Create a Protein with Your Mind

See now you have conflated the idea of a common ancestral sequence, with the idea of a common ancestral gene, and a common ancestral protein. Those are three distinct concepts, and you’ve sooo mysteriously decided to switch from one to the two others in the span of two posts.

Sal you are so transparent.

4 Likes

Ok, so do you think all genes descended from a universal common ancestral gene?

You really have to be more clear and specific.

2 Likes

Ok. I’ll try. That’s a fair criticism.

2 Likes

I don’t know. I would have to know how the first genes originated, and I don’t. So I don’t believe any particular model. I can envision multiple different and distinct scenarios but I don’t have any good reasons currently to come down hard on any one.

3 Likes

This train of thought is pretty surreal. We know for a fact that new genes arise all the time in the biosphere. Given this, why would anyone posit a single ancestral gene for all proteins?

(I guess the irony here - that @stcordova’s point here, cryptic as it may seem, aligns universal common ancestry with a core ID tenet regarding protein evolution - probably should be spelled out. So there, I’ve done so.)

4 Likes

2 posts were split to a new topic: Gpuccio Comments on Peaceful Science

I just bought the 2nd edition for 27 dollars through Kindle. The printed version cost about 150. I made the decision to buy because I was able to get a free sample and realized it’s a good book. Thank you for the recommendation!

My only complaint is that it characterizes Entropy as “order and disorder”. This in an antiquated view that has roots in a passing remark by Boltzmann! The late professor of chemistry, Frank Lambert, did the world a great service by advocating a better qualitative approximation for entropy in terms of energy dispersal, albeit the formally adopted definitions of Entropy are the Planck-Boltzmann definition:

S = k_BW

where S is entropy, k_B is Boltzmann’s constant, W is number of microstates. Or the more traditional Clausius definition:

\Delta S = \int \frac{dQ}{T}
or

dS=\frac{dQ}{T}

Yes, there was a discussion not long ago on a chemistry prof mailing list of Lambert’s legacy. Since my General Chemistry days (almost 20 years now) the major textbooks have slowly converted over, due in large part it seems, to Frank’s efforts.

I do think the “disorder or randomness” conception of entropy has its uses, especially in its conceptual simplicity compared to “energy dispersal”, but it doesn’t really have quantitative value so I move fairly quickly to the mathematical definitions.

1 Like

So much for the modifier “peaceful” in the name peaceful science. I have a question. What is being asked for in the OP? Is it a challenge against the intellectual capacity of mind to think up a useful protein from scratch or is it a challenge against the notion that a mind can influence matter?

Neither. What is being requested is an account of the process by which ID proponents believe a “mind” led to the existence of a physical protein, with the amount of detail that ID’ers expect of evolutionary accounts.

1 Like

The detail of evolution are observations of how things are now, and then extrapolating them back to explain how things evolved. Genetic drift is observed, and then postulated to be the way that the genome can bridge the gap of the current functioning gene to a new functioning gene. Is that the kind of detail? Is the thread asking for a narative of a sythetic biologist as the explanatory process?

What do you mean? Nobody is fighting here.

I have a question. What is being asked for in the OP? Is it a challenge against the intellectual capacity of mind to think up a useful protein from scratch

It’s exactly what is being asked. Can Bill (or you) type out the amino acid sequence of a protein that will be able to perform the function I request? Can you just think such a protein sequence up without having to do any kinds of biochemical experiments, without any sort of computer modeling work, without any trial and error?

or is it a challenge against the notion that a mind can influence matter?

That came later in this thread, but yeah I put that challenge out there too. Can you show me a disembodied mind that exists completely independently of a physical substrate(no brain, no body, no physical hardware of any kind), which can wish or will proteins, DNA, or living organisms into existence?

1 Like

As any historical science, including geology, astronomy and so on. How did this mountain range, or river form? What are all those “holes” on the moon’s surface? Could they be craters? When did they happen?

Scientists draw from observations, and build models to explain data that is the result of past events.

Genetic drift is observed, and then postulated to be the way that the genome can bridge the gap of the current functioning gene to a new functioning gene.

Genetic drift is one part of some models that explain how some genes changed over time.

Is that the kind of detail?

Since you’re speaking in vague generalities instead of specifics, no. Evolutionary biologists can actually give remarkably precise models for how certain genes evolved, and how they changed and diversified over time, and back it up with experiments that corroborate those models.

I’d be very impressed if IDcreationists could do something even remotely similar. Explain when some gene was created, how it was created, what mechanisms were involved. Especially if they could show the invisible disembodied spook that can use it’s occult powers to wish functional proteins, if not entire living cells, or large multicellular organisms, entire populations of them, into existence. That’d be truly amazing.

Is the thread asking for a narative of a sythetic biologist as the explanatory process?

No I wouldn’t put the bar that high, I think IDcreationists should first learn to crawl before we ask them to even dream about matching the explanatory power of evolution.

1 Like

If evolutionary models were at the same level as present ID creationist models, they would look something like this: “Things changed into other things.”

2 Likes

I really like this book! So this is what P-Chem is about? Nice. I had no idea what it might be like.

The first chapters read like my Statistical Mechanics book, Pathria and Beale, which is good because I need to review, review, review. I was impressed that Partition functions were mentioned so early on. Wow!

This was nice quote I stumbled on:

The Molecular Logic of Biology Is Encoded in Coupled-Binding Actions Biological machines are varied and powerful, like computers. The power of computers comes from the multiplicity of useful ways that you can link together a few elementary logic units, such as and gates, or gates, and bistable flip-flops. In a simple logic device, you have two inputs x and y. Each input is given to be in one of two states, call them 0 or 1. A truth table (Figure 29.7) describes the outputs for the different possible inputs. Biology uses this principle too. Biomolecules can act as logic elements.

Dill, Ken. Molecular Driving Forces (p. 595). CRC Press. Kindle Edition.

I’m thinking of starting a separate thread on P-Chem just to deposit some of my thoughts, but this is exactly how I see the modern view of biology, with lots of computer-like processing. I see it with a lot of the binding and releasing and chemical modification. I’m glad my perspective isn’t idiosyncratic, though I’ve been criticized by some of my detractors for saying there is massive information processing in biological systems. I see it a lot in the post-translational modifications in Eukarytic proteins. The sophisticatoin boggles the mind!

But, back to the topic, when we talk about creating proteins with our mind, one of the issues is not really the fold, but in some cases like histones, one of it’s roles is like an information repository that is managed by bio-logic processes. Visually the bits and bytes that are read/written/erased can be visualized this way:

Histone_Common_img1%5B1%5D

When I saw this, I had a different view of what it meant to design a protein in a complex eukaryotic creature. It requires thinking of the protein not merely as a catalytic molecule, but rather an information storing molecule!

I saw this from another textbook:

chemistry lies at the heart of all biology

Alberts, Bruce. Essential Cell Biology (Fifth Edition) (p. 39). W. W. Norton & Company. Kindle Edition.

Reminds me of this:

1 Like

And physics lies at the heart of all chemistry.

Yes. And all evidence suggests that a mind capable of merely understanding, never mind designing, a such a system can only exist if this mind, itself, arises from an storage system of such complexity. It becomes increasingly absurd to claim that a mind capable of “designing” such a system could be simple. Can you explain why people insist on making such a claim?

1 Like