Eukaryotic genome DNA is wrapped around core histones and forms a nucleosome structure. Together with associated proteins and RNAs, these nucleosomes are organized three‐dimensionally in the cell as chromatin. Emerging evidence demonstrates that chromatin consists of rather irregular and variable nucleosome arrangements without the regular fiber structure and that its dynamic behavior plays a critical role in regulating various genome functions. Single‐nucleosome imaging is a promising method to investigate chromatin behavior in living cells. It reveals local chromatin motion, (...) which reflects chromatin organization not observed in chemically fixed cells. The motion data is like a gold mine. Data analyses from many aspects bring us more and more information that contributes to better understanding of genome functions. In this review article, we describe imaging of single‐nucleosomes and their tracked behavior through oblique illumination microscopy. We also discuss applications of this technique, especially in elucidating nucleolar organization in living cells. (shrink)

The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA‐labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads (...) to new questions, the reinterpretation of previous findings, and revised models of mRNA export. In this review, we will briefly highlight some of these recent findings and discuss how live cell SMI approaches may be used to further our current understanding of mRNA export and gene expression. (shrink)

We here review primary methods used in quantifying and mapping 5‐hydroxymethylcytosine (5hmC), including global quantification, restriction enzyme‐based detection, and methods involving DNA‐enrichment strategies and the genome‐wide sequencing of 5hmC. As discovered in the mammalian genome in 2009, 5hmC, oxidized from 5‐methylcytosine (5mC) by ten‐eleven translocation (TET) dioxygenases, is increasingly being recognized as a biomarker in biological processes from development to pathogenesis, as its various detection methods have shown. We focus in particular on an ultrasensitive single‐molecule imaging technique (...) that can detect and quantify 5hmC from trace samples and thus offer information regarding the distance‐based relationship between 5hmC and 5mC when used in combination with fluorescence resonance energy transfer. (shrink)

Molecular interactions are at the origin of life. How molecules get at different locations in the cell and how they locate their partners is a major and partially unresolved question in biology that is paramount to signaling. Spatio‐temporal correlations of fluctuating fluorescently tagged molecules reveal how they move, interact, and bind in the different cellular compartments. Methods based on fluctuations represent a remarkable technical advancement in biological imaging. Here we discuss image analysis methods based on spatial and temporal correlation (...) of fluctuations, raster image correlation spectroscopy, number and brightness, and spatial cross‐correlations that give us information about how individual molecules move in cells and interact with partners at the single molecule level. These methods can be implemented with a standard laser scanning microscope and produce a cellular level spatio‐temporal map of molecular interactions. (shrink)

A kind of “ruthless reductionism” characterized the experimental practices of the first two decades of molecular and cellular cognition. More recently, new research tools have expanded experimental practices in this field, enabling researchers to image and manipulate individual molecular mechanisms in behaving organisms with an unprecedented temporal, sub-cellular, cellular, and even circuit-wide specificity. These tools dramatically expand the range and reach of experiments in MCC, and in doing so they may help us transcend the worn-out and counterproductive debates about “reductionism” (...) and “emergence” that divide neuroscientists and philosophers alike. We describe examples of these new tools and illustrate their practical power by presenting an exemplary recent case of MCC research using them. From these tools and results, we provide an initial sketch of a new image of the behaving organism in its full causal-interactive complexity, with its molecules, cells, and circuits combined within the single system that it is. This new image stands in opposition to the traditional “levels” image of the behaving organism, and even the initial sketch we provide of it here offers hope for avoiding the dreary metaphysical debates about “emergence” and “downward causation,” and even the reduction vs. anti-reduction dispute, all dependent upon the familiar “levels” image. (shrink)

Outer membrane proteins (OMPs) maintain the viability of Gram‐negative bacteria by functioning as receptors, transporters, ion channels, lipases, and porins. Folding and assembly of OMPs involves synchronized action of chaperones and multi‐protein machineries which escort the highly hydrophobic polypeptides to their target outer membrane in a folding competent state. Previous studies have identified proteins and their involvement along the OMP biogenesis pathway. Yet, the mechanisms of action and the intriguing ability of all these molecular machines to work without the typical (...) cellular energy source of ATP, but solely based on thermodynamic principles, are still not well understood. Here, we highlight how different single‐molecule studies can shed additional light on the mechanisms and kinetics of OMP biogenesis. (shrink)

Cryo‐electron microscopy allows the visualization of macromolecules in their native state. Combined with techniques of three‐dimensional reconstruction, cryo‐EM images of single molecules can be used to study macromolecular interactions. The ribosome, a large RNA–protein complex with multiple binding interactions, is an excellent test case illustrating the power of these new techniques. Conformational changes during the binding of tRNA and protein factors to the ribosome can now be studied without the interference of crystal packing. Now that the first X‐ray structures (...) of ribosomal subunits have become available, conformational changes observed by cryo‐EM in different functional states can be traced back to internal rearrangements of the underlying structural framework. Electron microscopy, X‐ray crystallography, and modeling should be used together in the endeavor to understand the functioning of the translational machinery. BioEssays 23:725–732, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Macromolecular interactions play a central role in many biological processes. Protein‐protein interactions have mostly been studied by co‐immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real‐time at the single‐molecule level. This technique is called single‐molecule pull‐down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single‐molecule fluorescence microscopy. SiMPull (...) is used to count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single‐molecule biochemical tool to perform functional studies on the pulled‐down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. (shrink)

Pointillistic based super‐resolution techniques, such as photoactivated localization microscopy (PALM), involve multiple cycles of sequential activation, imaging, and precise localization of single fluorescent molecules. A super‐resolution image, having nanoscopic structural information, is then constructed by compiling all the image sequences. Because the final image resolution is determined by the localization precision of detected single molecules and their density, accurate image reconstruction requires imaging of biological structures labeled with fluorescent molecules at high density. In such image datasets, (...) stochastic variations in photon emission and intervening dark states lead to uncertainties in identification of single molecules. This, in turn, prevents the proper utilization of the wealth of information on molecular distribution and quantity. A recent strategy for overcoming this problem is pair‐correlation analysis applied to PALM. Using rigorous statistical algorithms to estimate the number of detected proteins, this approach allows the spatial organization of molecules to be quantitatively described. (shrink)

New imaging methodologies in quantitative fluorescence microscopy, such as Förster resonance energy transfer (FRET), have been developed in the last few years and are beginning to be extensively applied to biological problems. FRET is employed for the detection and quantification of protein interactions, and of biochemical activities. Herein, we review the different methods to measure FRET in microscopy, and more importantly, their strengths and weaknesses. In our opinion, fluorescence lifetime imaging microscopy (FLIM) is advantageous for detecting inter‐molecular interactions (...) quantitatively, the intensity ratio approach representing a valid and straightforward option for detecting intra‐molecular FRET. Promising approaches in single molecule techniques and data analysis for quantitative and fast spatio‐temporal protein‐protein interaction studies open new avenues for FRET in biological research. (shrink)

Six years ago, the Singer lab published a landmark paper which described how individual mRNA particles cross the nuclear pore complex in mammalian tissue culture cells. This involved the simultaneous imaging of mRNAs, each labeled by a large number of tethered fluorescent proteins and fluorescently tagged nuclear pore components. Now two groups have applied this technique to the budding yeast Saccharomyces cerevisiae. Their results indicate that in the course of nuclear export, mRNAs likely engage complexes that are present on (...) either side of the pore and that these interactions are modulated by proteins present in the messenger ribonucleoprotein (mRNP) complex. These findings lend support to the notion that just before and/or after the completion of nuclear export, mRNPs undergo one or more maturation steps that prepare the packaged mRNAs for translation. These results represent new and exciting insights into the mechanism of mRNA nuclear export. (shrink)

While innovations in modern microscopy, spectroscopy, and nanoscopy techniques have made single molecule observation a standard in many laboratories, the actual design of meaningful fluorescence reporter systems now hinders major scientific breakthroughs. Even though the field of chemical biology is supercharging the fluorescence toolbox, surprisingly few strategies exist that make the transition from model systems to biologically relevant applications. At the same time, the number of microscopy techniques is growing dramatically. We explain our view on how the impact (...) of modern technologies is influenced not only by further hard‐ and software developments, but also by the availability and suitability of protein‐engineering tools. We identify how the largely independent research fields of chemical biology and fluorescence nanoscopy can influence each other to synergistically drive future technology that can visualize the localization, structure, and dynamics of molecular function without constraints. (shrink)

The recent development of single molecule detection techniques has opened new horizons for the study of individual macromolecules under physiological conditions. Conformational subpopulations, internal dynamics and activity of single biomolecules, parameters that have so far been hidden in large ensemble averages, are now being unveiled. Herein, we review a particular attractive solution‐based single molecule technique, fluorescence correlation spectroscopy (FCS). This time‐averaging fluctuation analysis which is usually performed in Confocal setups combines maximum sensitivity with high statistical (...) confidence. FCS has proven to be a very versatile and powerful tool for detection and temporal investigation of biomolecules at ultralow concentrations on surfaces, in solution, and in living cells. The introduction of dual‐color cross‐correlation and two‐photon excitation in FCS experiments is currently increasing the number of promising applications of FCS to biological research. BioEssays 24:758–764, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

The current revolution in biological microscopy stems from the realisation that advances in optics and computational tools and automation make the modern microscope an instrument that can access all scales relevant to modern biology – from individual molecules all the way to whole tissues and organisms and from single snapshots to time‐lapse recordings sampling from milliseconds to days. As these and more new technologies appear, the challenges of delivering them to the community grows as well. I discuss some of (...) these challenges, and the examples where openly shared technology have made an impact on the field. (shrink)

June 2022 A Revolutionary New Metaphysics, Based on Consciousness, and a Call to All Philosophers We are in a unique moment of our history unlike any previous moment ever. Virtually all human economies are based on the destruction of the Earth, and we are now at a place in our history where we can foresee if we continue on as we are, our own extinction. As I write, the planet is in deep trouble, heat, fires, great storms, and record flooding, (...) weather patterns drastic everywhere. Capitalism has been so successful in supplying us with an endless array of consumer items, that we have never noticed there is a cost. But there is a cost, the cost is the very life of the Earth herself, and now the day of reckoning is here. Days of reckoning are most often days of rath. But I am hoping that this is a day of major Awakening over the entire planet. We have caused a crisis so great for the Earth we can hardly get our minds around it. But I am proposing that deeply embedded in the crisis are ideas, about who and what the Earth is, Ourselves, and what we are here for. I am proposing that this is a call to all philosophy and philosophers to rethink ourselves from the ground up. The human race has never gotten the Earth right and now we must, for the Earth is the true foundation for civilization. We are in deep trouble with the Earth, and it owes to the fact that the great male thinkers never got the Earth right, they could never make the connection between the life of mind and the life of the Earth. I am proposing that deeply embedded in the crisis we are in are ideas. And that in fact the planet is in the grip of a false metaphysics, and scientific image of nature that really comes most recently from Descartes. His conviction that matter, and with it the Earth, are simply the weighable, the measurable the extended in space and time, utterly devoid of any inner life of mind thoughts or Consciousness. This view of matter and the Earth goes back to the very dawn of thought, Descartes is just its most recent and comprehensive version of things. This view of matter is really a false metaphysics that dominates most of the modern world and underpins the whole scientific image of nature itself. I am proposing this is a false metaphysics and offering a new version of things based on Consciousness. If there is a single idea fueling and driving the destruction of the planet, it is the conviction that the Earth is something without Consciousness. When you intend to ravage and savage the planet, turn it into consumer items to be converted into money in the bank, first pretend that all of the bright beings in the natural world are devoid of Consciousness, just “things” you do not have to have any conscious about destroying them. I am proposing that this term Consciousness, that has appeared as term and a problem for modern science, is the key to getting ourselves right with the Earth. I propose this new theory for science will ramify into every other disciplines as well, and the ways we think just about everything. This old paradigm based on a false theory of matter, has run its course, it has brought us to the brink of our own extinction. We need new ideas, and we need them now. You will find my recent work in the Scientific God Journal under the title: Consciousness as the Organizing Principle, and a very complete version of my arguments for this term Consciousness, along with radical reinterpretation of modern science itself, on the Galileo Commission site. It is a radical moment for all of the thinkers among us, take this as my small contribution to rethinking ourselves in new terms, based on my understanding that the true basis for the whole of Being, the Universe, the Cosmos, and with them Ourselves, is this term Consciousness. And unpack it. And I predict that with this term Consciousness every intractable human problem in both science and the modern world will go down like a line of dominos before it. And so, here are a few new ideas I would offer you. These are the times of the Reappearance of the Feminine, a great Awakening as of Springtime after a long dark and lonely Winter. We are leaving behind us an old civilization based on male dominance, fear lies and control, now in decay, disease, and death disintegrating all around us. We are moving into a whole new civilization based on Love and Truth. A new civilization requires new basic terms values and first principles. And so, I return to Descartes. 1. Just over 300 years ago a young man travelling with the army found himself stranded in a foreign town in a bare room lit by a candle with nothing to do but think. And in a couple of nights Descartes laid the entire thought foundations for modern science and most of the modern world. It isn’t clear that modern philosophers with their funding sources of grants, their graduate students, their reputation and all the perks and privileges of academia can do any better. Descartes claimed there are just two principles in the Universe, Matter and Mind. God was pure mind; human beings were mind and matter. And we are the only ones on the planet with mind. Everything else all of the bright array of beings who share the planet with us are simply matter. And matter? The weighable the measurable the extended in space and time utterly devoid of any inner life of thoughts, feelings, or Consciousness This classification was a boon for developing science. Scientists did not have to worry about any inner life in nature, ideas or Consciousness, they could just set about weighing and measuring, as they have until the present day. But it was a disaster for the Earth. Earth was once worshiped as a Goddess. With Descartes she became almost overnight “things.” Simply commodities and resources, an endless of supply of consumer items, to be turned into money in the bank. And now Descartes concept of matter is up for us. If there is a single idea that is enabling and driving the destruction of the Earth, it is the conviction that Earth is something without Consciousness. This whole scientific image of nature as something devoid of Consciousness is driving the destruction of the Earth, and driving us all insane, and it needs to change. Ever since Descartes formulated Dualism, scientists and philosophers have been trying to get rid of it. They have done this by attempting to make matter the fundamental term of reality, and to explain mind or Consciousness in terms of matter. And now, Consciousness has emerged as term and a problem for modern science. 2. The prevailing Universe picture has been mainly based on the belief that Consciousness appears only at the end of evolution in ourselves and some of the higher animals when matter attains “a certain state of complexity” and it is produced by neurons in the brain. But Consciousness is nothing real in itself, the neurons are doing the work, Consciousness is simply a byproduct of neural activity. As William James summed up this position, not his: Consciousness is to the brain as a shadow to the runner, it runs beside him but never influences his stride. And so, the great problem of neuroscience: How do neurons produce Consciousness? So far, no one has been able to say how. All we have is parallelism. Two processes are running in parallel a train of neural events and a train of Consciousness events. And so, which one is primary? The face of neuroscience and much of the modern world is that the neural events are what is really real, Consciousness is secondary. The conviction that Consciousness is something produced by neurons is so deeply held and has been so for so long, that it seems like an obvious fact. It is in fact an assumption and a theory, and it could all well be the other way around. The scientific image of nature as something devoid of Consciousness is now up for us. It has enabled the destruction of the Earth, and we are now at a unique place in our own evolution where we can foresee if we continue on as we are, our own extinction. And so, there are the best reasons for rethinking Descartes concepts of matter. Scientists and philosophers have been trying to escape dualism by making matter the fundamental term. And now, this has not worked. In a nutshell: The mind body problem, the “hard problem of Consciousness” ---how do neurons in the brain, atoms and molecules give rise to ideas thoughts and feelings and who what and where is the “I” who sees them? And then, the near-death experience. I remind you of the truth of the near-death experience. The body in the bed is brain dead eeg flat, but the patient, pure Consciousness is hovering at the ceiling watching the doctors work over the body below, able to read dials he could not have seen from the bed, sometimes able to events in the corridor beyond the room, all subsequently confirmed by the doctors. Evidence as good as it gets that the patient really was out of his body. And so, the patient is able to see without eyes, hear without ears and to think and remember without a brain. There is not a single scientific principle that can account for this. And I am proposing that the near-death experience is a threshold and a key for a much deeper understanding of the Universe. These three problems are so hard they cannot be solved by present scientific principles and therefore call all present principles and ways of thought into question. When your axioms cannot account for the data, it is time to drop them and find better fundamental terms. We have not been able to solve the problems of Consciousness with the assumption that matter is the most basic and fundamental term. And so, if Cartesian dualism is to be overcome at all, we need to try it the other way around. 3. We are in the position of Copernicus. Remember Copernicus? He was making his calculations on the assumption that the Earth was the center of the Universe until they became so unwieldy that he decided to try it all the other way around. To make the sun the center, the Earth revolving around it. And lo, all of his data fell neatly into place. I am proposing a whole new Universe picture. Evolution makes us continuous with every other being, Consciousness would not be in us if it were not in them also, and then, in the atoms and molecules and cells that make up living beings. I propose to make Consciousness the most basic term and see what follows. I am in fact, proposing a new Copernican Revolution, that Consciousness is the true basis for the Universe and the right fundamental term, for science itself all other disciplines as well, and the whole of the modern world. And I predict that every intractable problem in science or the modern world, will go down like a line of dominos before it. In a nutshell: Consciousness and not matter is “first and fundamental” in the Universe, it is there from the very “Beginning” everything has it and all of the true causalities, the explanatory principles belong to it. Not to matter. What then is matter? All matter is an Appearance of something much more real, Consciousness. All matter is an expression of Consciousness, even the least little bit of matter contains Consciousness, and is an expression of Consciousness. And so, we revise the scientific image of nature. Science at present is two termed, matter/energy. It needs to become three termed: Matter/energy/Consciousness, with the recognition that all of the basic principles, the true causalities of events, and of the Universe belong to Consciousness. And now physics. To accommodate this new Universe picture physics needs to alter just one term, energy. All energy contains Consciousness, that idea alone will change our world forever. The animals the trees the plants are just as conscious as we are, as is the Earth herself, a continuum of many forms of Consciousness of which our own is one. The Earth consists of interacting and intersecting forms of Consciousness, Consciousness within Consciousness within Consciousness within Consciousness. A remarkable work has just appeared entitled “Beyond Words What Animals Feel and Think.” Describing in detail how like ourselves all of the animals are. And the more we can see how like us everything else really is, the harder it will be for us to do them all in, in the interest of turning them into consumer items. And so, here is a new principle of understanding, that entails completely new forms of explanation, and a whole new Universe picture to be spelled out in terms of Consciousness and its various properties. This is a Universe that is aware awake and Enspirited throughout. And so, there is only one principle, not two. And so, how does Consciousness work? There is “no mind/body problem.” My Consciousness is aligning the Consciousness of neurons in the brain, that aligns the Consciousness of all other cells in the body, that aligns the Consciousness of molecules and atoms themselves. Mainly from the top down, but also interactive, and not reduction to the purely physical forces. 4. And so, here is a radical new Universe picture, and with it a new way to think about the Universe itself, the Earth, Ourselves, and Spirit. It requires a complete revision of both of the terms of modern science itself. The problem of the modern world owes in deep measure to Descartes concept of matter as something devoid of interior life. But he is only the most powerful and simple expression of a whole tradition of thought that predates him, that goes back to the very dawn of thought itself. It owes to the conviction of both Plato and Aristotle that the Earth was something devoid of reason, or mind, and therefore something to be held in complete contempt. We are emerging from a civilization based on contempt for the Earth, and down the road, it will become contempt for the body, sex, women, the Native people, and people of color everywhere. And so, this entire tradition is now up for us, it has brought us to the brink of our own extinction, and we need to get beyond it. I am proposing that this term Consciousness is the way out. The missing piece of the puzzle and the idea whose time has come. And it will enable us to move into a completely new civilization based on respect for the Earth, women, sex, people of color, that honors everyone and has a place for all. Revolutions in science occur when new data show up that cannot be accounted for by existing paradigms (Thomas Kuhns: The Structure of Scientific Revolutions). Consciousness, and all the properties and problems of Consciousness are just such data, and they compel a new scientific revolution. But we are a scientific age. A new Copernican revolution in science is such as revolution everywhere. And Consciousness is the key to getting every other reality at all levels and depths right as well. It will enable us finally to get the Earth right, get ourselves right with the Earth, and with one another. Archimedes: Give me a place to stand, and I will move the world. I am proposing a new synthesis among our fundamental terms in which this term Consciousness is the new lynchpin. And so, I return once more to Descartes. Descartes in the Mediations was a dualist, they were two realities interacting in the pineal gland mind and body. But Descartes age was high on “Cartesianisms,” on Descartes concept of matter. Animals were simply cleverly wired machines (Hobbes called them automata). Rumor had it that Descartes followers went about kicking dogs reasoning that their howls were not due to any feelings of pain, but simply the wiring of the machine. We have been doing this to the Earth ever since, and now the Earth is not going to stand for it any longer. It is time we all woke up. There is no matter in Descartes sense of it, or in Plato and Aristotle’s sense of it. This old concept of matter is embedded in all of the crisis and catastrophes---fires, drought, pandemics, over population, the disintegrating economies, our ways of life, capitalism and consumerism themselves. All matter is Enspirited, contains Consciousness, and is an expression of Consciousness. Now I tell you something about Descartes you may not know. In the Mediations was a dualist, there are minds and bodies. But by the end of his life, he knew the truth. Descartes guided his whole life by these vivid dreams, and toward the end of his life he had this dream: He saw the Universe as a giant machine and in the heart of the machine propelling the whole, was Consciousness. And so, out of the shades and shadows and into the light of day. Here is a renewed and a new science, a new cosmology. And with it, a revolutionary new metaphysics. The whole of the modern world is in the grip of a false metaphysics, based on Descartes theory of matter. Here is a new, and finally true metaphysics based on the single term, Consciousness. 5. And in all my works, I spell out this new metaphysics based on Consciousness, and what it means for how we think about virtually everything: The Universe, the Earth, Ourselves, and Spirit. Of who, what and where Spirit is, that we may connect with Spirit everywhere. There is only one term for the Universe, and not two, this single term Consciousness, that manifests itself in two modes: Consciousness in Form, Consciousness Formless. And so, here is a sketch of what this new term Consciousness really means. For four great aspects of the real, four new cornerstones for a whole new civilization on Earth, based on Love and Truth. A. For the Universe: New causalities, all matter is an expression of Consciousness, awake and aware, Enspirited throughout, which has a place for the causalities of love ideas intent plan and purpose, what Aristotle called final causality, that for the sake of which. And it has a place for subjectivity, the greatest mystery in the whole of the Universe, knowable only in ourselves, but there in everything else as well, bedrock in the chain of causalities. The buck stops here. Here are two very different Universe pictures. The Cartesian Universe consists of things, pushed, and pulled around by the physical forces that function blind. The true Universe consists of selves and not things. Selves at least in ourselves, are organized and focused about an I, an I am, or a sense of self in everything, ever other being dear to itself. Just one aspect of subjectivity. And so, it is Consciousness all the way down, and subjectivity all the way down. Science proceeds on the basis of the negligible of what it can leave out as unimportant. Subjectivity is the ultimate animating principle of the Universe. What Descartes really did was to strip from nature what is most essential about it, its animating principle Consciousness. And so, we come out of a long history of “clunk.” The great male thinkers have killed creation. First in concepts and now in the lived life. And so, after centuries of fruitless search, not all of it in vain, finally, and just in time the true basic principle for the Universe has shown up in virtually all disciplines, this term Consciousness. B. And so, the Earth: What does this term Consciousness really mean for the Earth? It means that all of the bright array of beings around us have Consciousness. And the more we can realize how like us they are, the harder it will be to do them all in. Is this what it really means to be “made in the image of Spirit?” To destroy ever other living being? The god of Genesis is a creator god who has created billions and billions of living forms. Man, taking himself to be made in the image of Spirit has destroyed virtually all of it. The Earth is not things, not commodities and resources, not an endless array of consumer goods. The Earth consists of conscious living spiritual beings like ourselves, who need to be honored and respected, nurtured and cared for, to be Loved. And if the human race can finally pull it off and bring Love here and start helping the Earth rather than destroying her, even our vast numbers now at 8 billion, may not matter. Deeply embedded in the modern world is a false cosmology based on the hitherto useful but ultimately false metaphysics of Descartes. In particular it owes to Descartes concepts of matter, and of the Earth, as something devoid of Consciousness. And now this concept is up for us. If there is a single idea enabling and driving the destruction of the planet, it is the conviction that the Earth is something devoid of Consciousness. And we all have a vested interest in keeping this false concept in place. When you intend to ravage and savage the Earth, to turn it into consumer items, and money in the bank, first pretend she has no Consciousness that way we need not have any conscious about it. We are in deep trouble with the planet. Virtually all human economies are based on the destruction of the Earth, and we are now at a place in our history where we can foresee if we continue on as we are, our own extinction. And so, here are a few new guiding principles for the planet, based on Consciousness. Consciousness has field properties. The Earth is Consciousness throughout, connected and interconnected throughout, intersecting and interacting fields of Consciousness of which our own is one. To harm one is to harm all. Only this understanding of the Earth can set our destructive technologies, and capitalism, their goals, and their limits. The real problem with capitalism, and with civilization itself is it has no true understanding of the Earth, all the exquisite networks and webworks that connect all beings with one another. Nor it is about to admit that the Earth is our “life support system,” reason gone insane in the modern world. We are destroying our life support system, capitalism is the full expression of the human death wish in the modern world, and it needs to change. And now, let the barriers between ourselves and all other beings go down. C. And so, Ourselves. This new Universe picture based on Consciousness opens into and has a place for new concepts of human identity. In particular, it has a place for reincarnation, a process whereby one Consciousness dons’ bodies again and again and lays them down. This is a process wholly impossible on materialistic theories. This new view of things puts a higher perspective on Freudian determinism, which is a partial knowing in a greater account. We are something more than the victims of genes drives and childhood. We are immortally eternal evolving spiritual beings who take on a cycle of earthly lives in order to achieve certain goals and abilities, and then, our earthly cycle complete, we depart the Earth plane for other areas of the Universe physical or purely spiritual, to continue our evolution elsewhere. The scientific evidence for reincarnation is increasing on all sides, see for example the work of Michael Newton, a mainstream scientist forced to confront the fact of reincarnation. A completely new reincarnational picture is now emerging everywhere. We choose our parents for abilities we could acquire through them. We all come here with reasons for being here, and we all have free will, an original property of Consciousness, and we work out our issues accordingly. We all come here with the same reason for being here. It is to experience the Earth plane and human society at all levels and depths, in every social role, every climate, both sexes male and female and in all races. We are all here to acquire a deep understanding of the Earth plane with all its challenges and all of its present problems. We are not here to devour and consume the Earth, but to honor her for the learning experience she makes available for us. And so, reincarnation is the great equalizer, the fundamental basis for any bill of rights. Many of the problems of the modern world owe to the fact that reincarnation has not been taught in the West. Reincarnation was the center piece of Jesus teachings. It was banned by a fourth century council that decided the populous could best be controlled through fear. They edited all mention of reincarnation from the scriptures, and inserted fear terms instead, a judgmental god, and so on. If reincarnation had been taught, there would have been no suppression of women, but the gift of both sexes would have been honored and developed. And there would have been no reason for contempt for people of color because who they are, we have been or will be. There is no reason to look down on anyone when we know that our own identity includes membership in theirs. The truth of reincarnation needs to be the foundation for getting ourselves right with the Earth, and with one another. D. And so, Spirit. This new Universe picture, based on Consciousness, has a place for Spirit as simply Infinite Consciousness. All universes all worlds are formed out of this Consciousness, divine and sacred throughout. And Spirit is everywhere in the Earth and can be connected everywhere. And the Native North American people had things right. Everything has its own Spirit, and without contradiction is also an expression of Spirit. And what I am really doing in terms of concepts of modern science is presenting the Native North American version of the Real. And this new Universe picture has a place for the essential insight of all religions almost smothered by church tradition: Love. Not an emotion but a great Oneness, that can be found everywhere, even in a busy city street. But especially in the Earth, that is levels and depths of Oneness everywhere. And so, for the first time in their long and bitter antagonistic history, science and religion now share a common base with this term Spirit, the lynchpin in a new conceptual framework. And I offer an interpretation of where we are in our history, this present moment of historical grace, and these tumultuous times in which we live, the return of the Goddess and the Divine Feminine, the Reappearance of the Feminine in history, the Advent of Women, this great Awakening, as of Springtime after a long dark Winter, the Awakening, the Second Coming. And so, stay tuned! (shrink)

Various techniques have attempted to localize imagery. However, early findings using single cell recordings of human receptive fields during imagery tasks have had little impact. Reports by Marg and his coworkers (1968) found no evidence for imagery in human Area 17, 18, and 19. Single cells from humans suggest later imagery-related activity in hippocampus, amygdala, entorhinal cortex, and parahippocampal gyrus.

Inspired by the application of CycleGAN networks to the image style conversion problem Zhu et al., this paper proposes an end-to-end network, DefogNet, for solving the single-image dehazing problem, treating the image dehazing problem as a style conversion problem from a fogged image to a nonfogged image, without the need to estimate a priori information from an atmospheric scattering model. DefogNet improves on CycleGAN by adding a cross-layer connection structure in the generator to enhance the network’s multiscale feature extraction (...) capability. The loss function was redesigned to add detail perception loss and color perception loss to improve the quality of texture information recovery and produce better fog-free images. In this paper, the novel Defog-SN algorithm is presented. This algorithm adds a spectral normalization layer to the discriminator’s convolution layer to make the discriminant network conform to a 1-Lipschitz continuum and further improve the model’s stability. In this study, the experimental process is completed based on the O-HAZE, I-HAZE, and RESIDE datasets. The dehazing results show that the method outperforms traditional methods in terms of PSNR and SSIM on synthetic datasets and Avegrad and Entropy on naturalistic images. (shrink)

A new field of gene expression regulation research is emerging that has previously been overlooked. This new area is concerned with distinguishing the expression of a single gene from the averaged expression of many gene copies within the cell population. This paper reviews research focused on individual genes in inducible gene expression systems. The main experimental strategy is to measure the gene expression level of a single cell containing a single reporter gene molecule. In contrast to (...) the commonly held belief, gene induction is found to be stochastic under certain conditions. The possible mechanisms and implications are discussed. (shrink)

Many employers assess their workforces with gendered and racialized imagery that can put groups of workers and applicants at a disadvantage in the labor market. Based on 78 interviews with white employers in Atlanta, the author reveals that some employers use a complex but widely shared stereo-type of Black working-class women as single mothers to typify members of this group. These employers use this single-mother image to explain why they think Black women are poor workers, why they think (...) Black women are reliable workers, and why they think Blacks are poorly prepared for the labor market. In focusing on these white employers' claims, the author concentrates not on the well-documented out-comes of labor market discrimination, such as differential rates of pay and promotion, but on how employers construct and use the images that may from the basis of it. This is especially relevant amid current attacks on affirmative action programs. (shrink)

Conformational changes of proteins and other biomolecules play a fundamental role in their functional mechanism. Single pair Förster resonance energy transfer offers the possibility to detect these conformational changes and dynamics, and to characterize their underlying kinetics. Using spFRET on microscopes with different modes of detection, dynamic timescales ranging from nanoseconds to seconds can be quantified. Confocal microscopy can be used as a means to analyze dynamics in the range of nanoseconds to milliseconds, while total internal reflection fluorescence microscopy (...) offers information about conformational changes on timescales of milliseconds to seconds. While the existence of dynamics can be directly inferred from the FRET efficiency time trace or the correlation of FRET efficiency and fluorescence lifetime, additional computational approaches are required to extract the kinetic rates of these dynamics, a short overview of which is given in this review. The functional mechanism of proteins is often driven by underlying conformational changes. These intramolecular changes and dynamics can be investigated using single pair Förster resonance energy transfer. The kinetic timescales of the dynamics in the range of nanoseconds to seconds is then quantified using different experimental and analytical implementations. (shrink)

Replication protein A (RPA), the major single‐stranded DNA‐binding protein in eukaryotic cells, is required for processing of single‐stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high‐affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single (...) class='Hi'>molecule studies showed that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error‐prone repair of double‐stranded breaks and promote error‐free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis. (shrink)

Previous research suggested a role of gaze in preference formation, not merely as an expression of preference, but also as a causal influence. According to the gaze cascade hypothesis, the longer subjects look at an item, the more likely they are to develop a preference for it. However, to date the connection between viewing and liking has been investigated predominately with self-paced viewing conditions in which the subjects were required to select certain items from simultaneously presented stimuli on the basis (...) of perceived visual attractiveness. Such conditions might promote a default, but non-mandatory connection between viewing and liking. To explore whether the connection is separable, we examined the evaluative processing of single naturalistic food images in a 2 x 2 design, conducted completely within subjects, in which we varied both the type of exposure (self-paced versus time-controlled) and the type of evaluation (non-exclusive versus exclusive). In the self-paced exclusive evaluation, longer viewing was associated with a higher likelihood of a positive evaluation. However, in the self-paced non-exclusive evaluation, the trend reversed such that longer viewing durations were associated with lesser ratings. Furthermore, in the time-controlled tasks, both with non-exclusive and exclusive evaluation, there was no significant relationship between the viewing duration and the evaluation. The overall pattern of results was consistent for viewing times measured in terms of exposure duration (i.e., the duration of stimulus presentation on the screen) and in terms of actual gaze duration (i.e., the amount of time the subject effectively gazed at the stimulus on the screen). The data indicated that viewing does not intrinsically lead to a higher evaluation when evaluating single food images; instead, the relationship between viewing duration and evaluation depends on the type of task. We suggest that self-determination of exposure duration may be a prerequisite for any influence from viewing time on evaluative processing, regardless of whether the influence is facilitative. Moreover, the purported facilitative link between viewing and liking appears to be limited to exclusive evaluation, when only a restricted number of items can be included in a chosen set. (shrink)

The human sensory experience of submolecular phenomena is only possible through complex technological mediations that include not just magnifications, but also manipulations of time and translations from one sense to another. In my creative moving image project Wildly Oscillating Molecules, I develop strategies for using an atomic force microscope (AFM) as a cinematographic instrument, specifically using its tactile mechanisms to generate video. Using the AFM over four years to generate experimental moving image installations, I examine my physical and psychological experiences (...) of this nanoscientific instrumentation. Although referred to by the philosopher of technology Don Ihde, the AFM's style of technological mediation has not been subjectively explored. Working to engage with an infinitesimal scale, the AFM has a unique style of spatial and temporal mediation that can be manipulated through the post-production and exhibition practices of the moving image. Wildly Oscillating Molecules provides insight into how the AFM influences human spatial and temporal perception of nanoscale phenomena and provides a new framework with which to analyse nanoscientific imaging practices. Understanding the nuances of technological mediation encourages science artists working with submolecular phenomena to adopt, evolve or transform properties of technological mediation when presenting their work to an audience. (shrink)

Some photographs show determinate features of a scene because the photographed scene had those features. This dependency relation is, rightly, a consensus in philosophy of photography. I seek to refute many long-established theories of photography by arguing that they are incompatible with this commitment. In Section II, I classify accounts of photography as either single-stage or multi-stage. In Section III, I analyze the historical basis for single-stage accounts. In Section IV, I explain why the single-stage view led (...) scientists to postulate “latent” photographic images as a technical phenomenon in early chemical photography. In Section V, I discredit the notion of an invisible latent image in chemical photography and, in Section VI, extend this objection to the legacy of the latent image in digital photography. In Section VII, I appeal to the dependency relation to explain why the notion of a latent image makes the single-stage account untenable. Finally, I use the multi-stage account to advance debate about “new” versus “orthodox” theories of photography. (shrink)

In developing a new theory of vision in Ad Vitellionem paralipomena Kepler introduced a new optical concept, pictura, which is an image projected on to a screen by a camera obscura. He distinguished this pictura from an imago, the traditional image of medieval optics that existed only in the imagination. By the 1670s a new theory of optical imagery had been developed, and Kepler's pictura and imago became real and virtual images, two aspects of a unified concept of image. The (...) new concept of image developed out of a synthesis of Kepler's determination of the geometrical location of a pictura as the limit, or focus, of refracted pencils of rays and the triangulation used by a single eye to determine the perceived location of an imago. The distinction between real and imaginary images was largely developed by Gilles Personne de Roberval and the Jesuits Francesco Eschinardi and Claude François Milliet Dechales. (shrink)

Major problems in cancer chemotherapy are toxicity, resistance, and cancer heterogeneity. A new theranostic paradigm has been proposed by the authors. Many million small molecules (SM) are bound to the proteins extracted from a patient's cancer. SM that also bind proteins extracted from normal human tissues are subtracted from the cancer protein bound SM leaving a large array of SM targeting many sites on each of the cancer biomarkers. Targeting many more than the conventional 1 – 4 cancer biomarkers will (...) reduce development of tumor resistance. After several cycles of selection and counter selection, DNA codes appended to the SM will be PCR amplified to provide templates for restricted libraries of the SM to improve selectivity and sensitivity. The large array of selected and counter selected SM assures that many of the compounds in the array will penetrate the cell membrane and bind to intracellular targets, low tumor resistance, low background for imaging, low therapeutic toxicity, and targeting of the diverse biomarkers present in the heterogeneous mixture of cells in primary and metastatic cancer. Theranostic use of radiolabeled SM binding many sites on many, not necessarily critical, biomarkers provides high cancer cell killing. Experiments to provide proof of principle of this novel concept suggested by the authors. -/- . (shrink)

The traditional formalism of quantum mechanics is mainly used to describe ensembles of identical systems (with a density-operator formalism) or single isolated systems, but is not capable of describing single open quantum objects with many degrees of freedom showing pure-state stochastic dynamical behaviour. In particular, stochastic 'line-migration' as in single-molecule spectroscopy of defect molecules in a molecular matrix is not adequately described. Starting with the Bohr scenario of stochastic quantum jumps (between strict energy eigenstates), we try (...) to incorporate more general pure-state stochastic dynamical behaviour into the quantum mechanical formalism.Probability distributions of (approximately) pure states, arising through the stochastic pure-state dynamics for long times, give rise to appropriate decompositions of thermal density operators. These decompositions of density operators into pure states mediate between quantum mechanics for ensembles of molecules and quantum theory for single molecules (or single dressed quantum objects). We suggest that such decompositions should be consistent with infinite limits (e.g. the Born-Oppenheimer limit for infinite nuclear masses) in the sense that quantum fluctuations (around classical behaviour in the infinite limit) die out asymptotically. (shrink)

The paper is an introduction to the third issue of the Journal for the Philosophy of Language, Mind and the Arts. The authors give an account of the theories that have most enriched the study of images since the second half of the twentieth century: analytical philosophy and visual culture studies. A distinction is made between the two philosophical traditions. On the one hand, in particular within the context of analytic philosophy, images have been studied as single entities in (...) relationship with both a referent and the perceptual or interpretive abilities of an observer. On the other hand, thanks in particular to the iconographic tradition inaugurated by Aby Warburg, images have been analyzed in their multiplicity, in their mutual relationship, both synchronically and diachronically. (shrink)

Ghost Image is made up of sixty-three short essays—meditations, memories, fantasies, and stories bordering on prose poems—and not a single image. Hervé Guibert’s brief, literary rumination on photography was written in response to Roland Barthes’s Camera Lucida, but its deeply personal contents go far beyond that canonical text. Some essays talk of Guibert’s parents and friends, some describe old family photographs and films, and spinning through them all are reflections on remembrance, narcissism, seduction, deception, death, and the phantom images (...) that have been missed. Both a memoir and an exploration of the artistic process, Ghost Image not only reveals Guibert’s particular experience as a gay artist captivated by the transience and physicality of his media and his life, but also his thoughts on the more technical aspects of his vocation. In one essay, Guibert searches through a cardboard box of family portraits for clues—answers, or even questions—about the lives of his parents and more distant relatives. Rifling through vacation snapshots and the autographed images of long-forgotten film stars, Guibert muses, “I don’t even recognize the faces, except occasionally that of an aunt or great-aunt, or the thin, fair face of my mother as a young girl.” In other essays, he explains how he composes his photographs, and how—in writing—he seeks to escape and correct the inherent limits of his technique, to preserve those images lost to his technical failings as a photographer. With strains of Jean Genet and recurring themes that speak to the work of contemporary artists across a range of media, Guibert’s Ghost Image is a beautifully written, melancholic ode to existence and art forms both fleeting and powerful—a unique memoir at the nexus of family, memory, desire, and photography. (shrink)

Single-sided deafness (SSD) or profound unilateral hearing loss obligates the only serviceable ear to capture all acoustic information. This loss of binaural function taxes cognitive resources for accurate listening performance, especially under adverse environments or challenging tasks. We hypothesized that adults with SSD would manifest both functional and structural brain plasticity compared to controls with normal binaural hearing. We evaluated functional alterations using magnetoencephalographic imaging (MEGI) of brain activation during performance of a moderately difficult auditory syllable sequence reproduction (...) task and assessed structural integrity using diffusion tensor magnetic resonance imaging (DTI). MEGI showed the SSD cohort to have increased induced oscillations in the theta band over the left superior temporal cortex and decreased induced gamma band oscillations over the frontal and parietal cortices between 175-475 ms following stimulus onset. DTI showed the SSD cohort to have extensive fractional anisotropy reduction in both auditory and non-auditory tracts and regions. Overlaying functional and structural changes revealed by the two imaging techniques demonstrated close registration of cortical areas and white matter tracts that expressed brain plasticity. Hence, complete loss of input from one ear in adulthood triggers both functional and structural alterations to dorsal temporal and frontal-parietal areas. (shrink)

Dichotomous Images in Ian McEwan's Saturday: In Pursuit of Objective Balance Saturday sets out to depict the contemporary world with its ambiguities and paradox. In the novel, like in a mirror painting, every event, character and conflict is highlighted from diverse, often contradictory, angles by the narrator's extensive commentary, flashback and reference to other books. The prevailing happiness of mass protests against the war on Iraq is countered by the recollection of mass graves, an element of Saddam's callous regime, the (...) real terrorist threat is contrasted with national paranoia, and the Prime Minister's performance of truthfulness is scrutinized by means of Paul Ekman's study of micro-expressions.The technique of dualistic depiction is further used in order to describe the characters. Reworking the idea of two sides of the same coin, McEwan offers the novel as a metaphorical study of the intricacies of human personality. Therefore, Baxter becomes simultaneously an offender and a victim, John Grammaticus turns from a successful poet into an alcoholic womanizer, and Lilian Perowne's physical and mental disintegration is contrasted with her past as a champion swimmer.McEwan's dichotomous description of the world echoes Barthes's binaries, not only in the duality itself, but also in the fact that the juxtaposition of contradictory images constitutes a more complete depiction of an event or a person. The contrast between the opposing ideas is further accentuated by the use of different jargons: the language of medicine, media, upper-class, working-class, and the like. The use of language throughout the novel seems to repeat the notion that by means of jargons people control and exclude others, highlighting their authority and constructing their position of supremacy.Saturday, which captures acutely the events of a single day in the life of a renowned neurosurgeon, Henry Perowne, presents issues, such as the terrorist threat or the creation of media reality, that appear international in consciousness. The essay illustrates how, with admirable artistry, McEwan incorporates meaningful images, visually complex descriptions and different kinds of language into a diary account, for readers to enjoy a more objective comment on the contemporary world. (shrink)

When we look at a tree, two images of it are formed, one on each of our retinas. Why, then, asks the child or the philosopher, do we not see two trees?1 Thomas Reid offers an answer to this question in the section of his Inquiry into the Human Mind entitled ‘Of seeing objects single with two eyes’. The principles he invokes in his answer serve at the same time to explain why we do occasionally see objects double. In (...) Part I of this essay, I examine the principles Reid uses to explain single and double vision. This part is mostly an exercise in the history of cognitive science, but it raises questions of interest to philosophers along the way. In Part II, I turn to a hard-core philosophical problem raised by double vision, namely, whether double vision constitutes an objection to the direct realist theory of perception, which was one of Reid's main philosophical purposes to promote. (shrink)

Is there a dominant global image—call it a world picture—that links the Occupy movement to the Arab Spring? Or is there any single image that captures and perhaps even motivated the widely noticed synergy and infectious mimicry between Tahrir Square and Zuccotti Park?

A photographic image is said to provide evidence of a photographed scene because it is a causal imprint of reflected light, an indexical trace of real objects and events. Though widely established in the history, theory, and philosophy of photography, this traditional imprinting model must be rejected because it relies on a “single-stage” misconception of the photographic process: the idea that a photographic image comes into existence at the time of exposure. In its place, a “multistage” account properly articulates (...) different production stages, such as registering and rendering, that are relevant to understanding the relation between a photographic image and the photographed scene. By denying that any photographic image is a causal imprint, the multistage approach proposes a more demanding evaluation of photographic evidence. This has implications for documentary film and photojournalism, along with specialized applications such as forensics, surveillance, and face-recognition technology. (shrink)

The paper focuses on the problematic of selfinterpretation and the correspondence between selfimage and the reality. Its presupposition is, that a human being is not committed to a single way of life, fully determined by his/her biological characteristics or by the dictate of his/her social background; first of all, he/she is not dependent on single ways of the interpretation of the world or of his/her selfinterpretation. It is his/her ability to accept certain characteristics as his/her own that makes (...) him/her a human being. There is usually a distinction between his/her own seeing himself/herself, which does not necessarily, leads to a failure. The strategies of survival are various and they need not to be rooted in true interpretations in all their aspects. In conclusion the author argues, that the critical thinking making its way into everyday life as well as into the public sphere offers the possibility of the variability of the ways of life and of a consensual coexistence on the basis of manifold interpretative structures and models. Enforcing a uniform view as a presupposition of human cooperation is replaced by an approach, respecting the legitimacy of the pluralistic image of the world and of the humans, for which this approach makes no obstacle in cooperative working of society. (shrink)

A comprehensive theory of the structure and cognitive function of the human imagination, and its relationship to perceptual experience, is developed, largely through a critique of the account propounded in Colin McGinn's Mindsight. McGinn eschews the highly deflationary (and unilluminating) views of imagination common amongst analytical philosophers, but fails to develop his own account satisfactorily because (owing to a scientifically outmoded understanding of visual perception) he draws an excessively sharp, qualitative distinction between imagination and perception (following Wittgenstein, Sartre, and others), (...) and because of his fatally flawed, empirically ungrounded conception of hallucination. In fact, however, an understanding of perception informed by modern visual science will enable us to unify our accounts of perception, mental imagery, dreaming, hallucination, creativity, and other aspects of imagination within a single coherent theoretical framework. (shrink)

While much has been written about verbal narratives, we still lack a clear account of what makes images narrative. I argue that there are narrative characteristics of images and show this with examples of single images. The argument proceeds in three steps. First, I propose that from a semantic perspective, the following two characteristics are necessary for an image to be narrative: a representation of an event and a representation of time. Second, I argue that there are paradigmatic characteristics, (...) such as at least two events, bridging connections, and unifying subjects between these events, characters with intentions, and the representation of goal-directed actions. Third, I show that it is possible to differentiate between narrative and non-narrative images while also accounting for the idea that narrativity is a matter of degree. While I do not provide a full definition of narrative images, my account constitutes a necessary first step in this direction. (shrink)

This dissertation works out a new approach to understanding what makes a representation pictorial and what makes a representation imagistic. Over the last thirty years, the most common approach to these problems has been to claim that what makes a representation pictorial is that normal perceivers can perceive it in certain ways. By contrast, my approach singles out structural features of representational systems as that which distinguishes pictures from other kinds of representations. Pictorial systems are those that are transparent, relatively (...) syntactically sensitive, relatively replete, and semantically rich. All pictures are images, but the converse relation does not hold because images need not be transparent, though they satisfy the weaker condition of being mimetic. This approach is similar to, but enjoys advantages over, Nelson Goodman's work on the topic. ;The account of what makes a representation pictorial or imagistic is then brought to bear on the imagery debate, which concerns whether the brain implements imagistic systems of representation, specifically in the early stages of perception. A review of what we know about the workings of the visual and auditory systems reveals that no representations in the brain are pictorial, though some are imagistic in quite limited respects. Though they fail to be imagistic in many interesting respects, the early stages of the visual and auditory systems are highly isomorphic to what they represent. ;The role of isomorphism in perceptual states has been much discussed in both philosophy and cognitive neuroscience. The last two chapters of the dissertation argue that perceptual representations of traditionally secondary qualities like colors and sounds are isomorphic to those properties to a lesser degree than representations of traditionally primary qualities like shapes. This distinction in how such properties are represented can affect out intuitions concerning the nature of those properties and the nature of perceptual experience. Furthermore, it is argued that isomorphism is an important feature of perceptual representations because of the role it plays in making information cognitively available. This role for isomorphism is maintained even if one is an information theorist, and therefore thinks that lawful causal generalizations fix the content of representations. (shrink)