A Simple Gene Origination Calculation

_{July 27, 2008

Intelligent Design}

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In this month’s Nature Genetics, there is an article by Zhou, et. al., dealing with the generation of new genes in Drosophila melanogaster—the fruit fly. While only having access to the abstract, I nonetheless was struck by one of their findings: the rate of new functional gene generation. As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

Here’s the link to the abstract.

Comments

I realized I never responded to Daniel at #203 regarding the status of biological objects as machines. 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.”
Patrick_{September 15, 2008
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Paul Giem and Patrick: 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, DanielDaniel King_{September 9, 2008
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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.Patrick_{September 8, 2008
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Daniel King, 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.Paul Giem_{September 2, 2008
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Hi, Patrick, 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?Daniel King_{September 2, 2008
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Modern hard drives (2008 models) have an average non-recoverable read/write error rate of 1 in 10^15 per hard drive. This is quite an improvement because I believe the error rate was around 1 in 10^13 just a few years ago and far worse 10+ years ago. And I just fixed a laptop where key OS files had been degraded. The machine was less than one year old. DNA viruses have error rates between 10^6 to 10^8 mutations per base per generation, while the human genomic error rate is at ~2.5x10^8 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: https://uncommondescent.com/intelligent-design/the-altenberg-sixteen/#comment-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?Patrick_{August 30, 2008
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Reply to Paul Giem #207, part 2:
"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.)Daniel King_{August 30, 2008
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Reply to Paul Giem #207, part 1:
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_{August 29, 2008
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bFast #208:
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.Daniel King_{August 29, 2008
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Oops, the studies are in #170.bFast_{August 28, 2008
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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.
Anyway, I’ve got to ask…if DNA is not a language, then what is it?
It’s a RECIPE!
One thing is clear, DNA seems to use a fundimentally different coding technique than we programmers use, a technique that may need to find its way into computer programming. This technique is well described as a recipe. Computer software has gone through a number of fundimental changes, from sequential, to block structured, to object oriented. Custom languages have used even different structures, like lisp and its list structure. In each case, the CPU needed to make no changes to adapt to the different coding styles. To describe the coding style in DNA as "recipe" style makes lots of sense. However, it does not change the fact that the underlying technology is a pretty straightforward computer. Note the wiki in 119 states: "it contains the instructions". This statement clearly defines DNA as computer code -- it is a bunch of instructions! As to your wiki definition of language, please note that computer languages do not meet the definition any better than DNA does.bFast_{August 28, 2008
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Daniel King, You said, (204)
As long as you understand that I do not accept your quoted statement, I agree that you understand my thinking about the QBeta work.
I agree that our agreement about the Qbeta work is not adequate to prove, or even reasonably prove, my quoted statement. That means that I wouldn't expect you to accept that statement without something else as evidence. All I wanted to point out is that the Qbeta work does not falsify the statement. It looks like we have agreement here. You said, (204)
Thanks very much for the clarification. I would, however, object to the aspersion of dishonesty among “some” abiogenesis researchers.
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. I suppose it might have made it easier for you if I had said "there are some OOL researchers that explicitly recognize this." But as you wish me to read them more charitably, I wish that you would read me more charitably. (I have run into people defending naturalism who insist that naturalism has solved the OOL problem. None of them, to my knowledge, are OOL researchers. I can name at least one name, if you wish. Otherwise, we can just move on.) To the question of how life came to be, you quote me (204, accurately) as saying,
But the same answer still applies. If it was done by an intelligence (or Intelligence), thousands, let alone billions, of years ago, do we have the right to demand that we can reconstruct the mechanism without asking any eyewitnesses? And if we can’t do so, and there are no earthly eyewitnesses, we’re kind of out of luck, aren’t we? That is, unless the one (or One) who did it tells us how, but let’s not go there right now.
You then reply,
On the contrary, we not only have the right to ask questions and to think about the past (no matter how far past), we have the obligation as thinking beings to do so. That’s what God gave us brains for. Eyewitnesses are not essential to a number of sciences, including history, astronomy, archeology, paleontology, geology, etc.
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.
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. Commenting on your (205),
A nice critique.
Thank you.
The work “commonly” is too vague, I think. Based on the Ferris work, “more commonly under some conditions” would be more accurate.
Let me try again. 8. Except in highly unusual and somewhat artificial situations, when nucleotides polymerize naturally into RNA, a significant number of linkages are 2',5' linkages rather than the 3',5 linkages normally found in RNA. Keep in mind that this is a fallible obstacle. If we discover that a montmorillonite from Antarctica can be simply added to ATP without pretreatment (or perhaps pretreatment with dilute seawater), and without HEPES, with the specificity noted by Kawamura and Ferris, then the obstacle will essentially fail. These obstacles are scientific, and therefore cannot be absolute. That's why I preferred to refer to them as obstacles rather than dealbreakers. But the possibility that they may be wrong is not evidence that in fact they are wrong. Currently, the assertion that they are wrong is a faith statement, and the evidence we have now argues that in fact they are right. I believe that faith has a place in our trying to sort out reality. I even believe on occasion without evidence, and occasionally against the evidence. Without that belief, I would never do research into a controversial subject that most scientists would consider closed. But I wouldn't dream of telling those who differ with me on the basis of evidence that they should just take it from me, in spite of the evidence, that they are wrong, let alone stupid for their belief.
Yes, it is evidence for. Possibly. A teeny weeny bit. We’re taking baby steps at this stage of development in the field. he 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. 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". 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 have much sympathy for the ID position. I wouldn’t have engaged in this discussion if I didn’t think there were issues worth analyzing. And I have enjoyed and profited from this engagement. I thank you especially for calling my attention to Shapiro’s Origins, which I now have in hand and am reading with pleasure. It is a beautiful example of scientific writing for non-scientists.
Thank you. And even though the conversation has had some rough edges at times, I think we've all learned from it. I know I have, and I have appreciated the opportunity to learn. You're certainly welcome regarding Shapiro. I agree wholeheartedly with your assessment of his writing. I'm glad I could introduce you to him.Paul Giem_{August 28, 2008
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Paul Giem #199:
You stated, My statement (1) was not an argument. It was a datum. An iota of evidence. Just as “hypotheses are not evidence,” so “evidence is not an hypothesis.” No hypothesis = no argument = no possibility of question-begging. But it is not a datum. Part of what I pointed out is that in fact, humans have designed DNA. Perhaps small pieces of DNA, but they have done so. Furthermore, without further evidence, one cannot say that humans did not create the DNA needed to start life, or to create the Cambrian explosion, or whales, or other humans. For all we know from science, the whole mess could have been created by a very intelligent graduate student )or series of graduate students) with a supersupercomputer. Now, that’s not what I think most likely happened. But I do think that it was some kind of intelligence. Your argument starts to sound like “we know it wasn’t aliens, and God either doesn’t exist or doesn’t muddy his hands with nature.” That is effectively an antitheist position. Don’t be too surprised if some of us find it unconvincing as the starting point for an argument.
Don't be surprised if I find your equivocations about current capabilities of human genetic engineers and the historic origin of DNA unconvincing. Here is my statement again:
computer machine language was designed by human beings :: DNA was not designed by human beings
Looks like a datum to me.
With your agreement that there is evidence for ID, at least in the case of OOL, one can dispense with this line of reasoning.
I have much sympathy for the ID position. I wouldn't have engaged in this discussion if I didn't think there were issues worth analyzing. And I have enjoyed and profited from this engagement. I thank you especially for calling my attention to Shapiro's Origins, which I now have in hand and am reading with pleasure. It is a beautiful example of scientific writing for non-scientists.Daniel King_{August 27, 2008
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Paul Giem #198:
I have finally been able to get a copy of Kawamura and Ferris (1994) [J. Am. Chem. Soc. 116, 7564–7572], and I have some comments. [...SNIP...] Given this paper, IMO, my obstacle 8 should be rewritten to read: 8. Except in highly unusual and somewhat artificial situations, when nucleotides polymerize naturally into RNA, they commonly form 2?,5? linkages rather than the 3?,5? linkages normally found in RNA. Would you dispute that obstacle using evidence from the literature?
A nice critique. In the current state of our ignorance, all experimental conditions may be judged artificial, so you may make as much of that as you like. The work "commonly" is too vague, I think. Based on the Ferris work, "more commonly under some conditions" would be more accurate.
Finally, how would you classify this paper? Is it evidence for a “plausible prebiotic scenario”, as the authors seem to think?
Yes, it is evidence for. Possibly. A teeny weeny bit. We're taking baby steps at this stage of development in the field.
Is it not relevant to OOL research, as you have stated about the Qbeta research?
Yes, it's relevant, as the QBeta work was not.
Or is it net evidence against abiogenesis?
How can it be evidence against? You have argued that it's not evidence for. Your opinion doesn't constitute evidence against.
Compare and contrast this work with the Qbeta work. I would be quite interested in your analysis.
The contrast is that the QBeta work was not directed at abiogenesis from its inception, and yielded no data relevant to the subject.Daniel King_{August 27, 2008
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Paul Giem #197:
Rather, my point was the narrow one that the Qbeta experiments were not evidence against the statement that "It’s the naturalistic OOL researchers that engage in speculation against the evidence." My understanding is that you would not regard it as evidence either for or against that proposition, and so it cannot serve as evidence against it. Do I understand correctly? If so, we have a deal, and in future lists of obstacles to evolution, at least until the other side brings it up, I would plan not to mention the subject.
As long as you understand that I do not accept your quoted statement, I agree that you understand my thinking about the QBeta work. As I believe I said above, I consider it to be irrelevant to abiogenesis.
Note that what I said was not that the quest was futile, not that it could not achieve its goal, but rather the more limited claim that it had not achieved its goal. And there are some OOL researchers that recognize this. See the extensive quotes by kairosfocus in (72), and read Shapiro’s Origins (which hopefully you will get soon through interlibrary loan). So I do not “mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest.” I was not talking about futility. 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.
Thanks very much for the clarification. I would, however, object to the aspersion of dishonesty among "some" abiogenesis researchers. Such ad hominems are bad form in scientific discourse. If you really want to make that kind of case, name names and back up your assertions with evidence.
My question was directed at HOW, not WHETHER. If a Creative Intelligence invented life, HOW did it do it? But the same answer still applies. If it was done by an intelligence (or Intelligence), thousands, let alone billions, of years ago, do we have the right to demand that we can reconstruct the mechanism without asking any eyewitnesses? And if we can’t do so, and there are no earthly eyewitnesses, we’re kind of out of luck, aren’t we? That is, unless the one (or One) who did it tells us how, but let’s not go there right now.
On the contrary, we not only have the right to ask questions and to think about the past (no matter how far past), we have the obligation as thinking beings to do so. That's what God gave us brains for. Eyewitnesses are not essential to a number of sciences, including history, astronomy, archeology, paleontology, geology, etc. Life was invented out of chemicals. Somehow.Daniel King_{August 27, 2008
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Patrick #196:
Would you also assert that the bacterial flagellum is not a machine?
Of course I would. The bacterial flagellum can be likened to a machine, such as an outboard motor - a device designed and built by human beings. Similarly, my exercise trainer used to tell me that he was going to transform me into a "Lean, mean, fighting machine." (He failed.) But I didn't take him literally, because I know that I am not a device that was designed and built by human beings. Giving a name to something does not make it into that thing. As a notorious ex-president of the US once said, "It depends on what the meaning of the word is is."Daniel King_{August 27, 2008
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Whoops! That was DaveScot (200)Paul Giem_{August 26, 2008
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DaveScot (201), You are quite right that a professional program will be write-protected and that therefore if you copy the backup copy onto another computer, the bug in the first computer's copy will not affect either the backup copy or the other computer. However, if you copy the first computer's copy to another computer, the bug will be replicated. And if the backup copy develops a bug, say, through a scratch, the bug will be replicated as well. If you lose the backup copy, or forgot to make one when you programmed (I know, I know, how stupid can one get? Pretty stupid!), you have only two choices; fix the bug (and make a backup copy), or live with a defective program. The point I was making, which is still valid, is that mistakes in computer code are heritable, just like DNA changes. It is interesting that DNA comes with a built-in backup copy. What a neat idea! It's almost like someone designed it that way!Paul Giem_{August 26, 2008
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Paul Giem I hate to tell you this, but if a program you are using develops a bug, and you copy it to another computer, the new copy will still have the bug. I don't mind telling you that you're quite wrong. If the program develops a bug while being used the bug won't be on the write-protected copy that software is distributed upon. Generally when software is copied onto a computer it will be from a write protected diskette or CD-ROM onto a hard drive. When the software is copied onto another computer it is generally from the original diskette or CD-ROM not the local copy on a hard drive.DaveScot_{August 26, 2008
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Daniel King, (194) You refer me to your response to bFast defending your claim that "computer machine language is not subject to random mutational change". You ask, innocently I presume,
There’s a heritable change in the machine code?
I hate to tell you this, but if a program you are using develops a bug, and you copy it to another computer, the new copy will still have the bug. You go on to ask bFast, "Other than possible employment in pedagogy, of what heuristic value is the analogy?" Which leads me to ask, have you ever programmed a computer? Because, to someone who has, your question sounds uninformed, to put it politely. You stated,
My statement (1) was not an argument. It was a datum. An iota of evidence. Just as “hypotheses are not evidence,” so “evidence is not an hypothesis.” No hypothesis = no argument = no possibility of question-begging.
But it is not a datum. Part of what I pointed out is that in fact, humans have designed DNA. Perhaps small pieces of DNA, but they have done so. Furthermore, without further evidence, one cannot say that humans did not create the DNA needed to start life, or to create the Cambrian explosion, or whales, or other humans. For all we know from science, the whole mess could have been created by a very intelligent graduate student )or series of graduate students) with a supersupercomputer. Now, that's not what I think most likely happened. But I do think that it was some kind of intelligence. Your argument starts to sound like "we know it wasn't aliens, and God either doesn't exist or doesn't muddy his hands with nature." That is effectively an antitheist position. Don't be too surprised if some of us find it unconvincing as the starting point for an argument. I will finish on a note of agreement. As you quoted me and commented,
Is there any reason to believe, on the basis of evidence, that ID is the correct explanation for OOL? The answer, judging from your own posts, is yes. You may call the evidence weak (although others will differ), but there is in fact evidence.
Well put, and agreed to.
This means that an ID approach to OOL issues is not simply a matter of "speculation", as you indicated in (57). I claimed in (59) that "There is a lot of experimental evidence to back us up." One may dispute how much "a lot" is, but is it good to see that we can at least agree that there is evidence for the proposition that ID is the correct explanation for OOL. You may not argue this way, but I have run into multiple people who will argue that there is no evidence for ID, and a lot of evidence for "evolution". This us usually related to the claim that ID is not science (because there is no evidence for it), and therefore must be religion, since it refers to God (DaveScot notwithstanding), whereas OOL research is scientific. This sets up a Science versus Religion debate, and the "religious" side is presumed to automatically lose, without even a need to consider the evidence. With your agreement that there is evidence for ID, at least in the case of OOL, one can dispense with this line of reasoning. :)Paul Giem_{August 26, 2008
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Daniel King, I have finally been able to get a copy of Kawamura and Ferris (1994) [J. Am. Chem. Soc. 116, 7564–7572], and I have some comments. First, judging from the products' reaction with RNase T2, the linkages of some parts of the experiment were nearly pure 3',5'-linked. So at first glance it would appear that 3',5' linkages can be made using natural materials. So the experiments seem to suggest one possible way that RNA can be made without 2',5' linkages. That would be a way around one of my obstacles. It is also interesting to note that the authors of the paper see this as related to OOL. The last 4 sentences of the paper (excluding the acknowledgment) were:
Structure analysis of the reaction products revealed that only the 3',5'-linked dinucleotide was formed in each reaction. The observation of the regiospecific formation of the corresponding 3',5'-linked dinucleotide was unexpected. This observation suggests that it will be possible to synthesize 3',5'-linked oligonucleotides on montmorillonite if the activated monomer, in this case ImpA, is the limiting reagent. This is also a plausible prebiotic scenario for regiospecific oligonucleotide synthesis since it is likely that the concentrations of activated mononucleotides were quite low on the primitive earth.
However, on second glance, things aren't quite what they seem. The montmorillonite (clay from weathered volcanic rock) isn't just dumped in. Only certain clays, ones from American Colloid Compound (unstated provenance), Japan, and Wyoming, would significantly cause the reaction. Clays from the San Diego, CA area (Otay), Arizona, and Texas "exhibit little or no catalytic ability". There is some evidence suggestion that iron may have something to do with the catalytic activity. But not only must we carefully choose the clay; we must also pretreat it with hydrochloric acid, then neutralize it with sodium hydroxide. This is a bit more difficult to visualize on the primitive earth. Then we must add magnesium chloride (calcium chloride is not nearly as effective). By this point we are starting to reach. We start to overbalance in our reach when we realize that HEPES (N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid) is added to the reaction. Where HEPES came from on the primitive earth is not clear. The starting compound, IMO, pushes us over the edge. It is the 5'-phosphorimidazolide of adenosine. Adenosine itself is hard enough to make. Now we must add a phosphate group, then remove an oxygen from that phosphate and add an imidazole group. The authors' laconic comment that "it is likely that the concentrations of activated mononucleotides were quite low on the primitive earth" is a breathtaking understatement. Of interest in this regard is that, judging from figure 5, the major reaction catalyzed by montmorillonite, consuming roughly 3/4 of the reagent (estimated from the graph) is simply hydrolysis of ImpA. That makes the reaction even less likely. And even in ideal circumstances, oligomers of 10 parts seems to be the practical maximum. The authors note that "The exclusive formation of 3',5'-linked dinucleotides under the condtions used for the kinetic studies was an unexpected finding." Presumably, most other experiments had found a significant number of 2',5' linkages. Given this paper, IMO, my obstacle 8 should be rewritten to read: 8. Except in highly unusual and somewhat artificial situations, when nucleotides polymerize naturally into RNA, they commonly form 2',5' linkages rather than the 3',5' linkages normally found in RNA. Would you dispute that obstacle using evidence from the literature? Finally, how would you classify this paper? Is it evidence for a "plausible prebiotic scenario", as the authors seem to think? Is it not relevant to OOL research, as you have stated about the Qbeta research? Or is it net evidence against abiogenesis? Compare and contrast this work with the Qbeta work. I would be quite interested in your analysis.Paul Giem_{August 26, 2008
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Daniel King, (193) Thank you for your responses (193 and 194). It looks like we almost have a deal, and the only sticking point is 3. My original statement was,
3. I would like an explicit acknowledgment that in this specific area, my claim (79) that
It’s the naturalistic OOL researchers that engage in speculation against the evidence.
has not been falsified.
Your response was,
3. If your blanket claim has been supported by anything other than quotations from Shapiro and Kacian et al., please advise. In any case, speculation against the evidence is a matter of opinion. From what I’ve seen from serious OOL researchers are good faith efforts to speculate in light of the evidence.
Your reply addresses the larger picture, not the very limited point I was making and trying to get agreement on. I specifically was not saying, and not trying to get your assent to, the proposition that my quoted statement from (79) had been proved, or was correct, or even had evidence for it. We can discuss that later. Rather, my point was the narrow one that the Qbeta experiments were not evidence against the statement that
It’s the naturalistic OOL researchers that engage in speculation against the evidence.
My understanding is that you would not regard it as evidence either for or against that proposition, and so it cannot serve as evidence against it. Do I understand correctly? If so, we have a deal, and in future lists of obstacles to evolution, at least until the other side brings it up, I would plan not to mention the subject. You said,
I assumed that you would find the Ferris review helpful as an overview.
As you can see, the overview had several significant defects, especially as regards the question of 2',5' versus 3'.5' linkages. It also has the inherent defect of being secondary versus the primary reporting of experiments. But I can appreciate your reasoning. You say,
“We should be honest enough to admit this fact…,” in reference to not being surprised about not finding a “pathway to life without intelligence…” I take this to mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest.
You have misinterpreted me. Let me make it clearer. My original statement was,
I just think that it is possible that there is no pathway to life without intelligence, and that if so we should not be surprised to not find one, and that if we do not find one we should be honest enough to admit this fact, and that this admission can be, and at present is, an evidence-based statement.
The pronoun "this" could be taken ambiguously. My intention was to take it in the following way: ". . . and that if we do not find one [a pathway to life without intelligence] we should be honest enough to admit this fact [the fact that we have not found a pathway to life without intelligence]" Note that what I said was not that the quest was futile, not that it could not achieve its goal, but rather the more limited claim that it had not achieved its goal. And there are some OOL researchers that recognize this. See the extensive quotes by kairosfocus in (72), and read Shapiro's Origins (which hopefully you will get soon through interlibrary loan). So I do not "mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest." I was not talking about futility. 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. You say,
My question was directed at HOW, not WHETHER. If a Creative Intelligence invented life, HOW did it do it?
But the same answer still applies. If it was done by an intelligence (or Intelligence), thousands, let alone billions, of years ago, do we have the right to demand that we can reconstruct the mechanism without asking any eyewitnesses? And if we can't do so, and there are no earthly eyewitnesses, we're kind of out of luck, aren't we? That is, unless the one (or One) who did it tells us how, but let's not go there right now.Paul Giem_{August 26, 2008
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Would you also assert that the bacterial flagellum is not a machine?Patrick_{August 25, 2008
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Patrick #191:
Last I heard people were working on using DNA for high density data storage with a MUCH longer shelf life than CDs/DVDs.
Yes, human beings are capable of manipulating DNA (among other entities) in imaginative ways for computing or other purposes. But in the context of my remarks to bFast, I was comparing DNA, as it functions in natural biological systems, to computer machine language.
Anyway, I’ve got to ask…if DNA is not a language, then what is it?
It's a RECIPE! See this:
A language is considered to be a system of communicating with other people using sounds, symbols and words in expressing a meaning, idea or thought. This language can be used in many forms, primarily through oral and written communications as well as using expressions through body language.
I assert that all other usages of the word "language" as employed by you and other worthy persons (including computer scientists) are figurative and therefore not probative. Are those figurative employments profitable for scientific purposes (except pedagogically)? Once again: What matters is the bottom line, which awaits a response from you and your colleagues:
What Further Fruitful hypotheses Follow from the hypothesis that DNA is a language?
Daniel King_{August 25, 2008
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Paul Giem #190:
I have to agree with bFast (188); your differences fail. The first and the last fail worst. The last one is the worst; it is a true FAIL. ROFL! Do you have any idea how many programs get corrupted every year? The problem isn’t that computer programs never change and DNA changes; the problem is that when computer programs change, the results are almost invariably either silent or deleterious. Come to think of it, the same is true for DNA. You have just outlined a similarity. Try again.
See my response above to bFast on this point.
1. Provenance - computer machine language was designed by human beings :: DNA was not designed by human beings. That is quite simply begging the question. The whole point of looking at the other similarities is to suggest that an intelligence somewhat similar to (although probably more intelligent than) human intelligence created DNA. You can’t list that as a significant difference unless you want to win the argument by fiat.
My statement (1) was not an argument. It was a datum. An iota of evidence. Just as "hypotheses are not evidence," so "evidence is not an hypothesis." No hypothesis = no argument = no possibility of question-begging. I was addressing bFast's claim of equivalence. You are free to deal with that datum as you wish and as you have done. I have agreed that your speculations have evidence to support them. Those speculations have led you to hypothesize:
Is there any reason to believe, on the basis of evidence, that ID is the correct explanation for OOL? The answer, judging from your own posts, is yes. You may call the evidence weak (although others will differ), but there is in fact evidence.
Well put, and agreed to.Daniel King_{August 25, 2008
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Paul Giem #189:
Regarding Kawamura and Ferris, the abstract you gave looks interesting. I am curious as to why you did not refer me to it first instead of to the Ferris review. I will reserve further comment until I have read the actual article.
I assumed that you would find the Ferris review helpful as an overview.
In (178) you state, You believe that scientific work on abiogenesis can tell us nothing about the real events that brought life about, since those events could not have occurred naturally (”without intelligence”). Moreover, you believe that it is dishonest to keep an open mind about the subject! This is either ignorant (which I prefer to believe) or dishonest.
I was referring to your statement that I quoted just above my comment:
I just think that it is possible that there is no pathway to life without intelligence, and that if so we should not be surprised to not find one, and that if we do not find one we should be honest enough to admit this fact, and that this admission can be, and at present is, an evidence-based statement.
"We should be honest enough to admit this fact...," in reference to not being surprised about not finding a "pathway to life without intelligence..." I take this to mean that persons who pursue research into naturalistic pathways are not honest enough to admit the futility of their quest.
You ask, “Have you no curiosity about how the Creative Intelligence invented life?” Well, yeah, but that doesn’t mean that I have the right to demand an answer compatible with naturalism. One has to be open to the possibility that such an answer will not be forthcoming, either because the events were unique enough that we never do find the right (or even a possible) combination, or because it didn’t happen without intelligence, or even naturalistically. (Remember, we’re supposed to be open here.)
My question was directed at HOW, not WHETHER. If a Creative Intelligence invented life, HOW did it do it?
On (179), it looks like we may have a deal. I would only ask for three more conditions. You say, Now will you desist from citing the QBeta work as evidence against abiogenesis research? 1. I would like the right to cite the relevant Qbeta work as evidence against abiogenesis if someone else (as Kacian et al. did) cites it as evidence for abiogenesis. 2. I would like your agreement that you will without prompting point out that the Qbeta work does not in fact indicate a pathway for abiogenesis if you run into someone who claims it does so (absent further evidence, of course). 3. I would like an explicit acknowledgment that in this specific area, my claim (79) that It’s the naturalistic OOL researchers that engage in speculation against the evidence. has not been falsified.
1. If you would like to continue to cite the QBeta work, please do so. 2. I agree without prompting and without reservation that if any person makes such a claim, I will laugh that person to scorn. 3. If your blanket claim has been supported by anything other than quotations from Shapiro and Kacian et al., please advise. In any case, speculation against the evidence is a matter of opinion. From what I've seen from serious OOL researchers are good faith efforts to speculate in light of the evidence.Daniel King_{August 25, 2008
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bFast #188:
1 - Provenance. This is a bit of a stretch, isn’t it.
A stretch? How so? What I said in #187 was:
1. Provenance - computer machine language was designed by human beings :: DNA was not designed by human beings.
Is that statement incorrect? Does it not point to a difference between DNA and computer machine code? A rather fundamental difference, I think. Remember, you said in #184:
DNA is a language in the same sense that a computer language — expressly machine language — is a language! It is EXACTLY the same thing!
It looks like there's some "stretch" to the meaning of EXACT in your mind. Here are some typical dictionary definitions:
Exact: 1 : exhibiting or marked by strict, particular, and complete accordance with fact or a standard Exact: 2 : marked by thorough consideration or minute measurement of small factual details.
There also seems to be some "stretch" to your concept of implementation:
2 - Implementation. “Computer machine language is executed by a central processing unit.” Not necessarily. The feature that set microcomputers apart from mainframes was the creation of the CPU. Prior to that the processing was done by an assemblage of electronic systems. DNA is processed by an assemblage of proteins that unwinds it, runs along it, produces an RNA copy, sends the RNA copy to be translated into a protein sequence which then folds it. As comuters have been known to work with an assemblage rather than a nice packet called a CPU, I fail to see the difference. You may point out that an organism is not limited to a single processing system running against the DNA. Well, modern computers have, effectively, four separate CPUs executing the memory at four separate locations. I have seen computers running up to 50 CPUs on the same chunk of code simultaneously.
Looks to me like you are defining the sequence of operations that lead from DNA through its transcription into RNA to its translation into protein as EXACTLY the same as "an assemblage of electronic systems."
Not all computers have writeback, especially small dedicated computers like the one in your microwave — though I understand that retroviruses actually use a writeback system.
So DNA is EXACTLY like the firmware in my microwave oven.
3 Instruction set. The size of the instruction sets in the range of modern computers is huge. The computer in your microwave likely has a very small instruction set. However, DNA does have an instruction set. Especially once you examine start and stop sequences, you must conclude that this is more than just a punch card — but an instruction set.
The start of translation is signaled by a particular codon; similarly, there are special termination codons. These are not "sequences." (A sequence is a series of codons.) Your analogy is comparable to saying that the use of a capital letter to start a sentence and the use of a period to end it are "instructions". Possibly useful pedagogically. But a deep insight?
I don’t know enough of how DNA is translated to know if scientists even understand the instruction set yet, but the discovery of intronic data would indicate that the instruction set is more complex than first thought. However, DNA translates the same way when the conditions are the same (translating differently when specific commands to translate differently such as “make a skin cell” is warranted). The fact that DNA follows such a tight discipline establishes that it follows a disciplined instruction set.
You don't know any more than "start" and "stop" about the hypothetical DNA instruction set, but you do know that it is EXACTLY like a computer machine language, because "DNA follows such a tight discipline".
4 Computers use binary code. Well, not all. The IBM System 32, for instance, used BCD code. I inderstand that some computers have at least been experimented with which use a tri-state system based on if a magnetic donut was positively charged, negitively charged or not charged. Furthermore, the punch-card systems used in looms are often seen as simple computers.
So, DNA is EXACTLY like the machine language used in microprocessors, microwave ovens, IBM System 32, and punch-card systems. The analogical possibilities seem to be unlimited.
5 - Versatility. To suggest that DNA lacks verstaility is ludicrous. While DNA is limited to act on living cells, computers are limited to act on their own memory, and some simple boolean I/O ports. Both systems are extremely versatile. They work in separate environments, but in both environments they offer incredible flexibility.
Please cite examples of DNA code versatility and flexibility for my edification.
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.
There's a heritable change in the machine code?
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.
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.
DNA is computer memory, the proteins that act on the DNA, the RNA intermediate, are the central processing system.
More precisely: DNA may be likened to computer memory, the proteins that act on the DNA, the RNA intermediate, may be likened to the central processing system. Other than possible employment in pedagogy, of what heuristic value is the analogy?Daniel King_{August 25, 2008
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While DNA is limited to act on living cells,
Eh? Last I heard people were working on using DNA for high density data storage with a MUCH longer shelf life than CDs/DVDs. Daniel King, Anyway, I've got to ask...if DNA is not a language, then what is it?Patrick_{August 24, 2008
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Daniel King (187), I have to agree with bFast (188); your differences fail. The first and the last fail worst. The last one is the worst; it is a true FAIL. ROFL! Do you have any idea how many programs get corrupted every year? The problem isn't that computer programs never change and DNA changes; the problem is that when computer programs change, the results are almost invariably either silent or deleterious. Come to think of it, the same is true for DNA. You have just outlined a similarity. Try again.
1. Provenance - computer machine language was designed by human beings :: DNA was not designed by human beings.
That is quite simply begging the question. The whole point of looking at the other similarities is to suggest that an intelligence somewhat similar to (although probably more intelligent than) human intelligence created DNA. You can't list that as a significant difference unless you want to win the argument by fiat. But probably more important, you appear to make two concessions that support my original thesis. You concede (181) that "I agree with you that analogous reasoning is a form of inductive inference. What one is doing is toting up similarities as evidences." You later try to take it back by saying, "I hope it is clear, from what I said above, that arguments from analogy are hypotheses. Hypotheses are not evidence." But if analogous reasoning is inductive inference, then the evidence behind that inductive reasoning is in fact evidence. That would mean that the similarities between DNA code and say, computer code, are in fact evidence which can be reasonably construed as supporting a hypothesis of intelligent design. In addition, you concede that "Of course, what you said in #79 qualifies as evidence that human intelligence can manipulate DNA for desired purposes." That means that we know with moral certainty that DNA code can be caused by intelligent agents. That is evidence that can be reasonably construed as supporting a hypothesis that an intelligent agent or agent caused some of the DNA code in living organisms. Thus it is fair to say that my claim (79) that "to say that we are engaging in speculation without evidence is incorrect" is in fact correct. You try to blunt the force of these observations by arguing that "the argument is formally valid, but the conclusion has not been proven." Nobody ever made that claim. The claim was about evidence, not proof. In fact, this is not the first time you have made that claim about proof, and I have pointed out that the dispute was not about proof. Please stick to the subject. Your point about proof is granted, but irrelevant to the subject. The question is about evidence. Is there any reason to believe, on the basis of evidence, that ID is the correct explanation for OOL? The answer, judging from your own posts, is yes. You may call the evidence weak (although others will differ), but there is in fact evidence.Paul Giem_{August 24, 2008
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Daniel King, In (177) you apparently missed my point. I could perhaps guess that ImpI had to do with inosine, although the article itself did not make this clear (it is also not clear from the article why ImpI was used instead of ImpG). But I was not implying that ImpU or ImpC were ambiguous so much as that they did not seem to have much to do with the question of 2',5' linkages versus 3',5' linkages. That was what I referred to when I said, "Unless you can explain what the discussion means, your reference is not of much help." Regarding Kawamura and Ferris, the abstract you gave looks interesting. I am curious as to why you did not refer me to it first instead of to the Ferris review. I will reserve further comment until I have read the actual article. In (178) you state,
You believe that scientific work on abiogenesis can tell us nothing about the real events that brought life about, since those events could not have occurred naturally (”without intelligence”). Moreover, you believe that it is dishonest to keep an open mind about the subject!
This is either ignorant (which I prefer to believe) or dishonest. Assuming that it is in fact ignorant, let me help make it less so. I do not believe that it is dishonest to keep an open mind about OOL, and in fact believe that it is preferable to do so. I have indicated this on a number of occasions. One example is at https://uncommondescent.com/intelligent-design/faith-and-reason-in-the-ool-context/#comment-292935 where after others label my obstacles as dealbreakers, I say,
I don’t look at these obstacles so much as dealbreakers as they are obstacles that must be dealt with if one is to have a good theory. I am prepared to be completely openminded about the origin of life. I’m not locking and barring the door if someone wants to go there. But if that person expects me to follow him/her, he/she needs to deal with the obstacles. If the obstacles are not dealt with, I see no reason why I should exercise faith that they will disappear. I have been told for decades that science has no room for faith. I could buy skepticism. What I can’t buy is selective skepticism.
Thus at least the last sentence in your quoted paragraph is incorrect, and I view the other two sentences as at least in theory overstatements. You ask, "Have you no curiosity about how the Creative Intelligence invented life?" Well, yeah, but that doesn't mean that I have the right to demand an answer compatible with naturalism. One has to be open to the possibility that such an answer will not be forthcoming, either because the events were unique enough that we never do find the right (or even a possible) combination, or because it didn't happen without intelligence, or even naturalistically. (Remember, we're supposed to be open here.) On (179), it looks like we may have a deal. I would only ask for three more conditions. You say,
Now will you desist from citing the QBeta work as evidence against abiogenesis research?
1. I would like the right to cite the relevant Qbeta work as evidence against abiogenesis if someone else (as Kacian et al. did) cites it as evidence for abiogenesis. 2. I would like your agreement that you will without prompting point out that the Qbeta work does not in fact indicate a pathway for abiogenesis if you run into someone who claims it does so (absent further evidence, of course). 3. I would like an explicit acknowledgment that in this specific area, my claim (79) that
It’s the naturalistic OOL researchers that engage in speculation against the evidence.
has not been falsified. In that case, we have a deal.Paul Giem_{August 24, 2008
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