That ghastly collection of homophobes and right-wing zombies, Focus on the Patriarchy, is starting a new initiative to take on the happily growing army of student atheists. They’re launching a series of ‘edgy’ videos called True U which feature grim Christians staring glumly at the camera while statistics scroll by (“Increasing numbers of college students are losing their faith!” “60% of all biology & psychology professors are atheist or agnostic!” Cheer up kids, it’s good news all the way!). Then to inspire them, they cut to a Christian fake college professor ranting away.
The ‘professor’ is…Stephen Meyer of the Discovery Institute! And the great thing is that he’s openly using the arguements of Intelligent Design creationism to counter atheism with assertions that science supports the existence of a god.
“The new atheism is the old atheism repackaged to make best sellers,” says Dr. Stephen Meyer, a presenter in the video, “but is completely out of touch with the most current developments in science.” Meyer, who holds a Ph.D. from Cambridge University in the History and Philosophy of Science, is a Senior Fellow at the Seattle-based Discovery Institute, an organization that promotes intelligent design. The Discovery Institute is behind the “Teach the Controversy campaign” that aims to teach creationist anti-evolution beliefs in United States public high school science courses alongside accepted scientific theories, claiming that a scientific controversy exists over these subjects.
It’s been settled for a long time, but this is one more nail in the coffin: Intelligent Design is simply a front for religious pitchmen. And not just any religion, but far right Christianity.
Also, his arguments are awful.
“When we find information in DNA molecules encoded in digital form, the best explanation is that that information also had an intelligent source.”
That’s what he babbled about endlessly in his dreary text, Signature in the Cell: nothing but rank assertions that genetic information is digital (really, it’s not), that it’s just like computer programs (nope), that computer programmers write computer code (OK, I’ll accept that), and therefore, there had to have been a Great Intelligent Space Programmer at the beginning of everything (can you say logic error, boys and girls? I knew you could). So now you know the next step, the part he wasn’t brave enough to say in his book…and that Super Programmer is Jesus.
At least I suspect that classroom is as fake as the one Ben Stein was yelling at in Expelled, since Meyer is no longer affiliated with any real university and spends all of his time flogging lies to his creakily fanatical colleagues and church audiences any more.
Please tell me that’s not Cambridge University, UK? As in, one of the two best Universities in the UK and the best University for science subjects in the UK?
Because that would be well embarassing…
His degree is in the “history and philosophy” of science.
Not science. He’s not a scientist. Never was. Never will be.
I’m continually amused that faith is not enough.
Man, that coffin has so many nails in it by now that it’s more metal than wood. I think we need to get a box to put next to the coffin, where we can throw each new nail.
Audley Z. Darkheart #3 wrote:
I’m continuously relieved that faith is not enough. It’s the only thing that gives us a fighting chance. The people who are “out of touch with the current developments in science” are not the atheists.
It’s when people emphasize faith as being enough — it’s an open heart and mind and a choice to believe — that I get worried. There’s no check on that. There’s no means to bring us in. We closed our hearts. Case closed.
If God is the celestial programmer who wrote the genetic code, then he is a terrible programmer.
The code is almost unreadable, to the extent that we have no idea what a lot of it does. He apparently took large pieces of it and copy-pasted it from one organism to another, just commenting out the chunks of it that weren’t needed anymore. And speaking of comments, has he even heard the word “documentation”? Because there isn’t any.
So baby Jesus really did make the phyla
Let’s test this construction by making a few substitutions.
It’s still stupid.
Sastra:
That too.
When creationism was rejected by the courts on First Amendment grounds, the creationists brought out Intelligent Design. ID is merely creationism with the name of God taken out and an unspecified “Intelligent Designer” substituted. (But we all know who they mean, nudge, nudge, wink, wink.)
ID is based on a lie, which not only makes it bad science, but bad religion as well. Yet the god-botherers pushing it are too stupid to realize this, or else too dishonest to admit it.
I got to “encoded in digital form” and I had to stop. I couldn’t take any more stupid. I’m not a scientist of any sort…just an interested lay person who knows practically nothing about biology…and I know that’s just stupid. The same sort of stupid as describing the brain as a computer.
Note that I made it past “looking at questions like…the reliability of the Bible.” I know something about that question, but I’m pretty sure he would dismiss the evidence that it isn’t reliable for anything. Certainly not science, biology and the like, and not even history.
Even if his Cambridge PhD is just in the “history and philosophy of science,” that’s no excuse. How could he study the history and philosophy of science and not know better? I studied the history and philosophy of science at a podunk Southern Baptist college and I learned more than that.
Plus, the whole smary ad is an act of rhetorical persuasion, not a presentation of evidence. Notice the feel-good moment as the attractive, young co-ed with good makeup smiles subtly and nods as if agreeing with him, as if “seeing the light,” as if…well, whatever. Advertising shtick at it’s best, or is that worst. If you’re a guy, you’ll buy.
I love the question: “Why can’t someone give me reasons for faith?” Why indeed? But it’s the wrong question. There are lots of reasons for faith and the preachers are happy to give them to you: fear of hell, for example. But where’s the evidence?
And what’s with all the lines? And why do all the guys look like such losers?
It’s more machine now than man, twisted and evil.
I’m sorry, what were you saying? I was distracted by that Liberty University ad.
I find it funny how quickly morons like him can assert just how ‘evident’ design is…just finished why evolution is true, and frankly it makes my head hurt knowing there are grown fucking men who still cling to this shit. Thankfully there are actual fucking scientists out there who care about doing SCIENCE. Pretty sure I’d lose it otherwise.
I must ask you for clarification on this point, as it seems wrong. The only thing that characterizes information as “digital” is that it is encoded in discrete, indivisible chunks, as opposed to “analog” information which is continuous. The genome is encoded in a quaternary system composed of 4 states per symbol (A, C, T, and G); there are no hybrids or intermediates for any of these states. I’ve seen this point made by Dawkins, I believe in his “Rebuttal to the Information Challenge” about those Australian Creationists that visited him. It didn’t sound like he was making a simile. Genetic information seems clearly and unambiguously digital.
Is there some hidden assumptions or meaning you have behind your use of the world “digital” beyond what I said above?
I also thought the best genome-to-computer-program analogy was also made by Dawkins. Can’t remember where it’s from, but he drew special attention to subroutines when explaining it. Just as subroutines will often do nothing more than call other subroutines, many genes have the sole function of regulating the expression of other genes. One of the example he mentioned: eyeless doesn’t actually make eyes, it just acts as a regulator that says “start the eye-making subroutine here”.
There are, of course, numerous ways in which a genome is not at all like executable code. All analogies break down when you take them too far beyond the few abstract properties they are meant to represent. Is there some issue with the specific “subroutine” analogy, or is it against other people taking the genome-to-computer-code analogy way too far?
Sastra @ 5;
Its a common go-to argument among a certain type of xian – they say that faith should be enough, and that as such atheists are closed-minded and hard-hearted and refuse to just wonder at how awesome their god’s supposed handiwork is. They cast rationality and a need to base truth claims on evidence as a personal defect, or even as being dangerous. Some then go on to attempt patronising pity of atheists supposedly too ‘enslaved’ to science to live a full life, while others prefer to paint us as monsters (claiming that we are all nazis-in-wating being a particular favourite) in an attempt to whip up fear and hatred of anyone who isn’t a good little bible-basher.
I understand why it worries you – if enough people accepted the idea that ‘faith should be enough’ and that evidence is at best irrelevant and at worst the enemy, then pogroms against atheists motivated by the notional ‘evils’ of unbelievers become that much more likely.
Hi There. This particular statement is of interest to me: “nothing but rank assertions that genetic information is digital (really, it’s not)” I get this argument from a creationist coworker of mine and I honestly don’t know enough about this area to speak about it. I’m an electrical engineer. He’s a biologist or his degree is in biology at least so he knows a lot more about DNA that I do. What is the response to this? Serious question. Please enlighten me.
The Dishonesty Institute’s public relations pimps must be having a cow. Meyer has a new book coming out in a few months about how the instantaneous Cambrian Explosion proves
Godthe Intelligent Designer Did It – Meyer’s book is all about sciency-sounding stuff and has nothing to do with religion, nosirree. And then this comes out! Good timing, Stevie!Well I listened to that ad, and PZ I want my minute and 56 seconds of lifespan back. He’s a fast, glib talker with out any facts, figures or numbers to check in that add. When he said “world view has the causal power”, I almost threw up. Sounded a lot like Karl Rove’s “We make our own reality”.
Secondly when he said something like: as one historian said ‘belief in god is more credible now than any time in the last century’, I’d like a citation. Since he’s a historian (well his degree is) I wonder if he’s citing himself?
What’s surprising to me is how long it’s taken to more or less just go out pushing straight theism. I mean, who has been fooled since Dover, at least, other than IDiots and the like? And they can be fooled that it’s science so long as it’s consistent with the Bible and theism, since to them “science” is simply theology in a cell.
And especially, they know they need donations from the religious, and people like Ham have been pounding away at the claim that they’re not religious enough. Of course they’re quite religious in fact, theists were supposed to see through the rhetoric, but they’re really less likely to see through it than the rest of society is.
Glen Davidson
Oooh, Focus on the Patriarchy, I like that a lot. Going to steal.
Small changes in the codon (swaps of one nucleotide) lead to small changes in the amino acids’ properties. Informaticians call this a Gray-code. This is the equivalent to continuity in the theory
of analytical functions, i.e.small changes on the x-axis lead to small changes on the y-axis (no sudden jumps).
That’s incredibly depressing and very worrying, so I agree with the video on that point.
That’s it???? Seems like it should be a lot higher.
markdowd @15: first off, to clarify, you’re responding to the rebuttal of an assumption.
which isn’t quite the same as asserting that genetic information is not digital. Only part of it is digital, specifically the strict reading of the base code itself. I’ll go on from here:
‘The genome’, the strict sequence of bases translatable by the genetic code, isn’t the only source of genetic information. How the sequence gets translated depends on secondary and tertiary structural effects, which might count as ‘hybrids or intermediate states’ by your definition. For instance, the sequence of bases next to a given base affects how the DNA molecule folds and how accessible the base is to being read. G-C pairs bond more strongly than A-T pairs, so a sequence with lots of G-Cs in it can be more prone to skipping. Affinity effects sometimes modify the transcript of a sequence as well as the efficiency with which it gets transcribed at all. Some letters in a sequence can even be more prone to mutation depending on their neighbors, which doesn’t sound very digital at all. (And because of redundancy in the code, some base substitutions don’t change the transcribed sequence at all – the only effects of the substitution are secondary ones.)
Going on, bases can be methylated or otherwise directly modified, which affects their binding and that of the sequence they’re in; sequences can be made less active or skipped over entirely because of blocking by assemblages of proteins; bases can be unreadable (see: nucleotide excision repair) and other bases can even exist besides ACTG. Look at cell differentiation, where cells activate and modify very different stretches of DNA even though they all contain the (mostly) identical and complete genomic information. And not all of these effects arise directly from the strict genomic sequence; some methylation gets imposed on an individual genome during the creation of germ cells inside the parents, for instance.
To mangle another metaphor, saying the ACTG code makes genetic information digital is a lot like saying the written musical notes on a page mean musical information is digital while eliding the notations of speed and volume, the glissandoes, the performer’s fingering, and what instrument the piece is written for.
Um, yes. That’s exactly what I’m doing right now.
Challenge accepted! *puts on godhat* *IQ drops twenty points*
Let’s do this.
Because God’s plan is beyond our power to understand.
How dare you second-guess your creator! Since God is by definition the greatest programmer, whatever method he uses must be the best. So, the proper way to describe this is that human programmers foolishly redesign things for improved performance and delete unnecessary code.
Oh yeah? How about the BIBLE? Checkmate athiests!
Are you ready to repent now?
Meyer just lies a lot. And he seems to be getting more vicious about it with age.
Which worldview? This is a central lie of Meyers. “There are two worldviews, fundie death cult xianity or atheism.”
There aren’t two worldviews. There are many. Depending on how you draw the lines, there are thousands, millions, or billions. You can make the argument that everyone has their own unique “worldview”.
Even most xians worldwide don’t share Meyers death cult worldview. Creationism isn’t a xian doctrine, it is a minority cult xian doctrine.
Worldview has the causal power. This is meaningless gibberish as it stands.
Causal power to do what? It’s not magic because magic doesn’t work. Meyer’s worldview has made him a hate filled, bigoted liar who is increasingly angry because his religion is dying. Dying, helped along by people like himself.
It’s a non sequitur, bafflegab.
Whether the code is digital or not has no bearing on how it arose and how it changes.
In point of fact, we know how the “program” has changed over the last 3.8 billion years. It evolves and we can see it in real time.
You… you mean… ID really ISN’T secular after all? I feel like a child who just found out there is no Tooth Fairy :/
They need to get the fuck off my campus with their bullshit.
Mark Dowd@15,
I think it is pretty clear that genetic information is not digital. The genetic code in each cell is the same. However, a cell becomes part of a liver or a brain depending on the cells around it. There are no “genes” for formation of wings or arms, and yet they form. At the very least, this means that the meaning of a “bit” depends on the state of the bits around it.
In a digital representation, the “2” bit has the same meaning regardless of the values of the bits around it. That is hardly true for the genetic code.
Well technically, thanks to the Planck length, all information in this universe is digital!
@NBWAW
For extremely large values of “now”, one presumes.
Love this.
The genetic code is also degenerate.
Multiple codons can specify the same amino acid. In some cases, up to 6 different codons specify the same amino acid. Wikipedia:There are three amino acids encoded by six different codons: serine, leucine
I don’t know enough about the formal definition of “digital code” to know if they can be degenerate but they might not. A 1 should always be a 1, a zero a zero.
Or the English language. Which is written in linear form using discrete units, i.e letters, words, sentences, and paragraphs.
Wrong! We know very well that most of it doesn’t do anything!
Over half of your genome consists of retrovirus corpses in all stages of decay, and most of the rest consists of repetitions that are caused by slippage of the replication or repair machinery.
Seconded.
Yes, and Pteryxx said so, just didn’t use the word. What Pteryxx didn’t quite mention is codon usage: there’s more tRNA for some synonymous codons than for others (different ones in different organisms), so some such codons cause faster translation while others clog the ribosome for a while.
The genetic code is also lopsided. There are 64 possible codons (i.e. there are 64 possible combinations of ACTG). With 20 standard amino acids, the most logical arrangement would be 3 codons per amino acid, with the remaining 4 codons encoding “stop.” Alternatively, rather than “start” always being “methionine,” there could be 2 dedicated “start” codons and 2 dedicated “stop” codons.
Needless to say, this is not what we have.
If DNA is proof of Gawds’ ineffable design, why is it in base 4? If we (humans, that is) are made in Gawds’ image, why do we have ten fingers? (though I do know people with 9. plus Frodo, of course)
I will never understand how it’s possible for someone like Stephen C. Meyer, who is clearly not stupid, to think the things he does.
*nod* I was trying to stick with just the As, Cs, Ts, and Gs, to answer the misinterpretation in #15:
Technically the ACTG sequence alone doesn’t provide any information beyond being replicable through its complementary strand. However, the physical molecules represented by that string of ACTGs come with shapes and affinities. To read proteins out of it, you need the genetic code: sets of three that encode specific amino acids or start/stop points.
Another reasonable arrangement would be to have the most degenerate codons code for the most abundant amino acids, or to have degenerate and similar codons code for *similar* amino acids, to mitigate mutation damage. Interestingly, even with evolutionary pressures we don’t have those either:
http://en.wikipedia.org/wiki/Codon_usage_bias
This HAS to be a reaction to…(ANNOUNCEMENT)MTV’s Savage U(/ANNOUNCEMENT), by Dan Savage.
Savage U is rather shallow compared to Savage’s column (or especially the podcast), but its pretty much the work of the devil to these people – it not only openly talks about non-marital sex (shock horror!), it aslo aknowledges and shows what college sex-life is like (while offering advice to protect youngsters from the risks of sex – shock horror! Abstinence is the only way!) Contraception! Condoms! Anonymous sex! Gays, Lesbians, Bisexuals, Transexuals and Queers! (shock doubleplus horror!) And even worse for the Discovery “Institute”, Savage actually criticises/contrasts/discusses fundamentalist Christian views (about sex and relationships) among the youth (shock, horror, onyourkneespraytobabyjesus horror!)
Everything about this ID clip – the trendy music, Meyers neck-showing and semi-shavedness, the “quotes” the “student life”, is an attempt to mimic the average Savage U episode. How afraid, how desperate have these culture warriors got…
OK, there are many issues one might have with Savage U as a format, a source of information, but it goes to show how freaked out these people are, at college students talking openly about their sexuality with a gay man.
* a gay atheist man (extra doubleplus horror!)
Plus thanks for the discussion of the non-digital nature of DNA. I thought I knew these things, but having them spelled out was great.
John Lev,
.
////Hi There. This particular statement is of interest to me: “nothing but rank assertions that genetic information is digital (really, it’s not)” I get this argument from a creationist coworker of mine and I honestly don’t know enough about this area to speak about it. I’m an electrical engineer. He’s a biologist or his degree is in biology at least so he knows a lot more about DNA that I do. What is the response to this? Serious question. Please enlighten me./////
.
Digital computer programs are strictly read in the sequence of 0 and 1. But DNA is not always read in the sequence of A,G,C,T. That’s because DNA is a chemical that interacts with other chemicals and the environment. These interactions/chemical reactions modify DNA, which changes the way the code gets manifested. It’s chemistry. Computer software & human language don’t have chemistry. IDiots ignore/don’t understand this fundamental difference.
Another way of putting it is that while the genetic code is indeed digital, the genetic code is only one part of how DNA actually works, and how DNA actually works is only one part of how biological information is encoded.
I thought I found a whole flight sim in it once, but, unlike the semi-competent people at Microsoft, it crashed the moment I started flapping my arms. And, yeah, there was, in one prior version of Windows, and actual easter egg, which if you figured out how to run it, was a precursor to MS Flight. lol
Actually, I would say that, if it was to be described as a “program language”, it would be one of these:
http://en.wikipedia.org/wiki/Esoteric_programming_language
Holy shit. I’ve seen that series at my former fundie school, right after it came out.
It is exceptionally mediocre. He butchers both scientific facts and religious beliefs to “prove” theism.
It was awful when I saw it and I doubt it’s gotten any better now.
Curious stuff.
The biblical worldview was that we were all just piles of meat and that God breathed his “Holy Vapor” into us and that we started walking. Ashes to ashes, dust to dust, and no DNA to remember you by. Now that we have a much more sophisticated understanding of biology it’s “too complicated” not to have been designed (by an undesigned yet far more complicated being, natch).
Once upon a time this was a question looking for an answer. Now it’s an answer that needs it’s question to stay alive.
Umm, DNA is digital. Information doesn’t need to be binary to be digital. A book is digital because letters are discrete. When you read a book out loud, you convert digital into analog. DNA has information encoded in discrete sequences/units.
Not only is DNA digital, it’s also programming. Those sequences provide instructions for machinery (when present) for how to perform actions (assemble/build other machinery). The fact that there are copying/execution errors is immaterial. The fact that the machines doing the work are proteins instead of silicon or gallium-arsenide logic gates is also immaterial. The fact that the presence of impurities/chemicals introduces alternate (undesirable?) behavior is immaterial. No (computer) program stands alone, it must execute within the confines of a physical device.
Both a silicon computer and our biological computers (specifically cellular machinery here, not brain) are subject to the same laws of physics including thermodynamics. Exceed operating temperatures? Both break down. Blast them with radiation? Both break down. Introduce impurities into structures? Both break down. Breaking down means not operating within the boundaries of the program. The break downs can occur in the storage/retrieval of the program, not just in the machinery running the program (bits on a CD can become unreadable). Are DNA/cell/multicellular computers more complex? Of course. But, that doesn’t change the underlying digital nature of the root instruction set.
Furthermore, we can (and may eventually) read every living species DNA. We can store those sequences as binary information inside a computer and recreate them as biological material. DNA is nature’s way of storing information (on this planet) about how to build and maintain a living thing. Given the right circumstances (machinery that interprets the programming), it does. That’s programming, folks.
Finally, don’t worry, saying DNA is digital/programming no more implies a programmer must have written it than saying DNA is very, very, very complex but it still wasn’t intelligently designed. You’re fighting the wrong fight. In fact, to say that DNA is digital and that we are simply machines at the root level represents to me the height of atheist thinking. To believe DNA is something more than digital smacks of orthodoxy and mythic thinking.
Don’t run from “DNA is digital”, embrace it for all its worth.
Yawn, not one citation from AP or evidence of expertise for the opinion.
No, andrewphilli
Whoops.
No, andrewphillips, DNA is not digital. The genetic code is digital (depending to some degree on how you define it), but DNA is actually more than just the genetic code.
@Nerd of Redhead…
I didn’t think folks around here accepted argument by authority. Nevertheless, I am a Software Developer, Electrical/Computer Engineer, Artificial Intelligence expert and Computer Security expert. Aside from the many programs I’ve written and programming languages I’ve learned, I’ve written my own computer languages and built a handful of computers. Lots of education and professional work in programming, computers, Information Theory, etc. FWIW, I know digitized information and a “programming” language when I see them.
@Amphiox – a CD with music is more than just bits. The question then remains: are any of the other non-information parts used? If they are used, then they become part of the (digital) language/mechanism. If they aren’t used, they aren’t relevant.
Everything about DNA smacks of digitized information. The mechanisms arrayed to reduce copying errors. The tolerance for copying errors in continued operation of the organism. Mechanisms which “read” the information and follow those instructions to make a very wide array of chemicals. The presence of start and stop codons. The way its transferred from one generation to the next in order to build that next generation. The language may (mostly) contain instructions for increasing or decreasing various chemical concentrations whose ultimate result is to build living things. The language doesn’t contain *easily* recognized instructions like “build an arm”. That doesn’t mean it’s not a program. More likely, this means it’s a really complicated program. That’s the kind of program I’d expect from billions of years of random chance working with the only mechanisms available (chemical concentrations and timing).
At this point, I’m going to need some clarification: What wouldn’t be digital information?
E.g. the grooves in a vinyl record will, under suitable magnification, show themselves to be composed of individual, discrete atoms, so isn’t that also digital? Is there anything that isn’t digital? Maybe I’m missing something?
Every single one of these examples you list applies to the genetic code, and not to DNA itself. I repeat, there is more to how DNA works than just the genetic code.
A CD is a medium that contains a digital code. That code is digital, but the CD is not. The size, shape, chemical composition, the fact it does not melt in water or spontaneously combust in the presence of oxygen, all that and more are also critical to its proper function. If you are going to call those things part of its digital “mechanism” then you have redefined both the words “digital” and the words “mechanism” so broadly as to render the very terms meaningless.
As I mentioned before, thanks to the Planck length, absolutely everything in this universe can be said to be digital, to the point where it is meaningless to even use the word.
Well, as far as a record is concerned (or just about everything else), it’s the information, the mechanism and the action that’s important. So, we’re working at a particular scale and examining behavior in and around that scale. Both “record groves made of atoms” and “everything can be seen at planck length” are really strawman arguments, reductions to the absurd.
Information can never exist outside of a physical object. Information is a thing we can measure, in fact, it has a unit of measure: the bit. We can compute the information content of an algorithm, too. Information cannot exist in a vacuum, it must be encoded on a physical object. That object is a real world thing and is subject to real world physics whether the information exists in your head, on a page, in a computer memory or disk drive, on a CD or in a strand of DNA. It can be mutated, crushed, altered and destroyed. Likewise, the information encoded can be altered without altering what we call the object. We can go round and round all day about whether the medium is the message or just contains it, but the message can never exist in some true platonic, non-corporeal form. It must have a physical presence.
I’m not in any way redefining Digital or Mechanism (although perhaps *your* understanding of what those words mean is changing).
Now, your turn. Give me a chance to prove my point and enlighten me. What else does DNA do other than encode genetic information?
Telomeres
Yeah, the argument has gone a bit too far, I think. It seems to be, basically, “DNA is the medium in which the information is encoded, so therefore DNA isn’t, itself ‘digital’.” OK, yeah, if someone wants to get that nit picky about it, then sure. But, that isn’t necessarily what is meant, any more than someone saying that a CD is digital means they think the physical media is, itself, and they are not that the “content” is.
Oh, and Pteryxx, Telomeres seem to be a) a error correction system, not unlike the way data is encoded on physical media, like CDs, or hard drives, or the old magnetic medias, where “buffer space” is needed, so that when reading/writing to them, you don’t read/write past the “sector”, or fail to read the entire contents of said sector. When the buffer gets corrupted, the sector becomes unusable, just the same as if you mangled the actual data. In the old days, on Apple IIs, you had to “manually” spin up the drive, pulse it as a set rate, and read a block of data from the floppy disk, which was like 4 times the size of the final digital results, then, basically, scan through this, to find the “start point” of the actual data, convert it to a usable form, then go to the next step, which was either read the next sector, or do something with the data. Due to how this worked, it was plausible, as long as you got the basic timing right, to encode sectors of entirely arbitrary numbers of actual “bytes” of real data. Even the 3.5″ disks, which later came out, had a quirk where, while the physical hardware did all the read/writes, you could find sectors on PCs encodes with, I think it is, 512 bytes per sector, and the MAC as 524 bytes, using the same encoding method (not GCR, but MFM). But, the principle is the same, you have a mess of “dead” space between sectors on such media, and its there as a buffer space, to prevent under/over reading.
In the case of DNA, this has also seemed to have been adapted to be a critical failure detection method, though not always a reliable one, to tell a cell, “Whoops! Your defective copy function has actually under-read the data, and made a defective copy, time to throw out this bad media.”
Neither of those functions are “non-digital”. Rather, they are what you might expect if your copy function is glitchy, someone got lazy about fixing it, and the “media” is sloppy enough, like a floppy disk, that you can’t afford to try to, unlike a circuit, cram two pieces of data, right on top of each other, without any buffer space between them, and get reliable results.
Just some examples. Everything DNA does is a chemical reaction. Rates of reaction and concentrations of reagents are critical, and these are manipulated as part of the regulation of gene expression and the like. As just one example, the whole sequence of changing gene expression in embryology begins with concentration gradients of transcription factors in the oocyte/zygote. These are critical to DNA function but are not encoded anywhere in the DNA sequence.
These things (reaction rates, concentration gradients, etc) are all analog,
The DNA “program” relies of both digital and analog information.
@kagehi thank you. I was formulating a response involving Error Correcting Codes, but I think your example is perfect.
@amphiox ok. A mechanism which relies upon analog behavior doesn’t make the instructions analog, those can still be digital. I can set the digital temperature on my oven’s digital computer with its LED digital readout to 371 degrees fahrenheit. When the very analog oven temperature reaches that value a little bell rings. Digital program interacting with analog operations. Happens all the time in engineering. So much so that entire sub discipline of control systems was created.
Hmm. Actually, I think I got my example “slightly” wrong, at least in details, you had to hunt the incoming data for a identifier, like a codon, which told you that you had the right sector data coming up, then, once you knew it was, funnel that data into the space you would later “translate” into the final result. And, yeah, analog being involved isn’t much different. The reason for the speed needing to be fairly precise, but not exact, on drives was due to signal strengths. Basically, this determines how strong the signal is, so if its below the detection threshold you get no usable result, and, if its “above it”, it can end up blurring the data, so, you still lose information. However, its simpler to do this, than have a lot of different states, but, in principle, there is no reason why you couldn’t have encoded, say a “low”, “neutral”, and “high” state into the design, at least in principle, and thus encoded more than a single bit into each data space.
But, yeah, both views on it are correct, in a sense. Its still a case of fairly precise encoding, combined with a very flexible “control system”, in a sense. Some of that being, in effect, just, “If there isn’t enough of something, X number of copies won’t do anything.”, sort of like a GPU, with unused cores idling. It “can” do more, but it doesn’t have the data to work on, so those cores don’t do anything. The amount of some chemical doesn’t just trigger something on/off, so much as fail to provide enough “inputs” to run all of the processes available (unless I am thinking about it wrong. lol)
@ Nerd of Redmond – Actually, these modifications aren’t problems, at all. Computer programs are not set in stone. It is possible for (some) programs to modify themselves, and there are programs out there that do this. A sub discipline of AI, Genetic Algorithms, is devoted to changing a program’s behavior by altering its code. I (and plenty of other programmers) have written programs that compile and link in new code on the fly.
Decades ago Alan Turing (yes, the Turing Test guy) proved we could never be certain a computer program would halt (the Halting Problem) by proposing a computational mechanism, Turing Machine, that could reprogram itself.
DNA codons changing over time poses no problem for the machinery converting those codons into proteins. It might be a problem for the cell or the organism. Or, it might be a boon. The codon change might cause a change in the concentration of some chemical (*that* would be analog). Nevertheless, the DNA continues to contain digitized instructions for making chemicals (proteins).
As for all those systems that “avoid interaction with the DNA”, what created the systems? Presumably, there’s no magic here, and everything in the biologics can be traced back to proteins arising from encodings in DNA. Now, if you tell me that there are some chemicals external to DNA that transfer from the environment (or the mother) into an organism and affect its development, I’ll accept that point and agree that that part of the process is in and of itself not “digital”. That’s a fair statement. However, I would argue that the organisms involved are most likely built in such a way that they are open to that interaction, the building of which was driven by their own DNA.
Andrew,
You’ll find that quite a few of us know who Turing was. I, like others here, share much of your expertise. Like you, I have nowhere near the expertise in biology or chemistry that the people you are arguing with have.
What exactly is your argument? That chemical reactions can be considered to be a digital system? I’m sure you could model them digitally, but that’s not the same thing.
People here keep confusing “system”, with, “language/encoding method”. No, the “system” isn’t, and doesn’t have to be, “digital”. You can store the same “data” on a CD, or a magnetic tape, the former being “digital”, since it doesn’t actually store analog data, the latter is, even though the data is “read off” based on thresholds, by parts that interpret the varying, noisy, data into clear 1s and 0s. You can also have, and do have, all sorts of systems that interact with, or even use, analog inputs, and even generate analog outputs, where everything “in between” is digital.
The argument is, “Just because parts of a ***system*** are not digital, or even most of it, this does not change whether or not the encoding/language/core of the system is, or not.” The alternative argument, which is being insisted on by some people here is, “It can’t be digital, look at all the parts of the system that are not digital!” Uh, no.. that’s not the point. The question is, “does the information encoded in the DNA, exist in what could be described as a digital media?” The answer is, “Yes, despite all the other things going on in the system, which do everything from changing a) if it gets executed, b) when it gets executed, c) how often if gets executed, and even, to some extent, d) what it does when executed.” All of that is “perfectly normal”, even for man made digital systems, if/when they interface with analog data sources.
That some creationists can’t understand “any” of the distinctions, isn’t relevant to whether or not the “language” is basically digital or not. And, all those distinctions are critical to why the system is an insane bloody mess, that doesn’t always work right, and shows no “design”, by any definition of “competency”, and thus either a) wasn’t, or b) if it was (as per their silly argument), didn’t know what they where doing, even by the standards of a two year old.
In the case of the concentration gradients in the zygote, the instructions are analog. Because the concentration gradient of transcription factors itself IS the instruction. The same is true for all the other concentration gradients that are critical for bodyform patterning in embryology. Spatial information is converted into a concentration gradient of a signally molecule which is converted to a concentration gradient of transcription factors which are converted to new concentration gradients of new transcription factors which cascade to trigger the next step of gene expression.
These gradients are all analog and they are not encoded in the sequence of the DNA base pairs, but without them embryology does not work at all.
I would go as far as to argue that, as far as we currently know, the DNA digital code does not actually contain any explicit “instructions” at all, and our use of the word “instruction” to describe its function is a human-invented metaphor that only approximates what is really going.
There is no “program” anywhere in the genetic code that gets “executed”.
The information in the genetic code is actually a “parts list” combined with regions that encode bonding affinities for the chemical reaction of a protein binding to DNA.
The actual “instructions” that “run” the DNA are emergent from the laws of protein chemistry. They are expressed in protein shape and chemical affinity. The genetic code contains no information about how proteins should fold, it only specifies the protein sequence. The folding “instructions” are derived from the laws of chemistry.
DNA does not “encode” protein shape, it “entails” protein shape. And it is protein shape, not sequence, that produces biological function.
@amphiox
#68 – I love this point about concentration gradient, it’s such a neat trick in the development of the embryo. That said, the fact that there is a gradient over a spatial expanse is an artifact of the physical nature of the embryo. I agree this is an analog system. I also understand that all of the cells in the system respond differently to the different concentration levels and that’s how the embryo body plan gets oriented and organized. The concentration gradient is actually a set of (analog) Signals. The Receiver of each Signal is an individual cell along the gradient, with each Signal causing a different Computational path to be taken in the Codon instruction set. The Sender of the Signal is at the top of the gradient, generating the transcription factors based upon instructions found within the Codons.
#69 – I appreciate your concern with using words that imply some sort of intelligence behind them. Does “instruction” mean some actor is “interpreting” this thing and doing what we or it “wants”? We can try to find different words, I’m happy to explore the thesaurus, but I don’t know any that carry quite the same meaning. I’d like point out that, ironically, your first sentence of #68 uses “instruction”.
From the computer science point of view, “instruction” assumes no intelligent actor, only an operation which tells some mechanism to take some action. The “program” is the entire DNA strand, and it is “executed” by everything that reads it, responds to signals from the surroundings and generates proteins from it. (Actually, there are millions/billions/trillions of copies of the program all over the organism residing in each cell each with its own protein reading mechanism. The program is mostly the same, but varies due to copy errors and behaves differently in each location due to environmental signaling and/or machinery changes/specialization of the cell).
In a computer, we have a microprocessor that reads machine instructions and executes them. The language of the microprocessor contains operations like: add, multiply, store, read. The discussion we are having and the pictures of a PZ cuttlefish are ALL ultimately sent through many such processors and pass through that language even though they and everything else we do with computers has such a richer meaning to us.
Likewise, the protein making machinery of the cell just links together the elements/molecules of the protein chain. Each Codon (there are small countable number – 4^3 or 64) is the instruction. The codons determine the order, which particular amino acids and how much. There’s nothing “fuzzy” or analog about the codons. Either they are one of the 64 instructions or they aren’t. If they aren’t, no protein chain (or an unexpected result). Otherwise, its behavior is predictable. That is a fantastic example of a digital system and the Codons are the instructions.
Nothing tells the protein how to fold, that is driven by the laws of chemistry and based upon protein organization. In fact, nothing tells the proteins what to do once they are created. They float around doing whatever they do, signaling (to amplify or dampen), catalyze, become a part of a membrane, etc.
If it were possible to measure degree of analog or digital nature, I grant you that practically all of an organism is analog. I reserve for debate three locations of digital nature: DNA (codons), parts of our mind (something about symbols as an emergent property, think of counting, that’s digital) and our fingers (we get the word digital from base 10 counting using our fingers/digits after all, someone with half a finger can still count to ten).
Analog systems can have emergent digital properties, Digital systems can drive analog systems (which have emergent properties).
Yawn True Believer™ still unconvincing. Life, biology, and chemistry is messy.
@echidna – not that chemical reactions are digital systems, because most chemical reactions are nothing of the kind. Only that some chemicals (DNA base pairs) are units in a language (quite literally, amino acid assembly language) and that the ribosome and its supporting structures are the instruction set reader/assembler. Everything that happens beyond that is interesting, but has no conceptual impact on this system. The variety of life around us, as incredible as it is, are emergent properties of very complex (analog) systems built upon that digital system.
I think that second sentence puts my point in a nutshell:
Codons == Amino Acid Assembly Language
Cheers.
Just to be clear, I personally don’t think a purely analog system gets you any place, in the first place. Even analog circuits are not built on “analog” rules sets, they are built with clear intent to “do” something with the data. But, that is a “human” produced process.
To get a non-created one, how ever it starts to produce something like life, needs to build a set of rules that are a bit more complex, on the whole, than, say, the rule that water follows the path of least resistance. Its needs to, eventually be able to, based on the same sort of analog data, opt to, instead, follow the path of greatest resistance, if the other path doesn’t provide what it needs to survive as a system. This requires not just a discrete, self contained rule set, but one that can modify, based on all that external data, which processes actually happen.
But, yeah, the problem here is that the system isn’t analog in the sense we consider analog, and its not exactly digital either, save in the most general sense of those terms, which is that large parts of the system are based on how strong the signals are, and a critical core part is made up of what we literally have no other word for, save for “instruction set”, which, as far as I know, don’t exist in “analog” systems.
In any case, I am not sure where the real argument is here. I don’t even think andrew is exactly arguing that the whole damn thing is digital, just the encoding of the instruction set, which lets it all work as a unit, not as a bunch of random chemical reactions. Having that at its core, in no way at all, implies anything else, other than, “There are discrete instructions in there, which, much like a program, decide which processes should happen, and when, based upon all that messy analog input.” It certainly doesn’t imply that anything “created” it, the way some people would like it to be. But, the argument seems to be purely semantics. Its ***not*** analog. Its not digital either. So, unless someone comes up with some intermediary word, that means, “sort of both, but neither”, we are left with imprecise terms, and the need to at least try to figure out how much, if any, of it they apply to. And, frankly, the DNA doesn’t fit the definition of analog, so…
Whether or not the other guy arguing this point means anything beyond that… is frankly his problem. lol
No creator, all atheists here. I went back and listened to his statement: “So, when we find information encoded in the DNA molecule in digital form, the best explanation is that that information also had an intelligent source.”
I agree with the first part (clearly), I absolutely disagree with the second part. It’s unsupported, and at this point, given Evolutionary Theory, completely wrong. I’d like to see his evidence/proof for an intelligent source.
Quite frankly, I think it’s the coolest thing that random chance created the first digital language billions of years before we humans did.
Decades ago Alan Turing (yes, the Turing Test guy) proved we could never be certain a computer program would halt (the Halting Problem)
I have just finished teaching our third-year course on theory of computation at Waterloo. If you had written this on my final exam, you would have gotten no credit at all. We certainly can be certain and routinely are certain that some given computer programs halt. Turing’s result speaks to the non-existence of a general method for unerringly solving the halting problem. Your characterization of his result is incorrect.
andrewphilips:
You are “finding” information encoded because you’re interpreting self-replication as a message rather than as a natural process; note it could be no less accurately be interpreted as analog information.
(Until it’s processed by a consciousness, information is but data)
shallit @75 – Umm, I certainly would not have written the above as my answer for the “Halting Problem” because that has nothing to do with the Halting Problem. Alan Turing was a pretty smart guy – he contributed to a lot of Comp Sci, not just whatever you happen to be teaching or studying right now. (Halting Problem http://en.wikipedia.org/wiki/Halting_problem – vs. Turing Test http://en.wikipedia.org/wiki/Turing_test).
Morales @76 – It’s both – a natural process and information describing self-replication along with a bunch of other stuff. No, consciousness has nothing to do with information vs. data. They are equivalent. Well, strictly speaking, I would think most people interpret data as information, but not necessarily the other way around, although I’m willing to be convinced the are equal. (Data as scientific collection of information rather than Information which may be known but not collected scientifically).
Consider this, if we (as thinking machines) weren’t here (read never evolved, died out) with all other things being equal, and we never discovered DNA or determined its behavior, DNA would still work the same and produce the wonders we see around us. It’s an interesting philosophical argument along the lines of trees falling in forests with no one to hear them and sill David Deutsch arguments about parallel universes popping into existence during photon double slit experiments, but in the end, it’s really just that – sophomoric perspectives attempting to make humans somehow important. Ribosomes and other cellular machinery processed the information encoded in our DNA for billions of years before anyone bothered to look and verify what was going on. Information and computation are embodied within the DNA molecule. Here, I am using the well-defined form of Entropy from Information Theory laid out by Claude Shannon (http://en.wikipedia.org/wiki/Entropy_(information_theory)). Yes, we can measure the Information content of the DNA Codons using this theory.
Umm.. Yes and no. See, the problem with trying to apply formula is that you need to know what “is” and “isn’t” data to start with. And, it doesn’t help when, as one of PZ’s videos nicely describes, even your “information”, is “encoded” in such a haphazard way that you can have the logical equivalent of 3 inches of code, on the logical equivalent of a 50 foot rope, with all the fragmented bits in between being “unused” in that sequence.
So much for “information”. Its more like trying to find one hidden stenographic word, in a picture of a balloon, and having the “its all meaningful” people insist that, despite the fact that only the hidden words that matter, the balloon itself is a “critical” part of the message. Its almost like watching the scene in Zoro, The Gay Blade, where the bad guy is trying to work out what sort of message is being sent to him, based no the fact that Zoro was wearing plum one day, and olive the next. Just.. no. Information is “contextual”. A lot of things will look like information, if all you do is run them through some equations. It doesn’t make them, outside of a clear context for what they *do*, actual information, equations or otherwise.
OK, so we agree there is information in there, just that we humans aren’t able to read all of its meaning. I’m assuming we agree that it *is* meaningful, however, to the cellular machinery. I agree that there’s a lot left for us to learn when it comes to “junk” DNA vs. meaningful DNA. None of this flies against my original point (or post, for that matter) that the stuff that is meaningful is digital and computational in the modern computer sense.
To recap, (I’m not allowing the goal posts to be moved here): the Codons contained within DNA represent Digital information used by the Organic Computational Cellular Machinery ultimately to Assemble Proteins. There’s plenty of Analog signaling going on within both the cell and within multicellular organisms that mediates the reading of DNA. Finally, although biological organisms contain and perform Digital Computation, this does not in any way imply the entire organism is a Digital Computer.
I would argue that its a hybrid Analog and Digital computer.