Theory of Intelligent Design, the best explanation of Origins

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Theory of Intelligent Design, the best explanation of Origins » Molecular biology of the cell » Metabolism » Biosynthesis and metabolism

Biosynthesis and metabolism

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1 Biosynthesis and metabolism on Thu May 07, 2015 5:59 pm


Biosynthesis and metabolism

A robotic assembly line   finds its equivalent in the biological world through biosynthesis and metabolic pathways  (also called biogenesis or anabolism) which  is a multi-step, enzyme-catalyzed ( robots ) process where substrates ( unfinished parts ) are converted into more complex products. In biosynthesis, simple compounds are modified, converted into other compounds, or joined together to form macromolecules. This process often consists of metabolic pathways. Some of these biosynthetic pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles. Examples of these biosynthetic pathways include the production of lipid membrane components and nucleotides. Also the biosynthesis of heme happens in mitochondria and cytosol. 1)

Metabolic activity makes it possible for organisms to extract energy from the environment and make life’s component parts. These processes allow organisms to grow, reproduce, maintain biological structures, and respond to changes in the environment. Metabolic processes within the cell’s interior are organized into pathways consisting of a series of chemical reactions that transform a starting compound into a final product via a series of small, stepwise chemical changes. Each step in a metabolic route is mediated by a protein (called an enzyme) that assists in the chemical transformation.

Metabolic pathways can be linear, branched, or circular. The chemical components that are part of a particular metabolic sequence sometimes take part in other metabolic pathways. These shared compounds cause metabolic pathways to be networked together.3)

Metabolism involves reactions of small molecules. A significant number of metabolic reactions produce small molecules used by the cell’s machinery as building blocks to assemble proteins, DNA, the RNAs and cell membrane bilayers. On the other hand, some metabolic activities breakdown compounds like glucose and other sugar molecules into smaller molecules to provide energy for the cell’s operations. Some metabolic activities prepare materials the cell no longer needs (cellular waste) for elimination. Other reactions detoxify materials harmful to the cell. 4)

METABOLISM - all biochemical reactions that transform matter, energy and information

3 basic stages:
1.  Uptake of substances (for example, across the plasma membrane)
2.  Transformation of substances (anabolism or catabolism - explained a bit later!)
3.  Release of substances (for example, the elimination of metabolic wastes across the plasma membrane) 2)

Metabolic pathway- the order in which reactions affecting a starting substance occur.  A metabolic pathway may be linear or circular and the product (end substance) of one pathway may be the reactant (starting substance) of another.  Often reactions in a pathway are reversible.

All pathways have the following participants:
1.  Substrates/reactants  - substances that enter the reaction    
2.  Intermediate products  - compounds formed between the start and the end of the reaction  
3.  Enzymes - proteins that catalyze (speed up) reactions
4.  Energy carriers  - usually ATP.  It donates energy to the reactions that need it and picks up energy from reactions that produce it.
5.  End products /metabolites  - substances produced at the end of the pathway.

Metabolic pathways in general are found to be ‘optimal’:

Metabolism: A Cascade of Design
Excerpt: A team of biological and chemical engineers wanted to understand just how robust metabolic pathways are. To gain this insight, the researchers compared how far the errors cascade in pathways found in a variety of single-celled organisms with errors in randomly generated metabolic pathways. They learned that when defects occur in the cell’s metabolic pathways, they cascade much shorter distances than when errors occur in random metabolic routes. Thus, it appears that metabolic pathways in nature are highly optimized and unusually robust, demonstrating that metabolic networks in the protoplasm are not haphazardly arranged but highly organized. 3)

Highly optimized, unusually robust, highly organized are atributes that i would rather ascribe to be the product of a intelligent agency,  than random evolutionary forces.

Given the dynamic environment of the cell, fluctuations in the levels of metabolites are bound to happen. When these unintended variations occur, they will travel throughout the networks. Some processes in the cell are sensitive to metabolite concentrations and will be negatively affected as a result. To combat these affects, metabolic systems have regulatory systems in place (based on engineering principles) that dampen concentration bounces, keeping them within tight bounds. In other words, metabolic pathways are optimized to withstand inevitable concentration changes of metabolites.

The paralleles to above factory example is clear. The optimization of the factory assembly line is a important design requirement ( maximal  flexibility in the line for demand and supply fluctuation ) and are best explained and achieved through the  rational planning and design of intelligent  minds.

The salient characteristics of biochemical systems, such as their optimization, are identical to features we would immediately recognize as evidence for the work of a human designer. The similarities between biochemical systems and manmade machines logically compels the conclusion that life’s most fundamental processes and structures stem from the work of an intelligent Agent.  4)

Well said.

So what are the best answers that our friends, proponents of natural mechanisms have on hand ?

Origin and evolution of metabolic pathways
How the major metabolic pathways actually originated is still an open question nice admittance !!  but several different theories have been suggested to account for the establishment of metabolic routes, as The Retrograde hypothesis (Horowitz, 1945), The Granick hypothesis, The Patchwork hypothesis (Ycas, 1974; Jensen, 1976), Semienzymatic origin of metabolic pathways (Lazcano and Miller,1996), The bioinformatic approach , The directed evolution experiments All these ideas are based on gene duplication. 7)

Is gene duplication a viable explanation for the origination of biological information and complexity?
Although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms.  8

If a certain line of reasoning  is not persuasive or convincing, then why do atheists not change their mind because of it? The more evolution papers are published, the less likely the scenario of gene duplication ( even questioned by peer reviewed papers, as shown above ) , mutation, and natural selection becomes.  We should consider the fact that modern biology scientific research  may have reached its limits on several key subjects, to which biosynthesis pathways belong. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios,  or in a confession of ignorance.  Fact is  there remains a huge gulf in our understanding. This lack of understanding is not just ignorance about some technical details; it is a big conceptual gap.  The reach of the end of the road is evident in regard of many, if not almost all major questions. The big questions of macro  evolutionary changes and abiogenesis  are very far from being clearly formulated, even understood,  and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, one day a solution will be found. Not only that, but it seems, the ones that less understand the subject, the more they believe to have the right answers and philosophical position, almost like religious fundamentalists.  Istn't that a prima facie of a " evolution of the gap" position ? We don't know yet, but evolution  and naturalism must be true anyway ? So, the God hypothesis remains out of the equation as a real possibility  in the beginning, and so  at the end, and never receives a serious and honest consideration. If the scientific evidence does not lead towards naturalism providing sactisfactory explanations, why should we not change your minds and look somewhere else ?


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2 Re: Biosynthesis and metabolism on Tue Aug 04, 2015 7:38 pm


Metabolic Pathways

Picture above: Glycolysis and the citric acid cycle are at the center of an elaborate set of metabolic pathways in human cells. Some 2000 metabolic reactions are shown schematically with the reactions of glycolysis and the citric acid cycle in red. Many other reactions either lead into these two central pathways—delivering small molecules to be catabolized with production of energy—or they lead outward and thereby supply carbon compounds for the purpose of biosynthesis.

To accomplish any major task, a cell requires a series of reactions occurring in an ordered sequence. This, in turn, requires many different enzymes because most enzymes catalyze only a single reaction, and many such reactions are usually needed to accomplish a major biochemical operation. When we consider all the chemical reactions that occur within a cell, we are talking about metabolism (from the Greek word metaballein, meaning “to change”). The overall metabolism of a cell consists, in turn, of many specific metabolic pathways, each of which accomplishes a particular task. From a biochemist’s perspective, life at the cellular level can be defined as a network of integrated and carefully regulated metabolic pathways, each contributing to the sum of activities that a cell must carry out. 

Question : how could this regulation have emerged, if there was no reason for intermediate states to arise? Life depends on these metabolic pathways, and they function only if fully setup and interlocked in a complex network. 

Metabolic pathways are of two general types. Pathways that synthesize cellular components are called anabolic pathways (using the Greek prefix ana–, meaning “up”), whereas those involved in the breakdown of cellular constituents are called catabolic pathways (using the Greek prefix kata–, meaning “down”). Anabolic pathways usually involve a substantial increase in molecular order (and therefore a local decrease in entropy) and are  endergonic(energy-requiring).

Order was therefore a prerequisite for life to emerge. No order, no life. Order is usually assigned to a intelligence causing it, and  sets it up. The contrary is chaos, wich we assign to random unguided events ( increase in entropy )

Polymer synthesis and the biological reduction of carbon dioxide to sugar are examples of anabolic pathways. Often, anabolic pathways synthesize polymers such as starch and glycogen from glucose units in order to store energy for future use. Certain steroid hormones, for example, are called anabolic steroids because they stimulate the synthesis of muscle proteins from amino acids. Catabolic pathways, by contrast, are degradative pathways that typically involve a decrease in molecular order (increase in entropy) and are exergonic (energyliberating). These reactions often involve hydrolysis of macromolecules or biological oxidations. Catabolic pathways play two roles in cells: They release the free energy needed to drive cellular functions, and they give rise to the small organic molecules, or metabolites, that are the building blocks for biosynthesis. However, a catabolic pathway is not simply the reverse of the corresponding anabolic pathway. For example, the catabolic pathway for glucose degradation and the anabolic pathway for glucose synthesis use slightly different enzymes and intermediates. As we will see shortly, catabolism can be carried out either in the presence or absence of oxygen (i.e., under  either aerobic or anaerobic conditions). The energy yield per glucose molecule is much greater in the presence of oxygen. However, anaerobic catabolism is also important, not only for organisms in environments that are always devoid of oxygen but also for organisms and cells that are temporarily deprived of oxygen.

ATP: The Universal Energy Coupler

The anabolic reactions of cells are responsible for growth and repair processes, whereas catabolic reactions release the energy needed to drive the anabolic reactions and to carry out other kinds of cellular work. The efficient linking, or coupling, of energy-yielding processes to energy-requiring processes is therefore crucial to cell function. This coupling is made possible by specific kinds of molecules that conserve the energy derived from exergonic reactions and release it again when and where energy is needed. 

In virtually all cells, the molecule most commonly used as an energy intermediate is the phosphorylated compound adenosine triphosphate (ATP). ATP is, in other words, the primary energy “currency” of the biological world. Keep in mind, however, that ATP synthesis is not the only way that cells store chemical energy. Other high-energy molecules, such as GTP and creatine phosphate, store chemical energy that can be converted to ATP. In addition, chemical energy is stored as reduced coenzymes such as NADH that are a source of reducing power in cells. These molecules are very important in shuttling energy between different metabolic pathways and processes in cells. Because ATP is involved in most cellular energy transactions, it is essential that we first understand its structure and function and appreciate the properties that make this molecule so suitable for its role as the universal energy coupler.

ATP Contains Two Energy-Rich Phosphoanhydride Bonds

ATP is a complex molecule containing the aromatic base adenine, the five-carbon sugar ribose, and a chain of three phosphate groups. The phosphate groups are linked to each other by phosphoanhydride bonds and to the ribose by a phosphoester bond, as shown for the ATP molecule below:

The compound formed by linking adenine and ribose is called adenosine. Adenosine may occur in the cell in the unphosphorylated form or with one, two, or three phosphates attached to carbon atom 5 of the ribose, forming adenosine monophosphate (AMP), diphosphate (ADP), and triphosphate (ATP), respectively. The ATP molecule serves well as an intermediate in cellular energy metabolism because energy is released when ATP undergoes hydrolysis—water is used to break the phosphoanhydride bond that links the third (outermost) phosphate to the second. Two products are formed: The terminal phosphate receives an —OH from the water molecule and is released as inorganic phosphate ( often written as ), and the resulting ADP molecule gets an and immediately loses a proton by ionization. Thus, the hydrolysis of ATP to form ADP and is highly exergonic. The reverse reaction, whereby ATP is synthesized from ADP and with the loss of a water molecule by condensation, is correspondingly endergonic. As you can see, energy is required to drive ATP synthesis from ADP and , and energy is released upon ATP hydrolysis. Biochemists sometimes refer to bonds such as the phosphoanhydride bonds of ATP as “high-energy” or “energy-rich” bonds, a very useful convention introduced in 1941 by Fritz Lipmann, a leading bioenergetics researcher of the time. However, these terms need to beunderstood correctly to avoid the erroneous impression that the bond somehow contains energy that can be released. All chemical bonds require energy to be broken and release energy when they form. What we really mean by “energy-rich bond” is that free energy is released when the bond is hydrolyzed. The energy is therefore a characteristic of the reaction the molecule is involved in and not of a particular bond within that molecule. Thus, to call ATP or any other molecule a “high-energy or energy-rich compound” should always be understood as a shorthand way of saying that the hydrolysis of one or more of its bonds is highly exergonic.

Endergonic (from the prefix endo-, derived from the Greek word ἔνδον endon, "within", and the Greek word ἔργον ergon, "work") means "absorbing energy in the form of work." Endergonic reactions are not spontaneous. By thermodynamic standards, positive work, a form of energy, is defined as moving from the surroundings (the external region) to the system (the internal region). Thus, an endergonic process, as contrasted with an exergonic process, is one where the system absorbs energy from the surroundings. As a result, during an endergonic process, energy is put into the system, if the transformation occurs at constant pressure and temperature, ∆G > 0. An endergonic reaction is a chemical reaction that absorbs energy in the form of work. A good example of a net endergonic process is photosynthesis.Photosythesis is a build-up or anabolic process that forms orgainic substances from inorgainic materials with the help of light energy . It is, therefore,an Endergonic process Also, in metabolism, an endergonic process is anabolic, meaning, that energy is stored. In metabolism, catabolic and anabolic processes are coupled by adenosine triphosphate (ATP).

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