This brought it to mind

I have two quotes from two references referring to the bacteria flagellum as a “nanomachine” and with parts such as a “drive shaft, bushings, mounting plate, and a switch complex.”

One from Current Biology Vol 18 No 16, by Howard C. Berg:

“The flagellar motor is a remarkably small rotary electric motor that includes a stator, drive shaft, bushings, mounting plate, and a switch complex. The motors are powered by protons or sodium ions, that flow through channels from the outside to the inside of the cell. Depending upon the configuration, the rod, hook, and filament are driven clock wise or counter clock wise. Other components include a rod cap, discarded upon rod completion, hook cap, discarded upon hook completion, hook-length control protein, and a factor that blocks late-gene expression.”

and another from Nature Reviews Microbiology volume 6 June 2008 p 455:

“The bacterial flagellum, one of the most remarkable structures in nature: a complex self-assembling nanomachine” where “dozens of proteins, many of which have intrinsic self-assembly properties, need to come together in an ordered assembly process to complete these molecular nanomachines.”

Your last two posts are so elegantly responsive and persuasive that I have concluded that I can add nothing more to this thread.

My thanks to you and bFast, and all the rest who have been so kind to engage with me here.

This will be my last post on Uncommon Descent. There are two reasons for this: Jack Krebs and Ted Davis. Perhaps we will meet again in other venues.

Best wishes,

Daniel

Thanks for adding more support for my point:

I would not say that…

DNA error rates are higher than computer hard drive reading rates. My guess is that reading error rates for solid state ROM are even lower than for hard drives.

The higher unrecoverable error rate in DNA is an engineering tradeoff based upon density/compactness and transfer rate. For example, increasing the transfer rate with a DVD burner increases the error rate. That’s a designed tradeoff. Besides, we are comparing machines that are as big as my hand to something that is sub-cellular. I’d LOVE to see if humans can produce a data storage at that scale that maintains better data integrity at similar transfer rates.

Never mind, the real question is, “how badly do I want to maintain data integrity”? As in, you can have many layers of error correction. Biology even has a backup system for error correction. Damage to the DNA can completely block the high-fidelity polymerases so a different DNA polymerase, termed zeta, copies over many types of DNA damage. Unfortunately, it is not very good at matching the right DNA base when there is no damage. But tests where zeta was removed resulted in dead cells and dead mice since without zeta there are breaks in the chromosome. It’s possible that genetic entropy has caused additional but not “necessary” error correction mechanisms to become deleted or scrambled over time. It is possible that zeta used to be more effective.

(On a side note that highlights the difference in how a Darwinist and an ID proponent would look at evidence. Let’s say we find a creature where zeta “functions better”. A Darwinist would say it’s “more highly evolved” while an ID proponent would see it as a conserved element that had managed to survive the damages of time.)

ROMs? Every single CD/DVD has errors on it. It’s been found by engineers that allowing errors to occur and then correcting during replication/reading actually allows for higher copying performance. The reading of compact discs have a huge number of read/write errors (call them mutations if you will) designed into the system which are then corrected via Reed-Solomon coding. One would be inclined to ask why not make more reliable read/write processes so error correction is not needed, and why deliberate design a system with a high error rate? The answer is that if one’s teleological goal are for compactness of storage, according to Shannon’s theorem, this is the optimal way to store data: “allow numerous errors and then correct afterward”.

The uninitiated however, upon looking at this method of information storage would be inclined to criticize the designers as incompetent. Biologists will say exactly that, “a competent designer would not have made DNA copy mechanisms which require error correction, he would have made a copy process which got it right on the first pass.” That is why they are biologists, not engineers.

Finally, the CD/DVD medium degrades fairly quickly within a decade, while apparently DNA can maintain data integrity in an inert state for quite a while.

Besides, biology NEEDS its error correction.

If you mean by “it” that DNA is a form of abstracted information, then I can only ask WHO is doing the abstracting?

I would say that is the wrong question to begin with. “WHAT is doing the abstracting” can be answered readily: it’s the physical mechanisms that know the conventions of the abstracted information and converts from one state to another. Unfortunately, we do not fully comprehend these conventions at this time since we cannot look at the information and say, “look, this information here is what makes a horse a horse and a fly a fly”.

As for the WHO, can you tell WHO designed a hard drive by analyzing the conventions and mechanisms? Yes, you could go to the patent office but unfortunately we don’t have that link-in-the-identification-chain for DNA. But you seem to be under the impression that ID proponents must identify the Designer(s) in order for core ID to be valid…but that assertion has been answered in book-form many times and I won’t reiterate it here.

I am happy to see you being so conciliatory and agreeable. Areas where we have substantial agreement will not be commented on, but they are still appreciated.

You continue to insist, speaking about my scientific view regarding the origin of life, that “your view has a theological basis.” You seem incapable of understanding that it is precisely the reverse; that my theology has a scientific basis.

Look at what you quoted in (211), your statement from (142),

Surely your faith does not rest on such a slender reed.

To this I replied (146), “WHy not? . . .”

Is it not obvious that my faith “rests on” science rather than vice versa?

You go on to recite an old, and in my case tired, canard:

Such persons [presumably persons who do not use miracles to sustain their faith] seem to be more comfortable with letting science go wherever curiosity leads it.

Do they really? Why the resistance to simply saying that, regarding OOL, “we don’t know how it happened without intelligence, we may never know, and it may not even be true”? Did you read the quote from Robert Shapiro in (114)? Let me quote it again:

Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin for life have failed unequivocally. Further, new geological evidence may indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. In such a case, some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.

Does that sound “more comfortable with letting science go wherever curiosity leads it”?

Look at what I wrote in (143) to Ritafairclough. I made it clear that my theology was based on science, rather than the reverse. I agree that the Catholic Church made a mistake regarding Copernicus and Galileo. I agree that it was part of a series of mistakes. But it is at least possible that by the time of Lyell and Darwin the pendulum had swung the other way.

And as far as the mistake went, it could even be argued that the church thought too much of traditional “science”, and that is why they made the mistake they did. After all, ask yourself which side the majority of the academics was on at the time. So much for consensus.

In fact, even in the case of Augustine and The Literal Meaning of Genesis this mistake was made; Augustine was arguing for instantaneous creation, rather than in 7 days, because a slow creation implied the lack of perfection in the incipient stages, and according to the dominant philosophy, God couldn’t create anything that wasn’t absolutely perfect. Besides, according to Ecclesiasticus, God made all things “simul” (a bad Latin translation), and why should light go around a round earth in 24 hours? It was easy for the sun to do it, but why disembodied light? Of course, now we don’t need light to go around the earth. The earth turns. Augustine just blew it, because he had too much respect for “facts which [infidels] have learnt from experience and the light of reason”. (These are my conclusions from my own reading of Augustine.)

Thank you for allowing me to be “absolutely entitled to [my] views”. I will be even more happy if you try to understand and accurately state them, rather than criticize views which I do not hold as if I held them.

You say,

Science can only grasp what it can reach. The miraculous is out of its reach. And therefore safe from science.

Are you saying that potentially there are some areas of physical reality that are out of the reach of science? Or that miracles aren’t physically real?

You (212) are right that your response to the Qbeta-montmorillonite comparison question had two parts. I addressed the first part in (207), and you did not respond. Once we settle that part, we can discuss the second.

Let me illustrate the problem with your difference another way. Supposing that some researchers were trying to create oil from methane using montmorillonite. They added ammonia, water, and calcium phosphate, and heated the mixture. When they examined the mixture, they discovered that it contained 0.01% ATP. Would you instantly denigrate that information on the basis that it wasn’t aimed at OOL research? Would you denigrate any further research in this area (say, trying to see if GTP or CTP could be created in this way) because the original research was not aimed at OOL?

On the question of whether there is a difference between computer code and DNA code regarding mutability, I read your response in (192) and responded to it in (199), and you didn’t respond to that. That is why I asked in (207), “Should I take your silence regarding your statement

6. Stability – computer machine language is not subject to random mutational change :: DNA is highly mutable.

that you no longer would maintain this argument?”

I am not arguing that there are no differences between DNA code and computer code. That is one reason why, in contrast to bFast, I have not argued against your calling the two groups of systems analogous rather than members of one group.

But your hard drive will eventually fail. If you want to keep you data pristine, you will eventually need a backup. I know from personal experience. Ram can introduce glitches, as you acknowledged. Even ROM can fail. I have had that happen too. And I just had to discard a disc because part of the data had been corrupted.

Look, make it easy on yourself. Without having to surrender your main point, that DNA code and computer code have significant differences, just admit that mutability is not one of those differences. That’s the “conciliatory and agreeable” thing to do.

Thanks for adding more support for my point: DNA error rates are higher than computer hard drive reading rates. My guess is that reading error rates for solid state ROM are even lower than for hard drives. Do you have any info on that?

Finally, no one can argue against it being a form of abstracted information. Or do you?

If you mean by “it” that DNA is a form of abstracted information, then I can only ask WHO is doing the abstracting?

DNA viruses have error rates between 10^6 to 10^8 mutations per base per generation, while the human genomic error rate is at ~2.5×10^8 per base per generation. Despite these estimated error rates people can still “count on” reproducing successfully.

Also, these error rates are estimates and under contention:

http://www.uncommondescent.com.....ent-177561

Now I could understand if you were asserting that “language” is too vague or not specific enough. But I find even “recipe” too vague. Now “code” would be better, but even that’s a subset of “language”, and you reject that because in your mind “code” signifies “human intelligence”…which does not explain SETI. Finally, no one can argue against it being a form of abstracted information. Or do you?

“The contrast is that the QBeta work was not directed at abiogenesis from its inception, and yielded no data relevant to the subject.”

Your evaluation of the difference, in my book, doesn’t fly. What a given experiment was aimed at does not determine its relevance. Let me give two relatively uncontroversial examples. The research that discovered the first antibiotic, penicillin, was in fact initially aimed at studying bacterial growth, not chemicals that are toxic to bacteria. It was nevertheless highly significant in the latter field. And the research that discovered the primary effect of Viagra was originally aimed at controlling angina, and Viagra was a failure in that regard. However, it has been extremely helpful in treating erectile dysfunction.
Perhaps you can find another difference between the Qbeta research and the montmorillonite reseearch.

My statement quoted above was in response to your request in #198:

Compare and contrast this work with the Qbeta work. I would be quite interested in your analysis.

My statement had two clauses. The first was “…the QBeta work was not directed at abiogenesis from its inception…” That is a truth, a datum, that distinguishes the QBeta work from the Ferris work. So it was responsive to your request. The second clause was “…yielded no data relevant to the subject.” It’s in the second clause that I addressed relevance.

I have already given you reasons for my opinion about the QBeta work (#149):

…knowing what I know about the Spiegelman and Haruna work on bacteriophage QBeta, I can state that their work is irrelevant to issuesof abiogenetic RNA syntheses.

QBeta is a small, icosahedral virus (bacteriophage) that infects E. coli. Its genome is a single-strand of RNA about 4,000 nucleotides in length, encoding three structural proteins and a replicase (RNA-copying enzyme). [see, for example, Klovins, J, Berzins, V and van Duin, J RNA 1998 4: 948-957]

In earlier work, [Haruna and Spiegelman Proc Natl Acad Sci U S A. 1966 Jun;55(6): 1539-54] had discovered an exquisite specificity of the phage replicase: it only works when provided with its own genomic RNA as a template for copying. This makes sense biologically, for if the replicase recognized and were bound as well as its own genome by the far more abundant messenger RNA molecules in infected cells, replication of the viral genome couldn’t get off the ground to generate new phage genomes. Another biological point: the phage is a highly evolved organism that replicates with maximum efficiency. It contains no genetic sequences that are not essential to its survival. There is no reason (no survival advantage) why its replicase should synthesize any additional information either in vivo or in vitro.

But if you want to consider the QBeta relevant to abiogenesis, that is your privilege.

Regarding (206), on your statement (1), perhaps we should just agree to differ, as we seem to differ on the definition of the word “datum”.

Call it a datum, call it an hypothesis, it still constitutes a difference between computer machine code and DNA. To the best of my knowledge, computer code was invented by human beings, whereas, to the best of my knowledge, DNA was not invented by human beings.

But if you want to argue that human beings invented DNA 3.5 billion years ago, that is your privilege.

Should I take your silence regarding your statement
“6. Stability – computer machine language is not subject to random mutational change :: DNA is highly mutable.”
that you no longer would maintain this argument?

See again #192, my response to bFast:

bFast: 6 Stability, “computer machine language is not subject to random mutational change” The computer techs are howling now! The reality is that periodically, too often, RAM slips a bit.

Daniel King: There’s a heritable change in the machine code?

bFast: Now, computers under normal operation twiddle with the memory in a very controlled fashion. Even there, however, computers will intentionally initialize memory to a random sequence. Certainly computer A will share executable segments with computer B, aka horizontal gene transfer.

Daniel King: Since you’ve brought my microwave oven into the big tent of computer machine language, please explain how the firmware is subject to random mutational change. Ditto for my CD player, dishwasher, cell phone, iPod, etc., etc.

I don’t think it should be up to me to clarify your analogies for you, but surely you are not equating the information in DNA (read-only memory) with occasional glitches in RAM electronics. If I couldn’t count on my BIOS to boot my machine, and if I couldn’t count on my hard drive to maintain the integrity of my operating system and programs, my computer wouldn’t be of much use.

But, if you want to equate DNA to RAM, that is your privilege.

(Note how conciliatory and agreeable I have become.)

All I wanted to point out is that the Qbeta work does not falsify the statement. It looks like we have agreement here.

The relationship, if any, of the QBeta work to your statement, “It’s the naturalistic OOL researchers that engage in speculation against the evidence,” is so remote that I am delighted to certify agreement here.

You are overreading. I said
“And there are some OOL researchers that recognize this. . . . I was talking about honesty about where the evidence is at present, and at least some of them are in fact honest about that fact.”
I was only stating what I could prove. It is possible that all OOL reserchers recognize explicitly that they have not reached the goal of showing how life developed from non-life, or could have developed. If so, I haven’t read it. Notice the “at least some”, which leaves open the possibility that “all” could fit the statement.

The only way to find out what all OOL researchers recognize explicitly would be to poll them.
But you have already noted with satisfaction that some of them criticize the work of others, which is an exemplary corrective.

But as you wish me to read them more charitably, I wish that you would read me more charitably.

I am doing the best I can to understand what you are saying.

I never said that we do not have the right to ask questions. I merely said that we don’t have the right to demand answers. There is a difference. There are some questions I’d like to ask about the first three flights on 9-11 that I’d like to know. Did any of the passengers think that they ought to take control of the airplane, and perhaps even try to do so but in a disorganized way? But I know of no way, either now or in the future, that we will ever know, or even have good evidence for a hypothesis regarding the question. Some things are just beyond our ability to discover. That doesn’t mean that we can’t ask the question. It just means that we can’t demand an answer.

(Emphasis added)

How does one determine those limits? Have we already reached those limits with respect to abiogenesis? From what you have written, it appears that you think so. And your view has a theological basis. For example:
You said in #114:

I am not sure that there is any other way to detect the existence of a deity than otherwise unexplained events in nature or
history (which is claimed as a part of nature by believers in naturalism).

To which I replied in #142:

Surely your faith does not rest on such a slender reed.

To which you responded in #146:

Why not? Did not the apostle Paul (1 Cor. 15) stake his entire belief system on the historicity of a miracle? Besides, I thought that a religion that was falsifiable would be superior to one that was not. A religion that is not falsifiable cannot, and for that reason, tell us anything about nature. It would seem to be an advantage for a religion to guide us when dealing with nature.

And let’s not forget your reference to Deuteronomy (#135)

It seems to me that you feel a need to protect the miraculous, so you oppose science that calls the miraculous into question. You are absolutely entitled to your view, of course. But for many other religious people, belief in the miraculous is not such a big issue; other consideratons sustain their faith. Such persons seem to be more comfortable with letting science go wherever curiosity leads it.

I was brought up a Catholic, and you may know that my Church has learned a lot from its conflict with Galileo and Copernicus. As I see it, the politics of the Counter-Reformation were a major factor in that blunder. St Roberto Bellarmino should have been more cognizant of what St. Augustine wrote in The Literal Meaning of Genesis:

Usually, even a non-Christian knows something about the earth, the heavens, and the other elements of this world, about the motion and orbit of the stars and even their size and relative positions, about the predictable eclipses of the sun and moon, the cycles of the years and the seasons, about the kinds of animals, shrubs, stones, and so forth, and this knowledge he hold to as being certain from reason and experience. Now, it is a disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics; and we should take all means to prevent such an embarrassing situation, in which people show up vast ignorance in a Christian and laugh it to scorn. The shame is not so much that an ignorant individual is derided, but that people outside the household of faith think our sacred writers held such opinions, and, to the great loss of those for whose salvation we toil, the writers of our Scripture are criticized and rejected as unlearned men. If they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the kingdom of heaven, when they think their pages are full of falsehoods and on facts which they themselves have learnt from experience and the light of reason? Reckless and incompetent expounders of Holy Scripture bring untold trouble and sorrow on their wiser brethren when they are caught in one of their mischievous false opinions and are taken to task by those who are not bound by the authority of our sacred books.

You also wrote (first quoting me):

“Life was invented out of chemicals. Somehow.”
Well, yeah. Science may or may not find out how. If science eliminates a whole category of causes, and the real answer lies within that category, then science will not find the answer. That much is guaranteed.

Science can only grasp what it can reach. The miraculous is out of its reach. And therefore safe from science.

Daniel King, thanks for the sited studies in post #179, I had missed this post. It’ll take me a while to absorb them, but I will.

Again, bFast, thanks for your interest. The people who seem (to me) to be doing the most interesting work on the RNA world are Jack Szostak, Gerald Joyce, and David Bartel. A good way to get free full text of many of their papers is to Google Szostak lab, or Joyce lab or Bartel lab and go to their bibliographies. Take a look at Szostak’s more recent work on artificial cells for some imaginative approaches to inventing life in the lab.

As to your wiki definition of language, please note that computer languages do not meet the definition any better than DNA does.

Exactly my point! “Computer languages” and “DNA as a language” are both figurative uses of the word “language.” And one of my objects here has been to criticize such figurative uses as sloppy talk that leads to faulty thinking.

I’m enjoying all of the agreement we’re reaching on this thread.