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What evidence is there for evolution being non-random?

cyborg said:
Hey Von, glad your conspiracy theories make you happy.

...
But you could have a career in sci-fi writing if you just didn't take yourself so damn seriously.
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Cyborg, ol' chum. I'd have to go back in archives to refresh my memory on what we went round and round on. Which particular conspiracy theory did you and I talk about? It's not that I forgot you, it's just I only stop in from time to time with 6 month hiati and forget who is who, and need a prompt.

You are correct that "taking oneself damn seriously" is very provoking--you probably instinctively know it is mere posture. I know it irritates the hell out of people but it is quite sporting. And your suggestion of a career for me shows you are very perceptive of my alter ego. That was actually kind of you to say.
 
articulett said:
Consider what Cyborg says about science fiction writing.
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Really? Thanks, Art'. I'll take that under consideration.:blush:

articulett said:
Oh, and since you're here--what is your definition of random?
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...since you ask...
vonNeumann's Definition of Randomness:
(Fanfare in brazen picolo trumpet in the key of C ....)
As my great uncle said "Any one who considers arithmetical methods of producing random digits is, of course, in a state of sin.'':)

Hehehehh! No, no, no. I'm not going to pretend to be an expert on this. I'm going to set a greater example than that. Even though it is tempting to do as Cyborg points out that I do..."I take myself too damn seriously."

Suffice to say that the subject of randomness is much deeper than I perceive most posters here give it credit. This OP asks a good question yet we can only poke at it.

I do have my opinions du jour , tentative and subject to change. I'll offer up some tidbits:
1. Quantum randomness is the only true randomness in our physical universe, the mechanism of which is apparently completely hidden from us.
2. Algorithmic Complexity as described by Gregory Chaitin, sheds new light on randomness from a meta-mathematical perspective. Chaitin says, "There's only one definition of randomness (divided into the finite and the infinite case for technical reasons): something is random if it is algorithmically incompressible or irreducible. More precisely, a member of a set of objects is random if it has the highest complexity that is possible within this set. In other words, the random objects in a set are those that have the highest complexity. Applied to the set of all n-bit strings this gives one of our definitions, applied to infinite binary sequences this gives our second definition. "

So Art', my answer is that my opinion on randomness is that Chaitin makes more sense on the essense of randomness than anything else I am currently aware of. It seems to me he has encapsulated what transpired from Hilbert->Goedel->Turing.

Since I believe quantum randomness is the only true physical randomness, and since mathematics models quantum mechanics even while we cannot see how quantum mechanics works, I believe therefore the explanation for randomness is best to be found in pure mathematics.
 
Hokulele said:
The bold is the key to my question. To uncover the second message, the frame has to be shifted. I am assuming that in your metaphor, the receiver is doing the shifting. To make this an analogy to nylonase, a similar shift has to occur. How could this shift happen, and what would you call that mechanism? If this shift cannot happen on its own, then your alien metaphor doesn't apply at all to nylonase.
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I am not trying to be thick on this, but I don't get your point. Do you mean that in the case of the metaphor, the receiver, being humans, are shifting the message until they find a frame they can decode?...so the frame shift in the metaphor is directed by intelligence? Yet in DNA expression, the starting point of transcription is frame shifted due to presumed error (if we rule out some other unknown mechanism)? So the fortuitousness of the expression into something different, and accidentally useful, is in itself an accident?

I do not understand why you take issue on how the shift can happen in the biological example. Is it not true that transcriptions commonly get out of synch and then get back in synch (hopefully) on their own?

To my point it is not important how the transcription of the data happens to be interpreted by starting in a different spot. My point is not on the decoding end but on the encoding end of things. My point is with regard to the elegance of the information at the time it was encoded. By the way, I have no knowledge on this, but I suspect that there are other polymers, besides just nylon, that the bacteria might have in its genetics the ability to transcribe the appropriate enzyme.
 
articulett said:
Look, Von,--Douglas Adams talking about artificial intelligence...you know, that Turing Machine
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I don't like Adam's SciFi. At least, I never could get past the first three pages of anything he ever wrote.

I need to elbow you on an error I've seen you make before and I see you make it here. You are confusing "Turing Machine" with "Turing Test". These are two entirely different things.
 
VonNeumann said:
Really? Thanks, Art'. I'll take that under consideration.:blush:


...since you ask...
vonNeumann's Definition of Randomness:
(Fanfare in brazen picolo trumpet in the key of C ....)
As my great uncle said "Any one who considers arithmetical methods of producing random digits is, of course, in a state of sin.'':)

Hehehehh! No, no, no. I'm not going to pretend to be an expert on this. I'm going to set a greater example than that. Even though it is tempting to do as Cyborg points out that I do..."I take myself too damn seriously."

Suffice to say that the subject of randomness is much deeper than I perceive most posters here give it credit. This OP asks a good question yet we can only poke at it.

I do have my opinions du jour , tentative and subject to change. I'll offer up some tidbits:
1. Quantum randomness is the only true randomness in our physical universe, the mechanism of which is apparently completely hidden from us.
2. Algorithmic Complexity as described by Gregory Chaitin, sheds new light on randomness from a meta-mathematical perspective. Chaitin says, "There's only one definition of randomness (divided into the finite and the infinite case for technical reasons): something is random if it is algorithmically incompressible or irreducible. More precisely, a member of a set of objects is random if it has the highest complexity that is possible within this set. In other words, the random objects in a set are those that have the highest complexity. Applied to the set of all n-bit strings this gives one of our definitions, applied to infinite binary sequences this gives our second definition. "

So Art', my answer is that my opinion on randomness is that Chaitin makes more sense on the essense of randomness than anything else I am currently aware of. It seems to me he has encapsulated what transpired from Hilbert->Goedel->Turing.

Since I believe quantum randomness is the only true physical randomness, and since mathematics models quantum mechanics even while we cannot see how quantum mechanics works, I believe therefore the explanation for randomness is best to be found in pure mathematics.
Click to expand...

I agree with you. It's a word with various shades of meaning. Nothing in the physical world may be "truly random" in that everything, so far, seems to have a cause (or a billion inputs creating the cause)... But you seem to be extracting a more general meaning that I think most people think of--where all possibilities are equally likely. Each dice number has an equal chance of being rolled...but no numbers on the dice can be rolled. Of course, all dice must be at least microscopically loaded in some way since they are made of atoms which contain mass which are affected by gravity...but most are "random enough" so that we cannot detect any preferences.

So what is your answer to the OP, or do you think the term is too ambiguous to give a simple answer too. Would you think it was necessary to define random first? How would you describe the randomness of evolution so as to distinguish it from tornado in a junkyard building a 747 creationist strawman? Or would you?

BTW, I last saw you engaging cyborg in regards to computers and something similar to a Turing Machine type argument...just to refresh your memory. Twas invigorating and brisk repartee as I recall.
 
VonNeumann said:
I am not trying to be thick on this, but I don't get your point. Do you mean that in the case of the metaphor, the receiver, being humans, are shifting the message until they find a frame they can decode?...so the frame shift in the metaphor is directed by intelligence? Yet in DNA expression, the starting point of transcription is frame shifted due to presumed error (if we rule out some other unknown mechanism)? So the fortuitousness of the expression into something different, and accidentally useful, is in itself an accident?

I do not understand why you take issue on how the shift can happen in the biological example. Is it not true that transcriptions commonly get out of synch and then get back in synch (hopefully) on their own?

To my point it is not important how the transcription of the data happens to be interpreted by starting in a different spot. My point is not on the decoding end but on the encoding end of things. My point is with regard to the elegance of the information at the time it was encoded. By the way, I have no knowledge on this, but I suspect that there are other polymers, besides just nylon, that the bacteria might have in its genetics the ability to transcribe the appropriate enzyme.
Click to expand...


The problem with your metaphor is that a signal must have both an encoding and decoding end, or else the message is useless. You cannot appreciate the elegance of the information unless you can interpret not only the original message, but the shifted one as well. To focus on only the encoding loses sight of the whole meaning of communication, and your metaphor. You suggest that several "meanings" may be incorporated into DNA, but unless there is a mechanism for accessing these other meanings, there is no point in speculating about them.

I guess my point is that the whole metaphor is completely inapplicable to a discussion of DNA unless you can adequately incorporate both ends of the transmission, which you have not been doing.
 
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Meadmaker said:
You started your question by saying that randomness isn't well defined. However, it is well defined. Of course, in common usage it has several definitions, but it is easy enough to specify exactly which one is in use, and that has been done here.

The paper by Chaitin looks interesting at a glance, but I don't see the relevance to evolution. I didn't read the whole thing, though. I just skimmed the abstract and a few paragraphs. Perhaps you could elaborate on why you think his perspective is relevant to the theory of evolution.
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I just posted in answer to Art' what I think are just a couple of things that come to my mind when I try to get a handle on "randomness". And I do not elaborate on why I think Chaitin's work is important and applicable to evolution except that it is pure mathematics and I believe the source of the source of randomness is quantum mechanics, which has NO explanation EXCEPT by pure mathematics. That still may seem unsatisfactory for an answer to your question. But it would be impossible for me to relate to you the answer without your not having the experience of studying what Chaitin's approach is. I wish I could chew Chaitin's stuff up into a little pure crystal of thought and put it in the mind of another person -- or that someone else could do it and port the condensed understanding directly into my mind. But it takes reading and study and each has to do his own.
 
VonNeumann said:
To my point it is not important how the transcription of the data happens to be interpreted by starting in a different spot. My point is not on the decoding end but on the encoding end of things. My point is with regard to the elegance of the information at the time it was encoded. By the way, I have no knowledge on this, but I suspect that there are other polymers, besides just nylon, that the bacteria might have in its genetics the ability to transcribe the appropriate enzyme.
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Hey Von...thanks for reminding me re: "Turing test"... my mistake.

Were you aware of this: http://blog.wired.com/wiredscience/2007/07/designer-virus-.html

By hacking a virus with artificial DNA, researchers at MIT and Boston University created a bacteria-killing machine that demonstrates the potential of synthetic biology

http://www.wired.com/science/discoveries/news/2007/07/synthetic_bio
http://www.nytimes.com/2007/06/29/science/29cells.html?ex=1184817600&en=408d08341dad5825&ei=5070

We can make the enzyme and insert it into a replicator.

You know how DNA is coded...triplicate codons coding for amino acids that fold into proteins and act as enzymes. A frame shift mutation would like if you added a letter to a sentence and got a new sentence with a whole new meaning or no meaning at all (some mutations make genes fail...which can confer an advantage too). In a dish...we can add the GATC and a template and build the protein we want...instead of waiting for nature to happen upon the "right" one...

A sentence isn't written so that you could add a letter and change the meaning completely, but if you were changing such things in texts all the time, you would end up changing the meaning of some sentences to the benefit of the reader. That is what happened in nylonase. The change was random in respect to whether it benefited the bacteria...it just so happened that such a change found itself in an environment where it could thrive.
 
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Hokulele said:
The problem with your metaphor is that a signal must have both an encoding and decoding end, or else the message is useless. You cannot appreciate the elegance of the information unless you can interpret not only the original message, but the shifted one as well. To focus on only the encoding loses sight of the whole meaning of communication, and your metaphor. You suggest that several "meanings" may be incorporated into DNA, but unless there is a mechanism for accessing these other meanings, there is no point in speculating about them.

I guess my point is that the whole metaphor is completely inapplicable to a discuss of DNA unless you can adequately incorporate both ends of the transmission, which you have not been doing.
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I am baffled on why we are having difficulty with this. The DNA gets decoded for two different enzymes. (in the sense of one enzyme before the frame shift "mutation" and the other enzyme after the frame shift mutation).The only difference is where you start the transcription. Right?

Do you think it was very lucky for this bacteria that the same code can specify two very useful but different things?

It would be as if I had one .exe file that I used for doing spreadsheets. Then I had a data error that wiped out the first instruction, and now the .exe file serves as a wordprocessor instead of as a spreadsheet program. I would suspect the versatility was in the .exe file all along and I just discovered the other utility by chance. If there were a mere GoTo that branched between two separate programs, I would not be impressed. But if it were two programs superimposed but shifted, it would be toe tingling.

The nylonase formula is superimposed on the other formula.
 
articulett said:
Hey Von...thanks for reminding me re: "Turing test"... my mistake.

Were you aware of this: http://blog.wired.com/wiredscience/2007/07/designer-virus-.html

By hacking a virus with artificial DNA, researchers at MIT and Boston University created a bacteria-killing machine that demonstrates the potential of synthetic biology

http://www.wired.com/science/discoveries/news/2007/07/synthetic_bio
http://www.nytimes.com/2007/06/29/science/29cells.html?ex=1184817600&en=408d08341dad5825&ei=5070

We can make the enzyme and insert it into a replicator.

You know how DNA is coded...triplicate codons coding for amino acids that fold into proteins and act as enzymes. A frame shift mutation would like if you added a letter to a sentence and got a new sentence with a whole new meaning or no meaning at all (some mutations make genes not work...which can be advantageous in themselves.). In a dish...we can add the GATC and a template and build the protein we want...instead of waiting for nature to happen upon the "right" one...

A sentence isn't written so that you could add a letter and change the meaning completely, but if you were changing such things in texts all the time, you would end up changing the meaning of some sentences to the benefit of the reader. That is what happened in nylonase. The change was random in respect to whether it benefited the bacteria...it just so happened that such a change found itself in an environment where it could thrive.
Click to expand...

Looks like interesting stuff and I hope to remember to get back to it later -- thanks for the links.

English is not very tolerant of frame shifts unless someone very very cleverly constructs special sentences that can give two meanings by starting the sentences in different places. One level of challenge is to get two grammatically correct sentences superimposed with frame shift, and the second level is to have them be semantically correct.

I could entertain this much better if there exist little molecular machines that constantly run up and down DNA, correcting errors. I know there is some of that going on, but i mean something yet to be discovered that may make "grammatical corrections" to the DNA (another metaphor). In computer programs, the language translator checks for syntax and form. The translator is not "smart enough" to test sematics. But if you start out with gibberish, and at least if it is forced to be grammatically correct, it has a much better chance at being sematically useful. Maybe during DNA self-repair, something as elegant as the superimposed coding can get formed over time. That's the kind of stuff I'm waiting to see be discovered.
 
VonNeumann said:
I am baffled on why we are having difficulty with this. The DNA gets decoded for two different enzymes. (in the sense of one enzyme before the frame shift "mutation" and the other enzyme after the frame shift mutation).The only difference is where you start the transcription. Right?

Do you think it was very lucky for this bacteria that the same code can specify two very useful but different things?

It would be as if I had one .exe file that I used for doing spreadsheets. Then I had a data error that wiped out the first instruction, and now the .exe file serves as a wordprocessor instead of as a spreadsheet program. I would suspect the versatility was in the .exe file all along and I just discovered the other utility by chance. If there were a mere GoTo that branched between two separate programs, I would not be impressed. But if it were two programs superimposed but shifted, it would be toe tingling.

The nylonase formula is superimposed on the other formula.
Click to expand...


I guess my problem with understanding your posts is that your analogies were originally brought up in reponse to Wings' question regarding how ID addresses nylonase. You have used the analogy of how two messages (or programs, or enzymes) can be encoded, but offer no explanation of how the decoding can happen. In your "message from aliens" example, you mention a frame-shift, and then when I question it, you say it doesn't matter. For an encoded message, some decoder would have had to work to discover the frame shift. This implies the decoding process is intelligently driven.

On the other hand, with this new programming example, you say you have a "data error", well, how does that happen? Is it just some random error that luckily transforms your spreadsheet to a word processor? That to me sounds like the standard evolutionary description of a mutation. The fact that it is useful to me, implies that my finding it useful represents the natural selection process. If the data error rendered the program useless, it would quickly be uninstalled. Unless you are suggesting that the data error itself is intelligently driven to force the new program to be useful.

To go back to the original question, with nylonase, if there are two options, why and how would one get shifted to another? To me, the simple explanation would be that you are describing a random mutation and it was lucky, or beneficial, or whatever you want to call it, that this particular shift is "good" for nylonase. However, the part I can't figure out is whether you are suggesting that this mutation does follow the standard explanation of evolution (random mutation ends up being beneficial and is propagated due to natural selection), or if you are suggesting that the shift from one enzyme to another is somehow directed by an outside intelligence, as would be required in the case of the alien transmission, or a data error that can only result in a shift from spreadsheet to word processor.
 
Yeah...Von...when you say one enzyme is superimposed upon another... it's sort of like saying that it was planned. I reminds me of people who find hidden meaning by applying a grid to the bible and decoding it...then they presume that code was there... You can do this with any book...and use any grid pattern you like...but it doesn't mean the code was there "on purpose"...

The words "bulls hit" has a different meaning when read all together. If you change one base pair in a frame shift mutation... every single codon could change...it would become an entirely different sequence of amino acids...and be an entirely different protein with a different shape... Most frame shift mutations will make a gene not function (which can be beneficial to an organism...you can prolong the healthy life of some organisms by knocking out key genes)-- but a frame shift mutation would be take this code 111 222 333 444 123 and turn it into this code 112 223 334 441 23X And each set of 3 digits codes for a specific amino acid... even though there is some redundancy. So, you can see, this would be a completely different protein--a completely different chain of amino acids.

It could happen all the time, but it wouldn't be useful until or unless in conferred a survival advantage. We don't know how many times the nylon digesting mutation arose in the eons before nylon...we just know that if a nylon digesting mutation evolves on an organism that happens to live on nylon, that organism will preferentially survive. It's not like organisms have DNA lying in wait to evolve... it's just that some have mutations that will give them preferential survival in whatever environment they find themselves in. This is exactly what goes on in antibiotic and chemotherapy resistance. Nothing is superimposed... it's just that these are cells that make lots of exponential copies of themselves which increases the likelihood that one of them somewhere will have something that allows it to preferentially survive whatever treatment we inflict upon it... The only thing necessary is a copying system that isn't entirely perfect...an occasional error can confer a survival advantage...
 
I've taken a look back at your original post, mijopaalmc. Now, I've noticed you used random in the sense of probability, therefore I'm assuming that you are using random to reference a probability distribution.

Now, using random or non-random in your original question was very ambigious. So I'm going to try and address the ambiguity before we can continue.

Taking a look back at your first post, your original question was.
"What evidence is there for evolution being non-random?"

Because random is an ambigious term, non-random is just as ambigious. What is meant by non-random?

Do you mean:
1. Predictable?
2. Ordered?
3. Without a probability distribution?
4. Determined?
5. Another word that better describes what is meant?

These questions may have already been addressed earlier, and if so, I apologize for bringing them up again. At least for me, I need clearer terms to understand what is being asked in the original question.
 
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VonNeumann said:
2. Algorithmic Complexity as described by Gregory Chaitin, sheds new light on randomness from a meta-mathematical perspective. Chaitin says, "There's only one definition of randomness (divided into the finite and the infinite case for technical reasons): something is random if it is algorithmically incompressible or irreducible. More precisely, a member of a set of objects is random if it has the highest complexity that is possible within this set. In other words, the random objects in a set are those that have the highest complexity. Applied to the set of all n-bit strings this gives one of our definitions, applied to infinite binary sequences this gives our second definition. "
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If you go back over my posts you will see that I have basically been arguing this point.

As such it rather puts a dent in the argument being made by people here who want to call evolution random as randomness does not have to represent a fundamentally different type of thing (that is to say one can explain the acausal causally and vice-versa - there is no more descriptive power in either one).

I don't see them getting that point of course.
 
In general, I think that this thread has thrashed enough about the issue for us to conclude that we will not agree anytime soon.

My own conclusion is that for some meanings of 'random' (especially a strict scientific meaning), evolution is random, and for some meanings of 'random' (particularly how it is used by mere mortals), evolution is non-random. I feel reassured that I am on the right track if I do not throw the R-word into a discussion myself, but waits until my opponent has done it, so that I can decide on how the word is used.

Just last week, on another board, a creationist used the old 'it is ridiculous to believe that random mutations should lead to the existence of man', and I felt quite comfortable in countering that "evolution is not random, though mutations are".

If I ever encounter a creationist with a more sophisticated concept of 'random', I might tread more carefully.
 
steenkh - a 'strict scientific meaning' of 'random' could mean everything is random or it might not.

It's really not hard to understand why using probability distributions to model something does not mean that something is random if one understands what it means to be predictable.
 
steenkh said:
Just last week, on another board, a creationist used the old 'it is ridiculous to believe that random mutations should lead to the existence of man', and I felt quite comfortable in countering that "evolution is not random, though mutations are".
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Well put. I try to point out to people that random mutations generate the variety of genes potentially available to the next generation. Non-random natural selection determines which of these genes will have greater reproductive success. So there is a random element within evolution that makes it non-deterministic, but the primary driving force behind evolution is non-random.
 
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