Reaping the Whirlwind: protein function without stable structure

Faith & Science Conversation
543

No not at all. I was asking why anyone would look at broken components and have their first guess be “design” not faulty inheritance from a common ancestor. Do you have an answer to that question that is not a variation of “God can do things however he wants to”?

Broken genes is a scientific argument. It doesn’t look to me like you have yet to say anything that presents “design” as anything other than a “meta-argument.” Also, all this talk about logic and tactics and Einstellung effects aren’t really scientific arguments either.

544

How did you determine they are broken?

545

You look at a related species that has the functioning version of the gene in the exact same place in the genome and see what it does.

546

My argument all along has been we don’t have enough information to conclude evolution is the best argument, and indeed with its tenuous evidence is a very weak one. I have never presupposed God wouldn’t have done something because humans think it would be a bad design. How do you rule out design. What you see as broken, God may well have intended exactly as it’s observed. How do you rule that out?

ID, on the other hand fully recognizes the lack of a complete evidence picture, and resorts to tried and true abductive reasoning. Try it sometime. I think you’ll like it if you can get past the Einstellung effect?

547

I read thousands of pages of science-related material over a period of about five years, and the compelling nature of the evolutionary model and the weaknesses of the design inference became obvious to me. So I changed my mind. I did not memorize all the data and arguments in those thousands of pages. You will have to explore for yourself. I will sleep fine at night if you come to a different conclusion.

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548

Reminds me of a famous quote by Ronald Reagan, “It’s not that Democrats don’t know very much, it’s rather the fact that what they do know is not true.” :wink:

549

:slight_smile: Part of the process involved changing the way I evaluated a source as trustworthy.

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550

You mean evolutionary narrative trumps science?:wink:

I need to get back to reading. Enough of this sparring. It is fun, however. Have a great day!

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551

Genes are usually several thousand nucleotides long, and have many specific, recognizable features - sequences that control when and where they are transcribed; sequences that control the amino acid sequence of the protein product, and on and on.

What we observe, over and over again, are sequences that have the vast majority of these features intact, but also have DNA sequence changes that cannot allow for a protein product to be made. One example, specifically, is mutations that produce “stop codons” in the middle of the sequence that should be determining the amino acid sequence of the protein product. Now, instead of being able to make a protein, this (now defective) gene cannot. Yet all the other features - thousands and thousands of nucleotides of them - are all still there and still match what we see in other species. And not only do they match the sequences of functional genes that we see in other species, they are sitting in exactly the same context in the genome - they’re next door to the same genes in both species.

If you were going to argue some sort of “God intended it this way and made it directly, apart from evolution” case you’d have to say something like God intentionally made two genes that happen to be identical for 99.9% of their sequences, and placed them into the same genome context in two different species, in order to perform two completely different functions - and that the strong appearance of common ancestry, strong though it is, is misleading.

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552

GULO is just one example–olfactory receptors are many others–and it’s experimentally straightforward to test key aspects of function of these “genes.” One type of experiment (as you know) involves expressing the gene in a cell in the lab, getting as close to the “right” kind of cell as you can. Then you can measure specific functions, biochemically or otherwise, and you can see whether the gene can even be expressed. This paper in Cell Reports from a few years ago is a perfect example:

https://www.cell.com/cell-reports/fulltext/S2211-1247(15)00639-7#secsectitle0015

But broken genes are the tip of the iceberg of failure for an “intelligent design” theorist who wants to paint the human genome (or any mammalian genome, for starters) as something that is a product of benevolent intelligent design. The human genome is not particularly big as animal genomes go–it’s about average–but it is absolutely chock full of mobile elements, most of which have been mutated just enough to make them no longer mobile. Many are still active, hopping around the genome during development (notably in the brain) and during formation of gametes. Whole systems of genetic regulation exist to suppress these damned things, but they break out with regularity. Their action underlies various causes of death and disease, and a high-profile paper just a couple weeks ago now links them conclusively to aging-related health decline. I started a discussion about that here on the forum.

Someday, maybe, an intelligent design advocate will start talking about mobile elements. Until then, there can be no coherent or honest consideration of intelligent design in the context of genomics. (I would say that in this case, ID most assuredly has something to hide). And until then, ID thought cannot be considered to be intellectually honest. It doesn’t have to be this way, but right now it is, and it has been since the founding of the ID movement.

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553

How do you know a sequence is not intact? Do all sequences code for proteins? I thought only a few do? If it doesn’t code for a protein, how can you rule out that it doesn’t have another function? How is seeing sequences from other species become the standard for assessing a sequence in another specie?

It may be misleading from man’s standpoint, but until we know more, the conclusion may be premature. After all, one of the goals of creation is show the foolishness of thinking outside God’s revealed way. He may have left a snare that you’ve fallen into? The safe approach is to get more facts before you begin concluding things may be in error.

Even if the coding similarities are true, I still don’t see how the common descent argument follows from the similarities in genes and their proximate organization. If God intended to create the world as we see it, could he not have designed it this way? I need a stronger argument to rule out design. Is there one?

I’ve read more of your book this morning and am seeing arguments that are more of the ilk where “is consistent with,” “can be account for,” “genetic fossils,” etc. are your preferred method. What I’m not seeing is substantive scientific arguments based on testing that confirms rather than “doesn’t nullify the hypothesis.” I was really taken aback at your argument that a theory is maintained unless proven wrong. If many tests can’t nullify a hypothesis, it must be right. How can that be called scientific?

554

Good question. I think that is one point where as you read more, it will be clearer. It’s repetitively true that there is evidence of broken and changed things, and the evidence of this comes in multiple areas. You’d think it could be possible an exception if it was only with regard to one case–but it’s over and over, and multiple disciplines (astronomy, genetics, geology, etc) support each other.

The omphalos hypothesis becomes a fall back–but then we wonder if God is deliberately trying to deceive us. I think you would agree that He doesn’t do that.

It really takes a long time to read this great stuff. You will bring your own unique talents to the conversation, and contribute in your own way, as you go.

I first became interested in apologetics when I was 10, and read some of the oldest books (Genesis Flood, etc). It took me at least 10 years to get to the point that EC could be true (with “Science Held Captive,” by Van Till, Young and Menninga), and it was 20 years later that I realized things weren’t concordant. Patience is terrific–everyone I met was patient with me, including my parents (who disagreed with me) and I think God is, too (better than we are). :slight_smile:

555

And…if we never do come to an agreement…that is still ok. I enjoy your thoughts. Thanks

556

Are you saying God has engineered these details into genomes to (potentially) deceive people?

557

A thought to consider when musing about why God would have created things the way He did is to recognize that when God created man to have free will, the creation itself must have options that allow man to choose for or against Him. I used to wonder that so much of what I see seems incompatible with a God who is righteous, just, and loving. Why is there so much apparent injustice in this world? Where is God? Is he just playing hide-and-go-seek with us for his personal amusement? Why doesn’t he respond to simple requests in a direct manner where there’s no question that He’s real and active in the world? Those are tough questions for young folks just starting out in life. Can the world we live in truly be one without a creator, and does it move along aimlessly without any moral compass? Is there even a place for morality in a world of just chemicals? What combination of chemicals is needed to produce self awareness, thought, values, etc? Where’s the threshold when it first appears?

We all seem very aware that we are more than chemicals. God formed Adam from chemicals, but before He was finished, he had to give life to the chemicals in a separate step. (Gen 2:7) Being in the image of God, Adam was given volition. For volition to be functional and Adam to have the ability to chose, he also was given choices. After the fall, the choices were manifest in the world as a whole so that we could choose an offer of redemption or chose a world with no God. Prov 25:2 is an interesting passage. It says:

2  It is the glory of God to conceal a matter,
But the glory of kings is to search out a matter.

If the world is the testing ground where God has given man the choice to come back to Him or seek his own apart from God, the world we see makes sense (partially anyway). This is where faith comes in. I see faith as believing something that cannot be proven. So that no man has any advantage over any other especially with regard to the ability to reason God’s existence with his intellect, God designed it this way. God designed us to recognize that He exists and is active in this world. Both the simple minded (like me) and the super intellects (like some of you) can find God and redemption. He even left a testimony of what reality is, the Bible. You won’t find God in the Cell Report. Folks who depend on their intellect and ability to reason scientifically will find it more and more difficult to understand their world. Each layer of this complex world that is peeled back reveals only more complexity. Interestingly, God uses this complexity to point us back to Him. Strangely, those who will not allow God in the door will never see it, but will rather depend on “Science” and claim that they will eventually come to a full understanding of the physical world, and will eventually arrive at the point where they can prove there is no God. Yet this complexity is the very mechanism God uses to graciously point us back to him and away from the Godless world view. He gives us example after example of intelligent design, e.g., Mt Rushmore, the Saturn V rocket, etc. and he gives us an ability (through our intellect) to recognize design and get it right 100 out of 100 times, unless it’s living even though it exhibits stunning levels of elegant design. Yet He is so clever that the most elegant design He has ever made cannot be recognized if one has first said No, God, I don’t have any use for you. Go away. Imagine the shock of those who reject Him when God shows them their folly at their last judgment. That’s going to be a really bad day for the unbeliever.

The centerpiece and perhaps the foundation of the world view with no God is evolution. Without evolution the Godless world has nothing. This is one of the reasons I’m puzzled that Christians are willing to embrace it even if only partially since it is the crux of a godless world view. To give it any form of sanction seems inconsistent with a Christian world view. So I ask myself a simple question, “What is it that the folks at BioLogs see that causes them to see merit in the evolution when it is the very core foundation of a Godless world view?” The scientific evidence for it is tenuous, theistic evolution stretches the Biblical narrative beyond recognition, and its conclusions are more the result of a consistent narrative than sound science and good engineering. I’m baffled!

Nonetheless, if God is using evolution to create and grow the world, then I need to understand it and embrace it. Thus, more reading…

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558

My response flirts with the boundaries of acceptable discussion on this forum, so I am flagging the @moderators and will completely understand if this post needs to be removed.

I know that there are some atheists (“Godless” to use the always-classy Isbellian lingo) who get comfort from evolution. It’s a narrow form of comfort, discussed most famously by Richard Dawkins (I wrote about it here) and historically outlined back at least to Hume (who almost pictured evolution but had to forego the “comfort” of an explanation).

But if you want to know about the relationship between unbelief and evolution, you might ask someone who used to believe and doesn’t anymore. I’m one of those, and I know scores more. For me and all of these people (I don’t claim to have stats on the extent to which we are representative), evolution itself was not involved in our deconversion. I never doubted common ancestry as a Christian and it never posed any challenge to my belief. (It made the fall hard to understand, but that never bothered me.)

The way that evolution eroded my faith was by showing me how faith failed to create or undergird integrity and honor in other believers. It gave me an unwanted case study in the effects of belief (evangelical belief specifically) on the functioning of minds and on the already-difficult task of maintaining faith with intellectual integrity. The argument above, that Christians ought to doubt evolution merely because it “helps” the “Godless,” was one I heard then, that eroded my confidence in faith. In short, this argument is an argument against faith, because it suggests that belief creates obstacles to clear thought and to integrity. I was still a Christian when I heard the testimony of numerous former believers, whose report to me was not that evolution itself made them atheists, but that Christian dishonesty about evolution made them question their beliefs.

If I wanted to help Christianity grow and thrive (I don’t), I would urge it in the strongest terms to see the “don’t give comfort to the Godless” argument as a sign of something gone very wrong. Maybe now I don’t care whether you do or not, because I think it’s already clear that the world will be better off without belief.

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559

@Raymond_Isbell, I’m glad you are going to keep reading. But I think you agree that God holds everyone honestly, knowing that they can only know what the intellect He gave them can grasp. Would you not say he will justly assess them according to what they know?

I would not say that faith is believing against truth or facts. Would it not be sinful of God to require that? Has he distributed truth equally to everyone?

I think you said you read “Benefit of the Doubt.” That really helps with intellectual honesty, to know that God won’t throw us into hell for not understanding. And it reminds us of His fatherhood.

Another point–how can we discuss anything with anyone of another faith if we cling to a presuppositional concept? If discussing with a Muslim, our reasoning of “the Bible is true because it is true, and also because I believe it that way” argues just as strongly from their point of view. We have no common ground to argue from–we can not disagree or agree over anything that we mutually observe.

Certain Hindu castes even believe that they are the only ones who can read the Bhagavad.

As Christians, we believe God is the God of truth; but more, He is a father. We can humbly say, “I am willing to examine all the evidence; and God is just–he will take us however we can use our finite minds, that He gave us, to understand them.” That gets rid of a lot of fear, doesn’t it?

Thanks.

560

I can understand your position. I tend to agree with the quote attributed (perhaps falsely) to Gandhi, ‘I like your Christ, I do not like your Christians. Your Christians are so unlike your Christ.’
I suppose that can apply to all of us at some time or the other.

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561

I resemble that remark. :slight_smile:

562

I think you missed the primary point I was making which is about free will having to be coupled to a world with choices if humans are to have a meaningful existence. There are basically two choices: 1) God designed and has a plan for this world that includes you and me, 2) There is no God, just chemicals.

Choice 2 is one that is looking for an alternative to a created world. Evolution fits the bill. Thus, I ask how is that Christians can find that the centerpiece of option 2, evolution, as palatable. That’s a fair question since it is a factor for an open minded person. Perhaps not all atheists believe in evolution, but most thinking ones do. Is there an alternative other than agnosticism?

Faith comes by hearing and hearing from the Word of God, not watching other believers. Believers are far from perfect. I don’t attend any church because of reasons similar to yours, but worse, they don’t do much to correct their lack of knowledge and understanding of biblical truth. I didn’t however give up on Christianity because of the bad behavior of other believers. Instead, I turned to focus on learning what the Bible really says. I’ve found that it is a marvelous story that makes complete sense, and I find no conflicts with good science. I’m in a good place and I haven’t had to compromise my intellectual integrity.

From what I can tell from what you’ve said and your writing in this forum is that you still haven’t found a good model for integrating science and faith. I would encourage you to get back to the Bible and learn it well. That’s hard in this day and age when we’re in a famine of knowledge of God (See Amos 8:11ff). It can be done. I did it. Now I’m trying to find out more about how science and faith are viewed as being in conflict. It’s a very interesting trek thru the evolution side that I’m seeing in Biologos.

Isa says (I forget the verse) God is tapping his foot waiting to bless us. For me blessing comes in the form of knowledge, and understanding.

Proverbs 2:6 -
3 Yes, if you cry out for discernment,
And lift up your voice for understanding,
4 If you seek her as silver,
And search for her as for hidden treasures;
5 Then you will understand the fear of the LORD,
And find the knowledge of God.
6 For the LORD gives wisdom;
From His mouth come knowledge and understanding;

The New King James Version. (1982). (Pr 2:3–6). Nashville: Thomas Nelson.