Intelligent Design, the best explanation of Origins
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Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity

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Intelligent Design, the best explanation of Origins » Origin of life » Genetics It is known that DNA is made up of of nonorganic elements found in dust

Genetics It is known that DNA is made up of of nonorganic elements found in dust

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It is known that DNA is made up of of nonorganic elements found in dust:

“The basic chemicals found in DNA are carbon, nitrogen, hydrogen, oxygen and phosphorous.”
Mitochondrial DNA Testing website, “What is DNA made of?” page.

These elements were thought to assemble into four chemical bases called adenine, guanine, cytosine, and thymine, which pair up with each other to form ‘base pairs’:
“The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T) … The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.
DNA bases pair up with each other, A with T and C with G, to form units called base pairs.”
Genetics Home Reference Handbook, “What is DNA?”

In a surprising twist, it has been recently discovered that there are actually six chemical bases, the additional two being modifications of cytosine:
“For decades, scientists have known that DNA consists of four basic units — adenine, guanine, thymine and cytosine. Those four bases have been taught in science textbooks and have formed the basis of the growing knowledge regarding how genes code for life. Yet in recent history, scientists have expanded that list from four to six.
Now, with a finding published online in the July 21, 2011, issue of the journal Science, researchers from the UNC School of Medicine have discovered the seventh and eighth bases of DNA.
These last two bases – called 5-formylcytosine and 5 carboxylcytosine – are actually versions of cytosine that have been modified by Tet proteins, molecular entities thought to play a role in DNA demethylation and stem cell reprogramming.”
University of North Carolina, “Scientists identify seventh and eighth bases of DNA,” July 21, 2011,

The order of these pairs make-up ‘sequences’ of code that creates the initial assembly of biological organisms as well as maintaining each of their features:
“Each base is also attached to a sugar molecule and a phosphate molecule. Together, a base, sugar, and phosphate are called a nucleotide. Nucleotides are arranged in two long strands that form a spiral called a double helix.”
Genetics Home Reference:Handbook, “What is DNA?”

The DNA sequences go through a ‘transcription’ and ‘translation’ process (refer to “The machine of DNA in real time” link below), which ultimately creates the proteins necessary to build and maintain life:
“To carry out these functions, DNA sequences must be converted into messages that can be used to produce proteins, which are the complex molecules that do most of the work in our bodies.”
National Human Genome Research Institute:Education, “What Does DNA Do?”

These are excellent videos that show some of these processes:
“DNA Structure”
“The machine of DNA in real time” from Walter Eliza Hall Institute of Medical Research.
“DNA: Secrete of Life” from PBS.
“Journey Inside The Cell” from Discovery Institute.

Geneticists once believed that the DNA sequences that code for proteins (genes) were the key to building and maintaining healthy cells. When all sorts of peripheral genetic elements were discovered in the last 50+ years, evolutionary geneticists referred to them as “junk DNA” on the assumption that they were nothing but useless genetic remnants left over from evolutionary predecessors.
Come to find out, these regulatory elements are the key to cellular health and development as well as the primary link to disease when not functioning properly:

“Many parts of DNA previously termed ‘junk’ by scientists are, instead, levers that control the genetic activity that can lead alternately to health or illness, according to reports published simultaneously today in the journals Science and Nature by the Encode international consortium.
Scientists previously thought that only genes, small pieces of DNA that make up about 1 percent of the genome, have a function. The new findings show that an underlying circuitry exists in which 80 percent of the DNA code within each human cell can contribute to disease. This may be why large studies targeting gene variants haven’t identified treatable causes for many complex maladies, the scientists said. The circuitry can be disrupted at several individual waypoints …
‘It’s like a brain in every cell,’ Stamatoyannopoulos said in a telephone interview.”, “DNA’s ‘Junk’ Now Seen as Lever Controlling Future Health,”
Refer to video explaining “ENCODE: Encyclopedia Of DNA Elements”:

Decades ago, it might have been excusable to believe that unguided forces could create such genetically complex life forms. But, considering what we now know about genetics, only a fool could believe in the fairy tale known as Darwinism.

If you still believe in Darwinism after reading these evolutionary-based research articles, please email us with a detailed step-by-step ‘naturalistic’ explanation for the origin of ANY one of these genetic materials, networks, or processes. If you make a good argument that is based on empirical science, we’ll open up “The ‘Let’s See How Evolution Works’ Game and Forum” once again:

“‘ATP is the fuel of life. It’s an energy currency molecule – the most important source of chemical and mechanical energy in living systems,’
Scientists for decades have worked to understand the critically important reaction but, until now, did not know how proteins in a cell extract and use the energy from ATP…
‘Conventional wisdom pointed toward the reactive agent that starts the ATP breakdown process as being something in the protein, such as an amino acid,’ notes Edward Wojcik, an assistant professor and another co-author on the paper.
But, it wasn’t an amino acid at all: It was a second water molecule that pulled the proton off the first water molecule …
‘For such a relatively simple molecule, water still has some tricks to teach us, and I am still amazed that we found it to play such a pivotal role in the motor protein machinery,’ Wojcik says.”
American Society for Biochemistry and Molecular Biology, “Researchers determine how ATP, molecule bearing ‘the fuel of life,” is broken down in cells,” March 1, 2010, Physorg.
“’To put our findings in perspective, the 6.4*1018 instructions per second that human kind can carry out on its general-purpose computers in 2007 are in the same ballpark area as the maximum number of nerve impulses executed by one human brain per second,’ they write.”
John Timmer, “World’s Total CPU Power: One Human Brain”, February 11, 2011, Ars Technica.
“RNA molecules aren’t always faithful reproductions of the genetic instructions contained within DNA, a new study shows. The finding seems to violate a tenet of genetics so fundamental that scientists call it the central dogma: DNA letters encode information and RNA is made in DNA’s likeness. The RNA then serves as a template to build proteins.
But a study of RNA in white blood cells from 27 different people shows that, on average, each person has nearly 4,000 genes in which the RNA copies contain misspellings not found in DNA…
What Li and her colleagues discovered is quite common. RNA molecules contained misspellings at 20,000 different places in the genome, with about 10,000 different misspellings occurring in two or more of the people studied. The most common of the 12 different types of misspellings was when an A in the DNA was changed to G in the RNA. That change accounted for about a third of the misspellings.
And the misspellings aren’t just rare, random mistakes. ‘When DNA and RNA differ from each other it happens in nearly every RNA copy,’ Li says.”
University of Pennsylvania Medical School in Philadelphia, “Central dogma of genetics maybe not so central”, originally posted November 5, 2010, ScienceNews.
“When the human genome was fully sequenced in 2004, approximately 20,000 genes were found. However, it was discovered that living cells use those genes to generate a much richer and more dynamic source of instructions, consisting of hundreds of thousands of genetic messages that direct most cellular activities. Frey, who has appointments in Engineering and Medicine, likens this discovery to ‘hearing a full orchestra playing behind a locked door, and then when you pry the door open, you discover only three or four musicians generating all that music.’
To figure out how living cells generate vast diversity in their genetic information, Frey and postdoctoral fellow Yoseph Barash developed a new computer-assisted biological analysis method that finds ‘codewords’ hidden within the genome that constitute what is referred to as a ‘splicing code’. This code contains the biological rules that are used to govern how separate parts of a genetic message copied from a gene can be spliced together in different ways to produce different genetic messages (messenger RNAs). ‘For example, three neurexin genes can generate over 3,000 genetic messages that help control the wiring of the brain,’ says Frey.”
University of Toronto, “Researchers crack ‘splicing code,’ solve a mystery underlying biological complexity”, May 5, 2010, Physorg.
“When a cell is preparing to grow or replicate, it starts the way a monarch planning to expand his territory might: by identifying and marshaling the necessary resources, loading them onto the appropriate vehicles, and transporting them to the front line.
For cells, that means connecting key molecules with so-called motor proteins, which are neatly equipped to recognize them and carry them to their designated positions at the intended site of growth.”
Cornell University, “Researchers ID molecular link key for cell growth”, January 24, 2011, Physorg.
“The apparently random self-assembly of molecular threads into the proteins that make the body work is far less frantic than previously thought, Michigan State University scientists say. That discovery could be a key to help unlock the nature of some diseases. How proteins spontaneously “fold” from wiggling chains of amino acids into a wide variety of functional – or malfunctioning – three-dimensional molecules is one of the biggest mysteries in biochemistry.”
Michigan State University, “Scientists post lower speed limit for cell-signaling protein assembly”, July 29, 2010, Physorg.
“The mechanism that controls the internal 24-hour clock of all forms of life from human cells to algae has been identified by scientists.
Akhilesh Reddy, from the University of Cambridge and lead author of the study, said: “We know that clocks exist in all our cells; they’re hard-wired into the cell. Imagine what we’d be like without a clock to guide us through our days. The cell would be in the same position if it didn’t have a clock to coordinate its daily activities.”
University of Cambridge, “Ancient body clock discovered that helps to keep all living things on time”, January 26, 2011, Physorg.
“Each gene serves as a recipe for building a protein molecule. When a particular protein is needed by the cell, the corresponding gene, made of DNA, is turned ‘on,’ or transcribed into a messenger RNA, which then carries the ‘protein recipe’ to the protein-making machinery of the cell.”
University of California-Santa Barbara, “Chemists Explain The Switchboards In Our Cells”, August 5, 2009, ScienceDaily.
“Had Amin Rustom not messed up, he would not have stumbled upon one of the biggest discoveries in biology of recent times …
Using video microscopy, they watched adjacent cells reach out to each other with antenna-like projections, establish contact and then build the tubular connections. The connections were not just between pairs of cells. Cells can send out several nanotubes, forming an intricate and transient network of linked cells lasting anything from minutes to hours…
Nothing in his experience could explain the phenomenon.”
New Scientist, “Tunnelling nanotubes: Life’s secret network”, November 18, 2008.
“In a report published in the June 25 issue of Cell, the team identified a near complete catalog of the DNA segments that copy themselves, move around in, and insert themselves here and there in our genome. The insertion locations of these moveable segments — transposons — in each individual’s genome helps determine why some are short or tall, blond or brunette, and more likely or less likely to have cancer or heart disease. The Johns Hopkins researchers say that tracking the locations of transposons in people with specific diseases might lead to the discovery of new disease genes or mutations.”
Johns Hopkins Medical Institutions, “Scientists identify DNA that may contribute to each person’s uniqueness”, August 13, 2010, ScienceDaily.
“Molecular motors, the little engines that power cell mobility and the ability of cells to transport internal cargo, work together and in close coordination, according to a new finding by researchers at the University of Virginia …
The new University of Virginia study provides strong evidence that the motors are indeed working in coordination, all pulling in one direction, as if under command, or in the opposite direction — again, as if under strict instruction.”
University of Virginia, “Molecular Motors In Cells Work Together, Study Shows”, February 25, 2009.
“‘Our results show that a molecular motor must take on a large number of functions over and above simple transport, if it wants to operate successfully in a cell,’ says Professor Matthias Rief from the Physics Department of the TU Muenchen. It must be possible to switch the motor on and off, and it must be able to accept a load needed at a specific location and hand it over at the destination. ‘It is impressive how nature manages to combine all of these functions in one molecule,’ Rief says. ‘In this respect it is still far superior to all the efforts of modern nanotechnology and serves as a great example to us all.’”
Physics Department of the TU Muenchen, “Intracellular Express: Why Transport Protein Molecules Have Brakes”, October 11, 2010, ScienceDaily.
“Gerstein and postdoctoral associate Nitin Bhardwaj analyzed regulatory networks of five diverse species, from E. coli to human, and rearranged those systems into hierarchies with a number of broad levels, including ‘master regulators,’ ‘middle managers’ and ‘workhorses.’ In most organisms, master regulators control the activity of middle managers, which in turn govern suites of workhorse genes that carry out instructions for making proteins.”
Yale University, “Molecular Middle Managers Make More Decisions Than Bosses”, March 29, 2010, Physorg.
“The researchers found that blood cells are directed by a multitude of transcription factors, proteins that turn on and off genes. While many previous studies have focused on individual transcription factors or types of blood cells, this study examined the expression and regulation of all transcription factors throughout blood development. The findings point to densely, interconnected circuits that control this process, suggesting that the wiring for blood cell fate is far more complex than previously thought.”
Broad Institute of MIT and Harvard, “Global View of Blood Cell Development Reveals New and Complex Circuitry”, January 20, 2011, ScienceDaily.
“Using a new technology called ‘differential epistasis maps,’ an international team of scientists, led by researchers at the University of California, San Diego School of Medicine, has documented for the first time how a cellular genetic network completely rewires itself in response to stress by DNA-damaging agents…
As researchers progress in mapping these networks, their dynamic nature is both enlightening and depressing, said Ideker. Scientists had hoped cellular networks might not change greatly across different conditions or from cell to cell. That they do so suggests greater challenges and complexities ahead.”
University of California-San Diego, “Rewiring of Genetic Networks in Response to DNA Damage”, December 7, 2010, ScienceDaily.
“’To put our findings in perspective, the 6.4*1018 instructions per second that human kind can carry out on its general-purpose computers in 2007 are in the same ballpark area as the maximum number of nerve impulses executed by one human brain per second,’ they write.”
John Timmer, “World’s Total CPU Power: One Human Brain”, February 11, 2011, Ars Technica.
“Every day, about 10 billion cells in a human body commit suicide. Cells infected by virus, that are transformed or otherwise dysfunctional altruistically sacrifice themselves for the greater good. Now, new imaging experiments have revealed a previously unseen order to this process, showing closely related cells dying in synchrony as a wave of destruction sweeps across their mitochondria, snuffing out the main source of energy that keeps cells alive…
Now the microscopy techniques are enabling a deeper understanding of apoptosis, says Bhola. ‘It’s one of those things where if you can’t see what’s going on, you tend to assume it’s random or all at once,’ he says. ‘But when you get a good look, you find it happens in a very organized fashion.’”
Rockefeller University, “Imaging Studies Reveal Order in Programmed Cell Death”, March 3, 2010, ScienceDaily.
“Like a film director cutting out extraneous footage to create a blockbuster, the cellular machine called the spliceosome snips out unwanted stretches of genetic material and joins the remaining pieces to fashion a template for protein production …
By molecular-scale standards, the spliceosome is a monster of a machine, made up of five RNA and 100 or more protein subunits that agilely assemble, step-by-step, into the giant complex when it’s time to carry out its work …
True to the movie director analogy, the spliceosome not only wields the scissors, it’s also ‘the brain that decides where to cut,’ Walter said. The ‘footage’ it works on is the genetic material contained in RNA molecules. RNA carries coded instructions for producing the proteins our body needs for building and repairing tissues, regulating body processes and many other sections called introns. The spliceosome’s task is to recognize and excise introns. Once the introns are removed, the spliceosome can stitch together exons in various combinations. Thanks to this mixing and matching of exons, a relatively small number of genes (a little over 20,000 in humans) can serve as blueprints for a great variety of proteins.”
University of Michigan, “Spying on a cellular director in the cutting room”, March 21, 2010, Physorg.
“’Essentially, proteins that search for specific information spin down the double helix of the DNA, like traveling along the threads of a screw, until they locate their target,’ said co-author Walter Mangel, a Brookhaven biophysicist …
For decades, scientists have known that proteins searching for genetic sequences are able to locate them at rates much faster than expected. They found that rather than moving around the entire three-dimensional space inside a cell, they moved in one-dimension, along DNA molecules. The Harvard group showed, in 2006, that the proteins slide back and forth in direct contact with the DNA as part of the search for specific sequences.”
Brookhaven National Laboratory, “Grooving down the helix: Researchers show how proteins slide along DNA to carry out vital biological processes”, December 3, 2009, Physorg.
“’For the first time, we have evidence to support the hypothesis that human cells have the widespread ability to copy RNA as well as DNA,’ said co-author Bino John, Ph.D., assistant professor, Department of Computational and Systems Biology, Pitt School of Medicine. ‘These findings emphasize the complexity of human RNA populations and suggest the important role for single-molecule sequencing for accurate and comprehensive genetic profiling.’”
University of Pittsburgh Schools of the Health Sciences, “Human cells can copy not only DNA, but also RNA”, August 10, 2010, Physorg.
“The primary cilium, the solitary, antenna-like structure that studs the outer surfaces of virtually all human cells, orient cells to move in the right direction and at the speed needed to heal wounds, much like a Global Positioning System helps ships navigate to their destinations.”
American Society for Cell Biology, “Primary cilium as cellular ‘GPS system’ crucial to wound repair”, December 17, 2008, Physorg.
“In fact, it looks so useless that, until recently, many scientists considered it to be just a leftover artifact of eons of evolution.
Recently, however, research has shown that defects in the development or function of primary cilia are associated with many human disorders, including polycystic kidney disease, skeletal malformations, neural tube defects, as well as obesity. Clearly there’s more here than meets the eye. Scientists have since decided that the primary cilium works as a kind of antenna to help the cell respond to outside chemical signals and mechanical forces.”
Stanford University Medical Center, “Mysterious cilium functions as cellular communication hub, study shows”, June 24, 2010, Physorg.

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