Critiques of Science as Currently Praticed

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What I was pointing out, was that epigenetic markers can get passed on to the next generation, but that as presently understood, these ultimately come off - there is no permanent heritable change.

Of course epigenetic marks signal something - the frequency of synthesis of the corresponding protein!
This is simply not what I am reading in modern literature. That flat denial that there is no heritable change from epigenetic signalling - is promoted by those conservative theorists who likewise - are still having trouble letting go of the metaphysical stance of Weismann.

Here is a recent paper whose conclusion is pretty clear that in the language of bio-signalling - changes in gene expression have generational effects.

Conclusions
The genomes of eukaryotic organisms are adaptable to non-genetic/environmental-driven changes through epigenetic modulation of gene expression across generation cycles (Fig. 3). Epigenetic modifications include DNA methylation and histone modifications. These have the ability to alter gene expression patterns without affecting the nucleotide sequence of the underlying genome, the only exception being deamination of 5-mC to thymine. Tight regulation of the activity of DNA methyltransferases as well as of demethylases plays a mechanistic role in the establishment, maintenance and transient erasure of DNA methylation patterns. Correspondingly, post-translational modifications of histones and of regulatory proteins were shown to play a role in hereditary transmission of chromatin composition and configuration states, both in mammals and in model organisms. Thus, epigenetic programs contribute to the transgenerational inheritance of complex traits, which may help accounting for the “missing heritability” in current GWAS studies.
bolding mine

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517414/

David - if I use the term "mutual information" would you know what I mean? It is not a qualitative expression, but a formal measurable in information theory (and one of C. Shannon's original equations). I would then discuss mutual information and how it may help us understand Darwin's view of what he observed as the inheritance of instinct.

A marker in chemistry is one thing and can be measured in terms of chemical bonds. A notation in language is at a different level, an informational level. I would have the view that DNA/RNA/Ribosomes are a natural language.
 
David - if I use the term "mutual information" would you know what I mean? It is not a qualitative expression, but a formal measurable in information theory (and one of C. Shannon's original equations). I would then discuss mutual information and how it may help us understand Darwin's view of what he observed as the inheritance of instinct.
What I suppose I would need, would be a way in which epi-genetically marked DNA (methyl and/or acetyl groups) could be converted into un-marked DNA that was somehow different. Without that, as I understand it, these changes are not permanently inherited.

David
 
What I suppose I would need, would be a way in which epi-genetically marked DNA (methyl and/or acetyl groups) could be converted into un-marked DNA that was somehow different. Without that, as I understand it, these changes are not permanently inherited.

David
Let's try this again
Correspondingly, post-translational modifications of histones and of regulatory proteins were shown to play a role in hereditary transmission of chromatin composition and configuration states,


DNA "speaks" thru mRNA and tRNA and a large array of other molecules. If epigenetic messages change histones and or regulatory proteins in future generations - they have changed the "conversations" that DNA can have in future generations. Are you aware that the opinion has developed in recent years that more traits are presented in nature as being heritable, (such as animal instinct), than are found encoded in the DNA codons?

The three roles of RNA in protein synthesis. Messenger RNA (mRNA) is translated into protein by the joint action of transfer RNA (tRNA) and the ribosome, which is composed of numerous proteins and two major ribosomal RNA (rRNA) molecules.
And epigenetic changes can happen in many individuals at once. Through epigenetic inheritance, some of the experiences of the parents may pass to future generations. ... Epigenetic inheritance may allow an organism to continually adjust its gene expression to fit its environment - without changing its DNA code.
I cannot explain what I mean - without you addressing whether you understand the concept of mutual information. David, you are a smart guy, you have credentials in a scientific field (unlike myself). Why not look at this with an open mind.
https://www.sciencedaily.com/releases/2017/07/170717100548.htm
 
Let's try this again

DNA "speaks" thru mRNA and tRNA and a large array of other molecules. If epigenetic messages change histones and or regulatory proteins in future generations - they have changed the "conversations" that DNA can have in future generations. Are you aware that the opinion has developed in recent years that more traits are presented in nature as being heritable, (such as animal instinct), than are found encoded in the DNA codons?

I cannot explain what I mean - without you addressing whether you understand the concept of mutual information. David, you are a smart guy, you have credentials in a scientific field (unlike myself). Why not look at this with an open mind.
https://www.sciencedaily.com/releases/2017/07/170717100548.htm
Speaking for myself, I didn't know what you meant by "mutual information". I looked at your reference and it doesn't mention the term: the paper looks to be about transgenerational transmission of methylation markers, and how those might be necessary for normal embryogenesis, possibly in addition to their having effects once the embryo has developed.

Why didn't you explain what mutual information is and how it applies in that paper? I myself didn't have a clue. There is a Wikipedia article on it here, but I find it doesn't provide a simple explanation I can readily grasp. Simple Wikipedia's explanation is somewhat better:

Mutual information measures how much more is known about one random value when given another. For example, knowing the temperature of a random day of the year will not reveal what month it is, but it will give some hint. In the same way, knowing what month it is will not reveal the exact temperature, but will make certain temperatures more or less likely. These hints or changes in likelihood are explained and measured with mutual information.​

OK - I get the gist of that. But why is it applicable in what you are talking about and the paper you cited?

PS: I know that epigenetic information can be passed from one generation to the next, sometimes for a number of generations: but the key question is whether or not epigenetic changes can become permanently fixed in a population -- I don't think David is denying epigenesis occurs, just asking the question about how the fixation might be achieved. As far as I can see, the eventual removal of the markers won't have changed the DNA or affected transcription to mRNA or translation of the code into amino acid sequences by tRNA/ribosomes. Just saying "mutual information" doesn't help. You need to explain how and why the term is relevant.

David has a PhD in chemistry; I have a Bsc in zoology. While he can show me a clean pair of heels in many scientific fields, I think I might have the edge in biology; nonetheless I didn't understand (and still don't) what you were on about, so why not give David a break and explain it for both of us?;)
 
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I don't think David is denying epigenesis occurs, just asking the question about how the fixation might be achieved. As far as I can see, the eventual removal of the markers won't have changed the DNA or affected transcription to mRNA or translation of the code into amino acid sequences by tRNA/ribosomes. Just saying "mutual information" doesn't help. You need to explain how and why the term is relevant.
You have nailed it - that was exactly my point! Receiving useful epi-genetic information from a parent, may be useful to you, but over the generations that information will fade away, so it can't (at least obviously) contribute to evolution.

There is another point, from what I have read, these epi-genetic tags work be increasing or decreasing the rate of transcription of the genes to which they are attached - so they are not relevant to the actual evolution of the DNA code contained in those genes.

DNA "speaks" thru mRNA and tRNA and a large array of other molecules. If epigenetic messages change histones and or regulatory proteins in future generations - they have changed the "conversations" that DNA can have in future generations. Are you aware that the opinion has developed in recent years that more traits are presented in nature as being heritable, (such as animal instinct), than are found encoded in the DNA codons?
I am really not a fan of using vague expressions like this unless we are talking about a subject that simply is not well understood - such as many of the topics on this forum.

I was trying to express my broader suspicion that mechanisms such as epi-genetics can greatly complexify any description of evolution, but it isn't clear that they will ultimately deliver some sort of short-cut that would permit, for example, a novel protein to evolve faster than would seem possible based on Darwinian selection - given that a half made protein will have no selective advantage at all, and will therefore be subject to the rigours of combinatorial explosion.

Paul A would argue, I think, that maybe the half made protein would have some value to the cell. However that really isn't the point - unless there is evidence that there are chains of useful proteins in 'protein space' so that natural selection can hop from one to another, the combinatorial explosion problem remains!

David
 
Receiving useful epi-genetic information from a parent, may be useful to you, but over the generations that information will fade away, so it can't (at least obviously) contribute to evolution.
If the natural language of life is chemistry - then this makes sense. If the natural language of life is more than chemistry and includes information, both formal and semantic - your statement is clearly false. I have complete respect for chemistry's role in our physical environment and especially for the conservation of materials discovered by Lavoisier and formalized by Emmy Noether. I understand your points that if the chemical "marker" is gone - then so is its ability to be a casual agent. My point -- as always -- is that science offers a second level of analysis. Informational analysis supersedes this context of "only chem is causal". It is the obvious fundamental cybernetic premise: that information feedback is the root cause of decision-making in the command and control of systems, which grounds the science.

Think of it this way: if someone offers reproductive facts in Spanish to a bilingual person and they understand these facts of life and can translate them to English to third person -- functionality is undisturbed. The concept of multiple realizability reveals that the "markers" in Spanish, when translated into English, can represent the same functionality for sex as the Spanish version. The original markers are gone - yet the mutual information is established in a new set of markers and can be measured after translation. The functional ability gained can likewise, be confirmed empirically and measured as a capability function such as Cp or CpK. F**cking is no different, as to the effect of sperm delivery, while the English and Spanish translations may vary in style. The variables are connected - in the first set of instructions - to the variables in the second set. The proof of the mutual information gained at a second or third location is confirmed by getting lucky in a procreative act.

Losing the methyl marker is immaterial to communication of the measurable mutual information connected to the recieved message after translation. The information is re-encoded in the RNA/Ribosome/Protein part of the communication system. Mutual information is a full-blown topic in Biology as exampled:

Matina Donaldson-MatasciThe fitness value of information in an uncertain environment.Abstract. Communication and information are central concepts in evolutionary biology. In fact, it is hard to find an area of biology where these concepts are not used. However, quantifying the information transferred in biological interactions has been difficult. How much information is transferred when the first spring rainfall hits a dormant seed, or when a chick begs for food from its parent? One measure that is commonly used in such cases is fitness value: by how much, on average, an individual's fitness would increase if it behaved optimally with the new information, compared to its average fitness without the information. Another measure, often used to describe neural responses to sensory stimuli, is the mutual information — a measure of reduction in uncertainty, as introduced by Shannon in communication theory. However, mutual information has generally not been considered to be an appropriate measure for describing developmental or behavioral responses at the organismal level, because it is blind to function; it does not distinguish between relevant and irrelevant information. There is in fact a surprisingly tight connection between these two measures in the important context of evolution in an uncertain environment. In this case, a useful measure of fitness benefit is the increase in the long-term growth rate, or the fold increase in number of surviving lineages. In many cases the fitness value of a developmental cue, when measured this way, is exactly equal to the reduction in uncertainty about the environment, as described by the mutual information.
http://math.ucr.edu/home/baez/nimbios/
 
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Bart V

straw materialist
Member
You have nailed it - that was exactly my point! Receiving useful epi-genetic information from a parent, may be useful to you, but over the generations that information will fade away, so it can't (at least obviously) contribute to evolution.

There is another point, from what I have read, these epi-genetic tags work be increasing or decreasing the rate of transcription of the genes to which they are attached - so they are not relevant to the actual evolution of the DNA code contained in those genes.


I am really not a fan of using vague expressions like this unless we are talking about a subject that simply is not well understood - such as many of the topics on this forum.

I was trying to express my broader suspicion that mechanisms such as epi-genetics can greatly complexify any description of evolution, but it isn't clear that they will ultimately deliver some sort of short-cut that would permit, for example, a novel protein to evolve faster than would seem possible based on Darwinian selection - given that a half made protein will have no selective advantage at all, and will therefore be subject to the rigours of combinatorial explosion.

Paul A would argue, I think, that maybe the half made protein would have some value to the cell. However that really isn't the point - unless there is evidence that there are chains of useful proteins in 'protein space' so that natural selection can hop from one to another, the combinatorial explosion problem remains!

David
I thought that the evidence given in this thread put the myth of a combinatorial explosion behind us.
BTW you never answered this question, from my last post:

So, David, given all that, i would really like to know, has this conversation changed your stance on the "hard to get protein" argument in any way?
Do you think the DI would ever remove this argument from it's repertoire?
 
If the natural language of life is chemistry - then this makes sense. If the natural language of life is more than chemistry and includes information, both formal and semantic - your statement is clearly false. I have complete respect for chemistry's role in our physical environment and especially for the conservation of materials discovered by Lavoisier and formalized by Emmy Noether. I understand your points that if the chemical "marker" is gone - then so is its ability to be a casual agent. My point -- as always -- is that science offers a second level of analysis. Informational analysis supersedes this context of "only chem is causal". It is the obvious fundamental cybernetic premise: that information feedback is the root cause of decision-making in the command and control of systems, which grounds the science.

Think of it this way: if someone offers reproductive facts in Spanish to a bilingual person and they understand these facts of life and can translate them to English to third person -- functionality is undisturbed. The concept of multiple realizability reveals that the "markers" in Spanish, when translated into English, can represent the same functionality for sex as the Spanish version. The original markers are gone - yet the mutual information is established in a new set of markers and can be measured after translation. The functional ability gained can likewise, be confirmed empirically and measured as a capability function such as Cp or CpK. F**cking is no different, as to the effect of sperm delivery, while the English and Spanish translations may vary in style. The variables are connected - in the first set of instructions - to the variables in the second set. The proof of the mutual information gained at a second or third location is confirmed by getting lucky in a procreative act.

Losing the methyl marker is immaterial to communication of the measurable mutual information connected to the recieved message after translation. The information is re-encoded in the RNA/Ribosome/Protein part of the communication system. Mutual information is a full-blown topic in Biology as exampled:


http://math.ucr.edu/home/baez/nimbios/
Do you understand this, David? Because I'm buggered if I do. If you can translate from Spanish to English, let me have it.
 
Do you understand this, David? Because I'm buggered if I do. If you can translate from Spanish to English, let me have it.
Evolutionary science has worked in the context of metaphysical materialism since the time of Darwin. Darwin himself did not. Darwinism as detailed by Charles Darwin maintained a primary role for mind and postulated mental evolution. https://en.wikibooks.org/wiki/The_Descent_of_Man/Chapter_III

Descent of Man Chapter III Darwin states that the object of this chapter is to show that "there is no fundamental difference between man and the higher mammals in their mental faculty."

First of all he discusses the instincts of man and apes. He even suggests that apes in the wild may learn things like which plants are poisonous from other apes. He also mentions how birds on deserted islands appear to inherit a fear of man while the sterile worker bees and ants appear to acquire their instincts spontaneously.

Darwin states that people "underrate the mental powers of the higher animals, and especially of man." He stresses the development of "the mental organs" through "variability" and natural selection. He quotes Wallace on the difference between how people learn to make things and how animals learn to make their homes. He comments on animal behavior that show they feel "pleasure and pain, happiness and misery" as well as terror, "courage", and "suspicion". Darwin also relates anecdotes about maternal behavior of female animals especially monkeys, and shame and playfulness in dogs.

In discussing the higher mental faculties, Darwin describes animal curiosity, the need for stimulation, and the abilities to imitate and focus attention.
The modern synthesis of evolution did not embrace Darwin's field observations and believed in only the chemistry of genes. Current evolutionary scholars are looking at a large gap in the amount and capability of the chemicals of encoded genes to be casual to cover the full range of observed hereditary behavior. (citations available on request)

This writer asserts that the information sciences are more germane than chemisrty in addressing observed behaviors in living things by understanding biological information processing. This field is exploding in use and is termed Bioinformatics. Bioinformatics can objectively address the measurable variables of mental activity and how mental capabilities are inherited. Further, the role of mentation and biological information processing can support pathways for an active causal agency in biological evolution itself. (see Darwin in the Genome - by Lynn Caporale)

The thought-experiment, which went unappreciated, was to point out the fact that epigenetic markers are not causal in terms of chemistry turning into codons, David points this out. Error-correction systems erase them. However, there are messages received and instructions that persist through information leaking into the DNA/RNA/Ribosome natural language. Birds can inherit a fear of man in a single generation. That fear can persit for many generation as instinct unless different instructions enter the "conversation". The markers are semantic notation, not a mechanism.

Through the processes of transcription, translation and cybernetic feedback, these markers encode meaningful information into the system through linguistic means as a natural language. I am aware that this flies in the face of what many people have been taught (wrongly), but it predicts a means detailing field observations of how living species adapt and evolve. The "markers" carry messages from the environment as detected by living things from their personal, social and species context) to the evolving genome and while organic chemistry is the channel - the functionality is in information processing about fitness in the future.

My next point would how this works and can be measured - but without speaking to an understanding of mutual information in action I should stop.
 
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Evolutionary science has worked in the context of metaphysical materialism since the time of Darwin. Darwin himself did not. Darwinism as detailed by Charles Darwin maintained a primary role for mind and postulated mental evolution. https://en.wikibooks.org/wiki/The_Descent_of_Man/Chapter_III

The modern synthesis of evolution did not embrace Darwin's field observations and believed in only the chemistry of genes. Current evolutionary scholars are looking at a large gap in the amount and capability of the chemicals of encoded genes to be casual to the extent of observed hereditary behavior. (citations available on request)

This writer asserts that the information sciences are more germane than chemisrty in addressing observed behaviors in living things by understanding biological information processing. This field is exploding in use and is termed Bioinformatics. Bioinformatics can objectively address the measurable variables of mental activity and how mental capabilities are inherited. Further, the role of mentation and biological information processing can support pathways for an active causal agency in biological evolution itself. (see Darwin in the Genome - by Lynn Caporale)

The thought-experiment, which went unappreciated, was to point out the fact that epigenetic markers are not causal in terms of chemistry turning into codons, David points this out. Error-correction systems erase them. However, there are messages received and instructions that persist through information leaking into the DNA/RNA/Ribosome natural language. Birds can inherit a fear of man in a single generation. That fear can persit for many generation as instinct unless different instructions enter the "conversation". The markers are semantic notation, not a mechanism.

Through the processes of transcription, translation and cybernetic feedback, these markers encode meaningful information into the system through linguistic means as a natural language. I am aware that this flies in the face of what many people have been taught (wrongly), but it predicts a means detailing field observations of how living species adapt and evolve. The "markers" carry messages from the environment as detected by living things from their personal, social and species context) to the evolving genome and while organic chemistry is the channel - the functionality is in information processing about fitness in the future.

My next point would how this works and can be measured - but without speaking to an understanding of mutual information in action I should stop.
Thank you, Stephen, for your effort in trying to express your ideas in more understandable English. However, while the English is clearer, some of the underlying concepts are still, to me at least, sketchy. You say that epigenetic markers aren't causal. Well, in the end, neither might DNA sequences be causal; rather than their causing this or that phenotypic trait, they may rather be the appearance to our perception (or its extension through instruments and/or logical constructions) of phenotypic traits at a fine level of granularity.

When we look at phenomenality, the habit of reductionism tends to put causation at the lowest level possible: e.g. we explain why the sky appears blue by talking about scattering effects occurring at the level of atoms and molecules, and thereby think we have explained the phenomenon. But what if the sky appears blue for some as yet dimly understood reason, and at the level of our perception/its extensions, we are imposing a causative narrative of "atoms and molecules"?

Rather than science discovering new mechanisms, it might be in the business of constructing consistent narratives. The fact that these narratives at some point always break down (however useful they might be within a certain range) could be flagging to us to the possibility that causation isn't bottom-up, but rather top-down. If that is so, the amazing thing is that the narratives appear so consistent over their effective range: good enough for us to be able to create hi-tech products, for example.

The temptation to assert scientists have their world view largely correct is almost irresistible: but in the end it could be merely an appearance of correctness, and entails us constructing insoluble "problems" such as the hard problem of consciousness (see Bernardo Kastrup's paper here), or the fact that relativity and Quantum theories are incompatible. These "problems", in the end, may be semantic artifacts of the way that scientists tend to think that the physical is fundamental rather than consciousness.

Now I don't know if any of that relates to what you are saying, and I'm still unsure what you mean when you say that mutual information is important. One of the reasons is that it's an area that seems to be shrouded in much mathematical rubric, and I'm not by any stretch of the imagination a mathematician, making it very difficult for me to get a handle on it. You insist that I have that understanding before you are willing to go further, and so it appears that we are at an impasse. Hence your understanding remains with you, and I still, essentially, have only the vaguest clue what you're saying. If you want to engage in meaningful communication, for me you would need to be less elliptical, I'm afraid.
 
Stephen, Let me say first, that I totally endorse what Michael has written. I'd also make the general observation that I feel you have taken on board a few ideas from the very fluid area of evolution, and found yourself a little out of your depth.
Evolutionary science has worked in the context of metaphysical materialism since the time of Darwin. Darwin himself did not. Darwinism as detailed by Charles Darwin maintained a primary role for mind and postulated mental evolution. https://en.wikibooks.org/wiki/The_Descent_of_Man/Chapter_III
This resembles something J.Scott turner has written in his recent book. Yes, it may well be that Darwin's original theory made more sense given what was known back then, and maybe if Darwin had been shown the actual structure of the gene - encoded in DNA - he might have abandoned his theory!
The modern synthesis of evolution did not embrace Darwin's field observations and believed in only the chemistry of genes. Current evolutionary scholars are looking at a large gap in the amount and capability of the chemicals of encoded genes to be casual to cover the full range of observed hereditary behavior. (citations available on request)
Well to be brutally honest, I think current scholars are chipping away at Darwin's theory while pretending to still support it - because they want to stay in post! I wish they would be a bit more honest sometimes, and admit that materialistic explanations of life are pretty near impossible to come up with.
This writer asserts that the information sciences are more germane than chemisrty in addressing observed behaviors in living things by understanding biological information processing.
Well of course as soon as the genetic code was understood this statement was true - that is why those DNA bases are so glibly reduced to single letters C,A,G, and T!
This field is exploding in use and is termed Bioinformatics. Bioinformatics can objectively address the measurable variables of mental activity and how mental capabilities are inherited. Further, the role of mentation and biological information processing can support pathways for an active causal agency in biological evolution itself. (see Darwin in the Genome - by Lynn Caporale)
Appeals to mental activity buck a lot of questions. I mean, a single cell doesn't have a brain! You either have to postulate huge amounts of lower level computation - say in microtubules (which I don't think would amount to mental activity) - or, I think you have to bite the bullet and assume that all life has a spritual/non-material (call it what you want) component.
The thought-experiment, which went unappreciated, was to point out the fact that epigenetic markers are not causal in terms of chemistry turning into codons, David points this out. Error-correction systems erase them.
I never mentioned error correction, but I think it is generally assumed that these tags do come off. From Nessa Carey's book on epigenetics, it would seem that these tags are primarily there to specialise the cells of the body for different tissues. They turn DNA on or off, to produce nerve cells, or liver cells, etc.
However, there are messages received and instructions that persist through information leaking into the DNA/RNA/Ribosome natural language. Birds can inherit a fear of man in a single generation.
Assuming that is true (I just don't know), and that the information can't be passed on from parent to chick in some more conventional way, I think again we need a non-physical entity to pass on that information.
That fear can persit for many generation as instinct unless different instructions enter the "conversation".
Sometimes people like to talk in metaphors that are dangerous because people can start to take them too literally. I think the use of 'conversation' is in that category. Again, I think this confusion is partly deliberate. Researchers want to get new ideas out without being too explicit, which might cost them their academic careers!
The markers are semantic notation, not a mechanism.
Well writing on a blackboard is also a semantic notation, but if it gets rubbed off - or perhaps there is no rubber available and people keep writing new information over the same surface - the meaning is lost!
Through the processes of transcription, translation and cybernetic feedback, these markers encode meaningful information into the system through linguistic means as a natural language. I am aware that this flies in the face of what many people have been taught (wrongly), but it predicts a means detailing field observations of how living species adapt and evolve. The "markers" carry messages from the environment as detected by living things from their personal, social and species context) to the evolving genome and while organic chemistry is the channel - the functionality is in information processing about fitness in the future.

My next point would how this works and can be measured - but without speaking to an understanding of mutual information in action I should stop.
Well, do you understand this explanation of mutual information:

https://en.wikipedia.org/wiki/Mutual_information

It would take a very considerable effort to understand that properly, and somehow I doubt if it would really help that much. Unfortunately, I think some people use maths as yet another obfuscation tool - basically because nobody in academia can actually speak their mind clearly in this area!

David
 
Sometimes people like to talk in metaphors that are dangerous because people can start to take them too literally. I think the use of 'conversation' is in that category. Again, I think this confusion is partly deliberate. Researchers want to get new ideas out without being too explicit, which might cost them their academic careers!

Well writing on a blackboard is also a semantic notation, but if it gets rubbed off - or perhaps there is no rubber available and people keep writing new information over the same surface - the meaning is lost!
David
The idea being defended is that the activity of mind can be examined under a methodological system of measurement that is similar to the materials based measurements of chemistry and physics. Conversation, as the passing of instructions and messages has a formal standing in two sciences, the mathematical theory of communications (MTC) and linguistics. Information transfer during a conversation has its primary process model: signal - channel - receiver. The MTC measures the coded notation transfer and linguistics addresses a complimentary level of communication which is the semantics of the messages. A message functions as the moving of "meaning" from source to receiving agents or storage locations.

Implicit in the blackboard example is that the writer of the notation is using a language of coded symbols. The formal information of the marks, denotes a message, which the marks represent. The writer may inscribe the blackboard and no other party may see or photograph it. However, when the writer encoded the blackboard with information - which she felt the need to channel - she created a state where that information was simultaneously encoded with the agent as the source and on the board. Communication of the message can be measured as to the source and the receiver having ensembles of tokens that represent the same state. These ensembles are mutual information. Any difference in the two representations can be attributed to noise in the channel, such as misspelling, missing instructions, etc.

Notice that the nervous system encoding within the agent (source code) and the coding in a language are different coding systems and different media, but since information objects can be realized in different media, the mutual information can communicated largely intact. We can copy from a hard drive to a DVD and play the DVD for a listener. There is mutual information in the each medium encoding the same message. (multiple realizability). Washing the black or whiteboard doesn't change the mutual information communicated, just stops the board form being a further source of signals of that message. The mutual information still resides with the agent.

If the board was seen or photographed - more copies of the mutual information are generated, with some measurable degree of fidelity. In fact if the message on the board was original - even if the notation is wiped - the agents who gained mutual information from reading it can carry that message throughout the world. If photographed - the mutual information originating in the mind of the agent can last for a long duration, even after all the agents die.

DNA/RNA/Ribosome epigenentic signals can encode instructions that reach-out to a colony and species and last for thousands of generations.

The assumptions behind this point-of-view are that bio molecules can be a natural language and that behavior instincts are observed to be hereditary.
 
I thought that the evidence given in this thread put the myth of a combinatorial explosion behind us.
BTW you never answered this question, from my last post:
Well look, this issue of the combinatorial explosion (or otherwise) involved in the formation of new proteins, is fairly well defined, so let's pursue it a bit.

First, it is worth noting that 'nylonase' is a misnomer, because this enzyme does not break down nylon, but a bi-product of its manufacture 6-aminohexanoic acid.
This is a fairly simple organic chemical, and it doesn't seem inconceivable that an enzyme to metabolise this already existed somewhere in the bacterial kingdom. Remember that bacteria can swap genes among themselves rather easily.

What I am saying, is that maybe this discovery didn't merit the fanfare that claimed that it proved that evolution could come up with new proteins so easily.

This Wiki article certainly suggests that protein space is very sparsely populated, but that there may be clusters of related proteins with a very similar structure.

https://en.wikipedia.org/wiki/Sequence_space_(evolution)

Note that that if this is true, then that would seem to rule out frame shift mutations. I am not sure if you know what these are, so consider part of a gene split up into the codons for successive amino acids:

CAG TAT CCA ACT G ...........

Now consider what happens if you delete one DNA base - i.e. perform a frame shift. You get:

AGT ATC CAA CTG ...........

This totally scrambles the protein, and if sequence space is sparse there is a negligible chance of ending up with something useful.

In fact, it would seem that it probably happened by a single mutation:

https://en.wikipedia.org/wiki/Nylon-eating_bacteria

David
 

Bart V

straw materialist
Member
Well look, this issue of the combinatorial explosion (or otherwise) involved in the formation of new proteins, is fairly well defined, so let's pursue it a bit.

First, it is worth noting that 'nylonase' is a misnomer, because this enzyme does not break down nylon, but a bi-product of its manufacture 6-aminohexanoic acid.
This is a fairly simple organic chemical, and it doesn't seem inconceivable that an enzyme to metabolise this already existed somewhere in the bacterial kingdom. Remember that bacteria can swap genes among themselves rather easily.

What I am saying, is that maybe this discovery didn't merit the fanfare that claimed that it proved that evolution could come up with new proteins so easily.

This Wiki article certainly suggests that protein space is very sparsely populated, but that there may be clusters of related proteins with a very similar structure.

https://en.wikipedia.org/wiki/Sequence_space_(evolution)

Note that that if this is true, then that would seem to rule out frame shift mutations. I am not sure if you know what these are, so consider part of a gene split up into the codons for successive amino acids:

CAG TAT CCA ACT G ...........

Now consider what happens if you delete one DNA base - i.e. perform a frame shift. You get:

AGT ATC CAA CTG ...........

This totally scrambles the protein, and if sequence space is sparse there is a negligible chance of ending up with something useful.

In fact, it would seem that it probably happened by a single mutation:

https://en.wikipedia.org/wiki/Nylon-eating_bacteria

David
About nylonase, repeating what i wrote in that thread :

I do not think the discussion about whether or not frame shift is in play negates the value of Nylonase as evidence for recent new function.
This essay:
Is it easy to get a new protein? A reply to Ann Gauger
goes more in to that.

But again you answer a post with several links to good peer reviewed research, with a post on a ID/creationist blog, run by the Discovery Institute.
My main argument in my previous post did not hinge on Nylonase in any way.
And from the wiki link in your post:

Role in evolution teaching[edit]
Main article: Nylon-eating bacteria and creationism
There is scientific consensus that the capacity to synthesize nylonase most probably developed as a single-step mutation that survived because it improved the fitness of the bacteria possessing the mutation. More importantly: The enzyme involved has been produced by a mutation completely randomizing the original gene. Despite this, the new gene still had a novel, albeit weak, catalytic capacity. This is seen as a good example of how mutations easily can provide the raw material for evolution by natural selection.[7][8][9][10]
As said, the arguments made in that thread certainly do not hinge on the case of nylonase.
In that exchange, i provided a decent number of papers that showed different approaches of how it would be easier to navigate protein space.
Most of them showed up in this post

So i also repeat my question from the last post in that thread:
So, David, given all that, i would really like to know, has this conversation changed your stance on the "hard to get protein" argument in any way?
Do you think the DI would ever remove this argument from it's repertoire?
Besides all that, is it not a pity we no longer can not discuss this in the original thread?
 
About nylonase, repeating what i wrote in that thread :



And from the wiki link in your post:
Nobody doubts that one-step mutations can happen, and if they are beneficial, they can be selected for.

Ultimately, the question is whether the whole set of proteins required by life can be obtained in that way.
As said, the arguments made in that thread certainly do not hinge on the case of nylonase.
Well nylonase was introduced as a supposed knock-down argument against ID.
In that exchange, i provided a decent number of papers that showed different approaches of how it would be easier to navigate protein space.
Most of them showed up in this post
OK - why don't you pick one that you think is most interesting, or maybe most accessible to both of us. Otherwise we get a branching tree of argument!
Besides all that, is it not a pity we no longer can not discuss this in the original thread?
You can argue that out with Alex if you want.

Are you aware that there is a block of biologists who have given up on conventional Neo Darwinism(ND), and are looking for something else.

http://www.thethirdwayofevolution.com/

They would not be doing that if there wasn't a problem with ND.

Now I don't think they will succeed, because I think the complete answer goes beyond materialistic explanations, but those scientists are certainly saying that Darwinian survival of the fittest isn't going to be the complete answer.

David
 

Bart V

straw materialist
Member
Nobody doubts that one-step mutations can happen, and if they are beneficial, they can be selected for.

Ultimately, the question is whether the whole set of proteins required by life can be obtained in that way.
And that is where the Discovery Institute claimed to have evidence that was impossible, that was what that exchange was all about.
In the end this evidence did not amount to much, just the claim that remained.


Well nylonase was introduced as a supposed knock-down argument against ID.
Again, this was about much more than only nylonase.

And let there be no confusion about the burden of evidence, it are the ID proponents who have to provide evidence against the theory of evolution by natural selection.
They make claims that are supposed to overturn a well established theory, they should bring the evidence.

OK - why don't you pick one that you think is most interesting, or maybe most accessible to both of us. Otherwise we get a branching tree of argument!
No, the fact that the literature has so many examples of evidence for easier pathways to protein function, means that the ID argument of 'hard to get protein' goes nowhere.

The 'hard to get protein' argument is a negative one, i assume you agree at least to that.

So it has to show it has tried every possible way we can imagine, and maybe even some we can not imagine at this time.
For this argument to make any sense, it should be able to give evidence over a broad range of subjects, but it doesn't.

In reality, it does the polar opposite, it relies on one or two papers that are exaggerated, misused, and misquoted.
It tries to give evidence on a very narrow path that does not lead very far.

We should not discuss these papers one by one, now that would result in an argument branching explosion.
The fact that these papers are easy to find, by an interested layman like me, is the actual argument.

There are probably much more that i do not even recognize as being relevant to the subject.

The fact that there is so much positive evidence for plausible pathways through protein sequence space, blows the weak negative argument by the DI out of the water, that is what we should be discussing.

Or rather that should be the conclusion.
 
And that is where the Discovery Institute claimed to have evidence that was impossible, that was what that exchange was all about.
In the end this evidence did not amount to much, just the claim that remained.
The discovery institute claimed that a frame shift mutation could not create a new viable protein, and I tried to explain to you why that is so. However, as I understand it someone has since come up with an ordinary mutation that achieves the same thing.

The real problem here is best attacked by an analogy - to try to take all the jargon out of it.

Imagine that you knew that someone had scattered some rocks filled with precious stones, on a stony beach, and you wanted to find them.

If they had scattered them randomly, that would be an almost impossible task, because every rock you chose, would have to be broken open to see if it contained precious stones. Now suppose that you learned that the scatterer had been rather careless and had dropped little heaps of stones rather than scattering them evenly, then with luck, if you found one stone full of gems, you might be lucky and find some more nearby! That seems to be roughly what is being claimed for the distribution of useful proteins among all possible proteins.

OK so what is still utterly unclear, is how even one stone can be found (and remember the protein space is vastly bigger than a beach, with many more dimensions).
Having found one cluster of proteins/stones, it is also not clear how you find the next cluster.

Imagine now, that you record the location of any stones found to contain gems by their gps coordinates, e.g. 50.7192° N, 1.8808° W. The nearest analogy to the frame shift mutation, is to imagine looking for your next stone at 1.8808° N, 50.7192° W ! In other words, the frame shift is as good as choosing a essentially random location to look for the next stone.

I know that analogy is a bit contrived, but I'd really like you to get an idea of what this is all about. You may be able to think of a better analogy, but we need to pull back from all the technical details, I think, to see why it is just unreasonable to claim that there is some magical short-cut to the search problem.

David
 

Bart V

straw materialist
Member
The discovery institute claimed that a frame shift mutation could not create a new viable protein, and I tried to explain to you why that is so. However, as I understand it someone has since come up with an ordinary mutation that achieves the same thing.
Fine, let us forget for a moment about frame shift mutation.
For the umpteenth time, The evidence for easier pathways through protein space does not hinge on frame shift mutations.

There is enough evidence to find in the literature that explore different, plausible, approaches.
It are the ID/creationists that claim this is not possible. It is one of their "10 reasons Darwinism is not true" arguments that will never die


The real problem here is best attacked by an analogy - to try to take all the jargon out of it.
No it is not, it is best attacked by looking at the evidence


......
I know that analogy is a bit contrived, but I'd really like you to get an idea of what this is all about. You may be able to think of a better analogy, but we need to pull back from all the technical details, I think, to see why it is just unreasonable to claim that there is some magical short-cut to the search problem.

David
No, first we have to look if there is a search problem, and that is what we did in that other thread.
In the end there really was no credible evidence that this search was impossible. There was, however enough evidence for plausible ways this search could have taken place.

That is what i wanted to discuss, and what you seem to want to avoid discussing.

Of course protein space navigation is not easy, the probabilities involved are indeed going to be incredibly small. But it also took billions of years to get to the incredible biodiversity we know.

Our intuition is completely useless in matters of probability and large numbers. So we would have to try to quantify this, problem is we do not have all the right factors to put into the equation.

For the Discoveroids to show that evolution is impossible, they have demonstrate that they know all the possible factors to put into the equation, which, IMO, is impossible.
The peer reviewed research, mentioned in that thread, showed at least a few different factors that would also have to be put in that equation

And yet they seem to claim they did exactly that.
In the thread we are discussing, i think it is shown that that was not true.

So, David, my question to you is simple.

Going on the scientific evidence presented by both sides in that thread, do you think the DI has quantifiably shown navigation through protein space is impossible?
 
No, first we have to look if there is a search problem, and that is what we did in that other thread.
In the end there really was no credible evidence that this search was impossible. There was, however enough evidence for plausible ways this search could have taken place.

That is what i wanted to discuss, and what you seem to want to avoid discussing.

Of course protein space navigation is not easy, the probabilities involved are indeed going to be incredibly small. But it also took billions of years to get to the incredible biodiversity we know.

Our intuition is completely useless in matters of probability and large numbers. So we would have to try to quantify this, problem is we do not have all the right factors to put into the equation.

For the Discoveroids to show that evolution is impossible, they have demonstrate that they know all the possible factors to put into the equation, which, IMO, is impossible.
The peer reviewed research, mentioned in that thread, showed at least a few different factors that would also have to be put in that equation

And yet they seem to claim they did exactly that.
In the thread we are discussing, i think it is shown that that was not true.

So, David, my question to you is simple.

Going on the scientific evidence presented by both sides in that thread, do you think the DI has quantifiably shown navigation through protein space is impossible?
Well I think there is a smoke and mirrors quality to this - smoke put up, not by you, but by the science community. Notice that it was 'they' who put up the idea that evolution might take place by frame shifts - yet when I went to the trouble of translating that into ordinary terms, you seem to recognise that frame shifts aren't going to cut it.

If you think there is another paper that represents the idea that the navigation through 'protein space' can be made easy, let's discuss it - just as we have discussed the issue of frame shifts. There would not be the entire "third way" movement coming out of biology right now, if the picture for evolution by natural selection was so rosy.

Here is a video by Dennis Noble - one of the Third Way leaders.


Wiki gives his qualifications thus: "Denis Noble CBE FRS FRCP FMedSci is a British biologist who held the Burdon Sanderson Chair of Cardiovascular Physiology at the University of Oxford from 1984 to 2004 and was appointed Professor Emeritus and co-Director of Computational Physiology."

Now, DN isn't arguing for ID as such, but he is saying that Neo Darwinism needs replacing because it can't explain life. I suspect he won't find an adequate materialist replacement, but at least he is looking! Note also that Jerry Coyne has him in is sights - basically because he is rocking the boat regarding Neo Darwinism! DN spends the first few minutes replying directly to Jerry Coyne (maybe one of your hero's?).

You said:
For the Discoveroids to show that evolution is impossible, they have demonstrate that they know all the possible factors to put into the equation, which, IMO, is impossible.
Well, no, really both sides should present their alternative viewpoints without claiming proof unless they actually have one!

David
 
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