Evolution vs. Design
How would we build a really complex system — such as a general artificial intelligence (AI) that exceeded human intelligence?
That is the question Steve Jurvetson addresses in yesterday’s Technology Review. He considers it as a choice between two options: evolutionary search algorithms or design, and his summary of the problems with each are illuminating:
… designed systems also tend to break easily, and they have conquered only simple problems so far.
In fact, biological evolution provides the only "existence proof" that an algorithm can produce complexity transcending that of its antecedents.
But evolved systems have their disadvantages. For one, they suffer from "subsystem inscrutability." That is, when we direct the evolution of a system, we may know how the evolutionary process works, but we will not necessarily understand how the resulting system works internally.
If biological evolution provides the only proof that evolutionary algorithms can produce complexity transcending that of its antecedents, but biological evolution happened by virtue of evolutionary algorithms producing that complexity, are we in some slight danger of circular reasoning?
Another question: how much inscrutability does positing unknown/unknowable evolutionary processes for a system add– in particular, processes we only know of because we assume that that system was produced by evolution? Is design or evolution more likely to be a science stopper in going into further research?
The article (available here) is worth reading and thinking about.
HT: IDesign@UCI
Update: ID the Future has a post up on the problems with Jurvetson’s analysis.
If biological evolution provides the only proof that evolutionary algorithms can produce complexity transcending that of its antecedents, but biological evolution happened by virtue of evolutionary algorithms producing that complexity, are we in some slight danger of circular reasoning?
I fail to follow your reasoning in suggesting that this is circular. Perhaps it is because you shortened “existence proof”, which I understand to mean “example”, with “proof”, which has multiple definitions but most commonly would mean evidence. There is plenty of evidence for the example of evolution: in the fossil record, in anatomy, in the genomes, in geographical distributions.
Is design or evolution more likely to be a science stopper in going into further research?
No question, design is the bigger science stopper. “God did it” just kills inquiry. With a hypothesis of evolution, I can always look for precursors, intermediates, obsolete artifacts, etc.
I will also note that the author is talking about humans using design and/or evolutionary algorithms to build things, this is a different question from figuring out which occured in past pre-human-technology days.
Comment by ivy privy — July 19, 2006 @ 7:32 pm
Sticking ot the original question about how we would build certain complex things, which is a completely different problem than figuring out whether existing biological things were designed or evolved (which you seem to effortlessly slide into)
He considers it as a choice between two options: evolutionary search algorithms or design
Why not both? I don’t see any reason for not mixing the two methods. You could design a basic frame work and use evolutionary algorithms to tweak or expand it. One property (weakness?) of evolution is that, while it can use exaption to accomodate new uses for existing parts, those parts are bound by their evolutionary history. Thus, evolution tends to produce solutions that may be suboptimal due to their history. An example would be bipeds with a spine clearly developed for use by quadrupeds.
Comment by ivy privy — July 21, 2006 @ 3:45 pm
>How would we build a really complex system — such as a general artificial intelligence (AI) that exceeded human intelligence?
Comment by Zero — July 22, 2006 @ 4:29 am
>How would we build a really complex system — such as a general artificial intelligence (AI) that exceeded human intelligence?
Comment by Zero — July 22, 2006 @ 4:41 am
Is design or evolution more likely to be a science stopper in going into further research?
No question, design is the bigger science stopper. “God did it” just kills inquiry. With a hypothesis of evolution, I can always look for precursors, intermediates, obsolete artifacts, etc.
The “God did it” cliche is foolish. How does it differ from “evolution did it”? I can look for biological function which is real and quantifiable. Precursor functions are intrinsically speculative.
I will also note that the author is talking about humans using design and/or evolutionary algorithms to build things, this is a different question from figuring out which occured in past pre-human-technology days.
Why would intelligence have properties that make it impossible to draw deductive inferences applicable to a general approach. Evolutionists routinely make deductions from evidence that conforms to an expected paradigm. For example, genomic similarities are considered evidence of common descent. The related argument cites evidence that is consistent with an evolutionary hypothesis. If two species are related by common ancestry this is what we would expect to see. IDers take the same approach with evidence. Genetic information, its means of expression and linguistic qualities have unmistakable parallels to intelligent processes and are exactly what one would expect to see in an inteligently designed system.
Comment by Wiliam Bradford — July 25, 2006 @ 3:05 am
Another question: how much inscrutability does positing unknown/unknowable evolutionary processes for a system add– in particular, processes we only know of because we assume that that system was produced by evolution? Is design or evolution more likely to be a science stopper in going into further research?
As I mentioned already, you are confusing two different things - how humans might best design something, and discovering whether existing biological structures & properties came to be. But supposing you had stuck with your original post on how humans should design things, and asked about avoiding inscrutability, the obvious solution would be documentation. Every step of the design process should be documented, with reasons given for deliberately introduced design elements and model parameters documented for evolutionary algorithm steps. This would go a long way towards limiting inscrutability in human-designed projects, and is just the sort of data we do not have for existing biological structures and properties.
Comment by ivy privy — July 27, 2006 @ 5:49 pm
How would we build a really complex system — such as a general artificial intelligence (AI) that exceeded human intelligence?
You could probably start by defining “intelligence” and even “general intelligence”, or at least explaining how you would quantify it, so that you would be able to decide when tha AI exceeded human “intelligence”.
Comment by ivy privy — July 27, 2006 @ 5:52 pm
The “God did it” cliche is foolish. How does it differ from “evolution did it”? I can look for biological function which is real and quantifiable. Precursor functions are intrinsically speculative.
Nonetheless, a gre3at deal of work has been done in identifying evidence of precursors in the fossil record as well as in the genomes. I note that I gave an actual example, whereas you can supply none.
Genetic information, its means of expression and linguistic qualities have unmistakable parallels to intelligent processes and are exactly what one would expect to see in an inteligently designed system.
Since, as we are repeatedly told, ID infers nothing whatsover about the identity, goals or methods of the Designer, what possible findings would be inconsistent with “an intelligently designed system”? Here we get to the lack of testability.
Comment by ivy privy — July 27, 2006 @ 5:58 pm
Why would intelligence have properties that make it impossible to draw deductive inferences applicable to a general approach. Evolutionists routinely make deductions from evidence that conforms to an expected paradigm. For example, genomic similarities are considered evidence of common descent. The related argument cites evidence that is consistent with an evolutionary hypothesis. If two species are related by common ancestry this is what we would expect to see. IDers take the same approach with evidence.
To take the stated example, which of these is consistent with an Intelligent Designer:
1) Genomes with shared genetic code, gene sequences with the appearance of divergence from a common ancestor through known genetic mechanisms (point mutations, recombination, gene duplication, etc) including similarities in non-coding regions and transposon insertion sites
2) Each genome and genetic code widely different, even within a species
The Designer “paradigm” is compatible with both of those, and any others. Meanwhile, evolutionary theory is incompatible with many conceivable possibilities which do not occur.
Comment by ivy privy — July 27, 2006 @ 6:07 pm
Nonetheless, a gre3at deal of work has been done in identifying evidence of precursors in the fossil record as well as in the genomes. I note that I gave an actual example, whereas you can supply none.
You only think you have identified precursors. Why would I give examples of precursors when the evidence does not point that way?
Genetic information, its means of expression and linguistic qualities have unmistakable parallels to intelligent processes and are exactly what one would expect to see in an inteligently designed system.
Since, as we are repeatedly told, ID infers nothing whatsover about the identity, goals or methods of the Designer, what possible findings would be inconsistent with “an intelligently designed system”? Here we get to the lack of testability.
Are the alphanumeric symbols of this exchange the product of intelligence or a random event like a pet walking across a keyboard or the banging of a toddler? Would spacetravelers on a distant planet conclude that the image of an animal-like creature in a mountain range was the result of natural forces or intelligence?
Comment by Wiliam Bradford — July 28, 2006 @ 3:24 am
Why would intelligence have properties that make it impossible to draw deductive inferences applicable to a general approach. Evolutionists routinely make deductions from evidence that conforms to an expected paradigm. For example, genomic similarities are considered evidence of common descent. The related argument cites evidence that is consistent with an evolutionary hypothesis. If two species are related by common ancestry this is what we would expect to see. IDers take the same approach with evidence.
To take the stated example, which of these is consistent with an Intelligent Designer:
1) Genomes with shared genetic code, gene sequences with the appearance of divergence from a common ancestor through known genetic mechanisms (point mutations, recombination, gene duplication, etc) including similarities in non-coding regions and transposon insertion sites
2) Each genome and genetic code widely different, even within a species
The Designer “paradigm” is compatible with both of those, and any others. Meanwhile, evolutionary theory is incompatible with many conceivable possibilities which do not occur.
The genetic code itself is highly consistent. Genomic sequences vary of course. The predictability of sequences cannot be predetermined by a natural force. If lysine had to follow arginine in sequences and valine had to succeed proline and glycine, tyrosine life would not exist. It is the lack of a deterministic outcome in sequences dictated by a force of nature that signifies the genetic code is the product of intelligence- not a series of organic chemical reactions. Variations in protein encoding genes and regulatory sequences are not inconsistent with design. Chemical determinism is.
Comment by Wiliam Bradford — July 28, 2006 @ 3:42 am
Bradford: Variations in protein encoding genes and regulatory sequences are not inconsistent with design. Chemical determinism is.
Nothing is inconsistent with design. Not even chemical determinism, but if you consider chemical determinism to be a problem for design, then the work by Bob Knight and others who have show evidence for stereochemistry in the genetic code may be of interest.
While the present day code is certainly independent of the chemistry of the proteins, there is good evidence that this has not always been the case. Yet as Pattee and others have observed, for evolution to be open-ended it is important that there exists a genotype to phenotype mapping which is not constrained by natural law.
Suggestion: Genetic code arose first as a necessity (stereochemistry) and then co-evolved to extend the coverage of the code to other amino acids and adapted to become more error resistent.
All three components have support in the genetic code, and the history of the origins of the genetic code shows how these processes can help understand how the genetic code may have arisen naturally.
Of course for ID which relies on absence of testable hypotheses, such hypotheses are quite problematic.
Comment by PvM — July 30, 2006 @ 10:27 pm
PvM: Suggestion: Genetic code arose first as a necessity (stereochemistry) and then co-evolved to extend the coverage of the code to other amino acids and adapted to become more error resistent.
How does a code arise? It is easy to throw out statements like this but what evidence is there to back this up. Not generalities; specifics. The co-evolving and adapting assertions are likewise meaningless in the absence of empirical evidence.
All three components have support in the genetic code, and the history of the origins of the genetic code shows how these processes can help understand how the genetic code may have arisen naturally.
Of course for ID which relies on absence of testable hypotheses, such hypotheses are quite problematic.
There is no history of the origin of the genetic code. Only speculations fueled by overactive imaginations. There is good evidence that a minimally functional genome requires a large complex of genes. Hypotheses centered around this are testable. Intelligence detected in the generation of complex encoded entities implicates the insufficiency of forces of nature alone in generating the same effect. Minimal genomes are problematic for naturalists.
Comment by Wiliam Bradford — July 30, 2006 @ 11:52 pm
Bradford How does a code arise? It is easy to throw out statements like this but what evidence is there to back this up. Not generalities; specifics. The co-evolving and adapting assertions are likewise meaningless in the absence of empirical evidence.
Of course, it’s easy to throw out statements, that’s my main objection to intelligent design. Therefore, I am more than happy to provide you with more specific details. For this we have to delve into the scientific literature and look at the work by Knight and Landweber.
Ready? Let me know and I will provide more details than just the references
Knight, The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations Ph.D. Thesis 2001
Knight, R. D. and L. F. Landweber (2000). “The Early Evolution of the Genetic Code” Cell 101(6): 569-572.
Knight, R. D., S. J. Freeland, and L. F. Landweber (1999). “Selection, history and chemistry: the three faces of the genetic code.” Trends Biochem Sci 24(6):241-7.
Bradford
There is no history of the origin of the genetic code. Only speculations fueled by overactive imaginations. There is good evidence that a minimally functional genome requires a large complex of genes. Hypotheses centered around this are testable. Intelligence detected in the generation of complex encoded entities implicates the insufficiency of forces of nature alone in generating the same effect. Minimal genomes are problematic for naturalists.
Nice attempt to redirect the issue. While I can appreciate that to some the idea, that science can in fact retrieve the history of the genetic code over a period of almost 3 billion years, may sound ridiculous, the simple fact is that science and scientists have found ingeneous ways to present and test hypotheses.
Let me know if you are interested. And in the mean time could you elaborate on your unsupported and meaningless claim that
Intelligence detected in the generation of complex encoded entities implicates the insufficiency of forces of nature alone in generating the same effect.
Comment by PvM — July 31, 2006 @ 1:32 am
PvM: Ready? Let me know and I will provide more details than just the references
If you wish to cite data in support of arguments you’re going to have to frame the main points and cite specific passages to back your points if necessary.
Bradford
There is no history of the origin of the genetic code. Only speculations fueled by overactive imaginations. There is good evidence that a minimally functional genome requires a large complex of genes. Hypotheses centered around this are testable. Intelligence detected in the generation of complex encoded entities implicates the insufficiency of forces of nature alone in generating the same effect. Minimal genomes are problematic for naturalists.
Nice attempt to redirect the issue. While I can appreciate that to some the idea, that science can in fact retrieve the history of the genetic code over a period of almost 3 billion years, may sound ridiculous, the simple fact is that science and scientists have found ingeneous ways to present and test hypotheses.
Let me know if you are interested. And in the mean time could you elaborate on your unsupported and meaningless claim that
Intelligence detected in the generation of complex encoded entities implicates the insufficiency of forces of nature alone in generating the same effect.
What force of nature (devoid of an intelligent component) would generate this encoded exchange or the underlying software enabling its transmission and posting? Intelligence is indicated by the insufficiency of forces of nature alone to effect the outcome.
Comment by Wiliam Bradford — July 31, 2006 @ 1:53 am
PvM: While I can appreciate that to some the idea, that science can in fact retrieve the history of the genetic code over a period of almost 3 billion years, may sound ridiculous, the simple fact is that science and scientists have found ingeneous ways to present and test hypotheses.
The issue is evidence. Your assertions as to what is scientific is limited to the extent that your beliefs are consistent with test results. Anything beyond that is a personal opinion to which you are entitled.
Comment by Wiliam Bradford — July 31, 2006 @ 2:39 am
What force of nature (devoid of an intelligent component) would generate this encoded exchange or the underlying software enabling its transmission and posting? Intelligence is indicated by the insufficiency of forces of nature alone to effect the outcome.
Of the four known forces of nature; strong nuclear force, weak nuclear force, electromagnetics, and gravity, electromagnetics plays the largest role in chemistry, and therefore, in biochemistry. Are you suggesting that chemistry is insufficient to account for gene transcription and translation? Do you believe that the workings of cells are ongoing miracles?
Or is it just that you are throwing around phrases such as “forces of nature” without a clear idea of what you are writing about?
Comment by ivy privy — August 7, 2006 @ 3:43 pm
What force of nature (devoid of an intelligent component) would generate this encoded exchange or the underlying software enabling its transmission and posting? Intelligence is indicated by the insufficiency of forces of nature alone to effect the outcome.
Of the four known forces of nature; strong nuclear force, weak nuclear force, electromagnetics, and gravity, electromagnetics plays the largest role in chemistry, and therefore, in biochemistry. Are you suggesting that chemistry is insufficient to account for gene transcription and translation? Do you believe that the workings of cells are ongoing miracles?
The phrase “forces of nature alone” should have been enough for you to realize that the intelligently generated codes I referred to were not posed as examples of contravention of natural laws but rather operation in accordance with them. Intelligence, as it relates to codes, is required to generate the observed outcome, even as that outcome occurs in accordance with natural laws. Biochemistry reveals the details of cellular function and molecular biology genomic features. What neither do is account for the origin of the genetic code and genomes functioning according to it. Are you suggesting that a series of organic chemical reactions in a prebiotic environment led to the transcription and translation functions?
Or is it just that you are throwing around phrases such as “forces of nature” without a clear idea of what you are writing about?
Read the adjective next to nature.
Comment by Wiliam Bradford — August 8, 2006 @ 1:04 am
Are you suggesting that a series of organic chemical reactions in a prebiotic environment led to the transcription and translation functions?
Yes. We know that organic chemical reactions happen. We do not know that there was an Intelligent Designer in the prebiotic world.
Comment by ivy privy — August 8, 2006 @ 10:23 pm
Are you suggesting that a series of organic chemical reactions in a prebiotic environment led to the transcription and translation functions?
Yes. We know that organic chemical reactions happen. We do not know that there was an Intelligent Designer in the prebiotic world.
Of course organic chemical reactions occur. Since the end result of these reactions eventually would produce a replicating cell and since the scientific evidence documenting such a process is nil your belief that the process occured is an expression of faith. Since observation of the prebiotic world is not possible all conclusions drawn are based on indirect evidence. Your assertion about what we do not know extends to a chemical process you have placed your faith in.
Comment by Wiliam Bradford — August 9, 2006 @ 2:17 am
Of course organic chemical reactions occur.
Aha! We agree on something. I see no reason to doubt that organic chemical reactions occured billions of years ago in the pre-biotic world.
Since the end result of these reactions eventually would produce a replicating cell and since the scientific evidence documenting such a process is nil your belief that the process occured is an expression of faith.
I disagree on the state of the scientific evidence. PvM has already cited scientific papers on OOL, your statement is false. Moreover, this viewpoint provides hypotheses for testing, and these are tested in ongoing research. Take for example a recent paper in Science on RNApol error correction:
Nikolay Zenkin, Yulia Yuzenkova, and Konstantin Severinov
Transcript-Assisted Transcriptional Proofreading
Science (2006) 313:518-520
Now let’s compare this to the scientific hypotheses generated by your Intelligent Designer idea, and the experimental programs for testing these hypotheses:
(nil)
Since observation of the prebiotic world is not possible all conclusions drawn are based on indirect evidence.
Do you have something against indirect evidence? It’s used all the time in science and in the courts. I think it’s better than no evidence at all.
Your assertion about what we do not know extends to a chemical process you have placed your faith in.
So you fed me a “suggestion” and have already transmogrified it to an “assertion”.
Could you explain what definition of faith you are using? Some of the local folk prefer their own definition.
Comment by ivy privy — August 9, 2006 @ 2:34 pm
My response of 2 days ago hasn’t shown up yet. I’ll repeat some of it:
Of course organic chemical reactions occur.
Ah, we agree on something! Organic chemical reactions happen today, and there is no reason not to believe that they happened in the prebiotic world.
Since observation of the prebiotic world is not possible all conclusions drawn are based on indirect evidence.
Do you have a problem with indirect evidence? It is used all the time in science and in the courts. If you’re one of those Ken Ham “Were you there?” types we can end the conversation right now. Indirect evidence is better than no evidence at all.
Comment by ivy privy — August 10, 2006 @ 2:37 pm
Your assertion about what we do not know extends to a chemical process you have placed your faith in.
The burden of proof is on you. Rhetorical attempts to invert the burden of proof will not be successful. You claim something other than organic chemical reactions led to the origin of life, you provide evidence for the existence of that something. Positive evidence. How did this Intelligent Designer intervene? Where is the evidence of that?
Comment by ivy privy — August 10, 2006 @ 2:55 pm
Since the end result of these reactions eventually would produce a replicating cell and since the scientific evidence documenting such a process is nil your belief that the process occured is an expression of faith.
You’re wrong about the evidence. There is a variety of evidence for various OOL scenarios. PvM has already cited some. Here’s more recent evidence:
Nikolay Zenkin, Yulia Yuzenkova, and Konstantin Severinov
Transcript-Assisted Transcriptional Proofreading
Science (2006) 313:518-520
What’s more, ideas about the naturalistic origins of life lead to testable hypotheses, which lead to more research and more evidence. ID does not provide testable hypotheses, and therefore has no way to increase the amount of pro-ID evidence, which is nil.
BTW, be careful about using that word faith. Some of the locals prefer to use their own definitions.
Comment by ivy privy — August 10, 2006 @ 3:05 pm
Another post not showing up, probably because it included links. I’ll try again.
Since the end result of these reactions eventually would produce a replicating cell and since the scientific evidence documenting such a process is nil your belief that the process occured is an expression of faith.
Nope. There is evidence for various naturalistic OOL scenarios. PvM has already cited some above. Here’s some more recent evidence:
Nikolay Zenkin, Yulia Yuzenkova, and Konstantin Severinov
Transcript-Assisted Transcriptional Proofreading
Science (2006) 313:518-520
What’s more, naturalistic scenarios for the origin of life lead to testable hypotheses; which lead to experiments which lead to more evidence. I.e. they are scientific.
The ID viewpoint does not supply any hypotheses, and therefore does not lead to experiments and new evidence. I.e. it is not scientific.
Comment by ivy privy — August 10, 2006 @ 3:09 pm
Of course organic chemical reactions occur.
Ivy: Ah, we agree on something! Organic chemical reactions happen today, and there is no reason not to believe that they happened in the prebiotic world.
And no reason to believe prebiotic organic chemical reactions led to an encoding genome.
Since observation of the prebiotic world is not possible all conclusions drawn are based on indirect evidence.
Do you have a problem with indirect evidence? It is used all the time in science and in the courts. If you’re one of those Ken Ham “Were you there?” types we can end the conversation right now. Indirect evidence is better than no evidence at all.
No evidence is an apt description for evidence that cells arise.
Your assertion about what we do not know extends to a chemical process you have placed your faith in.
The burden of proof is on you. Rhetorical attempts to invert the burden of proof will not be successful.
You have the burden of proof in showing that cells are produced from unspecifed chemical pathways.
You claim something other than organic chemical reactions led to the origin of life, you provide evidence for the existence of that something. Positive evidence. How did this Intelligent Designer intervene? Where is the evidence of that?
The evidence for intelligent causality lies in the encoding sequences of nucleic acids. Indirect evidence is used all the time in science.
Since the end result of these reactions eventually would produce a replicating cell and since the scientific evidence documenting such a process is nil your belief that the process occured is an expression of faith.
Nope. There is evidence for various naturalistic OOL scenarios. PvM has already cited some above. Here’s some more recent evidence:
Nikolay Zenkin, Yulia Yuzenkova, and Konstantin Severinov
Transcript-Assisted Transcriptional Proofreading
Science (2006) 313:518-520
Posting names of articles without URLs or summaries is unresponsive. If you read the article and understand it, it should not be difficult to point to the specific data supporting your case.
What’s more, naturalistic scenarios for the origin of life lead to testable hypotheses; which lead to experiments which lead to more evidence. I.e. they are scientific.
A testable hypothesis does not signify the test results confirm your hoped for belief. Only evidence is relevant.
The ID viewpoint does not supply any hypotheses, and therefore does not lead to experiments and new evidence. I.e. it is not scientific.
ID hypothesizes that a minimally functional genmome would not arise in that absence of intelligent direction.
http://www.pnas.org/cgi/content/full/103/2/425
Of course you can assert that unknown chemical reactions led to a minimal genome but that would not be scientific would it?
Comment by Wiliam Bradford — August 10, 2006 @ 5:18 pm
The evidence for intelligent causality lies in the encoding sequences of nucleic acids. Indirect evidence is used all the time in science.
That is not positive evidence. We already know that nucleic acids encode information, so post hoc claims that this supports ID fails to provide any predictive power, i.e. any scientifically testable hypotheses.
Posting names of articles without URLs or summaries is unresponsive. If you read the article and understand it, it should not be difficult to point to the specific data supporting your case.
That is a recent article in one of the most prestigious scientific journals. If you don’t have access to the scientific litereature, that tells me something about you.
The article discusses error-correction in RNA strands being copied from DNA templates by RNA polymerase. The mismatched RNA base takes part in the mismatch excision. I.e. there is inherent error correction capability in the strand of RNA which would have made early RNA World replication more reliable.
Comment by ivy privy — August 10, 2006 @ 8:30 pm
A testable hypothesis does not signify the test results confirm your hoped for belief.
You seem confused here. Even if ID were true, if it is not testable, it is not science. Write that down. Study it.
Only evidence is relevant.
And you don’t have any.
ID hypothesizes that a minimally functional genmome would not arise in that absence of intelligent direction.
I missed the part about how that is a scientifically testable hypothesis. I get the impression you are not familiar with this whole science thing.
Comment by ivy privy — August 10, 2006 @ 8:34 pm
ID hypothesizes that a minimally functional genmome would not arise in that absence of intelligent direction.
http://www.pnas.org/cgi/content/full/103/2/425
You seem to have badly misinterpreted that article,
Essential genes of a minimal bacterium
John I. Glass, Nacyra Assad-Garcia, Nina Alperovich, Shibu Yooseph, Matthew R. Lewis, Mahir Maruf, Clyde A. Hutchison, III, Hamilton O. Smith *, and J. Craig Venter
PNAS | January 10, 2006 | vol. 103 | no. 2 | 425-430
How would a requirement for a minimal bacterial genome place any restrictions on pre-bacterial entities? Specifically, if I had an RNA genome, such as is postulated for the RNA World, and as is the case in many viruses, I wouldn’t need any of the DNA replication enzymes, would I? That article explores the minimal number of genes required for a bacterium using a particular technology set. There is nothing in that article about an Intelligent Designer.
I’ll give you an analogy: I could tabulate a minimum parts list for an Indy racing car. This would place no limits on scooters, bicycles or go carts.
Comment by ivy privy — August 10, 2006 @ 8:44 pm
The evidence for intelligent causality lies in the encoding sequences of nucleic acids. Indirect evidence is used all the time in science.
That is not positive evidence. We already know that nucleic acids encode information, so post hoc claims that this supports ID fails to provide any predictive power, i.e. any scientifically testable hypotheses.
Abiogenesis predicts that codons of nucleic acids arrange in protein encoding patterns according to a prearranged code? You believe in miracles and attribute them to unknown and unspecified chemical pathways.
Posting names of articles without URLs or summaries is unresponsive. If you read the article and understand it, it should not be difficult to point to the specific data supporting your case.
That is a recent article in one of the most prestigious scientific journals. If you don’t have access to the scientific litereature, that tells me something about you.
It shows something about you that you are unwilling to summarize, briefly quote from or provide a link to what you reference unless pressed for it. This is not a private conversation. If you do not wish others to evaluate whatever you throw up on a screen then by all means just give a title and journal name.
The article discusses error-correction in RNA strands being copied from DNA templates by RNA polymerase. The mismatched RNA base takes part in the mismatch excision. I.e. there is inherent error correction capability in the strand of RNA which would have made early RNA World replication more reliable.
Reliability is not the strong suit of RNA. It is ill-suited as an information storage medium; a task better left to DNA. Of course error correction is fine but you have yet to explain how genetic information is acquired and expressed in the first place in this prebiotic world.
Comment by Wiliam Bradford — August 11, 2006 @ 12:46 am
A testable hypothesis does not signify the test results confirm your hoped for belief.
You seem confused here. Even if ID were true, if it is not testable, it is not science. Write that down. Study it.
Study this Ivypivey. Your belief that cells arise has been tested repeatedly without a single cell in evidence. In case you have not noticed there are only two options here. Either cells arose with intelligent input or woithout it. The zeros on your test report card suggest the only alternative.
Only evidence is relevant.
And you don’t have any.
ID hypothesizes that a minimally functional genome would not arise in that absence of intelligent direction.
I missed the part about how that is a scientifically testable hypothesis. I get the impression you are not familiar with this whole science thing.
I gather you did not understand that a test indicating that minimally functional genomes do in fact arise without intelligent direction would falsify the hypothesis. I’m not surprised because nothing can falsify abiogenesis.
Comment by Wiliam Bradford — August 11, 2006 @ 12:57 am
ID hypothesizes that a minimally functional genmome would not arise in that absence of intelligent direction.
http://www.pnas.org/cgi/content/full/103/2/425
You seem to have badly misinterpreted that article,
Essential genes of a minimal bacterium
John I. Glass, Nacyra Assad-Garcia, Nina Alperovich, Shibu Yooseph, Matthew R. Lewis, Mahir Maruf, Clyde A. Hutchison, III, Hamilton O. Smith *, and J. Craig Venter
PNAS | January 10, 2006 | vol. 103 | no. 2 | 425-430
How would a requirement for a minimal bacterial genome place any restrictions on pre-bacterial entities?
Pre-bacterial entities are the stuff of your dreams
Specifically, if I had an RNA genome, such as is postulated for the RNA World, and as is the case in many viruses, I wouldn’t need any of the DNA replication enzymes, would I?
If you had an RNA genome like a virus then good luck in your search for a host cell.
That article explores the minimal number of genes required for a bacterium using a particular technology set. There is nothing in that article about an Intelligent Designer.
The article indicates that even an obligate parsite requires hundreds of genes and a means to express them. Hundreds of encoding genes translated by means of an existing code which we’ll pretend resulted from unintelligent chemical reactions about which we are unable to specify very much. Other symbolic codes are the product of intelligence but not this one. Natural selection dunnit.
I’ll give you an analogy: I could tabulate a minimum parts list for an Indy racing car. This would place no limits on scooters, bicycles or go carts.
I gather a part of your Indy car includes a computer program specifying how the scooters, bicycles and go carts are assembled as well as the mechanisms of their function. Best of all the program was the product of unspecified and undirected chemical interactions. No intelligence involved.
Comment by Wiliam Bradford — August 11, 2006 @ 1:17 am
The evidence for intelligent causality lies in the encoding sequences of nucleic acids. Indirect evidence is used all the time in science.
Ivy: That is not positive evidence. We already know that nucleic acids encode information, so post hoc claims that this supports ID fails to provide any predictive power, i.e. any scientifically testable hypotheses.
The prediction: each time a new symbolic coding system is encountered anywhere in the universe and the cause generating the symbolic codes identified, an intelligent source, rather than a stochastic chemical process, will be implicated. As for post ad hoc claims, claiming that a living cell arose as a result of an unknown stochastic chemical process falls short of a predictive claim.
Comment by Wiliam Bradford — August 11, 2006 @ 2:44 am
Abiogenesis predicts that codons of nucleic acids arrange in protein encoding patterns according to a prearranged code? You believe in miracles and attribute them to unknown and unspecified chemical pathways.
You are rambling incoherently. You are very confused over who is invoking miracles.
It shows something about you that you are unwilling to summarize, briefly quote from or provide a link to what you reference unless pressed for it. This is not a private conversation. If you do not wish others to evaluate whatever you throw up on a screen then by all means just give a title and journal name.
1) I used links in a couple previous posts which have not shown up. No point in repeating that failure. 2) Nature is a subscription-only site. Even if I gave a link I’m not sure if you would have access to it. 3) I gave a publication quality citation, complete with volume and page numbers. It should be more than adequate for anyone with the wherewithal to be discussing science in public.
Reliability is not the strong suit of RNA. It is ill-suited as an information storage medium; a task better left to DNA. Of course error correction is fine but you have yet to explain how genetic information is acquired and expressed in the first place in this prebiotic world.
Yes, that piece of evidence was not a comprehensive explanation of all steps necessary to go from a pre-biotic state to the current DNA-RNA-protein cellular life forms by which we are surrounded. Is that what you’re complaining about? I provided a piece of evidence. You have provided none at all. Also, perhaps you could explain what “genetic information” would even mean in an RNA World.
Study this Ivypivey. Your belief that cells arise has been tested repeatedly without a single cell in evidence. In case you have not noticed there are only two options here. Either cells arose with intelligent input or woithout it. The zeros on your test report card suggest the only alternative.
No, there are many possible naturalistic explanations, which have not been exhausted. Are you saying ideas that haven’t even been thought up yet should have been already tested? The RNA World theory, for example, did not become popular until the 1980s, when the existence of catalytic RNA was firmly established.
I gather you did not understand that a test indicating that minimally functional genomes do in fact arise without intelligent direction would falsify the hypothesis.
Do you have a point here? Did the reference you cited establish that that cannot happen? You cited a reference that did not back up your claims about it. Then you try to twist the rhetoric to blame me for your failure.
Pre-bacterial entities are the stuff of your dreams
Meaningless rhetoric
If you had an RNA genome like a virus then good luck in your search for a host cell.
Do these useless rhetorical games amuse you? How about this wording: “If I had an RNA genome, as an RNA virus does.”
I gather a part of your Indy car includes a computer program specifying how the scooters, bicycles and go carts are assembled as well as the mechanisms of their function. Best of all the program was the product of unspecified and undirected chemical interactions. No intelligence involved.
More senseless rambling, and an attempt to stretch my instructive analogy too far. As I hope you know, machines such as Indy cars do not replicate themselves the way that biological organisms do.
As for post ad hoc claims, claiming that a living cell arose as a result of an unknown stochastic chemical process falls short of a predictive claim.
Since evolution entails precursors and intermediates, i.e. a history, that claim would lead to many more specific claims that could be tested through experiments, such as those already cited in this thread, and many more that I could cite. ID meanwhile, makes no testable predictions at all.
Comment by ivy privy — August 11, 2006 @ 2:46 pm
You are rambling incoherently. You are very confused over who is invoking miracles.
Asserting that something as intricate as a cell arises from unspecifed chemical reactions without the evidence to back the claim is the stuff of miracles.
It shows something about you that you are unwilling to summarize, briefly quote from or provide a link to what you reference unless pressed for it. This is not a private conversation. If you do not wish others to evaluate whatever you throw up on a screen then by all means just give a title and journal name.
1) I used links in a couple previous posts which have not shown up. No point in repeating that failure. 2) Nature is a subscription-only site. Even if I gave a link I’m not sure if you would have access to it. 3) I gave a publication quality citation, complete with volume and page numbers. It should be more than adequate for anyone with the wherewithal to be discussing science in public.
When you have a citation you have read at your fingertips as it appeared you did then providing links, summaries or qoutes from the article is no big deal. It is done all the time. Others are not going to take the time to run down every title you throw up on a screen. Why would you not want to take a little extra time to describe what you consider essential information?
Reliability is not the strong suit of RNA. It is ill-suited as an information storage medium; a task better left to DNA. Of course error correction is fine but you have yet to explain how genetic information is acquired and expressed in the first place in this prebiotic world.
Yes, that piece of evidence was not a comprehensive explanation of all steps necessary to go from a pre-biotic state to the current DNA-RNA-protein cellular life forms by which we are surrounded. Is that what you’re complaining about? I provided a piece of evidence. You have provided none at all. Also, perhaps you could explain what “genetic information” would even mean in an RNA World.
Genetic information is that which is biologically useful in enabling an organism to code for proteins and RNA. OOL literature is full of references to biologically useless RNA.
I gather you did not understand that a test indicating that minimally functional genomes do in fact arise without intelligent direction would falsify the hypothesis.
Do you have a point here? Did the reference you cited establish that that cannot happen? You cited a reference that did not back up your claims about it. Then you try to twist the rhetoric to blame me for your failure.
The citation provides a gauge by which minimal genomic function is measured. It is a starting point for future research. If minimal function entails hundreds of functional genes and prebiotic earth contains none you have a clear problem with selection value in any theorized process.
I gather a part of your Indy car includes a computer program specifying how the scooters, bicycles and go carts are assembled as well as the mechanisms of their function. Best of all the program was the product of unspecified and undirected chemical interactions. No intelligence involved.
More senseless rambling, and an attempt to stretch my instructive analogy too far. As I hope you know, machines such as Indy cars do not replicate themselves the way that biological organisms do.
It was you who introduced the inadaquate analogy.
As for post ad hoc claims, claiming that a living cell arose as a result of an unknown stochastic chemical process falls short of a predictive claim.
Since evolution entails precursors and intermediates, i.e. a history, that claim would lead to many more specific claims that could be tested through experiments, such as those already cited in this thread, and many more that I could cite. ID meanwhile, makes no testable predictions at all.
Abiogenesis does not entail precursors and intermediates. That is one of the difficulties with the belief. There are no intermediates to a genetic code and a minimally functional genome. You can assert the contrary but not based on the identification of functional intermediates.
As for a testable prediction, found universally are error detection and repair mechanisms that maintain genomic integrity. Causes of genomic mal-function include factors that were present on earth at life’s origins. The prediction is that such mechanisms are absolutely essential to the viability of a genome and a test involves observing replication without such mechanisms. If the rate of information loss exceeds gains a generation mechanism is fatally compromised.
Comment by Wiliam Bradford — August 11, 2006 @ 4:31 pm
Asserting that something as intricate as a cell arises from unspecifed chemical reactions without the evidence to back the claim is the stuff of miracles.
Now you are confused about who has provided evidence and who has not.
When you have a citation you have read at your fingertips as it appeared you did then providing links, summaries or qoutes from the article is no big deal. It is done all the time. Others are not going to take the time to run down every title you throw up on a screen. Why would you not want to take a little extra time to describe what you consider essential information?
Keep whining about this. It tells anyone else who might be reading this who is prepared to discuss science and who isn’t.
Genetic information is that which is biologically useful in enabling an organism to code for proteins and RNA. OOL literature is full of references to biologically useless RNA.
RNA was coding for RNA? You seem confused.
The citation provides a gauge by which minimal genomic function is measured. It is a starting point for future research. If minimal function entails hundreds of functional genes and prebiotic earth contains none you have a clear problem with selection value in any theorized process.
Future research? That paper did not support ID, and it does not indicate any future research that would support ID. As I already explained, “minimal function” involves a defined set of technology and a defined environment. For example, primates, including humans, do not manufacture their own vitamin C, they get it from their diet.
It was you who introduced the inadaquate analogy.
Yes, I did, as an instructive method to explain something. I did not claim that the analogy extended beyond the comparison for which I was using it. Apparently I overestimated your ability to rationally take in data.
Abiogenesis does not entail precursors and intermediates. That is one of the difficulties with the belief. There are no intermediates to a genetic code and a minimally functional genome. You can assert the contrary but not based on the identification of functional intermediates.
You seem to be at odds with the scientific community on this one. People have actually been researching the origin and evolution of the genetic code; i.e. exploring events which you claim didn’t happen. These papers were already cited in this thread, so you can’t claim ignorance:
Knight, The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations Ph.D. Thesis 2001
Knight, R. D. and L. F. Landweber (2000). “The Early Evolution of the Genetic Code” Cell 101(6): 569-572.
Knight, R. D., S. J. Freeland, and L. F. Landweber (1999). “Selection, history and chemistry: the three faces of the genetic code.” Trends Biochem Sci 24(6):241-7.
Why don’t you write the authors and share your wisdom with them; that they are wasting their time exploring something which doesn’t exist.
As for a testable prediction, found universally are error detection and repair mechanisms that maintain genomic integrity. Causes of genomic mal-function include factors that were present on earth at life’s origins. The prediction is that such mechanisms are absolutely essential to the viability of a genome and a test involves observing replication without such mechanisms.
Since evolution also predicts error correction, and error correction mechanisms have already been identified which might have operated in the RNA World, I have no idea what you might be predicting here that is unique to ID.
If the rate of information loss exceeds gains a generation mechanism is fatally compromised.
Do keep in mind the amplification due to replication.
Comment by ivy privy — August 11, 2006 @ 10:47 pm
Genetic information is that which is biologically useful in enabling an organism to code for proteins and RNA. OOL literature is full of references to biologically useless RNA.
RNA was coding for RNA? You seem confused.
No encoding nucleic acids have been produced or is that too difficult for you?
The citation provides a gauge by which minimal genomic function is measured. It is a starting point for future research. If minimal function entails hundreds of functional genes and prebiotic earth contains none you have a clear problem with selection value in any theorized process.
Future research? That paper did not support ID, and it does not indicate any future research that would support ID.
A completely irrelevant point. ID was not the focus of the study
As I already explained, “minimal function” involves a defined set of technology and a defined environment. For example, primates, including humans, do not manufacture their own vitamin C, they get it from their diet.
A minimal genome has nothing to do with technology or your garbled thoughts. It correlates function to minimal gene number.
As for a testable prediction, found universally are error detection and repair mechanisms that maintain genomic integrity. Causes of genomic mal-function include factors that were present on earth at life’s origins. The prediction is that such mechanisms are absolutely essential to the viability of a genome and a test involves observing replication without such mechanisms.
Since evolution also predicts error correction, and error correction mechanisms have already been identified which might have operated in the RNA World, I have no idea what you might be predicting here that is unique to ID.
Then study error and correction mechanisms. They apply to many different types of genomic disruption not addressed by the study you referenced.
If the rate of information loss exceeds gains a generation mechanism is fatally compromised.
Do keep in mind the amplification due to replication.
Do keep in mind that references to RNA replication evidence no biologically useful information. RRRRRR is replication, not information.
Comment by Wiliam Bradford — August 12, 2006 @ 1:54 am
Ivy: Since evolution also predicts error correction, and error correction mechanisms…
How is this relevant to a discussion of abiogenesis?
Comment by Wiliam Bradford — August 12, 2006 @ 1:58 am
A completely irrelevant point. ID was not the focus of the study
There you go. William Bradford, who doesn’t have the wherewithal to find a paper in a widely-read and widely-distributed scientific journal, thinks the fact that he has cited a reference somehow matters, even though the reference does not back his claims, and leads to no furhter experiements which might back up his claims.
A minimal genome has nothing to do with technology or your garbled thoughts. It correlates function to minimal gene number.
Minimal gene number for what? There you go again. William Bradford cannot or will not acknowledge that “minimal genome” entails a set of requirements on what must be encoded, and a set of requirements for what environment the genome can survive in.
As for a testable prediction, found universally are error detection and repair mechanisms that maintain genomic integrity. Causes of genomic mal-function include factors that were present on earth at life’s origins. The prediction is that such mechanisms are absolutely essential to the viability of a genome and a test involves observing replication without such mechanisms.
This is getting stranger all the time. William Bradford insists that replication must be observed without error-correction mechanism, even after research has been cited which demonstrates that error correction is inherent in the structure of RNA.
Do keep in mind that references to RNA replication evidence no biologically useful information. RRRRRR is replication, not information.
If William Bradford expressed a coherent thought somewhere in that jumble, I’m afraid it escaped me.
How is this relevant to a discussion of abiogenesis?
The discussion has ranged rather more widely than just abiogenesis. It appears you are having trouble keeping track.
That’s about enough for me. I will just point out to any readers of this thread that, no matter how badly William Bradford need tutoring in biology, I am not getting paid for this and it takes a great deal of effort to keep repeating points that he either forgets or ignores.
Bye now.
Comment by ivy privy — August 13, 2006 @ 6:15 pm
http://www.pnas.org/cgi/content/full/103/2/425
Essential genes of a minimal bacterium
John I. Glass, Nacyra Assad-Garcia, Nina Alperovich, Shibu Yooseph, Matthew R. Lewis, Mahir Maruf, Clyde A. Hutchison, III, Hamilton O. Smith *, and J. Craig Venter
PNAS | January 10, 2006 | vol. 103 | no. 2 | 425-430
…Herein, we identify 382 of the 482 M. genitalium protein-coding genes as essential, plus five sets of disrupted genes that encode proteins with potentially redundant essential functions, such as phosphate transport…
Whoops! Time for an update.
Smallest genome clocks in at 182 genes
Philip Ball, Nature News, Published online: 12 October 2006; | doi:10.1038/news061009-10
Let me check my math… yes, 182 is les than 382. Let me reiterate that a “minimal genome” is the minimum to encode a certain set of functions for a certain environment. Since the environment may have been different in the past, there is no theoretical roadblock to the development of minimal genomes.
Comment by ivy privy — October 17, 2006 @ 4:53 pm