Cell biology Intelligent Design Irreducible Complexity

Intelligent design and the origin of the visual cycle

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From commenter Otangelo Grasso, some thoughts: 

The irreducible process of phototransduction, 11 cis retinal synthesis, and the visual cycle, essential for vertebrate vision

http://reasonandscience.heavenforum.org/t1638-origin-of-phototransduction-the-visual-cycle-photoreceptors-and-retina#5753

William Bialek: More Perfect Than We Imagined – March 23, 2013
Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. 9

From the book: Evolution of Visual and Non-visual Pigments, page 106
Opsin—the protein that underlies all animal vision., has become a favorite research target, not only of vision scientists but of many researchers interested in the evolution of protein structure, function, and specialization. This level of focus has made the opsins canonical G-protein-coupled receptors (GPCRs) and arguably the most investigated protein group for its evolutionary radiations and diverse functional specializations.  Still, opsin’s early evolution REMAINS PUZZLING, and there are many questions throughout its evolutionary history for which we have partial, but tantalizingly incomplete, answers. Obviously, the invertebrates, with their astonishing diversity and with evolutionary hints of the most ancient animals in their genomes, functions, and even body plans, offer the best hope of answering many of these fundamental questions.

Rhodopsins and Cone opsins have two interdependent agents, namely 11 cis retinal chromophores, and opsins, to which they are attached. By absorbing a photon, 11 cis retinal isomerizes to trans retinal conformation, and that triggers a conformational change in opsins, which trigger the signal transduction cascade, which in the end, provokes the electrical signal, transmitted to the brain for processing.

11-cis-Retinal is a unique molecule with a chemical design that allows optimal interaction with the opsin apoprotein in its binding pocket, and this is essential for the formation of the light-activated conformation of the receptor. 2

There are many things that are functionally important, and must be JUST RIGHT, in order for these molecular mechanisms to work.

The fact that rhodopsin has been intensely studied, provides a WEALTH of information on a molecular level, which permits to make INFORMED CONCLUSIONS of its origins.

Now OBSERVE how many things must be JUST RIGHT and ESSENTIAL ( following is straightforward from the relevant scientific literature ) :

Rhodopsin Structure and Activation

Rhodopsin consists of an apoprotein opsin and an inverse agonist ( that’s like a mechanism which keeps a switch off ), the 11-cis-retinal chromophore, which is covalently bound through a Schiff base linkage to the side chain of Lys296 of opsin protein.

The binding of the chromophore to the opsin is essential to trigger the conformational change. That means, there had to be

– a Schiff base linkage 
– a Lys296 residue where chromophore retinal covalently binds
– the side chain of the residue
– an essential amino acid residue called “counter ion” key factor appears to be the protonation state of the Schiff-base counterion
– a pivotal role of the covalent bond between the retinal chromophore and the lysine residue at position 296 in the activation pathway of  rhodopsin
– A key feature of this conformational change is a reorganization of water-mediated hydrogen-bond networks between the retinal-binding pocket and three of the most conserved GPCR sequence motifs. 2

Residues important for stabilizing the tertiary structure

– (e.g. disulphide bridge (S-S),
– amino-terminal (N) glycosylation sites)
– activation/deactivation of photopigments (e.g. carboxyl-terminal (C) phosphorylation sites)
– membrane anchorage (e.g. palmitoylation sites)

For visible light absorption, all opsins contain an essential amino acid residue called “counter ion”, in addition to a retinal-binding site, Lys296 (in the bovine rhodopsin numbering system), where chromophore retinal covalently binds through a protonated Schiff base linkage . The proton on the Schiff base is necessary for visible light absorption, but energetically unstable within the opsin molecule. In opsin pigments, a negatively charged amino acid residue, counterion, stabilizes the protonated Schiff base, and is an essential amino acid residue for opsin pigments to absorb visible light.

Various types of opsin-based pigments with absorption maxima in the visible light region possess a “protonated” Schiff base linkage. In the protein moiety, the positive charge on the protonated Schiff base is unstable, and therefore a counterion, a negatively charged amino acid residue is needed to stabilize the positive charge. In vertebrate visual pigment, glutamic acid at position 113 serves as the counterion 11

Furthermore: movement of the cytoplasmic end of the sixth transmembrane helix is essential for pigment activation.

From the above information, it is clear that there is an evidently FINE- TUNED protein-protein interaction, that is, the 11 cis retinal chromophore physical constitution, and the opsin physical constitution, MUST BE JUST RIGHT from the beginning, and be able to interact PRECISELY to trigger the signal transduction chain.

Let’s suppose, opsin is able to interact with TRANSDUCIN. So what ?? If the signal transduction pathway is not fully setup, and able to go all the way through – no signal – no vision. So having such a precise protein-protein arrangement will make only sense, if down down there, after many complex molecular interactions, a visual image is generated in the brain. After two amplification steps, the goal is achieved, and a signal is sent to the brain. To get that signal, is a REMARKABLE SIGNAL AMPLIFICATION mechanism:

A single photoactivated rhodopsin catalyzes the activation of 500 transducin molecules. Each transducing can stimulate one cGMP phosphodiesterase molecule and each cGMP phosphodiesterase molecule can break down 1000 molecules of cGMP per second. Therefore, a single activated rhodopsin can cause the hydrolysis of more than 100.000 molecules of cGMP per second.

Following enzymes, molecules, and proteins are ESSENTIAL in the signal transduction pathway:

Rhodopsin  Rhodopsin is an essential G-protein coupled receptor in phototransduction.
Retinal Schiff base cofactor All-trans-retinal is also an essential component of type I, or microbial, opsins such as bacteriorhodopsinchannelrhodopsin, and halorhodopsin.
Transducin  Their function is to mediate the signal transduction from the photoreceptor proteins, the opsins, to the effector proteins, the phosphodiesterases 6
Guanosine diphosphate ( GDP ) Transducin is tightly bound to a small organic molecule called Guanosine diphosphate ( GDP )
Guanosine triphosphate GTP when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called  GTP, which is closely related to, but critically different from, GDP, binds to transducin. 
G-nucleotide exchange factor (GEF)    The exchange of GDP for GTP is done by a G-nucleotide exchange factor (GEF) 7
Cyclic guanosine monophosphate (cGMP) 
phosphodiesterase (PDE)  is necessary to transform cGMP to GMP. This closes the cGMP gated ion channel due to the decreasing amounts of cGMP in the cytoplasm 6
cGMP-gated channel of rod photoreceptors
Cyclic nucleotide-gated Na+ ion channels

Once the signal goes through,  a system is required to stop the signal that is generated and restore the opsin to its original state. For that task, other essential proteins are needed  to restore the initial state of rhodopsin:

Guanylate cyclase
Rhodopsin kinase
Arrestin

The biosynthesis of 11 Cis retinal, essential in the first step of vertebrate vision, is also REMARKABLE.

There is an INTRIGUING EVOLUTIONARY CONSERVATION  of the key components involved in chromophore production and recycling, these genes also have adapted to the specific requirements of both insect and vertebrate vision. Visual GPCR signaling is unique with respect to its dependence on a diet-derived chromophore (retinal or 2-dehydro-retinal in vertebrates; retinal and 3-hydroxy-retinal in insects). The chromophore is naturally generated by oxidative cleavage of carotenoids (C40) to retinoids.(C20). Then the retinoid cleavage product must be metabolically converted to the respective 11-cis-retinal derivative in either the same carotenoid cleavage reaction or a separate reaction. 3

All animals endowed with the ability to detect light through visual pigments need pathways in which dietary precursors for chromophore, such as carotenoids and retinoids, are first absorbed in the gut, and then transported, metabolized and stored within the body to establish and sustain vision.

Two fundamental processes in chromophore metabolism defied molecular analysis for a long time: the conversion of the parent C40 carotenoid precursor into C20 retinoids and the all-trans to 11-cis isomerization and cleavage involved in continuous chromophore renewal. Following proteins are essential in the pathway to synthesize 11 cis retinals :

retinal pigment epithelial (RPE)  The retinal pigment epithelium (RPE), a single layer of cuboidal cells lying betweenBruch’s membrane and the photoreceptors, is an essential component of the visual system.
Lecithin-retinol acyltransferase  Is Essential for Accumulation of All-trans-Retinyl Esters in the Eye and in the Liver 4
Retinyl ester hydrolase
11-cis-retinol dehydrogenases
Isomerohydrolase  It performs the essential enzymatic isomerization step in the synthesis of 11-cis retinal. 5
Retinoid-binding proteins
RPE retinal G protein-coupled receptor (RGR)

The absorption of light by rhodopsin results in the isomerization of the 11- cis -retinal chromophore to all- trans forming the enzymatically active intermediate, metarhodopsin II, which commences the visual transduction process.

Continuous vision depends on recycling of the photoproduct all-trans-retinal back to visual chromophore 11-cis-retinal. This process is enabled by the visual (retinoid) cycle, a series of biochemical reactions in photoreceptor, adjacent RPE and Müller cells.

Since the opsins lacking 11-cis-RAL lose light sensitivity, sustained vision requires continuous regeneration of 11-cis-RAL via the process called ‘visual cycle’. Protostomes and vertebrates use essentially different machinery of visual pigment regeneration, and the origin and early evolution of the vertebrate visual cycle is an UNSOLVED MYSTERY.

Restoration of light sensitivity requires chemical reisomerization of trans-retinal via a multistep enzyme pathway, called the visual cycle, in cells of the retinal pigment epithelium (RPE).

When a photon of light is absorbed, 11-cis retinal is transformed to all-trans retinal, and it moves to the exit site of rhodopsin. It will not leave the opsin protein until another fresh chromophore comes to replace it, except for in the ABCR pathway. Whilst still bound to the opsin, all-trans retinal is transformed into all-trans retinol by all-trans Retinol Dehydrogenase. It then proceeds to the cell membrane of the rod, where it is chaperoned to the Retinal Pigment Epithelium (RPE) by Interphotoreceptor Retinoid Binding Protein (IRBP). It then enters the RPE cells, and is transferred to the Cellular Retinol Binding Protein (CRBP) chaperone. 8

The visual cycle fulfills an essential task of maintaining visual function and needs therefore to be adapted to different visual needs such as vision in darkness or lightness. For this, functional aspects come into play: the storage of retinal and the adaption of the reaction speed. Basically vision at low light intensities requires a lower turn-over rate of the visual cycle whereas during light the turn-over rate is much higher. In the transition from darkness to light suddenly, large amount of 11-cis retinal is required. This comes not directly from the visual cycle but from several retinal pools of retinal binding proteins which are connected to each other by the transportation and reaction steps of the visual cycle.

This cycle is present only in vertebrates, as cephalochordates and tunicates do not possess the required enzymes. The isomerization of 11-cis retinal to all-trans retinal in photoreceptors is the first step in vision. For photoreceptors to function in constant light, the all-trans retinal must be converted back to 11-cis retinal via the enzymatic steps of the visual cycle. Within this cycle, all-trans retinal is reduced to all-trans retinol in photoreceptors and transported to the Retinal pigment epithelium (RPE). In the RPE, all-trans retinol is converted to 11-cis retinol, and in the final enzymatic step, 11-cis retinol is oxidized to 11-cis retinal. The first and last steps of the classical visual cycle are reduction and oxidation reactions, respectively, that utilize retinol dehydrogenase (RDH) enzymes.

To make things even more intriguing, there are at least 4 different pathways for regeneration of 11 Cis retinal. Protostomes and vertebrates use essentially different machinery of visual pigment regeneration, and the origin and early evolution of the vertebrate visual cycle is an unsolved mystery. In the vertebrate cycle, following proteins are ESSENTIAL :

Rhodopsin (also known as visual purple) is a light-sensitive receptor protein involved in visual phototransduction.
Photoreceptor cells are specialized type of cell found in the retina that is capable of visual phototransduction.
Retinal pigment epithelium (RPE) is the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells
Retinal G-protein-coupled receptor (RGR) is a non-visual opsin expressed in RPE. RGR bound to all-trans-RAL is capable of operating as a photoisomerase that generates 11-cis-RAL in the light-dependent manner
Interphotoreceptor retinoid-binding protein (IRBP), an abundant 140 kDa glycoprotein secreted by photoreceptors . The binding of retinoids by IRBP protects them from oxidation and isomerization.
β-Carotene 15,15′-monooxygenase (BCO) in RPE supplies all-trans-RAL to the visual cycle via central cleavage of β-carotene
Cellular retinaldehyde-binding protein (CRALBP)  binds 11-cis-ROL and 11-cis-RAL
Retinoid isomerase RPE65 (or isomerohydrolase) in the RPE. RPE65 is involved in the all-trans to 11-cis isomerization.

Retinoids need to be shuttled between different organelles and protected from isomerization, oxidation, and condensation. Thus, key retinoid-binding proteins are critical for maintaining proper retinoid isomeric and oxidation states. Cellular retinaldehyde–binding protein (CRALBP) in the RPE and Müller cells, and extracellular interphotoreceptor retinoid–binding protein (IRBP) are two major carriers involved.  The structure of CRALBP—with its unanticipated isomerase activity—has been elucidated, whereas the structure of IRBP has only been partially characterized. Inactivating mutations in either one of these binding proteins can cause retinal degenerative disease.  More.

 

15 Replies to “Intelligent design and the origin of the visual cycle

  1. 1
    polistra says:

    Waaaaaay tl;dr.

    Two much simpler facts about the retina:

    (1) Photoreceptors work backwards from most neurons. They generate the most output when light is dim and the least output when light is bright. Automatic gain control.

    (2) The photoreceptors are at the back of the retina, not the front. Why? So the glial cells, which run through the tissue from front to back, can filter and focus the right set of colors on each cone.

    Try to think of a “random” sequence that would produce either of those mechanisms.

  2. 2
    critical rationalist says:

    Argument from incredulity?

    Knowledge comes from authorative sources and neo-Darwinsism isn’t an authoraive source, so it couldn’t have been the source of said knowledge?

    Again the key issue here is an explanation for the growth of knowledge. Specifically, the knowlege of which transformation an organism should perform on raw materials to make a copy of itself. Yet, the explantions we get from ID proponents are either supernatural (and therefore inexplicable), absent or irrational.

    The current crop of ID itself is just one such example, it that it is based on selective inferences from experience which are arbitrary as compared to other possible inferences from experience, which are ignored.

    To use an example, every designer we’ve observed is itself a complex, knowelge laden entity that is well adapted for the purpose of designing things. The same knowlege of which transformations to perform in organisms would either need to be present in said designer or external to it. So, you have the very same problem including the knowlege of how to transform raw materials into the “perfect” carpet of retinal tissue. It’s the same problem, just pushed up a level, in that it too would exhibit the appearance of design. IOW, the proximate cause is the knowledge in organisms, which needs to be explained. Saying some abstract designer with no defined limitations put it there doesn’t explain the origin of that knowelge.

    If I bought a plan for how to build a boat online, then followed the instructions to the letter, did I design a boat? No, I did not. Can I choose to build a boat without possessing the knowelge of what transformation of matter are necessary to construct one? No, I cannot. So, how can mere choice and intent get a set of instructions for transformations raw materials into the supposedly “perfect” retinal carpet in eyes?

    Human beings are good explantion for human designed things because of our human limitations, such as limits on what we knew, when we knew it, etc. For example, how can we explain the specific details of the appearance of AC in automobiles?

    Well, human beings are conformable in a very narrow temperature range. We can only get rid of excess heat by sweating, which isn’t comfortable, especially when we wear clothing to protect ourselves, etc. So it’s not that we wouldn’t have chosen to build cars with AC or intended to build them with AC. So, why didn’t cars come with AC from the start?

    First, we didn’t know how to build cars, let alone AC systems. Then we knew how, but not at a scale that would be practical for use on an automobile. Then we know how to make such systems small enough, but not cheep enough, so the price was beyond what most customers could afford. Eventually, we created the knowlege of how to build AC systems that were efficient and cheep enough that they could be mass produced and the additional cost didn’t make the car unafordable for purchased by customers. Then AC appeared on automobiles. Note how all of these steps are based on necessay outcomes due to limitations of human designers, with finite resources, etc.

    Compare this explantion to “AC appeared on automobiles at that particular time because that’s just what the designer must have wanted”, which is what ID effectively presents, as its designer has no defined limations, such as limits on time, knowlege, resources, etc. And no such limitation will be forthcoming because, everyone knows, ID’s designer is actually God, which as no limitations beyond what is logically possible.

    Again, it’s not that I’m against ID as a theory, per-se. The current crop of ID fails to explain why eyes appear first as light sensitive patches of cells and end up as what we see in human beings, centrapods, etc. Since ID’s designer has no defined limitations on what it knew, when it knew it, etc. it could have created organisms with complicated eyes first, then eventually organisms with light sensible patches of cells, or both all at once. ID simply has no explanation for that order other than “eyes appeared in that order because that’s just what the designer must have wanted”, which explains nothing.

  3. 3
    Mung says:

    It is much easier to evolve an ear, which is why my current experiment involves evolving an ear from a sound-sensitive spot.

  4. 4
    Otangelo Grasso says:

    Critical rationalist: ” Saying some abstract designer with no defined limitations put it there doesn’t explain the origin of that knowledge.”

    God is not complex
    http://reasonandscience.heaven.....ot-complex
    God is a remarkably simple entity. As a non-physical entity, a mind is not composed of parts, and its salient properties, like self-consciousness, rationality, and volition, are essential to it. In contrast to the contingent and variegated universe with all its inexplicable quantities and constants, a divine mind is startlingly simple. Certainly, such a mind may have complex ideas—it may be thinking, for example, of the infinitesimal calculus—, but the mind itself is a remarkably simple entity

    Who designed the designer ?

    http://reasonandscience.heaven.....e-designer

    One need not fully understand the origin or identity of the designer to determine whether an object was designed. Thus, the question of the origin of the designer is irrelevant to whether we can detect design, the core focus of intelligent design theory. For example, if SETI were to detect a signal from an intelligent extra-terrestrial civilization, we would need not know how that life form arose to determine that there was indeed an intelligent entity that sent the signal. The question of the origin of the designer may be an interesting question, but answering this question is irrelevant to whether we can detect design.

    The question “Who designed the designer?” is most likely a philosophical / religious question that lies outside the domain of scientific inquiry, and thus is beyond the scope of intelligent design. Religious objections require religious answers. In that regard, many religions have proposed ideas about the origin of the designer. For example, Christianity postulates the that the designer is God who by definition is eternally existent and has no origin. This is akin to Aristotle’s ‘unmoved mover” — an uncaused cause. Postulating an uncaused cause is no philosophical problem, however, because every worldview has at its base an uncaused cause. Atheism/materialism, for instance, requires that the universe (or the chain of events that led to our universe) ultimately happened for no reason, just by chance. At its base, atheism proposes an uncaused cause. The right question is not “Is it a problem that Christianity has at its base an uncaused cause (God)?” because every worldview has at its base an uncaused cause. The right question asks: “Since every worldview has at its base an uncaused cause, whose uncaused cause is most reasonable?”

    Because we have no experience with something coming from nothing, or with blind and unguided causes creating complex and specified information we find in our universe, atheism’s “uncaused cause” fails. However, we do have experience with such complexity coming from an intelligent mind. This means that Christianity’s uncaused cause — God — is a far better explanation for the origin of our information-rich, meaning-filled universe compared to atheism.
    http://www.ideacenter.org/cont.....hp/id/1147

    W.L.Craig :
    First, in order to recognize an explanation as the best, one needn’t have an explanation of the explanation. This is an elementary point concerning inference to the best explanation as practiced in the philosophy of science. If archaeologists digging in the earth were to discover things looking like arrowheads and hatchet heads and pottery shards, they would be justified in inferring that these artifacts are not the chance result of sedimentation and metamorphosis, but products of some unknown group of people, even though they had no explanation of who these people were or where they came from. Similarly, if astronauts were to come upon a pile of machinery on the back side of the moon, they would be justified in inferring that it was the product of intelligent, extra-terrestrial agents, even if they had no idea whatsoever who these extra-terrestrial agents were or how they got there. In order to recognize an explanation as the best, one needn’t be able to explain the explanation. In fact, so requiring would lead to an infinite regress of explanations, so that nothing could ever be explained and science would be destroyed. So in the case at hand, in order to recognize that intelligent design is the best explanation of the appearance of design in the universe, one needn’t be able to explain the designer.

    http://www.reasonablefaith.org.....d-delusion

    ” ID simply has no explanation for that order other than “eyes appeared in that order because that’s just what the designer must have wanted”, which explains nothing.”

    ID theory is not about meaning, or the ” why’s “, but if we can detect design in nature. To which I believe, there is overwhelming evidence, as the example of the visual cycle, which could not function, unless with a minimal number of proteins in a minimal pathway, to go through.

    Your objections are entirely philosophical – to which I say: in order to reject the inference of design, and an intelligent designer, it is not enough to point out flaws on the theistic worldview. The opponent needs to be able to provide a better, more compelling explanation of origins. That’s the hard part – good luck with that !!

  5. 5
    Dionisio says:

    Very interesting. Thanks.

  6. 6
    Dionisio says:

    Embedded Variability Framework (EVF), fully designed and implemented within the biological systems. That’s all.
    The rest is speculative gossiping of the worst kind.
    Still don’t get it?
    Ok, let’s try another approach.
    Ever heard of MSFT .NET?
    No? OK, read about it: https://www.microsoft.com/net/
    Then you might understand what EVF is all about.

  7. 7
    Eugene S says:

    Critical Rationalist

    “Argument from incredulity?”

    You have already been told elsewhere that this is fallacious. What you are saying is not right because:

    (1) empirical evidence suggests that such systems (semantically closed self-replicating linguistic machines) can be produced by intelligence;

    (2) there is absolutely no evidence that such machines can come about by virtue of non-telic causation. On the contrary, evolution (RV+NS) starts given a population of such machines. Evolution, whatever its actual capabilities, is conditioned upon the existence of a population of these machines to start with, not the other way around.

    (1) and (2) together strongly suggest that such machines can only be produced by intelligence. The only here is a result of purely scientific abductive reasoning, i.e. inference to the best explanation, which has nothing to do with God-of-the-gaps or incredulity.

    Empirical evidence suggests that in the observable universe, apart from biological codes, the category of linguistic machines includes only correlates of intelligence – natural and formal languages (mathematics, programming languages).

    Your position is that of blind faith, because you adhere to it no matter what empirical support there is against it.

  8. 8
    Origenes says:

    CR @2

    CR: To use an example, every designer we’ve observed is itself a complex, knowelge laden entity …

    Are you capable of making a distinction between the inner world and the external world — between mind and body? If so, which of those two do you think is doing the design?

    CR: … that is well adapted for the purpose of designing things.

    You keep repeating this phrase over and over. Whose purpose are you talking about? I have asked that simple question several times, but you never answer.

    CR: The same knowlege of which transformations to perform in organisms would either need to be present in said designer or external to it.

    Why is that necessary? Provide an argument, instead of reasoning from an assumed truth of mind brain identity.

    CR: So, you have the very same problem including the knowlege of how to transform raw materials into the “perfect” carpet of retinal tissue. It’s the same problem, just pushed up a level, in that it too would exhibit the appearance of design. IOW, the proximate cause is the knowledge in organisms, which needs to be explained. Saying some abstract designer with no defined limitations put it there doesn’t explain the origin of that knowelge.

    If life on earth is designed, by say aliens, then this is the truth we have to deal with — irrespective of whether that fact answers ultimate questions about knowledge or not.
    If we must conclude that life is designed, and indeed we must, we may very well not have answered all fundamental questions, but to suggest that it therefore doesn’t solve anything is simply ludicrous. Excluding blind processes as the source and pointing to an intelligent origin for life on earth, is obviously a crucial step towards the truth.
    You are correct when you say that the design inference does not solve the origin of biological information, in the sense that it does neither solve the identity of the designer(s) nor their source of information. However that’s not what ID is about. ID is not about solving ultimate questions. ID is a modest inquiry as to whether things are designed.

  9. 9
    critical rationalist says:

    CR: ” Saying some abstract designer with no defined limitations put it there doesn’t explain the origin of that knowledge.”

    OG: God is not complex.

    So, the designer is God, and there is no explanation a to how God possessed that knowledge? Apparently, he “just was”, complete with that knowledge, already present? If so, it’s unclear why we have to go any further. Specifically, why couldn’t we more efficiently state that organisms “just appeared” complete with this knowledge, already present?

    And, are you suggesting that if the designer is not God, then we still have the same problem?

    One need not fully understand the origin or identity of the designer to determine whether an object was designed.

    We can determine if an object has the appearance of design. That is, it is well adapted to serve a purpose. That only happens when knowledge is present. So, the question is, what is the origin of that knowledge. How did it grow.

    Again, human beings are good explanations for human designed things, because of our very specific human limitations. You’re conflating this in respect to the biosphere.

    Because we have no experience with something coming from nothing, or with blind and unguided causes creating complex and specified information we find in our universe, atheism’s “uncaused cause” fails. However, we do have experience with such complexity coming from an intelligent mind. This means that Christianity’s uncaused cause — God — is a far better explanation for the origin of our information-rich, meaning-filled universe compared to atheism.

    If you’re going to exclude from the contents of theories things we have not experienced, we have no experience with other designers other than us, let alone designers that were present on earth at the right time, or are “non-material”. And we couldn’t have designed ourselves. So, you’re completely out of designers.

    First, in order to recognize an explanation as the best, one needn’t have an explanation of the explanation. This is an elementary point concerning inference to the best explanation as practiced in the philosophy of science.

    And the explanation for the features of organisms is knowledge in those organisms. They make entire copies of themselves, including the recipe they contain. That is the proximate cause. So, if we need not have a explanation of the explanation (knowledge) then it’s unclear why you feel the need to invoke a designer.

    Similarly, if astronauts were to come upon a pile of machinery on the back side of the moon, they would be justified in inferring that it was the product of intelligent, extra-terrestrial agents, even if they had no idea whatsoever who these extra-terrestrial agents were or how they got there. In order to recognize an explanation as the best, one needn’t be able to explain the explanation.

    Yes. The explanation for that machinery is knowledge. It could only be such. Otherwise you’d have the spontaneous appearance, like Lamarck’s mice appearing out of rags when the knowledge of how to transform raw materials into mice was not present in those rags.

    You’re assuming that knowledge is true justified belief that requires a knowing subject. Your assuming it comes from authoritative sources, like consciousness, or God. ID hinges on that assumption. Thats where we disagree.

  10. 10
    critical rationalist says:

    You’re assuming that knowledge is true justified belief that requires a knowing subject. Your assuming it comes from authoritative sources, like consciousness, or God. ID hinges on that assumption.

    IOW, ID hinges on a philosophical view of knowledge. It’s a question of epistemology.

  11. 11
    ET says:

    CR:

    Argument from incredulity?

    That is all you and yours have. You don’t even have a testable methodology to see if blind and mindless processes could produce it.

  12. 12
    Mung says:

    Science hinges on a philosophical view of knowledge. It’s a question of epistemology.

  13. 13
    Otangelo Grasso says:

    “it’s unclear why you feel the need to invoke a designer.”

    If you see a message on a sand dune, like ” John loves Sandy “. Would you intuitively and immediately recognize that someone past there a short time ago, and wrote the message on the sand dune? Or would you consider that rain and wind wrote the message randomly entirely through natural events? Even the most basic cell maintaining the most basic functions of life is far more complex than the most complex man-made machine. Would you say that it is plausible that random, unguided, natural events have enough statistical probability to create and give rise to the most sophisticated self-replicating factory of the universe? –

    Michael Denton writes in Evolution: A Theory In Crisis:
    “To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity.The complexity of the simplest known type of cell is so great that it is impossible to accept that such an object could have been thrown together suddenly by some kind of freakish, vastly improbable, event. Such an occurrence would be indistinguishable from a miracle. The cell is a veritable micro-miniaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world.

    The cell contains an informational code system and programming languages like our alphabet or a computer code, more versatile than C, Visual Basic, or PHP, and more robust and error-free than any other code system out of 1 million alternatives? – using a communication protocol which wastes far less space than TCP/IP and is more robust than Ethernet? – using furthermore a collection of rules and regularities of information coding for instructional complex texts? – defined by alphabet, grammar, a collection of punctuation marks and regulatory sites, and semantics? and then uses that code system to create a blueprint for a self-replicating factory, which requires about 1500 books, each with 300 pages, 300.000,00 characters per book, each containing the precise complex instructions and information to create this factory, and stored in the smallest storage device possible and known, a trillion times denser than a CD? How is it, that you would recognize immediately, that a simple message on a sand dune required intelligence, but above description of the simplest imaginable biological cell does not require a designer ?!

    Objection: Comparing living cells to man-made self-replicating machines, and books is a false analogy
    Answer: Talking about life getting together is similar to talking about cars forming themselves, or even basic computer programs making themselves. These things are not just improbable, they are impossible without intelligence.
    Marcello Barbieri writes in his book: Code Biology A New Science of Life, page 28
    Molecular biology has proved that there is a genetic code in every cell and that genes and proteins are molecular artifacts because they are manufactured by molecular machines. Coding and artifact-making, in other words, take place both in our society and inside the cell, and this does create a parallel between culture and molecular biology.
    In other words. Intelligence produces self-replicating machines and books. And so only intelligence can produce life, that depends on coded information, proteins, and molecular machines.

    If the analogy of two phenomena are very close and striking while at the same time, the cause of ONE of the phenomenon is very obvious; it becomes scarcely possible to refuse to admit the action of an analogous cause of the other phenomenon, though (the cause of the other phenomenon is) not so obvious in itself”
    — in “Preliminary Discourse on the Study of Natural Philosophy”, London, Longman, Rees, Orme, Brown and Green, 1831, page 149.

    When you see that:
    the way genetic information encoded in the DNA is exactly the same as what we humans would do to elaborate a blueprint to build a factory, full of complex machines, compartments, production lines, computers, etc;
    the way that the nucleus communicates with its ribosome is similar to how we humans have designed computers to communicate with one another,
    then one has to AT LEAST stop and wonder whether some intelligent being has designed the genetic code and made the communication system between the nucleus and its ribosomes….

  14. 14
    critical rationalist says:

    If you see a message on a sand dune, like ” John loves Sandy “. Would you intuitively and immediately recognize that someone past there a short time ago, and wrote the message on the sand dune? Or would you consider that rain and wind wrote the message randomly entirely through natural events? Even the most basic cell maintaining the most basic functions of life is far more complex than the most complex man-made machine. Would you say that it is plausible that random, unguided, natural events have enough statistical probability to create and give rise to the most sophisticated self-replicating factory of the universe? –

    And you wonder why people have a hard time taking ID proponents seriously?

    – An exposed sand beach is not good storage medium, as it would be washed away quickly
    – The content represents communication of a personal nature
    – The message contains proper nouns
    – The message is in English

    Should I go on?

    Talking about life getting together is similar to talking about cars forming themselves, or even basic computer programs making themselves. These things are not just improbable, they are impossible without intelligence.

    It’s not that I’m ignoring what we know about human designers. Rather, you’re ignoring what we know about the growth of knowledge.

    Why don’t you start out how “intelligence” results in those things, then explain how Neo-Darwnisnsm doesn’t fit that explanation.

    the way genetic information encoded in the DNA is exactly the same as what we humans would do to elaborate a blueprint to build a factory, full of complex machines, compartments, production lines, computers, etc;


    I’m not following you.

    That there is only one way to store information in physical mediums means that information was put there by an intelligent agent?

    What other means would any other process embedded information, which would indicate it did grow via variation and some form of criticism, as opposed to an intelligent agent?

  15. 15
    Otangelo Grasso says:

    ” Why don’t you start out how “intelligence” results in those things, then explain how Neo-Darwnisnsm doesn’t fit that explanation.”

    Problem no.1
    The genetic code system ( language ) must be created, and the universal code is nearly optimal and maximally efficient

    http://www.ncbi.nlm.nih.gov/pubmed/8335231
    The genetic language is a collection of rules and regularities of genetic information coding for genetic texts. It is defined by alphabet, grammar, collection of punctuation marks and regulatory sites, semantics.

    Origin and evolution of the genetic code: the universal enigma
    In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
    http://www.ncbi.nlm.nih.gov/pm.....MC3293468/

    The genetic code is one in a million
    if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
    http://www.ncbi.nlm.nih.gov/pubmed/9732450

    The genetic code is nearly optimal for allowing additional information within protein-coding sequences
    DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
    http://www.ncbi.nlm.nih.gov/pm.....rt=classic

    Problem no.2
    The origin of the information to make the first living cells must be explained.

    Determination of the Core of a Minimal Bacterial Gene Set
    Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes ( which code for 13 protein complexes ) Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell with the following features. These protein complexes could not emerge through evolution ( muations and natural selection ) , because evolution depends on the dna replication, which requires precisely these original genes and proteins ( chicken and egg prolem ). So the only mechanism left is chance, and physical necessity.
    http://mmbr.asm.org/content/68/3/518.full.pdf

    Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.

    Paul Davies once said;
    How did stupid atoms spontaneously write their own software … ? Nobody knows … … there is no known law of physics able to create information from nothing.

    Problem no.3
    The genetic cipher

    On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
    The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a “frozen accident” or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894784/

    The British biologist John Maynard Smith has described the origin of the code as the most perplexing problem in evolutionary biology. With collaborator Eörs Szathmáry he writes: “The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existence, or how life could have existed without it.” To get some idea of why the code is such an enigma, consider whether there is anything special about the numbers involved. Why does life use twenty amino acids and four nucleotide bases? It would be far simpler to employ, say, sixteen amino acids and package the four bases into doublets rather than triplets. Easier still would be to have just two bases and use a binary code, like a computer. If a simpler system had evolved, it is hard to see how the more complicated triplet code would ever take over. The answer could be a case of “It was a good idea at the time.” A good idea of whom ? If the code evolved at a very early stage in the history of life, perhaps even during its prebiotic phase, the numbers four and twenty may have been the best way to go for chemical reasons relevant at that stage. Life simply got stuck with these numbers thereafter, their original purpose lost. Or perhaps the use of four and twenty is the optimum way to do it. There is an advantage in life’s employing many varieties of amino acid, because they can be strung together in more ways to offer a wider selection of proteins. But there is also a price: with increasing numbers of amino acids, the risk of translation errors grows. With too many amino acids around, there would be a greater likelihood that the wrong one would be hooked onto the protein chain. So maybe twenty is a good compromise. Do random chemical reactions have knowledge to arrive at a optimal conclusion, or a ” good compromise” ?

    An even tougher problem concerns the coding assignments—i.e., which triplets code for which amino acids. How did these designations come about? Because nucleic-acid bases and amino acids don’t recognize each other directly, but have to deal via chemical intermediaries, there is no obvious reason why particular triplets should go with particular amino acids. Other translations are conceivable. Coded instructions are a good idea, but the actual code seems to be pretty arbitrary. Perhaps it is simply a frozen accident, a random choice that just locked itself in, with no deeper significance.

    That frozen accident means, that good old luck would have hit the jackpot trough trial and error amongst 1.5 × 1084 possible genetic codes . That is the number of atoms in the whole universe. That puts any real possibility of chance providing the feat out of question. Its , using Borel’s law, in the realm of impossibility. The maximum time available for it to originate was estimated at 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that’s universal. Put simply, natural selection lacks the time necessary to find the universal genetic code.

    Put it in other words : The task compares to invent two languages, two alphabets, and a translation system, and the information content of a book ( for example hamlet) being written in english translated to chinese in a extremely sophisticared hardware system. The conclusion that a intelligent designer had to setup the system follows not based on missing knowledge ( argument from ignorance ). We know that minds do invent languages, codes, translation systems, ciphers, and complex, specified information all the time. The genetic code and its translation system is best explained through the action of a intelligent designer.

    Bill Faint: The attribution of the design has to be to God or purely materialistic mechanisms. The gigantic pull to swallow in the second case is the fact that the output is the product of code, and that the molecular machinery needed to replicate the code (for inheritance/perpetuation), transcribe it, translate it into protein with many intermediate steps requiring highly specific operations, and to repair it in the foreseen event that it is damaged (to preserve/protect it) or destroy it in the event that it suffers irreparable damage (to forestall cancer) is just too big to swallow. DNA had an intentional purpose. That’s the only reasonable conclusion I can come to.

    Origin and evolution of the genetic code: the universal enigma
    http://reasonandscience.heaven.....sal-enigma

    The genetic code is nearly optimal for allowing additional information within protein-coding sequences
    http://reasonandscience.heaven.....-sequences

    The genetic code cannot arise through natural selection
    http://reasonandscience.heaven.....-selection

    The origin of the genetic cipher, the most perplexing problem in biology
    http://reasonandscience.heaven.....in-biology

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