Tick tock on the molecular clock

Posted by ERV on May 31, 2010
(26)
More »

I got a giggle from reading Larry (and then John Hawks) talking about time travel. Kinda. I mean, people using science to look back in time, and orient themselves in that different era to such a degree they can gain information about said time.

Scientists arent just guessing when they estimate when humans and chimpanzees split into different species, or where/how ‘new’ species like Ardi and Teh Hobbit fit into the tree– they are using two totally different arms of science figure out how species were oriented millions of years ago. We have estimates from fossils and how old they are and when/where we find them (estimates based on geology, anthropology). And then we have molecular clocks (estimates based on biochemistry, genetics).

These methods arent mutually exclusive– I think its normal to use fossils to ‘calibrate’ molecular clocks. The more info we have, the easier it is to see back in time.

But sometimes these two methods do give ‘answers’ that are too different for scientists (Larry):

The theoretical models agree on a human-chimp divergence time of 3-5 million years.

I’ve been skeptical of the fossil record calibrations for many years because they give some very unreasonable divergence times and because the so-called “fixed” standards also seem unreasonable. The molecular clock ticks at an approximately constant rate but we just don’t know what that rate is. I would have no problem accepting that humans and chimps diverged 6-7 million years ago.

Okay, so why did this make me giggle?

We kinda have the same issues with HIV-1. A LONG TIME AGO, in THE YEAR 2000, we thought HIV-1 crossed into humans 1931 (1915 – 1941).

Then ALL THE WAY BACK IN 2008 we found another ‘fossil’– HIV-1 from 1960. They used that fossil to recalibrate HIV-1s clock, and then the speciation event got thrown back to 1921 (1908 – 1933).

So as I was reading their posts, nodding and thinking ‘Ya, I totally know what theyre talking about’, the absurdity of comparing an event that happened millions and millions of years ago to an event that happened ~90 years ago made me lol.

LOOKING THROUGH THE SANDS OF TIME ALL THE WAY BACK TO 1921!!! THEY BARELY HAD MILITARY AIRCRAFT IN 1921!! One estimate was as low as 1873… OMG I CANT EVEN IMAGINE A WORLD WITHOUT COORS LIGHT! WHAT AN ALIEN TIME!

hehehehe 100 years ago, 5 million years ago, same thing :P

Keywords: ,
(26)
More »

Comments

  1. #1 Divalent
    May 31, 2010

    “OMG I CANT EVEN IMAGINE A WORLD WITHOUT COORS LIGHT!”

    Why do you find it impossible to imagine a better world?

  2. #2 Tommykey
    May 31, 2010

    THEY BARELY HAD MILITARY AIRCRAFT IN 1921!!

    Well, they did have some famous fighter pilots in WWI, like the Red Baron.

  3. #3 Tyler DiPietro
    May 31, 2010

    I’ve seen papers out there experimenting with using exponential distributed variables to compensate for the limitations of assuming a constant rate of divergence. Phylogenetics is pretty interesting stuff if you’re into statistics and cluster analysis.

  4. #4 Geoffrey
    May 31, 2010

    OMG I CANT EVEN IMAGINE A WORLD WITHOUT COORS LIGHT!

    What are you talking about? Cat’s have been able to piss for ages. :)

  5. #5 Optimus Primate
    May 31, 2010

    OMG I CANT EVEN IMAGINE A WORLD WITHOUT COORS LIGHT!

    One can dream.

  6. #6 complex field
    June 1, 2010

    Imagine there’s no Coors Light.
    It’s easy if you try….

  7. #7 Larry Moran
    June 1, 2010

    Coors light is my favorite beer, by far.

    I find it amusing that so many people have to go out of their way to show they don’t like it. What are they trying to prove other than the fact they would be happy to live in the nineteenth century? :-)

    Is beer snobbery replacing wine snobbery as the best way to show your pretense to cultural superiority? [Hint: It's not working.]

  8. #8 Dan Gaston
    June 1, 2010

    The problem with molecular clocks is that while the rate of divergence is relatively steady over very short intervals, and averages to a steady rate over very long intervals, it is, in actuality, quite variable. That is why so much work in molecular phylogenetics is being done on complicated covarion models of evolution that allow for rate variation across sites and along lineages. Two papers of interest on the issues of molecular clock estimates for divergence times are:

    Here: http://www.ncbi.nlm.nih.gov/pubmed/17556757

    and

    Here: http://www.ncbi.nlm.nih.gov/pubmed/16754613

    Molecular clocks are great… when they are well calibrated with fossils. For issues with dating hominids and most mammals this may not be too severe of an issue because there is a wealth of fossils but as you push back deeper into the tree they become very unreliable.

  9. #9 Dan Gaston
    June 1, 2010

    Larry: I think “snobbery” is only snobbery when it is done solely for the sake of being pretentious. These are the folks who will go on endlessly about how expensive or rare or hard to get their particular beverage, food, or item of interest is.

    On the other hand many people have their preferences purely on taste, in which case it isn’t snobbery to look down on mass-market relatively generic beer or wine any more than it is to think that home made mac n cheese is better than Kraft Dinner. Or that fresh caught salmon tastes better than fish sticks from a cafeteria.

    But its ok to like the other stuff if that is what you actually prefer.
    :)

  10. #10 SLC
    June 1, 2010

    Re Larry Moran @ #7

    As a life long teetotaler, I am not in a position to discuss the pros and cons of various alcoholic beverages. However, IMHO, much of the animosity against the products of the Coors company is due to their anti-union activities and their extreme conservative positions and the fact that they donate money to organizations that actively lobby for those positions.

  11. #11 harold
    June 1, 2010

    Lary Moran said –

    Coors light is my favorite beer, by far.

    I like almost all beer, but Coors Light is one of my least favorite. Different strokes for different folks. Someone mentioned the political element, as well, but I just don’t like it as much as the type of beers I enjoy more. I also can’t help noticing that beers that are very similar to Coors Light (including some made by Coors under a different brand) are available for a lower price.

    I can’t help wondering if maybe you claim to like Coors Light because you are into the politics associated with the Coors family, but whatever.

    I find it amusing that so many people have to go out of their way to show they don’t like it.

    What the hell is it to you if someone likes a different type of beer? More Coors Light for you.

    What are they trying to prove other than the fact they would be happy to live in the nineteenth century? :-)

    Does not compute.

    Yes, the average beer brewed in the nineteenth century was probably more to my taste than the average beer brewed in the US in the twenty-first century.

    But no, since I can easily get great beer in the twenty-first century, and also get antibiotics, public sanitation, modern science, all the music, film and television of the twentieth century, fast transportation, etc, etc, etc, no, I don’t “want to live in the nineteenth century”.

    Is beer snobbery replacing wine snobbery as the best way to show your pretense to cultural superiority?

    Nope, this comment is just an embittered reflection of your own insecurity.

  12. #12 harold
    June 1, 2010

    Larry Moran –

    Although I stand by my comments above, perhaps they are a bit strong.

    I have to admit that, as I am not crazy about the beer they brew or their brand of politics, Coors annoys me in two separate ways.

    On the other hand, there is NOTHING wrong with drinking the beer that you personally prefer, and it is 100% legal to be right wing.

  13. #13 natural cynic
    June 1, 2010

    OMG I CANT EVEN IMAGINE A WORLD WITHOUT COORS LIGHT!

    What are you talking about? Cat’s have been able to piss for ages. :)

    Nope. Coors is bear piss collected in the late summer-early fall. Coors Light is bear piss collected in the month following hibernation.

  14. #14 Jesse
    June 1, 2010

    @13 natural cynic:

    Nope, it’s horse piss, not bear piss. The light version comes from the horses that actually do drink when led to water.

    As for Coors, and its variants, Bud, etc… A real beer drinker does not learn how to choke them down. A real beer drinker learns how to enjoy them. Here’s why:

    1) You ever bring beer to a party where if it’s there, somebody will drink it? You can bring something real good and people will probably drink it. Often you won’t know all of them, but it’s your money they’re putting down their gullets. You can get a case of something good, or for less $$ you can get a 30 pack of Coors Light.

    2) Some people only drink Coors Light, Bud Light, Coors Original, etc… If they offer you a beer, it is nice to be able to enjoy the beer with that person rather than turning it down or pretending to enjoy it in the interests of politeness. (I still have to choke down Budwiser.)

    3) They’re cheap when purchased in bulk.

    4) Coors Light and it’s ilk are like sex in a raft. It’s fucking close to water. If you enjoy the act of drinking beer for more than just the effects of the alcohol, that’s more that you can drink before becoming inebriated.

    Give me a nut brown ale with the right amount of hops or a nice chocolate stout and I’m in heaven, but I won’t shy away from Coors Light or anything that is similar. Just keep the Budwiser away.

  15. #15 harold
    June 1, 2010

    Jesse –

    I completely agree with your comments.

    I would just add that, although they are somewhat stigmatized, there are products which are pretty much the same as Coor’s Light, for a lower price. Including the Keystone line, which is made by Coors (they may literally fill the cans with the same stuff for all I know), the ill-named Natural line (made by A-B), and all the other Milwaukee’s Best type stuff.

    Heck, even Pabst Blue Ribbon is cheaper than Coor’s Light.

    However, of course, as I said, those extremely similar but cheaper products are stigmatized. So judgment is required. Some Coor’s Light drinkers would be offended if you brought Natural Light to a party they were throwing.

  16. #16 Jesse
    June 1, 2010

    I can do just fine with Natty Light or Keystone Light. I’ve personally found that the difference in price between what I can find Coors Light for and Keystone Light for are negligible, but that’s only for large quantities and only at a few certain stores.

    At one of those certain stores I managed to pick up Killian’s Red for 10$/case last week.

  17. #17 Prometheus
    June 1, 2010

    “LOOKING THROUGH THE SANDS OF TIME ALL THE WAY BACK TO 1921!!!”

    Most people have an historical memory of about 70 years and their sensory memory is even worse.

    I have had to show 30 year olds how to use a rotary phone and had to re-teach a 68 year old.

    Why? ….when the power is out beyond your cell’s charge, you can still make and receive calls over a land line using an clunky old phone because the switching stations have huge battery banks and run current through the phone line.

    I have a beer drinking buddy who conjectures that the flaccid(his opinion) quality of U.S. mass production domestic beer has to do with a major portion of the U.S.population losing sensory memory during prohibition.

  18. #18 Tommykey
    June 1, 2010

    I have had to show 30 year olds how to use a rotary phone and had to re-teach a 68 year old.

    Being 40, I’m just old enough to remember rotary phones. We even had a black & white tv when I was a kid.

  19. #19 Tyler DiPietro
    June 1, 2010

    Beer tastes like ass. Why does anyone drink. I DEMAND TO KNOW!

  20. #20 Jesse
    June 1, 2010

    @19 Well, from the way you describe it, ass tastes good! Seriously though, don’t most guy’s lives revolve around chasing ass? Explains the love of beer, now doesn’t it?

  21. #21 Tyler DiPietro
    June 1, 2010

    Okay, so instead beer tastes like [insert bad tasting thing here].

    I get it, there is no arguing over taste. I fucking hate beer though. If our qualia are the same I have no idea why anyone drinks it.

  22. #22 Jesse
    June 1, 2010

    The way we experience it is clearly not the same then. It’s not surprising though. Fresh tomatoes make me sick. Literally. My dad says that I was that way as soon as I was old enough to eat solid foods. Even smelling them makes me unhappy, which is funny because I like to make my own cooked tomato sauces, and I have to endure the smell. There is something in them that my body perceives as nasty, rotten vegetables. I simply cannot fathom why people like them, but they do. Oh well, it’s more for them, I guess. I think it’s the same with beer for other people.

    P.S. After spending hours on my roof in the sun fighting with the one of the fucking swamp coolers, I am enjoying a nice, cold beer. I’m going to have to finish kicking its ass tomorrow.

    P.P.S I bet that ERV did not expect this blag post to turn into a discussion about beer and tastes.

  23. #23 John Scanlon FCD
    June 2, 2010

    If our qualia are the same I have no idea why anyone drinks it.

    If qualia can be said to exist at all, they depend on the messy, unreplicable bits of our heads. How could they be the same in different people?

    A lot of the fossil-based calibrations that have been used in vertebrate phylogeny are not well supported; the tendency for palaeontologists (especially palaeoanthropologists) to claim ‘firsties’, i.e. that their new scrap of bone is the oldest example of a popular clade (ceratopsians, hominins or whatever) clutters the literature with a lot of spurious identifications, that the molecular-clockers then glean from textbooks and reviews without much context or capacity to criticise. The effect on clock-rate estimates is to make them slower than the real rates, so that certain workers come alarmingly close to predicting rabbits in the Precambrian. The same people tend to assume the geological events (origin of islands and mountain chains) can be used to fix the divergence of animal clades by vicariance, but don’t seem to be too worried when their trees imply long-distance dispersal. Don’t they notice that invalidates their assumptions?

    Anyway, not only adding new calibration points, but critical review of previously accepted calibrations, are essential to getting it right. Righter, at least. That makes these questions about Ardipithecus really interesting.

  24. #24 Prometheus
    June 2, 2010

    “A lot of the fossil-based calibrations that have been used in vertebrate phylogeny are not well supported….”

    I agree with this.

    Morphology is really complicated because it is so loaded with presumptions, like shoehorning stuff into Linnaean taxonomy, the whole higher and lower order of beings thingy and creotards breathing down everybody’s necks looking for errors as evidence of Hebrew Fred Flintstone.

    I had a girlfriend who was an anthropologist. I was sitting around the display case lined lab waiting for her when I realized some old coot had organized the entire collection according to the medieval Great Chain of Being.

    There was an empty case at the end of the room so I put a little sticky note on it that said “Angel Skulls Only”.

    I thought it was kind of funny at the time but that crap pisses me off as a former curator. The kids were being forced to think like Thomas Aquinas just to find exemplars and this was a state college.

  25. #25 Azkyroth
    June 2, 2010

    OMG I CANT EVEN IMAGINE A WORLD WITHOUT COORS LIGHT!

    Strange; you never struck me as a pessimist. O.o

  26. #26 Alice Bluegown
    June 6, 2010

    While I appreciate the thrust of this post (and it’s a very interesting topic), I’m rather surprised no one has picked up on your statement “they barely had military aircraft in 1921″. Yes they did, largely thanks to a little thing called World War 1, which took the airplane from an army novelty to a primary weapon of war – such concepts as aerial reconnaissance, dogfighting and strategic bombing all evolved during that brutal conflict. WW2 would provide an even bigger quantum leap, taking us (roughly) from biplanes to jets and, ultimately, space rockets.
    This has been a message from your friendly neighbourhood GAG (Girly Aviation Geek) – you may now return to discussing beer.