We are as worms

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Genes in us multicellular eukaryotes are characterized by a peculiar feature: the DNA sequence is interrupted by stretches called introns that are transcribed into mRNA, but then cut out so that their sequence is not represented in the final protein product. The gene is spliced together out of portions called exons, excluding the introns, a bit of post-transcriptional editing that permits splice variants to be made, and that can increase the diversity of gene products. 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.

Continue reading "We are as worms" (on Pharyngula)

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Check this out:

http://creationsafaris.com/crev2005[…]tm#20051126a

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?

Sadly, these shysters are in my neck of the woods. One of them was on local TV a little whiel ago, bragging about the Allosaurus skeleton they jsut found. They were VERY careful not to mention that they think the skeleton is less than 10,000 years old and died in Noah’s Flood. (snicker) (giggle)

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

An impartial jury already ruled, over 100 years ago – a jury called “science”. Once upon a time, all scientists were creationists. Now, they’re not.

I doubt that this is due to every scientist on the planet suddenly converting to atheism.

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?

By doing scientific research into why this is so, formulating hypotheses that explain the evidence, doing further research to test the hypotheses and gather more evidence, developing the hypotheses into a theory or theories, lather, rinse, repeat. It’s called science.

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.

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?

Why don’t you ask Dr Fry?

Or are you too chicken-livered to spout your nonsense to people like him?

Read a bit more carefully:

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.

I see. But haven’t you, up front, decided that “evolution” did it? All the language about the scientific method is fine, in, and of, itself. 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, 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?

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

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!!! Now you have TWO things to explain–how do the “introns” NOT change, and, why the sequences DO change. One explanation CONTRADICTS the other–unless, of course, you’re a “believer”; then, of course, anything is possible. On the Darwinist’s shop front, a sign: “All ad hoc hypothesis welcomed.”

But haven’t you, up front, decided that “evolution” did it?

I’ve “decided” that evolutionary theory, being the result of 150 years of applying the scientific method to the question of origins, is very clearly the best mode of understanding the characteristics and diversity of species, until shown otherwise–by the scientific method. On the other hand, your perspective amounts to “gee whiz, that’s complicated, hard for evolution to explain in 30 seconds, musta been god/space aliens” (at least insofar as it amounts to a convincing argument for me to embrace a different theory).

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?

Like I said, I’ll ‘pause’ when I’m shown a theory that better fits the evidence, not an off-the-cuff nitpick that you think should make one question one of history’s best-supported and comprehensive scientific theories and start making assumptions that a different theory (which has nothing scientific to offer BUT vacuous nitpicks of evolution, plus a congenital need to come up with a metaphysical basis for reality by any means necessary) must be a better explanation.

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!!!

The sequences that aren’t changing (much) are the ones that code for parts of the protein. Note that the paper purposely focused on genes known to be present in very diverse species. Evolution predicts that most such genes will encode essential functions. If that’s so, then evolution also predicts that the coding regions of those genes will be relatively well conserved.

But introns aren’t part of the coding region. Most of the intron sequence isn’t important for gene function. (Some bits are, because they participate in the splicing reaction.)

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.

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

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?

Not really. Evolution contends that all extant organisms evolved from common ancestors. Thus, I expect some basic mechanisms should be traceable all the way back to Urbilateria (and even earlier).

I do not expect all biological “mechansims” to be traceable to the beginning. If that were the case, it would be support for the “front-loading” hypothesis. But in fact, the evidence indicates some mechanisms emerged early, and others much later. That’s consistent with the theory of evolution (but not with front-loading).

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,

Really? Isn’t it just a way of making a fantastic number of different proteins from a limited number of gene sequences? Sounds more like brilliant design.

I see. But haven’t you, up front, decided that “evolution” did it?

What alternative do you want to offer, Blast.

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

Says you. (shrug) Dr Fry has already demonstrtaed what an ignorant putz you are.

Stop quote-mining, Troll. The entire sentence:

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.

makes it clear that PZ is talking about introns, not the basic DNA->mRNA->tRNA->amino acid->protein translation - bacteria use the same process we do, albeit with much fewer introns. It is strange and inefficient that mRNA should carry non-coding codons.

This only makes it worse,

Fun research project for a creationism watcher: how many examples can you catalog of creationists responding with “this only makes it worse” when confronted with the evidence that they have no idea what they’re talking about? Right off the top of my head, the Wells “shrimp” mutation incident and Dembski’s orders-of-magnitude error pointed out by Shallit &/or Elsberry jump to mind. But I suspect that some serious research might reveal that this is, in fact, part of the official creationist playbook.

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!!!

And how, given a high-school understanding of evolution, could this possibly NOT be true? I’m reminding myself of “Russell’s Rule”, which is that if there is no evidence to believe that the foolishness of comments like Blast’s is not obvious to every reader, there’s no reason I should spend my time trying to correct misunderstandings that exist only in the minds of the willfully ignorant. But I do think it’s worth re-emphasizing that this is, as Kevin Vicklund pointed out, yet another prediction that evolution made, and - surprise, surprise! - is borne out. Not bad for a theory the creationists insist is “unfalsifiable”.

Qetzal asked:

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

Gonna tackle that one, Blast? Or should we just chalk it up as another example of The Designer moving in mysterious ways?

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.

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.

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.

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?

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.

Well, I agree with you that there are reasons that “introns” are “conserved.” There are recent studies showing that these “introns” actually play some role in the regulation of gene expression through a mechanism involving siRNA. So, I believe the reason they’re conserved is because they play a vital function in cellular life.

BUT, that doesn’t solve the problem. What it demonstrates is that the genome has the capacity to highly-conserve any portion of its sequence whenever it wants to–in fact, it can “conserve” for 8 nucleotides, e.g., and then turn around and NOT “conserve” for the next 12 or so nucleotides. The cunundrum is this: if you explain the “conservation”, then how do you explain “non-conservation” right next door? This is easily explained via an Intelligent Designer designing organisms to survive changing environmental factors, but is deadly to Darwinian theory. Unless, of course, you’re a “believer.”

[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?]

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.

BlastfromthePast Wrote:

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.

You’re wrong. The point of the article is that the locations of introns within the code has not changed much, not that the introns themselves have not changed. For example, if we let uppercase be exon and lowercase be intron, than ASddERTDqsdFDE is the same as DSedRTGHsqdFDE. They are different in sequence, but the introns (locations of the unused code) are the same.

BlastfromthePast Wrote:

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.

You’re wrong. The article did not mention sequence conservation.

BlastfromthePast Wrote:

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?

Without knowing the mechanism used to distinguish one from the other, I’d be hesitant to predict which would be more strongly conserved. For example, if the DNA sequence itself is used by the RNA to identify an intron, that I would expect introns to be much more strongly conserved in sequence, but more weakly conserved in location. On the other hand, if the assembly process just skips over triplets without looking at them, I would expect introns to be much more weakly conserved in sequence, but more strongly conserved in location. So, I don’t see where Darwinian theory makes a prediction without more detail on the mechanism.

BlastfromthePast Wrote:

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

Different mechanisms affecting these sequences.

BlastfromthePast Wrote:

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?

Gene duplication, among other things.

Blast,

Please see #60775, 60776, & 60782 for good responses to most of your points.

[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?

That’s wrong for several reasons, but the simplest is that it’s really all one mechanism: natural selection acting on ‘random’ mutation. The exon sequences code for parts of the protein. The intron sequences do not. Mutations in an exon are more likely to be deleterious because they frequently alter the protein. Thus, exon mutations are less likely to be passed on to future generations. Mutations in an intron are less likely to be deleterious, so they have a higher relative chance of being passed on.

Note that this doesn’t mean mutations occur more frequent in introns. Only that they are more likely to be essentially neutral (i.e. less likely to be counterselected when they do occur). Over evolutionary time, intron sequences are much more free to diverge compared to neighboring exon sequences.

Like Russell, I’m unfamiliar with your mouse deletion example, so I can’t comment on how it relates to any of this. Can you give us a reference?

W. Kevin Vicklund Wrote:

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).

This is incorrect. IIRC, most of the intron sequence plays no apparent role. There are a few important bases right at the junctions between intron and exon. There can also be small sequences within the intron that are necessary for proper splicing. But most of the intron sequence plays no particular role in splicing or translation.

It’s true that there are some places where an intron mutation could abolish splicing. That would lead to effects like you describe (e.g. extra amino acids incorporated in the protein). But most intron mutations would not have that effect.

As PZ Myers implies in 60776, intron position is what’s being conserved, not intron sequence.

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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.

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.

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.

Different mechanisms affecting these sequences.

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?

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

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?

Anton Mates Wrote:

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?

Let’s remember this quote.

Anton Mates Wrote:

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

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

Now, about that article 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.

Read it and weep. You’ll notice, Russell, that he’s talking about the LexA gene, and not the P53 protein.

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.

BlastfromthePast Wrote:

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

A few comments back. I said,

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.

And you said,

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.

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?

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.

You are aware that that quote isn’t from the Cirz et al. paper, yes? It’s from a ScienceDaily article about the paper.

Aside from that, since the Cirz paper itself notes that the measured mutation rate is never 0 under any circumstances, and since there’s no suggestion that the mutations themselves, whatever their rate, are non-random or genetically determined, I remain unsure of your purpose in citing it.

James Taylor wrote:

Random is an illusion (in computer programming).

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.

Like Kolmogorov complexity: http://en.wikipedia.org/wiki/Kolmog[…]v_complexity

BlastfromthePast quoted:

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.

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.

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.

Yes, the “SOS response”. It’s old news. Perhaps Blast just read about it in some creationist religious tract.

Anton Mates Wrote:

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?

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. 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.

Norman Doerring Wrote:

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

That’s not how Romesberg interpreted it.

Grey Wolf Wrote:

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.

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?

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

Hey, I thought it was ingenious. :) I’m not sure it would work, though…just thinking off the top of my head, but fan noise is spectrally filtered to some degree and if you looked at the last bit you might end up inadvertently sampling some harmonic. The output would definitely still be more random than any computer RNG, but it might have a very uneven and uncalculable distribution, and as you doubtless know a predictable distribution is almost as important to an RNG as the unpredictability of the individual values.

I guess I could just test it–I’ve got a microphone and Matlab–but it’ll have to wait a while. Let us know if you’ve seen anyone publish on it, though. I’m sure the electrical engineering types took a crack at it long ago…

Grey Wolf wrote:

James was already using that definition…

But Blast wasn’t. I think I see how Blast’s mis-reasoning works. 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.

People like Behe would be easier to argue with – he’ll come right out and tell you the attribute of mind he tries to demonstrate with irreducible complexity is “foresight.”

As DNA, evolution acquires a kind of memory and learned experience – two mind-like attributes – but not foresight.

Let’s parse this.

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

First of all, “IMO” in this case means squat - assuming we’re talking about biology. But what are “the models”?

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

Well, yes. The fact that mutation, by definition, alters the genome pretty much establishes a “connection”. But really all Romesberg has demonstrated is that this particular bug has evolved this particular mechanism to amplify a phenomenon that does, in fact, happen anyway: when the replicator is stressed, it makes more errors.

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.

Unless you’re a pre-committed creationist, there’s nothing in the Romesberg data to suggest anything of the sort.

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

We’re so relieved!

We’ll see where science takes us to.

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. But, hey! I’m not troubled by that at all, as long as they don’t try to wedge themselves into public education!

Blast wrote:

That’s not how Romesberg interpreted it.

How exactly do you interpret the reporter’s interpretation of Romesberg’s interpretation?

Do you think he claims there is foresight in the increased mutations?

Behe will come right out and tell you the attribute of mind he tries to demonstrate with irreducible complexity is “foresight.”

Will you?

BlastfromthePast Wrote:

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.

I’m not sure what “models” you’re referring to, as mathematical models of evolution have explored all sorts of mutation rates.

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.

Correction–the genome affects the rate of mutation, thereby affecting the rate of evolution (however that’s defined). Clearly many other factors play a part as well–the presence of mutagens, selection pressures, etc. And yes, the fact that there’s a genetic factor is indisputable, but also has been accepted by biologists for an awful long time.

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.

But science has already taken us past this. It’s utterly non-controversial that organisms can influence their own mutation rates and, for that matter, the recombination patterns in their offspring. I mean, that’s one of the big perks of sexual reproduction according to mainstream evolutionary theory–to increase genetic diversity and thereby improve, say, the parasite resistance of your descendants.

No one ever said mutation rates were random–it’s the individual mutations themselves which occur randomly, and you really haven’t presented any evidence to the contrary. Nor have you explained why genetic influences on mutation rate need be “built into” an organism, rather than being just another trait promoted by natural selection.

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?

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…

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

Thanks for giving us your, uh, expert opinion, Blast. (yawn)

Just to remind the audience once again, Blast is the same “expert” who wanted to tell us all about whale evolution but didn’t know what _Pakicetus_ was, then wanted to tell us all about bird evolution but didn’t know what _Caudipteryx_ was, THEN wanted to yammer about “snake genes are frontloaded”, only to tuck tail and run when Dr Fry himself told him he was full of crap.

I have neither the patience, time, nor inclination to respond to each point you make. Quite a bit of this, it’s clear, is simply how we care to interpret things. We can assume that there is a more “clear-sighted” interpretation, and then take the added step of assuming ours is the best interpretation.

I’ll just note the following:

Russell Wrote:

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.

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? When one steps back from Darwinism and looks at the explanations that evolution provides, it seems quite clear that they are tortured/circular/strained. It’s all relative, you know. Have you ever heard of the Parable of the Cave?

Anton Mates Wrote:

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…

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.” What computers can do, genetic code can do. Providing an “input” parameter is the easiest part of a RNG.

Norman Doerring Wrote:

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.

You’re half right. Yes, I’m convinced that only intelligence can explain the complexity that organic life displays. That seems like the right starting point. (Unless, like Darwin and his followers, I say to myself: “It just looks complex.”) But as to the “mindlessness” of randomness, it is the opposite to this that I’m pointing out: what appears to be “mindless” (=random), is, indeed, the work of intelligence—as is a RNG.

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

Nor the ability. (yawn)

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

You can change that in a New York Second, Blast, simply by (1) giving us a NON-materialistic explanation and (2) showing us how to test it using the scientific method.

Until then, you are simply all mouth. (shrug)

BlastfromthePast wrote:

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

Now, define intelligence. Do you think intelligence is something supernatural? Or natural?

You can’t just point to vague signs of intelligence – you have to be specific about which attributes of intelligence you can see functioning because a part is not a whole when talking about intelligence. A part does not indicate the presence of a whole:

“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

I would say that evolution does begin to display certain attributes of intelligence. In DNA evolution acquires a kind of memory and learned experience — two mind-like attributes. However, evolution seems to lack other attributes of intelligence, like foresight.

Today we create computer systems that we say are artificially intelligent. One of the tools we use to get computers to learn and create and invent are programs based on evolutionary algorithms - computer programs that model evolution.

http://library.thinkquest.org/18242/ga.shtml

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.

I love it when the fundies (sensu lato) go all PostModernist on us: “It all depends on your point of view, there is no ‘correct’ interpretation!” One wonders if they experience just a twinge of cognitive dissonance when they take the 180° opposite stand on matters of morality. But I digress.

Of course, I don’t know in an absolute sense of the word, anything. But note that pretty much every single scientist engaged in biological research - while they disagree on all sorts of particulars - sees the same overwhelming confirmation of at least the basics of what you like to call “Darwinism”. Does that not give you pause? Does that not cause you to suspect that possibly this “who’s torturing the data” puzzle is not necessarily consigned forever to PoMo uncertainty?

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

Correction: “when one with absolute pre-commitments not to accept it steps back from the overwhelming evidence that the “modern synthesis” of evolution is pretty sound…”

Otherwise, you’re asking us to believe that a few untrained outsiders who just happen to have religious precommitments, such as yourself, see clearly that the whole foundation of biology is misunderstood by all of us who have taken the trouble to actually study it. If that doesn’t give you pause - and I say this with no ad hominem intent nor any other ill will - there’s something seriously wrong with your cognitive processes.

Blast Wrote:

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?

A) You can’t program a computer code to produce random numbers. We have already explained why. I will continue to wait you to admit that you have shown to know nothing of computer code.

B) I fail to understand how DNA is coded to produce random numbers - in fact, all DNA does is copy itself and into useful molecules for the body. The only random part is mutations, which are *not* coded by DNA, except in your imagination, but by external sources. That is what studies say. To turn that around, you could produce a study that states that DNA is the cause for mutations, and then predict, from your own DNA (or any other) where the next mutation will happen, and then I will admit I was wrong. But you won’t - because you are wrong.

Again: DNA does not produce random patterns. It produces perfectly predictable patterns that any child can write down, since it is just “letter” substitution. Only in your feverish imagination does DNA code random numbers. I will continue to wait you to admit that you have shown to know nothing of DNA code.

C) If you are so sure it is easily programed, be scientific for once in your life and *produce that code*. I recommend you use visual basic - it is easy enough to learn to use and you will have an easy ready made GUI for your results.

Blast Wrote:

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.

D) Blast, if you had read the posts in this thread, you would have learned that no computer program can, unaided, be programmed into a TRNG. It needs to read an already random external input - and at that point the computer is no longer being computer-ish - it just digitalized the random input. No code needed beyond the driver for the microphone, or the Geiger counter, or the box opening hand that checks which of the three states the cat is in*.

And when you talk about the input value in genetic code, what the deuce are you talking about? Your parallel brakes down completely at this point, as in many others, since DNA takes no external input prior to copying itself, except in the form of mutations to its code, completely unlike a computer code which starts with a code and an input, and any mutations to the code render it completely useless. I assume you don’t see this, Blast, because you are as lacking in computer knowledge as you are in biology.

All in all, I (and about 4 others, at least) have shown you to be wrong, wrong, wrong in all counts. Again. As always. Ready to admit your ignorance, Blast?

Regarding my noise TRNG - I will not swear it is foolproof. It is, however, far cheaper than sing QP or Geiger counters, and with a certain care in the noise reading you should get close enough to the “coin throw” effect (after all, all you need is a truly random 1 or 0) that makes no difference.

Hope that helps,

Grey Wolf

*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.

Blast wrote:

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

Because we can use our knowledge in the real (material) world while you can only blather and argue.

A Darwinist can figure out where on the tree of life a fossil belongs, eventually. How do you organise your knowledge of fossils if not on a branching tree?

A Darwinist can set up experiments with fruit flies, bacteria and computer models to test his beliefs about evolution. How do you test your beliefs?

I’m sure the others here can add to my list of things Darwinists can do with their knowledge that IDers can’t do with theirs.

I Wrote:

*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.

After seeing that posted, I have felt a little bad about not explaining myself further, so without ado I include the relevant quote (approximate)

Terry Pratchett Wrote:

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.

Hope that draws a laugh,

Grey Wolf

BlastfromthePast Wrote:

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.

As previously explained by multiple programmers in this very thread, the above is simply false. No computer program in existence generates random numbers. They generate pseudorandom numbers which hopefully have some statistical properties “close enough” to random ones for whatever your purpose. (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.)

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

Again, as previously explained, false. The input required to generate true random numbers is not a single parameter, but a continuous data stream from some random external phenomenon such as radioactivity. Or, yes, Grey Wolf, fan noise. :)

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.”

Not so much false as nonsensical. As previously explained, the generated number sequence is not random, but it would hardly become more random by any measure if it were unaffected by the input value–quite the opposite!

No offense intended, but at this point it becomes impossible to believe that you actually and carefully read the preceding thread. If posts by multiple programmers haven’t been sufficient to show you the problems with what you said above, I’m not sure I can do any more to help.

Incidentally, it’s perfectly true that in principle there could be some sort of genetic algorithm to produce pseudorandom mutations, which could be sufficiently random-looking that we couldn’t tell the difference. It would be rather odd from both an evolutionary and (I imagine) an ID perspective–why waste DNA coding for pseudorandom mutations instead of just using the random ones which happen all the time?–but hey, science accepts odd theories, you just need evidence. Unfortunately, none has yet been provided.

Grey Wolf Wrote:

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

Electronics tend to generate a consistent audio frequency while running, hence the dull drone of computers and the pervasive whitenoise they produce. I am not sure how random the results would be. Since the audio output is a wave and the fan generates a consistent frequency, the wave would eventually catchup to itself and the same values would result. I think the results would be closer to the LCG than anything else. It is an interesting concept though.

Oops… sorry for the truncated quote Grey.

Blast Wrote:

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

Because we don’t stop with interpretation. We take the next step, and make testable predictions. We say, “I think things work like so. If I’m right, then this experiment should give this result. If I’m wrong, it should give that result.”

Then we perform the experiment, and let reality decide.

That’s the key to science, Blast.

Anton Mates Wrote:

(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.)

This brings up a very interesting point that programmers are well aware of and are constantly balancing out, optimization. The very long and complicated RNGs are a lesson in diminishing returns. Since only a single instruction can be carried out at a time in a processor, the more instructions piled through reduces the overall performance of an algorithm. It is therefore important to minimize the number of instructions to increase performance. Long and complicated algorthms tend to require exponentially more instructions than simple routines. Sometimes statements can be combined and parts of the algorithm eliminated if the process still works the same in the end (*cough* irreducible complexity). In the long run, better more complicated RNGs may not perform any better than the simplistic RNGs for a given application. A programmer must weigh performance against capability. The evolutionary algorithm can be viewed as programming DNA to work better with a significant balancing of capability (with possibly significant overhead) versus optimization (increase in efficiency) with enhancements vetted by natural selection.

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This page contains a single entry by PZ Myers published on November 29, 2005 5:03 PM.

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