Deconstructing Avida

Perhaps I’m being simplistic, but don’t people write computer programs to get them to do what they want them to do? Avida is an example of design. It’s a sad commentary on the state of learning that we need detailed refutations of this nonsense.

Right now, there are “grumble grumble” mouse-potato back benchers pouring over this article seeking ways to spin it negatively. What a strange and curious world they live in.

Congratulations Dr. Dembski et al. I look forward to reading this in detail.

Congratulations on this paper Dr. Dembski and I also look forward to reading it.

Its worth noting that Michael Behe publish Darwin’s Black Box in 1996. One of the claims he made in the book was that there was not one, single research research study in any peer reviewed scientific journal that provided a detailed, testable model of how evolution constructed any of the IC systems he discusses in the book. Lo these 13 years later and that is still the case. However, I have seen the Avida study cited quite often when I asked for such a citation, as the only such study. How ironic!

The hypocrisy here is breathtaking. On the one hand, we are told that ID is not science. On the other hand, articles in places like NATURE appear that are clearly motivated by ID. And yet, the articles themselves are scrupulous to avoid referencing ID, its proponents, or published writings lest we gain an entry in the Science Citation Index and thus can further strengthen the case that ID is indeed science.

An article on astronomy might well be motivated by a desire to refute the claims of astrologers. It does not follow that astrology is science or that it would be appropriate to refer to astrology in the article.

Let’s be frank…

Hey. Wait a minute…

Congratulations guys! Good to see this available!

Dr. Dembski, congratulations on yet another published paper. You and Dr. Marks are on a roll. I look forward to reading it.

kibitzer:

Perhaps I’m being simplistic, but don’t people write computer programs to get them to do what they want them to do?

Not always. There are several branches of experimental science in which people write programs to see what they’ll do. The degree to which Avida fits this description is disputed.

Eric Anderson has written an excellent essay on Avida:

Bits, Bytes and Biology: What Evolutionary Algorithms (Don’t) Teach Us About Biology

Dear Dr. Dembski,

congrats on your new paper. Just two quick annotations to your references: This is the fourth paper in a row in which the title of S. Christensen’s and F. Oppacher’s paper What can we learn from No Free Lunch? A First Attempt to Characterize the Concept of a Searchable Function got mutilated (by dropping the word function). And you are referencing your paper The Search for a Search: Measuring the Information Cost of Higher Level Search. Now, I understand some of your troubles with the delayed publication of this paper, as the Vol. 3, No. 4, 2008 of International Journal of Information Technology and Intelligent Computing (infact the whole years) seemingly hasn’t appeared yet…

Congratulations again, Dr Dembski, et al

Dr Dembski:

The hypocrisy here is breathtaking. On the one hand, we are told that ID is not science. On the other hand, articles in places like NATURE appear that are clearly motivated by ID. And yet, the articles themselves are scrupulous to avoid referencing ID, its proponents, or published writings lest we gain an entry in the Science Citation Index and thus can further strengthen the case that ID is indeed science.

I think the problem is that ID doesn’t make any positive predictions that can be tested. It only says that evolution can’t account for A, B and C. And then it turns out that evolution actually can account for A, B and C. And then ID says, but it can’t account for D, E and F. And so on. Until ID makes some useful predictions, it’s no wonder that scientists treat ID as a joke.

Science Citation Index and thus can further strengthen the case that ID is indeed science.

ID is obviously science and global warming — excuse me “climate change” and Darwinism are obviously politics and/or religion.

Well done, WD.

Omedeto, Dr Dembski!

I agree that scientific papers should be written straightforwardly to present evidence that supports or criticises specific intellectual positions, positions clearly identified by the authors. I look forward to papers from your group that actually cite Behe, even if he was ultimately wrong, as you say.

I think it is important that you were able to locate active information in the choice of instruction set and the reward schedule of Avida, since these function similarly to the physics and chemistry, and the initialization – the experiment’s “Big Bang” so to speak. It is important that no active information was smuggled into the experiment while it was running from an intelligent source, but that the rules and structure of the experimental Universe were identified as sources of active information. It would certainly make me cautious about drawing analogies between Avida experiments and the real world if you had found an “online” source of active information.

“…provided that these were also selectively favoured.”

If I’m not mistaken, we’ve already extensively covered the inadequacy of computer programs to demonstrate natural selection, with the “Weasel” posts and the like. Also, Dr. Meyer covers this area in a chapter in his book, with the observation that all of the computer models have a common component – the prior inputing of information, which render them irrelevant to Darwinian selection’s ability to develop and/or originate complex systems. They clearly beg the question – can complex systems develop without the prior input of specified complex information?

“These findings show how complex functions can originate by random mutation and natural selection.”

Hardly, they demonstrate how a randomized computer program can develop pseudo-selection once the information and goal are programmed into the system by an inteligent programmer with a mind.

Natural selection has the unique quality of not purposely needing to demonstrate itself. However, Darwinists have the unique quality of purposely needing to demonstrate natural selection – with a 0% success rate. The reason? If natural selection is a random process without plan or purpose, one cannot demnostrate it through a planned purposeful process.

I also look forward to reading the article.

I think the problem is that ID doesn’t make any positive predictions that can be tested.

Sure it does. It claims everything with CSI is designed. Show something that has CSI and is known not to be designed and you falsify ID.

Dr. Dembski, thank you for your work. Please pass on our thanks to your co-authors. Now, when are we going to see that “Complete Idiots Guide to D&M Papers”?

I mean, c’mon, help the critics out.

By the way, want to see Design Theory in action?

Check out Uri Alon’s work.

Perhaps I’m being simplistic, but don’t people write computer programs to get them to do what they want them to do?

Computer simulations are a great way to demonstrate the capabilities of unguided, unintelligent, processes, such as random changes and “natural” selection.

So while they may do an excellent job of showing how evolution itself is teleological, the evolutionary processes themselves, the “strategies” of evolution, quite obviously are not.

I think the problem is that ID doesn’t make any positive predictions that can be tested.

Really. So this D&M paper doesn’t advance any prior ID prediction? Astounding. Why then, did they write it?

It is important that no active information was smuggled into the experiment while it was running from an intelligent source, but that the rules and structure of the experimental Universe were identified as sources of active information.

This is just bizarre. If the information didn’t enter the program while it was running, how on earth did the program make use of it? Have we just refuted the D&M paper?

Nakashima,

Where do Dembski and Marks say that Behe was wrong, and about what?

By the way, want to see Design Theory in action?

Check out Uri Alon’s work.

Our lab also studies topics in evolution, experimentally and theoretically. We have measured the cost and benefit of gene expression in E. coli, and demonstrated in evolutionary experiments that protein levels evolve to maximize fitness within a few hundred generations. Other studies are on the origin of modularity in biological systems based on evolution in changing environments, and on the plasticity of the input functions of genes.

Another case of ‘Design Theory’ in action performed by one of those ‘evolutionists’.

In my prior post it is not immediately apparent that the quoted paragraph is from Uri Alon’s website.

By the way, want to see Design Theory in action?

Check out Uri Alon’s work.

Our lab also studies topics in evolution, experimentally and theoretically. We have measured the cost and benefit of gene expression in E. coli, and demonstrated in evolutionary experiments that protein levels evolve to maximize fitness within a few hundred generations. Other studies are on the origin of modularity in biological systems based on evolution in changing environments, and on the plasticity of the input functions of genes.

The hypocrisy here is breathtaking. On the one hand, we are told that ID is not science. On the other hand, articles in places like NATURE appear that are clearly motivated by ID. And yet, the articles themselves are scrupulous to avoid referencing ID, its proponents, or published writings lest we gain an entry in the Science Citation Index and thus can further strengthen the case that ID is indeed science.

One can not say that ID has been completely ignored by Nature and its sister journals. E.g.: Dr. Behe’s “Darwin’s Black Box” has been cited in Nature Immunology. Salvador Cordova and the IDEA centers have been presented in Nature. Dr. Dembski has been cited in EMBO reports published by Nature. Drs. Behe and Dembski have been mentioned in Nature. Also ID has been mentioned in Nature Medicine. Just recently EMBO reports cited Drs. Behe and Dembski again.
On the other hand one should be aware of the fact that the vast majority of scientist will never be mentioned in journals of the Nature Publishing Group.

20
tragic mishap
12/11/2009
11:23 pm

Nakashima,

Where do Dembski and Marks say that Behe was wrong, and about what?

It’s actually not in the paper but in Dr. Dembski’s post on the top of this page:

But it was also clear to them that addressing him forthrightly in a prominent scientific venue could backfire, indicating that Behe was on to something important even if he was ultimately wrong. Some scientific mistakes are illuminating.

#5

Mark Frank: How many articles in
NATURE or SCIENCE have you seen lately (like the in last 100 years) that refute astrology in the name of astronomy? And did any of them beat around the bush by not naming “astrology” explicitly even though that was their target?

Astronomy/astrology was a thought experiment. I have no idea if any astronomer has been motivated by a desire to refute astrology. The point is that even if they were so motivated, the subject of their article need not be astrology and they need not mention astrology in the article. There is a difference between what motivates the author – which they might well discuss informally – and what the paper is about.

To be more explicit. The point of the AVIDA paper was to show that mutation plus random selection is able to generate complex novel function (leave aside whether it succeeds for the moment). It is part of the theory of ID that this is not possible. But there are many other groups that hold this belief (and it is not the only thing that ID proponents believe).

The author may be particularly motivated by the writings of ID but the program and the paper are about a particular challenge to evolutionary theory not about ID.

#8

But, really, your analogy begs the question. You have to assume from the outset that ID is not scientific, and then make this kind of analogy.

Clive my point is that the motivation to write an article is not the same as the subject matter. This applies whether the motivation is a scientific theory or not.

When it comes to evaluating whether something is scientific or not, you have to look at the individual truth claims. Not some fluffy and barely defined heading under which many things are placed.

Each truth claim stands on it’s own as falsifiable or not.

Take some of these claims:

a) Certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

b) It is impossible for the bacterial flagella to have evolved by natural selection.

Can you imagine how the first one can be falsified? It says “best explained”. What does “best” mean? If I find a thing which can have evolved, or could have been put that way to begin with, what work should I do to determine which proposition is correct?

There isn’t any. The statement itself relies on words which are too undefined to be tested. It blatantly says all it is is doing is a subjective inference.

The second claim IS falsifiable. But, it’s beyond trivially falsifiable. It claims that something is IMPOSSIBLE. All it takes to falsify is to IMAGINE one POSSIBLE way that it could have evolved. Don’t have to do any lab work, because the statement has set itself up for a purely theoretical test. It’s so trivial that it’s just not worth spending time on.

When determining whether ID is ’science’ or not, one has to look at all the individual claims made by it’s proponents. One has to separate and analyze each claim. If those claims depend on each other, if they help each other, if they all play by the rules, then maybe ID would be science. But they don’t.

The best ID is now is a collection of various claims. Some of which are falsifiable, all of those trivially. And some of which are not falsifiable, and are little more than interesting philosophical questions. That’s basically what Judge Jones said.

wasabi,

You have a narrow view of what science is. Falsifiability is the not only criteria. Intelligent design means intelligent intervention and this is not the same process as observing the natural laws and trying to infer their interaction to explain a certain event. In fact an intelligent intervention would be the intervention of natural laws for some particular phenomena.

So what ID often looks for is where the natural laws did not seem to work. There is always the possibility that natural laws could explain the phenomena but through certain types of analysis using the tools of science one can come to the conclusion that the best explanation is the suspension of natural laws in a particular situation.

So the falsifiable/not falsifiable paradigm is not necessarily applicable in all science. There is no accepted definition of science and falsifiability and science are not equivalent.

ID is anything but trivial despite what some people assert.

Sure it does. It claims everything with CSI is designed. Show something that has CSI and is known not to be designed and you falsify ID.

What about showing something (that has CSI, or not) and is known to be designed?

Computer simulations are a great way to demonstrate the capabilities of unguided, unintelligent, processes, such as random changes and “natural” selection.

So while they may do an excellent job of showing how evolution itself is teleological, the evolutionary processes themselves, the “strategies” of evolution, quite obviously are not.

Where is the teleology in computer simulations?

Where or what are the strategies of evolution?

I believe many, both ID proponents as well as more general YEC or OEC creationists are hung up on the term ‘random mutations’ – thinking like “this random thing, how do they think that may amount to anything?”

But unless I am mistaken, mutations are not just some scrambling of genes. Many different modes of mutation has been identified. Gene duplication is one of them. Fully functional segments of DNA duplicated, and available for use in whatever capacity might be appropriate.

And what’s more, the duplicates may undergo slight mutations, point mutations, that may make them useful for further steps in an evolutionary process.

Mathematics and simulations are no substitute for the real thing.

that the best explanation is the suspension of natural laws in a particular situation.

Meaning the designer is not a designer in the sense we use the word, working in and with nature. Instead, it must be a magician employing magic methods. The way I see it, a god would be the best candidate for the job.

H’mm:

Seems the conclusion of the latest Dembski-Marks peer reviewed ID paper — congratulations — are also important:

_______________

>> III. CONCLUSIONS
A. Active Information
The Avida program uses numerous sources of active infor-
mation to guide its performance to successful discovery of the
EQU logic function. The sources include the following.
• Stair step active information. In the initial description of
Avida, the authors write [16]
“Some readers might suggest that we stacked the
deck by studying the evolution of a complex feature
that could be built on simpler functions that were
also useful.”
This, indeed, is what the writers of Avida software do
when using stair step active information. The importance
of stair step active information is evident from the inabil-ity to generate a single EQU in Avida without using it
[16].
• Active information from Avida’s initialization. The ini-
tialization in Avida recognizes the essential role of the
nop-C instruction in ?nding the EQU. Initializing using
all nonessential nop-A or nop-B instructions results in
the a decrease in NAIPI in Avida.
• Mutation, ?tness, and choosing the ?ttest of a number
of mutated offspring [5] are additional sources of active
information in Avida we have not explored in this paper.

B. Disclosure

According to the principle of conservation of information
[3], [4], [5], [7], [9], [10], [19], [20], [21], [22], [23], [28], [30],
all computer search algorithms of moderate to high dif?culty
require active information.
The conservation of information principle in computer
search, as manifest in the No Free Lunch Theorems, are [2]
“… very useful, especially in light of some of the sometimes outrageous claims that had been made of
speci?c optimization algorithms.”

To have integrity, computer simulations of evolutionary
search like Avida should make explicit
(1) a measure or assessment of the dif?culty, ?, of the
problem being solved,
(2) the prior knowledge that gives rise to the active infor-
mation in the search algorithm, and
(3) a measure or assessment of the active information,
either + or ?, introduced by the prior knowledge. >>
_______________

Have fun all.

GEM of TKI

PS: Been busy off-line and elsewhere, to those who inquired. (Some of it for not so happy reasons.) Cooking up some evil stuff. (have a look here at the functionally specific complexity of cellular metabolic reactions as a system. Compare to say the chemical reaction flows pathway of a petrochemicals plant. Then factor in our favourite 1,000 bit threshold and see where that gets ya.

Hi kairosfocus

I’ve just been having a look at your metabolic pathways link and the online presentation on compartmentalization by your (unnamed) biochemist who says he doesn’t believe in evolution. It’s pretty awesome stuff, and I must say that for sheer complexity, it leaves the petrochemicals plant in the dust.

They say that a picture is worth a thousand words, and your links are a perfect illustration of that saying.

Anyway, I’m glad to see you back.

Clive #35

That most assuredly was not your point, your point was to equate ID with astrology.

That was not my intention. I am sorry if I gave that impression. I chose astrology on a whim because of its links with Behe in the Dover trial. I could equally have chosen geology.

“Meaning the designer is not a designer in the sense we use the word, working in and with nature. Instead, it must be a magician employing magic methods. The way I see it, a god would be the best candidate for the job.”

Your entering the above text is an example of intelligent design. No natural laws imaginable would have produced this text. Are you a magician when you did this?

The point of the AVIDA paper was to show that mutation plus random selection is able to generate complex novel function (leave aside whether it succeeds for the moment). It is part of the theory of ID that this is not possible.

This is incorrect.

First, did you mean to say “random mutation plus selection” rather than what you actually wrote?

Second, ID theory accepts that it’s possible to do things like what the Dawkins WEASEL program does. Random variation and selection can indeed produce meaningful results. It is not true that “it is part of the theory of ID that this is not possible.”

Hi Clive,

Are you not aware of the prediction that supposed “junk dna” wouldn’t be “junk” after all on the assumption of ID? This was a useful and true prediction, so what is your next objection?

I have two problems with your ID analysis of junk DNA:

1. It’s not clear to me how the prediction of “no junk DNA” follows from a ID hypothesis. In science, predictions are derived deductively from hypotheses. For example, we can correctly predict when the next solar eclipse will occur, based on the current positions of the heavenly bodies and the equations of Newton’s laws. How exactly does your “no junk DNA” prediction follow from what ID hypotheses? I am asking you to lay out the deductive reasoning.

2. It’s actually not true that there is no “junk DNA”, as far as I know. For example, human DNA is riddled with remains of transposons and retroviruses. That stuff is pure junk. Unless you know otherwise, the ID prediction is simply not true.

IrynaB,

If life is designed in whole or in part, then it is unlikely that you will find many totally useless aspects of the organism. For example, most organs are not appendices. But, ID could have predicted that the appendix does end up having a use. It is not merely “vestigal.” Same with DNA. It is more likely in an ID scenario that most, if not all, of DNA will have a useful function. In a neo-darwin scenario, you need lots of junk DNA to have enough raw materials for variation and a lot of vestigal DNA that was useful once, but is useless now. It is unlikely that that would be the case in a design scenario, so this is a prediction that ID makes.

Cabal:

Where is the teleology in computer simulations?

If you have an argument for why the belief that a computer simulation is not teleological is a rational belief I’d love to hear it.

I daresay most readers here have at least some idea of what simulations are for.

hrun0815:

Another case of ‘Design Theory’ in action performed by one of those ‘evolutionists’.

Compare the design portion of the following text with the evolution portion:

Design:

The transcription network of E. coli contains numerous patterns of nodes and edges. Our approach will be to look for meaningful patterns on the basis of statistical significance. To define statistical significance, we compare the network to an ensemble of randomized networks. …Patterns that occur in the real network significantly more often than in randomized networks are called network motifs.

Evolution:

The basic idea is that patterns that occur in the real network much more often than in randomized networks must have been preserved over evolutionary timescales against mutations that randomly change edges.

Here we have evolution meaning not evolution.

#39

First, did you mean to say “random mutation plus selection” rather than what you actually wrote?

Yes – thank you for correcting my error.

Second, ID theory accepts that it’s possible to do things like what the Dawkins WEASEL program does. Random variation and selection can indeed produce meaningful results. It is not true that “it is part of the theory of ID that this is not possible.”

OK. I need to spell it out a bit more explicitly. It is not possible without incorporating the target into the selection algorithm (or words to the that effect). The important thing is that there any many other groups that believe that evolution cannot explain the origin of complex features. Avida is an attempt to show how this can be done. It is about evolution, not about ID.

#41

If life is designed in whole or in part, then it is unlikely that you will find many totally useless aspects of the organism.

Useless for what? Are you making some assumptions about the objectives of the designer? If so, can we count any instances which do not support these objectives as evidence against the design hypothesis?

VJT:

Great to hear from you.

I see from the above that AVIDA has more than a passing resemblance to some of the problems with Weasel. (And that somehow it has not hit home that an intelligently designed computer simulation is not a really likely context for getting a good empirical demonstration of the claimed wonderful — I am tempted to say “magical” — design powers of chance variation plus natural selection.)

Anyway, I need to add that the author of the chart is the the International Union of Biochemistry and Molecular Biology. [Bottom left. That is, this is NOT anonymous, nor dubious. (Note the original source . . . I thought BU had linked that but realise now they copied it to their own server; sorry. The exchange at BU was set off by a med doctor and lecturer at med schools whose lecture heads the thread there.)]

Compared to the cluster of integrated functional pathways and associated enzyme catalysis, provision of intelligent substrates and clever compartments etc to support the process, the petrochems plant is put to shame. FSCI, and well beyond 1,000 bits.

And AVIDA simulations come up short too. I would like to see the scale of a program that could within the 10^150 state limit on our observed cosmos, set up a random search strategy with realistic rewards that would get to a structure significantly like the real world one.

I think it is well beyond the reach of the resources of our cosmos, unlike a toy example like AVIDA, which exploits bootstrapping mechanisms — as Dembski and Marks et al show — to ease the pathway to what is actually a fairly simple task: create an equivalent to an EX-NOR gate array in software.

Are you not aware of the prediction that supposed “junk dna” wouldn’t be “junk” after all on the assumption of ID? This was a useful and true prediction, so what is your next objection?

True because it was predicted after function for some junk DNA had been found, no?

Does ID predict that all junk DNA has a function?

Since the concept of an unspecified designer could explain any observation it will accommodate both junk DNA and no junk DNA. The designer might have included mechanisms for utilizing or purging whatever was functionless DNA at any given time or he might have allow it to accumulate as long as it did not impose an intolerable burden on the organism. There is no way to decide without specifying the nature of the designer, something which ID resolutely refuses to do.

Collin: But, ID could have predicted that the appendix does end up having a use. It is not merely “vestigal.”

Vestigial doesn’t mean without use. It means without the primary function found in homologous structures of related organisms, but it may retain secondary fuctions.

The appendix is homologous to the end of the mammalian caecum, a pouch that holds a colony of bacteria that aid digestion of plant cellulose. In humans, cellulose digestion is not a significant aspect of diet, so this function is no longer as important as in its relatives. Secondary functions may include maintaining a shielded population of gut flora in case of bowel evacuation due to disease, and possible uses to the immune system.

Lack of strong positive selection in the appendix leads to wide variation in the size and structure of the appendix.

Collin: But, ID could have predicted that the appendix does end up having a use.

Ostrich wings are used for balance, but they’re still vestigial.

Collin: In a neo-darwin scenario, you need lots of junk DNA to have enough raw materials for variation and a lot of vestigal DNA that was useful once, but is useless now.

There is a cost associated with DNA replication, so a simplistic or first-order view of evolution would predict that excess DNA would tend to be weeded out by selection. Bacteria, which rely on rapid reproduction for success, have very streamlined genomes. That some DNA is clearly without function, means that this cost can be comparatively low in more complex organisms.

Zachriel,

I incorrectly conflated vestigal with useless.

It was my understanding that the appendix was evidence for unguided evolution because it was vestigal and useless. Since it was useless, it would never have been part of a design of human beings.

But a designer who is modifying one species with an appendix that performs its primary function, to a species that doesn’t need it for its primary function, may decide to keep the appendix for its secondary function. But any organ that has more cost than benefit will be discarded either by a designer or by evolution.

I said ” Collin: In a neo-darwin scenario, you need lots of junk DNA to have enough raw materials for variation and a lot of vestigal DNA that was useful once, but is useless now.”

You said:

“There is a cost associated with DNA replication, so a simplistic or first-order view of evolution would predict that excess DNA would tend to be weeded out by selection. Bacteria, which rely on rapid reproduction for success, have very streamlined genomes. That some DNA is clearly without function, means that this cost can be comparatively low in more complex organisms.”

Yet isn’t it true that the apparently high amount of junk DNA was used as evidence for evolution? Now the relative lack of truly junk DNA is evidence for evolution? Seems unfalsifiable.

Collin: But a designer who is modifying one species with an appendix that performs its primary function, to a species that doesn’t need it for its primary function, may decide to keep the appendix for its secondary function.

The problem is that without positing specific characteristics of the designer, you could just say He had his inscrutable purposes.

Collin: But any organ that has more cost than benefit will be discarded either by a designer or by evolution.

Discarding or modifying an organ by evolution takes time. That is the key difference. (That, and the nested hierarchy of common descent.) Note again that vestigial organs tend to have high variability, which is consistent with relaxed selection.

Collin: Yet isn’t it true that the apparently high amount of junk DNA was used as evidence for evolution? Now the relative lack of truly junk DNA is evidence for evolution? Seems unfalsifiable.

There are countervailing forces. Pressure to streamline the genome is pit against the limitations of population and generation time. It takes time to eliminate junk. And with slow reproducers, little advantage.

Since the concept of an unspecified designer could explain any observation it will accommodate both junk DNA and no junk DNA.

I have no idea what a concept of an unspecified something (designer, rock, fantasy) means.

I fail to comprehend how concepts of unspecified whatevers can explain anything.

If “designer” specifies something, then “unspecified designer” is a contradiction in terms.

I am at a loss to understand how a contradiction in terms can explain anything.