It’s not just the genes, it’s the links between them

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Once upon a time, I was one of those nerds who hung around Radio Shack and played about with LEDs and resistors and capacitors; I know how to solder and I took my first old 8-bit computer apart and put it back together again with "improvements." In grad school I was in a neuroscience department, so I know about electrodes and ground wires and FETs and amplifiers and stimulators. Here's something else I know: those generic components in this picture don't do much on their own. You can work out the electrical properties of each piece, but a radio or computer or stereo is much, much more than a catalog of components or a parts list.


Electronics geeks know the really fun stuff starts to happen when you assemble those components into circuits. That's where the significant work lies and where the actual function of the device is generated—take apart your computer, your PDA, your cell phone, your digital camera and you'll see similar elements everywhere, and the same familiar components you can find in your Mouser catalog. As miniaturization progresses, of course, more and more of that functionality is hidden away in tiny integrated circuits…but peel away the black plastic of those chips, and you again find resistors and transistors and capacitors all strung together in specific arrangements to generate specific functions.

We're discovering the same thing about genomes.

The various genome projects have basically produced for us a complete parts list—a catalog of bits in our toolbox. That list is incredibly useful, of course, and represents an essential starting point, but how a genome produces an organism is actually a product of the interactions between genes and gene products and the cytoplasm and environment, and what we need next is an understanding of the circuitry: how Gene X expression is connected to Gene Y expression and what the two together do to Gene Z. Some scientists are suggesting that an understanding of the circuitry of the genome is going to explain some significant evolutionary phenomena, such as the Cambrian explosion and the conservation of core genetic processes.

Continue reading "It's not just the genes, it's the links between them" (on Pharyngula)

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Myers says: Once upon a time, I was one of those nerds who hung around Radio Shack and played about with LEDs and resistors and capacitors; I know how to solder and I took my first old 8-bit computer apart and put it back together again with “im... Read More


Thanks, PZ, it’s always nice to wake up to a good exposition of breaking science at the Panda’s Thumb. And as usual these days, research that goes very far into biology runs right into evolution.

One bit from the extended article:

First, though, a little caveat. As in my introduction above, Davidson and Erwin use the language of electronic circuitry to explain what they are seeing. Metaphors are very dangerous things, and I have a feeling that they are pushing the metaphor a little too hard, at the risk of obscuring substantial differences between fluid gene interactions in a cytoplasm and a layout of wires and widgets on a circuit board. Metaphors are also powerful communication tools, an effective way to get an idea across, so I’m indulging in it here…just be warned, at some point we’ve also got to leave this metaphor behind and treat the epigenetic activity of the cell on its own terms. Just not today.

That said, here is a little background for the interested: Gene regulatory networks, - the basics, and the classical lac operon.

This post also brings up the much abused term ‘neoDarwinism’. Of course there was a time before DNA was known to be the genetic material. But soon after the famous double helix was discovered, research into genetic control took off. Tomorrow’s discoveries are not yet today’s “neoDarwinism” but gene regulation is now classic. It’s your father’s neoDarwinism even if not your grandfather’s.

I was wondering how long it would take some creationist to distort this metaphor into an “admission” that DNA is “designed”.

Looks like Dembski has done it himself.

The comments are track-backed below, but, since I’m procrastinating from real work…with my own “fisking” in italics..Dembski says…

“Good grief, Myers. This is a prime example why biologists aren’t qualified to recognize design.

This constant refrain is amazingly illogical. First of all, it assumes that all “biologists” are neatly seperated from other scientific disciplines - that no-one is a biologist AND and engineer - which is nonsense. There are innumerable cross-trained biologists, and anyone who wants a biology degree has to get some grounding in the other major scientific disciplines. That’s why math, physics, chemistry, etc are constantly and easily applied in modern biology. Actually, Myers’ early expertise in electronics is an example of such cross-training. This craziness also implies that actually learning about life and living organisms by studying them (ie practicing biology) makes you less able to understand them

What you think you’re just discovering is something I recognized decades ago.

It’s fairly obvious that PZ Myers isn’t “discovering” any agreement with Dembski, but merely drawing up a metaphor. However, it’s valuable to see how Dembski behaves when he thinks someone has been “converted” - with uncivil contempt.

The flagellum for example isn’t the sum of its proteins. While each individual protein is complex in its own right, the assembly instructions are the real specified complexity.

Define “specified complexity”. Explain how “complexity” is measured, and against what benchmark flagellar proteins are “complex” (note - I’m not saying they’re not). What do you mean by “sum of its proteins”? And why does any of this blather have anything to do with whether or not the bacterial flagellum evolved? These are just technical-sounding words.

Design engineers recognize that immediately

What the Sam Hill is a “design engineer”? How does their training and professional qualification compare to that of say, electrical, mechanical, or chemical engineers? And what do they recognize, in meaningful English this time? and it’s taken you what, 20 years to begin catching on?”

no comments here - the deluded arrogance of the statement speaks for itself..

Harold, It was Davescot who wrote that post, not Dembski. While I agree that his points are absurd, he is not incorrect in using the term design engineer. It refers to somebody who builds systems of things and can come from backgrounds in either electrical, computer or mechanical engineering.

Regarding DaveScot’s armchair claim that engineers knew this long ago, realize who’s doing the normal science here. Normal science, according to Kuhn, is what is made possible by a successful paradigm. Scientific breakthroughs are certified when they lead to lots of productive normal science. DaveScot can claim prior art all he wants, but his paradigm of design isn’t leading to any normal science. So far, it only led to sneering engineers such as DaveScot, making arrogant claims on web pages. The normal science is being done by the people with the most productive paradigm, the evolutionary biologists.

Dembski announced the failure of ID when he said it was not capable of explaining the “pathetic details”. He said, in other words, that ID can’t lead to normal science.

PZ Meyers show how the comments by Paul Nelson and Cordova on Uncommon descent about the recent work by Davidson et al totally miss the point.

Notice once again the total lack of any ID relevant hypothesis beyond the insistance to show that neo-Darwinian theory is incomplete? Duh.… the whole Evo-Devo movement is about reconciling evolution and development. ID proponents have since long quote mined people like Valentine, Davidson or Erwin to argue their ‘Cambrian explosion cannot be explained hence design’ thesis. Not only are these authors strongly opposed to ID, but their actual work shows how regularity and chance processes can explain the Cambrian explosion and many other features of life. While science is uncovered incredible details about life, and provides explanation, ID remains totally empty in the darkness of ignorance, a spot which is becoming increasingly smaller.

For some indepth analysis see PZ Myers excellent overview or The Fine Art of Quote-Mining by Steve Verdon.

Speaking of the vacuity of ID, when can we expect Paul’s book to be published? Was it not pre-announced almost a decade ago? And what about the paper on ontogenetic depth? Yet another concept that has failed to deliver?

Seem Paul has taken notice Reading comprehension tutorial. Not very convincing but Paul has shown that the list of 400 or so scientists doubting the sufficiency of natural selection hardly make a case for intelligent design. It basically conflates the fact that even Darwin did not believe that Natural selection was sufficient with the idea that there is a true controversy about evolution in the sense of ‘did evolution happen’ rather than ‘how did evolution happen’.

Neo-Darwinian theory reconciled Darwinism and the gene. It’s time to reconcile Neo-Darwinism and developmental evolution. Notice how Cordova on UcD seems to believe that there is something scandalous or that Davidson’s comments somehow undermine Darwinian theory. Science proceeds and while Neo-Darwinian theory, like Newtonian physics, was extremely able to explain data and observations, science has progressed and a new revolution which adds our increased understanding of the role of development in evolution to Neo-Darwinian theory may be long overdue.

I’d love to hear Davidson’s comments in context.

As Modulus argues

Had a look at the page. It quotes Eric Davidson as saying “Neo-Darwinism is dead,” but I can’t find the original quote. Note however, he didn’t say the Theory of Evolution. And also note that this is suspiciously similar to something Gould said 25 years ago: “the neo-Darwinism synthesis is effectively dead, despite its continued presence as textbook orthodoxy.” (Stephen Jay Gould, Is a New and General Theory of Evolution Emerging? 6 Paleobiology 119, 119—20 (1980)

And remember that Nelson and Wells ‘argued’

In this article we review in broad outline some of the major difficulties with the neo-Darwinian explanation of homology, in particular, the incongruent causal relationship between genes, development, and phenotypic form. Despite the standard textbook claims, homology has never been adequately explained by neo-Darwinism. The time is ripe, we contend, to reconsider biology’s exclusion of intelligent design as a possible cause.

While Nelson may not have mentioned ID he surely seems to believe that the lack of explanation of homology (at least according to Nelson) should be evidence to reconsider biology’s exclusion of ID. Of course, Davidson may have argued that Neo-Darwinism is failing in this area but rather than take Paul’s advice he has presented scientific explanations for these data.

ID activists take great effort in trying to create the impression that there is a controversy in evolution but in the end it all comes down to introducing ID as a possible cause.

But why? ID as a possible cause is scientifically vacuous?

And what is Davidson’s argument to state that neo-darwinism ‘is dead’? Nelson explains this in his ISCID chat

Paul Nelson Wrote:

Some authors have recently noted this explicitly, e.g., Davidson 2001. He writes: “ …classical Darwinian evolution could not have provided an explanation, in a mechanistically relevant way, of how the diverse forms of animal life actually arose during evolution, because it matured before molecular biology provided explanations of the developmental process.”

Davidson, Eric. 2001. Genomic Regulatory Systems: Development and Evolution. New York: Academic Press.

Quite a different picture. Neo-Darwinism is dead as much as Newtonian Physics is dead. The King is dead long live the king :-)

On thoughts from Kansas Josh Rosenau comments on Nelson’s claim

Paul Nelson quotes Eric Davidson as asserting that “standard single-base-pair mutations” are “the textbook neo-Darwinism every college biology student learns.” It may be that Nelson is misunderstanding, but to claim that the only sort of mutation is a “single-base-pair mutation” is stupid. The first phrase is Paul Nelson quoting Davidson, the second is me quoting Nelson paraphrasing something he thinks Davidson told him.

Paul Nelson and Cordova

Hey, bring those guys by. I have a few questions for both of them that they seem to keep running away from. …

Paul Nelson writes:

… some of you people need to calm the heck down. Have a beer. Watch the Olympics. Get your ass away from the computer screen for longer than five minutes.

Sorry, no deal, Paul. We have learned the price of complacency while anti-science forces plot their next big surprise. From now on, we’re going to be scrutinizing your every move, every word you write, and every talk you give. As we say in this neck of the woods, time to turn the lights on, and watch the roaches run.

Note how at UC DaveFascist makes an idiotic analogy of gears and chains. Is he writing from an asylum?[…]omment-24753

First of all, and I must say I never thought I’d say this, my apologies to Dembski, for confusing him with DaveScot.

Second of all, some here seem to believe that DaveScot refers to all engineers who design anything, that is, darn near any working engineer, when he refers to “design engineers”.

If so, he’s making a libelous statement. He’s essentially claiming that all engineers are “crID Proponentists”. I would urge all professional engineering societies, and as many individual engineers as possible, to a) request that he clarify or retract the statement and b) take appropriate legal action if he doesn’t.

What was it DaveScot said, unwittingly, about Paul Nelson…?

“You certainly don’t have to agree here with descent with modification from a common ancestor but I’m going to start clamping down on anyone positively arguing against it. It’s simply counter-productive to our goals and reinforces the idea that ID is religion because nothing but religion argues against descent with modification from a common ancestor.”

hehehehe SteveS Yeah that was pretty funny .…evil darwinbot Dave Scott breaks off the leash and monsters one of ‘Count’ Don DemQuixote’s pulp fiction buddies.

Must have got his gears and chains well and truly ‘adjusted’ after Dr William Strangelove got a call from Paul “I see no evilution” Nelson warning him about the damage to his retainers.

Ahhh .…you just can’t make this stuff up.


Paul Nelson quotes Eric Davidson as asserting that “standard single-base-pair mutations” are “the textbook neo-Darwinism every college biology student learns.”

If that’s the definition of “neo-Darwinism”, then we can all go home now.

I don’t know of anyone that subscribes to the notion that point mutations are the most important, let alone only, mechanism of evolution.

If Nelson really thinks that Davidson and Erwin’s issues have anything to do with “the” controversy being peddled by the Disco Inst, he’s seriously delusional. But then, being a self-proclaimed YECer, he must be comfortable with serious self-delusion.

Is this the science they think is being “censored” in Dover and in Ohio?

The thought of Paul traveling half-way around the world (I guess on the Disco Inst’s dime) to pester actual scientists with his Sunday school notions of biology is simultaneously touchingly pathetic and hilarious.


Seven years ago, I was sitting outside a hotel in China waiting for lunch to start (yes, I worked at gaining weight back then), when Caltech developmental biologist Eric Davidson walked up and asked me why I was carrying a diagram from one of his papers. The diagram depicted the complex control region of the Endo16 gene in sea urchins. I told him that I wanted to ask conference participants what process they thought had constructed the highly specified genetic circuitry (over a dozen DNA-binding proteins, interacting at nearly three dozen binding sites, to construct the sea urchin gut) – what Davidson described as “information processing units ‘wired’ into the regulatory network so that they receive multiple inputs” (2001, p. 7).

I can’t believe it, my co-worker just bought a car for $63326. Isn’t that crazy!

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This page contains a single entry by PZ Myers published on February 18, 2006 9:23 PM.

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