The Blind Atheist: The Unscientific Root of Atheism

[Happy Wonderer]

On a side note however I should say that I don't think that chloroform and the lack of water in his experiment is a realistic simulation of any supposed abiogenesis hypothesis. The part of his experiment that is relevant to the subject of information that we are discussing is the fact that the molecule he created self replicates.

Agreed, as I said this molocule is probably not the precursor to life on earth -- but it is a proof of possibility. Self-replicating molecules can arise through pure chemical processes. Now you are in the position of having to argue that only uninteresting self-replicating molecules can arise, or that they can only arise under conditions not like earth. That is a fairly weak position to be in.

But, it replicates perfectly.

This particular molecule replicates perfectly under normal conditions over a short period of observation. This fact is only interesting if one wants to make the claim that all non-DNA self-replicating molecules must always reproduce perfectly under all conditions. There is no evidence for such a claim.

I can design a machine that reproduces a product that I designed millions of times. That of course does not prove that intelligent design was not involved because both the original design and the machine that reproduced it were necessarily designed.

That is not the question (nor is it a valid counter-example as the 'machine' in question reproduces itself.) It is unprovable that "intelligent design was not involved", what can be proved is that it is unnecessary. I will happily concede that you can never disprove supernatural involvement in anything -- perhaps the car gods help my car to start in the morning. Proving that the supernatural must have been involved is a much tougher proposition, because you have to show that there must have been no naturalistic means (improbable or not) that could have lead to RNA's precursor. It is a bit like (dis)proving an alibi; the cops don't have to show exactly how you got across town in time to commit the crime, all they have to show that it was possible for you to.

In his experiment he forced the assembly of a molecule that replicates itself -- perfectly. Even if the copies were not perfect his experiment still would not touch the subject of information even if the best survived and were selected for an assumed future breeding.

This doesn't make sense to me. So you are saying that even if he had come up with a molecule with the capability to evolve, it doesn't prove that molecules could evolve? What possible test are you looking for, then? If we show how RNA could come about step-by-step from chemical processes that likely existed on the pre-biotic earth would that be enough -- or would the fact that as intelligent beings we did the experiment be enough to disprove it?

The experiment doesn't touch the "subject of information" because the question of whether the precursor to RNA arose from chemical processes on earth has precious little to do with information. (Actually the question is properly framed as 'which chemical processes lead to the precursor to RNA;' there is not much doubt about the former.)

As humans we overgeneralize; it is how we are wired and as an approximation it works very well. It can lead to magical thinking and irrational beliefs, however. While one can make a (very weak) analogy to a strand of RNA as a computer program, the differences between the two are vast. If you actually look into how codons are 'interpreted' (google Aminoacyl-tRNA) you will find a mechanism that is completely unlike a generalized computing engine. Codons are not abstract objects like bits are, they are three dimensional real objects whose 'interpretation' is strongly related to their structure. I can make an arbitrary assignment that '101111' = 'Hamlet', you cannot make the arbitrary assignment that CAG=<kevlar fibre>; the physics do not work. That is a crucial distinction between the types of 'information' in a computer program and that in RNA.

hw

 

[Happy Wonderer]

I think he did a great work and I deal with his claims and similar ones in my book. But his work does not touch the subject and the problem of information (that I will define in my next post).

Julius Rebek's work shows that it is possible for simple chemical processes to create a self-replicating molecule. You have a problem if you define this self-replicator as having no information; clearly it 'encodes' information about how to combine atoms to make a copy of itself. (Consider prions for a naturally-occurring example.)

On a side note however I should say that I don't think that chloroform and the lack of water in his experiment is a realistic simulation of any supposed abiogenesis hypothesis. The part of his experiment that is relevant to the subject of information that we are discussing is the fact that the molecule he created self replicates.

Yes, as I said nobody claims that this molecule is in any way the ancestor of RNA. There are two different questions: one that scientists are interested in and one that you are trying to argue. The scientists are trying to figure out which set of chemical reactions lead to RNA, you are arguing whether they can. It doesn't help your side at all to point out that a particular molecule doesn't 'work' for pre-biotic earth, if we can find that works in one environment there is no good reason to think that there doesn't exist a molecule that works in a different one.

But, it replicates perfectly. I can design a machine that reproduces a product that I designed millions of times. That of course does not prove that intelligent design was not involved because both the original design and the machine that reproduced it were necessarily designed.

It is impossible to "prove that intelligent design was not involved" and nobody is trying to claim that. As above, at most we can show that intelligent design is unnecssary. You have a difficult argument to make, which is that there is no (even implausable) natural process that could have led to RNA. Any evidence that shows how a molecule similar to RNA could have come about weakens your case.

In his experiment he forced the assembly of a molecule that replicates itself -- perfectly. Even if the copies were not perfect his experiment still would not touch the subject of information even if the best survived and were selected for an assumed future breeding.

This doesn't make sense to me. So even if he made (by natural processes) a molecule that could have evolved, it doesn't prove that an 'evolveable' molecule could have come about by natural processes? So what kind of proof would possibly satisfy you?

Wait a minute and I will explain more clearly what I mean by information (although I already did earlier in the thread).

More on this later, dinner awaits.

hw

EDIT: wow, I thought my first post had been lost when the site apparently went down, so I did a new article. If I seem to be repeating myself it is because I am!

 

[Zadok001]

Well, it's worth a shot.

RF:

Your argument stems from the idea that DNA is "coded," and that any code must come from an intelligent organism. I think you may simply be having an issue with semantics; just because we call it a "DNA Code" does not mean it's ENCODED. When we first discovered DNA, it was largely unclear what it DID, exactly. While we still don't understand the specific functions of most genes, we know know how base pairs interact, and what results from them.

Now, the key concept you're missing is this: EVERYTHING DNA CODES FOR IS "DECODED" ACCORDING TO THE LAWS OF CHEMISTRY, WHICH HOLD TRUE REGARDLESS OF INTELLIGENT INPUT.

Chemical laws govern DNA. No "codebook" exists that defines what DNA does outside of the laws of chemistry. That's why Notto keeps trying to get you to explain why the interaction of H and O are not encoded intelligently. The chemicals that make up a DNA chain react with one another *exactly* as they would in a laboratory. These reactions are exceedingly complex, and result in VERY complex organisms, but they're still JUST CHEMICAL REACTIONS.

Now, clearly, you want to claim otherwise. Therefore, we ask that you present SOME kind of evidence showing that the reactions of DNA are NOT simply following the rules of chemistry.

Either that, or hyrdrogen just grew a brain.

 

[Happy Wonderer]

Well, Zadok covers pretty much where I was going to continue but let me add a few points. It is a common misconception that DNA is the complete 'code' for an organism. Surprisingly, the fact is that it is not. You can't just plunk human DNA into an E. coli and have a human result. For mammals, embryo development is a complex interaction between the host and the fertilized egg. A lot of the 'information' that makes a human foetus is actually contained in the mother; her body responds to various hormones signaled by the egg, and the newly developing foetus responds to hormone signals from her body. If the female doesn't produce adequate estrogen at the appropriate time, for example, the foetus' liver will not mature.

So the critical point is that if an alien had complete understand of a human's DNA but no examples of a human female, the alien would be unable to produce a human from that DNA. This is a point that is so often overlooked that it bears repeating. DNA imparts no meaningful information (species reprodution-wise) on its own! It only makes sense in the (broad) context of the creature that is reproducing itself. Yes, foreign DNA can be introduced into species, but only fairly well related ones -- the famous 'ear on mouse' works because mice and men are closely related.

The thing about the real world is that it is very hard to capture in words, so having made the broad statement above I'll modify it. Viri, of course, are foreign DNA that can be introduced into a host. However, the point still stands -- if you knew only the DNA of a virius and nothing about cells then you would not know anything at all about how the virius worked. All you would have would be 'code' for a bunch of protiens expressed in some apparently random order. You have to know how those proteins interact in the context of a living cell to know what the virus does, or that it was in fact a virus.

All that the information in a DNA codon represents is one of 20 amino acids, which are relatively simple molecules that in turn are combined to make protiens. The DNA representation of this is extremely inefficient (most codons are duplicates and many are empty/STOP) -- which doesn't prove that it wasn't designed. However, it doesn't provide strong evidence of a designer.

DNA is not invariant, there are some slight variations in some species (usually a STOP codon is replaced by some amino.) This shows that the code can vary by natural means unless one wants to posit that these few organisms really needed yet another way to represent a particular amino.

It would be interesting for a biologist to explain the process that actually translates a codon into an amino. I sort of understand it, but not well enough to explain it coherently. When you look at the actual mechanism, you can begin to see how an undirected process could have generated it, and understand my point about how dependent the whole system is upon a living organism.

I think a lot of the confusion comes about from looking at RNA as a starting point, rather than as a very advanced stage in a complex development that we as yet know very little about.

hw

 

[Jet Black]

the famous 'ear on mouse' works because mice and men are closely related.

not to nitpick as such, because I may be wrong. But if I recall correctly, the famous ear on mouse experiment was carried out by constructing a 3dmesh in which cartilage cells could be grown, and this was shaped to look like an ear, rather than it being a real human ear. Whether the cartilace cells were human ones or mouse ones I do not recall. Furthermore, the mice had no immune system, explaining how it could be done "relatively easily".

 

[Jet Black]

just as a side note, the "language" is not as rigid as many thought. as has already been pointed out, sometimes a stop in one creature codes for an AA in another, also we get things like this:

http://www.acs.ohio-state.edu/units/research/archive/aminoacd.htm

out of interest, here is the codon table:

http://www.cbs.dtu.dk/courses/27013/codon.html

is there any relevance to the number of codons which codes for an amino acid, or is it fairly random?

 

[Happy Wonderer]

not to nitpick as such, because I may be wrong. But if I recall correctly, the famous ear on mouse experiment was carried out by constructing a 3dmesh in which cartilage cells could be grown, and this was shaped to look like an ear, rather than it being a real human ear. Whether the cartilace cells were human ones or mouse ones I do not recall. Furthermore, the mice had no immune system, explaining how it could be done "relatively easily".

You are correct, it is kind of a bad example but the most famous thing I could think of to make the point. That is the problem with trying to answer rebuttals before they are made, you often end up creating a straw man.

The interesting part of the experiment was a mouse being coopted to grow human cartilage, not that it was in the shape of an ear. This reinforces the idea that DNA really only makes 'sense' as a program in the context of the organism that it comes from.

hw

Speaking of ears, I hope you are doing better? Best wishes on that and get well soon!

 

[RFHendrix]

Well, it's worth a shot.

RF:

Your argument stems from the idea that DNA is "coded," and that any code must come from an intelligent organism. I think you may simply be having an issue with semantics; just because we call it a "DNA Code" does not mean it's ENCODED. When we first discovered DNA, it was largely unclear what it DID, exactly. While we still don't understand the specific functions of most genes, we know know how base pairs interact, and what results from them.

Now, the key concept you're missing is this: EVERYTHING DNA CODES FOR IS "DECODED" ACCORDING TO THE LAWS OF CHEMISTRY, WHICH HOLD TRUE REGARDLESS OF INTELLIGENT INPUT.

Chemical laws govern DNA. No "codebook" exists that defines what DNA does outside of the laws of chemistry. That's why Notto keeps trying to get you to explain why the interaction of H and O are not encoded intelligently. The chemicals that make up a DNA chain react with one another *exactly* as they would in a laboratory. These reactions are exceedingly complex, and result in VERY complex organisms, but they're still JUST CHEMICAL REACTIONS.

Now, clearly, you want to claim otherwise. Therefore, we ask that you present SOME kind of evidence showing that the reactions of DNA are NOT simply following the rules of chemistry.

Either that, or hyrdrogen just grew a brain.

Thanks for at least understanding the problem. Much of this thread seems to skirt around the issue which you seem to grasp.

The laws of chemistry are used as tools to produce a specific product. The manufacturing of that product is virtually inevitable because of the programmed information within DNA and the translation process. Saying that the "laws of chemistry" explain the information and the code is like saying that the laws of physics explain the words that a teacher writes on the board. The words come from thought and invisable intelligence. The laws of physics only explain the process of manifesting the information that originated mentally.

The problem is not the formation of RNA or DNA. There is no argument from me that they follow the laws of physics. The problem is what we have discovered in addition to those laws. Information is a different field of science and we need to use the applicable laws to deal with the information problem because chemical laws only manifest the mental process that must originate meaningful information. After all is said and done the genetic code MEANS something and that MEANING is accurately translated. There is no escaping that conclusion. Ordinary chemical processes do not translate or assign meaning. And that is true with or without a "code book" or if we can even translate the code ourselves. The code is imbedded within the machinery of life and the machinery know the meaning just as man made machines "understand" which componants are to be activated at particular times. Without the intelligent input we simply have a big fire.

Machiney can do everything you said the laws of physics can do. The most complicated computer can as well. The problem is not what makes the machine or computer work. The problem is the intelligent input within the machine and computer that remains invisible but is still an obvious requirement. Water and hydrogen and the normal chemical reactions within the universe have nothing to do with the origin of that intelligent input. Now, is the intillegent input required or not? And is life an information based machine or not? If it is we have an information problem which the laws of physics cannot solve unless we assume that those laws are somehow imbued with intelligence.

 

[RFHendrix]

Well, Zadok covers pretty much where I was going to continue but let me add a few points. It is a common misconception that DNA is the complete 'code' for an organism. Surprisingly, the fact is that it is not. You can't just plunk human DNA into an E. coli and have a human result. For mammals, embryo development is a complex interaction between the host and the fertilized egg. A lot of the 'information' that makes a human foetus is actually contained in the mother; her body responds to various hormones signaled by the egg, and the newly developing foetus responds to hormone signals from her body. If the female doesn't produce adequate estrogen at the appropriate time, for example, the foetus' liver will not mature.

So the critical point is that if an alien had complete understand of a human's DNA but no examples of a human female, the alien would be unable to produce a human from that DNA. This is a point that is so often overlooked that it bears repeating. DNA imparts no meaningful information (species reprodution-wise) on its own! It only makes sense in the (broad) context of the creature that is reproducing itself. Yes, foreign DNA can be introduced into species, but only fairly well related ones -- the famous 'ear on mouse' works because mice and men are closely related.

The thing about the real world is that it is very hard to capture in words, so having made the broad statement above I'll modify it. Viri, of course, are foreign DNA that can be introduced into a host. However, the point still stands -- if you knew only the DNA of a virius and nothing about cells then you would not know anything at all about how the virius worked. All you would have would be 'code' for a bunch of protiens expressed in some apparently random order. You have to know how those proteins interact in the context of a living cell to know what the virus does, or that it was in fact a virus.

All that the information in a DNA codon represents is one of 20 amino acids, which are relatively simple molecules that in turn are combined to make protiens. The DNA representation of this is extremely inefficient (most codons are duplicates and many are empty/STOP) -- which doesn't prove that it wasn't designed. However, it doesn't provide strong evidence of a designer.

DNA is not invariant, there are some slight variations in some species (usually a STOP codon is replaced by some amino.) This shows that the code can vary by natural means unless one wants to posit that these few organisms really needed yet another way to represent a particular amino.

It would be interesting for a biologist to explain the process that actually translates a codon into an amino. I sort of understand it, but not well enough to explain it coherently. When you look at the actual mechanism, you can begin to see how an undirected process could have generated it, and understand my point about how dependent the whole system is upon a living organism.

I think a lot of the confusion comes about from looking at RNA as a starting point, rather than as a very advanced stage in a complex development that we as yet know very little about.

hw

I agree that the life process is not simply contained in DNA (See the chapter in my book, Junk Science and Junk DNA) but how does that tend to detract from my argument? You said:

<blockquote>"DNA codon represents is one of 20 amino acids, which are relatively simple molecules that in turn are combined to make protiens. The DNA representation of this is extremely inefficient (most codons are duplicates and many are empty/STOP) -- which doesn't prove that it wasn't designed. However, it doesn't provide strong evidence of a designer."
</blockquote>

But as you stated above DNA requires a support system and a translation mechanism which is by no means simple. DNA is only a small part of the overall information processing system within life. The entire system must be in place before there is life so that only compounds the problem for my opponants. And it cannot be said that there is "inneficiency" with any degree of cerainty because of the extremely complicated and largely unknown communication within the life process.

 

[RFHendrix]

Hope to check back on this thread later. I don't have time today to debate this further.

 

[Jet Black]

I get the impression that you are jumping right to some language, rather than developing a language.
of course I am just talking off the top of my head here, but look at a possible scenario. We know that RNA can catalyse RNA polymerisation so if we start off with a basic string that does this, then mistakes will more than likely be made. however if we get to a stage where there is an RNA catalyst that selects more specifically for a particular base, then this would lower the amount of errors in a self reproducing RNA strand. now double the length of the strand (in a similar manner to polyploidy) and then there is redundancy since we now have one RNA section that codes for a more specific base (or a couple, or even three would be better than four) and one that codes generally and so on. This second strand is better than the first, since it is more likely to replicate itself completely than the others.... so the "language" actually develops with repeated trial and improvement.

 

[Zadok001]

"The problem is not the formation of RNA or DNA. There is no argument from me that they follow the laws of physics. The problem is what we have discovered in addition to those laws. Information is a different field of science and we need to use the applicable laws to deal with the information problem because chemical laws only manifest the mental process that must originate meaningful information. After all is said and done the genetic code MEANS something and that MEANING is accurately translated. There is no escaping that conclusion. Ordinary chemical processes do not translate or assign meaning. And that is true with or without a "code book" or if we can even translate the code ourselves. The code is imbedded within the machinery of life and the machinery know the meaning just as man made machines "understand" which componants are to be activated at particular times. Without the intelligent input we simply have a big fire. "

I love the sound points make when they go flying past...

Anyways, you missed my point rather completely. You're assigning "information" value to the reactions of DNA, but not to any simple chemical reaction. You posit the existence of a difference between the two. I don't see any evidence that such a distinction exists. The reactions of DNA and RNA are just complex chemical reactions. The difference between the genetic code and the formation of water is a difference of magnitude, not of type.

Now, I'll ask again: What leads you to believe that this distinction is anything other than a difference of magnitude?

 

[Jet Black]

I love the sound points make when they go flying past...

Anyways, you missed my point rather completely. You're assigning "information" value to the reactions of DNA, but not to any simple chemical reaction. You posit the existence of a difference between the two. I don't see any evidence that such a distinction exists. The reactions of DNA and RNA are just complex chemical reactions. The difference between the genetic code and the formation of water is a difference of magnitude, not of type.

Now, I'll ask again: What leads you to believe that this distinction is anything other than a difference of magnitude?
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his issue seems to be with where this "coding language" came from. It is not so much that the information is within the reactions of the DNA, but within the DNA itself, it is undeniable that there is a significant amount of information there. My problem with his argument though, is that he seems to think that this information must have popped into being in one shot, when there are other ways that this information could have come about, as I expressed. Granted my idea was nothing more than that, I have no evidence to back me up, but until it is eliminated as a possibility, it has to at least be considered.

"We must fall back upon the old axiom that when all other contingencies fail, whatever remains, however improbable, must be the truth." Sherlock Holmes.

 

[Osiris]

2. There exists in the world an intelligent source of information, i.e the human mind. This has been empirically proved and confirmed in several thousand years of human history and experimentation. There has never been even one verified example where information or intricate interactive machinery came into being without intelligent input.

Speculation: Perhaps the information within DNA and the associated machinery of life came into being by way of the laws of physics? Or perhaps there is an intelligent source of information within the universe?

I guess everything that seems to have a design, needs to have some sort of input and design in it...
if humans have a complex design, how much more complex is God? if you are going to use your logic, he must have a higher intelligent source of information above him...

or maybe something simple...
single celled organisms, are they complex in design? not really... what was their purpose? to eat? maybe after a while they probably found out that to get more food was to be in groups...

 

[Jet Black]

maybe after a while they probably found out that to get more food was to be in groups...

as a note, this has been observed, as a result of genetic mutation

 

[RFHendrix]

Julius Rebek's work shows that it is possible for simple chemical processes to create a self-replicating molecule. You have a problem if you define this self-replicator as having no information; clearly it 'encodes' information about how to combine atoms to make a copy of itself. (Consider prions for a naturally-occurring example.)

Yes, as I said nobody claims that this molecule is in any way the ancestor of RNA. There are two different questions: one that scientists are interested in and one that you are trying to argue. The scientists are trying to figure out which set of chemical reactions lead to RNA, you are arguing whether they can. It doesn't help your side at all to point out that a particular molecule doesn't 'work' for pre-biotic earth, if we can find that works in one environment there is no good reason to think that there doesn't exist a molecule that works in a different one.

It is impossible to "prove that intelligent design was not involved" and nobody is trying to claim that. As above, at most we can show that intelligent design is unnecssary. You have a difficult argument to make, which is that there is no (even implausable) natural process that could have led to RNA. Any evidence that shows how a molecule similar to RNA could have come about weakens your case.

This doesn't make sense to me. So even if he made (by natural processes) a molecule that could have evolved, it doesn't prove that an 'evolveable' molecule could have come about by natural processes? So what kind of proof would possibly satisfy you?

More on this later, dinner awaits.

hw

EDIT: wow, I thought my first post had been lost when the site apparently went down, so I did a new article. If I seem to be repeating myself it is because I am!

Making a molecule that can "evolve" further does not solve the problem because we are dealing with the formation of an information based machine. Or, the formation of a language that dictates the operation of an interactive, intricate biological machine that actually has a useful function. Surely everyone here realizes that it is only speculation without evidence (unless one uses the exact same evidence that ID uses, i.e., the universal code) that all life evolved from a single cell.

The problem is not making a blob of some type of theoretical proto-life form that we then assume evolves into a fully functioning life form. All life is information based. It does no good to escape that central issue by pretending that a "self replicating molecule" somehow continues to evolve into a coded language and machinery that is directed by the proper interpretation and translation of that language. Yes, it is interesting how steel and glass are formed but we are making a car here. The problem is the evolution of a useful language without intelligent input.

 

[RFHendrix]

I get the impression that you are jumping right to some language, rather than developing a language.
of course I am just talking off the top of my head here, but look at a possible scenario. We know that RNA can catalyse RNA polymerisation so if we start off with a basic string that does this, then mistakes will more than likely be made. however if we get to a stage where there is an RNA catalyst that selects more specifically for a particular base, then this would lower the amount of errors in a self reproducing RNA strand. now double the length of the strand (in a similar manner to polyploidy) and then there is redundancy since we now have one RNA section that codes for a more specific base (or a couple, or even three would be better than four) and one that codes generally and so on. This second strand is better than the first, since it is more likely to replicate itself completely than the others.... so the "language" actually develops with repeated trial and improvement.

If you agree that we are dealing with a language/information problem then there should be no problem proving that a meaningful language can evolve on a computer. You are suggesting that the laws of physics with the aid of natural selection is all that is necessary to evolve a useful language. You should be able to prove your assumption with a computer.

 

[RFHendrix]

Here is the essence of the problem whether we are talking about a computer solution or a chemical one:

The reason a computer or chemicals cannot design something on their own is because of value judgements that must be entered into the system by someone who can discern values. In other words, why is a word (codon) better than a letter (or nucleotide base)? Or, why is a sentence (or gene) better than a word? It seems like the word would be better at first glance because it is much more brief. Someone has to decide if the brevity is better or the more complete explanation is better. Is a tube better if it is porous and allows some of the liquid to seep through or is it better if it contains the liquid completely? Is a low electrical current better than a higher one? Is an image better than text or is text better?

The answers to the above questions may vary even within the same system. Who or what makes these decisions? Now, taking an intelligently designed computer program and watching it evolve a language is circular reasoning. Likewise, taking a viable life-form and saying that it can produce information is circular reasoning. We need to begin from the laws of physics and then evolve a meaningful language. Remember we are talking about the ORIGIN of meaningful information, and that problem needs to be solved either with chemicals or within a non-inteligently programmed computer. It cannot be assumed that somehow the information just evolved and we just haven't figured out how yet. It can be assumed however that it evolved (or was created instantly) by an intelligent being because that is where the evidence leads. There is no basis for assuming that a purely materialistic solution exists. That is mere speculation that contradicts available evidence. Theism is the default position, not atheism.

 

[bevets]

I guess everything that seems to have a design, needs to have some sort of input and design in it...
if humans have a complex design, how much more complex is God? if you are going to use your logic, he must have a higher intelligent source of information above him...

What is your opinion of the Aristotelean concept of 'Uncaused Cause'? Or the Thomistic distinction between contingent and Necessary beings?

 

[bevets]

Your whole argument seems to be one of "if you don't understand it, God did it".

Would you suggest that a better explanation for things we don't understand is 'Chance did it'?