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The theory of Darwinian evolution by natural selection is not the best description of reality

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A theory which, different from natural selection, Instead says that major evolutionary steps occur from DNA rearrangements which are carried out by cellular genetic engineering systems that are operating non-randomly.

This is not an intelligent design debate. If you wanted to go a step further of "how", Then I'd take the intelligent design route citing a few areas of cellular biology. However, that would be a different debate.

For this debate I'm simply taking the view of that evolution has been driven by cellular systems of natural, Non-random genetic engineering is a better theory than the defined natural selection.

One comparison between the two can be seen in the idea of mutations. Natural selection says the random mutations which are most favorable are passed on. The opposing theory would instead say that most mutations are not random. They result from the mis-pairing during DNA replication and the need to preserve a protein's function given a non-random read-write process.

Round 1
Pro
This discussion could go in different directions and we only have a small number of rounds. 

Ill start with a general overview and some points in contention with the idea of survival of the fittest by natural selection after random gene mutations. Once I get a feel for where you're coming from I can focus this down and apply more relevant info and sources. I think this theory has a lot of merit, but I went to school for physics, astronomy, and math. This is out of my wheelhouse and depth of knowledge. I hope still a discussion worth having. Although I make no claims of rigor. I'm simply doing my best here with what I've managed to learn and find from different scholarly sources over a long period of time. 

A high level view and summary of the claimed non-random gene mutation process can start as follows:

  • DNA operates as a type of data storage medium.
For my organismal generations: Within organismal generations, there's genetic storage in local
DNA sequences and long range chromosome structure.
There is epigenetic storage in covalent
modifications and stable chromatin configurations;
Within a single cell cycle there is computational storage in
meta-stable nucleoprotein complexes. 


  • DNA in addition to the data storage and "reading" ability has a sort of writing ability too. Like cd burning back in the day. Not only can we read cds but drives came out which allowed us to read and write (RW from the cd days haha) onto the storage medium. 
Genomes have different kinds of functional
information. Besides coding sequences, sort of data files in a way, determining the primary structure of
 RNA and various protein molecules, there is information for other essential processes such as packaging DNA molecules within the nucleoid or
nucleus and the replication of DNA and transmission of copies to progeny cells. 


This read write ability is driven by the non random cellular processes.


You can formulate a series of basic ideas that lead to seeing evolution as something like a systems engineering problem.

1. Genomes are formatted by repetitive elements. Then, they are organized in a hierarchy for multiple storage
 and transmission functions.
2. Major evolutionary steps occur by DNA rearrangements which arise in sophisticated, non-random genetic
engineering systems within the cell. 
3. Significant evolutionary jumps can when when the repetitive elements are altered which guide the formatting with genome system
architecture. This is beyond simply altering protein and RNA
coding sequences as in natural design. 
4. Evolutionary change is responsive to biological inputs, with respect to locating and timing of DNA rearrangements, which is regulated by cellular natural genetic engineering. 


The gene doesn’t have a special causal role. There are feedback loops from each and to each system. It’s based on a hierarchy and contains these different systems at each level. 










Con
Preface

Hello again! Hope you're doing well in these weird times! All that jazz. We've had a debate previously, so I'm going to mostly skip the introduction segment. To the reader - if you have any tips/advice in debate structure/rhetoric that would be appreciated. I'm still learning the nuances and jargon of DebateArt.

There are some truly ugly scientific terms in this debate. I'll do my best to define all the crazy terms used in my arguments in a dedicated category under Sources.

I apologise in advance for the size of this round. There was a lot to cover.

Definitions

There are several variations of the "theory of evolution" - the modern synthesis, Pigliucci's extended evolutionary synthesis, Koonin's post modern synthesis, etc, that could be said to be a better description of reality than Darwinism specifically. If PRO were to take the position that the modern synthesis, for example, is a better theory, I would have little choice but to concede. (For arguing that a 151 year old theory is superior to the modern version would be... difficult.)

However, the contention addressed in this debate arises not from the clash between these syntheses - but instead from the concept that:

"...evolution has been driven by ... non-random genetic engineering..."
...which is something that most if not all of the Darwin-based theories disagree with. In that sense, I propose the following (admittedly ugly) definition:

  • "Darwinian Evolution", or "Darwinism": The theory of evolution postulated by Darwin, in which all species of organisms arise and develop through the natural selection of small, inherited variations that increase the individual's ability to compete, survive, and reproduce.
For almost all other definitions, CON will defer to Merriam Webster. That said, the definition for "mutation" is extraordinarily verbose and unnecessarily technical, so it has been paraphrased. Link provided for full definition.

  • "Natural Selection": A natural process that results in the survival and reproductive success of individuals or groups best adjusted to their environment and that leads to the perpetuation of genetic qualities best suited to that particular environment. [1]
  • "Mutation": ... permanent change in hereditary material that involves either a change in chromosome structure or number ..., or a change in the nucleotide sequence of a gene's codons ... that occurs either in germ cells or in somatic cells ...". [2]
Structure

R1: Preface, Definitions, Structure, BoP, Rebuttal, Point 1.
R2: Rebuttal, Point 2.
R3: Rebuttal, Point 3.
R4: Rebuttal, Conclusion.

Burden of Proof *

In this case, as the instigator suggests a significant departure from a widely accepted scientific theory - and thus the burden of proof falls to PRO. 

  • PRO seeks to prove that evolution is guided by non-random genetic engineering. 
  • CON seeks to dispute PRO's assertion and reaffirm that Darwinism - rather, modern Darwinism, is the "best" available theory.
* If there's an issue with the BoP please contact me, UpholdingTheFaith. I'm still a little iffy on who is supposed to set forward the BoP, if it's necessary to be set forward, etc., and I'd be happy to rectify any issues.

Rebuttal

For my organismal generations: Within organismal generations, there's genetic storage in local
DNA sequences and long range chromosome structure.
There is epigenetic storage in covalent
modifications and stable chromatin configurations;
Within a single cell cycle there is computational storage in
meta-stable nucleoprotein complexes.
I say this as respectfully as I can - this is nigh nonsensical. The use of "my" - along with the poem-like spacing and lack of citation - seems to imply that this is something that you've written personally. I'm going to ignore this bit for the following reasons:

  1. No citation.
  2. Six undefined highly abnormal terms.
  3. Relevance to the topic is extremely unclear.
  4. Red herring: "a seemingly plausible, though ultimately irrelevant, diversionary tactic." [3]
"DNA in addition to the data storage and "reading" ability has a sort of writing ability too. Like cd burning back in the day. Not only can we read cds but drives came out which allowed us to read and write ... onto the storage medium."
Are you referring to protein synthesis or the manner in which the DNA sequence can change via mutation? Or mitosis? Or meiosis?

Genomes have different kinds of functional information. Besides coding sequences, sort of data files in a way, determining the primary structure of
 RNA and various protein molecules, there is information for other essential processes such as packaging DNA molecules within the nucleoid or
nucleus and the replication of DNA and transmission of copies to progeny cells. 
Again - a source would be helpful.

This read write ability is driven by the non random cellular processes.
Equating the existence of "non random cellular processes" that occur within the cell to evidence of "non-random evolution" is blatantly fallacious. Erythrocytes carry oxygen, osteoblasts build bone, macrophages consume pathogens - these processes are self-evidently not done randomly.

2. Major evolutionary steps occur by DNA rearrangements which arise in sophisticated, non-random genetic engineering systems within the cell. 
No evidence provided to support this claim - "non-random genetic engineering systems" are unreferenced and unmentioned.

3. Significant evolutionary jumps can when when the repetitive elements are altered which guide the formatting with genome system architecture. This is beyond simply altering protein and RNA coding sequences as in natural design. 
No evidence of "evolutionary jumps" provided. Evolution isn't known for its speed, [4] and the phrase "jump" seems to imply that PRO's theory of evolution occurs rapidly, which contradicts a wealth of documented evidence. [5

4. Evolutionary change is responsive to biological inputs, with respect to locating and timing of DNA rearrangements, which is regulated by cellular natural genetic engineering. 
No evidence provided to support this claim.

The gene doesn’t have a special causal role. There are feedback loops from each and to each system. It’s based on a hierarchy and contains these different systems at each level. 
  1. What systems?
  2. What feedback loops?
  3. What hierarchy?
  4. What levels?
  5. What gene?
Concluding Rebuttal Statement:

Aside from vague claims and unsupported statements, no discernible argument has been made in favour of the position of PRO.

CON Point 1: Darwinism as an Accurate Description of Reality

[In order to meet the BoP - to show that Darwinism is the best available theory - my first round is dedicated to show that it is, at least, description of reality.]

Sub-points: a) Convergent Evolution, b) Domestic Evolution.

a) "Convergent Evolution" refers to when two species of different lineages develop the same trait, absent in those lineages. There are multiple examples of this phenomena - where an arctic fox and an arctic bird develop a similar colour independently, when dolphins and sharks develop similar fin shapes - or even when songbirds from around the world develop a similar brain structure. [6]

The process of convergent evolution is an interesting illustration of evolution - and a perfect example of how the principles of Darwinism fit with reality. In the case of the arctic animals - a common selective pressure is present. The less visible the animal, the more likely they are to survive predators, and go on to reproduce. Despite being genetically dissimilar - bird and fox - the same colouring is evolved. 

b) An interesting facet of evolution is domestic evolution  - where a horse's selection pressure becomes its speed or endurance, or a dog's selection pressure becomes its ability to manage sheep, or simply 'be cute'. For instance: gradually, wolves - more specifically, the ancestor of modern day dogs, which we would likely call wolves - through small inherited variations - have become continually more docile and suited for human companionship. [7] This isn't a result of a selection pressure imposed by nature - but rather by the human race.

The more 'acceptable' the dog - mutations of colour, size, shape, demeanour - the more likely it is to be bred and reproduce. We manipulate Darwinism here deliberately - breeding animals for a range of purposes. I hardly need sources to say that domestic cats, cows, chickens, sheep, dogs, etc, aren't a result of nature.

Will be continued in my R2 - out of space. Lengthy rebuttal.

Sources

[1]: Regarding the definition of "Natural Selection", https://www.merriam-webster.com/dictionary/natural%20selection
[2]: Regarding the definition of "Mutation", https://www.merriam-webster.com/dictionary/mutation
[3]: Regarding the "red herring", https://en.wikipedia.org/wiki/Red_herring
[4]: Regarding the speed of evolution, P3, https://humanorigins.si.edu/education/introduction-human-evolution
[5]: Regarding evidence of gradual evolution, see Fossil Record, Common Structures, Distribution of Species, https://www.ncbi.nlm.nih.gov/books/NBK230201/
[6]: Songbird brain structure, (So awesome!), https://jarvislab.net/Publications/Evo_Vocal_Brain_Structures.pdf

Terms

Protein Synthesis: Production of new proteins. DNA is converted into RNA in the transcription phase, the protein is built by a ribosome in the translation - a component of almost all cells, what is referred to as an "organelle". (There's a hell of a lot more to it, but that's the gist.)
Erythrocyte: Blood cell.
Osteoblast: Bone-synthesising cell.
Macrophage: Literally "large eaters" in Greek, immune system cell.
Mitosis: Somatic (non-sex) cell becomes two identical cells.
Meiosis: Sex cell becomes four non-identical daughter cells.
Round 2
Pro
Perhaps my topic was too big especially given my depth of knowledge. Also. Something to remember for next time and I will call out in the description. Physics and astronomy i can go very deep on. Evolutionary biology not so much. I apologize if I came off as someone ready to have a upper level collegiate understanding here. I have perhaps a intro college level understand. With a gap of many years in using any of these terms, it's a slow process for this level of rigor. 

The theory im citing has some profound conclusions, one of which is that this idea of very long time periods is not only not necessary but shown to be incorrect by observation. That would be a big difference. There's many others. I'm seeking to better understand through a comparison that perhaps two college freshman could talk out. Cosmology, I can make calculus based arguments haha. 

Two things, we lost our babysitter for the next 3 days and so I'll have to push some work stuff to tonight and will not have anywhere near enough time to do this argument justice. 

My interest started after I found out about articles like this that were coming out:

Then a group of over 300 credentialed scientists got together in London in 2016 to hash it out. I followed some of that and was very interested  especially given the amount of data and experiments which seem to greatly conflict with the Darwinian ideas. 



Which leads to a book and paper which I've based most of trying to discuss this idea on, although clearly out of my league. I never had an issue talking astronomy things when the other had no basis in mathematics. It just meant the conversations were less cited and more high level discussions. Again, burden on me to define in debate description. Im learning a lot about what I dont know about what I know so thank you!

Check out this paper as my next argument if you'd like I suppose. If you find a flaw im not understanding is a flaw (often how those astronomy discussions ended) id really appreciate it. 

My current depth of knowledge as a basis, this theory looks well substantiated and more consistent with observation. It also explains a lot of the out of place observations that Darwin's theory doesn't account for like McClintock's findings in the 40s. 

Well. I thought compelling. I wouldn't normally have brought it here but that conference in London seemed to push for a new paradigm in the same way that I've seen it happen in astronomy over and over again. 


Main points from above. I used this paper to try and bolster some terminology above but was rushed and obviously failed. Either way thanks for your patience. If you don't want to review that paper I'm cool to run out the rounds and concede. Your call. I'm trying to learn and understand. I need to go to reddit or something, but the audience is far less rigorous there. We need to invent a new place. Discuss it out with rigor.com lol




Con
Note

"Two things, we lost our babysitter for the next 3 days and so I'll have to push some work stuff to tonight and will not have anywhere near enough time to do this argument justice."
Please don't stress - if you run out of time just waive a round and I'll do the same. 

Rebuttal - Addressing the Sources

Reviewing the sources that PRO has provided - specifically the third one, "A 21st Century View of Evolution", the paragraph that I criticised becomes drastically more clear. Evidently that was copy and pasted from there - and the weird poem-like spacing is a result of the original format being in dot point. (The context of "three different time scales" when included makes a lot more sense.) For the reader;

"One of the keys to a 21st Century vision of how genomes operate is to think about DNA as a data storage medium that operates over three different time scales:

  • Many organismal generations: genetic storage in local DNA sequences and long range chromosome structure;
  • Multiple cell generations: epigenetic storage in covalent modifications and stable chromatin configurations;
  • Within a single cell cycle: computational storage in meta-stable nucleoprotein complexes."
From PRO Source 3, link below.

As far as I can tell, quite a lot of PRO's Round 1 is cut and pasted from this source. Even the four steps at the end almost exactly match up to the conclusion of the study on page ninety seven: 

  • "Genomes are formatted by repetitive elements and organised hierarchically for multiple information storage and transmission functions.
  • Major evolutionary steps occur by DNA rearrangements carried out by sophisticated cellular natural genetic engineering systems operating non-randomly.
  • Significant evolutionary changes can result from altering the repetitive elements formatting genome system architecture, not just from altering protein and RNA coding sequences.
  • Cellular regulation of natural genetic engineering activities makes evolutionary change responsive to biological inputs with respect to timing and location of DNA rearrangements."

In response to the information presented in the source, CON points out the following:

  1. Copy and pasting academic articles without reference does not equate to an argument.
  2. While this is a "high level" scholarly source, it's not been universally accepted. The author's wikipedia page, [8], points out several reviews that criticise the findings. "It has been criticised by some." (Four articles are cited.)
  3. The conclusions made in the source don't come into conflict with the principles of Darwinism - it merely speaks of a mechanism through which evolution functions. Shapiro (the author) hasn't changed the tractor - he's changed a piston in the engine. Certainly a ground breaking change - but it's not an entirely new theory. From a review of the study by Paul R. Thompson: [9].
"Notwithstanding what many may assume from the title, this is not an update of a conventional account of evolution...". 
Granted - the article is fascinating, and it certainly differs from the original concept of Darwinism. But - no wonder! "The Origin of Species" was published in 1859 - DNA wasn't even identified until ten years later, in 1869. [10]. Darwin could never conceive the mechanisms behind the evolution of species, but his observations and his theory - that species change gradually over long periods of time according to natural selection - still stands firm in the more modern versions.

An explanation of this I'm rather fond of is from a source I can't link to - it's not accessible for free - but I'll quote it here. [11]

"The capacity for change, Shapiro points out, is itself adaptive."
As for the other two sources:


A good source, but the existence of "mutational hot spot[s]" on the genome isn't in itself and evidence for intelligent evolution.


Needless to say, I am not a fan of this source. It's emotional, it's biased, it references itself. Here are some outtakes:

“Evolution is too important to leave to evolutionary biologists.”
Which is not dissimilar to "medicine is too important to be left to doctors", or "physics is too important to be left to physicists". It's an absurd statement.

"Scientism and reductionism have been punched in the face. Empiricism is making a comeback."
Merriam Webster advises that "scientism" refers to "methods and attitudes typical of or attributed to the natural scientist", [12].

"Lamarck was right 200 years ago..."
Lamarckian evolution - from Brittanica.com, "a theory of evolution based on the principle that physical changes in organisms during their lifetime—such as greater development of an organ or a part through increased use—could be transmitted to their offspring." [13

Lamarck's theory is representative of his time - cellular biology was in its infancy, and the distinction between germ cells - sex cells that are passed on - and somatic cells - body cells - wasn't clear. The theory is clearly problematic when thinking of a genetic mutation that occurs during life in the somatic cells - cancer. Cancer risk in genes can be hereditary, but an individual with cancer does not automatically pass this on to their offspring.

Concluding Rebuttal Statement:

In this round, PRO has presented three sources. Aside from these sources, no argument has been made in the favour of PRO. 

CON Point 2: Mutation - The Clash Between Darwinism and 'Intelligent Evolution'

Sub-points: a) Understanding mutations, bSickle cell anaemia.

Note: In my previous Round I said that I would extend upon CON Point 1 here - but PRO's statement earlier about potentially having to skip a round brings this more important point to this round instead. If given the opportunity, CON Point 1 will be extended in R3.

a) The science of mutation is an incredibly complex topic, but for the purposes of this debate, CON seeks to talk only about germ line mutations and their effect on the offspring of organisms.

There are three outcomes that result from a change in the genetic code. 

  1. Silent - in which a mutation is present, but causes no phenotypical change. (No effect on organism.)
  2. Nonsense - in which a mutation is present, and causes a shortened or nonfunctional protein to be expressed. (e.g., cystic fibrosis.) [14]
  3. Mis-sense - in which a mutation is present and causes a different protein to be expressed. (e.g., sickle cell disease.) [15]
This is obviously a simplification - I skip polypeptide synthesis, chromosome mutations and the causes of mutation for brevity. If PRO requests more detail I would be happy to oblige - but this is all that's needed for the moment.

In the case of evolution, a beneficial mutation can only be the result of mis-sense, or, more rarely, nonsense mutations. PRO stipulates:

"The opposing theory would instead say that most mutations are not random."
Which begs the question - why would a non-random system deliberately develop harmful/neutral mutations? Why do silent mutations exist in a deliberate system?

This is explained quite well by Darwinism - because the mutations are random, there's no telling whether a mutation will be beneficial, neutral or harmful. Harmful mutations are eliminated by the process of natural selection, and thus they don't propagate in nature for more than a few generations.

b) Sickle cell disease (SCD) is a heritable disease that results in malformation of the red blood cell - leading to a host of life long symptoms. [16] SCD - at surface level - is harmful to an individual's likelihood to survive and reproduce. Then why is the gene so common, with 5% prevalence worldwide? [17]

We owe thanks for this anomaly to plasmodium falciparum, or "malaria". The specific nature of malaria's development in the human body is restricted by SCA - and so individuals with SCA are more likely to survive in areas where malaria is highly prevalent - and so the gene is allowed to propagate and spread, despite it's negative affects overall. 

Darwinism, again, explains this phenomena well - SCA is more prevalent where malaria is. How does a non-random system deliberately develop a half-effective, self damaging defence? 

Sources

[8]: Regarding criticism of "A 21st Century View of Evolution", https://en.wikipedia.org/wiki/James_A._Shapiro
[9]: Regarding Paul R. Thompson's review of "A 21st Century View of Evolution", page 385, https://www.jstor.org/stable/10.1086/668137
[10]: Regarding the discovery of DNA, https://www.yourgenome.org/stories/the-discovery-of-dna
[11]: Brooks, D.S. Book Reviews. J Gen Philos Sci 44, 235–245 (2013).
[12]: Regarding the definition of Scientism, https://www.merriam-webster.com/dictionary/scientism
[14]: Regarding nonsense mutations, https://en.wikipedia.org/wiki/Nonsense_mutation
[15]: Regarding mis-sense mutations, https://biologydictionary.net/missense-mutation/
[16]: Regarding sickle-cell anaemia, https://en.wikipedia.org/wiki/Sickle_cell_disease

Terms

No new unusual terms presented.
Round 3
Pro
I've got a lot of learning to do. Well thats in general. Even more here. Both in this field but also debate format. I won't have the time now to try and dive in and see where I fall given your awesome response. 

Anyone voting. Vote for my opponent. He's a beast. His format is rigorous and well organized. He's the type who make me realize I'm probably more looking for something like Reddit for discussions not formal debates as this site offers.

Jrob thank you! Your patience and willingness to put in that effort is beyond appreciated. I'm sorry this fell flat but part of it was the depth and level of your responses. Again. You're a beast. I can offer this. If there's an astronomy related debate I feel I got the depth of knowledge to go in on something. If there's a topic, I can't guarantee ill suddenly have a brand new format but if we expand the time to reply I should have time in a few days. Any time for that let me know. I'd like to be able to deeply communicate about stuff and give you the effort you deserve here. If not, man again I super appreciate it. 

Vote con!


Con
Conclusion

Thank you for your time and effort, UpholdingTheFaith. I found reading Shapiro's work to be very interesting, so thanks especially for bringing this topic to my attention. As I hope I have shown in my responses - Darwinism, or evolved Darwinism, if you will - still remains the best theory to explain the phenomena we observe in the natural world. Far be it from an online debate to determine that which the scientific community will wrestle with for decades to come, of course.

I must point out that your argument has a lot more merit than you may think - if you had held to the concept of that the chance of speciation is too tiny to be caused by natural selection - and instead proposed that there must be another mechanism at play, even citing Darwin's uncertainty in the Origin of Species, I would have had a significantly harder time in this debate. (Even to tie the "21st Century View of Evolution" paper into what MisterChris mentions in the comments.)

I suppose what I'm trying to say is - don't doubt yourself. 

"If there's an astronomy related debate I feel I got the depth of knowledge to go in on something."
Maybe Fermi's paradox, another time? I would likely be hopeless, but it sounds like good fun.

"If not, man again I super appreciate it."
To you as well! Until next time!

------------------------------------------------

All Sources

[1]: Regarding the definition of "Natural Selection", https://www.merriam-webster.com/dictionary/natural%20selection
[2]: Regarding the definition of "Mutation", https://www.merriam-webster.com/dictionary/mutation
[3]: Regarding the "red herring", https://en.wikipedia.org/wiki/Red_herring
[4]: Regarding the speed of evolution, P3, https://humanorigins.si.edu/education/introduction-human-evolution
[5]: Regarding evidence of gradual evolution, see Fossil Record, Common Structures, Distribution of Species, https://www.ncbi.nlm.nih.gov/books/NBK230201/
[6]: Songbird brain structure, (So awesome!), https://jarvislab.net/Publications/Evo_Vocal_Brain_Structures.pdf
[8]: Regarding criticism of "A 21st Century View of Evolution", https://en.wikipedia.org/wiki/James_A._Shapiro
[9]: Regarding Paul R. Thompson's review of "A 21st Century View of Evolution", page 385, https://www.jstor.org/stable/10.1086/668137
[10]: Regarding the discovery of DNA, https://www.yourgenome.org/stories/the-discovery-of-dna
[11]: Brooks, D.S. Book Reviews. J Gen Philos Sci 44, 235–245 (2013).
[12]: Regarding the definition of Scientism, https://www.merriam-webster.com/dictionary/scientism
[14]: Regarding nonsense mutations, https://en.wikipedia.org/wiki/Nonsense_mutation
[15]: Regarding mis-sense mutations, https://biologydictionary.net/missense-mutation/
[16]: Regarding sickle-cell anaemia, https://en.wikipedia.org/wiki/Sickle_cell_disease

Round 4
Pro
Thank you for the kind words. Really. 

Yeah it's an interesting theory gaining some traction. Ill be curious to see where it goes. The cell has always been super interesting to me. If you haven't seen it, this documentary on how something like a cold gets you sick from the cellular level was one of the most fascinating things I've ever seen. And it's narrated by my favorite Doctor Who hahaha



The Fermi Paradox sounds like a super fun one!! Yeah, please anytime. Well. At least a few days but shoot me a message or simply make the debate and tag me if possible. 


Thanks again!

Con
Waive.

------------------------------------------------

(Check out this one! It's narrator by the Doctor, but it's still worth a watch! https://www.youtube.com/watch?v=X_tYrnv_o6A)