This huge kidney stone website serves a large audience yet no one complains that I lack a kidney stone book. Its 85 articles comprise about 300,000 words, the size of a major textbook. Why would I add another book?

The book will connect the articles and integrate the knowledge into a plausible narrative that gives a sense of where we are right now concerning the science and medical practice of kidney stone prevention.

This introduction goes beyond the common use because in it I set out some of the key ideas and basic terms concerning science and medicine and the main themes I can recognize in the field of kidneys tone disease. So it is not a grace note or telling of what’s to come but an integral part of the book itself.

History and the Archipelago

I have sailed – cruised really, among the islands of the grecian archipelago, looked upon their monuments of undying intellect and the brilliant and sorrowful artifacts of the lost and elevated aristocracy that made them. Ruined palaces, tombs shaped in the shapes of beehives; a great playing field its running track shaded by rising slopes of grass where people might have lain or sat to watch the runners. An island like some children’s museum where I walked along the traces of a once gorgeous boulevard, and stood inside the low unroofed walls of a house whose windows faced the sea.

Guides would tell me names others had deciphered long before. Here, an ancient shrine to Helen and Menelaus, perhaps. There, Mycenae; Agamemnon ruled, perhaps, and was murdered by his own wife. And lovely Delos, sacred Delos, jewel of the Cyclades archipelago; were Apollo and Artemis born there? And Zeus, did he make that mountain his sanctuary?

All this is there to see. But what it means, how it made up a world – that requires more than scientists can disclose among its ruins. How can these scattered islands teach us the magnificence and violence of Greece, their separate histories frame what we call the West, except we know their story?

And that requires we learn their story from someone who can tell it.

The Painting

Lucas Cranach the Elder (1475 – 1553) painted the Judgement of Paris between 1512 and 1514. The painting hangs in the Metropolitan Museum of Art. Do Athena, Hera, and Aphrodite foresee Agamemnon dead, the burning towers, Hector at the gates of Ileum? Surely Paris, of his fateful judgment, knew nothing. And these violent, shape changing deities, why would they draw, thus, two civilizations into the fire?

The Closing of the Loop

We Tell About What We Cannot Observe

Facts are what we see, and they are here already. I have put them out among their articles.

The articles of this site lie scattered like Sybil’s leaves, like islands of an archipelago, each one the peak of an invisible mountain resting upon the bottom of the sea.

Deep indeed are the waters of the sea and, far beneath, the mountains join in ranges and furrows where once, perhaps, – before the flood – fertile river valleys shined all green and golden in the Summer sun. So what we see all scattered and alone, if we could find our way down to where all things begin, would be one thing, one great feature of the world, entire and comprehensible.

Come then, ride imagination down where flooded valleys mark the mountain’s feet, and set our facts along their way like diamonds in their natural tiara. They will blaze out like starfire the drowned mysterious patterns of the world.


Teller of Tales

But that imagining so like my metaphors must find its hold on what is real, and there, in that one phrase, we have it all. What shall we do with our imagined valleys, with the natural tiara of the world set out in blazing dreams – what shall we do when we awaken?

That is where science and metaphor part company – in a way.

Hear me now, for we are at a moment of importance.

What good is a metaphor except its vision finds some hold on what we plainly see? All poets know that. If the articles of this site are islands of an archipelago, they must be connected at their roots. What we can observe must be a minute fraction of what is there.

But dreams of how the world might come to be the way we find it – how can such dreams prove themselves when day has come? It is not enough to prove themselves as metaphors do – by suggestive linkages to obvious reality. They must do more.

Maker of Prophecies

The more they must do is this way. If a scientific dream be useful – the right word in the right place – one can use it as a prophet or prophetess might use a dream and say what will be found to come. But here the use is by a colder part of mind than prophecy, perhaps the coldest part of all. If the scientific dream be true, then by pure deductive logic something in the world that we can observe must be a certain way – not this, nor that, but the one certain way of all possible ways. That is what I mean by useful.

When a scientist dreams, that dream has value to the extent that from it one can deduce specific predictions about things that can be measured directly in the real world. A dream from which one cannot deduce a testable prediction, such a dream has no use.

What then?

Should that deduction prove true – and deduction it must be – the dream is not untrue. That is what science does. That is how we have about this one disease what we have now concerning how what all we can observe might come to be the way it is. We who have worked the fields here have dreamed, deduced our singular prophesies, gone out to try their worth and found them not untrue.

Medicine and Science

What Homer Said

Let me be clear. Homer never met Agamemnon, nor Paris, nor Helen. No one had who heard his tales of the great war. He imagined them out of fragments remembered from before his time, going back, perhaps, to when they might have lived.

But one can find some evidence of truth in them.

If one looks carefully, as scientists have, traces remain of Troy, perhaps, and the vast palaces of those who conquered it.

True or not in such external ways, the stories matter because of their internal truth. Men and women understand that his characters are true, that they behave as people will when so confronted by extreme realities. So stories have a dual sense of truth.

What Science Says

Science lacks one part of that duality. What it discloses must possess demonstrable reliability.

We Study What Is There

So it is we see before us phenomena in our patients and wonder at their origins.

The stones, traces of what be believe have caused of the stones, what the treatments that arise seem to accomplish for certain people over a certain time – these are observations. The word in science, induction. I myself have cataloged thousands of patients and published papers that describe them. Many more have done the same. From such observations come what I might call the general sense of what a ‘typical’ patient might be like.

In fact, the very mathematics tend toward the general sense. What else is a mean value?

We do this inductive research, and have done it for generations, because without a knowledge of what is there how can anyone imagine how what is there came to be the way it is? How can one imagine well about the causes of things he does not know, she does not know, in full detail?

We Imagine Causes

I do not imagine how many stones a patient made – I count them. Likewise for a thousand patients. But why they make them? Is it this, or that? Something in urine, something in kidneys, in the genes, the food, the life lived? And we want to know the causes in general, not for just this one patient but for the thousands of patients, the millions of them.


Because we tend that way as people. We dress the search for causes in a practical garment – know the cause to treat the cause, for example. But at heart there is a love in it – a love to discover, to pursue, to possess what we cannot observe.

We Deduce Predictions

Kidney stones form, we might imagine, because of conditions in urine that favor them. If so – thus deduction runs – then we must find in urine of people who produce stones conditions that differ from those who do not produce stones. Moreover, the differences must involve conditions that have plausible connections to the making of kidney stones. Fail to verify this prediction and the imagining is falsified. It is not a true dream and we can abandon it.

We Test the Predictions

If dreaming well requires imagination be free and ernest, and deduction requires an invincible intellect, testing requires a bent for practical ingenuity. The tests must somehow embody sufficient rigor in means simple enough for reasonable use. As an example, suppose someone else has contrived a long term observation program of men and women that seeks to link things about them to how things turn out in terms of diseases. Some of them, surely, must begin forming kidney stones as decades pass, and certainly most will not. Why then not get urine samples from both groups – those who do and those who do not – and compare them?

That was done, and indeed urines differed and in ways plausibly connected to the making of kidney stones.

We Build the Treasure House and Theory of a Field

That test tells us that the idea, the imagination, the ‘hypothesis’ to use a term of art, was not incorrect. Does that mean it is indeed correct? No. Another test will come, and another, and one day the idea may prove false. But right now the imagined cause of stones in differences of urine composition has use, predictive value, and we use it.

The idea, the tests that have been made of it, the details of what differences of urine chemistry track with stones and presumably cause stones, all these materials belong to the treasure house of the field of kidney stone research. We might just call it the established knowledge of the field. The presumed cause, urine composition, is part of what one might best call the theory of the field – not something one can observe directly but something imagined that has predictive power.

Be careful here.

Of course we can observe urine composition directly, and prove directly that this or that chemical component must have a role in stone production. But we cannot directly observe stones forming in people – it is impossible. We come after the fact of formation and seek to explain how it happened. That urine of stone formers and non stone formers differs, that is demonstrable. That the differences causes stones, that is imagined – and the collection of predictive imaginings are best called theory to separate them from what can be demonstrated directly.

What Physicians Get From Science

The Yield of Science

Physicians bring the yield of science to their patients. Certainly some physicians do science, but most do not and even those who can do not do science and patient care at the same time. These two actions differ.

The yield of science to medical practice is tests and remedies.

The tests have predictive value. Remedies cure or reduce the illness of disease. Most tests begin like the urine chemical differences – in imagination proven by predictive capacity. Remedies may arise from any corner of the world – from casual observations, folklore, all the way to genetically altered molecules invented out of pure dreams.

The Science of Trials

Classes of scientists specialize themselves in testing tests – how well they accomplish their predictions in practical settings. Likewise for remedies.

This kind of practical or applied science depends very little on imagination but quite a bit on practical ingenuity. It is, in principle, inductive in that the hypothesis simplifies to: This test predicts that outcome, that remedy produces this outcome. So the answer is not at all like that of tests of imagination. A test does this well or that well, a remedy the same. Whereas an imagination that predicted well may fail, a trial – the term of art for tests of tests and remedies – is what it purports: no more or less. It can be overturned because incomplete or in error, but not because imagination failed.

Practice of Medicine

It Depends on Science

If the tests and remedies arise from science, they benefit patients only via physicians. A patient with stones collects urine for testing because science has established links between such chemistry and stone formation. Science has established links between a change in such chemistries and reduction of stone formation. One might think the physician’s role trivial, a role that could be played by a machine.

It Enacts What Science Offers

But consider the reality. Urine composition varies with diet, fluids, activity and all these vary at the will of the person who makes that urine. Who can tell the physician if that sample represents when stones formed or not? Who can explain to patients that they must provide the right kinds of samples.

More. You must, a physician might say, do this or that with fluids or diet – and for perhaps a lifetime. Who will convince someone to do this? How?

Then, there is understanding. Will someone willingly alter life habits without some understanding of why? Can a physician counsel to this or that without an understanding of why?

Evidence arises in science, from science. The rest, its actuation into reality arises from something else – faith, personality, education, storytelling? We say evidence based medicine and our heads bow in affirmation – far superior to some arcane art of medicine. Foolishness. We need both. Always. People need people to enact change.

The Main Biologies of Kidney Stone Disease

The outcome of my generation and generations before me is the yield of science – the treasure house and theories. If I have undertaken to write a book here I did so to narrate what is in that treasure house, what those theories purport, and what supports their truth. I say narrate meaning that word – for the articles embody the details already; they lack the narrative.

What narrative?

Not a repetition of the facts or theories or tests, but analysis of the science that gave us the observations and tested the theories. Analysis means narration by parts, inspection of process, as in the story about Troy. To show is not to narrate; narrate, not to show merely but show in the service of story – direction, movement, meaning, integration into the greater themes as in the image of the diamonds at the roots of the world.

One Force, One Outcome, One Major Actor

That force is saturation, the outcome crystal formation.

All things arise from the work and shapes of the kidney. Of stones, actor principalis.

The kidney supersaturates the urine. Its cells are the surfaces on which crystals anchor, and those anchored crystals form the base on which common calcium stones form. By middle age or older, kidneys have usually accumulated some mineral deposits. But kidneys of stone formers generally have accumulated more deposits for any given age. This matter of deposit numbers vs. age deserves more study than we have given it.

Water Balance

Kidneys supersaturate tubule fluid and urine as they conserve water. Their work produces the free energy of supersaturation that may lie dormant in the fluid or dissipate in formation of crystals that can become kidney stones. But they supersaturate or not to serve the needs of systemic water balance, indifferent to such things as stone formation.

Kidney Anatomy

Supersaturation produces crystals anchored within the kidneys themselves. Local supersaturations and special tissue conditions determine where anchored crystals form. The stones we seek to prevent form on those anchoring sites.

Given normal kidneys and urinary tracts, the main two anchoring sites are plaque and tubule plugs. But any distortions of the collecting system – congenital ureteropelvic obstruction, bifid ureters as examples – offer a place for crystals to lodge. Innumerable tiny stones may form in the blind end cysts of medullary sponge kidney.

Kidney Physiology

Tubule cell transporters regulate the amounts of stone forming ions and molecules in tubule fluid and urine. Therefore, for any amount of water conservation they determine the resulting supersaturations.

Those transporters serve the needs of the body that regulates them. Perhaps over the dim uncertain eons we evolved to some compromises between systemic needs and the hazards stones pose to the flourishing of our species. Perhaps not. Certainly, gene variations commonly cause humans to vary in transporter function for calcium, and perhaps citrate and protons. Rarely, gene defects produce such kidney disorders that make stones inevitable.

Urine Polymers

Kidneys add many protein molecules and other large polymers to the urine. Some are filtered out of blood, many are too large for filtration and we presume kidney cells provide them. Many of these large molecules bind to crystal surfaces and affect their growth and whether they stick together. They can be surfaces on which ions in urine bind to form the initial crystal nuclei. Being so numerous as they are, over 1,000 in urine alone and not as yet enumerated in kidney tissues, no one knows which matter, if any, in kidney stone formation.

The many proteins in urine and many other large urine molecules lie between supersaturation and crystal formation. I think they glue crystals together so as to make out of their multitudes of tininess the full bulk of clinical stones.

No doubt gene variation, and epigenetic modulations so affect these polymers that perhaps no two people express quite the same mix. They are a dark continent, an almost unexplored world.

Systemic Diseases

Because they serve the body, diseases of the body that affect bone and mineral handling, or water balance, or acid base balance, or oxalate metabolism all can drive kidneys to make stones. Whereas we prevent common stones by altering diet and use of a few medications that affect urine composition, stones from systemic diseases require we treat the underlying diseases. Of their manifestations, stone are but one and not always the one most important. So emphasis shifts from stone formation to that disease.

Kidney Diseases

Inherited or acquired kidney tubules can lose functions from diseases. Some cause excessive amounts of stone forming material in urine. Some cause too alkaline or acid a urine. Of these diseases some progress to kidney failure. Stones are only a part of a more serious problem.

Behavior and Inheritance

Than kidney stones, no disease better illustrates how behavior and inheritance cross to cause human disease. For although our species fashioned everything about the kidneys as we evolved into what we are now, how we use the kidneys depends upon what we do. Culture, habit, accident, and chance much determine whether stones will form.

Fate and Choice

My themes run like the threads of a loom.

The kidneys, the whole body, even, string their warp on its tensioners. How kidneys work, how constructed, what polymers they put into their tubules and urine, and the entire vastness of bone and mineral metabolism, gastrointestinal functioning, liver metabolism, brain control of water balance  – all these await the thread of the weft.

And that, which runs through all the rest to make reality, is what we do. We choose the yarns and throw the shuttlecock.

The warp is what we start with, fair or poor as chance may have it.

The warp is the body of fate, the weft our will.

And the cloth what we make of what we are.

Accident and Chance

Uncertain indeed are the threads of the loom.

For they must separate, open a way for the shuttle to pass with threads above and threads below.

But threads can break or tangle, and the shuttle go wrong so the pattern disclose some waywardness to an expert eye.

All this is metaphor, of course, taken lightly, by way of imagistic explanation of things too deep for words. But we have the long threads, do we not, strung on their elaborate tensioners and only so long and so durable. We have indeed their separation into the two, between which runs the shuttlecock; is that not true? And the cloth, do we not throw our patterns on the long threads of the warp?

Of course we do not – we are not looms. Even so, cannot one striking image set imagination free, engage the mind, perhaps, in ways unthought of?

What I Will Make of This

Metaphor or not, for what might seem an airy dream of warp and weft the realities of this my one disease may make an earthly shape. Or, better said perhaps, let wash over it but the glamour and the flourish of a vision or metaphor and reality brightens, as gravity kindles commonness to blazing light.

How Long a Book?

Not long.

Enough to put the themes together, tell the story they can tell, and, in this one tiny corner of biology and medicine try to understand how things work. Separate what we know from what we think we know. And, how what we think came to be the way it is.

A Preferred Order of Reading

This TOC is for the kidney stone book. It runs differently from the sidebar TOC of the site that gives links to the articles. I intend my story book to run in the direction of this TOC and make no allowances for people who skip around. Things build on each other so if you want the story read it in order.

If you just want to look up things, the sidebar TOC was made for you.

Warning: This Book is in Preparation – Only 2 chapters exist so far

Chapter One: Kidney Stones in General

Chapter Two: How Kidney Stones Form