Darwin Unhinged: The Bugs in Evolution

Well it is a spiral chain of nucleotide bases, and in itself is nothing more. I mean it is only active in the sense that other molecules - proteins of various sorts -interact with it.

It is linear in the same sense that a human sentence is linear.

You may be referring to the definition of a gene as a linear stretch of DNA.  That is an abstract method to get to a "unit" of heredity.  But the action of the electro-chemistry in the DNA/RNA/Ribosome system of coding is best described as a complex and dynamic system.  The unit of a gene has itself evolved

My points are all aimed not at the chemical transformations - but what transformations of information objects and functional meanings are happening.  Look, the background for what is dynamic and what is linear in terms of the math equations is far out of my reach.  (and it is a math question)  First why the concept is dated in modern times.  

 Abstract
This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.

Keywords: function; gene; gene networks; regulation; structure; theory.

Copyright © 2017 by the Genetics Society of America.

Here is stuff at the cutting edge that gets me interested.  Twisted DNA used by nature to solve problems.  Crazy silly for a master design; brilliant as an on the fly adaptation.  My story is mind detected this use in the chemical/physical probabilities and then took a while to make function with meaning.

 Left-Handed DNA Has a Biological Role Within a Dynamic Genetic Code
In 1970, biochemist Robert Wells of the University of Alabama at Birmingham saw something strange in his X-ray images of a new synthetic DNA polymer. The DNA molecule was composed of the traditional sugar backbones and nucleotide pairs, but rather than the well-known right-handed spiral of the double helix structure, famously discovered by Watson and Crick in 1953, Wells’s polymer spiraled in the opposite direction, giving it a zigzag appearance.

Whether this bizarre form of DNA existed in cells and had any function, and what that might be, was hotly debated for nearly half a century. But research has recently confirmed its biological relevance. So-called Z-DNA is now thought to play roles in cancer and autoimmune diseases, and last year scientists confirmed its link to three inherited neurological disorders. Today, molecular biologists are beginning to understand that certain stretches of DNA can flip from the right- to the left-handed conformation as part of a dynamic code that controls how some RNA transcripts are edited. The hunt is now on to discover drugs that could target Z-DNA and the proteins that bind to it, in order to manipulate the expression of local genes.

https://www.the-scientist.com/features/l...code-67558

I have to address this because it is such a crucial fact - DNA is not linear -  as a potential source of a chemical signal or in its activity as information.


Stay with sources like James Tour.  Is this something he said?

The DNA code stored in a gene for a protein is necessarily linear. Certainly the physical arrangement of the nucleotide sequence in the gene may not be entirely linear.
From the Britannica and other sources:

Genetic code is the sequence of nucleotides in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) that determines the amino acid sequence of proteins. Though the linear sequence of nucleotides in DNA contains the information for protein sequences, proteins are not made directly from DNA.

During transcription, the enzyme RNA polymerase uses DNA as a template to produce a pre-mRNA transcript. The pre-mRNA is processed to form a mature mRNA molecule that can be translated to build the protein molecule (polypeptide) encoded by the original gene. A protein is the resulting linear polymer of amino acids linked together by peptide bonds.

The DNA code stored in a gene for a protein is necessarily linear. Certainly the physical arrangement of the nucleotide sequence in the gene may not be entirely linear.
From the Britannica and other sources:

ok -- on one hand - papers from the last couple of years by teams of scientists --- OR Encyclopedia Britannica with a dated report.

Yes much of the primary instructions are linear, but much - if not most - is open to dynamic responses.  Please find below a list of other signal pathways found as of 20 years ago.

 The discovery of intragenic recombination in the early 1940s and the establishment of DNA as the physical basis of inheritance led to the neoclassical concept of the gene, which prevailed until the 1970s. In this view the gene (or cistron, as it was called then) was subdivided into its constituent parts, mutons and recons, identified as nucleotides. Each cistron was believed to be responsible for the synthesis of a single mRNA and hence for one polypeptide. This colinearity hypothesis prevailed from 1955 to the 1970s. Starting from the early 1970s, DNA technologies have led to the modern period of gene conceptualization, wherein none of the classical or neoclassical criteria are sufficient to define a gene. Modern discoveries include those of repeated genes, split genes and alternative splicing, assembled genes, overlapping genes, transposable genes, complex promoters, multiple polyadenylation sites, polyprotein genes, editing of the primary transcript, and nested genes. 

We are currently left with a rather abstract, open, and generalized concept of the gene, even though our comprehension of the structure and organization of the genetic material has greatly increased.

https://pubmed.ncbi.nlm.nih.gov/7688132/
This has been the case for 50 years!  Why as a supposed defender of ID, do you always respond with materialist arguments ????

I don't think it would be that interesting.  This "Professor Dave" appears to be an internet personality and as such I don't see him as a SME.

I suppose it annoys me that people like him add the prefix 'professor' and don't even identify themselves, then present a really shallow response to a world famous chemistry professor.

I'd much rather see a thoughtful scientist working in and supportive of abiogensis respond to Tour's criticisms.  As you find them compelling, I do as well albeit I am a true layman when it comes to the related sciences (e.g., organic chem, etc.).

Well so would I, but a thoughtful man knows when he would be beaten.

I wish there were more debates on topics like this. 

I would like that too - if academics were expected to be up for debate (with exceptions for people like Stephen Hawkins) if they verbally attack someone else, I think it would help a lot.

ok -- on one hand - papers from the last couple of years by teams of scientists --- OR Encyclopedia Britannica with a dated report.

Yes much of the primary instructions are linear, but much - if not most - is open to dynamic responses.  Please find below a list of other signal pathways found as of 20 years ago.


https://pubmed.ncbi.nlm.nih.gov/7688132/
This has been the case for 50 years!  Why as a supposed defender of ID, do you always respond with materialist arguments ????

Because none of the above changes the fundamental problem of where the information came from. Each of the things you cite are complications, and relate to the all-important information, but they don't create the information.

Suppose someone marketed a program that, given a few keywords, would write a high quality novel of 1000+ pages, and each novel it wrote would be distinct.

Would you be satisfied that this wasn't a trick, with a human involved in the loop somewhere?

Because none of the above changes the fundamental problem of where the information came from. Each of the things you cite are complications, and relate to the all-important information, but they don't create the information.

Can we frame this in terms of science?  If we found an object - say a multilayer printed circuit board - we can ask how it was designed and built.  The glass, epoxy, copper and tin are all molecules that are defined.  The processes of drilling, imaging and plating have to be in its history.  We have information from a bill of materials and processes instructions that define physical construction.

Are they the same level of design as the logic gates of computation???  There is craftmanship in making electronic devises, focusing attention to specific regulation of measurable current flow.

The design of a PWB (pcb) starts with a Truth Table and the logic gates to actualize command outputs.  A level of design that is not physical, but able to be physically constructed.

The bio-information for evolution, comes from real-world events that are recipient forms of mind's decisions and their intentional outcomes to thrive and survive.  You want to talk about the moldy old arguments of Darwinism about material "genes".

I want to talk about how living things designed themselves by changing the probable information in the past and future to command and control the present.  Before eating was the desire to grow.

There is no science argument against a Divine Plan.  Nor is there science to support it.  Nature is pretty amazing in how it supports life and mind.

There is no science argument against a Divine Plan.  Nor is there science to support it.

This, I absolutely agree with and it's something that bugs me when people on both sides of a religion v science debate think that science proves something.  However, science very often exposes holes in the written-in-stone certainties that many scientists develop while thinking they are being totally objective.  It also challenges many tenets of faith dogma, although it hasn't come anywhere near to shaking Zion at its core yet.  

Can we frame this in terms of science?  If we found an object - say a multilayer printed circuit board - we can ask how it was designed and built.  The glass, epoxy, copper and tin are all molecules that are defined.  The processes of drilling, imaging and plating have to be in its history.  We have information from a bill of materials and processes instructions that define physical construction.

Are they the same level of design as the logic gates of computation???  There is craftmanship in making electronic devises, focusing attention to specific regulation of measurable current flow.

The design of a PWB (pcb) starts with a Truth Table and the logic gates to actualize command outputs.  A level of design that is not physical, but able to be physically constructed.

Well that cuts to the heart of the matter. Say an archaeologist dug up some PCBs, and he had a good enough microscope to see the details on the circuit board, and maybe even what was in the chips. I don't think he would talk about complex geo-information information flows or whatever, I think he would say, "Something made this!".

Now suppose that scientists back in Darwin's day and earlier had been able to see clearly what is really in a cell - right down to the DNA - I think they would have said the same thing, except that they would have used the word 'God' to avoid what happened to Giordano Bruno.

The bio-information for evolution, comes from real-world events that are recipient forms of mind's decisions and their intentional outcomes to thrive and survive. 

How can it? I mean, knowing that your physiology is getting poisoned by ethanol (say), doesn't translate into the understanding how to solve the problem by creating an enzyme alcohol dhydrogenase to metabolise ethanol.

You want to talk about the moldy old arguments of Darwinism about material "genes".

I only want to talk about Darwin, because I think he enters into the politics of science which dictates that scientists must not say that RM+NS is dead - certainly not in words that could attract a mass audience. Don't forget that in the US, schools have been more or less forbidden to teach alternatives to RM+NS. How would the science establishment cope with the loss of face if the truth were realised?

So the Third Way cloaks what it wants to say, so as not to appear too radical.

There is no science argument against a Divine Plan.  Nor is there science to support it.  Nature is pretty amazing in how it supports life and mind.

Well actually, there is quite a lot of science behind the idea that life was planned by one or more disembodied consciousnesses of some sort. A lot of the planning must have happened before there was life on earth, so the entities that did that work must have been disembodied.

David

So the Third Way cloaks what it wants to say, so as not to appear too radical.

Well actually, there is quite a lot of science behind the idea that life was planned by one or more disembodied consciousnesses of some sort. A lot of the planning must have happened before there was life on earth, so the entities that did that work must have been disembodied.

David

Well, actually you are imagining a narrative about Third Way, but in fact there is no political focus for religion.  The founders are aging scientists who have changed the landscapes in their fields and want to assert their stamp on Academia .  If you think there is cloaking - please point it out specifically.

Mind in an independent environment from a physical manifestation is predicted by my personal naïve version of IR.  It asserts information processing to organize reality's probabilities into a wave function that could select the one decohering into life and embodiment.

A superposition with real world structures of:  life & "not life yet" as possible outcomes.

Well, actually you are imagining a narrative about Third Way, but in fact there is no political focus for religion.  The founders are aging scientists who have changed the landscapes in their fields and want to assert their stamp on Academia .  If you think there is cloaking - please point it out specifically.

Mind in an independent environment from a physical manifestation is predicted by my personal naïve version of IR.  It asserts information processing to organize reality's probabilities into a wave function that could select the one decohering into life and embodiment.

A superposition with real world structures of:  life & "not life yet" as possible outcomes.

I think you would agree that Neo-Darwinism has remained the official explanation for evolution for many years, and I don't think you would disagree with my feeling that it should back off and let other people - such as the Third Way and the ID group - make their cases.

People pretend Neo-Darwinism is a sound theory, when they know damn well it is not - indeed you criticised me for going on about mouldy old Darwin - because you too know that theory is dead. However unfortunately they have to write in ways that avoid explicitly rejecting NeoDarwinism. So consider this quote from Torday and Miller:

Chapter 2: A highly contentious evolutionary debate has existed since Darwin’s
seminal “On the Origin of Species” in 1859. For many decades, the arguments were
dominated by skepticism regarding the role of natural selection. The rediscovery of
the pioneering work on heredity by Gregor Mendel in the early twentieth century
led to a general unification of natural selection with the new science of genetics.
Although this integrated approach that focuses on selection has gripped evolutionary
biology since the mid-twentieth century, continuous adjustments now lead to a
new approach through cognition-based cellular–molecular evolution.

You can't easily discern that they are rejecting RM+NS, as opposed maybe to extending it!

Then consider this:

Chapter 3: Although its origin is unknown, cognition is both central to life and
embodied within the basic cellular form.

The traditional biological view is that cognition is a process that happens exclusively in the brain, but here they are claiming that cognition occurs at the cellular level (something I agree about) - which is total heresy in conventional biology.

You yourself described a colleague who was almost sacked for publishing a book about Lamark, so you know full well the pressure on biologists to conform.

So an explicit (uncloaked) version of that might read:

We reject the traditional theory of Neo-Darwinism as a grossly inadequate explanation of evolution, and claim that organisms evolve using cognitive processes that seem to be present in every cell.
These cognitive processes don't require a brain, and so bring into question the conventional view of consciousness.

Isn't that what they want to say? If so, why don't they say it?