    Since carbon, oxygen, and higher elements are required for life, and those elements did not exist until early stars went supernova, it is not merely improbable, but actually impossible for life to have “always” existed.

    [Poetry snipped]

    Is that all you’ve got? Misunderstandings, and/or lies, and poetry?

  42. Owlmirror says

    Sometimes I see patterns. And I could be wrong about this particular pattern. But there was another commenter who argued vehemently that life “always existed”. And some basic quick checks shows that he lives in Hawaii. What a coincidence… “Kamehameha the Great”?

    Hm.

    PZ, his web pages suggest that Charlie Wagner isn’t a creationist per se. He’s a mystical steady-stater. Woo.

  43. says

    That thought occurred to me, too, Owlmirror, but I thought he was too sick at present to be posting. Maybe I’m wrong, but I thought he made his grand stage exit here some time ago.

    Does sound like him, though, I gotta say.

  44. says

    When the possibility of error is recognized, only then is it possible to be right.

    When errors are constantly sought and corrected, it becomes possible to be right a whole lot.

    If errors are not constantly sought out and corrected, you’re going to be wrong. A lot.

    If you’re not even admitting the possibility of error, you can no longer see there’s a difference between being right and being wrong.

    The best scientists are their own harshest peer review. Kudos to Jacobson.

  45. fletch says

    Yes. Science has an integrity and dedication to the honest evaluation of the evidence that religion lacks.

    Especially when it concerns “second-hand” smoke– or glowball warming…

  46. Ross Nixon says

    Science has integrity? That’s news to me, When did this happen?

    Good, let’s see how long it takes Leaky to recant.

    The skull of an alleged human ancestor Richard Leakey made famous in 1972 was poorly reconstructed, claims a paleoanthropologist who specializes in craniofacial biology. According to Dr. Timothy Bromage of New York University, Leakey employed nonstandard principles while assembling the bones of his “Skull 1470”, giving the face a flatter, more human-like profile. Many at the time of the discovery were stunned to find such a human-like face dated to 3 million years ago. (This date was later revised downward to 1.9 million years. The skull was later dubbed Homo rudolfensis and considered an ancestor in the direct line leading to modern man, Homo sapiens.)
    Employing rules that the eyes, ears and mouth of mammals must bear a precise relationship to one another, Dr. Bromage did his own reconstruction and found the skull “looked more apelike than previously believed.” The computer-aided reconstruction reduced the brain size to less than half that of a modern human. He said that the corrected skull has a “surprisingly small brain and distinctly protruding jaw, features commonly associated with more apelike members of the hominid family living as much as three million years ago.” Dr. Bromage criticized the famous paleoanthropologist, judging that “Dr. Leakey produced a biased reconstruction based on erroneous preconceived expectations of early human appearance that violated principles of craniofacial development…. Dr. Leakey produced a reconstruction that could not have existed in real life.” The erroneous interpretation, the article states, has been “widely accepted until now.”

    And will it take 100+ years to change the textbooks like it did in the case of Haeckel’s known faked drawings to support his embryonic recapitulation theory?

  47. Peter Ashby says

    In my PhD thesis I spend some time retracting the findings of my honours thesis (based on too small n-numbers). No embarrassment was entered into, they were honest mistakes based on a small sample size that was necessitated by the nature of the project. I could collect lots of data at one time point or small amounts of data from many time points. Such is life, those who never make mistakes never attempt anything. To make a mistake is to have made an effort. Making mistakes is not shameful, it is failing to learn from them that is shameful.

  48. Torbjörn Larsson, OM says

    Jacobson didn’t actually retract the entire paper, only a couple of sentences.

    Thanks John, that puts the matter in the proper perspective.

    And the refutation note seems solid and self-contained. (One could argue about references, but it seems pretty basic data is required. And the original paper remains and may contain such references.) One of several satisfying resolutions, IMO.

    we don’t want to get started on James Watson again, but… He announced his retirement today.

    He retires from a lab board, but I read his retirement letter as that he continues to research there:

    That the Cold Spring Harbor Laboratory is now one of the world’s premier sites for biological research and education has long warmed my heart. So I am grateful that its Board now will allow me to remain along my beloved Bungtown Road. Forty-nine years ago, as a newly appointed young Assistant Professor at Harvard, I gave my first course on this pernicious collection of diseases of uncontrolled cell growth and division.

    Cancer, then an intellectual black box, now, in part because of research at the Laboratory, is almost full lit. Though important facts remain undiscovered, there is no reason why they should not soon be found. Final victory is within our grasp. Strong in spirit and intensely focused, I wish to be among those at the victory line.

  49. Torbjörn Larsson, OM says

    Jacobson didn’t actually retract the entire paper, only a couple of sentences.

    Thanks John, that puts the matter in the proper perspective.

    And the refutation note seems solid and self-contained. (One could argue about references, but it seems pretty basic data is required. And the original paper remains and may contain such references.) One of several satisfying resolutions, IMO.

    we don’t want to get started on James Watson again, but… He announced his retirement today.

    He retires from a lab board, but I read his retirement letter as that he continues to research there:

    That the Cold Spring Harbor Laboratory is now one of the world’s premier sites for biological research and education has long warmed my heart. So I am grateful that its Board now will allow me to remain along my beloved Bungtown Road. Forty-nine years ago, as a newly appointed young Assistant Professor at Harvard, I gave my first course on this pernicious collection of diseases of uncontrolled cell growth and division.

    Cancer, then an intellectual black box, now, in part because of research at the Laboratory, is almost full lit. Though important facts remain undiscovered, there is no reason why they should not soon be found. Final victory is within our grasp. Strong in spirit and intensely focused, I wish to be among those at the victory line.

  50. Torbjörn Larsson, OM says

    Given powerful ionizing radiation and no liquid water, I think panspermia/cosmic origin is far less likely than earth-bound abiogenesis.

    I admit that I’m not overly fond of panspermia. It seems Earth life started so fast that it is an easy process. (Admittedly, this hypothesis is dependent on such circumstances that possible earlier life likely didn’t survive the Late Heavy Bombardment and other weakly supported ideas.)

    And while it seems one of the major panspermia proponents, Chandra Wickramasinghe, instead sees this short time period as a major problem and motivator, I must confess that his latest formulation of his research is intriguing.

    It turns out that many of our planets systems bodies can be suspected to contain vast bodies of liquid water. Venus, Earth and Mars once had or are conjectured to have such bodies on the surface. Venus later became a hot house, Earth survived its ice house events, and Mars dried out on the surface, but each seems to have enough time for abiogenesis before that.

    And there are still ~ 10 moons that are now suspected to have liquid oceans. Most will be trapped between ice sheets with precious little organics dissolved or injected by meteor impacts. But a few like Enceladus and Europe are thought to have minerals and organics enough.

    Wickramasinghe have applied such suspicions to the vast mass of cometary bodies. They have ice and possibly ice as hinted but not proved by probes. Wickramasinghe suggests that the solid material may possibly heat the ice to liquefaction by radioactivity.

    Because clay needs liquid water to form, Wickramasinghe says that suggests comets once had warm, liquid interiors due to heating from radioactive isotopes. Clay is also a favoured catalyst for converting simple organic molecules into complex biopolymers on the early Earth.

    Now, Wickramasinghe and his colleagues argue that the sheer volume of watery clay environments on comets makes them a far more likely site for the origin of life than our home planet.

    The team estimates that the volume of these environments on the early Earth would have been about 10,000 cubic kilometres. A single 20-kilometre-wide comet could offer about a tenth of that, but when you include all the comets in the outer solar system, volume arguments alone make comets 1012 times more likely than Earth to have spawned life, they say.

    He makes further speculations that bumps up this estimate, but as we don’t know much about
    abiogenesis it isn’t very convincing. The transport of such hypothsized life to early Earth is most tenuous, as the Late Early Bombardment was from inner system dry bodies.

    But such life may still be out there in a frozen state. The Bad Astronomer looks at and summarily distrusts another paper that similarly purports to show that cosmic radiation is a problem for genetic material:

    The researchers revived old microbes and found the younger ones (100,000 years old) fared better than older ones (8 million years old). Radiation damage was the culprit. The ice they used was 3-5 meters below the surface, so it seems to me the claim that this is an objection to panspermia is hollow; comets can be very large, so microbes could be buried a mile deep in the cometary ice.

  51. Torbjörn Larsson, OM says

    Given powerful ionizing radiation and no liquid water, I think panspermia/cosmic origin is far less likely than earth-bound abiogenesis.

    I admit that I’m not overly fond of panspermia. It seems Earth life started so fast that it is an easy process. (Admittedly, this hypothesis is dependent on such circumstances that possible earlier life likely didn’t survive the Late Heavy Bombardment and other weakly supported ideas.)

    And while it seems one of the major panspermia proponents, Chandra Wickramasinghe, instead sees this short time period as a major problem and motivator, I must confess that his latest formulation of his research is intriguing.

    It turns out that many of our planets systems bodies can be suspected to contain vast bodies of liquid water. Venus, Earth and Mars once had or are conjectured to have such bodies on the surface. Venus later became a hot house, Earth survived its ice house events, and Mars dried out on the surface, but each seems to have enough time for abiogenesis before that.

    And there are still ~ 10 moons that are now suspected to have liquid oceans. Most will be trapped between ice sheets with precious little organics dissolved or injected by meteor impacts. But a few like Enceladus and Europe are thought to have minerals and organics enough.

    Wickramasinghe have applied such suspicions to the vast mass of cometary bodies. They have ice and possibly ice as hinted but not proved by probes. Wickramasinghe suggests that the solid material may possibly heat the ice to liquefaction by radioactivity.

    Because clay needs liquid water to form, Wickramasinghe says that suggests comets once had warm, liquid interiors due to heating from radioactive isotopes. Clay is also a favoured catalyst for converting simple organic molecules into complex biopolymers on the early Earth.

    Now, Wickramasinghe and his colleagues argue that the sheer volume of watery clay environments on comets makes them a far more likely site for the origin of life than our home planet.

    The team estimates that the volume of these environments on the early Earth would have been about 10,000 cubic kilometres. A single 20-kilometre-wide comet could offer about a tenth of that, but when you include all the comets in the outer solar system, volume arguments alone make comets 1012 times more likely than Earth to have spawned life, they say.

    He makes further speculations that bumps up this estimate, but as we don’t know much about
    abiogenesis it isn’t very convincing. The transport of such hypothsized life to early Earth is most tenuous, as the Late Early Bombardment was from inner system dry bodies.

    But such life may still be out there in a frozen state. The Bad Astronomer looks at and summarily distrusts another paper that similarly purports to show that cosmic radiation is a problem for genetic material:

    The researchers revived old microbes and found the younger ones (100,000 years old) fared better than older ones (8 million years old). Radiation damage was the culprit. The ice they used was 3-5 meters below the surface, so it seems to me the claim that this is an objection to panspermia is hollow; comets can be very large, so microbes could be buried a mile deep in the cometary ice.

  52. Torbjörn Larsson, OM says

    Oh, I forgot to mention a tangential on the possibility of abiogenesis in funny places. Kin blogger Steinn Sigurðsson of Dynamics of Cats has a paper out on possibly habitable lone planets:

    [From the abstract]

    … An interaction between a giant planet and a protoplanet binary may have one of several consequences, including the delivery of volatiles to the inner system, the capture of retrograde moons by the giant planet, and the ejection of one or both of the protoplanets. We show that an interesting fraction of terrestrial-sized planets with lunar sized companions will likely be ejected into interstellar space with the companion bound to the planet.

    The companion provides an additional source of heating for the planet from tidal dissipation of orbital and spin angular momentum. This heat flux typically is larger than the current radiogenic heating of the Earth for up to the first few hundred million years of evolution. In combination with an atmosphere of sufficient thickness and composition, the heating can provide the conditions necesary for liquid water to persist on the surface of the terrestrial mass planet, making it a potential site for life.

    We also determine the possibility for directly detecting such systems through all-sky infrared surveys or microlensing surveys. Microlensing surveys in particular will directly measure the frequency of this phenomenon.

    IIRC they get that 5 % of the ejected planets will retain water and companion both. And a sizable fraction will be detectable.

    Wððt!

  53. Torbjörn Larsson, OM says

    Oh, I forgot to mention a tangential on the possibility of abiogenesis in funny places. Kin blogger Steinn Sigurðsson of Dynamics of Cats has a paper out on possibly habitable lone planets:

    [From the abstract]

    … An interaction between a giant planet and a protoplanet binary may have one of several consequences, including the delivery of volatiles to the inner system, the capture of retrograde moons by the giant planet, and the ejection of one or both of the protoplanets. We show that an interesting fraction of terrestrial-sized planets with lunar sized companions will likely be ejected into interstellar space with the companion bound to the planet.

    The companion provides an additional source of heating for the planet from tidal dissipation of orbital and spin angular momentum. This heat flux typically is larger than the current radiogenic heating of the Earth for up to the first few hundred million years of evolution. In combination with an atmosphere of sufficient thickness and composition, the heating can provide the conditions necesary for liquid water to persist on the surface of the terrestrial mass planet, making it a potential site for life.

    We also determine the possibility for directly detecting such systems through all-sky infrared surveys or microlensing surveys. Microlensing surveys in particular will directly measure the frequency of this phenomenon.

    IIRC they get that 5 % of the ejected planets will retain water and companion both. And a sizable fraction will be detectable.

    Wððt!

  54. Peter Ashby says

    Torbjörn Larsson quoted:
    “The researchers revived old microbes and found the younger ones (100,000 years old) fared better than older ones (8 million years old). Radiation damage was the culprit. The ice they used was 3-5 meters below the surface, so it seems to me the claim that this is an objection to panspermia is hollow; comets can be very large, so microbes could be buried a mile deep in the cometary ice.”

    The problem with this is a mile below the surface is not the sort of place to find liquid water, clay and nucleic acids. How he squares the different requirements for biogenesis and subsequent survival I don’t know

  55. David Marjanović, OM says

    It requires fewer miracles to believe that life has always existed.

    But you know full well that there is no “always”. Firstly, the age of the universe is not infinite. Secondly, first-generation stars cannot have planets, because the Big Bang only produced hydrogen, helium, and trace amounts of lithium; heavier elements are only produced in stars, and elements heavier than iron are only produced in supernovae. The sun seems to be a third-generation star.

    To deny this, you need to be a steady-stater. And to be a steady-stater, you need to ignore all research in the field done in the last 30 years. It’s just like being a creationist, except that there it’s upwards of 130 years rather than just 30.

    Also, it is clear that an ordinary atmosphere is chemically quite unlike life (you failed to cite anything, but methane and ammonia fall apart when the sun shines — they can’t stand UV), but that merely means life didn’t arise in the air! Try the ocean. Perhaps a hydrothermal vent or something.

    BTW, methane and ammonia falling apart due to UV produces a haze high in the atmosphere like Titan’s. It has the added benefit of working like an ozone layer in the absence of ozone. Was in Scientific American a few years ago.

    Poetry is nice, but not an argument. If you want to make a point, do that instead of telling us a poem.

    —————–

    Once you’ve conceded that you were wrong then and you are still wrong now (though less wrong, by your measurements), the creationist would just reply that the Bible is right.

    Then just say “Yeah, right.”

    I can’t guarantee that there will be a way to continue the “debate” after that, however. But then, debate is whatcha put on de hook to catch de fish…

    ————–

    Concerning Homo rudolfensis, some call it Kenyanthropus rudolfensis (thus referring it to the same genus as Kenyanthropus platyops), and nobody considers it either very important or very surprising. In most textbooks it’s not even mentioned.

    Concerning Haeckel’s inter- and extrapolations… oh boy. PZ has posted about this several times. Use the search engine near the top left corner of this page.

    —————–

    IIRC they get that 5 % of the ejected planets will retain water and companion both. And a sizable fraction will be detectable.

    Problem is that very few such planets, ejected or not, seem to exist in the first place. We’re talking about 5 % of a very small number.

  56. David Marjanović, OM says

    It requires fewer miracles to believe that life has always existed.

    But you know full well that there is no “always”. Firstly, the age of the universe is not infinite. Secondly, first-generation stars cannot have planets, because the Big Bang only produced hydrogen, helium, and trace amounts of lithium; heavier elements are only produced in stars, and elements heavier than iron are only produced in supernovae. The sun seems to be a third-generation star.

    To deny this, you need to be a steady-stater. And to be a steady-stater, you need to ignore all research in the field done in the last 30 years. It’s just like being a creationist, except that there it’s upwards of 130 years rather than just 30.

    Also, it is clear that an ordinary atmosphere is chemically quite unlike life (you failed to cite anything, but methane and ammonia fall apart when the sun shines — they can’t stand UV), but that merely means life didn’t arise in the air! Try the ocean. Perhaps a hydrothermal vent or something.

    BTW, methane and ammonia falling apart due to UV produces a haze high in the atmosphere like Titan’s. It has the added benefit of working like an ozone layer in the absence of ozone. Was in Scientific American a few years ago.

    Poetry is nice, but not an argument. If you want to make a point, do that instead of telling us a poem.

    —————–

    Once you’ve conceded that you were wrong then and you are still wrong now (though less wrong, by your measurements), the creationist would just reply that the Bible is right.

    Then just say “Yeah, right.”

    I can’t guarantee that there will be a way to continue the “debate” after that, however. But then, debate is whatcha put on de hook to catch de fish…

    ————–

    Concerning Homo rudolfensis, some call it Kenyanthropus rudolfensis (thus referring it to the same genus as Kenyanthropus platyops), and nobody considers it either very important or very surprising. In most textbooks it’s not even mentioned.

    Concerning Haeckel’s inter- and extrapolations… oh boy. PZ has posted about this several times. Use the search engine near the top left corner of this page.

    —————–

    IIRC they get that 5 % of the ejected planets will retain water and companion both. And a sizable fraction will be detectable.

    Problem is that very few such planets, ejected or not, seem to exist in the first place. We’re talking about 5 % of a very small number.

  57. Owlmirror says

    Because I was curious, I went and looked up the work on rudolfensis. I see that Afarensis and John Hawks have already commented on it:

    http://scienceblogs.com/afarensis/2007/03/31/hawks_on_the_1470_reconstructi/

    http://johnhawks.net/weblog/fossils/habilis/er/bromage_1470_2007.html

    So the craniofacial reconstruction isn’t quite as large a difference from the original Leakey construction in the first place. Did Leakey do it wrong? Probably, yes. Reconstructing a 3-dimensional puzzle from shattered and scattered pieces is not an easy task.

    But Hawks points out a problem with Bromage’s additional claims: Why should the skull have a smaller capacity just because the face is further forward?

    Finally, should Leakey retract his work? The whole point of science is to find the truth as best you can. I think Leakey did as well as anyone might expect.

    Indeed, the retraction in the original post probably wouldn’t have happened if creationists hadn’t started exploited the contentious sentences.

    Mistakes happen, in science as in everywhere. A scientist might leave out a crucial word, or make a typographical error; or the mistake might happen during typesetting or printing. Usually, those would be corrected in an errata update. In this case, while these sloppily-worded sentences could have simply been corrected, even at this late date, I think the point of issuing a retraction is to make it very clear to creationists that no, the science does not support them, in any way shape, or form.

    When will creationists retract Genesis, since that work has been so thoroughly refuted by all of the branches of modern science? Heck, when will the Discovery Institute retract ID, since it is not even a scientific theory?

  58. Torbjörn Larsson, OM says

    Peter Ashby:

    The problem with this is a mile below the surface is not the sort of place to find liquid water, clay and nucleic acids.

    I assume that if a “muddy iceball” liquefies from radiation heat it will sort itself out gravitationally and thermally (i.e. with ice on top). So I’m not sure what you are trying to say here, unless you are discussing measurements you didn’t make a reference to.

    David Marjanović:

    Problem is that very few such planets, ejected or not, seem to exist in the first place.

    You mean with a large companion? Dunno, I have to check the papers.

    But Sigurðsson was excited because both planet and companion were detectable in a few percent of the cases. As he expects detection, I assume the model builders see enough of them to be a sizable amount in our near neighborhood.

  59. Torbjörn Larsson, OM says

    Peter Ashby:

    The problem with this is a mile below the surface is not the sort of place to find liquid water, clay and nucleic acids.

    I assume that if a “muddy iceball” liquefies from radiation heat it will sort itself out gravitationally and thermally (i.e. with ice on top). So I’m not sure what you are trying to say here, unless you are discussing measurements you didn’t make a reference to.

    David Marjanović:

    Problem is that very few such planets, ejected or not, seem to exist in the first place.

    You mean with a large companion? Dunno, I have to check the papers.

    But Sigurðsson was excited because both planet and companion were detectable in a few percent of the cases. As he expects detection, I assume the model builders see enough of them to be a sizable amount in our near neighborhood.