A thought experiment about OOL


#41

So how does that work for DNA? How do you determine if a sequence of nucleotides or amino acids fits this pattern? Here is the amino acid sequence for human cytochrome c:

MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE

If that was a string of Scrabble tiles, would you say that it was designed?[quote=“bjmiller, post:40, topic:36944”]
The key issue is that the sequence of the nucleotides (letters in the message) is not determined by the underlying chemistry of the RNA/DNA medium. See here for more details or the link in my previous post. This point becomes clear when one recognizes that the same information resides in a protein and in a gene; although, the chemistry of the media are different.
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How does the same information reside in a DNA sequence and in a protein? Please explain.[quote=“bjmiller, post:40, topic:36944”]
In the case of occlusions, imagine their arrangement in some crystal matches some external pattern, such as a series of numbers ranging between 0 and 9, which happen to match the phone numbers of the last five previous researchers. I suspect the inference to design would be clear.
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What DNA, RNA, or protein sequences match phone numbers of the last five previous researchers?[quote=“bjmiller, post:40, topic:36944”]
One has to be careful equating the energy released from a smoker to the production of the specific high-free-energy molecules which could drive the reactions needed to generate life.
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Why? You claim that free energy is a problem and yet there are tons of sources of energy, be it lightning, smokers, hot springs, etc.


(Brian J Miller) #42

So how does that work for DNA? How do you determine if a sequence of nucleotides or amino acids fits this pattern? Here is the amino acid sequence for human cytochrome c:
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
If that was a string of Scrabble tiles, would you say that it was designed?

If you had given me this string, I would ask three questions:

  1. Is the string the product of some algorithm or law-like process?

  2. Is the string highly improbable?

  3. Does the string match some external pattern or category of patterns?

  4. Since Scrabble letters are free to be arranged in any order, no law-like process was operational. I could also test to see if the sequence demonstrated correlations which would point to some law-like process, or does the sequence appear close to random.

  5. The number of letters is large enough to preclude the possibility of pure chance. In contrast, if the string had been CAT, the pattern matches a word, but such a short sequence could happen by chance.

  6. Finally, I would attempt to match the pattern to some known pattern. I might start with attempting to match the sequence to a sentence in some language. Ideally, I would eventually recognize that the letters matched amino acids. I would then run a BLAST search to see if the pattern matched closely enough to the sequence of some known protein to rule out chance. I would then find a match and know that the sequence was designed.

In the case of the origin of life, a minimally functional cell requires a precise set of reactions to take place in an enclosed space. However, reactions in cells rarely proceed quickly enough to maintain the metabolism. Even more problematic many of the reactions are energetically unfavorable - they move to higher free energy. Therefore, they need enzymes which will link reactions moving downhill (ATP --> ADP + P) with the desired cellular reaction. Such a linking requires an enzyme which targets all of the right molecules and then drives the two reactions in the right order. The minimal cell requires a whole suite of such enzymes, and each enzyme requires that amino acids (or nucleotides) link together in the right order. The probability of such fortuitous arrangements of letters in numerous chains is fantastically improbable. To give an example, the likelihood of random amino acids forming a functional cytochrome c was calculated by Robert Sauer from MIT to be 1 in 10^65 (Reidhaar-Olson, J. F., & Sauer, R. T. (1990) “Functionally Acceptable Substitutions in Two -Helical Regions of Repressor”, Proteins: Structure, Function, and Genetics 7, 306-316.).

Finding all of those enzymes in the right vicinity to drive a functional cell is as striking as finding an occlusions pattern with phone numbers. In the occlusion example, the number sequences derived from the crystal matched phone numbers that happened to be the numbers of researchers in the lab. In the case of the enzymes, the sequences of amino acids (or nucleotides) are the right sequences to correspond to enzymes which match the required reactions for the cell. The sequences of amino acids represent information.
The analogy is as follows:
AA sequences --> sequences of numbers (information)
Function enzymes --> operational phone numbers
Needed reactions for cell --> phone numbers of scientists who worked in lab

The challenge is that information is typically contained in a medium which is disconnected from the functional goal of the information. The blueprint for a house is contained on paper, not the materials which make up the house. In contrast, the information representing the right order of amino acids is contained in the sequence of amino acids which is both the medium and the goal of the information. The goal is for the sequence to fold into the right shape to drive the right reactions. This result would be like the ink making up the blueprint for a house causing the paper containing the ink to fold into the form of the desired house.

(To be continued)


#43

Previously, you said that the order of letters had to spell out English words in order to have information. Seems that requirement has gone out the window.[quote=“bjmiller, post:42, topic:36944”]
2) The number of letters is large enough to preclude the possibility of pure chance. In contrast, if the string had been CAT, the pattern matches a word, but such a short sequence could happen by chance.
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How did you determine that the number of letters is large enough to preclude the possibility of pure chance? I could arrange the same number of letters at random.

Then what is stopping you? You claim that these sequences contain information, yet you seem unable to measure it.[quote=“bjmiller, post:42, topic:36944”]
In the case of the origin of life, a minimally functional cell requires a precise set of reactions to take place in an enclosed space. However, reactions in cells rarely proceed quickly enough to maintain the metabolism. Even more problematic many of the reactions are energetically unfavorable - they move to higher free energy. Therefore, they need enzymes which will link reactions moving downhill (ATP --> ADP + P) with the desired cellular reaction. Such a linking requires an enzyme which targets all of the right molecules and then drives the two reactions in the right order. The minimal cell requires a whole suite of such enzymes, and each enzyme requires that amino acids (or nucleotides) link together in the right order. The probability of such fortuitous arrangements of letters in numerous chains is fantastically improbable. To give an example, the likelihood of random amino acids forming a functional cytochrome c was calculated by Robert Sauer from MIT to be 1 in 10^65 (Reidhaar-Olson, J. F., & Sauer, R. T. (1990) “Functionally Acceptable Substitutions in Two -Helical Regions of Repressor”, Proteins: Structure, Function, and Genetics 7, 306-316.).
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You haven’t even shown that life would require cytochrome c, and the rest of that paragraph is full of bare assertions.

This is another bare assertion. You need to show all possible combinations of nucleotides and proteins that can result in life before you can even calculate these probabilities, and from what I have seen we simply don’t know what combinations result in life. Therefore, such probabilities are impossible to calculate.

This is the same type of information found in H2O that allows it to form hexagonal crystals.


(Brian J Miller) #44

The issue with DNA is much less complicated than proteins. At some point, a hypothetical cell precursor transitioned to using proteins as catalysts for needed reactions. The challenge is that proteins degrade fairly quickly. Even if a miracle happened and a fully functional cell formed by whatever means, most proteins would not last for more than a few days. They would then need to be replaced. Unfortunately, proteins do not self-replicate, so the amino acid sequences would have to be stored in some other medium. RNA also has a rather short shelf life, so DNA would be needed rather quickly. The question then becomes how did the genetic code originate when strong chemical affinities do not exist between any particular amino acid and any particular codon (set of three nucleotides). In other words, one would not observe in a vat with all of the amino acids and codons the different amino acids strongly attaching to particular codons, thus revealing a code.

The origin of life theorist Eugene Koonin reviewed the different theories and determined that the code was a frozen accident not related to the direct chemical interactions between amino acids and codons. If no physical/chemical connection exists, no physical process could explain the encoding. The model presented by Yarus could only potentially help explain decoding, not encoding. The encoded information in DNA corresponding to the amino acid sequences then represents a tell-tale example of specified complexity. The chances of nucleotides randomly assembling in the right order to encode proteins are too improbable to happen by chance. In this case, the probability could be calculated directly. And, the sequence of codons would correspond to the neighboring protein sequences. The DNA would thus contain information corresponding to the proteins.

In addition, even if some extraordinary process encoded the DNA, that encoding would be useless unless a decoding process came into being before the miracle cell disassociated. Now let’s assume some decoding process came into being. That process would be unconnected to the encoding process, so the encoding and decoding would not use the same code. All of the stored information would then be lost. The code has to preexist the cell, so the encoding and decoding can be coordinated properly. Origin theorists could argue that the decoding mechanism came into being through some graduate selective process, but that process would have to be guided by the intelligence which decided on the code. Else, the chances of the coding matching the encoding are virtually nonexistent.


#45

That simply isn’t true. I have worked with proteins and they can survive for years in the right environments. Proteins like Taq polymerase can survive near boiling temperatures and still have activity. You can store antibodies for years or even decades in the fridge and they stay active.[quote=“bjmiller, post:44, topic:36944”]
The encoded information in DNA corresponding to the amino acid sequences then represents a tell-tale example of specified complexity.
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As already shown by previous posts, the term “specified complexity” is a meaningless term that is not measurable, is not scientific, and is only thrown about to make it look like you have an argument. You might as well claim that pizzas have specified complexity, or rainbows have specified complexity. It seems that you will claim anything has specified complexity since there are no meaningful criteria for measuring or detecting specified complexity.[quote=“bjmiller, post:44, topic:36944”]
The chances of nucleotides randomly assembling in the right order to encode proteins are too improbable to happen by chance.
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And yet we don’t see those calculations, only the bare assertion that it is too improbable.

Yet another assertion. Even now, RNA is used to make DNA so I don’t see what the problem would be.[quote=“bjmiller, post:44, topic:36944”]
Origin theorists could argue that the decoding mechanism came into being through some graduate selective process, but that process would have to be guided by the intelligence which decided on the code. Else, the chances of the coding matching the encoding are virtually nonexistent.
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Yet another bare assertion.