# Can God be a useful "scientific" hypothesis? Yes

**URL:** <https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699>\
**Category:** Side Conversation\
**Tags:** Science, Design\
**Created:** [May 9, 2021, 10:15pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699 "2021-05-09T22:15:33Z")\
**Posts on this page:** 20\
**Page:** 5

<div class="post-metadata">

**Author:** ![nwrickert](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/nwrickert/32/810_2.png) [@nwrickert](https://discourse.peacefulscience.org/u/nwrickert)\
**Post date:** [May 21, 2021, 3:39am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/82 "2021-05-21T03:39:44Z")

</div>

> [@Meerkat\_SK5](#):
>
> For example, if a Divine Intelligence is guiding evolution, the logical consequence is that this being is all-powerful, all knowing, and all-good. We can test this by looking for an underlying positive benefit to the species or population or other species within sinister designs that seem to bring harm and degeneration.

A logical consequence is an abstract thing. How do we test for that?

Yes, people can have opinions about that. But how do we come to a clear unambiguous decision?

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [May 21, 2021, 4:09am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/83 "2021-05-21T04:09:28Z")

</div>

> [@Meerkat\_SK5](#):
>
> For example, if a Divine Intelligence is guiding evolution, the logical consequence is that this being is all-powerful, all knowing, and all-good.

None of those are logical conclusions.

> [@Meerkat\_SK5](#):
>
> We can test this by looking for an underlying positive benefit to the species or population or other species within sinister designs that seem to bring harm and degeneration.

Much too vague to test. What do you even mean by “harm and degeneration”?

> [@Meerkat\_SK5](#):
>
> We can also test this by examining whether the designer had a different design goal in mind that achieves maximum efficiency from bad designs.

And that’s more word salad. This is hopeless.

And for the fifth time (though I may have lost count): how do you explain the end-Permian mass extinction? Is everything really for the best in this best of all possible worlds?

> [@Meerkat\_SK5](#):
>
> But now, I’m starting to think it is not necessary but only recommended at best. What do you think?

What isn’t necessary?

---

<div class="post-metadata">

**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [May 21, 2021, 4:47am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/84 "2021-05-21T04:47:20Z")

</div>

> [@Meerkat\_SK5](#):
>
> Well first off, I am not obligated to support a claim you made.

No @Meerkat_SK5, and _more importantly_ **I was not asking you to.**

I _do_ expect you to substantiate your own claims, such as this one:

> [@Meerkat\_SK5](#):
>
> I would agree if we were talking about a Deistic God, but a theistic God is Personal, which would allow us to constrain the hypothesis within the context of human behavior, as I explained before.

Your claim that we can “constrain the hypothesis within the context of human behavior” (i) is unsubstantiated, and (ii) (as I pointed out) appears to be contradicted by the doctrine of Divine Ineffability (according to which doctrine God is beyond description and comprehension).

And this one:

> [@Meerkat\_SK5](#):
>
> That is in regards to God’s relationship with mankind NOT with his relationship with nature and the animal kingdom.

This claim is also unsubstantiated. And, given that I’ve seen Theodicy (part of “that” theology) discussed in connection to the animal kingdom, I also find it highly dubious.

> [@Meerkat\_SK5](#):
>
> You are the one who is claiming theology suggests God behaves in a mysterious way before and after the inception of humans without even providing an article or source to support your contention . I merely responded to your assertion.

As should be obvious to any _reasonable_ reader, I was only bringing up those theological issues _in order to impeach your claims_.

> [@Meerkat\_SK5](#):
>
> Secondly, I have actually indirectly responded to this objection in a different post.

Given the shear volume of your blather on this thread, that is a _thoroughly unhelpful claim_!

Link to the post please and, given how lengthy your posts generally are, indication of which part of that post you are refering to.

> [@Meerkat\_SK5](#):
>
> For instance, “God is ineffable because the structure of his intrinsic nature is infinite” according to an article I looked up on the subject of Ineffability. However, this actually makes it more testable. For instance…
> 
> 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](https://en.wiktionary.org/wiki/conventional) [empirical interpretation](https://en.wikipedia.org/wiki/Evidence-based_practice).[[A]](https://en.wikipedia.org/wiki/Falsifiability#cite_note-thematerialrequirement-1) Thus the theory must be about [scientific evidence](https://en.wikipedia.org/wiki/Scientific_evidence) and it must prohibit some (but not all) possible observations. For example, the statement “All [swans](https://en.wikipedia.org/wiki/Swan) 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?

I have three problems with this ‘reply’ (and I use the word so loosely, to the point that it has fallen apart in a heap on the floor):

1. This appears to be _irrelevant_ to the issue I was raising.

2. It appears to be utter balderdash, as I believe has been pointed out to you by numerous others.

3. “How can you say this is still unfalsifiable …?” The answer is simple: I **never stated this**. I’d probably agree with the claim of unfalsifiability (see 2 above), but have not _myself_ actually articulated it. Which makes it strange that you ask this question.

---

<div class="post-metadata">

**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [May 21, 2021, 9:04am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/85 "2021-05-21T09:04:54Z")

</div>

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > Experiments involving natural selection say nothing about God-driven or human-driven evolution, because these experiments are meant to test hypotheses about natural selection _itself_ .
> 
> I agree, but it has nothing to do with natural selection but so-called “random” mutations. I was arguing that we can test whether it was non-random or not.

By “random mutations”, evolutionary biologists mean that mutations occur regardless of their consequences. It is one of the most supported claims in evolutionary biology.

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > Second, precisely define what you mean by “new genetic information”.
> 
> I don’t know. My definition of it would probably be described in this article that I can’t access it fully:

You don’t know what “new genetic information” means, but you claimed it wasn’t gotten in Lenski’s LTEE. You then go on to cite a paper, which doesn’t define what it meant by “new genetic information”. Aren’t you confused?

The paper authors seem confused as well. Their _E_. _coli_ lines evolved the cit+ trait, just like in Lenski’s LTEE, but they deny its new. They made a conclusion contrary to their data.

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > Your misunderstanding still remains because the Lenski’s LTEE and PACE experiments are concerned with processes that drove evolutionary change _after_ the earliest lifeforms arose. In other words, these experiments depend on the existence of preexisting life forms, so they cannot show you how those life forms arose in the first place.
> 
> Well first off, there is no established consensus on the definition of life and life could have arisen outside our biosphere under conditions as-yet unknown to us.

The definition of life is completely irrelevant to our conversation, so is the issue of whether life originated in other places. This response further confirms you don’t really understand the things you say.

Remember you claimed the LTEE and PACE experiments (PACEE from now on) can be used to simulate the origin of the first cells and I pointed out that this wasn’t possible because both experiments depend on the existence of already existing lifeforms like the _E_. _coli_ (which both use). Biological evolutionary experiments in general are only concerned with how life changed or changes following the origin of the earliest forms from organic matter. The origin of prebiotic life is completely out of the scope of modern evolutionary biology and its experimental methods like LTEE and PACEE.

> [@Meerkat\_SK5](#):
>
> Secondly, the intelligent designer is a life form as well in this context. So we can potentially show whether or not a God guided evolution, which is my point. Again, I am not suggesting I know there is a Divine intelligence guiding evolution or how he did it. Instead, I am arguing that we can scientifically test to see whether or not those claims are true.

If you feel you could scientifically test for God-driven evolution, go ahead and develop your methodology, validate and publish a peer-reviewed report of its performance, accuracy and other important details. Stop trying to use unsuitable experiments like LTEEs and PACEEs.

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > Furthermore, Lenski’s LTEE and PACE experiments have nothing to offer on the evolution of body plans because they use microbes which lack body plans.
> 
> I agree. I was arguing that we can potentially use God to explain the origin of body plans. Sorry for the confusion.

You are free to postulate God is responsible for body plans, but that hypothesis is unscientific until you put into a format that is testable.

> [@Meerkat\_SK5](#):
>
> We can test this by looking for an underlying positive benefit to the species or population or other species within sinister designs that seem to bring harm and degeneration.

We have been through this already. If this is one way to falsify your hypothesis of God-driven evolution, then your hypothesis is falsified because of the inactivity of GULOP in our genome.

In the absence of dietary vitamin C, we and other organisms who need it to survive die. If God drove our evolution to that point, then there is nothing good or loving about him. In contrast, if our evolution was unguided, the formation of GULO makes complete sense.

---

<div class="post-metadata">

**Author:** ![Roy](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/roy/32/3799_2.png) [@Roy](https://discourse.peacefulscience.org/u/Roy)\
**Post date:** [May 21, 2021, 11:08am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/86 "2021-05-21T11:08:56Z")

</div>

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > > [@Meerkat\_SK5](#):
> > >
> > > I was referring to major body plans and new genetic information being produced.
> > 
> > …  
> > Second, precisely define what you mean by “new genetic information”.
> 
> I don’t know. My definition of it would probably be described in this article that I can’t access it fully:
> 
> [Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA - PubMed (nih.gov)](https://pubmed.ncbi.nlm.nih.gov/26833416/)

So you _ **literally** _ don’t know what you’re talking about.

A few side points:

- You _should_ be able to access it fully, since it’s free access ([here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4800869/)).
- The only definition they provide for “new genetic information” (novel gene function) _is_ on the page you linked to.
- That definition is completely at odds with the Yockey quote you’re so fond of using.

---

<div class="post-metadata">

**Author:** ![Faizal\_Ali](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/faizal_ali/32/12416_2.png) [@Faizal\_Ali](https://discourse.peacefulscience.org/u/Faizal_Ali)\
**Post date:** [May 21, 2021, 6:56pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/87 "2021-05-21T18:56:17Z")

</div>

> [@Meerkat\_SK5](#):
>
> I don’t know. My definition of it would probably be described in this article that I can’t access it fully:

This may be the most perfect pair of sentences ever written by a creationist. The existence of this entire thread has now been justified.

---

<div class="post-metadata">

**Author:** ![Meerkat\_SK5](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/meerkat_sk5/32/11938_2.png) [@Meerkat\_SK5](https://discourse.peacefulscience.org/u/Meerkat_SK5)\
**Post date:** [May 22, 2021, 3:32am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/88 "2021-05-22T03:32:45Z")

</div>

> [@John\_Harshman](#):
>
> Much too vague to test. What do you even mean by “harm and degeneration”?

**Benevolent Design Hypothesis**

This explanation entails that sinister designs that seem to bring harm and degeneration have an underlying positive benefit to the species or population or other species. The positive benefit would involve maintaining or enhancing either survival or reproductive capabilities, or the ability to fit different environments.

We can test this by studying nociceptive sensitizations in animals. For example, injury in animals can lead to long-lasting distress, whereby frequent exposure to pain-producing stimuli causes a progressively amplified response well after the injury has healed. This phenomenon has been referred to as “nociceptive sensitization.” Biomedical researchers have long viewed nociceptive sensitization as maladaptive because, in humans, it is associated with anxiety.

However, researchers have studied nociceptive sensitizations in squids and concluded that heightened sensitivity to pain helps these creatures evade predation. Since nociceptive sensitization is pervasive, it likely serves a similar benefit among other animals, as well.

[Nociceptive Sensitization Reduces Predation Risk: Current Biology (cell.com)](https://www.cell.com/current-biology/fulltext/S0960-9822(14)00335-2)

We can also test this by studying carnivores or predators. They often are responsible for producing mass extinctions within herbivore populations. However, studies show how animal death and carnivorous activity play a necessary role in preventing the fixation of harmful viruses within populations that would potentially cause a herbivore population to become extinct.

[Predators indirectly control vector-borne disease: linking predator-prey and host-pathogen models - PubMed (nih.gov)](https://pubmed.ncbi.nlm.nih.gov/19474078/)

**Design Tradeoff hypothesis**

This explanation involves the situational decision to deliberately diminish or lose one quality, quantity, or property of a design in return for gains in other aspects. In other words, one thing increases, and another must decrease.

We can test this by examining those bad designs from an engineer’s perspective and look for other qualities that may have increased. This would show the designer had a different goal in mind for that design then originally thought. As one professional engineer has suggested:

“…there are practical limitations to the width and length of vehicles, and heavier bumpers can reduce gas mileage and the maneuverability of the vehicle. The reality is that virtually every feature in a designed structure such as a car is a compromise between competing objectives: safety, comfort, aesthetics, cost, ease of manufacturing, ease of repair (an objective often overlooked), stability, speed and acceleration, and so forth. Generally, not every desirable objective can be met”.

[Intelligent Design and Design Flaws: Jury-Rigged Design in Nature? (jefflindsay.com)](https://www.jefflindsay.com/DesignFlaws.shtml)

There are examples of this found in nature already:  
[Glycolytic strategy as a tradeoff between energy yield and protein cost | PNAS](https://www.pnas.org/content/110/24/10039.short?rss=1)

[An optimal bronchial tree may be dangerous - PubMed (nih.gov)](https://pubmed.ncbi.nlm.nih.gov/14961120/)

> [@John\_Harshman](#):
>
> And for the fifth time (though I may have lost count): how do you explain the end-Permian mass extinction? Is everything really for the best in this best of all possible worlds?

Simple, mass extinctions allows for a surge in biodiversity:

“Analysis of the fossil record of microbes, algae, fungi, protists, plants, and animals shows that the diversity of both marine and continental life increased exponentially since the end of the Precambrian.”

More importantly, Biodiversity benefits all life:

[Biodiversity enhances the multitrophic control of arthropod herbivory | Science Advances (sciencemag.org)](https://advances.sciencemag.org/content/6/45/eabb6603.full)

[Science Journals — AAAS (sciencemag.org)](https://advances.sciencemag.org/content/advances/6/45/eaba1715.full.pdf)

> [@John\_Harshman](#):
>
> What isn’t necessary?

Arguing that previous observations suggest that if there is a Divine intelligence that guided evolution, it probably operates and mimicks human behavior rather than natural law. In other words, it’s offering justification for a rational God for the operation of nature.

> [@Tim](#):
>
> Your claim that we can “constrain the hypothesis within the context of human behavior” (i) is unsubstantiated, and (ii) (as I pointed out) appears to be contradicted by the doctrine of Divine Ineffability (according to which doctrine God is beyond description and comprehension).

The evidence suggests that if there is a Divine intelligence that guided evolution, it mimics the behavior of humans NOT natural law:

“ _There is nothing in the physico-chemical world [apart from life] that remotely resembles reactions being determined by a sequence [the genome] and codes between sequences [the genetic code]. The existence of a genome and the genetic code divides living organisms from non-living matter._ ” (Computers and Chemistry, 24 (2000) 105-123)

“ _Only the measurement of information in the genome and the transcription of information from DNA to RNA to protein are mathematically identical to the measurement of information and the transcription of written language._ ”

[Microsoft Word - 2005-11-16\_Hubert\_Yockey\_reply\_to\_FTE\_amicus.doc (ncse.ngo)](https://ncse.ngo/files/pub/legal/kitzmiller/2005-10_amicus_briefs/2005-11-16_Hubert_Yockey_reply_to_FTE_amicus.pdf)

“ _For experiments aimed at demonstrating chemically more complex processes, **such as multistep syntheses mimicking biochemical pathways or genetic replication,** repeated interventions by the experimentalist have been necessary_ .”

[Prebiotic chemistry and human intervention | Nature Communications](https://www.nature.com/articles/s41467-018-07219-5)

> [@Tim](#):
>
> This claim is also unsubstantiated. And, given that I’ve seen Theodicy (part of “that” theology) discussed in connection to the animal kingdom, I also find it highly dubious.

No, this is your claim that you have not substantiated. You need to provide the article you are suggesting that makes this connection so I can properly address it. BTW, I was not trying to argue for the Christian God under this topic. The God of classical theism is the subject of this discussion.

> [@Tim](#):
>
> This appears to be _irrelevant_ to the issue I was raising.

Yes, my mistake. It was the wrong example. If God is infinite or non-contingent, then we would not get flawed designs in nature. That’s all I was suggesting.

> [@Michael\_Okoko](#):
>
> By “random mutations”, evolutionary biologists mean that mutations occur regardless of their consequences.

Yes, that’s one of the definitions of “random” mutations I am going off on but what is your point by telling me this.

> [@Michael\_Okoko](#):
>
> You don’t know what “new genetic information” means, but you claimed it wasn’t gotten in Lenski’s LTEE. You then go on to cite a paper, which doesn’t define what it meant by “new genetic information”. Aren’t you confused?

Alright, here is my definition. New genetic information would be a new transporter, a new promoter, or a new metabolic pathway.

> [@Michael\_Okoko](#):
>
> If you feel you could scientifically test for God-driven evolution, go ahead and develop your methodology, validate and publish a peer-reviewed report of its performance, accuracy and other important details. Stop trying to use unsuitable experiments like LTEEs and PACEEs.

Sure, that’s fine. The experimental procedure I laid out before was mainly there to show that my hypothesis is testable at least in principle, which was my overall objective under this topic.

---

<div class="post-metadata">

**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [May 22, 2021, 4:31am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/89 "2021-05-22T04:31:50Z")

</div>

> [@Meerkat\_SK5](#):
>
> > [@Tim](#):
> >
> > Your claim that we can “constrain the hypothesis within the context of human behavior” (i) is unsubstantiated, and (ii) (as I pointed out) appears to be contradicted by the doctrine of Divine Ineffability (according to which doctrine God is beyond description and comprehension).
> 
> The evidence suggests that if there is a Divine intelligence that guided evolution, it mimics the behavior of humans NOT natural law:

1. Even if your statement _were_ true, it does not “constrain the hypothesis within the context of human behavior” – even if the purported Divine Intelligence _does_ mimic human behavior **does not** mean that they _must_ on all occasions mimic it.

2. Your spammed quote-mines **do not** provide evidence for your claim. They do not in fact make any mention of anything resembling a “Divine intelligence” at all. I’m fairly certain that the authors whose work you are abusing would be _thoroughly confused_ as to how you think their statements support your claim.

3. [Addendum] Your second Yockey quote is pulled _out of context_ from a section whose stated purpose is to **directly contradict** your claim that the material supports a (Divine) Intelligence:

> **Point Two: Information theory is not concerned with “patterns of intelligence”**

So @Meerkat_SK5, you have merely succeeded in turning one unsubstatiated claim into _two unsubstantiated claims_. The original one being:

> [@Meerkat\_SK5](#):
>
> I would agree if we were talking about a Deistic God, but a theistic God is Personal, which would allow us to constrain the hypothesis within the context of human behavior, as I explained before.

> [@Meerkat\_SK5](#):
>
> > [@Tim](#):
> >
> > This claim is also unsubstantiated. And, given that I’ve seen Theodicy (part of “that” theology) discussed in connection to the animal kingdom, I also find it highly dubious.
> 
> No, this is your claim that you have not substantiated.

I merely mentioned that to explain _why_ I found your claim to be “dubious”. It is therefore peripheral to the discussion. I read it a week or two back in connection to the question of whether animals go to heaven, and did not bookmark it. The fact that I cannot immediately produce it _does not change_ the fact that the following statement (which I was referring to above) **is unsubstantiated** :

> [@Meerkat\_SK5](#):
>
> That is in regards to God’s relationship with mankind NOT with his relationship with nature and the animal kingdom.

[Addendum: I could not find the original article I read, but [this article](https://www.jstor.org/stable/20014122) seems to cover similar territory.]

So @Meerkat_SK5, you now have three unsubstantiated claims at issue with me (and I’m sure more with other members).

Do I need to point out to you that any _further_ attempts to ‘substantiate’ these claims about a “Divine intelligence” and theology, with quote-mines from scientific sources _that make no mention of such issues_, will not only not be acceptable, but will be treated with outright derision? They are simply a _non sequitor_.

In any case this all seems to be approaching the stage of _flogging a dead horse_. If ‘God can be a useful scientific hypothesis’ (which I strongly doubt, and would suspect most theist scientists would doubt as well), it would appear (from the failure of this lengthy discussion) that @Meerkat_SK5 is not the right person to advance the claim.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [May 22, 2021, 1:01pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/90 "2021-05-22T13:01:25Z")

</div>

> [@Meerkat\_SK5](#):
>
> This explanation entails that sinister designs that seem to bring harm and degeneration have an underlying positive benefit to the species or population or other species. The positive benefit would involve maintaining or enhancing either survival or reproductive capabilities, or the ability to fit different environments.

Notice that you didn’t even answer my question. And this covers too much ground to be useful, especially when the benefit may accrue to “other species”. Further, what you mention here would seem to be similar to what’s expected from natural selection. How would you tell the difference?

> [@Meerkat\_SK5](#):
>
> They often are responsible for producing mass extinctions within herbivore populations.

Apparently you don’t know what mass extinction is. Or even what extinction is. No, what you’re talking about here is death. Death is not extinction, and extinction is not mass extinction. Beyond that, your model is confused. If predation were merely good for the predator, wouldn’t that also fit your model? If it’s bad for the harmful virus, you’re free to ignore that. As long as you can find something good for somebody, somewhere, you declare victory.

> [@Meerkat\_SK5](#):
>
> This explanation involves the situational decision to deliberately diminish or lose one quality, quantity, or property of a design in return for gains in other aspects.

Why do you say “deliberately”? Again, wouldn’t natural selection produce a similar result?

> [@Meerkat\_SK5](#):
>
> Simple, mass extinctions allows for a surge in biodiversity:

Only in recovery from a major loss in biodiversity. Now of course that may benefit some of the survivors, but you ignore most species, the ones that die, to concentrate on the few survivors. Once again, your model is vague enough to accommodate anything, and so is useless.

Please stop with the naked quotes from unattributed sources and inappropriate citations of papers you have not read.

> [@Meerkat\_SK5](#):
>
> Arguing that previous observations suggest that if there is a Divine intelligence that guided evolution, it probably operates and mimicks human behavior rather than natural law. In other words, it’s offering justification for a rational God for the operation of nature.

More word salad. Please stop.

---

<div class="post-metadata">

**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [May 22, 2021, 1:42pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/91 "2021-05-22T13:42:27Z")

</div>

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > You don’t know what “new genetic information” means, but you claimed it wasn’t gotten in Lenski’s LTEE. You then go on to cite a paper, which doesn’t define what it meant by “new genetic information”. Aren’t you confused?
> 
> Alright, here is my definition. New genetic information would be a new transporter, a new promoter, or a new metabolic pathway.

Excellent. Let’s recap the line of thought leading to this point. It started with this:

> [@Michael\_Okoko](#):
>
> > [@Meerkat\_SK5](#):
> >
> > Again, I admitted that the experimental procedure I laid out would not and could not apply to current ongoing evolution because humans and animals exist now and the goal of creating and developing the life forms today is achieved.
> 
> How do you know (with empirical evidence) there was any such goal of creating living things? More so, if the goal of the creation and development of life forms has been achieved, kindly explain the contradictory observation that life forms are still evolving?

You then clarified what you meant by that goal being achieved:

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > More so, if the goal of the creation and development of life forms has been achieved, kindly explain the contradictory observation that life forms are still evolving?
> 
> I was referring to major body plans and new genetic information being produced.

Thus, its clear that you think new genetic information cannot be produced in extant organisms. I further pressed you to clarify what you meant by new genetic information and you replied as follows:

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > You don’t know what “new genetic information” means, but you claimed it wasn’t gotten in Lenski’s LTEE. You then go on to cite a paper, which doesn’t define what it meant by “new genetic information”. Aren’t you confused?
> 
> Alright, here is my definition. New genetic information would be a new transporter, a new promoter, or a new metabolic pathway.

To summarize, you believe new genetic information cannot be produced because God has achieved his creative goals and you even went ahead to specify what you meant by new genetic information. Thus, if I find examples of genes getting new promoters or new metabolic pathways evolving, then it falsifies your claim that evolution was or is guided by God, because if it was guided the production of new genetic information should have ceased (according to you).

In the first case, the emergence of a new promoter, Lenski’s LTEE provides a classic example. The diagram below beautifully refutes your claims, because it shows how the _citT_ (citrate/succinate antiporter) gene was given a new promoter.

 ![nihms402795f2](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/9/9b437c67891016a260060517e971a4ebf12f12c9.jpeg)

Prior to its duplication ( **fig a** ), the _citT_ gene (blue segment, fig a) could only be expressed in the absence of oxygen. See those arrows which go down and take a turn to the right, they indicate promoter regions which are currently directing DNA transcription into RNA and for this context _in the presence of oxygen_. The promoter sequence of _citT_, if it were shown wouldn’t have had any arrow attached to it, because it would be bound by a repressor protein, preventing the transcription of genes downstream to it. This repressor protein is active in the presence of oxygen.

Lenski’s LTEE rolls on and one day, boom!, that _citT_ gene is duplicated (alongside bits and pieces of its neighbours, **fig b** ). This duplication event places _citT_ downstream of the _rnk_ promoter which is before the _rnk_ gene (pink segment in fig a). The _rnk_ promoter can be bound by RNA polymerase _in the presence of oxygen_ to initiate transcription. The new location of _citT_ allows it to be co-transcribed with bits of the _rnk_ gene under oxygen-rich conditions.

If what I wrote is unclear, just know that what happened here is akin to transferring an employee (_citT_) to work with a “new” boss (_rnk_ promoter) who has a different work schedule. See the source paper below for more details

> **[Genomic Analysis of a Key Innovation in an Experimental E. coli Population](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3461117/)**
>
> Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit\[+\] ), in an experimental...

For the second case, the emergence of new metabolic pathways, I present to you the PCP degradation pathway which newly emerged in the bacterium called _Sphingobium chlorophenolicum_. PCP is a man-made chemical which is quite toxic to living organisms including microbes. Serendipitously, the aforementioned bacterium was found to facilitate its degradation by some researchers many decades ago. Molecular investigations revealed the presence of a new, but still inefficient, metabolic or biotransformative pathway the bacterium evolved to degrade PCP. This is the pathway:

 ![Screenshot_20210522-140904](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/b/b43ac4739b5231d0b451849b96fc0d9992c4f1ce.png)

Some of the enzymes in the pathways were derived from HGT events (transfer of genetic material between bacteria without their asexual mode of reproduction), while others were derived from its common ancestor with a sister _Sphingobium_ species.

> **[The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into...](https://academic.oup.com/gbe/article/4/2/184/556989)**
>
> Abstract. Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicu

An aside. In both examples I provided, we see a similar pattern in the evolution of new traits, which is inefficiency of those new traits post-actualization. When a trait is newly evolved. In Lenski’s LTEE, the earliest mutants with the Cit+ trait, utilized citrate quite poorly. The trait had to undergo further refinement, and it did through further mutations, enabling better utility of citrate as a carbon source. The PCP degradation pathway is currently in the “actualization” stage (just like the earliest CitT+ strains) because it is highly inefficient at degrading PCP, but will need to undergo refinement either in nature or in Copley’s (or maybe my) lab 😉

With these examples, your version of the hypothesis of God-driven evolution is falsified, because new genetic information to use citrate under oxic conditions and degrade PCP via a new metabolic pathway were produced, even though it should have stopped according to you.

---

<div class="post-metadata">

**Author:** ![Meerkat\_SK5](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/meerkat_sk5/32/11938_2.png) [@Meerkat\_SK5](https://discourse.peacefulscience.org/u/Meerkat_SK5)\
**Post date:** [May 22, 2021, 7:18pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/92 "2021-05-22T19:18:13Z")

</div>

> [@Tim](#):
>
> - Even if your statement _were_ true, it does not “constrain the hypothesis within the context of human behavior” – even if the purported Divine Intelligence _does_ mimic human behavior **does not** mean that they _must_ on all occasions mimic it.

I already explained why it does in previous posts because God is supposed to be bound by his own nature. For instance, the attributes of God have to work in accordance with each other in a logically consistent manner because he is who he is (i.e. the law of identity) and cannot not be who he is at the same time (i.e. law of non-contradiction).

This means that God cannot make himself cease to exist because this would conflict with him being a necessary being. God cannot make a square circle because this would conflict with his omniscience. God cannot lie because it would conflict with his omnibenevolence. God cannot make a rock so heavy that he cannot lift because it would conflict with his omni-potency.

God cannot create and develop a world that does not have God intimately involved in the process every step of the way because it would conflict with his “Personal’ nature. Thus, God must be true to “all” his attributes, because to do otherwise would be to deny his own self.

> [@Tim](#):
>
> Your spammed quote-mines **do not** provide evidence for your claim. They do not in fact make any mention of anything resembling a “Divine intelligence” at all. I’m fairly certain that the authors whose work you are abusing would be _thoroughly confused_ as to how you think their statements support your claim.

I agree, I was not trying to provide evidence that a Divine intelligence guided evolution. Instead, I was arguing that IF there is a God guiding evolution, we have good reasons to believe that this causal agent is _probably_ Personal or relatable like us rather than mysterious. Thus, we can test it in accordance to human behavior by allowing human intervention to take place in experiments and have it count as potential evidence for or against the hypothesis. In other words, it was just an educated guess.

> [@Tim](#):
>
> [Addendum: I could not find the original article I read, but [this article](https://www.jstor.org/stable/20014122) seems to cover similar territory.]

I encourage you to read this article. It’s basically a response to your article:

[Where is God When Bad Things Happen? Why Natural Evil Must Exist (godandscience.org)](https://www.godandscience.org/apologetics/natural_evil_theodicity.html)

> [@John\_Harshman](#):
>
> Notice that you didn’t even answer my question.

What I mean by “harm and degeneration” is a feature of an organism that is designed to impede on that organism or other organisms’ ability to survive, reproduce, and fit an environmental niche.

> [@John\_Harshman](#):
>
> And this covers too much ground to be useful, especially when the benefit may accrue to “other species”.

I am not sure what you mean by this.

> [@John\_Harshman](#):
>
> Further, what you mention here would seem to be similar to what’s expected from natural selection. How would you tell the difference?

Correct, I made it very clear that this hypothesis is an improvement of the Modern synthesis or add-on to what we already know, which means this is not about natural selection but it is about random mutations being undirected. I am merely arguing that mutations was never really random. That’s pretty much it.

> [@John\_Harshman](#):
>
> Apparently you don’t know what mass extinction is. Or even what extinction is. No, what you’re talking about here is death. Death is not extinction, and extinction is not mass extinction. Beyond that, your model is confused. If predation were merely good for the predator, wouldn’t that also fit your model?

I guess I don’t know what your objection entails. Maybe you can pinpoint what exactly conflicts with my hypothesis or at least tell me why you think your objection is not based on a definition of species that I have not agreed upon yet?

> [@Michael\_Okoko](#):
>
> With these examples, your version of the hypothesis of God-driven evolution is falsified, because new genetic information to use citrate under oxic conditions and degrade PCP via a new metabolic pathway were produced, even though it should have stopped according to you.

The trait and the genetic arrangement may be novel, but \*the mechanisms, genes, promoters, and metabolic pathways are NOT novel.\*I am going to have to refer you to Hugh Ross to explain further:

"Well, it isn’t utterly new for _E. coli_ to utilize citrate as a primary food source. _E. coli_ utilizes citrate via a citrate fermentation cycle under anaerobic conditions just fine. Under anaerobic conditions, the bacteria produce a citrate/succinate antiporter that allows transport of citrate from the environment into the bacteria. Also, as mentioned before, citrate utilization by _E. coli_ , although rare under aerobic conditions, has been observed before. In those instances, the acquisition of this novel function, like many acquisitions of new traits in microbes, is through the horizontal (from bug to bug) transfer of small circular pieces of DNA (known as plasmids) encoding new functional genes. They can grow aerobically on citrate because they produce a citrate transporter encoded by the plasmid DNA and regulated by plasmid promoters. The citrate transporter allows citrate uptake, and citrate is metabolized via the citric acid cycle.

But that’s not what’s going on in the Cit+ _E. coli_ in the LTEE. It’s not horizontal gene transfer. It’s not due to contamination of the cultures. The citrate transporter is not being co-opted from another system. It’s not exaptation. All Cit+ bacteria in the Ara-3 lineage harbor a ~3 kb tandem repeat of a portion of the endogenous _citT_ operon, resulting in the introduction of additional _citT_ genes in the _E. coli_ genome. (See figure below.) The critical (but not sole) changes hinge on the duplication of an endogenous promoter ( _rnk_ ) that is active under aerobic conditions, the duplication of the _citT_ gene, encoding a citrate transporter, and the juxtaposition of these elements in tandem repeats. The tandem copies of the _citT_ gene are no longer under the regulatory control of the endogenous _citG/citT_ promoter but are under the regulation of copies of an endogenous, downstream _rnk_ promoter. The _rnk-citT_ element allows the production of a citrate transporter under aerobic conditions, and this allows Cit+ _E. coli_ to utilize the citrate in the growth media via mechanisms and metabolic pathways already present.

 ![](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/b/bf55b1167648a13bcb93aa621219c7f64dd39376.png)

The Ara-3 Cit+ bacteria utilize citrate through the preexisting metabolic pathway (citric acid cycle). The ability to do so is facilitated by production of citrate/succinate antiporters from a preexisting gene sequence that is now expressed under aerobic conditions by simply switching the promoter that controls its expression. It is a novel trait, but the mechanisms underlying it are not innovations of new genes or new promoters. The Cit+ bacteria did _not_ evolve a new transporter, a new promoter, or a new metabolic pathway."

> [@Michael\_Okoko](#):
>
> We have been through this already. If this is one way to falsify your hypothesis of God-driven evolution, then your hypothesis is falsified because of the inactivity of GULOP in our genome.

And I told you already that this does not falsify the hypothesis.

---

<div class="post-metadata">

**Author:** ![Witchdoc](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/witchdoc/32/10610_2.png) [@Witchdoc](https://discourse.peacefulscience.org/u/Witchdoc)\
**Post date:** [May 22, 2021, 9:03pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/93 "2021-05-22T21:03:10Z")

</div>

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > We have been through this already. If this is one way to falsify your hypothesis of God-driven evolution, then your hypothesis is falsified because of the inactivity of GULOP in our genome.
> 
> And I told you already that this does not falsify the hypothesis.

Of course it does.

You said God behaves like humans.

A human wouldn’t design humans with a broken vitamin C gene so that we get scurvy, or a broken uricase gene so that we get gout.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [May 22, 2021, 10:05pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/94 "2021-05-22T22:05:16Z")

</div>

> [@Meerkat\_SK5](#):
>
> **Benevolent Design Hypothesis**
> 
> This explanation entails that sinister designs that seem to bring harm and degeneration have an underlying positive benefit to the species or population or other species.

Scientific hypotheses are not mere explanations. A scientific “Benevolent Design Hypothesis” would involve a mechanism underlying design, not any explanation or justification for it.

You appear to have multiple misunderstandings about the scientific method.

> [@Meerkat\_SK5](#):
>
> We can test this by studying nociceptive sensitizations in animals.

No, we really can’t, because your hypothesis is in no way mechanistic.

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > By “random mutations”, evolutionary biologists mean that mutations occur regardless of their consequences.
> 
> Yes, that’s one of the definitions of “random” mutations I am going off on but what is your point by telling me this.

It’s the only biologically relevant definition.

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > You don’t know what “new genetic information” means, but you claimed it wasn’t gotten in Lenski’s LTEE. You then go on to cite a paper, which doesn’t define what it meant by “new genetic information”. Aren’t you confused?
> 
> Alright, here is my definition. New genetic information would be a new transporter, a new promoter, or a new metabolic pathway.

Why aren’t the new antibody sequences generated by mutation + selection during the immune response new information?

---

<div class="post-metadata">

**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [May 22, 2021, 10:56pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/95 "2021-05-22T22:56:27Z")

</div>

> [@Meerkat\_SK5](#):
>
> > [@Michael\_Okoko](#):
> >
> > With these examples, your version of the hypothesis of God-driven evolution is falsified, because new genetic information to use citrate under oxic conditions and degrade PCP via a new metabolic pathway were produced, even though it should have stopped according to you.
> 
> The trait and the genetic arrangement may be novel, but \*the mechanisms, genes, promoters, and metabolic pathways are NOT novel

I am glad you figured out how evolution could operate ( **Addendum: on further reading of your comment, its obvious you blindly echoed Ross’ erroneous claim about no new promoter emerging in Lenski’s LTEE** ). Don’t forget evolution works like a tinkerer: it takes preexisting parts (ranging from biomolecules to organs) and modifies or rearranges them to get novel features and it uses a collection of well-known mechanisms like gene duplications, fusions, HGT, etcetera to achieve these novel changes. Furthermore, I showed you a new metabolic pathway which evolved in _S_. _chlorophenolicum_ that allowed it to degrade PCP (a pesticide that did not exist until humans created it).

Merely bringing this up shows you don’t understand how evolution operates, but I hope you do now.

> [@Meerkat\_SK5](#):
>
> I am going to have to refer you to Hugh Ross to explain further:

Oh well, let’s see:

> [@Meerkat\_SK5](#):
>
> Well, it isn’t utterly new for _E. coli_ to utilize citrate as a primary food source

This is completely irrelevant, because no one denies this. What’s relevant is that several _E_. _coli_ lines in the LTEE evolved the ability to use citrate as a carbon source **under oxic conditions** , by expressing the formerly suppressed citrate/succinate antiporter.

> [@Meerkat\_SK5](#):
>
> The citrate transporter is not being co-opted from another system. It’s not exaptation.

The citrate/succinate antiporter wasn’t co-opted, but the _rnk_ promoter was.

> [@Meerkat\_SK5](#):
>
> The critical (but not sole) changes hinge on the duplication of an endogenous promoter ( _rnk_ ) that is active under aerobic conditions…

This is false in two ways.

First, this is temporally false because the earliest Cit+ mutants had no duplicate _rnk_ promoters, but were still able to uptake citrate. Later mutants, however, had duplicate _rnk_ promoters.

Second, in a non-temporal sense this is false because whether we have two or more _rnk - citT_ modules/duplicates, the CitT+ trait _only_ depends on the **duplication of the _citT_ gene** and its **relocation downstream of the _rnk_ promoter** (or any other promoter that works under oxic conditions). In one of the CitT mutants, the duplicate _citT_ was placed downstream of the _rna_ promoter, not the _rnk_ promoter.

> [@Meerkat\_SK5](#):
>
> The Ara-3 Cit+ bacteria utilize citrate through the preexisting metabolic pathway (citric acid cycle).

No surprise here. Its how evolution works. Using what you have at present to make or do something new. The citric acid cycle itself was once new as well, built from other parts by the hands of that tinkerer called evolution.

In addition, it goes beyond just using catabolizing citrate in the citric acid cycle, but now doing so _under oxygen-rich_ conditions. That’s novel.

> [@Meerkat\_SK5](#):
>
> It is a novel trait, but the mechanisms underlying it are not innovations of new genes or new promoters.

Again no surprise here at how evolution could operate. The frequency at which Ross emphasizes this point about using preexisting parts and/or mechanisms to generate evolutionary novelties as if it were a counterpoint suggests the man, like Meerkat, does not understand how evolution works.

> [@Meerkat\_SK5](#):
>
> The Cit+ bacteria did _not_ evolve a new transporter, a new promoter, or a new metabolic pathway."

Which is just horrendously false with regards to a getting a new promoter. The Cit+ mutants evolved a new promoter for their _citT_ gene to be transcribed under oxic conditions.

In addition, its quite easy to evolve new promoters from scratch. Happy reading:

[https://www.nature.com/articles/s41467-018-04026-w](https://www.nature.com/articles/s41467-018-04026-w)

Word of advice. Stop getting your biology knowledge from an astronomer. If a blind man leads a blind man, both will fall into a pit.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [May 22, 2021, 11:01pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/96 "2021-05-22T23:01:03Z")

</div>

> [@Meerkat\_SK5](#):
>
> What I mean by “harm and degeneration” is a feature of an organism that is designed to impede on that organism or other organisms’ ability to survive, reproduce, and fit an environmental niche.

Then you are mixing up two quite different things. Any feature that’s “designed” to impede that organism’s abilities would be evidence of God, though a malevolent one. Natural selection works to improve those abilities, not degrade them. A feature that impedes other organisms abilities (such as the teeth and claws of predators) would be an improvement for the predator, and would likewise be evidence of natural selection. Now, Darwin famously said that any feature of an organism that existed solely for the benefit of a different species would argue against his theory. Maybe you should concentrate on finding those. But as it is, your ideas are confused and useless.

> [@Meerkat\_SK5](#):
>
> I am not sure what you mean by this.

I mean that you have constructed a mishmash of many different sorts of phenomena, real examples of which either do not exist or are consistent with unguided evolution.

> [@Meerkat\_SK5](#):
>
> Correct, I made it very clear that this hypothesis is an improvement of the Modern synthesis or add-on to what we already know, which means this is not about natural selection but it is about random mutations being undirected. I am merely arguing that mutations was never really random. That’s pretty much it.

You made none of this clear at all. And it has nothing to do with whether mutations are directed. You have so far said nothing at all about mutations. Also, I don’t know if you were following the argument about what “random” means, but it isn’t clear that you know what you mean by it.

> [@Meerkat\_SK5](#):
>
> I guess I don’t know what your objection entails. Maybe you can pinpoint what exactly conflicts with my hypothesis or at least tell me why you think your objection is not based on a definition of species that I have not agreed upon yet?

I don’t think you know what anything I’m saying means. No, this has nothing whatsoever to do with the definition of “species”. I’m pointing out that your hypothesis is so all-encompassing that anything at all would count as evidence for it in your mind. As long as some event or feature benefits some individual, or species, or segment of the biosphere, you count it as evidence for design. This is hopeless.

---

<div class="post-metadata">

**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [May 22, 2021, 11:03pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/97 "2021-05-22T23:03:52Z")

</div>

> [@Meerkat\_SK5](#):
>
> And I told you already that this does not falsify the hypothesis

There is no significant benefit to losing GULO activity. If you don’t get vitamin C in your diet or via supplements, you will die. That’s a massive design flaw.

---

<div class="post-metadata">

**Author:** ![Tim](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/tim/32/9381_2.png) [@Tim](https://discourse.peacefulscience.org/u/Tim)\
**Post date:** [May 23, 2021, 4:20am UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/98 "2021-05-23T04:20:30Z")

</div>

> [@Meerkat\_SK5](#):
>
> I already explained why it does in previous posts because God is supposed to be bound by his own nature.

You have not in fact demonstrated that _it is in God’s nature_ to mimic humanity, merely _claimed_ (not particularly convincingly) that he _does_ (at times) mimic humanity.

> [@Meerkat\_SK5](#):
>
> Instead, I was arguing that IF there is a God guiding evolution, we have good reasons to believe that this causal agent is _probably_ Personal or relatable like us rather than mysterious.

Given that _neither_ of your _quote-mined_ passages were talking about God “mimic[ing] the behavior of humans”, and in fact one of them was quote-mined from a section explicitly stating that “Information theory is not concerned with ‘patterns of intelligence’”, they do not constitute “good reason” for this claim. They do not in fact constitute _any reason at all_ for accepting it.

> [@Meerkat\_SK5](#):
>
> I encourage you to read this article. It’s basically a response to your article:
> 
> [Where is God When Bad Things Happen? Why Natural Evil Must Exist (godandscience.org)](https://www.godandscience.org/apologetics/natural_evil_theodicity.html)

1. I offered the article as a _refutation_ of your claim that theodicy was unrelated to the animal kingdom, **not** because I accepted its claims.

2. In any case, why would I be interested in an article on the subject by Rich Deem, who (i) has no qualifications in theology, and (ii) is a professional creationism apologist (a group for which I have _zero_ confidence in the honesty of)?

---

<div class="post-metadata">

**Author:** ![Meerkat\_SK5](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/meerkat_sk5/32/11938_2.png) [@Meerkat\_SK5](https://discourse.peacefulscience.org/u/Meerkat_SK5)\
**Post date:** [May 24, 2021, 2:36pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/99 "2021-05-24T14:36:54Z")

</div>

Alright, I am going to bring some more clarity to what I am trying to argue. According to Ayala,

“Mutations are random or chance events because (i) they are rare exceptions to the fidelity of the process of DNA replication and because (ii) there is no way of knowing which gene will mutate in a particular cell or in a particular individual. However, the meaning of ‘random’ that is most significant for understanding the evolutionary process is (iii) that mutations are unoriented with respect to adaptation; they occur independently of whether or not they are beneficial or harmful to the organisms. Some are beneficial, most are not, and only the beneficial ones become incorporated in the organisms through natural selection.”

The central thesis I am trying to argue is that the “random” in mutations is an appearance.  
For instance, ever since the ENCODE results, numerous studies have revealed that most, if not all, of these non-coding regions play an important role in the accurate functioning of the DNA in regards to neutral mutations ([http://www.lncrnablog.com/](http://www.lncrnablog.com/)).

The vast majority of mutations in regions that do encode proteins but are deleterious appears to be fine-tuned to lower the risk of harmful genetic changes. For instance, mutations have been shown to be guided by both the physical properties of the genetic code and the need to preserve critical protein function.

[Evolution: are the monkeys’ typewriters rigged? | Royal Society Open Science (royalsocietypublishing.org)](https://royalsocietypublishing.org/doi/10.1098/rsos.140172)

Moreover, I argue that harmful mutations that do arise are regulated in a way that ensures the timely death of individuals so that resources are available for the young and preserve a balance between predator and prey populations because too many predators or prey can cause a collapse of the ecosystem.

[Species with a Large Impact on Community Structure | Learn Science at Scitable (nature.com)](https://www.nature.com/scitable/knowledge/library/species-with-a-large-impact-on-community-13240710/)

Lastly, I argue that beneficial mutations have not always been rare but directed. For instance, researchers performed a statistical study of the fossil record, using the origin and radiation of dicynodonts and sauropod dinosaurs as case studies to understand what caused the rapid increase in biodiversity for these dinosaur groups at specific points in history. They discovered that these animals did not show large biodiversity when they initially appeared on the scene. Instead, it took several million years before these two groups underwent radiation events. In both cases, bursts in biodiversity occurred after an extinction event. Thus, biological improvement was not connected with the first appearance of dicynodonts and sauropods that initiated an increase in biodiversity. Instead, the trigger appeared to be the extinction of other groups of organisms. [Just ask for reference]

Thus, I am saying that God has directed mutations over the course of history to either choose beneficial, neutral, or harmful mutations in order to guide evolution to improvement of either survival, reproductive abilities or to fit ecological niches.

I already I explained how we can theoretically test this additional mechanism to the evolutionary mechanism. So I will just move on and address everyone’s latest objections

> [@Witchdoc](#):
>
> A human wouldn’t design humans with a broken vitamin C gene so that we get scurvy, or a broken uricase gene so that we get gout.

The reason why falsifying my hypothesis this way is problematic is because it could be an example of Design Tradeoffs. This involves the situational decision to deliberately diminish or lose one quality, quantity, or property of a design in return for gains in other aspects. In other words, one thing increases, and another must decrease.

For example, Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) is the most abundant protein in nature that plays a crucial role in photosynthesis. However, the carbon fixation reaction happens gradually and inadequately. Moreover, rubisco can catalyze the reaction of oxygen with ribulose 1,5-bisphosphate to form unwanted compounds.

This seemingly inefficient enzyme has compelled researchers to focus their efforts on developing genetically engineered plants with better forms of rubisco that function with greater efficacy than those found in nature (Liu et al., 2010). As a result, genetically modified plants would boost food production around the world. Ellis wrote a commentary on this work, referring to it as “a superb example of unintelligent design” (Ellis, 2010).

However, previous research revealed that the difficulty of rubisco to discriminate between oxygen and carbon dioxide is not because of defective design, but instead stems from the inherent chemical nature of these two gases. To overcome this “confusion,” the enzyme slows down the carbon fixation reaction. Rubisco faces a trade-off between rate of reaction and discrimination between carbon dioxide and molecular oxygen (Tcherkez, et al. 2006). Moreover, in a response to Ellis’ commentary, Porter & Wollenweber (2010) argued that the efficiency of rubisco has no bearing on crop yields. [Just ask for references]

Thus, there could be different goals the designer had in mind or maybe there is an underlying function that may be found in the future like other psuedogenes.

> [@Mercer](#):
>
> Scientific hypotheses are not mere explanations. A scientific “Benevolent Design Hypothesis” would involve a mechanism underlying design, not any explanation or justification for it.

The mechanisms would be “directed” mutations and natural selection

> [@Mercer](#):
>
> Why aren’t the new antibody sequences generated by mutation + selection during the immune response new information?

According to a following study, “We hypothesized that the isolation of such mutants should be relatively easy, would follow the same genetic trajectory as that identified in the LTEE, and would utilize **information present on the chromosome and _not_ involve evolution of new information (novel gene function)**. As such, we predicted that the extremely long time required for E. coli to evolve to Cit+ status **was due to the LTEE conditions** and _not_ to potentiating genetic events requiring 33,000 generations.”

> [@Michael\_Okoko](#):
>
> Again no surprise here at how evolution could operate. The frequency at which Ross emphasizes this point about using preexisting parts and/or mechanisms to generate evolutionary novelties as if it were a counterpoint suggests the man, like Meerkat, does not understand how evolution works.

No, it’s you who does not understand what I am arguing. This is not about refuting evolution but showing how my hypothesis could be refuted. As you suggested, we would not expect this from an unguided process but we would expect this from a guided one. So if we saw innovations of new genes and new transporter and new metabolic pathway, then it would show a possible condition in which advanced life could have arose without human intervention and thus falsifying the hypothesis. So thank you for proving how God is a testable hypothesis.

> [@Michael\_Okoko](#):
>
> Which is just horrendously false with regards to a getting a new promoter. The Cit+ mutants evolved a new promoter for their _citT_ gene to be transcribed under oxic conditions.
> 
> In addition, its quite easy to evolve new promoters from scratch. Happy reading:

But this is not how we test for my hypothesis because it readily allows that natural selection can effect _some_ changes in populations. The right question is not ‘Can natural selection do anything?’ but rather ‘Can natural selection do _everything_ on its own without human intervention?’

> [@Michael\_Okoko](#):
>
> There is no significant benefit to losing GULO activity. If you don’t get vitamin C in your diet or via supplements, you will die. That’s a massive design flaw.

Or it could be a design tradeoff. For instance, the bronchial system in the human lung is not optimally designed to produce maximum efficiency in distributing air with minimal dissipation and it is relatively oversized. However, it has been suggested that the design actually is optimal when one considers physiological variability: a more optimal design of the bronchial tree would result in many more humans suffering from asthma and other lung disorders . [just ask for reference]

> [@John\_Harshman](#):
>
> Any feature that’s “designed” to impede that organism’s abilities would be evidence of God, though a malevolent one.

Again, the attributes of God have to work in accordance with each other in a logically consistent manner because he is who he is (i.e. the law of identity) and cannot not be who he is at the same time (i.e. law of non-contradiction). God must be true to “all” his attributes, because to do otherwise would be to deny his own self.

So NO. If it was truly a Sinister design, it would be evidence against my hypothesis.

> [@John\_Harshman](#):
>
> Now, Darwin famously said that any feature of an organism that existed solely for the benefit of a different species would argue against his theory. Maybe you should concentrate on finding those.

As I told Michael, thank you for showing how my hypothesis is testable because it involves God “directed” mutations and natural selection.

> [@John\_Harshman](#):
>
> You made none of this clear at all. And it has nothing to do with whether mutations are directed. You have so far said nothing at all about mutations. Also, I don’t know if you were following the argument about what “random” means, but it isn’t clear that you know what you mean by it.

I addressed this at the top

> [@John\_Harshman](#):
>
> I’m pointing out that your hypothesis is so all-encompassing that anything at all would count as evidence for it in your mind. As long as some event or feature benefits some individual, or species, or segment of the biosphere, you count it as evidence for design.

No, it just means that it is not the best way to falsify it, as I explained to another user.

> [@Tim](#):
>
> You have not in fact demonstrated that _it is in God’s nature_ to mimic humanity, merely _claimed_ (not particularly convincingly) that he _does_ (at times) mimic humanity.

I explained logically how and why God must be consistent with his nature based on the laws of logic. Do you want me to copy and paste this again?

> [@Tim](#):
>
> Given that _neither_ of your _quote-mined_ passages were talking about God “mimic[ing] the behavior of humans”, and in fact one of them was quote-mined from a section explicitly stating that “Information theory is not concerned with ‘patterns of intelligence’”, they do not constitute “good reason” for this claim.

I already explained how all three observations COMBINED gives us reason to infer that it is probably personal like us. You have yet to explain why those observations do not show it. Instead, all you did was cherry picked one of them and isolated it from the other observations to make your conclusion. I never argued that that one observation suggests patterns of intelligence.

> [@Tim](#):
>
> I offered the article as a _refutation_ of your claim that theodicy was unrelated to the animal kingdom, **not** because I accepted its claims.

No, this was not my argument. I merely responded to your assertion that our inability to comprehend, understand, and predict God’s actions applies to both nature and humanity. It has nothing to with Theodicy and even if it does, I already addressed it by explaining the Benevolent design hypothesis.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [May 24, 2021, 3:24pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/100 "2021-05-24T15:24:22Z")

</div>

> [@Meerkat\_SK5](#):
>
> …numerous studies have revealed that most, if not all, of these non-coding regions play an important role in the accurate functioning of the DNA in regards to neutral mutations ([http://www.lncrnablog.com/](http://www.lncrnablog.com/)).

Where does anyone on that blog reveal any such thing?

> [@Meerkat\_SK5](#):
>
> > [@Mercer](#):
> >
> > Why aren’t the new antibody sequences generated by mutation + selection during the immune response new information?
> 
> According to a following study, “We hypothesized that the isolation of such mutants should be relatively easy, would follow the same genetic trajectory as that identified in the LTEE, and would utilize **information present on the chromosome and _not_ involve evolution of new information (novel gene function)**. As such, we predicted that the extremely long time required for E. coli to evolve to Cit+ status **was due to the LTEE conditions** and _not_ to potentiating genetic events requiring 33,000 generations.”

My question was about antibody genes, not the LTEE. Why would you quote my question and follow it with a non-answer?

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [May 24, 2021, 3:36pm UTC](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699/101 "2021-05-24T15:36:02Z")

</div>

> [@Meerkat\_SK5](#):
>
> I am going to bring some more clarity to what I am trying to argue.

You may think so, but you never really do.

> [@Meerkat\_SK5](#):
>
> The central thesis I am trying to argue is that the “random” in mutations is an appearance.  
> For instance, ever since the ENCODE results, numerous studies have revealed that most, if not all, of these non-coding regions play an important role in the accurate functioning of the DNA in regards to neutral mutations ([http://www.lncrnablog.com/](http://www.lncrnablog.com/)).

Case in point: That paragraph conflates two quite separate ideas. The randomness of mutations (or not) has nothing to do with the existence (or not) of junk DNA. And the ENCODE results are a joke. And showing that one or a few lncRNAs are functional does nothing to imply that the entire genome is functional. Finding a black swan doesn’t tell you that all swans are black.

> [@Meerkat\_SK5](#):
>
> For instance, mutations have been shown to be guided by both the physical properties of the genetic code and the need to preserve critical protein function.
> 
> [Evolution: are the monkeys’ typewriters rigged? | Royal Society Open Science (royalsocietypublishing.org)](https://royalsocietypublishing.org/doi/10.1098/rsos.140172)

You have confused mutation with fixation, though the authors of the study did not.

> [@Meerkat\_SK5](#):
>
> Moreover, I argue that harmful mutations that do arise are regulated in a way that ensures the timely death of individuals so that resources are available for the young and preserve a balance between predator and prey populations because too many predators or prey can cause a collapse of the ecosystem.

You can argue that, but do you have any evidence? Your reference certainly has nothing to do with your claim.

> [@Meerkat\_SK5](#):
>
> Lastly, I argue that beneficial mutations have not always been rare but directed.

Vast confusion on your part here. Dicynodonts are not dinosaurs. You present no evidence of directed mutation. That mass extinctions decrease diversity, which subsequently recovers, is no surprise and needs no divine intervention.

> [@Meerkat\_SK5](#):
>
> Thus, I am saying that God has directed mutations over the course of history to either choose beneficial, neutral, or harmful mutations in order to guide evolution to improvement of either survival, reproductive abilities or to fit ecological niches.

Still word salad. There has been no improvement in your argument. Perhaps you could use some divine intervention. Certainly extinction of most of your words would improve it.

> [@Meerkat\_SK5](#):
>
> I already I explained how we can theoretically test this additional mechanism to the evolutionary mechanism.

You haven’t. If both beneficial and deleterious mutations are directed, and if both extinction and radiation are directed, there’s nothing that could falsify divine intervention.

> [@Meerkat\_SK5](#):
>
> Thus, there could be different goals the designer had in mind or maybe there is an underlying function that may be found in the future like other psuedogenes.

You have once again demonstrated that no evidence can falsify your claims, since anything could have a function we haven’t discovered. This is just another version of the “mysterious ways” defense.

> [@Meerkat\_SK5](#):
>
> This is not about refuting evolution but showing how my hypothesis could be refuted.

Instead you have shown that your hypothesis can’t be refuted by any conceivable data.

> [@Meerkat\_SK5](#):
>
> If it was truly a Sinister design, it would be evidence against my hypothesis.

Only because your hypothesis is specifically about a benevolent god. But benevolent toward whom? Not, apparently, toward trilobites or pantodonts, or upwards of 99% of all species that have ever lived. He does seem to really like filaria worms, but that interferes with his liking for humans. Very confusing.

> [@Meerkat\_SK5](#):
>
> As I told Michael, thank you for showing how my hypothesis is testable because it involves God “directed” mutations and natural selection.

Not so fast. First you will have to find a feature that exists solely for the benefit of a different species. Have you?

> [@Meerkat\_SK5](#):
>
> I addressed this at the top

Sadly, no.

> [@Meerkat\_SK5](#):
>
> I explained logically how and why God must be consistent with his nature based on the laws of logic.

True, but you never managed to explain why his nature has to be what you claim. Very little in any of your conclusions actually follows from your premises, so invoking the laws of logic is ironic at best.

[Previous page](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699.md?page=4)

[Next page](https://discourse.peacefulscience.org/t/can-god-be-a-useful-scientific-hypothesis-yes/13699.md?page=6)