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Author
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Topic: The Origin of Biological Information
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David L. Hagen
Member
Member # 323
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posted 09. March 2006 23:00
Have you applied for your patent on it yet?
That is the most recognized method of identifying and publishing principles of intelligent design. If it can do what you claim, you could make a billion $.
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Doug Wedel
Member
Member # 1901
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posted 10. March 2006 08:03
quote:
Have you applied for your patent on it yet? That is the most recognized method of identifying and publishing principles of intelligent design.
I have just been granted a patent on a _completely_ unrelated matter. It took 5 years and $15,000.
So no -- and I really was trying to avoid any _grandiose_ statements about what I am doing, because I certainly don't regard it as grandiose. I am simply extending von Neumann's work. It's just that I don't know how to talk about this CSI stuff ;-)
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Stephen Wright
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Member # 195
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posted 10. March 2006 18:09
quote:
“I in my own small way am trying to do the same thing that Professor Dembski is trying to do, which is to figure out the interrelationship of information to life, and how to correctly describe and symbolize and discuss the various elementary components of the system.”
Doug,
I am enjoying following the posts in this thread. You have elicited a response from Professor D. and some well considered opinions from Micah. I am very interested in an expanded ontological view of “information”. You might look through S. Cordova’s “2nd law – 4th law” thread here on Brainstorms and especially note the diagram of Chris Beling at the end of the 6th page. Further, as to the relations of information theoretic pathways and “life” – Werner Loewenstein’s, Touchstone of Life, is an excellent exposition of the bioinformational paradigm.
This writer suggests that your “third leg”, as data, is giving the broader category of information the short-sheet treatment. IMHO, a comprehensive view of the subject needs to include three categories, each represented by formalized models of information transforms. They are communication theory, logic and thermodynamics. I would map data to communication: logic to meaning and negentropic information to thermodynamics.
Data, as bits, detail the characteristics for transfer of the non-semantic form of information and just do not cover enough information territory. They speak to the objective nature of information quantification and present as if they are a structural component. The other two categories are needed to have a complete picture: semantic meaning and changes in potential increase or decrease of functional productivity within systems.
The math formulas of Shannon and Weaver cover only this structured aspect or “outer covering” of information. While data’s digital semiotic representation is the clearest and cleanest of the math formalisms – they do not, by themselves, connect with the semantic content where “meaning” occurs. Further, they don’t completely grasp the conversion of energy to organization in a physical system that can be seen as an increase in negentropy.
Suggested in this response is a view of the subject through the visualized modeling of information objects or OOP’s (object oriented programs). If an inner logic is added, as specified relations, to the other two categories – data and entropic analysis - there is a unity established among them. I am aware this is not a normative way to think, but there is a developing school of thought to this end. An information object can be ascertained that is complete and comprehensive. The data structures can have logic as in-dwelling orientation that gives it meaning. This combination of structure and logic then can have relations to the greater environment. When this relationship is determined to be functional; then the further descriptions of thermodynamics apply. Three types of informational math are needed to describe the full range of its influence. They loosely correspond to the famous “form, fit and function” – of engineering.
Here in the early days of ISCID – Professor Dembski participated in an interactive forum. I was able to ask the simple question “do you think information is real and does it have structure?” He answered strongly to the affirmative on the first part but didn’t address the second part about structure.
What do you think of the mapping I offer and further, do you think information may have ontological structure? A naïve view of CSI can come of this approach. I will probably not be able to follow the math you promise – but appreciate the time you have taken to connect with the others here. You may find this tripartite approach to your liking – it was suggested by J. Von Neumann.
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Doug Wedel
Member
Member # 1901
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posted 10. March 2006 21:25
Stephen,
Thanks for your interesting post. Some of the things you said I _completely_ agree with, some I'm not sure about. I want to respond, but before I do I just want to clear up a couple of (to me) ambiguities.
You say
quote:
I am very interested in an expanded ontological view of “information”.
Could you tell me a little more about your use of the word "ontological" here?
And also, in your second paragraph, when you say
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This writer suggests
are you referring to the author of the Touchstone of Life (which I've read) or to yourself as the poster ;-)
Thanks.
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David L. Hagen
Member
Member # 323
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posted 11. March 2006 23:05
Doug
Regarding your questions, recommend you read:
Hubert P. Yockey Information Theory, Evolution and the Origin of Life (2005) Cambridge University Press, ISBN13 978-0-521-80293-2; ISBN-10 0-521-80293-8. Ch 11 “Randomness, complexity, the unknowable, and the impossible.” (Though with a grain of salt.)
Yockey (2005) p 166: “Decimal sequences representing some transcendental numbers” “pass standard tests for randomness” “pi and e included” (Parthia, 1962; Pincus and Kalman, 1997; Pincus and Singer, 1998; Stoneham, 1965).
Yockey (2005) p 167: “it is impossible to” “prove a given sequence to be random”. Chaitin, 2001a)
Yockey (2005) p 168: “. . .almost all long sequences are indistinguishable from random ones (Wolfram, 2002).” “Gregory Chaitin (1999, 2001a, 2001b) has proved that no procedure exists to determine whether a given sequence can be calculated from a computer program. Consequently, it is impossible to determine whether a given sequence is random or not.”
Yockey (2005) p 168: “Thus, both random sequences and highly organized ones are complex because a long algorithm is needed to describe each one (Wolfram, 2002). Information theory shows that it is fundamentally undecidable whether a given sequence has been generated by a stochastic process or by a highly organized one.”
Yockey (2005) p 171: From Turing (1936), “If the Turing machine stops, the number is computable, otherwise the number may be random and incomputable. By the same token, no computable number is random.”
Yockey exhibits curious contradictions: He gives clear examples of critical elements for life:
Yockey (p 2) Pasteur demonstrated chiral molecules are “an essential and unique element in biology.” “The existence of the genome and the genetic code divides living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” Gregor Mendel and Watson & Crick showed that “the message in the genetic information system is segregated, linear, and digital.” and “resembles an algorithmic language”. He then gives strong arguments that all methods proposed as the origin of life and information cannot explain chirality and the genetic code etc.
However, Yockey advocates Darwin’s belief “that the origin of life is unknowable or undecidable. Then he assumes naturalistic evolution as basis for all increases in complexity and argues against Intelligent Design!
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Doug Wedel
Member
Member # 1901
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posted 12. March 2006 13:55
Thanks, David, for the interesting quotes -- I have read Yockey and all the others you mention, too. The distiniction between randomness, complexity and this third thing, order, is something so important that I tried just now to address it separately in a separate post: Simplicity, Complexity & Order.
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Bruce Fast
Member
Member # 924
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posted 12. March 2006 17:40
Doug, I read this entire thread yesterday. It frustrated me beyond belief. You seem to have an idea which you are afraid to bring to light until you have established certain definitions. It seems that your concern is that you will say, "hey, my co-evolutionary algorithm demonstrates 'something'" only to have people say, you don't know what "something" is, and your algorithm doesn't demonstrate that.
I feel for you, you have caused me to believe that there is no nice, clean, precise definition for CSI. Further, it feels to me that any definition of CSI is being carefully tuned to assure that certain presumptions about CSI, namely that only "intellignece" could generate it, is being artificially protected.
(As to patenting your algorithm goes, let me present to you what I do with wonderful ideas because I am uninterested in spending $15,000 or thereabouts on pointless patents. (I have 7 patents in my name and 2 actively in the works.) You may want to look into the joys of provisional patents. (Provisional patents give you one year of protection.) I don't waste time with patent searches, or patent lawyers. I just compose very clearly, not trying to keep anything as secret, exactly what my idea is, and specifically, how to get there from here. With software the latter is often really easy, I include a listing of a program that does the thing. I send that with a check and a small form to the uspto. I believe it's about $80. At that point, my idea has real protection, and I am not broke.)
I, personally, am dying to see your co-evolutionary algorithm. I wonder if it could be presented without any specific claims as to it's significance to the design debate.
By the way, I am planning my own thread to query for a simple, "you don't have to have read the book" definition of CSI.
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Stephen Wright
Member
Member # 195
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posted 12. March 2006 21:10
quote:
“This transit from real to virtual photon, we shall see, is the bridge between the nonbiological and biological organizations in the universe; it is the window through living beings let the cosmic information in.” – Werner Loewenstein
Emphasized by Italics on Page 21 in the paperback edition of ToL - subtitled Molecular Information, Cell Communication, and the Foundations of Life.
The expression, “this writer”, was an example of my poor prose and while Loewenstein is a real writer; the suggestion was mine.
The use of the word ontological was intended to make the distinction that virtual events are as “substantial” and real as events in the material domain. The quotation above, from Touchstone of Life, addresses the foundations of life, as promised in the book’s subtitle. At issue is what life and phenomena essentially are and not about how we observe them.
Talking about information is trying. It is easy to say - such and so concept has “power” or a certain idea is “energizing”. However power, work, force or energy are physical concepts, which have precisely defined models. In an informational domain, events similar to these terms happen, so they are just metaphors. It leads to an inappropriate feeling that all information is metaphor, abstraction or vapor. It is in this sense that the word structure is applicable but only in a corresponding way.
It would be nice if there were common language expressions that made the distinction between mental work and physical work. From a transformational viewpoint, mental effort that organizes concepts is parallel to the physical effort to arrange mechanical components. Material transforms, directed by energetic vectors, determine science laws that we can observe and give assent to their predictability. The material domain and methodological materialism, as a tool to follow conserved transformations, are solid venues in the science worldview. I merely project the same status to a virtual (informational) domain and the math and science methods we have to track the vectors. Comparing these transforms, as separate analysis pathways for a single event, leads to a “depth perception” in observation. Like when Watson and Crick used both the chemical bonds and the need for information duplication - to solve the structure of DNA.
I hope to follow your demonstration. If any of these comments of mine have validity, the process will follow the route where material transforms gradually arrange virtual potentials. During the process, a logical intent or purpose will be inserted into the data structure or information object. Now, with a logical purpose indwelling, this virtual potential can manifest CSI by retreiving it as design.
[ 12. March 2006, 21:12: Message edited by: Stephen Wright ]
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Doug Wedel
Member
Member # 1901
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posted 13. March 2006 16:15
Bruce,
Thanks for your post.
quote:
Doug, I read this entire thread yesterday. It frustrated me beyond belief. You seem to have an idea which you are afraid to bring to light until you have established certain definitions.
It's not that I'm "afraid" -- I just want to be careful where I throw my pearls ;-)
Actually, while I, like you, found the process rather frustrating, nevertheless, there is (almost always) good will and high intelligence to be found in here, and this grinding back and forth on matters of definition and exact precise meaning can be of great value sometimes.
Thanks for your thoughts on patenting -- interesting!
quote:
I, personally, am dying to see your co-evolutionary algorithm. I wonder if it could be presented without any specific claims as to it's significance to the design debate.
I can certainly present it using my own definitions ;-), but I just don't want to play any "gotcha games".
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Bruce Fast
Member
Member # 924
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posted 13. March 2006 16:22
Please do. I think your sincerity is established. Further, I think that clear concise, and established definitions for the terminology you are using are not established, therefore your definitions are as adequate as the definition you ascribe to them.
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Doug Wedel
Member
Member # 1901
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posted 13. March 2006 16:34
Stephen,
Thanks for the clarifications. The quote from Lowenstein is striking
quote:
This transit from real to virtual photon, we shall see, is the bridge between the nonbiological and biological organizations in the universe; it is the window through living beings let the cosmic information in.
But I wonder, why does he give such exclusive status to the virtual photon? There are "virtual smells" in the chaotic swirl of olfactory gases which must be transduced by one of the thousand or so discrete smell receptors. There are "virtual sounds" which must be picked out from background noise. It seems to me that there are a handful of I/O channels that life uses in which patterns of physical signals are transduced into data and then processed (data mined to use the buzz words) for meaningful patterns.
quote:
Talking about information is trying. It is easy to say - such and so concept has “power” or a certain idea is “energizing”. However power, work, force or energy are physical concepts, which have precisely defined models. In an informational domain, events similar to these terms happen, so they are just metaphors. It leads to an inappropriate feeling that all information is metaphor, abstraction or vapor. It is in this sense that the word structure is applicable but only in a corresponding way.
I strongly sympathize with your view here. I view the "work done" by information as influencing decisions made by an organism. Hence, information has an impact on the evolutionary probabilities of the organism (survival/reproduction). This is a very different kind of "work" that what is done in terms of "force over time."
quote:
It would be nice if there were common language expressions that made the distinction between mental work and physical work. From a transformational viewpoint, mental effort that organizes concepts is parallel to the physical effort to arrange mechanical components. Material transforms, directed by energetic vectors, determine science laws that we can observe and give assent to their predictability. The material domain and methodological materialism, as a tool to follow conserved transformations, are solid venues in the science worldview. I merely project the same status to a virtual (informational) domain and the math and science methods we have to track the vectors. Comparing these transforms, as separate analysis pathways for a single event, leads to a “depth perception” in observation. Like when Watson and Crick used both the chemical bonds and the need for information duplication - to solve the structure of DNA.
I find these remarks very intriguing but somewhat elusive ;-) I very much like your idea that the mental effort involved in forming concepts can be broken down into its parts and analyzed as a transactional process.
quote:
I hope to follow your demonstration. If any of these comments of mine have validity, the process will follow the route where material transforms gradually arrange virtual potentials. During the process, a logical intent or purpose will be inserted into the data structure or information object. Now, with a logical purpose indwelling, this virtual potential can manifest CSI by retreiving it as design.
It's amazing how many different "rubrics" there are for talking about this stuff! I do think you are on to something, but I'm not sure about the statement "During the process a logical intent or purpose will be inserted into the data structure or information object." Could you clarify a little?
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Doug Wedel
Member
Member # 1901
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posted 13. March 2006 19:10
Stephen,
I'm finally now responding to your very interesting original post!
When you say, speaking of the third leg of my stool, the DATA leg...
quote:
that your “third leg”, as data, is giving the broader category of information the short-sheet treatment. IMHO, a comprehensive view of the subject needs to include three categories, each represented by formalized models of information transforms. They are communication theory, logic and thermodynamics. I would map data to communication: logic to meaning and negentropic information to thermodynamics.
You think the fundamental name of the "stuff" should be "information", is that it, as in
MATTER - ENERGY - INFORMATION
I thought DATA was more appropriate here at this level of abstraction than INFORMATION. Data is the raw stuff, like matter and energy. Like matter and energy, it "manifests" in a number of different discrete forms, eg. visual data, auditory data, conceptual data, et cetera.
But maybe I'm wrong ;-) Maybe data is more like the "atom" in matter, the irreducible systemic component.
Let me try to briefly address the three subdomains you articulate in the comment above -- communication theory, logic, and thermodynamics.
As I am coming to view biological information processing in the following steps:
1. Physical signals -- photons, sound waves, molecules -- physically impinge on the organism. This "impingement" comes at a thermodynamic cost, i.e. the cost of the rhodopsin metabolic function that first registers the signal.
2. The signal is transduced into data. This clearly takes more energy stored in ATP in the cell.
3. Initial processing occurs to detect clusters of data which may contain patterns of significance. Here, we are getting into thermodynamic mysteries, because we have no idea how the organism stores data, much less processes it, but it seems safe to conclude that any kind of switch setting and/or switch reading takes some quantum of thermodynamical energy.
4. Data clusters of interest are now separated from background noise and somehow encoded for transmission to the brain centers corresponding to the input device, eg. visual cortex.
5. Further processing is required to refine the incoming pattern into a form that it can be used effectively to search through a pattern library.
6. If a pattern match is found, the pattern is evaluated.
7. Depending on the evaluation function, the pattern may directly influence the organism's choice at one node in the vast hyperbranching tree of options in real organic life.
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Data, as bits, detail the characteristics for transfer of the non-semantic form of information and just do not cover enough information territory. They speak to the objective nature of information quantification and present as if they are a structural component. The other two categories are needed to have a complete picture: semantic meaning and changes in potential increase or decrease of functional productivity within systems.
You see "data" as a non-semantic "objective" form of information. I see information as a compound thing that is built up only in part from input data.
I totally agree with you about the importance of emphasizing semantics. One aspect of my project is to show how to automata the acquisition of information that contains what we could call "semantics", i.e. deep structure.
quote:
The math formulas of Shannon and Weaver cover only this structured aspect or “outer covering” of information. While data’s digital semiotic representation is the clearest and cleanest of the math formalisms – they do not, by themselves, connect with the semantic content where “meaning” occurs. Further, they don’t completely grasp the conversion of energy to organization in a physical system that can be seen as an increase in negentropy.
You are spot on here. Shannon's formulas capture only the most superficial possible "order", the kind of order that distinguishes all messages with meaning from pure random noise. Kolmagorov, et al, opened the doors for compression based on _understanding_ and _meaning_, but they did not fully accommodate these ideas in their system, leaving us with an Aglorithmic Information Theory in which SIMPLICITY = ORDER.
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Suggested in this response is a view of the subject through the visualized modeling of information objects or OOP’s (object oriented programs).
I like your suggestion, and indeed, it is a very important part of the little proof I am offering. As you may know, from the very earliest days of the cellular automaton, in the days when Stanislaw Ulam was playing around on one of the world's first computers in Los Alamos, was to create a visual mathematical matrix so that he could see on the computer screen a visualization of hte outcomes of his formulas.
Down through the subsequent half-century almost all of us who have become deeply ensared in the cellular automata briar patch have been lured there by the ability to do mathematics visually.
What is Wolfram's book "A New Kind of Science," if not a paean to the visualization of symbolic logic?
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What do you think of the mapping I offer and further, do you think information may have ontological structure?
I very much like your analysis although more debate is required concerning the appropriate abstractions.
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You may find this tripartite approach to your liking – it was suggested by J. Von Neumann.
Thank you for pointing that out. I probably got my ideas first from von Neumann. I have spent a _lot_ of time with his profound ideas and his bracing way of thinking the unthinkable.
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KBC1963
Member
Member # 1868
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posted 17. March 2006 23:25
Might I put in a few words from my understanding of what CSI is and what separates it from random formations.
Any randomly generated string of numbers or on offs hold the potential to mean something, the key to determining whether it has real information content is the point when it is consistently understood by something separate from itself. Intelligent information requires a consistent formation to be consistently acted upon by a separate formation.
I see chemistry and chemicals as low level bits of information that consistently form and show consistent reactions to these forms. Now at this level all actions that occur during the interaction of two distinct chemicals we can call 're'actionary and their only constraints are normally occuring forces and proximity.
In contrast complex information provided by a certain form which then interacts with a separate form initiates a 'pro' active action by the second form that is unrelated to the informational first form.
In essence when we see two forms interact and we can see consistently, an action occur involving only the second form and it is the same after each interaction of the two forms then we can conclude that the first form provided information that was understood and acted upon by the second form. The proof of the information being complex and specified would be the consistent action being performed by the second form that would have no logical natural reason to perform that action.
Evolution posits that all that exists is a result of reactionary actions that eventually buildup into proactive forms by small changes over time. The problem with this line of thinking is that, where information is involved there must be the informational form that changes or grows larger and a second form that can continue to understand the information as it changes and alters its actions accordingly.
This relationship between the informational form and acting form is what I believe is irreducibly complex. They must at all times remain in sync in order for information exchange to occur and elicit reliable actions on the part of the second form.
This relationship is what I consider to equal 'control'.
Consider if you will the ribosome / DNA relationship. The DNA acts as the informational form and the ribosome is the proactionary form. The ribosome never affects the DNA so its relationship to DNA is not 're'actionary, it consistently performs actions that cannot logically be infered as a result of these two forms interacting thus we can conclude complex specified informations presence. The actions of the ribosome being proactive confirm the presence of information. The sum of the actions observed reveal the complexity of the information being transfered and the observation that the ribosome performs these actions consistently confirms that the information is specified.
I would think that the only way to test to see if natural causes can acheive this type of relationship without being constrained intelligently would be to have two separate computer programs that begin with small randomly generated chemical forms that can acheive this type of relationship as displayed by the ribosome / DNA in the timeframe prescribed for the life of the chemical forms it would be required to imitate. We must never lose sight of the fact that the more complex the chemical form is the more suceptible it is to naturally occuring degrading forces. Only after the information level reaches an amount that equals a closed balanced system such as the cell will the informational form enjoy a respite from these degrading influences and possibly go on to evolve in an evolutionary defined way.
I hope my post is in line with the reasonings and intents of the founders of CSI and that it in some way helps to relay the monumental events that would need to happen in order for CSI to naturally occur. In my own reasoning there would be no way conceivable for anything to ever find a natural path to acheive this type of relationship as the actionary form must always 'evolve' in a highly constrained way to match the informational form and acheive continuity of existence (replication).
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John A. Davison
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Member # 1425
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posted 18. March 2006 11:03
I think this comment from Grasse may be of some interest.
"But according to Darwinian doctrine and Crick's central dogma, DNA is not only the depository and distributor of the information but its SOLE CREATOR. I do not believe this to be true."
Evolution of Living Organisms, page 224. (his emphasis).
My own prejudice is that the Big Front Loader (BFL) loaded an unknown number of intitial forms an unknown number of times with all the necessary information to provide for all of evolution and all of ontogeny. I see no role whatsoever for the environment in any of this beyond that of acting as a releaser for endogenous latent and highly specified information. I am not alone in this view.
"Evolution is in a great measure an unfolding of pre-existing rudiments."
Leo Berg, Nomogenesis, page 406
I would modify this by substituting "was" for "is" and for "in a great measure" I would substitute "entirely."
I believe that everything we are now learning favors this interpretation.
"A past evolution is undeniable. A present evolution is undemonstrable."
John A. Davison
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