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.
- DNA operates as a type of data storage medium.
- 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.
"...evolution has been driven by ... non-random genetic engineering..."
- "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.
- "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. 
- "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 ...". 
- 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.
For my organismal generations: Within organismal generations, there's genetic storage in localDNA sequences and long range chromosome structure.There is epigenetic storage in covalentmodifications and stable chromatin configurations;Within a single cell cycle there is computational storage inmeta-stable nucleoprotein complexes.
- No citation.
- Six undefined highly abnormal terms.
- Relevance to the topic is extremely unclear.
- Red herring: "a seemingly plausible, though ultimately irrelevant, diversionary tactic." 
"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."
Genomes have different kinds of functional information. Besides coding sequences, sort of data files in a way, determining the primary structure ofRNA and various protein molecules, there is information for other essential processes such as packaging DNA molecules within the nucleoid ornucleus and the replication of DNA and transmission of copies to progeny cells.
This read write ability is driven by the non random cellular processes.
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.
- What systems?
- What feedback loops?
- What hierarchy?
- What levels?
- What gene?
"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."
"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."
- "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."
- Copy and pasting academic articles without reference does not equate to an argument.
- While this is a "high level" scholarly source, it's not been universally accepted. The author's wikipedia page, , points out several reviews that criticise the findings. "It has been criticised by some." (Four articles are cited.)
- 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: .
"Notwithstanding what many may assume from the title, this is not an update of a conventional account of evolution...".
"The capacity for change, Shapiro points out, is itself adaptive."
“Evolution is too important to leave to evolutionary biologists.”
"Scientism and reductionism have been punched in the face. Empiricism is making a comeback."
"Lamarck was right 200 years ago..."
- Silent - in which a mutation is present, but causes no phenotypical change. (No effect on organism.)
- Nonsense - in which a mutation is present, and causes a shortened or nonfunctional protein to be expressed. (e.g., cystic fibrosis.) 
- Mis-sense - in which a mutation is present and causes a different protein to be expressed. (e.g., sickle cell disease.) 
"The opposing theory would instead say that most mutations are not random."
"If there's an astronomy related debate I feel I got the depth of knowledge to go in on something."
"If not, man again I super appreciate it."