Why do you never see in science articles asking questions like this ? What emerged first, Genes, or the gene regulatory network, and the information to pick or suppress the right genes at the right time? Simple. Because such simple questions make it evidently clear why naturalism fails. No Nobel price needed... btw.....
Interdependence of the DNA double helix, the genetic code, and the machinery to transcribe and translate the code to make proteins 3
Can a alphabet arise without a intelligent mind inventing it ? What good is a alphabet for, if there is no medium like ink and paper to write a message on the paper, if there is no one to actually write a message, and no one to read and understand it upon common agreement of meaning of words and language, between sender and receiver ??
Can the DNA code arise without a intelligent mind inventing it ? What good is the DNA code for, if there is no medium like the DNA double helix, to encode the information required to make proteins ? What good is the DNA code for, the software, and the DNA double helix, the hardware, if there is no machinery to read, transcribe and translate the message stored in DNA to make proteins ? Must not all come into existence all at ones , otherwise, if one is missing, the others have no function ?
The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics.
Must not only the alphabet, but also the storage medium be invented ? - That can be ink and paper, the hardware of a computer, or the morse code in various mediums ?
Must not only the DNA code, but also the storage medium , the double helix, AND also the machinery to read and transcribe the message be invented, otherwise the first two have no function ?
In the cell, things are however far more complex. There is a whole chain of subsequent events that must all be fully operational, and the machinery in place, in order to make the final product, that is proteins. That chain is constituted by INITIATION OF TRANSCRIPTION, CAPPING, ELONGATION, SPLICING, CLEAVAGE,POLYADENYLATION AND TERMINATION, EXPORT FROM THE NUCLEUS TO THE CYTOSOL, INITIATION OF PROTEIN SYNTHESIS (TRANSLATION), COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING. In order for evolution to work, the robot-like working machinery and assembly line must be in place, fully operational. So the origin of the machines cannot be explained through evolution. All there is left, are random chemical reactions, or design. Chose which explanation seems more fitting the evidence.
Interdependence of the promoter region in DNA, transcription factors, and RNA polymerase II 4
Transcription is the process of making RNA from a DNA template. Several key factors are involved in this process. Including, DNA, transcription factors, RNA polymerase, and ATP. This is a irreducible complex system. DNA, transcription factors, RNA polymerase, and ATP must be present, otherwise transcription cannot occur. What came first, the TATA Box in the promoter region in DNA, or transcription factors, controlling the rate of transcription of genetic information from DNA to messenger RNA ? What use does one have without the other ? Both must have come into existence in the right exact time. And the RNA polymerase machine as well, since the other two without it have no function either. That is extremely sophisticated, interdependenet machinery that had to come into existence all at once. Thats best explained through a designer. There are many more molecular machines involved in the process, namely additional proteins such as coactivators, chromatin remodelers, histone acetylases, deacetylases, kinases, and methylases etc..... this is a interdependent, highly coordinated complex machinery, where the single parts have no use, unless in conjunction with all other parts. This is one more prima facie example of intelligent design in micro biology.
In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. 1
For the transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase. These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expression.
In eukariotic cells, the response elements in promoter regions are Pribnow box, TATA box, BRE, CAAT box
The cell is irreducibly complex 7
The cell is an interdependent functional city. We state, “The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.” The notion of the theoretical first cell arising by natural causes is a perfect example of irreducibly complexity. Life cannot exist without many numerous interdependent complex systems, each irreducibly complex on their own, working together to bring about a grand pageant for life to exist.
Cell Membranes, origins through natural mechanisms, or design ? 6
According to this website : The Interdependency of Lipid Membranes and Membrane Proteins
The cell membrane contains various types of proteins, including ion channel proteins, proton pumps, G proteins, and enzymes. These membrane proteins function cooperatively to allow ions to penetrate the lipid bilayer. The interdependency of lipid membranes and membrane proteins suggests that lipid bilayers and membrane proteins co-evolved together with membrane bioenergetics.
My comment: The nonsense of this assertion is evident. How could the membrane proteins co-evolve, if they had to be manufactured in the machinery , protected by the cell membrane ?
The cell membrane contains various types of proteins, including ion channel proteins, proton pumps, G proteins, and enzymes. These membrane proteins function cooperatively to allow ions to penetrate the lipid bilayer.
The ER and Golgi apparatus together constitute the endomembrane compartment in the cytoplasm of eukaryotic cells. The endomembrane compartment is a major site of lipid synthesis, and the ER is where not only lipids are synthesized, but membrane-bound proteins and secretory proteins are also made.
My comment: So in order to make cell membranes, the Endoplasmic Recticulum is required. But also the Golgi Apparatus, the peroxysome, and the mitochondria. But these only function, if protected and encapsulated in the cell membrane. What came first, the cell membrane, or the endoplasmic recticulum ? This is one of many other catch22 situations in the cell, which indicate that the cell could not emerge in a stepwise gradual manner, as proponents of natural mechanisms want to make us believe.
Not only is the cell membrane intricate and complex (and certainly not random), but it has tuning parameters such as the degree to which the phospholipid tails are saturated. It is another example of a sophisticated biological design about which evolutionists can only speculate. Random mutations must have luckily assembled molecular mechanisms which sense environmental challenges and respond to them by altering the phospholipid population in the membrane in just the right way. Such designs are tremendously helpful so of course they would have been preserved by natural selection. It is yet another example of how silly evolutionary theory is in light of scientific facts.
Nucleosomes and irreducible complexity 8
A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. This structure is often compared to thread wrapped around a spool. The basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies of each histone H2A, H2B, H3 and H4. Linker histone H1 binds the DNA between nucleosomes and facilitates packaging of the 10 nm "beads on the string" nucleosomal chain into a more condensed 30 nm fiber.
Histones are among the most highly conserved eucaryotic proteins. For example, the amino acid sequence of histone H4 from a pea and from a cow differ at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate a given histone gene in uitro andintroduce it into the yeast genome in place of the
normal gene. As might be expected, most changes in histone sequences are lethal; the few that are not lethal cause changes in the normal pattern of gene expression, as well as other abnormalities.
If a change in histone sequences are lethal, how could it probably come to be in gradual steps, or trial and error ? As long as the correct sequence is not reached, no function.....
Nucleosome assembly following DNA replication, DNA repair and gene transcription is critical for the maintenance of genome stability and epigenetic information.
In assembling a nucleosome, the histone folds first bind to each other to form H3-H4 and H2A-H2B dimers, and the H3-H4 dimers combine to form tetramers. An H3-H4 tetramer then further combines with two HZA-H2B dimers to form the compact octamer core, around which the DNA is wound.
The assembly is a sequential multistep process, requiring several folds and steps in a highly organized, regulated and precise manner, and must have been programmed and functional right from the beginning. Histone chaperones play important roles in regulating the intricate steps involved in folding of histones together with DNA to form correctly assembled nucleosomes, furthermore assembly, disassembly and histone exchange to facilitate DNA replication, repair and transcription. There is a need for histone chaperones to guide the process and each step along the assembly pathway is carefully controlled and regulated by these histone chaperones. It is evident that a stepwise evolutionary fashion of development of histone chaperones to guide the process would result in a disaster. They had to be there fully working and programmed to do their job right from the start.
Furthermore, to add to the already amazing machine like performance, (linker histones) have to participate at each step in the processes of nucleosome assembly, disassembly and histone exchange during different genomic processes. Linker histone H1 is an essential component of chromatin structure ( so its irreducible ). H1 links nucleosomes into higher order structures.
Nucleosome formation is dependent on the positive charges of the H4 histones and the negative charge on the surface of H2A histone fold domains. Acetylation of the histone tails disrupts this association, leading to weaker binding of the nucleosomal components. Histone acetyltransferases (HATs) and Histone deacetylase ( HDAC ) are also essential enzymes, that remove through acetylation the positive charge on the histones, and as a consequence, the condensed chromatin is transformed into a more relaxed structure that is associated with greater levels of gene transcription. This relaxation can be reversed by HDAC activity.
So we can conclude that all these parts, DNA, Linker histone H1, histones H2A, H2B, H3 and H4,and acetyltransferases (HATs) and Histone deacetylase ( HDAC ) form a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system, while Histone chaperones are also essential to build the since they guide the process and each step along the assembly pathway.
Eye / brain is a interdependent and irreducible complex system 9
The visual system is made of three major parts: the eyeballs with retina, the optic nerve, and the visual cortex. The eye ball has at least individual 16 parts, while the visual system, consisting in the optic nerve and visual cortex, en-globes total at least another individual 14 parts. These items are minimal requirements for vision of humans. The question is, which evolved first: the retina (eyeball), the optic nerve, or the visual cortex ? Since all of these are interdependent, they would have had to arise and evolve at the same time, either interconnect since the beginning, or at the right time all togheter, once fully evolved. Not one of the three items could have preceded the others, as they would be useless. It is unimaginable to think of a different use that could be assigned to each part individually, and how each could individually have function and advantage of survival. If any one to three of these items were partially evolved, no vision would be achieved. There would be no possible advantage, and evolution could not continue.
The thalamus relies on electrochemical codes to the visual cortex. The visual cortex then interprets the signals and converts the signals into light, color, and visual images. Light, color, and visual images do not exist at all outside of a receptive brain. In fact they don’t exist at all inside of our visual cortex. Our visual images are pure perception. Tehy don’t exist in reality. The brain “manufactures” the light that we see, as well as the odors that we smell, sound we hear, taste, and texture. Without a brain’s visual cortex to interpret the signals it gets from the retina, the electromagnetic waves from the sun would only be useful in warming and energizing the planet earth. How would evolution “know” that if it evolved this incredibly complex vision system, light, color, and incredible images would be at the finish line.
If a change in selective pressures favored a dimpled eyespot with a slight increase in visual acuity, pretty soon the majority of the population would have dimpled eyespots. The problem with this notion is that no population of creatures with flat eyespots shows any sort of intra-population range like this were even a small portion of the population has dimpled eyespots to any selectable degree. This is a common assertion, but it just isn't true.
the first step in vision is the detection of photons. In order to detect a photon, specialized cells use a molecule called 11-cis-retinal. When a photon of light interacts with this molecule, it changes its shape almost instantly. It is now called trans-retinal. This change in shape causes a change in shape of another molecule called rhodopsin. The new shape of rhodopsin is called metarhodopsin II. Metarhodopsin II now sticks to another protein called transducin forcing it to drop an attached molecule called GDP and pick up another molecule called GTP. The GTP-transducin-metarhodopsin II molecule now attaches to another protein called phosphodiesterase. When this happens, phosphodiesterase cleaves molecules called cGMPs. This cleavage of cGMPs reduces their relative numbers in the cell. This reduction in cGMP is sensed by an ion channel. This ion channel shuts off the ability of the sodium ion to enter the cell. This blockage of sodium entrance into the cell causes an imbalance of charge across the cell's membrane. This imbalance of charge sends an electrical current to the brain. The brain then interprets this signal and the result is called vision.
Many other proteins are now needed to convert the proteins and other molecules just mentioned back to their original forms so that they can detect another photon of light and signal the brain. If any one of these proteins or molecules is missing, even in the simplest eye system, vision will not occur
The question now of course is, how could such a system evolve gradually? All the pieces must be in place simultaneously. For example, what good would it be for an earthworm that has no eyes to suddenly evolve the protein 11-cis-retinal in a small group or "spot" of cells on its head? These cells now have the ability to detect photons, but so what? What benefit is that to the earthworm? Now, lets say that somehow these cells develop all the needed proteins to activate an electrical charge across their membranes in response to a photon of light striking them. So what?! What good is it for them to be able to establish an electrical gradient across their membranes if there is no nervous pathway to the worm's minute brain? Now, what if this pathway did happen to suddenly evolve and such a signal could be sent to the worm's brain. So what?! How is the worm going to know what to do with this signal? It will have to learn what this signal means. Learning and interpretation are very complicated processes involving a great many other proteins in other unique systems. Now the earthworm, in one lifetime, must evolve the ability to pass on this ability to interpret vision to its offspring. If it does not pass on this ability, the offspring must learn as well or vision offers no advantage to them. All of these wonderful processes need regulation. No function is beneficial unless it can be regulated (turned off and on). If the light sensitive cells cannot be turned off once they are turned on, vision does not occur. This regulatory ability is also very complicated involving a great many proteins and other molecules - all of which must be in place initially for vision to be beneficial.
The complexity of transcription through RNA polymerase enzymes and general transcription factors in eukaryotes 10
Transcription is the process of making RNA from a DNA template. Several key factors are involved in this process. Including, DNA, transcription factors, RNA polymerase, and ATP.
Many proteins (well over 100 individual subunits) must assemble at the start point of transcription to initiate transcription in a eucaryotic cell.
This is a irreducible complex system. DNA, transcription factors, RNA polymerase, and ATP must be present, otherwise transcription cannot occur.
Transcription begins with a strand of DNA. It is divided into several important regions. The largest of these is the transcription unit. This portion of the DNA will be used to produce RNA. Upstream of the transcription unit is the TATA box. An enhancer region may also be involved.
Several complexes, known as transcription factors, are required for successful transcription. The first is TFIID, the largest of the general factors. A component of this factor, TBP, binds to the DNA using the TATA box to position TFIID near the transcription initiation site. Other transcription factors, including TFIIA and TFIIB, then attach.
These complexes prepare the DNA for the successful binding of RNA polymerase. One RNA polymerase is bound, other transcription factors complete the mature transcription complex.
Now, energy must be added to the system for transcription to begin. This energy is provided by the reduction of ATP into ADP and Pi.
RNA polymerase then synthesizes an RNA template from the strand of DNA. Most factors are released after transcription begins. When the end of the transcription unit is reached, the RNA polymerase dissociates, and the newly formed strand of RNA is released.
All the parts must come into existence at the same time, one has no function without the others. Also the whole sequence of events must be coordinated, and all parts must fit precisely together. There is no feasable mechanism producing this complex system randomly and in a stepwise fashion. Evolution is not a option, since transcription is required to make proteins, which are required to make replication work, which is essential upon which evolution works.
Catch22, chicken and egg problems in biology and biochemistry
A list of irreducible complex systems
8 ) https://reasonandscience.catsboard.com/t2051-nucleosomes-function-and-design?highlight=nucleosomes
Last edited by Otangelo on Thu Jan 07, 2021 8:20 am; edited 12 times in total