Is there really information being conveyed within a cell?

Conversation
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Yes, there is some misunderstanding going on here.

The fact that I agreed with Massimo Pigliucci (or Charles Darwin, or @John_Harshman or @sfmatheson) rather than you about the importance of explanation in science doesn’t mean that I was talking about you, let alone that I was looking to trade barbs with you on this or any other topic. I was happy to reply to @John_Harshman mainly because I agreed with him and had something to add, but also because he doesn’t strike me as insufferably peevish, pedantic and contentious. (He can always correct me later, lol.)

Okay, so when you said earlier that “science isn’t advanced by arguments,” you meant only arguments by ID pseudoscientists who don’t produce new data (and thus presumably far better explanations)? If so, I think for consistency’s sake you should also mention the arguments of historians, forensic pathologists, paleontologists and others who devise hypotheses regarding past events based largely, if not entirely, on previously existing data.

There’s one sure way to find out… Only $9.99 at Amazon. :laughing:

No, John, my book does not contain any testable hypotheses. In fact, I say or suggest just the opposite in a number of places:

“Even if an accurate representation of reality, as I believe it is, the model of creationism I propose would not make a lot of testable predictions” (p. 25).

“…[C]reationists would be well advised to present the narrative account of the creation in Genesis not as some sort of testable scientific theory, but rather a divinely revealed historical-theological truth for which there happens to be considerable scientific evidence” (p. 59).

“Arguably…, creationism and Evolution are strictly neither testable scientific theories nor documented historical events, but more like untestable theories of prehistorical events” (p. 59).

“A systematically complex biological world created by the direct action of a transcendent God could well be one reality that is strictly beyond the power of a scientific theory to reasonably explain” (p. 60).

“With a basic understanding of this kind of organized structure and systematic coordination in place, we can begin building a modified creation model emphasizing its apparent systematic, technological character – as opposed to being a ‘testable scientific theory’ to rival Evolution” (p. 106).

“When I speak of my ‘model,’ then, I mean a static model of how the biosphere is presently structured and what such a structure may suggest about origins, rather than a testable model of some process that would explain how the biosphere may have originated – the latter being more commonly associated with science” (pp. 158-159).

With all that noted, if you still feel a need to lump me in with “ID pseudoscientists” in order to reinforce a stereotype, go right ahead. I won’t try to stop you.

Here’s what I would expect to see if you were wrong: I would expect to see you falling all over yourself trying to explain that scientific explanations are far superior to and orders of magnitude more powerful than all other explanations because they come from hypothesis testing – and yet conspicuously failing to test a relevant hypothesis to support your explanation.

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We weren’t disagreeing about the importance of explanation. We were disagreeing about the importance of arguments.

The misunderstanding is yours.

You have quite a talent for the straw man. I mean that testing hypotheses is the center of science.

I don’t see why, because all of those people, unlike you, routinely test the hypotheses they devise.

We see this dull creationist trope all the time. The hypothesis has to predict something you don’t currently know, not necessarily something that happens in the future. IOW, if I clone and sequence a new gene, common descent predicts where it will be when we construct a tree based solely on sequence differences. It’s still a prediction, even if the events that produced the differences happened millions of years ago.

The quotes from your book emphasize that trope, especially this one:

Putting aside your failure to understand that evolution is a phenomenon and evolutionary theory pertains to the mechanisms underlying it, in what way is evolutionary theory not testable?

That’s some impressive word salad! Hypotheses are a subset of explanations. Hypotheses and explanations are supported by evidence. One tests a hypothesis to attempt to falsify it, not to “support an explanation.”

Let’s see if you can grasp hypothesis testing as well as the third-graders I have taught:

  1. Joe hypothesizes that his dog understands English words.
  2. Jim hypothesizes that Joe’s dog understands intonation, not actual words.

Note that Joe and Jim have no need to make any arguments or publish books; if they are being scientific, they shouldn’t be investing any ego in their hypotheses anyway–they can both figure out how they could be falsified.

Can you see how both hypotheses can be tested at once? Third-graders can.

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I’m peevish, pedantic, and contentious, but not insufferably so.

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That’s your central problem. New data don’t have to be happening after the hypothesis is formed. They just have to be unknown when the hypothesis is formed. Fossils, DNA sequences, and such are in fact data about the past and are able to test hypotheses of evolution and creation. Of course evolution wins, contrary to your opinion. Try presenting a real hypothesis here and see how it goes.

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Exactly. A corollary of this is that private hypothesis testing is a great way to learn. IOW, even when all the evidence is available somewhere, one can formulate testable hypotheses and go looking for those existing answers.

Try it sometime, Don, even for a subject outside of biology!

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Welcome back, @Don_Mc! I saw when your book came out. :slight_smile:

You know that cuts both ways, right?
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.

That said, I have wandered off-topic, so I’ll leave it at that. I can split the thread if anyone really wants to grind this out again (but let’s don’t and say we did). :slight_smile:

ETA: It was unfair of me to ignore this …

I appreciate the first part, and I can deal with the second part being addressed to a Creationist audience. Thank you for putting that in writing.

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Sort of off-topic, but a really good example of a code in nature.

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That hypothesis has, in fact, been tested and confirmed, and continues to be tested and confirmed, with every discovery and piece of knowledge obtained thru the scientific method.

If you dispute this conclusion, perhaps suggest a non-scientific method that has produced anything even close to similar results.

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Thanks for that, @Dan_Eastwood!

One incidental bit about that book: a brainy engineer friend who reviewed it (and disagreed with the better part of it) was put off by the subtitle – The Failed Dogma of Evolution and a Fresh Model of Creationism – because in his view evolution is a genuine scientific theory and not a dogma. Yet I chose it not simply to be provocative but to suggest that evolution fails as dogma, i.e., when presented and promulgated as an unchallengeable truth. I take it that precisely because evolution is a genuine scientific theory, it is (in principle at least) only provisionally confirmed and always amenable to potential falsification like any other. I say that to clarify that I’m not just trying to be offensive for offense’s sake.

– none of which really matters, since I’ve sold maybe two copies over the last three months. :sweat_smile:

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. That’s why I embrace a third way, which is to leave scientists and educators to their work, essentially promote creationism (or ID, teleology, etc.) as a branch of apologetics rather than science education, and (informally) encourage the teaching of systems theory rather than evolution as a neutral unifying theoretical paradigm of biology. I don’t know of anyone who agrees with me, though.

Fair enough. In that case I will just mention in passing that I was ready, though certainly not eager, to acknowledge an error (regarding my evident misreading of @Mercer’s “retrospective explanations”); then push back a bit on @John_Harshman’s reply; then reply again to @Mercer re: his take on explanatory power and hypothesis testing. But if you’d rather let the thread die, I would just as soon get back to things that cause me less stress anyway.

Thanks likewise for that acknowledgement.

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I agree, but I don’t know anyone doing that.

It is in principle and in practice. You’re probably missing that because you don’t seem to be using “theory” in the collective sense. In reality, it’s a group of theories that have changed over time. And as I pointed out, they are tested all the time. You can test them too.

I do not see how systems theory or biology is (or can be) in any way an alternative to (or in opposition to) evolutionary theory or biology. I’m all but certain that none of the systems biologists whom I know, or the even larger number I have met, would see that either. Can you elaborate? What is the meaning of “neutral” there?

And if you’re modestly leaving “scientists and educators to their work,” isn’t encouraging systems theory as some sort of alternative to evolutionary theory an explicit rejection of leaving scientists and educators to their work?

Finally, from my work on my local public school curriculum committee, science textbooks for more than 20 years have improved, focusing far more on teaching students that hypothesis testing is the core of science (educators tend to call it “inquiry-based”) than they do on presenting evolution (or any other aspect of biology) as some sort of dogma.

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I can understand that. That’s why I tried to define information in my first post.

By information I mean any physical property or characteristic of matter that is used to represent something that it is not.

As a software engineer (and fellow creationist), the definition of information that creationists and ID are (usually) talking about can be found in the dictionary.

1b

: the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (such as nucleotides in DNA or binary digits in a computer program) that produce specific effects

So, not a physical property of the nucleotide itself, but the sequence of the bases.

This is the same as all computer code (programs and files like documents/spreadsheets/digital photos, etc). All are functional sequences of ‘1’ and ‘0’.

I guess what you are saying is that the code is like a mechanical code. It’s just matter doing as matter would be expected to do, and not like a man made code that requires an assigned value or abstraction.

There are several reasons why this isn’t true.

First of all, there are many instances where a man made code is coded/decoded mechanically. Computers for example. When you press a key on your keyboard, it is converted to the appropriate string of 8 bits (a byte) that corresponds to whatever codeset the computer is using (like ASCII) to be stored in memory and then it is converted back to the letter that you see on your screen. A DVD being played in a DVD player is another example.

The second reason is that it isn’t “matter doing as matter would be expected to do”.

Consider that all proteins are made from the same set of 20 amino acids (with a few very rare exceptions). How can all of the tens of thousands of different proteins have different functions if it’s just chemicals doing what chemicals do? The answer is that proteins and functional rna are also sequential objects. When a protein is expressed, it is first produced as a sequential string (polymer) of amino acids. Once translation is complete, it folds into a 3D shape (some proteins have portions that remain unfolded). It is this shape that gives the protein its function. In other words, sequence is primary, chemistry is secondary. This goes back to Crick himself.

The last reason that I’ll mention is that amino-acyl tRNA synthetases are produced like all other proteins - by means of the translation process. The genetic code is used to produce the amino-acyl tRNA synthetases. It’s a chicken and egg type situation.

The abstraction of the genetic code is the relationship of codon to amino acid. There is no law of chemistry that requires a particular codon to code for an particular amino acid. If the 3 bases of a codon went through a chemical reaction and the amino acid was the product, then it would be non-abstract.

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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.

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.

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I just put that in your Title. Let me know if you prefer something else? :slight_smile:

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Allow me to stop you right there and savor this moment. :laughing:

I do appreciate the questions and comments, and will try to say more in a few days after I get caught up on other activities that are (unlike some of my interactions here) not far out of my comfort zone.

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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.

False. It folds as it is being translated.

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

Why start out with false claims?

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

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

And if it was important for you to note that:

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

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It’s not false at all, much less “spectacularly” so. Why did you write that? Do you intend to quibble about the phrase “very rare exceptions”? Did you misunderstand “made from the same set” to mean that all proteins contain the same aa’s? I don’t get it. @theaz101 was writing simple textbook biology. Care to explain?

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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.

Knowing/admitting this makes it much more obvious that the system was “designed” by an iterative process.

I am confident that I understood the writer’s intended meaning to be functional composition, not initial assembly, given the much more obviously false claims that preceded it.

But hey, we can ask the writer him/herself. 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.

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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! :wink:

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Ideology can be a problem, but maybe you haven’t looked far enough? I can point you to several good FB groups (like this one).

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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.

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