Thursday, December 30, 2010

672)The Miracle Of Ribosome(The Cell's Protein Factory) Assembly Evolution; Quotes from Blogpost Four Hundred.

"In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

"Indeed, one strength of Islam has always lain in its belief that creation is not static but continuous, that through scientific and other endeavours, God has opened and continues to open new windows for us to see the marvels of His creation"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"Islamic doctrine goes further than the other great religions, for it proclaims the presence of the soul, perhaps minute but nevertheless existing in an embryonic state, in all existence in matter, in animals, trees, and space itself. Every individual, every molecule, every atom has its own spiritual relationship with the All-Powerful Soul of God"(Memoirs of Aga Khan III, 1954)

"The God of the Quran is the One whose Ayats(Signs) are the Universe in which we live, move and have our being"(Aga Khan III, April 4th 1952, Karachi, Pakistan)

"In fact this world is a book in which you see inscribed the writings of God the Almighty"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet)

Kathalika yubayyinu Allahu lakum ayatihi la'allakum ta-'aqiloona: "Allah thus makes clear to you His Signs that you may intellect"(Holy Quran 2:242)

"One hour of contemplation on the works of the Creator is better than a thousand hours of prayer"(Prophet Muhammad, circa 632CE)

http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html




Cornelius Hunter
Friday December 24th 2010

The Miracle of Ribosome Assembly Evolution

New research is uncovering the details of how the cell’s protein factory—the ribosome—is constructed. The ribosome translates messenger RNA molecules—edited copies of DNA protein-coding genes—into a string of amino acids, according to the genetic code. The ribosome has two major components (one smaller and one larger), each made up of both RNA and protein molecules, and is constructed via a complex sequence of events.

The RNA components of the ribosome are copies of DNA genes. These ribosomal RNA molecules—known as rRNAs—are initially in a raw copy of DNA which eventually is edited. For instance, one of these copies of DNA may contain many rRNAs, separated by spacer segments. The spacer segments need to be removed, leaving the individual rRNAs ready for assembly.

One of the findings of the new research is that in the early stages of assembly, one of the DNA copies folds up such that a spacer segment binds to one of the rRNAs. In particular, the spacer binds to the special segment of the rRNA that reads the messenger RNA molecules, in the final, assembled ribosome. When the spacer is removed, the rRNA switches to its correct shape, for function in the ribosome. One implication of this finding is that ribosome construction can be regulated by this switch. Remove the spacer and ribosome construction proceeds. Leave the spacer, and ribosome construction halts. As the researchers concluded:

"our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes."

RNA tends to fold up into a variety of shapes. In this case, as lead researcher Katrin Karbstein suggests, RNA folding properties are part of the design:

"Perhaps, nature has found a way to exploit RNA’s Achilles’ heel—its propensity to form alternative structures … Nature might be using this to stall important biological processes and allow for quality control and regulation."

But of course this mechanism brings yet more complexity:

"What is interesting is that as the organism becomes more complex, the number of cleavages needed increases. This may make the process more accurate and that may be an evolutionary advantage, but even in bacteria this cutting is not done in a simple way. We still don’t know exactly why that is."

Karbstein suggests that the strictly ordered cutting and pasting steps in ribosome assembly are introduced to produce singularly perfect intermediates. As she explains:

"Ribosomes make mistakes rarely, on the order of one in 10,000 amino acid changes. A lot of this accuracy depends on conversations between different parts of the ribosomes, so if the structure of the RNA isn’t correct, these conversations can’t happen. And that means more mistakes, and that’s not good because it can lead to any number of disease states."

Ribosomes don’t just happen. They are not easily assembled and the evolution of this choreography calls for several just-so heroics. Yes, this fine-tuned set of mechanisms makes for fantastic regulation of the cellular protein making factory, but it means that evolution must have gone through a stage where life didn’t work. For the spacer segment that binds to the rRNA is a show-stopper. It would be selected against instantly.

The only way to resolve this problem is to have the spacer removal mechanism already in place, before the spacer sequence itself evolved. As usual, evolutionists would need to rely on the needed mechanism just happening to serve some other useful purpose, and when the spacer sequence happened to arise for no reason, the removal mechanism found new work for itself. In other words, mutations arose that caused the DNA copy to fold, rendering ribosome synthesis—and life itself—impossible. But as luck would have it, there just happened to be the right molecular machine lying around that removed the problematic segment at just the right time and place. Not only was the fatal flaw obviated, but a brilliant new means of regulation invented. Amazing. Over time, further mutations happened to refine its actions and today we have the fine-tuned ribosome assembly process.

There you have it—evolution’s just-add-water version of science. For the umpteenth time evolution becomes a charade. Behind the scenes, in deep-time where no one can see it working, evolution once again performs miracle after miracle.

http://darwins-god.blogspot.com/2010/12/miracle-of-ribosome-assembly-evolution.html



Easy Nash
http://apps.facebook.com/blognetworks/blog/science_and_religion_in_islam_the_link/
http://gonashgo.blogspot.com/2009/08/500blogpost-five-hundred-is-blogpost.html
http://gonashgo.blogspot.com/2009/03/453a-blog-constructed-within.html

In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God: Aga Khan IV(2008)
The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)

671)The Bacterial Flagellum – Truly An Engineering Marvel!; Quotes From Blogpost Four Hundred.

"Every particle of the Creation has a share of the Command of God, because every creature shares a part of the Command of God through which it has come to be there and by virtue of which it remains in being and the light of the Command ofGod shines in it. Understand this!"(Abu Yakub Al Sijistani, 10th century Fatimid Ismaili cosmologist, d971, Kashf al-Mahjub("Unveiling of the Hidden"))

Kathalika yubayyinu Allahu lakum ayatihi la'allakum ta-'aqiloona: "Allah thus makes clear to you His Signs that you may intellect"(Holy Quran 2:242)

"In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

"......The Quran tells us that signs of Allah’s Sovereignty are found in the contemplation of His Creation - in the heavens and the earth, the night and the day, the clouds and the seas, the winds and the waters...."(Aga Khan IV, Kampala, Uganda, August 22 2007)

"....in Islam, but particularly Shia Islam, the role of the intellect is part of faith. That intellect is what seperates man from the rest of the physical world in which he lives.....This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives. Of that I am certain"(Aga Khan IV, Dar-es-Salaam, Tanzania, August 17th 2007)

"Of the Abrahamic faiths, Islam is probably the one that places the greatest emphasis on knowledge. The purpose is to understand God's creation, and therefore it is a faith which is eminently logical. Islam is a faith of reason"(Aga Khan IV, Spiegel Magazine interview, Germany, Oct 9th 2006)

"In sum the process of creation can be said to take place at several levels. Ibda represents the initial level - one transcends history, the other creates it. The spiritual and material realms are not dichotomous, since in the Ismaili formulation, matter and spirit are united under a higher genus and each realm possesses its own hierarchy. Though they require linguistic and rational categories for definition, they represent elements of a whole, and a true understanding of God must also take account of His creation. Such a synthesis is crucial to how the human intellect eventually relates to creation and how it ultimately becomes the instrument for penetrating through history the mystery of the unknowable God implied in the formulation of tawhid."(Azim Nanji, Director, Institute of Ismaili Studies, London, U.K., 1998)

"Education has been important to my family for a long time. My forefathers founded al-Azhar University in Cairo some 1000 years ago, at the time of the Fatimid Caliphate in Egypt. Discovery of knowledge was seen by those founders as an embodiment of religious faith, and faith as reinforced by knowledge of workings of the Creator's physical world. The form of universities has changed over those 1000 years, but that reciprocity between faith and knowledge remains a source of strength"(Aga Khan IV, 27th May1994, Cambridge, Massachusets, U.S.A.)

"The Divine Intellect, Aql-i Kull, both transcends and informs the human intellect. It is this Intellect which enables man to strive towards two aims dictated by the faith: that he should reflect upon the environment Allah has given him and that he should know himself. It is the Light of the Intellect which distinguishes the complete human being from the human animal, and developing that intellect requires free inquiry. The man of faith, who fails to pursue intellectual search is likely to have only a limited comprehension of Allah's creation. Indeed, it is man's intellect that enables him to expand his vision of that creation"(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11, 1985)

"The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims. Exchanges of knowledge between institutions and nations and the widening of man's intellectual horizons are essentially Islamic concepts. The Faith urges freedom of intellectual enquiry and this freedom does not mean that knowledge will lose its spiritual dimension. That dimension is indeed itself a field for intellectual enquiry. I can not illustrate this interdependence of spiritual inspiration and learning better than by recounting a dialogue between Ibn Sina, the philosopher, and Abu Said Abu -Khyar, the Sufi mystic. Ibn Sina remarked, "Whatever I know, he sees". To which Abu Said replied," Whatever I see, he knows"."(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11th 1985)

"In Islamic belief, knowledge is two-fold. There is that revealed through the Holy Prophet (s.a.s.) and that which man discovers by virtue of his own intellect. Nor do these two involve any contradiction, provided man remembers that his own mind is itself the creation of God. Without this humility, no balance is possible. With it, there are no barriers. Indeed, one strength of Islam has always lain in its belief that creation is not static but continuous, that through scientific and other endeavours, God has opened and continues to open new windows for us to see the marvels of His creation"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"Our religious leadership must be acutely aware of secular trends, including those generated by this age of science and technology. Equally, our academic or secular elite must be deeply aware of Muslim history, of the scale and depth of leadership exercised by the Islamic empire of the past in all fields"(Aga Khan IV, 6th February 1970, Hyderabad, Pakistan)

"Islamic doctrine goes further than the other great religions, for it proclaims the presence of the soul, perhaps minute but nevertheless existing in an embryonic state, in all existence in matter, in animals, trees, and space itself. Every individual, every molecule, every atom has its own spiritual relationship with the All-Powerful Soul of God"(Memoirs of Aga Khan III, 1954)

"Islam is fundamentally in its very nature a natural religion. Throughout the Quran God's signs (Ayats) are referred to as the natural phenomenon, the law and order of the universe, the exactitudes and consequences of the relations between natural phenomenon in cause and effect. Over and over, the stars, sun, moon, earthquakes, fruits of the earth and trees are mentioned as the signs of divine power, divine law and divine order. Even in the Ayeh of Noor, divine is referred to as the natural phenomenon of light and even references are made to the fruit of the earth(Aga Khan III, April 4th 1952, Karachi, Pakistan)

"The God of the Quran is the One whose Ayats(Signs) are the Universe in which we live, move and have our being"(Aga Khan III, April 4th 1952, Karachi, Pakistan)

"Nature is the great daily book of God whose secrets must be found and used for the well-being of humanity"(Aga Khan III, Radio Pakistan, Karachi, Pakistan, February 19th 1950)

"In fact this world is a book in which you see inscribed the writings of God the Almighty"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet)

"O brother! You asked: What is the [meaning of] `alam [world] and what is that entity to which this name applies? How should we describe the world in its entirety? And how many worlds are there? Explain so that we may recognize. Know, O brother, that the name `alam is derived from [the word] `ilm(knowledge), because the traces of knowledge are evident in [all] parts of the physical world. Thus, we say that the very constitution (nihad) of the world is based on a profound wisdom"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet, from his book "Knowledge and Liberation")

“The physician considers [the bones] so that he may know a way of healing by setting them, but those with insight consider them so that through them they may draw conclusions about the majesty of Him who created and shaped [the bones]. What a difference between the two who consider!”(Abu Hamid Al-Ghazali, Muslim Theologian-Philosopher-Mystic, d1111CE)

"Tarkib' is composition as in the compounding of elements in the process of making more complex things, that is, of adding together two things to form a synthesis, a compound. Soul composes in the sense of 'tarkib'; it is the animating force that combines the physical elements of the natural universe into beings that move and act. Incorporating is an especially apt word in this instance. It means to turn something into a body, as in 'composing'. But it is actually the conversion of an intellectual object, a thought, into a physical thing. Soul acts by incorporating reason into physical objects, the natural matter of the universe and all the things composed of it"(Abu Yakub Al-Sijistani,10th century Fatimid Ismaili cosmologist, d971CE, from the book, 'Abu Yakub Al-Sijistani: Intellectual Missionary', by Paul Walker)

"One hour of contemplation on the works of the Creator is better than a thousand hours of prayer"(Prophet Muhammad, circa 632CE)

"All human beings, by their nature, desire to know."(Aristotle, The Metaphysics, circa 322BC)

http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html



24 December 2010

The Bacterial Flagellum – Truly An Engineering Marvel!

Jonathan M

A few weeks ago, I had the opportunity to attend a lecture by microbiologist Phillip Aldridge, of the University of Newcastle. The topic of his lecture was “The Regulation of Flagellar Assembly”. Being an ID proponent, I had a natural interest in what Aldridge was going to say, and I had been looking forward to the event for some time. I was already familiar to a degree with several of the key mechanisms and regulation of flagellar biosynthesis. Nonetheless, the lecture succeeded in re-kindling my passion for biology, and inspired me to do some in-depth research on my own with regards the workings of this engineering marvel.

I must confess that I was blown away. If one thought that the functional-specificity of arrangement with respect to the flagellum’s key components may well provide adequate grounds for a design inference, the mechanisms of flagellar construction take this intuition to a whole new level. So mesmerized I was by the motor’s intrinsic beauty and elegance, that I decided to provide a sketch overview of this amazing process for the benefit of readers of this blog. Of course, there are variations in the flagellum’s overall construct from species to species. The archetypical flagellum, however, is probably that of the closely related species, Escherichia coli, Salmonella enterica, and Salmonella typhimurium. It is this that I want to primarily focus on.


An overview of the flagellum’s construct

As with a typical man-made motor, the unit which provides rotary motion (which is embedded in the inner cell membrane) revolves within a stationary component (stator). The rotor is a tube-like structure which extends from within the cell, through the membrane, to the outside, where the flagellar filament (which serves as a propeller) is attached via a flexible joint.

The flagellum consists of a basal body (which is embedded in the cell wall) and two axial structures, the book and filament. The basal body is made up of the MS ring, rod, and L- and P- rings. Parts of the axial structure are exported from the cell by the type III secretion system (T3SS). The T3SS is composed of several proteins from the MS ring and a peripheral hexameric ATPase FliI that drives the export process.

The motor is anchored in the cytoplasmic membrane and cell wall. The motor consists of a central rod that passes through a series of rings. In gram-negative bacteria, an outer ring (the L ring) is anchored in the lipopolysaccharide layer. Another ring (the P ring) is anchored in the peptidoglycan layer of the cell wall. A third set of rings (the MS and C rings) are respectively found within the cytoplasmic membrane and the cytoplasm. Gram positive bacteria, by contrast, do not have an outer membrane, and thus only possess the inner pair of rings. A series of proteins, called Mot proteins, surround the inner ring and are anchored in the cytoplasmic membrane. The structures of the L, P, C and MS rings, in combination with the central rod, are collectively referred to as the “basal body”. In addition, a class of proteins called the Fli proteins function as a ‘switch’ for the reversal of motor rotation, which is plugged into an elegant signal transduction mechanism for receiving feedback from the environment — I will discuss this further in due course.

The flagellar filament (propeller) is constructed from subunits of the polypeptide flagellin. There is a wider region at the base of the filament (the ‘hook region’), which connects the filament to the motor component of the base. These subunits are arranged in a tight helical structure to produce a stiff hollow rod. Each subunit contributes to a small propeller blade to the outside of the structure.

The driving force behind the flagellum’s rotary motion comes from a proton motive force, to which I shall return in due course.


Chemotaxis and Signal Transduction

Chemotaxis refers to the means by which bacteria direct their movements in response to environmental chemical signals. This mechanism allows the bacteria to locate food by swimming towards the highest concentration of food molecules (such as glucose). The default direction of flagellar rotation is anticlockwise. This directionality of rotation can be reversed by virtue of a classic two-component signal transduction circuit (discussed below). When the direction of rotation is switched to clockwise, the flagellar bundle breaks apart, and the bacterium physically “tumbles” in place. The overall movement of a bacteria can be described in terms of a series of alternating swimming and ‘tumbling’ phases. When the bacterial cell ‘tumbles’, it re-orientates itself. By repeatedly evaluating its course, the bacterium is able to find favourable locations with the highest concentration of attractant (possibly a food source).

A two-component signal transduction circuit essentially involves a histidine protein kinase that catalyses the transfer of phosphoryl groups from ATP to one of its own histidine residues, and a response regulator that catalyses the transfer of phosphoryl groups from the histidine kinase to its own aspartate residue. In the chemotaxis system, the histidine kinase, CheA, associates with chemoreceptors (a distinct class of transmembrane receptor proteins) which interact with chemicals in the surrounding environment. The switch in flagellar direction is induced by CheY, which interacts with a flagellar switching protein, FliM, inducing the change from counter-clockwise to clockwise rotation.

The chemoreceptors which form a part of the chemotaxis system are Tsr, Tar, Tap, Trg, and Aer. In combination with CheA and CheW, they act to form receptor-signalling complexes that function to integrate sensory information to regulate CheA autophosphorylation, hence controlling its activity. This, in turn, controls the phosphorylation of the response regulator (CheY). Ordinarily, CheY is reversibly bound to CheA. When it becomes phosphorylated, however, it dissociates with CheA and quickly diffuses to the flagellar motors. The CheY then acts as an allosteric regulator to promote the clockwise rotation of the flagellar bundle, which results in the ‘tumbling’ motion. An attractant stimulus interacts with the chemoreceptors, inhibiting the activity of the CheA kinase. This results in a decrease in phosphorylated CheY. Thus, the propensity of the bacterium to re-orient itself by “tumbling” is decreased.

When CheB is activated by CheA, it acts as a methylesterase, and removes methyl groups from glutamate residues on the cytosolic side of the receptor. It acts antagonistically with CheR, which adds methyl residues to the same glutamate residues. If the attractant’s concentration is high, the level of CheA phosphorylation (and, hence, CheY and CheB phosphorylation) stays relatively low. The bacterium thus swims relatively smoothly. Because the phosphorylated CheB is not available to demethylate, the level of methylation of the chemoreceptors increases.

Methylation, however, inhibits the chemoreceptors from responding to the attractant. Thus, the level of phosphorylated CheA and CheB increases and the bacterial cell tumbles, regardless of whether the level of the attractant is high. The availability of CheB-P now means that the chemoreceptors can be demethylated, and the receptors become available again to respond to attractants. In the case of repellants, the system works in exactly the opposite way — whereby more methylated chemoreceptors respond most and the lesser methylated chemoreceptors respond least!

A diagrammatic illustration of this system is to be found in the figure below:


Proton Motive Force

A proton motive force drives the rotation of the bacterial flagella. Electrochemical energy is converted into torque via an interaction between the stator and the rotor. Torque is then transmitted from the C-ring by the MS ring to the rod and then to the hook region. From there it is transferred to the propeller (filament). When the filament rotates, the torque is converted into thrust, allowing the bacterial cell to move.

The rotary engine is located at the flagellum’s anchor point on the inner membrane. A flow of protons across the membrane, resulting from a concentration gradient, drives the motor. Protons are transferred across the membrane by the rotor, and the rotor is turned in the process. The speed at which the motor turns can be increased or decreased as a direct result of changes in the strength of the proton motive force.

But it only gets better. An interesting 2008 study by Blair et al. demonstrated that an operon required for the biosynthesis of the biofilm matrix in Bacillus subtilis also encodes a molecular clutch, called EpsE. When associated with a flagellar basal body, EpsE disables the biological motor by disengaging the drive train from the power source! Those hungry for further reading are invited to read Howard Berg’s 1995 paper on Torque generation in the bacterial flagellar rotory motor.


Flagellar Assembly

The processes of flagellar assembly, and its regulation, is my personal unparalleled favourite area of study in the discipline of microbiology. For an informative documentary on the assembly of this nanomachine, I highly recommend viewing this video.

The self-assembly of the bacterial flagellum requires the co-ordinated expression of more than 60 gene products (which encode for both structural and regulatory proteins). Bacteria are intriguingly able to detect the stage of progress with respect to flagellar assembly, and subsequently use this information in the co-ordination of gene expression.

The mechanisms of flagellar assembly are so complex and so sophisticated that justice can hardly be done to them here. Interested readers who desire a fuller discussion of these mechanisms are advised to read a 2002 paper, authored by Phillip Aldrige and Kelly T Hughes, appearing in Current Opinion in Microbiology. In addition, a technical book, Pili and Flagella: Current Research and Future Trends features a detailed discussion of this topic. The book is typically priced at £150/$310, but a significant portion of the book may be accessed via Google Books. The book discusses studies of flagellar mutants that fail to complete their flagella. In so doing, they discern which proteins are absolutely indispensible to flagellar assembly, and which are not — something any ID proponent should be interested in.

Flagellar assembly begins in the cytoplasmic membrane, progresses through the periplasmic space, and finally extends outside the cell. As previously alluded to, the flagellar apparatus consists of two main parts: the secretion system and the axial structure. The main components of the axial structure are FlgG for the rod, FlgE for the hook, and FliC for the filament. All of these assemble with the help of a cap protein (FlgJ, FlgD and FliD respectively). Of those, only FliD remains at the filament’s tip — the other two are not present in the finished product. Other components of the axial structure (FlgB, FlgC and FlgF) connect the rod and MS ring complex. The hook and the filament are connected by FlgK and FlgL

The MS ring complex is the structural foundation of the apparatus. When the C ring and C rod attach to the M ring (at its cytoplasmic surface), the complex begins to secrete flagellar proteins.
With the assistance of a cap protein (FlgJ), the rod structure is constructed through the peptidoglycan layer. But its growth is terminated when it reaches the outer membrane (which represents a physical barrier such that it cannot pass through unaided). But not to worry! The outer ring complex cuts a hole in the membrane. The hook then begins to grow beneath the FlgD scaffold until it reaches approximately 55nm in length. When the hook reaches this critical length, the substrates which are being secreted switches from the rod-hook mode to flagellin mode. FlgD is then replaced by HAPs (hook associated proteins) and the filament continues to grow — note that this can only take place in the presence of FliD (the cap protein), otherwise the flagellin monomers are lost.


The Regulation of Flagellar Assembly

The energy costs of assembling flagella make these nanomachines expensive systems to run. This entails the necessitude for systems and mechanisms to regulate the co-ordination of assembly. The flagellar system of Salmonella (the paradigm organism for this system) possesses three classes of flagellar promoters which are organised into a transcriptional hierarchy. The Class I promoter drives the expression of the enteric master regulator, FlhD4C2. In association with the sigma factor, σ70, this master regulator turns on the Class II promoters which are responsible for the gene expression of the hook-basal-body subunits and its regulators, including σ28, and its anti-sigma factor, FlgM. σ28 is required for the activation of the Class III promoters. This class of promoters is responsible for the expression of flagellin monomers, the chemotaxis system and the motorforce generators. Interaction with its anti-sigma factor (FlgM), thus keeping it away from the RNA polymerase holoenzyme complex, inhibits the activation of σ28 prior to the completion of the Hook Basal Body. When the Hook Basal Body is finished, the FlgM is secreted through the flagellar structure via the Type III Secretion Apparatus substrate specificity switch. This means that the Class III promoters can now be activated by their sigma factor (σ28) because its anti-sigma factor (which represses its action) has been removed. This allows the flagellum to be completed.

This brief overview of flagellar assembly has barely scratched the surface of this intricate process. Nothing will please me more than if, after having read this description, at least a few readers reach for the relevant literature to find out more.


The Bacterial Flagellum — A Paradigm for Design?

In writing the above descriptions, I hoped to treat the educated layperson to a flavour of the magnificence of this rotary motor. As previously stated, nothing will bring me more satisfaction than having provided someone with the inspiration to pursue further information. The question does arise, however, as to whether this system bears the hallmarks of design — or is it, as so many biologists maintain, merely the product of blind, purposeless and impersonal natural processes of chance and necessity? To me, the answer is very clear. This system certainly appears to be designed technology. It certainly appears to bear the hallmarks of design logic. And it does seem that the burden of proof must, at this present time, lie with he who rejects this proposition — that is, he who ascribes this system to blind natural processes. The handwaving gestures of Kenneth Miller, who asserts that the Darwinian explanation for this system is more appropriate in light of the presence of the Type III Secretion System, can no longer be considered a satisfactory rebuttal to the design postulate. Such gestures may, at first glance, appear convincing to the uninitiated, unfamiliar with the complexities of these systems. But when one examines the molecular structure and orchestration of these systems, one loses satisfaction with the vague discussions of protein sequence homologies. Kathryn Applegate and Ard Loius seem to be under the impression that this assembly process parallels the processes of Darwinian evolution — I will allow readers to judge for themselves on that one.

As has been pointed out by Stephen Meyer and Scott Minnich, there is an even more fundamental challenge to the standard Darwinian line with regards this system. Firstly, the phylogenetic evidence is strongly suggestive that the T3SS is an evolutionary biproduct of the flagellar system, rather than the other way round (see, for instance, here). Secondly, if flagellum biosynthesis were to be expressed simultaneously with the Yop T3SS, flagellin monomers would likely be exported out the needle-like structure as well as the flagellar basal body, potentially limiting the efficiency of both systems. Meyer and Minnich argue in their paper that the potential for cross-recognition between Type III exported proteins in the same cell explains why the segregation of these systems by specific environmental cues is necessary. Expression of a flagellum under host conditions would result in a loss of polarised secretion of Yop proteins into the cells of the host. Flagellin is also a potent cytokine inducer – display of flagellin to the macrophages by direction injection via the Ysc secretin would strongly countermand the Yersinia’s anti-inflammatory strategy.

http://www.uncommondescent.com/intelligent-design/the-bacterial-flagellum-truly-an-engineering-marvel/



Easy Nash
http://apps.facebook.com/blognetworks/blog/science_and_religion_in_islam_the_link/
http://gonashgo.blogspot.com/2009/08/500blogpost-five-hundred-is-blogpost.html
http://gonashgo.blogspot.com/2009/03/453a-blog-constructed-within.html

In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God: Aga Khan IV(2008)
The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)

670)Mark Tapson Offers Ten Good Suggestions On How To Make Islam Respectable; Quotes Of Easy Nash, Jason Kenney and Orestes Brownson.

Sunday, December 26, 2010

How to Make Islam Respectable
Mark Tapson

Regardless of whether one subscribes to the notion of a clash of civilizations, I think we can all agree that relations between “the Islamic world” and “the West,” however one defines those labels, are, well, strained. President Obama was elected at least partly because, with childhood roots in Muslim Indonesia and an Arabic middle name no one was allowed to mention until after the election, the Left believed him to be the perfect candidate to heal that rift – when he wasn’t healing the racial divide, America’s reputation abroad, and the planet.

So right out of the gate, Obama made his first order of business an appearance on al-Arabiya TV, in which he made seven references to “respecting” the Muslim world, his flashing neon semaphore to them that he was no imperialist exploiter like his predecessor (Daniel Pipes notes here how common a motif the word “respect” was for Obama, ironically so for a man who commands none either at home or abroad). Then it was on to a self-important speech from Cairo, in which Obama flattered the Islamic world so effusively that one wondered if he was angling to ask it to the prom. And of course, who can forget his show of contemptible dhimmitude – I mean deep respect – to the Saudi King?

His efforts haven't exactly mellowed the clash of civilizations into a Kumbiya campfire circle. And yet Obama was at least theoretically on the right track. Because a recent poll by the new Abu Dhabi Gallup Centre reports that a large majority of Muslims say that the best way for the West to improve relations with them is to “respect Islam.” But the West has made every effort at “Muslim outreach” and bent over backwards to make social and cultural concessions to its Muslim citizens. President Bush himself expressed a distasteful degree of deference toward Islam, and Obama far surpassed even that; so how much more respect will it take to make the Muslim world feel sufficiently respected?

The issue needs to be reframed. Since even our most gushing genuflection seems to have accomplished nothing except to incite further expectations of respect, it’s time for the West to take charge of this dialogue on our terms. We in the West – apart from Obama and his sycophants – are accustomed to the understanding that respect cannot simply be expected, much less demanded; it has to be earned. So now the question becomes, what must that majority of Muslims who want respect for their religion do to earn it? How can they make their religion, well, more respectable?

What follows are ten suggestions (a few of which mirror Robert Spencer’s five ways to end Islamophobia) for those Muslims cited in the Gallup poll to take to heart – those who, like Rodney Dangerfield, lament that they can’t get no respect.


10) STOP WAGING VIOLENT JIHAD

Let’s get the most obvious one out of the way first. If Muslims are tired of having the words
“Muslim” and “terrorist” linked (on those rare occasions when our leaders and media actually do link them), a painfully obvious solution leaps to mind: stop committing acts of terrorism in the name of Allah and Mohammed.

Ending atrocities against innocents and non-combatants (as we define them, not as the Islamists define them), and striving to actually live up to Islam's Religion of Peace™ label, would be a nice good-faith gesture to lay the groundwork for better relations with the West. It's certainly the most urgent step to take, and the most necessary - without it, none of my subsequent suggestions will matter.

For Muslims who already are not plotting or committing acts of terrorism, confront your co-religionists who are and nip them in the bud. After all, as it’s often pointed out, they constitute a TME - Tiny Minority of Extremists ™ - that should easily be overwhelmed by the moderates' superior numbers. At the very least, report the TME to the authorities – which brings us to suggestion number nine…


9)COOPERATE TO THE FULLEST WITH LAW ENFORCEMENT TO ROOT OUT THE TERRORISTS IN YOUR MIDST:

A New York Times article last week noted that Rep. Peter T. King of New York, who will become the chairman of the House Homeland Security Committee, complained about a lack of cooperation in terror investigations:

When I meet with law enforcement, they are constantly telling me how little cooperation they get from Muslim leaders.

He cited the case of Najibullah Zazi, arrested last year for plotting to bomb the New York subway system. Ahmad Wais Afzali, a Queens imam had tipped off Zazi that he was the target of a terror investigation.

Salam al-Marayati, the executive director of MPAC, the Muslim Public Affairs Council*, “expressed deep concern” that [King] basically wants to treat the Muslim-American community as a suspect community.

I’m sorry to break this news to Mr. Marayati, but the Muslim-American community is suspect – not because of bigotry or Islamophobia, but because the terrorists and radicals in its midst have made it so, and resisting cooperation with law enforcement naturally lends even more weight to that suspicion. It doesn't help when Muslim community leaders cry “civil rights violations” while claiming that people like King are undermining the relationship that Muslim leaders had sought to build with law enforcement officials around the country.

Relationship? Law enforcement officials nationwide are complaining that there isn't one. Short of infiltration, which Muslim leaders also oppose, law enforcement has no way of knowing what radical activities may or may not be going on inside the mosques. And that brings us to our next recommendation...

*Check out the Investigative Project on Terrorism’s devastating piece about MPAC’s unfitness to serve as a liaison with law enforcement.


8) DE-RADICALIZE YOUR MOSQUES:

Estimates are that upwards of 80% of all mosques in the United States are controlled by the fundamentalist Wahhabi strain of Islam promoted by the Saudis’ bottomless funding. Preaching Jew-hatred, the supremacy of sharia, and the downfall of democracy isn’t likely to win us over. I'm just sayin'.

Now former Iranian Revolutionary Guard Reza Khalili reports that Iran is using mosques and Islamic cultural centers in Europe and the U.S. as centers of terrorist recruitment and planning:
They recruit, they train, they sell the ideology of martyrdom, and many, many are guided and connected to terrorist groups.

Robert Spencer comments that there is no surprise in this, except for those Westerners who buy the politically correct line that mosques are benign houses of worship that are never used for any nefarious purposes. In reality, mosques have been used to preach hatred; to spread exhortations to terrorist activity; to house a bomb factory; to store weapons; to disseminate messages from bin Laden; to demand (in the United States) that non-Muslims conform to Islamic dietary restrictions; to fire on American troops; to fire upon Indian troops; or to train jihadists.

If Muslims don't want their mosques infiltrated or investigated by non-Muslim law enforcement, then it's up to them to clean house and rid themselves of the elements - including the imams themselves - who might be fomenting and plotting subversion, hatred, and terror.


7) START RESPECTING THE RIGHTS OF WOMEN:

One of the West's bigger bones to pick with the Muslim world is the latter's (mis)treatment of women, which rockstar scholar Reza Aslan angrily insists isn’t an issue:

If you’re somehow arguing that Islam has a different conception of women in society than Europe does, it’s just wrong.

Women such as Ayaan Hirsi Ali and my friends Brigitte Gabriel and Nonie Darwish beg to differ.* Here is how Nonie’s must-read book Cruel and Usual Punishment begins:

For the first thirty years of my life, I lived as a virtual slave. I was a bird in a cage; a second-class citizen who had to watch what I said even to my close friends. Under Islamic law I had to live in a gender-segregated environment and always be aware that the legal and social penalty for “sin” could end my life. This is what it is to live as a woman under Sharia law.

Last week it was reported that each year an estimated 600,000 lashes are dealt to women in the sharia wonderland known as the Sudan, for such shockingly heinous crimes against humanity as wearing pants. Women in sharia-controlled Saudi Arabia must conceal their seductive charms in black Hefty bags and veil their faces in public, of course; but now even that’s not enough for the Saudi “Commission for the Promotion of Virtue and Prevention of Vice.” A Commission spokesman announced that

The Commission members have orders to tell any women in public to cover up her face if they find that her eyes are seditious.

Ah, seditious eyes – potentially more threatening than seditious bare ankles, although the Commission doesn’t explain what constitutes “seditious.” No word either on how the Commission feels about “Bette Davis Eyes.”

* Not that Aslan will listen. In 2009 I attended an event at which Aslan was speaking, and Nonie Darwish rose in the audience to challenge him about the condition of women under sharia. After conceding one small point, he said, “Everything else you said is wrong” – and turned away from her, ending their discussion.


6) START RECIPROCATING RELIGIOUS TOLERANCE:

There is no more religiously tolerant country in history than the contemporary United States, although you’d never know this from the constant wailing refrain of “Islamophobia!” from Islamists and their leftist sympathizers. The notion of a tsunami of Muslim-hatred washing over the nation is a shameful PC myth, as a November “hate crimes” report reveals. Muslim-Americans enjoy as much, if not more, religious freedom here as anyone else.

By stark contrast, no Bibles, churches, temples or synagogues are allowed on the Arabian peninsula, the home of Islam. Non-Muslims are not even allowed in Mecca. Under Islamic rule elsewhere, no new non-Muslim houses of worship are allowed to be built, and existing ones may not be repaired.

Then there is the violent persecution of non-Muslims. My friend Mark Durie, the brilliant scholar of Islam, notes in his The Third Choice that

The human rights situation of Christians in many Muslim countries has been getting steadily worse over the past half-century. This deterioration has been directly linked to the worldwide Islamic revival and reinstatement of sharia law.

A report last month at the Hudson New York think tank states that

Christians in Arab countries are no longer being persecuted; they are now being slaughtered and driven out of their homes and lands.

And then, of course, there’s the Koran-mandated Jew-hatred and Muhammad’s command of death for those who leave Islam.

Muslims want us to respect Islam? End the persecution of non-Muslims, reciprocate religious tolerance, and abolish the death penalty for “apostasy.” Then we’ll talk.


5) UPDATE YOUR PENAL CODE FROM "MEDIEVAL"

While our own legal system has a far-from-perfect record of dispensing justice, and punishment can be harsh (that’s why it’s called “punishment”), sharia is the very definition of draconian. This “cruel and usual punishment,” as Ms. Darwish calls it, includes lashings for drinking alcohol, amputations for thievery, beheadings for more serious crimes, being hanged or thrown from a roof for homosexuality, and – the real gem in sharia’s crown – the stoning of adulterers.

This last method of execution requires that the stones used be neither too small to do serious damage nor large enough to cause a quick death. So it’s clear that the ordeal is intended to be as excruciating and prolonged as possible.

Say what you will about our own electric chairs and firing squads, which we’ve largely abandoned in our search for the most humane method of execution (itself reserved for only the most heinous of crimes); sharia’s punishments are characterized by barbarism. News flash: barbarity doesn’t generate respect.


4) LET THE WHOLE CARTOON THING GO:

Speaking of barbarity…

This would seem to be a no-brainer, but apparently it bears explaining: "taking offense" is not license for frenzied rioting, murder and mayhem. The most notable example is the worldwide rage over a set of cartoons published years ago in a Danish newspaper, which no one outside of that tiny country would have seen if not for the cartoons' shrewd distribution by Islamists themselves eager to unite the ummah, the worldwide Muslim community, against the blasphemous West. That murderous outrage is ongoing: Danish cartoonist Kurt Westergaard was recently set upon in his home by a Muslim attacker seeking vengeance.

Similar, more recent examples include the threats to kill the South Park creators for their tame, satirical, animated take on that same hypersensitive hysteria, and the death fatwa issued against cartoonist Molly Norris, who has since "gone ghost" in fear for her life. Not to mention the death threats, explicit or implied, over innumerable other things that offend many Muslims.

Apologists like to point out that many Muslims take disrespect toward Islam, Allah, and his prophet very seriously, and they suggest we tiptoe respectfully around that religious sensibility. I would like to point out that such apologists are cowards, appeasers, and religious hypocrites, and remind them that violent lunacy is not deserving of respect. And this segues into suggestion number three...


3) STOP PRESSING FOR LIMITS ON FREE SPEECH AND FOR THE CRIMINALIZATION OF ISLAMOPHOBIA:

From the Salman Rushdie affair to Molly Norris' sad vanishing, the list of Islamist assaults on our precious freedom of speech is far too long to do justice to here. And the West has too often responded not with firm resistance, but by preemptively censoring itself: witness Random House rescinding its offer to publish The Jewel of Medina, a novel that an academic warned might outrage Muslims, or the Yale University Press publishing a book about the Danish cartoons that will not include the cartoons themselves.

Islamists know that the key to winning the war of ideas against the West is to keep hammering away at our freedom of speech - our right and our ability to critique and denounce a totalitarian ideology that is hell-bent on bringing the West under its heel. Criminalizing blasphemy, defamation of religion, "Islamophobia" and the like will put us at a mortal disadvantage. Indeed, the world's largest Islamic assembly, the Organization of the Islamic Conference, has made the criminalization of religious defamation, specifically "Islamophobia," its number one priority - and Obama has sent a sympathetic envoy to that party to help them achieve it.

To earn our respect and the beginning of trust, you must embrace, not threaten, our freedoms and our values.


2) STOP LETTING THE MUSLIM BROTHERHOOD SPEAK FOR YOU:

For decades now, the Muslim Brotherhood has shrewdly worked to establish its subversive presence in America through a complex network of front groups and “legacy groups” which includes virtually every recognized Muslim organization in this country. Over time these groups – most notably the ubiquitous CAIR, the Council on American Islamic Relations – have gradually muscled their way into position as the representative voice of all Muslim-Americans.

Maddeningly, our government, law enforcement, and media have taken the bait and embraced these groups unquestioningly – blindly engaging an enemy that seeks the “elimination of Western civilization,” as an internal Brotherhood document proclaims. Such Islamist groups completely control this country’s dialogue with our Muslim citizens.

Americans have been asking since 9/11/01:

Where are the moderate Muslims? Why have they not risen up en masse to show that they stand with us against the extremists?

For Muslims to earn the respect of the West, those moderates in America and around the world must prove first that they exist - by uniting, organizing, promoting themselves not only to the media and government but to the public, and fearlessly confronting the deeply-rooted network of Brotherhood groups. And they must also speak out forcefully in unqualified solidarity with the West against their co-religionists' terrorism and stealth agenda.


1) START TAKING RESPONSIBILITY FOR YOUR OWN DESTINY INSTEAD OF BLAMING THE WEST:

In contrast to Western notions of self-reliance and free will, the Arab world suffers from what Hugh Fitzgerald calls an “Islam-inculcated inshallah-fatalism” characterized by the habitual mantra “Inshallah,” or “If God wills it,” used in reference to virtually every action. As Fitzgerald writes,

Why try very hard when, in the end, every fiber in your individual or collective being tells you that, in the end, it's all up to Allah, and he will intervene, quite inexplicably and suddenly, whenever he wants?

This is fatal to cultural, technological, scientific, economic, and spiritual development.
Without the culturally ingrained confidence that human beings can, through their own decisions and choices, impact the external world and to a large extent steer their own destinies, a people is doomed to stagnation, jealousy, and parasitism, and tends to look outside themselves to affix blame.

To earn the West’s respect, such Muslims must stop shrugging “inshallah” about all things great and small, stop laying the blame for their conditions on conspiracy theories of Western imperialism and thievery, and actively take responsibility for a better future and a peaceful, shared destiny with the West.

(This article first appeared on NewsReal Blog, 12/26/10)

http://marktapson.blogspot.com/2010/12/top-10-ways-islam-can-earn-wests.html



Easy Nash
If there are 23,000 jihadist websites and blogsites out there in cyberspace, there is no reason why we should not create 100,000 non-jihadist websites and blogsites: easynash(2007)

Quotes Of Canadian Minister Of Citizenship, Immigration And Multiculturalism Hon. Jason Kenney(2009):
1)When you become a citizen, you're not just getting a travel document into Hotel Canada.
2)I think it's scandalous that someone could become a Canadian not knowing what the poppy represents, or never having heard of Vimy Ridge, Passchendaele, Dieppe or Juno Beach.
3)We mention freedom of conscience and freedom of religion as important rights but we also make it very clear that our laws prohibit barbaric cultural practices, they will not be tolerated, whether or not someone claims that such practices are protected by reference to religion.
4)I think we need to reclaim a deeper sense of citizenship, a sense of shared obligations to one another, to our past, as well as to the future, a kind of civic nationalism where people understand the institutions, values and symbols that are rooted in our history.
5)New Canadians are naturally conservative in the way they live their lives: they are entrepreneurial; they have a remarkable work ethic; they are an aspirational class; they want stability; they are intolerant of crime and disorder; they have a profound devotion to family and tradition, including institutions of faith; that whole spectrum of values is conservative.

Orestes Brownson's noble hope: "that we have reached the term of our downward tendency; that radicalism has had its day; that a reaction has commenced, and that the mass of our people will recover from their folly, and henceforth not fear to be conservative."

Thursday, December 16, 2010

669)Two Japanese Scientists, A Couple Of Boogers, Claim That Snot Has The Power To Alter Scents; Quotes from Blogpost Four Hundred.

"In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

"Islamic doctrine goes further than the other great religions, for it proclaims the presence of the soul, perhaps minute but nevertheless existing in an embryonic state, in all existence in matter, in animals, trees, and space itself. Every individual, every molecule, every atom has its own spiritual relationship with the All-Powerful Soul of God"(Memoirs of Aga Khan III, 1954)

"Nature is the great daily book of God whose secrets must be found and used for the well-being of humanity"(Aga Khan III, Radio Pakistan, Karachi, Pakistan, February 19th 1950)

http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html



Snot has the power to alter scents

Mice studies show sense of smell can be modified by mucus

By Laura Sanders
Tuesday, November 30th, 2010

A rose sniffed through a snotty nose may not smell so sweet. Enzymes in mice’s nasal mucus transform certain scents before the nose can detect them, a new study finds. The results, published December 1 in the Journal of Neuroscience, show that lowly mucus may feature prominently in the sense of smell.

“It is completely unexpected that snot would play a potential role in changing how we perceive odors,” says neuroscientist Leslie Vosshall at Rockefeller University in New York City. “Most people and most scientists pay no attention at all to mucus.

”But there’s more to mucus than what meets the nose: The thick goo that serves to lubricate the nose is teeming with proteins and protein-chopping enzymes. Some of these molecules are thought to catch smells and shuttle them to odor receptors in the nose. Other components may protect the body from toxic chemicals by chopping them up into less harmful pieces. But no one knew whether this chopping action had any effect on smell perception.

In the new study, Ayumi Nagashima and Kazushige Touhara of the University of Tokyo added particular odorants to tiny amounts of mucus sucked out of a mouse’s nose and tested the resulting chemical composition of the mix. After five minutes of sitting in mucus, about 80 percent of almond-smelling benzaldehyde was converted into benzyl alcohol (a scent found in some teas and plants) and the odorless benzoic acid. Inactive enzymes in boiled mucus couldn’t do this odor conversion, the team found.

Snot enzymes can cut up aldehydes and molecules with chemical features called acetyl groups, the researchers reported. Scents from these kinds of molecules are common in flowers, plants and animals (and perfumes: aldehydes feature prominently in Chanel No. 5’s formulation).

This odor transformation happened inside the mice’s noses and was reflected in their brains, too, the researchers found. Parts of the mouse brain called glomeruli get signals from mice’s smell-sensing nerve cells. When the researchers inactivated a scent-chopping enzyme in the mice’s noses (in effect, removing the effect of the mucus), the pattern of glomeruli activation changed, suggesting that the snot enzymes affect what the mouse smells.

Mice’s behavior confirmed this altered sense of smell. Mice were trained to associate sugar with a particular odor. Later, the mice were presented with two smells, one that usually comes with a treat and one that doesn’t. Normally, the mice spent more time nosing around the smell that came with a treat. But when mucus enzymes were inactivated, the mice spent less time sniffing around the treat-linked smell, suggesting that they could no longer recognize the odor.

That the mucus enzymes could act on the odors before the nose could detect them was unexpected, says neuroscientist Sigrun Korsching of the University of Cologne in Germany, “but the behavioral tests are convincing in that respect.”

Whether humans experience this same mucus effect is unclear. Some of the same mucus enzymes are also found in people, and preliminary data from other researchers suggest that nasal enzymes can change odorant quality for humans, Touhara says.

In addition to showing how mucus can change smells, the study answers a vexing mystery that has been lurking in the olfactory field — experiments in lab dishes give slightly different results than experiments in a live animal. Korsching says that the new study offers a convincing explanation for this difference — snot.

http://www.sciencenews.org/view/generic/id/66832/title/Snot_has_the_power_to_alter_scents



Easy Nash
http://apps.facebook.com/blognetworks/blog/science_and_religion_in_islam_the_link/
http://gonashgo.blogspot.com/2009/08/500blogpost-five-hundred-is-blogpost.html
http://gonashgo.blogspot.com/2009/03/453a-blog-constructed-within.html

In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God: Aga Khan IV(2008)
The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)

668)Ibn Sina Or Avicenna: An Encyclopedia Article By Dr Nader El-Bizri Of The Institute Of Ismaili Studies; Quotes From Blogpost Four Hundred.

"The truth, as the famous Islamic scholars repeatedly told their students, is that the spirit of disciplined, objective enquiry is the property of no single culture, but of all humanity. To quote the great physician and philosopher, Ibn Sina: "My profession is to be forever journeying, to travel about the universe so that I may know all its conditions." "(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims. Exchanges of knowledge between institutions and nations and the widening of man's intellectual horizons are essentially Islamic concepts. The Faith urges freedom of intellectual enquiry and this freedom does not mean that knowledge will lose its spiritual dimension. That dimension is indeed itself a field for intellectual enquiry. I can not illustrate this interdependence of spiritual inspiration and learning better than by recounting a dialogue between Ibn Sina, the philosopher, and Abu Said Abu -Khyar, the Sufi mystic. Ibn Sina remarked, "Whatever I know, he sees". To which Abu Said replied," Whatever I see, he knows"."(Aga Khan IV, Aga Khan University Inauguration Speech, Karachi, Pakistan, November 11th 1985)

http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html



Ibn Sina or Avicenna

Dr Nader El-Bizri

This is an edited version of an article that was originally published in Medieval Islamic Civilization: An Encyclopaedia , Vol. 1, pp. 369-370, ed. Josef W. Meri , Routledge (New York-London, 2006).

Download PDF version of the article

Abu ‘Ali al-Hasan Ibn Sina (ca. 980-1037 CE), known in Latin as Avicenna, was a physician, natural philosopher, mathematician, poetic mystic, and princely minister. Of Persian descent, he was born in Afshana in the province of Bukhara. His chief philosophical work, Kitab al-shifa’ (Book of Healing), which was known in Latin as Liber Sufficientia, together with its condensed revision, Kitab al-najat (Book of Deliverance), led many to regard him as being the authoritative Neoplatonist integrator of the Aristotelian corpus. However, his intellectual acumen elevates his station beyond that of a commentator and lets him stand as an insightful thinker in his own right. His philosophical investigations covered mathematics, music, logic, physical and psychical sciences, as well as metaphysics and theology.

In geometry, he critically examined Euclid’s Elements and attempted to prove its fifth postulate. In his Aristotelian intromission conception of vision, he showed that the velocity of light had a finite magnitude. Partly influenced by Porphyry's Isagoge, Aristotle's Organon, and Galen's logical investigations, he eventually developed intricate forms of propositional logic.

Furthermore, he founded a proto-theory of meaning that was partially embodied in his work Kitab al-hudud (Book of Definitions), wherein he arrived at definitions by way of a rigorous distinction among concepts. Unlike most Platonists, he celebrated the merits of the art of persuasion and rhetoric. In astronomy, he endeavoured to systematise his observations that were grounded in Ptolemy's Almagest, and in mechanics he built on the theories of Heron of Alexandria while also seeking to improve the precision of instrumental readings. In his physical inquiries he studied different forms of energy, heat and force, while presenting a more coherent account of the interconnection between time and motion than what is habitually associated with Aristotle's Physics. One of his important achievements in natural philosophy was his account of the soul in Kitab al-nafs (Treatise on the Soul), which was preserved in his al-Shifa and al-Najat, and was translated into Latin under the title De Anima. Therein, he presented an affirmation of the existence of the soul that rested on a radical mind-body dualism in an argument that is customarily referred to as “the flying person argument,” which anticipates Descartes's “cogito ergo sum.” He also elucidated the notion of “intentionality” in the workings of the internal sense of the facility of estimation (wahm) and its pragmatic entailments.

Ranking among the most influential of metaphysicians in the history of philosophy, Ibn Sina offered an original elucidation of the question of “being” (al-wujud) that was mediated by a methodical distinction between essence and existence and oriented by an ontological consideration of the modalities of necessity, contingency, and impossibility. Taking the contingent to be a mere potentiality of being, whose existence or nonexistence did not entail a contradiction, Ibn Sina construed all creatures in actuality as being necessary existents due to something other than themselves. Consequently, any contingent had its essence distinct from its existence while being existentially dependent on causes that are external to it, which lead back to the One Necessary Existent due to Itself Whose Essence is none other than Its Existence. In this, Ibn Sina eschewed Aristotle’s reduction of “being” into the Greek conception of ousia (substance or essence), and he conceived the Deity as being the metaphysical First Cause of existence rather than being the physical Unmoved Cause of motion. Although his consideration of Divine creation was primarily mediated by an attempt to found a synthesis between Aristotle’s naturalism and monotheistic creationism, his ontology remained more akin to Neoplatonist emanationism, which took the One Necessary Existent to be the Source of all existential effusion. In this processional hierarchical participation in “being”, the Active Intellect played a necessary role in the genesis of human knowledge.

Following Plato, Ibn Sina held that knowledge, consisting of grasping the intelligible, ultimately determined the fate of the rational soul in the hereafter. Believing that the universality of our ideas was attributed to the mind itself, he additionally held that our passive individual intellects are in a state of potency with regard to knowledge, unlike the Active impersonal and separate Intellect that is in a state of actual perennial thinking. Consequently, our passive intellect qua mind acquires ideas by being in contact with the Active Intellect without compromising its own independent substantiality or immortality. In a mystical tone that becomes most pronounced in Kitab al-isharat wa-l-tanbihat (Book of Hints and Pointers), Ibn Sina also maintained that certain elect souls are capable of realising a union with the Universal Active Intellect, thereby attaining the station of prophecy.

His philosophical views were debated by Averroes and Maimonides, criticised by al-Ghazali, and integrated by intellectual authorities in medieval Europe, such as Thomas Aquinas, Duns Scotus, and Roger Bacon. His thinking also impacted the course of development of the ontotheological systems of prominent Muslim scholars such as Suhrawardi, Tusi, and Mulla Sadra. In all of this, his philosophical wisdom did not outshine his celebrated reputation as a physician, and his classic Kitab al-qanun fi’l-tibb (The Canon in Medicine), which was translated into Latin in the twelfth century CE (Liber Canonis), commanded an authority that almost surpassed that of Hippocrates and Galen and acted as the decisive compendium of the Greco-Roman- Arabic scientific medicine, and as the reference Materia Medica, throughout the medieval period and up to the Renaissance.


Primary Sources
Ibn Sina. Kitab al-shifa’, al-ilahiyyat. Edited by Ibrahim Madkour, George Anawati, and Said Zayed. Cairo: al-Hay’a al-misriyya al-‘amma lil-kitab, 1975.
---. Kitab al-shifa’, Kitab al-nafs. Edited by Fazlur Rahman. Oxford: Oxford University Press, 1960.
---. Kitab al-najat. Edited by Majid Fakhry. Beirut: Dar al-afaq al-jadida, 1985.
---. Kitab al-hudud (Livre des definitions). Edited and translated by A. M. Goichon. Cairo: Institut francais d’archeologie orientale du Caire, 1963.
---. Kitab al-‘isharat wa’l-tanbihat (Le livre des directives et remarques). Edited and translated by A. M. Goichon. Paris: J. Vrin, 1999.


Further Reading

Afnan, Soheil. Avicenna: His Life and His Works. London: Allen and Unwin, 1958.
Corbin, Henry. Avicenne et le recit visionnaire, Tehran: Societe des monuments nationaux de l’Iran, 1954.
Gardet, Louis. La connaissance mystique chez Ibn Sina et ses presupposes philosophiques. Cairo: Institut francais d’archeologie orientale du Caire, 1952.
Goichon, A.M. Lexique de la langue philosophique d’Ibn Sina. Paris: Desclee de Brouwer, 1938. ---. “Ibn Sina.” In The Encyclopaedia of Islam. Vol. III. Leiden: E. J. Brill, 1960.
---. La philosophie d'Avicenne et son influence en Europe medievale. Paris: Librairie d’Amerique et d’Orient, 1971.
Goodman, Lenn E. Avicenna. London: Routledge, 1992.
Gutas, Dimitri. Avicenna and the Aristotelian Tradition. Leiden: E. J. Brill, 1988.
Hasse, Dag Nikolaus. Avicenna’s De Anima in the Latin West. London: The Warburg Institute, University of London, 2000.
Janssens, Jules, and Daniel De Smet (Eds). Avicenna and His Heritage. Leuven: Leuven University Press, 2002.

http://www.iis.ac.uk/view_article.asp?ContentID=112130



Easy Nash
http://apps.facebook.com/blognetworks/blog/science_and_religion_in_islam_the_link/
http://gonashgo.blogspot.com/2009/08/500blogpost-five-hundred-is-blogpost.html
http://gonashgo.blogspot.com/2009/03/453a-blog-constructed-within.html

In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God: Aga Khan IV(2008)
The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)

Sunday, December 5, 2010

667)Bacteria Growing With Poisonous Arsenic Instead Of Vitalizing And 'Indispensable' Phosphorous Changes The Debate On The Origins Of Life On Earth.

Kathalika yubayyinu Allahu lakum ayatihi la'allakum ta-'aqiloona: "Allah thus makes clear to you His Signs that you may intellect"(Holy Quran 2:242)

"In fact this world is a book in which you see inscribed the writings of God the Almighty"(Nasir Khusraw, 11th century Fatimid Ismaili cosmologist-philosopher-poet)

"Nature is the great daily book of God whose secrets must be found and used for the well-being of humanity"(Aga Khan III, Radio Pakistan, Karachi, Pakistan, February 19th 1950)

"The God of the Quran is the One whose Ayats(Signs) are the Universe in which we live, move and have our being"(Aga Khan III, April 4th 1952, Karachi, Pakistan)

"Islam is fundamentally in its very nature a natural religion. Throughout the Quran God's signs (Ayats) are referred to as the natural phenomenon, the law and order of the universe, the exactitudes and consequences of the relations between natural phenomenon in cause and effect. Over and over, the stars, sun, moon, earthquakes, fruits of the earth and trees are mentioned as the signs of divine power, divine law and divine order. Even in the Ayeh of Noor, divine is referred to as the natural phenomenon of light and even references are made to the fruit of the earth(Aga Khan III, April 4th 1952, Karachi, Pakistan)

"In Islamic belief, knowledge is two-fold. There is that revealed through the Holy Prophet (s.a.s.) and that which man discovers by virtue of his own intellect. Nor do these two involve any contradiction, provided man remembers that his own mind is itself the creation of God. Without this humility, no balance is possible. With it, there are no barriers. Indeed, one strength of Islam has always lain in its belief that creation is not static but continuous, that through scientific and other endeavours, God has opened and continues to open new windows for us to see the marvels of His creation"(Aga Khan IV, Aga Khan University, 16 March 1983, Karachi, Pakistan)

"Of the Abrahamic faiths, Islam is probably the one that places the greatest emphasis on knowledge. The purpose is to understand God's creation, and therefore it is a faith which is eminently logical. Islam is a faith of reason"(Aga Khan IV, Spiegel Magazine interview, Germany, Oct 9th 2006)

"......The Quran tells us that signs of Allah’s Sovereignty are found in the contemplation of His Creation - in the heavens and the earth, the night and the day, the clouds and the seas, the winds and the waters...."(Aga Khan IV, Kampala, Uganda, August 22 2007)

"....in Islam, but particularly Shia Islam, the role of the intellect is part of faith. That intellect is what seperates man from the rest of the physical world in which he lives.....This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives. Of that I am certain"(Aga Khan IV, Dar-es-Salaam, Tanzania, August 17th 2007)

In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God"(Aga Khan IV, July 23rd 2008, Lisbon, Portugal)

http://gonashgo.blogspot.com/2008/09/400blogpost-four-hundred-knowledge.html

Bacterium grows with arsenic

Microbe uses toxic element instead of phosphorus
By Rachel Ehrenberg

Web edition : Thursday, December 2nd, 2010

EnlargeONE MICROBE'S POISONThe microbe known as strain GFAJ-1 grows when fed arsenic and deprived of phosphate, a crucial ingredient of life. Evidence suggests the bacterium is using arsenic as a building block for molecules, such as DNA, that normally require phosphate.Courtesy of Science/AAAS

When cooking up the stuff of life, you can’t just substitute margarine for butter. Or so scientists thought.

But now researchers have coaxed a microbe to build itself with arsenic in the place of phosphorus, an unprecedented substitution of one of the six essential ingredients of life. The bacterium appears to have incorporated a form of arsenic into its cellular machinery, and even its DNA, scientists report online December 2 in Science.

Arsenic is toxic and is thought to be too chemically unstable to do the work of phosphorus, which includes tasks such as holding DNA in a tidy double helix, activating proteins and getting passed around to provide energy in cells. If the new results are validated, they have huge implications for basic biochemistry and the origin and evolution of life, both on Earth and elsewhere in the universe.

“This is an amazing result, a striking, very important and astonishing result — if true,” says molecular chemist Alan Schwartz of Radboud University Nijmegen in the Netherlands. “I’m even more skeptical than usual, because of the implications. But it is fascinating work. It is original and it is possibly very important.”

The experiments began with sediment from eastern California’s Mono Lake, which teems with shrimp, flies and algae that can survive the lake’s strange chemistry. Mono Lake formed in a closed basin — any water that leaves does so by evaporation — making the lake almost three times as salty as the ocean. It is highly alkaline and rich in carbonates, phosphorus, arsenic and sulfur.

EnlargeARSENIC AND OLD MUDNASA scientist Felisa Wolfe-Simon samples sediment cores from California's Lake Mono that yielded a bacterium that appears to use arsenic instead of phosphorus in its metabolism, a result that suggests the chemistry of life is more flexible than thought.© 2010 Henry Bortman

Led by Felisa Wolfe-Simon of NASA’s Astrobiology Institute and the U.S. Geological Survey in Menlo Park, Calif., the researchers cultured microbes from the Lake Mono sediment. The microbes got a typical diet of sugar, vitamins and some trace metals, but no phosphate, biology’s favorite form of phosphorus. Then the team started force-feeding the critters arsenate, an analogous form of arsenic, in greater and greater quantities.

One microbe in particular — now identified as strain GFAJ-1 of the salt-loving, mostly marine family Halomonadaceae — was plucked out and cultured in test tubes. Some were fed loads of arsenate; others got phosphate. While the microbes subsisting on arsenate didn’t grow as much as those getting phosphate, they still grew steadily, doubling their ranks every two days, says Wolfe-Simon. And while the research team couldn’t eliminate every trace of the phosphate from the original culture, detection and analytical techniques suggests that GFAJ-1 started using arsenate as a building block in phosphate’s place.

“These data show that we are getting substitution across the board,” Wolfe-Simon says. “This microbe, if we are correct, has solved the challenge of being alive in a different way.”
Arsenic sits right below phosphorus in the periodic table and so, chemically speaking, isn’t that different, Wolfe-Simon notes. And of the six essential elements of life — carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur (aka CHNOPS) — phosphorus has a relatively spotty distribution on the Earth’s surface. If a microbe in a test tube can be coerced to live on arsenic, perhaps life’s primordial home was also arsenic-rich and life that used phosphorus came later. A “shadow biosphere” of arsenic-based life may even exist unseen on Earth, or on some lonely rock in space.

“It isn’t about arsenic, and it isn’t about Mono Lake,” says Wolfe-Simon. “There’s something fundamental about understanding the flexibility of life. Any life, a microbe, a tree, you grind it up and it’s going to be CHNOPS. But we have a single sample of life. You can’t look for what you don’t know.”

Similarities between arsenic and phosphorus are also what make the element so poisonous. Life often can’t distinguish between the two, and arsenic can insinuate itself into cells. There, it competes with phosphorus, grabs onto sulfur groups, or otherwise gums up the works, causing cell death. Some microbes “breathe” by passing electrons to arsenic, but even in those cases the toxic element stays outside the cell.

Researchers are having a hard time wrapping their minds around arsenate doing the job of phosphate in cells. The ‘P’ in ATP, the energy currency for all of life, stands for phosphate. And the backbone of the DNA double helix, the molecule containing the genetic instructions for life, is made of phosphate. Basic biochemistry says that these molecules would be so unstable that they would fall apart if they were built with arsenate instead of phosphate.

“Every organism that we know of uses ATP and phosphorylated DNA,” says biogeochemist Matthew Pasek of the University of South Florida in Tampa. He says the new research is both fascinating and fantastic. So fantastic, that a lot of work is needed to conclusively show exactly how the microbe is using arsenate.

Both phosphate and arsenate can clump up into groups, and with their slightly negative electric charge, slightly positive DNA would be attracted to such clumps, says Pasek. Perhaps the arsenic detected in the DNA fraction was actually a nearby clump that the DNA wrapped itself around, he speculates.

The microbe may be substituting for phosphate with discretion, says geochemist Everett Shock of Arizona State University in Tempe, using arsenic in some places but not others. But Shock says the real value of the work isn’t in the specifics. “This introduces the possibility that there can be a substitution for one of the major elements of life,” he says. Such research “stretches the perspective. Now we’ll have to see how far this can go.”

http://www.sciencenews.org/view/generic/id/66953/title/Bacterium_grows_with_arsenic

Related:http://www.washingtonpost.com/wpdyn/content/article/2010/12/02/AR2010120203102_2.html

Easy Nash
http://apps.facebook.com/blognetworks/blog/science_and_religion_in_islam_the_link/
http://gonashgo.blogspot.com/2009/08/500blogpost-five-hundred-is-blogpost.html
http://gonashgo.blogspot.com/2009/03/453a-blog-constructed-within.html

In Shia Islam, intellect is a key component of faith. Intellect allows us to understand the creation of God: Aga Khan IV(2008)
The Qur'an itself repeatedly recommends Muslims to become better educated in order better to understand God's creation: Aga Khan IV(2007)
The Quran tells us that signs of Allah's Sovereignty are found in the contemplation of His Creation: Aga Khan IV(2007)
This notion of the capacity of the human intellect to understand and to admire the creation of Allah will bring you happiness in your everyday lives: Aga Khan IV(2007)
Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation: Aga Khan IV(2006)
The Holy Qu'ran's encouragement to study nature and the physical world around us gave the original impetus to scientific enquiry among Muslims: Aga Khan IV(1985)
The first and only thing created by God was the Intellect(Aql): Prophet Muhammad(circa 632CE)