Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Origin of life » The cell, the most advanced, irreducibly complex and sophisticated factory in the universe

The cell, the most advanced, irreducibly complex and sophisticated factory in the universe

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The cell, the most advanced, irreducibly complex and sophisticated factory in the universe

All living systems, irrespective of size, are made up of cells and that each type of cell exhibit many common features and carry out analogous, if not identical, processes. An understanding of the structure and activities of cells is, therefore, vital to all who work within the sphere of biology. The purpose of this chapter is to generate an overview of some key aspects of the factory-like processes, and why the evidence of these working principles point to inteligent design as the best explanation of how Cells, and therefore life must have come to be.   All living systems are capable of bringing about an enormous number of chemical changes.  Living systems are superb chemical factories, taking in one set of chemicals (nutrients) and converting them into new products. The range of chemicals made are far greater than all of the chemicals produced by man-made factories. Cell factories are composed of complex structures, and use specific “tools” which are used and managed in a co-ordinated manner to provide an effective and efficient unit. The term 'cell' was first applied, by Robert Hooke in 1665, to the box-like structures he found in plant material. First Naegeli (1854) and then Virchow (1858) were able to claim that all living things were constructed of units (cells) each of which owed its origin to the pre-existence of other units (cells). The term protoplasm, first coined by Purkinje in 1859, became widely accepted for the jelly-like contents of cells. The development of the electron microscope during the 1950's led to much greater resolution of the fine structure of cells. These studies clearly demonstrated that cells can be divided into two quite distinct types described as prokaryotic and eukaryotic. Eukaryotic cells are structurally the more complex of the two and are found in all types of plants and animals including the microscopic forms (eg algae, fungi, protozoans). Prokaryotic cell organisation is confined to the bacteria. The chemical analysis of cells also revealed that prokaryotic cells can be divided into two sub-groups. Those which contain chemicals similar to those of eukaryotic cells were called the true bacteria or, more properly, the eubacteria. Those which were chemically quite distinct (especially in the structure of the fats they contained) from eukaryotes were called archaebacteria. Currently we accept that there are three basic cell groups; the eukaryotic, the eubacterial and the archaebacterial types. Within the cell wall is a membrane called a plasma membrane  which encloses a jelly-like substance called the cytoplasm. Embedded in the cytoplasm is the genetic material (DNA) which stores the information needed for the cell to carry out its functions. Copies of this information are passed onto daughter cells when the cell multiplies. The cytoplasm is the site where many of the chemical changes take place. These chemical changes include those processes which lead to production of a usable form of energy, reducing power and a series of simple organic molecules. These processes we may describe as the fuelling reactions of the cell. The products of the fuelling reactions are used to drive the synthesis of new chemicals (biosynthesis) which may be assembled into new cell structures Thus we may view the cytoplasm and its surrounding plasma membrane as being the workshop of the chemical factory. The fuelling reactions and biosynthesis of new cell material are together referred to as metabolism. In the cell factory we see the genetic material as the management of the factory specifying and controlling its processes, whilst the the cytoplasm and plasma membrane are the place where the processes take place.

Eukaryotic cells
Cells displaying eukaryotic features are characteristic of all plants and animals. They may exist singly as in the unicellular algae and protozoans or, more commonly, in larger groups in the macroscopic plants and animals. In these multicellular forms, diferente cells within the same organisms display different features. They are said to be differentiated. Differentiation is therefore a process by which cells develop specialised features to carry out specific functions. Some for example may be involved with the transport of nutrients, others with defence against infection while others are involved with excretion. There is therefore a division of labour amongst the cells in multicelular systems. Cells of related function are often grouped together into tissues. In turn, tissues may be grouped together into organs such as the lungs and hearts of animals, and the leaves and flowers of plants, each of which perform specific tasks in maintaining and propagating the system. Despite this specialisation, certain features of the cells are common to all.

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2 Proteins on Sun Jan 06, 2019 3:41 pm

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Proteins
We shall begin by considering proteins. The reason is that proteins are polymers constructed from amino acids. Thus by establishing the importance of proteins, we can more readily appreciate why amino acids are of enormous importance for life. Of all the types of compounds found in cells, proteins are amongst the most important. Proteins are present in large quantities in cells. Human Cells, for example, contain a staggering 2,3 billion proteins. Their importance is in part a result of the enormous variety of structures (and hence properties) which is possible through the manner of their construction. They fulfil a huge range of requirements. The ability of proteins to fulfil these roles is a consequence of the enormous range of three-dimensional structures which proteins can take - each protein has a precise three-dimensional structure, Underpinning an understanding of proteins is the need to understand the components from which proteins are composed, amino acids.

Amino Acids Are the Building Blocks of Proteins
Proteins are composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur. The monomers of proteins are amino acids, compounds with a structure in which a carbon atom, called the α-carbon, is linked to an amino group (—NH2) and a carboxyl group (—COOH). The α-carbon also is linked to a hydrogen atom and a side chain, designated with the letter R. Proteins are polymers of amino acids. When an amino acid is dissolved in water at neutral pH, the amino group accepts a hydrogen ion and is positively charged, whereas the carboxyl group loses a hydrogen ion and is negatively charged. The term amino acid is the name given to such molecules because they have an amino group and also a carboxyl group that acts as an acid. All amino acids except glycine exist in more than one isomeric form, called the d and l forms, which are enantiomers. Only l-amino acids are found in proteins. d-amino acids are not found in most cells. An exception is the cell walls of certain bacteria, where they may play a protective role against molecules secreted by the host organism in which the bacteria live.

What Are the Structures and Properties of Amino Acids?
As implied by the root of the word (amine), the key atom in amino acid composition is nitrogen. The ultimate source of nitrogen for the biosynthesis of amino acids is atmospheric nitrogen (N2), a nearly inert gas. However, to be metabolically useful, atmospheric nitrogen must be reduced. This process, known as nitrogen fixation, occurs only in certain types of bacteria. Even though nitrogen is one of the most prominent chemical elements in living systems, N2 is almost unreactive (and very stable) because of its triple bond (N≡N). This bond is extremely difficult to break because the three chemical bonds need to be separated and bonded to different compounds. Nitrogenase is the only family of enzymes capable of breaking this bond (i.e., it carries out nitrogen fixation). These proteins use a collection of metal ions as the electron carriers that are responsible for the reduction of N2 to NH3. All organisms can then use this reduced nitrogen (NH3) to make amino acids. In humans, reduced nitrogen enters the physiological system in dietary sources containing amino acids. All organisms contain the enzymes glutamate dehydrogenase and glutamine synthetase, which convert ammonia to glutamate and glutamine, respectively. Amino and amide groups from these two compounds can then be transferred to other carbon backbones by transamination and transamidation reactions to make amino acids. Interestingly, glutamine is the universal donor of amine groups for the formation of many other amino acids as well as many biosynthetic products. Glutamine is also a key metabolite for ammonia storage. All amino acids, with the exception of proline, have a primary amino group (NH2) and a carboxylic acid (COOH) group. They are distinguished from one another primarily by, appendages to the central carbon atom. 1



1. https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445#

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The 20 amino acids found in living organisms. 
Amino acids have different chemical properties (for example, nonpolar versus polar) due to the nature of their different side chains. These properties contribute to the differences in the three-dimensional shapes and chemical properties of proteins, which, in turn, influence their biological functions. Amino acids are fundamental to biology as the structural units of the enzymes, which are responsible for the vast and varied catalytic repertoire of cells, and other cellular structural proteins. 7 Amino acids are not simple chemicals , but made in all lifeforms by enzymes through complex biochemical manufacturing processes. ( Enzymes by themselves require amino acids to be made ).  In the 1953 Miller–Urey experiment, trace amounts of some amino acids were made without enzymes. 

Synthesis of amino acids on a prebiotic earth
As with other biomonomers, there are two prebiotically relevant sources of amino acids: endogenous and exogenous syntheses. From both pathways a wide variety of amino acids can be obtained, but here we will focus on α-amino acids, given their major relevance in biochemistry.  The exogenous formation and delivery of amino acids have been evaluated by analyzing the composition of different carbonaceous chondrites. The amino acid set in this carbon-rich class of meteorites comprises more than 70 species with most of them being α-amino acids and including at least eight proteogenic ones. The chemistry involved in their extraterrestrial synthesis is at least partly based on nonselective photochemical and radical processes.1

The endogenous production of amino acids on the primitive Earth has been investigated for the last six decades. Even if the particular conditions (e.g., the recreated reductive atmosphere) in which Miller’s original experiments were carried out are eventually discarded as unrealistic.

An interview from 1998 with exobiology pioneer, Dr. Stanley L. Miller, University of California San Diego 3
We've shown that either you have a reducing atmosphere or you are not going to have the organic compounds required for life. If you don't make them on Earth, you have to bring them in on comets, meteorites or dust. Certainly, some material did come from these sources. In my opinion, the amount from these sources would have been too small to effectively contribute to the origin of life. The amount of useful compounds you are going to get from meteorites is very small. The dust and comets may provide a little more. Comets contain a lot of hydrogen cyanide, a compound central to prebiotic synthesis of amino acids as well as purines. Some HCN came into the atmosphere from comets. Whether it survived impact, and how much, are open to discussion. I'm skeptical that you are going to get more than a few percent of organic compounds from comets and dust.

Nobel laureate Christian de Duve, who called for “a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry.”  That rules out starting with complex molecules like DNA, RNA, and proteins.

A central problem for the prebiotic synthesis of biological amino acids and nucleotides is to avoid the concomitant synthesis of undesired or irrelevant by-products. 2

Prebiotic selection of proteinogenic amino acids. 
The prebiotic origins of amino acids have been investigated for over 60 years. However, no reported prebiotic synthesis or meteoritic amino acid sample provides the restricted set of amino acids assigned to the genetic code. For example, recently Sutherland and coworkers demonstrated the stepwise prebiotic syntheses of 12 aminonitrile proteinogenic amino acid precursors, but, paradoxically, essential ketones—such as acetone , monohydroxyacetone  and dihydroxyacetone —are required during the assembly of the branched carbon framework of valine and leucine.

1. https://pubs.acs.org/doi/abs/10.1021/cr2004844
2. https://www.nature.com/articles/nchem.2703

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Scientists finish a 53-year-old classic experiment on the origins of life 1
March 21, 2011
Even if our young planet had the right conditions to produce amino acids, that’s a less impressive feat than it appeared in the 1950s. “Amino acids are old hat and are a million miles from life,” says Nick Lane. Indeed, as Miller’s experiments showed, it’s not difficult to create amino acids. The far bigger challenge is to create nucleic acids – the building blocks of molecules like RNA and DNA. The origin of life lies in the origin of these “replicators”, molecules that can make copies of themselves. Lane says, “Even if you can make amino acids (and nucleic acids) under soup conditions, it has little if any bearing on the origin of life.” The problem is that replicators don’t spontaneously emerge from a mixture of their building blocks, just as you wouldn’t hope to build a car by throwing some parts into a swimming pool. Nucleic acids are innately “shy”. They need to be strong-armed into forming more complex molecules, and it’s unlikely that the odd bolt of lightning would have been enough. The molecules must have been concentrated in the same place, with a constant supply of energy and catalysts to speed things up. “Without that lot, life will never get started, and a soup can’t provide much if any of that,” says Lane.

Extraterrestrial input of amino acids
Blank and her NASA team  claimed that amino acids can survive a comet’s entrance into Earth’s atmosphere and subsequent surface impact. But this  presents a big problem. Calculations and measurements show that both events generate so much heat (atmosphere = 500°+ Centigrade while the collision = 1,000°+ Centigrade) that they break down the molecules into components useless for forming the building blocks of life molecules. This was confirmed by NASA when they sent the Stardust Spacecraft to the comet 81P Wild in 2004 to recover samples, which were returned to Earth and analyzed for organic molecules. The only amino acid indisputably detected in the sample was glycine at an abundance level of just 20 trillionths of a mol per cubic centimeter 2

Amino Acids Are Chiral Molecules
There is one general feature of the molecules constituting all known living systems on Earth, and in particular of biopolymers, which needs to be addressed and explained within the problem of origins: their homochirality. Most molecules of life are homochiral, that is, they possess the same handedness or chirality. Homochirality of biological molecules is a signature of life. The  chirality or sense of handedness of the amino acid molecules is an important problem. Figure above shows two versions, or enantiomers, of the amino acid alanine. Each contains exactly the same number of elements with the same types of chemical bonds, and yet they are the mirror image of each other. A molecule that is not superimposable on its mirror image is chiral. When a molecule with a definite sense of handedness reacts chemically with one that is symmetric (or otherwise does not have a particular handedness), the left- and right-handed amino acids have similar properties. Likewise, the chemical properties of an interaction between two left-handed molecules or two right-handed molecules are the same. However, neither of these interactions is the same as when a left- and right-handed molecule are interacting with each other. Hence, the handedness of biological molecules such as amino acids or nucleotides plays a role in their functionality.


Biologically synthesized amino acids, for instance, occur exclusively in their levorotatory (L) form, while the sugar constituents of nucleic acids are all dextrorotatory (D)The chemistry explaining how primitive homochiral peptides and RNA molecules could have been formed is not obvious, considering that most prebiotic routes toward nucleotides and amino acids start from achiral precursors such as formaldehyde, formamide, cyanoacetylene, etc. There is also the possibility of finding elsewhere life forms based on biopolymers with opposite chirality to the ones present in our biological world. Secular science does not know if the choice of L-amino acids and D-sugars was deterministic or accidental. Science does  not even know whether homochirality arose first for amino acids or sugars.  The issue is inherently complex  and involves a high level of technicalities present in the specialized literature. Theories on the origin of homochirality in the living world can be classified into two major types: biotic and abiotic. The first ones suggest that selection and amplification of one of the enantiomers of chiral biomolecules took place at an early stage in life. This view is, however, not consistent with the notion that biopolymers need to be composed of chiral monomers in order to perform their functions. Proteins constituted by mixtures of L- and D-amino acids cannot form well-defined tertiary and quaternary structures. Ribose must have been in its D form for the first RNA molecules to adopt functional structures, which cannot occur with random mixtures of D- and L-nucleotides. An abiotic source of homochirality then seems more compatible with the principles of biology, but it implies the presumption of some kind of symmetry-breaking process leading to enantioenriched biomonomers. It is also plausible that enantioenrichment could have happened along the synthesis of biopolymers rather than at the monomeric molecular level. A compromise solution between both extremes would be that chiral monomers were only partially enantioenriched before they polymerized. The competition to build biopolymers would then be gradually won by the majoritarian enantiomer, leading to more efficient chiral selection as the complexity of biopolymers increased. 3






The two mirror-image enantiomers of the amino acid alanine.


1. https://uncommondescent.com/intelligent-design/pardon-me-if-i-am-not-impressed-dr-miller/
2. https://tnrtb.wordpress.com/2011/11/07/homochirality-and-the-origin-of-life/
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857173/

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