Theory of Intelligent Design, the best explanation of Origins

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76 Re: My articles on Wed Mar 08, 2017 2:21 am



In photosynthesis, 26 protein complexes and enzymes are required to go through the light and light-independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose and O2 as end products. A good part of the protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and oxygen, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, and no advanced life would be possible on earth.

So, photosynthesis is a interdependent system that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage -- all happened by a series of natural events that we can call ad hoc mistakes "formed in one particular moment without ability to consider any application," to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to "feed" ATP synthase nano motors to produce ATP, and so on? Such independent structures would have not aided survival.

Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning, various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function. So it seems that photosynthesis falsifies the theory of evolution, where every small step needs to provide a survival advantage.

Fun and games with Otangelo Grasso about photosynthesis

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77 Re: My articles on Wed Mar 29, 2017 5:53 pm


Chromosome condensation, amazing evidence of design

Imagine trying to stuff about 10,000 miles of spaghetti inside a basketball.  Then, if that was not difficult enough, attempt to find a unique one inch segment of pasta from the middle of this mess, or try to duplicate, untangle and separate individual strings to opposite ends.  This simple analogy illustrates some of the daunting tasks associated with the transcription, repair and replication of the nearly 2 meters of DNA that is packaged into the confines of a tiny eukaryotic nucleus.  The solution to each of these problems lies in the assembly of the eukaryotic genome into chromatin, a structural polymer that not only solves the basic packaging problem, but also provides a dynamic platform that controls all DNA-mediated processes within the nucleus.

Every second, the cells constituting our bodies are replaced through cell division. An adult human consists of about 50,000 billion cells, 1% of which die and are replaced by cell division every day. In order to ensure cell survival and controlled growth of these new cells, the genetic information, stored in DNA molecules, must first be correctly copied and then accurately distributed during cell division. Moreover, to fully ascertain that the new cells will contain the same genetic information as the parental cells, any damage to the DNA, which is organised into several chromosomes, must be repaired.

Quite a bit is known about two of these complexes. One of them, cohesin, keeps the DNA copies together such that they do not separate too early; while the other, condensin, makes the chromosomes more compact, making the separation easier.

During the first stage of mitosis, that of prophase, the duplicated chromosomes are prepared for segregation and the mitotic machinery is assembled. The nucleus of an interphase cell contains tremendous lengths of chromatin fibers. The extended state of interphase chromatin is ideally suited for the processes of transcription and replication but not for segregation into two daughter cells. Before segregating its chromosomes, a cell converts them into much shorter, thicker structures by a remarkable process of chromosome compaction (or chromosome condensation), which occurs during early prophase

Research on chromosome compaction has focused on an abundant multiprotein complex called condensin.

Packing ratio is the length of DNA divided by the length into which it is packaged.

The shortest human chromosome contains 4.6 x 107 bp of DNA (about 10 times the genome size of E. coli). This is equivalent to 14,000 µm of extended DNA, or about 2 meters. In its most condensed state during mitosis, the chromosome is about 2 µm long. This gives a packing ratio of 7000 (14,000/2). That means, it becomes 7000 times shorter !!

To achieve the overall packing ratio, DNA is not packaged directly into final structure of chromatin. Instead, it contains several hierarchies of organization. The first level of packing is achieved by the winding of DNA around a protein core to produce a "bead-like" structure called a nucleosome. This gives a packing ratio of about 6. This structure is invariant in both the euchromatin and heterochromatin of all chromosomes.

The second level of packing is the coiling of beads in a helical structure called the 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes. This structure increases the packing ratio to about 40.

The final packaging occurs when the fiber is organized in loops, scaffolds and domains that give a final packing ratio of about 1000 in interphase chromosomes and about 7,000 in mitotic chromosomes.

Thats a amazing change , from a ratio of 6, to 7.000 !!

Squeezing DNA Into A Small Space

To fit 2 meters of DNA into a tiny nucleus is a monumental engineering feat. DNA is highly compacted yet has to be instantly available to rapidly make proteins in neurons with a momentary change of thought. This regulation is different in each type of cell. . It has been known for some time that the shape of proteins determines their function and the folding is very complex involving four levels of folding . Now it appears that the shape of the chromatin, also, determines function, with new secondary and tertiary structures discovered.

Condensins: universal organizers of chromosomes with diverse functions

Condensins are multisubunit protein complexes that play a fundamental role in the structural and functional organization of chromosomes in the three domains of life. It is a molecular machine that helps to condense and package chromosomes for cell replication. It is a five subunit complex, and is “the key molecular machine of chromosome condensation."

Condensin produces “supercoils” of DNA, one of many steps in packing the delicate DNA strands into a hierarchy of coils that results in a densely-packed chromosome.  “It is not entirely clear how the DNA is held in this supercoiled state,” they say, “but several studies suggest that the V-shaped arms of the condensin complex may loop and clamp the DNA in place.”  This clamping is “rapid and reversible.”  Scientists watching the process in both bacteria and humans are “showing that both vertebrate and bacterial condensins drive DNA compaction in an ATP-dependent fashion with a surprising level of co-operativity that was not fully appreciated.” The condensin molecules work as a team; if not enough condensin is around, nothing happens.     These authors point out also that condensin is just one of many enzymes involved in chromosome formation.  Think about how remarkable it is that during each cell division, the chromosomes are structured so reliably that they can be labeled and numbered under the microscope.  “Our own proteomic analysis,” they claim, “has identified over 350 chromosome-associated proteins, so there is clearly more work to be done.”

How could these nano machines arise by natural means, in a gradual stepwise manner ?   Unless someone can demonstrate a series of small steps to climb mount unprobable (as Richard Dawkins calls the challenge of evolving complex, information-rich, functional biological structures), this is wishful thinking.  The mountain is not a series of small steps, but a sheer cliff with slippery vertical walls.  And why would a mindless molecule even want to go climb uphill against its natural inclinations? The discoveries in biochemistry are making evolution increasingly untenable.  Here we see highly complex molecules, made up of building blocks (amino acids) arranged in precise sequences to build functioning machines.  The complexity is mind-boggling, and it exists all the way down in the very simplest single-celled life forms, with no precursors.  Without these machines, the cell could not divide. Proposing intelligent design is not a argument of ignorance. We know that intelligent minds are capable of projecting complex machines where ideas of problem solutions are required. Intelligent minds are able to store large quantities of information into small spaces, computer chips are a good example.  As conclusion, Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.

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