Comments on: Waiting for the Electrician, or Someone Like Him

By: judy halper

judy halper — Mon, 07 Aug 2006 07:53:11 +0000

Uri Alon is actually an associate professor at the Weizmann Institute, not Tel Aviv University

By: marcel

marcel — Wed, 19 Jul 2006 19:09:53 +0000

Oops. I should read the comments before submitting my own. I’m just too late to the party today.

By: marcel

marcel — Wed, 19 Jul 2006 19:07:12 +0000

“If our genes are wired like circuits, does that mean nature is an electrician?”

Nah. Nature is a civil engineer. Who else would put a sewage canal right in the middle of a recreational area?

By: luca

luca — Wed, 19 Jul 2006 06:45:23 +0000

Carl, you may want to check this press release on bacteria bulding electrical networks…

http://www.pnl.gov/news/release.asp?id=171

just an idea for another post following the thread bacteria/circuits…

Luca

By: Josh

Josh — Wed, 19 Jul 2006 01:26:56 +0000

I’ve always though of engineering firms as somewhat monotheist, where the plebs do the designing and the general manager takes all the credit.
Perhaps this is feudalism?

I don’t really care, if God has to have some plebs do the dirty work for him so be it. He got the job done in the end

http://www.theonion.com/content/node/29057

By: Owlmirror

Owlmirror — Tue, 18 Jul 2006 21:17:20 +0000

This looks like there's a typo:

In 1979 Stephen Jay Gould and Richard Lewontin spandrel. argued that many structures in living things got their start through no help from natural selection.

It would make more sense if it read:

In 1979 Stephen Jay Gould and Richard Lewontin argued that many structures in living things got their start through no help from natural selection.

By: King Aardvark

King Aardvark — Tue, 18 Jul 2006 14:39:10 +0000

Well, that settles it. God is a multi-disciplinary engineering design firm, with an EE department, chem eng department, and a civil (enviro) department. So does this prove that the correct form of ID is multiple designers?

By: Josh

Josh — Tue, 18 Jul 2006 08:55:33 +0000

I always thought of spandrels as more of a structural concept rather than an organisational one, which is what these feed-forward loops seem to be. I think this is an important conceptual difference since the way things are organised as opposed to the way they are built operate along a different premise.
Spandrels are just thrown around liberally with no real policy as to what they actually constitute. If you can’t explain something by natural selection then does it have to be a spandrel? Perhaps an adaptation, but a gene network?
The gene regulatory networks look remarkably like the diagrams that ecologists were doing for keystone species back in the 70s and 80s. This is where one species has a seemingly disproportionate effect on the ecosystem. Surely keystone species cannot be spandrels, but perhaps my analogy is wrong.
I would still say an organisation principle is just an organisation principle, and a spandrel is just a fluke, a chance hapening that turns out to have some benefit, not something that you would expect again and again.

By: snaxalotl

snaxalotl — Tue, 18 Jul 2006 06:35:59 +0000

you might have rushed to wikipedia too quickly. there are two meanings for feedforward. In the biological sciences (especially neural networks) feedforward usually just means “without feedback”, i.e. an output doesn’t loop back to provide input to an earlier stage of the chain. In engineering, and I believe this is the older and certainly less namby-pamby version, feedforward generally means a feedback control system where the thing that is being monitored is not the desired outcome variable, but a predictor of the desired outcome. For example, instead of a heater monitoring (and responding to) the temperature of a room, you can monitor the difference between outside and inside temperature, use the wall insulation value to predict the temperature in five minutes, and pump in the amount of energy which will counteract that predicted effect. The example you show in figure 1 is the first sort, but where there is any sort of loop you would usually be talking about the second sort, although I haven’t looked through the material enough to work out which sort any of the examples are talking about.

By: SMgr

SMgr — Tue, 18 Jul 2006 01:49:25 +0000

re: the above link. Remove the period and it works.

By: SMgr

SMgr — Tue, 18 Jul 2006 01:35:24 +0000

Also related would be John R. Koza's work in Genetic Programming that has been able to reproduce a sizable number of electronic circuits using Darwinian principles. A partial online list is available at http://www.genetic-programming.com/humancompetitive.html. His book "Genetic Programming III" has some wonderful sequences of circuits gradually becoming more accurate and complex over a number of generations. For example, Chapter 31, "Synthesis of an Asymmetric Bandpass Filter".

By: tdj

tdj — Mon, 17 Jul 2006 20:56:18 +0000

Three engineers are discussing the nature of God. The electrical engineer says, “God is a EE! It’s all circuits and neural nets.”

The chemical engineer replies, “Nah, God’s a ChemE. Those circuits all boil down to diffusion and chemical kinetics.”

The civil engineer pauses, then says, “I’m pretty sure God is a civil engineer. Only a civil engineer would put a wastewater line through a recreational facility.”

By: Timothy Chase

Timothy Chase — Mon, 17 Jul 2006 20:56:03 +0000

Some of the more interesting work being done in the investigation of gene regulatory networks is by Michael Levine and Eric Davidson. What they have found, for example, is that there exist gene regulatory network kernels which tend to be conserved once they have been developed even among fairly distant species over hundreds of millions of years. Much of the rest of the network will change, but typically through the addition of later GRN kernels.

Here is a link to one of their papers. I can look up more later.

PERSPECTIVES
Gene regulatory networks for development
Michael Levine, and Eric H. Davidson
PNAS | April 5, 2005 | vol. 102 | no. 14 | 4936-4942
http://www.pnas.org/cgi/content/full/102/14/4936

Now it has been argued that modularity tends to be the result whenever gene duplication takes place, and this may very well be the case in the long run, and no doubt this tends to explain how much of the modularity we see comes into existence. However, in the case of the bat wing (as studied by comparing gene regulation in the fruit bat, a species of mouse and humans) there are times when two proteins will play essentially the same role in the network. This too, I believe is to be expected as the result of a form of network redundancy which results in developmental and environmental robustness.

Taking this somewhat further, what we have seen so far in gene regulatory networks is a kind of scale-free, small world – similar to those found in many areas – and which tend to arise systemically simply as the result of the natural evolution of networks. (For comparison, bacteria evidently also employ the same sort of network for lateral gene transfer involving drug resistance and pathogenicity. Likewise, phages play an important role in such networks and appear to be fairly modular in terms of how they are constructed and trade in genetic components.) However,in some cases, there appear to be at least local violations to scale-free structures in gene regulatory networks. For example, I remember reading not too long ago that the network for yeast (which has been largely mapped) involves an exponential core – perhaps a preserved relic from the origin of the network itself.

Two points which are a bit more tangential:

1. It has been recognized that a great deal of genetic variation is cryptic and thus is not expressed at the level of phenotype. This, it has been suggested, is largely the result of of the canalization of such networks as is required for robustness. However, when perhaps a one or another key gene is knocked out or is subject to mutation, a fair amount of this variation is unmasked, consequently being made visible to selection and results in the release of evolutionary potential. At some later point, evolutionary developments are stablized by further mutations, resulting in the recovery of robustness.

2. With respect to the bat wing, it appears that what occurs is a shift in the expression of HOXd13 towards the posterior late in the embryonic development of the bat, increasing the expression of bone morphogenic protein 2 by 30%, lengthening the “forearm” by a factor of 2 and at least two digits by a factor of 6 to 8. Such shifting HOX zones seems to be the cause of much of the modification of tetrapod bodyplans – and goes a long way towards explaining the allometric relationships between fairly divergent species which were discovered quite some time ago.

By: RPM

RPM — Mon, 17 Jul 2006 20:48:50 +0000

Is the next post on scale free networks?

By: Scott Belyea

Scott Belyea — Mon, 17 Jul 2006 18:21:31 +0000

FYI ... http://www.firesigntheater.com/albums/album.php?album=wfte is the correct URL, but it isn't clickable in the post because the actual link was messed up ...