how does the reading frame shift and still have the appropriate start and stop codon? It seems as if a shift in the reading frame would lead to a non-expressed gene, not a gene that now will code for another protein.

Joy answered:

I suspect you'll find answers to "how" in yet another level of coding, this one in the histones, as part of chromatin dynamics.

Joy,

Doug asked about frameshifts within the standard code, not about alternate codes.

Doug,

In the shifted reading frame, you will no longer have a start and stop codon at the original locations, but there can still be a start codon and a stop codon.

Here is a toy example using mRNA codons to demonstrate the principle:

Original frame:

AUG Start
AAU Asparagine
GAC Aspartic acid
CUC Leucine
AGU Serine
AAC Asparagine
CAG Glutamine
GUA Valine
AAC Asparagine
UAG Stop

Now shift the frame forward by one nucleotide:

UGA —-
AUG Start
ACC Threonine
UCA Serine
GUA Valine
ACC Threonine
AGG Arginine
UAA Stop
ACU —-
AGx —-

So in this case you can actually get two proteins from the same gene by shifting the reading frame forward by one nucleotide.

In other cases, as you suspected, you won't see a start codon in the shifted frame, so the gene won't be expressed in that frame. It all depends on the exact nucleotide sequence of the gene in question.

To see this, look at what happens when we shift the reading frame forward by two nucleotides, using our toy example:

GAA —-
UGA —-
CCU —-
CAG —-
UAA Stop
CCA —-
GGU —-
AAA —-
CUA —-

In this case we hit a stop codon before we see a start, so the gene is unexpressed.

It sounds very exciting; but how does the reading frame shift and still have the appropriate start and stop codon? It seems as if a shift in the reading frame would lead to a non-expressed gene, not a gene that now will code for another protein.

I suspect you'll find answers to "how" in yet another level of coding, this one in the histones, as part of chromatin dynamics.

There was interesting research released just today on how useful it's proving - New Method for Reading DNA, about gene expression 'suites' necessary for cell differentiation being part of this dynamic.

Coding of multiple proteins by overlapping reading frames is not a feature one would associate with eukaryotic genes. Indeed, codependency between codons of overlapping protein-coding regions imposes a unique set of evolutionary constraints, making it a costly arrangement. Yet in cases of tightly coexpressed interacting proteins, dual coding may be advantageous. Here we show that although dual coding is nearly impossible by chance, a number of human transcripts contain overlapping coding regions. Using newly developed statistical techniques, we identified 40 candidate genes with evolutionarily conserved overlapping coding regions. Because our approach is conservative, we expect mammals to possess more dual-coding genes. Our results emphasize that the skepticism surrounding eukaryotic dual coding is unwarranted: rather than being artifacts, overlapping reading frames are often hallmarks of fascinating biology.

(Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei Kosakovsky Pond, Anton Nekrutenko, "A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes," PLOS Computational Biology, Vol. 3(5) (May, 2007), emphasis added.)

It sounds very exciting; but how does the reading frame shift and still have the appropriate start and stop codon? It seems as if a shift in the reading frame would lead to a non-expressed gene, not a gene that now will code for another protein.

me: It doesn't make unintelligent evolution scientific by default either.

aag:
Evolution by mutations random in regard to fitness and natural selection isn't scientific by default, its been observed, and it makes useful predictions.

I don't doubt evolution. But words like 'random' should be used with care. First, mutations are physical events, covered by the laws of physics, and those laws look designed to me, not least quantum mechanical laws***. Second, Russian roulette, state lotteries, random-number generators in gaming consoles, etc, and sweeping leaves in a yard with a brush, are all instances of, or exhibit evidence of, intelligent design. So, the word 'random' does not entail blind through and through, or un-designed, or unintentional, or unintelligent per se.

***

As a final example, the fact that nature obeys the principles of quantum theory is highly important for the possibility of life. It turns out that matter would not be stable in a non"“quantum world. People generally suppose that the Heisenberg Uncertainty Principle makes the world, at least at the atomic level, a fuzzier and more indefinite place. However, paradoxical as it may sound, that principle is ultimately responsible for the fact that subatomic particles form stable atoms with well"“defined chemical properties. Were it not for the principles of quantum theory, matter would be amorphous and protean to such a degree that it is hard to imagine a living organism being possible"¦..

"¦..In the final analysis one cannot escape from two very basic facts: the laws of nature did not have to be as they are; and the laws of nature had to be very special in form if life were to be possible. In my view these facts lend themselves most naturally to a religious interpretation. Certainly, they tend to undercut the claim so often confidently made by materialists that the discoveries of
science point to a universe without meaning or purpose, in which man is an accidental by"“product.

That's from a particle physicist at the Bartol Research Institute, U. of Delaware. More here.

It doesn't make unintelligent evolution scientific by default either.

Evolution by mutations random in regard to fitness and natural selection isn't scientific by default, its been observed, and it makes useful predictions.

Breaking into a rousing rendition of The Matterdidit Somehow Chorus isn't what it takes to make a scientific case for Impersonal Nature filling in gaps in our knowledge either.

Of course not, what it takes is research, which scientists are constantly engaged in, but IDists do very little of.

, like all theists, already and openly appeal to one unobservable entity. If naturalists denounce us for doing that, and end up doing it themselves by appealing to numberless unobservable entities, intellectual bankruptcy is an apt term to describe it.

I am a theist as well, I simply don't think God can be studied scientifically. We are aware of multiple species which have made and used tools: several species of homos and chimpanzees, but we don't have scientific evidence of an unobservable entity which intervenes in the natural universe.

Well, it depends on whether one is talking about actual science or ideal science. Who knows what the latter is capable of? It might actually specify criteria for, and find instantiated evidence of, cosmic and biological design.

IDists keep saying that, but they never actually do it, or even seem to have research proposals to try to do it.

ID may achieve something of a breakthrough in human understanding. But not if the supporters of these ideas are continually subject to scorn and hostility and hounded from the Academy.

The DI has its own research institute now, at which IDists should be able to engage in research free from persecution, so we will see what amazing breakthroughs it produces. I'm not holding my breath.

me: Well, 'The Will of God' and 'Laws of Nature' are empirically equivalent hypotheses.

Aag:
They are not equivalent, because a miracle can be invoked to justify any result, making the hypothesis untestable and useless.

me:
Er, so can Laws of Nature! Have you heard of, say, quantum vacua and virtual particles? Or has human understanding of the world ever been changed by an unexpected observation?

aag:
Of course it has. The difference is that there are definable limits which can be placed on natural phenomenon; even quantum events fall within realms of probability. There are no such limits on God.

No, that's simply a blatant misconception as I've explained before, including to you.

me: As a matter of plain historical fact, there have been lots of different scientific theories. There still are. Now we've got string theories and multiverses coming out our ears, for pete's sake.

Aag: There have been lots of scientific theories, which have been replaced by other theories which provide better explanations of the evidence. Religions aren't sustained by evidence, but by faith, so they simply proliferate, each claiming to have the "truth".

Belief in a transcendent, rational and moral creator is one of the most stable beliefs ever recorded. So is the belief in matter existing independently of perception. It's hard to see what could falsify belief in the latter, since it's hard to know what difference it would make if the null hypothesis was true. But that doesn't stop materialists believing in completely mind-independent matter or 'Laws of Nature'.

Science is simply a disciplined form of study which seeks to develop useful models of reality. Some believers now want their faiths to get the "scientific" label because they believe the success science has had using methodological naturalism promotes philosophical naturalism, your own concern. But that isn't science's purpose and never has been.

Well, tell it to Dick Dawkins.

me: It has taken all other species millions of years to get, er, nowhere near even Newtonian physics. Why are we so special? Just a freak accident of evolutionary history? I refuse to purchase that notion, without proper evidence. Evolution hasn't explained sets, or propositions, or lots of other things that are part and parcel of math and science. So once it does that, then it can try to figure why one species out of lots also discovered quantum physics.

aag: Humans are uniquely intelligent, but there are many species which are unique in one way or other compared to other species.

Humans are uniquely lots of things compared to all other species on the planet. We speak English, Chinese, etc. We've been to the Moon. We grow wheat for export.

And the fact that scientists haven't figured out everything yet doesn't make ID scientific by default.

It doesn't make unintelligent evolution scientific by default either.

IDism doesn't provide plausible explanations of anything at all. IDists have to do more than point to gaps in our current knowledge to make a case for intelligent design.

Breaking into a rousing rendition of The Matterdidit Somehow Chorus isn't what it takes to make a scientific case for Impersonal Nature filling in gaps in our knowledge either.

The actual data says, we're the only species afawk in the universe with a theory of not only the Big Bang, but any theories whatsoever. And if you're going to appeal to millions of hypothetical, unobserved, and unobservable-by-us entities such as alien civilizations for which there isn't a shred of evidence in order to shore up a naturalistic theory of human mathematical accomplishment, then I leave as an exercize for other readers to figure out why that would expose the hollowness, if not outright intellectual bankruptcy, of your charges against ID.

You are contradicting yourself, stunney.

That's a nice big baloney sandwich you've got there.

I said: "And if you're going to appeal…". Notice the conditional. I, like all theists, already and openly appeal to one unobservable entity. If naturalists denounce us for doing that, and end up doing it themselves by appealing to numberless unobservable entities, intellectual bankruptcy is an apt term to describe it.

Before you said

me: And there seems to be no clear reason in principle why minds cannot be posited in the same way as other theoretical entities. In fact, we take the existence of minds other than our own for granted. What it is exactly that licenses that belief is really what ID is all about. The same goes for Strong AI.

Aag: When its for ID, other minds is what ID is all about. When I argue it, its "intellectual bankruptcy". You'll have to be more consistent than that.

Oh, I'm consistent. It's the naturalists who're not.

There's no contradiction between believing in science and believing in other minds, be they human, alien, or transcendent. But see my remark above for an example of inconsistency.

me: Once more, I refuse to purchase the naturalist theory. It's far too implausible to be reasonable. A transcendent creator who is the source not only of the ordered physical world but of moral and aesthetic order and value as well seems to me to be more rationally credible than the heap of implausible, 'just-so', unfalsifiable hypotheses that naturalism piles up and would have us accept.

Aag: Thats fine; if in fact the universe isn't naturalistic, then science lacks the capacity to accurately describe it.

Well, it depends on whether one is talking about actual science or ideal science. Who knows what the latter is capable of? It might actually specify criteria for, and find instantiated evidence of, cosmic and biological design.

Also, if theism is true, God is the most natural reality there is, since God exists solely by virtue of God's eternal nature as the unique being which exists of metaphysical necessity. All other beings are contingent.

Several centuries of incredible scientific breakthroughs, however, argue that science is an enormously powerful tool for gaining new understanding about the universe.

Does anyone at TT ever deny this?

It may well be that intelligent life is the exception; in that case, the best science can do is say "we don't know".

Let's not pre-judge the findings of science. The 'fine-tuning' data regarding the cosmos garnered in the past few decades could hardly have been dreamed of when The Origin of Species was published, and would have delighted Paley (not sure about Darwin). It's well under 100 years since Big Bang cosmology began to be developed. AI, or string theory, or ID may achieve something of a breakthrough in human understanding. But not if the supporters of these ideas are continually subject to scorn and hostility and hounded from the Academy.

Well, 'The Will of God' and 'Laws of Nature' are empirically equivalent hypotheses.

Aag:
They are not equivalent, because a miracle can be invoked to justify any result, making the hypothesis untestable and useless.

Er, so can Laws of Nature! Have you heard of, say, quantum vacua and virtual particles? Or has human understanding of the world ever been changed by an unexpected observation?

Of course it has. The difference is that there are definable limits which can be placed on natural phenomenon; even quantum events fall within realms of probability. There are no such limits on God.

As a matter of plain historical fact, there have been lots of different scientific theories. There still are. Now we've got string theories and multiverses coming out our ears, for pete's sake.

There have been lots of scientific theories, which have been replaced by other theories which provide better explanations of the evidence. Religions aren't sustained by evidence, but by faith, so they simply proliferate, each claiming to have the "truth". Science is simply a disciplined form of study which seeks to develop useful models of reality. Some believers now want their faiths to get the "scientific" label because they believe the success science has had using methodological naturalism promotes philosophical naturalism, your own concern. But that isn't science's purpose and never has been.

It has taken all other species millions of years to get, er, nowhere near even Newtonian physics. Why are we so special? Just a freak accident of evolutionary history? I refuse to purchase that notion, without proper evidence. Evolution hasn't explained sets, or propositions, or lots of other things that are part and parcel of math and science. So once it does that, then it can try to figure why one species out of lots also discovered quantum physics.

Humans are uniquely intelligent, but there are many species which are unique in one way or other compared to other species. And the fact that scientists haven't figured out everything yet doesn't make ID scientific by default. IDism doesn't provide plausible explanations of anything at all. IDists have to do more than point to gaps in our current knowledge to make a case for intelligent design.

The actual data says, we're the only species afawk in the universe with a theory of not only the Big Bang, but any theories whatsoever. And if you're going to appeal to millions of hypothetical, unobserved, and unobservable-by-us entities such as alien civilizations for which there isn't a shred of evidence in order to shore up a naturalistic theory of human mathematical accomplishment, then I leave as an exercize for other readers to figure out why that would expose the hollowness, if not outright intellectual bankruptcy, of your charges against ID.

You are contradicting yourself, stunney. Before you said

And there seems to be no clear reason in principle why minds cannot be posited in the same way as other theoretical entities. In fact, we take the existence of minds other than our own for granted. What it is exactly that licenses that belief is really what ID is all about. The same goes for Strong AI.

When its for ID, other minds is what ID is all about. When I argue it, its "intellectual bankruptcy". You'll have to be more consistent than that.

Once more, I refuse to purchase the naturalist theory. It's far too implausible to be reasonable. A transcendent creator who is the source not only of the ordered physical world but of moral and aesthetic order and value as well seems to me to be more rationally credible than the heap of implausible, 'just-so', unfalsifiable hypotheses that naturalism piles up and would have us accept.

Thats fine; if in fact the universe isn't naturalistic, then science lacks the capacity to accurately describe it. Several centuries of incredible scientific breakthroughs, however, argue that science is an enormously powerful tool for gaining new understanding about the universe. It may well be that intelligent life is the exception; in that case, the best science can do is say "we don't know".

Not true, bees have complex codes which were not intelligently designed. The nonrandom evolutionary process has been shown to have the capacity to genrate such codes in fact.

So much for Common Descent!

No, my point was, whatever is true of bees, there are no observed cases of codes arising unintentionally from non-code stuff.

Well, 'The Will of God' and 'Laws of Nature' are empirically equivalent hypotheses.

Aag:
They are not equivalent, because a miracle can be invoked to justify any result, making the hypothesis untestable and useless.

Er, so can Laws of Nature! Have you heard of, say, quantum vacua and virtual particles? Or has human understanding of the world ever been changed by an unexpected observation?

Science needs limits, so that it can develop testable models which become ever more accurate with time. "Scientific" theories which invoke miracles would simply proliferate like religious sects, each claiming to be "true".

As a matter of plain historical fact, there have been lots of different scientific theories. There still are. Now we've got string theories and multiverses coming out our ears, for pete's sake.

1) Einsteinian relativity, and quantum mechanics (and multi-dimensional space as per string theory), are incredibly counter-intuitive. And hence, they are intuitively extraordinarily far removed from being probably the result of a long history of unintentional and largely random physical processes. They're also nothing like what would be useful to a dog. Or to a cat. Especially Schrodinger's kitty.

Aag: First, evolution isn't a random process.

Bits of it are.

Second, the counterintuitiveness of relativity and quantum mechanics is probably why it took us 10,000 years after the rise of civilization to develop those theories.

It has taken all other species millions of years to get, er, nowhere near even Newtonian physics. Why are we so special? Just a freak accident of evolutionary history? I refuse to purchase that notion, without proper evidence. Evolution hasn't explained sets, or propositions, or lots of other things that are part and parcel of math and science. So once it does that, then it can try to figure why one species out of lots also discovered quantum physics.

If naturalism were true, and this ability is not all that improbable in the universe, then we should have encountered some evidence of other species having that sort of ability by now, given, again the age of the universe and the age of life on this planet -Fermi's Paradox. We should have received a visit or a card by now. And we haven't encountered any such evidence (unless life here is construed as such evidence, or if you believe in UFOs.)

Aag: If the evolution of intelligent life capable of, and actually successful in, developing technological civilization was rare enough that at any given time there was on average only about one such civilization per galaxy, there could be billions of such civilizations in the universe that we would lack the capacity or luck to have observed.

Yeah, there could be. But you don't have the data. The actual data says, we're the only species afawk in the universe with a theory of not only the Big Bang, but any theories whatsoever. And if you're going to appeal to millions of hypothetical, unobserved, and unobservable-by-us entities such as alien civilizations for which there isn't a shred of evidence in order to shore up a naturalistic theory of human mathematical accomplishment, then I leave as an exercize for other readers to figure out why that would expose the hollowness, if not outright intellectual bankruptcy, of your charges against ID.

3) There is no reason why aesthetic considerations should be a good heuristic procedure in theoretical physics given naturalism. Beauty is inextricably linked to consciousness. But why should an impersonal universe care about what it's going to look like to conscious mathematicians and physicists who will be living in it at some point billions of years in the universe's future?

aag: We evolved to fit this universe, the universe wasn't designed to fit us. If there are recurring patterns at many different levels of the universe, including ones observable by us when we were evolving, it would be natural for us to evolve to find them aethetically pleasing.

Well, no other species evolved to engage in great art, appreciate wonderful music, delight in elegant equations, enjoy having a house with a gorgeous view of the ocean, etc. So why didn't more of them evolve to fit the universe's myriad aesthetic properties? And no, I don't mean mechanisms of sexual attraction.

And it's not just mathematical and other forms of beauty that we appear to have lucked out on. It's the capacity for experiencing moral value, the capacity for religious experience, the capacity to study history, the capacity to not believe our species merely lucked out to become so different across different dimensions of experience. For instance, we can imagine a mathematically talented species which knew nothing of morality or aesthetics. Or a very ethical species which was hopeless at math. Or a wonderfully artistic species which was also amoral. But we got all three. Hmmm.

Once more, I refuse to purchase the naturalist theory. It's far too implausible to be reasonable. A transcendent creator who is the source not only of the ordered physical world but of moral and aesthetic order and value as well seems to me to be more rationally credible than the heap of implausible, 'just-so', unfalsifiable hypotheses that naturalism piles up and would have us accept.

I keep erasing what I've written, so I'm going to keep this response short. First, I didn't mean any negative connotation by the term "inhuman."

As for an example, I would say DNA is one such. From a scientific point of view, it is warranted to say, based on observationally derived and mathematically informed evidence, that DNA involves or constitutes a code; and also warranted to say that all other codes we know of were intelligently designed, and hence on inductive grounds, (and logical grounds concerning whether codes can even in principle arise unintentionally) that it's more probable than not that DNA was intelligently designed.

Not true, bees have complex codes which were not intelligently designed. The nonrandom evolutionary process has been shown to have the capacity to genrate such codes in fact.

Well, 'The Will of God' and 'Laws of Nature' are empirically equivalent hypotheses. Scientists frequently invoke the latter, thus revealing an empirically unwarranted bias in favor of philosophical naturalism. I think it's important that science be conducted without being presumptively biased in favor of a controversial philosophical worldview, since such bias will tend to color the choice of questions, answers, and interpretations of data in logically illegitimate ways.

They are not equivalent, because a miracle can be invoked to justify any result, making the hypothesis untestable and useless. Science needs limits, so that it can develop testable models which become ever more accurate with time. "Scientific" theories which invoke miracles would simply proliferate like religious sects, each claiming to be "true".

1) Einsteinian relativity, and quantum mechanics (and multi-dimensional space as per string theory), are incredibly counter-intuitive. And hence, they are intuitively extraordinarily far removed from being probably the result of a long history of unintentional and largely random physical processes. They're also nothing like what would be useful to a dog. Or to a cat. Especially Schrodinger's kitty.

First, evolution isn't a random process. Second, the counterintuitiveness of relativity and quantum mechanics is probably why it took us 10,000 years after the rise of civilization to develop those theories.

If naturalism were true, and this ability is not all that improbable in the universe, then we should have encountered some evidence of other species having that sort of ability by now, given, again the age of the universe and the age of life on this planet -Fermi's Paradox. We should have received a visit or a card by now. And we haven't encountered any such evidence (unless life here is construed as such evidence, or if you believe in UFOs.)

If the evolution of intelligent life capable of, and actually successful in, developing technological civilization was rare enough that at any given time there was on average only about one such civilization per galaxy, there could be billions of such civilizations in the universe that we would lack the capacity or luck to have observed.

3) There is no reason why aesthetic considerations should be a good heuristic procedure in theoretical physics given naturalism. Beauty is inextricably linked to consciousness. But why should an impersonal universe care about what it's going to look like to conscious mathematicians and physicists who will be living in it at some point billions of years in the universe's future?

We evolved to fit this universe, the universe wasn't designed to fit us. If there are recurring patterns at many different levels of the universe, including ones observable by us when we were evolving, it would be natural for us to evolve to find them aethetically pleasing.