Comments

1. #1 G Felis

   January 22, 2009

   Actually, there’s something that, to my mind, makes this even worse. I am certain I have read more than one well-written, non-hyped explanation of horizontal gene transfer and the web-not-tree of life… in the pages of New Scientist.

   NS usually manages to find a fairly decent balance between a bit of interest-generating sensationalism for their cover stories and solid science content, but once every few months they simply blow it one way or the other – too much hype on the cover or not enough balance in the content, and occasionally both in the same story (like this one). It’s especially frustrating, both because NS is good in so many other ways – and because there isn’t a better science weekly to read instead.

2. #2 MrG

   January 22, 2009

   JR, you’re probably aware that Paul Nelson, the DI’s resident YEC, has been trying to race the dead horse of “horizontal gene transfer as a gross embarrassment to Darwin” for several years now. Sigh, although I tire of reading UNCOMMON DESCENT and EVOLUTION NEWS & VIEWS in a second, curiosity compels me now to check as to when they will pounce on this NEW SCIENTIST article.

   Physicist Murray Gell-Mann, not noted for his tact, once told an interviewer from SCIENTIFIC AMERICAN that popular science writers were “idiots”. I think Gell-Mann picked up that opinion from the various books trying to link his work in particle physics to Eastern mysticism. Bob knows what Gell-Mann would have said if he’d been an evo scientist. Cheers — MrG

3. #3 Dan

   January 22, 2009

   Look at the positive side. Jonathan Wells claims that the “tree of life” is an “Icon of Evolution” that the “dogmatic Darwinists” would never give up. This article proves that scientists are not committed dogmatically to the “tree of life icon”. And if we’re not committed to it, then certainly it’s not an “icon”.

   Perhaps Wells will be honest and change the title of his book to “Popular Misconceptions that Creationists hold concerning Evolution”.

   Don’t hold your breath.

4. #4 MrG

   January 22, 2009

   Dan, that would be a cold day in the underworld. A quick check at EVOLUTION NEWS & VIEWS shows that Robert Crowther — a new name to me — playing up articles along exactly the same lines run from THE GUARDIAN and THE TELEGRAPH in the UK.

   I would suspect all three articles have some “evolutionary relationship” among them, lighting doesn’t strike thrice in the same place at the same time. I’m just thankful it doesn’t seem to have been a Reuters dispatch. But maybe I speak too soon. Cheers — MrG

5. #5 Charles L. Clarke

   January 22, 2009

   I fail to grasp the significance of horizontal gene transfer, to the prove of Darwins’s Theory on Evolution.

   Question, I hold that although any two individuals will only share approximetly 95%, the same DNA, Any pair of individuals of a species, would given enough time, would mutate 100% the DNA of a species. The point, genetic drift, is not consequencial to evolution. Finally no two individuals, could survive, to replicate a species, without Intelligent Design.

   The above truth by itself puts Darvins Theory of evolution, in scientific question.

   I do have more knowledge of gentics than I’ve used here.

   I am not a believer in god, however, I do fall into a category of believing in UFO’s. Nope never seen one.

   I have no Idea of how Intelligent Design came about, but for Einstein, to be able to set down, and think, play his violin, and change his formula’s, and finally come up with the theory of relativity.

   The Universe defies, just Kabooom.

   Thanks Respectfully

   Charles L. Clarke
   6710 Gladstone Ave.
   Shawnee, Kansas 66218

   913 631 0446

6. #6 MrG

   January 22, 2009

   There was an interesting article in AAAS SCIENCE some months back about how horizontal gene transfer makes big headaches for taxonomy in microbiology. Not sure if the article’s online but I wrote up a notes in my blog:

   http://www.vectorsite.net/g2008m10.html#m18

   Interesting reading. Cheers — MrG

7. #7 Mike Warner

   January 22, 2009

   Darwin, not Darvin

   Pretty sure that two individuals of the same species share more that 95% of DNA.

8. #8 Jedidiah Palosaari

   January 23, 2009

   I wonder if the writing for New Scientist is similar to many other magazines and many books- where the author of the article has little to no say over the title of the article. It may be that this was a decision by the editors of New Scientist, concerned purely about advertising and sales, and against the will of the article’s author.

9. #9 Scott Hatfield, OM

   January 23, 2009

   Charles, you appear to be off your meds. I counted ten unconnected clauses in your post before I gave up. I am sure in your mind they were all connected, but unfortunately I can’t read your mind. Thus, I can’t really follow what you are saying.

10. #10 Dave Luckett

    January 23, 2009

    May I venture the (probably inadequate) analogy that HGT (in fact, modern microbiology) stands to the the Theory of Evolution somewhat as Einstein’s work stands to Newton’s – that is, as an illuminating and enabling extension of knowledge to areas unknown to the original theorist, with profound consequences. Did Einstein invalidate Newton? Of course not. What Newton wrote was true. Same here.

11. #11 Charles L. Clarke

    January 23, 2009

    This is more a search for a blog , or chat that is about the ID and Evolution, subject.

    I wrote earlier about horitzontal genetic exchange, it’s a no brainer. You have all these bacteria invading plant and animal host.

    Sorry you can’t offer one exchange of genetic material as evidence.

    I can’t seem to find anything but chat rooms with porn and people wanting to meet. You have any idea where you’re exchanging ideas, and not looking for sex.

    I’m 64 years old, not interestested, in anything but discussing mostly ID and evolution.

    If you could help, I would apprciciate, if not, thanks anyway.

12. #12 DaveH

    January 23, 2009

    Interesting that the tree image was produced by Darwin at the very first moment of his insight into common descent. By the end of The Origin he had rather famously changed to a “tangled bank”.

    That said, I think that popular science journos using a provocative “Was X wrong?” come-on can be effective. I well remember the National Geographic issue a couple of years ago with a “was Darwin wrong?” cover. Then the same on the contents page. Then the same (by itself) on the first page of the article in huge scary type “WAS DARWIN WRONG?”. Then over the page the first paragraph of the article proper was,basically, “No. And here’s why…” As the young kids say; I LOLed. It may well have drawn in some non-reality-based types, eager for “ammunition” from such an iconic magazine.

    Best regards, DaveH

13. #13 SteveF

    January 23, 2009

    Jason,

    Whilst I largely agree with you, in this instance it appears likely that the scientists themselves could also be to blame. In the article, Eric Bapteste (unless he has been quoted out of context) said:

    “We have no evidence at all that the tree of life is a reality”

    Sigh. It’s a battle when the journalists are producing overhyped nonesense, without the scientists themselves doing it. You can bet that quote will be a creationist favourite for years to come.

14. #14 Dave Wisker

    January 23, 2009

    HGT gives the tree of life a more realistic root system. So the tree of life metaphor is actually more like a tree than ever.

    IDers are just ridiculous.

15. #15 SLC

    January 23, 2009

    It might be of interest to note that the same numbnuts George Johnson also wrote an article several years ago bad mouthing Murray GellMann. Anyone who has seen Mr. Johnson on Blogging Heads TV knows that he rivals Maureen Dowd for lack of intelligence.

16. #16 novparl

    January 23, 2009

    Heh heh. I thought that’d set the cat among the pigeons when I read it in the Guardian, quoting New Scientist, quoting 2 researchers at the Curie Inst. in Paris.

    Btw – Why don’t women take an interest in evolution?

17. #17 Joe Felsenstein

    January 23, 2009

    DaveH wrote:
    

    By the end of The Origin he had rather famously changed to a “tangled bank”.

    Unless I misunderstand, Darwin’s famous “tangled bank” was not a model of the genealogy, but instead an image of the complexity of interactions of life.

    I agree with SteveF that Eric Bapteste’s blanket statements about the nonexistence of a tree are irresponsible self-promotion. So when we look at a bunch of birds we are to expect no signal of a tree, just rampant HGT and hybridization? Really?

    Finally, MrG said:
    

    although I tire of reading UNCOMMON DESCENT and EVOLUTION NEWS & VIEWS in a second, curiosity compels me now to check as to when they will pounce on this NEW SCIENTIST article.

    Look at Uncommon Descent, Paul Nelson has “pounced”. But it’s more like a belly-flop than a pounce. The elephant in the room that creationists like Nelson are deliberately ignoring is that even if there is a total reticulated mess rather than a tree, that is still common descent, a common genealogy of life.

18. #18 novparl

    January 23, 2009

    That should be Pierre & Marie Curie Univ. It was thinking about Marie & her pitchblende made me ask my naughty question.

    The NS article also quotes Prof Michael R. Rose. Who’s in Wikipedia.

19. #19 Jud

    January 23, 2009

    Charles wrote:

    I do have more knowledge of genetics than I’ve used here.

    If, as you say, you’d like to have a conversation about evolution (and wherever did you get that stuff about porn and sex you keep mentioning?), then I’d suggest it would be a great idea to learn still more about genetics, evolution, and related topics.

    Two very fine and highly readable books I can recommend by scientists doing current work are “Endless Forms Most Beautiful” by Sean B. Carroll, and “Your Inner Fish” by Neil Shubin. Happy reading!

20. #20 Graham Lawton

    January 23, 2009

    Hey Jason
    Thanks foe blogging about my story.I have a couple of beefs with your post.
    1) my article says explicitly that uprooting the tree of life doesn’t invalidate the theory of evolution, it enriches it. To imply otherwise is grossly unfair (ie “Like I said, this is old news, and is not anything that is relevant in our little dust-ups with the creationists…) That implies I said it did. Please can you amend it? Or at least say, explicitly, that I am NOT an apologist for creationism.

    2) There is news to report, and it’s in there. The field has moved on a lot since Dolittle’s piece in Scientific American. Obviously, though, the real peg is that we are approaching Darwin’s 200th birthday. As a self-appointed critic of the science media I thought you would realise that. Maybe not…

    In the spirit of mutual criticism, can I suggest that you learn something about how the media works before pontificating about it? Or does your admonition that “writers should understand the work about which they are writing” not apply to you?

    Keep up the good work!

21. #21 eric

    January 23, 2009

    Novparl wrote:

    Btw – Why don’t women take an interest in evolution?

    LOL. Novparl, it usually helps to READ the article on which you are commenting. That way you can avoid looking like a fool. For instance, this particular article begins “Recently, ScienceBlogs own Abbie Smith…”

22. #22 Matt G

    January 23, 2009

    Charles-

    We share far more than 95% of our DNA with other humans. We are thought to share about 99.5 – 99.9% of our DNA with Neanderthals, based on sequences reported a few months ago. Check out work by Svante Paabo at the Max Plank Institute.

    Matt

23. #23 Wes

    January 23, 2009

    Graham,
    Your response to Jason doesn’t do much to address his criticisms.

    1.) As I read Jason’s critique, he wasn’t calling you an “apologist for creationism” or implying that you were. He was saying that the irresponsible title on the cover of the magazine was going to become fodder for creationist spin, and that scientists and teachers (not journalists) would end up having to do damage control as a result.

    2.) The issue is not whether the field has or has not moved on since 2000. It’s that horizontal gene transfer (and Darwin’s ignorance thereof) is not new, and putting “Darwin was wrong” on the cover in order to report on some recent developments in an area that’s been well-known for several years now is irresponsible sensationalism. You can’t tell me your editors didn’t put that title there because they knew it would attract the eyes of people thinking someone had disproven evolution. The title is misleading and does not represent the substance of the issue of horizontal gene transfer.

24. #24 Cheshire

    January 23, 2009

    In the spirit of mutual criticism, can I suggest that you learn something about how the media works before pontificating about it? Or does your admonition that “writers should understand the work about which they are writing” not apply to you?

    Graham:

    You shouldn’t sacrifice accuracy to sell a few copies. I think that’s what Rosenhouse is trying to say.

    Most of what I got from his complaints is that you published a headline that could be easily taken out of context to make the article mean something it clearly doesn’t. You might not have meant to do that…your intention was undoubtedly to get the magazine off the shelves as fast as you can. However to us science types, we want our work to be represented as accurately as possible and portraying small bits and bounds as ‘TEH HOOJ FRIGGEN BRAKETHRU’ really doesn’t accurately portray what’s going on in the lab.

    You repeatedly up-played a concept that hasn’t been integral to evolutionary biology for quite some time. HGT’s been familiar to biologists for a very long time. We’ve known that life is a web for a good, long while. This is hardly new and hardly controversial. There might be a bit of quibbling over how large a role horizontal gene transfer played in the evolution of life on earth, but all my classes have mentioned some form of horizontal gene transfer whether it’s through viruses or endosymbionts like wolbachia. It’s already in the classroom-it’s a settled debate.

    Here in this post, we already have a bright and shiny example of how creationists refuse to read any sort of science material courtesy of Charles L. Clarke. Believe me…you’re going to see your article again presented in a context that it wasn’t intended.

    You messed up, dude. It’s OK, it happens to the best of us. However, it’s a major pain in the ass for us scientists…especially at a time when religious fanatics are trying to conquer the largest textbook market in the US.

25. #25 MrG

    January 23, 2009

    I will not crticise Mr. Lawton’s comments — the responses so far are more than sufficient — but I would point to him that the article in question, probably unintentionally, hit some raw nerves on the evo science folks.
    The evo science people are very used to confrontations with Darwin-bashers, and are sensitive to certain issues — one being the way the Darwin-bashers like to pile up every stone they can find to throw at evo science.

    It is admittedly not reasonable to worry overmuch about how Darwin-bashers will exploit one’s writing — they’re going to do that no matter what. But it prudent to write clearly to begin with, and certainly prudent not say to say: “Darwin Was Wrong!” — and simply hand the Darwin-bashers another stone for no particular good reason.

    The complaint here is not that the article actually presents false information, it’s just that it serves it up in a tone that gives a strongly implied negative impression about evo science. I suppose that might be missed in the UK since they don’t have to defend Darwin in court every few years … yet. Cheers — MrG

26. #26 doppelganger

    January 23, 2009

    NASA YEC David Crappedge, I mean Coppedge, is joining the chorus of YEC/IDiots drooling over this - complete with the requisite embellishments and unwarranted extrapolations, not to mention the smarmy commentary…

27. #27 Matt G

    January 23, 2009

    Science journalists aren’t the only ones doing this. I was appalled to see a highly respected scientist doing the same thing in a book written for a broad audience. I can’t remember the author, but he used words like “doctrine” and “orthodoxy” to dismiss his critics. While there are certainly some scientists who cleave a bit too strongly to their favorite theories and hypotheses (forgetting the part about being dispassionate), using words like these is ill advised. While probably more justified than when creationists do it, it still smacks of the same slimy tactics: 1) appeal to emotion/sympathy (“my views are being suppressed,” “I’m being persecuted for unconventional ideas,” etc.); 2) going to the popular press when you can’t convince other scientists; 3) publishing your views in non-peer reviewed media; 4) presenting the views of critics in your own words, and not letting them speak for themselves, etc.

    I’m torn between wanting to ignore creationists entirely and just serving the science straight up, and writing in a manner which is mindful of how it might be misrepresented by creationists.

28. #28 TexMex

    January 23, 2009

    http://www.danottesymposium.com/

29. #29 Jason Rosenhouse

    January 23, 2009

    Graham -

    Thank you for the comment.

    1) my article says explicitly that uprooting the tree of life doesn’t invalidate the theory of evolution, it enriches it. To imply otherwise is grossly unfair (ie “Like I said, this is old news, and is not anything that is relevant in our little dust-ups with the creationists…) That implies I said it did. Please can you amend it? Or at least say, explicitly, that I am NOT an apologist for creationism.

    I’ll revise my opening post to make this explicit as soon as I post this comment. Just to be clear, though, I certainly did not say, and I don’t think I implied, that either you or the editors of NS are apologists for creationism. My point, as Wes has also observed, is that both the inappropriately sensational cover and in several places the tone of your article have needlessly handed the creationists a big propaganda victory. I realize that’s less of an issue in England, but around here, even in an Obama administration, science education is relentlessly under attack.

    2) There is news to report, and it’s in there. The field has moved on a lot since Dolittle’s piece in Scientific American. Obviously, though, the real peg is that we are approaching Darwin’s 200th birthday. As a self-appointed critic of the science media I thought you would realise that. Maybe not…

    The fact remains that the main point of your article was that horizontal gene transfer is causing scientists to question the metaphor of an evolutionary tree of life, and that was precisely the point of Doolittle’s article nine years ago. I would add that Doolittle’s article was far more sedate in tone.

    I’ll accept the criticism that I shouldn’t have said your article “has only” the old news about horizontal gene transfer. I should have said your article is mostly old news, with not enough that is sufficiently new or significant to justify any great hype. Better?

    Of course I understand that the peg was the Darwin bicentennial. Nice job honoring the old man.

    In the spirit of mutual criticism, can I suggest that you learn something about how the media works before pontificating about it? Or does your admonition that “writers should understand the work about which they are writing” not apply to you?

    Fair enough! Which aspect of science journalism, were I to understand it better, would cause me to revise any of the opinions I expressed in the post?

    Keep up the good work!

    Will do! Er, assuming that wasn’t sarcastic…

30. #30 MrG

    January 23, 2009

    I think with JR’s comment the issues have been laid out as well as needed. But that leads to the question for Mr. Lawton and NS:
    Does NEW SCIENTIST stand by their presentation of the article? Or will the editors be so kind as to issue an, ahem, “clarification”?

31. #31 David Marjanović, OM

    January 23, 2009

    Btw – Why don’t women take an interest in evolution?

    Why did Napoleon cross the Mississippi?

    I’m trying to say that there is such a thing as a wrong question: a question that is based on an assumption which is just flat-out wrong.

32. #32 heddle

    January 23, 2009

    David Marjanović, OM,

    Why did Napoleon cross the Mississippi?

    To get to Waterloo.

33. #33 Karen S.

    January 23, 2009

    Btw – Why don’t women take an interest in evolution?

    Who says they don’t? I find the topic fascinating. And isn’t the executive director of the National Center for Science Education a woman?

34. #34 Graham, for the last time

    January 23, 2009

    Thanks for you response, Jason. I appreciate it.

    On science journalism in general, I think that you (and a lot of other bloggers) have a naive view of what it’s all about. You think that our role is simply to educate the public by faithfully disseminating the findings of scientists in a way that scientists approve of, and that if we only did that competently the world would be a better place.

    Problem is, there are plenty of media outlets that do exactly that – Nature and Science, for example (not to mention thousands of blogs that nobody ever reads). But they have minuscule readership among the general public, proving that the model doesn’t work. To get noticed, you have to play the game to some extent. You have to find exciting new stories and sell them in exciting, sexy (and sometimes controversial) ways. That doesn’t go down well with the purists, but I’d always argue that it’s better to have a million people reading a “dumbed down science rag” than a few hundred people reading real science and everybody else doing something else.

    And yes, keep up the good work.

35. #35 ponderingfool

    January 23, 2009

    That doesn’t go down well with the purists, but I’d always argue that it’s better to have a million people reading a “dumbed down science rag” than a few hundred people reading real science and everybody else doing something else.
    *******************************************
    Not if they are getting the wrong impression of what the actual science is. Then it is just poor journalism.

36. #36 MrG

    January 23, 2009

    Mr. Lawton seems to be saying: “We stand by the article as it is presented” and “we will say nothing publicly about its misuse by the Darwin-basher community.” Possibly I overreact, but I would be delighted to be corrected.

    Somehow a quote from only three days ago that has already become famous seems applicable here: “We reject as false the choice between our safety and our ideals.”
    The same could be said about choosing between popularization and integrity. NS could have chosen a wide range of interesting ways of presenting the article but they chose to play the tabloid headline route. (How about including a “Page 3″ in NS? That would get my attention. As long as you’re popularizing, why worry about appropriateness?)

    I think that protests to Mr. Lawton having had no effect, protests should be taken to the editors. PZ Myers has contact with Dawkins, I suspect that a letter to the editors from Dawkins might get their attention in a way that protests here have failed to make the slightest dent on the solid Mr. Lawton.

37. #37 Larry Moran

    January 23, 2009

    Graham Lawton says,

    On science journalism in general, I think that you (and a lot of other bloggers) have a naive view of what it’s all about. You think that our role is simply to educate the public by faithfully disseminating the findings of scientists in a way that scientists approve of, and that if we only did that competently the world would be a better place.

    I think the role of a science journalist is exactly that. Your job is to faithfully disseminate the findings of scientist in a way that scientists approve of. In other words, your job is to be accurate.

    It’s not your only job but it’s the most important. If you are not faithfully disseminating accurate information then it doesn’t matter what else you do ’cause you aren’t being a good science writer.

    To get noticed, you have to play the game to some extent. You have to find exciting new stories and sell them in exciting, sexy (and sometimes controversial) ways.

    We understand that part. Being a good writer and being exciting are components of science journalism.

    But don’t forget that the top three criteria are:
    1. scientific accuracy
    2. scientific accuracy
    3. scientific accuracy

    Everything else is window dressing.

38. #38 slpage

    January 23, 2009

    I think that the science journalists may want to examine their own naivete a bit.
    As predicted and expected, a number of creationists are plastering the title – not the information in the article, but the title – all over the internet and proclaiming a victory of sorts. In the cases I have seen, even when the content of the article is quoted for them falsifiying their ‘conclusions’, they simply dismiss them. Many people DO NOT READ beyond the title, that or they do not care what the articles actualy state. They have their “juicy quote”, and that is all that matters.

    Some of us may recall hearing about a Worldnetdaily article that came out a year or so ago titled “University Bans Bibles”. The religious right had a field day with that one, using it as ‘proof’ that academia was atheistic and intolerant. But when one pointed out that all that had actually happened was that the U of Edinburough had denied the Gideons access to their dorms to put bibles in every room due to student complaints, as indicated in that very article, they shrugged it off and ran with their original take based solely on the title!

    Do not assume that the American public is clever – or intellectually curious/honest – enough to actually read an article to see whether or not a hyperbolic title is designed just to get attention or if it is an accurate preview of what the article indicates.

39. #39 Kevin

    January 23, 2009

    “I’ll accept the criticism that I shouldn’t have said your article “has only” the old news about horizontal gene transfer. I should have said your article is mostly old news, with not enough that is sufficiently new or significant to justify any great hype. Better?”

    OH much much better Jason….its not an old moldy boot! its an old moldy boot with new shoelaces!

    shorter “Posted by: Graham, for the last time”

    “We need to tart up our re-hashed stories with some sexy bits or no one will ever read them!”

    (not even Charles)

40. #40 Graham Lawton

    January 23, 2009

    MrG, I think you’re conflating my article and the cover of the magazine. The article is called “Uprooting Darwin’s tree”, it is a report on how many biologists believe the tree of life concept has outlived its usefulness and are now moving towards a richer concept of how all living things are related and yes, I do stand by it.

    The cover of the magazine says “Darwin was wrong – uprooting the tree of life”.

    The editorial says “None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that “New Scientist has announced Darwin was wrong”. Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not.”

    So, please, stop posturing. Why are you attacking me, instead of the IDiots and creationists? They’re the real enemy.

41. #41 Orac

    January 23, 2009

    Why are you attacking me, instead of the IDiots and creationists? They’re the real enemy.

    Because through carelessness, you gave them ammunition, even though you did not intend to?

42. #42 Johnny

    January 23, 2009

    Well if nothing else, N.S. is definitely getting plenty of play in the blogosphere!

    I linked my blog back to here: http://ecographica.blogspot.com/2009/01/whys-graham-so-glum-lawton-critiqued.html

43. #43 Wes

    January 23, 2009

    Graham,
    You seem to be missing the point entirely.

    No one is denying that journalists have to report “sexy” or “exciting” things. Carl Zimmer does the same thing. But Carl Zimmer does not use misrepresentation to “sex up” his stories. He just seeks out stories (say, viruses that affect the cognitive processes of their hosts) which are exciting in themselves.

    The charge against you is not that you sexed up the story. It’s that the title and several portions of the story misrepresent the issue in order to sex it up.

    Sexy and exciting is fine. Misrepresentation in order to be sexy and exciting is not. Misrepresentation in order to be sexy and exciting which gives creationist more propaganda fodder is bad news.

44. #44 MrG

    January 23, 2009

    WE’s comments about Carl Zimmer were spot on. I’m not actually much of a fan of Zimmer’s writing — he’s shooting at the naive reader and if I’m not high the ladder I’m a few rungs above that. No reason to read through a book for a newbie when a chapter would do for me.

    However, I respect CZ, because I know perfectly well writing for the naive reader is hard, and these are the people who really need to be reached. He does a bangup job of it, more power to him, I hope he makes good money off his books because he deserves it.

    I see no need to comment on any comparisons between CZ and others.

45. #45 Jason Rosenhouse

    January 23, 2009

    Graham –

    To get noticed, you have to play the game to some extent. You have to find exciting new stories and sell them in exciting, sexy (and sometimes controversial) ways.

    Well, yes, I understand that. It’s no different in the blogosphere, where one must shout a bit to get noticed.

    Sensationalism is part of the journalism biz, and is hardly limited to the science section. But I’m sure you also understand that there comes a time when sensationalism can do actual harm. This is one of those times. How long do you think it will be before some state school board has this cover thrust in their face by some representative of the religious right? Do you want to be the one to have to explain that actually the cover means simply that one particular metaphor used by Darwin is not as widely applicable as previously thought?

    How long do you think it will be before we see the following sentences in some creationist publication:

    As science journalist Graham Lawton notes, “The tree-of-life concept was absolutely central to Darwin’s thinking, equal in importance to natural selection.” But even Lawton, himself a Darwinist, is forced to concede that the notion of one universal tree of life, “lies in tatters, torn to pieces by an onslaught of negative evidence.” Nice of him to notice! Creationists have been saying that for years!

    Don’t even bother protesting that the first quote was actually from Doolittle. The creationists don’t care.

    Surely some balance must be struck between being provocative enough to attract readers, while not being so provocative that your story is inaccurate and misleading. Your editors showed poor judgment in choosing their cover. As did you in using such florid language to describe research that did not merit such treatment.

46. #46 Jeffrey Shallit

    January 23, 2009

    I have nothing against science journalists – my father was one. But I’ve noticed something about the current crop of science journalists — they simply cannot gracefully accept any kind of correction from people who know more than they do. Perhaps it is a defensive reaction to the looming death of traditional journalism.

47. #47 MrG

    January 23, 2009

    Y’know … I’ve seen flame wars take over boards and blogs, but this is the first one I’ve personally noticed that spread over an entire community of them in a flash …

    … and with, as far as I can see, only one person handling the fight on the other side.

48. #48 söve

    January 23, 2009

    thanks.

49. #49 ERV

    January 23, 2009

    That doesn’t go down well with the purists, but I’d always argue that it’s better to have a million people reading a “dumbed down science rag” than a few hundred people reading real science and everybody else doing something else.

    Oh my god! Is Grahams second response a joke? Can Jason verify email?

    Tell me that was a joke.

    You dont think there is a gradient between dumbed down sensationalized shit and top-tier science journals?

    Tell me that was a troll post.

50. #50 Spartan

    January 23, 2009

    Hmmm, I tend to side with Graham a little on this one. Although the text ‘Darwin Was Wrong’ is too large on the cover, there is a sub-title in smaller text but not tiny, which Jason oddly did not mention, that says ‘uprooting the tree of life’, not ‘uprooting evolution’. If it just said ‘Darwin was Wrong’, then I think it’s an obvious misrepresentation; with no other qualifier, Darwin equals evolution. The web article is titled ‘Why Darwin was wrong about the tree of life’; does anybody think that title is unfair? The fact that the cover will become creationist fodder isn’t the fault of New Scientist; creationists pluck statements out of actual scientific papers to their advantage but we don’t scrutinize those and criticize them when they write a paragraph or sentence that may be quote-mined. From the end of the article:

    Instead, they see the uprooting of the tree of life as the start of something bigger. “It’s part of a revolutionary change in biology,” says Dupré. “Our standard model of evolution is under enormous pressure.

    What’s less accepted is that our whole fundamental view of biology needs to change.”

    Is it fair to criticize Dupre (philosopher of biology, whatever that is) for that prime ammo also?

    I hedge from that position somewhat based on was quoted in the post, mainly ‘Without it the theory of evolution would never have happened.’. I think the article is trying to say that the tree of life framework was essential to Darwin coming up with his theory, which I don’t know is the case, but that sentence seems to be about as close as the article comes to suggesting that the ToE is incorrect. But that’s not that close, and the article itself is specifically about the ‘tree of life’ model itself. The creationist’s main (only) tactic is to misrepresent others; seems a little unfair to then admonish the victims.

51. #51 Eric Murphy

    January 23, 2009

    Since when is a metaphor the most important concept in a scientific theory? The “tree of life” is a metaphor for an actual thing, a phylogeny. I doubt any evolutionary biologist doubts that there is One True Phylogeny of all life on earth (although the concept of common descent, of genes at least, is blurred by LGT). The question of whether that phylogeny is strictly “tree-shaped” is hardly a central issue in evolutionary theory.

52. #52 Spartan

    January 23, 2009

    Since when is a metaphor the most important concept in a scientific theory?

    I don’t think it says that; it says it was central to Darwin’s thinking, mainly that the theory of evolution was developed to explain the observation, the metaphorical ‘tree of life’.

53. #53 roland

    January 23, 2009

    I believe that the sensational cover title made it problematical. I guess “Darwin being modified” does not have the same impact as “Darwin was wrong”.

    Unfortunately the creationist clap-trap has already begun with the highlighted, underlined, upper-case commentary, which, when one replies to, makes it look as if one is making excuses for poor Darwin, yet again.

    I think the tree of life is still there, at least when it comes to complex, multi-cellular life. Now however, it comes with lots of lines cross-joining the thicker branches.

    How does one present this more nuanced explanation to creationists?

    Journalists really need to work hard at presenting headlines that are both catchy and accurate. I suspect this is not an easy thing to do, and at times the consequences of failing, can backfire badly.

    I like New Scientist and think its journalism is great. This time, it goofed. Unfortunately, because I frequent YEC/ID boards, cleaning up the mess now has to be done.

    Oh well.

    Regards, Roland

54. #54 Eric Murphy

    January 23, 2009

    re: “I don’t think it says that; it says it was central to Darwin’s thinking, mainly that the theory of evolution was developed to explain the observation, the metaphorical ‘tree of life’.”

    The tree isn’t the observation. Nested hierarchies of character traits are the observation. Common descent is the hypothesis that explains that observation. A “tree of life” is the metaphor, which describes (accurately or not) the shape of the branching evolutionary process which results in the hypothesized phylogeny. What Darwin was wrong about was the shape of the phylogeny, not that the phylogeny exists. The article definitely implies that there is no evidence that the phylogeny exists: “”We have no evidence at all that the tree of life is a reality,” says Bapteste.”

    Is Bapteste saying there is no phylogeny, or that the phylogeny is not strictly tree-shaped? The article strongly implies the former.

55. #55 mezzobuff

    January 23, 2009

    *de-lurk*
    As someone with little science education, people like me depend upon journalists to accurately (and sometimes simplistically) describe and define what is going on in the world with regard to science. I tend to read articles and then refer to the science blogs to get clarification on the issues that interest me. I am certainly not the norm, yet if the general public is getting incomplete or ‘muddled’ information (as seems to be the case here), even if simply in the “sexy” headlines of a journalistic piece, then we are being done a disservice. We do not need “dumbed down,” sensationalist scientific journalism: We only need to understand the ideas and their importance in any given field. Funny that Graham derides blogs so much: this is where I find I get a better understanding not only through the posts themselves, but also through the comment sections and the lively debate that goes on within them. I agree with Wes and others: Zimmer is my ideal.
    *back to lurking…*

56. #56 Spartan

    January 23, 2009

    Is Bapteste saying there is no phylogeny, or that the phylogeny is not strictly tree-shaped? The article strongly implies the former.

    Eric, keep reading:

    “Both he and Doolittle are at pains to stress that downgrading the tree of life doesn’t mean that the theory of evolution is wrong – just that evolution is not as tidy as we would like to believe. Some evolutionary relationships are tree-like; many others are not. “We should relax a bit on this,” says Doolittle. “We understand evolution pretty well – it’s just that it is more complex than Darwin imagined. The tree isn’t the only pattern.”"

    That pretty much specifically says the latter.

57. #57 Peter Henderson

    January 23, 2009

    The UK’s Daily Torygraph has already picked up on this:

    http://www.telegraph.co.uk/scienceandtechnology/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claim-scientists.html

    Charles Darwin’s tree of life, which shows how species are related, is ” wrong” and “misleading”, claim scientists.

    They believe the concept misleads us because his theory limits and even obscures the study of organisms and their ancestries.

    Evolution is far too complex to be explained by a few roots and branches, they claim.

    I would expect something in AiG’s so-called “news to note” tomorrow.

58. #58 Jonathan Abbatt

    January 23, 2009

    As a regular UK reader of New Scientist, and normally a fan, I was disappointed with this piece. The content exaggerated the case for any overthrow of Darwin’s work. HGT at the roots of the ‘tree’ is not news, and the Bapteste quote obviously needs putting in context. This is evolution not revolution. Darwin remains the Newton of biology and no Einstein equivalent has emerged yet to create a new paradigm. Controversy sells of course but the ill-chosen cover shows insensitivity to the culture wars over public education which are a real issue in the US. You can do better than this NS.

59. #59 derwood

    January 23, 2009

    Hi Roland!

60. #60 John Kwok

    January 23, 2009

    Graham,

    You seem as guilty of trying to do as much sensationalism in your science journalism as your colleague over at Newsweek, Sharon Begley, has done in its current issue, proclaiming the resurgence of “Neo-Lamarckism” as a “scientific” challenge to “Darwinism”. What Wes, jason and a few others have tried to note is the fact that a reputable journalist like Carl Zimmer – whose undergraduate training was in English, not science – is quite good at what he does simply by conveying the excitement of scientific discovery, not by trying to make inane commentary regarding how a successful scientific experiment or discovery will challenge current orthodox thinking.

    While I understand the “logic” behind the “slant” of Ms. Begley’s piece, I am utterly mystified by yours, especially when you work for a journal that strives to be as objective as the journals Science and Nature. I earnestly hope you will take seriously our criticism and do some considerable reflection before reporting on yet another scientific “scoop”.

    Respectfully yours,

    John

61. #61 zy

    January 23, 2009

    Maybe OT but offered as advance warning, expect a spate of articles about how a new species of catfish that can climb rocks has overturned everything we knew about evolution. OH NOES!

62. #62 John Kwok

    January 23, 2009

    Jason,

    While this is slightly off topic, I should note that even the eminent New York Times has been irresponsible lately in its science journalism as noted here, in this article published yesterday:

    http://www.nytimes.com/2009/01/22/education/22texas.html?_r=1

    The local reporter covering the Texas State Board of Education science standards hearing seemed more interested in giving a “balanced” perspective, by giving equal weight to the comments of Discovery Institute Senior Fellow Stephen Meyer and several Texan anti-evolution supporters. While this may be newsworthy, it was done at the expense of reporting what is at stake in Texas, and that was noted only in the final paragraph.

    Regards,

    John

    P. S. I was underwhelmed by that Abbie Smith post, which, sadly, seemed a typical example of some of her more adolescent behavior that she does show occasionally at ERV.

63. #63 Robert O'Brien

    January 23, 2009

    Oh my god! Is Grahams second response a joke? Can Jason verify email?

    Tell me that was a joke.

    You dont think there is a gradient between dumbed down sensationalized shit and top-tier science journals?

    Tell me that was a troll post

    I was wondering when the Lilo of lab-monkery would drop in.

64. #64 SLC

    January 24, 2009

    Re John Kwok

    P. S. I was underwhelmed by that Abbie Smith post, which, sadly, seemed a typical example of some of her more adolescent behavior that she does show occasionally at ERV.

    Criticizing Ms. Smith for adolescent behavior is rich coming from a birther like Mr. Kwok.

65. #65 John Kwok

    January 24, 2009

    @SLC,

    Ms. Smith missed completely the implications of the Proceedings of National Academy of Sciences paper which P Z Myers noted correctly, in a recent, rather inane post of hers:

    http://scienceblogs.com/erv/2009/01/latent_evolutionary_potential.php

    Before commenting on a paper which addresses the issue as to how organismal body size increased over time in response to changes in the chemical composition of Earth’s atmosphere from approximately 4 billion years ago to the present, maybe she ought to learn something about paleobiology and evolutionary ecology. Her ignorance is almost as bad as Behe’s, unfortunately.

    Respectfully yours,

    John Kwok

66. #66 John Kwok

    January 24, 2009

    @SLC,

    I’m not sure what a “birther” means, but if you are trying to suggest that I am a “forced-birther” – which is slang for an abortion opponent – then you’re quite mistaken, since I’ve NEVER opposed the right of women to have abortions and I would like to see drugs like RU-486 made freely available to those women who need them.

    An inane, adolescent observation of yours merely reinforces my point regarding Ms. Smith’s occasionally adolescent behavior online, since it has apparently garnered the enthusiastic support of yet another “adolescent”: yourself.

    Respectfully yours,

    John

67. #67 Gary Hurd

    January 24, 2009

    Graham Lawton wrote above,
    

    You have to find exciting new stories and sell them in exciting, sexy (and sometimes controversial) ways. That doesn’t go down well with the purists, but I’d always argue that it’s better to have a million people reading a “dumbed down science rag” than a few hundred people reading real science and everybody else doing something else.

    Mr. Lawton, I find your attitude reprehensible. You think it is better that you have mislead millions of people, rather than a few hundred that read “real science.” That certainly makes the New Science cover more understandable. Maybe next week you can run with “Darwin had sex with his cousin!”

68. #68 Douglas Theobald

    January 24, 2009

    Spartan wrote:

    “The web article is titled ‘Why Darwin was wrong about the tree of life’; does anybody think that title is unfair?”

    Yes. Darwin’s tree considered essentially only animals. For what he applied the tree metaphor to, he was right and he still is. I also find it annoying that it’s news to proclaim that Darwin was wrong. He was wrong about lots of stuff. It would be nice, at the very least, if the science journalists could accurately report what he was actually right about and what he wasn’t.

    But then again, I guess Graham knows better than me, lowly “naive” scientist that I am, with my silly “purist” concerns for truth and accuracy. Science journalism isn’t about being truthful.

69. #69 Robert O'Brien

    January 24, 2009

    An inane, adolescent observation of yours merely reinforces my point regarding Ms. Smith’s occasionally adolescent behavior online, since it has apparently garnered the enthusiastic support of yet another “adolescent”: yourself.

    I concur, although, I think you are being too generous with “occasionally.”

    Maybe next week you can run with “Darwin had sex with his cousin!”

    LOL.

70. #70 Johnny

    January 24, 2009

    Lawton’s pursuit of truth reveled; he just posted to my site.

    Graham writes:

    “Why am I posting all over the shop?

    I’m defending myself against scurrilous accusations spread by you and other hysterical bloggers. I’m not going to sit back and let you drag my name through the mud based on some flimsy and lazy supposition about the content of my article.

    Let me set the record straight one more time. I wrote an article saying that many biologists now argue that one important aspect of the theory of evolution needs modifying in the light of new evidence, Whether you like it or not, that is true.

    See for example: http://centres.exeter.ac.uk/egenis/research/QuestioningtheTreeofLife.htm

    True. Truth. Remember it?”

    What he’s responding to: http://ecographica.blogspot.com/2009/01/whys-graham-so-glum-lawton-critiqued.html

71. #71 SLC

    January 24, 2009

    Re John Kwok

    Obviously, Mr. Kwok doesn’t follow Ed Braytons’ blog or he would have known what a birther was. Just for his information, birther has nothing to do with abortion. It has to do with Mr. Kwoks’ rather interesting notion that President Obama was born somewhere other then Honolulu, Hawaii. Myself and the commentors over at Mr. Braytons’ blog have christened such individuals birthers. For the benefit of those who don’t visit Pandas’ Thumb, Mr. Kwok got into a lengthy discussion with myself and others over this issue. I would suggest that for Mr. Kwok to place himself in the company of nutcases like Alan Keyes, Joseph Farah, the clowns over at the Israelinsider, and the even more wacky clowns who reside over at onenewsnow does not indicate good judgment on his part.

72. #72 MrG

    January 24, 2009

    > Yes. Darwin’s tree considered essentially
    > only animals. For what he applied the tree
    > metaphor to, he was right and he still is.
    > I also find it annoying that it’s news to
    > proclaim that Darwin was wrong.

    I like to use the Wright Brothers as something of an ironic stand-in for Darwin, and I was thinking along such lines of the scenario:

    “The Wright Brothers were WRONG!”

    “Why?”

    “Because they didn’t know how to build a helicopter!” True enough, it wasn’t until the late 1930s that anyone came up with a workable helicopter — the technology’s not all that closely related to that of fixed-wing aircraft.

    I’m writing up an outline of THE ORIGIN OF SPECIES for my website and going through the book fairly carefully. This little flap over the NS article got me to thinking: THE ORIGIN OF SPECIES, as far I have been able to penetrate it, never uses microorganisms as an example.

    They’d known about microorganisms for a long time by 1859, but they had very little knowledge of their details and lifestyles. Darwin’s thinking was generally accurate for the eukaryotic organisms he considered; the prokaryotes were generally outside of his field of vision, and that part of the vision had to be added by later generations. The interesting thing is that, since prokaryotes broadly speaking don’t work like eukaryotes, the rules are different for prokaryotes — but having factored in those rules, Darwin’s thinking is just as applicable for prokaryotes than it is for eukaryotes.

73. #73 John Kwok

    January 24, 2009

    @ SLC,

    Have no interest in regurgitating the November 2008 presidential election with you, since I have stated elsewhere that I am delighted with most of Obama’s Cabinet picks (Incidentally two of his key advisors, David Axelrod and Eric Holder, are fellow alumni of my prominent New York City public high school.) and his most impressive may have been choosing eminent marine ecologist Jane Lubchenco to run NOAA.

    I’m sorry you’re so interested in supporting Ms. Smith, that you haven’t commented on my remark that she was wrong in misinterpreting what P Z Meyers wrote regarding that PNAS paper. Here’s yet another recent example where she’s confused convergent evolution with the exchange of genetic material across kingdoms (which is relevant for obvious reasons in this very thread on inane science journalism):

    http://scienceblogs.com/erv/2009/01/hiv_tomato_tomahto.php#more

    Again my advice to Abbie is that she ought to try doing her homework with respect to understanding evolutionary ecology, especially with regards to coevolution. Otherwise she runs the risk of becoming almost as irrelevant as Denyse O’Leary. As for you, you’re starting to sound like Uncommon Dissent’s DaveScot Springer, who had the temerity of dubbing me the “Jekyll and Hyde of Paleobiology”.

    Respectfully yours,

    John Kwok

74. #74 SLC

    January 24, 2009

    Re John Kwok

    Abbie Smith is hot.

75. #75 John Kwok

    January 24, 2009

    @ SLC,

    Oh sure, “Abbie Smith is hot” if that’s all you really care about. But is that really a remark worthy of posting here at Science Blogs? But regardless of whether or not she is “hot”, does she understand what she is talking about with respect to evolution? I think not. Moreover I think it is demeaning to her and to other, far more credible, women graduate students and scientists to evaluate them on whether or not they are “hot”.

    In her latest post, her most accurate observation about coevolution was this: “*blink* Evolution is an arms race, man.” However, that’s not quite true if one forgets such issues like kin selection, group selection, and indeed, perhaps all of sociobiology.

    There is nothing in her latest post that demonstrates that she understands well either coevolution or convergent evolution (A classic example of convergent evolution is of course the evolution of fins in fishes, ichthyosaurs, and cetaceans.).

    Let’s continue our discussion solely on her merits – or sadly, lack thereof – with regards to how well she understands the general concepts of modern evolutionary biology.

    Respectfully yours,

    John

76. #76 SLC

    January 24, 2009

    Re John Kwok

    If Mr. Kwok has some issues with Ms. Smiths’ knowledge and expertise in evolutionary biology, why doesn’t he post his complaints over at her blog? I suspect the reason is that he is afraid that she will hand him his head, just as she did with Michael Behe.

    Just out of curiosity, what does Mr. Kwok do for a living? Does he earn his daily bread by working in some area of science or technology?

77. #77 Mike of Oz

    January 25, 2009

    Well there are good points on both sides. It is fair to say that magazines like New Scientist are good for disseminating easily digestible and enjoyable science reading to the public. As a non-scientist (though a scientifically literate one) who doesn’t have time to pour over in-depth and often complex journal articles, I personally find it very informative.

    On the other hand to approve such a cover was a bit silly of New Scientist. It spells “ammunition” in capital letters. No-one including the naive, sensationalist, and scientifically illiterate mainstream media will even bother trying to comprehend the article. The cover says all they want to know, even though it was never intended to cause such problems. Surely the Editor could’ve seen this coming a mile away.

78. #78 Douglas Theobald

    January 25, 2009

    Surely the Editor could’ve seen this coming a mile away.

    Of course the editor saw it — the editors at NS aren’t stupid idiots. The fact that they published it anyway speaks volumes. They don’t care what the message is, because they’re trying to make money by selling issues. It’s a tough economy out there right now.

79. #79 AnthonyK

    January 25, 2009

    Yes, I too think the cover was grossly misleading and gives succour to creationist nutjobs. For higher organisms, the “tree of life” analogy is still accurate, and useful; for New Scientist to say otherwise represents something of a nadir it its presentation of scientific ideas. It’s a constant battle over here for newspapers and journals to avoid sensational, misleading headlines; scientific articles are particularly prone to being misrepresented by sub-editiors in search of dumbed-down copy. To see this in our premier popular science journal is very sad.
    Darwin was wrong in the same way that the “orbiting satelites” model of atoms is wrong – a very useful picture and conceptual framework, still presented in science lessons worldwide, but lacking sophistication and utility at higher levels. Ever tried presenting chemical bonding models to school pupils using quantum mechanics?
    Darwin was more right than wrong – “Darwin Updated” would have been a far better headline.

80. #80 John Kwok

    January 25, 2009

    @ SLC,

    Obviously you are guilty of selective reading, period, and unable to accept that Ms. Smith’s knowledge of evolutionary biology isn’t as extensive as you think. I am a former paleobiologist who has had extensive training in paleobiology and evolutionary ecology. If I didn’t then how could I write these reviews over at Amazon:

    http://www.amazon.com/Why-Evolution-True-Jerry-Coyne/dp/0670020532/ref=pd_bbs_sr_1?ie=UTF8&s=books&qid=1232904150&sr=8-1

    (My review of Jerry Coyne’s “Why Evolution is True”.)

    http://www.amazon.co.uk/review/product/0743296206/ref=cm_cr_dp_synop?%5Fencoding=UTF8&showViewpoints=0&sortBy=bySubmissionDateDescending#R2T5JV3BE3M4ID

    (My review of Michael Behe’s “The Edge of Evolution”, which was posted originally at Amazon’s USA website. It is still posted there.).

    http://www.amazon.co.uk/Evolution-What-Fossils-Say-Matters/dp/0231139624/ref=sr_1_1?ie=UTF8&s=books&qid=1232904443&sr=1-1

    (My review of Donald Prothero’s “Evolution: What the Fossils Say and Why It Matters”, which was posted originally at Amazon’s USA website. It is still posted there.)

    I am a computer programmer/data manager/data analyst, photographer and writer.

    If I could post my observations about Ms Smith’s ignorance and poor understanding of some of the most important concepts in contemporary evolutionary biology, then I most certainly would. However, it is a sign of her adolescent immaturity that she no longer allows me to post there.

    Ms. Smith’s claim to fame is having pwned Michael Behe with regards to his understanding of the origins of HIV/AIDS (having received extensive technical assistance from Dr. Ian Musgrave) and alerting us to Bill Dembski’s apparent theft of the Harvard University cell animation video produced for it by the film production company XVIVO. For these reasons she has garnered ample interest and attention not only from fellow supporters of evolution, but from the anti-evolution crowd too. If I was Ms. Smith, I would try to assume more responsibility for posting accurately on my blog about evolutionary biology by taking immediately, the necessary steps required to educate myself about the important concepts of modern evolutionary biology.

    Respectfully yours,

    John Kwok

    P. S. SLC, what are your qualifications to write in defense of Ms. Smith’s behavior and her understanding of evolutionary biology?

81. #81 SLC

    January 25, 2009

    Re John Kwok

    In response to Mr. Kwoks’ question I have no qualifications whatever to defend Ms. Smiths’ musings about evolutionary biology and I have not done so anywhere on this thread. Having a PhD in elementary particle physics does not provide such a qualification.

    As for banning people from commenting on ones blog, I have no idea as to why Ms. Smith would ban Mr. Kwok, although, in recalling his idiotic comments relative to President Obamas’ birth certificate on a Pandas’ Thumb thread, I can well believe that he made himself obnoxious on her blog and was treated accordingly. For instance, Larry Fafarman has been banned on several blogs, including this one and Robert O’Brien and Colin Brendemuehl have been banned over at Ed Braytons’ blog, because they deteriorated into obnoxious trolls.

82. #82 tomh

    January 25, 2009

    @ SLC
    Mr. Kwoks’ rather interesting notion that President Obama was born somewhere other then Honolulu, Hawaii.

    Now that’s hilarious, plus it tells me everything I need to know about Mr Kwok’s attitude on ideology vs. critical thinking. Ideology trumps logic and evidence every time.

83. #83 John Kwok

    January 25, 2009

    @tomh and SLC,

    There are other, far more prominent, conservatives who accept the scientific validity of evolution and whom I presume were critical of Obama, starting with conservative commentator John Derbyshire of the National Review. Had I known last fall what I know now of Obama’s plans – as well as the overall excellent composition of his cabinet – I would have voted for him.

    I find it fascinating that you seemed more interested in commenting about my prior political views instead of addressing my concerns that Ms. Smith’s knowledge of evolutionary biology may not be up to the task of commenting accurately about it at her blog.

    Respectfully yours,

    John Kwok

    P. S. I possess undergraduate and graduate degrees in geology and biology, culminating in a M. S. degree in Geosciences. Therefore I am well qualified to comment accordingly about paleobiology and evolutionary ecology.

84. #84 tomh

    January 25, 2009

    @John Kwok

    I’m sorry, it’s just that the fact that you seriously questioned Obama’s place of birth puts you so far out on the wingnuttery spectrum that anything you write induces a paroxysm of laughter. I’m sure it’s just a shortcoming of mine.

85. #85 John Kwok

    January 25, 2009

    @ tomh,

    There have been others who have expressed serious reservations, and frankly, I wished Obama would have released an official, notarized copy just to silence the critics. I have to trust the judgement of a fellow high school alumnus, Eric Holder, whom I am sure has seen the original copy.

    It’s too bad your “paroxysm of laughter” doesn’t include Ms. Smith’s abysmal understanding of convergent evolution, and especially, coevolution, which, ironically, is almost as bad as Michael Behe’s, which he demonstrates again and again in his dismal “The Edge of Evolution”. No, on second thought, if I am correct about my assertion of Ms. Smith’s knowledge, then it should induce tears, not laughter. It’s really something not worthy of laughter IMHO.

    Respectfully yours,

    John Kwok

86. #86 SLC

    January 25, 2009

    Re John Kwok

    1. As I stated, I am not competent to comment on Mr. Kwoks’ differences of opinion with Ms. Smith and have not done so and will not do so. I can’t speak for Mr. tomh.

    2. The issue isn’t whether Mr. Kwok was critical of President Obama. Many people, both liberal and conservative have been, are now, and will be in the future critical of him. The issue is that Mr. Kwok engaged in long arguments claiming that President Obama was not born in Honolulu, Hawaii and therefore was ineligable to be elected to the ofice of POTUS. I find it amusing that Mr. Kwok now says that President Obama is A OK, even though Mr. Kwok has claimed that he is illegally occupying the office.

87. #87 tomh

    January 25, 2009

    @John Kwok

    There have been others who have expressed serious reservations …It’s too bad your “paroxysm of laughter” doesn’t include Ms. Smith’s…

    No, it’s strictly limited to your absurd speculations regarding Obama’s birthplace. These “others” you refer to are certainly a fine lot to associate yourself with. Way, way out there on the wingnut spectrum. Why are you so sure that your fellow high school alumnus has seen the original copy? Perhaps he simply accepted the evidence, instead of believing in some insane, conspiratorial ramblings.

88. #88 John Kwok

    January 25, 2009

    @ SLC,

    You are indulging in that favorite creationist pastime, quote mining. Simply because you think Abbie Smith is “hot”, you seem prepared to shift the discussion back to whether or not I think President Obama is “A OK” even if “…he is illegally occupying the office.” It’s too bad that you, a physicist who is apparently ignorant of basic principles of evolutionary biology, seem interested in acting like a creationist.

    I hope your judgement of any female physicist colleagues isn’t nearly as distorted as your appraisal of Ms. Smith’s understanding of evolutionary biology, simply because she is “hot”.

    In fairness to Ms. Smith, however, I have met quite a few molecular biologists and biochemists who are not fully conversant with basic principles of evolutionary biology. I suspect that may be due to their training, not because they are inclined to embrace ID and other forms of “scientific creationism” due to their religious beliefs. Conversely, I have admitted my own ignorance of some aspects of molecular biology and biochemistry and have deferred to others, like, for example, biochemist and molecular epidemiologist David Levin – who posts often over at Amazon.com – to make the pertinent remarks explaining why data in his respective fields support the scientific validity of evolution.

    If Ms. Smith is unwilling to learn more about evolutionary biology, then she should refrain from making some of the inane recent commentary that I have noted here. Or at the very least, admit her ignorance and recommend that others should read the remarks of those more qualified to comment.

    Respectfully yours,

    John Kwok

89. #89 John Kwok

    January 25, 2009

    @ tomh,

    Eric Holder – whom I have not met, but we do have mutual friends and/or acquaintances – was Obama’s chief legal advisor both during the campaign and the post-election transition. He is also a highly respected attorney. So I have to presume that Holder did indeed look at the original documentation.

    See my remarks that I just posted addressed to SLC. Like him you are wasting your time and mine by acting like a creationist.

    Respectfully yours,

    John Kwok

90. #90 tomh

    January 25, 2009

    @John Kwok

    So I have to presume that Holder did indeed look at the original documentation.

    You presume way too much. Do you think the Supreme Court went to Hawaii to inspect the original also? No, they denied the frivolous lawsuits based on evidence, as any pea-brained idiot could do.

    Like him you are wasting your time and mine by acting like a creationist.

    I have no idea what you are talking about, all I did was laugh at you when it was mentioned that you promoted the idea that Obama wasn’t legally qualified to be president. As for me wasting your time, that’s illogical on the face of it. Your time is your own to use as you see fit. Apparently, you’ve used some of it pursuing a wingnut conspiracy theory.

91. #91 Robert O'Brien

    January 25, 2009

    Both tomh and SLC are engaging in pseudo-argumentation. It does not matter if John Kwok is Cuckoo for Cocoa Puffs* in another area or in every other area. All that matters is if his arguments are sound in the context of this thread.

    *I’m not saying he is; I don’t know either way.

92. #92 SLC

    January 25, 2009

    Re tonh

    Attached is a link to the Pandas’ Thumb thread in which Mr. Kwok made an ass of himself.

    http://pandasthumb.org/archives/2008/10/nature-endorses.html#comment-panels

    Re John Kwok

    I only wish that I could name some female physicists as hot as Abbie Smith or Sheril Kirchenbaum. It would appear that the good looking females who go into science tend toward the life sciences.

    I will repeat once more, I am not going to comment on the issues between Mr. Kwok and Ms. Smith as I am incompetent to do so. If she or Mr. Kwok care to comment on the issue of quantum entanglement, I would be happy to comment on that!

93. #93 tomh

    January 26, 2009

    @ SLC

    Thanks for the link to the PT thread, I’m very glad I missed it the first time around. What an embarrassment. I had no idea Mr. Kwok was so unhinged or I never would have responded to him.

94. #94 Anton Mates

    January 26, 2009

    John Kwok,

    I find it fascinating that you seemed more interested in commenting about my prior political views instead of addressing my concerns that Ms. Smith’s knowledge of evolutionary biology may not be up to the task of commenting accurately about it at her blog.

    What’s the basis for your concerns, exactly? It’s not clear to me what you think Abbie got wrong. What claim did she make about “latent evolutionary potential” that doesn’t jibe with what PZ or the original paper said, or what the original paper said? And did the HIV-1 paper by Qian et al. actually state that the Tat/P19 functional similarity is due to horizontal transmission rather than convergent evolution?

95. #95 John Kwok

    January 26, 2009

    @ Anton,

    Abbie missed completely the implications of both the Proceedings of National Academy of Sciences paper:

    http://www.pnas.org/content/106/1/24.full.pdf+html

    and what P Z Myers had to say about it:

    http://scienceblogs.com/pharyngula/2009/01/organismal_size_over_evolution.php

    by launching into a rather curious riff on “quasispecies” which started with this inane observation of hers:

    “Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks. Case in point: PZs post yesterday on ‘latent evolutionary potential’.

    “Ah, the realization of latent evolutionary potential. Did you know that you have latent evolutionary potential? Sure. If we put you and your family and friends in a novel environment, and let the generations tick by, we’ll discover that certain sets of traits will become more prominent as selection and drift take their toll. The phrase does not imply that there is a purposeful arrangement of genes in your body that are there with a preexisting intent to allow you to thrive in a particular situation. You are complex, you have many properties that may in your current situation be superfluous or useless, but could be utilized in different situations.”

    Heck yeah! We have to deal with ‘latent evolutionary potential’ all the time when we are dealing with HIV-1, because HIV-1 behaves as a quasispecies– a HUGE, dynamic population of viruses, where each virus is totally unique, yet they are all still related to one another. Its just genetic drift to the extreme. hehe!”

    First, she misses the point – which ironically the folks over at Uncommon Dissent picked up on – that the authors of the Proceedings of the National Academy of Sciences paper – who included eminent evolutionary ecologist James H. Brown -
    discovered that organismal body size seems to have been correlated with changing composition of the Earth’s atmosphere, with substantial increases occurring after the Earth’s atmosphere became increasingly oxygen-enriched after approximately one billion years ago. Second, I have to raise my eyebrows at her notion of a “quasispecies”, and recommend strongly that she consults with someone who really knows speciation – such as noted evolutionary geneticist Jerry Coyne – before making a similar observation again.

    As for her more recent posting on the paper by Qian et al., she apparently is confusing convergent evolution with horizontal transmission of genomic material and is also erroneously implying that convergent evolution has occurred in those viruses, when, as you have pointed out correctly, it was horizontal transmission, not convergent evolution, identified by these researchers. I wish she didn’t say this:

    “This is, quite possibly, one of the weirdest examples of convergent evolution I have ever seen.”

    Sincerely yours,

    John

96. #96 John Kwok

    January 26, 2009

    @ SLC,

    I strongly object to reading whenever someone observes that eminent physicist Lisa Randall is “hot” (In the interest of full disclosure, both she and her high school classmate, physicist Brian Greene, are fellow alumni of my high school, and I do vaguely remember Brian.). You’re ducking the issue by not admitting that your sole criterion for judging Abbie Smith’s worthiness to comment on evolutionary biology is the “fact” that she is “hot”.

    Once more you are engaging in a classic creationist tactic by indulging in “quote mining” about what I did say with regards to President Obama, but have since recanted.

    Respectfully yours,

    John Kwok

97. #97 John Kwok

    January 26, 2009

    @tomh,

    No, I am not presuming too much at all when I noted yesterday that Holder probably looked at the original documentation since he was Obama’s chief legal advisor both during and after the presidential campaign (This was an observation I had ignored originally by someone who knows Holder.).

    Apparently you are so obsessed with trying to “expose” me simply because I am pointing out errors made by Ms. Smith. Maybe you ought to pause, catch your breath, and consider seriously what Robert O’Brien said:

    “It does not matter if John Kwok is Cuckoo for Cocoa Puffs* in another area or in every other area. All that matters is if his arguments are sound in the context of this thread.”

    Respectfully yours,

    John Kwok

98. #98 John Kwok

    January 26, 2009

    @Anton,

    As a postscript to my previous comment, I should note I am making my observation on the Qian et al. paper based on what I have read from their abstract. If they did use the term “convergent evolution”, then they’re mistaken, since if what they described as convergent evolution was truly convergent evolution, then there would have to be two different kinds of viruses in plants and animals – genetically unrelated to each other – that have evolved over time to have exactly the same features reported in their paper (Again, as I noted a few days ago, a classic example of convergent evolution is the evolution of fins in fishes, ichthyosaurs and cetaceans.).

    Sincerely yours,

    John

99. #99 John Kwok

    January 26, 2009

    @Anton,

    I’m guilty of a little oversimplification in my most recent post, since what I should have said was, “…. convergent evolution, there would have to be two different kinds of viruses in plants and animals – genetically unrelated to each other – that have evolved over time to have similar features….” Since the paper said that the features are identical, then there’s two possibilities, and neither includes convergent evolution. Either this is an excellent example of genetic transfer of the same viruses from plants to animals (or vice versa) or an elegant molecular example of viruses showing plesiomorphic traits (what a cladistic systematist would refer to as shared “primitive” traits – plesiomorphies – as defined by the father of cladistics, German entomologist Willi Hennig), and thus, therefore, an elegant molecular example supporting common descent. So, if my interpretation is correct, there is no reason why Abbie Smith should have regarded this as an example of convergent evolution.

    Sincerely yours,

    John

100. #100 John Kwok

     January 26, 2009

     @SLC,

     Your inane comment regarding how “hot” Abbie Smith and Sheril Kirshenbaum (Incidentally, she is a “friend” of mine online elsewhere, and she isn’t a graduate scientist) makes me wonder how you would greet eminent high energy particle physicist Lisa Randall at a scientific meeting comprised of fellow physicists. Hopefully you’ll display better judgement – especially tact – towards her at such a meeting.

     Regardless, you’ve merely demonstrated to me that you don’t care what Abbie says, as long as she says it, merely to fulfill your own sexual fantasies. Right?

     John Kwok

101. #101 eric

     January 26, 2009

     Getting back to the original subject of the post, I think I can summarize the action as follows:
     1. Mr. Lawton writes an article about Darwin which is not entirely accurate, but ‘spiced up.’
     2. Mr. Rosenhouse takes him to task for that in his blog.
     3. Mr. Lawton complains that Mr. Rosenhouse’s blog is bad journalism because his summary of Lawton’s article is not entirely accurate and ‘spiced up.’

     Hmm…

102. #102 John Kwok

     January 26, 2009

     @eric,

     Yes, I think yours is a terse and excellent summary of the main action.

     John

103. #103 SLC

     January 26, 2009

     Re John Kwok

     After reading the comments by Mr. Kwok here, I can see why Ms. Smith banned him from her site. He is clearly a schmuck and an obnoxious putz to boot. And by the way, I have made no appraisal of Ms. Smiths knowledge and expertise in evolutionary biology and Mr. Kwoks’ claim that I have is totally without foundation.

     As for Dr. Randall, I have never met here or seen her, and, in fact, prior to Mr. Kwoks’ mention of her in one of his comments, I had never heard of her. Back when I was active in physics a million years ago, here were very few women in physics and I can’t recall any who were attractive.

     Of course, Mr. Kwoks’ apparent disinterest in the physical appearance of Ms. Smith and Ms. Kirchenbaum indicates that he might much prefer, say, Brent Corrigan.

104. #104 John Kwok

     January 26, 2009

     @ SLC,

     Sure, I’ve met a number of very attractive scientists and recently told one – whom I had last seen shortly after we had both graduated from our high school – that she has grown into a beautiful woman. So who said I am not interested in “the physical appearance of Ms. Smith” and Ms. Kirshenbaum (You are misspelling her name BTW.)? It’s not relevant to this discussion IMHO. Nor should it be.

     I am quite surprised that you call yourself a physicist and not heard of Harvard University physicist Lisa Randall, especially for her important contributions to high energy particle physics, string theory and cosmology ( I don’t pretend to understand any of her work BTW, but am aware of it.). That’s almost analogous to claiming that you’re an evolutionary biologist and have never heard of Stephen Jay Gould, Richard Dawkins or E. O. Wilson.

     Thanks again for reaffirming my observation that your only interested in Abbie Smith because she’s “hot”. What a classic example of breathtaking inanity from someone who claims to be a scientist!

     Respectfully yours,

     John Kwok

105. #105 Robert O'Brien

     January 26, 2009

     An inane, adolescent observation of yours merely reinforces my point regarding Ms. Smith’s occasionally adolescent behavior online, since it has apparently garnered the enthusiastic support of yet another “adolescent”: yourself.

     Of course, Mr. Kwoks’ apparent disinterest in the physical appearance of Ms. Smith and Ms. Kirchenbaum indicates that he might much prefer, say, Brent Corrigan.

     Quod erat demonstrandum.

106. #106 John Kwok

     January 26, 2009

     @SLC,

     You’re not good in reading comprehension either. I said that you seem uninterested in commenting on Abbie Smith’s comprehension of modern evolutionary biology, but rather, more interested in commenting her on her “physical appearance”. Your frequent comments to this thread merely confirm my observation.

     Respectfully yours,

     John Kwok

107. #107 John Kwok

     January 26, 2009

     @Robert,

     Thanks for trying to inject some sanity into this thread. It’s a shame that both SLC and tomh
     seem uninterested in addressing the merits of what I have had to say about several rather stupid remarks from Abbie at her blog with respect to modern evolutionary biology. Instead they believe it is more important to attack the messenger than to deal with the substance of his message.

     Appreciatively yours,

     John

108. #108 SLC

     January 26, 2009

     Re John Kwok

     1. I said I had a PhD in physics. Nowhere did I claim to be a physicist as I haven’t been active in the field for a long time, probably long before Prof. Randall came online.

     2. Mr. Kwok should be ashamed of himself for associating with an asshat like Robert O’Brien after whom Ed Brayton has named the O’Brien trophy for idiot of the month. Since Mr. Kwok stated on the Pandas’ Thumb that he had a high regard for Mr. Brayton, he might take that into consideration.

109. #109 Anton Mates

     January 26, 2009

     John Kwok,

     First, she misses the point – which ironically the folks over at Uncommon Dissent picked up on – that the authors of the Proceedings of the National Academy of Sciences paper – who included eminent evolutionary ecologist James H. Brown -
     discovered that organismal body size seems to have been correlated with changing composition of the Earth’s atmosphere, with substantial increases occurring after the Earth’s atmosphere became increasingly oxygen-enriched after approximately one billion years ago.

     This appears to be a non-issue to me, since she wasn’t writing about the original paper; she neither cited nor quoted it. She was writing about PZ’s observation, and her post is entirely relevant to that, particularly his line: “You are complex, you have many properties that may in your current situation be superfluous or useless, but could be utilized in different situations.” That certainly applies to the HIV mutants she describes, which happen to be resistant to drugs they haven’t even met yet.

     Second, I have to raise my eyebrows at her notion of a “quasispecies”, and recommend strongly that she consults with someone who really knows speciation – such as noted evolutionary geneticist Jerry Coyne – before making a similar observation again.

     What’s wrong with it? As far as I can tell from authorities, that’s exactly what a viral quasispecies is. From one paper, for instance: “Rather than being homogeneous, RNA virus populations consist of complex distributions of mutant (and sometimes also recombinant) genomes, in a type of population structure known as quasispecies.”

     Since the paper said that the features are identical, then there’s two possibilities, and neither includes convergent evolution. Either this is an excellent example of genetic transfer of the same viruses from plants to animals (or vice versa) or an elegant molecular example of viruses showing plesiomorphic traits (what a cladistic systematist would refer to as shared “primitive” traits – plesiomorphies – as defined by the father of cladistics, German entomologist Willi Hennig), and thus, therefore, an elegant molecular example supporting common descent. So, if my interpretation is correct, there is no reason why Abbie Smith should have regarded this as an example of convergent evolution.

     But the paper didn’t say that the TAT RSS (RNA silencing suppressor) and the P19 RSS are identical. It said that they are similar and function equivalently, but it also identified them as heterologous. That’s pretty much the definition of convergent evolution, no? Moreover, the paper explicitly said that the RSS is conserved within plant viruses. Evidently the authors believe that plant virus RSS’s have a common origin but that HIV-1′s RSS arose independently. They also mention Ebola’s VP35 as a third example of this, and if you read the cited paper, it states that there are several heterologous RSS’s in animal viruses–Influenza A, Hepatitis C and Vaccinia among others.

     So it seems to me that Abbie is, again, quite right. According to the researchers working in this area, at least, this is a matter of convergent evolution.

     Perhaps you were confusing the viral suppressors with the RNA silencing mechanism they attack? The latter is a matter of common descent, according to the paper; animal and plant RNA silencing pathways are homologous.

110. #110 neo-anti-luddite

     January 26, 2009

     While it is undeniably true that:

     “It does not matter if John Kwok is Cuckoo for Cocoa Puffs* in another area or in every other area. All that matters is if his arguments are sound in the context of this thread.”

     [quote from Robert O'Brien]

     …I believe that anyone who emulates standard creationist tactics warrants having any claim s/he makes subject to a greater degree of scrutiny. Once someone has proven that s/he is willing to lie for his/er ideologies, this seems the only sensible course of action.

     In my opinion, Mr. Kwok’s claims in the above-mentioned Panda’s Thumb thread regarding President (then Senator and later President-Elect) Obama’s citizenship, the nature of certain aspects of the US Constitution (especially his laughable claim that the military is legeally required to enact a coup d’etat if a lawfully-elected president enacts specific economic policies), and the generally weasely nature of his “arguments” regrading subjects varying from the political orientation of Chancellor Merkel to the inherent “Socialism” of redistributive taxation fit that standard to a T.

     The fact that when it comes to the evolution-vs.-creationism fight, he’s our unhinged wingnut does nothing to alter Mr. Kwok’s underlying unhinged wingnutitude.

     That being said, however, why don’t we all agree to just get along.

     Remember: Big Dembski is watching you….

111. #111 Mike of Oz

     January 26, 2009

     Thanks for the link to the PT thread, I’m very glad I missed it the first time around. What an embarrassment. I had no idea Mr. Kwok was so unhinged or I never would have responded to him.

     Wow, I’m a fairly regular browser of PT and I missed that whole exchange too! I have to admit that during reading it today I let out a few rounds of bellicose laughter. Very amusing. And mildly disturbing……

112. #112 John Kwok

     January 26, 2009

     @Anton,

     She cites the reference by P Z Myers about that PNAS paper co-authored by, among others, noted evolutionary ecologist James H. Brown, and she misses completely the point which P Z made. Using that as a jumping off point to discuss quasispecies is not only dubious, but a bit disingenuous.

     I am by training an organismal biologist, not a virologist, but I am still puzzled by that “term” quasispecies. Would be better if she consulted with someone who understands speciation – especially at the microbial level in her case – like microbial ecologist Richard Lenski, and perhaps too, evolutionary geneticist Jerry Coyne.

     Unfortunately, I don’t have a subscription to PNAS, so I can’t comment directly on the paper, except for the abstract which I have noted, and remember, I did SAY that I am confining my remarks to what I read in the abstract. Given the information you provided, however, yes, that would qualify as a microbial example of convergent evolution, and, potentially a rather fascinating one. But “one of the weirdest examples”, I think not, assuming yours is an accurate interpretation of this paper.

     John

113. #113 SLC

     January 26, 2009

     Rer Mike of Oz

     There have been several threads on Ed Braytons’ blog with contributions of folks equally as nutty as Mr. Kwok (e.g. someone calling himself John Adams). The disturbing part is that one of these whackjobs may take it into his head to do something about it. IMHO, they are all full of hot air and are just blowing off steam but you never know.

114. #114 John Kwok

     January 26, 2009

     Dear neo-anti-luddite,

     If you truly believed “why don’t we all agree to just get along”, you wouldn’t be bringing up points I have repudiated. As for our “buddy” Bill Dembski, there’s obvious not a dime’s worth of difference between you or him.

     I should note that a European friend who was well aware of my political discussions is more than dismayed that people like yourself are still interested in bringing it up, instead of focusing our efforts on attacking those like Dembski. If you’re really serious about “why don’t we all agree to just get along”, then I’d appreciate an acknowledgement from you that recognizes my change of heart.

     Otherwise, you’re no better than a Dishonesty Institute IDiot Borg drone like DaveScot Springer, who dubbed me the “Jekyll and Hyde of Paleobiology” after a heated exchange between Heddle and myself over at Abbie Smith’s blog. So you’re right…. “Big Dembski” is indeed watching.

     Live Long and Prosper (as a DI IDiot Borg drone),

     John Kwok

115. #115 John Kwok

     January 26, 2009

     @SLC,

     Thanks for your most recent inane comments. Clearly you seem uninterested in defending yourself against my accurate observation that you’re more interested in Abbie Smith because – and yes, I do admit it – she’s physically attractive, not because she may or may not have anything worthwhile to say about evolutionary biology.

     John Kwok

116. #116 tomh

     January 26, 2009

     @ John Kwok If you truly believed “why don’t we all agree to just get along”, you wouldn’t be bringing up points I have repudiated.

     You are truly amazing. You told lie after lie in that thread, never admitting any of them even after being confronted with indisputable proof, just piled on more lies, now you complain that people are bringing up points you’ve “repudiated.” Unbelievable. By the way, I see the Court denied another wingnut citizenship suit today. How’s that “Constitutional crisis” coming, now that we have a Marxist-Leninist president, as you repeatedly claimed. Are the troops in the streets yet?

117. #117 Tyler DiPietro

     January 26, 2009

     “If I could post my observations about Ms Smith’s ignorance and poor understanding of some of the most important concepts in contemporary evolutionary biology, then I most certainly would. However, it is a sign of her adolescent immaturity that she no longer allows me to post there.“

     No John, it’s a sign of your intellectual immaturity that you demanded she ban Dustin, windy etc. for having to temerity to laugh at your temper tantrums over their criticisms of your various inanities, then having the audacity to threaten her through email after she got sick of babysitting your sorry, crazy ass. Get some fucking help.

118. #118 Mike of Oz

     January 26, 2009

     @SLC

     Yeah I never paid much attention to these personalities before but now they’ve aroused my curiosity (more from a psycho-analysis point of view than anything else).

     The citizenship stuff made me laugh out loud. I mean, the guy couldn’t have even got as far as the Senate without that being thoroughly looked at (AFAIK it’s a requirement for any elected rep). It seems pretty moronic to even bring it up.

     As for the rest of the anti-Obama tirade (and excessive use of the word “inane” and references to school education), well, for a non-member of any political party and fairly centre-orientated person like myself, it all just got a bit bizarre!

119. #119 windy

     January 27, 2009

     Anton:

     But the paper didn’t say that the TAT RSS (RNA silencing suppressor) and the P19 RSS are identical. It said that they are similar and function equivalently, but it also identified them as heterologous. That’s pretty much the definition of convergent evolution, no?

     I agree with your interpretation.

     Would be better if she consulted with someone who understands speciation – especially at the microbial level in her case – like microbial ecologist Richard Lenski, and perhaps too, evolutionary geneticist Jerry Coyne.

     The Richard Lenski that was one of the authors of this paper?

     According to quasi-species theory, selection favours the cloud of genotypes, interconnected by mutation, whose average replication rate is highest. Here we confirm this prediction using digital organisms that self-replicate, mutate and evolve.

     Btw, does John’s namedropping strike anyone else as rather Dan Brown-esque? “Noted evolutionary geneticist Jerry Coyne staggered through the halls of the University of Chicago…”

120. #120 The Chimp's Raging Id

     January 27, 2009

     Kwok’s name dropping reminds me of some with a desperate and childish need for attention. Since the thread looks to have been derailed already, I’ll say no more on the subject.

121. #121 Anton Mates

     January 27, 2009

     John,

     She cites the reference by P Z Myers about that PNAS paper co-authored by, among others, noted evolutionary ecologist James H. Brown, and she misses completely the point which P Z made.

     Which point? PZ made many of them in that post. Among them, that any population of organisms contains “latent evolutionary potential” which can be exploited in a changing environment. Abbie quoted that bit and ran with it. I don’t see why she’s obligated to discuss either the rest of his post or the paper he was covering, no matter how illustrious its authors; we have his post for that.

     Using that as a jumping off point to discuss quasispecies is not only dubious, but a bit disingenuous.

     So it’s not that she’s wrong, she just doesn’t follow proper introductory-quote etiquette?

     I am by training an organismal biologist, not a virologist, but I am still puzzled by that “term” quasispecies. Would be better if she consulted with someone who understands speciation – especially at the microbial level in her case – like microbial ecologist Richard Lenski, and perhaps too, evolutionary geneticist Jerry Coyne.

     Lenski seems to agree with her usage of the terminology, as windy points out. In any case, we do have a working virologist available, who is presumably familiar with how the term is used within virology. That would be Abbie.

     Given the information you provided, however, yes, that would qualify as a microbial example of convergent evolution, and, potentially a rather fascinating one. But “one of the weirdest examples”, I think not, assuming yours is an accurate interpretation of this paper.

     “Weird” is subjective. It’s certainly very unusual to have convergence to this level of perfection on a molecular level, I would think–and with so many independent origins, to boot.

122. #122 Gerdien

     January 27, 2009

     Despite HGT, the tree of life seems to resolve much better than the Doolittle diagram in textbooks suggests:
     Ciccarelli et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science. 311:1283–1287.
     Dutil het al, 2008. Signature Genes as a Phylogenomic Tool. Mol. Biol. Evol. 25:1659–1667.

123. #123 neo-anti-luddite

     January 27, 2009

     Mr. Kwok,

     Since you seem incapable of admitting error, then I take it back; let’s not agree to get along.

     The fact that you believe anyone who calls you on your crap is working with the DiscoTute is of a kind with the lies, omissions, weaseling, and ridiculously irrelevant name-dropping you displayed in the Panda’s Thumb thread referenced above. (By the way, is that supposed to be some sort of argument-from-authority-by-association? It seems to be positively pathological with you.)

     As far as I can tell, you have repudiated nothing except your own belief regarding the type of person Obama would appoint to his Cabinet. Unless, of course, you count this as a repudiation:

     “I AM ASSUMING that Obama is a natural-born United States citizen merely because of his excellent judgement [sic] so far with respect to virtually all of his cabinet picks. Don’t get me started please if I am mistaken.”

     [quote from John Kwok – page 11 on the PT thread]

     You are mistaken, Mr. Kwok; a person’s judgment has absolutely no bearing whatsoever on his/er legal status as a citizen of the United States of America. And the fact that you are willing to overlook what you believe to be a breach of the US Constitution simply because Obama started doing things that you approve of speaks three very short but eloquent words about your character, your honesty, and your integrity:

     You have none.

     You seem to believe that people are either with you or against you, and if they are with you, then all is forgiven. If those are the only options, sir, then I will stand against you every time because the sort of facts-be-damned mentality that you displayed (and that, ironically, you fight so ardently against in the creationists on PT and elsewhere) is poison to both science and democracy.

     Now I’m going to go cash my paycheck from the DiscoTute, if you don’t mind. (And that was sarcasm, in case you missed it.)

124. #124 John Kwok

     January 27, 2009

     @Anton,

     Abbie Smith obviously can’t tell the difference between an important scientific paper and one that isn’t, judging by her comments on “latent evolutionary potential” and “quasispecies. I thought it was important to mention in this thread, since she’s as guilty as Graham Lawton is in not doing her homework and reporting responsibly on important scientific research. There’s a very good reason why PNAS has made the Payne et al. paper available as a free download to the general public; because they recognized its potential importance as one of the most important papers in biology published this year.

     John

     P. S. See my next comment

125. #125 John Kwok

     January 27, 2009

     @Anton,

     This PNAS paper cited by P Z Myers, the dishonest folks over at Uncommon Dissent and by yours truly, is important for several reasons. A collaborative effort on the part of several paleobiologists, ecologists and statisticians, it is the first quantitative attempt to look at the evolution of body size through time for all life on Planet Earth, and how that evolution has been affected by changes in the chemical composition of Earth’s atmosphere. The study suggests that body size was constrained by the Earth’s oxygen composition, increasing in two steps of similar magnitude, to account for three-quarters of the overall increase in body size, expanding eventually to 16 orders of magnitude. The first of these steps occurred approximately 1.9 Gya, at the time when the first eukaryotic cells are recognized in the fossil record. The second step occurred after oxygen levels began to increase towards present day levels during the interval recognized as the latest Neoproterozoic and early Paleozoic eras (0.6-0.45 Gya), coinciding with the initial diversification of metazoans (known incorrectly as the “Cambrian Explosion”). The authors have concluded therefore that latent evolutionary potential for all organisms was attained soon after the last remaining environmental constraints – in this case sufficient oxygen concentration in the atmosphere – were removed.

     P Z Myers did such a good job in summarizing the importance of this paper that I am reposting most of his comments here:

     Now that is the point of this new paper by Payne and others. They have taken a big picture examination of the distribution of fossil sizes over Earth’s history, and asked whether the range has varied smoothly over time, as you’d expect if the outer bound were simply diffusing to higher levels. And the answer is no, it is not, there are a couple of discrete jumps in the maximum size that imply limits to earlier expansion that were overcome at specific periods in history. There was a wall of some sort to the left of the staggering mass of life, and they speculate a bit about what it might have been.

     How do we explain these sudden upward surges in maximum size? Unsurprisingly, it isn’t by postulating a being of unimaginable magical or technological power who visits Earth at that time and inoculates his chosen species with size boosting genes. There is absolutely no evidence for that, and no need to invent such a silly hypothesis. Instead, there are two very good explanations that are actually supported by measurements and observations (and strangely, scientists prefer those kinds of explanations). One is a change in the environment, and the other is an intrinsic change in a subset of life.

     The environmental change is illustrated in the chart. The periods when the maximum organism size increased are correlated with periods when free oxygen levels in the atmosphere increased. Basically, the atmosphere was modified by the byproducts of organic metabolism in a way that allowed aerobic organisms to grow to a larger size — Earth accumulated enough rocket fuel in its atmosphere that some organisms could use to burn and grow. This is actually a fairly old story; we’ve been teaching about the oxygen increase in introductory biology for at least the last decade that I’ve been doing it.

     The other part of the explanation is the one that has made our poor confused creationists so giddy, I’m afraid. The authors say,

     These size steps coincide with, or slightly postdate, increases in the concentration of atmospheric oxygen, suggesting latent evolutionary potential was realized soon after environmental limitations were removed.

     Ah, the realization of latent evolutionary potential. Did you know that you have latent evolutionary potential? Sure. If we put you and your family and friends in a novel environment, and let the generations tick by, we’ll discover that certain sets of traits will become more prominent as selection and drift take their toll. The phrase does not imply that there is a purposeful arrangement of genes in your body that are there with a preexisting intent to allow you to thrive in a particular situation. You are complex, you have many properties that may in your current situation be superfluous or useless, but could be utilized in different situations.
     You see, we have a good idea of exactly what intrinsic capabilities contributed to the ‘latent potential’ that led to certain lineages growing larger at those two transitions, and they both have natural precursors. We don’t need a designer to explain the shifts, because the changes are expressions of known properties!

     The abrupt increase in the Paleopterozoic, for instance, is the product of growth in size of the relatively recently evolved eukaryotes. You’ve probably heard of the endosymbiote hypothesis: eukaryotes are the product of a merger of multiple prokaryotic organisms into a single whole. Single celled organisms combined, with different specializations — organelles in our cells called mitochondria, for instance, are thought to be descendants of an incorporated prokaryote. Our mitochondria have the primary function of burning carbon and oxygen to produce energy. This was “latent evolutionary potential” that could be exploited by eukaryotes as oxygen availability rose. And so, following the rise of increasing oxygen concentrations, the size of some eukaryotes staggered upwards to a new maximum.

     The second surge in the beginning of the Phanerozoic was also a consequence of a property with precursors in the existing single-celled populations: multicellularity. This is another biological property rich in “latent evolutionary potential”. Again and unsurprisingly, simply combining multiple cells into one organism is a fast-track to larger organismal size, and we see multiple lineages exploring this capability, many of which failed and died out, such as the Ediacaran fauna, and others in the Cambrian that expanded rapidly. Multicellularity itself is not an abrupt, binary choice. We have precursors: modern choanoflagellates show that protists can find selective advantage in transient assemblies, colonial organisms show the virtues of more permanent arrangements, and creatures like sponges exhibit cooperativity and specialization in internal function. Chance creates the potential, and selection can drive an agency-free promotion of greater expression of that potential.

     I must emphasize that this is not a paper endorsing any form of intelligent design creationism, and the creationists’ appropriation of its conclusion depends entirely on their distortion of its contents. Here is the authors’ full conclusion.

     Although increase in maximum size over time can often be accounted for by simple diffusive models, a single diffusive model does not appear capable of explaining the evolution of life’s overall maximum size. Approximately 3/4 of the 16-orders-of-magnitude increase in maximum size occurred in 2 discrete episodes. The first size jump required the evolution of the eukaryotic cell, and the second required eukaryotic multicellularity. The size increases appear to have occurred when ambient oxygen concentrations reached sufficient concentrations for clades to realize preexisting evolutionary potential, highlighting the long-term dependence of macroevolutionary pattern on both biological potential and environmental opportunity.

     The way the creationists have abused that is by pretending that this implies that the evolution of the eukaryotes and of multicellularity had to have been purposeful events. This is simply not true. All this is saying is that the limits of growth are properties of both organismal and environmental constraints, and that we can map those out by looking at the fossil record.
     ________________________________________
     Payne JL, Boyer AG, Brown JH, Finnegan S, Kowalewski M, Krause RA Jr, Lyons SK, McClain CR, McShea DW, Novack-Gottshall PM, Smith FA, Stempien JA, Wang SC (2009) Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Proc Natl Acad Sci U S A. 106(1):24-7.

126. #126 John Kwok

     January 27, 2009

     P. S. to my two most recent comments:

     I am a bit dismayed that virtually all of those interested in condemning me for political views I had since recanted, are behaving exactly like those over at Uncommon Descent in their slavish fawning over their “Messiah”, Dr. Bill Dembski (As eminent vertebrate paleobiologist Donald Prothero has noted recently in a public lecture here in New York City, only creationists seem interested in acknowledging one’s title; he himself prefers to be referred to as Mr. Prothero when he isn’t wearing the hat of a vertebrate paleobiologist.).

     Since Abbie’s blog is read avidly by both evolution supporters and those who are opposed, then it is really incumbent upon her to get her facts right. Why refer to the Payne et al. paper, and make an inane opening comment that asserts how laboratory work is somehow superior to research done over the time span of millions – indeed in the case of Payne et al. billions – of years, as though she’s channeling biochemist Michael Behe? If she can’t say anything meaningful about the Payne et al. paper, then don’t mention it, or say something along the lines like, “P Z Myers has a terrific interpretation of this paper which I don’t really understand too well.”.

     Respectfully yours,

     John Kwok

     P. S. I pointed out the Paine et al. paper to a college classmate, a noted astrobiologist/planetary geologist, and he thinks it’s so interesting, he’s going to reference it in a public lecture he’s giving soon.

127. #127 John Kwok

     January 27, 2009

     @neo-anti-luddite,

     I suggest you have a chat with Frank J and Dave Luckett over at Panda’s Thumb, who have forgiven me for not supporting President Obama in the recent presidential elections. Maybe have a chat too with Jeff Eyges, who – to my amazement and for which I am still most grateful, recently observed over at PT:

     “John, btw, I said this to you a couple of weeks ago on Roger Ebert’s blog, in the ‘Expelled’ thread, but I don’t think you noticed it – I admire the way you tackle creationists on Amazon. I haven’t the stomach for it. If anyone I know is ever tempted to harbor any hope for the future of humanity, I direct them to the comments on Amazon. That cures them of it pretty quickly!”

     “In any case, you’re a better man than I.”

     This was a ringing endorsement which Dave Luckett strongly seconded.

     Live Long and Prosper (as a DI IDiot Borg drone),

     John Kwok

     P. S. I’ll regard you as a DI IDiot Borg drone until you apologize for your online conduct against me.

128. #128 neo-anti-luddite

     January 27, 2009

     Mr. Kwok,

     Your opinion of me is utterly irrelevant, and to be frank, I don’t care who you voted for either.

     I freely admit that you’ve done some good work refuting creationist crap; hell, that’s why it’s so puzzling (and frankly infuriating) to see you emulate creationist tactics. I will also freely admit that as far as I can tell, you have made no errors of fact when you discuss evolution (but as a layperson, I make no great claims to accuracy on scientific minutiae).

     None of this, however, exempts you from following the basic precepts of honest debate, and my position is (as it has always been and likely always will be) that if you are willing to engage in deceptive debate tactics in any area of discourse, then you cannot expect people to take you at your word, even if you happen to be on “our side” in any given debate (or even if you happen to be telling the truth this time). Indeed, it is such a willingness to overlook fallacious reasoning and dishonest tactics in service of an ideological position that is the very hallmark of anti-evolutionists. The fact that you don’t appear to use those tactics in the evolution debate is great, as far as it goes; but that you’re willing to use such tactics at all is deeply disappointing.

     I don’t care whether you support Obama or not. I do care whether you are honest in your positions and in your presentation of the facts, and I believe that others who read your posts should know that you are willing to lie when it serves your ideological position. Please note that this does not mean that I believe everything you say is a lie; I’ve found that very few things are so black and white. I speak up when I see error, and I fully expect others to point out when I myself am in error. I have no trouble admitting my faults, and perhaps my distaste for lying is one of them.

129. #129 windy

     January 27, 2009

     Abbie Smith obviously can’t tell the difference between an important scientific paper and one that isn’t, judging by her comments on “latent evolutionary potential”

     Again, it looks like she took PZ’s post as an opportunity to discuss a different case of latent evolutionary potential. This does not mean that she denied the importance of the Payne paper.

     and “quasispecies.

     Which is a commonly used concept in evolutionary virology, and one that Richard Lenski evidently approves of, as I demonstrated above. What’s the problem?

130. #130 tomh

     January 27, 2009

     John Krok wrote:
     I am a bit dismayed that virtually all of those interested in condemning me for political views I had since recanted,…

     Actually, accusing someone of lying about their place of birth, of forging official documents, of hiding the truth in order to circumvent the law, these are not political views. Lying about what someone has said, whether it’s Obama in his book or Farrakhan in his newspaper, and then simply ignoring the evidence when it’s pointed out to you, and repeating the lies, these are not political views. Accusing someone of trafficking with terrorists and planning a “Marxist-Leninist” takeover of the US, all without a shred of evidence, these are not political views. Do you accuse others whose political views you disagree with of all these things, or was it only Obama? You have never recanted a single one of these lies.

     And now, with one more huge lie, you try to sweep all this drek together under the heading of “political views” and claim you have recanted them. Your pathological name-dropping is simply mildly amusing, but this facade you’re trying to project, that you have somehow repudiated all the lying you engaged in, is completely untrue and dishonest.

131. #131 John Kwok

     January 27, 2009

     @ windy,

     I really don’t see what Abbie saw as “latent evolutionary potential” and it is rather presumptuous of her to regard it as such, when the very term was defined for the first time in the Payne et al. paper (I have a reasonably good guess as to who, among the coauthors, actually came up with the term, evolutionary ecologist James H. Brown, since he’s been interested in years in the ecological consequences of evolving body size and, has coined the term “macroecology” as the ecological equivalent of macroevolution.).

     No, windy, in this case you are absolutely wrong in defending Abbie for citing the Payne et al. paper without doing a good job of explaining it. At least, to his everlasting credit, P Z Myers recognized just how important a paper it is (though sadly, he had to be reminded about it from a rather delusional post over at Uncommon Dissent.).

     John Kwok

     P. S. Your steadfast sycophantic defense of Abbie sounds all too much like what I’ve read from Bill Dembski’s supporters over at Uncommon Dissent.

     P. P. S. But thanks for your tip regarding Lenski’s acceptance of “quasispecies” (IMHO it’s a bad term, and I was painfully reminded how much we really don’t know about speciation at the microbial level when I attended the Rockefeller University evolution symposium back in May, 2008. BTW Abbie was supposed to write summaries of the talks and post them at her blog, but she hasn’t done them as of it yet. I wish she would, since much of the material was almost incomprehensible to someone trained in organismal biology (Or rather, to use Eugenie Scott’s term – she was there and we briefly compared notes afterwards – “rough sledding” for an organismal biologist like herself.).

132. #132 John Kwok

     January 27, 2009

     @ neo-anti-luddite,

     I don’t care what you think of me, except that I expect you keep your thoughts to yourself. Moreover, when other, far more respectable PT posters like Frank J and Dave Luckett have not just “buried the hatchet” with me regarding what I had thought initially of President Obama, but indeed, have gone out of their way to praise me for some of my comments over at PT, maybe it’s time you start “singing” a different tune about me.

     If you can’t refrain from acting like a jackass each time you criticize me, then you’re really no better than the delusional IDiots posting over at Uncommon Dissent. Why don’t you start “playing” with them for a change.

     Live Long and Prosper (as a DI IDiot Borg drone),

     John Kwok

133. #133 John Kwok

     January 27, 2009

     @Anton,

     What I’ve always thought – and still do – as really “weird” from the perspective of convergent evolution is that classic example, the Panda’s Thumb. There’s really nothing “weird” in the Qian et al. paper with regards to documenting an instance of convergent evolution from a molecular perspective; apparently the editors of PNAS thought so too, or else they would have made that paper freely available for public download in .pdf format, which, I remind you, is exactly what they did with the Payne et al. paper.

     Respectfully yours,

     John

134. #134 Anton Mates

     January 27, 2009

     No, windy, in this case you are absolutely wrong in defending Abbie for citing the Payne et al. paper without doing a good job of explaining it.

     She didn’t cite the Payne et al. paper. She didn’t say one word about it. That wasn’t what her post was about.

     She cited PZ’s post, which was largely about the paper, but the passage of his which she chose to discuss was making a much more general point.

135. #135 neo-anti-luddite

     January 27, 2009

     Mr. Kwok,

     You seem bound and determined to misunderstand me; yet another weasely creationist-style move. My beef with you has nothing to do with what you thought or think of Obama. My beef with you is –and has always been – that you repeatedly and vehemently lied in service of your ideological position, then lied about lying, and then tried to sweep it all under the rug. If you had pulled that kind of crap when talking about John McCain, I’d have called you on it just as quick. It’s the lying that’s the problem, Johnnie, not what you happen to think of Obama at any point in time.

     Get that through your skull.

     It’s interesting that you seek to stifle discourse rather than improve it. In the course of our interactions, you have expressed a desire that I die (i.e. “I wish you well in achieving room temperature soon.”), claimed that I am working for the DiscoTute (above), and engaged in all manner of huffiness and hissy-fits, but you have never once addressed the substance of any of my complaints regarding your claims in the Obama thread on PT. In that thread you said:

     “If there are no valid issues regarding his birth certificate, then the Messiah should have released it. Rightly or wrongly, the longer he does a “song and dance” routine with regards to its potential press release, the easier it is for me and many others to believe that he’s hiding something like the fact that he is not a “natural born United States citizen” as required by the U. S. Constitution for any prospective Presidential candidate.”

     [quote from John Kwok – page 3 on the PT thread]

     I offer you a modified version of your own words to consider: Rightly or wrongly, the longer you do a ‘song and dance’ routine with regards to the claims you made, the easier it is for me and many others to believe that you’re lying.

     So here’s your opportunity, buddy. Just type these simple words here, on this bog, right now:

     “I was wrong when I claimed that Obama’s status as a U.S citizen was suspect.”

     Since you claim to have recanted it shouldn’t be hard, and it would be a first step towards salvaging some semblance of your reputation.

     I look forward to not seeing those words show up anytime soon.

136. #136 neo-anti-luddite

     January 27, 2009

     Cue John Kwok claiming that Anton Mates is working with Dembski in 3…2…1….

137. #137 Anton Mates

     January 27, 2009

     Perhaps I should mention that I have no idea what Abbie Smith looks like. (And for purposes of neutrality, I’ll try to prolong my ignorance as long a I can!)

138. #138 Aureola Nominee, FCD

     January 27, 2009

     I see you’re being haunted by your intellectual dishonesty, Mr. Kwok. Don’t say you hadn’t been warned: with your lying, you destroyed your credibility. And contra your claim that those who called you on your lies were behaving “like creationists”, note the support you’ve been given in this very thread by Robert O’Brien.

139. #139 windy

     January 27, 2009

     I really don’t see what Abbie saw as “latent evolutionary potential” and it is rather presumptuous of her to regard it as such, when the very term was defined for the first time in the Payne et al. paper

     Presumptuous?? Payne et al
     a) don’t define a new term; the phrase only appears in the abstract.

     b) were not the first to use the phrase in a scientific paper – for example,
     “The primary motivation for this study was to explore latent evolutionary potential of shape traits in the wing.” Weber et al. 2005, Genetics 169: 1461–1475

     c) are using a redundant phrase for something that is already widely discussed in the literature under ‘evolutionary potential’ and ‘evolvability’ (it is not necessary to add ‘latent’)

     P. S. Your steadfast sycophantic defense of Abbie sounds all too much like what I’ve read from Bill Dembski’s supporters over at Uncommon Dissent.

     Umm what? Based on the two short comments above? Apparently sycophancy is easier than it used to be.

     (sorry for feeding the kwok everyone, it’s like staring at a car wreck.)

140. #140 neo-anti-luddite

     January 27, 2009

     You know, Johnnie, if you hadn’t proven yourself a liar, I’d be giving you the benefit of the doubt in your little tiff with windy because I’ve read a fair number of your postings and as far as I know, this thread is the fist time I’ve read anyting windy has posted.

     But unfortunately for you, I’ve read a fair number of your postings regarding Obama’s citizenship. Now do you see how this works, ol’ buddy, ol’ pal?

     Hi, windy, and welcome to the “DI IDiot Borg drone” collective! Would you like to enroll in direct deposit for your DiscoTute paychecks?

141. #141 John Kwok

     January 27, 2009

     @anton,

     Sorry, but Abbie had no good reason to quote from P Z Myers, when he was referring to “latent evolutionary potential” with regards to clade diversification, NOT microbial evolution. Myers recognized correctly that Payne et al. has some intriguing insights into the past history of life on Earth, and in fact, noted that in the concluding paragraph of his post, which I am noting again for your benefit:

     “The way the creationists have abused that is by pretending that this implies that the evolution of the eukaryotes and of multicellularity had to have been purposeful events. This is simply not true. All this is saying is that the limits of growth are properties of both organismal and environmental constraints, and that we can map those out by looking at the fossil record.”

     How do I know this, you might ask? Stylistically the Payne et al. paper resembles some classic papers – which included mathematical modeling of what could be described euphemistically as “clade success” – published back in the mid to late 1970s – coauthored by paleobiologists and ecologists such as notable figures like David Raup, J. John Sepkoski, Daniel Simberloff, Stephen Jay Gould, and, incidentally, James W. Valentine (the very PNAS editor of the Payne et al. manuscript). These were papers I read in graduate school and often discussed with others, including one of my graduate school professors, none other than evolutionary ecologist James H. Brown, one of the co-authors of the Payne et al. paper.

     Abbie Smith’s improper usage of “latent evolutionary potential” should be understandable to anyone who has read not only the Payne et al. paper but also P Z Myers’ excellent interpretation of it. If Abbie wants to comment on large-scale evolutionary patterns and processes, then she had better devote some time towards studying them and understanding them, not by writing inane blog posts which open with comments so reminiscent of what I have read from Michael Behe (who thinks the fossil record is irrelevant towards understanding evolution), such as: “Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     John Kwok

142. #142 Anton Mates

     January 28, 2009

     Sorry, but Abbie had no good reason to quote from P Z Myers, when he was referring to “latent evolutionary potential” with regards to clade diversification, NOT microbial evolution.

     Abbie can quote from Alice in Wonderland if she wants. Why shouldn’t she?

     And in what way is

     The abrupt increase in the Paleopterozoic, for instance, is the product of growth in size of the relatively recently evolved eukaryotes…This was “latent evolutionary potential” that could be exploited by eukaryotes as oxygen availability rose. And so, following the rise of increasing oxygen concentrations, the size of some eukaryotes staggered upwards to a new maximum.

     not a statement about microbial evolution?

143. #143 SLC

     January 28, 2009

     Since Mr. Kwok likes to name drop, I’ll do a little name dropping of my own.

     During my time as an undergraduate and graduate student in physics, I took courses from 4 Nobel Prize winners. They included Owen Chamberlain, Emilio Segre, Steven Weinberg, and Julian Schwinger. How about them apples Mr. Kwok.

144. #144 neo-anti-luddite

     January 28, 2009

     And in what way is

     The abrupt increase in the Paleopterozoic, for instance, is the product of growth in size of the relatively recently evolved eukaryotes…This was “latent evolutionary potential” that could be exploited by eukaryotes as oxygen availability rose. And so, following the rise of increasing oxygen concentrations, the size of some eukaryotes staggered upwards to a new maximum.

     not a statement about microbial evolution?

     C’mon Anton, you know the answer to that one:

     ‘Cause the Kwokster said so, and he knew someone who knew [insert gratuitous name-dropping here], so just shut the hell up, you DI IDot Borg drone, you.

     The Kwokster doesn’t have to back up his claims; the Kwokster knows people….

145. #145 John Kwok

     January 28, 2009

     @ Anton,

     If you really paid attention to how the authors collected the data, then you’ll see that they were referring to CLADES not microbial species (look at their methods section). That’s something which P Z Myers recognized and made note of in his excellent summary of the paper.

     Again it is really presumptuous of Abbie to assert that she has found viral evidence of “latent evolutionary potential”, especially when the authors of the paper include several scientists with distinguished reputations in their respective fields, including, for example, evolutionary ecologist James H. Brown, whose work has been cited frequently with regards to ecological implications of body size evolution, species area relationships in biogeography, and other aspects of ecology, such as community, behavioral and physiological ecology. He is the co-author of one of the very best – if not the best – textbook on biogeography:

     http://www.amazon.com/Biogeography-Third-Mark-V-Lomolino/dp/0878930620/ref=sr_1_7?ie=UTF8&s=books&qid=1233160129&sr=1-7

     So I would trust Jim’s rationale for coining the term “latent evolutionary potential” over that of a graduate student in virology, one Abbie Smith, who does not have the decades-long distinguished publishing record in ecology for which he is well noted.

     John Kwok

146. #146 John Kwok

     January 28, 2009

     @ SLC,

     So you studied physics at Harvard University or at the University of Texas, Austion (or both) with Steven Weinberg (who, incidentally, is an alumnus of my high school alma mater’s arch rival; Weinberg’s high school alma mater is the only one – public – or private – that has seven Nobel Prize laureate alumni)? Obviously your knowledge of physics has atrophied since then, especially when you weren’t aware of Harvard University physicist Lisa Randall – who is on the editorial board of SEED magazine – the sponsor of Science Blogs – if my memory is correct.

     Are you going to make the inane assertion that Abbie Smith’s understanding of “latent evolutionary potential” is better than distinguished evolutionary ecologist James H. Brown’s, especially since he was probably the one who coined the term as one of the co-authors of the Payne et al. paper?

     But I forget, you probably think Abbie Smith is “right” since she’s so “hot”. Am I right?

     John Kwok

147. #147 John Kwok

     January 28, 2009

     @neo-anti-luddite,

     If I didn’t know what I was talking about, do you think I’d be praised for my comments on evolution and the so-called creation vs. evolution debate by the likes of Frank J, Dave Luckett and Jeff Eyges, among others, over at Panda’s Thumb.

     I haven’t seen Jim Brown in years, and I doubt he’ll remember me. But I am sure that if you spoke to an ecologist at your local college or university, then I’m sure that that professor would recognize him and agree with my assessment of his work.

     Thanks for demonstrating once more that you are indeed worthy of your membership in the Dishonesty Institute IDiot Borg Collective.

     Peace and Long Life (as a DI IDiot Borg drone),

     John Kwok

     P. S. If Abbie wants to be regarded as a credible scientist, then she ought to admit to her mistake in grossly misinterpreting the Payne et al. paper.

148. #148 SLC

     January 28, 2009

     Re John Kwok

     Mr. Kwok has incorrectly deduced that I took a course from Prof. Weinberg at Harvard or UT. Actually, Prof. Weinberg was at UC Berkeley at the time but the venue of the course I took from him was Brandais, Un. And by the way, the late Prof. Schwinger was also a graduate of the Bronx School of Science.

     As for Prof. Randall, as I stated previously, I have been out of physics for a long time and am quite sure that I am unfamiliar with any number of current stars in that field.

     As for Ms. Smith, she indicates on her blog that Mr. Kwok is a cyber stalker, as well as a troll. I would suggest that Mr. Kwok not follow up his cyber stalking with physical stalking as Ms. Smith has a pit bull for a pet.

149. #149 John Kwok

     January 28, 2009

     @ SLC,

     If I didn’t know better, I would think that you are a cyberstalking sockpuppet of Abbie Smith OR one of the Discovery Institute’s delusional IDiot Borg drones pretending to be an Abbie Smith sockpocket.

     On a more serious note, if Abbie Smith wants to be taken seriously as a commentator on evolutionary ecology, then she better learn something about it. Judging from her recent posts, that is something I remain highly skeptical of.

     John Kwok

150. #150 John Kwok

     January 28, 2009

     @ SLC,

     Nobel Prizes are not awarded in ecology, evolution or geology, so the fact that you’ve studied with four Nobel Prize laureates, including two who are distinguished alumni of the Bronx High School of Science, would be comparable to saying that Bill Dembski was a National Science Foundation graduate scholarship recipient and studied with several notable mathematicians at the University of Chicago for his Ph. D. degree in mathematics (both observations are indeed true).

     It’s a pity you refuse to dmeonstrate any interest in trying to evaluate critically, Abbie Smith’s understanding of certain aspects of evolutionary biology (which several other retired and active physicists have done in the ongoing struggle against creationists, by carefully weighing their “evidence” for their inane beliefs) – namely paleobiology and evolutionary ecology – which she has misinterpreted in two of her most recent posts over at her blog, or listen carefully to someone who has (namely yours truly).

     John Kwok

151. #151 John Kwok

     January 28, 2009

     @ SLC,

     I remain interested in reading how you would defend as appropriate, Abbie Smith’s incorrect usage of the term “latent evolutionary potential”, after I have posted my recent comments to you and Anton on this very matter.

     John Kwok

152. #152 SLC

     January 28, 2009

     Re John Kwok

     I am not going to rise to the bait of Mr. Kwoks’. As I have previously stated, I am not competent to comment on the difference of opinion between Mr. Kwok and Ms. Smith and will not do so so quit wasting Prof. Rosenhouses’ disk storage.

     It appears that there are other commentors here who are not in agreement with Mr. Kwok and who appear competent so I suggest that he argue with them.

     I responded to Mr. Kwoks’ name dropping with name dropping of my own. Now that he has been trumped, he whines.

153. #153 John Kwok

     January 28, 2009

     @ Anton,

     For your benefit, I am reposting these remarks that I wrote last night:

     “Sorry, but Abbie had no good reason to quote from P Z Myers, when he was referring to “latent evolutionary potential” with regards to clade diversification, NOT microbial evolution. Myers recognized correctly that Payne et al. has some intriguing insights into the past history of life on Earth, and in fact, noted that in the concluding paragraph of his post, which I am noting again for your benefit:

     ‘The way the creationists have abused that is by pretending that this implies that the evolution of the eukaryotes and of multicellularity had to have been purposeful events. This is simply not true. All this is saying is that the limits of growth are properties of both organismal and environmental constraints, and that we can map those out by looking at the fossil record.’”

     Again, you can read the Payne et al. paper in .pdf format here:

     http://www.pnas.org/content/106/1/24.full.pdf+html

     I suggest you read the paper, before rising to the occasion to defend Abbie for her inappropiate usage of the term “latent evolutionary potential” or making an inane remark like this one:

     “Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     Respectfully yours,

     John Kwok

154. #154 John Kwok

     January 28, 2009

     @ SLC,

     It would be “name dropping” if I said I knew personally all of those paleobiologists whose names I cited. But did I? No, I pointed out that they had done important work in the mid to late 1970s that is echoed in the Payne et al. paper. Indeed, that work led eventually to the recognition by Raup, Sepkoski and their successors at the University of Chicago of periodic mass extinctions over the past five hundred and a half million years of earth history.

     Thanks for demonstrating that you’re just a stupid sockpuppet of Abbie Smith’s and that you suspend any semblance of credible scientific reasoning any time her name is mentioned, simply because you think she is “hot”.

     John Kwok

155. #155 John Kwok

     January 28, 2009

     @ SLC,

     Actually, the correct time span is approximately 545 million years ago, which is also referred to as the Phanerozoic Eon. What Raup and Sepkoski were interested in initially was trying to apply the MacArthur – Wilson model of equilibrium island biogeography to the marine invertebrate fossil record. A few years later, using the same data set assembled for that research, they discovered that there is an approximately 26 million year-long interval between mass extinctions over the past two hundred and fifty million years using sophisticated Fourier analysis. It is now recognized that there were approximately
     seven or eight really major mass extinctions in the last five hundred forty five million years.

     Tell me now whether you still think that Abbie Smith is a credible commentator now on paleobiology and evolutionary ecology. I think the answer is obvious.

     John Kwok

156. #156 windy

     January 28, 2009

     Sorry, but Abbie had no good reason to quote from P Z Myers, when he was referring to “latent evolutionary potential” with regards to clade diversification, NOT microbial evolution.

     PZ’s statement quoted by Abbie does not refer to clade diversification either! It refers to evolutionary potential in a human population consisting of “you and your family and friends”. PZ did the same thing you are castigating Abbie for: gave an example of variation below the species level to explain the general concept of evolutionary potential.

     So I would trust Jim’s rationale for coining the term “latent evolutionary potential” over that of a graduate student in virology

     He didn’t coin the term, it appeared in a paper in 1995! Which, I might add, also referred to intraspecific variation.

     SLC, I remain interested in reading how you would defend as appropriate, Abbie Smith’s incorrect usage of the term “latent evolutionary potential”, after I have posted my recent comments to you and Anton on this very matter.

     By your own criteria SLC should trust me, an evolutionary biologist with a Ph.D., over a geoscientist with a M.S. I tell you it’s not incorrect.

     And you can’t attempt to pull Brown’s rank on me, since you have no evidence that you aren’t falsely attributing your view to him, in the same way you mistakenly assumed that Lenski wouldn’t approve of ‘quasispecies’.

157. #157 John Kwok

     January 28, 2009

     @ Windy,

     You’re right, I don’t need to pull rank with respect to James H. Brown. He’s presumably a much better thinker than you’ll ever be, simply because of the fact that his work is widely cited in the literature (I’d be interested in seeing that reference to that 1995 paper BTW, though I remain correct – and if you read carefully P Z Myers’ own interpretation of the Payne et al. paper, he apparently agrees with me – in noting that the term “latent evolutionary potential” is used here to describe clade diversification of not just microbes, but more importantly, of multicellular plants and animals.). But now, forgive me for name dropping, but I still regard myself as being fortunate for having had the opportunity of learning from – and on at least one occasion, rendering some invaluable assistance to – Brown’s former colleague, ecologist Michael L. Rosenzweig.

     You may have a Ph. D. in ecology, but you seem incapable of agreeing with me that in her analysis of the Qian et al. she made the rather odd remark that “evolution is an arms race, man”. Is it really? What about kin selection, group selection, or perhaps, all of sociobiology? It is fair to say that much of coevolution may consist of a co-evolutionary arms race, but to say that is all of it, then you’re overlooking some other, equally important, aspects of it.

     Respectfully yours,

     John Kwok

158. #158 John Kwok

     January 28, 2009

     @ SLC,

     The data set that Raup and Sepokoski used, in conjunction with ecologist Daniel Simberloff and paleobiologist Stephen Jay Gould, in trying to determine whether the marine fossil record supported MacArthur – Wilson equilibrium island biogeography was used by Sepkoski – with some additions – to yield the interesting result of uncovering three “evolutionary faunas” which Sepkoski noted in the late 1970s. He added some more data to do the mass extinction analysis with Raup, but it was essentially the same data that he had worked from for the paper co-authored with Raup, Simberloff and Gould.

     This is merely a minor postscript to what I wrote beforehand.

     John Kwok

159. #159 John Kwok

     January 28, 2009

     @ Windy,

     I recommend reading carefully the materials section of the Payne et al. paper. Like Sepkoski, they collected data from higher taxonomic categories. They were NOT interested in species, speciation or intraspecific variation, simply because the geological record doesn’t preserve such detail over the billions of years covered in that analysis. Myers was well aware of it, which is why he referred repeatedly to clades – which is what Payne et al. were studying after all – in his summary of their paper. So my interpretation as to what Payne, Brown and their colleagues meant by “latent evolutionary potential” is correct, while Abbie’s is sadly, quite mistaken.

     John

160. #160 windy

     January 28, 2009

     You’re right, I don’t need to pull rank with respect to James H. Brown. He’s presumably a much better thinker than you’ll ever be, simply because of the fact that his work is widely cited in the literature (I’d be interested in seeing that reference to that 1995 paper BTW

     I already gave it: Weber et al. 2005, Genetics 169: 1461–1475 “The primary motivation for this study was to explore latent evolutionary potential of shape traits in the wing.”

     though I remain correct

     How would you know if you were wrong?

     and if you read carefully P Z Myers’ own interpretation of the Payne et al. paper, he apparently agrees with me – in noting that the term “latent evolutionary potential” is used here to describe clade diversification of not just microbes, but more importantly, of multicellular plants and animals.

     PZ’s example was not about clade diversification, fool! “If we put you and your family and friends in a novel environment, and let the generations tick by, we’ll discover that certain sets of traits will become more prominent as selection and drift take their toll.” That would be change along a single lineage, not diversification of lineages.

     But now, forgive me for name dropping, but I still regard myself as being fortunate for having had the opportunity of learning from – and on at least one occasion, rendering some invaluable assistance to – Brown’s former colleague, ecologist Michael L. Rosenzweig.

     What does this got to do with anything?

     You may have a Ph. D. in ecology

     No, I don’t. There’s more to biology than ecology.

     you seem incapable of agreeing with me that in her analysis of the Qian et al. she made the rather odd remark that “evolution is an arms race, man”. Is it really? What about kin selection, group selection, or perhaps, all of sociobiology?

     That statement does not imply that evolution is nothing but an arms race.

     So my interpretation as to what Payne, Brown and their colleagues meant by “latent evolutionary potential” is correct

     But you are sadly mistaken in assuming that that’s the only kind of “latent evolutionary potential” there is.

161. #161 John Kwok

     January 28, 2009

     @ windy,

     He was referring to clades, as demonstrated by his observations on lineages in these paragraphs:

     “The abrupt increase in the Paleopterozoic, for instance, is the product of growth in size of the relatively recently evolved eukaryotes. You’ve probably heard of the endosymbiote hypothesis: eukaryotes are the product of a merger of multiple prokaryotic organisms into a single whole. Single celled organisms combined, with different specializations — organelles in our cells called mitochondria, for instance, are thought to be descendants of an incorporated prokaryote. Our mitochondria have the primary function of burning carbon and oxygen to produce energy. This was ‘latent evolutionary potential’ that could be exploited by eukaryotes as oxygen availability rose. And so, following the rise of increasing oxygen concentrations, the size of some eukaryotes staggered upwards to a new maximum.”

     “The second surge in the beginning of the Phanerozoic was also a consequence of a property with precursors in the existing single-celled populations: multicellularity. This is another biological property rich in ‘latent evolutionary potential’. Again and unsurprisingly, simply combining multiple cells into one organism is a fast-track to larger organismal size, and we see multiple lineages exploring this capability, many of which failed and died out, such as the Ediacaran fauna, and others in the Cambrian that expanded rapidly. Multicellularity itself is not an abrupt, binary choice. We have precursors: modern choanoflagellates show that protists can find selective advantage in transient assemblies, colonial organisms show the virtues of more permanent arrangements, and creatures like sponges exhibit cooperativity and specialization in internal function. Chance creates the potential, and selection can drive an agency-free promotion of greater expression of that potential.”

     As for his examples of the origins of eukaryotes and multicellularity as examples of “latent evolutionary potential”, then they are what Payne et al. were referring to, and for Abbie to leap suddenly from the observations of Payne et al. to virology is dubious, and disingenuous.

     Myers was being a bit “sarcastic” in the quote you’ve posted (toward the creationist IDiot who had posted his own inane summary of the Payne et al. paper over at Uncommon Dissent) that was the start of Abbie’s rather bizarre riff, after, of course, her inane opening comment that one could make as much significant progress in evolutionary biological research by studying HIV-1 viruses as doing “big-stuff” biology of the kind done by Payne et al.

     You’ve apparently missed my comment regarding Abbie’s gross oversimplification of “…evolution is an arms race, man” in a later post of hers. Care to comment on that?

     I thought you were an ecologist, so I mentioned Michael Rosenzweig since his is another, quite distinguished, evolutionary ecologist. I consider myself fortunate to have studied with both.

     John

     P. S. I recommend you read carefully the Payne et al. paper if you haven’t already. That it is available as a free public download, really implies how important a paper it is.

162. #162 John Kwok

     January 28, 2009

     @ Windy,

     I can’t believe that Abbie would treat the fossil record with as much disdain as Michael Behe has done with a comment like, “Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     Again she missed the significance of the Payne et al. paper – which may be the key reason why PNAS is offering it as a free download – to talk instead about “latent evolutionary potential” in virology.

     Are we going to discuss the meaning of “is” now with this observation of yours in reply to my observation:

     “…you seem incapable of agreeing with me that in her analysis of the Qian et al. she made the rather odd remark that “evolution is an arms race, man”. Is it really? What about kin selection, group selection, or perhaps, all of sociobiology?”

     “That statement does not imply that evolution is nothing but an arms race.”

     Someone who knows nothing about biology – like the IDiots over at Uncommon Dissent who follow religiously Abbie’s every word – might conclude otherwise. Abbie shouldn’t have made such an irresponsible statement, without making some acknowledgement of kin selection, group selection, and perhaps sociobiology too.

     John

163. #163 John Kwok

     January 28, 2009

     @ Windy,

     It’s more than a bit hypocritcal of Abbie to criticize journalists like Graham Lawton if she, herself, is guilty of making similar errors at her own blog. You may not think so, but I think I’ve provided enough evidence to state my case. It’s for these reasons that I have been commenting about her comments here in this discussion thread.

     My intent is not to bash Abbie, but hopefully, to encourage her to do her homework first before posting. I really don’t care what she thinks of me now, but I’m available to render assistance to her, if she requests it.

     John

164. #164 neo-anti-luddite

     January 28, 2009

     Man, your reading comprehension skills suck, Johnnie-boy. You’d never have made it through my 1101 class (which kinda makes me wonder about that “quality education” you claim to have).

     I never said that you don’t know what you’re talking about when you’re addressing evolutionary issues. In fact, I even said that as far as I can tell you have been accurate when discussing any evolutionary matter that I have knowledge of.

     What I did say was that you have a demonstrated track record of lying, so all other things being equal, I’ll give someone I don’t know the benefit of the doubt before I’ll give it to you, because you have already proven that you are willing to lie in online debates.

     When you can back up what you say by providing empirical evidence to support your claims, I’ll happily agree that you’re not lying in that particular instance. But unless you can provide some proof that you’re not lying again, it seems only prudent to assume that you might be. You’ve done it before, after all, and then lied about it to boot….

     And here’s a little hint, ol’ buddy; name-dropping isn’t proof. Even if you could prove that you actually do know any of the people you claim to, it still wouldn’t be proof of anything other than the fact that you’re a prat.

     But hey, don’t take my word for it; I once took a class from some guy who studied under Einstein.

165. #165 neo-anti-luddite

     January 28, 2009

     @neo-anti-luddite

     If I didn’t know what I was talking about, do you think I’d be praised for my comments on evolution and the so-called creation vs. evolution debate by the likes of Frank J, Dave Luckett and Jeff Eyges, among others, over at Panda’s Thumb.

     Okay, Johnnie, let’s quit pussyfooting around: back up your implied claim that I said you don’t know what you’re talking about with regards to the evolution vs. creationism debate.

     Go ahead, quote me saying anything like that.

     Please.

     Anything.

     No?

     So you’re just lying again, and for all on this thread to see, no less.

     Damn, you’re dumb.

166. #166 John Kwok

     January 28, 2009

     @ Windy,

     I thought you said that there was a 1995 paper defining the term “latent evolutionary potential”, but you gave me a reference instead for a 2005 paper. Is this the same one?

     I just looked again at Payne et al. and noticed that they did not define “latent evolutionary potential” or gave a citation to a prior definition it, so it is entirely possible that Payne et al. came up independently with this term, without prior knowledge of the paper you’ve cited. So my suspicion that James H. Brown derived this term independently may still be correct. If so, that’s even more of a reason why Abbie shouldn’t have referred to the Payne et al. paper (or rather, preferably speaking, devote a post solely to the Payne et al. paper).

     John

167. #167 neo-anti-luddite

     January 28, 2009

     …and just to provide a counter-example (and to back up my own claim), here’s a relevant quote from me from this very thread, in a post that you replied to:

     I freely admit that you’ve done some good work refuting creationist crap; hell, that’s why it’s so puzzling (and frankly infuriating) to see you emulate creationist tactics. I will also freely admit that as far as I can tell, you have made no errors of fact when you discuss evolution (but as a layperson, I make no great claims to accuracy on scientific minutiae).

     I don’t needle you because of your position on Obama, or because I don’t think you know anything about evolution, Johnnie-boy; I needle you because you’re a lying, weasely ideologue and I really don’t like lying, weasely ideologues. End of story.

     And by the way, you have my deepest thanks for proving me right about you.

168. #168 John Kwok

     January 28, 2009

     @ neo-anti-luddite,

     Pity you can’t carry an intelligent discussion, instead sounding a lot like DaveScot Springer, who dubbed me the “Jekyll and Hyde of Paleobiology” over at Uncommon Dissent, after he read a heated exchange between heddle and myself at Abbie’s blog last year (BTW, heddle and I have patched things up and I regard him as a friend. I hope the same will be true between Abbie and myself.).

     Instead, what I said about SLC definitely applies to you too:

     “An inane, adolescent observation of yours merely reinforces my point regarding Ms. Smith’s occasionally adolescent behavior online, since it has apparently garnered the enthusiastic support of yet another “adolescent”: yourself.”

     However, you’ve just proved twice in row how moronic you are.

     I see you are still enjoying your membership in the Dishonesty Institute IDiot Borg Collective.

     Live Long and Prosper (as a DI IDiot Borg drone),

     P. S. The next time you collect a paycheck from DI, please remind them that both Bill Dembski and DaveScot Springer owe me some expensive Leica and Zeiss Ikon rangefinder camera equipment as just compensation for their inane attacks on me.

169. #169 neo-anit-luddite

     January 28, 2009

     And yet you can’t provide no actual evidence to back up his claims regarding me.

     Thanks for once again proving me right.

170. #170 John Kwok

     January 28, 2009

     P. S. to my last comment:

     Neo-anti-luddite, thanks for demonstrating for a third time, that you’re a moronic DI IDiot Borg drone.

     If you truly believed this (see below), then you wouldn’t be using every opportunity lately to find some way of trying to bash me:

     “I freely admit that you’ve done some good work refuting creationist crap; hell, that’s why it’s so puzzling (and frankly infuriating) to see you emulate creationist tactics. I will also freely admit that as far as I can tell, you have made no errors of fact when you discuss evolution (but as a layperson, I make no great claims to accuracy on scientific minutiae).”

     What the late Billy Martin said about George Steinbrenner and Reggie Jackson, probably applies to you too: “One was born a liar. The other was born convicted”.

     Live Long and Prosper (as a DI IDiot Borg drone),

     John Kwok

171. #171 Tyler DiPietro

     January 28, 2009

     Kwok is kinda reminding me of John A. Davison.

172. #172 John Kwok

     January 28, 2009

     P. S. Neo-anti-luddite,

     You’re absolutely hopeless, did you know that? No wonder why the state of American education has declined so precipitously. You’re demonstrating why as a “sterling” product of such.

     Peace and Long Life (as a DI IDiot Borg drone),

     John Kwok

173. #173 windy

     January 28, 2009

     I thought you said that there was a 1995 paper defining the term “latent evolutionary potential”, but you gave me a reference instead for a 2005 paper. Is this the same one?

     Yes, sorry about that, I meant the 2005 one.

     I just looked again at Payne et al. and noticed that they did not define “latent evolutionary potential”

     That’s what I told you several posts ago- they haven’t defined a new term, it’s just a phrase, so Payne et al do not have any sort of exclusive rights to it!

     So my suspicion that James H. Brown derived this term independently may still be correct. If so, that’s even more of a reason why Abbie shouldn’t have referred to the Payne et al. paper

     Yes, if there’s one thing distinguished scientists hate, it’s people referring to their papers.

174. #174 neo-anti-luddite

     January 28, 2009

     I’m not sure how my last comment got so screwed up, but since I had to click “Submit” three times to get it to post, I guess something got mangled.

     Anyway, your ideological blindness is showing again, Kwokster; as I’ve said before, just because in the evo-creo debate you happen to be our lying sack-o-crap, that doesn’t mean you get a free pass from me regarding following the precepts of honest debate.

     One of the most glaring differnces between us is that you are not honest in your interactions with people you disagree with, while I am not willing to compromise my integrity just because we happen to agree on one particular issue. You are a liar, and I’m treating you like I do any other liar (though I admit those liars are usually creationsits).

175. #175 John Kwok

     January 28, 2009

     @ Tyler DiPietro,

     Doing your best to be yet another Abbie Smith sockpuppet, right:

     “Kwok is kinda reminding me of John A. Davison.”

     Maybe you ought to read again her inane comments, which opened with an absurd, backhanded compliment of the fossil record, and one that sounds so much like Michael Behe’s:

     “”Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     I hate to correct her of this inane observation of hers, but she has ignored in that one comment, in addition to paleobiology, everything from sexual selection to community ecology, and long-term field studies of microevolution at work, such as, for example, the ongoing decades-long elegant work on Darwin’s Finches by evolutionary ecologists Peter and Rosemary Grant.

     Abbie’s blog is widely read by both supporters of evolution and acolytes of organizations like the Dishonesty Institute and AiG. She should remember that the next time she even thinks of writing something as inane as that quote.

     John Kwok

176. #176 neo-anti-luddite

     January 28, 2009

     …and you still haven’t provided a shred of evidence to support your bald-faced lie that I said you “didn’t know what you were talking about” in terms of evolution.

     In the immortal words of Stan Lee:

     ‘Nuff said!

177. #177 John Kwok

     January 28, 2009

     @ windy,

     Obviously you missed the importance of the Payne et al. paper since it is available for free public download. May I suggest that you read it BEFORE COMMENTING again, so then maybe we’ll have an intelligent discussion of it AND remind Abbie what she missed.

     John

178. #178 John Kwok

     January 28, 2009

     @ windy,

     I think “distinguished scientists” like James H. Brown want people to refer to their papers, provided, of course, they’re not a DI IDiot Borg drone lurking over at Uncommon Dissent. Unfortunately, there was one lurker who made an inane comment on that paper, so P Z Myers felt compelled to write an excellent summary of it and post it on his blog.

     You may have missed my note that I alerted a college classmate of mine to the Payne et al. paper – he’s an astrobiologist/planetary geologist – and he thinks it is so interesting, that he intends to mention it in his next public lecture. So if he finds it interesting, then maybe you ought to read it too, instead of reading a distorted commentary from Abbie Smith, and an excellent, but still second-hand, report, from P Z Meyers.

     John

     P. S. I’ll admit my mistakes when I think I’m wrong, but since I’m a graduate of that famous New York City public high school…. (Just kidding about that of course. I just don’t think that I’ve made any mistakes for which I should apologize for in this thread. If you read my commentary elsewhere, however, you’ll find that I am all too willing to acknowledge my mistakes.

179. #179 windy

     January 28, 2009

     Obviously you missed the importance of the Payne et al. paper since it is available for free public download. May I suggest that you read it BEFORE COMMENTING again, so then maybe we’ll have an intelligent discussion of it AND remind Abbie what she missed.

     I have read it. What you fail to realize that the paper in no way precludes discussion of latent evolutionary potential in other contexts. I’m sure Payne, Brown and the other authors would be embarrassed at the suggestion.

     In fact, if you weren’t such a poser on evolutionary biology, you might have realized that the paper is only tangentially related to the issue of evolutionary potential/evolvability – as you yourself noted, they don’t quote any prior literature on it!

180. #180 Tyler DiPietro

     January 28, 2009

     Hey, I’m no biologist, nor do I pretend to be one. Your reasons for calling that quote “inane” seem vague enough for the actual biologists here not to be able to pin them down, anyway. All I see is repetitive and insane behavior a la John A. Davison, right down to the idiotic closing phrase (“I love it so!” versus “_____ is a DI IDiot borg drone”).

     All you’re doing is trolling for her attention, you need to get a life.

181. #181 neo-anti-luddite

     January 28, 2009

     If you read my commentary elsewhere, however, you’ll find that I am all too willing to acknowledge my mistakes.

     Yeah, Johnnie-boy, you’re going to have to provide some evidence to back that claim up, too.

     Anything?

     No?

     Completely unsurprising.

182. #182 neo-anti-luddite

     January 28, 2009

     @neo-anti-luddite

     If I didn’t know what I was talking about, do you think I’d be praised for my comments on evolution and the so-called creation vs. evolution debate by the likes of Frank J, Dave Luckett and Jeff Eyges, among others, over at Panda’s Thumb.

     Johnnie can’t provide an actual quote to back up his implied claim that I said he didn’t know what he was talking about regarding evolution, but he still says with a straight face:

     I just don’t think that I’ve made any mistakes for which I should apologize for in this thread.

     While this last doesn’t count as a lie, since I’m sure the Kwokster doesn’t think that he’s wrong (most likely ever), I’m quite certain that anyone with the slightest shred of intellectual integrity can see from the above quotes that he is in fact a lying, weasley ideologue of a kind with the creationists he condemns.

183. #183 John Kwok

     January 28, 2009

     @ windy,

     Terrific, but maybe you ought to realize that I’m really EXCITED that this paper has given us such important insights into the evolution of body size, especially during the Pre-Cambrian, since I was reminded of our relative ignorance of that during two days of talks I attended at Rockefeller University last spring. Granted this is an initial effort – and the authors acknowledge that – but it is still important for having discovered two “discrete Jumps” – as P Z Myers has noted – in the evolution of body size.

     I’m not going to discount the existence of “latent evolutionary potential”, but here, it is noted in the context of the diversification of clades – the evolution of lineages – over the span of not just hundreds of millions, but also, billions of years. Abbie is merely conflating the issue by making a quick observation on the Payne et al. paper and then jumping on her interest in “latent evolutionary potential” in virology. That, IMHO does a grave disservice to anyone who might have wondered what the fuss is about – and believe me it is quite noteworthy – with regards to the contents of the Payne et al. paper (such as why has an IDiot paid attention to it, commenting on it over at Uncommon Dissent) and why Abbie seems to have a rather flippant, almost adolescent, reaction to it.

     Both you and Tyler should realize that I am not commenting on Abbie’s posting to get her attention. Since hers is a popular science blog read by both evolution supporters and creationists, then she ought to ensure that her comments really pass muster. It’s really incumbent upon her not to make inane remarks like:

     “”Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     or

     “…evolution is an arms race, man”.

     Creationists are going to read these comments AND BELIEVE that she’s really telling the “truth” about evolution. I know she’s quite smart, and may yet be a good scientist. But she better be a responsible one too, commenting accurately on evolutionary biology.

     So, contrary to what Tyler asserts, I am not “trolling for her attention”. I expect her to act responsibly (And I was made aware of that responsibility when I had my online tussle with heddle over at her blog, which caught the attention of DI IDiot Borg drone DaveScot Springer. This was so amusing to Springer that he dubbed me the “Jekyll and Hyde of Paleobiology” and posted a blog entry at Uncommon Dissent in my honor.).

     Let me close with a comment I heard, in private, from Ken Miller. “We’re all in this together”. He doesn’t object to sharing his material with others as long as it serves the overarching goal of defeating ID creationists and other creationists. I suggest that you, Tyler, neo-anti-luddite, and others, including Abbie, bear this in mind. When I saw heddle was getting abused over at PT, I finally thought “Enough is enough” and stepped in, reminding the others that heddle is one of the good guys. So am I. Please treat me as such.

     Respectfully yours,

     John Kwok

184. #184 neo-anti-luddite

     January 28, 2009

     @ Tyler DiPetro

     Oo, snap!

     I’ve got to say, comparing the Kwokster to JAD is old-school cold, but you make a very compelling case.

     Or, more accurately, Johnnie-boy insists on making your case very compelling.

185. #185 W. Kevin Vicklund

     January 28, 2009

     John Kwok, may I suggest you read Abbie’s post, PZ’s post, and the Payne et. al. paper before further commenting? Having read all three several times, it is obvious that you have either not read or you have failed to understand them.

186. #186 John Kwok

     January 28, 2009

     @ Tyler,

     Again, for your benefit, I am reposting this:

     “‘Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.’”

     “I hate to correct her of this inane observation of hers, but she has ignored in that one comment, in addition to paleobiology, everything from sexual selection to community ecology, and long-term field studies of microevolution at work, such as, for example, the ongoing decades-long elegant work on Darwin’s Finches by evolutionary ecologists Peter and Rosemary Grant.”

     In plain English, by making such an inane observation, she foolishly asserts that one can learn as much about evolution by studying HIV-1 in a few weeks, as one can by studying the evolution of lineages over the course of billions of years. But that’s wrong, QUITE wrong. Microbial evolution is really a very small subset of what encompasses evolutionary biology. Evolutionary biology encompasses everything from studying evolutionary developmental biology – better known as “evo – devo” – to sequencing genomic data to determine phylogenetic relationships in molecular systematics, and of course, studying patterns and processes of evolution from the fossil record in paleobiology, and last, but not least, studying microevolution in Darwin’s Finches for decades as an excellent example of evolutionary ecology. It really speaks to her immaturity by making such a flippant comment like that without realizing that others, including nonscientists like yourself. but especially, creationists, will believe that what she is saying is true.

     For similar reasons I am critical of her observation:

     “..evolution is an arms race, man”

     She ignores in that statement the fact that there ample instances of cooperative interspecific behavior documented by generations of behavioral ecologists who have shown the existence of mutualism. It also dismisses the possibility of kin selection at work, and perhaps group selection too, and maybe, just maybe, all of sociobiology as well.

     As someone trained in evolutionary biology, I expect her to act responsibly whenever she posts about it. I’m not, by any means, “trolling for her attention”.

     Respectfully yours,

     John Kwok

187. #187 W. Kevin Vicklund

     January 28, 2009

     Shorter John Kwok: I don’t like how ERV writes, so I’m going to falsely accuse her of not understanding biology. Why is everyone attacking me?

188. #188 John Kwok

     January 28, 2009

     @ W. Kevin,

     I’ve read the Payne et al. paper more than once. That’s how ecstatic I am about it. I have also read critically what P Z Myers and Abbie have written. My criticism of Abbie still stands, however, because she goofed in not indicating the importance of the Payne et al. paper. Why refer to it, even tangentially, via P Z Myers’ excellent summary of it, if she wasn’t going to discuss it at length.

     Respectfully yours,

     John Kwok

189. #189 neo-anti-luddite

     January 28, 2009

     Let me close with a comment I heard, in private, from Ken Miller. “We’re all in this together”. He doesn’t object to sharing his material with others as long as it serves the overarching goal of defeating ID creationists and other creationists. I suggest that you, Tyler, neo-anti-luddite, and others, including Abbie, bear this in mind. When I saw heddle was getting abused over at PT, I finally thought “Enough is enough” and stepped in, reminding the others that heddle is one of the good guys. So am I. Please treat me as such.

     Then start acting like one of the good guys, John. Don’t lie, don’t deliberately misread what people say, and own up to your mistakes.

     Here’s an olive branch from me to you, a little story from my childhood:

     My father is a professor of biochemistry and genetics at a Tier 1 research university, and in a fit of mid-life crisis, he ended up marrying one of his grad students. She made the mistake of taking one of his classes after they were married, and she seemed to think that their relationship would guarantee her a good grade in his class.

     He flunked her.

     You see, my father holds those whom he cares about to a higher standard than everyone else, and while I recognize (very personally, I might add) just how fundamentally crappy that can be, I found that as I grew up, I understood where he was coming from.

     John, I don’t dislike you; I dislike the tactics you have displayed. I’ve been reading and occasionally posting on PT for a number of years, and in that time I’ve found your posts both funny and occasionally informative. I took you at your word when you spoke about evolutionary matters, John, in part because I never saw you write anything inaccurate (as far as I could tell), and in part because I’m a sci-fi geek and I appreciate the Star Trek references.

     Your behabvior in the Obama thread, however, seemed to come straight from the creaotard playbook. I expect that kind of crap from the Fundies. I don’t expect that kind of crap from people who I respect to any degree.

     I admit that I’ve been even more harsh with you than I have been with the various creationists I’ve hounded, but damn it, man, you lied! You know better, because you are better!

     At least I thought you were.

     I will say this one last time, without venom or snarkiness, and I hope that you take as I mean it:

     I don’t care whether you support Obama or not; all I care aobut is whether you are honest in your positions and in your statements of fact. If you can admit that you were in error regarding Obama’s birth certificate, I will take you at your word again.

     I know you don’t care what I think of you, John, but believe it or not, I care what other people think of you, if only because on this very important issue, you represent not just yourself when you speak, you represent us all. In this areana, you are absolutely correct to note that we are all in this together.

     And wihtout snark this time, let me say once more:

     “Why don’t we all agree to just get along.”

     I’ll stop pestering you until you give me reason to start again, John, whether you admit your lies or not. But I really hope you admit that error, because I don’t like having to Venn you in with the creotards.

190. #190 John Kwok

     January 28, 2009

     @ W. Kevin Vicklund,

     Thanks for demonstrating that you’re merely a trolling Abbie Smith sockpuppet:

     “Shorter John Kwok: I don’t like how ERV writes, so I’m going to falsely accuse her of not understanding biology.”

     If she could be as funny as Stephen Colbert, then I couldn’t care less. BUT I EXPECT HER TO BE ACCURATE. It’s not her writing style that I’m criticizing, but instead, it is its content.

     John Kwok

191. #191 john Kwok

     January 28, 2009

     @ neo-anti-luddite,

     I wish I didn’t have to say this:

     I wish you well in assuming room temperature soon.

     John Kwok

192. #192 W. Kevin Vicklund

     January 28, 2009

     Because she was referring to the first half of PZ’s post, which did a very good job of describing a concept, rather than the second half, which did a very good job of summarizing a paper that utilized a concept. Payne’s paper cited other papers. Should we castigate PZ for not discussing those papers? Your objections are, quite frankly, inane.

193. #193 neo-anti-luddite

     January 28, 2009

     So, just for the record, John, was your last post at me (the one at 5:55 pm) in response to my last post to you (the one at 5:52 pm) or my second-to-last post (the one at 5:18 pm)?

194. #194 W. Kevin Vicklund

     January 28, 2009

     If you actually think ERV was inaccurate, then I go back to my initial suggestion: you clearly don’t understand what was written.

     But I think you know that ERV is accurate, and you are just trolling.

195. #195 John Kwok

     January 28, 2009

     @ W. Kevin,

     I am criticizing Abbie for not recognizing the important discovery made by Payne et al. that Myers devoted most of his post to. In fact, let me remind you what Myers said in closing:

     “The way the creationists have abused that is by pretending that this implies that the evolution of the eukaryotes and of multicellularity had to have been purposeful events. This is simply not true. All this is saying is that the limits of growth are properties of both organismal and environmental constraints, and that we can map those out by looking at the fossil record.”

     Myers wrote the post as a rebuttal to the inane commentary about the Payne et al. paper posted over at Uncommon Descent:

     http://www.uncommondescent.com/biology/preexisting-evolutionary-potential-now-a-scientific-fact/

     Your interpretation of Myers’ reason for writing his blog entry about “latent evolutionary potential” is absolutely incorrect. Myers’ reason for his blog entry was to write accurately about “latent evolutionary potential” as seen by Payne et al. in their PNAS paper. So, again, why did Abbie refer to Myers’ blog if she wasn’t going to comment extensively too on the Payne et al. paper? What she did instead was dubious and frankly, also disingenuous.

     John Kwok

196. #196 John Kwok

     January 28, 2009

     @W. Kevin,

     I think you need a course in reading comprehension. May I suggest a worthy teacher in oen Frank McCourt:

     “But I think you know that ERV is accurate, and you are just trolling.”

     @neo-anti-luddite,

     If you can demonstrate that you’re as funny as Frank McCourt, then I’ll apologize for my previous post. But I haven’t seen anything from you that’s as funny as anything I’ve heard from my favorite high school teacher.

197. #197 John Kwok

     January 28, 2009

     @W. Kevin,

     If you’ve read my posts carefully here, then you ought to realize that I’ve given a quick synopsis on some of the important work done in paleobiology since the mid 1970s and how and why it is relevant to the Payne et al. paper. For example, I observed that Payne et al. collected data in a manner similar to what Sepkoski did in his classic papers from the mid and late 1970s and early 1980s. Most of the authors of the Payne et al. paper are either paleobiologists, like the lead author, or are ecologists familiar with the paleobiological literature, such as, most prominently, James H. Brown.

     So I hate to shatter your illusion, my dear Abbie Smith sockpuppet, but I’m not the one trolling. If anyone is, it is you.

     John Kwok

     P. S. I am certain Frank McCourt, who was my high school creative writing teacher, would agree with me. Incidentally his current wife is a fan of evolutionary biology.

198. #198 neo-anti-luddite

     January 28, 2009

     So this:

     Let me close with a comment I heard, in private, from Ken Miller. “We’re all in this together”. He doesn’t object to sharing his material with others as long as it serves the overarching goal of defeating ID creationists and other creationists. I suggest that you, Tyler, neo-anti-luddite, and others, including Abbie, bear this in mind. When I saw heddle was getting abused over at PT, I finally thought “Enough is enough” and stepped in, reminding the others that heddle is one of the good guys. So am I. Please treat me as such.

     …was just another one of your lies.

     That’s a pity.

199. #199 John Kwok

     January 28, 2009

     @ neo-anti-luddite,

     I’m not a Christian, but I am willing to forgive and to forget. However, YOU HAVE NOT given me any credible reason to do so.

     You can start by apologizing for calling me a liar in this thread, not once, but many times. You can also add that my criticisms of Abbie Smith have merit, especially now that I have provided a link to that inane Uncommon Dissent posting on the Payne et al. paper that was so incredulous, that P Z Myers felt compelled to post an accurate summary of the Payne et al. paper over at his blog.

     When you do that, then maybe I’ll be willing to stand by what I said in that quote of mine. But until then, you better start demonstrating your worthiness – and I’m not being sanctimonious, but rather, angry, very angry, at you – for me to apologize for my unkind remark about you that is posted above.

     John Kwok

200. #200 tomh

     January 28, 2009

     John Kwok wrote:
     If you read my commentary elsewhere, however, you’ll find that I am all too willing to acknowledge my mistakes.

     That may be true for some “commentary” somewhere, but on the PT thread “Nature Endorses Obama” there are no less than 47 instances where you were untruthful/in error/and-or willfully contradicting known facts. Each time you were shown indisputable evidence showing you to be in error, yet not once did you acknowledge your error. None of this was opinion about politics, it was always a factual matter. And now you claim that you are all too willing to acknowledge errors. I’m afraid I would have to see it to believe it.

201. #201 john Kwok

     January 28, 2009

     @ tomh,

     Hope you’ve noted too the endorsements I have received from the likes of Frank J, Dave Luckett and Jeff Eyges, among others, over at PT recently. Have you tablulated those as well? Need I remind you that I regard Obama now as my president too? Or have you forgotten that? He will get my support as long as he governs in a manner that I believe is worthy of it.

     Too bad you’re so hung up about my political commentary that you seem incapable of deciding whether or not I am correct in criticizing Abbie Smith, especially for failing to recognize – unlike her mentor P Z Myers – the importance of the Payne et al. paper.

     John Kwok

202. #202 John Kwok

     January 28, 2009

     @ neo-anti-luddite,

     I am not going to wait an eternity for you to apologize and to endorse my fair criticism of Abbie’s commentary. If you want me to apologize for my own unkind remark towards you, then I expect you to follow my advice as noted in my most recent post addressed to you.

     John Kwok

203. #203 Anton Mates

     January 28, 2009

     John Kwok,

     If you really paid attention to how the authors collected the data, then you’ll see that they were referring to CLADES not microbial species (look at their methods section).

     Since when did evolution not apply to CLADES?

     Two paragraphs after the one Abbie quoted, PZ says:

     You’ve probably heard of the endosymbiote hypothesis: eukaryotes are the product of a merger of multiple prokaryotic organisms into a single whole. Single celled organisms combined, with different specializations — organelles in our cells called mitochondria, for instance, are thought to be descendants of an incorporated prokaryote. Our mitochondria have the primary function of burning carbon and oxygen to produce energy. This was “latent evolutionary potential” that could be exploited by eukaryotes as oxygen availability rose. And so, following the rise of increasing oxygen concentrations, the size of some eukaryotes staggered upwards to a new maximum.

     Are unicellular prokaryotes and eukaryotes not microbes?
     Is a heritable increase in the size of a certain lineage not evolution?
     How is this not referring to microbial evolution?

     In plain English, by making such an inane observation, she foolishly asserts that one can learn as much about evolution by studying HIV-1 in a few weeks, as one can by studying the evolution of lineages over the course of billions of years.

     No, in plain English, she does not assert that. She says that there are some facts about evolution that the HIV-1 researcher can discover in a few weeks, whereas the researcher studying large organisms needs millions of years of observations to discover them. Which is quite true. Or do you disagree that viruses, in many ways, evolve faster than, say, mammals?

     She does not, of course, mean that big-stuff-biologists need to wait around for millions of years before they figure this out. In fact, I’m almost sure she’s aware that the science of biology is less than one million years old. But I can see how you might think differently, since you apparently believe she’s a lunatic.

     For similar reasons I am critical of her observation:
     “..evolution is an arms race, man”
     She ignores in that statement the fact that there ample instances of cooperative interspecific behavior documented by generations of behavioral ecologists who have shown the existence of mutualism. It also dismisses the possibility of kin selection at work, and perhaps group selection too, and maybe, just maybe, all of sociobiology as well.

     Oh, for the love of…you’re not even trying anymore, are you?

     Here, I’ll play along. Abbie’s blog subtitle claims that “If we’re made in Gods image, God’s made of gag, pol, and env.” Yet she has no theological justification whatsoever for claiming that the supreme being is, or could be, composed of these three proteins!! Clearly she knows nothing about biology.

     Yeesh.

     And yes, I’m an Abbie Smith sockpuppet. In fact, the entire Scienceblogs commenter community consists of Abbie Smith and a random name/email generator.

204. #204 John Kwok

     January 28, 2009

     @ Anton

     So what prompted P Z Myers to write about the Payne et al. paper in the first place in his blog entry?

     He admitted that he wrote it in response to this:

     http://www.uncommondescent.com/biology/preexisting-evolutionary-potential-now-a-scientific-fact/

     Myers may have put a “spin” on it, emphasizing aspects of cellular and developmental biology, but again, let me note his rationale for writing his post, as he noted in the closing paragraph:

     “The way the creationists have abused that is by pretending that this implies that the evolution of the eukaryotes and of multicellularity had to have been purposeful events. This is simply not true. All this is saying is that the limits of growth are properties of both organismal and environmental constraints, and that we can map those out by looking at the fossil record.”

     I think you too need to take a private reading comprehension course from Frank McCourt.

     Last, but not least, thanks for admitting that you, too, are yet another Abbie Smith sockpuppet (BTW, I knew that already.).

     John Kwok

     P. S. Congratulations. So you know what a clade is. Could it be possible that somewhere, in your rather intellectually-challenged mind, that you are refusing to admit that I, a former paleobiologist, could be right in my criticisms of Abbie Smith’s commentary. Maybe you should start thinking seriously of such a possibility.

205. #205 John Kwok

     January 28, 2009

     @ Anton,

     You are in dire need of a reading comprehension course. Go ask McCourt if he will accept you as his student.

     Again, here’s what I said in reply to a similar comment from Tyler, which you deliberately left out:

     “I hate to correct her of this inane observation of hers, but she has ignored in that one comment, in addition to paleobiology, everything from sexual selection to community ecology, and long-term field studies of microevolution at work, such as, for example, the ongoing decades-long elegant work on Darwin’s Finches by evolutionary ecologists Peter and Rosemary Grant.”

     “In plain English, by making such an inane observation, she foolishly asserts that one can learn as much about evolution by studying HIV-1 in a few weeks, as one can by studying the evolution of lineages over the course of billions of years. But that’s wrong, QUITE wrong. Microbial evolution is really a very small subset of what encompasses evolutionary biology. Evolutionary biology encompasses everything from studying evolutionary developmental biology – better known as “evo – devo” – to sequencing genomic data to determine phylogenetic relationships in molecular systematics, and of course, studying patterns and processes of evolution from the fossil record in paleobiology, and last, but not least, studying microevolution in Darwin’s Finches for decades as an excellent example of evolutionary ecology. It really speaks to her immaturity by making such a flippant comment like that without realizing that others, including nonscientists like yourself. but especially, creationists, will believe that what she is saying is true.”

     I didn’t say that she can’t learn something about evolution from HIV-1; of course she can. But she’s mistaken in trying to generalize by saying that “Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     That’s not just foolish, but it is also quite immature of her to make such an inane declaration.

     Again, microbial evolution IS BUT A SMALL SUBSET of evolutionary biological research. I hope you are capable at least of comprehending that.

     Since hers is a blog popular with both evolution opponents and those who accept its scientific validity, I do expect her to be more responsible in her commentary in the future.

     John Kwok

     P. S. I knew already that you’re an Abbie Smith sockpuppet. Why? You behave like the usual Dishonesty Institute IDiot Borg drone in your inane reasoning. Maybe you’ll wise up just once to realize that this former paleobiologist has some valid criticisms to note with regards to Abbie’s inane, and adolescent-sounding, commentary.

206. #206 Anton Mates

     January 28, 2009

     Id respond, but I have a hard nights work ahead of me revising copies of Our Dear Leader’s birth certificate. Cant spare the time, alas.

     –Abbie

207. #207 John Kwok

     January 28, 2009

     @ Anton,

     Now that is something I’d expect Frank McCourt would say, if he read this:

     “Id respond, but I have a hard nights work ahead of me revising copies of Our Dear Leader’s birth certificate. Cant spare the time, alas.

     –Abbie”

     Maybe there’s hope for you after all. Hahahaha!!!

     John

208. #208 John Kwok

     January 28, 2009

     @ Anton,

     Oh and please tell Abbie that I’ll be dedicating my first novel to her. I’ll even send her a signed copy.

     John

209. #209 tomh

     January 28, 2009

     John Kwok wrote:
     …you’re so hung up about my political commentary

     This is pathetic. There is NO political commentary involved. There is only you lying about factual matters, and refusing to admit it when confronted with evidence.

     Have you tablulated those as well?

     You mean I should tabulate the praise you received from a few random commenters about some review you wrote on Amazon to balance out the large number of outright lies you told on PT? And that’s related how?

210. #210 Tyler DiPietro

     January 28, 2009

     LOL! Even the fucking hint that he got attention from Abbie is enough to make the guy cream his pants.

211. #211 John Kwok

     January 28, 2009

     @ tomh,

     I’ve written a lot of Amazon reviews of evolutionary biology and creationist books. Those reviews are far more important than my political commentary, and I have had ample praise not just from a “few random commentators” at PT, but from others as well. I’m not going to start naming names, however, since I’m not interested in giving you more ammunition for your obvious hatred of me.

     The election was held on November 4th. Today is January 28th. Barack Obama is – and has been for eight days – my president. I am delighted with many of his cabinet picks, especially eminent marine ecologist Jane Lubchenco as the head of NOAA. Two of his most trusted advisors, David Axelrod and Eric Holder, are prominent alumni of our high school alma mater. What more can I say to convince you of my sincerity? Obviously not a single word….

     And that’s a pity.

     John Kwok

212. #212 John Kwok

     January 28, 2009

     @ Tyler,

     Thanks for demonstrating that you’re a real, inane jerk, like those I have read over at Uncommon Dissent and at Amazon.com, who are zealous advocates of creationism, especially ID creationism.

     Why don’t you spend your time wisely by learning something about paleobiology and evolutionary ecology? If you did, then maybe you might realize that my criticisms of Abbie’s inane commentary have merit.

     Meanwhile, I trust you’ll enjoy your newly earned membership in the Dishonesty Institute IDiot Borg Collective.

     Live Long and Prosper (as a DI IDiot Borg drone),

     John Kwok

213. #213 tomh

     January 28, 2009

     John Kwok wrote:
     Two of his most trusted advisors, David Axelrod and Eric Holder, are prominent alumni of our high school alma mater. What more can I say …

     No one cares. You’re a proven liar, that’s enough for me.

214. #214 W. Kevin Vicklund

     January 28, 2009

     If you’ve read my posts carefully here, then you ought to realize that I’ve given a quick synopsis on some of the important work done in paleobiology since the mid 1970s and how and why it is relevant to the Payne et al. paper. For example, I observed that Payne et al. collected data in a manner similar to what Sepkoski did in his classic papers from the mid and late 1970s and early 1980s. Most of the authors of the Payne et al. paper are either paleobiologists, like the lead author, or are ecologists familiar with the paleobiological literature, such as, most prominently, James H. Brown.

     Yes. So what? All that demonstrates is that Payne et. al. properly used the term in their paper. No one involved in this discussion, not PZ, nor ERV, nor anyone on this thread disputes that. What it doesn’t do is prove that ERV is using the term wrong. You have shown no evidence that ERV is wrong to use ‘latent evolutionary potential’ the way she has. Name-dropping doesn’t prove it either. Nothing in Payne’s paper demonstrates that she uses it inaccurately, nor does anything in PZ’s post. You have presented no evidence of your central claim.

     ERV doesn’t engage much in nuance. Someone who utilizes nuance would be more inclusive. All of your other complaints revolve around this fact. Thus, all these complaints are due not to inaccuracies, but rather to her writing style. I don’t care if you don’t like her writing style – I understand that it’s not for everyone, and you are entitled to criticize her if you see fit. But you’re hiding what would be an honest disagreement over style behind a false accusation in order to denigrate her. This is dishonest, vindictive behavior.

215. #215 windy

     January 28, 2009

     I’ll admit my mistakes when I think I’m wrong

     You have made some fleeting nods in that direction but you seem to be incapable of learning from your mistakes. You were wrong about the Qian paper and HGT, wrong about Lenski and quasispecies, etc, but that does not deter you in the slightest, you just come up with a new horrible scientific transgression that Abbie must have committed.

     Myers’ reason for his blog entry was to write accurately about “latent evolutionary potential” as seen by Payne et al. in their PNAS paper.

     So let me get this straight, PZ using “stumbling drunks” and “venomous crocoducks” to illustrate an evolutionary point is perfectly in accord of your high standards whereas using HIV evolution to illustrate a point about evolution is “disingenuous” and “inane”?

216. #216 Aureola Nominee, FCD

     January 28, 2009

     Keep squirming, John. Did President Obama say, in his victory speech, that “ours did not become a great nation until his election”? Yes or no?

217. #217 W. Kevin Vicklund

     January 28, 2009

     To expand on the last paragraph of my previous comment, when you wrote the following in your second comment on this thread:

     P. S. I was underwhelmed by that Abbie Smith post, which, sadly, seemed a typical example of some of her more adolescent behavior that she does show occasionally at ERV.

     I have no problem with you writing that. It is simply an expression of opinion, relevant to the topic of the thread. While I may disagree (or not), it is honest, forthright, and a potentially valid criticism.

     It is the events immediately following that post that I object to. You made false accusations as to her knowledge, and have offered nothing to support those accusations. Not only that, but I believe that she grokked the implications of the paper more fully than you have. Not only does the paper tell us some important stuff about how evolution has proceeded in the past, but the same concepts can be applied to modern life, in real time, life-and-death situations. In ways that impact lives on a personal level. This visceral importance is much more likely to sway hearts and minds. Both types of knowledge are important, of course, but what ERV wrote about is what will convince the person on the street that it matters. By all means, criticize her for her style, if you think it’s off-putting. But to claim she’s wrong and to disparage her knowledge without offering any supporting evidence is to engage in the very tactics we ought to be decrying.

218. #218 neo-anit-luddite

     January 29, 2009

     @ neo-anti-luddite,

     I’m not a Christian, but I am willing to forgive and to forget. However, YOU HAVE NOT given me any credible reason to do so.

     You can start by apologizing for calling me a liar in this thread, not once, but many times.

     And yet you have lied at least once in this very thread, with no need to reference any other threads or posts. You lied, ergo you are a liar. This is not some sort of ad homenim insult, John, it’s merely a statement of fact.

     You can also add that my criticisms of Abbie Smith have merit, especially now that I have provided a link to that inane Uncommon Dissent posting on the Payne et al. paper that was so incredulous, that P Z Myers felt compelled to post an accurate summary of the Payne et al. paper over at his blog.

     First off, whether your criticisms of Abbie Smith have merit or not is in no way supported by the link you provided; all that proves is that the UD crowd are a bunch of idiots.

     We already knew that.

     Second of all, my opinion of the merit of your criticisms has no bearing on their validity either. That you seem to crave such validation from an admitted layperson is interesting to say the least, especially in light of the fact that at least one actual working scientist (Abbie) obviously disagrees. Argument from authority is only a fallacy if one isn’t an authority on the subject in question.

     So your demand seems more like some sort of petty dominance game than anything else. You know, the kind kids in middle school like to play.

     When you do that, then maybe I’ll be willing to stand by what I said in that quote of mine. But until then, you better start demonstrating your worthiness – and I’m not being sanctimonious, but rather, angry, very angry, at you – for me to apologize for my unkind remark about you that is posted above.

     Once again, John, either your reading comprehension skills are extremely poor, or you are lying. Again. It’s getting hard to tell the difference, really.

     I don’t want you to apologize for the unkind remark about me that you posted above. By all means, point out where I demanded, asked, or even implied that I was looking for an apology from you. You can’t do it, John, because I never asked you to apologize for anything, just like I never claimed you didn’t know what you were talking about when you speak about evolution.

     All I did was ask you to finally, at long last, admit that you were wrong when you claimed that Obama’s citizenship was suspect. And you were wrong, John. Verifiably, empirically wrong. You’ve stopped spouting that drivel, true, but you’ve never admitted to that error (or any other that I’ve seen you make).

     As I said before, your opinion of me is utterly irrelevant. So are your insults.

     But apparently mine aren’t irrelevant to you.

     You see, the reason your insults have no impact on me is because they are laughably false. It’s like a five-year-old calling me a poopie-head; I have absolutely no uncomfortable suspicion that any of the insults you fling at me might be accurate. But obviously some part of you recognizes your own lies or you wouldn’t get angy at me – “very angry” even – for calling you a liar.

     It wouldn’t bother you at all if you didn’t know it was true, John.

     I am not going to wait an eternity for you to apologize and to endorse my fair criticism of Abbie’s commentary.

     I’m afraid you’re wrong yet again, John; you will indeed wait an eternity for me to apologize to you for accurately desccribing you as a liar.

     If you can actually prove that your criticism is of Abbie is vaild, however, I’ll admit it. But like so many of the things you claim, John, you just don’t seem capable of backing it up.

     And now you’re becoming both redunadant and boring. The next time you spout some crap on a new thread, I’ll happily shove your skeletons into the light for all to see, but I think my work on this thread is done.

     Good night, John. Sleep well.

219. #219 Robin

     January 29, 2009

     DiPietro:

     All you’re doing is trolling for her attention, you need to get a life.

     Clearly after a week of posting virtually non-stop this is true. I would say he needs medical attention as well…

220. #220 Robin

     January 29, 2009

     Terrific, but maybe you ought to realize that I’m really EXCITED that this paper has given us such important insights into the evolution of body size, especially during the Pre-Cambrian, since I was reminded of our relative ignorance of that during two days of talks I attended at Rockefeller University last spring. Granted this is an initial effort – and the authors acknowledge that – but it is still important for having discovered two “discrete Jumps” – as P Z Myers has noted – in the evolution of body size.

     The problem with your argument, John, is that while you may indeed be excited by the implication of the PNAS research, the fact is Ms. Smith is under NO OBLIGATION to feel the same way. And even if she does feel the same way, she is under NO OBLIGATION to write about it. The particular blog topic that you are having a childish meltdown over doesn’t even address this paper, and while she certainly addresses subjects that the paper addresses, again she is under NO OBLIGATION to even reference the paper, let alone go into a lengthy discussion of it. The fact that you feel her presentation is immature is irrelevant. I can’t say that I’m all that fond of your presentation, but quite frankly such is irrelevant to the fact that your argument holds no merit.

221. #221 Robin

     January 29, 2009

     I’ve read the Payne et al. paper more than once. That’s how ecstatic I am about it. I have also read critically what P Z Myers and Abbie have written. My criticism of Abbie still stands, however, because she goofed in not indicating the importance of the Payne et al. paper. Why refer to it, even tangentially, via P Z Myers’ excellent summary of it, if she wasn’t going to discuss it at length.

     I’d like to think she did it because she knew it would bend you out of shape, but something tells me that isn’t that case. I’m betting however she did it because it had little to do with the point she made. That you feel she overlooked (lacking the expertise to understand the significance of the paper) the responsibility to address the PNAS paper simply because her point tangentally touches upon the research presented in the paper is…how should I put this…irrelevant. You are welcome to start your own blog and write verbosely on the subjects you want to write about; Ms. Smith, OTOH, gets to write about what she wants to write about on her blog with no obligations to reference ANYTHING if she so chooses. That you feel her choices damage her credibility as a serious scientist is of course your opinion, but your opinion is (as evidenced hereon) not shared universally in the scientific community. I for one find her writing style and choices of subjects, not to mention her referencing and explanatory capabilities, exceptionally good and entertaining and thus find her to be quite credible scientifically. Now I’m sure you can drop some fancy name of someone that you think somehow gives your opinion some added weight, but quite frankly such tactics merely make you look desperate and insecure and I find nothing remotely authoritative about your opinion in this particular thread.

222. #222 John Kwok

     January 29, 2009

     @ Robin,

     Ask yourself why Abbie would ignore the Payne et al. paper, especially when it garnered the attention of an IDiot poster over at Uncommon Descent and the reaction was so ridiculous, that P Z Myers felt compelled to write an entire blog entry about what that IDiot missed with regards to the Payne et al. paper. Why do you think PNAS made this paper available for free public download? Perhaps because they recognize its potential importance as one of the most important papers on evolution published this year?

     As I noted yesterday with regards to P Z Myers’ rationale for commenting on the Payne et al. paper:

     “He admitted that he wrote it in response to this:

     http://www.uncommondescent.com/biology/preexisting-evolutionary-potential-now-a-scientific-fact/”

     Ordinally I agree with you that Abbie is a fine commentator, BUT she needs to be more responsible in her posting lest creationists – and those who are not scientifically literate – accept as “gospel” truth:

     “Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     or this:

     “..evolution is an arms race, man.”

     It is not a matter of her “bending me out of shape”. It is however, an obligation that I DO EXPECT OF HER to be as accurate as possible before making a post pertaining directly to science. I couldn’t care less if she tried to emulate a comedian like Stephen Colbert or a funny memoirist like Frank McCourt, but she really ought to strive to getting her science right, or don’t bother commenting on it at all, period.

     John Kwok

223. #223 John Kwok

     January 29, 2009

     @ Robin,

     There’s a typo to one of my sentences above, which I am correcting now:

     Ordinarily I agree with you….

     Actually that sounds awkward, so am rephrasing it as,

     Usually I will agree with you that Abbie is a fine commentatior…..

     John

     P. S. I am a former paleobiologist who has acquired too extensive knowledge in evolutionary ecology. I think you should heed my criticisms which are not meant to bash Abbie, but rather instead, to encourage her to do the best possible job she can.

224. #224 Robin

     January 29, 2009

     Ask yourself why Abbie would ignore the Payne et al. paper, especially when it garnered the attention of an IDiot poster over at Uncommon Descent and the reaction was so ridiculous, that P Z Myers felt compelled to write an entire blog entry about what that IDiot missed with regards to the Payne et al. paper. Why do you think PNAS made this paper available for free public download? Perhaps because they recognize its potential importance as one of the most important papers on evolution published this year?

     I know EXACTLY why she didn’t reference the PNAS paper – it was unnecessary to reference it to get her point across. Pure and simple.

     As I noted yesterday with regards to P Z Myers’ rationale for commenting on the Payne et al. paper:

     “He admitted that he wrote it in response to this:

     http://www.uncommondescent.com/biology/preexisting-evolutionary-potential-now-a-scientific-fact/“

     Which is great – that was HIS point for writing what HE wrote. It wasn’t Ms. Smith’s point, however, and I’m sorry John, but she wasn’t writing it to appease *your* particular excitement about the PNAS paper either. Her reason for writing her piece had nothing to do with the ID nonsense. And guess what? She didn’t *have* to address it since PZ already did a fine job of trashing that ID nonsense. But what you don’t seem to understand is that even if PZ hadn’t addressed the ID nonsense, Ms. Smith would still not be obligated to do so. I can’t fathom how you seem not to understand this. She can write about anything she wants to, John, and doesn’t need (and apparently could care less about) your approval to do so.

     Ordinally I agree with you that Abbie is a fine commentator, BUT she needs to be more responsible in her posting lest creationists – and those who are not scientifically literate – accept as “gospel” truth:

     “Gawd I love doing HIV-1 research. Stuff that takes big-stuff-biologists millions of years to watch, we can figure out in a few weeks.”

     or this:

     “..evolution is an arms race, man.”

     No, John, she doesn’t. She doesn’t need to do anything. Period. She is not under ANY obligation to do anything as far as posting on her blog is concerned. Period. However, specifically, She CERTAINLY isn’t under any obligation to meet your innane standards and seek your approval. That you happen to think she’s doing a disservice to the scientific community and offering opportunity to the ID crowd is not an opinion shared by other scientists or lay readers, so your point is really quite moot. You can believe we are all wrong, but frankly it’s quite clear the majorty doesn’t find your opinion credible on the subject and is going to dismiss it, particularly since you haven’t supported your claims.

     It is not a matter of her “bending me out of shape”. It is however, an obligation that I DO EXPECT OF HER to be as accurate as possible before making a post pertaining directly to science. I couldn’t care less if she tried to emulate a comedian like Stephen Colbert or a funny memoirist like Frank McCourt, but she really ought to strive to getting her science right, or don’t bother commenting on it at all, period.

     John Kwok

     The only problem here is that her science is correct as far as her particular point is concerned. Again, that you feel that her lack of referencing the PNAS paper was an amateurish oversight is your opinion, not (as exemplified by the counter opinions hereon) a fact. And she didn’t get the concept of convergent evolution wrong, in fact she made a quite deft real-world example of why such is so important. Such did not require her to mention ANYTHING about the PNAS paper, and guess what? She didn’t mention it. She used PZ’z comments to lead into her point. Nothing wrong with that.

     Further, her comments about HIV-1 research demonstrating in weeks what Big-Stuff-Biologists must wait millions of years for and evolution being an arms race were spot on. That you feel that those comments are all inclusive rather than being generalizations about aspects of evolutionary research is your reading comprehension problem. The rest of us get her point it seems and understand that such is true in that specific subset of evolutionary research. You can argue all you want that such is an immature way of stating her point, but then you are commenting on her style, not the accuracy of her content. Since most of us seem to be quite clear on the point she was making, it appears that the accuracy of her statements cannot be a problem.

225. #225 John Kwok

     January 29, 2009

     @ Windy,

     Oh boy, can’t you see Myers was trying to be funny in his post, before he launched into a substantial, quite accurate, summary of the Payne et al. paper, while also making some pertinent observations relevant to cellular and developmental biology too?

     REPEAT AFTER ME, PLEASE. Myers wrote his rebuttal in response to this:

     http://www.uncommondescent.com/biology/preexisting-evolutionary-potential-now-a-scientific-fact/”

     I think I’ve noted ALREADY in a series of rebuttals to SLC yesterday that the Payne et al. paper follows in the grand tradition of papers written by such eminent paleobiologists as Stephen Jay Gould, J. John Sepkoski, David Raup and James W. Valentine (who was the PNAS editor of the Payne et al. paper) back in the mid 1970s to early 1980s. Maybe you ought to search the literature for the appropriate references – which I don’t have unfortunately – and start reading these papers.

     You might also search for “incumbent replacement” and Rosenzweig and McCord’s paper on that, since when you find it – it was published in Paleobiology back in the early 1990s – you might recognize my name listed in its Acknowledgements Section.

     I find it hysterical that I’m arguing with someone who hasn’t even tried to read the paleobiological literature, and that I am remembering all of this even though I have been out of the field since the early 1990s.

     John Kwok

226. #226 Robin

     January 29, 2009

     There’s a typo to one of my sentences above, which I am correcting now:

     Ordinarily I agree with you….

     Actually that sounds awkward, so am rephrasing it as,

     Usually I will agree with you that Abbie is a fine commentatior…..

     John

     Thank you John. I noticed that I inferred what you meant, but I appreciate the correction.

     P. S. I am a former paleobiologist who has acquired too extensive knowledge in evolutionary ecology. I think you should heed my criticisms which are not meant to bash Abbie, but rather instead, to encourage her to do the best possible job she can.

     I am well-aware of your credentials from reading your posts both here and on PT. That said, I do not find your criticisms valid in this instance.

227. #227 John Kwok

     January 29, 2009

     @ Robin,

     Sorry, but your increasingly inane defense of Abbie’s ignorance of what Payne et al. were trying to say with regards to “latent evolutionary potential” misses the point THAT IT IS POTENTIALLY ONE OF THE BEST PAPERS ON EVOLUTION PUBLISHED THIS YEAR and that Abbie made a major goof by not commenting on it accurately.

     John

228. #228 Robin

     January 29, 2009

     Sorry, but your increasingly inane defense of Abbie’s ignorance of what Payne et al. were trying to say with regards to “latent evolutionary potential” misses the point THAT IT IS POTENTIALLY ONE OF THE BEST PAPERS ON EVOLUTION PUBLISHED THIS YEAR and that Abbie made a major goof by not commenting on it accurately.

     John, for the umpteenth time, she didn’t refer to the PNAS paper. There’s NO WAY you can assertain Ms. Smith’s knowledge of the paper when she didn’t refer to it at all. You are being disingenuous at best. Her use of “latent evolutionary potential” was perfectly accurate and in no way hindered by not refering to the PNAS paper. Further (as I and others have noted) she isn’t obligated to address anything about the paper, regardless of the fact that you happen to think it’s the best work since Star Trek: The Wrath of Khan. It matters not one wit that she didn’t note that she had it framed and has it hung both in her bed room and her lab or that she dismissed it as merely another interesting piece of research. She is not obligated to note it at all since it would have added nothing to her particular point. That you do not understand her point and her work enough to appreciate such is not her shortcoming.

229. #229 John Kwok

     January 29, 2009

     @ Robin,

     You’re right only in the sense that she referred to P Z Myers’ hysterically funny observation on “latent evolutionary potential”. But if she was going to do that, then WHY FOR HEAVEN’S SAKE DIDN’T SHE RECOGNIZE HOW IMPORTANT THE PAYNE ET AL. PAPER IS.

     Contrary to what others have asserted here, Myers did not decide to write about “latent evolutionary potential” and then, at random, choose the Payne et al. paper to provide a suitable example. NO, HE WROTE ABOUT IT in response to a rather silly, quite stupid, Uncommon Dissent IDiot “review” of the Payne et al. paper.

     I showed this paper to a college classmate of mine, an astrobiologist/planetary geologist – whom you may have heard of (but I’m not going to mention the scientist’s name lest people accuse me again of “name dropping”) – and he recognizes that is very interesting, and SO INTERESTING that he intends to mention it during a forthcoming public lecture. Now if an astrobiologist/planetary geologist could find Payne et al. interesting, then why not a virology graduate student too?

     John

230. #230 Robin

     January 29, 2009

     You’re right only in the sense that she referred to P Z Myers’ hysterically funny observation on “latent evolutionary potential”. But if she was going to do that, then WHY FOR HEAVEN’S SAKE DIDN’T SHE RECOGNIZE HOW IMPORTANT THE PAYNE ET AL. PAPER IS.

     Simple – because she didn’t need to to make her point.

     Contrary to what others have asserted here, Myers did not decide to write about “latent evolutionary potential” and then, at random, choose the Payne et al. paper to provide a suitable example. NO, HE WROTE ABOUT IT in response to a rather silly, quite stupid, Uncommon Dissent IDiot “review” of the Payne et al. paper.

     I have read every comment posted here and can’t find one wherein someone implies they think that Myers choose the PNAS paper at random. OTOH I see a great number of posts noting that Myers wrote his piece specifically as a response to the UD piece, so I’m not sure where you got the former impression.

     I showed this paper to a college classmate of mine, an astrobiologist/planetary geologist – whom you may have heard of (but I’m not going to mention the scientist’s name lest people accuse me again of “name dropping”) – and he recognizes that is very interesting, and SO INTERESTING that he intends to mention it during a forthcoming public lecture. Now if an astrobiologist/planetary geologist could find Payne et al. interesting, then why not a virology graduate student too?

     You’ve mentioned this multiple times now, and as happy as I am that your former classmate found the paper fascinating and appears to share the same level of enthusiasm about it that you have, John, the anecdote is really a non-sequitur. No one is disputing that the paper is compelling and that some people are enthusiastic about the research’s implications. That said, just because it is fascinating doesn’t mean everyone has to note it, jump up and down about it, and/or write about it. I understand that as someone who finds the paper extraordinary, you can’t fathom how someone who understands these implications could just pass it over, but again that Ms. Smith didn’t address the paper doesn’t mean she either didn’t understand it or didn’t find it fascinating. It only means she didn’t address it. And as noted, it really wouldn’t have added anything to her point to address it. Maybe she’s waiting to address the paper – who knows? But she isn’t under any obligation to do so, so arguing that her post on her blog is shoddy for not referencing it just doesn’t make sense.

231. #231 John Kwok

     January 29, 2009

     @ Robin,

     I think the fact that Payne et al. is available for free public download from the PNAS site should speak volumes to you as to its potential importance. None of the recent papers which Abbie has cited share its distinction.

     So no matter how you want to “spin” it, I remain correct in asserting that Abbie goofed by not commenting on a paper whose importance P Z Myers recognized by devoting such an extensive blog entry to it at his blog.

     John

232. #232 John Kwok

     January 29, 2009

     @ Robin,

     I believe Anton was under the mistaken impression that P Z Myers was writing solely on “latent evolutionary potential” and somehow plucked the Payne et al. paper out at random merely to provide a concrete example of “latent evolutionary potential”. And if it’s not him, then it might have been W. Kevin.

     John

233. #233 Robin

     January 29, 2009

     I think the fact that Payne et al. is available for free public download from the PNAS site should speak volumes to you as to its potential importance. None of the recent papers which Abbie has cited share its distinction.

     I’m not arguing that it isn’t an important work, John – on the contrary I’ve noted that it holds fascinating implications. That said, this too is a non-sequitur. She isn’t obligated to cite it no matter how profound it is and there is nothing lacking in her work for not doing so.

     So no matter how you want to “spin” it, I remain correct in asserting that Abbie goofed by not commenting on a paper whose importance P Z Myers recognized by devoting such an extensive blog entry to it at his blog.

     John

     It is your personal opinion she “goofed”, not a fact. At least, you’ve not provided any evidence that her point was lost because she didn’t refer to the paper, and since as far as I can tell her point would not have been enhanced in the least by referencing the paper, never mind going into any kind of lengthy discussion of it, I will continue to disagree with and dismiss your opinion on this. Again, I realize you think the paper is incredible and I’m not arguing against that, but such does not place any onus on anyone else to reference it. It just doesn’t.

234. #234 W. Kevin Vicklund

     January 29, 2009

     It was neither Anton nor me. It was one of the strawmen you have erected in a desparate attempt to deflect attention from the fact that you have utterly failed to support your assertations. The reason PZ wrote what he did is utterly irrelevant to whether ERV was correct in her usage of the term.

235. #235 neo-anti-luddite

     January 29, 2009

     I know I said I was done here, but has it struck anyone else that John’s posts here, especially lately, seem to contain a whole lot more cut-and-paste phrases and even paragraphs than they used to?

     I’m not sure what, if anything, can be made of that, but I find it quite unusual.

236. #236 windy

     January 29, 2009

     I think the fact that Payne et al. is available for free public download from the PNAS site should speak volumes to you as to its potential importance.

     Oh, for the love of… Open access in PNAS is something that the authors have the option of paying for, not some special favor bestowed upon a select few! If PNAS had thought this paper was so supremely important, they could have made it a Feature Article or at least put it on the goddamn cover! The cover of that issue has dogs on it! The PNAS editors thought DOGS were more important than your once-in-a-lifetime paper!

     For those keeping score at home, that’s yet another instance where John had no idea what he was talking about.

237. #237 Robin

     January 29, 2009

     I think the fact that Payne et al. is available for free public download from the PNAS site should speak volumes to you as to its potential importance.

     Oh, for the love of… Open access in PNAS is something that the authors have the option of paying for, not some special favor bestowed upon a select few! If PNAS had thought this paper was so supremely important, they could have made it a Feature Article or at least put it on the goddamn cover! The cover of that issue has dogs on it! The PNAS editors thought DOGS were more important than your once-in-a-lifetime paper!

     For those keeping score at home, that’s yet another instance where John had no idea what he was talking about.

     LOL! I was really trying to be more subtle about this point, but this is a great (and very funny – thank you) way to illustrate the issue. Thanks Windy!

     As I noted this is a non-sequitur; even if it was the MOST important research work to come out in the last 10 years, Ms. Smith would still not be obligated to address it. I don’t know how many different ways to present this to Mr. Kwok, but as much as he feels this work deserves attention and that Ms. Smith obviously dropped the ball in not giving the attention he feels it deserves, in reality the onus is not on her to address it and the point she did make cannot be validly assessed against that lack of reference since it would have added virtually nothing to her point.

238. #238 John Kwok

     January 29, 2009

     @ Robin,

     Yes I know that open access at PNAS is something available to the authors at special expense, but I am sure that PNAS would not have granted it too if they didn’t think that there was something rather special about the paper. An assessment that P Z Myers apparently agreed with, since he spent so much time defending and explaining it over at his blog.

     John

239. #239 John Kwok

     January 29, 2009

     @ Windy,

     You may have forgotten this, but I haven’t:

     “He didn’t coin the term, it appeared in a paper in 1995! Which, I might add, also referred to intraspecific variation.”

     You later told me that the paper was actually published in 2006. How curious.

     Maybe I – as a former paleobiologist with a M. S. degree in Geosciences – have a much better grasp of the historical significance of the Payne et al. paper – and am therefore well qualified to comment upon it, and to stress its importance, than reading increasingly inane comments from you objecting to my defense. You know, it’s really as though we’re squabbling over the meaning of the word “is”. Does that have a familiar ring to it?

     John

240. #240 windy

     January 29, 2009

     You may have forgotten this, but I haven’t:
     “He didn’t coin the term, it appeared in a paper in 1995! Which, I might add, also referred to intraspecific variation.”
     You later told me that the paper was actually published in 2006. How curious.

     Err, I already replied to you and apologised for writing 1995, when I meant 2005. I had previously given the correct ref for the 2005 paper and my point still stands. And since you yourself confused 2005 with 2006 just now, I’d say we are even

     *sigh* is this the best you got?

241. #241 John Kwok

     January 29, 2009

     @ Kevin,

     In your own words from yesterday, you note this:

     Because she was referring to the first half of PZ’s post, which did a very good job of describing a concept, rather than the second half, which did a very good job of summarizing a paper that utilized a concept. Payne’s paper cited other papers. Should we castigate PZ for not discussing those papers?”

     I am only guilty of exaggerating when I said that someone had thought that Myers had plucked randomly the Payne et al. paper. No, by your own words, you are admitting that Myers’ intent was to write solely about “latent evolutionary potential” when his ACTUAL purpose was a successful defense and interpretation of it, rebutting the rather inane Uncommon Dissent review of it.

     John

242. #242 John Kwok

     January 29, 2009

     @ Windy,

     Sorry, but I’m not going to concede the point. I think I’ve been demonstrating over the past few days that I have an excellent understanding of the recent history of science behind the Payne et al. paper. Maybe you should start following some of the leads I have provided.

     Have you GOOGLED “incumbent replacement” yet and come up with the Rosenzweig and McCord paper? I presume your library does subscribe to Paleobiology, so I recommend you search its stacks for that paper, and once you find it, look at the acknowledgements section.

     John

243. #243 Robin

     January 29, 2009

     Robin,

     Yes I know that open access at PNAS is something available to the authors at special expense, but I am sure that PNAS would not have granted it too if they didn’t think that there was something rather special about the paper. An assessment that P Z Myers apparently agreed with, since he spent so much time defending and explaining it over at his blog.

     John

     A) Any writer of a PNAS article can pay the fee to have his/their work available through open-access, John. The fact that the Payne, et al. paper has open-access does not indicate anything about its importance. Your speculation regarding PNAS granting the open-access is noted, but without some substantiation that the editors actually cared and/or judge various pieces for open-access in some manner, I just don’t find the claim compelling.

     B) A repeat since apparently my previous statement to this point didn’t sink in: even if this was the MOST IMPORTANT research conducted in the last 10 years, Ms. Smith would still not be obligated to comment on it and/or write about it. Get over it John. Ms. Smith may well be even MORE excited than you about the results from Payne, et al.’s work – we do not know since she hasn’t said anything about it. But to the point, there is no intellectually honest way to assess her opinion or understanding of the work based on her blog piece. She didn’t mention the Payne, et al. paper, but she didn’t have to so any assessment about her feelings, knowledge, grasp, and/or insight into said paper is quite moot.

244. #244 John Kwok

     January 29, 2009

     @ neo-anti-luddite,

     Since you are determined to add some more lines of breathtaking inanity, then my paraphrase of a now famous sarcastic remark uttered by a well known conservative radio talk show host (whom I don’t take seriously at all BTW) still applies.

     I might add to it, by expressing an interest in being present at your last rites, if you don’t mind your Ps and Qs. You truly have a long way to go with me, and if you wish to have the semblance of a decent online relationship, then you ought to respond favorably to what I have demanded from you.

     John

245. #245 John Kwok

     January 29, 2009

     @ Robin,

     Just to shift this discussion back to where it properly belongs, with regards to Graham Lawton’s sensationalist reporting on the tree of life, I will say it once more:

     Abbie has a major responsibility to grow up as a science commentator, by making sure that her comments could not be wrongly interpreted by myself, by those who don’t have a science background, and especially, by creationists. I’ve already reminded those reading this thread that I was the subject of some abuse over at Uncommon Dissent after one of its primary posters avidly read an exchange I had with heddle – who is truly, more so than either Abbie or yours truly – one of the great warriors in the ongoing struggle against the dark forces of irrationality represented by the DI and AiG, among others – over at Abbie’s blog that he found so amusing.

     My issue with her isn’t just the Payne et al. article. It’s really, more fundamentally, making silly comments like those I have cited a few times already. As I noted yesterday, I don’t care if she’s striving to be as funny as comedian Stephen Colbert or memoirist Frank McCourt. All I care about is that she expresses herself in such a way that whatever she conveys is accurate and not subject to potential misinterpretation.

     John

246. #246 windy

     January 29, 2009

     Robin:

     I don’t know how many different ways to present this to Mr. Kwok

     I don’t think there is a way to get through to him. But for some reason I can’t stop. This thread is like being stuck in the Twilight Zone. “You are entering another dimension, a dimension of John Kwok’s mind. Didudidu didudidu…”

     you replied to John:

     I am well-aware of your credentials from reading your posts both here and on PT. That said, I do not find your criticisms valid in this instance.

     I have been surprised to see people in this thread refer favorably to John’s evolution-related (not Obama-related) posts at the PT. I haven’t been following them, but here on SB I’ve never seen him demonstrate much actual understanding of evolutionary biology. It’s mostly arguments from authority (of course we have some pretty good authorities in evolutionary biology so often you can seem pretty knowledgeable that way!)

247. #247 tomh

     January 29, 2009

     Robin, if you are ever called upon to talk to a wall, you will be well prepared.

248. #248 W. Kevin Vicklund

     January 29, 2009

     No, by your own words, you are admitting that Myers’ intent was to write solely about “latent evolutionary potential” when his ACTUAL purpose was a successful defense and interpretation of it, rebutting the rather inane Uncommon Dissent review of it.

     Sorry John, but I said jack about PZ’s intent. The fact remains, regardless of his intent, that his post is in two parts, one giving a good description of the term and one defending the use of the term in the paper. Granted, the parts are interleaved. Nonetheless, he has expanded the concept past the way it was used in the paper.

     So what did ERV do? She got excited ablout the concept. She showed how it applies directly to her line of work, in the form of a newly released paper. She showed how it actually matters to people in real life, rather than just an important but abstract concept. And finally, part of the reason she wrote it was to combat what was published last year by the lead scientist of the DI.

     PZ may have shown why the creationists are wrong, but ERV showed why it matters that they are wrong.

249. #249 neo-anti-luddite

     January 29, 2009

     I have been surprised to see people in this thread refer favorably to John’s evolution-related (not Obama-related) posts at the PT. I haven’t been following them, but here on SB I’ve never seen him demonstrate much actual understanding of evolutionary biology. It’s mostly arguments from authority (of course we have some pretty good authorities in evolutionary biology so often you can seem pretty knowledgeable that way!)

     I’m beginning to think that the reason John seemed knowledgable on PT is that he was essentially repeating basic biological facts in response to serious creotard bullshit. It doesn’t take much to seem reasonable in the face of gibbering moronity.

     If you hold a stained styrofoam cup up next to a rusted-out can, the cup looks pretty good; put it in among the lead crystal, though, and it looks quite pathetic indeed.

250. #250 SLC

     January 29, 2009

     Re anti-Kwok posters

     It would appear that Mr. Kwok has some sort of obsession with Ms. Abbie Smith. What happened Mr. Kwok, did you make a run at her and your advances were rejected? I don’t want to play psychiatrist here but your obsession is quite unhealthy and is a symptom of a serious mental problem. I agree with Mr. DiPietro, you should get help.

251. #251 Robin

     January 29, 2009

     @ Robin,

     Just to shift this discussion back to where it properly belongs, with regards to Graham Lawton’s sensationalist reporting on the tree of life, I will say it once more:

     Abbie has a major responsibility to grow up as a science commentator, by making sure that her comments could not be wrongly interpreted by myself, by those who don’t have a science background, and especially, by creationists. I’ve already reminded those reading this thread that I was the subject of some abuse over at Uncommon Dissent after one of its primary posters avidly read an exchange I had with heddle – who is truly, more so than either Abbie or yours truly – one of the great warriors in the ongoing struggle against the dark forces of irrationality represented by the DI and AiG, among others – over at Abbie’s blog that he found so amusing.

     I will repeat another of my points that it seems you missed: Ms. Smith has no responsibility or obligation as a science blogger (highly specialized area of science I might add) to meet your particular standards of science commentary. Period. Whether Heddle is the GREATEST warrior against irrationality makes no difference and really doesn’t add anything to the discussion. That your comments were a target of abuse at UD really doesn’t add anything to the discussion either except as yet another example that the folks at UD like to abuse people’s statements with regard to science and rational thinking, usually without any basis, but this really isn’t news to those of us who follow their antics.

     My issue with her isn’t just the Payne et al. article. It’s really, more fundamentally, making silly comments like those I have cited a few times already. As I noted yesterday, I don’t care if she’s striving to be as funny as comedian Stephen Colbert or memoirist Frank McCourt. All I care about is that she expresses herself in such a way that whatever she conveys is accurate and not subject to potential misinterpretation.

     I understand that you don’t like her style and that you feel that because she engages in silliness, her comments could be more easily misunderstood. Having perused the comments on her blog, however, I’ve not found any yet that indicate that even a small minority of readers find her explanations confusing. Further, I’ve not yet seen her comments targeted by anyone from UD or any other creationist site, so while potentially it could happen, I doubt her specific area of expertise and the subjects she blogs on lend themselves to the type of mischaracterizations that seem to indicate support for ID. While I can certainly appreciate your concern and I share such concern in general with regard to the communication of scientific concepts to the general public, I just don’t find Ms. Smith’s explanations regarding convergent evolution and latent evolutionary potential inaccurate or poorly articulated.

252. #252 windy

     January 29, 2009

     Abbie has a major responsibility to grow up as a science commentator, by making sure that her comments could not be wrongly interpreted by myself, by those who don’t have a science background, and especially, by creationists.

     She wasn’t misrepresented by creationists in this case, Payne et al. were! Don’t they have this responsibility you speak of?

     making sure that her comments could not be wrongly interpreted by myself

     That would be impossible, because you choose to misinterpret them.

253. #253 Robin

     January 29, 2009

     Robin:

     I don’t know how many different ways to present this to Mr. Kwok.

     I don’t think there is a way to get through to him. But for some reason I can’t stop. This thread is like being stuck in the Twilight Zone. “You are entering another dimension, a dimension of John Kwok’s mind. Didudidu didudidu…”

     It is beginning to feel a bit like that…

     I am well-aware of your credentials from reading your posts both here and on PT. That said, I do not find your criticisms valid in this instance.

     I have been surprised to see people in this thread refer favorably to John’s evolution-related (not Obama-related) posts at the PT. I haven’t been following them, but here on SB I’ve never seen him demonstrate much actual understanding of evolutionary biology. It’s mostly arguments from authority (of course we have some pretty good authorities in evolutionary biology so often you can seem pretty knowledgeable that way!)

     Just to be clear, I wasn’t providing any evaluation of Mr. Kwok’s evolution-related comments, either pro or con. I merely noted that I am aware of his credentials given his reference to them both here and at PT.

254. #254 Jason Rosenhouse

     January 29, 2009

     Okay folks, enough is enough. I think it’s time to move on to other things. I’ll be closing the comments on this post.