Everything you need to know about ID

It's a wonder that these people know how to tie their own shoes. I was sent a link to Perry Marshall's Intelligent Evolution Quick Guide, and it is certainly a fine example of the kind of reasoning that allows creationism to thrive. It's a short guide, but it goes on for over a page, when the essential syllogism that defines ID is actually presented in three all-encompassing lines.

  1. DNA is not just a molecule - it is a coding system with a language & alphabet, and contains a message

  2. All languages, codes and messages come from a mind

  3. Therefore DNA was designed by a Mind

As I'm sure all of you sensible readers can immediately detect, his first premise is a deeply flawed analogy and his second is simply undemonstrated and entirely false, so his "therefore" is unwarranted. Three lines, three errors: a perfect representation of creationist thought.

I give to you the cockroach. It contains DNA, and it copies it and propagates it to the next generation of cockroaches, yet is it even aware of its DNA? Does it use its tiny little cockroach mind to construct a complex molecule? No. Mindless chemistry does it. There is no thought behind the synthesis and modification of the DNA molecule at all, yet it is true that it carries out complex activities with the aid of other molecules in the cytoplasm…but without the assistance of any intelligent beings at all.

Similarly, I give you the creationist. They contain DNA, and a large brain as well, but they don't use that brain at all in producing progeny. After a little embarrassed tickle and grunt, mindless chemistry takes over in fertilization and development, and 9 months later, another mind emerges from one of their unencephalized wombs. We can trace the origins of that DNA back and back and back, and at no point in its history does it seem to be produced by conscious design, and the farther back we look, the less available potential there was for intelligent intervention. Bacteria are even less clever than cockroaches, you know.

If you want to understand our history and our evolution, the first concept you have to be able to grasp is that natural processes produce all the complexity and diversity of extant life without the guiding hand of any external agents. Once you've realized that, it becomes apparent that we can work backwards through our ancestry without invoking magic or cosmic helpers — that Intelligent Design creationism is a superfluous hypothesis that can be dismissed in the absence of any corroborating evidence.

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Cockroaches = Creationists?

But come on, human sex can be be even more mindless than the example given!You know, like when the embarrassed tickle and grunt happens when the XY partner is passed out from too much Boone's Farm.

Maybe it's best to look at creationism as a meme. It's a meme that if it gets beyond the intellectual level of moron, then morons won't be able to understand it. Ideas like that are for the scientifically illiterate, the mentally ill and Robert Byers (who is in a category of his own).

Argh. XY should have been XX. Although I guess it could have been the original assertion, too. I understand they like to be caught unawares.

So to speak..

I was pondering (2) for a bit, since it seems almost tautological... and then I remembered our good old friends from psychology, paradolia and apophenia. And the recent finding that suggests that human minds that are under stress may actually be more likely to tend to perceive patterns that simply are not there. And that religion and other superstitions might therefore be self-reinforcing loops of stress and pattern recognition... Hm.

By Owlimirror (not verified) on 11 Oct 2008 #permalink

Er... I'm not sure the cockroach analogy works. It just moves the POV up a level. Couldn't the IDiot just say the roach was designed that way by the DNA coder?

By Yet Another Mike (not verified) on 11 Oct 2008 #permalink

" . . . his second [premise] is simply undemonstrated and entirely false . . ."

It is undemonstrated, but I believe it to be true -- as far as it goes. The question is: which mind creates the message?

Perhaps it is the duty of the ostensible receiver of a message to prove that there really was a message to be received.

I don't know about the rest of you, but I am totally conscious of every copy of my DNA that is made and, in fact, control the process. My DNA is coded in Español. Thats right, I'm God.

Aquaria, that goes both ways, though... It's not just when XX is passed out, sometimes XY is the unconscious one also...

I don't know about the rest of you, but I am totally conscious of every copy of my DNA that is made and, in fact, control the process. My DNA is coded in Español. Thats right, I'm God.

Using this "logic", could one argue that genetic illnesses come about when the big sky daddy stutters?

By Janine ID AKA … (not verified) on 11 Oct 2008 #permalink

Humans represent information using their languages. This is not the same as information BEING a language, a message, or an alphabet.

And I see the author has as much idea of information as he has of mutation.

All in all: FAIL.

Let's see. There is a Nobel prize waiting for someone who proves evolution is wrong. But the ID crowd is too cowardly to try to publish their work in the science literature so they could get a chance for the prize. Therefore, one must conclude that they know they are running a scam that cannot stand up to any scrutiny. QED

By Nerd of Redhead (not verified) on 11 Oct 2008 #permalink

This reminds me of the scene in Cryptonomicon where Lawrence Waterhouse philosophizes that, when the Japanese get a new boat into the sea in Japan, some ripples and waves are produce. These ripples affect the movements of the surface of the water in small but chaos-theoretically recursive ways that eventually reach the US West Coast. Thus, if one had an advanced enough mathematics (plus ripple-observation powers), one could determine how many ships the Japanese are constructing in Tokyo simply by looking at the waves that arrive in San Diego.

By analogy with the ID crowd, Waterhouse could have said that the waves of the ocean are a language, and that since all languages are created by a mind, then it must have been the Japanese who created the ocean!

Nerd of Redhead #14: That's where you invoke the conspiracy to keep creationism and other non-facts out of science, or whine about how They're Being Mean To Us.

By chancelikely (not verified) on 11 Oct 2008 #permalink

I think it bears repeating that DNA is not a code, nor a language, and it does not have an alphabet.

Codes and languages are abstractions. We use the symbol "T" to stand for a certain phoneme. It needn't be that particular symbol. We could have used "%" instead and the language works just as well. Similarly "AGCTTCAT" is a code that represents a DNA sequence. We could just as easily write "12344314" to stand for the same sequence.

None of that is true for actual DNA. You cannot simply replace every instance of an adenine base with, say, benzene and have everything work out as before. DNA doesn't stand for something, it is the thing.

VII. The Atheist's Riddle: "Show me a message that does not come from a mind."

So simple, any child can understand; so complex, no atheist can solve.

Why attempt a serious argument, when you can just declare victory?

IV. What is information? What Makes a Message?

1) Symbolically represents something other than itself (i.e. a book is more than paper and ink)

2) Requires a speaker ("transmitter") and a listener ("receiver")

3) Contains the elements of language - alphabet, syntax, meaning and intent

Point 3) is soooooo adorable. I guess tree rings don't count as messages, even though they are precisely that -- information coded in symbolic form, because there was no "intent", in their creation. But DNA -- why, it's just obvious that there is intent there.

Just a wee bit circular, this.

By zaardvark (not verified) on 11 Oct 2008 #permalink

To me, point 1 sounds like its more or less correct. If you take language to be a formal language such as a programming language, then the bases and larger scale patterns are just part of the syntax and semantics of the DNA-based language for a particular type of cell. He has conflated the concept of DNA and language though as the DNA is just the embodiment of the language, the language itself is defined by the way the cell reacts to the molecule. DNA is a program, the cell's machinery a computer.

Point 2 is demonstrably false though. You could write a program to encode information of particular events using random words and grammar. It wouldn't be a 'mind' creating the language, it would be the random number generator. With enough data another program could learn and interpret that language. You would have two things communicating without a mind designing the detail of the language. Of course, you could use a genetic algorithm to deduce the rules of the language.

There's obviously a bit of equivocation going on here with different meanings of the words "code" and "messages." But Perry Marshall may have accidentally hit on a way to actually demonstrate Intelligent Design -- if it were true.

Remember the fuss several years back about the "Equidistant letter sequences in the Book of Genesis?" This was a poorly-done paper published in a statistics journal that inspired an even worse book, The Bible Code. I remember it -- all these apologists were trumpeting that there was now a mathematical and verifiable proof that the Bible could not have been the work of ordinary humans.

If you laid the original letters from the Torah (or other Bible books) out in a grid pattern and selected letters equally spaced according to some starting "skip" number, you would find coded messages in encrypted form which made predictions, included predictions for the 20th century. Only God could do that!

Trouble was, anyone could do it, because it was all very sloppy, and computers can always find some sort of pattern in noise. You could find messages in any book, including War and Peace -- and statistics buffs had a field day "finding" loopy messages.

BUT, there could have been a tighter evidence for a real hidden code, had everything been clear, consistent, and specific. Carl Sagan, in the book Contact, hypothesized a similar proof of a cosmic Designer with codes hidden in pi.

It almost sounds as if Marshall is proposing a kind of equidistant letter sequences in DNA -- which spell out "HI THERE" or "I GOD MADE THIS STUFF DAWKINS YOU DOPE" over and over. He's not (I think).

But if he were -- and it really worked -- and it persuaded experts in the related fields -- then yes, I think that would indicate Intelligent Design. Empirical evidence FOR, as opposed to the usual attempts to disprove "Darwinism."

Instead, he's just using an old bait 'n switch with talk of "messages" and "codes." Disappointing.

If you take language to be a formal language such as a programming language, then the bases and larger scale patterns are just part of the syntax and semantics of the DNA-based language for a particular type of cell.

Nonsense. All languages are arbitrary. DNA is not. At best, one could say DNA is a template, but not a code. At least not at all like the code of language or software. PZ has it right, DNA and the reactions that create proteins are just chemistry. That guanine pairs only with cytosine or adenine only with thymine is not arbitrary. The language/code analogy completely falls apart given this fact.

Marshall's argument has been thoroughly demolished and PWND all over the web. See this thread at IIDB for just one example.

PZ, why do you still waste so much time on something so obvious?

The code contained in DNA
Is evidence, or so they say,
God's handiwork, there on display, the product of His Mind.
It's plainly seen by any fool
It's more than just a molecule
But rather, a precision tool that shows that we're designed!

This molecule contains the clues
Creationists can gladly use
To show we did not come from ooze, through natural selection;
No "nature, red in tooth and claw"
But God, in wonderment and awe
Created, like a man of straw, his image in reflection.

Rest of poem here.

Nonsense. All languages are arbitrary. DNA is not. At best, one could say DNA is a template, but not a code.

In the sense in which the term "code" is used in information theory, this is just not true. DNA clearly is a code.

At least not at all like the code of language or software.

Sure it is. Whether or not the "meaning" (whatever that is) is not qualitatively the same as a human language has no bearing on whether or not you're looking at a code.

PZ has it right, DNA and the reactions that create proteins are just chemistry.

And a radio transmitter sending messages is just physics.

That guanine pairs only with cytosine or adenine only with thymine is not arbitrary.

Doesn't have to be for information to be encoded. There are a large number of permitted sequences, and which sequence you have encodes information which can be retrieved.

The language/code analogy completely falls apart given this fact.

The problem here is that it isn't an analogy. DNA isn't like a code. It is a code.

The flaw in the original argument isn't in point 1. It's in point 2, for which there is no support. The example of tree rings by zaardvark at #18 is a pretty good example.

By Brain Hertz (not verified) on 11 Oct 2008 #permalink

there is no empirical evidence that truly random processes create significant evolutionary progress

Ever get the feeling that whenever anyone else speaks they just jam their fingers in their ears and "La-la-la-I-can't-hear-you" ? How else could they honestly keep saying such idiotic things.

...oh, right. Honestly. Nevermind.

Cuttlefish, you sly ol' slut - your link leads to a 'no page found' for the Digital Cuttlefish. Keeping the naughty bits of DNA in your personal stash what, what?!

I've had it! There is no reasoning with these people. They are fuck tards and I can't take it any more. Let's get all of us atheist and agnostics together and liquidate all of our possessions to buy our own island somewhere. When the credulous fuck tards realize that the people who make the largest contributions to civilization have left and life for them begins to move back toward the dark ages, MAYBE THEN THEY MIGHT WAKE THE F>>> UP!
Sorry, I just had an encounter with two guys (mormons) riding bicycles before reading this post! Can't deal with that much stupidity inside a 15 min. time span.....

By Another Primate (not verified) on 11 Oct 2008 #permalink

"All known examples of evolution (genetic programs, social progress) have an ability to Evolve that is designed in."

It really torques me when people equate evolution in the biological sense to some sort of colonial notion of the onward march of civilisation.

Then there's this gem: Under natural patterns like hurricanes and snowflakes it says "Everyday interactions of matter & energy produce these things" but under plans, human language, computer language and DNA it says "Always require a designer". Ummm, DNA dimerization and all the other processes of biochemistry ARE everyday interactions of matter and energy.

That entire page reads like something a 15 year old christian apologist would write for a high school rhetoric class.

one could determine how many ships the Japanese are constructing in Tokyo simply by looking at the waves that arrive in San Diego.

I always read things like this (the butterflies causing hurricanes being another common example), but wouldn't the effects be completely dampened out beyond a certain distance, or irretrievably swamped by other sources of noise? It makes for a fanciful thought experiment, but I just can't see it working like that in the real world. It sounds like something out of an episode of "24" where they magically process a blurry security cam photo of a person to such a level of clarity they can just read his genetic code right off the image.

I guess it's my years of communication link design speaking. I know how easy it is for information to become irrevocably lost due to noise and channel distortions. That's what they pay me the big bucks to mitigate. :-) Generally, it involves doing things at the information source before you transmit.

Everything is a communication channel of a sort, be it the atmosphere with tiny winds from a butterfly wing or the ocean with waves from a ship entering the water. The Shannon limit is going to stomp your information at some point.

Even if you could somehow isolate the effects of the Japanese ships in the water near San Diego, the data would be corrupted beyond usefulness. Imagine trying to spot a small pattern few molecules in height relative to the surrounding landscape. And the landscape is the Himalayas. And you have to do it from a satellite. In orbit around the Moon. :)

By Quiet_Desperation (not verified) on 11 Oct 2008 #permalink

@Sastra #20

You mean this? http://cs.anu.edu.au/~bdm/dilugim/moby.html

Pretty good stuff. I've encountered bible code nuts fairly recently, they'll never accept that they've been pwned.

As to Sagan's "messages in pi" stuff. They're there! If you calculate pi to enough decimal places, you will come across a section of 1s and 0s which will translate into the ASCII code for "Worship the tentacled one, O ye sluts!" Fact!

Like the experts in economics who have not anticipated this particular crisis, a lot of evolutionists have a very narrow perspective.They remind me of early priests, who are so tied to there belief/understanding, they simply do not have the capacity to think outside the box of their specialty. There is waiting in the wings a version of Intelligent Design, which if true is indeed earthshaking - if one does not take this one seriously, then presumably one does not take the issue of nuclear weapons and the dangers of nuclear war seriously.Wonder when the ' penny is going to drop' , before the bombs or after.Until the scientific community starts to take this particular theory more seriously, our humanity is collectively doomed by it's own stupidity.Where is the evidence you may ask, and I would reply, it is all around you - world RELIGIONS, history, UFOS, population increase in last 65 years,environment changing.27000 nuclear weapons, and what science is doing today.If our scientists are doing what they are doing , why not more advanced scientists, in other solar systems. This theory is offering a PREDICTION. and not mysticism. Requires one to make an interdisciplinary synthesis of all the information available in the world.Wake up we are in the 21st century and connect up the dots.

The IIDB thread (linked by a commenter above) is instructive, for those who want to follow people patiently, and sometimes not so patiently, explaining to dense people what an analogy is. Calling DNA a code, and what it does language, is an analogy, but fundies seem to have their Morton's Demons working full time to keep that simple notion away from anything moist and gooey inside their craniums.

BTW, I think I show up in that thread -- I did in one on the subject there -- under my handle anthrosciguy.

He could have brushed up on his understanding of semiotics as well. If DNA is a message, who is the receiver? What community agreed on it's denotative meaning? By his logic any phenomenon observed is just as valid as a sign or message and the bit about DNA is irrelevant.

Like the experts in economics who have not anticipated this particular crisis, a lot of evolutionists have a very narrow perspective.They remind me of early priests, who are so tied to there belief/understanding, they simply do not have the capacity to think outside the box of their specialty. There is waiting in the wings a version of Intelligent Design, which if true is indeed earthshaking - if one does not take this one seriously, then presumably one does not take the issue of nuclear weapons and the dangers of nuclear war seriously.Wonder when the ' penny is going to drop' , before the bombs or after.Until the scientific community starts to take this particular theory more seriously, our humanity is collectively doomed by it's own stupidity.Where is the evidence you may ask, and I would reply, it is all around you - world RELIGIONS, history, UFOs, population increase in last 65 years,environment changing.27000 nuclear weapons, and what science is doing today.If our scientists are doing what they are doing , why not more advanced scientists, in other solar systems. This theory is offering a PREDICTION. and not mysticism. Requires one to make an interdisciplinary synthesis of all the information available in the world.Wake up we are in the 21st century and connect up the dots.

Of natural patterns like hurricanes and snowflakes it says: Everyday interactions of matter & energy produce these things

No, no, no!
Hurricanes, cyclones, blizzards ect. aren't mindless everyday interactions of matter & energy--they are messages from god telling us how bad the Darwinists, atheists, gays, femminists and Democrats are!!! Doesn't the author know that?? And he calls himself a believer?

Scheesh! FAIL

Serious brain-wrong here:

There is waiting in the wings a version of Intelligent Design, which if true is indeed earthshaking - if one does not take this one seriously, then presumably one does not take the issue of nuclear weapons and the dangers of nuclear war seriously.

Nuclear weapons are a problem because they work, which implies that our understanding of nuclear reactions is essentially correct. (We're smart enough to build 'em and dumb enough to use 'em.) Taking the issue of nuclear weapons seriously means understanding the power of scientific knowledge. The same goes for "the dangers of nuclear war", since we know about hazards such as fallout and nuclear winter because we do science.

So: Michael seems to equate credence in a myth (Intelligent Design) with understanding of science (nuclear physics). I think somebody missed a step.

Michael,

Seriously. What the hell are you talking about? That made no sense whatsoever.

Hmm.. Take a million wooden boards, fire a million random nail guns at them, then pick the 100 that "work" like pachinko machines (where you drop the ball in and the pins direct it to fall into different slots on the bottom, for anyone who doesn't know what that is, or in case I misspelled it. lol) Are the nails a "code"? Is there some "message" involved? Hell, even though, in this case, you can prove someone fired the damn nail gun, was it "intelligently designed"? Well - 1) Only if you presume #3, 2) Not really, even if you "do" presume #3, and 3) Not unless you have no damn clue how they actually where made. Yet, some imbecile who wanted to prove that all pachinko machines where "designed" would make precisely that argument, and a lot of other imbeciles would believe it.

Yeah. Not a terribly believable argument for DNA being a fracking intelligent language.

Michael @ #34- You know it, man!
I need to talk about my cat. For a long time, I have had a growing suspicion that she may be trying to communicate a message through her meows. I sense something vital in her intent. I can see the earnestness in her gaze. If I could only understand!!
It is for this reason I have decided to eat nothing but cat food for the next month. I know it is my slavish, almost priestly devotion to the old ways of knowing, and it is my backwards reliance on things like the english alphabet, words and sentences and stuff, that are holding me back. And I have decided to alter my body chemistry nutritionally so I can begin to understand the feline wisdom I am so obviously blocking myself to. Soon I will know what she is trying to say, and my life will be richer.

I am on the verge of a great discovery.

Michael is a raelian...

Michael, science will go where the evidence takes it. Right now there is no proof for god, and various religions on earth are just proof that humans band together under various banners. No more, no less, and no god. There is also no proof that aliens seeded the earth. At the moment, I have a program running the background looking for these aliens via Seti@Home. So far, ET is being elusive. Science is well aware of the seed theory and will investigate it as new information becomes available.

By Nerd of Redhead (not verified) on 11 Oct 2008 #permalink

#17:

You cannot simply replace every instance of an adenine base with, say, benzene and have everything work out as before.

But you can replace thymine with uracil in RNA, and everything does work out, in the sense that the information encoded is not altered by the substitution.

#21:

That guanine pairs only with cytosine or adenine only with thymine is not arbitrary.

But the choice of particular triplets of base pairs to represent particular amino acids is (as far as we know) arbitrary. That's established by the set of available transfer RNAs, not by the fundamental chemistry of DNA. You could in principle replace the existing tRNAs with an entirely different mapping, and recode all the DNA accordingly, and things would still work. In fact I seem to recall that this has actually been done experimentally, although I don't have a citation; can anyone verify? There are also naturally occurring variations to the standard genetic code.

By Gregory Kusnick (not verified) on 11 Oct 2008 #permalink

There may be no proof that aliens seeded the earth, but we sure have one that spooky slime has seeded his head...

In the sense in which the term "code" is used in information theory, this is just not true. DNA clearly is a code.

That is not at all the sense with which Marshall was employing it. Or did you miss that? As I stated, DNA is not a code in the way language or software is code. The latter can be described as abstract symbols used to convey a message. DNA and its process isn't anything like that. One could only call it a code in the very narrow sense of the term, that is, as a process that maps a specific input to a specific output. This is how the term "genetic code" was originally meant. It was simply a description of the biochemistry linking a sequence of nucleotide triplets to a sequence of amino acids for synthesis of a spefice chain of peptides or proteins (i.e., a specific input to a specific output).

IDiots and creotards love to conflate and equivocate these two very different meanings of code.

JD: "PZ has it right, DNA and the reactions that create proteins are just chemistry."

And a radio transmitter sending messages is just physics.

You left this somewhat vague, but if by sending a message by radio you meant a human transmitted message, then there's the equivocation of definitions I was referring to.

Unlike every human made code, "DNA to protein" is completely contained within the physical layer. There are no higher levels of arbitrary abstractions. DNA sequences don't symbolically represent anything. They are simply physical entities (chemical molecules) that chemically react to form other chemicals. In the sense Marshall was clearly implying, DNA is no more a code than water (oxygen codes hydrogen?) or table salt (Na codes chlorine?). Nor is the sun code for a clock.

JD, "The language/code analogy completely falls apart given this fact.

The problem here is that it isn't an analogy. DNA isn't like a code. It is a code.

False. The analogy fails right at step 1. because Marshall equivocates two very different meanings of code. DNA is not a code in the way language or software are codes and that clearly is what he asserts.

Rick R wins the thread!

And best of luck, Rick, in your quest for feline enlightenment! Maybe if you're successful you'll be able to translate Michael's post.

From his website :

"Once one has this scientific concept in mind, then the original function of all the world religions becomes more understandable . This is against a backdrop of there having been many humanities on this very ancient planet, which have disappeared for the rather self-evident reasons we can see today, namely nuclear war, over population and environmental degradation. Further the planet is indeed very ancient and is a sort of a "living machine. Man is a "disease" of the universe and there are an infinite number of human races "out there". "

Codes and languages are abstractions. We use the symbol "T" to stand for a certain phoneme. It needn't be that particular symbol. We could have used "%" instead and the language works just as well. Similarly "AGCTTCAT" is a code that represents a DNA sequence. We could just as easily write "12344314" to stand for the same sequence.

But but but God designed DNA using the Western alphabet! (Just kidding!)

Here's another way to think of it:

Sudoku puzzles don't need to use numbers to work, and you don't need to be literate to solve them. For the purposes of the Sudoku puzzle, you can use words, letters, or pictures, or anything else that can be seen and depicted on paper. (I've seen baseball Sudokus that use the common shorthand for player positions: SS, P, C, 1B, 2B, etc.)

"What does God want with a starship?" inquired Captain James T. Kirk in one of very many geeky movies.

And: "Why does God need an engineer to prove His existence?" inquires Weemaryanne.

By weemaryanne (not verified) on 11 Oct 2008 #permalink

Re: #47

From his website :....Further the planet is indeed very ancient and is a sort of a "living machine. Man is a "disease" of the universe and there are an infinite number of human races "out there".

Sounds like he's another woo-tard mesmerized by the Gaia hypothesis.

Give NOT to me the cockroach, please. Somebody did that for me already this morning. I nuked it with Raid. Fortunately, I have, to this point, not had an infestation of creationists in my apartment.

Michael @ 31

Turn off Coast to Coast radio for a couple of weeks, your brain is melting.

That is not at all the sense with which Marshall was employing it. Or did you miss that?

I disagree; I think that's exactly the sense in which he was using the term "code". DNA encodes information, which can correctly be referred to as a "message". That term doesn't imply that it was generated by anybody sentient or has an intended recipient. The flaw in his argument is in step 2, not step 1.

As I stated, DNA is not a code in the way language or software is code.

And I continue to disagree.

The latter can be described as abstract symbols used to convey a message. DNA and its process isn't anything like that.

It isn't? The symbols are concrete, of course, but why does that make it not a code?

One could only call it a code in the very narrow sense of the term, that is, as a process that maps a specific input to a specific output.

Why is that narrow, and why does it not apply here?

This is how the term "genetic code" was originally meant. It was simply a description of the biochemistry linking a sequence of nucleotide triplets to a sequence of amino acids for synthesis of a spefice chain of peptides or proteins (i.e., a specific input to a specific output).

I guess I'm not seing the "simply" part. But in any case, complexity doesn't alter what it is. DNA most certainly encodes information.

IDiots and creotards love to conflate and equivocate these two very different meanings of code.

What they're conflating is the use of the term "message" to imply that there must be some sort of sentient generator and intended recipient. There's nothing in the use of the term "code" which implies that.

By Brain Hertz (not verified) on 11 Oct 2008 #permalink

Isn't he the same asshole with ads all over google? I wonder how much money he makes selling merchandise and milking the gullible fools.

By LotharLoo (not verified) on 11 Oct 2008 #permalink

Shorter: IDiots do not mean to ask questions, they intend only to assert their assumptions again and again. Everything subsequent to such nonsense has shown that assertion is their only goal.

What one should say is that life needs something like DNA in order to evolve, that is, something quite conservative, yet able to change randomly from time to time. The fact is that these two abilities were predicted via neo-Darwinism well before DNA was found, so in a sense (in some aspects, that is) properties of DNA were predicted by evolution/genetics.

The mere fact that a code is needed for life indicates that life would have a code if it exists. Once the code is found, one has to look to see what the causes behind the coded information are. And these causes do not differ meaningfully from what is predicted of random mutation and natural selection, plus a few other factors.

Glen D
http://tinyurl.com/2kxyc7

"Requires one to make an interdisciplinary synthesis of all the information available in the world."

And a metric assload of crack cocaine, apparently.

Quoting Another Primate #27.
"I've had it! There is no reasoning with these people. They are fuck tards and I can't take it any more. Let's get all of us atheist and agnostics together and liquidate all of our possessions to buy our own island somewhere."

Not to minimize your apparent anger and frustration but I have had the same thought recently but with a different slant. If all the atheists and like-minded agnostics lived on their own island together I think you would still be annoyed, ticked-off, and frustrated much of the time. It wouldn't be the utopia you imagine. You are letting people irk you.

So what, that some people think differently than you do and you can't change their minds. It is wonderful that we do not all think alike because collectively we can solve problems that one person alone never could.

By Louise Van Court (not verified) on 11 Oct 2008 #permalink

Michael being wrong again:

Like the experts in economics who have not anticipated this particular crisis,

Actually millions of people saw this crisis coming a year ago including many or most economists. Also myself who took appropriate measures in the 401K plan over a year ago. Tens of millions saw it coming months ago in the USA alone. Hank Paulson, the treasury secretary and Bernanke the fed guy saw it coming two weeks ago. Bush is still trying to figure it out.

This was a failure of leadership, mostly the GOP's fault although the Dems didn't help anything.

Your points go downhill from there.

Several years ago there was an interminable thread on IIDB with Marshall, second in length only to the infamous "Ed Thread," in which Marshall basically ignored every critique. He has latched onto the analogy described in PZ's OP, holding to it like grim death, and will never understand that analogies are not evidence.

What they're conflating is the use of the term "message" to imply that there must be some sort of sentient generator and intended recipient. There's nothing in the use of the term "code" which implies that.

Are you not paying attention? As I stated the word code has different meanings. There is not a single one that covers every context. Dictionary.com lists FIFTEEN different meanings for the word code.Of those, only the last one applies to DNA:

15. Genetics. to specify the amino acid sequence of a protein by the sequence of nucleotides comprising the gene for that protein: a gene that codes for the production of insulin.

IOW (as I stated previously) "a specific input to a specific output. "

Marshall's use of the word code in his argument most certainly does "imply a message and a sentient generator" In fact, that is what his argument is all about. It fails, however, in that it equivocates the different meanings of the word code. DNA is not arbitrary nor is it at all like the use of code to describe software or language. From The Alliance for Telecommunications Industry Solutions, whose aim is to develop and promote standards for information and communications technologies, the word code is defined as:

1. A set of unambiguous rules specifying the manner in which data may be represented in a discrete form. Note 1: Codes may be used for brevity or security. Note 2: Use of a code provides a means of converting information into a form suitable for communications, processing, or encryption. 2. [In COMSEC, any] system of communication in which arbitrary groups of letters, numbers, or symbols represent units of plain text of varying length. .... and 4. A set of rules that maps the elements of one set, the coded set, onto the elements of another set, the code element set.

The genetic code could be described by definition #4, but clearly not by other definitions. For example, software or language could be described by definition #2, but DNA couldn't.

JD: "As I stated, DNA is not a code in the way language or software is code."

And I continue to disagree.

No apparently, like the IDiots, you wish to make up your own definitions or usurp the standard meanings of well defined words.

If you believe DNA is a code like software, then please show us how the completely physical process of
DNA --> mRNA --> protein that is completely contained in the physical layer is REQUIRED to be abstracted at higher levels the way ALL software is. Also, if DNA is a code like software why isn't table salt or water also information containing codes? Or are you claiming all chemicals are really analogous to software?

Marshall argument (and yours) fails because he either doesn't realize or understand that the term "code" has different meanings in different contexts or he does know, but deliberately equivocates them.

I'd say JD is right. the difference between the way science uses "code" and the way it's used colloquially is the same issue as "theory" and "theory". they blorr the distinctions to make a point

In the scientific sense, there's no symbolic information. the information is stored withing a small set of transcribable building-blocks. the information directly derives from the physical, chemical composition and combination of the building-blocks.
In the colloquial sense, "code" is a form of encryption. the building blocks are inherently meaningless and useless, and can be substituted by ANYTHING, in ANY combination. the meaning is mounted onto them symbolically.

symbolical coding requires a mind usually (though i suppose the randomly generated computer language from an earlier post disproves even that), and THAT is why they argue that DNA needed a mind that imbued it with its meaning. They're wrong, because DNA coding isn't symbolic at all.

I'd say JD is right. the difference between the way science uses "code" and the way it's used colloquially is the same issue as "theory" and "theory". they blorr the distinctions to make a point

Yes, it's a similar situation. When scientist say "genetic code" they mean it in a very specific sense of the word (input maps output). And just like with the word "theory," context is everything.

and to make a human-scale comparison for the way DNA transmits information:

a non-symbolic way of getting "hot" across would be to pour boiling water on your hand. I could make the same point in a few other ways (stab you with a hot poker, hold your hand into a fire...), but the number of substitutions possible is limited by the physical attributes of the medium. pouring cold water over your hand will NOT convey "hot" to you.

that's how DNA transfers meaning. language on the other hand doesn't need to burn you to transfer the meaning of "hot", because it's an agreed upon, symbolic representation.

It is wonderful that we do not all think alike because collectively we can solve problems that one person alone never could.

It's the fundamentalists who are causing problems, in case you didn't notice.

In the battle between JD and Brain Hertz, I am siding with JD at this point. I find the analogy of DNA to code (as used by Marshall) to be tortured. If DNA is code, when do we know information has been encoded vs. a random string of nonsense? It is not like someone watches the various transcriptions and says at some point "Aha! now we are getting somewhere -- we have a membrane!".

In all cases for real codes, their is a distinguishing point by some entity at which random noise gives way to meaning, and therefore information. DNA does have the property of persistence of certain randomly produced sequences, but this is an attribute of the underlying chemistry involved. Languages and codes retain information because the arrangement of symbols has a useful meaning outside the language itself. DNA has no external meaning that I know of.

"Michael is a raelian..."

Damn.

I had my money on Michael being either Gene Ray or Sollog.

By WhenDanSaysJump (not verified) on 11 Oct 2008 #permalink

1. Bozo the clowns nose is red.
2. Red is the color of fire.
3. Fire is a tool of the devil.

Therefore it is a well known fact that Bozos nose is evil incarnate.

By Eric Paulsen (not verified) on 11 Oct 2008 #permalink

Comment 63 nails it.

Who is Sollog?

By David Marjanović, OM (not verified) on 11 Oct 2008 #permalink

This would be a reasonable syllogism (but proving far less than the creationists want it to), except for the change of "come from" in point 2 to "designed" in point 3.  That is the unwarranted leap!  A mind that creates a language string need not be conscious, such as the "hive mind" that creates the dances of bees.

With point 3 corrected, this syllogism is basically just the Gaia Hypothesis, that it is useful to think of the entire biosphere as a meta-organism where DNA mutations constitute Gaia's "thoughts".  In no way does it prove that it is even useful to think of the universe as being ruled by a bearded guy sitting on a throne in the clouds.  Fail, as usual.

The Ken Ham School of Logic/Business Plan:

Phase 1. Spout creationist nonsense.
Phase 2. ???
Phase 3. Profit. Get it?

This argument is bad enough without mischaracterising it as you have, PZ. They are not saying the organism with DNA must have a mind but that DNA, as a message, must be the product of a mind (presumably God's). Nothing in the argument requires attributing intelligence to cockroaches (or even creationists), making most of your post just look foolish.

Not quite as foolish as what you mock, mind you, but still very weak indeed. You've done better. Your blog is increasingly proof that passionately opposing sides will eventually meet in the middle -- a ground that is still pretty stupid. You should raise your standards.

Eric Paulsen @67 wrote:

1. Bozo the clowns nose is red.
2. Red is the color of fire.
3. Fire is a tool of the devil.
Therefore it is a well known fact that Bozos nose is evil incarnate.

Hmm, you might be on to something....

JD has already touched upon this point, but it warrants amplification: if all things that map specific inputs to specific outputs are considered "codes", you could similarly reduce just about any physical phenomena. This is what has lead to Wolframian confusions about the laws of physics being "computational" or computation "underlying" physics.

Actually, DNA is a coding system, and (as Conway-Morris points out) one that approaches, but falls just short of, optimization in terms of efficiency and reliability. It is possible to imagine codes that are more efficient at storing information and which are less prone to errors, but such would be a vanishingly small portion of the set of all possible codes.

And, since evolution actually requires variation, it may well be that the code we have strikes just the right 'Goldilocks' balance between reliability and the occasional novel variant to make evolution likely to occur. If the code was a little more reliable, there would be much less variation in populations due to the lowered mutation rate, decreasing the likelihood of fortuitous variation being present within populations in a changing environment, which would have the effect of stymieing natural selection. Conversely, if the process was a little bit less efficient or less reliable, populations would become swamped with deleterious mutations, and again this would tend to keep populations small in terms of both genetic diversity and absolute size, and again selection would tend to be hindered.

So, to that extent one might say that the code we observe does appear to be optimized ('fine-tuned') for life. Narrowly considered, Marshall's initial premise is worthy of our attention in the same way that the value of the fine-structure constant or the charge of an electron is worthy of our attention. It is worth asking why they have the values or parameters that they do!

Where Marshall's argument fails, however, is in the second premise, which is the leap to a conscious agency. The fact that DNA is relatively optimal compared to other possible codes as a basis for an evolving system does not constitute evidence for its design per se. There is no reason to believe that natural causes can not be evoked for any proximal explanation of the code's properties, if it can be shown that other possible codes would be less optimal than the one we see....and in fact, it is a relatively simple matter to show why this is so.

It would've been nice to see a discussion of this point at the 'Origins' conference I attended last weekend at Cal Tech, but abiogenesis only received a gloss in just one of the wide-ranging lectures, of which I hope to start posting soon.

If DNA is a message, what is it saying? What is it ultimately trying to tell us?
Perhaps, "We apologize for the inconvenience."

The Ken Ham School of Logic/Business Plan:
Phase 1. Spout creationist nonsense.
Phase 2. ???
Phase 3. Profit. Get it?

(with apologies to Sidney Harris)

And then a miracle occurs.

Or, at least, given the fulsome inanity of much creationism, something akin to a miracle, because Ken Ham's organization is making quite a bit of money.

Scott,

The point about equivocating definitions still stands. If argument for design from DNA is only that it works really well (which I'm not in a position of expertise to dispute), then it has the same basic form as arguing for design via bacterial flagella or the eye. But the argument being made by the guy quoted in the OP is a bit more complicated: he's arguing that we can know DNA is designed for the same reason we know a Haskell98 compiler is designed: it's a coded message which requires a sentient creator almost by definition. That is, as I understand, what is under dispute by JD, myself and others.

Scott Hatfield said:

Actually, DNA is a coding system, and (as Conway-Morris points out) one that approaches, but falls just short of, optimization in terms of efficiency and reliability.

DNA is a code as Conway-Morris defines it. His definition supports his (not so mainstream) conjectures well, but may not apply here.

Conway-Morris, while highly qualified in his area, does not represent an authority for this discussion (in my opinion).

I still have not seen a good refutation of the core problem -- if DNA is a code, what does it code for, in terms of information? A "program" that can produce many equally "good" results produces no "meaning" (in the human sense of course).

As far as DNA code being optimized, since no a priori requirements were placed on DNA in terms of the information it stores, how does one critique its reliability and efficiency?

If DNA is a message, what is it saying? What is it ultimately trying to tell us?

Since DNA self-reproduces, and acts in the service of its own self-reproduction, a four-letter Anglo-Saxon monosyllabic imperative verb (which can mean, among other things, "commence reproduction") comes to mind...

By Owlmirror (not verified) on 11 Oct 2008 #permalink

JD @ #50

As far as I know, there is nothing 'woo' about the Gaia hypothesis, which simply states that there are feedback loops linking all systems and a change in one can affect others. I suspect that AGW is an excellent example of that.

Or am I missing your point?

By Gary Bohn (not verified) on 11 Oct 2008 #permalink

Since DNA self-reproduces, and acts in the service of its own self-reproduction, a four-letter Anglo-Saxon monosyllabic imperative verb (which can mean, among other things, "commence reproduction") comes to mind...

ROFLMAO

subtle.

very subtle.

...Hark! I think I hear that siren song even as I write this...

Gosh, looks like a valid syllogism to me. I'll just swap a term:

1. DNA is not just a molecule - it is a coding system with a language & alphabet, and contains a message

2. All languages, codes and messages come from humans.

3. Therefore DNA was designed by a human.

(tee hee)

Tyler wrote:

If argument for design from DNA is only that it works really well (which I'm not in a position of expertise to dispute), then it has the same basic form as arguing for design via bacterial flagella or the eye.

I agree. An ID creationist would doubtless stub their toe on the optimality of DNA and say, 'Oho! A watch!'

...he's arguing that we can know DNA is designed for the same reason we know a Haskell98 compiler is designed: it's a coded message which requires a sentient creator almost by definition.

As I said in my previous post, this second premise (conscious agency) does not follow from the first claim, and if I didn't make it clear, I regard that claim with skepticism, in part because (as R.C. Moore and others have argued elsewhere) #1) those making that argument seem to be deliberately conflating different senses of the word 'information', and #2) even if we admit the relationship between a technical definition (such as 'Shannon information') and everyday usage, the claim of the necessity of a conscious agent is still not demonstrated.

As a theist, I would be completely at home with any clear, unmuddied argument that demonstrates not only the sufficiency, but the necessity for a conscious agent in scientific terms. As a science teacher, however, I do not see that such an argument exists. The main purpose of this line of reasoning appears mainly to make technicians like Percy Marshall appear to be profound, original thinkers. Just to make things clear, I don't think that follows, either!....:)

Computer languages: HTML, JPG,C++, TCP/IP, USB

Eh? JPG is a language ? USB is a language ?

As far as DNA code being optimized, since no a priori requirements were placed on DNA in terms of the information it stores, how does one critique its reliability and efficiency?

Well, reliability has to do with how often the message is correctly copied vs. not. Efficiency, I don't know how that was defined, but it's in the book 'Life's Solution.' Unfortunately, my copy is currently in storage, so I can't give the primary source that Conway-Morris cites, much less the technical details. Perhaps someone else here can?

#60:

...the completely physical process of DNA --> mRNA --> protein that is completely contained in the physical layer...

#61:

the information directly derives from the physical, chemical composition and combination of the building-blocks.

You guys are still ignoring tRNA, where the actual translation takes place. A codon does not select a specific amino acid through inevitable physico-chemical processes. It does so through the medium of tRNA, which embodies an arbitrary mapping from codon to amino acid. As far as I'm aware, there's nothing in the physics or chemistry of DNA transcription and protein synthesis that makes this particular mapping inevitable, or an alternative mapping impossible. (And indeed, we find variant mappings in nature.) In software terms, the genetic code is table-driven. You need tRNA, or some other mechanism for representing arbitrary [codon, amino acid] pairs, to perform the translation. A gene therefore is not a physical analog of a protein, as you guys seem to be arguing; it's a symbolic representation that requires information processing (the tRNA table lookup) to realize.

By Gregory Kusnick (not verified) on 11 Oct 2008 #permalink

JD: I clicked on your Wikipedia link for "Gaia hypothesis" and was amused to see that "citation needed" is liberally sprinkled throughout the first paragraph of the entry -- such as, for example, here: "Lovelock and other supporters of the idea now regard it as a scientific theory, not merely an hypothesis, since it has passed predictive tests.[citation needed]"

2 false premises and 1 non-sequitur.

3 logical fallacies in 3 phrases. Wow. Impressive.

By The Blind Watchmaker (not verified) on 11 Oct 2008 #permalink

Efficiency, I don't know how that was defined

By natural selection.

A gene therefore is not a physical analog of a protein, as you guys seem to be arguing; it's a symbolic representation that requires information processing (the tRNA table lookup) to realize.

Well, yes, but this is also done physically, by enzymes that fit one tRNA and one amino acid much better than all other combinations. It's still a fully automatic and mindless process.

The origin of the genetic code may be due to natural selection: most other codes would lead to considerably higher mutation rates.

By David Marjanović, OM (not verified) on 11 Oct 2008 #permalink

if DNA is a code, what does it code for, in terms of information?

While I can't improve on Owlmirror's answer @79 for wit, I can at least play straight-man.

The information (in the colloquial sense of "meaning" which is the term all ID arguments of this variety really want, even those couched in supposedly sophisticated formalisms, like Dembski's) in DNA tells how to build a machine in a given developmental environment to survive and reproduce in a given niche. It's "about" that developmental regime and that niche.

It's still a fully automatic and mindless process.

I never said otherwise, and I'm certainly not defending Marshall's woo. I'm just objecting to the argument that "mindless" necessarily means "devoid of symbolic content".

By Gregory Kusnick (not verified) on 11 Oct 2008 #permalink

(Note, this is shorter than it looks - I put a quick primer on deduction vs induction at the bottom, which makes it longer)
(Yeah, I haven't read the whole thread so pardon any duplications)

Technically, line (1) is mostly correct. DNA is a language, and follows the expected rules of such. The only problem with it (line 1) is that it implicitly claims DNA carries exactly one message. C, Python, Java, Assembly, these are all languages too.

The full series, however, should be:

1) DNA is not just a molecule - it is a coding system with a grammar (codons, introns, exons, etc) & alphabet* (A,T,C,G), and the ability to convey messages (codon strings).
[true]

2) Any coding system that has (a) a grammar, (b) an alphabet, AND** (c) the ability to convey messages, is called a language. [true to the best of my knowledge***]

3) Therefore, DNA is a language.
[conclusion 1]

4) All previously known languages have originated from an intelligent being.
[may or may not be true - historical counter-examples, anyone? Probably subjectively true, however]

5) DNA is not known to have originated from an intelligent being.
[true]

6) Therefore, not all languages may originate from an intelligent being.
[conclusion 2]

Now, I skipped over some more formal stuff (eg, 5 & 6 should have been declaratives in stead of possibilities if this were formal logic), but the basic error comes clear: the original fell pray to inductive error, this particular one being analogous to the 'no black swans' problem. This being that, to a Western European prior to the discovery of Australia, no swan had ever been observed that was black, and so it was thought that ALL swans must be not black. Sometime after the discovery of Australia, they found black swans there, illustrating the 'problem' with a conclusion from inductive logic - ie, that it can never be completely proven true without checking EVERY possibility for a counter example to the premise(s)
(see primer below if you don't understand, or want to see more about, what I'm talking about).

Since science is primarily inductive in nature (see primer first if you want to complain), I imagine that grasping the relevance of this particular problem, and the deductive equivalent may be one of the root reasons some people don't 'get' science, thinking that if something is proved 'wrong' or 'incorrect' or if it's possible that it could be, everything related to it must be, or that if something is currently known to be true, it must be absolutely true.

*for simplicity, I'm including ideographs(?)[like used in Chinese] and such in the term 'alphabet'.
**Logical 'and' in capitals, grammatical 'and' otherwise.
***Either way though, this is meant to be the logical form 'P => Q' so even if languages exist that don't follow that rule, that statement may still be true (ie, a subset of languages).

Let's start with the difference in the respective 'truthiness' of the conclusions from Induction and Deduction:

o Conclusion from Inductive Syllogism:
1) Can not be proven completely true, given that the premises are true, without checking every possibility (ie, every item in the applicable universe) in some cases.
2) Can be proven false by counter-example.
3) Can be proven false by falsifying any or all inductive premises (as this is equivalent to providing a counterexample of the inductive premise(s)).
4) But can not be proven false by falsifying any other premise(s).

o Conclusion from Deductive Syllogism:
1) Can always be proven true given the premises are true.
2) Can not be proven false by falsifying any or all premises (which is not equivalent to providing a counterexample).

(This all assumes the logical relations were applied correctly and that we're not considering restatements of a premise [ie, P(said one way) => P(said another way)])

Or, in short,
o Both can be proven false by counter-example, and
o Neither can be proven false by disproving any non-inductive premise(s),
but
o Induction requires checking the ENTIRE applicable universe to prove that the inductive premises truly are general.

The primary reason for this difference it that:
o In induction, you try to go from specific cases to general properties (some swans -> all swans), whereas
o In deduction, you try to go from known/defined general properties to specific cases (all swans -> some swans).

As such, there's an 'extra' type of premise in inductive logic (what I'm calling an 'inductive premise') which is true only within the scope of the available examples, but is not known to be true or false outside of that. However, as the amount of observations supporting that premise increases, with a lack of any counter-examples, the greater the likelihood that the premise is true in general - thus it's use in inductive logic (and the importance of the mathematics of probability). Deduction does not allow this type of premise, as it seeks to go from the general to the specific.

You may be wondering about that 'neither can be proven false by falsifying the premises' bit. The deductive equivalent of the Black Swans problem should clarify easily:
For the syllogism
o Some animals are mammals.
o All mammals are white.
o This animal is a mammal.
o Therefore this animal is white.
All premises are false when the animal is an albino alligator, but the conclusion is still true - the alligator, being an albino, IS white.

Note however, that it IS possible to prove a negative, by (among other methods) proving it's negation false.

On a final note:
o Science is Inductive by nature - everything starts from specific examples to find general laws.
o Mathematics are Deductive by nature - everything starts from generalities¹ to find specifics
o Check out the term 'pons asinorum' for a laugh..

¹: Since the beginning axioms of any branch of mathematics is ultimately a group of general 'meaningless' definitions and arbitrarily defined relations between those definitions, it is not inductive.
Statistics is a bit of a mix between science and mathematics - many basic elements are strict mathematics, but some of the higher level stuff includes "magic numbers" from experience.

DNA tells how to build a machine in a given developmental environment [including constraints] to survive and reproduce in a given niche. It's "about" that developmental regime and that niche.

even that would be a rough language at best. constraints particular to the organism in question are one of the things that prevents optimal tracking of said "niche", and so would tend to interfere with any ability to utilize DNA to "track" a specific set of selective pressures relating to say, the localized environment.

It's one of the things that really limits the applicability of fitness-space models, IMO.

God is love.

Love is blind.

Stevie Wonder is blind.

Therefore, Stevie Wonder is God.

If you accept his assumptions even a madman sounds reasonable.

Actually, I am perfectly fine with DNA + RNA representing a sort of "code". One can write applications whose sole code function is to generate their own code, and one could even, presumably, make one that would generate variations (though that falls into genetic algorithms). The problem is, as has been pointed out, it doesn't mean that a) something *created* the code, or that b) it qualifies as being... C++, instead of something like Befunge, reMorse, Whirl, Intercal, Lolcode, Chef, Brainfuck, and numerous others that are exercises in designing "idiot" systems, that basically work, but which no sane engineer would consider actually coding a project in.

So, God has a very sick sense of humor and decide to code life using some sort of esoteric system that is just plain idiotically stupid? Suppose its possible. lol

And the PEDANT OF THE BLOG AWARD™ goes to......
Dreikin!

By Sui Generis (not verified) on 11 Oct 2008 #permalink

Ok, there seems to some issue as to whether DNA is a code/language.

1) DNA is symbolic - each base is a symbol, and each codon a word.
2) DNA conveys a message - most basically, it is "add this amino acid: ___", though there are others as well, both in abstraction and meaning (eg, make this RNA; Make a protein X that causes translation of protein Y to decrease in relation to the concentration of Z floating around).
3) The Symbol : Meaning mapping is arbitrary - there is no reason that DNA must be the conveyor of the message (lookup: cDNA libraries - the DNA is the message, not the protein or RNA; RNA viruses - they don't use DNA for their coding).

Now, Mr JD at #60 <2008-10-11 16:18EDT> wrote a rather long post that I'd like to address, but I won't quote all of it.

1) Dictionary: As you pointed out, dictionaries aren't a particularly good source for this type of discussion, as they tend to include all accepted/normal/popular meanings, but do not necessarily include their logical relations (eg, "Is definition 1 a subset of definition 2? Dictionary doesn't say.."

2) "DNA is not arbitrary [continued..]": Yes it is. See above.

3) "[..here] nor is it at all like the use of code to describe software or language.": Yes it is. With respect to software code (and I'm using your implied meaning of at least a middle-level language like C, not the low-level assembly languages which would be more appropriate), DNA is the source code, and the produced proteins and RNA are the resultant program. With respect to _Natural_ (ie, human) languages, DNA is the conveyance of an abstract message (Do this action) in physical form (letters and codons) to another entity (ribosome, polymerase, etc).

4) Alliance for Telecommunications Industry Solutions definitions:
(a) DNA clearly falls under the first definition: it is unambiguous (each codon has only one translation, and each triplet has only one codon ['stop' codons may be longer, as they are actually a class of non-triplet codons, analogous to the UTF-8 mechanism]), it encodes data (the elements of the proteome and RNA-some) in a discrete form (the nucleotides in a chain), and provides a method for converting that information into a form suitable for processing - mRNA. In fact, it self-contains the method for it's own conversion, which many of the codes that definition applies to don't (compiler source code is an example exception).
(b) Note that COMSEC at the beginning of the second definition? That means "Communication Security" - ie, cryptography and the like. It's use of 'arbitrary' is meant to indicate that the 'code' (rather, the ciphertext) should not be decipherable without a conversion mechanism and or some 'private' bit of information. The 'plain text', as any cryptographer will confirm, need not be human readable - it could be a base64-encoded picture or program, for example. This is outside of the scope of the obvious meanings we're debating, it would seem, and therefore irrelevant. And it doesn't describe source code or natural language either, for the same reasons.
(c) What was definition 3? (just curious and lazy)

5) All software source code is NOT required to be abstracted - and even for that which is, the brainfuck software language would obviously indicate the irrelevance of that 'abstraction'. Software can be coded at as low a level as you would like, as long as you know the format(s) and rules. Just take a hex editor, set it to binary representation, and start typing 1's and 0's. Or, get some olde Vaxen and start punching cards, or get even older - ENIAC, and manipulate the physical elements of the machine to program it. Aside from which, DNA is analogous to assembly code, mRNA to the assembly code as stored in the compiler-readable form (or sometime it's similar to java byte-code), and protein to the compiled program.

6) Salt and water aren't information containing codes (in the respect we seem to be debating) for several reasons. Most importantly, they're generally uniform and disordered - each piece of salt is just like any other piece at the word-level, and the same goes for water, and neither is in any way linear normally. Further, there's no translation mechanism - they're not operationally mapped into something else unambiguously.
However, it could be done - differently sized/shaped/space-grouped salt and/or water _crystals_ could be mapped by a (set of) nanomachine(s) into something else - say, a nanostructure composed of different elements, with each element taking the place of each crystal and chosen according to the size of the crystal. Or for a mechanism more similar to computers, combine the water and salt: high salinities correspond to 1's, and lows to 0's.

Sui Generis:
YES!!!!
Thank you, Thank you all! I would like to thank all the people who made this possible (God not included, of course). Satan, first of all, for introducing me to this wonderful thing called logic, Linus and Stallman and Gnu and every one else in the FLOSS community, de Saussure for the introduction to Linguistics...

(hehe, I saw that before I posted my last volume to this thread - does two of them in the same thread make me a square PoW? :-D )

Gee, in point 2 he assumed his conclusion. That's called begging the question, I think. Or maybe you could just say that he made an unwarranted and unprovable statement.

The information (in the colloquial sense of "meaning" which is the term all ID arguments of this variety really want, ... in DNA tells how to build a machine in a given developmental environment to survive and reproduce in a given niche.

The information in DNA also builds machines that crash and burn on a regular basis. You are giving DNA a goal I think it is quite unaware of. So again, what is the information in the sense of Perry Marshall's usage. And if there is no information encoded, then is DNA a code? (again, in Marshall's usage).

he assumed his conclusion. That's called begging the question, I think.

Yeah, that's what it's supposed to mean, but I think the battle may be lost (at least in the U.S.). Now, "begging the question" is mostly being used to mean "raises the question" or "brings to mind the question."

I agree completely with your point, however. I'm not a biologist, but it seems to me that talk about "symbols" and "messages" is just anthropocentric. It makes sense that we evolved to be anthropocentric, but we have to recognize it and discount for that bias when thinking scientifically.

Are you not paying attention? As I stated the word code has different meanings. There is not a single one that covers every context. Dictionary.com lists FIFTEEN different meanings for the word code.Of those, only the last one applies to DNA:

I'm paying attention perfectly well, thank you. It's just that I disagree.

I do not see how the fact that the words in question might have multiple meanings has any bearing on the question, which is whether Marshall's point 1 can be considered incorrect.

Since there is a reasonable meaning, in that context, of the term "code" (specifically that which would be used by somebody designing or analyzing a communication system, which happens to be my field) which renders the statement accurate, you can't claim to be entitled to substitute a different meaning and then declare him wrong.

The flaw in the argument is in the assumption appearing in point 2 that something that codes information must have "meaning" and must be a conveyance from one sentient being to another, which just isn't so.

By Brain Hertz (not verified) on 11 Oct 2008 #permalink

The last paragraph of the article says:

"If you want to understand our history and our evolution, the first concept you have to be able to grasp is that natural processes produce all the complexity and diversity of extant life without the guiding hand of any external agents."

Since "the guiding hand of (an) external agent"
was involved:

Genesis 1:1 (NIV)
In the beginning
God created the heavens and the earth.
http://www.biblegateway.com/passage/?search=Genesis1-11;&version=31;

and

Isaiah 48:13
My own hand
laid the foundations of the earth,
and my right hand
spread out the heavens;
http://www.biblegateway.com/passage/?book_id=29&chapter=48&version=31&c…

If you go on the premise
that it all happened:
"without the guiding hand of any external agents"
the results
will not be science,
but rather science fiction
. . .
or,
in the words of the Bible:

Ecclesiastes 10:13 (New King James Version)

The words of his mouth
begin with foolishness,
And the end of his talk
is raving madness.
http://www.biblegateway.com/passage/?search=Ecclesiastes10:13;&version=…;

Since God was there "In the beginning"
It would be wise to rely on His account
of how things happened.

As we are advised:
"God...does not lie"
Titus 1:2
http://www.biblegateway.com/passage/?book_id=63&chapter=1&verse=1&end_v…

I call Poe on JosephU #104

No one could really be that stupid.

In case I'm wrong, JosephU, c'mon. You can't cite the bible's assertion that is is factually accurate as proof that the bible is factually accurate. How could you not understand that?

Replace DNA with "religion" and molecule with "belief system" and re-read it. OMG, It has a designer too!

Religion is not just a belief system - it is a coding system with a language & alphabet, and contains a message.

All languages, codes and messages come from a mind.

Therefore religion was designed by a mind.

Since God was there "In the beginning"
It would be wise to rely on His account
of how things happened.

So God authored the bible? Here I was thinking that men wrote it. No self-respecting deity would ever claim credit for that load of dribble.

I'm not about to enter this debate (!), but for all those debating the validity of the first point, could I suggest that you take into account that only a portion of the DNA codes for RNA (be it mRNA, snRNAs, miRNAs, tRNAs, etc). DNA is structured inside the nucleus, not a linear ticker tape of "code". Portions of the DNA are involved in setting up and maintaining that structure, e.g. MARs (not the planet, Matrix Attachment Regions, and not "that" Matrix, either, for fans of the films!); NORs (not 'Not ors' but Nucleolar Organizing Regions); insulator sites / boundary elements; cohesion binding sites; association points with nuclear pores, Cajal bodies, PML bodies, the lamina, etc., etc. There is the higher-order structuring of the chromatin to think about at many levels, from histones and the classical temporal transcription factors up to the whole-nucleus level. Then there are the epigenetic modifications of the proteins the DNA is bound to and whole host of other things tying into how DNA is "used" including non-coding RNAs, co-factors, various "signal" molecules, etc...

The portions of DNA that code for mRNAs, after being transcribed to mRNA, do provide a series of adjacent binding sites for tRNA anticodons, but the total of the DNA in a nucleus is a collection of quite complex molecular systems that just happen to physically connected though a relatively small number of molecules, each being the DNA molecules in each of the chromosomes of the organism in question.

The point is that by considering only the mRNA-encoding portions of DNA (or only the mRNAs themselves), a lot is being left out, pretty much the entire nature of DNA in a nucleus, IMO!

(As I'm not joining the debate, I'll leave my opinion out, but I'll drop this in for those wanting to "play" to chew on. Have fun!)

By BioinfoTools (not verified) on 12 Oct 2008 #permalink

I'll drop this in for those wanting to "play" to chew on

"mmmmmm, Intron-jerky..."

/homer

#104... what is it like to have a reality so small it can fit in one 2,000-year-old book?

Think of the things a flagellum would tell 'em
If only they knew how to open their eyes
The stuff they could see through their glasses surpasses
Their presuppositions, distortions and lies
If all they believe is the bible, they're liable
To miss a real world that is there to be seen
But gladly the biblical thinkers wear blinkers
And try to decipher the code of the gene

It's hard to imagine a finer designer
Than blind evolution and millions of years
But this explanation's (quite oddly) ungodly
And quickly rejected for fanning their fears
They cannot accept evolution's solutions
And make up a God who's the cause of it all
Myself, I can't use that religion, one smidgen
It's selfish and petty; I can't think that small

http://digitalcuttlefish.blogspot.com/2008/10/ignorance-aint-bliss-for-…

@109:

A lot more than introns, too ;-)

@Everyone:

For anyone who misreads post 108 as me jerking people around, I certainly didn't mean it that way. Don't let my points stop you having fun :-) I'm just saying that there is much more to "DNA" than just a coding sequence and you might want to add the other things DNA is involved in to your debate if you're so inclined.

By BioinfoTools (not verified) on 12 Oct 2008 #permalink

This one's been kicking around for a while now.

My own take was that even if 1. is true, 2. is demonstrably untrue as many interpretable patterns can arise from non living mechanisms.

Weather is a great example. I know for example that if a warm off shore wind is blowing in my part of the world, it usually precedes a cold front system. Despite being hot today, I can load the extra blankets on the bed for tonight.

3. Is therefor clearly false.

A Few Observations

1. DNA is just a part of the machinery.

2. Cats are trying to communicate with us. They have meows for "I'm hungry" and "Whatcha doin'?" Cats vocalize at us because we vocalize at them, and cats are polite in their own feline way.

Now for Evolution Made Real Simple

Mistakes happen.

Sometimes the mistake works out well.

Sometimes the mistake works out so well it comes to replace the original method.

That's right, evolution is like cooking.

If one checks the definition for a theory one finds that it is a premise which contains the possibility that it can be proven wrong - that the basic idea it is wrong and that a better solution exists. The theory of Intelligent design (if you can call it that by any stretch of the imagination) contains no such condition. One can never prove or disprove the existance of an intelligent designer. Therefore, it isn't science and isn't a theory as science demands a proof of principle. Tt is really just a philosophical idea..

By David C. Harmer (not verified) on 13 Oct 2008 #permalink

If one checks the definition for a theory one finds that it is a premise which contains the possibility that it can be proven wrong - that the basic idea it is wrong and that a better solution exists. The theory of Intelligent design (if you can call it that by any stretch of the imagination) contains no such condition. One can never prove or disprove the existance of an intelligent designer. Therefore, it isn't science as science demands a proof of principle and isn't a theory. Tt is really just a philosophical idea..

By David C. Harmer (not verified) on 13 Oct 2008 #permalink

One can never prove or disprove the existance of an intelligent designer.

you can even go one step further.

even if you COULD somehow prove there was an extra-sapien "intelligence" remotely capable of biological design, to actually formulate a hypothesis as to whether a specific bit of biota was "designed", you'd also have to have a model of exactly how that "intelligence" interacts with the environment.

IOW, the proponents of ID (and let's face facts, that means 99% Abrahamic religionauts), would have to know how God actually interacts to "make" things.

...and I always tell them:

"good luck with that. call us when you know as much about god as an anthropologist does about humans."

ID supporters simply can't even formulate a testable hypothesis, even if they COULD prove that god exists!

It's a complete non-starter.

beyond a waste of time.

Hey, now that I think about it, I think if I ever title a book on my investigations into cdesign propenentists, I'll title it:

"Beyond a Waste of Time: Researches into projections of the cognitively dissonant."

that way, the religionauts can simply dismiss my book via the title, without having to even make the effort of creating all those strawmen like they do for Dawkins' books.

Not sure I agree with the cockroach analogy. The creationists are saying that god creates DNA, not people. They're not saying that we have brains, and we have DNA, therefor our brains create DNA.

You know, I wonder how well this article would fly with other IDers and creationists. If you go back and look over his actual arguments, you will notice that he is making the case that ONLY DNA shows signs of being created. By this definition, then, his designer has been removed from every other aspect of the universe besides biological life. Apparently God created the universe, then strolled away for a few billion years on vacation, then came back again once the Earth had cooled to take up the job again. What a slacker!