A Simple Gene Origination Calculation
| July 27, 2008 | Posted by PaV under Intelligent Design |
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.
218 Responses to A Simple Gene Origination Calculation
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Reply to Paul Giem #207, part 1:
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.
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.
I am doing the best I can to understand what you are saying.
(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:
To which I replied in #142:
To which you responded in #146:
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:
You also wrote (first quoting me):
Science can only grasp what it can reach. The miraculous is out of its reach. And therefore safe from science.
Reply to Paul Giem #207, part 2:
My statement quoted above was in response to your request in #198:
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):
But if you want to consider the QBeta relevant to abiogenesis, that is your privilege.
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.
See again #192, my response to bFast:
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.)
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 ~2.5×10^8 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?
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?
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,
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),
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:
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:
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,
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
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.
I would not say that…
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.
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.
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,
Daniel
I realized I never responded to Daniel at #203 regarding the status of biological objects as machines.
This brought it to mind