Can God be a useful "scientific" hypothesis? Yes

[Meerkat_SK5]

INTRODUCTION

In this article, I am going to be showing how God can be a useful scientific hypothesis in the fields of biology and biochemistry. This means that I will be showing how we can test whether a Divine intelligence has and continues to guide evolution, which would make this an improvement of the Modern synthesis rather than a separate explanation. However, this time it will NOT be about trying to prove that God guided evolution or prove God exists at all. It will also not be about whether God used common design or common descent. Instead, it’s all about finding out whether there is a Divine intelligence guiding evolution.

The God of classical theism is generally defined as “Necessary” and “Personal”, which sums up the totality of God’s attributes. What I mean by “Personal” is a common designer that can expressly manifest the immaterial properties of digital information and apply it to the physical-chemical world. “Necessity” means an intelligent designer that needs to exist in order to guide evolution. I made this inference based on…

1. The comparison between the genome and computers that have been shown to be more than just metaphorical but literal. For instance, researchers created a biotech version of an e-reader, with one of the highest storage capacity to date. Church_Science_12.pdf (harvard.edu)

2. The high similarity between the genetic text and human written language. For instance, Hubert P. Yockey:

“It is important to understand that we are not reasoning by analogy. The sequence hypothesis [that the exact order of symbols records the information] applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical.”
Microsoft Word - 2005-11-16_Hubert_Yockey_reply_to_FTE_amicus.doc (ncse.ngo)

3. The required assistance of the biochemist to obtain meaningful results within prebiotic experiments:

“…After all, it is not easy to see what replaced the flasks, pipettes and stir bars of a chemistry lab during prebiotic evolution, let alone the hands of the chemist who performed the manipulations. (And yes, most of us are not comfortable with the idea of divine intervention in this context.)" [emphasis added]

Prebiotic chemistry and human intervention | Nature Communications

EVOLUTION BY DIVINE INTELLIGENCE

Falsification

The best example of a successful experiment demonstrating, in a legitimate way, how lifelike molecules can emerge from prebiotic chemistry evolution is the Miller-Urey experiments. Researchers have provided a potentially useful criteria for the amount of observer interference acceptable, which should make sure biochemist successfully disprove the hypothesis completely (Thaxton 1984 p.99-110; Jekel 1985). Thaxton, C.B., Bradley, W.L. & Olsen, R.L. (1984) The Mystery of Life’s Origin, Philosophical Library Inc., New York.

The best example of a successful experiment demonstrating, in a legitimate way, how random mutations can potentially produce new traits more often is Lenski’s world-famous long-term experiment on E. coli. In order to successfully disprove the hypothesis, the Lenski experiment needs to produce results similar to what we see from a protein engineer, such as this study:

The intelligent design of evolution | Molecular Systems Biology (embopress.org)

Verification

When the observer chooses a particular set of natural conditions to work on, the observer has to first test and determine whether or not life can be developed within that condition without interference. Then, the observer must perform the same experiment with the same set of natural conditions following the previous one but impose unrealistic interference in the second round of experiments.

The combined outcomes of these experiments would produce evidence for the hypothesis. This is because even though the experimenter who guides evolution within each natural condition is finite and contingent, there could not be any conscious life before simple life emerged, hence why we have to include the first experiment to support the “necessary” attribute of this common designer .

The Phage-assisted continuous evolution (with the apt acronym “PACE”) experiment and In-vitro selection experiments from prebiotic simulations would be the best approaches to confirm the hypothesis. The protein design experiment I suggested above could also be a good approach as long as researchers follow the procedure laid out here.

Furthermore, since we are dealing with a flawless designer, the discovery of optimality within so-called design flaws would also potentially confirm the hypothesis.

For instance, we should find many more examples of designs that are optimized to fit a particular environment better than another organism from alleged suboptimal design flaws.

We should find more trade-offs between conflicting design goals from allegedly bad designs that are considered to be poorly constructed for its perceived function.

We should find a positive function for sinister designs that seem to only bring harm and degeneration upon that organism or to other organisms. [Just ask for examples]

WHY GOD IS USEFUL

This hypothesis should encourage researchers to do and explain the following things…

1. Re-examine the alleged design flaws to find optimality in organisms.

2. Expand and test different environmental conditions to potentially find a new law of nature.

3. Find out whether there is a divine intelligence guiding evolution or not.

4. Find out how God guided evolution (I.e. common design versus common descent).

5. Explain the origin of life and species.

One more thing, feel free to just copy your previous objections from other topics and paste them here, if you feel they still have not been addressed under this topic. This will save everybody time and effort.

[John_Harshman]

@Meerkat_SK5

What I mean by “Personal” is a common designer that can expressly manifest the immaterial properties of digital information and apply it to the physical-chemical world. “Necessity” means an intelligent designer that needs to exist in order to guide evolution.

That isn’t what “Personal” and “Necessary” mean either in theology or in ordinary language. Might I suggest that instead of just re-writing while retaining most of your old text, you also re-think what you mean to say?

Most of what follows is a rehash of your former claims, without even an acknowledgment that those claims have been taken apart, or at least contested, the last several times you made them.

@Meerkat_SK5

In order to successfully disprove the hypothesis

What hypothesis? You haven’t stated a hypothesis. There’s no way to test an unstated hypothesis.

@Meerkat_SK5

One more thing , feel free to just copy your previous objections from other topics and paste them here, if you feel they still have not been addressed under this topic. This will save everybody time and effort.

No, it will save you time and effort while costing other people time and effort. And why repost objections when you ignored them the first time? Einstein’s definition of insanity would seem to apply.

[swamidass (S. Joshua Swamidass)]

DNA is not a computer code…

Just like the silicon in sand, it can be used by humans to store digital data. That doesn’t make it computer code.

[Meerkat_SK5]

@swamidass

DNA is not a computer code…

I know. I never said it was. I mentioned Church and his colleague’s experiment to give credence to the idea that the medium (i.e. the genome) in which the genetic text is stored is literally similar to human computers or were you referring to the Genome when you said this? If so, then you can omit it since it is not necessary for the argument to hold.

[Timothy_Horton]

What would falsify your “hypothesis”? If it’s not falsifiable even in principle it’s not science.

[swamidass (S. Joshua Swamidass)]

@Meerkat_SK5

@swamidass

DNA is not a computer code…

I know. I never said it was.

I think you did…

@Meerkat_SK5

The comparison between the genome and computers that have been shown to be more than just metaphorical but literal.

You are saying the comparison between genomes and computers is not merely a metaphor, but that it is literally not just about similarities, as if this some how provides a case for design.

There are good reasons to wonder if God created all things, as I believe. This is not one of those good reasons.

[Meerkat_SK5]

@John_Harshman

That isn’t what “Personal” and “Necessary” mean either in theology or in ordinary language.

Can you give me a source for this?

@John_Harshman

Might I suggest that instead of just re-writing while retaining most of your old text, you also re-think what you mean to say?

Sure, let me rephrase this then to be more clear. When I say “personal” I just mean an intelligent designer like us where we have “certain capacities or attributes such as reason, morality, consciousness or self-consciousness, and being a part of a culturally established form of social relations…” according to wikipedia.

“Necessary” just means a being that needs to exist in order for something to come about no matter what the situation, which would only include our life under this topic.

@John_Harshman

Most of what follows is a rehash of your former claims, without even an acknowledgment that those claims have been taken apart, or at least contested, the last several times you made them.

Yes and I made the proper adjustments accordingly. If I have not in your eyes, then it is just an issue of not explaining well enough rather than on the merits.

@John_Harshman

No, it will save you time and effort while costing other people time and effort. And why repost objections when you ignored them the first time? Einstein’s definition of insanity would seem to apply.

Again, its not an issue in regards to the merits of the my case but just how I explain or convey my case in a way that is comprehensible to others, which was what I was referring to when I said users can copy and paste old objections if they feel it was not addressed. I will just explain it a different way for them if need be.

@John_Harshman

What hypothesis? You haven’t stated a hypothesis. There’s no way to test an unstated hypothesis.

A Divine intelligence formed the first life and the anatomical structures of multicellular life from the physical-chemical world and continues to maintain these structures by ensuring organisms fit the environments it occupies to survive, reproduce, and fill the biosphere.

In other words, God guides the entire process of evolution.

[Meerkat_SK5]

Wikipedia:

“a theory is falsifiable (or refutable ) if it is contradicted by possible observations —i.e., by any observations that can be described in the language of the theory, which must have a conventional empirical interpretation.[A] Thus the theory must be about scientific evidence and it must prohibit some (but not all) possible observations. For example, the statement “All swans are white” is falsifiable because “Here is a black swan” contradicts it.”

An intelligent designer must exist to guide all life on earth. This is falsifiable because “Here is an experiment showing life could have evolved by a unguided process” would contradict it. How can you say this is still unfalsifiable despite it being formulated in almost the exact same way that Karl Popper has suggested?

[Meerkat_SK5]

@swamidass

You are saying the comparison between genomes and computers is not merely a metaphor, but that it is literally not just about similarities, as if this some how provides a case for design.

No, I was not trying to make the case for intelligent design based on that particular experiment. What I was ultimately trying to argue is that IF there is a designer we can infer ,based on that experiment and observations, that this designer probably operates in the same manner that we do. In other words, it was an educated guess that would exclude other possible designers, such as aliens or unconscious computer-like designers from potentially explaining those experiments and observations.

[Puck_Mendelssohn]

@Meerkat_SK5

Yes and I made the proper adjustments accordingly. If I have not in your eyes, then it is just an issue of not explaining well enough rather than on the merits.

And there lies the problem. You are under the impression that you have got hold of an insight that is so penetrating and wonderful that others are blinded by its brilliance, and fail to comprehend it. When they object, you mistake their withering substantive criticisms as a failure on their part to understand the genius of the thing.

Alas, this isn’t how things actually are. The many objections offered by others here are substantive; they go to the merits; and they are fatal. You need to discard this whole notion and start completely fresh on something worthwhile.

[John_Harshman]

@Meerkat_SK5

When I say “personal” I just mean an intelligent designer like us where we have “certain capacities or attributes such as reason, morality, consciousness or self-consciousness, and being a part of a culturally established form of social relations…” according to wikipedia.

Much better than what you said originally.

@Meerkat_SK5

“Necessary” just means a being that needs to exist in order for something to come about no matter what the situation, which would only include our life under this topic.

That isn’t quite what theologians mean. You could ask them.

@Meerkat_SK5

Yes and I made the proper adjustments accordingly. If I have not in your eyes, then it is just an issue of not explaining well enough rather than on the merits.

How do you know that?

@Meerkat_SK5

A Divine intelligence formed the first life and the anatomical structures of multicellular life from the physical-chemical world and continues to maintain these structures by ensuring organisms fit the environments it occupies to survive, reproduce, and fill the biosphere.

In other words, God guides the entire process of evolution.

I doubt you actually mean what you have said here, and you really mean something untestable. But if we take your words as given, then the hypothesis is falsified by the simple observation that most species are extinct, the great majority without descendants. The structures have not been maintained. In fact, at the end of the Permian, somewhere around 90% of marine species disappeared. How well did they fit their environments then?

[Timothy_Horton]

@Meerkat_SK5

This is falsifiable because “Here is an experiment showing life could have evolved by a unguided process” would contradict it.

No this wouldn’t falsify the hypothesis because your hypothesized God could always be using supernatural powers which exactly mimic unguided natural processes. Your hypothesis is still not falsifiable and still not science.

[Mercer (John Mercer)]

@Meerkat_SK5

@John_Harshman

What hypothesis? You haven’t stated a hypothesis. There’s no way to test an unstated hypothesis.

A Divine intelligence formed the first life and the anatomical structures of multicellular life from the physical-chemical world and continues to maintain these structures by ensuring organisms fit the environments it occupies to survive, reproduce, and fill the biosphere.

What is the mechanism by which the Divine Intelligence forms and maintains? Without any mechanism, it’s not a scientific hypothesis.

[Tim]

@John_Harshman

@Meerkat_SK5

“Necessary” just means a being that needs to exist in order for something to come about no matter what the situation, which would only include our life under this topic.

That isn’t quite what theologians mean. You could ask them.

I take you mean “necessary” in this sense:

https://plato.stanford.edu/entries/god-necessary-being/

[Michael_Okoko]

@Meerkat_SK5

This means that I will be showing how we can test whether a Divine intelligence has and continues to guide evolution,

Can you apply your test to the evolution of SARS-CoV-2 and HIV-1 M, which are responsible for two current pandemic? Let’s know if this divine intelligence is currently guiding the evolution of both deadly viruses.

@Meerkat_SK5

The comparison between the genome and computers that have been shown to be more than just metaphorical but literal. For instance, researchers created a biotech version of an e-reader, with one of the highest storage capacity to date. Church_Science_12.pdf (harvard.edu)

Computers have a wide array of functions, unlike genomes which just sit inside cells waiting to be transcribed or replicated. Stop getting it twisted.

@Meerkat_SK5

The required assistance of the biochemist to obtain meaningful results within prebiotic experiments:

Every experiment requires experimenter interference as I have pointed out before. By your logic, a divine intelligence is responsible for all cancers because investigators can interfere more or less with in vitro or in vivo carcinogenesis experiments.

@Meerkat_SK5

“…After all, it is not easy to see what replaced the flasks, pipettes and stir bars of a chemistry lab during prebiotic evolution, let alone the hands of the chemist who performed the manipulations. (And yes, most of us are not comfortable with the idea of divine intervention in this context.)" [emphasis added]

Modifying this quote:

@Meerkat_SK5

“…After all, it is not easy to see what replaced the flasks, pipettes and stir bars of a chemistry lab during [tumorigenesis studies], let alone the hands of the [medical oncologist] who performed the manipulations. (And yes, most of us are not comfortable with the idea of divine intervention in this context.)" [emphasis added]

See how it sounds?

@Meerkat_SK5

The best example of a successful experiment demonstrating, in a legitimate way, how lifelike molecules can emerge from prebiotic chemistry evolution is the Miller-Urey experiments.

There have been other successful experiments. Keep up with the field.

@Meerkat_SK5

The best example of a successful experiment demonstrating, in a legitimate way, how random mutations can potentially produce new traits more often is Lenski’s world-famous long-term experiment on E. coli. In order to successfully disprove the hypothesis, the Lenski experiment needs to produce results similar to what we see from a protein engineer, such as this study:

@Meerkat_SK5

In order to successfully disprove the hypothesis, the Lenski experiment needs to produce results similar to what we see from a protein engineer, such as this study:

The intelligent design of evolution | Molecular Systems Biology (embopress.org)

The press article you linked discussed the findings from this study:

Designed divergent evolution of enzyme function - PubMed

After going through the study abstract:

Abstract

It is generally believed that proteins with promiscuous functions divergently evolved to acquire higher specificity and activity, and that this process was highly dependent on the ability of proteins to alter their functions with a small number of amino acid substitutions (plasticity). The application of this theory of divergent molecular evolution to promiscuous enzymes may allow us to design enzymes with more specificity and higher activity. Many structural and biochemical analyses have identified the active or binding site residues important for functional plasticity (plasticity residues). To understand how these residues contribute to molecular evolution, and thereby formulate a design methodology, plasticity residues were probed in the active site of the promiscuous sesquiterpene synthase gamma-humulene synthase. Identified plasticity residues were systematically recombined based on a mathematical model in order to construct novel terpene synthases, each catalysing the synthesis of one or a few very different sesquiterpenes. Here we present the construction of seven specific and active synthases that use different reaction pathways to produce the specific and very different products. Creation of these enzymes demonstrates the feasibility of exploiting the underlying evolvability of this scaffold, and provides evidence that rational approaches based on these ideas are useful for enzyme design.

it became obvious you either didn’t read it or failed to understand what you read. Those protein engineers simply copied a natural strategy for protein evolution, called divergent molecular evolution, where a promiscuous enzyme evolves into a more highly specific and active form. This in no way resembles what Lenski hoped to achieve with the LTEE.

@Meerkat_SK5

Verification

When the observer chooses a particular set of natural conditions to work on, the observer has to first test and determine whether or not life can be developed within that condition without interference. Then, the observer must perform the same experiment with the same set of natural conditions following the previous one but impose unrealistic interference in the second round of experiments.

Lets modify this as well:

When the observer chooses a particular set of natural conditions to work on, the observer has to first test and determine whether or not [tumors can develop] within that condition without interference. Then, the observer must perform the same experiment with the same set of natural conditions following the previous one but impose unrealistic interference in the second round of experiments.
[/quote]

Whether we sparingly or heavily interfere with tumorigenesis experiments, it says nothing about whether an intelligent mind was involved in the process. That applies as well to OoL experiments.

@Meerkat_SK5

The combined outcomes of these experiments would produce evidence for the hypothesis. This is because even though the experimenter who guides evolution within each natural condition is finite and contingent, there could not be any conscious life before simple life emerged, hence why we have to include the first experiment to support the “necessary” attribute of this common designer .

By this logic God is the cause of all cancers because finite investigators guide the induction of tumors in their experiments.

@Meerkat_SK5

Furthermore, since we are dealing with a flawless designer, the discovery of optimality within so-called design flaws would also potentially confirm the hypothesis.

For instance, we should find many more examples of designs that are optimized to fit a particular environment better than another organism from alleged suboptimal design flaws.

We should find more trade-offs between conflicting design goals from allegedly bad designs that are considered to be poorly constructed for its perceived function.

We should find a positive function for sinister designs that seem to only bring harm and degeneration upon that organism or to other organisms. [Just ask for examples]

GULOP stares hard at you.

@Meerkat_SK5

One more thing , feel free to just copy your previous objections from other topics and paste them here, if you feel they still have not been addressed under this topic. This will save everybody time and effort.

Obviously you did not learn much from your previous exchanges. This might turn out to be another waste of time.

[Roy (30-year veteran)]

@Meerkat_SK5

2. The high similarity between the genetic text and human written language. For instance, Hubert P. Yockey:

“It is important to understand that we are not reasoning by analogy. The sequence hypothesis [that the exact order of symbols records the information] applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical.”
Microsoft Word - 2005-11-16_Hubert_Yockey_reply_to_FTE_amicus.doc (ncse.ngo)

That text does not occur in that reference.

You are lying about your sources again.

One more thing , feel free to just copy your previous objections from other topics and paste them here, if you feel they still have not been addressed under this topic. This will save everybody time and effort.

I am saving time and effort by starting by checking one of your references, noting that you’re still deliberately misquoting and misrepresenting your references, and not bothering to read what else you say.

[John_Harshman]

@Roy

@Meerkat_SK5

“It is important to understand that we are not reasoning by analogy. The sequence hypothesis [that the exact order of symbols records the information] applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical.”

Microsoft Word - 2005-11-16_Hubert_Yockey_reply_to_FTE_amicus.doc (ncse.ngo)

That text does not occur in that reference.

But it does apparently appear in another paper by Yockey: Hubert P. Yockey, 1981. Self Organization Origin of Life Scenarios and Information Theory. Journal of Theoretical Biology, 91:13-31. One may suspect that @Meerkat_SK5 didn’t read that one either.

I say “apparently” because I so far can’t find the actual full text anywhere on the web, only quotes.

[Tim]

@Michael_Okoko

@Meerkat_SK5

The comparison between the genome and computers that have been shown to be more than just metaphorical but literal. For instance, researchers created a biotech version of an e-reader, with one of the highest storage capacity to date. Church_Science_12.pdf (harvard.edu)

Computers have a wide array of functions, unlike genomes which just sit inside cells waiting to be transcribed or replicated. Stop getting it twisted.

@Meerkat_SK5 you have made your “more than just metaphorical but literal” claim 1, 2, 3 times previously by my count.

I am getting heartily sick of your argumentum ad nauseam.

This is particularly true, as this claim is false, as I’ve already pointed out to you.

Church et al no more demonstrate that the genome is a computer than that a Wham!'s Greatest Hits CD or a book of Shakespearean sonnets are. That genomes, optical disks and paper-and-ink can be used as storage media does not demonstrate that they are computers.

I would further point out that Church’s “biotech version of an e-reader” cannot interpret a biological genome any more than a living organism’s processes can interpret the results of Church’s device, rendering this comparison still weaker.

I would suggest that the last thing this world needs is yet another apologist trying to make ‘scientific’ claims whilst being unwilling and/or unable to come to grips with the underlying scientific research.

If you want to make the world a better place, then become an aid worker.

[Tim]

@John_Harshman

But it does apparently appear in another paper by Yockey: Hubert P. Yockey, 1981. Self Organization Origin of Life Scenarios and Information Theory. Journal of Theoretical Biology, 91:13-31. One may suspect that @Meerkat_SK5 didn’t read that one either.

Given that this quote appears in a number of apologetic sources, most notably God’s Undertaker by John C. Lennox, this seems to be a safe bet.

Parrot_SK5 rides again.

[Roy (30-year veteran)]

@John_Harshman

But it does apparently appear in another paper by Yockey: Hubert P. Yockey, 1981. Self Organization Origin of Life Scenarios and Information Theory. Journal of Theoretical Biology, 91:13-31.

Not with the bit in [square brackets] - that seems to have originated in (and been copied repeatedly from) an article by Thaxton from 2002.

I have no idea if the addition reflects the original paper, which (as you say) doesn’t appear to be available - and nor does @Meerkat_SK5. Given it’s origin, I doubt it.