Reaping the Whirlwind: protein function without stable structure

(Stephen Matheson) #563

My model is perfect, actually. It integrates science, faith, psychology, and moral philosophy. Since I haven’t discussed my “model for integrating science and faith,” you couldn’t know anything about it.

(Randy) #564

Do you think that the fact that we know how the baby grows in his mother’s womb (yes, chemicals, proteins, enzymes, DNA) negates that God is involved? I don’t understand. It sounds like you have a false dichotomy here. Is it wrong to try to understand things? Are there places we can’t look?

I just listened to Stephen Hawking’s “A Brief History of Time,” in which he said that the Pope told scientists, " Just don’t dig into anything behind the Big Bang–because that’s where God started it all." I don’t know exactly what the Pope said, and think maybe Hawking misunderstood that–but is that seriously the mandate we have–not to look? I hope I’m misunderstanding you, but it sounds like looking is presumptuous?

Or can we only look for evidence that fits what we think is the truth? I don’t think that’s where you’re going, is it?

Thanks for your discussion…

Re going to church–man, I’m sorry you had a tough time. Sometimes you can’t attend a church; but I personally do find it helpful. I attend a solidly YEC church and learn a lot from my friends there. You don’t have to have all the science right to be mature–and many of them are more mature than I. Another reason it is fun to talk with you and others–I can learn a lot. Thanks.

(Christy Hemphill) #565

Actually, evolution says nothing about how creation got here or life began. So, no it does not fit the bill at all. All it explains is the mechanism for the diversity of life, once life exists.

(Raymond Isbell) #566

I guess my writing leaves a little to be desired. The two options (more simply stated) are 1) God, 2) No God. A possible 3rd is “Don’t know.” The 3rd usually ends up at 1 or 2.

Group 2 recognizes that life comes from non-life (chemicals), and I have read that some of those call Abiogenesis evolution. Evolution fits their bill nicely, and many of them use it to justify their unbelief.

(Christy Hemphill) #567

Evolution may fit their worldview nicely, but that doesn’t make it derivative of their worldview. That is a problem I see in the rhetoric of many anti-evolution Christians. Because creationism is derivative of their worldview and they feel ideological conflict with evolution, they assume that because there is no conflict between an atheistic worldview and evolution, that evolution is somehow derivative of atheism. It isn’t. And it’s silly to assume that the 99% of biologists (including plenty of theists) who accept the model do so because of prior ideological commitments, not because of scientific observations. It’s even sillier to think that the many Christians in science who either move from creationism to accepting evolution or who never had a problem with evolution to begin with come to those terms because they are somehow embracing an atheist worldview.

(Dennis Venema) #568

You’re paraphrasing Romans 10:17, but I think you’re not quite getting the picture.

The “Word of God” in this verse is not the “Bible”. How could it be? Most of New Testament wasn’t written yet. It’s not even the Old Testament, since if it was that, Paul would have used his usual word for that - “the scriptures”.

What Paul is saying here is this: pistis (not to get into the whole other debate we’ve been having, but here I’m seeing an emphasis on loyalty and allegiance) comes from hearing the message of the gospel (spoken and lived by the believers).


The analogy breaks down when you consider a single mutation may have zero downstream results. Where is your explanation for the fact that many mutations in our genome have no effect on the final outcome. Have you considered that fact that your DNA is so unique that it can be used to prove you were at the scene of a crime and yet even with this fantastically large number of differences to other people’s DNA you are here and walking around upright. BTW, we know the DNA comes from our parents so if you want to argue that it is intelligently designed to work out this way it has to be worked out using only your parents DNA and any mutations you acquire.

(Chris Falter) #570

Hi Raymond,

I appreciate that you are doing a lot of reading and asking a lot of questions. Much respect.

You also mention later that someone can choose not to choose. (“I don’t know.”)

Your presentation of the choice is, in my opinion, an example of what Ravi Zacharias would call “The Fallacy of the Excluded Middle.”

The middle option is that we see chemicals and physics–yea, even quantum mechanics!-- as descriptions of how God has created the world.
Even though the behavior of every observed phenomenon in these realms conforms to rigorous mathematical laws, we need not accept the deistic explanation that God created the universe and its laws in the past, but now no longer touches a thing. Instead, a Christian can affirm that in some mysterious way we do not fully understand, God holds all things together-- even as they seem fully explained by science, at least from the scientific perspective.

Let’s take a concrete example. A hurricane is a highly complex, dynamic system with interdependent components. How would you explain its origins, Raymond? Are the meteorological explanations valid? If so, how is meteorology, which uses only the laws of physics (fluid dynamics, temperature gradients, etc.), not godless?


(Chris Falter) #571

This is a good question, Raymond. It has a good answer.

Biologists have observed that a single nucleotide substitution results in the change of at most a single amino acid in a protein. Most single nucleotide changes have no effect whatsoever, either because the DNA segment is non-coding (approx. 90% of the human genome, IIRC), or because the nucleotide change in a coding segment does not change the coded amino acid sequence.

Thus the hash function analogy is almost always incorrect in genetics. Does that make sense?

Now a frameshift mutation in a coding segment would have much bigger effects. If the effects were deleterious, though, the mutation would probably be removed from a population by negative selection. A few other rare types of mutations can rarely have large effects, but the same population dynamics would apply there.


(Raymond Isbell) #572

Hmmm… You don’t believe anymore, and yet your model for integrating science and faith (which you don’t have anymore) is perfect? I would ask you to explain, but that’s none of my business, so I’ll let it go. I still wonder, however, why you stay in the forum if you’re no longer Christian, i.e., you don’t believe (your words).

(Raymond Isbell) #573

I think you misunderstand me. Choice #1 says that God is real and involved. I’m not sure how you inferred that I believe God is not involved with details such as a baby’s growth in its mother’s womb. Quite the contrary. Let me explain.

Actually, I believe God is in complete moment by moment control of history including the states of all matter and energy. He also allows man a degree of freedom of will/volition sufficient that He can justly hold man responsible for his choices/actions. Taken together, viz., God controls matter and energy and allows man a range of freedom, how can He control history if man is free to go a way that is inconsistent with God’s intentions for history? I submit that with God’s foreknowledge of how man will react to every contingency, he can manipulate circumstances that present to man to ensure outcomes that are consistent with his plan. Think of God as having a complete math model of the world (an infinite set of non-linear differential equations) where he has a large number of parameters he controls and independent variables (man’s choices). He can see every possible solution to every value of the independent variables, and He chooses the one solution that provides the “history” He intends. As a result, He accomplishes His plan perfectly while simultaneously allowing man a responsible level of free choice. In my view, this is how God “Predestines” everything from the foundation of the world. Thus, Rom 8:29-30,

29 For whom He foreknew, He also predestined to be conformed to the image of His Son, that He might be the firstborn among many brethren. 30 Moreover whom He predestined, these He also called; whom He called, these He also justified; and whom He justified, these He also glorified.

That God knows beforehand everything that will happened, and that he uses that foreknowledge to predestine everything, can be seen by comparing passages like Rom 8:29 with Matt 11:20ff where he knows that the folks in Tyre and Sidon would have repented long before if they had seen the miracles that Jesus had performed before those in Chorazin and Bethsaida. It appears that He can see the effects of actions He takes before He performs them using his foreknowledge (προγινώσκω). Add to this that the Lord causes the heart of Kings to do as He wishes (Prov 21:1), you have good evidence that God is actively controlling history while at the same time allowing man freedom of will. To me this removes the tension we see in the biblical themes of election and predestination.

If there is no God and man came from chemicals and will return to the same, then there is no control by God. All that happens is by chance unless there are other controlling forces out there that we know nothing about.

This is a bit complicated, but it tells me how God can both control history and allow man freedom of will. The reason we see death, suffering, hypocrisy, cheating, lying, stealing even among believers as Stephen correctly observes, is that God must allow a sufficient level of volitional freedom for every man whether to do good or bad. If God stopped every evil act by man, man would no longer be able to manifest his free will to the extent that his freedom would be meaningful and he could be held responsible. Remember that Jesus cried at Lazarus’ death. I suspect that allowing man to do evil is painful for God to allow and watch, but it’s required if the elect are to have a meaningful eternal existence. Our freedom and God’s desire for us to have a meaningful eternity with Him comes at a high price to God, both emotionally (watching our pain), but also directly to God himself as Jesus went to the cross and suffered that horrible judgment for the sin of mankind. Ouch!

Taken further, this proposition offers an incentive to pray. God knows our prayers and requests via His foreknowledge and can integrate it into his plan before the plan is executed. He literally will (and does) change history to answer our prayers. However, he also may choose not to answer because it could conflict with a higher priority in the bigger plan. Once in heaven, we could ask why He didn’t answer a particular prayer. I expect He would say that answering the prayer would have generated ripple effects down thru history that would conflict with other higher priority objectives that even we would agree with.

To sum up, yes, God is involved, and I believe it is to a degree that is far more than we realize.


(Randy) #574

Sorry if I misunderstood you; good thoughts, which definitely bear careful consideration. I will think about them. Thanks.

(Raymond Isbell) #575

My point in all of this is simply that we don’t understand the full effects of changes even at the single nucleotide level as they propagate up to the phenotype level. Certainly we observe some repeatable effects of a small change at the beginning (nucleotide level), but do we really know what is going on in the middle steps as that change propagates forward? Could it be that the change sets in motion other effects that may not show up until later, e.g., effects of carcinogens that result in cancer much later. I was stationed at Camp Lejeune in the Marine Corps and along with all the Marines at that base in the late 1970’s were exposed to some industrial chemicals in the base drinking water. In 1998 (about 20 yrs later) I was diagnosed with bladder cancer. It was attributed to that exposure. Fortunately, my cancer was caught early, and I survived. Others did not. But the point is that effects of mutations may have delayed effects and it should give us pause before we draw conclusions about cause/effect. Should evolutionists also pause before concluding that evolution explains so much based on simple observations?

The notion of “non-coding” genes is an interesting one. Is it true that evolutionists attribute some if not all to “junk?” The term “fossil genes” was used earlier, and also points to “non-function” for certain genes. I find it strange that evolutionists are willing to attribute this phenomenon (non-coding genes/fossil genes) to a by-product of evolution. Given how much we don’t know about what’s going on in the cell, is it possible these “fossil genes” are actually functional and we simply haven’t found the relationship between them (genes and function)?

The hash function analogy was really a very simple one intended to illustrate that an input going into an algorithm/complex system (e.g., cell) may have a wide range of outputs and looking in the reverse direction, we cannot attribute the effect to the input. (you can’t reason your way backward to get the input, the same as with a one-way function.)

(Stephen Matheson) #576

Your point is either wrong or irrelevant. We know that some changes can cause effects, that we can measure, and some might cause effects, but we haven’t looked, but that the enormous majority do nothing of consequence at the phenotype level. This fact is so striking that, in its early days, it required extra explanation. Hence the subfield of evolutionary capacitance and robustness, mentioned repeatedly to you.

The logic you are employing is so bad that it’s ridiculous. It’s like arguing that we don’t really know that most meteorites that burn up in the atmosphere don’t cause harm to humans even though they don’t hit anything. That’s technically true, since we don’t follow up on the meteorites. To argue that this knowledge gap is relevant to anything is to shuffle toward insanity.

Yep. You are describing the large and busy field of molecular genetics.

(Raymond Isbell) #577

At least I don’t contradict myself in the same sentence and again in the same post.

Terms/phrases that from what I’ve seen give scholarly level labels to concepts that reflect what we don’t understand other than at a descriptive level, i.e., it’s happening, but we have no clue how it works, and for sure we must disguise it so that Creationist don’t use it against us. And for sure, we can’t rule out that it was designed in.

(Dennis Venema) #578

Raymond - you’ve had several people, me included, try to explain facets of this to you. Biologists understand quite a bit about how robustness works. We’ve tried to explain parts of it to you. This isn’t a reasonable response, friend.

(Stephen Matheson) #579

This kind of typing paints you as both ignorant and dishonest. Your ignorance is abundantly clear. Whether you lack integrity, as you so frequently project onto others, I do not know. What I do know is that you cannot be trusted to carry on a discussion.

(Raymond Isbell) #580

If I’m wrong about the state of knowledge of how the cell works, and 90% of DNA is non-coding, please tell me how that 90% is used. Also, while you’re at it, explain how proteins navigate around the cell, how they know where to go when, and what to do when they arrive. How is that arrival broadcast to all the other proteins that use that information to commence new processes that depend on the arrival of that process? Also, tell me how the microtubules know when to self-construct including where to start, where to end, and what to do when they’re done. Where’s the command and control function hosted in the cell that orchestrates and coordinates all these activities. How is computational function performed and where? Computational function is used to compute directions to support various protein navigation data, coordination, and other functions. Where’s memory for all of this stored? Where’s the central executive software managing all of this?

The materials you have been giving me to read are full of phrases like, “is consistent with,” “it must work like” or other phrases that suggest neither you nor anyone else understands it sufficiently to be able piece is all together into a coherent description.

Where’s the process flow for all the cell functions documented? I never see an end-to-end description from nucleotide to phenotype with each intermediate component and process identified that is coherent and shown to comply with known science.

I’m trying to understand this, but you guys are pushing a narrative that simply doesn’t close.

(Raymond Isbell) #581

Your explanations are anecdotal with very little science behind them other than they appear consistent with a theory. I’ve seen some of your explanations which are more of a narrative that sews together extrapolated data points that cannot otherwise be joined except with some creative imagination. I don’t mind the conjectures, but how is that better than the design argument? Where’s a scientific strategy to get to a good explanation?

In your book you point out that a theory stands until an experiment comes along that shows it to be false. That might be a good approach if you could also show that all possible test scenarios have been identified and tested and that there are no systems states and no possible interactions in it environment or interaction with other systems that have been overlooked and not tested. How can you do that with cell given how much you don’t know?

How is my response unreasonable when I ask for a profession, thorough and complete explanation. What do we say about your attempts to conclude evolution is sound when the only support you have for it is extrapolated data with many, many unknowns remaining unaddressed?

(Raymond Isbell) #582

Am I seeing the “Einstellung effect” in full flower? Seeing those who disagree with you as dishonest and ignorant? You seem like a troubled individual. Don’t give up, however. There’s hope if you return to the Bible and embrace its truths.