Uncommon Descent Serving The Intelligent Design Community

The First Gene: An information theory look at the origin of life

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email
The First Gene: The Birth of Programming, Messaging and Formal Control

Here, edited by David Abel, The First Gene: The Birth of Programming, Messaging and Formal Control :

“The First Gene: The Birth of Programming, Messaging and Formal Control” is a peer-reviewed anthology of papers that focuses, for the first time, entirely on the following difficult scientific questions: *How did physics and chemistry write the first genetic instructions? *How could a prebiotic (pre-life, inanimate) environment consisting of nothing but chance and necessity have programmed logic gates, decision nodes, configurable-switch settings, and prescriptive information using a symbolic system of codons (three nucleotides per unit/block of code)? The codon table is formal, not physical. It has also been shown to be conceptually ideal. *How did primordial nature know how to write in redundancy codes that maximally protect information? *How did mere physics encode and decode linear digital instructions that are not determined by physical interactions? All known life is networked and cybernetic. “Cybernetics” is the study of various means of steering, organizing and controlling objects and events toward producing utility. The constraints of initial conditions and the physical laws themselves are blind and indifferent to functional success. Only controls, not constraints, steer events toward the goal of usefulness (e.g., becoming alive or staying alive). Life-origin science cannot advance until first answering these questions: *1-How does nonphysical programming arise out of physicality to then establish control over that physicality? *2-How did inanimate nature give rise to a formally-directed, linear, digital, symbol-based and cybernetic-rich life? *3-What are the necessary and sufficient conditions for turning physics and chemistry into formal controls, regulation, organization, engineering, and computational feats? “The First Gene” directly addresses these questions.

As we write, it is #2 in biophysics, and the trolls haven’t even got there yet.

Here’s Casey Luskin’s review:

Materialists Beware: The First Gene Defends a Strictly Scientific, Non-Materialist Conception of Biological Origins:

The First Gene investigates a number of different types of information that we find in nature, including prescriptive information, semantic information, and Shannon information. Prescriptive information is what directs our choices, and it is a form of semantic information — which is a type of functional information. In contrast, Shannon information, according to Abel, shouldn’t even be called “information” because it’s really a measure of a reduction in certainty, and by itself cannot do anything to “prescribe or generate formal function.” (p. 11) Making arguments similar to those embodied in Dembski’s law of conservation of information, Abel argues that “Shannon uncertainty cannot progress to becoming [Functional Information] without smuggling in positive information from an external source.” (p. 12) The highest form of information, however, is prescriptive information:

Comments
Timbo, It appears that you are talking to yourself as your position is the empty plate that cannot muster a testable hypothesis. And obviously that bothers you...Joe
November 28, 2011
November
11
Nov
28
28
2011
04:15 AM
4
04
15
AM
PDT
If I may cut in, it is not a boring question at all, especially in view of the "only right" naturalistic materialism. This can change the perception of science in the heads of millions of people. That I cannot describe as boring. It is terribly important. Another reason why I don't think it's boring is given two conflicting explanations (spontaneous origin vs. purposeful design) finding out which one's right is actually very interesting in its own right as well as in terms of its possible ramifications (philosophy of science e.g.).Eugene S
November 28, 2011
November
11
Nov
28
28
2011
04:06 AM
4
04
06
AM
PDT
Scott,
I’d love to hear how or why detecting design would bring research to a screeching halt. It sounds clever until you scratch your head and realizes that it has no basis in reality and in fact nullifies several other fields of science.
Could you develop this a bit.Eugene S
November 28, 2011
November
11
Nov
28
28
2011
03:59 AM
3
03
59
AM
PDT
Timbo,
I’m not attempting to reframe any questions or to refute ID. At the moment there is nothing to refute. I can’t say life wasn’t designed until a model of how that process might have worked is put up.
How do you model design? Tell me something you've designed, and then model the mental activity of designing it. If you can't then you're making this up as you go along. If you can then you've just written the hypothesis.ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
11:22 PM
11
11
22
PM
PDT
I'm not attempting to reframe any questions or to refute ID. At the moment there is nothing to refute. I can't say life wasn't designed until a model of how that process might have worked is put up. You put down of darwinism ironically still contains far more scope for investigation and discussion than ID does. Problem is, you have an empty plate and no apparent hunger.Timbo
November 27, 2011
November
11
Nov
27
27
2011
08:02 PM
8
08
02
PM
PDT
You're correct, if I were claiming to offer a mechanical narrative of the manufacture of life. Having failed to refute ID, you keep attempting to reframe the question. Refute what it does state if you can rather than shifting the question. Exactly what gold standard does either abiogenesis or darwinism hold up in the hypothesis department anyway? Last I checked the hypothesis was 'a little of something like this and a little of something like that and something got selected and something drifted (we're not sure exactly which) and some other mechanism we haven't thought of yet or all of them together or any combination of the above.' Test that if you can. But, now that you mention it, empty plate + hunger > heaping crap platter.ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
06:57 PM
6
06
57
PM
PDT
So you are not curious enough to come up with a hypothesis? You've got an empty plate, not a 1oz steak.Timbo
November 27, 2011
November
11
Nov
27
27
2011
04:56 PM
4
04
56
PM
PDT
Timbo, It is a bit strange that you talk about hypotheses when your position cannot even muster one.Joe
November 27, 2011
November
11
Nov
27
27
2011
04:11 PM
4
04
11
PM
PDT
Very well. My opinion is that matching attributes of a thing of unknown origin to the observed signature of design in countless artifacts of known origin is not necessarily the same endeavor as determining the mechanism of manufacture. You can invalidate a conclusion by showing its logical fallacies or contradictory evidence. That it leaves unanswered questions does not invalidate it. You're skipping past the evidence leading to conclusion to the unanswered questions. ID is not reverse engineering. Rather, it tells you what can be reverse engineered. That conclusion, with all of its unanswered questions, is preferable to a theory that endlessly adds new mechanisms, never applies them in any specific manner to what it proposes to explain, and is also preposterous and without any precedent. 1oz steak + hunger > heaping crap platter. Not trying to be rude, just trying to clearly isolate and illustrate the point. Plus, once you eat the tiny steak you can still look for some more nutrition. It's not the end. The #2 option is just more filling.ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
03:34 PM
3
03
34
PM
PDT
I'm interested in your opinion.Timbo
November 27, 2011
November
11
Nov
27
27
2011
03:15 PM
3
03
15
PM
PDT
I pity the frustrated soul who wrote the FAQ that no one reads.ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
03:11 PM
3
03
11
PM
PDT
An explanation would be nice, let alone a more detailed one. Science works by making a hypothesis and then modelling that. Can you even come up with a hypothesis that can then be modelled and tested?Timbo
November 27, 2011
November
11
Nov
27
27
2011
03:10 PM
3
03
10
PM
PDT
Petrushka,
The question of whether evolution is sufficient is purely a question of the attributes of the landscape.
I'll go with that.
So it’s between an explanation that is sufficient depending on the landscape (and the landscape is amenable to being studied), and an explanation that is nothing at all and has no prospects for research.
Again, this bizarre reasoning that the potential for future research is better than accuracy. I'd want to know the truth even if that meant no prospects for research. I'd love to hear how or why detecting design would bring research to a screeching halt. It sounds clever until you scratch your head and realizes that it has no basis in reality and in fact nullifies several other fields of science. Looking for a natural explanation if its existence is not a historical reality does provide infinite potential for research. It's like looking for the wreck of a ship that never existed. As long as the funding holds up the search never ends. Except for the funding part, explain again how that's better?ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
03:08 PM
3
03
08
PM
PDT
Timbo,
In my view, whether something is designed or not is ultimately a rather boring question. I need to know how and why. Don’t you?
I won't hold my breath for "Intelligent Design - The Motion Picture" either. A more detailed explanation would be nice. I'd like that too. But an accurate observation with no explanation is better than a really bad explanation. Sort of like knowing that arsenic is bad for you without knowing why is better than ten inaccurate reasons why it's good for you. Let me boil that down a little more: accurate is better than inaccurate. More is not always better. I'd rather eat a one-ounce steak than a heaping platter of crap, even if it leaves me hungry. How do you not see that?ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
02:59 PM
2
02
59
PM
PDT
Please, share with us the details of the largest landscape traversed. Otherwise all the abstract terminology in the world amounts to nothing. That is what it is, by the way, it's purely abstract, floating ideas with no concrete implementation.ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
02:49 PM
2
02
49
PM
PDT
ScottAndrews2, accepting that your first sentence is correct, do you actually have an alternative explanation? Because this is a site about an alternative explanation I thought, but for some reason most of the posts are actually engaged in what you complain about: that is attacking another explanation. You yourself, put a lot of time into attacking evolution. You do not believe the evolution that is observed acting today is capable of producing the biological diversity we see in the world. You think that evolution can only produce "insignificant" changes (I think that is the word you have used, but forgive me if I am wrong). But I don't believe you have ever laid out your explanation. How do you think the significant changes are carried out? Saying they were "designed" doesn't explain how. If I said to my friend, "how did you make that beautiful gratin?" and he said "I designed it", I would be none the wiser. If he said that he took some potatoes and par-boiled them, then sliced then very thin, and that placed them in a layer with just the sides overlapping, then placed some knobs of butter on them and then another layer of potatoes and then some cream and then baked it at 450 for 10 minutes then turned it down to 350 for 40 minutes, I would have useful information. In my view, whether something is designed or not is ultimately a rather boring question. I need to know how and why. Don't you? As I understand Petrushka, it is impossible to design a protein that works without evolving it. This is because there are so many different combinations that are possible and no way of knowing which ones are good beforehand. So I would just like to know if you have any thoughts on how the designer might have done it? Or do you believe the designer is omniscient?Timbo
November 27, 2011
November
11
Nov
27
27
2011
02:33 PM
2
02
33
PM
PDT
OK, the characteristics of the landscape determines whether evolution can traverse it. That's a given. the argument is not about whether evolution works, but about whether the landscape supports incremental change. We've known that since around 1940, when the landscape metaphor was first described. All the other arguments about probability are rubbish.Petrushka
November 27, 2011
November
11
Nov
27
27
2011
10:17 AM
10
10
17
AM
PDT
Umm your GA has a goal if "It is driven by the landscape of pronounceability,". If it was NOT so driven it would never produce any 10 letter words.Joe
November 27, 2011
November
11
Nov
27
27
2011
07:45 AM
7
07
45
AM
PDT
My program demonstrates the effects of connectability in landscapes, because it runs in several different languages with exactly the same code. The only difference is in how easy it is to move around with small steps. Some languages have spelling rules that make words and pronounceable syllables close together, and other languages are sparse. So the program models smooth and rugged landscapes.Petrushka
November 27, 2011
November
11
Nov
27
27
2011
07:44 AM
7
07
44
AM
PDT
Cannot be built incrementally via blind and undirected chemical processes. If you cannot grasp that then you do not belong here.Joe
November 27, 2011
November
11
Nov
27
27
2011
07:41 AM
7
07
41
AM
PDT
Having coded GAs that do something at least one ID denizen said was impossible -- produce 10 letter words approximately a billion times faster than a random search -- I have some basis for arguing that your central point is false. The question of whether evolution is sufficient is purely a question of the attributes of the landscape. and that landscape is being explored by researchers like Lenski and Thornton. So it's between an explanation that is sufficient depending on the landscape (and the landscape is amenable to being studied), and an explanation that is nothing at all and has no prospects for research. Your best guy in this debate openly admits that directed evolution may be required in order to design. That says something. I'll point out that my program has no target and will just as frequently create pronounceable non-words as it will produce dictionary words. It is driven by the landscape of pronounceability, not a dictionary. It does not produce the same output from the same starting point in multiple trials.Petrushka
November 27, 2011
November
11
Nov
27
27
2011
07:38 AM
7
07
38
AM
PDT
In what reality is an alternate explanation even required in order to dismiss a poor, inadequate one? How odd. Even without the faintest clue of how the functions of proteins could be encoded in DNA, the observation that it is in fact function encoded in symbolic language cannot be poofed away. So we don't know how to encode it? Okay, we don't know. From that rock-solid evidence of intelligent agency you make the leap to A) we don't know to encode it so it must be impossible, and then B) having illogically ruled out intelligent agency, spontaneous self-organization is the answer requires stalwart allegiance to an ideology. This is especially noteworthy because while you rule out one because the mechanism can't be explained, you're perfectly content to wait for a check in the mail from the other. When someone asserts principles of logic and then applies them selectively, even if that means discarding highly relevant evidence, it gives away that the underlying motivation is anything but an intent to follow the evidence where it leads.ScottAndrews2
November 27, 2011
November
11
Nov
27
27
2011
07:19 AM
7
07
19
AM
PDT
There must not be a replication function. Replicators must replicate, really replicate. If they replicate better, because they have create better functional information to replicate, they will. No need for “points” or enything measured.
That is utterly confusing, I described an agent with a neural network that allows it to interact with the environment, and with a system that allows it to replicate at a rate that is variable and dependent on how it interacts with the environment. Now you tell me that it can't include a function - a part of its coding - that allows it to replicate, it must 'really' replicate'? Earlier you said this:
The replicators can be programmed any way that is considered appropriate, and the rules of random variations in them can be set as appropriate.
Just so long as it isn't programmed to replicate !!! I described something that was within the constraints you imposed, now you object. Why is that? Now you said this about an operating system:
It is designed, but not to demonstrate anything about NS. That’s enough.
Yes - it is designed to manage access to system resources and prevent - by design - software from copying its self and consuming resources in an unrestricted way. An OS is designed, in part, to prevent software doing the things you want to test for. I guess this is why you are so keen to argue for it as a good environment eh! ;) I said this, and you replied:
We are talking about how to model biology and an OS has very little in common with the natural environments we actually observe – it is not a good analog for the thing we are trying to model
It is impossible to model biology. That is out of question. Modeling biology would mean to model protein space and biological reproduction, metabolism, and so on. It’s simply impossible.
You are getting very confused I think! We are talking about environments, the conversation was about whether a computer operating system was a good analog of real world environments. We were not discussing creating a model of a replicator that matched biological replicators exactly, as you yourself suggested here:
The replicators can be programmed any way that is considered appropriate, and the rules of random variations in them can be set as appropriate.
What matters here is that we use an environment that is a good analog of the environment that real replicators exist in - we are testing the idea that replication with variety in nature can generate fsci because that variety leads to different replication rates. Just picking an environment that was designed for something totally different is not enough because you may be picking an environment that excludes features that are found in real environments, and which contribute to the generation of fsci. It would be like testing an hypothesis about the development of wings by picking an environment where aerodynamics and gravity have no analog. Wings would not develop, but that would not prove that wings cannot develop in nature, just that you picked an environment in which wings could not develop, or indeed one where the idea of 'flight' was meaningless.
Why? Nothing can be biased by design if those who designed it were not aware of the purpose (in this case the development of new functions). That’s why the environment must be blind to the experiment. Exactly my point.
I agree that it can be biased by intent but a 'blind' environment can still be biased by design - like a well designed OS it can be designed to prevent unrestricted copying and consumption of memory and compute cycles - OS designers are not blind to replication, computer viruses are a big problem. Look at it this way, you want to test something about rabbits breeding, so you pick a 'blind' environment. After dropping the rabbits into the middle of the pacific and observing them drown you conclude that rabbits cannot breed.
In general, all forms of blinding have the purpose to avoid that a cognitive bias in the experimenters can alter the results.
blinding is used to prevent accidental communication of experimental intent between an experimenter and a subject. I don't think you can apply this concept to the way computer models are constructed - you are blinding yourself to aspects of the system you are actually trying to understand. In this instance one thing that needs to be understood is if there are any properties of the environment that biological replicators exist in that contribute to the generation of fsci. Picking a test environment that lacks these features (because you are blind to them) and concluding that natural selection cannot generate fsci would be to pull the wool over your own eyes - just as dropping rabbits into the pacific does not demonstrate that rabbits cannot breed.GCUGreyArea
November 27, 2011
November
11
Nov
27
27
2011
01:41 AM
1
01
41
AM
PDT
Since gpuccio claims that protein domain coding sequences are irreducible and cannot be built incrementally, I eagerly await the demonstration of an alternative method.Petrushka
November 27, 2011
November
11
Nov
27
27
2011
12:52 AM
12
12
52
AM
PDT
I eagerly await any design advocate who proposes a method of biological design that does not include variation, fecundity and selection. Particularly since this is how pharmaceutical engineering is done. An approach that could produce de novo protein domains from first principles rather than using evolution would be most welcome.Petrushka
November 27, 2011
November
11
Nov
27
27
2011
12:22 AM
12
12
22
AM
PDT
Oh My, then I am happy to await GP's response - for that is an argument in which you are surely to prevail. ;)Upright BiPed
November 26, 2011
November
11
Nov
26
26
2011
11:10 PM
11
11
10
PM
PDT
Firstly, instead of trying to toss incoherent insults at me
I wasn't addressing you. If I had been addressing you I would have posted under your post, and it would have been indented under your post.Petrushka
November 26, 2011
November
11
Nov
26
26
2011
07:30 PM
7
07
30
PM
PDT
Petrushka: I suppose the Designer likes His games played on a level field. Why not? Or there is more than one designer. There are many reasonable possibilities.gpuccio
November 26, 2011
November
11
Nov
26
26
2011
02:48 AM
2
02
48
AM
PDT
Petrushka,
In the software industry your design theory would be known as vaporware.
Firstly, instead of trying to toss incoherent insults at me, its is the evidence you need to address. This is Empiricism 101. When the evidence itself indicates that your objections are based upon formalities which you just take for granted, then it is the evidence you must address - otherwise, your objections simply fail. Do you understand? Secondly, I did not give you a "design theory". I made the evidence-based argument that the transfer of recorded information from the genome is semiotic, just like every other observed transfer of recorded information. That transfer has specific physical dynamics. Those dynamics are coherently understood, and that understanding creates a short list of four physical requirements (entailments) which are observed in such transfer - without exception. Each of those entailments are satisfied in the obervation of genetic information transfer, which consequently confirms its semiotic state. I have asked you to attack those physical dynamics in earnest, but you have chosen to simply continue taking them for granted, and you maintain your objections as if such evidence didn't matter. In fact, you said as much explicitly. In the presence of such a disregard for observable evidence, I am not sure what else can be said. You seem to be operating under the belief that being non-responsive to physical evidence is a valid form of empirical methodology. It isn't.Upright BiPed
November 25, 2011
November
11
Nov
25
25
2011
03:59 PM
3
03
59
PM
PDT
suppose I’m most curious why the Designer gave disease causing organisms the ability to evolve around and even subvert the immune system.
Perhaps that is due to generations of random effects on our immune system.Joe
November 25, 2011
November
11
Nov
25
25
2011
02:53 PM
2
02
53
PM
PDT
1 2 3 4 5 6 9

Leave a Reply