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December 04, 2009

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DNA makes natural selection possible, but can other things also make natural selection possible? Helper T-cells have T-shaped appendages that have different molecular configurations on different cells, but they all have the same DNA. A T-cell that encounters an invader whose surface molecular configuration matches that of the T cell will replicate itself, with the result that a large number of T-cells will be produced to go against that particular invader. In other words, selection. This selection process is not DNA-based. Therefore, the possibility that DNA could be acted upon by some sort of non-DNA selection has not been disproved.

I have the book, it is awesome. A powerful work that deserves a read by folks on both sides of the debate. Good stuff!

Johnnie-

The issue here is not how to change DNA once you've got it. The issue is how you get DNA in the first place. This cannot be explained by natural selection because DNA is a sine qua non of natural selection (even in the T-cell story told above).

Can an Evangelical Christian Accept Evolution?

http://www.youtube.com/watch?v=Of0PjoZY4L0

Wisdom lover:

The T-cells do not change DNA. DNA has nothing to do with the selection process that T-cells are involved in. The T-cells are a counterexample to your claim that the DNA is a sine qua non of natural selection.

Ted,
Evolution as it pertains to molecules to man is patently absurd - it has never been observed, there is no evidence for it (fossils don't show anything even remotely resembling it) and is as much a science as the just-discovered man-caused-global-warming-I-can-fudge-numbers fiasco.

Natural selection - the diversification of species is observable and is completely compatible with the Bible.

Nagel - that's a great recommendation. Good to see.

Kpolo,

Have you ever observed God creating a species? And what, precisely, do you mean by "diversification of species"?

Johnnie-

So T-Cells have no DNA. That's news to me.

Your response, Johnnie, is a classic example of a Red Herring Fallacy. The point of the argument is that natural selection cannot give rise to DNA. You are attempting to change the subject and talk about some complex mechanism involving T-Cells that is utterly impossible in a world without DNA. The hope, I suppose, is that your interlocutor will quickly find himself in over his head and give up.

Wisdom Lover,

T-cells have no DNA? That would be news to me, to, since it is the opposite of what I said.

If you want a natural selection process whose agents do not have DNA, consider the sorting of sand, gravel, and rocks by size on beaches, around promontories, and between the shore and nearby islands. The sorting is done by wave and tidal action, which is not DNA.

In regard to an interlocutor, the only Interlocutor I have is the same one that you show reverence for in your username.

Hi Johnnie, to compare the complex design signature of DNA to random sorting of beach sand as being similar seems to me to be another red herring.

Wisdom lover and brad:

The subject of this thread is the assertion that DNA makes natural selection possible. Introduction of counterexamples is not a case of red herring arguments (changing the subject). Counterexamples don't change the subject, they demolish the subject.

Hi Johnnie, I am just saying that your "counterexample" is not directed to the objection that WisdomLover was making. It seems to me that your making comparisons between DNA and its role in directing life is NOT really like random sorting of sand and pebbles on the shore. Sand and pebbles aren't governed and directed by a complex internal guidebook that may or may not resist the random sorting tendencies of waves and tides. I still think you are furthering a side argument which I'm now debating with you as proof that this is what it is.

Maybe you should start with demonstrating that waves and tides or some other natural physical process can account for DNA in the first place to prove that environment can order changes or alternations in DNA also.

Brad:

Wisdomlover has not yet answered to my sand and pebble counterexample, and when he does, his answer will probably be on point.

But your answer to the sand and pebble counterexample is completely off point. As in your use of the phrase "random sorting". Sorting by its very definition is the opposite of random. Sand and pebbles don't resist randomness imposed on them by waves and tides; waves and tides impose a sorting on sand and pebbles which is not random.

Johnnie, WisdomLover said, "The point of the argument is that natural selection cannot give rise to DNA." Then you gave the natural process that occurs that sorts sand from pebbles as evidence that natural selection can happen without DNA. But you've missed the idea that a natural, random process is not enough to explain the particular kind of complexity of DNA.

The difference is that the sorting you are talking about depends on a physical property of the sand and pebbles--i.e., their size. The physical property determines where each one ends up. This is very different from DNA. When DNA developed, there was no specific physical property of C, G, T, and A that determined the order they ended up in (as is the case with the sand and pebbles).

Because no physical property determines the order, they can, in fact, be joined in millions of ways, just like the 26 letters of the alphabet can be joined together in countless ways because there's no physical property of the letters that determines that all the vowels come together in a certain order and all the consonants come together in another, physically predetermined order.

The chance of DNA coming together in a meaningful way completely randomly is beyond miniscule. In your sand sorting illustration, the sorting is not random, but determined by physical properties of waves, size of the rocks, etc.

What is meant by the phrase “particular kind of complexity of DNA”? What is “meaningful DNA”? How do you know if DNA is “meaningful” or not?

Are there any natural processes that can create meaningful DNA? Can the As, Cs, Gs and Ts ever start in a “non-meaningful” state and end up in a “meaningful” state via a natural process? If you don’t think that such natural processes exist, given that human knowledge is incomplete, how do you know that these processes don’t exist? Isn’t ID “theory” really just a matter of “we don’t know where DNA came from, so God did it”?

Has anyone ever observed God manipulating the atoms in nucleotides in such a way as to create meaningful DNA? That is, have we ever seen God make DNA? Has anyone ever observed the DNA “develop” by a non-natural mechanism? Has anyone ever seen the As, Cs, Gs and Ts arrange themselves in a meaningful way by a non-natural or non-physical means? If not, how do we know that God made DNA?

Did God place every nucleotide in its proper place in the human genome? Did God directly manipulate the atoms in the human DNA molecule to create human DNA? If not, which base sequences in the human genome are the direct products of God’s hand and which are the product of a natural process? How can you tell the difference?

Let’s play God of the Gaps. As a place holder, let’s say that God created the DNA in the first cell. Ok, now is it possible that the millions of species that we see today are the product of natural processes that have acted since the first cell was created? If not, why not?

Amy,

My original post had nothing to do with WisdomLover, it had to do with the argument that Brett made (either quoting from Meyer or paraphasing) that DNA cannot be explained by natural selection BECAUSE (emphasis mine) it makes natural selection possible. That's the argument as stated. WisdomLover changed the argument, not I. I refuted Brett's qualifying clause, so Brett's argument has to be restated as "DNA has not been explained by natural selection". Period.

To Amy on physical properties:

Natural selection (I think) is always a physical process. If we define natural selection as any selection not done by God or not done by humans, we have a wide range of possible processes, but they are likely to be all physical. Selection on sand and pebbles depend on the physical property of sand and pebbles. Selection on living things depend on the physical properties of the living things. Gazelles are swift because cheetahs select the not-so-swift ones. A female selects big muscular males because they are likely to be better vehicles for the bringing of her offspring to sexual maturity.

As for the physical properties of A, G, C, and T, the order in which they appear in the neucleotide is not predetermined, as you say, but their physical properties enable only one complement to make the link to the opposite strand, and all four had to be the right size to fit into the double helical structure. A selection problem, to be sure, but one that might be solveable under more than one theory.

Hey folks, Johnnie is totally correct. DNA is *not* the "sine qua non" of natural selection. What is the proof of the claim that it is? What we do know is that in recent history, DNA has been the mechanism of natural selection. But this does not mean that natural selection could not have happened differently in the distant past, with some other mechanism (such as RNA, for example, in a hypothesized "RNA world"). Those who mainly seem to like evolution in order to debunk religion, as opposed to because they are objective scientific investigators, are jumping all over Nagel because his endorsement language makes it seem as if he himself thinks, erroneously, that DNA is the "sine qua non" of evolution. What he should have said is that it is difficult to explain, not how life arose, but how a system with a sophisticated enough mechanism of natural selection arose. This system need not have been life as we now know it at all, as long as it had enough power to evolve great complexity through natural selection. It is explaining the origin of this sort of system which Nagel should have described as "fiendishly difficult", because there is no "just so story" available to support it as there is once natural selection is in place. Unlike the spittle spewing religion haters, I am willing to charitably assume this is what Nagel really meant; otherwise, indeed, he is quite ignorant (and also, illogical, confusing a priori and empirical issues, and that is hard to believe of such a noted philosopher).

>>it had to do with the argument that Brett made (either quoting from Meyer or paraphasing) that DNA cannot be explained by natural selection BECAUSE (emphasis mine) it makes natural selection possible.

My point responds to what you say here. The kind of selection you're talking about works because the physical properties of the things sorted are ordered based on their physical properties. Therefore when you use that to explain how DNA could have come into existence by showing sorting taking place in nature, that does not work as a counter-example because the order of DNA is not determined by physical properties.

>>As for the physical properties of A, G, C, and T, the order in which they appear in the neucleotide is not predetermined, as you say

That is why your example is not relevant.

>>A selection problem, to be sure, but one that might be solveable under more than one theory.

Well, to compound the problem, because there is no predetermined order, the chance of a short, functional protein happening by accident (considering all the total possibilities) is 1 chance in 10 to the 125th power, which I believe is more than the number of all the atoms in the universe (don't quote me on that one, I'm not sure about that).

Probability...

http://www.talkorigins.org/faqs/abioprob/abioprob.html

http://www.epicidiot.com/evo_cre/65_dice.htm

Amy,

You still don't get it. "The order of DNA is not determined by physical properties" is not true. Consider an error in DNA transcription, or alteration of the code by impact of a high-energy cosmic particle, or an inversion (extremely rare). The resultant DNA is likely to be selected out because the individual it leads to will not have the physical properties that will enable it to leave progeny. But occasionally, a mutation might be beneficial (just like drawing to an inside straight does pay off sometimes). The physical properties of the individual weigh on the continued existence of the particular DNA sequence that gave it its form.

I read or heard somewhere that handwritten Torahs are carefully checked against a known exact copy. An error of only one letter means that the new Torah is destroyed. No possibility of it producing more copies of itself.

>>The order of DNA is not determined by physical properties" is not true.

Johnnie, you're missing what I'm saying. I'm not talking about existing strands of DNA that are selected for or against, based on what they do in the creature. I'm talking farther back than that--at the beginning of DNA coming together to build the first creature, not after the information in DNA is already doing its job and reproduction is happening. I'm not talking about the resulting physical properties of the creature, I'm talking about the physical properties of the parts of DNA itself--C, A, G, and T. There's nothing physically in C by itself that requires it to join with an A next, then a T, etc.

This situation is the opposite of something like a water molecule, where, when hydrogen and oxygen come together, the physical properties of each require them to come together in a specific way. This is very different from the way the DNA came together in the first place--that is, the original coming together could have happened in an unbelievably large number of ways, most of which would not have worked to direct the cell at all. But despite the fact that nothing in A, C, T, and G physically predetermined that the DNA would come together in a meaningful way, it just happened to.

Do you see what I'm explaining now?

Amy,

Every combination of A, C, T, and G has a meaning; that is, for every different combination of A, C, T, and G, there is a different creature. So for every meaningful creature we see, and for every meaningful creature we don't see, the DNA came together to give meaning to that creature. Everything, not nothing, in A, C, T, and G physically predetermines that DNA will come together in a meaningful way.

Do you see what you are explaining now?

Johnnie, huh? Most combinations of ACTG are not going to code for an organism. And of course, not only that, no combinations of ACTG are going to be able to do anything outside of a specially tuned environment that facilitates their deployment.

rcogitans,

How do you know? Let's say that chimeras, griffins, and centaurs cannot be deployed outside of a specially tuned environment. Yet chimeras, griffins, and centaurs have meaning. Give Adam any ACTG coding, and he will give a name for it.

rcogitans followup:

I say that all ACTG combinations have a meaning, but for most of them the meaning is going to be "lunch".

Johnnie, I don't know a lot about this subject, but it is common sense. It would be incredibly remarkable if every sequence of DNA coded for an organism.

Even DNA copying is not a trivial task. In order to be copied, it has to be broken apart. It is a well-defined sequence of the DNA that is needed by the copying mechanism in order to know where to break it apart and start copying. This is known as a "replication origin". Figuring out how DNA works is difficult enough that this specific sequence has been difficult to identify. In humans, there are a number of these, each is several thousand nucleotides long. If they are not there, the genome cannot be replicated. (See MBOC p260 for discussion).

This is just one small example of the highly specific nature of a genome required in order to get anything at all. Not a useful organism, not even succesfully creating all the parts for one single cell, but even DNA replication itself.

rcogitans,

The whole point of my ascribing meaning to every ACTG coding is that Amy is being arbitrarily restrictive when she talks about DNA having come together in a meaningful way. At any particular instance in time, there is a set of AGCT codings in existence. About any particular member of that set, we may have to withhold judgment about what will happen to it. Will it replicate? Will it become food for another AGCG sequence? Will it break apart? Will it combine with another ACGT sequence? Suppose that these are the only four possibilities and we assess a set of probabilities for those possibilities. This assessment is what we call meaning. Whether this meaning=organism is pretty easy to figure out now, but at the start, when genomes were a lot shorter, maybe not so easy. It's a lot harder to figure out who's going to win a marathon at the start than later on. But every genome is in the race, and each has a meaning.

Johnnie, Amy isn't interested in the current time, where meaningful DNA sequences already exist, as she has clearly stated. She is interested in where the meaningful DNA came from in the first place, as is the book in question. That is the issue under discussion here, which you simply are not addressing.

Anyone ever going to define "meaningful"?

...but in any case, I'm not interested in waffling discussion with who knows who about this stuff! I only wanted to point out the error that Nagel had made in his endorsement, and to suggest that it is reasonable to charitably overlook it (and I'll add now, pending some indication that it was a slip on Nagel's part, and not simply his ignorance and poor reasoning. His reply to Fletcher in the TLS suggests this charity is in fact reasonable).

>>Every combination of A, C, T, and G has a meaning; that is, for every different combination of A, C, T, and G, there is a different creature.

Johnnie, this is just false. There are very few combinations that function. There are very, very many possible non-functioning combinations that would not work at all at the most basic level.

>>Everything, not nothing, in A, C, T, and G physically predetermines that DNA will come together in a meaningful way.

Because the first part is false, this part is also false. But in addition to that, you're still not getting why your counter-example is not analogous. There is nothing physically about A that requires it to join to C, then to a G, etc. in a particular combination (unlike hydrogen and oxygen in a water molecule where the combination is determined by the physical properties of H and O). Nothing physically prevents them from coming together in any combination, and neither does anything physical compel them into a particular combination. Instead, A, C, T, and G can come together in countless different combinations to make many different sequences just as letters in an alphabet can be brought together in different ways to form many words because they're not confined to specific patterns. And as with letters in the alphabet, they're more likely to randomly end up in nonsense (sjkdlgf js jkdlf jkljk) than in a meaningful sentence (how are you?).

This is different from the sand and pebbles whose physical qualities determine where they end up, and it works the same way every time.

A meaningless grouping of A, C, T, and G is meaningless because it does nothing, it accomplishes nothing, it codes for nothing. It would be like me writing computer code--complete nonsense, nothing but random clutter. It would be like a sentence that read: "Sjfkdl skdj jk yenbksosk enghsoby!" It's a meaningless grouping of letters that does nothing. Again, you're still talking about existing creatures, but I'm talking about something much more basic than that.

>>At any particular instance in time, there is a set of AGCT codings in existence. About any particular member of that set, we may have to withhold judgment about what will happen to it.

You're talking about functional coding in existing creatures. It's meaningful. It may not be optimal, but it's meaningful. This is not what I'm talking about.

Amy and rcogitans,

I'm not talking about only DNA coding at the present time. I'm talking about DNA coding at any and all times and gave a definition of meaning that fits for any and all times. Maybe the word "creature" puts you off. It normally means what we call a living organism. But not always. Its universal definition is something that owes its existence to someone or something else. And I'm not equating meaning with accomplishment. Maybe Joe could help us with a definition of meaning. I will offer one conception of meaning: worthy of commentary. Consider the marathon example again: before the race we have a list of the runners and their numbers. Each is a potential winner, but few are likely to get extra commentary at the start. But all get the commentary of a name and a number. After the race begins, more attention will be focused on the front runners. They get more attention because their being front runners has more meaning. The race ends. The winners get trophies and more commentary. They accomplished something. Did the race have meaning for only those runners that passed some threshold of accomplishment, or did it have meaning for all of them?

And how much commentary will a pile of meaningless groupings of molecules that aren't organized in any functional way and therefore don't run at all get?

Actually, "sjfkdl skdj jk yenbksosk enghsoby" does mean something in Tralfamadorian. It means that we still don't have a definition of "meaningful".

Hast hit it, friend Joe.

Since Amy was the one who introduced the term "meaningful", maybe she could tell us what she "means"?

In order for something to be meaningful, it has to conform to a preset pattern in order to communicate meaning. There is no Tralfamadorian to which this sentence conforms in order to communicate. That sentence does not communicate anything whatsoever to anyone, and your claim that it does is imaginary.

In the case of DNA, certain patterns will accomplish ordered tasks in a functioning creature. When the DNA conforms to those functioning patters, it is meaningful. If the various parts of DNA were to find themselves together in one place and then joined together randomly, they would far more often than not write the same kind of "sentence" as the one I posted above that would not conform to any effective pattern (any of the meaningful possibilities) that would work within a functioning organism.

In computer code, certain codes will meaningfully communicate instructions because they conform to the way computers work. If I type kajldjkfksj into computer code, what I typed is meaningless and transfers no information, gives no instructions, does not function at all. It is meaningless. Random is meaningless. Complexity that conforms to a meaningful pattern that is later decoded to accomplish a purpose is meaningful.

As with computers, in biological organisms, you're limited by reality. You can't just claim fake possible languages exist when they don't. In reality, most possible combinations would be meaningless because they would not conform to patterns that actually work to accomplish something in biological organisms.

Amy:

Thanks for your comments on meaningfulness. I would add that meaningfulness has a tense in relation to the thing that it has meaning for. A thing that existed in the past may have meaningfulness now, thus "a pile of meaningless groupings of molecules that aren't organized in any functional way and therefore don't run at all" may have meaningfulness to someone later based on what happened to particular molecules in the pile. Is it not written somewhere that a stone that was rejected by the builders became the head of the corner? Some passages of Ezekiel don't seem to make much sense now, but maybe they will later when the proper context is set. When Luke wrote that the figurehead of the ship that bore Paul from Meleta was Castor and Pollux, was he adding a little more salt to his salty sea story, or does it have some deeper meaning as well?

“In order for something to be meaningful, it has to conform to a preset pattern in order to communicate meaning.”

I’m afraid that saying “meaningful things communicate meaning” is a bit circular.

“There is no Tralfamadorian to which this sentence conforms in order to communicate. That sentence does not communicate anything whatsoever to anyone, and your claim that it does is imaginary.”

Actually, you don’t know if this is true or not. It's true that Tralfamadorians are a product of Kurt Vonnegurt’s imagination, but that doesn’t eliminate the possibility that your sentence has meaning somewhere in the universe. You may well have accidentally created something that means something to some intelligent being somewhere out there in the great beyond. It all depends on what “reads” the sentence. Whether or not a string of symbols means something depends on the mind of the intelligent sender and the mind of the interpreting, intelligent recipient, and it’s one of many reasons why symbolic language is a poor analogy for DNA. In addition, symbolic language is known to be the creation of minds, but new DNA can come into existence by natural processes. In short, symbolic language is not the same as DNA.

“In computer code, certain codes will meaningfully communicate instructions because they conform to the way computers work. If I type kajldjkfksj into computer code, what I typed is meaningless and transfers no information, gives no instructions, does not function at all. It is meaningless. Random is meaningless. Complexity that conforms to a meaningful pattern that is later decoded to accomplish a purpose is meaningful.”

Like symbolic language, computers and computer codes are poor analogies for DNA. What does a random symbolic computer code have to do with the ways atoms in cells interact with each other? Take DNA for what it is. Put aside the analogies and just look at DNA as it is.

"In the case of DNA, certain patterns will accomplish ordered tasks in a functioning creature."

Whoa, when did we jump to “functioning creatures”? Wasn’t Johnnie taken to task for talking about “existing creatures”? What is that you want to talk about? Do you want to talk about where DNA came from to begin with or do you want to talk about DNA in “functioning creatures”?

“When the DNA conforms to those functioning patters, it is meaningful.”

What is a functioning pattern? What is the function to which you refer here?

“If the various parts of DNA were to find themselves together in one place and then joined together randomly, they would far more often than not write the same kind of "sentence" as the one I posted above that would not conform to any effective pattern (any of the meaningful possibilities) that would work within a functioning organism.”

Could an “effective pattern that would work within a functioning organism” ever be the product of a natural process? Why or why not?

In everything we study there is always going to be at least some possibility of another explanation no matter how small the percentage of deviation may be. In order to make sense of anything in this world we rely on an inference to the most probable explanation. Sense the DNA in living organisms is made out of the ATCG nucleotides and these need to be in a specific order in order to create anything at all, it is most likely that some language has already been created that determines what is a "meaningful" sequence. The physical properties respond to the message. This means the message has to proceed the molecules themselves. Without that language already in place, the probability of any organism coming about by chance is virtually too small to take into consideration. Therefore anything that claims anything other than divine design is not the most probable theory.

The word, 'design' absolutely predicates both intelligence and purpose. Merely to describe 'design' as 'intelligent', as if, alternatively, it might have been random, displays an ignorance of the English language and the limits of the meanings of words that is so fundamentally stupid, it angers me.

That the implicitly imbecilic question has been raised by its proponents, who would presumably like to believe themselves reasonably intelligent people speaks volumes about the dire process of dumbing down that scientificism has exerted on the minds of people initially endowed with an appreciable measure of worldly intelligence.

Moreover, the concepts of intelligence and purpose are, themselves, mutually implicit, so I can't even recommend that they coin a new term, for the absurd tautology, 'intelligent design'.

I was too late to comment on a thread, here, concerning Dawkins materialist mindset, in which he tried to wriggle out of addressing the question of the provenance of the Big Bang, with some nonsense about what's north of the north pole.

Well, there is no need to go back as far as the Big Bang, or to go back at all, since it is surely clear that:

a) Even though light interacts with space-time, it is not proper to it, but belongs to a different order of reality, not governed by Special Relativity. So, how in Hades, can Dawkins be so bombastic about the all-ecompassing scope of scientific enquiry?

b) The implication of Special Relativity is that it is personalised/customized for each observer, its speed never varying in relation to him, irrespective of the constant speed of his own motion in the same direction.

A philosopher of science much admired by Einstein(understandably, in view of the above), but whose name I couldn't even find on Google, couldn't interpret it in the obvious way, as the personalised/customized action of a personal God, because of the totally hegemonic, prevailing paradigm scientists are held in thrall to, right up to the present day.

Presumably, on the same basis, philosophers of science concluded that there was no such thing as objective observation, but, rather, it would most aptly described as 'inter-subjective'. Maybe, the old Jewish mystics knew a thing or two, when they said that when any man dies, a whole world dies with him.

As a result, he stated that, in some mysterious way, before the light of a far distant galaxy set off on its journey, it must have known, so many billions of years ago, that its observer would be there. Evidently, all-powerful and all-knowing.

Well, ever since the Galileo business, the Christian, notably, Roman Catholic Church, has been 'on the back foot'.

There is also the socio-economic aspect to consider, i.e. that the hierarchy has tended to be drawn from families belonging to the kind of classes materially profiting more than the masses, from the perforce reductionist focus proper to such a basic and rudimentary study as the physical world, namely, science. So, a certain diffidence towards the prevailing 'scientismificist' paradigm would have been understandable enough.

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