Doesn't darwinian theory fall apart on ontological grounds?

[QuinticNon]

It doesn't contain. It represents. It expresses. It points to an immaterial agent that predetermines a specific manifestation into physical reality.

Information is immaterial. Nothing immaterial may be contained.

---------- Post added 11-28-2009 at 01:28 AM ----------

Originally Posted by paulhanke

...the gene regulation network, in which such observations (e.g., what are the chemicals in the immediate environment?) play a key part in deciding which genes should be expressed...

How do chemicals decide? We must be careful not to personify chemicals. This is the work of RNA. And the Nobel Prize Winner Barbara McClintock was demonized for two decades having to take her work underground until her findings could no longer be ignored that gene regulation was in fact controlled, and non random at all. James Schapiro and many others have confirmed her work. You'll notice a protein alphabet at the end of Yockey's model.

Originally Posted by paulhanke

... the next thing missing from Yokey's model is an encoder...

Yockey's model starts with the double helix. It has already been encoded. We don't know how. That's what we're trying to figure out in this discussion. Where did the genesis source of information come from? He simply takes us from double helix to final protein.

Originally Posted by paulhanke

... that is, for DNA to be a code (or, more specifically, the result of a code that maps alphabet A to alphabet B), it must be alphabet B ...

Yes, DNA is technically alphabet B. RNA is technically alphabet C. We don't know the source for the original alphabet A. Yockey's model does not address the original encoding of DNA. We've seen the physical mechanism, when genes are selected from both parents and assembled into one new double helix. We just don't know what drives or instructs that mechanism to do so.

My personal theory is that RNA is reading non coding pseudogenes, actively selecting the best it has to offer, and thereby instructing the two codes to combine. The Russians are making progress with this, as they are beginning to see that DNA/RNA is not binary, but has the efficiency of quaternary/ternary logic to process in a holographic manner.

I'm moving this weekend. But will attempt to provide the research as soon as I can. Thanks!

[jeeprs]

I went to get Yockey's book out of the library previously, but it is technically challenging. But I do recall that there is a chapter addressing the issue of 'intelligent design' and denying that his book amounts to evidence for it. Although from the Amazon reviews, it seems that according to his theory, the 'origin of the code' (or life, as such) is not something we know or are likely to. (Of course this leaves a lot of space, which personally I am OK with. Space presents many possibilities.)

The second point that comes back to me was from lectures from the professor I had for Indian Philosophy, Dr Arvind Sharma. A phrase he used frequently in explaining Indian cosmology and the nature of Being, was that 'what was latent, becomes patent'. This is the idea that Brahman was always already 'latent' within the universe, (in the immanent aspect) and becomes manifest as living beings. Rather an Hegelian idea, but the phrase stayed with me.

I think what is coming out of all of this, for me, is the idea of the heirarchy of being. Of course Western material science is primarily concerned with one level of this heirarchy, namely the material level, which in the various traditional philosophies was understood as the lowest level. (Mind you, a lot has been done with it as a result of this concentration.) However it seems that various discoveries in all of the main sciences are unavoidably pointing towards other levels of the heirarchy of being. The nature of meaning is one such indication, but there are many others.

---------- Post added 11-28-2009 at 09:00 PM ----------

Originally Posted by paulhanke

. I think you would need to show that evolution itself is sentient ...

So this idea of 'the latent becoming patent' does that in that there is a kind of 'latent intelligence' in the universe which gradually becomes manifest in sentient beings. So again, this is the idea that intelligence doesn't evolve, our capacity for it evolves.

Whereas in the 'current scientific model', intelligence emerges only at the end of a very long evolutionary process having really been completely absent until it bootstraps itself into existence.

[QuinticNon]

Originally Posted by jeeprs

But I do recall that there is a chapter addressing the issue of 'intelligent design' and denying that his book amounts to evidence for it.

Yes, I've read elsewhere that Yockey is an atheist. In fact, as far as I know, all of my references are atheists or don't speak on the matter. Claude Shannon had a co-author to his book, Mathematical Theory of Communication, Weaver. I believe he is the only self proclaimed theist in the bunch. But I myself don't even know what the term theist means any longer. It's so, so... vague?

Intelligent Design is wrought with lies, ego, agenda... ignorance. It's embarrassing to be considered in that "camp", lumped together with hard 7 day creationists and the self proclaimed Name it and Claim it mega church pew parkers. Most of whom reject evolution altogether, but have no idea why.

I hope to promote the term, Intelligent Evolution. Noting that Darwin never mentioned the term Random Mutation in Origin of Species. He did however mention the need for an as yet unknown mechanism for Natural Selection to act upon. In the race to find that mechanism, Random Mutation was born. They may as well have called it Singularity. It means, "We don't know, but we can't let you know that. What would happen to our grants and funding?"

Barbara McClintock has handily demonstrated Controlled Mutation as the likely mechanism. I believe that quaternary(DNA)/ternary(RNA) logic is the next necessary acknowledgment to provide answers for the decision making capacity of the genome. Binary is just switches, yes or no, on or off, susceptible to cause and effect only. Quaternary/ternary can emulate "knowing".

Originally Posted by jeeprs

...the nature of Being, was that 'what was latent, becomes patent'.

Yes. More of this please. Very compatible with Bhartrihari and any teaching directed at principles of The Word, or The Way. Remember that Christianity was first called The Way. It wasn't called Christianity until religion got a hold of it.

Originally Posted by jeeprs

...idea of 'the latent becoming patent' does that in that there is a kind of 'latent intelligence' in the universe which gradually becomes manifest in sentient beings.

Sound eerily familiar to Terrence McKenna and his rap about the Great Attractor. Rather than a Singularity that pushes outward from the beginning of time, this Great Attractor is actually pulling us inward, towards it, meeting at the end of time. His Novelty Theory concludes that time as 12/21/12 (independently of the Mayans or Hopi). Interesting fun side note, that 122112 maps to ABBAAB. Hebrew, as read left to right, is BAABBA. BA ABBA translates in English as "Father Returns".

[Dave Allen]

Originally Posted by QuinticNon

I hope to promote the term, Intelligent Evolution. Noting that Darwin never mentioned the term Random Mutation in Origin of Species. He did however mention the need for an as yet unknown mechanism for Natural Selection to act upon. In the race to find that mechanism, Random Mutation was born. They may as well have called it Singularity. It means, "We don't know, but we can't let you know that. What would happen to our grants and funding?"

Well there's a few slurs against scientists (good scientists anyway) in there.

I don't know what you mean when you say "random mutation was born" as if to say scientists now sum evolution up as random mutation. The random elements of reproduction are actually downplayed by most scientists - and exaggerated wildly by those who hope to equate randomness with chaos in order to reduce evolution to an absurdity.

Evolution is evolution. It doesn't need rebranding just because a single aspect of it is under some scrutiny as to exactly how big a role it plays (and even Barbara McClintock was working on the assumption that randomness plays a role).

As for scientists not admitting they don't know. I think that's pretty unfair. On a quest for knowledge you need be skeptical and admittedly ignorant in order to make the incremental steps required to edge closer to your goal. Scientists speaking honestly will admit they don't know - that they even don't know what they are sure of - and describe the implcations of what is known using tentative language. "It is thought that Tiktaalik provides a perfect example of a transitional form between fish and tetrapod", etc.

What scientists do like to do is hypothesise "it could be this, it could be that" - but that's just part of the process needed to forge ahead with the search - it isn't "please don't take our money away" anymore than any other justification for any other profession.

Barbara McClintock has handily demonstrated Controlled Mutation as the likely mechanism.

She demonstrated a number of things, and factors favouring a degree of ability in some cellular processes to positively select for some mutations over other ones, or some unmutated stretch of genetic material over a mutated bit, are among them.

Her personal theological beliefs in regard to her study are not science.

Saying "she thinks transposition implies some sort of external intelligence, so if she's right about the science of transposition she must be right about the intelligence" is like saying "Richard Dawkins finds justification for atheism in his understanding of evolution, therefore evolution is atheist".

Wrong.

Her (or his) scientific understanding can inform her (or his) metaphysical philosophy all it wants - but that doesn't mean she (or he) has demonstrated the philosophy - just the science.

To state that that's "the likely mechanism" for natural selection is to jump ahead of oneself, because it's more apparent that natural selection resulted in the "error checking" processes.

---------- Post added 11-28-2009 at 11:03 AM ----------

Originally Posted by QuinticNon

Remember that Christianity was first called The Way. It wasn't called Christianity until religion got a hold of it.

The Roman and Hebrew words for 'heresy' were probably the first names it had.

[Aedes]

Originally Posted by QuinticNon

Are you not familiar with its role with pseudogenes? mRNA is a full blown operating system. It runs the entire show.

I'm quite familiar, though I'm not sure pseudogenes are what you're thinking of. Pseudogenes are genes that do not get expressed, and this is often because they lack a promoter sequence. It would be very easy in the lab to pick up pseudogene expression, you can do reverse transcriptase-based PCR to amplify RNA transcripts, so any RNA gene product of a pseudogene would be picked up. There was one that I worked on -- no mRNA expression and no polypeptide at all. You may be thinking of gene silencing, which is partly done by siRNA (not mRNA). But I also don't want to hijack the discussion with too much scientific nuance, I mean we can talk about gene regulation and epigenetics all day but in the end, a lot of people here have very little scientific background and it's sufficient to just focus on the so-called "central dogma" of genetics for the purposes of this discussion.

It's been a pleasure.

Likewise.

---------- Post added 11-28-2009 at 12:45 PM ----------

Originally Posted by QuinticNon

Noting that Darwin never mentioned the term Random Mutation in Origin of Species. He did however mention the need for an as yet unknown mechanism for Natural Selection to act upon.

And that's provided by molecular genetics -- whether or not one ascribes conscious agency to it.

Originally Posted by QuinticNon

In the race to find that mechanism, Random Mutation was born.

Mutation is not random. It's probabilistic. But even if it were 100% totally random, that's fairly unimportant: the real issue behind selection as one (of several) mechanisms of population genetic evolution is that mutations are not preserved randomly, even if they arise randomly.

Also, again, realize that when one mentions mutation, we are really talking about allelic or haplotype polymorphisms -- these may be single nucletoide polymorphisms, they may be crossovers, they may be duplications, deletions, etc. There are lots of alterations in gene sequence that get lumped together as mutation here.

[QuinticNon]

Originally Posted by Dave Allen

Well there's a few slurs against scientists (good scientists anyway) in there.

Who will now come forth to defend the Creationists I've slurred?

Just kidding friend. I certainly did not mean to suggest that all science is bad or driven by personal agenda. What I refer to is a human ego problem, and not directed at any one group over another. My sincere apology if I have offended you. It is the human propensity for fixity of assumptions that concerns me. That being a dogmatic trap to those who cannot release themselves from it.

Originally Posted by Dave Allen

I don't know what you mean when you say "random mutation was born" as if to say scientists now sum evolution up as random mutation.

Darwin never mentioned it. The concept was "born" out of a desire to identify a mechanism for natural selection to act upon. And no, absolutely not, most current scientists do not "sum evolution up as random mutation". It pleases me greatly to see (what I call) NeoNeo Darwinism downplay the role of randomness in light of new discoveries. Classic Darwinism (sans random mutation) is therefore reinforced.

Originally Posted by Dave Allen

The random elements of reproduction are actually downplayed by most scientists...

A positive turn of trends.

Originally Posted by Dave Allen

...and exaggerated wildly by those who hope to equate randomness with chaos in order to reduce evolution to an absurdity.

Would you please explain what you consider the difference to be between randomness and chaos?

Originally Posted by Dave Allen

Evolution is evolution. It doesn't need rebranding just because a single aspect of it is under some scrutiny as to exactly how big a role it plays...

Well, the fundamental principles may be solid, but the intricacies of the theory have evolved, like any other theory has, does, will, and should. How to best distinguish this evolution without rebranding? Isn't that a fundamental principle of evolution, to rebrand (note the change) of when mutations arise?

Originally Posted by Dave Allen

...and even Barbara McClintock was working on the assumption that randomness plays a role...

Perhaps at the beginning, as taught to her from others. But her recognition is not from running with the pack of the times, under the "assumption" of "randomness". Her recognition is attributed to her evolving beyond those assumptions.

"A goal for the future would be to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a "thoughtful" manner when challenged."
Gifts of Speech - Barbara McClintock

Originally Posted by Dave Allen

Her personal theological beliefs in regard to her study are not science.

I have no idea what her personal theological beliefs are. I only know her research.

Originally Posted by Dave Allen

Saying "she thinks transposition implies some sort of external intelligence...

I never said that. You've misread me. I don't know of any "external" intelligence reference ever made from Barbara McClintock.

"Over the years I have found that it is difficult if not impossible to bring to consciousness of another person the nature of his tacit assumptions when, by some special experiences, I have been made aware of them. This became painfully evident to me in my attempts during the 1950s to convince geneticists that the action of genes had to be and was controlled. It is now equally painful to recognize the fixity of assumptions that many persons hold on the nature of controlling elements in maize and the manners of their operation. One must await the right time for conceptual change".
Barbara McClintock
Barbara McClintock - Wikipedia, the free encyclopedia

The fixity of assumptions she refers to are from those who were threatened by her discovery of controlled mutations. Those who's research was founded around an ill conceived (and heavily funded) concept random mutation.

[Dave Allen]

Originally Posted by QuinticNon

Would you please explain what you consider the difference to be between randomness and chaos?

I think Aedes just did by citing probables.

But if you like - a dice provides a certain number of results that are as likely or not as one another (or maybe not if it's poorly cut).

So there's a random factor in there - you can't predict the result even if you can guess at it.

But it isn't pure chaos - you'll get a number, or maybe a sexual position or something depending on the dice - I dunno. But you won't get chaos, despite the random factor.

The random factor's influencing the changes in DNA from the moment it splits to the moment it recombines are greater than those of a dice (any dice we could feasably make anyway).

So it's random in the sense of not knowing what the results will be.

But it's not chaos in the sense of the results might be anything, or are ungoverned by factors that limit them to set types, or that you can't say what they might be with some insight or general confidence.

I never said that. You've misread me.

Very possibly. There was some talk on another thread of basing some metaphysical beliefs on her research. I'm possibly being unfair to her to claim she was responsible for such a thing herself, the testimony on that thread is pretty doubtful after all.

So if you aren't proposing the interferance of external intelligence I apologise for assuming you did.

However, even transposition results in some unpredictability, and may itself have arose out of natural selection of earlier processes that were even more unpredictable.

[Aedes]

Originally Posted by QuinticNon

Would you please explain what you consider the difference to be between randomness and chaos?

To be random means that all possible outcomes have equal probability, at least when "random" is not being used colloquially.

In its colloquial use, it's often interchanged with chaos, i.e. unpredictability.


By analogy, think about car accidents. Car accidents are a great example of chaos. At the beginning of the day, you cannot predict which two cars will collide with one another at the end of the work day, 10 hours later. The number of initial variables is too great, and the outcome partially dependent on so many of them. This is the so-called "butterfly effect".

But car accidents are NOT random. Elderly drivers, teenage drivers, males, distracted drivers, drunk drivers, speeders, etc are all more likely to be in accidents than sober, middle aged soccer moms driving the speed limit with their kids in the back. In other words, not all cars are equally likely to be in a collision.

[paulhanke]

Originally Posted by QuinticNon

How do chemicals decide? We must be careful not to personify chemicals.

... perhaps I should have phrased it as "...the gene regulation network, in which such observations (e.g., what are the chemicals in the immediate environment?) play a key part in the decision which genes should be expressed..." ... that is, it is the gene regulation network that "observes" and "decides" - not disorganized chemicals floating around in the environment

Originally Posted by QuinticNon

Yockey's model starts with the double helix. It has already been encoded. We don't know how.

... but isn't this begging the question? ...

Originally Posted by QuinticNon

Yes, DNA is technically alphabet B. RNA is technically alphabet C. We don't know the source for the original alphabet A. Yockey's model does not address the original encoding of DNA. We've seen the physical mechanism, when genes are selected from both parents and assembled into one new double helix. We just don't know what drives or instructs that mechanism to do so.

... but this is not encoding, this is recombination ... DNA doesn't have to be a code to be recombined - it just has to be information ... and the resulting DNA is not a code in the Shannon sense, either, as the recombination is never reversed (decoded) to recover the original DNA of the parents (would this even be possible to do in principle?) ...

---------- Post added 11-28-2009 at 02:16 PM ----------

Originally Posted by jeeprs

So this idea of 'the latent becoming patent' does that in that there is a kind of 'latent intelligence' in the universe which gradually becomes manifest in sentient beings. So again, this is the idea that intelligence doesn't evolve, our capacity for it evolves.

Whereas in the 'current scientific model', intelligence emerges only at the end of a very long evolutionary process having really been completely absent until it bootstraps itself into existence.

... but if latency is how the universe works, does that mean that matter was latent until the universe evolved the capacity for it? ... that carbon was latent until the universe evolved the capacity for it? ... that stars, galaxies, life, me, you, etc., were latent until the universe evolved the capacity for them? ... and what of the other almost infinite number of possibilities that never were and never will be realized by the universe - do they all exist as unfulfilled latencies? ... or does it make more sense that the universe simply creates new things (matter, carbon, stars, galaxies, life me, you, etc.) during its long, long trajectory through its state space of possibilities? ...

[Aedes]

Originally Posted by paulhanke

but this is not encoding, this is recombination ... DNA doesn't have to be a code to be recombined - it just has to be information ... and the resulting DNA is not a code in the Shannon sense, either, as the recombination is never reversed (decoded) to recover the original DNA of the parents (would this even be possible to do in principle?)

It's certainly possible to do if you have parental DNA as a reference.