DNA and Information

[CraigD]

Despite being an information theory enthusiast (not an uncommon trait among math students matriculated into computer programmers), I’ve avoided this thread until now because it seemed more a theological debate than a discussion of molecular biology. However, I feel compelled to chime in, as I believe an important point has not yet been raised. From post #1 of this thread:

DNA, on the other hand, represents a complete plan for a living organism. DNA is an encoding / decoding mechanism that contains code, or language, representing the organism.

DNA is a information storage medium. It does not contain a mechanism for decoding or copying its information. This is done by a variety of large, complex protein complexes, such as DNA polymerase.

 

To make a computer hardware analogy, DNA corresponds to the platters of a hard disk, while these protein “factors” are the read/write heads. Without these factors, and the cell necessary to support them, the data contained in DNA can’t build a living organism, just as without its read/write heads and the mechanism necessary to manipulate them, the data on a hard disk can’t be accessed for any purpose. Thus, a virus contains DNA, but can’t make use of it without borrowing the machinery of a host cell, rather like removable magnetic media.

 

In principle, a properly made collection of machines – protein or otherwise – could read “genetic” information from practically any media. Such a media would be hard-pressed to approach the information density of DNA, though – a “bit” of DNA information requires barely 30 “CHON” atoms, while all the supporting cellular “hardware” increases it to only about 10^6 atoms/bit. By comparison, the most efficient magnetic hard drives require about 10^17 atoms/bit!

 

The use of DNA in biological organisms allow them to exploit this tremendous information density to do all the amazing things that biological organisms can do. There’s no fundamental qualitatively difference, I think, between a biological organism, and any other object built from a large collection of data, such as a ship or an airplane, built by human beings using machines and working from paper blueprints, or a physical artifact built by a computer-controlled robot. The difference comes from a huge quantitative difference in information density and speed of use.

[hallenrm]

While DNA may be a code, it in itself is not really information. Just as an alphabet is a code, the information is the combined result of the letters and not really intrinsic upon the code itself. Just as Cyrillic and Greek alphabets differ, they can still impart pretty much the same information. The fact that there is a code is really unimorptant, IMO. DNA is nothing more than the letters.

Wrong, while nucleic acids in DNA may be likened to the alphabet of a language (DNA is deoxyribose nucleic acid) the DNA molecule is like a sentence and a sentence can contain information.

[TRoutMac]

To make a computer hardware analogy, DNA corresponds to the platters of a hard disk, while these protein “factors” are the read/write heads. Without these factors, and the cell necessary to support them, the data contained in DNA can’t build a living organism, just as without its read/write heads and the mechanism necessary to manipulate them, the data on a hard disk can’t be accessed for any purpose.

 

This is a really fantastic explanation of "irreducible complexity"… thank you!

 

I have compared DNA to a computer disk (I used a CD-R) many times… it's a great analogy. To get more specific, DNA's backbone is like a formatted (but blank) hard disk. (magnetic or optical, makes no difference) and the base pairs are like the little 1s and 0s that are stored on the platter. And you're absolutely right, you can't access the data on a hard disk without the ancillary hardware… the rest of the computer!! It's an excellent analogy to be sure.

 

There’s no fundamental qualitatively difference, I think, between a biological organism, and any other object built from a large collection of data, such as a ship or an airplane, built by human beings using machines and working from paper blueprints, or a physical artifact built by a computer-controlled robot.

 

Again, absolutely correct. Said another way, all machines, whether organic or man-made, must operate at every level within the bounds of physics. Organic machines exploit the laws of physics at a sub-microscopic level (as well as a macro level) and, well, us humans are getting there with our developments in nano-technology, but we've got a long way to go yet.

 

The fact that the information density in DNA is so much higher than any information storage system we've devised does, in fact, say something important about DNA and where the information it carries came from.

 

Thank you for lending even more support to the computer analogy.

[C1ay]

The fact that the information density in DNA is so much higher than any information storage system we've devised does, in fact, say something important about DNA and where the information it carries came from.

It may say something important about DNA but it says nothing about where it came from. We have zero observable evidence on the origin of DNA.

[TRoutMac]

It may say something important about DNA but it says nothing about where it came from.

 

It most certainly does say something about where it came from. Information theorist Henry Quastler said this: "information habitually arises from conscious activity."

 

We have zero observable evidence on the origin of DNA.

 

But we most certainly do have observable evidence as to the origin of every other information storage and processing system. That origin is "Intelligence".

 

On a scientific basis, we can say with a great degree of certainty that the information in DNA points towards an intelligent cause. Apart from concluding that this intelligence is far beyond our own capabilities, we really don't know anything else about that intelligence. At least not on scientific grounds.

[questor]

giving a little thought to this ongoing discussion, i was struck by a sudden

intuition : human beings are not necesarily descended from monkeys--we are probably descendants of trees or slime. after all, trees and biotic slime preceeded man, and if genetic code replicates itself, why were not our first ancestors slime or plants ? whatever the first life form was,we are supposed to believe that all life ensued from this organism. this means flora and fauna.

do we share DNAcode with trees? lizards? mollusks? and all forms of life? if not, why not? if we all evolved from the seminal lightning strike on the primordial soup we should share similar code. some of you may want to read some of the more recent findings on this subject at:

http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html

[coldcreation]

giving a little thought to this ongoing discussion, i was struck by a sudden

intuition : human beings are not necesarily descended from monkeys--we are probably descendants of trees or slime. after all, trees and biotic slime preceeded man, and if genetic code replicates itself, why were not our first ancestors slime or plants ? whatever the first life form was,we are supposed to believe that all life ensued from this organism. this means flora and fauna.

do we share DNAcode with trees? lizards? mollusks? and all forms of life? if not, why not? if we all evolved from the seminal lightning strike on the primordial soup we should share similar code. some of you may want to read some of the more recent findings on this subject at:

http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html

 

To answer your question Questor, yes, we share the DNA code with all life forms on earth. We are very similar in composition to worms. The slime you write about quite often, as if it were a bad thing that one celled life forms could evolve into complex creatures over millions of years, does too have something in common with us: both the animal and plant types. The process of reproduction, be it miosis or mitosis are remarkably similar.

 

Watching Cosmos on TV as a kid I was struck by the fact that we, humans, are made of the same elements as nails, sea salt, dust, rocks and a host of other common things found around us every day. The difference between people and these elements is the degree of complexity with which they are composed.

 

Evolution is not a bad thing questor. There is nothing wrong with life having evolved from simple organic material floating around in space or at the bottom of an ocean. On the contrary. Its a good thing. That way we can argue over it.

 

cc

[C1ay]

It most certainly does say something about where it came from. Information theorist Henry Quastler said this: "information habitually arises from conscious activity."

That may be true of information generated by humans but it says nothing conclusive about any information generated by nature.

 

 

But we most certainly do have observable evidence as to the origin of every other information storage and processing system. That origin is "Intelligence".

 

On a scientific basis, we can say with a great degree of certainty that the information in DNA points towards an intelligent cause. Apart from concluding that this intelligence is far beyond our own capabilities, we really don't know anything else about that intelligence. At least not on scientific grounds.

That is only true of human generated information. We have no conclusive observable evidence about any information generated by nature except that it exists. We don't know how.

 

BTW, if DNA was intelligently designed, do you accept the possibility that it could have been done by extraterrestial life, aliens, from somewhere else in the universe, even our own galaxy?

[questor]

CC, i see nothing wrong in evolution, i think the process enabled us to be here

the question is how did it all start and how was it directed. of course all earthly objects are composed of whatever building blocks exist on the planet.

live and inert objects are composed of the existing elements. the big difference is that some objects are alive and sentient, the others just sit there for eternity. you might want to agree that life was ''created'' when the lightning bolt hit the pile of slime just at the right moment and ''created'' some RNA or whatever started the self replication biosyntheses. the fact that

quite a few physical laws, elements, carbon, hydrogen, oyxgen, gravity and the other forces, spin, et cet. all had to be present was just a lucky confluence of almost supernatural coincidence.

[coldcreation]

CC, i see nothing wrong in evolution, i think the process enabled us to be here

the question is how did it all start and how was it directed. of course all earthly objects are composed of whatever building blocks exist on the planet.

live and inert objects are composed of the existing elements. the big difference is that some objects are alive and sentient, the others just sit there for eternity. you might want to agree that life was ''created'' when the lightning bolt hit the pile of slime just at the right moment and ''created'' some RNA or whatever started the self replication biosyntheses. the fact that

quite a few physical laws, elements, carbon, hydrogen, oyxgen, gravity and the other forces, spin, et cet. all had to be present was just a lucky confluence of almost supernatural coincidence.

 

Hmmm, lucky confluence, perhaps, directed-supernatural coincidence, certainly not.

 

The question of how it all started depends on how far back you are willing (or able) to consider. There really is no begining. There may be no fine line between what is inert and what is alive, but a smooth gradation. Consider now a starting point of 'slime' and lightning. Fine. But then we can ask where the slime came from. The further we ponder, the further back we can go.

 

Ultimately one need to go back beyond 4.5 Gyrs, when the dust, gas, and elements were just a cloud rotating around a second generation star. And back further still, when the first generation star shed material into the outer reaches of the proto-solar system, material that would collect, group and aglomerate into long chains of carbon and other essential elements: the proto-seeds of complex life forms. Evolution does start, it continues.

 

The supernatural would have been fine had no physical evidence been available to study. Alas that is not the case. I'm not sayig all the answers have been provided, but that it is just a question of time before that happens.

 

cc

[coldcreation]

''created''

''created''

.

 

Yes, it would be nice to know how DNA came to be as we know it.

[TRoutMac]

That may be true of information generated by humans but it says nothing conclusive about any information generated by nature.

 

That presupposes precisely the point at issue… that nature generates information. Geez… have you folks ever heard of objectivity?

 

That is only true of human generated information.

 

How could you possibly know that this is only true of human-generated information? Henry Quastler's quote said information arises from "conscious activity". Do you not believe that extra-terrestrial aliens engage in "conscious activity"? You're trying to pull a fast one here because, if I'm not mistaken, you have said in the past that you believe alien (non-human, extra-terrestrial) intelligence exists. If you believe that, then you're contradicting yourself. Information (off the sort we're speaking of) is the product of intelligence and is not in fact, limited to human intelligence.

 

BTW, if DNA was intelligently designed, do you accept the possibility that it could have been done by extraterrestial life, aliens, from somewhere else in the universe, even our own galaxy?

 

As an abstract possibility, yes. However, the problem with that scenario is that I would then have to explain how and why the extra-terrestrial life exists. And if I attributed them to another extra-terrestrial being, then I'd be faced with the same problem all over again. So, that gets me nowhere.

[C1ay]

That presupposes precisely the point at issue… that nature generates information. Geez… have you folks ever heard of objectivity?

So you are saying nature generates no information? The rings of a tree carry no information of it's age? The canyons carved by rivers reveal nothing of the past? That redshift of the stars conveys nothing to us about the universe? Bottom line, is it your claim that these things are not information if they didn't result from conscious activity?

 

How could you possibly know that this is only true of human-generated information? Henry Quastler's quote said information arises from "conscious activity".

I'll rephrase. You cannot extrapolate the how or why of nature's processes solely from the observation of human processes. If there is information in nature we cannot assume that it could only be the result of a process similar to human processes.

 

Do you not believe that extra-terrestrial aliens engage in "conscious activity"? You're trying to pull a fast one here because, if I'm not mistaken, you have said in the past that you believe alien (non-human, extra-terrestrial) intelligence exists. If you believe that, then you're contradicting yourself. Information (off the sort we're speaking of) is the product of intelligence and is not in fact, limited to human intelligence.

Talk about fast one. Just because any aliens that might exist have would have conscious activity does not allow the leap to conclude that information can only come from conscious activity.

 

 

As an abstract possibility, yes. However, the problem with that scenario is that I would then have to explain how and why the extra-terrestrial life exists. And if I attributed them to another extra-terrestrial being, then I'd be faced with the same problem all over again. So, that gets me nowhere.

 

Just because it gets you nowhere doesn't mean it's not a possibility and there's no reason to believe it's any less possible than some mythical designer. Surely you're not claiming that you have observable evidence of what the designer you believe in can or cannot be.

[questor]

Clay, there is quite a difference in information that is gathered by observing

the result of a natural occurrence ( tree rings ). that information goes into YOUR brain, and gives no subsequent activity. the information stored in DNA exists in the DNA itself and is responsible for subsequent specialized and directed activity.

[coldcreation]

Clay, there is quite a difference in information that is gathered by observing

the result of a natural occurrence ( tree rings ). that information goes into YOUR brain, and gives no subsequent activity. the information stored in DNA exists in the DNA itself and is responsible for subsequent specialized and directed activity.

 

Yes. For example inside the fertilized seed that will grow to be a tree there is much information about the tree which determines its subsequent formation. In addition to that information combined with random mutations there are external factors that will play a role in its development, e.g., soil quality, soil depth before hitting solid rock, water quantities, thermal conditions, altitude, feeding animals that strip bark or remove leaves and fruit, birds or insects that eat the leaves or dig holes through the trunk, sunlight, wind, etc.

 

So, in addition to the DNA, RNA information stored inside each cell, there are those external factors to which each cell will adapt. And because each cell is part of the whole, the physical structure of the tree (or human being) will change.

 

And here is the most amazing thing: The cells will memorize, i.e., there will take place a modification in the DNA, that can be passed on to the following generation. The progeny will then be able to adapt better to the different factors than without the new information. Certainly this process is not infiable. There are many errors along the way (some even cause species to die out) and it is not always the fittest or most well adapted who survive. But it is a evolutionary process that over timescales of hunders, thousands, millions and ultimately billions of years yeild most astounding results. So astounding, in fact, it is hard to believe the complexity of what has developed.

 

This information is generated, stored and modifiable at any given time. It is not nature that generates information, but it is a natural outcome of a long series of interactions (chemical, ect.) and reactions (chemical, etc).

 

No designer is needed to move protons, neutrons and electrons around. No designer is needed to produce the observed outcome of billions of years of modifications. On the contrary though, to produce a designer human beings are needed. Yes, indeed, humans are required to produce an all mighty designer.

 

As far as the possibility for life existing elsewhere. There is little doubt. As far as the possibility of them comming to visit us hear on earth: highly unlikely.

 

cc

[C1ay]

Clay, there is quite a difference in information that is gathered by observing

the result of a natural occurrence ( tree rings ). that information goes into YOUR brain, and gives no subsequent activity. the information stored in DNA exists in the DNA itself and is responsible for subsequent specialized and directed activity.

And that has what to do with trying to learn the source of DNA? My point is that there are signs of information throughout nature. That the information exists tells us nothing more than that, it exists. It is also fair to acknowledge that the information contained in DNA is much more complex than the information contained in the rings of a tree or the spiral of a conch shell. That only means it is complex though, it says nothing conclusive about it's source. Anyone that concludes it must have come from here or there simply because it's complex is leaping to that conclusion without using science to get there.

[questor]

the action and results of action by DNA seem almost SUPERNATURAL, do they not ?