How much did God affect evolution?


#84

Please give more reference and where we can read about it.


(GJDS) #85

If you Google ‘Nobel prize chemistry 2018’ you can find the description of the work. If you have access to the scientific literature you may search for ‘directed evolution’ to find technical discussions - if not I think Wikipedia may be helpful.

A very brief description may be that of utilising engineered variation to enable a selection of desired enzymes based on a number of induced variations - I am a chemist so my brief statement may not be typically given by a biologist. The interesting aspect is that a scientist can use variations and gene modification to obtained desired enzymes - while avoiding the extremely complicated chemical synthetic steps that would be used by conventional methods.


(Chris) #86

“If” being the operative word. The hypothesis is far from proven and can’t be advanced as proof that it did happen.
Some possibilities are

  1. it didn’t happen
  2. it happened through the action of an intelligent agent
  3. it happened entirely through natural processes

If you want to argue for 3 then you need to show that it CAN happen. You need to show in the present beneficial gain of function mutations. So far none of the examples discussed in this thread show that.


(Chris) #87

For some comment on this (Nobel prize in chemistry)
It’s Not “Evolution” — A Nobel Prize for Engineering Enzymes
The Nobel Prize and Intelligent Evolution


(GJDS) #88

I am not sure that the work on directed evolution supports ID - my impression is that there is more to biology than random mutations and natural selection. At this point in time however, biologists cannot articulate what this “more than…” could be.


(Stephen Matheson) #89

I can’t quite tell what your question is, but I’ll give this a try: directed evolution does not imply the existence of, or relevance of, powers outside of nature. Directed evolution, in my view, is simply the harnessing of the power of variation and selection, specifically by creating or facilitating variation (that’s the most innovative part, IMO) and designing an effective selection process.

I can certainly see how a believer could take note of directed evolution and point out that a deity, like a talented chemist or biologist, could manipulate the variation + selection mechanism to achieve particular goals. And no atheists could ever provide evidence against that.


(GJDS) #90

If I understand directed evolution correctly, some genetic engineering is used and the modified DNA is added to bacteria (I guess this may need to be selected?), and from this many variations are produced, and the bio-scientist has devised a method by which the desired product is manipulated, or selected, or isolated. This approach is far more effective than synthetic routes.

While I admire the talent and skill displayed, I think there is lots and lots of directed activity. I do not view this as “evidence” for God or some supernatural power, but rather, how much random variation would you consider in this context? And how does this fit with random mutations, variations and natural selection of Darwinian evolution?


(George Brooks) #91

aarceng responds to my earlier question:

@aarceng

Well, naturally I choose #2! “It happened through the action of an intelligent agent”

AND #3 "It happened [strike word entirely] through natural processes.

You’ve got a wording problem though… you use the word “entirely” in #3. That’s a little too tricky for a Christian audience, don’t you think?

And the reason I choose BOTH #2 and #3 is because it is biblical!

Genesis 1:20-21
[First half of couplet: God command Nature to make the Creatures]
And God said, Let the waters bring forth abundantly the moving creature that hath life, and fowl that may fly above the earth in the open firmament of heaven.

[2nd half of couplet: God confirms that he is “ONE” with the Creation of the Earth]
And God created great whales, and every living creature that moveth, which the waters brought forth abundantly, after their kind, and every winged fowl after his kind: and God saw that it was good.

If you think it is a fluke… it happens yet again… just a few verses later:

Genesis 1:24-25
[First half of couplet: God commanded Nature to Make the Creatures]
And God said, Let the earth bring forth the living creature after his kind, cattle, and creeping thing, and beast of the earth after his kind: and it was so.

[2nd half of couplet: God confirms that he is “ONE” with the Creation of the Earth]
And God made the beast of the earth after his kind, and cattle after their kind, and every thing that creepeth upon the earth after his kind: and God saw that it was good.

You apparently haven’t read the Mission Statements for BioLogos:

Please note points [6] and [9]

[6] We believe that God typically sustains the world using faithful, consistent processes that humans describe as “natural laws.” Yet we also affirm that God works outside of natural law in supernatural events, including the miracles described in Scripture. In both natural and supernatural ways, God continues to be directly involved in creation and in human history.

[9] We believe that the diversity and interrelation of all life on earth are best explained by the God-ordained process of evolution with common descent. Thus, evolution is not in opposition to God, but a means by which God providentially achieves his purposes. Therefore, we reject ideologies that claim that evolution is a purposeless process or that evolution replaces God.

https://biologos.org/about-us/our-mission/

According to the Mission Statement, #3 , BY ITSELF, is probably not even an option!

@Jpm, what are your thoughts on Option #3 (if listed by itself) in the list above? Would that even pass muster?


(Stephen Matheson) #92

That’s just one way to create the variants, and it was the approach used in older experiments. One of the Nobels recognized the phage display technique, for example. Directed evolution now uses more sophisticated approaches with higher throughput. But the basic idea is the same: you need to somehow generate a lot of variation, and you need to devise a way to select the variants you want. Phage display is one particularly brilliant trick, because the thing you’re selecting (a peptide) is connected to the DNA that encodes it.

For the approach to be most successful, I think you want as much randomness as possible, so that the sequence space is sampled in an unbiased way. For this reason, one key technical challenge in any directed evolution experiment is the generation of diversity. One approach is to replicate the DNA (or RNA) using polymerases designed to be error-prone. Even then, one has to worry about whether the resulting variation is truly random, and not biased in any particular way. In practice, this is probably not perfectly achievable.

I think the main way it differs, conceptually, is at the selection step, in which the experimenter is subjecting the pool of variants to very intense selection based on very focused criteria. In the real world, selection is never that intense and is based on more diffuse “criteria” such as survival and reproduction of whole organisms. Otherwise, conceptually, the process is not different in any way that I can see.


(GJDS) #93

I am pasting an introductory quote from: ChemBioChem 2018, 19,239–246

Methodology Development in Directed Evolution: Exploring Options when Applying Triple-Code Saturation Mutagenesis Ge Qu,[a] Richard Lonsdale,[b, c] Peiyuan Yao,[a] Guangyue Li,[b, c] BeibeiLiu,[a] Manfred T. Reetz,[a, b, c] and ZhoutongSun

which says (from what I can see) that random approaches make things difficult, and the scientist seeks ways to reduce these difficulties.

“In the directed evolution of stereo- and regioselective enzymes as catalysts in organic chemistry and biotechnology, saturation mutagenesis (SM) at sites lining the binding pocket (CASTing) and iterative saturation mutagenesis (ISM) have emerged as efficient techniques.[1] Upon applying NNK codon degeneracy encoding all 20 canonical amino acids to randomization sites larger than two-to-three residues, the screening effort increases drastically.[2] Therefore, reduced amino-acid alphabets were introduced in SM/ISM with generation of smaller and higher quality mutant libraries that require less screening. We recently showed that triple-code saturation mutagenesis (TCSM) constitutes a viable compromise between structural diversity of mutants and the screening effort, provided the choice of the three amino acids as combinatorial building blocks is made correctly.[3a]”

In the hope that I can avoid comments on areas outside my expertise, my impression is the technique enables use of multiple reaction routes in a complex system, and direction is required to steer the events towards the desired outcome. While multiple routes in a complex system may appear random, my view is the degree of complexity is relevant, as random is, when all is said and done, the opposite of directed.


(Stephen Matheson) #94

I read that quote to be about how to generate diversity of protein structure, efficiently and practically. I don’t think that the quoted paper is about multiple reaction routes in a complex system. It seems to be about how to get the protein variants into the screen, without creating so many of them that the screen is not practical to carry out. I don’t think the paper has anything at all to do with steering events.


(T J Runyon) #95

I have it. It isn’t too fun


(Chris) #96

@gbrooks9, so you would like a 4th option
4. It evolved without direct intervention within the natural laws established by God during creation. ?

But you also hold that God CAN intervene at any point to produce a specific event either within normal laws of nature or contrary to them.


(Chris) #97

Haemochromatosis? At least there is medical treatment available today. I can be thankful for that for a couple of health issues I have myself.


(George Brooks) #98

@aarceng

Option Four? As it reads here, it looks perfect… as long as you ADD the statement after it!

But you also hold that God CAN intervene at any point to produce a specific event either within normal laws of nature or contrary to them.

and is 100% consistent with the BioLogos Mission Statement.

Why don’t you adopt an AMENDED Option 4 as well!?

ADDENDUM:

Are you willing to AMEND option 4? Or make an OPTION 5?


#99

You call any change in gene expression patterns as a loss in function. Therefore, if you were to watch every mutation that led to humans from a common ancestor shared with chimps you would call each and every mutation a loss in function, even as humans evolved bigger brains and bipedality.


(Chris) #100

@gbrooks9, sure. How’s this?
Some possibilities are

  1. It didn’t happen
  2. It happened through the action of an intelligent agent
  3. It happened entirely through natural processes
  4. It evolved without direct intervention within the natural laws established by God during creation, but noting that God CAN intervene at any point to produce a specific event either within normal laws of nature or contrary to them.

(Chris) #101

No, but I do distinguish between a gain of function mutation and one that is conditionally beneficial.

Genotype-Phenotype

In the case of adult lactose tolerance we know from all other mammals and over 50% of humans what the pattern of expression of lactase should be, and therefore we can confidently identify the mutation as a loss of function since it fails to turn off lactase production at the normal time.

Similarly if the regulatory system fails to turn lactase production on in infancy that is also a loss of function. This happens in children that are born lactose intolerant.

Now NYLONASE is probably a gain of function, although a trivial one. This took an enzyme that had low activity on nylon and tweaked it to have much higher activity. (Now you should probably ask why I consider it trivial.)

But since that didn’t happen it is purely hypothetical.


(Phil) #102

I have not followed this closely, Chris, but am curious which of the four you would choose, and how would you show that it has taken place?

If I am reading you right, you are getting to a question addressed here in other posts, which is, “How does God act through evolution?” I must say that I have found it a good question, and not having a clear answer, but I am content with the mystery.


(George Brooks) #103

@aarceng:

Well, that’s got the technicalities down… but it sounds a little awkward. Do you really think God is conducting an INTERVENTION when he does a miracle? Who is he intervening against when a miracle makes a tornado go away?

Is he intervening in himself? How about this instead:

REVISED [4] “God can create living things either by miraculous engagement with the Universe, or by using Evolutionary principles, like Natural Selection and Mutation, as manifested through for lawful natural operations.”

“engaging” and “engaged” is closer to the truth than “intervening” and “intervened”. The left hand can’t intervene with the right hand is doing.