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Date: 2003/01/19 01:45:45, Link
Author: lpetrich
Taken from two postings in the thread "The Multi-Design Inference" over at the Internet Infidels.

This is an inference that multiple designers had designed some entities; this is a natural extension of Dembski's "Design Inference". And it is an inference often made about human designers.

This is an essential part of efforts to detect forged signatures; handwriting styles are individualized, and a close examination of a signature may reveal whether it was written with an imperfect imitation of someone else's style.

Handwriting analysis has also been useful in archeology; by that means, it was shown that the various Mycenaean Linear B tablets had been written by several scribes, each of whom had written several tablets.

Such stylistic analyses have been used in other fields; much of the debate about the authorship of various parts of the Bible has been based on stylistic analyses -- characteristic vocabulary, preoccupations, etc. More recently, the Unabomber was identified when someone recognized some familiar styling in the text of his manifesto.

Applying that to the world of life, one concludes that if many features had been designed, then there had likely been more than one designer. Camera-like eyes are sometimes pointed to as examples of design, but those of vertebrates have one characteristic architecture and those of cephalopods have another. So could there have been a separate designer for each? Charles Darwin himself, in his creationist years, had concluded that Australia's distinctive fauna might suggest that "there had been two Creators at work."

Likewise, predator-prey relationships suggest multiple designers, one for the predators and one for the prey, because predators are adapted for finding and catching prey, and prey are adapted for avoiding and resisting predators. Multiple food-chain levels suggest additional designers. Thus, in a grass-deer-wolf food chain, with deer eating grass and wolves eating deer, the grass, deer, and wolves had had separate designers.

Host-parasite relationships are a close analogue of predator-prey relationships, with parasites being adapted to live off of their hosts and hosts being adapted to resist their parasites. Thus, in this example, the wolves can be afflicted with fleas, heartworms, and distemper viruses, adding yet another designer to the list.

In an attempted rebuttal, Walter ReMine has claimed to have demonstrated that there had only been one designer, but I've yet to see his "proof".

The multi-design inference must be an embarrassment for the Intelligent Design movement, because it goes against the theological predilections of many of its participants. However, I doubt that those like the Raelians would be terribly bothered by a multi-design inference.

However, it must be conceded that single superpowerful designer can imitate several less-powerful designers. But the trouble is that such a hypothesis tends to lack falsifiability; for sufficiently powerful designers, it would be difficult to rule out hypotheses like creation with apparent age, like Philip Gosse's Omphalos hypothesis.

Also, there is a parallel to the single-powerful-designer hypothesis in Biblical criticism.

Among present-day scholars, the favorite hypothesis of the authorship of its first five books is the JEDP hypothesis, which posits four separate sets of authors, each with a characteristic vocabulary and preoccupations.

The traditional hypothesis, however, is that all those five books had been written by Moses and only Moses, and its present-day defenders maintain that he had repeatedly switched stylistic gears as he wrote.

Date: 2003/01/19 02:20:58, Link
Author: lpetrich
William Dembski apparently believes that beavers intelligently design their dams.

However, beavers have some sort of dam-building instinct that consists of placing sticks and mud wherever they hear rushing water, such as at an underwater speaker playing that sound. This document on beaver control warns about that, and understanding that has enabled the design of a Beaver Deceiver fence around a culvert inlet.

I find it curious that both supporters and critics of Intelligent Design theory have said so little about the question of intelligent design by species other than Homo sapiens, because there is an abundance of seeming evidence of such design, like beaver dams, spiderwebs, and so forth. And if much of that is true intelligent design, then we have an abundance of nonhuman intelligent design right under our noses, in a sometimes very literal sense!

Animal-intelligent-design capability is part of a lot of folklore, and many pet owners seem to think that their pets have that capability. And the reputable biologist George Romanes had offered numerous seeming examples of that capability in the late 19th cy. Only to be repeatedly ridiculed later as an example of how not to do animal-behavior research.

Much animal behavior has been found to be a combination of instinct and simple forms of learning, though the instincts involved may be very complicated, and though instinct and learning are often closely intertwined. For example, web-building spiders know how to build their webs without being taught, and the webs they build have a stereotyped, species-specific architecture, despite their complexity. There has been some simulated-spider research that implements web building with a combination of algorithms with the form of "if you feel this configuration of nearby strands, go here".

And much animal learning would be hard to call intelligent design on the animal's part; this includes mechanisms like

Imprinting (Konrad Lorenz became the "mother" of some geese)
Habituation (not responding to "meaningless" stimuli)
Latent learning (wandering around and picking up detail)
Classical/Pavlovian conditioning
Instrumental/operant conditioning

There is an exception:

Insight learning (pausing and then implementing a solution)

This may be called a form of intelligent designing. But it has been seen in only a few species, most notably chimpanzees. So one reasonably concludes that the intelligent-design ability is rare in the animal kingdom. And the closeness to our species of the main counterexample is consistent with what one would expect from evolutionary biology -- in fact, Wolfgang Koehler had used evolutionary biology to decide on an experimental subject for his pioneering experiments.

And what, precisely, might Koehler's chimps have been doing? An analogy with human problem-solving suggests that they were manipulating a mental model of their solution before implementing that model. Thus, a chimp who sees a lot of crates and an out-of-reach banana may imagine crates stacked on other crates to reach that banana before actually trying to stack those crates.

So performing intelligent design may simply be manipulating a mental model of something before building it. Thus, if I wish to build a dam across a creek, I don't get seized with an uncontrollable urge to collect mud and sticks and place it where I hear rushing water. Instead, I picture in my mind that dam and imagine where best to place it and how I'd build it.

By contrast, intelligent-design advocates generally treat intelligent design as some sort of unanalyzable fundamental principle.

And from the occurrence of structures that appear to be produced by intelligent design, but that are not, one obtains a powerful counterargument to the "design inference".

One counterargument is that spiders, beavers, etc. were designed with their instincts, but that does not change how the appearance of design had been produced by a non-design mechanism. The ultimate origin of those instincts is an entirely separate question.

Date: 2003/01/20 04:09:01, Link
Author: lpetrich
Thanx. I downloaded and read the whole book; it was nice to discover that it also referred to mental modeling as an important ability.

There was an interesting experiment mentioned in it (chapter 9) for finding out how chickens and chimpanzees find their way around obstacles:

It turns out that chickens and chimpanzees differ markedly on the Umweg task. Whereas chickens can solve the problem only if their frantic movements bring them by chance to a spot where they can see the path around the obstacle, chimpanzees can more calmly examine the situation and then simply walk around the barrier to obtain the object. So chickens must rely on the variation and selection of overt behaviors, but larger-brained chimps are able to substitute the variation and selection of mental processes for overt behavior.

Thus, chimps can do intelligent designing, while chickens cannot -- at least as judged from their behavior.

Date: 2003/01/24 22:28:11, Link
Author: lpetrich
Self-recognition is an ability possessed by very few species. Human children acquire that ability at about 18 mos - 2 years of age, but great apes acquire that ability at adolescence. Outside of Pongidae/Hominidae (Pongohominidae?), the only species that show evidence of self-recognition are the bottlenose dolphin and the Asian elephant (the most common captive cetaceans and proboscideans, however).

And self-recognition may be a byproduct of a more general mental-modeling capability, with the model being of oneself.

Date: 2003/02/02 17:14:46, Link
Author: lpetrich
I wish to propose an analogy that may be helpful in understanding the evolution of irreducible complexity.

Honeybee societies.

Honeybee hives contain a queen, as many as 10,000 workers, and some drones (male bees). The queen depends on the workers for all her needs -- food, shelter, protection, etc., while the workers depend on the queen to replenish their numbers. Queens cannot exist without workers, and workers cannot exist without queens. Thus, irreducible complexity.

This total dependency extends to the founding of new hives. Workers do all the work of founding; they scout for hive locations and then go to whichever one attracts the most interest. And then they do all the work of construction in that location.

Compare solitary bees, in which a female does all the tasks that honeybee queens and workers do, though with much simpler nests.

Which makes it seem difficult to picture how honeybee societies could have been a result of evolution by natural selection, or at least that's what an entomological counterpart of Michael Behe would say.

But fortunately, the diversity of life offers examples with a very plausible intermediate state: bumblebees. A bumblebee queen overwinters in isolation and founds a hive in the coming spring, constructing it and bringing food to her offspring in the fashion of a solitary bee. But her offspring become workers who help her with the next generations over the year.

Thus, the evolution of honeybees can be broken up into two steps:

1. Some of a female's daughters staying home and helping to raise that female's other offspring, thus the evolution of the queen/worker distinction.

2. A queen recruiting some workers to help found a hive, thus giving that queen "instant" workers at that new hive. This makes it unnecessary for a queen to do anything but lay eggs all day.

Michael Behe's work, it seems to me, focuses on the molecular equivalent of honeybees; the challenge for understanding the origin of these features is to find the molecular equivalent of bumblebees, or at least work out some plausible scenario for their occurrence. And biologist Kenneth R. Miller has attempted to do exactly that, finding plausible bumblebees for the bacterial flagellum's honeybee.

I think that he'd have a bit more respect if he simply decided that the origin of what he discusses is a mystery. he could have been like Robert Shapiro, who has criticized various origin-of-life scenarios in detail without claiming that that means that the Earth had been "seeded" with its first organisms.

Date: 2003/02/11 01:38:28, Link
Author: lpetrich
Over in this Internet Infidels thread, I had posted some interesting recent research into the evolution of life before the Last Universal Common Ancestor (LUA, LCA, LUCA) of all known cellular Earth life. To summarize, both papers I'd looked at point to the earliest Earth life as being closer to prebiotic chemistry than more recent life. And the second paper points to evidence of much less complexity in the earliest life.

The enormous volume of genetic data collected over the last few decades, including the sequencing of over 100 genomes, has made possible the reconstruction of several of the genes and proteins contained by the Last Universal Common Ancestor.

The amino-acid content of these proteins is interesting; according to the work of Brooks DJ, Fresco JR, Lesk AM, Singh M, the LUCA's proteins were enhanced in amino acids known to be produced in prebiotic-synthesis experiments, and depleted in amino acids known to be rare or absent in such experiments. This adds support to the hypothesis that the original source of amino acids was prebiotic synthesis; the earliest organisms simply eat some Primordial Soup.

By comparison, Brian K. Davis's work focuses on 10 proteins, and uses a different criterion for assigning amino-acid origin time; how many metabolic steps are necessary to produce some amino acid from a Krebs-Cycle predecessor. Aspartate and glutamate, for example, score very low, while lysine and arginine score very high. The low scorers are also those relatively abundant in prebiotic syntheses, which suggest that biosynthesis of them was developed as a substitute for Primordial-Soup eating (the Horowitz hypothesis).

The "code age" of a protein he determined by finding the average score of its amino acids; he used this to work out the proteins' order of appearance.

The oldest of these proteins was ferredoxin, a biosynthesis enzyme that contains iron-sulfur clusters and that transfers electrons (hydrogen-atom equivalents). This protein he reconstructs as having a negatively-charged tail; this can stick to positively-charged objects like mineral surfaces with their metal ions -- which is consistent with the view of Gunter Wachtershauser that life originated from iron-sulfur-associated chemical reactions on mineral surfaces, and that the Krebs Cycle dates from this time. Note that the Krebs Cycle's members are all acids -- negatively-charged ions -- meaning that they can stick to mineral surfaces.

This suggests that the earliest life had not had well-defined cells, that it had been a sort of Haeckelian Urschleim living in the mud of hydrothermal vents.

Not much younger than ferredoxin is a protein involved in cell division and an ATPase component that resides in cell membranes; as a consequence, nearly all the rest of Brian Davis's scenario takes place in distinct cells, including the acquisition of "difficult" amino acids like the benzene-ring and alkaline ones.

Also after the origin of cells but before the LUCA is the origin of DNA; enzymes for synthesizing DNA nucleotides from RNA ones, copying DNA to RNA, and copying RNA to DNA date from this period. So DNA is younger than both RNA and proteins.

However, DNA-to-DNA copying systems are much more difficult to place in this period, since those of the (eu)bacterial and the archaeo-eukaryotic lineages are very different, suggesting separate elaboration -- or even separate origin. The LUCA could have had a DNA-RNA genome, with DNA being copied to RNA and back.

Brian Davis's paper did not address the RNA-world question, but his work suggests that an RNA world, if it had existed, had been pre-cellular.

An interesting result is that the earliest Earth life is closer to various sorts of prebiotic chemistry than later Earth life. This poses an interesting conundrum for the hypothesis that some designer had "seeded" the Earth with some organism that became the ancestor of all its later life. Why this choice of "seed"? Why not a "seed" with a chemistry more like that of present-day organisms?

Also interesting is the absence from the earliest life of DNA, distinct cells, and several amino acids; this indicates the absence of the enzyme systems necessary for constructing and handling them. Thus, the origin of life has to account for much less complexity than one would expect from present-day cell architecture.


Brooks DJ, Fresco JR, Lesk AM, Singh M.
Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.
Mol Biol Evol  2002 Oct;19(10):1645-55
At this PubMed entry.

Davis BK.
Molecular evolution before the origin of species.
Prog Biophys Mol Biol  2002 May-Jul;79(1-3):77-133
At this PubMed entry.

Date: 2003/04/13 19:20:52, Link
Author: lpetrich
I'm posting my announcement here because I don't know where a good place for it is; it's not YEC, and it's not explicitly "Intelligent Design".

Here is one of that debate's home pages. Walter ReMine has just submitted his final contribution, the final one of the debate. The subject:

"Comparisons of molecules (proteins, DNA) of various species provide independent and compelling support for the hypothesis of biological macro-evolution"

It seems to me that Dave Thomas has made a much more reasonable case than Walter ReMine, who liked to wander all over the place without really explaining what his "Message Theory" was. ReMine often seemed to me to not really understand what he was talking about, and he has apparently spent a sizable amount of time working in a quote mine.

Date: 2003/10/09 15:29:29, Link
Author: lpetrich
Has anyone tried to explore why creationism has been so politicized? Politicization is not very common among pseudoscientists, even those who advocate very popular beliefs.

Astrologers, for example, are apolitical; they don't seem to want equal time for astrology in astronomy classes.

But a better comparison is with vitalism, the view that the processes of living things are due to some "vital force." It is a centuries-old view that survives as the "theoretical justification" of certain "alternative medical therapes." Aristotle had even identified three kinds of this force: the vegetable soul, the animal soul, and the rational soul.

But vitalism has suffered defeat after defeat after crushing defeat over the last few centuries, and it has become totally discredited among respectable scientists. Though there are still plenty of physiological puzzles, "vitalism of the gaps" is never thought worth considering.

Vitalists can easily make arguments parallel to creationists, like mentioning physiological processes that continue to be puzzles, the simplicity of "VitalForceDoesIt", how teenagers would be more likely to commit suicide and kill their classmates if they believe themselves to be biochemical robots rather than animated by some "vital force", etc.

Yet vitalists are apolitical, not wanting equal time for vitalism in classrooms. And creationists who appear to believe in some form of vitalism do not make an issue out of it, and coexist with apparently non-vitalist creationists like Michael Behe.

Notable politicized pseudosciences in the past have been Hanns Hörbiger's Welteislehre (Cosmic Ice Theory) and Lysenkoism.

The advocates of the Cosmic Ice Theory would apply pressure to get people to accept the theory; they were known to heckle astronomers' meetings with "Out with astronomical orthodoxy! Give us Hörbiger!". They even aligned themselves with Nazism, though the Nazi Party never officially endorsed it.

Trofim Lysenko had claimed that he could breed improved crop plants by altering their heredity; he believed that genes do not exist. He claimed impressive "results", but his experimental procedures were shoddy beyond belief -- he had no conception of a controlled experiment, and he believed that doing statistics is a waste of time. However, he got the support of Joseph Stalin himself, and mainstream geneticists were forced to recant, sent to gulags, or executed. Even the great biologist Nikolai Vavilov could not escape; he was sent to prison for allegedly being a British spy, dying there.

Date: 2003/10/24 01:25:40, Link
Author: lpetrich
An article in , How I decoded the human genome, features this comment from someone with a long career in programming:
Kent spoke to me in nerdspeak, with geekoid locutions such as the use of "build" as a noun: "That's the most recent build of the genome. Build 31." I was used to hearing biologists talking about the elegance of DNA with what might be called reverence. By contrast Kent spoke of DNA as if it were the most convoluted, ill-documented, haphazardly maintained spaghetti code -- not God's most sublime handiwork, but some hack's kludge riddled with countless generations of side effects, and "parasites on parasites."

"It's a massive system to reverse-engineer," he said. "DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes ... the analogy breaks down at the margins but offers useful insights." It was nearly impossible to tell the working code from cruft, Kent said. "That's why a lot of people say, 'The genome is junk.'" But that's what he found interesting: a high-quality programmer's code is always self-evident, but legacy assembler handed down from generation to generation of bricoleurs (I'm paraphrasing again) provides a real challenge for people who like puzzles.

A bricoleur is a tinkerer, someone who constructs with whatever is available.

Date: 2003/11/15 09:42:49, Link
Author: lpetrich
The problem there is that different Christian sects vary widely in how political they are, no matter what the Bible says. Never underestimate the ability of a believer in a sacred book to argue away awkward parts of that book.

So one must look at fundamentalism, especially American fundamentalism, more closely -- and even a cursory glance reveals that some fundies are almost obsessively political. So one has to ask why they make a big issue out of creationism, and not vitalism.

Date: 2005/02/10 06:46:01, Link
Author: lpetrich
And Dembski has it all wrong about the methods of SETI.

SETI researchers devise their strategies by trying to work out what some extraterrestrial-signal designer might want to design, rather than use some measure of "complex specified information" or "specified complexity" or whatever.

For instance, most search strategies have involved searching for very narrowband signals, something like 1 Hz bandwidth for a typical frequency of 1.4 GHz or thereabouts. No known astrophysical source can produce such narrowband signals, while radio-transmitter technology can easily do so. Also, narrowband signals are more prominent against the interstellar background than broadband ones, because their power is concentrated in a smaller frequency range.

Date: 2005/02/10 07:00:04, Link
Author: lpetrich
Archdeacon Paley and the Museum of Watches

Let's imagine that Archdeacon Paley, of watches-need-watchmakers fame, could come to our time and visit some museum of watches and clocks and other timepieces over the centuries. He'd see:

Purely-mechanical clocks and watches
Electromechanical clocks and watches
Purely-electrical clocks and watches

Their displays would be:

Their timing would be controlled by:
The Sun
Falling sand
Quartz crystals
Oscillating atomic nuclei (in atomic clocks)

Archdeacon Paley might scratch and scratch his head and ask who designed all these timepieces. There are two main possibilities:

1. A single master designer who has designed every timepiece there ever was.
2. Multiple designers of timepieces over the centuries and at each time.

Would Archdeacon Paley try to argue (1)? And argue that all that single designer's designs are the best possible, in Panglossian fashion? Or would he recognize that it is (2) that had actually happened?

Turning to the Earth's biota, I think that a strong case can be made that if much or most of its features was designed, then this designing would be designed evolution in (2) fashion.

Back in his creationist days, Charles Darwin was inspired by Australia's distinct fauna to note in his diary that:
A Disbeliever in everything beyond his reason might exclaim "Surely two Creators must have been at work".

And over at The Panda's Thumb, there is a nice article discussing Multiple Designers Theory, which is (2) applied to the Earth's biota.

Also, How I decoded the human genome featured this comment from someone with a lot of experience in computer programming:
Kent spoke to me in nerdspeak, with geekoid locutions such as the use of "build" as a noun: "That's the most recent build of the genome. Build 31." I was used to hearing biologists talking about the elegance of DNA with what might be called reverence. By contrast Kent spoke of DNA as if it were the most convoluted, ill-documented, haphazardly maintained spaghetti code -- not God's most sublime handiwork, but some hack's kludge riddled with countless generations of side effects, and "parasites on parasites."

"It's a massive system to reverse-engineer," he said. "DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes ... the analogy breaks down at the margins but offers useful insights." It was nearly impossible to tell the working code from cruft, Kent said. "That's why a lot of people say, 'The genome is junk.'" But that's what he found interesting: a high-quality programmer's code is always self-evident, but legacy assembler handed down from generation to generation of bricoleurs (I'm paraphrasing again) provides a real challenge for people who like puzzles.

To sum up, it looks like (2) rather than (1) to that experienced designer.

I think that it is a good test of the open-mindedness of IDers whether they are willing to take seriously the possibility of multiple designers. And one can ask why they present ID in opposition to evolution and natural selection. Evolution can proceed by ID (evolution by genetic engineering), and ID and natural selection can coexist as mechanisms of evolution -- they are NOT mutually exclusive, despite what some IDers seem to think.

I have, however, seen some counterarguments offered to the multiple-designers hypothesis.

One of them is that nearly all Earth organisms use DNA as their molecule of heredity, something that somehow implies only a single designer doing all the designing.

If you people find it hard to keep yourselves from laughing, you have my sympathy, because that argument is almost absurdly weak. It's like Archdeacon Paley maintaining that all those clocks and watches had a single master desginer because they all measure time in the same units -- 1 day = 24 hours, 1 hour = 60 minutes, 1 minute = 60 seconds.

I wrote "nearly all", because RNA viruses are an exception, and apparently the only one. But RNA is a close chemical relative of DNA, making that exception a weak one.

I note in passing that it seems to me that DNA is often described as some sort of "magic molecule of life" in quasi-vitalist fashion. Though it's the nearly-universal carrier of genetic information, that appears to be its only function. What makes a living thing alive is the interaction of its various parts, not any particular substance.

Another counterargument is that one superpowerful designer is somehow a simpler hypothesis than a multitude of less-powerful designers. In my watch-museum example, it is deciding on hypothesis (1) rather than (2) -- even though (2) is what has happened. Unless one wishes to believe that there was some superpowerful designer behind these designers' thoughts and efforts, a case of (1) having the appearance of (2).