The evidence increasingly supports the concept of an intelligently designed and created biological system

Stunning Intelligence: The Cell Reprograms Its Splicing Mechanism After Gene Loss

The intricate complexity of cellular mechanisms offers compelling evidence for intelligent design. A striking example is how cells adapt to gene loss through alternative splicing, a process that suggests an underlying intelligent programming. When a gene function is lost, the cell reprograms its splicing machinery to compensate, enhancing its efficiency. This remarkable ability points to a sophisticated system designed to preserve functionality and maintain life.

1. Intelligent Design in Alternative Splicing

The alternative splicing mechanism is a marvel of biological engineering, allowing a single gene to produce multiple protein variants. This process involves the selective inclusion or exclusion of RNA segments, producing diverse proteins from the same DNA template. The fact that cells can modify this already complex system in response to gene loss suggests an intelligent design rather than random mutation and selection. Such reprogramming requires a deep understanding of the organism's needs and a capacity to implement intricate changes rapidly and efficiently.

2. Human Understanding of Alternative Splicing

Despite significant advances in molecular biology, our understanding of alternative splicing remains limited. Scientists have only scratched the surface of this elaborate code. The complexity of alternative splicing involves numerous factors and regulatory elements that interact in highly specific ways. Our limited comprehension underscores the sophistication of the system, further pointing to an intelligent origin.

3. Factors Influencing Alternative Splicing

Several factors influence alternative splicing, each adding a layer of complexity to the process:

• DNA Methylation Profiles: Methyl groups added to DNA can affect splicing decisions by altering the accessibility of splicing machinery to specific regions.
• Histone Modifications: Chemical modifications to histone proteins, around which DNA is wrapped, can influence the splicing machinery's access to genetic information.
• RNA Molecules: Various non-coding RNAs can interact with the splicing machinery, guiding it to specific splice sites or altering its activity.

These factors collectively contribute to the regulation of alternative splicing, demonstrating an orchestrated system of checks and balances designed to maintain cellular functionality.

The Cell can produce thousands of different proteins by using the same pre-mRNA. There's no need to alter DNA. This is the most significant mechanism behind the protein diversity and adaptation of organisms.

4. DNA Rearrangement for Efficiency

When faced with gene loss, cells not only reprogram splicing mechanisms but also rearrange their DNA to maximize the use of remaining genetic information. This process involves selectively retaining or discarding DNA segments, and prioritizing sequences that enhance cellular efficiency and functionality. Such rearrangement requires a highly organized and intelligent system capable of evaluating and responding to genetic changes dynamically. This also emphasizes the role of DNA as a passive information storage for the cell.

Conclusion

The ability of cells to reprogram their alternative splicing mechanisms and rearrange DNA in response to gene loss highlights an intelligent design behind these processes. The sophisticated nature of these adaptations points to a system that is not the product of random mutations but of deliberate, intelligent programming. As we continue to unravel the complexities of alternative splicing and DNA rearrangement, the evidence increasingly supports the concept of an intelligently designed and created biological system.

References

• News-Medical. (2023). Alternative splicing plays a role in compensating for loss of gene function. Retrieved from News-Medical
• Nitschke, L., et al. (2023). Loss of MBNL1 leads to compensatory alternative splicing of MBNL2. Baylor College of Medicine.
• DNA Methylation and Histone Modifications in Gene Regulation. (n.d.). Nature Education.
• The Role of Non-coding RNAs in Alternative Splicing. (n.d.). Frontiers in Molecular Biosciences.

Histone Modifications Regulate Alternative Splicing Mechanism

The role of Histone Code in protein diversity seems to be very significant

https://www.frontiersin.org/articles/10.3389/fgene.2019.00122/full (18th Feb 2019)

Excerpt: "Alternative splicing is a process that can generate multiple mRNA isoforms from a single gene by splicing pre-mRNA molecules in different ways. As an important process of gene expression, alternative splicing ensures the diversity of gene expression products. It has been estimated that alternative splicing occurs in approximately 90% human genes. Alternative splicing is reported to closely correlate with apoptosis, embryonic development and even a series of diseases. Although great efforts have been made on studying alternative splicing, the mechanisms of cell type-specific and stage-specific alternative splicing are still unclear.

Recently, Shindo et al. (2013) found that the alternative splicing of the BIN1 gene in IMR90 cell was regulated by the cooperation of H3K36me3, H3K4me3, H2BK12ac, and H4K5ac. These results strongly indicate that histone modifications play important roles in RNA splicing regulation and are key clues for revealing the regulatory mechanism of alternative splicing.
 

Based on these experimental results, several computational methods have been proposed to predict the alternative exons in exon skipping event based on histone modifications. The pioneer work was proposed by Enroth et al. (2012), in which a rule-based model was developed to classify included and excluded exons based on histone modification combinations. Later on, based on Enroth et al.’s (2012) dataset, Chen et al. (2014) proposed a quadratic discriminant (QD) function method and obtained an accuracy of 68.5% for classifying the included and excluded exons in the exon skipping event. More recently, a random forest based method was developed for the same aim and obtained an accuracy of 72.91% in the 10-fold cross validation test (Chen et al., 2018b). These results strongly indicate that histone modifications play important roles in RNA splicing regulation and are key clues for revealing the regulatory mechanism of alternative splicing. These results indicate that we should find the novel splicing code from the epigenome information.

Conclusion

Based on the Pearson correlation coefficients, the casual relationships of histone modifications in the process of RNA splicing were deduced by constructing their Bayesian networks. The results indicate that the inclusion or exclusion of exons is influenced by combinatorial patterns of histone modifications. Some of the histone modifications contribute directly to RNA splicing (e.g., H3K36me3 and H3K79me1), while other histone modifications indirectly contribute to the RNA splicing.

The result that H3K36me3 and H3K79me1 can affect RNA splicing is consistent with previous studies which have demonstrated that H3K36me3 and H3K79me1 are enriched in included exons. The H3K36me3 can regulate alternative splicing by interacting with polypyrimidine tract-binding protein (PTB). By interacting with the Tudor domain of TP53BP1, the H3K79me1 was also reported to interact with that interacts with snRNP.

By relaxing the chromatin structure, the H3 and H4 acetylation were also reported to regulating inclusion or exclusion of the skipping exon. Besides the histone modifications located in exon regions, histone modifications located in intragenic regions can also influence RNA splicing by regulating RNAPII elongation rates, or by directly binding to splicing factors and hence mediating their binding to pre-mRNA."

My comment: Histone code is a complex database being able to store epigenetic information that strongly affects DNA transcription, pre-mRNA splicing and post-transcriptional modifications of mRNA. It's clear that the histone code regulates organismal characteristics. By using histone epigenetic markers cells are able to convert digital (marker) information to analog information. The histone code is an indication of Intelligent Code of life, complex biological information that is designed by our Creator. The histone code is maintained by writers, readers and erasers which points to Intelligent Design. However, there is no mechanism for evolution, because epigenetic mechanisms only regulate pre-existing biological information. Don't get lost.

Speciation is not evolution - Epigenetic mechanisms behind organismal change

Speciation can occur rapidly and there's no need for a single change in DNA

https://news.mit.edu/2012/rna-splicing-species-difference-1220

Excerpts:"When genes were first discovered, the canonical view was that each gene encodes a unique protein. However, biologists later found that segments of genes can be combined in different ways, giving rise to many different proteins.
This phenomenon, known as alternative RNA splicing, often alters the outputs of signaling networks in different tissues and may contribute disproportionately to differences between species, according to a new study from MIT biologists.

After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns — which determine the segments of those genes included or excluded — vary from species to species."

"Alternative RNA splicing (a discovery for which MIT Institute Professor Phillip Sharp shared the 1993 Nobel Prize in medicine or physiology), controls the composition of proteins encoded by a gene. In mammals, genes — made of DNA stored in the cell nucleus — consist of many short segments known as exons and introns. After the DNA is copied into an RNA transcript, all introns and frequently some exons are excised before the messenger RNA (mRNA) leaves the nucleus, carrying instructions to make a specific protein.

This process allows cells to create a much wider variety of proteins than would be possible if each gene encoded only one protein. Some proteins, including Dscam in fruit flies and neurexin in humans, have thousands of alternate forms. These variant proteins can have vastly different functions, Burge says."

"Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says. “Splicing seems to be more malleable over shorter evolutionary timescales, and may contribute to making species different from one another and helping them adapt in various ways,” he says.

The new study is the first large-scale effort to look at the role of alternative splicing in evolution, says Brenton Graveley, a professor of genetics and developmental biology at the University of Connecticut Health Center. “It provides a lot of new insight into the potential role of alternative splicing in driving differences between species,” says Graveley, who was not involved in this study."

My comment: Alternative RNA splicing is regulated by epigenetic factors and mechanisms, such as DNA methylation profiles, histone epigenetic markers and non coding RNA molecules. Alternative splicing (AS) makes it possible to have alternate forms (The Bible: 'After its kind') from the same organism. This might happen in adaptational events. During and after the AS procedure, NO NEW information is generated, but pre-existing information is regulated, shuffled and re-used along the adaptational needs. Alternative splicing is a basic mechanism in both prokaryotes and eukaryotes. In humans, the AS works like a masterpiece; our cells can produce millions of different proteins just by reading ~19,000 strands of DNA. This kind of use of DNA also points out that DNA is just a passive data base. Evolution never happened. Don't get lost.

Keywords: alternative splicing speciation, alternative splicing phenotypic novelty

DNA has no control in cellular processes

Alternative splicing points to Intelligent Design

Alternative splicing is a complex mechanism that helps us understand that DNA does not control cellular mechanisms. Many people still think that one gene encodes one protein. Actually, the whole idea of ​​DNA genes encoding something is completely incorrect, at least within eukaryotes. 

It is important to understand the principles of alternative splicing. Without going into deep scientific terminology, I will briefly explain how alternative splicing works.

The cell reads certain DNA sections from which it builds a so-called pre-mRNA. The cell modifies this RNA transcript using a complex protein complex called a spliseosome. The spliseosome will carefully cut off that pre-mRNA from certain sequences to construct exactly the RNA sequence required by the cell for the required protein production. From one and the same DNA sequence, the cell is thus capable of manufacturing up to thousands of different proteins using this technology. For example, using the fruit fly Dscam gene the cell can produce as many as 38,016 different proteins. Without changing the DNA sequence! In the human genome there are only about 19,600 DNA sequences used to protein production, that is, less than that of a roundworm, but the number of different proteins in our body is up to two million according to some estimates. The ingenious alternative splicing mechanism makes this possible. In recent years, it has also been found that even most long non-coding RNA molecules go through alternative splicing procedure.

 

Alternative splicing is guided and controlled by several epigenetic factors such as DNA methylation profiles, histone epigenetic markers, and epigenetic markers of non-coding RNA molecules known in more than 140 different types.

More than 90% of human DNA-genes are read into an alternative splicing procedure. The number has risen from year to year as the research progresses. It is a clever and complex  mechanism that allows the implementation of alternative programs in the cell and hence the whole organism morphology and other features. Knowing the alternative splicing mechanism will help us understand that DNA is a kind of library information in the cell that it needs to produce the necessary proteins and to transmit epigenetic information about the environment to the organism's cells. DNA is passive information that does not control anything. DNA genes may overlap or embed with each other. The cell chooses different  strands of the DNA and constructs complex RNAs. Organisms may actually modify their own genome with many different mechanisms. This is done by nutrition, climate, stress factors, sensory stimulus etc. It has also been found that even our thoughts and attitudes can modify our DNA.

The alternative splicing mechanism points out that all changes in organisms are based on the alternative epigenetic regulation of existing biological information OR for gradual but unavoidable information corruption, ie genetic degeneration (whereby the alternatives are reduced). Therefore there is no mechanism for evolution. So do not be lost, good people.

Rapid Speciation by Epigenetic Mechanisms

Speciation occurs rapidly and it's based on Dynamic and Reversible Epigenetic Mechanisms - Evolution never happened

Introduction

Speciation, the process by which new species arise, has traditionally been viewed through the lens of genetic mutations and natural selection. However, recent research has unveiled the pivotal role of epigenetic mechanisms—dynamic and reversible modifications that regulate gene expression without altering the DNA sequence—in driving rapid speciation. Unlike permanent genetic changes, epigenetic modifications offer a flexible and swift response to environmental changes, enabling organisms to adapt quickly and potentially form new species. This article delves into the mechanisms behind epigenetic speciation, how they operate, and why these changes, despite their significant impact, do not constitute evolution in the classical sense due to their reversible nature.

Mechanisms of Epigenetic Regulation in Speciation

Epigenetic regulation encompasses various processes, including DNA methylation, histone modification, alternative splicing, and RNA editing. These mechanisms can produce heritable phenotypic changes that contribute to speciation.

DNA Methylation and Histone Modification

DNA methylation involves the addition of a methyl group to DNA, often resulting in gene silencing. Histone modification, including acetylation and methylation, alters chromatin structure, influencing gene expression. Both mechanisms can lead to significant phenotypic variations, enabling populations to adapt to different environmental conditions.

Alternative Splicing

Alternative splicing allows a single gene to produce multiple protein isoforms, enhancing the diversity of the proteome. This process is regulated by epigenetic factors and can generate functional differences crucial for adaptation and reproductive isolation.

RNA-Editing

RNA-editing modifies RNA molecules post-transcriptionally, altering the protein-coding potential without changing the underlying DNA sequence. This mechanism can introduce phenotypic variability, facilitating rapid adaptation to environmental changes.

Case Studies of Epigenetic Speciation

Several examples illustrate how epigenetic mechanisms drive speciation in various organisms:

1. 

   Heliconius Butterflies:

   • Mechanism: DNA methylation and histone modification.
   • Outcome: Wing pattern diversification leading to mimicry and mate selection, promoting reproductive isolation​ (Frontiers)​​ (Oxford Academic)​.
     

2. Lycaenid Butterflies:

   • Mechanism: Environmental stress-induced epigenetic changes.
   • Outcome: Heritable wing pattern modifications contributing to population divergence and speciation​ (Frontiers)​.

3. Pea Aphids (Acyrthosiphon pisum):

   • Mechanism: DNA methylation and histone modification.
   • Outcome: Adaptation to different host plants, leading to distinct ecotypes and speciation​ (Oxford Academic)​.

4. Bumblebees (Bombus terrestris):

   • Mechanism: Alternative splicing.
   • Outcome: Differences in behavior, physiology, and morphology, promoting ecological diversification and speciation​ (Oxford Academic)​.

5. Drosophila (Drosophila melanogaster):

   • Mechanism: Alternative splicing and RNA-editing.
   • Outcome: Sensory perception and mating behavior variations leading to reproductive isolation and speciation​ (Oxford Academic)​.

6. Lake Whitefish (Coregonus clupeaformis):

   • Mechanism: DNA methylation patterns.
   • Outcome: Adaptation to different ecological niches and reproductive isolation​ (Oxford Academic)​.

7. Black Poplar (Populus nigra):

   • Mechanism: Epigenetic variation.
   • Outcome: Rapid adaptation to environmental changes and population divergence​ (Christophe Ambroise)​.

8. House Sparrows (Passer domesticus):

   • Mechanism: Epigenetic variation.
   • Outcome: Adaptation to diverse environmental conditions, potentially leading to reproductive isolation and speciation over time​ (SpringerLink)​​ (Oxford Academic)​.

9. Polyploid Plants:

   • Mechanism: Epigenetic reprogramming in polyploid species.
   • Outcome: Stabilization of hybrid genomes leading to the formation of new species, as seen in the case of wheat (Triticum aestivum)​ (Oxford Academic)​​ (SpringerLink)​.

10. Darwin's Finches:

    • Mechanism: Epigenetic modifications, particularly DNA methylation patterns.
    • Outcome: Adaptive radiation and formation of new species due to changes in beak morphology and feeding behaviors​ (SpringerLink)​.

11. Cichlid Fish (Astatotilapia calliptera):

    • Mechanism: Divergent epigenetic patterns and alternative splicing.
    • Outcome: Adaptation to different ecological niches within Lake Masoko, leading to reproductive isolation and speciation​ (Oxford Academic)​.

12. Sunflower Speciation (Helianthus annuus and Helianthus petiolaris):

    • Mechanism: Alternative splicing.
    • Outcome: Splicing differences contributing to adaptation and ecological divergence, promoting reproductive isolation and speciation​ (Oxford Academic)​.

13. Head and Body Lice (Pediculus humanus):

    • Mechanism: Significant differences in gene expression due to alternative splicing.
    • Outcome: Adaptation to distinct environments and hosts, leading to ecological speciation​ (Oxford Academic)​.

14. House Mice (Mus musculus domesticus):

    • Mechanism: Alternative splicing and differential gene expression.
    • Outcome: Rapid adaptation to different environments, contributing to the divergence of populations and speciation​ (Oxford Academic)​.

Why Epigenetic Modifications Don't Lead to Evolution

Despite their profound impact on phenotypic variability and speciation, epigenetic modifications differ from genetic mutations in that they are reversible and dynamic. While genetic mutations are permanent changes in the DNA sequence, epigenetic marks can be added or removed in response to environmental cues. This flexibility allows organisms to rapidly adapt to changing conditions without committing to irreversible genetic changes. This transient nature means that epigenetic changes never lead to assumed evolution. Instead, epigenetic regulation results in inevitable genetic entropy.

Conclusion

Epigenetic mechanisms play a crucial role in driving rapid speciation by enabling organisms to quickly adapt to environmental changes through reversible modifications in gene expression. These processes, including DNA methylation, histone modification, alternative splicing, and RNA editing, create phenotypic diversity that can lead to reproductive isolation and the emergence of new species. However, the dynamic and reversible nature of these changes distinguishes them from genetic mutations, highlighting their unique role in speciation without contributing to long-term evolution.

Sources

1. Heliconius Butterflies: Frontiers in Ecology​ (Frontiers)​, Genetics​ (Oxford Academic)​
2. Lycaenid Butterflies: Color-pattern Evolution in Response to Environmental Stress in Butterflies​ (Frontiers)​
3. Pea Aphids: BioScience​ (Oxford Academic)​
4. Bumblebees: Genetics​ (Oxford Academic)​
5. Drosophila: BioScience​ (Oxford Academic)​
6. Lake Whitefish: Coregonus clupeaformis Epigenetic Speciation​ (Oxford Academic)​
7. Black Poplar: Epigenetic Variation in Tree Evolution: a case study in black poplar (Populus nigra)​ (Christophe Ambroise)​
8. House Sparrows: Frontiers in Ecology​ (SpringerLink)​​ (Oxford Academic)​
9. Polyploid Plants: BioScience​ (Oxford Academic)​​ (SpringerLink)​
10. Darwin's Finches: Frontiers in Ecology​ (SpringerLink)​
11. Cichlid Fish: BioScience​ (Oxford Academic)​
12. Sunflower Speciation: Genetics​ (Oxford Academic)​
13. Head and Body Lice: Genetics​ (Oxford Academic)​
14. House Mice: [BioScience](https://academic.oup.com

Epigenetic mechanisms and factors behind protein diversity

Instructions for protein production are not stored in DNA

The cell is able to use DNA very efficiently. By reading the same DNA sequence, a cell can produce thousands of different proteins without altering DNA. The best known DNA sequence from which a cell can produce up to 32,000 different proteins by alternative splicing is the Dscam sequence of a fruit fly. Such multifunctional utilization of DNA indicates not only the passive nature of DNA as a digital repository of information, but also that DNA doesn't provide instructions for protein production.

The accompanying study states quite unequivocally that alternative splicing, which is thus behind protein diversity, is driven by epigenetic mechanisms and factors.

https://www.cell.com/fulltext/S0092-8674(10)01378-4

Excerpts: "These insights suggest that epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced."

"A major recent discovery is that chromatin structure and epigenetic histone modifications act as key regulators of alternative splicing."

"Consistently, inhibition of histone deacetylation, DNA methylation, H3K9 methylation, and downregulation of heterochromatin protein 1α (HP1α) abolishes the siRNA-mediated effect on exon E33 splicing, suggesting a role of these modifications in alternative splicing regulation."

 

"These observations point to a role for epigenetic modifications in the regulation of alternative splicing, and this regulation may involve the modulation of RNA Pol II elongation rate."

"An advantage of such a histone-based alternative splicing regulatory system is that it would provide an epigenetic memory for splicing decisions that could be passed on during proliferation of a cell population and could be modified during differentiation without the requirement to establish a new set of alternative splicing rules at each step of differentiation. Obviously, an epigenetic alternative splicing memory would still require the proper expression of splicing factors, a process that itself may be controlled by epigenetic mechanisms. Regardless of mechanisms, it appears that epigenetic regulation is not limited to controlling what regions of the genome are expressed, but also how they are spliced."

Variation without changes in DNA

Epigenetic regulation of alternative splicing

https://science-explained.com/theory/one-gene-many-proteins-alternative-splicing/

Excerpt: "Just as it is possible to make different dishes by using some ingredients but leaving out others, it is also possible to make different proteins by including or leaving out certain “ingredients” of genes. This process is called alternative splicing and it makes it possible to produce different proteins from the same gene (these different protein versions from the same gene are called isoforms). In this way, our bodies can produce over 100.000 proteins from only 20.000 genes." (My add: Probably millions of different proteins according to latest research.)

"But what about alternative splicing? The principle is the same, a pre-mRNA is produced and spliced, a 5’ cap is added and a poly-A tail is added. The only difference is, that instead of just splicing the introns out, some exons might be spliced out too. This leads to different proteins, one in which all 3 exons are used and one in which only exon 1 and 3 are used. So one gene for two proteins (see figure below).

The example discussed here concerns a gene with only 3 exons. Although this keeps the explanation simple, it does not provide the potential of many different isoforms. If we would have more exons that would mean more flexibility in the number of proteins that can be formed from a single gene. The gene Dscam from the fruitfly (Drosophila melanogaster) has 95 exons and can form 38.016 different proteins. So this one fly gene can form more different proteins than the number of genes we humans have in total!  

All in all, alternative splicing is an essential part of complex animals like us. The use of alternative splicing makes it possible to have many different proteins to fulfil all the different tasks necessary in our lives without the need of a gigantic genome."

Alternative splicing (AS) is regulated by epigenetic mechanisms:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325479/

"Generally, AS can be coupled with transcription and subjected to epigenetic regulation, such as DNA methylation and histone modifications. In addition, ncRNAs, especially long noncoding RNAs (lncRNAs), can be generated from AS and function as splicing factors (“interactors” or “hijackers”) in AS."

My comment: Differences in the DNA are not the reason for human phenotypic variation. Genetically identical twins might have different colours of skin, hair and eyes. The most significant reason for variation in organismal characteristics can be found in epigenetic mechanisms and factors that regulate and mediate the alternative splicing mechanism. We should remember that genetically (DNA) all people are 99.9 % similar. The 0.1% difference is strongly related to hereditary diseases. This is why evolution believers hardly find fully beneficial DNA mutations. Evolution has no mechanism. Don't get lost.

The cell is able to compensate for a loss of gene function by programming alternative splicing to function more efficiently

This discovery helps us understand better the reasons for DNA rearrangements.

https://www.news-medical.net/news/20230221/Alternative-splicing-plays-a-role-in-compensating-for-loss-of-gene-function.aspx

Excerpt: "Living organisms have a knack for persisting in the face of challenges. For instance, when genes malfunction, organisms may be able to compensate by activating redundant genes with similar functions, called paralogs.

One example of such compensation are two genes of the muscleblind-like (MBNL) family of RNA-binding proteins that lose their function in Myotonic Dystrophy Type 1, the most common cause of adult-onset muscular dystrophy. Loss of MBNL1 increases the levels of its paralog MBNL2 in tissues where protein expression is low, allowing MBNL2 to functionally compensate for MBNL1 loss. In animal models, loss of one paralog results in no or only minor functional consequences, whereas loss of both paralogs leads to a severe condition and lethality.

"Although this form of compensation for loss of gene function has been widely observed, the underlying molecular mechanisms and roles in preventing or modifying disease severity are not well understood. In this study, we discovered how loss of MBNL1 leads to the compensatory increase of MBNL2 protein." 

Dr. Larissa Nitschke, first author, postdoctoral associate of pathology and immunology in Dr. Thomas A. Cooper's lab at Baylor College of Medicine

MBNL proteins are deeply involved in RNA processing, including alternative splicing, a process that allows cells to make many different proteins from a limited number of genes.


"To make proteins, genes in the DNA are transcribed into RNA, which is then translated into protein. Before RNA is translated into protein, it is processed and the fragments spliced in a certain way," said Cooper, R. Clarence and Irene H. Fulbright Chair and S. Donald Greenberg Chair in Pathology. He also is the corresponding author of the work.

"In almost all genes, the RNA is spliced in more than one way. That is alternative splicing; it allows one gene to make many different proteins. It would be like putting together different bracelets by combining a limited number of beads in unique ways."

Nitschke, Cooper and their colleagues found that loss of MBNL1 leads to the formation of MBNL2 with two new segments spliced to it, called exon 6 and exon 9.

"The inclusion of these exons gives MBNL2 new properties that enable it to compensate for the lack of MBNL1 function," Nitschke said. "Inclusion of exon 6 promotes a more efficient transit of MBNL2 into the nucleus of the cell where this protein conducts its function. Adding exon 9 makes the protein less susceptible to degradation and more stable, which allows it to effectively compensate for MBNL1 loss of function."

The researchers found evidence of redirection of splicing in an animal model of Myotonic Dystrophy Type 1, which suggests that the compensatory mechanism also may be active in human patients.

"Our findings could also provide an explanation for the high variability of the disease in terms of its features," said Cooper, a member of the Dan L Duncan Comprehensive Cancer Center at Baylor. "Myotonic Dystrophy Type 1 can be very severe or mild, even in the same family. Individual differences in the ability to conduct these compensatory measures may explain the differences in severity."

"The discovery of the compensatory mechanism also supports further studies to explore if, similar to the splicing-enhancing drugs in Spinal Muscular Atrophy, the mechanism could be leveraged for therapeutic purposes in Myotonic Dystrophy Type 1," Nitschke said.

"We are very excited about our findings," Cooper said. "We uncovered new insights into a little studied biological mechanism that impacts Myotonic Dystrophy Type 1 severity but also is applicable to other diseases and how the body maintains the status quo." "

Summary and conclusions:

• After loss of gene function the cell is able to reprogram alternative splicing mechanisms in order to compensate for the loss of information.
• Reprogramming of alternative splicing machinery requires rearrangement of DNA.
• This discovery emphasizes the passive role of DNA.
• This also points to an incredible, sophisticated and intelligent programming solution. The alternative splicing machinery is epigenetically programmed to work more efficiently after genetic errors have caused loss of information.
• Again, random mutations and selection have no role in these complex programming events.

Enormous protein diversity results from alternative splicing - Not from random mutations

Alternative splicing is regulated by epigenetic factors - the most significant mechanism for organismal changes

http://cbm.msoe.edu/images/contentImages/smartTeams/alumni/2011-12/Valders.pdf

Excerpt: "Alternative splicing allows more than one protein to be made from one gene.
Enormous protein diversity results from alternative splicing. Mammals are much more complex than nematodes and fruit flies, yet the genomes of these organisms differ by less than 2 fold (about 25,000, 20,000 and 14,000 genes, respectively). The extent to which alternative splicing contributes to the complexity of eukaryotic organisms is a question that remains unanswered, but a strong correlation exists between complexity and intron number and alternative splicing. One fact that remains clear though, is that alternative splicing is important for generating protein diversity."

How many different proteins is it possible to produce by using only one DNA strand (a gene)?

An example: If all combinations were used, the cell is able to produce 38,016 different protein isoforms by editing and manipulating pre-mRNAs made from only one Dscam gene template.

https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-post-translational-modification.html

Humans have fewer protein-coding genes (~19,600) than an earthworm (~20,470). This means that the genes we thought made us who we are, don't.

According to latest research, there are only ~19,000 DNA strands used for protein production in a human genome. But the number of different proteins in a human body is up to several millions.

What factors and mechanisms regulate this complex splicing procedure? 

1. DNA methylation profiles
2. Histone markers

3. Non coding RNA molecules
4. Transcription factors (proteins that bind to methylated regions).

These are epigenetic factors. Modifications in epigenetic information layers will never result in any kind of evolution, because it's only about switching between alternative biological programs.

Any change in organisms is due to epigenetic regulation of pre-existing biological information. DNA mutations are associated with genetic diseases and corruption of biological information. That's why there's no mechanism for evolution.

The central term of genetics— “the gene”—can no longer be defined in simple terms

Reasons why it's difficult to define a gene and why DNA is just a passive information library

http://www.genetics.org/content/205/4/1353

Summary:

• The hypothesis of “one gene—one mRNA—one polypeptide” as a general description of the gene and how it works started to expire, however, when it was realized that a single gene could produce more than one mRNA, and that one gene can be a part of several transcription units. This one-to-several relationship of genes to mRNAs occurs by means of complex promoters and/or alternative splicing of the primary transcript.
  
• Multiple transcription initiation sites, i.e., alternative promoters, have been found in all kingdoms of organisms, and they have been classified into six classes (Schibler and Sierra 1987). All of them can produce transcripts that do not obey the rule of one-to-one correspondence between the gene and the transcription unit, since transcription can be initiated at different promoters. The result is that a single gene can produce more than one kind of transcript (Schibler and Sierra 1987).
  
• The discovery of alternative splicing as a way of producing different transcripts from one gene had a more complex history. In the late 1970s it was discovered, first in animal viruses and then in eukaryotes, that genes have a split structure. That is, genes are interrupted by introns (see review by Portin 1993). Split genes produce one pre-mRNA molecule, from which the introns are removed during the maturation of the mRNA by pre-mRNA splicing. Depending on the gene, the splicing pattern can be invariant (“constitutive”) or variable (“alternative”). In constitutive splicing, all the exons present in a transcript are incorporated into one mature mRNA through invariant ligation of consecutive exons, yielding a single kind of mRNA from the gene. In alternative splicing, nonconsecutive exons are joined by the processing of some, but not all, transcripts from a gene. In other words, individual exons can be excluded from the mature mRNA in some transcripts, but they can be included in others (Leff et al. 1986; Black 2003). Alternative splicing is a regulated process, being tissue-specific and developmental-stage-specific. Nevertheless, the colinearity of the gene and the mRNA is preserved, since the order of the exons in the gene is not changed.
   
  
• In addition to alternative splicing, two other phenomena are now known that contradict a basic tenet of the neoclassical gene concept, namely that amino-acid sequences of proteins, and consequently their functions, are always derivable from the DNA of the corresponding gene. These are the phenomena of RNA editing (reviewed by Brennickle et al. 1999; Witzany 2011) and of gene sharing originally found by J. Piatigorsky (reviewed in Piatigorsky 2007). The term RNA editing describes post-transcriptional molecular processes in which the structure of an RNA molecule is altered. Though a rare event, it has been observed to occur in eukaryotes, their viruses, archaea and prokaryotes, and involves several kinds of base modifications in RNA molecules. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence (Brennickle et.al. 1999). The concept of gene sharing describes the fact that different cells contain identically sequenced polypeptides, derived from the same gene, but so differently configured in different cellular contexts that they perform wildly different functions. This phenomenon, facetiously called “protein moonlighting,” means that a gene may acquire and maintain a second function without gene duplication, and without loss of the primary function. Such genes are under two or more entirely different selective constraints (Piatigorsky and Wistow 1989).
  
   

Severe cracks in the concept of the gene

Matters changed, however, when the sequencing projects revealed still more bizarre phenomena:
These new findings have shown that there are multiple possible relationships between DNA sequences and the molecular products they specify. The net result has been the realization that the basic concept of the gene as some form of generic, universal “unit of heredity” is too simple, and correspondingly, that, a new definition or concept of “the gene” is needed (Keller 2000; Falk 2009; Portin 2009). Several observations have been crucial to this re-evaluation, and one of us has reviewed these relatively recently (Portin 2009). They are worth summarizing here:

1. In eukaryotic organisms, there are few if any absolute boundaries to transcription, making it impossible to establish simple general relationships between primary transcripts and the ultimate products of those transcripts.
   
   Hence, the structural boundaries of the gene as the unit of transcription are often far from clear, as documented particularly well in mammals (reviewed by Carninci 2006). In reality, whole chromosomes, if not the whole genome, seem to be continuums of transcription (Gingeras 2007). Furthermore, the genome is full of overlapping transcripts, thus making it impossible to draw 1:1:1 relationship between specific DNA sequences, transcripts and functions (Pearson 2006). Indeed, convincing evidence indicates that the human genome is comprehensively transcribed from both DNA strands, so that the majority of its bases can be found in primary transcripts that compendiously overlap one another (The FANTOM Consortium and RIKEN Genome Exploration Group 2005; The ENCODE Project Consortium 2007; 2012). Both protein coding and noncoding transcripts may be derived from either or both DNA strands, and they may be overlapping and interlaced. Furthermore, different transcripts often include the same coding sequences (Mattick 2005). The functional significance of these overlaps is still largely unclear, but there is an increasing number of examples in which both transcripts are known to have protein-coding exons from one position in the genome combined with exons from another part of the genome hundreds of thousands of nucleotides away (Kapranov et al. 2007). This was wholly unanticipated when the 1960s definition of the gene was formulated.
   
   
2. Exons of different genes can be members of more than one transcript.
   Gene fusion, at the level of transcripts, is a reality, and is completely at odds with the “one gene—one mRNA—one protein” hypothesis. And this is not a rare phenomenon. It has been estimated that at least 4–5% of the tandem gene pairs in the human genome can be transcribed into a single RNA sequence, called chimeric transcripts, encoding a putative chimeric protein (Parra et al. 2006).
   
   
3. Comparably, in the organelles of microbial eukaryotes, many examples of “encrypted” genes are known: genes are often in pieces that can be found as separate segments around the genome.
   Hence, in addition to the fusion of two adjacent genes at the level of transcription, different building blocks of a given mRNA molecule can often be located, as modules, on different chromosomes (reviewed in Landweber 2007). Some evidence indicates that, even in multicellular eukaryotes, protein-coding transcripts are derived from different nonhomologous chromosomes (reviewed in Claverie 2005).
   
   
4. In contradiction to the neoclassical definition of a gene, which posits that the hereditary information resides solely in DNA sequences, there is increasing evidence that the functional status of some genes can be inherited from one generation of individuals to the next, a phenomenon known as transgenerational epigenetic inheritance (Holliday 1987; Gerhart and Kirschner 2007; Jablonka and Raz 2009).
   
   
5. Finally, in addition to protein coding genes, there are many RNA-encoding genes that produce diverse RNA molecules that are not translated to proteins.

My comment: Defining a gene seems to be very complex. This points to Intelligent Design and Creation. 

Gene Duplications don't lead to Evolution

Gene Duplications Point to Intelligent Design and Creation

"By faith we understand that the universe was formed at God's command, so that what is seen was not made out of what was visible." (Hebrews 11:3, NIV)

Gene duplications are remarkable processes that underscore the complexity and precision of genetic mechanisms, pointing towards Intelligent Design and Creation. Unlike the gradualistic explanations offered by evolutionary theory, the evidence suggests that gene duplications are epigenetically controlled and regulated events, enabling organisms to adapt rapidly and efficiently to environmental changes.

Epigenetically Controlled Gene Duplications

Gene duplications are not random occurrences but are guided by epigenetic mechanisms. These mechanisms include histone modifications, DNA methylation, and non-coding RNAs, which together ensure that duplications occur in a controlled manner. For instance, histone acetylation can relax chromatin structure, making specific genomic regions more accessible for duplication. DNA methylation patterns can change in response to environmental triggers, such as stress or dietary changes, initiating the duplication process. Non-coding RNAs, such as microRNAs, can further regulate gene expression by binding to mRNA transcripts and preventing their translation.

Once a gene is duplicated, the cell must manage the additional genetic material. This often involves DNA loss mechanisms, such as unequal crossing over during meiosis, which help maintain genomic integrity by removing excess DNA. This dynamic balance ensures that the genome does not become unwieldy while still allowing for genetic adaptability.

Harmfulness of Gene Duplications in Diploid Organisms

In diploid organisms, like humans, gene duplications can often be detrimental. Duplications can disrupt the balance of gene dosage, leading to genetic disorders and diseases. For example, the duplication of certain genes has been associated with conditions like Charcot-Marie-Tooth disease and some forms of cancer. This indicates that while gene duplications can provide adaptability, they also carry significant risks if not precisely regulated.

Regulatory Mechanisms Necessary for Controlled Gene Duplication

For gene duplications to occur in a controlled manner, several regulatory mechanisms must be precisely in place:

1. Epigenetic Marks: Histone modifications and DNA methylation patterns must be established and maintained to identify which genes can be duplicated.
2. Non-coding RNAs: MicroRNAs and long non-coding RNAs must regulate the stability and translation of mRNA transcripts.
3. Transcription Factors: Specific proteins must bind to promoter regions to initiate or suppress gene expression.
4. CpG Islands: Regions rich in cytosine and guanine nucleotides must be appropriately methylated to control gene expression.
5. 4D Genome Architecture: The spatial organization of the genome within the nucleus must facilitate the accessibility and replication of specific regions.

These mechanisms highlight the complexity and precision required for gene duplications, reinforcing the concept of Intelligent Design.

Gene Duplications and Biological Information

Contrary to evolutionary claims, gene duplication does not create new biological information. Instead, it results in the copying of existing genetic material. The duplicated gene may undergo intentional alterations or acquire new functions (by using different splice variants), but this is a modification of pre-existing information rather than the creation of novel information. Specific enzymes, such as ADAR, A3G, and AID can also target duplicated genes for intentional modifications. For instance, ADARs and APOBECs can edit RNA transcripts from duplicated genes, leading to changes in protein function or gene regulation. In some cases, these edits can create new splice variants or alter mRNA stability, thereby modulating the expression and function of the duplicated gene copies​ (BioMed Central) Intelligent Design posits that the original genetic information was created with the capacity for such modifications, allowing organisms to adapt without the need for new genetic information to evolve from non-information.

The Human AMY Gene Family

The human AMY gene family, which includes genes responsible for amylase production (AMY1 for salivary amylase and AMY2 for pancreatic amylase), showcases the complexity of epigenetic control of DNA. These genes can produce multiple splice variants (different mRNAs) through alternative splicing, a process that is itself highly regulated and complex.

Alternative Splicing

Alternative splicing allows a single gene to produce multiple mRNA variants, leading to the production of different protein isoforms. For a gene duplicate to function, several epigenetic mechanisms and factors must be precisely in place:

• DNA Methylation: Influences which exons are included in the final mRNA transcript.
• Histone Modifications: Affect chromatin structure and gene accessibility.
• RNA Molecules: Non-coding RNAs can bind to mRNA transcripts, influencing splicing choices.
• Transcription Factors: Bind to enhancer or silencer regions to regulate splicing.
• CpG Islands: Act as regulatory regions that can enhance or suppress transcription.
• 4D Genome: The spatial arrangement of DNA within the nucleus affects gene expression and splicing outcomes.

The sophisticated regulation of the AMY gene family through alternative splicing underscores the complexity and precision of genetic mechanisms, pointing to an intelligent design rather than random evolutionary processes.

Conclusion

If gene duplication mechanisms are so vital for the survival of polyploid organisms, evolutionary theory would suggest that selective pressure should favor the preservation and development of such mechanisms in diploid organisms, like humans. However, it can be observed that gene duplications in humans and other diploid organisms are generally harmful, raising questions about evolution's ability to explain the uneven distribution of these mechanisms.

Gene duplications and their regulation provide compelling evidence for Intelligent Design and Creation. The intricate mechanisms that control gene duplications, the potentially harmful effects of duplications in diploid organisms, and the complexity of processes like alternative splicing all point to a designed and purposeful genetic system. This aligns with the Biblical view of a Creator who designed life with the ability to adapt and thrive in a changing world.

References

1. Epigenetic regulation of gene expression: how the environment influences our genes, Nature Reviews Genetics.
2. The role of non-coding RNAs in gene regulation, Cell.
3. Gene duplications and their impact on human disease, Journal of Medical Genetics.
4. Alternative splicing: a means to an end or an end to a means? Nature Reviews Molecular Cell Biology.
5. 4D genome organization and its implications for gene regulation, Genome Biology.

Protein coding genes are just raw data

An astonishing similarity of protein coding genes in humans, pigs, mice, dolphins, kangaroos, spiders etc.

https://proteomics.cancer.gov/whatisproteomics

Excerpt: "The human genome contains about 21,000 protein-encoding genes, but the total number of proteins in human cells is estimated to be between 250,000 to one MILLION."

My comment: Newest studies have confirmed the number of human protein coding genes to be about 19,000. RNA-directed cellular mechanisms are able to build thousands of different proteins by using raw data of one gene, without changing the gene's sequence. Mechanism is called alternative mRNA splicing. Based on DSCAM gene in Drosophila Melanogaster, the fruit fly's cell is able to build even 38,016 different proteins, without changing the sequence. The way of how the cell uses protein coding genes tells us that genes are not drivers. Instead, they are just raw data, libraries for RNA-directed mechanisms.

http://www.sciencedirect.com/science/article/pii/S0092867400001288

 

The alternative splicing is the most significant mechanism inducing the ecological adaptation and organisms' variation. The clever question arises: how come variation of organisms happen if the sequences of protein coding genes are not to be changed? Mutations in protein coding genes could be extremely harmful and they would cause a huge mess in genomic stability and integrity.

Serious science has the answer:
Epigenetic Control of Gene Expression. The alternative splicing mechanism is regulated by several epigenetic factors. The three main regulators are:

1. The DNA methylation.
http://www.cell.com/trends/genetics/abstract/S0168-9525(15)00040-2

2. MicroRNA downregulation.
https://www.lakeforest.edu/live/news/4451-co-regulation-of-mirna-biogenesis-and-alternative

3. Histone methylation
https://www.ncbi.nlm.nih.gov/pubmed/27606339

By the way, did you know that the C. Elegans, a tiny multicellular nematode worm, that is assumed to be a simple type of organism, has 20,450 protein coding genes? More than us! It is not a simple life form! It also uses the alternative splicing machinery for regulating its proteins in 1031 cells it has.

Protein coding genes are very similar in most animals. For example, human and mice genomes differ only at 2.5%.

https://www.newscientist.com/article/dn2352-just-2-5-of-dna-turns-mice-into-men/

Human and pig genomes are also extremely similar.

http://www.nationalhogfarmer.com/news/human-to-pig

"We took the human genome, cut it into 173 puzzle pieces and rearranged it to make a pig,” explains animal geneticist Lawrence Schook. “Everything matches up perfectly. The pig is genetically very close to humans."

Human protein coding genes are also very similar to kangaroos, dolphins, spiders etc. These are very inconvenient facts for believers of the evolutionary theory that is misleading people by maintaining the heresy of human-chimp genomic similarity. They don't tell you that the famous 98% is true only with these protein coding genes. But when we compare the alternative splicing mechanism and epigenomes, the differences are quite remarkable.

Everything points to Design and Creation. Don't get misled.