The question of the plausibility of the RNA world scenario has come up on the Information Content of Proteins thread. So I thought I better start an RNA world thread quick, before it takes over the discussion of proteins. So Gringo Royale and others, bring your discussion over here, please.
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| The Design Matrix: A Consilience of Clues by Mike Gene |
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| Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body |
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| Catalyzing Inquiry at the Interface of Computing and Biology |
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| System Modeling in Cellular Biology: From Concepts to Nuts and Bolts |
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| The Plausibility of Life By Marc W. Kirschner and John C. Gerhart |
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| Agents Under Fire by Angus Menuge |
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| Life's Solution by Simon Conway Morris |
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| Information Theory, Evolution and the Origin of Life by Hubert P. Yockey |
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| The Fifth Miracle by Paul Davies |
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| Nature, Design, and Science by Del Ratzsch |
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| Origination of Organismal Form by Muller & Newman |
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| Biased Embryos and Evolution by Wallace Arthur |
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| Rare Earth by Peter Ward and Donald Brownlee |
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| The Privileged Planet by Guillermo Gonzalez and Jay Richards |
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| The Way of the Cell by Franklin Harold |
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| The Volitional Brain by Benjamin Libet |
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| Evolution in Four Dimensions by Eva Jablonka & Marion Lamb |
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| The Evolution-Creation Struggle by Michael Ruse |
August 21st, 2009 at 6:00 pm
GringoRoyale:
Yet there is more at issue than the stability of single molecules. The fragility of a putative process and weak selection criteria is noteworthy. What is the strength of evidence for a continuous prebiotic process that culminates in a cell? That's what needs to be analyzed.
Comment by Bradford — August 21, 2009 @ 6:00 pm
August 21st, 2009 at 6:28 pm
One interesting "review of a review" I came across on this topic, related to the RNA world topic, is Rob Sheldon's.
Submitted for general interest here.
Comment by nullasalus — August 21, 2009 @ 6:28 pm
August 21st, 2009 at 6:38 pm
Bradford:
It is being analyzed as we speak, and as more experiments are being performed, more evidence comes in. It seems that you have already made up your mind. If anybody around here is closed-minded, it's you.
Comment by Raevmo — August 21, 2009 @ 6:38 pm
August 21st, 2009 at 6:51 pm
The pot calling the kettle black. What's the matter with withholding judgment until convincing empirical evidence is produced? Doesn't quite satisfy the NA narrative does it? You and some of your fellow swampies exemplify bigotry and close mindedness.
Comment by Bradford — August 21, 2009 @ 6:51 pm
August 22nd, 2009 at 3:52 am
On fairness.
@ Bradford:
Is it fair to lock Raevmo out of the thread and then ask him questions? Is "fellow swampies" a synonym for "actual scientists"?
You call the moderation shots here, fair enough, but sometimes you exemplify (thanks for the word) the parable of the mote and beam. (déjà-vu moment)
Comment by Alan Fox — August 22, 2009 @ 3:52 am
August 22nd, 2009 at 7:47 am
Sheldon mentions
All ID advocates need to do is demonstrate such a force, and they're in business. Without it they have nothing.
Comment by John Wendt — August 22, 2009 @ 7:47 am
August 22nd, 2009 at 9:14 am
I asked him questions. He responds with a contentless comment intended to make me the object of attention. Olegt and others have complained when insulting language is directed at someone they support in the political world yet never object when examples are right in front of them in internet forums. I want a forum where vigorous debate is possible. Where people can strongly but civilly disagree. We just saw that happen in aiguy's guest post thread. The focus was issues. That's where it should stay.
Fellow swampies is a reference to gossipy ladies who need to find something better to do with their time.
Comment by Bradford — August 22, 2009 @ 9:14 am
August 22nd, 2009 at 9:32 am
Bradford,
I see nothing insulting in Raevmo's comments in this thread. He said you were closed-minded and you reciprocated in kind.
In fact, you keep suggesting that we (the "swampies") toe a new-atheist line. That's actually insulting—to me, at least. I asked you several times to provide evidence of that and you always deflect. Sauce for the gander, I suppose.
Comment by olegt — August 22, 2009 @ 9:32 am
August 22nd, 2009 at 9:33 am
Bradford wrote:
Is that a thinly-veiled disinvitation from your blog? Do tell.
Comment by olegt — August 22, 2009 @ 9:33 am
August 22nd, 2009 at 1:54 pm
John Wendt,
And ID advocates seem to believe such a force has been demonstrated. Amply. Hell, it's being demonstrated right in this thread by their measure.
Comment by nullasalus — August 22, 2009 @ 1:54 pm
August 22nd, 2009 at 2:23 pm
Re:"
'impossibility of any forces in nature except those due to material causes (physics) –Darwinists accept this, ID doesn't.'
All ID advocates need to do is demonstrate such a force, and they're in business. Without it they have nothing.
"
what is the definition of 'nature' in this context. I presume it refers to the 'natural world', so before we get to 'the force' we would have to determine whether or not anything in 'nature' is non physical in nature.
Related questions: is the space between particles regarded as 'physical'?
If everything that is happening is physical, ultimately, is what was happening a split second ago physical or no longer existent since everything that was there (physically) then is no longer there physically now in exactly the same configuration.
If something is real (physical) one moment but a split second later no longer real, and/or a new reality has been created, in what sense is it 'physical'?
So the two root questions are:
'what is the definition of nature?'
'what is the definition of 'physical'?'
Only than can either of the above two cited introductory statement/questions be debated, let alone resolved.
Comment by ash — August 22, 2009 @ 2:23 pm
August 22nd, 2009 at 2:23 pm
Is this the argument that humans exercise intelligent design, therefore there must be something non-human that can also exercise intelligent design?
Comment by John Wendt — August 22, 2009 @ 2:23 pm
August 22nd, 2009 at 2:29 pm
Suggestion for the nature of such a 'force', or at least a good place to start in scientific investigation:
what is the agency (of whatever nature this is) that provides for the seeming continuity of structure at both the particulate, elemental and organismic level that provides for continuity of such structure from one moment to the next?
Is it a binding factor, an organisational field, inheritance of momentum/density based on the relative weight or strength of the structure that carries it through, or whatever? What is it that provides stability/continuity in the midst of onging flux?
To continue or not to continue, that is the question!
Comment by ash — August 22, 2009 @ 2:29 pm
August 22nd, 2009 at 2:29 pm
Is there another one?
Comment by Alan Fox — August 22, 2009 @ 2:29 pm
August 22nd, 2009 at 2:33 pm
John Wendt,
You said that what ID proponents "need to do is demonstrate such a force, and they're in business. Without it they have nothing." I simply replied that, according to ID proponents, the existence of that "force" is clear and obvious.
Are you saying now that their "force" clearly exists, but isn't necessarily needed to explain what they seek to explain? I can understand that argument, but it would be different from what you first offered here.
Comment by nullasalus — August 22, 2009 @ 2:33 pm
August 22nd, 2009 at 6:24 pm
Why don't you just explain to me what the force is?
Comment by John Wendt — August 22, 2009 @ 6:24 pm
August 22nd, 2009 at 6:34 pm
John Wendt,
An intervening mind.
Comment by nullasalus — August 22, 2009 @ 6:34 pm
August 22nd, 2009 at 7:56 pm
"An intervening mind" is the non-material force?
It is indeed obvious that there is intelligence at work in this thread. But never in human experience have we seen a mind, or an intelligence, do anything directly. Human design activity starts with electric activity in the brain (material and somewhat measurable). The electrical patterns couple to motor nerves, which produce chemicals that allow muscle fibers to contract. The energy for the contraction is supplied by ATP, which is the result of atoms moved about by energy from glucose, which is the result of atoms moved about by photons from sunlight.
But even human activity can't do what would be necessary for intelligent design of life. ID activity must be able to move specific atoms into specific places. Humans do that only with sophisticated equipment. How does an "intervening mind" do it? Where does the Intelligent Designer's energy come from?
Comment by John Wendt — August 22, 2009 @ 7:56 pm
August 22nd, 2009 at 8:22 pm
John Wendt,
Talk of materiality and immateriality in mind is part of a very interesting discussion in another thread (Aiguy's guest post and the ensuing discussion has been fantastic, in my view), but I haven't brought it up here. I assume you'd be willing to grant that an intentional mind (the nearest example: humans) can produce an OoL. That's enough for that ID "force" to get some traction, without having to immediately get into any deeper debates about whether minds (or the universe, for that matter) are wholly material, wholly immaterial, some combination, etc.
Interesting. Are you telling me flat out that humans will never intelligently design life, or create life from non-life in a laboratory? I doubt you are, but that's how this line came across.
There's this fun quote, I think credited to Carl Sagan. Roughly, "In order to make an apple pie from scratch, you have to go back to the Big Bang." Good point as far as it goes, but in my years of cooking I've never had to worry about quantum physics all that much – even when the microwave gets involved. Many times you just don't need every detail in place to get work done, draw valid conclusions, or entertain real possibilities.
Applied here: There are at least some instances where I can reasonably infer that a given artifact or event was designed, even if I have no clue how this was precisely accomplished. Would you agree?
Likewise: There are at least some instances where I can reasonably infer the intentional design of an artifact or event, even if I can't reach that conclusion with certainty. Would you agree? (Divje Babe flute would be a good example here, I think.)
(Note: I don't recall speaking with you before. Greetings, nice to meet you. I don't think Intelligent Design (or it's philosophical opposite) is science. But I like to present what I see as their basic approach and rationale in a straightforward way.)
Comment by nullasalus — August 22, 2009 @ 8:22 pm
August 22nd, 2009 at 10:28 pm
Humans consume other organisms for energy. That energy powers their muscles and brains. They also harnass other energy sources, such as fire and electricity, to heat food in order to change its chemical composition. Hands exert force, not intelligence.
This is all quite well-understood. The fact that cooking is artificial doesn't change the fact that the energy-matter ledger is in balance. The question above concerned the mechanism the posited intelligence used to manipulate the matter involved in the origin of life.
Even if true, it doesn't justify "an intervening mind" as the *force*.
The Divje Babe artifact is posited to have been created by humans. These interesting creatures consume other organisms for energy then use their muscle-powered hands to manipulate objects.
Comment by Zachriel — August 22, 2009 @ 10:28 pm
August 23rd, 2009 at 12:07 am
Zachriel,
We're already studying exactly that question in OoL labs and related areas – and with luck, we'll find out one (at least) path to how an intelligence can create life that way. Aside from pondering about it via philosophers, of course.
Thankfully, the specific means by which any intelligent force acted is a tertiary question for ID proponents. They seem more concerned with identifying the work of minds, not just 'minds with hands'. Don't knock tentacles, the squids may wise up one day.
Are you telling me, Zach, that the debate over the Divje Babe flute comes down to ascertaining whether or not anyone was around at that time who had hands? I suppose SETI could also be renamed to SETH – the Search for Extra-Terrestrial Hands.
Comment by nullasalus — August 23, 2009 @ 12:07 am
August 23rd, 2009 at 8:35 am
Humans will probably create artificial life one day. Is your claim that the origin of life was due to animals who ran research labs four billion years ago? There is no evidence of such research labs. There is evidence that primordial conditions could have led to a spontaneous origin. Then there's the cause and effect problem of explaining the origin of life by pointing to existing life.
If the object was associated with the Cretaceous, then yes, a claim that it is an artifact from that period would be highly questionable. The history of artifacts is one of technological development, from stone and fire to metals to plastic to computers. One interesting analysis is by Douglas Adams, the Four Ages of Sand.
Tentacles are structures found on animals who acquire their energy by consuming other organisms. Are you claiming that the origin of life was due to animals with tentacles running research labs billions of years ago? That would be positing that animals existed before their energy source did. Then there's the problem of evolution. We know that tentacled animals evolved from more primitive organisms. The cart before the horse.
Comment by Zachriel — August 23, 2009 @ 8:35 am
August 23rd, 2009 at 10:27 am
nullasalus wrote:
Sorry, couldn't resist. The Philosophers' Football Match.
Comment by olegt — August 23, 2009 @ 10:27 am
August 23rd, 2009 at 3:39 pm
Zach,
I'm not making any claims here. I'm pointing out what ID proponents are arguing (or at least what I take them to be arguing) – and they'll typically agree that they can't say word one about the designer. So even they wouldn't claim the OoL was due to 'animals who ran research labs' or anything else. Just "designers", full stop.
And what's wrong with the "cause and effect problem of explaining the origin of life by pointing to existing life"? That didn't and doesn't disqualify panspermia hypotheses – their view suggests that the origin of life didn't start on earth, which if true is an advance of knowledge. Admittedly it keeps the OoL itself a problem (at least we can stop worrying about 'initial conditions on earth' in that case) but it's a viable solution to the "OoL on Earth" problem, at least to a degree.
As for "no evidence it was designed" versus "evidence it was spontaneous", I think that comes down to an interesting reworking of how to classify "evidence".
Please inform SETI that what they're really looking for, first and foremost, are hands.
He was a fine scientist, wasn't he? I particularly admired his speculation about the existence of a spacegoing immortal striving to insult everyone in the universe in alphabetical order, or his engineering proposal to create a species of pig that enjoyed being eaten. Stunning stuff.
How could I be? We both know what the single most important factor is when it comes to creating complicated artifacts – hands. Hands, Zach. No Hands, no artifacts. This is biology 101.
Anyway, Zach, I'm not that interested in talking about this with you – I'm going to try and be as amiable as possible, and not point out why. But maybe John Wendt has some more responses, even though I'm dead positive he's going to end up strongly disagreeing with any ID project. (As I said, I have my own reasons for disagreeing with "ID as Science" too.)
Comment by nullasalus — August 23, 2009 @ 3:39 pm
August 23rd, 2009 at 5:31 pm
I agree this is the key. Specifically, ID proponents cannot say that "just designers, full stop" excludes spontaneous natural processes.
Yes, I agree it's important to consider these statements carefully, as it is easy to read more into them than is there. At the same time, it's also important to recognize "no evidence it was designed" really means "no evidence for something called 'a designer' other than natural processes", and "evidence it was spontaneous" really means "the evidence doesn't rule out known spontaneous processes."
The bottom line is proof of existence: ID doesn't have it, natural processes does. That means ID still has one step to take before it even gets to the level of natural processes as an explanation. ID proponents admit, without embarrassment, that they have absolutely no actual explanation for how "a designer" created life, yet their fundamental argument against natural processes is that there's no explanation based on them, either.
Comment by don provan — August 23, 2009 @ 5:31 pm
August 23rd, 2009 at 5:58 pm
don provan,
I can reverse that and argue that people advocating 'spontaneous natural processes' get into a whole lot of trouble once we start to really investigate what is 'spontaneous' and what is 'natural'. "Spontaneous natural processes" can be employed by intelligent agents/designers, after all – a good example of that would be the directed panspermia hypothesis, though that applies more to evolution than the OoL strictly considered.
I'd say evidence rather than proof. In any event, ID proponents would disagree, and I can see a few ways how they could. Our own existence and activity is limited proof-of-concept. Every advance we make in technology and natural sciences just serves to illustrate what "intelligent designers" are capable of. Hell, maybe Andrei Linde is right and humans can eventually design universes as well. Or maybe Nick Bostrom is correct about his own view of "designed universes". Neither of these guys are ID proponents, of course. Well, I suppose technically they are. James Gardner certainly is, even if he definitely doesn't fit the normal mold of ID proponent.
Anyway, the fact remains that technology marches forward. We may not know the ultimate metaphysics of nature (not really a question for science anyway), but we can certainly know just what we ourselves make in laboratories and factories. And the evidence there is clear: Intelligent designers can accomplish one hell of a lot. I'd agree that science has zero to say one way or the other about the existence of big-D Design and guidance in nature. Scientists have their hands full with far more modest aims besides.
Comment by nullasalus — August 23, 2009 @ 5:58 pm
August 23rd, 2009 at 7:16 pm
"But never in human experience have we seen a mind, or an intelligence, do anything directly. Human design activity starts with electric activity in the brain (material and somewhat measurable). The electrical patterns couple to motor nerves, which produce chemicals that allow muscle fibers to contract. The energy for the contraction is supplied by ATP, which is the result of atoms moved about by energy from glucose, which is the result of atoms moved about by photons from sunlight."
1. When Harry met Sally they made baby Jane doing unmentionable things under the covers. Does this not qualify as 'doing something directly?' – a new life form is created after all – or does it not count because it is not the product of conscious thought and so is not human intelligence? Or maybe it's just because it's under the covers and that's not fair because you can't prove they actually did anything or not!
2. The next section is a great, concise description of materialist view. However, I wonder if there is any proof at all for the initial premise-statement: 'Human design activity starts with electric activity in the brain (material and somewhat measurable).'
How do we know that it starts with electrical activity in the brain rather than ends, or at least that there is not something before the electrical activity which, as you pointed out, is part of a physical relay process of moving things from one part of the organism to another.
Personally, I very much doubt that mental activity, let alone deeper levels of intelligence, start with 'electrical activity'. That makes us into little more than sophisticated toasters on some level. It's not that I'm insulted, it's just that it sounds far too simplistic/ reductionist and belief-based an explanation.
Comment by ash — August 23, 2009 @ 7:16 pm
August 23rd, 2009 at 8:18 pm
Sure you are.
You are more than merely stating what ID advocates believe. My concern was was that you were apparently conflated intelligence with force.
Comment by Zachriel — August 23, 2009 @ 8:18 pm
August 23rd, 2009 at 9:54 pm
nullasalus: "SETH – the Search for Extra-Terrestrial Hands"
heh heh, good one.
Comment by kornbelt888 — August 23, 2009 @ 9:54 pm
August 24th, 2009 at 8:47 am
We were talking about energy, not hands specifically. Hands, and tentacles, are moved by muscles, which are transducers that use electrical impulses in nerves to regulate release of energy from ATP, in order to take the action desired by a designer, either human or cephalopod.
Atoms move in accordance with energy gradients. To move them in particular ways requires introducing energy in particular places and amounts.
Why "thankfully"? Because it's a rhetorical way to avoid a hard question? If it's not possible for unaided mind to control the energy gradients in a system, talk about "the work of minds" is empty.
I'm all in favor of ID projects. I do object to announcing conclusions before they have any data, and I don't see anything in ID theory that they can use to get data.
Comment by John Wendt — August 24, 2009 @ 8:47 am
August 24th, 2009 at 5:27 pm
I don't see how that reverses anything. You can investigate for yourself exactly what spontaneous natural processes are. No trouble at all. The same is not true for any pre-biological intelligent agent.
Just so. The intelligent agent is an additional claim that, unlike natural processes, lacks a proof of existence. We have good evidence that natural processes have operated as they operate today going back several billion years.
Call it whatever you want: the intelligent design explanation doesn't have it.
The concept of "intelligent design" is not being questioned, only the existence of anything capable of intelligent design before life was created.
Are you suggesting that humans existed before life was created? If not, then how are these points relevant to ID's proof of existence problem? Yes, there is evidence for intelligent designers. That evidence supports their existence going back a few million years, tops.
What are talking about, then, if it isn't what we can say about design and guidance in nature?
Comment by don provan — August 24, 2009 @ 5:27 pm
August 26th, 2009 at 7:00 pm
Returning to the original question: What exactly was it that made the RNA World so plausible?
I checked. The Wiki's say: "The RNA world hypothesis proposes that a world filled with life based on ribonucleic acid (RNA) predates the current world of life based on deoxyribonucleic acid (DNA). RNA, which can both store information like DNA and act as an enzyme, may have supported cellular or pre-cellular life."
Except that both DNA and protein perform both those functions: store information and catalyze processes.
?
Comment by Rock — August 26, 2009 @ 7:00 pm
August 26th, 2009 at 10:52 pm
Rock,
Maybe plausible is not the correct word. I think that the reasoning here is, at least in principle, that it is easier to accidentally evolve 1 kind of molecule that that performs both functions than to evolve 2 kinds of molecules separately. There are of course other problems. The chief among these is the “chicken and egg problem“. DNA needs protein to replicate and protein needs DNA to be replicated. Supposedly RNA is not plagued with this problem.
This of course is why some people doubt that, at least for the present, known natural causes are sufficient to explain the origin of life.
Comment by JOHN_A_DESIGNER — August 26, 2009 @ 10:52 pm
August 26th, 2009 at 10:58 pm
So has the RNA world hypothesis been demonstrated or not?
Comment by kornbelt888 — August 26, 2009 @ 10:58 pm
August 27th, 2009 at 9:20 am
The existence of ribozymes was an important discovery as it resolved the “chicken and egg problem“. RNA can exhibit autocatalytic properties, including activity associated with self-replication.
No. However, there have been a variety of important confirmed results.
No one claims that "known natural causes" constitute a complete theory of abiogenesis. However, multiple lines of evidence point to some natural origin, and no evidence points to the involvement of some outside teleological agent.
* The sterile origin of the Earth.
* The Theory of Evolution demonstrating that extant organisms evolved from a primitive common population.
* The facility of complex organic compounds to spontaneously self-assemble under a variety of conditions.
* The ability of random amino acid and nucleotide sequences to form functional enzymes.
* Specifics of abiogenetic theory, including hydrothermal, cycling, and impact events.
However, none of this is conclusive as to any particular abiogenetic history.
Comment by Zachriel — August 27, 2009 @ 9:20 am
August 27th, 2009 at 9:40 am
Wake me up when it has been.
Comment by kornbelt888 — August 27, 2009 @ 9:40 am
August 27th, 2009 at 9:51 am
Consider that for many years it wasn't known whether the Moon was formed by a collision, capture, accretion or by spinning off. Though no one knew which of these, or some other theory, would be shown correct, the vast majority of astronomers were confident some natural origin occurred due to their knowledge of plausible, known mechanisms. The collision theory is now considered strongly supported (because it explains mineral and isotope distributions), but there is always some uncertainty in science. So sleep.
Comment by Zachriel — August 27, 2009 @ 9:51 am
August 27th, 2009 at 10:13 am
Zachriel,
Ah, confidence by promissory note. You hang on to that hope. Wake me up when it comes true.
Comment by kornbelt888 — August 27, 2009 @ 10:13 am
August 27th, 2009 at 10:59 am
It's must be hard to read with your eyes adroop.
Science is based on the testing of hypotheses. The various theories of the Moon's origins have been tested against empirical observations. For instance, isotopes on the Moon imply it was created of the same material as the Earth. The lack of an iron core implies that it was not formed by accretion. Detailed computer modeling based on standard physical equations demonstrates that a collision is consistent with the data. Perhaps some extraterrestrial visitor tossed a beer bottle into the primordial nebula, seeding the Earth; then urinated behind the Sun, seeding life. But there is no evidence of this occurring.
Of course, like all scientific findings, the collision theory of the Moon's origin is considered tentative and subject to being discarded or revised in the light of new evidence—your lack of curiosity being irrelevant.
Comment by Zachriel — August 27, 2009 @ 10:59 am
August 27th, 2009 at 11:02 am
Let me ask this. Is it scientifically reasonable to tentatively conclude that the Moon had a natural origin? Was it scientifically reasonable in 1970 to tentatively conclude that the Moon had a natural origin?
Comment by Zachriel — August 27, 2009 @ 11:02 am
August 27th, 2009 at 11:05 am
Well, the so called RNA world POV has created if a lot of enthusiasm. But enthusiasm is not the same as supporting evidence. Robert Shapiro gives a fair minded critique in in an Sci Am article entitled. “A Simpler Origin for Life.” He writes:
Shapiro goes on to then expose what is the major problem with the theory.
In other words, if you begin with RNA it solves some of the major OoL problems like the “chicken and egg problem.” However, that leaves unsolved the problem, where did the RNA come from
Comment by JOHN_A_DESIGNER — August 27, 2009 @ 11:05 am
August 27th, 2009 at 11:46 am
Zachriel, last I heard, the moon has nothing to do with the RNA world hypothesis. Blah blah blah. The answer is still no. I said to wake me up when that hypothesis is demonstrated. Not when some hypothesis about the moon is demonstrated. But you keep boring me with irrelevant things about the moon.
ZZZZZZZZZZzzzzzzzzzz
Comment by kornbelt888 — August 27, 2009 @ 11:46 am
August 27th, 2009 at 11:48 am
So did cold fusion. Scientists can be as enthused all they want. That's none of my business. An enthused consensus is not a scientific argument, nor is it part of the scientific method.
Comment by kornbelt888 — August 27, 2009 @ 11:48 am
August 27th, 2009 at 11:51 am
Exactly the point that I was trying to make.
Comment by JOHN_A_DESIGNER — August 27, 2009 @ 11:51 am
August 27th, 2009 at 12:16 pm
It has to do with what is meant by scientifically "plausible". It is quite easy to meaninglessly wave your hands. I note you didn't answer the two questions.
That's correct. RNA First is not quite the same as RNA World. The evidence from the structure of ribosomes points strongly to the existence of RNA World, but whether RNA World was preceded by something else is not known at this time. Prebiotic chemistry still has troubles accounting for large enough concentrations of nucleotides, but RNA can appararently catalyze the production of nucleotides which resolves the problem of a continuous supply of nucleotides required for RNA World.
However, it is quite likely that RNA World is an over-reductionist view of a very complex phenomena.
Comment by Zachriel — August 27, 2009 @ 12:16 pm
August 27th, 2009 at 1:18 pm
Lol! Severe overstatement.
Severe understatement.
Comment by chunkdz — August 27, 2009 @ 1:18 pm
August 27th, 2009 at 1:32 pm
Hmm. It's you ringing my buzzer again and waking me up. Still no word on whether the RNA hypothesis has been demonstrated, eh. Stop stalking me.
ZZZZZZZzzzzzzzzzz
Comment by kornbelt888 — August 27, 2009 @ 1:32 pm
August 27th, 2009 at 1:41 pm
This is a bit like saying that even though we can't actually demonstrate that the Milton Bradley game "Mousetrap" can catch mice, the discovery of a mouse sized cage included in the game resolves the problem of whether the game can catch mice.
Comment by chunkdz — August 27, 2009 @ 1:41 pm
August 27th, 2009 at 1:47 pm
You do understand that nucleotides may form in low concentrations, but the problem is the continuous supply necessary to the RNA World Hypothesis.
Unrau & Bartel, RNA-catalysed nucleotide synthesis, Nature 1998.
Comment by Zachriel — August 27, 2009 @ 1:47 pm
August 27th, 2009 at 2:40 pm
Oh the problem is much bigger than that.
But yes, the basket is big enough to fit a mouse, thus resolving the problem of being able to catch a mouse. I wonder why I haven't caught any mice with my Milton Bradley game…?
Comment by chunkdz — August 27, 2009 @ 2:40 pm
August 27th, 2009 at 3:22 pm
Please be specific.
(The ID comments on this thread have been thoroughly lacking in substance.)
Comment by Zachriel — August 27, 2009 @ 3:22 pm
August 27th, 2009 at 3:39 pm
I'm sorry this hasn't been made clear: no, the RNA hytpothesis has not been demonstrated. I'm not sure why you're even asking, since I don't know of anyone that would say otherwise.
Rock asked the much more interesting question of whether the RNA world is plausible, and the answer to that is decidedly yes. Zachriel has discussed some of many limitations of that claim, including the fact that while it's plausible as a step before DNA, its origins themselves have not been explained.
The important point is that the RNA world is plausible in specific, concrete ways. We can consider what such a world was like, we can consider how such a world could lead to a DNA world, etc. This doesn't make it more likely to be true, but it does make it useful. In contrast, ID is only "plausible" in the sense that nothing could possibly contradict it, not because it says anything that can be investigated.
Comment by don provan — August 27, 2009 @ 3:39 pm
August 27th, 2009 at 6:34 pm
You mentioned Unrau and Bartel. Their experiment was done in vitro under stringently controlled artificial conditions, with artificially amplified concentrations of designer RNA's.
If I etherize a mouse and place him under the basket have I demonstrated that Milton Bradley's Mousetrap is a plausible mousetrap?
We expect better from our critics than arrogant posturing. Clean up your act, please.
Comment by chunkdz — August 27, 2009 @ 6:34 pm
August 27th, 2009 at 6:49 pm
Amplified concentrations of *random* RNA sequences, consistent with the RNA World Hypothesis. The study does not purport to demonstrate abiogenesis. It only answers the particular objection concerning the continuing availability of nucleotides to support RNA World.
Milton Bradley's Mousetrap is not an evolving population of replicators.
Comment by Zachriel — August 27, 2009 @ 6:49 pm
August 27th, 2009 at 7:04 pm
Not true. The families that were amplified were all artificially selected for autocatalysis – by design.
Yep. If we artificially select ribozymes and artificially amplify their concentrations we can achieve limited nucleotide synthesis.
And if we hog tie a mouse, etherize him, and carefully place him under the basket, we have proven that Milton Bradley has made a working mousetrap.
Comment by chunkdz — August 27, 2009 @ 7:04 pm
August 27th, 2009 at 7:44 pm
Paul Davies is another authority who highlights the many difficulties that an RNA first scenario presents. He writes:
The summarize the point that Davies is trying to make: from what we presently know it is virtually impossible to extrapolate what we have learned in the lab to some hypothetical process that may have occurred, out there someplace, a long, long time ago “in the wild.”
Is such a hypothesis still plausible? I guess if you hypothesize scientifically advanced alien biochemists in white coats it’s plausible. But, from a natural evolutionary perspective it is dead end, if not a non starter.
Comment by JOHN_A_DESIGNER — August 27, 2009 @ 7:44 pm
August 27th, 2009 at 7:56 pm
Remove "hands" and insert "beaks", "tails", "teeth", and any other appendage you can think of and you'd think that any creatures on earth that "consume other organisms for energy" and then "manipulate objects" can design cars, space shuttles and computers!
If biological life was a novel invention, then – by necessity and by definition – the inventor could not itself be of the class "biological life".
Pretending that that is what ID is proposing is a strawman.
This illustrates an important point. It is only for those who have accepted the premise that life formed naturally, that the discovery of ribozymes "resolved the 'chicken and egg problem'".
Zachriel has not only accepted that premise, he is fully committed to it. For him, the issue is said to be "resolved" with a discovery that may show some promise. The truth though, is that even without the discovery of ribozymes, ol' Zach would still be fully committed to that premise and the issue would still be "resolved" in his mind. He'll remain committed to that premise for as long as he chooses to interpret all evidence through that filter.
You're fully transparent Zachriel.
Comment by Daniel Smith — August 27, 2009 @ 7:56 pm
August 27th, 2009 at 8:07 pm
Artificially selected from a random library, not amplified "designer RNA's".
Milton Bradley's Mousetrap is not an evolving population of replicators.
Comment by Zachriel — August 27, 2009 @ 8:07 pm
August 27th, 2009 at 8:22 pm
Yes, that's right. There is a mechanism that converts energy from one form to another.
Yes, that's right too. Hence, my mention of the traditional order of horse and cart.
In fact, many IDers conflate intelligence with force or mechanism.
The premise is called a hypothesis and is tentatively held for the purpose of generating testable predictions. RNA World has led to many confirmed empirical predictions. Intelligent Design is without scientific merit because it doesn't generate testable scientific hypotheses.
Not at all. But as long as people continue to say there is scientific evidence for ID, then it is important to point out that the claim is false.
Thank you. But that's not an argument, you know.
Comment by Zachriel — August 27, 2009 @ 8:22 pm
August 27th, 2009 at 8:30 pm
As you are quoting Davies, I assume you agree that once life began, then evolutionary processes can explain the balance of the data.
Comment by Zachriel — August 27, 2009 @ 8:30 pm
August 27th, 2009 at 8:34 pm
Hmm. No edit function.
So where does Paul Davies think we should look to understand the origin of life? Does he posit life is probably a natural consequence of rare natural conditions perhaps?
Comment by Zachriel — August 27, 2009 @ 8:34 pm
August 27th, 2009 at 8:50 pm
Artificially selected, artificially isolated, and artificially amplified toward high concentrations.
Not "amplified concentrations of *random* RNA sequences" as you said earlier.
Do you really feel that artificially selected, artificially isolated, artificially amplified designers RNA's are "consistent with the RNA World Hypothesis"?
I measured a mouse and it fits perfectly in the basket. Does that make Milton Bradley's MOUSETRAP a plausible trap to catch mice with?
Comment by chunkdz — August 27, 2009 @ 8:50 pm
August 27th, 2009 at 9:02 pm
Of course it is. RNA World posits that primordial RNA networks catalyzed their own replication. The problem is that such sequences would quickly deplete the local supply of nucleotides. But we *know* from this experiment that if there are large numbers of random sequences, then there will be some that catalyze the production of nucleotides from simpler components, i.e. sugars and bases. Networks that include these catalysts would be preferentially selected.
Comment by Zachriel — August 27, 2009 @ 9:02 pm
August 27th, 2009 at 9:16 pm
These ribozymes don't have to be amplified to exist in nature. Given random collections of RNA sequences, such as might be catalyzed by montmorillonite, they are inevitable. It also shows that RNA World can form a primitive metabolism. And all this allows RNA World to bootstrap from very humble beginnings.
Comment by Zachriel — August 27, 2009 @ 9:16 pm
August 27th, 2009 at 9:17 pm
From the paper:
The RNA's were optimized by evolution, they were engineered in vitro, and they were artificially selected.
What part of the RNA World Hypothesis proposes ancient in vitro engineering and artificial selection?
I placed a drugged mouse under the basket. When I turned the crank, the basket eventually fell and trapped the mouse. Is Milton Bradley's MOUSETRAP a plausible catcher of mice?
[This is the third time I've asked you this question. I expect you to answer without evading next time.]
Comment by chunkdz — August 27, 2009 @ 9:17 pm
August 27th, 2009 at 9:22 pm
We *know* from this experiment that if there are large numbers of random sequences, then there will be some that catalyze the production of nucleotides from simpler components. They don't have to be artificially constructed or amplified.
Comment by Zachriel — August 27, 2009 @ 9:22 pm
August 27th, 2009 at 9:25 pm
I'm not an expert on Milton Bradley's MOUSETRAP, so I have no idea. But from what I understand, it's not an evolving population of replicators.
Comment by Zachriel — August 27, 2009 @ 9:25 pm
August 27th, 2009 at 9:35 pm
They do if they want the population to grow. Otherwise the catalytic RNA's are just as likely to degrade just as easily as any other.
Or to put it another way, the plastic basket in MOUSETRAP is demonstrably capable of holding a drugged mouse. Does this mean it can plausibly catch a mouse?
Then I'll give you the answer. It's NO.
Unfortunately, your boring and evasive obfuscations mean you lose your turn. See ya!
Comment by chunkdz — August 27, 2009 @ 9:35 pm
August 27th, 2009 at 9:37 pm
Trying again. Milton Bradley's MOUSETRAP is a board game for children and not meant to act as a mousetrap. You are drugging the mouse to represent helping the game in the process of catching the mouse. Without this help, the game would not be a plausible mousetrap. And that's apparently your point.
Of course, that is not the situation with RNA-catalyzed nucleotide synthesis. Given random nucleotide sequences, these ribozymes occur naturally. They will catch mice (catalyze nucleotide synthesis) without any help whatsoever. Furthermore, as part of an evolving network, they will be naturally selected, i.e. amplified.
Comment by Zachriel — August 27, 2009 @ 9:37 pm
August 27th, 2009 at 10:02 pm
The purity of the putative mixture will have something to do with what theoretical rybozymes react with. Homeostatic mechanisms are non-existent at this point in time.
Comment by Bradford — August 27, 2009 @ 10:02 pm
August 27th, 2009 at 10:07 pm
"I measured a mouse and it fits perfectly in the basket. Does that make Milton Bradley's MOUSETRAP a plausible trap to catch mice with?"
You should know by now that the MB mousetrap is consistent with catching mice. Isn't that enough for you? No? I'm shocked. SHOCKED!
Comment by kornbelt888 — August 27, 2009 @ 10:07 pm
August 27th, 2009 at 10:25 pm
No, the question is not simply whether nucleotide synthesis is possible. (just as the question is not simply whether a mouse can fit in the basket.)
The question is whether a population of RNA's in nature will survive simply because 1 out of every quadrillion or so of them can catalyze the creation of a nucleotide. (Or, can the MOUSETRAP really catch a mouse?)
Unfortunately, this experiment does not address this question.
But now we know that the mouse can fit in the basket. It's a major advance in origin of life studies, really.
Comment by chunkdz — August 27, 2009 @ 10:25 pm
August 28th, 2009 at 8:11 am
The RNA world as we now think of it is improbable, although with large populations and long times even improbable things can happen.
But as far as anyone can tell us, the kind of control needed for telic design of life-as-we-know-it is impossible.
Matthew 7:3-5 is worth pondering.
Comment by John Wendt — August 28, 2009 @ 8:11 am
August 28th, 2009 at 8:38 am
Matthew 7: 3-5
It's a good passage but what does it have to do with the plausibility of an RNA World?
Comment by Bradford — August 28, 2009 @ 8:38 am
August 28th, 2009 at 8:59 am
You don't listen at all, do you? We keep harping on the emptiness of ID's forensic strategy: You emphasize the weaknesses of the chemical approach, which all biochemists acknowledge, yet you ignore the bald fact that ID has no strengths.
Comment by John Wendt — August 28, 2009 @ 8:59 am
August 28th, 2009 at 9:36 am
You can harp all you wish but if a chemical approach is implausible another approach must be the way to truth. The recognition of symbolism in molecular systems signifies a mapping and a prior conceptualization of its meaning to rational minds. You can think such developments are the product of mindless covalent bonding if you prefer but you have no evidence supporting this. It's a personal preference you are entitled to. In any case this has nothing to do with removal of one's own sin prior to casting judgments on others unless we focus on the false allegation of not listening.
Comment by Bradford — August 28, 2009 @ 9:36 am
August 28th, 2009 at 11:23 am
ID may or may not have any scientific strengths as of yet, but it has a pragmatic, or common sense, strength: nature is not known to create coded information systems. Only entities with goals and foresight can do that, that we know of. Therefore, pragmatically, a telic source is a much better suspect for the source of the DNA coding system.
But as long as we're quoting Jesus, you might read Matthew 16:3.
Comment by kornbelt888 — August 28, 2009 @ 11:23 am
August 28th, 2009 at 11:24 am
Why is editing disabled?
Comment by kornbelt888 — August 28, 2009 @ 11:24 am
August 28th, 2009 at 11:27 am
I'll try to find out kornbelt. dp just posted a comment which does not appear when clicked on. Does anyone else experience this problem?
Comment by Bradford — August 28, 2009 @ 11:27 am
August 28th, 2009 at 12:00 pm
Editing is disabled because the preview function now works like it should.
Press 'Preview' and your post appears below the window. You can edit and preview as much as you want but once you 'Post Comment', no more editing is allowed.
Comment by Daniel Smith — August 28, 2009 @ 12:00 pm
August 28th, 2009 at 12:56 pm
Really? I'd like to see the specifics, Provan.
Comment by chunkdz — August 28, 2009 @ 12:56 pm
August 28th, 2009 at 2:42 pm
Let me guess… If you isolate and arrange molecular structures in a manner similar to what exists in life, these structures will perform some of the functions we see in life.
Close?
So basically life will do what it's designed to do.
How does that confirm the RNA world hypothesis?
Comment by Daniel Smith — August 28, 2009 @ 2:42 pm
August 28th, 2009 at 2:48 pm
So, according to Zachriel, all it takes to design cars, space shuttles and computers is a means to convert one form of energy into another and appendages.
It's really true… No intelligence allowed!
Comment by Daniel Smith — August 28, 2009 @ 2:48 pm
August 28th, 2009 at 3:52 pm
What else is there? Chemistry is founded on a combination of Brownian motion and quantum mechanics. Brownian motion is the random jostling of atoms and molecules in solution, QM shows how atoms will form compounds if Brownian motion brings them close enough together. There are lots of experiments that show random RNA strings folding into shapes that have biological activity. (Of course only some strings are active; others don't matter. ) The question now is whether there's enough production to sustain something like life.
To make design plausible, you have to show something that can move atoms into positions that Brownian motion can't produce. It seems that no one in the ID community has ever tried to do this, or even knows how to start.
Begging the question of whether such minds actually exist, or can exist, or can have the capability necessary to achieve such a plan. You can represent the DNA-RNA-ribosome-protein sequence in symbols, but the shape of the molecules is what moves other atoms into position to form compounds. In the protein information thread I quoted a report that proteins can be regarded as "slightly edited random strings". No intelligence necessary.
One of the central goals of science is that the evidence should be such that personal preference is not an issue. The RNA World isn't there yet, although the non-necessity of intelligent action has been accepted for a long time. Show us how a designer moves atoms around and we'll reconsider.
Personal preference has been a notably poor guide to science. The most tragic example was Einstein: saying "God does not play dice" he rejected the random aspect of quantum mechanics, thereby doomed himself to spend the last 40 years of his life in a fruitless search for a classical formalism to unify gravity with atomic forces. Such a search may yet be found, but it will be quantum in nature.
Comment by John Wendt — August 28, 2009 @ 3:52 pm
August 28th, 2009 at 4:12 pm
The recognition of symbolism in molecular systems signifies a mapping and a prior conceptualization of its meaning to rational minds.
As opposed to begging the question of the sufficiency of unknown chemical pathways to generate the same result.
It's a personal preference you are entitled to.
Then follow through and admit that science is unable to answer origin questions. As I said your personal preference is as legitimate as any other as far as your right to your own opinions is concerned.
You don't know there is non-necessity unless you can demonstrate it which you cannot. This is just atheism striving to control the beliefs of others.
Comment by Bradford — August 28, 2009 @ 4:12 pm
August 28th, 2009 at 4:20 pm
Like intuition, a consensus among the majority of scientists is neither a scientific argument not part of the scientific method.
Designers do it all the time. The screen you're reading was made by designers moving atoms around.
Show us how chance + law can build coding/decoding systems as per the DNA/ribosome system and I'll reconsider my position.
Comment by kornbelt888 — August 28, 2009 @ 4:20 pm
August 28th, 2009 at 4:46 pm
Bradford wrote:
Bradford, aren't you tired of asking people to admit that the OOL question has not been settled by science? I have said as much here. Why do you need an affirmation of that every now and then?
And unable to answer is a bit vague, so maybe you should make yourself clear. Do you mean to say that science can't answer that question now or are you implying that it cannot answer it in principle?
Lastly, personal preferences are fine, but not every personal preference can serve as a basis for a scientific theory. As someone pointed out, the actions of a designer are unpredictable (even in the statistical sense, I suppose), so while it may be gratifying to inject God into scientific gaps, it's a totally useless idea from the scientific standpoint.
Comment by olegt — August 28, 2009 @ 4:46 pm
August 28th, 2009 at 4:58 pm
John Wendt,
I agree. There is no evidence that the so called RNA first hypothesis is scientifically plausible. Several ID’ist like Shapiro and Davies have given solid arguments as to why it isn’t. So why have you brushed these criticisms aside.
It sounds to me like you are desparately clinging to the RNA world come hell or high water. Why is that? Personal preference?
Who has said it is necessary? I have always argued that from what we presently know ID is the best explanation for the origin of life. I am more than willing to reconsider. How much more open minded can I be?
Show us how life can emerge from non-life by unguided and undirected natural forces and you will win us over to your position. Let’s take a poll and see how many other ID’ists agree with that. Bradford? Bilbo? chunkdz?
Comment by JOHN_A_DESIGNER — August 28, 2009 @ 4:58 pm
August 28th, 2009 at 5:09 pm
correction: Several non-ID’ists like Shapiro and Davies have given solid arguments as to why it isn’t. So why have you brushed these criticisms aside.
Comment by JOHN_A_DESIGNER — August 28, 2009 @ 5:09 pm
August 28th, 2009 at 5:13 pm
No, because the people I ask are convinced that origin issues are on the way to resolution i.e. they are providing me with their faith based opinions while cloaking those views in nice sciency garb.
My exchange was with JW, not you.
Picking between the two options is itself a subjective opinion. I prefer to note that scientific boundaries are evidenced by our ability to make accurate predictions. I know I've said that before too but am not reluctant to keep repeating myself as long as others pretend their non-scientific feelings are more valid than mine.
Speaking of injecting into gaps I have an upcoming blog entry showing that the injections are not always administered by those believing in the existence of God.
Comment by Bradford — August 28, 2009 @ 5:13 pm
August 28th, 2009 at 5:40 pm
Olegt, JW and other skeptics gather round. Make yourselves comfortable and hear this. Stuart Kauffman et. al. have physical data they can cite to explain consciousness and free will which is at least as plausible, or in my view, more plausible than the physical evidence cited by RNA Worlders in advancing the view that a causally unexplained rybozyme catalyzed reaction pathways leading to a cell.
Comment by Bradford — August 28, 2009 @ 5:40 pm
August 28th, 2009 at 5:55 pm
Bradford,
Here is what JW wrote:
That was a pretty unequivocal acknowledgment that a scientific theory of life's origin is lacking at this point. What more do you want?
Well, that's a non-answer. Come on, spit it out: are you willing to bet that science will never figure out how life originated?
Stuart Kauffman has some wild speculations, and I don't find them particularly interesting. That topic, however, has nothing to do with the origin of life.
Comment by olegt — August 28, 2009 @ 5:55 pm
August 28th, 2009 at 6:25 pm
Olegt:
I'm surprised you even bother to ask that question since the answer is obvious. I've made this belief clear on many occasions namely, that the origin of life entailed purposeful direction- an element which is presently excluded from the analytical mix. If you exclude a key causal element you are going to end up with the same meager results OOL research has delivered for many decades now.
Comment by Bradford — August 28, 2009 @ 6:25 pm
August 28th, 2009 at 6:33 pm
I thought we were talking about science. If you want to talk religion, I won't waste your time any more.
Comment by John Wendt — August 28, 2009 @ 6:33 pm
August 28th, 2009 at 6:53 pm
I thought we were talking about science too but the sufficiency of scientific answers needs to be empirically documented and not presumed. My experience has shown me that unless someone is willing to consider the option of advanced intelligence preceding life rather than being an emergent property of matter, ID will be a non-starter for them. That does not make it a non-starter in reality.
Comment by Bradford — August 28, 2009 @ 6:53 pm
August 28th, 2009 at 7:08 pm
Please delete my comment (Bradford or whoever is here, I will link to an external site). Thanks!
Comment by computerist — August 28, 2009 @ 7:08 pm
August 28th, 2009 at 7:19 pm
Olegt:
I'd place a wager with you that the origin of life will remain a mystery. But a thousand years from now I won't be around to collect the money.
Comment by Bradford — August 28, 2009 @ 7:19 pm
August 28th, 2009 at 7:24 pm
I'm only half joking, Bradford. Extraordinary claims require extraordinary evidence. That science will never be able to solve the problem of the origin of life is an extraordinary claim. What are the grounds for this belief? Just personal incredulity?
Comment by olegt — August 28, 2009 @ 7:24 pm
August 28th, 2009 at 7:42 pm
Chemistry does not give rise to the coding systems evidenced in cells. That's an observation that has yet to be falsified. Why would anyone expect to see mappings of nucelotide sequences to amino acids until translation mechanisms and cellular structures are already in place? Why from a naturalistic POV?
Comment by Bradford — August 28, 2009 @ 7:42 pm
August 28th, 2009 at 8:03 pm
Perhaps a better question would be whether or not the definition and scope of science will have to change in order for science to "explain" the Origin of Life, among other things. Or whether such an explanation will be markedly different from other explanations science has offered.
I mean, we already have one explanation onhand: The multiverse did it. IT IS SCIENCE!
Comment by nullasalus — August 28, 2009 @ 8:03 pm
August 28th, 2009 at 8:17 pm
Bradford wrote:
Let me see if I understand the logic. Chemistry has not been able to explain the origin of life. Therefore science will never be able to explain the origin of life.
This fails at two levels. First, the task may not necessarily fall to chemistry as we know it. (Nullasalus, you are on to something.) I strongly recommend reading P.W. Anderson's essay More Is Different, which you can easily find on the web. Reductionism is often the wrong approach.
Second, if we remedy the first problem by expanding chemistry to science in general, your proposal reduces to this: science has not been able to explain the origin of life so far, so it won't be able to explain it ever. There are plenty of exeamples to the contrary.
Comment by olegt — August 28, 2009 @ 8:17 pm
August 28th, 2009 at 9:04 pm
Olegt,
If you're saying that science will certainly one day solve the OoL, but that the scope and definition of science may need to change in order to accomplish that, it doesn't sound like you're saying much. I dare say the answer sounds similar to what I've heard some ID proponents argue. Perhaps you meant something else.
Either way, I'd tentatively agree that reductionism of that variety is only so useful. Though, again, I also tend to hear that out of ID proponents as well, so go figure.
Comment by nullasalus — August 28, 2009 @ 9:04 pm
August 28th, 2009 at 9:05 pm
Say what, Bubba? That dog don't hunt.
Comment by kornbelt888 — August 28, 2009 @ 9:05 pm
August 28th, 2009 at 9:09 pm
Nope. Chemistry shows no indicators that reactions proceed to create symbolic coding systems. That's a directed task.
Comment by Bradford — August 28, 2009 @ 9:09 pm
August 28th, 2009 at 10:55 pm
nullasalus wrote:
Again, I recommend reading Anderson's essay. He argues that biology is not applied chemistry: it has its own theoretical structure, its own fundamental laws.
In addition, I can offer the classic example of thermodynamics. The 19th century saw the development by Boltzmann and others of the kinetic molecular theory of gases that has provided a microscopic basis for thermodynamics. The kinetic theory of gases is essentially classical mechanics of colliding particles. It successfully explained the nature of pressure (constant bombardment of the container's walls by molecules), temperature (the average kinetic energy of a molecule), and heat transfer (exchange of kinetic energy).
There was, however, one problem: mechanics was unable to explain irreversible phenomena such as viscosity, which are associated with the arrow of time. Loschmidt has posed the problem very sharply in the form of the reversibility paradox. The motion of individual particles, including their collisions, is fully reversible: film a collision of two molecules, run it backwards, it still would obey all the laws of Newtonian mechanics. However, we know well that a gas can behave irreversibly. For example, molecules initially occupying one half of a container quickly fill up the entire container and never spontaneously gather in the original location. Loschmidt's paradox demonstrated that classical mechanics alone can never explain irreversibility in thermodynamics.
Just think about it. Classical mechanics was the best developed and most trusted branch of physics at the time. It explained lots of things about thermal phenomena, yet it was clearly unable to explain irreversibility. A dead end? Of course not. The explanation of irreversibility required the development of statistical mechanics, in which we do not keep track of the individual positions and velocities of molecules but only of their statistical averages. A statistical description is necessitated by our imperfect knowledge about the molecular positions and velocities. No matter how small the initial uncertainty is, the chaotic nature of molecular motion makes the uncertainty grow in time until we completely lose the ability to predict which molecule will end up where. That's where entropy comes from. It wasn't in classical mechanics, it had to be invented from scratch.
I can give other examples along similar lines: classical physics is unable to explain the existence of para, dia, and ferromagnets. They are not supposed to exist in classical physics. There is a theorem proved by Bohr to that effect. A rigorous mathematical theorem totally forbidding magnetism. Hand of God? Nope. Quantum mechanics had to be invented in order to explain magnetism, among other things.
These are the kinds of developments I was talking about. They are revolutionary, but they do not redefine science in the way creationists want to.
Comment by olegt — August 28, 2009 @ 10:55 pm
August 28th, 2009 at 11:18 pm
Then Anderson is not saying much. We know that biological organisms are unique. Biochemistry is a distinctive branch of chemistry. I've pointed out before that Nullasalus, I and most other IDists agree with you about most all of science. There are likely fundamental laws governing the behavior of biological systems revealing not yet known predictive capabilities consistent with downward causation analysis. Origin analytics though begin within a prebiotic earthly environment. If pathways to life were not the consequence of undirected reactions involving biochemical precursors then what other candidates do you suggest? And if such pathways are said to lead to cells then how is this not a chemical paradigm?
Comment by Bradford — August 28, 2009 @ 11:18 pm
August 28th, 2009 at 11:31 pm
Although it took some of humanity's greatest geniuses to reveal the secrets of fundamental forces of nature the targets of analysis are less complex than a single cell. The success of reductionism in physics can provide a false sense of optimism that biological origins will lead to the same type of resolution. BTW, mathematical models of physical phenomenon say nothing about the causal origins of the universe and the dynamics that led to the particular mathematical values. The fact that forces of nature yield to mathematically detailed descriptions is not an argument against the hand of God. More likely it is merely a restatement of LaPlace's observation that God was not needed to figure out the math.
Comment by Bradford — August 28, 2009 @ 11:31 pm
August 28th, 2009 at 11:38 pm
olegt,
Actually, they really do – especially if you're going to include just about every theist under the sun as a "creationist". The inadequacy of reductionism to comprehensively explain the world happens to be one thing that diverse group typically is united in pointing out – and there really are people out there who take the opposite viewpoint (that biology really is just applied chemistry, etc. The whole "nothing buttery" perspective.) Now, you may think it's a waste of time to argue as much because it's clearly obvious that biology is not, in fact, just applied chemistry – and if so, I'd disagree with you. (More about whether it's a waste of time than anything else.)
You also seem to think that any theist (hell, anyone who rejects materialism?) is just itching to go "Hand of God!" and leave it at that. Now, I know you have a pretty low view of philosophy – a view I share here and there – but again, it gets more complicated. There really are arguments and discussion about whether or not things like "information" should be seen as a real and actual constituent of reality, rather than some fictional idea we use as a placeholder, or for illustrative purposes, etc. Just as there are arguments about which narrative understanding of evolution is most apt (and why Lynn Margulis, who I think is clearly not a fan of ID, will nevertheless argue strongly against Neo-Darwinism's associated "survival of the fittest" concept).
Which is why it's not just a question of whether or not the OoL is ever resolved by science, but how it's resolved. The expansion/change of science from classical mechanics to inclusion of quantum physics was a blow to materialists and reductionists that they're still striving to recover from. Just how "science" may have to change to best explain certain things, like the OoL, can easily go a way that "creationists" may celebrate. No, "God did it" is not going to become a scientific explanation (Probably not, anyway, but I don't believe it should be – anymore than 'God did not do it' should be). But whatever that explanation is, it may line up more with their explanations and thoughts about the universe than anyone else's.
Comment by nullasalus — August 28, 2009 @ 11:38 pm
August 28th, 2009 at 11:42 pm
Bradford wrote:
Good questions, Bradford. Now put yourself in the shoes of a 19th-century physicist and try to answer this:
Can you answer these questions without first developing a new branch of physics known as statistical mechanics? Do you understand now that your question cannot be answered prior to the development of an actual theory of life's origin?
Comment by olegt — August 28, 2009 @ 11:42 pm
August 29th, 2009 at 12:06 am
nullasalus,
I am not arguing that everyone in science agrees that "biology is not applied chemistry." If that were the case, there would be no need for Anderson to write the essay. That it remains relevant to this day is obvious because reductionism is alive and well among particle theorists just as it was 37 years ago.
Neither am I directing my criticism at theists: a theist is not necessarily a creationist. Theism is much more subtle. I am sure you understand that as a fan of Thomas Aquinas.
I don't care whether the advent of quantum mechanics was a blow to materialists. As you noted, I have little interest in philosophy. I also don't care whether a future scientific theory will resonate with Genesis as the Big Bang did. But I don't expect people like Bill "the Isaac Newton of information theory" Dembski or Mike Gene to leave their mark on science. Their approach amounts to little more than navel gazing. And you know that.
Comment by olegt — August 29, 2009 @ 12:06 am
August 29th, 2009 at 12:40 am
olegt,
Hey, I can only respond to you based on what you say. You brought up "creationists" in response to people pointing out problems with OoL proposals or who have something to say about the scope of science, and I qualified my response. And referring to every theist as a creationist is a favorite past-time nowadays. (At least it lets me refer to Ken Miller and Conway Morris as very successful creationists.)
I know what? That you have a low opinion of Dembski and Mike Gene? Sure, I managed to divine that somehow.
That their approach "amounts to little more than navel gazing"? That I disagree with. I may not have the view that ID is science, but I think the indirect contributions to science ID has made are considerable and important. (For one thing, they've helped people recognize the line between science and philosophy, and how others have and can blur that line.) Mike Gene doesn't claim to be making a mark on science, or really, doing science at all from what I see – right now he mostly encourages an approach to investigating natural science, particularly biology, that I find valuable. Dembski, I'm less prepared to evaluate, though I've been trying to read up on the general field of information theory.
But I don't think the ID debate – from the point of view of critics, or proponents – has ever been about "making a mark on science" anyway. Or hell, about science fundamentally at all. That's a subject we don't have to discuss, though.
Comment by nullasalus — August 29, 2009 @ 12:40 am
August 29th, 2009 at 1:33 am
Olegt:
Of course not.
Without an accurate theory- yes.
Comment by Bradford — August 29, 2009 @ 1:33 am
August 29th, 2009 at 2:12 am
JOHN_A_DESIGNER said:
Hi JAD,
Since there is much talk about weasel (plus JAD's request) I thought I'm probably missing out on all the hype and fun so to pass up on the opportunity to code a weasel implementation would be like a kid passing up the opportunity to bag candy during halloween.
Here is the external link (since I'm unable to syntax highlight/format on TT's) to the C code for anyone who is interested:
http://computerist29.wordpress.com/
Just compile and run!
Comment by computerist — August 29, 2009 @ 2:12 am
August 29th, 2009 at 3:31 am
To add to my previous comment, I'm not pretending the program what Dawkins or Dawkins-fans says it should do, its a very simple latching implementation, I'm sure Dawkins-fans out there have more "realistic" implementations. Weasel type algorithms show nothing except that it takes intelligence to select potential pre-function to reach functional "targets" from the onset and that these algorithms take advantage of intelligently designed computers. If you find a weasel program/algorithm that doesn't run on top of a intelligently designed system please give me a shout. If weasel simulates evolution in any way it should also be true that the same algorithm applies to explain all the pre-existing hardware and software its running on top of.
Comment by computerist — August 29, 2009 @ 3:31 am
August 29th, 2009 at 11:37 am
Hi computerist. You inspired me.
Comment by Bradford — August 29, 2009 @ 11:37 am
August 29th, 2009 at 11:56 am
Bradford, computerist,
If you, guys, are so excited about Weasel, why don't you take some time and learn what this program was about? From your comments it is clear that you rely on second-hand accounts to judge what it does and what is wrong with it.
As a result, you completely miss the point Dawkins made. Weasel was not meant to illustrate how evolution works. It was not meant to illustrate the creativity of a blind watchmaker. It was meant to illustrate one specific aspect of biological evolution: cumulative selection acting in a slowly mutating population. Replacing it with a partitioned search a la Dembski and Marks throws all of that out of the window.
Repeating their mistake is hardly educational. Read Dawkins's book instead and learn directly from the source. Or if you can't get your butt to the library, read the Wikipedia description for starters.
Comment by olegt — August 29, 2009 @ 11:56 am
August 29th, 2009 at 12:55 pm
I was familiar with Weasel long before computerist put up his comment. It was a very clumsy illustration of cumulative selection. Very oversimplified and hardly illustrative of a blind process.
Comment by Bradford — August 29, 2009 @ 12:55 pm
August 29th, 2009 at 2:47 pm
What would you do differently, Bradford, if you were to illustrate cumulative selection?
Comment by olegt — August 29, 2009 @ 2:47 pm
August 29th, 2009 at 3:39 pm
Olegt:
Dawkins' use of an emerging English language phrase to model cumulative selection is a good model for front loaded evolution. The end goal is evident and the process itself makes a specifiable functional outcome inevitable. This watchmaker has a purpose.
The problem with evolutionary analogies to phrases reminds us of Behe's IC point. A gradual buildup of letters forming words becomes functionally intelligible only after considerable "evolution" has occurred. The meaning is recognizable before all parts are in place and fine grammatical tuning after this mimicks standard evolutionary concepts, including cumulative selection. But where is the selection value at the outset? Reminds me of the origin of life.
Dawkins would have been better advised to utilize a physical process to make an analogy to cumulative selection. The successive buildup of underwater sediments resulting from repeated ocean floor volcanic activity can produce an island. Each eruption places one layer on top of another until the surface is broken. This is an unguided process with no apparent inevitablity to it. Some buildups never reach the surface. No analogies are perfect but phrases, in which letters are selected because they satisfy an outcome but have no utility until reaching a certain threshold of intelligibility, provides no indication of selection value at early stages.
Comment by Bradford — August 29, 2009 @ 3:39 pm
August 29th, 2009 at 4:41 pm
Bradford,
Cumulative selection is a process where (1) a parent organism produces offspring with slight random modifications and (2) the most fit—in some well-defined, non-random sense—children survive and reproduce further. Dawkins was explaining the distinction between random mutations alone (1) and systematic selective pressure acting on random mutations (1+2). In the former case, it is highly unlikely that an organism will reach a peak of fitness: a random search would take a long time to find the maximum. In the latter, cumulative selection gets to a peak very quickly.
It does not matter whether fitness is expressed as the proximity to a meaningful phrase (Weasel) or as reproductive success (nature). Cumulative selection works all the same. Your aversion to Darwin's theory clouds your reasoning and does not let you see Dawkins's point. That's too bad.
As to your own example, it illustrates ballistic random deposition, a process that has nothing to do with cumulative selection.
Comment by olegt — August 29, 2009 @ 4:41 pm
August 29th, 2009 at 4:46 pm
Me thinks it is like a weasel. That's a nice target. Is that how cumulative selection should be explained? Set the target up and program selection so that a bullseye is inevitable?
Comment by Bradford — August 29, 2009 @ 4:46 pm
August 29th, 2009 at 4:55 pm
It would help if you or Dawkins would explain the selective value of
M_ ___k_ _t i_ _i__ a w___e_
It gets you closer to the target right Dawkins? But since Darwin posited intermediate selection values en route and Dawkins chose the grammatical analogy then what is the answer to the above question?
Comment by Bradford — August 29, 2009 @ 4:55 pm
August 29th, 2009 at 5:04 pm
Bradford,
If you bothered to read Dawkins you would know that he was responding to the oft-cited example of monkeys banging randomly on keyboards. You would have to wait a long time before any given phrase emerged (whether meaningful or not). His weasel was meant to show that selective advantage on top of slight random variations increases fitness of the surviving organisms much faster than random mutations would alone. That's not controversial at all.
And yes, a bullseye is inevitable: a fitness function always has maximum. Usually more than one.
Comment by olegt — August 29, 2009 @ 5:04 pm
August 29th, 2009 at 5:09 pm
Dawkins is selecting letters to fit a predefined target. Of what relevance is this to biology?
Except he does not show this.
Nice verbiage. Sounds philosophical. Nothing analogous to a physical process in any of this.
Comment by Bradford — August 29, 2009 @ 5:09 pm
August 29th, 2009 at 5:12 pm
Olegt, you did not answer this:
It would help if you or Dawkins would explain the selective value of
M_ ___k_ _t i_ _i__ a w___e_
It gets you closer to the target right Dawkins? But since Darwin posited intermediate selection values en route and Dawkins chose the grammatical analogy then what is the answer to the above question?
Don't talk about fitness functions without being able to define intermediate steps.
Comment by Bradford — August 29, 2009 @ 5:12 pm
August 29th, 2009 at 5:16 pm
Bradford wrote:
For God's sake, Bradford! It's a made-up example! The weasel phrase has no advantage over any other phrase in real life!
Do you also rail against problems in math and physics textbooks? They, for the most part, are also made up. But that does not make them useless pedagogically.
I can't believe we are having this discussion.
Comment by olegt — August 29, 2009 @ 5:16 pm
August 29th, 2009 at 5:33 pm
Olegt:
Right. It's a trivial program saying "Make pretend children, that when the right letter arises in the correct slot then there is a physical basis for selection as opposed to the real one which is a predefined target." A poor way to teach evolution unless front loading is the point.
Comment by Bradford — August 29, 2009 @ 5:33 pm
August 29th, 2009 at 5:44 pm
Bradford,
Yes, it's a trivial* program! We use trivial, made-up, unrealistic problems to teach science and math. Let me give you an example if you don't believe it.
<Bradford> What kind of an idiot shoots a bullet into a wooden block? How can a spring be massless? And why do we neglect air resistance? </Bradford>
Pedagogical examples aren't always realistic. In fact, most of the time they aren't. Have you heard the expression toy model?
*Yet somehow the Isaac Newton of Information Theory and an IEEE Fellow failed to implement it correctly. I wonder why.
Comment by olegt — August 29, 2009 @ 5:44 pm
August 29th, 2009 at 6:06 pm
Olegt, try something that is actually biologically relevant or have you become an advocate of FLE?
Me thinks it is lkke a weasel.
Each letter represents an amino acid. Make an amino acid substitution which enhances fitness. Not as dramatic as Dawkins' example but more realistic. Dawkins is actually misleading and reinforces Behe's point about sloppy intermediate pathways.
Comment by Bradford — August 29, 2009 @ 6:06 pm
August 29th, 2009 at 6:13 pm
Olegt provided the following Dawkins quote on another thread:
So in other words, Dawkins assumes a priori that evolution occurs slowly and gradually step-by-step in such a way that every intermediate step is somehow a “meaningful” step. (Meaningful in terms of “simple survival or, more generally, reproductive success.) By analogy that would be an algorithm that operates without a target sequence but gradually evolves step-by-step syntactically and grammatically correct English sentences from start to finish. So why didn’t he program his computer to do something like that. That would have much more obvious pedagogical value than pre-selecting a target sequence, wouldn’t it? Maybe computerist should try his hand at writing a program like that.
The problem with people, like Dawkins, who assert that the origin and subsequent evolution of life can all be explained by a dysteleological (blind, unplanned, unguided, undirected etc.) process is that they do not consistently hold to that position. Indeed, after slamming the front door they, more often than not, quietly smuggle teleology in some form back into science through the back door. Of course they’ll insist that what they have allowed in is not really teleological. A little redefining of some terms, and a little rhetorical sleight of hand and… “Aha! we can have our cake and eat it too!” (unless, of course, someone catches them in the act)
In his book, Darwin’s Black Box, Michael Behe gives a great example of this. He begins by quoting Elliot Sober, quoting Richard Dawkins–with allusions to Michael Ruse and Daniel Dennett who use similar arguments.
Sober, in his book, Philosophy of Biology, is commenting on the METHINKSITISAWEASEL analogy that Dawkins uses in his book, The Blind Watchmaker. Dawkins was referring to a computer program that generates the phrase: METHINKSITISAWEASEL after a “reasonably probable” number tries beginning with a purely random set of letters. This he then uses to illustrate the power of natural selection.
Sober, perhaps to further simplify the analogy, uses the idea of something like a combination lock (using letters instead of numbers) to carry out the same thought experiment.
“How many different combinations of letters,” he asks, “may appear in the windows? There are 26 possibilities on each disk and 19 disks in all. So there are 2619 possible sequences… The probability that METHINKSITISAWEASEL will appear…is 1/2619 …a very small number indeed.
But now imagine that a disk is frozen if it happens to put a letter in the viewing window that matches the one in the target message… the message can [now] be expected to appear after a surprisingly small number generations of the process.” (p220)
The problems with the Dawkins-Sober analogy is that it doesn’t explain where the target sequence comes from. It cannot be a target sequence unless it is pre-selected, something that a blind, unintelligent process cannot do.
“Why METHINKSITISAWEASEL?” asks Behe. Why not “MY
DARLINGCLEMENTINE or MEBETARZANYOUBEJANE?
As a disk turns, who is deciding which letters to freeze and why?
Instead of an analogy for natural selection acting on random mutation, the Dawkins-Sober scenario is actually an example of the very opposite: an intelligent agent directing the construction of an irreducibly complex system. The agent (Sober here) has the target phrase (lock combination) in his mind and guides the result in that direction.” (p221)
METHINKS-BEHE-HAS-A-POINT
Of course, maybe we shouldn’t give Dawkins then Sober such hard time for their inaccurate and misleading analogy. After all, in DBB Behe uses the analogy of a mouse trap in illustrate irreducible complexity. Did his critics give him a hard time for that?
Comment by JOHN_A_DESIGNER — August 29, 2009 @ 6:13 pm
August 29th, 2009 at 7:06 pm
JAD:
Excellent point. Olegt did you applaud the mouse trap as a fine pedagogical example?
Comment by Bradford — August 29, 2009 @ 7:06 pm
August 29th, 2009 at 7:56 pm
JOHN_A_DESIGNER wrote:
You, guys, are a riot. Maybe because the analogy would never be perfect? English sentences are not subject to cumulative selection. They don't have offspring. Any parallel between an English sentence and a population of reproducing organisms is vague.
For the umpteenth time, Weasel is a made-up model, inspired by the equally made-up picture of furiously typing monkeys. It nonetheless has every feature of cumulative selection: organisms that reproduce (asexually) with slight variations and are subject to strong selective pressure. The fitness function in this imaginary example is the distance to a particular phrase taken from Shakespeare. It would take the monkeys (random search) bazillions of years to generate that phrase, while Weasel (cumulative selection) got it in 11 minutes on Dawkins's old computer.
Point well made. Caveats explained. And yet, creationists, having totally missed the point, are having a field day because Weasel is not a realistic model of evolution. Of course it's not! Dawkins said so in that same book. Get over it.
Comment by olegt — August 29, 2009 @ 7:56 pm
August 29th, 2009 at 8:01 pm
Bradford wrote:
No, I didn't read Behe's book.
However, I remember getting a laugh when Casey argued that bicycles were irreducible.
Comment by olegt — August 29, 2009 @ 8:01 pm
August 29th, 2009 at 8:03 pm
Olegt:
Take your own advice and get to the library.
Comment by Bradford — August 29, 2009 @ 8:03 pm
August 29th, 2009 at 8:04 pm
Bradford, why does it matter what I think about Behe's mouse trap? I don't challenge this example on every corner as you do. I even admit readily that I haven't read his book, so I can't even evaluate the quality of the example.
Comment by olegt — August 29, 2009 @ 8:04 pm
August 30th, 2009 at 4:31 am
Hi Bradford,
Yes I think your spot on; Dawkins weasel implementation is closer to front-loading governed by a high-degree of active info (I believe this is what Dembski/Marks is referring too) running parallel to reach targets then it is to a blind watchmaker. Not only is the target sequence selected for but so is the starting bit width (or character width in this case), throughout the process sub-sequences are selected for fitness, ie: an 'A' in x position is more meaningful in terms of fitness then 'A' at y position. The "knowledge" to decide what to select is present throughout the process, even assuming that evolution has no "targets" within the pre-specified character width (27 which has 27^27 possible combinations). We could also start at the bit level, randomize and select 8-bit sequences which would encode ASCII characters instead of dealing with raw characters.
,
JAD said:
A weasel implementation of this type would require a lookup table the size of Texas (hehe, just kidding). I say that because there needs to be some type of start and stop instruction somewhere along the way. The stop instruction for Darwinian evolution would supposedly be "has selected better function for this environment", the start instruction would be simply natural selection itself acting on random mutations. In terms of english sentences, we'd have to ask what would make sentence x more meaningful then sentence y in the english language. To do that we'd need encyclopedia's as lookup tables, the lookup table would correspond, for example, to sentences related to physics, these sentences would then be selected amongst physicists as more meaningful or accurate or whichever standard of measurement/cost they apply to the selective process. Having said that, I simply don't think its possible to get something meaningful in any context without some type of reference point as well as a tracking mechanism. If its simply a matter of generating sentences and if everyone feels that is a more correct representation then if I find the time this week I will code a new program.
Comment by computerist — August 30, 2009 @ 4:31 am
August 30th, 2009 at 4:38 am
Actually, he's defining "fitness" and then showing a random process moving towards it.
It isn't relevant to biology. It addresses an objection of ID by demonstrating how a random process can "create information".
So you say, but since ID doesn't clearly define "create information", it's hard for us to determine whether he shows it or not.
Comment by don provan — August 30, 2009 @ 4:38 am
August 30th, 2009 at 4:57 am
Not at all. The target sequence is defined by the example. There's no mystery about where it comes from at all.
In biology, the "target sequence" is, of course, reproductive success, i.e., "fitness". This isn't a concrete goal such as the examples use, but it's a goal, and it affects the development of organisms via undirected processes in much the same way as the concrete targets of the examples.
Fitness is a target that's simply the consequence of differential survival. In what way is it not the result of a blind, unintelligent process?
He didn't try to simulate evolution because it would have made the example far more complex without showing the essential point as well. Dawkins's point is quite simple: ID claims random processes are impossibly inefficient, but by introducing a measure of quality that can be mindlessly applied to randomly generated attempts, we can see that random processes can be quite efficient, far more efficient than probability calculates such as Dembski's suggest.
Comment by don provan — August 30, 2009 @ 4:57 am
August 30th, 2009 at 5:00 am
It would help if you or Dawkins would explain the selective value of
M_ ___k_ _t i_ _i__ a w___e_
It gets you closer to the target right Dawkins? But since Darwin posited intermediate selection values en route and Dawkins chose the grammatical analogy then what is the answer to the above question?
Don't talk about fitness functions without being able to define intermediate steps.
Yes, the only way M_ ___k etc… would have selective value is if it already performed a function. So if its simply a matter of selection among existing function, then all Dawkins has shown is micro-evolution in action. Dawkins has to still figure out the algorithm to account for the CPU, memory etc…
Have fun with that one Dawkins, the Darwin of our time!
Comment by computerist — August 30, 2009 @ 5:00 am
August 30th, 2009 at 5:02 am
(sorry, please ignore my last comment)
Bradford said:
Yes, the only way M_ ___k etc… would have selective value is if it already performed a function. So if its simply a matter of selection among existing function, then all Dawkins has shown is micro-evolution in action, which is what Darwinian evolution is quite capable of producing. Dawkins has to still figure out the algorithm to account for the CPU, memory etc…
Have fun with that one Dawkins, the Darwin of our time!
Comment by computerist — August 30, 2009 @ 5:02 am
August 30th, 2009 at 5:11 am
Wouldn't the target have to be somehow built into the initial random sequence in order for this to be front loading? In Weasel, it's external information built into the fitness function.
But in general your point is correct: the target is a fabrication of an intelligent mind. Weasel illustrates the process, not the creation of the target.
Does Dawkins bring up Weasel the context of the blind watchmaker? I can understand why you'd be confused if Dawkins said Weasel was a simulation of the blind watchmaker's behavior.
Evolution has no start or stop, of course: it's continuous. Weasel and this more complicated example need a start condition and a stop instruction because they are examples, not because random processes require start and stop.
Comment by don provan — August 30, 2009 @ 5:11 am
August 30th, 2009 at 5:16 am
The ID claim involves the creation of information. Can you tell me how how to measure whether the information created by a series of events exceeds the limits of "micro-evolution"?
Comment by don provan — August 30, 2009 @ 5:16 am
August 30th, 2009 at 5:24 am
Can you tell me how how to measure whether the information created by a series of events exceeds the limits of "micro-evolution"?
How can micro-evolution, which selects from pre-existing function, create new function? Micro-evolution works top-down while Macro-evolution works bottom up. Do you have any of those bottom-up examples of evolution in action?
Comment by computerist — August 30, 2009 @ 5:24 am
August 30th, 2009 at 5:24 am
Dp said:
How can micro-evolution, which selects from pre-existing function, create new function? Micro-evolution works top-down while Macro-evolution works bottom up. Do you have any of those bottom-up examples of evolution in action?
Comment by computerist — August 30, 2009 @ 5:24 am
August 30th, 2009 at 5:30 am
Just to make it clearer in my last comment I stated micro-evolution works top-down, well it does. It starts with exisiting function and works its way down while Macro-evolution works its way up, the problem is that Dawkins weasel says nothing about Macro-evolution, how you get function in the first place.
Comment by computerist — August 30, 2009 @ 5:30 am
August 31st, 2009 at 4:54 pm
No, I cannot tell you anything about the limits of "micro-evolution". I don't know of any limits to "micro-evolution". You brought up micro-evolution as if it presented some kind of limit to information creation, so I was hoping you'd be able to back it up with some idea about how we could measure whether something was exceeding those limits.
I don't understand. Evolutionary changes are selected from variations. What limiting mechanism are you suggesting that prevents a variation from including "new function"? Wouldn't any variation will be "a new function" in some sense?
You seem to have some idea of micro-evolution and macro-evolution as two entirely different processes that operate in two different ways. Can you clarify that? The only process I know of is variation and selection. I would call that "bottom-up", but you seem to be calling it "top-down", so I guess I have no idea what we're suggesting by those terms.
Comment by don provan — August 31, 2009 @ 4:54 pm
August 31st, 2009 at 6:06 pm
computerist:
Well said. This illustrates the problem with the Dawkins weasel. Function is analogous to meaning in a grammatical setting. Words in a sentence have meaning even if the sentence conveys a meaning different from the individual words. A letter in a word containing five letters conveys no meaning at all. Therefore no function and no selection value. You get no increase in biological complexity when no selection criteria exists.
Comment by Bradford — August 31, 2009 @ 6:06 pm
September 1st, 2009 at 12:11 pm
You seem to be viewing Weasel as some kind of simulation of biological evolution. But, as I've explained, Weasel is demonstrating how the process of mutation and selection generates information. It is not simulating how biological systems are selected in real life. In nature, successful systems survive because of how they interact with the environment, and that interaction does involve function. But Weasel introduces an entirely different artificial selection mechanism that doesn't involve interacting with anything, so it doesn't involve any function, and we shouldn't expect to see anything analogous to function.
Weasel avoids the extraneous complexity of biological evolution and focuses directly on information creation. That's why I suggested earlier that the mathematical calculations of CSI and such should be applied in a careful analysis of Weasel in order to show exactly how information is or is not leaking through from the simulation into the results. As long as you keep trying to argue that Weasel fails to model real life, you're missing its critical point, and you're also missing the nature of its vulnerability to the mathematical methods of information detection that ID has produced.
Comment by don provan — September 1, 2009 @ 12:11 pm
September 1st, 2009 at 2:59 pm
dp:
"Selection" is the product of predetermined intelligent input. Reaching the search target is a foregone conclusion which is why the simulation teaches nothing of use. Unless it is that front loading a mechanism to realize a target simulates how a front loaded evolutionary process would work.
Comment by Bradford — September 1, 2009 @ 2:59 pm
September 1st, 2009 at 5:03 pm
Bradford wrote:
Yes, reaching any target is also a forgone conclusion in a random search. Is not the point of the simulation rather to demonstrate the speed of cumulative selection compared to a random search? Also, if Weasel teaches nothing about selection, why does leading ID theorist Dr Dembski keep bringing it up? Perhaps he disagrees with you.
Comment by Alexei — September 1, 2009 @ 5:03 pm
September 1st, 2009 at 5:13 pm
Bradford wrote:
"Selection" is the product of predetermined intelligent input. Reaching the search target is a foregone conclusion which is why the simulation teaches nothing of use.
This is not just any target. It's a target that is specified in advance. Do you believe that mutations are random with respect to fitness? If so consider tRNA synthetases as targets. Reaching that target was a foregone conclusion of an evolutionary process right? How would you demonstrate that?
The letters were chosen, not selected by any criteria that resembles natural selection.
He likely brings up Weasel as a target of ridicule.
Comment by Bradford — September 1, 2009 @ 5:13 pm
September 1st, 2009 at 5:33 pm
Bradford wrote:
Yes indeed the target was specified in advance. But I believe that served the purpose of keeping the model simple, for pedagogical reasons. After all, Dawkins wrote for an audience of lay people, mostly not trained in parsing the technical scientific literature. In reality, the 'target' is higher survival and/or fertility than competitors, but there are many different ways an organism can be changed to accomplish that. Dawkins could have shown a model that would demonstrate the efficiency of cumulative selection, while allowing for a less specified target, but that would probably have been too difficult or perhaps too boring to read. Surely you do not doubt that biologists have devised such more elaborate models?
Why do you ask if I believe that mutations are random wrt fitness? It is not a matter of believe. One can look up the scientific literature.
Speaking of which, in your opinion have Dembski & Marx correctly depicted the model of Dawkins in there recent IEEE paper?
Comment by Alexei — September 1, 2009 @ 5:33 pm
September 1st, 2009 at 5:37 pm
In Weasel, the selection process is invented by a human, correct.
The point of Weasel is how much time it takes to reach the target. Reaching any search target is a foregone conclusion, given enough time.
On a tangential note, someone else said something like this, and I asked why this is anything like frontloading since the target is in the simulation, not in the data.
But, anyway, you still seem to be thinking Weasel says something about the goal. Perhaps you could expand on why you see the human invented selection process within Weasel having a different impact on the random-variation/selection process in the simulation than the selection process of differential survival has on the random-variation/selection process that led to modern species. As far as I can see, while the two targets are obviously fundamentally different, they have the same impact of directing the same process towards their respective goals. In analyzing either case, the selection process is a black box — "Is this better? Is this better?" — and the human origin of the Weasel selection processes, unavoidable since Weasel is a human designed simulation, seems to be isolated from the variation/selection process being simulated.
Maybe if you answer this question, it would help me see your point: what if instead of a quote from Shakespeare, the target were a string of characters randomly generated at the start of the simulation? Would the absence of a human origin for that target change anything about your analysis?
Comment by don provan — September 1, 2009 @ 5:37 pm
September 1st, 2009 at 5:50 pm
don provan makes a good point I think:
In Weasel, the target string is meant to indicate a optimal phenotype dictated by an external environment. The algorithm evolves the string to reach that optimum much (really, MUCH) faster then a random search. One could say that the string is a genotype that has incorporated information from the selective environment.
Comment by Alexei — September 1, 2009 @ 5:50 pm
September 1st, 2009 at 5:51 pm
There is no competition in this simulation. Another reason why it is a poor way to introduce lay people to natural selection. Lay people are taught that Dawkins knows how to spell. I was charitable and willing to stipulate that in advance.
Comment by Bradford — September 1, 2009 @ 5:51 pm
September 1st, 2009 at 5:55 pm
Alexei:
The external environment being English language conventions.
Of course. The search is front loaded for that purpose.
One could say that a program can be devised that guarantees a grammatical outcome.
Comment by Bradford — September 1, 2009 @ 5:55 pm
September 1st, 2009 at 6:17 pm
Bradford wrote:
There really is. In the simulation there is a population of strings that compete for representation in the next generation. The strings that most resemble the target string will increase their frequency, while the competing strings that resemble the target less will see their frequency diminished. This is the essence of natural selection, formulated in an abstract way. You should not let the abstraction (English words rather than biological phenotypes, and fitness rather than resemblance to target string) distract you from the equivalence between the mechanism in the simulation and the mechanism of natural selection in the real world. Do you also complain about physics models that in the real world there are no equations but rather particles? I do not think so, so why do you mind about this abstraction?
Alexei wrote:
Bradford answred:
But in the random search the target is also loaded up front. Still the cumulative selection search is much faster. So the front loading is not relevant.
Comment by Alexei — September 1, 2009 @ 6:17 pm
September 1st, 2009 at 6:31 pm
Of course. Intelligent selection tends to have that effect.
This is an intelligently designed outcome. Nothing natural about it.
There is no equivalence. What we witness is a poorly designed model of the real world.
Comment by Bradford — September 1, 2009 @ 6:31 pm
September 1st, 2009 at 6:36 pm
ricolfsubcwudlshne
There's a randomly generated string. What are the odds that an r would arise in the first position if all letters have equal odds?
Comment by Bradford — September 1, 2009 @ 6:36 pm
September 1st, 2009 at 6:47 pm
Or one could say that an environment can be devised that guarantees a biological outcome.
Comment by kornbelt888 — September 1, 2009 @ 6:47 pm
September 1st, 2009 at 6:58 pm
Bradford replies
So now you seem to agree that there is indeed competition, in contrast to your previous statement, but you now have objection because the selection is intelligent? What is intelligent about the selection? You cannot mean that simply because a human being made the model, that is proof selection in nature is also due to intelligent beings? It sounds a bit, how shall I say, as if you do not grasp the concept of modeling. No offense.
Please, read again what I wrote before. The model is pedagogical. Not meant to represent the real world. Neverless, there is close correspondence between the mechanisms in the simulations and the mechanisms of natural selection. You disagree, but you do not give arguments, I am sorry to say.
Assuming there are 26 letters, I would say 1 in 26. Do you wish to make a point with this trivial exercise?
Comment by Alexei — September 1, 2009 @ 6:58 pm
September 1st, 2009 at 7:05 pm
There is no competition among letters and nothing to mimick natural forces. We witness letters selected for a purpose.
You're making progress. The real world simulated- this is not.
What natural forces are approximated by this silly program?
What biological structure has a one in twenty six chance of selection?
Comment by Bradford — September 1, 2009 @ 7:05 pm
September 1st, 2009 at 7:09 pm
Very good kornbelt.
Comment by Bradford — September 1, 2009 @ 7:09 pm
September 1st, 2009 at 7:16 pm
It is you and Dawkins who make no arguments. Weasel shows absolutely nothing about evolution, because you and Dawkins assume that evolution works that way. You assume that function comes from primarily selection. Selection can vary function, but it does not create it, it starts its way with function and works its way down – that is what weasel shows. You assume that function can come about via simply selection and random mutations, you assume not only that it can be created but than changed willy nilly – this is because you assume function can be practically anything.
Comment by computerist — September 1, 2009 @ 7:16 pm
September 1st, 2009 at 7:31 pm
computerist wrote:
That is not true. The models of selection are used by animal and plant breeders, and experimental microbiologists, to correctly predict outcomes of selection. Therefore, the models have been verified, and since they contain same basic mechanisms as Weasel, that has also been verified. Perhaps you are not familiar with scientific models?
You continued:
You are wrong in many ways. Environment says what phenotype has highest fitness. Function can therefore not be 'practically anything'. If we start with a viable genotype, and the environment changes (maybe a new predator), then mutant genotypes that are less easy to catch by predator will be selected. Weasel works in same way.
Comment by Alexei — September 1, 2009 @ 7:31 pm
September 1st, 2009 at 7:43 pm
Yes, these models show that with existing function you can generate adaptive function through a selection criteria.
Thats what can happen when a phenotype starts out with existing function. In programming, function can be selected from existing libraries to adapt to code. The better fit function suited for the problem is utilized, while you can say the rest just sit there waiting for some type of adaptive significance.
Comment by computerist — September 1, 2009 @ 7:43 pm
September 1st, 2009 at 8:04 pm
Are you sure? I thought the simulation involved generating several variations, and then selecting the best among them. Isn't that a competition?
No, the external environment is the simulation. It has nothing to do with the English language. As I pointed out, it could be a random collection of characters, or a random collection of anything else you want, for that matter. The selection criteria involves only the relative distance of the variation from the target.
How is the search front loaded? All the search does is generate random variations and judge them against a criteria. How does the nature of the criteria make this procedure front loaded?
One could say whatever one wanted, but I'd be more interested in someone explaining why the simplified selection criteria invalidates the illustration. The vary/select process has no clue that the goal is created by a human, and could care less that it was created by a human. The important point is that it achieves the goal through a random process.
Comment by don provan — September 1, 2009 @ 8:04 pm
September 1st, 2009 at 8:11 pm
Watch this dp. I'm about to demonstrate selection in action. I'm currently rejecting many possible letter combinations because they do not meet the fitness criteria. The fitness criteria is defined by those sequences that best model the message I wish to convey. Holy cow. Natural selection in action. Computerist will devise the appropriate program which will express these sentences in cout commands. There you have it dp. Selection in action. Amazing.
Comment by Bradford — September 1, 2009 @ 8:11 pm
September 1st, 2009 at 8:12 pm
As long as you continue to think that Weasel is supposed to model the real world, you're going to continuing missing the point. I've tried to help you, but as long as you continue missing the point, there's really no point is discussing it further.
Comment by don provan — September 1, 2009 @ 8:12 pm
September 1st, 2009 at 8:15 pm
While Weasel is selecting phrases mindlessly based on a mathematical calculation.
Comment by don provan — September 1, 2009 @ 8:15 pm
September 1st, 2009 at 8:15 pm
dp, I like my selection model better.
Comment by Bradford — September 1, 2009 @ 8:15 pm
September 1st, 2009 at 8:25 pm
Weasel is programmed to select a particular message. I used an advanced mathematical formula to produce my cout.
Comment by Bradford — September 1, 2009 @ 8:25 pm
September 1st, 2009 at 8:33 pm
It might help to review Dawkins's own words about the infamous Weasel program. The Weasel program doesn't merit much attention.
In fairness to the good prof, he doesn't claim the Weasel program is a true analogy of biological evolution. Only that it illustrates how features can be accumulated in small steps. The thing is, he might have just as well used an analogy of pulling random colored blocks from an opaque bag and only piling up the blue ones, until it reached a predetermined height. Cumulative selection is cumulative selection, and this example is as good as the weasel program for that.
Comment by kornbelt888 — September 1, 2009 @ 8:33 pm
September 1st, 2009 at 8:37 pm
Me thinks this artificial selection is a weasel way out. 1 in 26, 1 in 26… The man is playing with half a deck.
Generation 01: WDLMNLT DTJBKWIRZREZLMQCO P
Generation 02: WDLTMNLT DTJBSWIRZREZLMQCO P
Generation 10: MDLDMNLS ITJISWHRZREZ MECS P
Generation 20: MELDINLS IT ISWPRKE Z WECSEL
Generation 30: METHINGS IT ISWLIKE B WECSEL
Generation 40: METHINKS IT IS LIKE I WEASEL
Generation 43: METHINKS IT IS LIKE A WEASEL
Comment by Bradford — September 1, 2009 @ 8:37 pm
September 1st, 2009 at 8:48 pm
It achieves the goal using random inputs against a non-random goal. One thing is clear in the Weasel program, the random input is of the proper range of values such that it not only can, but necessarily must, lead to the goal. We may not be able to predict the order, but it's guaranteed success. (Actually, we can predict the order, if we're using a pseudo-random generator.) If I put a limit on the random number generator so that "E" was never generated, the target would never be reached.
I don't think many IDers and critics of blind-evolution-as-complete-story have much of a problem with natural selection being part of the process of life's evolution. It's the nature of the variation that's "fed" into selection. While – as Zachriel will be quick to point out – the blind view of evolution is consistent with what is known about sources of variation, there is no gap free demonstration that it was actually was sufficient. The Weasel program is of no help here.
Comment by kornbelt888 — September 1, 2009 @ 8:48 pm
September 2nd, 2009 at 2:47 am
Yes, as I've pointed out a few times now. Perhaps Bradford will listen when you say it.
There's some truth in what you say, but this example wouldn't have demonstrated the effect of variations in several directions or the competition between variations, and I'm not sure whether anyone could say that a stack of blue blocks exhibits complex specified information.
Correct. Just as we can see happening in nature.
Again, the ID objection is not that the goal will not be reached, but only that it would take an impossibly long time. Weasel demonstrates that the time required is dramatically less than what Dembski calculates based on a purely random search.
Quite true. And if you take out the part that varies the choices, that would also cause the simulation to fail. What do you think that shows us? I think it just shows us that it's a simulation.
OK, good topic. What is the significant difference between the nature of the variations fed into Weasel's selection process and the nature of the variations fed into nature's selection process? Can you think of a way to change Weasel's variations to eliminate the difference?
The point isn't to show that it's sufficient, only to show that claims that it is insufficient don't hold water: the simulation shows that the calculations used to justify that the process is insufficient do not agree with the experimental results.
Comment by don provan — September 2, 2009 @ 2:47 am
September 2nd, 2009 at 2:55 am
This is imprecise to the point of being deceptive. Weasel is programmed to guess randomly about a particular message in a way that allows it to learn which guesses are better than others. Again, this is just like real life. The process itself is mindless and undirected even though the desired result is predefined.
Comment by don provan — September 2, 2009 @ 2:55 am
September 2nd, 2009 at 8:48 am
This is deceptive to the point of being wicked. The only randomness simulated is the 1 in 26 possibility for each position during each iteration (itself a departure from real life where odds are considerably longer). Then that randomness ceases when the predefined desired letter appears and no further variation occurs. The outcome is predetermined at the outset and the only variable is the number of iterations required to get there. The process is not mindless but rather programmed to artificially stop "mutations" when the desired letter appears in the designated location. This is perfect fodder for Behe's irreducible complexity for it artificially assigns fitness of parts to the whole based on the fitness of the whole without regard to intermediate fitness criteria.
The program is unlike evolutionary biology as I was taught. Whether blue eyes appear in a species is not an inevitable preprogrammed process but rather is linked to the interaction of mutations to environmental factors. There is no variable environment in weasel. The environment is static and guaranteed to generate only one possible outcome. No contingency with respect to outcomes.
The whole bit is typical of the intellectual dishonesty of Darwinists (as opposed to evolutionists) who seek to insert their non-scientific views through a science door.
Comment by Bradford — September 2, 2009 @ 8:48 am
September 2nd, 2009 at 10:47 am
No. The fitness function does not identify which letters to mutate and which to fix in subsequent generations. Fitness is assessed only on the whole string.
Try running the Proximity Reward Search from the Weasel GUI at EIL. I did, and got the following from one run using 50 offspring per generation and a mutation rate of 40%:
1. BFNCQRZU <- the initial (random) string. Note lucky hit in first position.
2. BRNCQRZU
3. BRNCQRRW
4. BRVTQMRW
5. BRVTQZRW
10. BRADQJRC
15. BRADXFRS
20. BRAJMWRD
30. BRAVFRRD
40. BRAQFOCD
50. BRAGFORS
60. BRFDFORH
63. BRUDFORD <- so close to the solution. Alas…
64. BRWDFORD
65. BRWDFORD
66. BRBDFORD
67. IRBDFORD <- the 1st character mutates away from the goal!
68. QRVDFORD
75. BRZDFORD <- it’s back
77. BRADFORD <- goal
I had to run the mutation rate up to see letter reversions because the GUI only reports the best fit out of the population. You can see letter reversions in the above at several locations.
77 generations, or 3,850 fitness queries. This was a lucky run; on average (from a set of 100 runs) the goal was found in 160.95 generations (8047.5 fitness queries). Not bad when compared with the median number of queries estimated for unassisted random search (1.96e+11).
Comment by Tom MH — September 2, 2009 @ 10:47 am
September 2nd, 2009 at 11:14 am
However, the random number generator is guaranteed to generate fit values for all positions. Try putting a filter on it that eliminates the "B" character and see how long it takes to "BRADFORD."
The weasel approach only demonstrates cumulative selection. It is of no benefit whatsoever, if the search is open ended, in determining whether the variation generator is sufficient to generator the right values for the target string.
Comment by kornbelt888 — September 2, 2009 @ 11:14 am
September 2nd, 2009 at 12:30 pm
It is a misleading with respect to cumulative selection. The only type of selection that would be relevant is single value substitutions like proteins, for example, where amino acids are the base unit. It is completely misleading with respect to biochemical pathways or gross anatomical structures. The former can consist of dozens of enzymes each with hundreds of amino acids. The latter can consist of countless proteins and non-proteins. The 1 in 26 odds is severely misleading and since I was told this was intended for lay people with little knowledge of biological details, this type of teaching borders on irresponsibility. BTW, how many functional peptides consist of eight amino acids (Bradford)? If creationists pulled this sort of thing they would be pilloried. But Dawkins is an icon to many.
One other point. Someone may say that 8 amino acids refers to certain sequence orders within proteins. But that too would be misleading because the protein is the unit relevant to fitness and then it is highly likely this protein interacts with others. The point is the model is grossly inadaquate.
Comment by Bradford — September 2, 2009 @ 12:30 pm
September 2nd, 2009 at 12:54 pm
METHINKS IT IS LIKE A WEASEL The total possible combinations would be 26^23 correct?
Comment by Bradford — September 2, 2009 @ 12:54 pm
September 2nd, 2009 at 1:25 pm
Not correct
METHINKSITISLIKEAWEASEL = 26^23
METHINKS*IT*IS*LIKE*A*WEASEL = 27^28
Comment by Karla — September 2, 2009 @ 1:25 pm
September 2nd, 2009 at 1:37 pm
Bradford, you mischaracterized weasel and I ran a simple case to illustrate the mischaracterization. The case I ran showed that the model does not artificially stop when the desired letter appears in the designated location (your claim). And you still don't get it:
Every single position in the string is allowed to mutate in every single offspring in every single generation. It's not limited to single value substitutions.
Surely you are joking.
Comment by Tom MH — September 2, 2009 @ 1:37 pm
September 2nd, 2009 at 1:56 pm
Glutathion has only three aminoacids but is functional. It is so functional that it is used as buffer in redox sensitive reactions.
Comment by Karla — September 2, 2009 @ 1:56 pm
September 2nd, 2009 at 1:57 pm
You got there in 77 generations right? That's 77 tries at piecing 26^8 of possiblities correct?
Comment by Bradford — September 2, 2009 @ 1:57 pm
September 2nd, 2009 at 2:02 pm
Each generation had 50 offspring, so that was 77 x 50 = 3850 tries.
Comment by Tom MH — September 2, 2009 @ 2:02 pm
September 2nd, 2009 at 2:06 pm
26^8 = 208,827,064,576
Comment by Bradford — September 2, 2009 @ 2:06 pm
September 2nd, 2009 at 2:09 pm
So of a total number of 208,827,064,576 possibilites you got there in 3850 tries correct?
Comment by Bradford — September 2, 2009 @ 2:09 pm
September 2nd, 2009 at 2:16 pm
Correct, although the search rarely require that many tries. Statistically the median number of searches is ln(2) of the number of combinations for large numbers of combinations. So make it ~144,750,000,000. (MATLAB round-off there.)
Comment by Tom MH — September 2, 2009 @ 2:16 pm
September 2nd, 2009 at 2:18 pm
Over 100 trials I got there in an average of 8047.5 tries (160.95 generations).
Comment by Tom MH — September 2, 2009 @ 2:18 pm
September 2nd, 2009 at 2:25 pm
Why would that be do you suppose?
Comment by Bradford — September 2, 2009 @ 2:25 pm
September 2nd, 2009 at 2:25 pm
Correct.
I modeled both these strings on weasel, using 100 offspring per generation and a mutation rate of 5%. The first string took weasel an average of 6286 queries. The second string took an average of 8129 queries, or 1.3 times as many as the first, even though its search space is (27^28)/(27^23) = 14 million times as large.
Comment by Tom MH — September 2, 2009 @ 2:25 pm
September 2nd, 2009 at 2:28 pm
Weasel stops when it reaches the target string.
"Why is it the car keys are always in the last place I look?!"
Comment by Tom MH — September 2, 2009 @ 2:28 pm
September 2nd, 2009 at 2:40 pm
That is to say, the search algorithm stops when it reaches the target string, regardless of the algorithm. The algorithm referred to here is random search, not weasel.
And as for "weasel": I am using the model located here, which implements several search algorithms. The one I am euphemistically referring to as "weasel" is the Proximity Reward Search. Sorry for muddling my terminology.
Comment by Tom MH — September 2, 2009 @ 2:40 pm
September 2nd, 2009 at 2:42 pm
Tom:
Tom, I'm not asking you why you would stop when reaching the target. I'm asking why you arrive at a target having the enormous number of possible pathways we see in the above figures in so few tries. Luck or something more to this program you are not telling?
Comment by Bradford — September 2, 2009 @ 2:42 pm
September 2nd, 2009 at 2:48 pm
Tom:
Consider this:
65. BRWDFORD
66. BRBDFORD
8 letters. All free to "mutate" yet only one does. How incredible is that!
Comment by Bradford — September 2, 2009 @ 2:48 pm
September 2nd, 2009 at 3:05 pm
No luck required, no tricks involved. The magic is the fitness function, which ruthlessly selects from the offspring only the best match to the target. This is why GAs are popular among engineers for solving combinatorially difficult problems. The payoff versus blind random search is enormous.
I'm not using code I wrote (buyer beware, I know, I know) but it can be downloaded (in java) from the site I linked. A version in C which only implements the weasel search algorithm can we downloaded from here. Being a MATLABer I will probably mutate the C version into MATLAB and have at it. It is not a particularly complex set of code.
What would be good would be to see the inner details to illustrate just how potent the approach is. Unfortunately, the model I've linked to in the above posts only shows the one survivor at each generation. If I can get my MATLAB version to show the "whole family" it might be possible to walk through some examples.
For your amusement.
Comment by Tom MH — September 2, 2009 @ 3:05 pm
September 2nd, 2009 at 3:08 pm
So then all letters are not free to mutate. The fitness function constrains randomness (mutations) and directs toward the target.
Comment by Bradford — September 2, 2009 @ 3:08 pm
September 2nd, 2009 at 3:15 pm
"(66) BRBDFORD" was the best fit out of the 50 mutated offspring of "(65) BRWDFORD". The remaining 49 were further away from the target string and were therefore discarded.
The mutation rate is 40% at each character position. That means there is a 1.12% chance of an offspring having only one mutation (0.6^7 times 0.4). Offspring with no mutations are slightly more probable (0.6^8, or 1.68%). No matter; the one closest to the target is the winner.
Comment by Tom MH — September 2, 2009 @ 3:15 pm
September 2nd, 2009 at 3:22 pm
No. Selection drags the population (subsequent generations) towards the target, but the letters in the offspring of each generation are nonetheless free to mutate, regardles of whether they match the target or not. What the offspring are NOT free to do is survive with equal probability. The one closest to the target survives; the others die.
Comment by Tom MH — September 2, 2009 @ 3:22 pm
September 2nd, 2009 at 3:50 pm
BTW my math here is slightly hosed. Haven't done binomial probabilities in a while.
The chance of one and only one mutation is 8*(0.6)^7*(0.4) = 8.96%, not 1.12%.
So in a set of 50 offspring, we'd expect 4-5 of them would have only one mutation (given a 40% chance per letter in an 8-character string).
Comment by Tom MH — September 2, 2009 @ 3:50 pm
September 2nd, 2009 at 3:51 pm
Because it's a cumulative search. Far from "not telling": the effectiveness of a cumulative search is exactly what Weasel was created to demonstrate.
Comment by don provan — September 2, 2009 @ 3:51 pm
September 2nd, 2009 at 4:09 pm
Tom, you wrote,
I never claimed that the model stopped. My claim was that the letters are not free to mutate once the desired letter is in place. I've pointed out from the start that Dawkins' program is consistent with front loaded evolution or Mike Gene's concept of foresight embodied in an evolutionary process. Dawkins unwittingly endorses a prominent IDist position with weasel.
Comment by Bradford — September 2, 2009 @ 4:09 pm
September 2nd, 2009 at 4:16 pm
Tom:
More accurately fitness for individual letters is assessed by the whole string. As I've previously pointed out this feeds into Behe's IC point about the lack of apparent function for intermediate pathways. If the target is Methinks and an initial string is Lugxqars, a subsequent iteration yielding Mugxqars confers no fitness except with reference to an evolutionary process having foresight. But such a process is not symbolized by a blind watchmaker.
Comment by Bradford — September 2, 2009 @ 4:16 pm
September 2nd, 2009 at 4:29 pm
The following sounds like something Dawkins could say about his weasel program:
Comment by Bradford — September 2, 2009 @ 4:29 pm
September 2nd, 2009 at 5:46 pm
Is that still your claim? If so, we are not making much progress here.
To be consistent with FLE, the inital string (which is where the front-loading occurs, right) would have the target embedded in it somehow, yes? So it would have to be something like
JHS*IENVLSPFQ*NSGTELFIH*INZDMETHINKS*IT*IS*LIKE*A*WEASEL
We would use the target pattern to extract its image from the string, discarding the rest, and voilá! One query would do the trick — and good thing, too, since the 40% mutation rate (if we do NOT select on the front-loaded portion of the string) is liable to render the embedded target string into gibberish after several generations. AFAIK Dawkins proposed no means of keeping it intact.
Comment by Tom MH — September 2, 2009 @ 5:46 pm
September 2nd, 2009 at 7:08 pm
No. To be consistent with front loading the initial string would have to be part of a process that is biased with respect to future outcomes.
Comment by Bradford — September 2, 2009 @ 7:08 pm
September 2nd, 2009 at 8:24 pm
Tom let's backtrack a bit. I've repeatedly complained that when fitness is assessed at the level of the string the lottery winners show evidence of foresight in a process since there is no fitness at the individual letter position that has an intermediate fitness function of its own. I've also repeatedly pointed out that this is essentially Behe's point with respect to irreducuble complexity. Intermediate structures are often unidentified in an evolutionary process and theoretical ones lack a precise fitness assessment. I take the responses or lack of them to indicate your agreement with this or am I wrong about that? When you peg letter winning (the fitness of a part) to the fitness of the whole (the string) you give up on intermediate fitness assessments using the grammatical logic Dawkins chose. You can say that when an initial string Ndulxiff evolves to Bdulxirf that the second string is closer to the fitness of the target string (Bradford) but it is still completely dysfunctional. No reason to count the B and r as winners at their respective positions as the string itself shows no identifiable function. OTOH, if the intermediate had been Bradleyy one could argue for intermediate function albeit imperfect function (a misspelling) because the intended word is discernable. Since the Dawkins program omits consideration of intermediate fitness on any criteria other than the target fitness the program fails as a realistic model of cumulative selection.
Comment by Bradford — September 2, 2009 @ 8:24 pm
September 2nd, 2009 at 9:00 pm
A couple of points. Yes, Behes critics did give him a hard time. For example, critic Ken Miller for example writes:
However, I think Millers attempt here at ridicule backfires. I think it is ridiculous that anyone would actually wear a real mousetrap as a tie clip. Furthermore, once you understand the concept of irreducible complexity the mousetrap illustration is no longer needed. So its just plain silly to keep arguing about it. In DBB Behe shows us some real systems inside the cell and explains why he thinks they are examples of IC systems. Whether you agree with him or not he is talking about real functioning systems inside a real functioning cell.
What is the real functioning system that the Weasel analogy is supposedly illustrating? Remember in this context we are talking about the origin of life and pre-biotic natural selection– if there is such a thing. That means we are beginning with either a strand of free floating protein or a strand of free floating RNA. Take your pick, you still have the same problem. Once they were polymerized why would these free floating strands change, evolve or do anything? In other words right at stage one you are literally dead in the water. I mean is there any evidence that the nucleotides AUCG (U substitutes for T in RNA) spontaneously rearrange themselves according to some abstract fitness function? How would these sequences ever know when the lottery hit the jackpot? I think you run into the same problems if you begin with a protein strand.
It seems to me that before we start talking about either protein or RNA we need to hypothesize that there existed some real feedback mechanism and/or real selection mechanism that was already in existence in the abiotic environment. I am talking about something real made out of real atoms and molecules drawing its energy somehow from the environment. What is that thing (or things) and how the hell does it work? Please spare us anymore of this abstract fitness function nonsense.
Comment by JOHN_A_DESIGNER — September 2, 2009 @ 9:00 pm
September 2nd, 2009 at 9:13 pm
Bradford,
I don't know how many times it needs to be pointed out that fitness in Weasel is defined as the number of letters in the right places. Once the fitness function is defined, you can compare how cumulative search stacks up against random search. Weasel shows that cumulative search reaches the peak of fitness much, much, much faster than does random search. Do you have any objection against that? No? I thought so.
And that is all Weasel was supposed to show. It was not intended to be a realistic model of natural selection. If you want to investigate how that works in a model that better represents evolution in a population of organisms, write your own god-damned model.
This thread is a great confirmation of results in education research, which show that listening to a lecture is the worst mode of learning. If you are really interested in learning about evolution then quit whining and do something hands-on. A good first step would be to just find an online simulation of Weasel and play with it. That will clarify the confusion evident in this comment like no amount of lecturing would.
Comment by olegt — September 2, 2009 @ 9:13 pm
September 2nd, 2009 at 9:16 pm
Or alternatively explain precisely how it applies to intermediate structures. That requires:
1. Identifying intermediates.
2. Specifying fitness criteria for the intermediate i.e. identify intermediate function.
3. Demonstrate that the intermediate meets the criteria.
Comment by Bradford — September 2, 2009 @ 9:16 pm
September 2nd, 2009 at 9:20 pm
JOHN_A_DESIGNER wrote:
John, how about reading the eff-ing book? The relevant passage has been cited at least a couple of times in this thread alone. O wait, you cited it yourself here! How about reading the excerpt and pondering it a bit?
Weasel does not illustrate a biological system. It illustrates the principle of cumulative search. See my comment just above.
Comment by olegt — September 2, 2009 @ 9:20 pm
September 2nd, 2009 at 9:25 pm
I don't know how many times this needs to be pointed out but assigning fitness based on outcome gives up on intermediate fitness functions which in turn invalidates cumulative selection. Do you evaluate the likelihood that an ancient limbless fish will evolve limbs and lungs and adapt to the land by ignoring how intermediate structures on the way to limbs and lungs confer a selection advantage? Or do you mindlessly assign any evolved structure that appears to be an intermediate as having selection value by that very fact without consideration of actual intermediate function?
Comment by Bradford — September 2, 2009 @ 9:25 pm
September 2nd, 2009 at 9:25 pm
Sorry, but weasel shows at most micro-evolution in action.
A more realistic model is required to generate something like the bacterial flagellum.
*flagellum operates with each of its parts interacting with one another synchronously
*each object/sub-function is producing a specific depended upon function, each sub-function anticipates (input is directly related to output)
*functional integrity is a requirement of the system
*current state of the sub-function/object, control and timing is essential
*thus, precision placement and order of execution is a must
These are just a few things that are obviously required for evolution via rm & ns to explain.
A target sentence/phrase which conveys meaning has to have all these variables taken into the equation.
Please tell me how Dawkins Weasel explains this, pretend if you must.
On a secondary note, I'll be working on this type of program when I find the time this week, but off the bat it does not look very good for Darwinism.
Comment by computerist — September 2, 2009 @ 9:25 pm
September 2nd, 2009 at 9:28 pm
Bradford,
You are barking up the wrong tree. Dawkins used Weasel to made a simple point: cumulative search works better than random search. Do you agree with that point?
Don't tell me that Weasel's fitness function is unrealistic. I know it. Dawkins knew it. That is not the point.
Concentrate.
Comment by olegt — September 2, 2009 @ 9:28 pm
September 2nd, 2009 at 9:30 pm
Olegt:
Cumulative search as opposed to cumulative selection on any basis other than target fitness (as opposed to the fitness of intermediates). That makes the program not just not biological. It makes it antithetical to evolutionary principles which are dependent on step by step selection of identifiable functions.
Comment by Bradford — September 2, 2009 @ 9:30 pm
September 2nd, 2009 at 9:34 pm
Olegt:
Concentrate on this Olegt. You have retreated from cumulative selection to cumulative searches without acknowledging it. The difference is the problem of intermediate function I have highlighted. Cumulative searches based on target fitness makes a trivial point.
Comment by Bradford — September 2, 2009 @ 9:34 pm
September 2nd, 2009 at 9:39 pm
Bradford,
I did not retreat anywhere. I see no difference between these terms. (Dawkins calls random search "single-step selection".) But if you are a stickler, I will rephrase that sentence:
Dawkins used Weasel to made a simple point: cumulative search selection works better than random search single-step selection. Do you agree with that point?
Comment by olegt — September 2, 2009 @ 9:39 pm
September 2nd, 2009 at 9:40 pm
Sorry, that was messed up in formatting. Once again:
Dawkins used Weasel to made a simple point: cumulative
searchselection works better thanrandom searchsingle-step selection. Do you agree with that point?Comment by olegt — September 2, 2009 @ 9:40 pm
September 2nd, 2009 at 9:51 pm
Olegt:
Cumulative selection requires intermediate selection along the way. That is assessed based, not on target fitness, but rather on the fitness of the intermediate. Target fitness guiding intermediate selection is not cumulative selection. Call it something else if you wish but not that.
Comment by Bradford — September 2, 2009 @ 9:51 pm
September 2nd, 2009 at 9:56 pm
Olegt, you ask questions while ignoring mine:
Comment by Bradford — September 2, 2009 @ 9:56 pm
September 2nd, 2009 at 10:03 pm
Bradford,
Don't make excuses. Don't deflect. Just answer my question.
Pretty please.
Comment by olegt — September 2, 2009 @ 10:03 pm
September 2nd, 2009 at 10:03 pm
Olegt:
So, please clarify. In your opinion cumulative search/selection has something to do with evolution? Or, nothing to do with evolution?
Comment by JOHN_A_DESIGNER — September 2, 2009 @ 10:03 pm
September 2nd, 2009 at 10:03 pm
Glad you asked, John.
I think it does.
Comment by olegt — September 2, 2009 @ 10:03 pm
September 2nd, 2009 at 10:11 pm
And Dawkins' program has nothing to do with cumulative selection (as defined by anything other than target fitness which renders it trivial) or evolution. But it is clearly not sold that way.
Comment by Bradford — September 2, 2009 @ 10:11 pm
September 2nd, 2009 at 10:17 pm
Olegt:
The problem with the last sentence is Dawkins' target selection criteria for intermediates does not illustrate the cumulative selection of biological evolution. You should have stopped with the prior sentence Olegt.
Comment by Bradford — September 2, 2009 @ 10:17 pm
September 2nd, 2009 at 10:27 pm
A search guided by the target works better than a random search. Seriously Olegt (and Dawkins) this stuff is so obvious even a swampie can see it. But why not produce a search methodology that utilizes intermediate fitness values en route to the target. Or is that too challenging?
Comment by Bradford — September 2, 2009 @ 10:27 pm
September 2nd, 2009 at 10:28 pm
Bradford,
Fitness function is defined in Weasel as a distance to a known target. But that is not essential to the principle of cumulative selection. We can define a fitness function without knowing the target in advance. Cumulative selection will work equally well. Do you disagree? Do you need a specific example?
Comment by olegt — September 2, 2009 @ 10:28 pm
September 2nd, 2009 at 10:49 pm
Indeed you can define a fitness function without knowing the target in advance. You can look to biological organisms for examples.
Comment by Bradford — September 2, 2009 @ 10:49 pm
September 3rd, 2009 at 8:18 am
Bradford, I am amazed that you are still flogging the dead horse. I see no reason to continue with this, so I will summarize (again!) the situation and move on.
Dawkins wrote Weasel to demonstrate the efficiency of cumulative selection in comparison to a random search. He chose a fitness function that minimizes the distance to a specific target and demonstrated that cumulative selection works great in this case. He then commented that this fitness function is not realistic. Let's quote him for the third time in this thread. I will helpfully add emphasis where it counts.
In this thread—and in creationist circles at large—criticisms are invariably concentrated on Dawkins's choice of the fitness function. You have latched onto it like Gordon E. Mullings onto a ratchet.* Give it up already! Cumulative selection is a totally separate issue. Cumulative selection works well for a variety of fitness functions. Whether the fitness function "knows" about the target or just maximizes some expression, cumulative fitness gets you to the top** and does so much, much, much faster than a random search would.
I—along with several other commentators—have tried in vain to explain this to the local gang over the last few days. Hundreds of comments later you are still criticizing Dawkins's choice of the fitness function. I don't know what it is—a lack of reading comprehension, unwillingness to engage the brain, mere stubbornness or personal feelings towards the former Oxford professor for public understanding of science—but something interferes with your ability to see that your criticism has already
been addressed by Dawkins in that same book. And that makes for a truly pathetic spectacle.
*A swamp inside joke.
** Quite often the fitness function has multiple peaks (local maxima), so it usually delivers you to one of peaks, and not necessarily to the highest one. If you repeat the process starting from another initial state you may get to a different fitness peak.
Comment by olegt — September 3, 2009 @ 8:18 am
September 3rd, 2009 at 8:20 am
The formatting is again messed up. It would be a good idea to return the Edit button.
Comment by olegt — September 3, 2009 @ 8:20 am
September 3rd, 2009 at 8:35 am
Another typo: cumulative fitness should have been cumulative selection.
Can I haz Edit button?
Comment by olegt — September 3, 2009 @ 8:35 am
September 3rd, 2009 at 8:54 am
The analogy (weak as it is) is that the initial string is the initial genotype. (It is also the initial phenotype, one of the weaknesses in the analogy.) It is selected at random so I am failing to see the FLE analogy. But we can leave it there.
Comment by Tom MH — September 3, 2009 @ 8:54 am
September 3rd, 2009 at 9:29 am
BRADLEYY would be functional and would have a high fitness score (relative to BDULXIRF) if the fitness function was "proximity to names popular in the United States c.2000". Probably would not score as well against BEOWULF if we raplaced "United States c.2000" with "Olde English heroic poetry". But wait a few years, and who knows? "Beowulf" may come back in vogue…
In either case, the dictionary of names we were using to assess fitness would serve as targets; thus we have replaced one target with many. They would constitute local maxima on the fitness landscape; hill-climbing algorithms that are searching for global maxima need techniques to avoid be trapped into local maxima that are below the global peak. This is all well understand in the field of evolutionary computation.
More importantly, it is unneccesary to have a target (or dictionary of targets) at all to demonstrate the power of cumulative selection! Blondie24, a checkers-playing AI, had at it's core a set of neural net weights that were developed by evolutionary techniques. Cloning with mutation produced a small set of genetically-related competitors that then played against each other in a round-robin tournament. The top scorers were retained and cloned (with mutation) for the next set of competitors. And so on. After many generations the programmers took the Nth generation winner on-line to compete against human players ("Blondie24" was the program's handle, which was chosen to hide the fact that she was not a human player…and to attract male competitors, heh.) Turned out to be a very successful checkers-playing AI, even good enough to defeat CHINOOK, the top-rated (rated expert) checkers AI at the time. Maybe aiguy knows more about it and will weigh in here?
The creators of Blondie24 were very scrupulous to avoid the "expert systems" approach of injecting human-developed heuristic knowledge. See this paper or read their book (an enjoyable book). Mr. Fogel in particular was rather dismissive of expert systems, and felt that they placed human limitations on potential algorithmic capabilities.
Weasel works with a target as the fitness function, and that is its limitation. It demonstrates the power of cumulative selection, something already well-understood by engineers who use evolutionary techniques to solve combinatorily complex problems. It does not adequately model biological evolution, though it certainly points in a promising direction. It is a tiny scrap of code not nearly deserving of all the attention it is getting. But if we cannot understand weasel then we're not going to get very far with more complex models, assuming that more complex models are an important part of the current path of biological research into origins and evolution. (I wouldn't know.)
Comment by Tom MH — September 3, 2009 @ 9:29 am
September 3rd, 2009 at 9:59 am
No, it sounds like something Dembski would say.
Comment by Tom MH — September 3, 2009 @ 9:59 am
September 3rd, 2009 at 10:36 am
I duly noted the Dawkins quote in an earlier post, and I understood that he was acknowledging the programs limitations. Then I wrote this:
In other words, I was asking for a revised weasel type program that was more analogous to the way that evolution actually worked. It appears that both computerist and Bradford picked up on that. I assumed that that is what the discussion has been about for the last couple of days. Not Dawkins original weasel program but how you could perhaps revise that kind of program to be more analogous to real world evolution. Is that even possible? I don’t know I’m not a computer programmer. However, my intuition is that it is not.
My apologies if I didn’t make that more clear, but the discussions on threads like this tend to be very informal if not a bit wild and wooley.
So are we free to look for a better analogy or not?
Comment by JOHN_A_DESIGNER — September 3, 2009 @ 10:36 am
September 3rd, 2009 at 10:47 am
Problem specific information included in the programming. Fits weasel to a T.
Comment by Bradford — September 3, 2009 @ 10:47 am
September 3rd, 2009 at 10:53 am
The analogy entails a process, correlating to evolution, which biases the outcome toward an evolutionary objective namely, the specific Methinks string which would represent either an organism or specific traits of an organism. Foresight is evident in the search facilitating problem specific information loaded into the program.
Comment by Bradford — September 3, 2009 @ 10:53 am
September 3rd, 2009 at 11:05 am
Well said. A program analogous to evolution would not evoke the type of critique seen in this thread. Unless, that is, critics are willing to acknowledge the plausibility of front loading evolution. Front loading for a specified outcome could be renamed weaseling.
Comment by Bradford — September 3, 2009 @ 11:05 am
September 3rd, 2009 at 11:49 am
The string METHINKS might be analogous to an enzyme that supports rapid catalytic rates. Deviations from this (e.g. METHIFKS) support lower catalytic rates. Let's assume a mechanism that favors (selects for) higher catalytic rates, and another mechanism that permits the enzyme to be reproduced with some random variation. Weasel demonstrates the effectiveness of cumulative selection in driving the population from {random_input} to METHINKS.
So the front-loading is the potentiality of METHINKS to support rapid catalysis. But METHINKS is just a molecule. It does not need to learn how to catalyze reactions, or be told how to do it; its catalytic properties are a function of basic chemistry and physics. Thus the "front-loading" consists of the laws of physics, and the properties of things like electrons and atomic isotopes, which behave the same way under the same conditions always and everywhere.
Every protein and every ribozyme and every form of RNA and every other biochemical of importance were possible from the instant of the Big Bang. They have always been targets.
Comment by Tom MH — September 3, 2009 @ 11:49 am
September 3rd, 2009 at 12:02 pm
The issue for me is how targets are modeled.
Comment by Bradford — September 3, 2009 @ 12:02 pm
September 3rd, 2009 at 12:43 pm
Tom MH:
So how exactly does this all work? There is a repository or library of un-embodied information floating out there someplace? How do you get that information into primitive genomes at the opportune time and place in the correct sequence?
BTW in principle I have no problem with such and idea, I just have no idea how it would work. So, enlighten me if you can.
Comment by JOHN_A_DESIGNER — September 3, 2009 @ 12:43 pm
September 3rd, 2009 at 12:50 pm
Obviously there's problem specific information included in the programming. That's true of any simulation. I'd be more impressed if you actually made a case for the problem specific information included in the programming leaking into the simulated environment. As far as I can see, the only external input into the simulation is the fitness function. If you have some reason to say that the fitness function in the simulation affects the environment differently than the fitness function in nature, could you spell it out for us? All I see is you saying, effectively, that since it's a simulation, by definition it is unable to simulate an environment that has no intelligent input.
How targets are modeled is certainly an interesting issue, but it has nothing to do with Weasel. The target in Weasel is just an arbitrary text string. Weasel doesn't do anything to try to model targets, only to model the application of a fitness function.
Comment by don provan — September 3, 2009 @ 12:50 pm
September 3rd, 2009 at 1:05 pm
The problem specific information included makes this simulation antithetical to the way evolution is said to work for reasons I've already stated. That makes weasel worse than useless. As yooz guys might say it is anti-science. And you know how horrifying that is.
Comment by Bradford — September 3, 2009 @ 1:05 pm
September 3rd, 2009 at 2:30 pm
JOHN_A_DESIGNER wrote:
That's great, John. You're neither a biologist, nor a programmer, but somehow you know that this would be impossible—without even trying. That's not intuition, it's prejudice.
Comment by olegt — September 3, 2009 @ 2:30 pm
September 3rd, 2009 at 2:38 pm
JOHN_A_DESIGNER wrote:
Of course you are. In fact, you should. That's exactly what I wrote yesterday. I look forward to seeing your code. Or Bradford's. Or computerist's.
Comment by olegt — September 3, 2009 @ 2:38 pm
September 3rd, 2009 at 3:09 pm
The repository is the physical properties of atoms. Certain atoms joined in a certain way can form an amino acid. Certain amino acids joined in a certain way can form an enzyme. Even if that constellation of atoms and amino acids has never existed in the entire history of the universe, the possibility that they could form that enzyme has always existed, and the properties that the enzyme would have, once formed, have always been the same.
Therefore it is perfectly valid for weasel to employ a target. My only regret is having suggested that this somehow is a weakness of the model. It is not.
Descent with modification. Of course, this requires that you put up with a lot of INcorrect information getting into primitive genomes at INopportune times and places and in INcorrect sequence. That would be the 49 offspring that do not survive to the next round in weasel. C'est la vie!
Comment by Tom MH — September 3, 2009 @ 3:09 pm
September 3rd, 2009 at 4:03 pm
Comment by computerist — September 3, 2009 @ 4:03 pm
September 3rd, 2009 at 4:08 pm
Sorry, unable to delete last comment. Here goes again:
Tom MH said:
Let me rephrase that:
The repository is the physical properties of atoms. Certain atoms joined in a certain way can form semi-conductor crystals, certain semi-conductor crystals can form a transistor. Even if that constellation of atoms and transistors has never existed in the entire history of the universe, the possibility that they could form that transistor has always existed, and the properties that the transistor would have, once formed, have always been the same.
NO SHIT, Tom MH, it could pretty much apply to ANYTHING!
This is the type of deluded Darwinian nonsense ID proponents have a fun time pointing out.
Comment by computerist — September 3, 2009 @ 4:08 pm
September 3rd, 2009 at 4:11 pm
JAD and Bradford might find this comment interesting.
Comment by olegt — September 3, 2009 @ 4:11 pm
September 3rd, 2009 at 4:11 pm
Can you humor me by explaining it in my terms? The problem specific information is unavoidable because it's a simulation, but can you explain how it is antithetically leaking into the simulated environment? The simulated environment involves a random process and an opaque measure of desirability. Where's the problem specific information?
I'm not entirely sure I understand your distinction between "cumulative selection" and "cumulative search", so perhaps you could clarify this. I would say that Weasel is a search based on accumulating results from an arbitrary fitness function. Perhaps that makes it a cumulative search based on selection?
Indeed, Weasel is trivial. It is intended to be a simple and obvious example of information creation by a random process.
When judging value, you know or care nothing whatsoever about the details such as lungs or linbs, and instead judge the entire organism in its current state for a single quality to be valued. In nature, that value is survival. In Weasel, that value is a measure of closeness to the target. Weasel simplifies the case so you don't get lost in the weeds, but you just complain because there are no weeds to get lost in.
Comment by don provan — September 3, 2009 @ 4:11 pm
September 3rd, 2009 at 4:16 pm
Tom MH said:
And is XZFFFDDS analogous to an enzyme that supports much much much less rapid catalytic rates?
Comment by computerist — September 3, 2009 @ 4:16 pm
September 3rd, 2009 at 4:34 pm
Indeed. Some people might even try to use evolutionary computation to lay out circuits filled with those transistors.
And once a novel circuit design is thus achieved, what will you say to JAD to explain where the "un-embodied information" was and how it got into the circuit? Obviously my approach didn't work.
Comment by Tom MH — September 3, 2009 @ 4:34 pm
September 3rd, 2009 at 4:36 pm
Yes.
Comment by Tom MH — September 3, 2009 @ 4:36 pm
September 3rd, 2009 at 5:01 pm
Going back to the thread's central theme take me through a step by step explanation (with documentation) showing how cumulative selection operates in an RNA World.
Comment by Bradford — September 3, 2009 @ 5:01 pm
September 3rd, 2009 at 5:05 pm
Getting off the dead weasel, Bradford?
Comment by olegt — September 3, 2009 @ 5:05 pm
September 3rd, 2009 at 5:07 pm
So a phrase XZFFFDDS, offset in some positions by about 20 or more characters in the alphabet supports much less catalytic rates!
Using Weasel as the driver, you will have no problem demonstrating how XZFFFDDS supports much less rapid catalytic rates and without the problem being defined from the start.
And once a novel circuit design is thus achieved, I will ask for the problem specific info that's embedded into the software, the specific parameters and the target to be reached defined by the intelligent agent handling the program. A simple FCSI check on the circuit design software itself won't hurt either.
Comment by computerist — September 3, 2009 @ 5:07 pm
September 3rd, 2009 at 5:32 pm
You will find all manner of problem specific info, of course. That would be the point of writing the program. What you won't find is the information that describes the solution, since that is unknown and doesn't even exist when the program is written. But that information — newly created information — is printed out as a result after the mindless, unguided, unsupervised, impersonal process finishes. Where did that information come from if it was not created by the mindless, unguided, unsupervised, impersonal process?
Comment by don provan — September 3, 2009 @ 5:32 pm
September 3rd, 2009 at 5:39 pm
Weasel is incapable of doing any such a thing. It is not a simulation of enzymes and catalytic processes — that was just an analogy.
In this application of evolutionary computation, a target is not used, since the engineer does not know what the final design should be, only the constraints. The circuit design that results would not necessarily be one conceived of by the engineer at the start of the process.
Comment by Tom MH — September 3, 2009 @ 5:39 pm
September 3rd, 2009 at 5:45 pm
What information would that be?
Comment by Bradford — September 3, 2009 @ 5:45 pm
September 3rd, 2009 at 5:58 pm
The information describing the novel circuit design .
Comment by don provan — September 3, 2009 @ 5:58 pm
September 3rd, 2009 at 5:59 pm
Thus the constraints are specified. Constraints are simply another way of reaching objectives. If I defined a program as what its not supposed to do rather then what it is, I can equally arrive at the same objective.
Comment by computerist — September 3, 2009 @ 5:59 pm
September 3rd, 2009 at 6:04 pm
How was that a mindless result?
Comment by Bradford — September 3, 2009 @ 6:04 pm
September 3rd, 2009 at 6:08 pm
Someone show me the code for the IDers' design algorithm.
Comment by Rock — September 3, 2009 @ 6:08 pm
September 3rd, 2009 at 6:09 pm
Yes, each problem requires different problem specific info. Transistors are made out of semi-conductor crystals, but that is an entirely different problem then designing a latch or a counter or JK-flip flop. Each require different problem specific info or "constraints" if you will. Thus the constraints should be well-defined, for example, to explain a rotary mechanism.
Comment by computerist — September 3, 2009 @ 6:09 pm
September 3rd, 2009 at 7:59 pm
Time to confess the truth. Weasel has nothing to do with biology we are told. It is merely about cumulative selection. And of course noone thinks biology when hearing the phrase cumulative selection.
In fact we're quite sure biologist Dawkins never even had biology in mind while popularizing Weasel. 
This is good bait and switch strategy. Know that most people will think biological evolution when hearing cumulative selection but if that is overtly challenged the correct response should be "Are you kidding? Don't you know that Weasel has nothing to do with biology?"
Comment by Bradford — September 3, 2009 @ 7:59 pm
September 3rd, 2009 at 8:22 pm
Bradford,
As I promised, I am not going to argue with you about Weasel. I'll just say that twisting other people's words is shameful.
Comment by olegt — September 3, 2009 @ 8:22 pm
September 3rd, 2009 at 9:03 pm
I'm told the passage was meant for a popular audience i.e. not biologists, computer programmers etc. An honest answer. When the average person hears selection he thinks biology or more specifically evolution- true or false?
Comment by Bradford — September 3, 2009 @ 9:03 pm
September 3rd, 2009 at 9:18 pm
Bradford, you are playing gotcha games and not to well.
Weasel is a good model of cumulative selection. Cumulative selection is part of theory of evolution. That does not mean that Weasel models a biological system. That's not hard to understand.
Again, as I said before, if you don't like the fact that Weasel's fitness depends on a specific target, write your own program where a target is not specified and the fitness function is some property of the phrase. I can think of numerous examples related to physics (like an Ising-type spin model) where an algorithm with cumulative selection can quickly find the state with the lowest energy—even if I don't tell the program what it is.
But I'm not holding my breath.
Comment by olegt — September 3, 2009 @ 9:18 pm
September 3rd, 2009 at 9:26 pm
Because it was the result of a mindless process.
Comment by don provan — September 3, 2009 @ 9:26 pm
September 3rd, 2009 at 9:29 pm
Of course. What's your point? Evolution has the similar information, except defined by chemistry and physics instead of existing technology. How does that change the fact that a random process developed the novel circuit design?
Comment by don provan — September 3, 2009 @ 9:29 pm
September 3rd, 2009 at 9:35 pm
What is hard for the ideologically blinded to understand is that average people think biological systems when encountering Weasel. What is worse is that Weasel not only does not model biological cumulative selection, it distorts that concept by incorrectly linking evolutionary steps to the fitness of a target. When I point this out the only defense is to maintain that Weasel does not model a biological system. So we have a world famous biologist touting a model of cumulative selection to readers with no particular technical expertise and we are to believe that there is no biological message intended for the common folk. Those promoting the Weasel concept should apologize to the Dover PA defendants because teaching false biology, albeit with a fallback excuse that it is not a biological model, is at the heart of Weasel. Average readers do not spend the time computerist and I devote to distinguishing Weasel selection from the real thing.
Comment by Bradford — September 3, 2009 @ 9:35 pm
September 3rd, 2009 at 9:36 pm
If it is a model it is not mindless.
Comment by Bradford — September 3, 2009 @ 9:36 pm
September 3rd, 2009 at 9:39 pm
Bradford,
Average people also have the reading comprehension and the attention span required to get to the point where Dawkins describes the limitations of his model. He does not mislead the reader.
You clearly heard about Weasel from a second-hand creationist source. I cannot vouch for the accuracy of its account. Maybe you should take your complaint to them.
Comment by olegt — September 3, 2009 @ 9:39 pm
September 3rd, 2009 at 9:40 pm
Bradford,
I'm sorry you misunderstood Weasel's point. I honestly don't think that's Weasel's fault since the descriptions I've seen have been fairly clear and easy to understand. Weasel is relevant to evolution and biology, of course, but it is not a simulation of evolution, which is apparently what you thought. I'm not sure why you misunderstood what Weasel tells us, but my guess is that your mind simply seized up rather than face the fact that one of the pillars of ID — that a random process cannot create complex, specified information — could so easily be disproved through such a trivial simulation.
Comment by don provan — September 3, 2009 @ 9:40 pm
September 3rd, 2009 at 9:45 pm
Olegt:
I've said since the outset of the discussion that Weasel infers a front loading concept favored by IDists. If the author of Weasel were named Mike Gene rather than Richard Dawkins ID critics would not be so indulgent of the program.
Comment by Bradford — September 3, 2009 @ 9:45 pm
September 3rd, 2009 at 9:47 pm
I understand the point perfectly well. It has as much sophistication as a two year old.
Comment by Bradford — September 3, 2009 @ 9:47 pm
September 3rd, 2009 at 9:48 pm
How perfectly stupid to contend that loading a program to hit an intended target proves anything at all.
Comment by Bradford — September 3, 2009 @ 9:48 pm
September 3rd, 2009 at 9:49 pm
Bradford wrote:
Bradford, you sound desperate. Call Dawkins what you want, but stupid he is not.
Chill down, dude.
Comment by olegt — September 3, 2009 @ 9:49 pm
September 3rd, 2009 at 9:51 pm
No, it's a process, and it is mindless. Random variation, opaque evaluation, random variation, oqague evaluation. Completely mindless.
Comment by don provan — September 3, 2009 @ 9:51 pm
September 3rd, 2009 at 9:52 pm
If a process which one and if a model you are confusing the process with the model.
Comment by Bradford — September 3, 2009 @ 9:52 pm
September 3rd, 2009 at 10:25 pm
My point is you should consider how much problem specific-FCSI is required for each subsequent problem/function in biology, it is vast! Consider all that "constrained" information processing that is required to generate not-function x which creates the exception to function y.
Comment by computerist — September 3, 2009 @ 10:25 pm
September 3rd, 2009 at 10:53 pm
What do you mean "which one"? I'm talking about the mindless unguided process that randomly picks designs and then looks at which ones work best, over and over. If that looks anything like a "model", I don't see how.
Comment by don provan — September 3, 2009 @ 10:53 pm
September 4th, 2009 at 8:50 am
Fair enough. The constraints in a string search algorithm are that the candidate strings are limited to fixed length and drawn from a fixed alphabet, and the test string must match the target. Weasel shows that RV+NS takes a randomly selected initial state to the target much faster than random search.
In biochemistry, the candidate strings are limited to atoms or molecules (the "alphabet"). String formation is further constrained by the physics of chemical bonding; of particular importance is the energy required to make or break any particular bond. Enzyme behaviour is further constrained by topology (protein folding, template matching). Random variation is limited in what offspring can be formed, but apparently there a large number of sources of variation for genomes (I don't have a link to it but Allen MacNeil has a website that lists dozens). Energy must be added to the system; nothing is going to take place at absolute zero, so at a minimum we need some heat. This is all much more complicated than text string searches, but even so, the analogy is useful.
I take it then that you agree that the constraints on the system are sufficient to explain the emergence of "active information" or "FCSI" in the resultant string or protein?
Yes, and evolutionary processes, as demonstrated by weasel, are a way to reach those objectives much more rapidly than random search.
Here endeth the lesson.
Comment by Tom MH — September 4, 2009 @ 8:50 am
September 4th, 2009 at 10:16 am
Sorry Tom, but the lesson has only begun for you and Dawkins!
The constraints required are themselves FCSI.
Comment by computerist — September 4, 2009 @ 10:16 am
September 4th, 2009 at 10:19 am
The laws of chemistry and physics are FCSI? Why do we need a new term?
Comment by Tom MH — September 4, 2009 @ 10:19 am
September 4th, 2009 at 10:37 am
computerist,
Where can I buy an FSCI meter? Is there a manual describing how to measure the quantity? You know, in a lab?
Comment by olegt — September 4, 2009 @ 10:37 am
September 4th, 2009 at 10:43 am
In any event, computerist, you didn't answer my question:
The designer would then be whoever decided that the laws of nature should be what they are. I'm fine with that; it pushes the origions of life question back to the origins of the universe, and leaves us free to try and comprehend the details of the natural processes behind abiogenesis, and evolution, here on Earth. E.g. form and test hypotheses, such as 'RNA World', without the need to invoke the meddling influence of some unknown causal agent.
One of those natural processes would be cumulative selection. It would be useful, from a pedgological POV, to have a simple illustration of cumulative selection to show the lay person the tremendous search advantages that cumulative selection has over random search (and to dispel the 'tornado in a junkyard' arguments related to the latter). Weasel does that job quite nicely.
Comment by Tom MH — September 4, 2009 @ 10:43 am
September 4th, 2009 at 10:50 am
Hi, olegt. I was going to ask computerist the same question, after he suggested running "a simple FCSI check on the circuit design software" upthread. If I asked my software engineers to do that I would be greeted with a blank stare, even though we are an SEI level 5 software engineering facility.
Comment by Tom MH — September 4, 2009 @ 10:50 am
September 4th, 2009 at 11:00 am
Yes, and evolutionary processes, as demonstrated by weasel, are a way to reach those objectives much more rapidly than random search.
Here endeth the lesson.
Comment by Tom MH — September 4, 2009 @ 8:50 am
Before you endeth, I was wondering how much faster the program converges if letters of the alphabet are not drawn with equal probability, but drawn according to the frequency they occur, say, in Shakespeare?
DRAM Ratchet
http://www.its.caltech.edu/~heathgrp/Papers/Paperfiles/2007/naturememory.pdf
This goes on my list of “cool devices,” I’ll probably never have.
Comment by Rock — September 4, 2009 @ 11:00 am
September 4th, 2009 at 11:27 am
I am not an expert but it seems to me that using evolutionary algorithms to make antennas simply is a method looking for optimum fitness; not targeted at particular antenna design? (Even more intelligent than a human
)
http://ti.arc.nasa.gov/projects/esg/research/antenna.htm
Comment by Satolep — September 4, 2009 @ 11:27 am
September 4th, 2009 at 11:31 am
You mean when doing random search? Good question. Once I get weasel.m up and running, I will try that. Test strings are drawn randomly from the alphabet, but the alphabet can be modified to emulate the relative frequency of occurrence of letters in English.
My guess is that hill-climbing (weasel) is still considerably faster. Pencil-and-paper cryptanalysts are familiar with letter frequencies — and even digraph and trigraph frequencies — but they also know a GA can blow past them (and ruin their fun) in solving cyptograms. Still, you raise an interesting question.
Sony Playstation 4. Or 5.
Comment by Tom MH — September 4, 2009 @ 11:31 am
September 4th, 2009 at 11:56 am
You got the idea! The concept is to find improved designs that human engineers cannot achieve, or are very unlikely to in a reasonable amount of time. (We always under cost and schedule limits.)
"Optimum" can be hard to establish; supercomputers take time and money, too, so the practical reality is, we snap the process off once some desired level of performance is achieved, or no further improvement is seen. In the latter case we may be locally optimum but we might not know if we are at a local maximum that is below a global maximum. Time-permitting, one tries to re-seed the process at different parts of the landscape landscape to test this.
And now I too must invoke time limitations, and sign off for the remainder of the day, and the weekend. See ya'll Monday!
Comment by Tom MH — September 4, 2009 @ 11:56 am
September 4th, 2009 at 12:14 pm
*First off, I don't agree that randomizing "strings" AND a fitness function generates FCSI, the FCSI is already built into the algorithm, the algorithm expects certain constraints for each specific problem. Thereby, the algorithms complexity is a function of its constraints.
*Randomizing a biological executable is not something that is as tolerable as running an executable on a computer with a Kernel managing the I/O between the hardware and software.
*Nobody happens to know the selective value of a rotary mechanism (as one example) to begin with (sure ,you may assume), the requirement so far is a rotary mechanism from the onset.
*In the real world, function is not randomized willy nilly, especially in biological systems (this is why you Tom MH, should read the Edge of Evolution and see the real limits of “evolution” in action).
*In the real world, software starts with UML: defining objects, its subsequent functions and properties and object interaction. Defining the problem top-down may not apply to cumulative selection, but the fact is that before object interaction can take place between “words”, a word must be fixed in the correct position before all other words, object interaction can be more complex and important to obtaining the objective then the sub-function itself, and yet a “space” in Weasel is treated equally as a character.
*Weasel randomizes "phrases", perhaps the target does not have to be specified in cumulative selection but various things must be, such as the character-bit width. Weasel assumes that after the first randomized phrase selective value is incurred, as you have already said yourself Tom MH.
Comment by computerist — September 4, 2009 @ 12:14 pm
September 4th, 2009 at 1:02 pm
The algorithm is "vary, test, vary, test". Testing is opaque: the algorithm has no idea what the test involves, it only knows the results. Now in Weasel, the test obviously is of human design because the entire simulation is of human design. In evolution, the test is simply survival. Where's the FCSI in that?
Tom MH and olegt are being flippant when they ask for an FCSI meter, but behind that is a very important point: since you believe FCSI is a valid measure, you should be able to apply it to the various aspects of Weasel to see where FCSI is and isn't and how it gets from where it is to where it shouldn't be. It would be a fabulous victory for ID if you could show how the unavoidable human footprint on the machinery of the simulation leaks into the simulated environment itself.
But, instead, you say that since FCSI is in Weasel — no one can deny that — that unavoidable means FCSI will leak into the simulated environment. As I recently pointed out to someone else, that's just the bogus claim that an unguided process cannot be simulated. This is going to come as a blow to people that have been simulating nuclear reactions: for decades now that've been thinking the reactions they're simulating can be made free of human effects.
Comment by don provan — September 4, 2009 @ 1:02 pm
September 4th, 2009 at 1:33 pm
Good place for you to show us this unguided process. After all the thread is titled: The Plausibility of the RNA World.
Comment by Bradford — September 4, 2009 @ 1:33 pm
September 4th, 2009 at 1:38 pm
I don't know if you need a new term but you do need a new paradigm. Chemicals forming information storage and retrieval systems outside biological organisms and without a guiding intelligence is unexplained by any known chemistry.
Comment by Bradford — September 4, 2009 @ 1:38 pm
September 4th, 2009 at 2:41 pm
Oh, sorry. I was just following the other conversation. I didn't realize you were offended that they had strayed from the topic. But at least now I can understand why you don't understand what unguided process generating information they were talking about, since it's obvious to someone following that conversation.
Comment by don provan — September 4, 2009 @ 2:41 pm
September 4th, 2009 at 3:40 pm
I'm not offended. It's Bilbo's thread. I was just hoping you had some real world evidence to substitute for silly computer algorithms. Guess not.
Comment by Bradford — September 4, 2009 @ 3:40 pm
September 4th, 2009 at 4:05 pm
I don't know what you've been smoking lately DP, don't pretend that I or other ID proponents do not understand Weasel.
Weasel generates phrases, the next generated phrase is based on a fitness test, a conditional test for survival – "best suited for the environment" in terms of how closer the phrase is to the target phrase or the current environmental context which defines the constraints (defines which characters not to select) – the greater percentage in terms of the current phrase is relative to the target/objective propagates into the next "generation", while the competing phrase does not even if it had a latched in "character" at the correct position, it doesn't go on to the next generation, so the previous phrase is indirectly in competition with the next phrase (program can be multi-threaded for multiple "phrases").
Yes, I believe FCSI is quite a valid measurement, especially for these types of tests.
I'll be working on it Don (yaa know this stuff doesn't just magically appear out of thin air), I'll be programming a bunch more (much more "realistic") Weasel implementations and check the results for myself.
Comment by computerist — September 4, 2009 @ 4:05 pm
September 4th, 2009 at 6:05 pm
Just to add to my previous comment:
*Weasel can equivocally show that function mutates until it is lost, its simply a matter of assumption, its a double edged-sword and it works both ways. Consider the environmental context (which defines the constraint), natural selection and random mutations. Tom thinks any phrase subject to those conditions is favorable to a certain outcome, while he and I could say it reaches "targets" I can say it reaches targets with no function. Therefore, Weasel works both ways, it depends on the assumption beforehand, personally I think it leads to a loss of information.
As for the Nasa antenna, yes intelligent selection works, it can work to select the best signal.
See Don, it was just a matter of time.
Comment by computerist — September 4, 2009 @ 6:05 pm
September 4th, 2009 at 6:28 pm
What intelligence is involved in determining which antenna produces the best signel? What intelligent is involved in randomly varying the antenna? What is significantly different between the mindless process that produces an antenna with the best signal and the mindless process that produces creatures with the best survivability?
Comment by don provan — September 4, 2009 @ 6:28 pm
September 4th, 2009 at 7:21 pm
The difference is your assumptions. The best signal is chosen when a signal between the antenna and transceiver is already set beforehand – NASA did not evolve an antenna, they simply chose the best signal by bending the antenna around an existing working platform – these generated different frequencies, the one with the strongest signal "unwinds" to the top which inevitably is chosen by the NASA engineers for the implementation phase.
On a side not: Those odd days you're unable to remember a certain thing you approximate your thought around a certain area until you find the closest/ exact answer – its thought the right side of the brain is a parallel pattern-match processing while the left side is serial-sequential processing (of course, everyone knew that already). Curiously, the processing of the right side of the brain resembles micro-evolution (selecting out of existing function, improving it, being creative and innovative) while the left is macro-evolution (designing and developing new function).
Comment by computerist — September 4, 2009 @ 7:21 pm
September 4th, 2009 at 7:36 pm
No, it generates phrases at random. Generation has nothing to do with the fitness test. The fitness test is only applied to see which of the competing randomly generated phrases is selected.
That's great! Can you give me an example?
I'll look forward to that, but I was thinking you'd just describe the FCSI in the existing code first before you could know how to change it. (Well, actually I'm not sure why you'd change it, since if you can show it's broken, you've proved your point.)
Comment by don provan — September 4, 2009 @ 7:36 pm
September 4th, 2009 at 8:02 pm
I thought I already made it clear that when I mean "generates" I mean generates randomly.
Comment by computerist — September 4, 2009 @ 8:02 pm
September 4th, 2009 at 8:07 pm
How can it be both random and based on a fitness test? The latter precludes the former, as far as I can see.
Comment by don provan — September 4, 2009 @ 8:07 pm
September 4th, 2009 at 8:20 pm
That agrees with my assumptions. The bottom line is still the mindless application of trial-and-error, just like evolution, generating an original design. No one clained the process invented antennas.
Comment by don provan — September 4, 2009 @ 8:20 pm
September 4th, 2009 at 8:34 pm
Here's a real world example of why cumulative selection is an impotent mechanism:
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
The question is: What is easily evolved by gradual, cumulative selection?
Comment by Daniel Smith — September 4, 2009 @ 8:34 pm
September 4th, 2009 at 8:56 pm
The randomly generated phrase is subject to a fitness test, I thought you knew that already.
Comment by computerist — September 4, 2009 @ 8:56 pm
September 4th, 2009 at 9:05 pm
"Subjected to a fitness test" is entirely different than "Based on a fitness test." "Based on" would mean the fitness test was in some way part of the generation. Since that's apparently not what you meant, could you go back and restate whatever it was you were trying to say when you said, "Weasel generates phrases, the next generated phrase is based on a fitness test…"? That might help.
Comment by don provan — September 4, 2009 @ 9:05 pm
September 4th, 2009 at 9:12 pm
Yes Don, because we are dealing with phrases, the current phrase and the next phrase. The next phrase (the one going on to the next "generation") is based on a fitness test, its a result of the previous (current) phrase being subject to a fitness test.
Comment by computerist — September 4, 2009 @ 9:12 pm
September 5th, 2009 at 3:51 am
OK, I guess we'll just have to admit we're speaking different languages. "Based on" means nothing like that to me. "Based on" says that information actually flowed from the fitness test to the phrase, but that's not the case if the fitness test merely scored the phrases so that the best could be selected.
Comment by don provan — September 5, 2009 @ 3:51 am
September 5th, 2009 at 4:41 am
Computerist states his belief:
But you seem to have forgotten this thread where you were going to provide some links to how FSCI has already been calculated and also show us how to calculate FSCI. All you did so far was to produce figures which boil down to just a simple count of the number of residues in a linear polymer.
Comment by Alan Fox — September 5, 2009 @ 4:41 am
September 5th, 2009 at 8:44 am
Selected based on target fitness criteria which makes Weasel trivial.
Comment by Bradford — September 5, 2009 @ 8:44 am
September 5th, 2009 at 11:14 am
Bradford;
Precisely. Dawkins pointed this out right at the start. Weasel was an aid to explaining the power of cumulative selection, nothing else.
Comment by Alan Fox — September 5, 2009 @ 11:14 am
September 5th, 2009 at 11:27 am
…which makes Weasel trivial.
Dawkins pointed out that Weasel is trivial?
A narrow type of cumulative selection based on target fitness. That's what makes it trivial.
Comment by Bradford — September 5, 2009 @ 11:27 am
September 5th, 2009 at 11:38 am
Bradford, you can't seem to wrap your brain around a simple idea: cumulative selection and fitness function are two separate notions. Whatever fitness function you provide, cumulative selection works much better than random search.* Your criticism therefore is directed at Dawkins's choice of the fitness function, and on that score Dawkins is with you. So your critique adds nothing to what Dawkins already said in the book.
Stop flogging the dead weasel already.
*Provided the fitness function is smooth.
Comment by olegt — September 5, 2009 @ 11:38 am
September 5th, 2009 at 12:48 pm
And in the case of English phrases, ID works better than both.
What's the point again?
Comment by Daniel Smith — September 5, 2009 @ 12:48 pm
September 5th, 2009 at 1:26 pm
A genetic ratchet?
http://en.wikipedia.org/wiki/Muller's_ratchet
What happens if Dawkins doesn't terminate the program?
Seems to me that in biology even exactly matching a fitness function doesn't result in the termination of the process. The illusion of cumulative selection is created by terminate the process, but does the notion of "cumulative selection" have any real relevance in evolutionary theory (other than in Richard Dawkins' mind)?
It does smack a bit of pre-destination, teleology, orthogenetic and progressive evolution, doesn't it.
Comment by Rock — September 5, 2009 @ 1:26 pm
September 5th, 2009 at 1:33 pm
Rock:
Well said Rock.
Exactly, yet you know that it was not Dawkins' intent to promote teleology or pre-destination.
Comment by Bradford — September 5, 2009 @ 1:33 pm
September 5th, 2009 at 1:44 pm
As you say. And as Dawkins says himself. Watchmaker was only meant to illustrate one point about cumulative selection. The environmental niche that acts as an engine of selection is dynamic and chaotic, not fixed.
Comment by Alan Fox — September 5, 2009 @ 1:44 pm
September 5th, 2009 at 2:42 pm
As I understand it the Weasel algorithm was an attempt to answer the question: Which is a more efficient means of arranging 27 letters and spaces so that they spell out "METHINKS IT IS LIKE A WEASEL" – random search (RS) or cumulative selection (CS)?
CS won hands down – due to the fact that any matching letter or space was deemed "more fit". Of course if "fitness" had been defined as "spelling out exactly METHINKS IT IS LIKE A WEASEL", CS would have no advantage over RS.
In either case – since the answer to the question is known – ID would beat both contenders by a mile. Most intelligent designers would get it right on the first attempt.
So how does this relate to real biological evolution? It's funny how defenders of Dawkins will say "it doesn't" while at the same time arguing that it shows the power of cumulative selection – one of evolution's many mechanisms.
In the paper I cited above, we see an example of real world evolution that required historically contingent evolution in order for a strain of e. coli to develop a means to metabolize citrate. This evolution could not occur easily by cumulative selection – despite the fact that e. coli already has a means of metabolizing citrate and only lacks a citrate transport system. It required – in essence – that METHINKS be in place before IT IS LIKE, and that both become fixed before A WEASEL be added. Based on Dawkin's model, you'd think that this would actually be easier, but it is not – since only METHINKS is considered fit, then only METHINKS IT IS LIKE, and finally only METHINKS IT IS LIKE A WEASEL.
This is an example of real world evolution that demonstrates just how difficult it is to develop something "simple". In the end, these scientists speculate that an existing transport system was coopted and used for transporting citrate. So – even though a means of metabolizing citrate was in place, and even though existing transport systems existed – coopting a transport system for citrate transport required over 30,000 generations of historically contingent evolution.
That's how it works in the real world.
Comment by Daniel Smith — September 5, 2009 @ 2:42 pm
September 6th, 2009 at 11:26 am
Hi Rock, you said:
From the POV of Darwinian Evolution and Darwinians, it doesn't matter whether the program is terminated – evolution is continuous as Tom MH and other Darwinian's will tell you. Cumulative selection "works", regardless of the exit condition such as "if reached target". If the current selected function is "best fit" relative to the niche, the current state will be "remembered" (a stop instruction) so to speak. It can be lost only if competing selected function is better fit for he niche. Offspring mutate randomly, natural selection "weighs" them (mutations) against each other, and the fitness function determines which one goes on to the next generation (the primary of importance being survival of the fittest).
Comment by computerist — September 6, 2009 @ 11:26 am
September 6th, 2009 at 11:34 am
Of course, as I have pointed out, the program demands assumptions from the start. If you assume the program increases function, it does. If you assume it the program decreases function, it does. I find that the evidence for decreasing function is more inline with the program and with science. The EoE tells us exactly what the capabilities of DE really are. Nature inevitably destroys, downgrades or whatever you want to call it, it turns metal into rust so to speak. The problem now is if biology can create faster then nature can destroy.
Comment by computerist — September 6, 2009 @ 11:34 am
September 6th, 2009 at 12:57 pm
Not if the fitness function is Fitness = METHINKS IT IS LIKE A WEASEL (no intermediates are any more "advantageous" than any other, only the whole string "works"). In that case cumulative selection and random search are equally effective.
Comment by Daniel Smith — September 6, 2009 @ 12:57 pm
September 6th, 2009 at 1:09 pm
Hi Daniel,
Your fitness function is flat except for a single extremely narrow peak (nerds would say a bit like a delta function). Thus, it violates olegt's explicit assumption of smoothness. For more or less continuous biological traits, his assumption seems more plausible than yours.
Comment by JarrodF — September 6, 2009 @ 1:09 pm
September 7th, 2009 at 3:06 pm
Catching up here (again). Hi, Daniel. Your post makes a nice seque to a point I want to make about weasel and CS.
Much has been made here about the use of a fitness target in weasel, and how this constitutes embedded FCSI or how it allows ID to find the target in the manner Daniel describes. Fine – let's remove it.
Instead of a test against a target, permit weasel to only call a completely separate process called the Oracle of Strings. The Oracle accepts as an input a candidate string, and supplies as an output the score. (And only the score — Oracle never reveals the target string.) In psuedocode:
fitness_score = Oracle_of_Strings(input_string)
Now weasel no longer contains the target information, and ID (other than omniscient ID) is no more likely* than random search to guess the target on the first try. In fact, it might even be provable that ID (that is, a human operator) can do no better than weasel in searching for the target, and that furthermore the only way a human operator can match weasel's performance is by using the exact same process.
*It is possible that a human operator could improve his search performance by choosing candidate strings that adhere to the known frequency of occurrance of letters (and digraphs, and trigraphs, and words…) in the English language. That would out-perform random search. To level the playing field, we will stipulate that nothing is known a priori about the target string (Oracle ain't telling). For all we know it could be in a foreign language. Or random gibberish.
While this answers Daniel's challenge, it probably does not dispel the FCSI challenge, as I am sure by now many of you are ready to point out that the FCSI is still in the system, even if it is hidden from view by the Oracle of Strings. Let me address that next.
Comment by Tom MH — September 7, 2009 @ 3:06 pm
September 7th, 2009 at 3:31 pm
To address the FCSI issue, let's abandon the Oracle of Strings for a second and talk about the Oracle of Organic Chemistry. This Oracle is similar to the other one in that it accepts as inputs a string and returns a fitness measure. The difference is that here the input string is a variable-length polypeptide chain, and the fiteness measure is the catalytic rate that peptide chain would have as an enzyme. Psuedocode:
catalytic_rate = Oracle_of_Organic_Chemistry(polypeptide_chain)
Of course, a well-designed interface to the Oracle of Organic Chemistry might need to be a little more complicated than that. For example, we might want to add fields to specify co-factors, and to identify the substrates and products, and specify things like temperature, pressure, the presence or absence of things like inhibitors, and so forth. But certainly you can see the resemblance.
Another difference between the O-Chem Oracle and the String Oracle is that this one accepts inputs of variable length. But the biggest difference is that the O-Chem Oracle has no target. If you stick to a specific set of substrates and products, and use cumulative selection exactly in the manner of weasel, you should be able to use repeated calls on the O-Chem Oracle to rapidly synthesize enzymes of extremely high catalytic rates.
Question for the TT commentariat: does the O-Chem Oracle contain FCSI?
Comment by Tom MH — September 7, 2009 @ 3:31 pm
September 8th, 2009 at 2:57 pm
I take it that you are beginning with an existing protein then? If not, then the first fitness criteria would be how (or whether) the peptide chain folds.
Then, of course there's the availability of substrate and the location of the newly formed protein.
Of course, then there's the issue of regulation.
Are we talking single-celled or multicellular organism? Because there are many other factors that come into play in higher organisms.
This is the problem when constructing a "simple" algorithm to explain an evolutionary process. It's pretty much impossible to do realistically.
Comment by Daniel Smith — September 8, 2009 @ 2:57 pm
September 8th, 2009 at 3:42 pm
Daniel, those are interesting but irrelevant questions. Make whatever assumptions you want. My question remains:
Comment by Tom MH — September 8, 2009 @ 3:42 pm
September 8th, 2009 at 4:43 pm
Highly efficient enzymes are your target? Within what context?
Comment by Bradford — September 8, 2009 @ 4:43 pm
September 8th, 2009 at 5:07 pm
Not precisely. Highly efficient enzymes as the goal. But absolutely no specification of what the target is. The calling program does not have a target it is trying to reach, and the Oracle does not have one to compare the input strings to.
Comment by Tom MH — September 8, 2009 @ 5:07 pm
September 8th, 2009 at 5:42 pm
I was wondering how much faster the program converges if letters of the alphabet are not drawn with equal probability, but drawn according to the frequency they occur, say, in Shakespeare?
“Once I get weasel.m up and running, I will try that.”
Any results?
Comment by Rock — September 8, 2009 @ 5:42 pm
September 8th, 2009 at 5:49 pm
"Much has been made here about the use of a fitness target in weasel… Instead of a test against a target, permit weasel to only call a completely separate process called the Oracle of Strings."
I'm sure IDers would find appeals to "Oracles" appealing.
I don't.
Let's try something different: See if the Weasel program produces any meaningful English language phrase, and how often.
No prespecified target, not of that weaseling and oracle-petitioning.
What are the chances?
Comment by Rock — September 8, 2009 @ 5:49 pm
September 8th, 2009 at 5:51 pm
Sorry, Rock! No results. I, er, found other diversions this weekend.
Comment by Tom MH — September 8, 2009 @ 5:51 pm
September 8th, 2009 at 5:54 pm
You need a measure of fitness. Without the Oracle, weasel merely creates modified (mutated) strings.
Comment by Tom MH — September 8, 2009 @ 5:54 pm
September 8th, 2009 at 5:57 pm
"You need a measure of fitness."
No truer words were spoken, TomMH.
Comment by Rock — September 8, 2009 @ 5:57 pm
September 8th, 2009 at 6:00 pm
Of course, any "meaningful English language phrase" is also a target.
Try to quantify it! LOL
Comment by Rock — September 8, 2009 @ 6:00 pm
September 8th, 2009 at 6:08 pm
Fitness functions are intrinsically teleological. The best an anti-telican can do is argue for a causal source for an initial, stable replicator that is grounded in "brute forces of nature." IOW, predefined as non-telic.
Comment by Bradford — September 8, 2009 @ 6:08 pm
September 8th, 2009 at 6:41 pm
Bradford:
What do you mean by this?
My understanding of a fitness function is that it is (essentially) a mathematical function into which one inputs the genome, and out of which one gets a fitness measure. (This is in the case of a genetic algorithm). In the real world, the fitness function is the environment, into which an organism is put (by birth, hatching, poofing, whatever), and the output is the number of descendents at some time later. But the fitness function is basically set at any particular point in time, and then varies over time as the organism's environment changes.
Comment by congregate — September 8, 2009 @ 6:41 pm
September 8th, 2009 at 6:56 pm
congregate, try setting a fitness function for initial conditions and I'll show you how teleology sneaks in.
Comment by Bradford — September 8, 2009 @ 6:56 pm
September 9th, 2009 at 8:52 am
A fitness function for a string of characters in the English language would indeed be intrinsically teleological because orthography, pronunciation, and meaning are all defined by human convention. So at a minimum it must have a target string (or set of strings, such as a dictionary).
Is there an intrinsic teleological property required for the target-less fitness function I described for the O-Chem Oracle (the catalytic rate for a candidate protein)? Does it necessarily contain FCSI?
Comment by Tom MH — September 9, 2009 @ 8:52 am
September 9th, 2009 at 9:01 am
Before I would answer a question about the fitness function of an enzyme I would want to know context. That's particularly important in assessing teleology.
Comment by Bradford — September 9, 2009 @ 9:01 am
September 9th, 2009 at 10:23 am
Feel free to make any assumptions about temperature, solution Ph, salt concentration level, whatever you think matters. Or make those inputs in the call to the Oracle. What does it matter? The question is, does the Oracle need FCSI to be able to generate the fitness measure: the catalytic rate of the enzyme?
Comment by Tom MH — September 9, 2009 @ 10:23 am
September 9th, 2009 at 10:42 am
Bradford-
Well, as I said, the fitness function in the real world is basically the environment, isn't it? I don't see how the environment is intrinsically teleological.
I'm not sure what you mean by initial conditions. Do you mean at the time biological life or its precursors first appeared on earth? At that time the fitness function varied depending on where on the planet one looked. If the "organism" or "proto-organism" or "prebiotic molecule" under consideration was in a location where there was lots of water, its fitness would be greater if it had the capacity to survive and reproduce in wet conditions. If in a dry desert, the opposite.
Comment by congregate — September 9, 2009 @ 10:42 am
September 9th, 2009 at 11:19 am
Oracles are crutches used by computer theorists to solve problems by cheating. In theory, the oracle plays the role of the computer theorist’s intuition—which he has failed to reduce to the mechanical operations of computation. Dawkins is the oracle in the Weasel program. Tom MH’s “Oracle”is just the string “ME THINKS…” Tom MH your oracle adds nothing to the program. (Other than non-functional pseudocode!)
Comment by Rock — September 9, 2009 @ 11:19 am
September 13th, 2009 at 3:31 pm
I'm not really concerned about FCSI. My point was that; if you want to make an algorithm that resembles the real-world evolution of enzymes, you'll have far too many variables to consider.
IOW, there are no algorithms that support actual real-world biological evolution since they are all essentially isolated from reality.
If you were to try to approximate real world evolution utilizing language (as weasel does) , you'd have to evolve something – a phrase or a sentence for example – in the context of something else – i.e. a paragraph. Even then, it would have to fit into larger contexts – a chapter, a book, and finally the English language as a whole – while, in all of it's intermediate forms, doing no damage to the overall meaning. IOW, if at any point the story makes no sense , the organism "dies".
Comment by Daniel Smith — September 13, 2009 @ 3:31 pm
September 18th, 2009 at 2:02 pm
Wow, I really need to install comment paging.
Comment by Guts — September 18, 2009 @ 2:02 pm
September 18th, 2009 at 2:37 pm
The individual dies. The species lives on to try again.
That's true. There are so many possibilities in real life that interesting things are bound to happen.
No, weasel doesn't try to approximate real world evolution. How many times does that have to be repeated?
Comment by don provan — September 18, 2009 @ 2:37 pm
September 18th, 2009 at 7:04 pm
I didn't word that very well did I? I didn't mean that weasel tries to approximate real world evolution – only that it utilizes language. Probably should have just left off the "(as weasel does)".
Comment by Daniel Smith — September 18, 2009 @ 7:04 pm