PZ Myers. 2004 Jun 12. Bicoid, nanos, and bricolage. <http://pharyngula.org/index/weblog/bicoid_nanos_and_bricolage/>. Accessed 2009 Jul 04.
Posted on M00o93H7pQ09L8X1t49cHY01Z5j4TT91fGfr on Saturday, June 12, 2004
Bicoid, nanos, and bricolage
Intelligent Design creationists are extremely fond of diagrams like those on the right. Textbook illustrators like them because they simplify and make the general organization of the components clear—reducing proteins to smooth ovoids removes distractions from the main points—but creationists like them for the wrong reasons. "Look at that—it's engineered! It's as if God uses a CAD program to design complex biological systems!" They like the implication that everything is done with laser-guided precision, and most importantly, that every piece was designed with intent, to fill a specific role in an apparatus that looks like it came out of a high-tech machine shop at a Boeing aerospace lab.
This is, of course, misleading. Real organelles in biology don't look glossy and slick and mechanical; they look, well, organic, with fuzziness and variability and, most importantly, mistakes and slop. What these biological machines look like is not the precisely engineered output of a modern machine shop, but like bricolage. Bricolage is a term François Jacob used to contrast real biology with the false impression of nature as an engineer. It's an art term, referring to constructions made with whatever is at hand, a pastiche of whatever is just good enough or close enough to the desired result to make do. It covers everything from the sculptures of Alexander Calder to those ticky-tacky souvenirs made from odd bits of driftwood and shells glued together that you can find at seashore gift shops.
The closer we look at the developmental biology of organisms, the more apparent the impromptu, make-do nature of their construction is. This is not to imply that they don't work well or efficiently, but only that the signature of intent is missing. What we see is function cobbled together out of scrap from the junkyard. One clear example of this property is a gene, nanos, in Drosophila.
First, a brief review. Previously, I wrote about maternal effect genes . Some genes, the maternal effect genes, are expressed in the mother's genome and are essential for packaging information into the egg before it is laid. The example I used was bicoid, a gene that is expressed in the mother fly's ovaries and which produces a gene product that is stored in high concentration at the front end of the egg, and at low concentration at the back end. When the embryo is developing, cells can detect the concentration of bicoid and turn on their own, zygotic genes accordingly. The first zygotic genes in the fly are called the gap genes, and they turn on in discrete bands along the length of the embryo. For instance, one gap gene is called hunchback, and it is turned on only where the bicoid concentration is high, at the front end, and it is not turned on at all in the back half of the embryo, and there are other genes that are only active in the back half, and are turned off in the front.
The story is a little more complicated than that. There is this lovely gradient of the bicoid morphogen that is essential for specifying the front end of the animal; lose it by mutation, and the embryo can't make a head. However, there is also a posterior gradient, a substance that is in high concentration in the back and low in front, that is essential for specifying posterior structures. That substance is called nanos, another maternal effect gene. Flies with a mutant nanos gene produce embryos that lack abdomens.
So, the fly actually has two complementary gradients, one of bicoid and another of nanos, both essential for determining the anterior-posterior organization of the animal. The fly invests a lot of effort into setting up these gradients; there is an army of genes (staufen, valois, oskar, vasa, tudor, to name a few) dedicated to making sure that the nanos gradient is set up properly, and another, smaug, that works to prevent any nanos that leaks into the wrong places from getting expressed. Obviously, nanos is mission-critical stuff that has to be in exactly the right place at the right time. What does it do?
I've already explained what bicoid does: it's a transcription factor that binds to DNA and turns genes off and on. Nanos is a little bit weird. All it does, as far as we know, is bind to hunchback RNA and modify it so that it can't be translated. That's it. It's an inhibitor of hunchback activity.
The reason the fly needs that is also illustrated in the diagram above. There's bicoid high at the anterior end, and nanos high at the posterior end, and...hunchback all over the place. Remember that I told you that hunchback is a zygotic gene that is turned on in the embryo in response to bicoid? That's true, but there's another complication: the mother fly also packs the egg with a low level of maternal hunchback RNA. We don't know why. It seems rather useless, and actually interferes with normal development. If nanos is not present, it is the elevated levels of hunchback at the posterior end of the embryo that confuses cells there, and makes them develop into more anterior structures. What the nanos protein does is illustrated here—it simply purges hunchback from the posterior end of the embryo.
There's a telling experiment that reveals how trivial the function of nanos is. We can make flies in the lab that lack maternal nanos. We can make flies that lack maternal hunchback. We can make flies that lack both maternal nanos and maternal hunchback, and here's the kicker, these flies produce embryos that develop completely normally. Maternal hunchback RNA is a mistake, a sloppy bit of unnecessary secretion that does nothing for the embryo, and maternal nanos is an elaborate, Rube-Goldberg mechanism that has been patched in to correct the stupid mistake.
Now if I were an intelligent designer building a fly from scratch, and I saw this little design defect, the way I would correct it is the obvious one: I'd fix the fly ovaries so that they weren't dribbling a completely useless protein into the egg. I wouldn't assemble a complex of a half-dozen proteins that were integrated into the cytoskeleton and pump a hunchback-suppressor to the right place, with other proteins floating around to make sure my hunchback-suppressor didn't do damage in the places where hunchback is supposed to be turned on.
As design, the nanos posterior gradient simply doesn't make sense. As bricolage, however, it's perfectly reasonable. Evolution does not demand a best or elegant solution, only one that works well enough. We suspect that other insects have more essential gradients of posterior positional information, and that Drosophila has inherited this mechanism from ancestors that relied more on it. Flies have some oddities to their development, though, and they've come to depend more and more on the bicoid gradient, and the posterior gradient system has been declining in importance. Nanos localization is a module that's been sitting in the Drosophila junkyard, and now it persists to compensate for a little slack in the mRNA packaging system of the ovaries.
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Dr Myers wrote:
This is not to imply that they don't work well or efficiently, but only that the signature of intent is missing. What we see is function cobbled together out of scrap from the junkyard.
Paul,
The "signature of intent" [B]IS[/B] that they work well and efficiently. You're not seeing the forest for the trees. Look at my web site as an example. I'm not a programmer and I've had to "cobble together" function "out of scrap from the junkyard". No respectable programmer would have done it the way I did it. Does this mean that it wasn't intelligently designed? Intelligence is the ability to solve problems, the ability to coax function out of co-opted materials, making use of what's available. When a chimp fashions a stick in such a way that he can insert it into a termite nest and pull out food, he's using intelligence. The fact that he (or she) used materials "cobbled" from the surroundings does not diminish this accomplishment.
Back when I was teaching computer science to high school students, back in the mid-seventies when 6502 assembler and Basic were common tools, I often asked my students to design simple programs, using the tools that I gave them. Every program was a little different, some used a lot of GOTO's many used FOR-NEXT loops, some employed GOSUBS. But they all worked! Should I have concluded that they were not the product of intelligent design simply because they weren't the most elegant or efficient solutions to the problem?
And what about "bricolage"? Does it not require intelligent input to cobble together function out of scraps? Everything you write points to the inevitable concusion that living systems are not the product of random, accidental occurrences. Everything you explain makes it more obvious that intelligent input is an absolute requirement. I'm really sorry that you don't see that.#: Posted by Charlie Wagner on 06/12 at 03:55 PM -
Hi PZ,
Great post. I guess Charlie goes in for the "third-rate programmer" theory of ID. Still, even a third rate programmer would get around to removing uneccessary bits like maternal nanos and maternal hunchback after a few million years, don't you think?
What I find interesting is that this appears to be an example of "unnecessary irreducible complexity" -- two "parts" that mess things up if either one is alone, but that if they are both removed everything is fine. One of Behe's favorite stories is how Doolittle mistakenly read this notion into a paper on blood-clotting in mice, but here it is in another system. -
Soooo... let me get this straight:
An absolutely perfect and wondrously efficient biological system would be evidence of intelligent design, because it's supposedly too perfect to be the result of natural processes.
A substandard and inefficient biological system would be evidence of intelligent design, because supposedly the only way for random shit to come together into a functioning whole is by intelligence.
So what exactly sort of biological system would *not* be evidence for intelligent design?
Anyway. Enough of the IDiocy... excellent post, Mr. Myers... this sort of stuff is my favorite part of this blog :D#: Posted by on 06/12 at 05:34 PM -
Well obviously God is punishing the unborn flies for something morally wrong that they will do in the future. Like the Oedipus thing. Obviously.
#: Posted by on 06/12 at 06:36 PM
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Charlie Wagner says:
Does it not require intelligent input to cobble together function out of scraps? Everything you write points to the inevitable concusion that living systems are not the product of random, accidental occurrences.
I'm not sure I see the need to attribute "intelligence" to any force that creates "functional" systems. And nobody has argued that living systems are purely the product of "random, accidental occurrences." Natural selection is a well-documented force that acts upon biological variation (random or otherwise) to produce functional systems. Insistence on using words like "intelligence" and "design" to describe living systems does not help us understand how those systems arose.#: Posted by on 06/12 at 07:22 PM -
Patrick wrote:
So what exactly sort of biological system would *not* be evidence for intelligent design?
One that had no structures and no processes and performed no functions. It probably would look something like this:
#: Posted by Charlie Wagner on 06/12 at 07:55 PM -
Charles Winder wrote:
[QUOTE]
Natural selection is a well-documented force that acts upon biological variation (random or otherwise) to produce functional systems.
[/QUOTE]
Natural selection can only act on what is already present. It has no power to produce functional systems or to create new structures or processes. Functional systems require insight to create and insight requires intelligence. Random processes can never produce functional systems because only a designer can know what the intent of the system is and only the designer can determine whether the system is doing what it was intended to do.#: Posted by Charlie Wagner on 06/12 at 08:03 PM -
Charlie, that structure obviously "functions" as an awesome rock-climbing subject, and secondarily as a habitat for plants and animals.
#: Posted by on 06/12 at 08:05 PM
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oic
#: Posted by on 06/12 at 08:07 PM
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Charlie, random processes can indeed create novel variants of existing systems. It's important to keep in mind that evolutionary change happens because of the combination of random mutation and non-random selective processes. Perhaps you are thinking of mutation as something that spontaneously creates "lucky monsters" that deviate greatly from their progenitors, when in fact this is rarely the case. Mutation creates variation in biological characters, and this variation serves as the raw material for directional change in characters over time (in response to selection and other forces). So you're right that natural selection per se doesn't create new variants, but remember that mutational processes do. Events such as genome duplication and reorganization, hybridization, and changes in regulatory genes can greatly amplify the amount of variation available to natural selection, the 'bricoleur.'
#: Posted by on 06/12 at 08:30 PM
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Charles Wagner wrote:
One that had no structures and no processes and performed no functions. It probably would look something like this:
Then, by definition, isn't that a non-living entity?#: Posted by on 06/12 at 08:49 PM - I loved those little "virtual machine" diagrams in primary and high school. They're great when you're starting out on the prickly and mind-bogglingly complex subject of molecular biology. But that's all they are: simplistic teaching aids.
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zed wrote:
Then, by definition, isn't that a non-living entity?
Right. There are no living systems that are not evidence for intelligent design. Only non-living systems show no such evidence.
The photo is Half Dome in Yosemite National Park in California, one of the most beautiful places on earth.
I've probably annoyed Paul enough for one day, so I'll end for this evening with some last thoughts on Ronald Reagan:
http://makeashorterlink.com/?S57222D88#: Posted by Charlie Wagner on 06/12 at 09:04 PM - It sure looks kludgy to me! But one question: If a fly without maternal hunchback develops normally, then wouldn't it be simpler (and therefore more likely to show up) for the hunchback gene to simply get disabled by a mutation? IOW, it sounds like whatever is causing the maternal hunchback RNA to flood the embryo from the mother is a neutral mutation, not harmful. In which case, how come the nanos gene needed to appear in the first place?
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"But they all worked!"
I think that was evidence not of intelligent design but of sloppy program reading/testing.
"Should I have concluded that they were not the product of intelligent design simply because they weren't the most elegant or efficient solutions to the problem?"
In many cases, yes.
-Peter, former TA in comp.sci.#: Posted by on 06/13 at 05:54 AM -
You can't simply knock out hunchback with a mutation. The fly needs a copy for her normal development; no hunchback, and she doesn't make a head. And it is that copy of the gene that is used to make the maternal hunchback she packs into her eggs.
The way it is deleted in the experiments is tricky. The fly is a mosaic, with hunchback deleted in the germ line, where it isn't needed, and left intact in the somatic tissues. -
Quote from Charles Wagner:
Does it not require intelligent input to cobble together function out of scraps?
Ok, going all the way back to the first post, Charles Wagner claims that this jury-rigged design also points to a designer. Several people have done a good job in explaining why that isn't true (no designer is needed), so instead I'd like to point out the consequences of following where Charles Wagner seems to be going.
So is Charles saying that God is incompetent? That God is all-powerful but can't come up with better designs than the idiotic designs like this that we see all over the animal and plant kingdoms? That billions of people worship someone so stupid that they would quickly be fired by any competent engineering manager? Is Charles saying that God flunked out of godschool?
Or instead is Charles saying that God isn't incompetent, but chooses the stupid design anyway? Is that done to trick innocent people so he can eternally torture them in Hell (2Thes 2:11)? Or is it done to cruelly force animals (including us) to suffer with sub-optimally designed bodies? If these bad designs are evidence of intelligent design, then what kind of sadistic intelligence is that? How does anyone know then that the devil didn't create everything, and has God tied up in the back yard, or buried there? Does any upright person really want to worship the creator devil?
If I've offended anyone, I'm sorry. As I said before, I don't see the bad designs as evidence for intelligence. I'm just pointing out that anyone who supports intelligent design is saying some awful things about God (Mk3:29).#: Posted by Jon Cleland Host on 06/17 at 10:38 AM