OK. Still vague as to how much change constitutes new and meaningful.
This is what you fail to understand, it’s not about “how much change”, it’s about “what kind of change”, how the process unfolds and what would the specific steps entail.
Again, a gene is not just any random DNA sequence; a gene is a specific code for a function. And remember we are not talking about merely new traits or alleles of the same genes; we are talking about new genes with new codes to allow for new meaningful functions.
Evolution is not a planned step-by-step progress towards a purpose but rather a slow accumulation of random meaningless changes without any purpose.
Random replacement of the
entire sequence of a gene is not equal to a new gene that encodes a new specific protein for a new meaningful function.
Considering the number of the bases in a single gene, mathematically, the chance to get a random sequence to specifically encode a new meaningful function is literally 1 in infinity, but regardless the ToE doesn’t assume that a new function would appear suddenly but rather through the accumulation of numerous purposeless steps that are not necessarily meaningful or functional, in fact, these random changes are mostly damages to the original code/function (especially after significant accumulation of random changes) or at best some changes may have neutral effect. Selection can neither see nor plan for the future. meaning, unless every random step along the way could cause some fitness advantage,
selection wouldn’t keep it or allow it to accumulate based on a hope for further potential that didn’t materialize yet. Hence, the random progress towards a future function is not possible. on the other hand, if every step along the way necessarily causes fitness advantage, then the process is not random.
The fact is that the DNA replication errors that allow random wrong bases to escape proofreading are not fitness advantages. The very definition of “pseudogene” is a previously functional gene that is no longer capable of coding for a protein
due to accumulated random mutations.
Pseudogene (genome.gov)
Regardless, even for the sake of argument if selection could keep the numerous meaningless accumulations of changes to the point that now the new sequence encodes a new gene with a new function that also happened to be beneficial for possible transformation towards a new body plan, but unless the new function offers an immediate fitness advantage to the organism itself, it wouldn’t be kept by selection. Selection doesn’t / can’t plan for a future potential.
Even for the sake of argument if the new function happened to be somehow beneficial to the organism itself as well as a future body plan, what about the
original function (of original gene) that was lost due to the accumulated change? The loss of the original function would impact fineness and still trigger elimination by selection.
The change process is always about alleles/traits not new genes. Change in phenotype happens due to the accumulation of alleles across multiple genes not the accumulation of random bases within the same gene towards some new function that would never materialize and even if it did, it may not necessarily offer a fitness advantage especially considering the loss of original function.
The bottom line is, there is no route towards encoding new meaningful gene function through random changes.
If I give you the machine language code (binary numbers, 1's & 0's) for some software such as “Microsoft Word”, you start random changes to the code hoping that someday you would transform the code into another meaningful function such as “Microsoft Excel” or any other meaningful software.
How much change would you need? How much change would render the original function void? If original function is already nullified, could the process still continue? Would you ever get there? What are the chances? How much junk would you produce along the process? How much junk is needed to terminate the process due to lack of benefit?
Do you understand what the notion of randomness entails?
But why introduce "random junk" into the discussion?
I didn’t introduce Junk. Scientists did. It’s a scientific term.
”Pseudogenes”, which are also labeled “
junk DNA" were considered to be failed copies of genes that were previously functional but during the evolution of genomes
lost their protein-coding ability due to accumulated random mutations.
Random changes are mostly DNA replication errors, such errors are mostly damages to the gene code or at best some of it could be neutral. And yes, such replication errors are merely random junk.
Junk DNA simply means “non-coding DNA”. It’s a scientific term.
Sure, some genetic variations will be neutral or harmful, but some will confer a competitive advantage in the phenotype, and these are selected for and accumulate. How many such improvements make a change new or meaningful? I'd say all of them, but you can define them differently if you like.
Random changes are not equal to improvements. Competitive advantage in the phenotype doesn’t happen due to the accumulation of random changes within a specific gene but rather the accumulation of “beneficial” traits across multiple genes.
The adaptation process is what gives rise to competitive advantage in the phenotype; such beneficial mutations that cause beneficial traits are not random. Adaptations are encoded in the genes (preprogrammed) and take effect through cell-mediated processes not random change such as the clear example of “Antimicrobial Resistance" (AMR) and “Escherichia Coli” developing the ability to utilize citrate through a cell-mediated adaptive process that activated
an existing but previously silent citrate transporter (Lenski’s experiment). See #8108
It’s important to understand the fact that the change process is always about traits/alleles that may accumulate across multiple genes. If the genome of an organism includes gene A with allele a1, gene B with allele b1, gene C with allele c1, etc. then the accumulation of change is about gene A with allele a2, gene B with allele b2, gene C with allele c2, etc. The process may repeat with more allele changes (a3, b3, c3) but regardless of the allele variants that may accumulate in multiple genes, and even if all alleles in all genes have changed but the original functions of the genes A, B & C continue to be the same, these genes do not transform into genes X, Y & Z with new foreign functions to the organism.
This is the problem we're having with new genes - no clear definition of what constitutes new,
Absolutely not, the definition is very clear. A “new gene” equals “new function”. Numerous random steps are not new functions. You imagine that along the long process of random alterations to the sequence, the genes continue to retain its original function or somehow perform some imaginary new functions, i.e., continues to be genes. It’s simply not true. The gene stops being a gene once it loses its original ability to perform a function (becomes a pseudogene). At this point it’s neither a new gene nor a new random function would pop out of nowhere instead of the old one.
Yes, alleles frequency continues to change all the time, but the process never encodes new gene functions that are foreign to the organism. We must understand the limitations of the process.
For example, you keep changing your car tires, new color, maybe also replace the engine or transmission, at what point your car would transform into a boat or aircraft? The function of the car will always be the same regardless of changes of “traits”. Traits never change the original functions of the system. Original functions (genes) continue to be the same.
But to retain the original functions, it’s imperative that you change the tires or other components (traits) with similar or better components of the same type (advantageous traits), if you replace the components with any random components without any purpose, such as wood blocks instead of tires, cardboard instead of glass, throw away some parts of the engine, maybe put some mashed potatoes instead of gas, would your car still perform its original function? Is your car still a car at this point? At what point it stopped being a car? Simply at the point when original function was lost due to the accumulation of purposeless changes. At this point, it's neither a car nor an airplane, merely some junk. at best, we may call it a "pseudocar"
.