Let me tell you about my day.
I’ve got a full schedule of labs, classes, and meetings today, and it’s advising week at UMM as well.
Late this afternoon, when my last class lets out, I’m bolting out the door and running for my car, and then in a squeal of burning rubber, racing for the airport. We had our first snow today. I estimate that I’ll arrive in Minneapolis sometime around the tail end of rush hour. I’m cutting it close.*
I’m flying to O’Hare. I arrive at about 10:30pm. My connecting flight to Nashville leaves at 7am. I have no idea what I’m going to do for 8½ hours. Maybe rewrite my talk.
I arrive in Nashville at 8:30am. I’m giving a talk at CSICon at 11:15am.
I’m explaining a difficult and fundamental topic in evolutionary biology: the role of chance. I just noticed that I have to do this in a half hour. I think I will be rewriting big chunks of my talk.
At 11:50am I intend to collapse somewhere.
The good news, though, is that finishing up my obligations early means I get to mostly relax and enjoy the weekend, and I really really need that. Except that I’m also bringing a stack of grading with me, and also have to prep a lecture for Monday (fortunately, the topic for that is regulation of cell division, and I know that stuff inside and out.**)
Anyway, all that just to let you know…posting may be light for the next 30+ hours. You can cope, right? Also, bonus: partying Friday and Saturday night, so maybe I can compensate with mildly inebriated posting (no drunk posting for me, I’m too old for that crap anymore.)
* But have no fear, I won’t compromise on traffic laws. I shall get there safely or not at all!
** Wait, I know everything in this class inside and out — I still suffer in fussing over all the details.
Ugh. The potentially never ending loop of talk re-writing. I have variously considered leaving all of that up to chance at times, but a predicted lack of coherent talk-evolution and rapid selection of myself from the talk-pool has kept me doing the boring mundane.
I much prefer being able to stroll into the centre of town, hop on the TGV, have a beer or three before arriving at the centre of the other town, and — with luck — being able to stroll to the hotel. What’s all this nonsense with burning tyres (is that some sort of a magic spell to make the airplane fly?) and general rushing around…
Have a safe if frantic trip, Professor poopyhead!
I won;t really be peeling out of my driveway, but it is a three hour drive on a good day, so I don’t have any slack time at all.
I used to have a “don’t drink and blog” rule. But I found it interfered too much with my drinking, so, you know, it had to go.
PZ I worry about your safety of course, but also your health. Travel is tough enough under even the best of circumstances; adding extra pressure and stress on top of it is bound to take a toll on you. : |
PZ, do you know if CSICon will be recording your talk and making it available online? The topic sounds fascinating, and I’d love to listen to it.
Safe travels!
@2: Oh, quit lording your fancy-schmancy Yuropeen socialist high speed trains over us. As a true American is is my God-given right to spend two hours each day crawling through traffic to and from work while spending a significant portion of my stagnant paycheck for payments on my very own car, insurance, and gasoline – oh, sorry, petrol.
PZ, you could try sleeping. You do sleep, don’t you?
Sleep? Isn’t that what the peons do?
grilled cheese for lunch?
Hey, if PZ has time to spare he could always open up comments on YouTube, and spend the time moderating them!
Or he could do something worthwhile I suppose.
PZ, if you’re getting in to O’Hare about 10.30 pm, & flying out at 7.00 am, i guess there isn’t much time for sleep. Unless you’re one of those folk who get by on five hours a night.
The peons sleep? I guess they’re not being driven hard enough, eh. But you’re not suggesting that … no, surely not!
Snow? It’s getting up to 80 here today in Cleveland and we’re expecting snow on Sunday. It’s like that here.
Is sleeping in the airport what people normally do with delays overnight? Do people put their belongings in a locker and hope no one gropes them while they are unconscious? Do any airports have those nap lockers like in Japan?
Are you sure you’re not getting burned out?
You sounded kind of out of it during your recent interview with Reap Paden.
Errm, what interview with Reap Paden? You clearly have me confused with someone else.
And no, I’m not getting burned out. Tension, exhaustion, and anger are the fuels that keep me burning, and there seems to be an inexhaustible supply.
PZ,
You bring back memories for me. I remember taking that grading with me everywhere – I even took it with me when I flew to Florida for my mother-in-law’s funeral.
And even for a lowly high school teacher, it’s a constant job to rewrite and tailor those lesson plans and lectures for each class.
This is why I get so pissed at the conservatives who claim that teachers and professors have it so easy. I think that most of the ones making the most noise would be stark raving mad after one semester – heck, probably after one week!
I am at work in Eden Prairie, MN and it is, as PZ said, snowing.
The rain I endured while driving to work has turned into the first snowfall. PZ sholdn’t worry though, this early snowfall is melting as soon as it hits the ground.
Light snow in downtown Minneapolis, too, but it seems to be letting up. Hope you find clear, dry roads & have safe travels PZ!
PZ:
I feel for you.
On September 5, I came to work expecting a normal day. At 9:30, I got a call that I was heading to Covelo, CA to a forest fire. I spent the next hour making flight, rental and hotel arrangements and was on a plane at 2:00pm (luckily, I can fly out of an airport that is really close by). Flew to Charlotte, SC. Then to LAX. Then to Sacramento where I waited almost an hour for my second checked bag (the one with the tent and air mattress in it), rented my car (they tried to rent me a Suburban but I said I wanted something smaller so they offered a Nissan Armada. I said, “What part of ‘smaller’ do you not understand?’ and ended up with a Jeep Wrangler (worst vehicle I have ever had at a fire) and drove to the hotel and checked in at 4:00am EDT. So I was up and going for just under 20 hours. Then, to get my mandatory work/rest ratio back in sync., I had to do nothing for 10 hours. (well, I showered, watched TV, had breakfast and lunch, found a cigar store) So I left the hotel at 11:00am local time (2:00pm my time (as long as I am travelling, I keep the same time zone, otherwise I lose hours) and drove the seven hours to the fire.
So I do feel for you. Really. I do.
But, on the bright side, the travel was in pay status, so Thpppt!
I had an annoying stopover in a small airport recently, where I flew in around midnight, and my flight didn’t leave until around 9 am the next morning. I thought ‘no big deal’, I’ll just crash in the waiting area. Then I heard my name paged to collect my luggage. It seems the airport shut down for the night, I had to collect my luggage and then re-check it in the morning, and since I had to leave the secure waiting area to get my luggage, I could not re-enter. So I was stuck hanging around the airport for the night, with no place to crash, dragging my luggage around.
My parents-in-laws will be there! So jealous. Be nice (but be a dick too, they have certain expectations of you!)
Overnight at an airport? *Shudder* seems like a suitable venue for a less-than-optimal afterlifre…
I have an issue with the role of chance in evolution that has always bugged me and I’m hoping PZ or anyone else with some wisdom on the subject can comment or at least suggest a paper or two that addresses it. Creationists say that “all things bright and beautiful can’t result from random…yada yada, airplanes and tornadoes paintings, painters, irridiculous complexity..blah, blah…” I think that’s accurate.
Scientists say that natural selection is the opposite of random, but that mutation is random. While probably true (in the sense that any DNA locus is about as likely as any other to be affected by one of myriad possible events that cause changes), it’s not really relevant unless the change (in a germ cell) happens to also avoid all error-correcting mechanisms.
I don’t see how anyone can label mutation as “random” without qualification!
I assume that these are not random. I’m guessing that tinkering with enzymes that chop up and re-anneal DNA in germ cells must be an incredible investment of resources since small changes can have drastic consequences and you can’t have enzymes running around like Leatherface chopping up DNA willy-nilly. Most of these mechanisms — I’m guessing– must have been figured out in bacteria and I know that DNAses (and endonucleases too) are very sequences-specific, and topoisomerases and ligases also. From this a couple of hypotheses cross my mind.
First, mutation is not that random and a mutation in let’s say a hemoglobin gene is going to be less likely than in, say, a gene for eye colour.
As well, certain genes are selected by “molecular Darwinism” to be more hospitable to binding error-repair enzymes, and perhaps ARE less subject to initial mutagenic events by acetylation for example, or conformational differences with non-coding or “less important” genes.
This, of course would apply to most-non-coding DNA, excluding I guess, regulatory regions and other binding domains.
Is this plausible? Has anyone published work that touches on any of these hypotheses? Can mutation be truly random once viable cell lineages have been established?
I would appreciate any comments or reading suggestions. Thanks.
Best of luck on your talk, PZ. I hope it’s filmed.
Mutation is random. It not only comes about by mistranscription, but decay of carbon 14 in the purine/pyrimidines that make up the DNA. What isn’t random is natural selection, which is very powerful if there is any advantage to the mutation. Your idea ignores that, hence it is nonsense.
Snow, oh my. I saw a flake or two one night last week when I was out taking photos but thankfully it has not been that cold up here in Ottawa and the long range forecast looks pretty decent for the next week or so at least.
On the topic of being drunk, are there any drinking plans set up in Ottawa while PZ is here?
Professor Myers, your tireless efforts on behalf of godlessness should not go unrewarded.
Tweet when you’re in a hotel bar, give me an hour or so, and I guarantee that the mysterious young atheist woman who smiles provocatively and sits down next to you will make you forget completely about Rebecca Watson.
(For a while, anyway.)
Saying that mutations occur randomly says nothing about the frequency with which they occur.
Relevant to what, exactly?
You seem to be confusing “mutation” with something like “viable and potentially successful phenotype”.
You seem to be confusing “mutation” with something like “viable and potentially successful phenotype”.
seems that way to me too.
@Isumak:
Just because a mutation can cause a lethal change in a particular DNA locus doesn’t mean it can’t still occur.
I’d probably deal with this misconception first, before trying to introduce more subtle concepts like what the distribution shape of mutation rates at various loci are, but yeah, the point is that mutations are stochastic, not deterministic.
First, mutation is not that random and a mutation in let’s say a hemoglobin gene is going to be less likely than in, say, a gene for eye colour.
the other thing you might be confused about are mutations in DNA vs fixation of genes in a population.
things that are (or were) strongly selected tend to become relatively fixed as phenotypes within the population. Thus, you see less variability in the structure of human hemoglobin, say, that you do with eye color, for which there isn’t really a strong selection pressure.
this has nothing to do with whether or not a mutation could still occur at the loci involving the relevant genes to each phenotype.
make sense so far?
As well, certain genes are selected by “molecular Darwinism” to be more hospitable to binding error-repair enzymes, and perhaps ARE less subject to initial mutagenic events by acetylation for example, or conformational differences with non-coding or “less important” genes.
well, sort of. there are examples of loci where specific mutagenic events are less likely that others, but it does not limit the overall stochastic nature of mutations, only limits the chances at specific loci, and there are very few examples of what you’re mentioning.
Is this plausible? Has anyone published work that touches on any of these hypotheses?
still not clear on exactly what it is that you are asking?
are you asking if selection has favored non random mutation rates?
if the latter, you can only put that question wrt specific sources of mutation, not “mutation” in general, as there are many, MANY, sources of mutations. what would limit the chances of one source of mutation for one loci, might actually INCREASE it for another.
so if you’re asking whether there has been work done looking at whether selection favors reduction of mutation rates at specific loci for specific mutagens, then yes, it has. I’d have to dig up specific references, but by the time I do, someone else will likely have beaten me to it.
if you’re asking whether the conclusion of all that work has been that there is overall a trend away from thinking mutations in the genome as a whole do not have a random distribution, then the answer is no.
Sleep? Isn’t that what the peons do?
Plenty of time to sleep once you’re dead, that’s what I say.
*drinks 5th cup of coffee*
….it’s not really relevant unless the change (in a germ cell) happens to also avoid all error-correcting mechanisms.
but… error correction mechanisms are subject to selection.
PZ, don’t stay up all night at O’Hare. I did that years ago and believe me, you don’t want to. I hope the situation has changed for that, but go to one of the expensive airport hotels and get a few hours sleep, and hope your hosts at CSICon will compensate you for it.
If a student asked you whether they should stay up all night studying for the exam, what would you advise them? Well then, take your own advice!
Ichthycic, I am defining “mutation” as a HERITABLE change in base sequence of an organism’s DNA. I think that is the way it is usually defined, at least in evolutionary biology. Changes to non-gametes producing evolution is a form of Lamarckianism, right? Changes in base sequence that occur in somatic cells are irrelevant to evolution–I’ll leave out the effects of cancer since it probably has little effect on species-wide evolution. T
Many changes to gamete DNA –harmful or not (I wasn’t making that distinction)– are repaired by the various repair mechanisms. I’m thinking of base mismatch errors, deamination, depurination and oxidations, produced by everything from ionizing radiation to chemical mutagens to DNA replication errors. There are more but it’s been a while since I studied molecular biology. These errors are detected and repaired at a very high rate by mechanisms which distinguish single-strand and double strand errors. Any errors that slip through can be potentially passed on to offspring and on doing so are what I –and I thought everybody else– call “mutations”.
Now, I’m not suggesting there isn’t a random component to the initial change. Of course there is. I’m suggesting that it is nor purely random, meaning that you can’t divide the number of bases or nucleotides by the mutation rate and obtain that number as the probability of a mutation occurring at every locus of every chromosome. I’m suggesting that repair mechanisms are not random, that they have sequence-specific, or perhaps location or conformation-specific probabilities for their successful detection and repair of errors. Natural selection, which crafted them, would insure that. They are probably reasonably parsimonious in their use of resources. At least they are probably worth their cost in terms of enhanced survival, but the fact they are not 100% effective is probably due to the advantage of variability on a species’ adaptive potential.
Because error repair is not random, mutation rates are not totally random. My hypothesis hinges on whether there is any reason to expect that enzymes involved in DNA repair might find more recognition sites around “important” genes than other genes.
I can’t see that this would work for the initial error-detecting proteins. Also, we know that if the damage is too severe, the affected cell becomes apoptotic and disappears.
“what would limit the chances of one source of mutation for one loci, might actually INCREASE it for another.”. Agreed. This is what I was trying to convey with my eye colour/hemoglobin suggestion.
The higher mutation rate observed in mitochondrial DNA and in non-coding regions of the genome illustrates that mutation IS non-random in any case, because they are somewhat shielded from selection pressures for different reasons and thus their DNA mutates at a higher rate than coding DNA. |I am merely wondering if there is any evidence that this non-randomness extends to recognition sites for DNA repair signalling molecules and/or enzymes.
Many changes to gamete DNA –harmful or not (I wasn’t making that distinction)– are repaired by the various repair mechanisms.
and many are missed, and many are created by faulty repair mechanisms, and many are not even recognized.
still not getting what you’re after here.
Many changes to gamete DNA –harmful or not (I wasn’t making that distinction)– are repaired by the various repair mechanisms. I’m thinking of base mismatch errors, deamination, depurination and oxidations, produced by everything from ionizing radiation to chemical mutagens to DNA replication errors. There are more but it’s been a while since I studied molecular biology.
insertions, deletions, duplications, all these things are very different and actually matter quite a lot. All of them are things that can be missed by “repair” mechanisms because they happen during recombination, for example.
Any errors that slip through can be potentially passed on to offspring and on doing so are what I –and I thought everybody else– call “mutations”.
right, so all you’ve done so far is talk about frequency, NOT distribution. Are you understanding this?
Because error repair is not random, mutation rates are not totally random.
No, as I said before, it IS random wrt to the idea that heritable mutations are NOT predictable overall, they are stochastic in distribution, not deterministic.
“not totally random” is meaningless. all you’re really saying here is that that they don’t have a perfectly normal distribution, that has nothing to do with whether they are considered deterministic or not.
do you understand what I am saying? I need to be clear that you do before I continue responding.
Uh-oh. When Joe Felsenstein tells me to get a hotel room, I better get a hotel room.
That isn’t the standard definition. Rethink your idea using the standard definition. Science doesn’t like you defining terms willy-nilly like that…
*Quick Evodevoman, to the Squidmobile!
[Deploys stout spray]
[Makes escape in a cloud of roasted malty blackness]
I really don’t know how you do it man! As mentioned above, I found that blogging sober interfered too much with drinking. But I must admit there was the odd day when I woke up, checked the blog and went “oh crap, did I really post that”.
And now I’m off to the airport to fly to SE Asia…But not for giving a talk.
I really don’t know how you do it man!
me either. often have wondered how in the hell PZ manages to find time to do all this stuff.
I’m happy if I can get a day’s regular work in, spend ANY time blogging, get a few minutes in that contribute to any of my other hobbies, and still get the regular cleaning and maintenance done.
at the end of a day where I manage to do all those things, I’m totally friggen exhausted.
yet.. PZ teaches, handles students, blogs, goes to conferences, manages a family…
HOW??
PZ,
Just saw this, which is about a Princeton study on non-randomness in evolution. According to the article,
“Princeton University research published in the journal Science suggests that knowledge of a species’ genes—and how certain external conditions affect the proteins encoded by those genes—could be used to determine a predictable evolutionary pattern driven by outside factors. Scientists could then pinpoint how the diversity of adaptations seen in the natural world developed even in distantly related animals.”
You’ve probably already seen it, but FYI in case. Might be an interesting reference for your talk.
I have the power of The Lord.
Heh. Not really.
hm… PZ the Travelling Ungod Salesman ?
The power of Greyskull is much more potent than the power of the Lord.
Nerd of Redhead: agreed about the definition of “mutation”. Heritability doesn’t enter into the definition, but is necessary for the mutation to have any evolutionary effect. Henceforth, I will use the word to mean changes to an organisms DNA.
Ichthyic: “and many are missed, and many are created by faulty repair mechanisms, and many are not even recognized.”
As I have been saying…
“insertions, deletions, duplications, all these things are very different and actually matter quite a lot. All of them are things that can be missed by “repair” mechanisms because they happen during recombination, for example.”
Agreed. Didn’t mention those specifically, but yup, they fall under the general heading “changes”, and of course meiosis is probably the main source of intraspecies variability. However, because as you say, they are not subject to proofreading and correction, they are not relevant to what I am suggesting, which concerns selection pressure on repair mechanisms and if there is any evidence that certain genes have “protected” status.
“right, so all you’ve done so far is talk about frequency, NOT distribution. Are you understanding this?”
No, because I haven’t said anything about frequency except to suggest that there exist estimates of # of changes per/ # of bases called mutation rates. I HAVE mentioned distribution, by noting that mutation rates vary, depending on location in the genome: Mitochondrial vs Somatic and pseudogene vs gene (though i used the dichotomy coding vs non-coding).
“not totally random” is not meaningless, although it is very clumsily expressed and I think that this is where people are taking issue with what I was asking in my original post. What I am getting at can be summarized in the concept of the “loaded dice”. Loaded dice might not give the same result on every throw, but one side has been weighted to make a certain outcome more probable than simple probability theory would dictate.
Nonetheless, the result is still governed by chance.
Alternatively, imagine you wanted to play poker and had a choice of betting your life savings on a game with a group of children to whom you had just explained the rules or a group of professional card-players. In both cases, the cards dealt are governed by chance. However, the resulting tallies of wins and losses will not be the same for you in both situations. If you think it would, there is a cold beer and an open chair waiting for you at my poker table ;).
Do you see that although both situations have an element of chance, the probabilities that govern the possible distributions of dice throws or poker hands will not dictate the outcomes of throwing the dice or your patterns of wins and losses, the way throwing fair dice would?
I’ll stop here, because if we can’t at least agree on the fact that systems which contain stochastic elements do not necessarily produce strictly random results, then we won’t get any further.
Mutation is random. Selection starts with survival to birth. If you’re wondering where the bad mutations went, look at the miscarriage rate–for humans, about 40% of fertilized eggs.
“not totally random” is not meaningless
yes, it is.
take a course in probability and statistics. It would assist your thinking on this greatly.
until then… ta.
Nope, still failing. Mutation need not do anything. Mutation is only the opportunity for natural selection to work on something for a difference in result. Learn some real science, and quit trying to tell real scientists you know something when you obviously don’t. Using non-standard definitions, not understanding what you are talking about, not understanding statistics while using them…
Why don’t you write up and submit a paper if you have a real idea. Submission policies for Science and Nature. Write the paper and see what real scientists/peers think of your flatuence.
That’s the sign of a good professor, in my opinion. As a student I can tell you that we really appreciate professors who go over their material every semester and who obviously put effort into their classes. Your students are very lucky to have you, as is the atheist community. So, umm, take care of yourself, ok?
Wow! What hostility!
Since none of you were any help, and Nerd of Redhead clearly can’t read nor understand what it reads, I guess this is not the place to speculate beyond a first-year undergrad level. N.O.R, at least I know more than you have demonstrated in your snippy little posts.
Ithyic, thanks for trying. The poker invitation is still open. The absolute dichotomy between random/non-random was covered in my stats courses, but if you learn a little more, you’ll find that the distinction is not so simple:
http://plato.stanford.edu/entries/chance-randomness/
What I was looking for was something like this:
http://www.the-scientist.com/?articles.view/articleNo/27910
I mistakenly thought people like the commenters on that website existed here. My mistake. Bye.
For any who can read and comprehend and are interested in what I now know is more than just my idle speculation:
Nature. 2012 May 3;485(7396):95-8.
Evidence of non-random mutation rates suggests an evolutionary risk management strategy.
Martincorena I, Seshasayee AS, Luscombe NM.
“Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases. Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection. Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.”
Unsurprisingly, my emphasis on repair mechanisms was simplistic and possibly just wrong and the authors do not suggest a definitive cause.
Last post, really. Link to an intelligent discussion of what I was getting at:
http://sandwalk.blogspot.co.uk/2012/08/an-example-of-directed-mutation-and.html