Is there really information being conveyed within a cell?

[Mercer (John Mercer)]

Edited to provide a more complete picture.

[theaz101]

That looks simple, elegant, and designed in a textbook.
However, in terms of the information required for function (the context of this topic), that is spectacularly false. When you look beyond a high-school textbook, you’ll see literally hundreds of posttranslational modifications that are anything but elegant. That’s why only a small minority of human proteins can be expressed in functional form in bacteria.

Are these modifications random, or based on the specific protein (based on sequence)?

False. It folds as it is being translated.

The folded shape is still determined by the amino acid sequence, right?

Here’s a source that talks about chaperone proteins assisting the protein fold before translation is complete. It says:

It is important to note that chaperones do not convey additional information required for the folding of polypeptides into their correct three-dimensional conformations; the folded conformation of a protein is determined solely by its amino acid sequence.

Is that source wrong?

Only partially. You’re leaving out a very important aspect that does not suggest intelligent design.

Such as?

It appears that you are denying a fundamental characteristic of catalysis, as well as ignoring a lot of research that has been done.

Such as?

How does it become abstract when multiple chemical reactions are involved instead of one?

My claim was that there isn’t a reaction that turns the codon into the corresponding amino acid. Are you disagreeing with that?

how do you explain the nature of peptidyl transferase, the enzyme that catalyzes the formation of peptide bonds in all of your proteins?

The peptidyl transferase is the part of the ribosome that joins the amino acids together as the amino acid polymer is being formed. What does that have to do with anything I said?

[theaz101]

Because massive numbers of proteins have many of those 20 changed posttranslationally, particularly at their amino termini. They are indeed initially assembled from the set of 20, but functional proteins are in no way limited to 20 amino-acid residues. They have plenty of other moieties attached. These modifications are often required for function or they significantly alter function.
…
But hey, we can ask the writer [himself].

My point is (hopefully) pretty simple. It’s that proteins are sequence based. Function primarily comes from sequence and chemistry is secondary. If there are post-translational modifications that are tied to sequence and are not simply random, then they (the modifications) don’t refute my point.

The point is the same–that intelligent design would never have needed to add all of these posttranslational kludges that evolution did, particularly since the genetic code has so many redundancies.

The notion that we humans can judge what a designer (God, in my case) would or wouldn’t have to do is the epitome of hubris.

[sfmatheson (Stephen Matheson)]

@theaz101

When you look beyond a high-school textbook, you’ll see literally hundreds of posttranslational modifications that are anything but elegant. That’s why only a small minority of human proteins can be expressed in functional form in bacteria.

Are these modifications random, or based on the specific protein (based on sequence)?

Either can apply. This kind of dichotomous thought is often a big hindrance to understanding biology and especially molecular biology and signal transduction (to take two examples).

[theaz101]

@sfmatheson

Not a syllable of that is contradicted by the simple textbook statement written by @theaz101. None of the rest of what you wrote is relevant to it. Maybe you meant to quote something else, I dunno. It looks to me like you are attacking his ID position (which, I’m sure, is preposterous) and doing so carelessly and clumsily.

Thanks for the support. It’s appreciated.

As far as my position goes, I’m a creationist, not an IDist. While the two share many features, the main difference is that ID says that it can determine that something is designed using scientific methods. However, since science can’t examine the supernatural, I don’t worry about such an effort.

[RonSewell (RonS)]

@theaz101

My claim was that there isn’t a reaction that turns the codon into the corresponding amino acid.

Binding is a chemical reaction.

@theaz101

Function primarily comes from sequence and chemistry is secondary.

There is no primary and secondary, and why would sequences be closer the heart of God than chemistry?

[Faizal_Ali]

@theaz101

The notion that we humans can judge what a designer (God, in my case) would or wouldn’t have to do is the epitome of hubris.

That’s a good point against ID. And, at the same time, if it can be demonstrated that a process can occur without the intervention of a “designer”, and there is no evidence to show the involvement of a “designer”, then that is sufficient reason to conclude a “designer” was not involved.

[Dan_Eastwood]

@Faizal_Ali

then that is sufficient reason to conclude a “designer” was not involved.

A quibble: We can’t falsify a designer this way, only show a designer is not required. This is where ID fails as science, because ID doesn’t say anything about a designer that could ever be falsified.

[theaz101]

@RonSewell

Is there a dichotomy? Proteins are chemicals, so of course they do what chemicals do, even if there is emergent systemic functionality. That is why it is called biochemistry. The 3D shape is the result of polar interactions, part of what chemicals do. Sequence and chemistry cannot be teased apart any more than any chemical formula can be disassociated from the properties of that chemical.

I’m certainly not denying the role of chemistry in how the protein folds or functions. I’m just saying that the particular fold and function is determined primarily by sequence. Chemistry is secondary.

@RonSewell

True, but I am not sure what you are implying in terms of the physical implication. The laws of chemistry apply in that changing the code requires changing the cellular chemistry. A given code is chemically fixed.

You’re confusing chemistry and sequence. If you wanted to change the code, you would have to change the sequence of at least some of the cellular machinery that translates the code.

[theaz101]

@Dan_Eastwood

That’s a really good question. You already noted that a natural code may be “mechanical”, operated on by the laws of physics or chemistry. I’d say a created code may have some attached meaning, written out by the sender and decoded by the receiver.

Having a code processed mechanically (according to the laws of nature) does not mean that the code originated naturally. We are both using devices that were designed to process codes mechanically. But no one (in their right mind) would claim that the code originated naturally (without an intelligent mind).

@Dan_Eastwood

I think the difference here is the intent to convey information; created codes require intent.

How do you determine intent?

[Dan_Eastwood]

@theaz101

I’m certainly not denying the role of chemistry in how the protein folds or functions. I’m just saying that the particular fold and function is determined primarily by sequence. Chemistry is secondary.

I’m not following the distinction. Without chemistry you don’t have folding or function (or even a sequence).

@theaz101

You’re confusing chemistry and sequence. If you wanted to change the code, you would have to change the sequence of at least some of the cellular machinery that translates the code.

And here. Why it is meaningful to talk about changing the code or machinery? The only meaningful “encoding” for codon sequences are the laws of chemistry, and we can’t change chemistry.

Perhaps I’m reading to much into your intention.

[Roy (34-year veteran)]

@theaz101

My point is (hopefully) pretty simple. It’s that proteins are sequence based. Function primarily comes from sequence and chemistry is secondary.

But function is a result of shape, especially the shape and chemistry of any binding sites, and there can be billions of different sequences that produce the same shape and hence the same function. Meanwhile, prions show that the same sequence can have different functions depending on what shape that sequence is folded into. The shape(s) a protein adopts are the result of chemical bonds between the amino-acids at different points in the sequence, so it more appropriate to say that chemistry is primary, shape is secondary and sequence is tertiary.

You’re also missing that RNA can also provide functionality with a completely different type of sequence.

[Rumraket (Mikkel R.)]

@Dan_Eastwood

@theaz101

I’m certainly not denying the role of chemistry in how the protein folds or functions. I’m just saying that the particular fold and function is determined primarily by sequence. Chemistry is secondary.

I’m not following the distinction. Without chemistry you don’t have folding or function (or even a sequence).

Absolutely.

@theaz101 the sequence only matters because it is a sequence of chemicals. Amino acid residues in the protein polymer have different chemical properties, and it is only because of this that the sequence matters. You can’t somehow separate the chemistry from the sequence and say one is more important than the other for protein structure and function.

[RonSewell (RonS)]

@theaz101

If you wanted to change the code, you would have to change the sequence of at least some of the cellular machinery that translates the code.

What you there state, albeit awkwardly, is that you would have to change the cellular chemistry.

[Don_Mc (Don McIntosh)]

@Mercer

@Don_Mc

@Dan_Eastwood

Maybe even harder the other way. For example, a review of the defense of ID claims made by ID proponents would support this. There has never been any admission of error or retractions in the ID literature, and there are some pretty big errors.

All I can say is it wouldn’t completely surprise me. I won’t pretend to be an unbiased observer of the situation, but often it seems to me like ideology has infected the dialogue to the point that maybe Peaceful Science simply cannot be had.

I’m not following you here. It appears that you are ignoring that Dan was pointing out that your side fails to correct errors. I would say the vast majority of errors, but I won’t attribute that to Dan. So are you saying that your side is infected by ideology? If so, we agree again!

If it really appears I was ignoring what Dan suggested about “my” side, it may be that I simply failed to communicate well (it wouldn’t be the first time). But I don’t think it really appears that way.

Note first that Dan appeared to acknowledge a problem that “cuts both ways” just before he said “Maybe even harder the other way.” Then he said that there are no admissions of error or retractions in the ID literature despite notable errors. I replied that “it wouldn’t completely surprise me” (which is not to say that I take him entirely at his word). Doesn’t that sound like an acknowledgement of his point? Then I said that it seems ideology has infected the dialogue – dialogue involving two parties – after which I advocated a “third way.”

So to clarify, yes, I do think ideology has contaminated both sides of the debate, which obviously includes “my” side. (I say that with some hesitation, not only because I’m not 100% on board with the ID agenda myself, but because I got to hear and meet some of the leading ID spokesmen in Dallas last year and I have a lot of respect for them. Just in case any of them are reading…)

But I think your remarks ironically highlight the problem. Even if I agree, somehow you have to read disagreement into it instead. For another recent example, the uncontroversial proposition that “all proteins are made from the same set of 20 amino acids (with a few very rare exceptions)” is perfectly acceptable when your colleagues say it, but “spectacularly false” when someone from the creationist/ID crowd says it. Seems we can’t even agree on basic facts in evidence. That sort of thing makes meaningful or productive dialogue, hence the stated mission of Peaceful Science, nearly impossible.

[sfmatheson (Stephen Matheson)]

@Don_Mc

the uncontroversial proposition that “all proteins are made from the same set of 20 amino acids (with a few very rare exceptions)” is perfectly acceptable when your colleagues say it, but “spectacularly false” when someone from the creationist/ID crowd says it. Seems we can’t even agree on basic facts in evidence.

First, thanks for your post. It’s reasonable and thoughtful and maybe worthy of a thread on its own. The topic is not new here at PS, not hardly, but IMO it’s important and valuable to explore regularly.

Re the comments about amino acids, I do think that was a mistake that is mostly due to this medium (quoting snippets from previous posts and responding to them). Nevertheless, IMO John was nitpicking and was careless, and I think there has been an overall failure to try to address simple comments (from @theaz101) in the spirit in which they were made. I might ask you to note that John corrected the mistake, and to further note that error correction is a theme of this part of the thread. The major mouthpieces of the ID movement seem never to do this. A discussion of that specific topic, which might include examples that show my impression to be wrong, would be valuable IMO.

Still, you are right that to whatever extent the discussion is “us” vs “them” with “sides,” there will automatically be barriers to “productive dialogue.” You can call that “ideology” but I think it’s more basic, more animal, than that. It’s human tribalism and it requires effort to negate. Is such dialogue “nearly impossible”? Call me naive and romantic (it happens a lot actually) but I disagree. Maybe one first step is to refuse to see another person as a member of a side or tribe, and to engage them as a human. Maybe a second step is to all agree that ideas are not protected or worthy of special respect, but that people are. And then maybe an additional critical step is to acknowledge and even expect people to fail, even spectacularly, and then expect them to apologize.

Sorry for the long response; FWIW I thought you deserved one.

[Mercer (John Mercer)]

@theaz101

Is that source wrong?

Does “information” imply a designer?

@theaz101

My claim was that there isn’t a reaction that turns the codon into the corresponding amino acid. Are you disagreeing with that?

I’m a biochemist, and I have no idea what you meant by “Turning the codon into the corresponding amino acid”. Why would there have ever been such a reaction(s) if we are thinking about the evolution of this mechanism, regardless of whether you accept evolution or not? I’m talking chemistry only.

@theaz101

how do you explain the nature of peptidyl transferase, the enzyme that catalyzes the formation of peptide bonds in all of your proteins?

The peptidyl transferase is the part of the ribosome that joins the amino acids together as the amino acid polymer is being formed.

My question is about the nature of it, not what it does. You wrote:

@theaz101

The last reason that I’ll mention is that amino-acyl tRNA synthetases are produced like all other proteins …

So my question is, since you very clearly think ^that^ was an important point to mention, is peptidyl transferase “produced like all other proteins”? It’s kinda important.

@theaz101

My point is (hopefully) pretty simple.

It’s far too simple, as others have pointed out. You have to go much deeper to see the complexity, which is the kind of complexity we expect from a relentlessly iterative process that is incapable of true redesign.

@theaz101

I’m certainly not denying the role of chemistry in how the protein folds or functions. I’m just saying that the particular fold and function is determined primarily by sequence. Chemistry is secondary.

There is no such dichotomy that would allow any such ranking, as others have explained. One thing they didn’t note is that “particular fold” is completely irrelevant evolutionarily, as folds are structural, not functional, classifications.

I’m more interested in what you think is important about amino-acyl tRNA synthetases. Please answer two questions:

1. What does catalysis do, chemically?
2. What can’t catalysis do, chemically?

[theaz101]

Binding is a chemical reaction.

Binding doesn’t turn the codon into its corresponding amino acid. The bond joins the corresponding amino acid to the growing peptide chain.

Function primarily comes from sequence and chemistry is secondary.

Primary in the sense that a protein and its function starts with a DNA sequence. The protein can’t be produced without transcribing and translating the sequence.

… and why would sequences be closer the heart of God than chemistry?

Why does one have to be “closer” than the other?

[theaz101]

That’s a good point against ID.

I don’t believe that ID is saying “the Designer would or wouldn’t do something this way”. ID is basically saying, “Natural (non-intelligent) processes and natural laws don’t account for ‘x’ and imply a Designer”, which I something I agree with. I think they are also saying that they can use scientific methods to distinguish between the two, but that isn’t something I’m concerned with.

And, at the same time, if it can be demonstrated that a process can occur without the intervention of a “designer”, and there is no evidence to show the involvement of a “designer”, then that is sufficient reason to conclude a “designer” was not involved.

I think it’s been demonstrated that there are processes (not necessarily random) that can effect small changes to existing organisms, but none that can account for the origin of life or for the variety of organisms that exist.