We are as worms

What's most amazing about both these stories is not the genes. It is the psychology of Darwinists. They can hang on to a theory no matter how much contrary evidence comes to light. Invented terms like "conserved genes" and "slow-evolving species" mask their desperation. They are clinging to a dogmatic evolutionary position in spite of evidence that looks like creation: abrupt appearance, stasis, and loss of original complexity. Simultaneously, they accuse creationists of accepting their view on "faith" while bluffing that "there is no controversy among scientists about evolution." Yet how would an impartial jury rule, based on the empirical evidence alone, with no evolutionary presuppositions?

Check this out: http://creationsafaris.com/crev200511.htm#200511...

Yet how would an impartial jury rule, based on the empirical evidence alone, with no evolutionary presuppositions?

The big step in evolution was the jump from prokaryotes to eukaryotes. Since then, everything (including us) has just been minor variations on the same basic theme.

Even the appearence of multicellularity wasn't that big a deal. We're all just basically tubes, with various things sticking out the sides.

How are the believers of evolution going to explain how "introns" are "highly conserved" for over half a billion years, while the "exons" change? Why one, and not the other?

How are the believers of evolution going to explain how "introns" are "highly conserved" for over half a billion years, while the "exons" change?

How are the believers of evolution going to explain how "introns" are "highly conserved" for over half a billion years, while the "exons" change? Why one, and not the other?

While sequences have diverged, the way the genes are organized in blocks has been conserved.

As opposed to your IDiot approach of deciding up front that yet another piece of evidence has been found to support your assumed conclusion, then moving on to the next "god did it" lie.

While sequences have diverged, the way the genes are organized in blocks has been conserved.

But haven't you, up front, decided that "evolution" did it?

To the contrary, this finding suggests that basic mechanisms were present from the beginning, that is, stasis, more than variation, and almost no time for development---all opposite of what Darwin would have expected. Doesn't this give you pause?

This only makes it worse, since you have some sequences changing while, at the SAME time, you have some sequences, "introns", right next to the changing sequences, which DON'T change---after HALF A BILLION YEARS!!!

To the contrary, this finding suggests that basic mechanisms were present from the beginning, that is, stasis, more than variation, and almost no time for development---all opposite of what Darwin would have expected. Doesn't this give you pause?

Actually, Blast, conservation of introns makes perfect evolutionary sense, to me at least. All but one of the 22 amino acids have multiple codon arrangements. Therefore, a certain amount of variation in codons can still result in the same amino acid being produced (let alone the amount of change in amino acids a protein can handle and still keep its function). But an intron represents a special case for the translation algorithm. The intron must exactly fit the special condition at the level of codons, not amino acids. So a single-point mutation of a codon in an intron may cause the translation algorithm to treat the codons normally, producing extra amino acid(s) and causing the resulting protein to lose or change functionality - even though the intron and its mutation correspond to the same amino acid(s).

In other words, once an intron gets in, it is very difficult to change or get rid of it, short of total excision.

Note: this is actually a prediction. I am predicting, based upon my knowledge of evolution, genetics, and algorithms, that we will find that introns are less amenable to variation than coding regions for the reasons I attempted to express above. It is something that I predicted when I first learned of the existence of introns several years ago - I was trying to figure out how to make sense of introns. It is nice to see a personal hypothesis supported by experimental evidence. I am a layman, not a biologist, so do not take my arguments as authoritative. Frankly, we need to know a lot more about introns and how they can exist. Perhaps someone with more knowledge of the mechanisms involved can shed additional light.

DNA that codes for proteins can vary without bad consequences not only because, as Kevin Vicklund rightly points out, 22 amino acids have multiple codon arrangements but also because many proteins retain their function when some of their amino acids change.

O.K

Blast I see your problem.

You can't accept evolution "did it" because you that would mean you have to "believe" in Darwin.

You are in fact a "Darwinist" in the truest sense. Nobody on this side of the fence "believes" (the way you do) *in* Darwin.

Darwin has been demonized by the Fundy Church's the same way Hitler was during WW2 by the allies to motivate the army of followers of the anti Darwin church cause, through propaganda and creation of a Myth through ...lets say bending the truth to get a desired result. It was a case of fighting fire with fire to support the cause. It did however do great damage to actual factual real honest to god truth as perceived by the followers, not the outside world truth which is purely secular.

The Church's Myth attempts to subsume the minds of the followers belief in a creation God by taking for God what is Caesar's and taking from Caesar what is God's.

No problems if you only want to go to school inside the box of the Church's mind.

A true Church of Mammon no wonder they fight so hard.
They actually don't believe in a non material God.

Have a long think about that Blast.

God is not Money or material Blast and has no effect on the creation of things other than what you make yourself for dinner - you should thank yourself for that.

This has to be one of the best arguments for the state setting guidelines on how religion is taught.

You can't believe in the truth because the truth has been hidden from you through Obscuration by Obscurantist's indulging in Solipsistic Tautology
promoting a private Myth (a lie) which you believe. They destroy truth, beauty and nature by doing so.

But strangely you intuitively know it is a lie(a little voice of god in the back of your mind), you can't accept that people you look up to as the persona of god could actually lie to you so to prove they are not liars you have to prove to yourself that the outside world, to that Myth, is in fact a lie itself.
or you are an Obscurantist self deluded liar yourself.

How can this happen ?

Read "Lolita" by Nabokov.

It's still a very strange and inefficient way to go about making proteins,

I see. But haven't you, up front, decided that "evolution" did it?

But the basic question SHOULD be this: does this finding conform with/support Darwin's theory of variation and NS? To the contrary, this finding suggests that basic mechanisms were present from the beginning

It's still a very strange and inefficient way to go about making proteins, though, and one that isn't necessary---bacteria, for instance, get along just fine without this intron nonsense.

This only makes it worse,

since you have some sequences changing while, at the SAME time, you have some sequences, "introns", right next to the changing sequences, which DON'T change---after HALF A BILLION YEARS!!!

Out of curiosity, how does ID account for the difference in divergence between introns and exons?

Evolution predicts that the intron sequences should be much more divergent than the coding sequences (exons) in these genes. Which perfectly explains why you have changing sequences right next to unchanging sequences. If the intron sequences were just as homologous as the coding sequences after half a billion years, that would be a challenge to evolution.

Note: this is actually a prediction. I am predicting, based upon my knowledge of evolution, genetics, and algorithms, that we will find that introns are less amenable to variation than coding regions for the reasons I attempted to express above.

If it codes for something important, natural selection will conserve it. If it's just "junk" - filler, spacer, randomly transposed DNA - natural selection will not conserve it. It's just as simple as that.

If you really want to discuss this mouse DNA deletion result, I wonder why you provided no link or reference? Could it be that you're more interested in generating fog than clarity?

What has been conserved are the splicing sites.

Blast makes a Monkey out of himself again.
Anymore gods in those gaps Blast ?
Why do you bother ? You already know God did it so what have you got to prove?

..oh thats right you don't actually beleive in god, because you know that what you are saying is the "broken truth TM".

Find out who stole it, because you won't find it here ...and that is a promise.

Correct me if I'm wrong, but the point of the article is PRECISELY that the "introns" haven't changed in over half a billion years. Vertebrates are "slowly evolving", it says.

— BlastfromthePast

You say that evolution predicts that "intron" sequences should be more divergent than the coding sequences, but, in actual fact, just the opposite is being reported.

— BlastfromthePast

That's part of my point. The other part is my observation that if you come up with an explanation for why one type of sequence is changing, then this contradicts any explanation as to why the other type of sequence isn't changing. In other words, if both were changing at roughly the same rate, this would conform to Darwinian theory. But that's not what we see. Doesn't that bother you?

— BlastfromthePast

The cunundrum is this: if you explain the "conservation", then how do you explain "non-conservation" right next door?

— BlastfromthePast

N.B. Before we go off into the "it's highly-conserved" because it's so vital to life, and so it's NS working", let me remind you of the experiment in mus musculus wherein they excised a "million" nucleotides in a "highly-conserved" region of junk-DNA, and found that the progeny were.......COMPLETELY NORMAL MICE! How do you explain that one?

— BlastfromthePast

[I]f you come up with an explanation for why one type of sequence is changing, then this contradicts any explanation as to why the other type of sequence isn't changing. In other words, if both were changing at roughly the same rate, this would conform to Darwinian theory. But that's not what we see. Doesn't that bother you?

Actually, Blast, conservation of introns makes perfect evolutionary sense, to me at least. All but one of the 22 amino acids have multiple codon arrangements. Therefore, a certain amount of variation in codons can still result in the same amino acid being produced (let alone the amount of change in amino acids a protein can handle and still keep its function). But an intron represents a special case for the translation algorithm. The intron must exactly fit the special condition at the level of codons, not amino acids. So a single-point mutation of a codon in an intron may cause the translation algorithm to treat the codons normally, producing extra amino acid(s) and causing the resulting protein to lose or change functionality - even though the intron and its mutation correspond to the same amino acid(s).

— W. Kevin Vicklund

To the contrary, this finding suggests that basic mechanisms were present from the beginning, that is, stasis, more than variation, and almost no time for development---all opposite of what Darwin would have expected. Doesn't this give you pause?

From the begginning? The beginning of what? Life?
If they are talking about a species that lived 500 million years ago, that time period is not what's considered to be the "beginning" of life on this planet.

Also, this doesn't look like stasis to me. I mean going from a world of worms, mollusks, fish, etc. to a world of worms, mollusks, fish, reptiles, birds, mammals, etc. not to mention all the different species of plants alive today too that did not exist 500 million years ago.

I don't see how any of these findings dispute evolutionary theory, so no it doesn't give me pause.

To the contrary, this finding suggests that basic mechanisms were present from the beginning, that is, stasis, more than variation, and almost no time for development---all opposite of what Darwin would have expected. Doesn't this give you pause?

Blast, why on earth do you insist on displaying your uninformed ignorance so publicly?

Is it part of that massive martyr complex that all fundies seem to have?

Lenny there is a "rapture" in the perverse rape of truth and beauty

Call it one of those "intuitive flashes" a search revealed Hitchens has picked that up as well in Nabokov's "revenge" on Solipsistic tautology of the Fundamentalists.

Hurricane Lolita.

Gene duplication, among other things.

Different mechanisms affecting these sequences.

Over evolutionary time, intron sequences are much more free to diverge compared to neighboring exon sequences.

Blastofhotair, you were asked for a cite to this research so that people with more expertise in such matters could see what the actual evidence is and correct your misconceptions about it.

Despite being asked by at least one person, you have continued to blather on without providing any hint as to what you are talking about.

It's as if facts are irrelevant to your position - which is unsurprising.

Or maybe you're just a coward, afraid of having your ignorance dissected and laid out in detail... again.

Well, if Blast isn't give us a source for that experiment, I may as well mention the experiment that was done recently where an elephant evolved from a beaker full of amino acids in a week and a half.

It was quite a small elephant, of course.

Blast have you heard of "Intelligible Design"

Download the MP3's from this site

http://www.pandasthumb.org/archives/2005/11/zimmer_on_evolu.html#comment-60905

What I don't understand here

This doesn't address the crucial issue. If, as you say, the normal mice are the result of gene duplication providing the needed information, then why is this region "highly-conserved", since, obviously, it's not needed. What vital role does it play---------Remember, the theory is is that "conservation" takes place because of its importance to the organism.

— BlastfromthePast

But if there is a "mechanism" for "conservation", and a "mechanism" for variation, then it would seem that variation is not directed by "blind chance" but by some underlying causal mechanism, right?

— BlastfromthePast

What I don't understand here is this: if the introns "diverge", then how are they recognized as introns? I know PZ Myers says that it is the splicing sites that are conserved, but how in the world are they recognized if they are not sequence specific?

— BlastfromthePast

Think of a protein as an essay broken up into paragraphs. What this result is saying is that the paragraph structure is maintained, and I suspect that the "themes" of the protein domains within them are retained to some degree, but the spelling and word use has changed.

If you ever have to grade student writing, you'll see echoes of the 5 paragraph essay format still hiding in their style.

One Brow wrote: I'm not sure anyone has an answer. There might not even be one answer

If, as you say, the normal mice are the result of gene duplication providing the needed information, then why is this region "highly-conserved", since, obviously, it's not needed. What vital role does it play---------Remember, the theory is is that "conservation" takes place because of its importance to the organism.

What I don't understand here is this: if the introns "diverge", then how are they recognized as introns?

Don't have your own theory? Attack that of the "other".

Don't have your own research? Attack that of the "other".

Attacks do not produce understanding. Attacks preclude understanding and, if successful, can forever destroy its possibility. Some people's goals couldn't be more obvious if bounded by a net.

- AC, Glorified Chemical Processing Tube

P.S. Is that article available without a subscription to The Atlantic, k.e.?

See if it is in the latest newsstand issue.
Or get it out of the library either the mag. or the book especially .... the mind games are nothing short of ...well mind blowing.
I read the book a fair while ago so I didn't need to go thru the rest of the article ...although I'd read it in the mag. if available.

It always cracks me up when IDiots refer to things like DNA, introns, extrons as being inconsistent with "Darwinism"

They have this caricature picture of science that a conceptual framewrok that was conceived over 140 years ago should be discarded in favor of "godidit" rather than incorporate new emprircal data and findings into it. One wonders how any actual science would get done if the folks had their way, which, I suppose, is the entire point of the ID/creationist movement.

( n.b. Darwin writes Origin of the Specis circa 1860 CE,
Watson and Crick describe the structure of DNA crica 1960 )

Gene duplication doesn't allow you to to evade the need to conserve both copies. If you lose one copy, your offspring are very suseptible to losing the second copy. Over the long run, you would have to expect the creature with two copies to be more durable.

If the mechanism for variation is randomly applied, it will produce random variations. Meanwhile, the mechanisms for conservation are anything but random.

The article did not say, and I'm not sure anyone has an answer. There might not even be one answer. Two possibilities are the exons themselves code the gaps and the RNA translator is pre-programmed for the gaps.

Now you can take the well-characterized gene from that organism, and search the DNA of other organisms for a similar gene. If the gene is conserved, you'll be able to recognize it by direct comparison of DNA sequences. You already know the exact coding sequence of the first gene, so it's relatively easy to identify the coding sequence of the related gene, even if it's not identical.

Hint, Blast: having a text is not enough; you need to actually read it.

Further hints: a molecular biology text may well be a perfectly-adequate resource in some areas, but it may not the best resource for trying to understand overarching issues in evolution. And, in any event, an eleven-year-old text may not be your best guide to current thinking in this fast-moving area (though it's an improvement on your habitual reliance on creo websites and 80-100 year ago thinkers!).

You might want to try Douglas J. Futuyma's Evolution, just out this past May.

Or not, as I have deep doubts about the sincerity of your interest in actually educating yourself in this area, as nothing you've been taught here to date has seemed to stick...

Posted by BlastfromthePast on December 1, 2005 03:10 PM (e) (s) ... As to the experiment, it's already been discussed on this blog before. There was an article in New Scientist in June of last year about the experiment. Why don't you just do a google search: mice-highly-conserved junk-DNA? It's easy. http://www.newscientist.com/article.ns?id=dn5063......

Well, one implication might be that there's not a whole lot of critical "front-loaded" information hiding in all that junk DNA...

The genome doubtless holds many surprises, but Blast's hoped-for "hypothetical" detailed-advance-instructions for "unfolding" everything that evolution has accomplished since eukaryotes arose are running short on places to hide.

Gene duplication doesn't allow you to to evade the need to conserve both copies. If you lose one copy, your offspring are very suseptible to losing the second copy. Over the long run, you would have to expect the creature with two copies to be more durable.

— BlastfromthePast

Not convincing; but plausible. As to the experiment, it's already been discussed on this blog before. There was an article in New Scientist in June of last year about the experiment. Why don't you just do a google search: mice-highly-conserved junk-DNA? It's easy. http://www.newscientist.com/article.ns?id=dn5063... Here's how it starts:It is not often that the audience at a scientific meeting gasps in amazement during a talk. But that is what happened recently when researchers revealed that they had deleted huge chunks of the genome of mice without it making any discernable difference to the animals.

If the mechanism for variation is randomly applied, it will produce random variations. Meanwhile, the mechanisms for conservation are anything but random.

— BlastfromthePast

But that is the very point I'm making: what "appears" random is not random. So, for example, is a "random-number generator" something that was "randomly" put together?

As to the experiment, it's already been discussed on this blog before. There was an article in New Scientist in June of last year about the experiment. Why don't you just do a google search: mice-highly-conserved junk-DNA? It's easy. http://www.newscientist.com/article.ns?id=dn5063... Here's how it starts:It is not often that the audience at a scientific meeting gasps in amazement during a talk. But that is what happened recently when researchers revealed that they had deleted huge chunks of the genome of mice without it making any discernable difference to the animals.

— BlastfromthePast

You old parody,you, Mr. Paley.

Nah, that can't be the real ghosty. The phraseology was much too pleasant.

Lilting, almost.

It's quite possible to make a random number generator whose future values can not be predicted. For example, the thousandths of a second digit from a human keystroke.

— One Brow

WRTO Blast's article:
The original research is here:
Megabase deletions of gene deserts result in viable mice.
and there's a recent review on the topic here:
Conserved non-genic sequences - an unexpected feature of mammalian genomes.

So my prediction was wrong; it is still a puzzle for "standard biology". The authors (being dogmatic Darwinists, of course) continue to thnk that the conservation reflects some function not detected in their survey of mouse "normalness", and seem to think that this will lead to interesting discoveries about hitherto unknown DNA functions. IDers, on the other hand, don't expect any particular relationship between conservation and functionality, and will therefore not waste their time trying to find it.

It's quite possible to make a random number generator whose future values can not be predicted. For example, the thousandths of a second digit from a human keystroke. Similarly for the genome, the mutation events are random in that they are not predictable.

So my prediction was wrong; it is still a puzzle for "standard biology". The authors (being dogmatic Darwinists, of course) continue to thnk that the conservation reflects some function not detected in their survey of mouse "normalness", and seem to think that this will lead to interesting discoveries about hitherto unknown DNA functions. IDers, on the other hand, don't expect any particular relationship between conservation and functionality, and will therefore not waste their time trying to find it.

But you see, "random" is "designed"---note James Taylor's comments. (viz. "Randomness is an illusion.")

— Blast

It was Darwinists who called it "junk-DNA", not IDers. It was IDers who said that the genetic code contains "information" and that code and information are synonymous, and who find it humorous to hear that 98% of the human genome is "junk." It was the Darinist's who didn't spend time looking into the "junk DNA" so convinced they were that "genes" control everything and can explain everything. So, here, you want to mock me for proposing something like "front-loading"---which might make sense of the 98% of the un-transcripted genome, and then at the same time mock me for "not being interested" in the other 98%, while pretending that Darwinists are the only ones interested in "real" science. It just doesn't fly.

It's not your interest or even your disinterest which arouse mockery, Blast.

It's your disingenuous evasion of the import of the evidence.

And your inability to resist quote-mining of material you fail to understand (most recently the "randomness" comment here) does little to avert future mockery.

Blast: I think if you look carefully at the literature, you'll find that the term "junk DNA" was used because biologists didn't know what function, if any, the noncoding DNA had - i.e. "apparent junk". I believe, also, that you will find that where functions have been discovered for noncoding DNA, the scientists making those discoveries would all answer to your concept of "Darwinists".

And yes, I do consider "front-loading" an eminently mockworthy notion. What mechanism - if not natural selection - do IDers propose to account for the sequence conservation in this situation? What research are they undertaking to validate it?

More powerful RNGs usually use other RNG algorithms to produce seed values in order to produce a quasi random starting seed point, but current computing methods cannot create a TRUE random number.

It was IDers who said that the genetic code contains "information"

Whatever evolutionary scientists may or may not have expected to find in the "junk" portion of the genome, Blast, at least they have laid their expectations and hypotheses out there and, of course, they have continued to investigate the content of the "junk" and to publish their findings, regardless of whether the findings raised more questions--temporarily--than they could answer.

What specific predictions, expectations, or hypotheses have the ID-preaching "scientists" expressed regarding the "junk" and, much more importantly, what research, investigation, and publication have they done to follow up any vague hand-waving speculations which they may have sputtered?

You know the answer as well as we do, Blast: zip, nada, zilch, zero, none.

Any idea why your crowd are such aimlessly inept, miserably poor, and just plain lazy scientists, Blast?

Hint: ID isn't science and ID-proponents aren't scientists. And wouldn't know how to start actually doing science even if they suddenly became "inspired" to become scientists.

Let us know anytime you get tired of piggybacking your lame speculations on the backs of the results performed by the real working scientists, Blast, and want to sincerely learn something about this tremedously exciting field. At times, I do detect signs of a genuine curiousity hiding back there behind the lockstep fundamentalist front that you insist on presenting to the world, Blast. Someday you ought to let that curiousity come out to play, unfettered by your preconceptions of how things ought to be.

Is this;
http://www.newscientist.com/article.ns?id=dn5063......

an indication that "junk DNA" is precisely that, Just junk?
Sounds like this would have implications on the % of relative closeness on species DNA.

But that is the very point I'm making: what "appears" random is not random.

At least it provides a good starting point for Dembski's algorithms to work their magic.

— tGoP

So, here, you want to mock me for proposing something like "front-loading"---which might make sense of the 98% of the un-transcripted genome, and then at the same time mock me for "not being interested" in the other 98%

while pretending that Darwinists are the only ones interested in "real" science. It just doesn't fly.

With regard to computer algorithms. You have inferred more than what was written. Random is an illusion (in computer programming).

— James Taylor

Why, it's that sections are evolutionarily conserved, indicating that selection has preserved them.

— RBH

Selection can preserve them only if they have some selectable function, hence one looks for those functions because they're evolutionarily conserved. That's a clue that's not available to IDists.

— RBH

"Darwinians" have sequenced whole genomes and actually interpret and make use of your pecious information.

— CJ O'Brien

What specific predictions, expectations, or hypotheses have the ID-preaching "scientists" expressed regarding the "junk" and, much more importantly, what research, investigation, and publication have they done to follow up any vague hand-waving speculations which they may have sputtered? You know the answer as well as we do, Blast: zip, nada, zilch, zero, none.

— Steveipinhead

Actually, no need to use Heisenberg or Geiger counters to build a truly random RNG - all you need is to use the microphone of the computer to listen to the noise being made by the computer (when this idea was explained to me, it required the microphone to be inside the computer case, next to the processor, but I don't think there is need). The idea goes thus: you make the fans of the computer start working, so you get a nice, random noise. You listen to the noise and digitalise it. You take the last bit of each of the resulting numbers (sampling at 44 Hz you build up a good amount in little time), and those bits are used to form the random numbers. As far as I can tell, it is a good RNG (Heisenberg and Geiger might be better, of course, but are expensive and a tad dangerous).

James Taylor wrote:

With regard to computer algorithms. You have inferred more than what was written. Random is an illusion (in computer programming).

Blast answered:
Aren't we talking about genetic code? Can't you see the parallel?

I answer:

Blast, that is a very ignorant statement so far. Computer code that has to be compiled is *nothing* like genetic code. For one thing, computer code is extremely sensitive to change - a single letter of the code changed is normally enough to make it stop working, while random mutations in genetic code are mostly neutral (what was it, 99% of them?).

Hope that helps,

Grey Wolf

I suggest you all pop another tab or two of Prosac.

And how many young scientists who are excited about ID will you give Ph'Ds to, allow to work in labs, and then allow their experiments to be published?

And, of course, Darwinists started up with these investigations only because of the embarrassment of the human genome project showing that chimps and humans are almost identical

One of the points I made when first I got on this blog was that Darwinists would eventually figure everything out---that they were wrong and that ID had the right idea---but that they would do so in an ineffecient way.

I still hold to the same opinion

With regard to computer algorithms. You have inferred more than what was written. Random is an illusion (in computer programming).

And, of course, Darwinists started up with these investigations only because of the embarrassment of the human genome project showing that chimps and humans are almost identical, and that humans have about a third as many "genes" as was expected---two embarassments that made it obvious that---contrary to the Darwinian Dream Machine---everything CANT be explained by invoking "genes." All of this should be a clue that you've been barking up the wrong tree for a 150 years now.

There is no parallel, Blast. James was discussing the ability or lack thereof of computer code to generate random values. But mutations are not generated by the genetic code. They're changes that occur to the code, driven by external physical phenomena---a UV photon, a reactive molecule, a replication error.

— Anton Mates

Aren't we talking about genetic code? Can't you see the parallel?

— Blast

What I'm suggesting is that what "appears" to be random mutation---and here we're talking almost exclusively about bacteria---could easily be the result of a built in program within the DNA.

— Blast

And how many young scientists who are excited about ID will you give Ph'Ds to, allow to work in labs, and then allow their experiments to be published?

— Blast

Yes, of course. But the cell has a way of "cleaning the mess up." There are cellular processes that repair these kinds of mutations.

— Blast

Blast, I am a computer engineer. Your pop-sci-level understanding of computing, code, programs, and DNA is both common and grossly inaccurate.

— AC

There is no parallel, Blast. James was discussing the ability or lack thereof of computer code to generate random values. But mutations are not generated by the genetic code. They're changes that occur to the code, driven by external physical phenomena---a UV photon, a reactive molecule, a replication error.

— BlastfromthePast

Yes, of course. But the cell has a way of "cleaning the mess up." There are cellular processes that repair these kinds of mutations. What I'm suggesting is that what "appears" to be random mutation---and here we're talking almost exclusively about bacteria---could easily be the result of a built in program within the DNA.

As to "genes": they're only part of the picture---a fact that should have been evident 40 years ago when the "genetic" component of chromosomal DNA was found to be so small.

Granted, we don't know all of the mechanisms within a cell and the nature of all of the operations they carry out, but if the genetic algorithm is truly an algorithm, then it is incapable of generating a TRUE random number for the same reasons that I mentioned before by its own process, unless of course the Heisenberg Uncertainty Principle is utilized by genetic algorithms. Since the genetic algorithm must follow the same limitations as computer algorthms, then the TRULY random changes must be attributed to outside forces; otherwise the mutation is not random, but probable and predictable. If mutations simply follow algorithmic principles, it would be possible to predict the next mutation of a cell with proper understanding of the genetic RNG function. If no RNG function exists in the genetic code, then it is impossible for a genetic code to alter itself into a new arrangement spontaneously. In essence, outside forces must alter the genetic code to produce the random mutation. Since we know random mutations do occur in genetic code, then either outside forces somehow altered the code, eg. gamma rays, viral infection, etc. or there is a highly successful and sofar undetected and unreproduced RNG embedded in the DNA sequence. This would be very significant news to computer science were it ever discovered as computational systems would have a model upon which a true RNG algorithm could be developed. So Blast, find the RNG in the human genome and you may have found your beloved evidence for frontloading. It is the only plausible mechanism to produce what you have argued for. If however, there is no RNG in the human genome, then frontloading is implausible. By finding and decrypting the supposed genome RNG, one could effectively run the simulation forward and possibly backward as much as one pleased and see all of the frontloaded permutations that the designer put in the system. I'll leave the How up to you.

One correction, if we actually set out to prove frontloading, we would have to find a more run of the mill RNG such as the LCG because the frontloaded seeds could not be TRUE random values. It must be a know sequence since the progression is already preprogrammed. If any RNG were found in the human genome, it would be yet another mechanism for evolution. Anything that allows randomness, even pseudo-randomness, enhances evolution.

Wait, you don't like genes?

But the cell has a way of "cleaning the mess up." There are cellular processes that repair these kinds of mutations.

And likewise, when we think we're increasing the mutation rate in bacteria or Drosophila by exposing them to mutagens, their cells are really just pretending to be affected? Is this Satanic Design Theory?

So cancer comes from the Devil?

Even if The Designer/Great Programmer From Beyond had tried to frontload instructions to produce all of the current diverse biome (and the future biome, too, presumably...forever? or just until the ever-imminent Judgment Day?) into--what? the first eukaryote, the first bacteria, the first cell, the first proto-living replicator?--then the fact that random physical forces do cause genetic mutations would long ago have screwed the pooch, er, upset the long-term plan.

Unless Blast thinks he has some evidence that random genetic mutations don't actually occur...

Or unless he wants us to believe that The Designer/Etc. somehow also "programmed" in a feature to predict which specific "random" mutations would occur in which manner to which replicating organism at which time and then, um, negative, er, repair the unplanned ones, all the while leaving undisturbed the, um, planned ones, inserted just to fool all the future programmed-to-be-dumb scientists...

Or does Blast's (hack, cough!) theory just come down to the tired old we-can't-trust-what-reality-tells-us-'cause-all-existence-could-just-be-Designerly-"street theater" omphalos crapola load of bull, er, line of baloney?

In which case, why does Blast ever bother supplying us with his "versions" of scientific studies?

So when you chainsmoke or chug radioactive waste and then come down with cancer or have a baby with genetic defects, it's not really that certain chemicals or radiation induced mutations in your cells that messed them up? Instead, your cells repaired all those mutations and then cleverly substituted their own mutations that just look random instead? And likewise, when we think we're increasing the mutation rate in bacteria or Drosophila by exposing them to mutagens, their cells are really just pretending to be affected?

— Anton Mates

Don't be so smug.

Don't start with all the cite this, cite that, you're a liar nonsense

So when you chainsmoke or chug radioactive waste and then come down with cancer or have a baby with genetic defects, it's not really that certain chemicals or radiation induced mutations in your cells that messed them up? Instead, your cells repaired all those mutations and then cleverly substituted their own mutations that just look random instead? And likewise, when we think we're increasing the mutation rate in bacteria or Drosophila by exposing them to mutagens, their cells are really just pretending to be affected?

— BlastfromthePast

So, is your theory that evolution is driven by UV radiation?

Don't be so smug.

In the last year there is a study out---discussed here---saying that they can get bacteria to stop mutating (It's already been discussed. Don't start with all the cite this, cite that, you're a liar nonsense).

And, there's a study saying that around 20% of bacteria seems to always be changing---almost seems like this is programmed, doesn't it?

So cancer comes from the Devil? HA! Great minds think alike, eh?

— 'Rev Dr' Lenny Flank

ID could then be summarized as "Everything looks like God made it, except for the stuff that Satan made, which therefore doesn't count."

I don't believe I've ever called you a liar, and offhand I can't recall asking you to cite anything.

— Anton Mates

So how exactly does this help your claim that organisms repair all their spontaneous mutations while self-inducing directed mutations?

— Anton Mates

I don't believe I've ever called you a liar, and offhand I can't recall asking you to cite anything.

— BlastfromthePast

Perhaps you haven't; but others do. The remark was for the lurkers.

Is it your contention, then, that organisms, including higher organisms, do not have in place any machinery whatsoever for repairing errors to their DNA?

Why not visit this site on DNA repair mechanisms?.... http://en.wikipedia.org/wiki/DNA_repair

One form of DNA damage is alteration of a nucleotide (a mutation), altering the information carried in the DNA sequence. Because DNA mutation and recombination are the main means for evolution to occur, the rate of DNA repair influences the rate of evolution. With a very high level of DNA repair rate, the rate of mutation is reduced, resulting in corresponding reduction in the rate of evolution. Conversely, high mutation rates increase the rate of evolution.

— Some Wikipedian good Samaritan

Sigh...

I just posted a comment describing what I thought was the self-evident foolishness of the creationist MD who tried to convince the board of education that evolution was impossible because we have DNA repair machinery.

Then along comes Blast with... exactly the same argument.

I just posted a comment describing what I thought was the self-evident foolishness of the creationist MD who tried to convince the board of education that evolution was impossible because we have DNA repair machinery. Then along comes Blast with... exactly the same argument.

Why not visit this site on DNA repair mechanisms?.... http://en.wikipedia.org/wiki/DNA_repair

Honestly, I doubt your description of the Cirz et al. paper will help assuage said lurkers' suspicion. Perhaps look upon it as a challenge to summarize more accurately in the future?

— Anton Mates

A useful site, yes. Did you notice that it refutes your claim that spontaneous mutations are always repaired and don't contribute to evolution?

— Anton Mates

Your point, Blast?

It's interesting, and not all that surprising to us "standard biologists" that organisms might evolve mechanisms to modulate evolvability. What we would find really surprising, and would make us rethink the whole evolution thing, would be if someone demonstrated that "baseline" error rates in nucleic acid replication were not important in speciation.

Organisms' being able to accelerate evolution only enhances the "evolutionists'" position. What you need to demonstrate is that organisms can somehow stop evolution. Good luck with that. LexA is of no more use in this regard than p53.

Blast, you're blithering again.

In the first quote you talk about summarizing more accurately. Now, pray tell, where did I EVER claim that spontaneous mutations are always repaired?

But mutations are not generated by the genetic code. They're changes that occur to the code, driven by external physical phenomena---a UV photon, a reactive molecule, a replication error.

Yes, of course. But the cell has a way of "cleaning the mess up." There are cellular processes that repair these kinds of mutations. What I'm suggesting is that what "appears" to be random mutation---and here we're talking almost exclusively about bacteria---could easily be the result of a built in program within the DNA.

Now, about that study of Cirz, here's a quote: This brought Romesberg to the conclusion that mutation is a programmed stress response --- a survival mechanism. If the cell senses damage, and if the damage persists beyond its ability to repair it, the cell will turn on its mutation machinery and open the floodgates for evolution.

Random is an illusion (in computer programming).

This brought Romesberg to the conclusion that mutation is a programmed stress response --- a survival mechanism. If the cell senses damage, and if the damage persists beyond its ability to repair it, the cell will turn on its mutation machinery and open the floodgates for evolution.

Norman said:
I think we need a more sensible definition of "random." Something like "in principle it is unpredictable" with no conotations about any mental activity absent or present.

I answer:
James was already using that definition - in fact, a far harder one: random is that which cannot be predicted from the previous random occourence. A truly random sequence has a series of characteristics about distribution of the numbers, chances of repeated numbers, etc, and also given one number, you cannot deduce the next one in the sequence. A computer's pseudorandom algorithm produces all the characteristics (if it is good!) except the last one, since it is an algorithm that takes a seed and then produces exactly the same sequence every time from the same seed.

In this particular case: you take C language's RNG and, if you know what number it produced (exactly), and you have a hand calculator, you can "predict" (i.e. calculate) the next number. If you take a given organism's latest mutation, nothing but a sheer amount of luck allows you to predict where the next one will be.

I also want to note Blast's selective blindness: he has been shown to have no idea of the topics he tried to participate in, and now refuses to answer questions put to him, or even acnowledge that he was in error. Be a man, Blast, and admit you had no idea of what you were speaking when you tried to equate computer RNG with DNA mutations.

Hope that helps,

Grey Wolf, a little hurt no-one commented on his noiseTRNG (True RNG)

That only means that stressed organisms copy DNA poorly compared to non-stressed organisms. That's all. They roll more genetic dice with each replication. They evolved to evolve. If it doesn't kill them (when they're dying anyway), it may make them more fit. It happens naturally and requires no foresight on the part of the organism or a designer.

So when you said, "There are cellular processes that repair these kinds of mutations," you didn't mean to imply that this repair process always works, and therefore that there's a need to posit directed mutations as well? If that's not what you meant, my apologies for misinterpreting you. In that case, what is your claim, how does it conflict with standard evolutionary theory, and how does the Cirz article support it?

— Anton Mates

That only means that stressed organisms copy DNA poorly compared to non-stressed organisms.

— Norman Doerring

I also want to note Blast's selective blindness: he has been shown to have no idea of the topics he tried to participate in, and now refuses to answer questions put to him, or even acnowledge that he was in error. Be a man, Blast, and admit you had no idea of what you were speaking when you tried to equate computer RNG with DNA mutations.

— Grey Wolf

Grey Wolf, a little hurt no-one commented on his noiseTRNG (True RNG)

James was already using that definition...

IMO the rates are too low for the models to be plausible.

This is direct evidence, then, of a connection between the genome and mutation rates.

For me, this suggests that it's a more likely scenario that mutation rates high enough to bring about significant change in frequencies is something that is "built into" organisms than something that is driven randomly.

Now, you may not agree. I'm not troubled by that at all.

We'll see where science takes us to.

That's not how Romesberg interpreted it.

Mathematical models of evolution presume a very low rate of mutation. There are replication errors, and errors of other sorts. IMO the rates are too low for the models to be plausible.

— BlastfromthePast

And, I had Cirz article in the back of my mind since it came out in June and there was back and forth. What the article demonstrates is that the genome itself regulates the rate of evolution---at least in bacteria. This is indisputable.

Does the rate fall to "0"? No, but as the quote makes evident, when the organism needs to react to some stressor, it turns up it's rate of evolution. This is direct evidence, then, of a connection between the genome and mutation rates. For me, this suggests that it's a more likely scenario that mutation rates high enough to bring about significant change in frequencies is something that is "built into" organisms than something that is driven randomly. Now, you may not agree. I'm not troubled by that at all. We'll see where science takes us to.

The suggestion was straightforward, really. You have computer code, binary digits, that can, in turn, be programmed to produce random numbers. DNA is a coded language. It, too, can be programmed to produce random numbers. How can you argue otherwise?

IMO the rates are too low for the models to be plausible.

Some of us have a proven record of not seeing where science takes us, but rather either ignoring or torturing every piece of data into a religiously predetermined straitjacket.

— Russell

But it's just been explained repeatedly in this very thread that computer code can't produce random numbers, and that moreover if you want random numbers you need to set up your program to take input from some external phenomenon. Just like, well, DNA already does by virtue of being a sensitive and easily damaged molecule. Honestly, all this stuff is right there, just scroll up the page...

— Anton Mates

He attributes the quality of "mindlessness" to randomness and is trying to demonstrate a quality of mind/intelligence called foresight in the appearance of evolution. He is missing his target badly.

— Norman Doerring

I have neither the patience, time, nor inclination to respond to each point you make.

how do you know that it isn't YOU who are "torturing every piece of data into a materialist predetermined straitjacket?

I'm convinced that only intelligence can explain the complexity that organic life displays.

"What magical trick makes us intelligent? The trick is that there is no trick. The power of intelligence stems from our vast diversity, not from any single, perfect principle. - Marvin Minsky, The Society of Mind, page 308

This is where your blindness comes in: how do you know that it isn't YOU who are "torturing every piece of data into a materialist predetermined straitjacket?... It's all relative, you know.

When one steps back from Darwinism and looks at the explanations that evolution provides, it seems quite clear that they are tortured/circular/strained.

The suggestion was straightforward, really. You have computer code, binary digits, that can, in turn, be programmed to produce random numbers. DNA is a coded language. It, too, can be programmed to produce random numbers. How can you argue otherwise? Add to this the sensible assumption that the DNA "program" produces random nucleotide sequences rather than random numbers, or, perhaps, the combination of random nucleotides at random intervals. This could easily be programmed using computer code. The same applies to nature's DNA code. Why don't you be a man and admit that you were wrong when you thought I didn't know what I was talking about?

— Blast

Have you ever heard of a random number generator? Have you ever heard of computer generated random numbers? The answer, just to help out here, is "yes" to both questions, because both things happen. The "input" you're talking about is simply an "input" parameter, which can be easily supplied to a computer program. The point here is is that one can "change" the string of random numbers generated by "changing" the "input" value, and thus, these "random" numbers, are not so "random." What computers can do, genetic code can do. Providing an "input" parameter is the easiest part of a RNG.

— Blast

how do you know that it isn't YOU who are "torturing every piece of data into a materialist predetermined straitjacket?

*If you are thinking "3 states? The cat can only be in 2 states!" you haven't read enough Pratchett and do not own a cat. I suggest Science of Discworld for good laughs and nice science.

— I

In fact, the mere act of opening the box will determine the state of the cat, although in this case there were three determinate states the cat could be in: these being Alive, Dead, and Bloody Furious.

— Terry Pratchett

Yes, Anton, it is right there. Have you ever heard of a random number generator? Have you ever heard of computer generated random numbers? The answer, just to help out here, is "yes" to both questions, because both things happen.

The "input" you're talking about is simply an "input" parameter, which can be easily supplied to a computer program.

The point here is is that one can "change" the string of random numbers generated by "changing" the "input" value, and thus, these "random" numbers, are not so "random."

Actually, no need to use Heisenberg or Geiger counters to build a truly random RNG - all you need is to use the microphone of the computer to listen to the noise being made by the computer (when this idea was explained to me, it required the microphone to be inside the computer case, next to the processor, but I don't think there is need). The idea goes thus: you make the fans of the computer start working, so you get a nice, random noise. You listen to the noise and digitalise it. You take the last bit of each of the resulting numbers (sampling at 44 Hz you build up a good amount in little time), and those bits are used to form the random numbers. As far as I can tell, it is a goo

— Grey Wolf

Oops... sorry for the truncated quote Grey.

[H]ow do you know that it isn't YOU who are "torturing every piece of data into a materialist predetermined straitjacket?

— Blast

(But I can tell you that mathematicans are frequently very frustrated by the inability to get "sufficiently random" numbers...and many very long, very complicated RNGs turn out to show surprising regularities in their output.)

— Anton Mates