I'm on my way home, and am actually using a fast internet connection at the airport — I'd forgotten what it was like! I quickly uploaded a few essential files, and my mail software is downloading my email. Unfortunately, I'd need a really fast connection to handle all that — the number of messages pouring in might actually hit 5 digits. If you're hoping for a reply to anything, you might well be out of luck here.
Atlanta has been very pleasant, with friendly people and good company. I'll have to come back sometime. The meeting itself was challenging for a mere biologist, but I might have absorbed a few glimmerings. At least it'll help me dig into the literature a little more.
As for my talk, and since I haven't had time to put much science here lately, I'm making my GECCO 2008 talk available as a pdf. These presentations are always a little cryptic when handed out without my explanatory overview, but at least in this one I've included my presenter notes, which might help a little bit. The first half is an overview of some concepts in evo devo, which includes those little reminders of what I was supposed to say; the last half is a description of two experiments, and I'm afraid my notes are a little thin there — the data in the research always seems self-explanatory to me. Sorry about that, you should have registered for the conference!
Email download complete: it didn't quite hit 5 digits, only 9865 messages in the last few days. Maybe if I included the spam that gmail filters out for me…
Ack! I couldn't add this note from the airport because "Your computer was automatically blacklisted (blocked) by the network due to an abnormal amount of activity originating from your connection." Curse you, Boingo! What good are you if I can't even download email without you suspecting I'm up to no good?
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"Science"? What is this "science" of which you speak?
I thought this was a magical-baked-goods blog!!!!1!
Looks pretty straightforward, actually.
I do wonder about saying that evolvability is not "encoded into the genome" but is simply the result of plasticity and modularity. Wouldn't those who say that "evolvability has evolved" avoid saying anything like it's being "encoded into the genome", but would simply say that evolution maintains evolvability as plasticity, mutability, and modularity?
Anyhow, that's how I see it. DNA and RNA themselves are essentially what was predicted from an understanding of evolution plus heredity (neo-darwinism), because, of course, DNA allows for plasticity and modularity, along with the requisite conservation.
Minor point, yes. I just think that plasticity and modularity are components of the "evolvability" that evolution maintains.
Glen Davidson
http://tinyurl.com/2kxyc7
"Evolvability" has become a bit of a buzzword, and there's a tendency towards reifying it. Most people I've talked to are perfectly willing to admit that it could easily simply be a property of plasticity and modularity.
Of course, then we have to push it back. Those two things aren't there in the genome, either: I also made the case that modularity is a consequence of the hierarchical pattern of fate restrictions in development, and plasticity is a reduction of buffering/constraint on development. I was really thinking in terms of addressing comp sci people with godlike powers of control over their models and simulations -- the answer to building development into their work isn't to encode high level abstractions like modularity, plasticity, and evolvability into their models, but to design the substrates they're working from so that those properties emerge.
But I think they already knew all that.
I recognize the mouse-bat stuff from TAM 6; it was sandwiched in between witty insults directed at Phil Plait.
Thanks for the response, PZ. I now see better what you mean, especially when you say that "evolvability" is becoming a buzzword.
Glen D
http://tinyurl.com/2kxyc7
5 digits?! That's kind of scary. How do you sort out the crap and get your important e-mails? o_____o
What's with all the science talk on this site that's not related to a "particular stage in the development of the vertebrate embryo." I mean the site is called pharyngula for god's sake. I don't come here to learn about the evolution of crackers.
Yes,
PZ you need to come back to Atlanta, you have to come to Skeptrack and not leave Phil Plait to his own devices... ;)
Any chance for future conferences in Hawaii? We're in such dire need of intellectual rigor. Apart from the pleasant weather, the nice people, wonderful environment, we're in a mental desert. I know the University of Hawaii has many interesting lectures, so if Richard Dawkins can visit, PZ should be able to.
page 9 of the pdf is cut-off.
Perhaps PZ ought to set up filters to sort any emails containing the word "cracker" "Catholic" "Donohue" "Donahue" "Eucharist" "pray", etc. into a separate folder. Might save some time.
Can anyone recommend a good book about evo devo?
good book on evo devo: Endless Forms Most Beautiful
http://www.amazon.com/Endless-Forms-Most-Beautiful-Science/dp/039332779…
Thanks for posting the presentation. I was getting comfortable reading along with your presenter notes, then all of a sudden page 13 comes along and I was all alone. To be fair, I WAS warned. =P
This is very nice to hear. I'm very devo, my wife, I might say, is even worse. That is, more devo. We're practically Pro-Cro-Magnum, a couple of regular Neanderthals. No that's not our last name, so forget it, spammers!
Every night we pray we'll wake up tomorrow on a lower, safer limb on the Tree of Life. I get vertigo up here. What it's like for you guys, I couldn't even imagine!
The latest from DI. http://www.evolutionnews.org/2008/07/a_case_study_in_darwinian_ethi.htm…
You guys gotta read this shit.
PZ,
Sorry I missed you. I'll be at the Atlanta airport Thursday, too late to meet.
Cheers,
Stephanurus
I doubt any of us expect replies, especially seeing the numbers), e.g. from what I know from my colleagues here in Canada many of us have cc'd you via email the letters of support to your prez but none of us would expect a reply on such a "for your files" task lest you want to spend the next 144 hours straight trying just to say "thx" to all individually, especially when few of us know you personally other than via the blog or occasional emails in the past.
It is clear you've been kind enough to say thanks on the blog and to ask people not to send hate mail to the fracking nutbars; save your email time for stuff that really needs attention like cataloguing the loons who send you hate mail.
5 digits - and I thought the 200 plus non spam emails I get every day was bad...
Yes, as per #10, a few pages are cut off in the pdf.
TheNaturalist (#13) wrote:
I second that! Fascinating and informative book. It's a must-read, in my humble opinion.
Alex @ #6
Ahem.. If I may reference xkcd yet again... though I'm pretty sure all the pros use Beyesian filtering instead.
I thought everyone knew that if they're not to go in the spamfilter, they have to include [TENTACLE] in the subjectline ...
http://copache.wordpress.com/2008/07/16/pz-myers-notice-me/
*cough*
I sent an email about this too. Doesn't hurt, does it?
"The first half is an overview of some concepts in evo devo,..."
If development is hierarchal, as you said in your talk, why shouldn't evolution likewise be hierarchal?
Why would you imagine that it is sequential, as described by modern evolutionary theory?
Just as the growth and development of an individual organism is uniquely controlled by information in the genome, so it is likely that the evolution of life itself was programmed into the genome from the very beginning, from the moment that it first arrived on earth, and that all subsequent "evolution" is nothing more than the unfolding of an algorithm that resides in the pool of genetic material found on the earth.
After all, you've got to account for the origin of the "toolkit" too.
Evolution is both sequential and hierarchical (anagenesis and cladogenesis for aficianados).
I am not familiar with your usage of the word "likely"...
If I had over 10,000 (or over 9000 for the 4channers* out there) emails in my inbox, I would probably shit my pants then and there.
I probably didn't help much. At least 3 of the emails you got in the past week were form me. =\
* Rules 1 and 2 don't mention talking about 4chan.
Um, St. Mike, a major point of PZ's presentation is that the growth and development of an individual organism is NOT uniquely controlled by information in its genome, but that environmental contingencies play crucial roles as well.
The "origin of the toolkit" IS being accounted for, as we speak. It's a major avenue of research.
For those readers not familiar with the term "evo devo"...
The "devo" part does NOT refer to "de-evolution." That term is basically moribund.
"Devo" refers to "developmental" as in "evolutionary developmental biology."
We now return to our regularly scheduled program....
Evolvability was originally defined as: "The ability of a population to respond to artificial or natural selection." (Houle, D. (1992) Comparing Evolvability and Variability of Quantitative Traits. Genetics, Vol 130, 195-204)
If you look at this original definition, I can think of various mechanisms that will increase the evolvability of species. For example, mutation rates are genetically determined, and a change in the mutation rate will affect the evolvability of the system. So, any coded mechanism that will alter the production or retention of new mutations will alter the evolvability of the species. AS such, evolvability can evolve itself.
Plasticity, as far as I can tell, will reduce evolvability because it hard codes the option to respond to an environmental change. Modularity to the contrary will make it easier, as it becomes easier to change function of a single module (as defined by a larger than average number of connections within the module and less than average number of connections between modules) as the number of affected connections between other modules is limited. Lower number of connections make it easier to modify a module.
Dear Dr Myers,
I hope I'm not clogging up your blog too much with this, but I heard today that you said no one has tried to explain the reasons why Catholics are upset about how you have been talking about the Eucharist. I wanted to direct you to the following article: http://www.ignatiusinsight.com/features/ceo_eucharist_sept04.asp
It doesn't go into detail as to the "whys" of what we believe, but it might help you to understand where we're coming from and why your words have done so much damage. If you want to look into the whys, there are plenty of places to look online. When I looked into the whys seven years ago it changed my life for the better.
Sally,
The question is why do Catholics think they can resort to violence and death threats?
If oranges are orange, why shouldn't apples be orange, too?
But it isn't in the genome. Read it and gaze in wonderment: it just simply isn't there!
What toolkit?
What utter nonsense. Even if PZ were utterly uneducated and too stupid to read Wikipedia, he was still brought up as a Lutheran, and the Lutheran beliefs about the Eucharist are almost identical to the Catholic ones.
Why did you even rely on a second-hand source in the first place? Why didn't you just snoop around his blog a little? Evidently you didn't even know this topic has generated several thousand comments so far on his blog alone -- did you really think none of those comments would have explained the Catholic beliefs about the Eucharist, had that been necessary, and did you really think none of the 9865 e-mails mentioned above explained the same?
PZ knows full well what Catholics believe about the Eucharist, and he thinks it's ridiculous. That's what's going on here.
#29 re evolvability. Carl Zimmer's "Microcosm" has a chapter on E. coli in hostile environments. The bacterium has a precise DNA-repair chemistry (enzyme?) that it uses in normal times. But when it suffers a lot of damage, a fast but sloppy chemistry takes over (different enzyme?). It makes more mistakes but it might keep more bacteria alive.
The result is that in a really hostile environment, e.g. flooded with antibiotics, the bacteria begin to mutate at a rate a hundred times faster than their usual rate. If I read your definition correctly, they increased their evolvability by the same factor. As a result, they evolve at startling rates. That's probably what happened when bacteria were sent into space and came back with an unexpectedly high number of mutations to help them survive.
When the environment settles down, they go back to using the more precise repair chemistry and the mutation rate falls back to its usual level.
I'd like to see Mike Behe and Bill Dembski explain that solid research finding.
Monado, indeed, one of the many mechanisms that can alter evolvability, and a excellent example of how plasticity in the DNA-repair mechanism can lead to changes in evolvability, and a counter example to my idea that plasticity works against it. I stand corrected.
I do believe this is in order:
I'm waiting for poster #24 to tell us what the "unfolding evolutionary algorithm" has in store for us next. Since it is apparently programmed into the genome, and since the human genome in its entirety is already known (and available for free, I think), we stand on the brink of knowing the evolutionary destiny of our species from now to the end of time.
Or not.
"Um, St. Mike, a major point of PZ's presentation is that the growth and development of an individual organism is NOT uniquely controlled by information in its genome, but that environmental contingencies play crucial roles as well."
Agreed.
"I'm waiting for poster #24 to tell us what the "unfolding evolutionary algorithm" has in store for us next. Since it is apparently programmed into the genome, and since the human genome in its entirety is already known (and available for free, I think), we stand on the brink of knowing the evolutionary destiny of our species from now to the end of time.
Or not."
Evolution is basically done with. All we can expect to see in our future is extinction and decimation.
Michael
PZ, might I suggest that you use something like IMAP rather than POP3? You wouldn't need to download all your mail, just the headers. It would save a lot of bandwidth, and it might prevent security systems from triggering as well.
If he used IMAP, he would have nothing to do on the plane (I guess I could scan through headers, but that's kind of boring).
I can't believe I missed out on Crackergate... damn vacations!
damn... He, not I could scan through the headers...
Selection can be hierarchical. For instance group selection.
But I suspect that's not what you mean by saying that evolution ought to be considered as a hierarchical process. So what are the different hierarchies in your view?
This is a prime example of weak induction.
What is this algorithm? What specific instructions were encoded?
Well, considering a large proportion of our genes are ancestral, many are paralogous duplicates, and others likely arose from events like exon shuffling, we can at least partly account for the origin of the "toolkit" of several extant organisms.
PZ,
I was at GECCO in Atlanta and enjoyed your talk. Thank you.
Yes: The wireless there was brutally slow.
I saw that several of our GDS guys queued up to talk with you, so you probably got these questions already, but since I squandered my opportunity to ask them in Atlanta, here goes ...
In EC, our notions of evolvability are somewhat different. Since we have ultimate control over the details and mechanisms of our evolutionary processes, underlying representation, ... and, in the case of GDS (generative & developmental systems), the developmental process ... when we focus of evolvability, we are typically focussing on the mechanisms & representations in our synthetic system that will encourage good/useful/interesting solutions will arise from the evolutionary process.
In some ways biologists have it harder: certainly real evolutionary and developmental systems are vastly more complex and not subject to radical re-wiring. But in some ways, we have it harder: You can focus on studying existing systems as they have arisen, whereas we have to construct systems that will assemble complex items (e.g., solutions) from scratch.
So I was particularly interested in Nic McPhee's "toolbox" question after the talk, but I would have phrased it differently: What (in your view) are the crucial and fundamental mechanisms at work in evolution and development that afford these properties of plasticity and modularity? For example, our GDSs often eschew this question building an explicit bias toward modularity directly into the representation and developmental process.
Have you any thoughts for how your more thorough understanding of natural evolutionary and developmental systems can inform our engineered systems in terms of bootstrapping the process? My view of our EC+GDS systems is that at one extreme we have elegant representations and mechanisms that rarely lead to useful solutions for serious problems without heavy kuldging (e.g., evolution of production rules in L-systems), or at another extreme we have highly tuned engineering-oriented approaches that solve some problems well but drift quite a bit from the more general developmental metaphors inspired by biology. Still a third extreme are those that try to construct as biologically plausible a system as possible, at the expense of clarity and complexity when applied to real problems.
Of course, at the end of the day, most of us are computer scientists and engineers, so biological plausibility is nice but not strictly necessary. And finding the right level of abstraction and the right way to incorporate effective search bias is a difficult problem for virtually every computer scientist. Still, I wondered if your knowledge of the real systems we are (very loosely) mimicking might be useful here.
So, those questions ... or any other constructive reaction to my ramblings, etc.
Thanks.
Sally #30
Sincerely hope you will see this comment and reply, if only with a rasberry.
There never have been any gods and there never will be any.
There never have been any fairys and there never will be any.
There is no heaven and no hell. This is our only life; here and now on this wonderful planet.
These constructs are imaginary. It is one of the strange abilities of humans to have poetical thoughts. Some of us are as good at it as Cuttlefish, OM; but ordinary humans can take delight in the fictions, and then proceed on with regular life.
Sally, just because persons you consider as experts and authorities told you that a cracker can become flesh, they are not telling you a fact. It is fanciful poetry.
About athiests; there are many in the congegations and even in the pulpits. PZ Myers is calling them to be honest. His encouragment brought me out of the closet. The first time I said out loud "I am an athiest"; wow, and shivers with shiny smile. The person I said it to replied, "So am I."
Sally, please respond.
We can embed pictures?!!!
I smell abuse!
So Bishop Pontoppidan, who can't spell himself, is none less than Michael the Archangel? Cool.
But he still hasn't learned to support his wild assertions with the tiniest spark of evidence.
You see, you have fallen among the scientists. Saying something doesn't make it so.
For starters, why can't we see the instructions of our past evolution in our genome? How would that even work, given that genes code for proteins or for regulatory RNA, not for mutations?!?
I get the... nagging suspicion that perhaps, just perhaps, you don't have the slightest inkling what you're talking about.
Posted by: Kim | July 16, 2008 6:06 PM
Sally,The question is why do Catholics think they can resort to violence and death threats?
KIM-- I WOULD ARGUE THAT THESE CATHOLICS AREN'T LIVING OUT THEIR FAITH, OR THAT THEY ARE MISREPRESENTING THEMSELVES IN THEIR POSTS.
Posted by: David Marjanović, OM | July 17, 2008 2:52 PM:
Even if PZ were utterly uneducated and too stupid to read Wikipedia, he was still brought up as a Lutheran, and the Lutheran beliefs about the Eucharist are almost identical to the Catholic ones.
BUT THEY REALLY ARE VERY DIFFERENT BELIEFS. WILL YOU HEAR ME OUT? I WAS RAISED LUTHERAN AS WELL (ELCA). BASICALLY MOST LUTHERAN DENOMINATIONS TEACH THAT THE "CRACKER" BECOMES CHRIST ONLY AT THE TIME IT IS CONSUMED BY A BELIEVER SO IT IS NEVER CHRIST IF IT ISN'T CONSUMED; WHEREAS CATHOLICS BELIEVE THAT ONCE THE "CRACKER" IS CONSECRATED BY A PRIEST, IT REMAINS THE BODY, BLOOD, SOUL AND DIVINITY OF CHRIST.
Why did you even rely on a second-hand source in the first place? Evidently you didn't even know this topic has generated several thousand comments so far on his blog alone
I DID, BUT ADMITTEDLY I WAS SHORT ON TIME AND DIDN'T WANT TO PERUSE THE COMMENTS. I HAD UNDERSTOOD FROM AN INTERVIEW WITH DR. MYERS THAT HE WAS RECEIVING MANY THREATS AND PEOPLE OFFERING TO PRAY FOR HIM BUT NO RATIONAL EXPLANATIONS FOR CATHOLIC BELIEFS, BUT NOW UPON RE-READING THE INTERVIEW I UNDERSTAND THAT HE ACKNOWLEDGED THAT HE DID RECEIVE SOME RATIONAL POSTS FROM CATHOLICS. I DIDN'T ATTEMPT TO EXPLAIN THE CATHOLIC BELIEFS B/C I DIDN'T WANT TO CLOG UP THE COMMENTS ANYMORE - I JUST DIRECTED DR. MYERS TO AN ARTICLE (THANKS FOR TAKING THE TIME TO READ IT DAVID) THAT EXPLAINED WHY PEOPLE WERE SO EMOTIONAL ABOUT THIS ISSUE (WHICH I HOPED WOULD RESONATE WITH DR. MYERS' CONSCIENCE) AND REMINDED HIM THAT HE COULD DO HIS OWN RESEARCH, WHICH I HOPE HE WILL TAKE THE TIME TO DO. SO I'M SORRY TO YOU DAVID AND ALSO TO YOU DR. MYERS FOR THE FURTHER CLOGGING. THIS TOPIC IS JUST CLOSE TO MY HEART B/C I LOVE MY NEWFOUND FAITH SO MUCH AND ALSO B/C I ATTENDED UMM FOR A CLASS ONE SUMMER IN HIGH SCHOOL.
Kim, why are you SHOUTING AT ME!!???
SALLY!!!! I MEA...sorry, I meant "Sally."