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Biology

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  • Evolution = atheism, no purpose. ‘Let me summarize my views on what modern evolutionary biology tells us loud and clear … There are no gods, no purposes, no goal-directed forces of any kind. There is no life after death. When I die, I am absolutely certain that I am going to be dead. That’s the end for me. There is no ultimate foundation for ethics, no ultimate meaning to life, and no free will for humans, either.’
  • Janine Benyus: Biomimicry in action. Posted August, 2009. Amazing examples of design in nature. Here she reveals dozens of new products that take their cue from nature with spectacular results. Also see: AskNature.org.

Creationism and Arguments for Design (some are YouTube videos)

The debate over origins is between the concepts of (intelligent) "design" versus (laws of) chance and (laws of) nature. In other words, can the origin of life be best explained from chance and inherent laws of nature or does it require an outside source of intelligence (i.e. information, knowledge, design, etc). That is, can the complexity of life (design) best be explained with or without a designer.

The properties of information are: (1) not bound to its medium, (2) massless, (3) intangible, (4) immaterial (e.g. technologies, works of art, biological systems), and (5) abstract construct of mind. "There is no known natural law through which matter can give rise to information, neither is any physical process or mateiral phenomenon known that can do this."

More than just matter + energy. There is also "information".

  • What are the most abundant proteins in a cell?
  • Discoveries Make the "Junk DNA" Rubble Bounce. Published 1/24/2013. In a process called alternative splicing, a single gene could code for multiple proteins with different biological functions. In this way, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.
  • Human genome at ten: Life is complicated. The more biologists look, the more complexity there seems to be. Few predicted, for example, that sequencing the genome would undermine the primacy of genes by unveiling whole new classes of elements....We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it's not. Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary....It seems like we're climbing a mountain that keeps getting higher and higher. The more we know, the more we realize there is to know....Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. "Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive.
  • Stephen Meyer - Genetics Proves Design and Disproves Evolution PT 1 of 2.
  • Stephen Meyer - Genetics Proves Design and Disproves Evolution PT 2 of 2.
  • 250 million yr old bacteria revived? Throw him under the bus! Reference this article: Alive...after 250 million years. Ancient bacteria trapped in a state of suspended animation for 250 million years are the world's oldest living things, claim US scientists. The microbes are ten times older than any previously discovered living organism...The bacteria were found in salt crystals buried almost 609 metres (2,000 feet) below ground at a cavern in south-east New Mexico, US.
  • How DNA Killed Evolutionism pt 1 of 4.
  • The Miller-Urey experiment. Refutation of the experiment which produced a handful of amino acids. Headings: (1) Irrelevant atmosphere - required absence of oxygen and nitrogen, and inclusion of unstable compounds (ammonia decomposes within 30,000 years; methane decomposes in 1% of the earth's lifetime; hydrogen does not exist in element form on this planet). (2) Irrelevant conditions - required a circulatory system, cooling system to isolate and protect from further reactions, and directed energy source. (3) Low yield - tiny quantities. As the amino acids were formed they reacted with reducing sugars, forming a brown tar around Miller's apparatus. (4) Wrong forms of amino acid - left versus right-handed amino acids. It is not a simple process to separate them and there is no natural system that can do so. In fact, L-amino acids have a tendency with age to undergo a chemical inversion to the D-form. This is called racemization.

Miller-Urey experiment

The Miller-Urey experiment. Refutation of the experiment which produced a handful of amino acids. Headings:

  1. Irrelevant atmosphere - required absence of oxygen and nitrogen, and inclusion of unstable compounds (ammonia decomposes within 30,000 years; methane decomposes in 1% of the earth's lifetime; hydrogen does not exist in element form on this planet).
  2. Irrelevant conditions - required a circulatory system, cooling system to isolate and protect from further reactions, and directed energy source.
  3. Low yield - tiny quantities. As the amino acids were formed they reacted with reducing sugars, forming a brown tar around Miller's apparatus. That is, the destruction of the key compounds by the prevailing conditions or by other chemical by-products.
  4. Wrong forms of amino acid - left versus right-handed amino acids. It is not a simple process to separate them and there is no natural system that can do so. In fact, L-amino acids have a tendency with age to undergo a chemical inversion to the D-form. This is called racemization.
  5. The problem of building a protein - We now need the amino acids to join together (polymerise) to form proteins. It requires the removal of water molecules. This does not occur naturally. Proteins range in chains of 25 to 50,000 amino acids. What are the odds of producing just one average protein of 150 amino acids by chance? The math: 20 to the 150th power. However, a living cells contains thousans of proteins. A simple bacteria has over 4,000. Humans have over 2 million and counting. BUT, assume a protein was formed, the next problem is the correct "folding" of the protein. Incorrect folding makes it biologically inactive.
  6. Other chemicals needed for life - Carbohydrates, lipids, and nucleic acids.
  7. No DNA/RNA formation - There has been no experimental indication of the formation of either RNA or DNA in a Miller-type synthesis.

    The problem of the origin(s) of life remains. All that has been outlined is speculation and, despite tremendous advances in biochemistry, answers to the problem remain hypothetical. … Details of the transition from complex non-living materials to simple living organisms remain a mystery.

Cell Biology (all are YouTube videos)

RNA Polymerase

  • RNA Polymerase. First RNA: RNA is a versatile molecule. In its most familiar role, RNA acts as an intermediary, carrying genetic information from the DNA to the machinery of protein synthesis. RNA also plays more active roles, performing many of the catalytic and recognition functions normally reserved for proteins. In fact, most of the RNA in cells is found in ribosomes--our protein-synthesizing machines--and the transfer RNA molecules used to add each new amino acid to growing proteins. In addition, countless small RNA molecules are involved in regulating, processing and disposing of the constant traffic of messenger RNA.

    The enzyme RNA polymerase carries the weighty responsibility of creating all of the different RNA molecules the cell uses. RNA polymerase is a huge factory with many moving parts. It is composed of a dozen different proteins. Together, they form a machine that surrounds DNA strands, unwinds them, and builds an RNA strand based on the information held inside the DNA. Once the enzyme gets started, RNA polymerase marches confidently along the DNA copying RNA strands thousands of nucleotides long.

DNA and Protein Synthesis -- by Craig Savage (all are YouTube videos)

Enzymes in DNA/RNA synthesis (YouTube videos)

  • Helicase. In humans, 95 non-redundant helicases are coded for in the genome, 64 RNA helicases and 31 DNA helicases.[2] Many cellular processes, such as DNA replication, transcription, translation, recombination, DNA repair, and ribosome biogenesis involve the separation of nucleic acid strands that necessitates the use of helicases.
  • Primase. Primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer (for temporary DNA elongation).
  • Topoisomerase. Topoisomerases are enzymes that regulate the overwinding or underwinding of DNA. The winding problem of DNA arises due to the intertwined nature of its double helical structure. For example, during DNA replication, DNA becomes overwound ahead of a replication fork. If left unabated, this tension would eventually grind replication to a halt (a similar event happens during transcription.) (YouTube) Topoisomerase 1 and 2.
  • Polymerase. A polymerase is an enzyme whose central biological function is the synthesis of polymers of nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, generally by copying a DNA or RNA template strand using base-pairing interactions.
  • Ribosome. The ribosome (from ribonucleic acid and the Greek soma, meaning "body") is a large and complex molecular machine, found within all living cells, that serves as the primary site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. Ribosomes consist of two major subunits—the small ribosomal subunit reads the mRNA, while the large subunit joins amino acids to form a polypeptide chain. Each subunit is composed of one or more ribosomal RNA (rRNA) molecules and a variety of proteins.
  • Transfer Molecules.

DNA to Protein (YouTube videos)

It is estimated that the human body may contain over two million proteins, coded for by only 20,000 - 25,000 genes. The total number of proteins found in terran biological organisms is likely to exceed ten million, but nobody knows for sure. Data is available on just over a million proteins, taken mainly from information found in the ~100 genomes which have been fully sequenced as of 2007....The longest known protein, titin, also known as connectin, contains 26,926 amino acids. Titin is found in muscle and contributes to its passive stiffness.

The word protein comes from the Greek prota, meaning "of primary importance". This is a suitable name, as the central importance of proteins in the human body can not be overestimated. All biological organisms can be seen fundamentally as protein structures filled with water and sometimes supported by mineralized tissues called bone. For almost every protein there is another protein that can break it down. Proteins sometimes coalesce into mutually cooperative units called complexes, which perform useful biological functions. Every section of useful genetic information, found in DNA and some RNA, codes for a corresponding protein which goes on to fulfill a useful biological role.

Chromosomes

The human (Homo sapiens) genome is the complete set of human genetic information, stored as DNA sequences within the 23 chromosome pairs of the cell nucleus, and in a small DNA molecule within the mitochondrion. The haploid human genome (contained in egg and sperm cells) consists of three billion DNA base pairs, while the diploid genome (found in somatic cells) has twice the DNA content.

The haploid human genome contains approximately 20,000 protein-coding genes, significantly fewer than had been anticipated. Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, introns, and sequences to which no function has yet been assigned.