Pharyngula

Evolgen disputes my explanation!

RPM of Evolgen disagrees with my definition of synteny! This is terribly distressing. Especially since, strictly speaking, he is precisely correct. The word has evolved in its usage from the pure form that RPM is describing to a more colloquial, pragmatic, somewhat sloppier sense as used by people looking at comparative genomics rather than classical Drosophila genetics.

If you read contemporary evo-devo papers, my definition is more useful in comprehending what they’re saying. If you want to read Drosophila genetics papers, you better know what RPM is talking about, or god help you (and there is no god).

Comments

  1. #1 Alex
    June 30, 2008

    Wait, so now words evolve? You Darwinists. Geesh.

  2. #2 Helioprogenus
    June 30, 2008

    To those asshole creationists who think PZ’s the proverbian amoral deamon set to destroy the world through lies and disinformation, ask yourselves if you would ever link to dissenting opinions from your own. Your delusional belief that throwing evidence out the window and embracing faith will lead to a higher moral and ethical calling is utterly stupid. If you had the moral fortitude to actually practice what you preached, you would have to constantly acknowledge that your beliefs are wrong. Yet, you lie, cheat, and steal, whilst believing in your own ignorant grandeur. This is how science works you ignorant creationist fucks, not through obfuscating facts, but analyzing all avenues that fit within observation and EVIDENCE. Take your faith and shove it in recesses that will never see the light of day, because in the end, all you have is a pile of dried out 2000 year old horseshit that in the end, will amount to a waste of life.

  3. #3 Gene
    June 30, 2008

    No worries, PZ. Lots of words have more than one meaning. One of my favorites is “sanction.” It’s almost an antonym to itself.

    http://www.merriam-webster.com/dictionary/sanction

  4. #4 shifty
    June 30, 2008

    holy crap that’s an awesome rant for only #2!

  5. #5 Steve LaBonne
    June 30, 2008

    I missed PZ’s original post so I’m a bit late to this party, but: Couldn’t the genomics types have coined a new word instead of misusing a long-established genetics term? Sheesh.

  6. #6 Alex
    June 30, 2008

    Did I spark #2?

    Well done Helioprogenus. Nice rant. I have to apologize if my comment brought that on. For I am the choir, full of sarcasm usually. I was kidding with that quip.

  7. #7 Jeff Arnold
    June 30, 2008

    Be careful.. It’s this type of dissention among scientists that helps the creos PROVE that darwinism is not true! Don’t you know that in order to be a scientist we have to all agree on everything all the time?? Otherwise our ‘science’ isn’t reliable and time-tested like the Bronze Age writings of desert nomads…

  8. #8 BlueIndependent
    June 30, 2008

    Helioprogenus, gees hold off with the shot across the bow. At least until one of them comes around here and drops some of that quote “2000 year old horseshit”.

    You’re at an 11, you need to be at a 1 right now.

  9. #9 Helioprogenus
    June 30, 2008

    Sorry to burst your bubble Alex, but you didn’t spark the tirade, it was a pre-emptive strike laid against that idiot Stan I figured would eventually Trollerina his way into this thread as well.

  10. #10 Patricia
    June 30, 2008

    Perhaps that fellow doesn’t realize what a huge diversity of education your gang of thugs comes from, and that in fairness to we lesser fry, you bang it down a notch once in awhile? If he does know, then he is a smart alec with a poorly filled trouser.

  11. #11 Alex
    June 30, 2008

    No apology necessary Helio. I just wanted to make sure my handle wasn’t the target of that firey rant…at least as much as possible.

  12. #12 Patricia
    June 30, 2008

    Free grog & swill for Helio #2!

  13. #13 frog
    June 30, 2008

    Strictly speaking, RPM & PZ & RPM’s commentators are wrong — since we’re speaking English.

    According to RPM: I disagree. While this is what many genomicists mean when they write or talk about synteny, they are wrong.

    Unlike other languages like Spanish or French, in English words mean what most people mean to mean, not what it originally meant, or what it should mean. That may be a feature, or a bug — but it’s clearly the rule!

    It may still carry as a minor meaning what Drosophila folks mean to mean, but the major meaning is what most folks mean to mean.

    For ESOL folks, this has been your update on English semantics — we prefer the caterpillar in Alice’s tale. Common usage trumps logic and history.

  14. #14 stly
    June 30, 2008

    Strictly speaking, evolution is wrong — since we’re speaking common sense.

  15. #15 mattmc
    June 30, 2008

    @#14

    Strictly speaking, you are an assclown. If “evolution is wrong”, what then is “right”?

  16. #16 Owlmirror
    June 30, 2008

    If “evolution is wrong”, what then is “right”?

    Lysenkoism, as all good Bolshevist Comrades know – except when they don’t.

    Comrade stan is being shy all of a sudden, da?

  17. #17 JoJo
    June 30, 2008

    Strictly speaking, evolution is wrong — since we’re speaking common sense.

    Evolution is much more commonsensical than 6000 years ago The Big Guy In The Sky made the universe and life and all that stuff in just six days.

    However, there’s another point. Science is not commonsense. As George Gamow put it, “common sense tells us that the speed of light is infinite and planck’s constant is zero.” A lot of physics seems very weird because these two numbers are not infinity and zero.

  18. #18 Heliprogenus
    June 30, 2008

    Who still thinks my pre-emptive tirade was ill placed. As I figured, Stan the trollerina would find his way on this thread and get back to laying down his theory of creationism through spontaneous deistic megalomanism. If this imaginary being created you in his image, well, I’m not impressed.

  19. #19 Helioprogenus
    June 30, 2008

    As for my question marks and grammatical ommissions, they’re as non-existant as stan’s deity.

  20. #20 clinteas
    June 30, 2008

    PZ,
    youre way too humble and apologetic today man,whats going on LOL .

    First the ” Catching up” thing,now this,get a grip Sir,its not all that bad,youre still doing fine !!

    I personally think that ” synteny for pharyngulites 101″ will just do fine,and the 2 and a half hardcore drosophilistas here can go to RPM to get their fix !

  21. #21 windy
    June 30, 2008

    It’s possible that stly was making a point about common sense definitions of words – if evolution means whatever the majority believes, and the majority believes evolution = “dogs giving birth to cats”, then evolution is wrong. Or something like that.

  22. #22 flo
    June 30, 2008

    I like drosophila genetics … also once did a ”
    paper/presenation thing about them … really interesting.

  23. #23 Patricia
    June 30, 2008

    Hey wait a minute – didn’t PZ call Stan a fucktard and warn him that he was about to be shuffled off to his cell? Teal curtains? Or am I confused… :( It’s all that twirling.

  24. #24 PZ Myers
    June 30, 2008

    I DID NOT CALL HIM ANY SUCH THING!

    I said he was a fuckwit. Let’s be accurate, OK?

    I told him to try and pay attention and respond substantively. So far, he hasn’t. I may have to give him a cell. I don’t know what all the talk about curtains is, since it won’t have any windows and is only decorated with manacles, chains, and decaying bones.

  25. #25 Tex
    July 1, 2008

    ‘When I use a word,’ Humpty Dumpty said, in a rather scornful tone,’ it means just what I choose it to mean, neither more nor less.’
    ‘The question is,’ said Alice, ‘whether you can make words mean so many different things.’
    ‘The question is,’ said Humpty Dumpty, ‘which is to be master – that’s all.’

    Through the Looking Glass Lewis Carroll

    RPM is right. PZ is wrong.
    The misuse of ‘synteny’ is just the newest in a long line of abuse of well-established terms from other fields by biologists. This bastardized use of ‘synteny’ is similar to the illegitimate use of ‘homology'(as in ‘these two genes are 85% homologous’) or ‘ortholog’ on occassions when there is no freakin’ way to tell whether homologous genes from different species really owe their separate existance to a speciation event or whether they were already separate genes in the last common ancestor.

    All of this reminds me of small children using a newly discovered word in every possible context until repeated coprrections from their elders refine their understanding of its proper meaning.

    We True Believers have almost succeded in stamping out the ‘homology’ heresy, and we are hard at work putting out the ‘ortholog’ revolt. Apparently it is time to man the barricades and fight back against Humpty-Dumptyization of ‘synteny.’

  26. #26 Barry Pearson
    July 1, 2008

    Alex at #1:
    “Wait, so now words evolve? You Darwinists. Geesh.”

    See: “Linguistic evolution is an evil lie from SATAN!!!”
    http://youtube.com/watch?v=uEcgpiQy7w8

    (Nice spoof).

  27. #27 truth machine
    July 1, 2008

    RPM is right. PZ is wrong.

    Since PZ wrote “Especially since, strictly speaking, he is precisely correct”, your statement is self-contradictory. It also suggests that your impression of what PZ wrote is quite distant from what PZ actually wrote:

    The word has evolved in its usage from the pure form that RPM is describing to a more colloquial, pragmatic, somewhat sloppier sense as used by people looking at comparative genomics rather than classical Drosophila genetics.

    This non-normative statement is factually correct.

    If you read contemporary evo-devo papers, my definition is more useful in comprehending what they’re saying.

    Regardless of one’s views on linguistics and bastardization, this judgment is likely correct

    If you want to read Drosophila genetics papers, you better know what RPM is talking about, or god help you (and there is no god).

    This judgment is certainly correct.

    Apparently it is time to man the barricades and fight back against Humpty-Dumptyization of ‘synteny.’

    The best way to do that is to offer alternative terminology. If you can’t, your cause is lost. (Truthfully, it’s lost anyway.)

  28. #28 truth machine
    July 1, 2008

    Strictly speaking, evolution is wrong

    Strictly speaking that’s ungrammatical. Claims and actions can be wrong, but “evolution” is neither. Had you said “Strictly speaking, the theory of evolution is wrong”, you might have had something, if you had also pointed out what it gets wrong.

    – since we’re speaking common sense.

    Strictly speaking, one doesn’t speak common sense, one speaks about it, or employs it. On the former: what one is speaking about has no bearing on whether a claim is true unless it affects the meaning of the claim — which applies to “synteny” but not to evolution and common sense. On the latter: there are many sorts of common sense, of varying degrees of validity. One thing that common sense tells us is that well educated, informed, smart people employing a self-correcting methodology are more likely to be right than uneducated, ignorant, unintelligent people clinging to the mythologies of ancient goatherds.

  29. #29 frog
    July 1, 2008

    Tex: All of this reminds me of small children using a newly discovered word in every possible context until repeated coprrections from their elders refine their understanding of its proper meaning.

    Except we ain’t talkin’ ’bout children. In the case of children, they aren’t the concensus — the elders are. But in this case, the argumentum ad populam is the correct argument. Sorry Tex, you can spend centuries manning (and womanning) the barricades, but at the end English words are defined by popular vote — unless you can convince the masses (in this case of geneticists) that they should be wrong, and convince them to change their way, they’re right.

    And as of today, they’re right, since they outnumber you. If you don’t like it — go speak French!

  30. #30 Gregory Earl
    July 1, 2008

    Frog, you may or may not be right with respect to the meaning of words in colloquial speech in English (although I don’t know what makes you think that French or Spanish would work differently). However, you are definitely wrong with respect to the meaning of scientific terminology, which are not defined by popular vote but by experts in the relevant fields. If you want to understand what synteny means, you cannot go with the majority, you have to go with the experts. As PZ points out, this means that you have to be aware that experts in different fields may use different definitions.

  31. #31 frog
    July 1, 2008

    Gregory: Frog, you may or may not be right with respect to the meaning of words in colloquial speech in English (although I don’t know what makes you think that French or Spanish would work differently).

    What makes it different is that both those languages have language committees. English is what ever is found in dictionaries, which are produced by private bodies — the most authoritative of which is the OED. French is defined by L’Académie française, and Spanish is defined by La Real Academia Española. They define the standard language, from the level of vocabulary down to grammer and spelling.

    English is different, and it isn’t a matter of specialized vs. colloquial. In French, “synténie” means what the Academy says it means – the Academia is normative, and one would assume that they would use the most “expert” definition, and not necessarily the most common meaning. (Which, as a matter of fact, is not a word according to the Academy).

    On the other hand, English is defined by usage — “expert” status is irrelevant, common usage in context is what defines it, whatever you happen to prefer. English does not have a normative body — so a word “means” what people mean to say, even if it annoys purists. As I said, that may be a feature or a bug — but it’s the reality. If I could get most people to mean “ribosome” when they say “chromosome”, that would go into dictionaries as the common meaning, with a mark as to its historical meaning and minor meaning.

    Now, to go to the most authoritative source, the Drosophila meaning is still the meaning in the OED and Webster’s. Wikipedia of course has both meanings, while Britannica uses synteny with the linkage meaning. The best analysis then is that best usage of synteny today primarily is “being on the same chromosome”, but the meaning is shifting. If Tex doesn’t really do a bang-up job on the barricades, the OED will expand the meaning to the less “correct” one in the next decade or so — they are more conservative than the Encyclopedia Britannica.

    Whether you like it or not, that’s the way it is, empirically and factually. While in Spanish there is no ‘sintenia’ since the RAE says there is no ‘sintenia’ (and it’s an unused word), and in French there is no ‘synténie’ since the Academy says there’s no such word, even though it is used. That’s one of the reasons why there are so many words in English, with so many meanings per word – jargon, even the most absurd, eventually gets official imprimatur if it’s common enough and lasts long enough — since official only means what most dictionaries think they can sell.

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