Psience Quest

(2017-11-25, 09:32 PM)malf Wrote: [ -> ]I’m relatively comfortable with an idealist view of the world*. If ‘all is mind’ that’s fine... but in terms of this argument it doesn’t really add much, unless you are trying to force some ‘extra mind’ into the evolutionary process? Otherwise, what one person calls ‘a property of mind’ can equally called ‘a property of matter’ by another. It resolves nothing really.

(*we will still have to sort out Paul’s trees in his yard though)

Well, it does allow for the "realm of mind" extending to the non-physical, or spiritual, to give it another name. That, for idealism, isn't a problem but it is for physicalism. So, in order to remain within the bounds of physicalism you really have to dismiss all that evidence we discuss here - whether it be evidence for teleology in biology or the NDEs, etc., I mentioned above. 

I am not a philosopher so can't give you a proper theory of mind. I don't know how it works and I can't stand apart from it as an external observer. I don't know what makes me different to the table I'm sitting at - all I can think of is that there is some creative process at work always and everywhere. This process creates a diversity of forms and environments and the laws which define them. Some of those forms have conscious awareness in varying degrees.

I'm sorry I can't do better but that's more or less where I stand.

Kamarling Wrote:So basically you are saying: give the physicalists more time and they will get to the answers and prove physicalism. Personally I think things like transcendent experiences, NDEs and the whole field of parapsychology should at least give you cause for concern that the physicalists might be wrong after all. It beggars belief for me that you can continue to dismiss all that. I know why my son does - because he doesn't bother to engage with that kind of material but you do and you still remain where you always have been.

Yes, I think it is probably all bad science. But there is the possibility that it might not be and I await something fantastic to convince me. Meanwhile, of what advantage is to me to decide that physicalism is dead? Do I suddenly learn something wonderful about the world? Especially when it's possible I just erred in the opposite direction?

Quote:As for what a nonphysical thing would look like - all things are essentially non-physical in my worldview. Just manifestations of mind. Something like a very detailed dream or virtual reality of the mind. Of course, that's idealism: everything is mind stuff. There are proponents here who are dualists though and would give both of us a good argument.

And you may be correct. As I've said many times, if we could work out all the details of physicalism and idealism, so that they both explain all our observations, then I'd bet they would be indistinguishable modulo terminology.

The bottom line for me is that there is more work to be done and I probably won't know the answer in my lifetime. If we survive death, then I'll buy you a beer in the next world. If we do not, I won't know.

~~ Paul

I'll look forward to that beer Paul.

(2017-11-25, 06:08 PM)malf Wrote: [ -> ]It’s a very interesting study and I’m sure is very exciting to anyone working in the field. You have made Shuker’s comments look quite prescient by linking to a shameless propaganda spin piece right at the end of your post.

Is it your contention that god/MAL is actively encouraging the methylation process in this cave fish?

I haven't contended anything. I'm offering the article plus a link to comments on it; it's up to you how those strike you. As for me, I have agreements and disagreements with them. You shouldn't think they reflect my own opinions merely because I linked to them.

At the moment I'm unsure what to think about the possibility that epigenetic changes can play into evolution. But I am amused by the effect the assertion is having. The Shuker quote especially was funny, showing his rigid attachment to the idea that the only allowable agency in evolution is genetics, and his paranoia that any other idea must be religiously motivated. As I pointed out, the third way people, who are open to the possible importance of epigenetics in evolution, aren't religious types.  

I have no idea how MAL might be operating in what appears to us as the "world". A word like "encouraging" is so very anthropomorphic, and also, intrinsically dualistic, implying that there is a separation between MAL and "objects" or "concepts" like "intelligence". MAL, as I conceive of it, is the totality of all, only apparently differentiated into separate entities that we label in all sorts of ways as we try to make sense of the mystery of existence.

(2017-11-22, 07:30 PM)Paul C. Anagnostopoulos Wrote: [ -> ]I find it interesting that no one is willing to pursue specified complexity as a potential source of evidence. Why is that?

 
The subject of CSI is a can of worms, that has been debated and hashed over on the Internet for at least 10-12 years with hundreds of pages of posts. There are plenty of threads where every conceivable aspect, in particular the math, of CSI has been argued to death. It still boils down to hard-held opinion on both sides. 

A good popularization of Complex Specified Information (CSI) is at https://dennisdjones.wordpress.com/2013/...omplexity/ (About 16 pages). 

One of the better brief discussions on complex specified information that I have found is here. This is summarized and paraphrased in the following:

There doesn't seem to be a fundamental problem with defining information, and defining complex at least has some criteria. For instance something highly complex is highly improbable (just one of many possibilities). For instance the sequence of cards in a well shuffled deck of cards. This is complex to a degree without having been independently specified. 

But there is a fundamental problem with specification. It is a subjective measure. But it is not hard to understand and intuitively recognize. Let's say you find a 52-card deck perfectly ordered by rank and suit. If the deck was shuffled it could have any of approximately 8 x 10**67 possible arrangements. That's the complexity part. The number of possible arrangement of parts is huge, and is not determined by any physical laws. 

The perfect ordering is a specification. Specification can be defined as an independently given pattern. We recognize function in a machine as a kind of specification. The problem is that although this is real, it is subjective. It is a product of mind. 

Of course materialists don’t believe that any sort of information can exist in the “spiritual” or mind realm separate from matter. That is, materialists always believe that information, whether specified or non-specified, must be encoded on some sort of material medium. 

There may not be any objective formula that distinguishes specification from non-specification. But that does not negate the fact that specification is real and tangible and can be practically employed to discriminate between chance and design as we can see with the ordered deck of cards example. This pattern is specified because it is a pattern that has been identified in advance. If we claim the perfectly ordered deck came about by a random process the process had to have enough time to go through a good portion of all the possible combinations - not likely. To shorten the time the random variation process would have to have had a goal - but this is not allowed. 

Now let's look at an example of specified complexity that exists in all living things. There is an enzyme called a topoisomerase, involved in the replication of DNA. This enzyme is far more complex than a deck of cards. It is a sequence of hundreds of amino acids in a folded chain. Any link in the chain can be any one of 20 different amino acids. The order determines how it will fold and what biological activity it will possess. Does it have specification, does it exhibit function, does it exhibit complex specified information? You must be the judge of that.

According to the faith-based secular religion of neo-Darwinism an unintelligent RM + NS process supposedly created all innovative new biological forms and mechanisms including the topoisomerase enzyme. This process is based on a symbolic code. 

Do we have any examples of complicated mechanical arrangements with function and specification where the origin can actually be determined, whose causal history is known, that are not assembled by an intelligence? The only complicated mechanical  arrangements with function and specification where the origin is causally known ("known" defined as "perceived directly, having direct cognition of"), is where the origin was via intelligent agency. 

First, show how an unintelligent process can create a symbolic code. DNA is a digital symbolic code composed of triplets of base 4 numerals represented by 4 nucleic acids. It even has start/stop symbols like human designed serial codes. The codes go through a lookup table to determine what action to take. This is all very familiar computer technology. Mathematical symbolism is a product of mind and a relatively advanced mind at that.

Then show how the RM + NS process worked to create topoisomerase before there was the DNA replication enzyme. 

Then show in detail with falsifiable models how this process created the various examples of that special class of high-CSI biological mechanisms - irreducibly complex systems.

(2017-11-29, 04:09 PM)nbtruthman Wrote: [ -> ] 
The subject of CSI is a can of worms, that has been debated and hashed over on the Internet for at least 10-12 years with hundreds of pages of posts. There are plenty of threads where every conceivable aspect, in particular the math, of CSI has been argued to death. It still boils down to hard-held opinion on both sides. 

A good popularization of Complex Specified Information (CSI) is at https://dennisdjones.wordpress.com/2013/...omplexity/ (About 16 pages). 

One of the better brief discussions on complex specified information that I have found is here. This is summarized and paraphrased in the following:

There doesn't seem to be a fundamental problem with defining information, and defining complex at least has some criteria. For instance something highly complex is highly improbable (just one of many possibilities). For instance the sequence of cards in a well shuffled deck of cards. This is complex to a degree without having been independently specified. 

But there is a fundamental problem with specification. It is a subjective measure. But it is not hard to understand and intuitively recognize. Let's say you find a 52-card deck perfectly ordered by rank and suit. If the deck was shuffled it could have any of approximately 8 x 10**67 possible arrangements. That's the complexity part. The number of possible arrangement of parts is huge, and is not determined by any physical laws. 

The perfect ordering is a specification. Specification can be defined as an independently given pattern. We recognize function in a machine as a kind of specification. The problem is that although this is real, it is subjective. It is a product of mind. 

Of course materialists don’t believe that any sort of information can exist in the “spiritual” or mind realm separate from matter. That is, materialists always believe that information, whether specified or non-specified, must be encoded on some sort of material medium. 

There may not be any objective formula that distinguishes specification from non-specification. But that does not negate the fact that specification is real and tangible and can be practically employed to discriminate between chance and design as we can see with the ordered deck of cards example. This pattern is specified because it is a pattern that has been identified in advance. If we claim the perfectly ordered deck came about by a random process the process had to have enough time to go through a good portion of all the possible combinations - not likely. To shorten the time the random variation process would have to have had a goal - but this is not allowed. 

Now let's look at an example of specified complexity that exists in all living things. There is an enzyme called a topoisomerase, involved in the replication of DNA. This enzyme is far more complex than a deck of cards. It is a sequence of hundreds of amino acids in a folded chain. Any link in the chain can be any one of 20 different amino acids. The order determines how it will fold and what biological activity it will possess. Does it have specification, does it exhibit function, does it exhibit complex specified information? You must be the judge of that.

According to the faith-based secular religion of neo-Darwinism an unintelligent RM + NS process supposedly created all innovative new biological forms and mechanisms including the topoisomerase enzyme. This process is based on a symbolic code. 

Do we have any examples of complicated mechanical arrangements with function and specification where the origin can actually be determined, whose causal history is known, that are not assembled by an intelligence? The only complicated mechanical  arrangements with function and specification where the origin is causally known ("known" defined as "perceived directly, having direct cognition of"), is where the origin was via intelligent agency. 

First, show how an unintelligent process can create a symbolic code. DNA is a digital symbolic code composed of triplets of base 4 numerals represented by 4 nucleic acids. It even has start/stop symbols like human designed serial codes. The codes go through a lookup table to determine what action to take. This is all very familiar computer technology. Mathematical symbolism is a product of mind and a relatively advanced mind at that.

Then show how the RM + NS process worked to create topoisomerase before there was the DNA replication enzyme. 

Then show in detail with falsifiable models how this process created the various examples of that special class of high-CSI biological mechanisms - irreducibly complex systems.

http://scienceblogs.com/dispatches/2007/...obability/

Some added depth in the comments too

nbtruthman Wrote:There doesn't seem to be a fundamental problem with defining information, and defining complex at least has some criteria. For instance something highly complex is highly improbable (just one of many possibilities). For instance the sequence of cards in a well shuffled deck of cards. This is complex to a degree without having been independently specified.

But there is a fundamental problem with specification. It is a subjective measure. But it is not hard to understand and intuitively recognize. Let's say you find a 52-card deck perfectly ordered by rank and suit. If the deck was shuffled it could have any of approximately 8 x 10**67 possible arrangements. That's the complexity part. The number of possible arrangement of parts is huge, and is not determined by any physical laws.

The perfect ordering is a specification. Specification can be defined as an independently given pattern. We recognize function in a machine as a kind of specification. The problem is that although this is real, it is subjective. It is a product of mind.

http://www.talkreason.org/articles/eandsdembski.pdf

Quote:There may not be any objective formula that distinguishes specification from non-specification. But that does not negate the fact that specification is real and tangible and can be practically employed to discriminate between chance and design as we can see with the ordered deck of cards example. This pattern is specified because it is a pattern that has been identified in advance. If we claim the perfectly ordered deck came about by a random process the process had to have enough time to go through a good portion of all the possible combinations - not likely. To shorten the time the random variation process would have to have had a goal - but this is not allowed.

The ordered deck of cards is a human artifact. I don't think you can find an objective way to determine whether natural artifacts are specified. And if you could, you still wouldn't have a proof that some particular specified natural artifact must have been designed. You have no proof that specification cannot be accomplished naturally.

I wish people would stop claiming that evolution has to make a random search. There is plenty of literature about mechanisms that narrow the search to fruitful subspaces of sequence space.

Quote:Do we have any examples of complicated mechanical arrangements with function and specification where the origin can actually be determined, whose causal history is known, that are not assembled by an intelligence? The only complicated mechanical  arrangements with function and specification where the origin is causally known ("known" defined as "perceived directly, having direct cognition of"), is where the origin was via intelligent agency.

Which says nothing about natural artifacts.

Quote:First, show how an unintelligent process can create a symbolic code. DNA is a digital symbolic code composed of triplets of base 4 numerals represented by 4 nucleic acids. It even has start/stop symbols like human designed serial codes. The codes go through a lookup table to determine what action to take. This is all very familiar computer technology. Mathematical symbolism is a product of mind and a relatively advanced mind at that.

A natural process can create a code based on chemistry given enough time. The question is: has there been enough time? If you think that evolution of a code is impossible in principle, I'd love to hear why.

There is no lookup table. There are individual tRNAs that carry an amino acid and bind to a particular codon. Please don't overemphasize the computer sciencey feel of it.

Quote:Then show how the RM + NS process worked to create topoisomerase before there was the DNA replication enzyme.

https://www.ncbi.nlm.nih.gov/pubmed/17293019

https://academic.oup.com/nar/article/37/3/679/1079742

http://www.annualreviews.org/doi/abs/10....196.003223

Note that a lack of detailed description of the evolution of topoisomerases says nothing about the description of the purported intelligent design of them.

~~ Paul

PS: Fun video: https://www.youtube.com/watch?v=k4fbPUGKurI

Another interesting bit of research.

Quote:When physics gives evolution a leg up by breaking one

Quote:In a new study, physicists and evolutionary biologists at the Georgia Institute of Technology have shown how physical stress may have significantly advanced the evolutionary path from single-cell to multicellular organisms. In experiments with clusters of yeast cells called snowflake yeast, forces in the clusters' physical structures pushed the snowflakes to evolve.
"The evolution of multicellularity is as much a matter of physics as it is biology," said biologist Will Ratcliff, an assistant professor in Georgia Tech's School of Biological Sciences.
The bigger they are...
Like the first ancestors of multicellular organisms, in this study the snowflake yeast found itself in a conundrum: As it got bigger, physical stresses tore it into smaller pieces. So, how to sustain the growth needed to evolve into a complex multicellular organism?
In the lab, those shear forces played right into evolution's hands, laying down a track to direct yeast evolution toward bigger, tougher snowflakes.
"In just eight weeks, the snowflake yeast evolved larger, more robust bodies by figuring out soft matter physics that took humans hundreds of years to learn," said Peter Yunker, an assistant professor in Georgia Tech's School of Physics. He and Ratcliff collaborated on the research that documented the evolution and measured the physical properties of mutated snowflake yeast.


Read more at: https://phys.org/news/2017-11-physics-ev...g.html#jCp

[Cellular packing, mechanical stress and the evolution of multicellularity]

[Partial] Abstract:
[/url]The evolution of multicellularity set the stage for sustained increases in organismal complexity[url=https://www.nature.com/articles/s41567-017-0002-y#ref-CR1]1,2,3,4,5. However, a fundamental aspect of this transition remains largely unknown: how do simple clusters of cells evolve increased size when confronted by forces capable of breaking intracellular bonds? Here we show that multicellular snowflake yeast clusters6,7,8 fracture due to crowding-induced mechanical stress. Over seven weeks (~291 generations) of daily selection for large size, snowflake clusters evolve to increase their radius 1.7-fold by reducing the accumulation of internal stress. During this period, cells within the clusters evolve to be more elongated, concomitant with a decrease in the cellular volume fraction of the clusters. The associated increase in free space reduces the internal stress caused by cellular growth, thus delaying fracture and increasing cluster size. This work demonstrates how readily natural selection finds simple, physical solutions to spatial constraints that limit the evolution of group size—a fundamental step in the evolution of multicellularity.

https://www.nature.com/articles/s41567-017-0002-y

(2017-11-30, 02:16 AM)Paul C. Anagnostopoulos Wrote: [ -> ]A natural process can create a code based on chemistry given enough time. The question is: has there been enough time? If you think that evolution of a code is impossible in principle, I'd love to hear why...

There is no lookup table. There are individual tRNAs that carry an amino acid and bind to a particular codon. Please don't overemphasize the computer sciencey feel of it.

The thing about codes is that to be codes, they necessarily have to have a lookup table or its equivalent. You claim there is no lookup table for tRNAs. I beg to differ. At one end, tRNAs contain anticodons (the name, which I didn't originate, should be a clue that they're something to do with codes)  that match codons on mRNA; and those are are specified by DNA. Hence DNA ultimately contains the lookup table for tRNAs. If you deny that tRNAs are specified by triplets in DNA, then you're denying that DNA is a code, and if so, you're challenging entirely conventional biological opinion.

As to your assertion that codes can arise through "natural process", first off you're going to have to come up with an example that is not DNA, because you've already, effectively, denied that DNA is a code. Please, snowflake me no snowflakes. Name me one code that has arisen through natural process without the help of any intelligence external to it. Explain to me how it arose, why it is a code, and what form its lookup table assumes.


For the benefit of anyone who'd like to understand the genetic code, transcription and translation, here's a useful video:

(2017-11-30, 12:30 AM)malf Wrote: [ -> ]http://scienceblogs.com/dispatches/2007/...obability/

Some added depth in the comments too

From the linked article arguing against CSI (complex specified information):

Quote:  Experiment after experiment on enzyme function, including some generated by ID advocates themselves (see Axe 2000 and 2004), have shown that you can make significant substitutions in enzymes and still have the enzyme function.

This fact used to argue against Dembski's version of CSI - is at the heart of my own arguments!!!!!!!  Unintentionally this author has opened the Pandora's box of bio-evolution.  If others are really interested we can look together in the Third Way literature where it is discussed.  The question is: if DNA is a language, how is it not proof that life has used information science principles to develop from the start.  The idea that information is "special" in the hands of a human - must be lost.

A Panda with low iron in its blood is chemically in the same boat as his human counterpart.  A Panda with a hot tip on a stock, doesn't have the same range of probable activity as does a human with the same info and a couple of bucks.  Likewise, a bamboo location for the human may not be profitable.  We live in informational environments as well as physical ones.

Axe, et all -- found that the exact chemistry of enzyme function is unlike a straightforward chemical process.  There are process control operations that regulate toward a functional goal.  The function proceeds, even with some garble in the instructions.  How it appears to work - is like a language!  A message can trigger a functional process, from an array of wordings.  In chemistry. without catalysts - reactions proceed to equilibrium.  If they preform a "function" it is by accident.  There is no "god of elements" speaking to the molecules to statistically obey.  Materialism allows no organizing process coming from the natural intentions of living things.
  
Yet, organizing their environments is a fundamental function exhibited by living things.   Intentional behavior is what defines life.


The measurement system to judge environmental organization through behavior guided by feedback -- is informational.  The entropy of environments around living things decreases in direct proportion to the mutual information they store about it.  Having a natural language like the one underlying bio codes in DNA, RNA, Ribosomes, Enzymes and Proteins - appears to be a prerequisite for life as we know it.  It is an information transfer system and it is inherently purposeful.  Communication isn't measured in the terms of chemical bonding or electro-static charge.

That there is structured information that results from the minds of living things is so simple a concept. 

Life is natural.  Life involves communication of intent through activity that logically supports survival.  The first living things were converters of raw facts into strategic behavior to eat, each ions, rest and reproduce.  Life is described better and better from a chemical viewpoint.  But if you want to understand the bigger picture science offers - life's ability to process information is required as well.