Hello all. I’m new here and this is my first post.
Firstly, I’d like to thank Dr. Joshua Swamidass for creating this wonderful platform and giving opportunity for everyone to post their personal opinions.
I’m a Design supporter as I’m convinced that design is the most rational explanation for the origin of specified biological information as opposed to strictly naturalistic explanations.
However, I neither deny evolution altogether nor the scientifically-determined age of fossils. I hold that organisms are designed to evolve with varying time and conditions.
Popular books on Evolution and college textbooks have long been teaching that variations occur by chance or random accidents. All genetic mutations, they taught, are unintended disruptions in the genetic code.
 “Where does this genetic variation come from? Mutations— accidental changes in the sequence of DNA that usually occur as errors when the molecule is copied during cell division.”
(Why Evolution is True, 2009)
 “Traditional thinking holds that mutation happens by accident and then spreads in the population by either natural selection or random genetic drift.”
Of course, some mutations occur by chance. For example, mutations introduced by DNA copying errors, reactive oxygen species and environmental factors.
However, are all heritable genetic changes unintended disruptions of the genetic code? Do organisms have the ability to generate variations? The answer to this question has great implications in the origins debate, I believe.
Think of meiotic recombination, a process that is known to us for decades. The new allele combinations produced through this process may be random but the event itself is not. Its a programmed and regulated process orchestrated by the cell that helps to generate variations. Its mediated by multiple biomolecules within the cell. In other words, the cell or the organism’s physiology has an active role in the generation of heritable genetic variations.
Somatic Hypermutation, a programmed process of mutation that has been known to us since 1980s, also points to the cellular capability to generate alterations in DNA. Although it doesn’t generate heritable variations, SHM shows that cells can target and mutate specific gene segments at specific time.
The CRISPR-Cas-system, which facilitates adaptive immunity in bacteria and archae, also illustrates the built-in cellular ability to modify genome.
Thanks to the advancement in biology, now we know of more built-in programmed mechanisms that generate heritable variations (especially during stressful & changing environments).
■ Stress induced mutations aid organisms to adapt to a stressful condition
︎ In prokaryotes -
This 2004 work showed that
preventing induction of the SOS response by interfering with the activity of the protease LexA renders pathogenic E coli unable to evolve resistance against the antibiotics ciprofloxacin & rifampicin.
︎ In Eukaryotes -
This 2014 work showed that induced mutations in yeast cells help them adapt to a challenging environment.
︎In humans -
This 2021 study found that de-novo HbS mutation rates are substantially higher in people living in malaria-prone regions.
Some had criticized the later study. (See: Brian Charlesworth on the errors of a new paper supposedly showing that a fundamental assumption of neo-Darwinian evolution is wrong – Why Evolution Is True)
However, the authors responded by showing that those criticisms do not hold merit.
A search on Pubmed will list hundreds of studies & reviews on Stress-induced mutagenesis. I recommend reading them to get a better understanding.
For example, refer this 2022 review paper: (doi: https://doi.org/10.1128/mbio.01074-22)
An important thing to keep in mind is, I do not claim that all mutations generated by this mechanisms are evolutionarily significant. Mutations generated so may or may not end up contributing to the evolution of organism. The key point is that cellular physiology has an active role in the generation of these variations rather than being passive. They are not random accidents or unintended disruptions in the genetic code.
■ Stress induced Transposable Element insertion in Drosophila contributes to resistance against oxidative stress.
Mobile DNA elements have been found to be playing significant role in rewiring and innovating transcriptional regulatory networks in evolution. They can reposition promoters, enhancers, heterochromatin markers, insulators, splicing signals, and other cis-acting control elements that are embedded in their sequences.
Refer this review paper to learn more: (doi: Regulatory activities of transposable elements: from conflicts to benefits | Nature Reviews Genetics)
■ CNV generated through recombination offers anti-fungal drug resistance to Candida (doi: https://doi.org/10.7554/eLife.58349)
■ Horizontal Gene Transfer
■ Transgenerational Inheritance of Epigenetic modifications.
For example, this 2011 study found the multigenerational Inheritance of extrachromosomal information in the form of small RNAs, viRNAs, which are induced by an episode of viral replication and which are propagated through the germline in a non-template-dependent manner.
■ Evolutionary changes driven by Developmental plasticity which is an intrinsic property of developmental systems.
Examples: (a) The morphology of white water-buttercup (Ranunculus aquatilis) leaves depends on their environment. Submerged leaves are branched into 20 or more thread-like segments. Floating or exposed leaves are scalloped.
(b) The water flea Daphnia longicephala develops protective crests and tail spines in response to its water bug predator, Notonecta.
(c) Adaptive Transgenerational plasticity in the plant Polygonun persicaria in drought.
■ Ability to mask/buffer Cryptic genetic variations in normal conditions and releasing them during stress or particular environments
Example: (doi: https://doi.org/10.1126/science.1240276)
■ Genome restructuring mediated by TEs during interspecific hybridization
(Doi: Drosophila Females Undergo Genome Expansion after Interspecific Hybridization | Genome Biology and Evolution | Oxford Academic)
■ Modular organization of biological systems (such as gene regulatory networks, protein interaction and metabolic pathways) promotes Evolvability.
In all the aforementioned mechanisms, evolution begins with a minimum level of cellular complexity. Several information-rich biomolecules, especially a number of different proteins, are necessary for the generation of variations through these processes. For example, refer this review to learn about the biomolecules involved in Horizontal Gene Transfer - (Doi: https://doi.org/10.3389/fmicb.2018.02154)
Evolutionary innovations mediated by all the aforementioned mechanisms are entirely compatible with Intelligent Design theory because its the organismal built-in mechanisms that generate variations and promote evolution. In other words, organisms are designed to evolve with varying time and conditions.
This is the reason why the concepts put forwarded by biologists such as James Shapiro and Rosenberg are gaining wide acceptance among Design proponents. (although all these biologists are unsupportive or even critics of ID). No sensible design proponent would argue against evolution mediated by built-in mechanisms. Fact is, until a few years back, no design proponent had thought of this possibility. The ability of cell/organismal physiology had been greatly underappreciated.
■ In addition to these, there is another important and widespread mechanism of evolution that too is compatible with Intelligent Design. Evolution by loss-of-function mutations or Reductive Evolution. Its top-down evolution since it begins with greater biological information content.
Examples: (a) Loss of function in SLC30A8 is associated with reduced risk of type 2 diabetes in humans.
(b) Experimental evolution in Pseudomonas aeruginosa resulted repeatedly in loss-of-function mutations in nfxB, conferring antibiotic resistance.
Overwhelming number of scientific papers points to the active role of organisms’ physiology in the process of evolution. Although the authors of all aforementioned papers believe that the ability to evolve itself was evolved, they do not offer an explanation. In fact how can they? If evolution we observe in real-time require sophisticated cellular mechanisms, one cannot invoke evolution to explain the origin of these cellular tools in the first place. Doing so would be a logical contradiction. This raises a challenge for design deniers - the evolutionary kick off.
EVOLUTIONARY KICK OFF - an underappreciated problem in the Origins debate
In my opinion, this is one of the best arguments that a design proponent can put forward in the Origins debate. However, as far as I know, this problem has been hardly identified or described in any design literature.
The concept is simple: According to naturalistic explanations, the process of biological evolution must have begun once the first (hypothetical) self-replicating systems originated in the primitive earth. Evolution had to kick off from that point. Its on the shoulders of evolution to form the first cellular life from these primitive self-replicating systems. In fact, its very first task.
Keep in mind that all the aforementioned built-in mechanisms such as horizontal gene transfer, transposition, recombination and stress induced mutagenesis are non-existent for a primitive self-replicating system. The only evolutionary mechanism that can be invoked is random accidental mutations getting fixed by selection or drift. But do we know of any significant biological innovation that originated solely through this mechanism of evolution? As far as I know, no emperical data suggests so.
In a 2021 Bioessays paper, prominent evolutionary biologists explains:
"…Our understanding of the origin of novel complex traits remains poor, apart from the realization that key evolutionary innovations such as the vertebrate eye, the insect wing, and the mammalian placenta cannot be explained by selection on random genetic mutations per se."
If selection on random genetic mutations by itself couldn’t have formed key evolutionary innovations such as eye, wings and placenta, how on earth it could have produced an enormously complex cell from a hypothetical primitive self-replicating system? This is the ‘evolutionary kick off challenge’ in brief.
I welcome all design deniers on this forum to give your thoughts on the above described ‘kick off’ problem. I’d greatly value healthy criticisms too.