The Blue Question by Cryberg

Wild type is the sole basis for all of biology. It was well established long before Darwin or Mendel were even born, much less before the field of genetics began to be understood in even a minor way. It is still today the sole basis for making sense and order in biology. In fact, the rudiments of the wild type idea probably trace back for 1000 years or more. It is pretty hard to pin down an exact date when it was first recognized, nor who the first person was who recognized it. If you do not understand wild type you do not understand anything about biology that has happened for at least the last 300 years.

The first person to formalize wild type was Carl Linneaus in the middle 1700s. Linneaus recognized that plant and animal species differed from each other in measurable physical characteristics. A given species differed in physical characteristics within that species far less than those same physical characteristics differed from other species. Based on this observation he developed a classification scheme that is still in use today. Today’s version follows an order where each step down represents a group that is more and more closely related. The steps are Life, Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. This is something taught in high school biology. At the end, species, you are talking about one single species. One level up, genus, you are talking about a number of species which are closely related based on phenotypic similarity.

It is not always an easy decision if two populations that are very closely related are one species or two species. In pigeons, for instance, some have argued at times that wild populations that were checked were a different species than wild populations that are barred. In fact variation in wild population from one location to another location is perfectly normal and to be expected. So biology has people who are called lumpers and others who are called splitters. A lumper would consider barred and checked populations of pigeons as one species. A splitter would call them two species. The lumper and splitter disagreement is unending, even today, in some cases. In general though, this disagreement is eventually resolved on one side or the other. Often today. things like DNA sequence data are brought to the table as part of the argument; as well as observations on interbreeding and gradation in phenotype in the geographic areas between the two different population centers. Today we also realize, that at times phenotypes can be so close to identical, that two species can be difficult to tell apart simply by physical examination. So DNA evidence is becoming more important all the time.

This idea that members of a species share more phenotypic traits with each other than they share with any other species was very well established by Darwin’s time in the middle 1800s; and formed a considerable amount of the background information he used to formulate his ideas about how one species evolved into another species. Darwin’s thought was if a population of one species was geographically isolated from other members of the same species that isolated population would live under unique conditions and that with time it would evolve traits that allowed it to better survive in its local environment. What Darwin recognized was wild type was not forever stable but could change as a result of what he called survival of the fittest. Like most new ideas in science this idea was not warmly embraced by some people. A great deal of his thinking was in fact based on domestic pigeons. But, a great deal was also based on his observations of finches on the Galapagos Islands. Each island had finches which were different in some specific ways from finches on the other islands. Often beak sizes and shapes differed dramatically. We know today these beak differences are not even due to differing genes. They are caused by changes in switches that turn genes on and off. Darwin recognized that these finches were all very closely related and probably all evolved from one single finch species. He was correct.

In the case of domestic pigeons, man interfered with nature and selected for physical traits man found desirable. The result was different breeds that had greatly different phenotypes. Yet he knew these different breeds would mate and produce young which were perfectly vigorous and fertile. And further these crosses generally looked much more like the well recognized wild type for pigeons than either parent breed. Darwin had no clue at all how this was possible. He came to these conclusions many years before Mendel’s work on peas became available. About all that was well understood at Darwin’s time in domestic animals was if you selected for some given trait you could over time develop that trait and exaggerate the difference from wild type. In fact, every domestic animal and plant was recognized as having been so selected by man to the point that in some cases it was not obvious what the original ancestor wild species had been.

Gregor Mendel published a paper in 1865 about peas concerning what we today call inheritance; and it became instantly ignored. In the next 35 years, only three scientists even referenced his work. The thinking at that time was that inheritance was a blending operation of some sort in spite of Darwin’s observations on pigeons which clearly refuted any such idea. It seems the idea that there could be units that were passed from parent to offspring that survived intact without dilution was more than biology at that time could accept. The net result was Mendel’s work lay dead until 1900.

Hugo de Vries and Carl Correns rediscovered Mendel’s idea of unit inheritance in 1900 and rediscovered Mendel’s earlier papers and gave him proper credit. Not uncommonly, in science, an idea is originated that is simply before its time and lays dormant for many years. That is exactly what happened to Mendel. Suddenly in 1900 the study of what we now call genetics exploded. As is typical in any explosion this new science instantly became disorganized and fragmented and filled with many ideas that today seem insane. The early students of genetics largely lost the idea of wild type or at least made a pigs ear of it. Much of the reason this happened is understandable today and probably was inevitable. Understanding of statistics was rudimentary at that time except when applied to games of chance and nonexistent in the biological sciences. There was no clue at all what these units of inheritance were or where they resided. Biochemistry knowledge consisted mainly of how to make bread, beer, wine and booze and not much more. And, even with bread, beer, wine and booze the physical process was understood but not much that was happening on a molecular level.

The net result was in early papers on genetics some things were proposed that today we view as amazing and can not understand how such a thing could possibly have ever been suggested. It took many years of experimental breeding programs carefully gathering data before it became obvious that things like the color of a pigeon involved a whole host of wild type genes and alteration of any single wild type gene could lead to a new phenotype. Early on the thinking was more along the line that color, or any other phenotypic trait in pigeons was probably the result of only one or two genes. The lack of understanding statistics also lead people to make some mating, raise three young and draw conclusions as to some trait being dominant or recessive. It is easy to understand such errors when you realize that the general wisdom was most of the time only one gene was involved in any kind of trait. For example, with the thought process at the time all crests on pigeons could well be considered due to different variations of one single gene that when mutated gave crest phenotypes. Or all the different forms of feathered feet and legs could be due to variations in one single gene that when mutated in different ways gave various feather patterns and sizes.

The first paper on inheritance in pigeons of any significance was published by Leon Cole in 1914¹. In that paper he stated “Red may be called the fundamental color in pigeons as is probably the case in fowls and most mammals. It appears to be potentially always present, and if we let the factor for its production be represented by the letter R, we may say that apparently the factor R is never lacking from the gametic formula of pigeons.” The red to which Cole refers is what we today call recessive red. In two prominent, short sentences Cole discards the whole concept of wild type that was the basis of all of biology for the prior 200 plus odd years! It was another decade or decade and a half before the science of genetics had made the progress to understand that there were three total disasters in Cole’s two short sentences. He not only discarded wild type but far worse he gave a unitary name and symbol to his newly defined wild type. It is not clear at all why he happened to assign R rather than r to red. It is clear he understood dominants and recessives. He assigned S to spread and B for blue for example. His gametic formula for a red was RRbbSS so he recognized that good reds at times have spread as one component. His formula for blue was RRBBss and black was RRBBSS. It is pretty hard to understand how in the world errors of this nature could possibly have ever happened unless you study history. If you study history you will learn that such errors were inevitable and are simply a pretty normal, although discouraging, part of how any science develops over time. When you are operating with very fragmented knowledge and only have tiny bits and pieces of actual data to study and think about and when you have not allowed enough time for other fields of science to weigh in and cast a vote, errors happen. This was true in the case of genetics in 1914 as genetics was only a 15 year old branch of biology at that time. The net result is a pretty normal high school student today can easily have a much more sophisticated understanding of genetics than the best living scientist had in 1914. We simply have to remember that in 1915 no one had any clue what a gene was or even where in the cell genes were located. No one had discovered DNA. A perfectly reasonable person in 1915 could have thought a gene was simply some bit of protein or carbohydrate that floated around in the cells cytoplasm. We Also must remember that in 1914 there was no reason to realize, as we clearly realize today, that for every mutant gene there exists a wild type gene. And, at least for recessive mutant genes that wild type gene does things that are absolutely critical in making a wild type phenotype. It was not at all understood back then that if you removed the wild type form of the recessive red gene you would not get a blue pigeon. This is so clearly understood today that a high school kid can understand the reasons. But, in 1914 it simply was not understood at all. Even today, almost no pigeon persons understands what would happen if the wild type form of the recessive red gene was removed. Thus it is reasonable to give Cole a lot of forgiveness.

You could make exactly the same type of disparaging observations about Newton failing to recognize the theory of relativity for example. After all, he had every single tool available needed to recognize relativity as inevitable. In fact, he knew every physical principal and the needed math. He knew the math far better than Einstein knew it; as Newton invented the needed math and Einstein was a miserable math student and learned little in school about the topic. Newton was in a vastly better position to recognize relativity back when he did his work, than Cole was in, to understand pigeon genetics in 1914. The wonderful part of science is it has a built in self correcting process that takes care of such errors with time. That is why science demands disclosure of all relevant data when a paper is published. With data, it is possible for another worker to go back and not only replicate experiments but also do added tests to confirm or deny claimed results as well as explore new possibilities. Thus the statement, no data, no science.

Unfortunately, experience has taught me that most of the pigeon hobby has a current understanding level such that they still largely fail to understand wild type. There likely is no cure as science had corrected Cole’s wild type errors within a decade, yet many people in the hobby still talk about a blue gene. They totally ignore the fact that a blue gene is forbidden by the naming rules because there are so many genes that equally deserve the name blue gene.

The corrections to Cole’s errors came more from fruit fly studies than any other single place. Fruit fly studies showed that any given phenotypic trait is frequently impacted by mutants at multiple different locations. In some cases, mutants at two clearly totally different locations could lead to exactly the same phenotype or at least so close it can be hard to tell the two mutants apart simply by looking at phenotype. This forced the genetics community to regroup and go back to the old standards that biology had accepted for centuries, namely wild type. And part of going back was to forbid the practice of giving wild type genes for a phenotype due to the vast confusion that resulted. This happened in the 1930s. As we have come to understand the biochemistry involved in heredity and life; it has simply become more obvious that naming or symbolizing a wild type gene based on phenotype is a fool’s errand. Today’s rule is simple and unambiguous. Wild type is named for the first discovered mutant at that locus. For example, wild type at brown is a proper name for a particular wild type gene in pigeons. Other examples would be wild type at dilute, wild type at recessive red, etc. The exception is if the exact biochemical function of that wild type gene becomes known and the gene’s DNA has been sequenced. If both criteria are satisfied it is perfectly acceptable to name it for its biochemical function. For example the wild type at albino gene is also properly named the tyrosinase gene as tyrosinase is the enzyme that wild type gene produces. It is symbolized Try. Both biochemical function and DNA sequence are absolute requirements for such a name. Absent either no name is permitted.

Cole made other errors in his 1914 paper. A major error he made concerned blue. Cole never looked at pigeon feathers under the microscope. Rather, he states clearly that he is accepting the unpublished findings of Lloyd-Jones as his source of information. Lloyd-Jones published his paper² in 1915. As Lloyd-Jones was in Iowa and Cole in Rhode Island in those days probably all communication between them was by letter. Further, Lloyd-Jones did not have photographic equipment available so he had to hand draw things he viewed in the microscope. Between slow communications and hand drawings there was much opportunity for errors to creep into the understanding of what pigment granules look like and how they are distributed within the feather. Cole was the first to state that pigment granules are clumped in blue feathers. He states that what we call blue “is in reality not a blue but a neutral shade of gray. It corresponds to Ridgeway’s ‘gull gray.’ The optical effect is due to a different arrangement of the pigment in the barbules from that which obtains in blacks. In blues the pigment is aggregated into clumps, while in blacks it is spread uniformly throughout the barbules.”

I am sure if Cole had ever actually looked at a blue feather under a microscope even at 100X magnifications he would never have said something so foolish. This is not even approximately true of a blue feather. Nor is it what Lloyd-Jones reported in his paper a year later entirely accurate. Yet, from 1914 to today the idea has persisted that somehow pigment clumping has something to do with production of the blue in a pigeon feather. It seems I must be the first person since Lloyd-Jones to actually look at blue pigeon feathers under a microscope at a variety of magnifications! Clumping does not exist. It is an invention by people who do not have any idea what the distributions of pigment actually looks like because they have not looked at feathers themselves with a microscope and because they have not read Lloyd-Jones 1915 paper carefully nor my paper published on Huntley’s web site³.

Unfortunately Lloyd-Jones picked a sample preparation technique that lead to considerable loss of detailed data at lower magnifications. His sample preparation method involved cutting feathers apart with scissors, embedding the jumbled parts in wax then cutting thin sections with a microtome. I am skipping a number of staining and clearing steps he also took. The problem with this sample preparation method is he could not always tell exactly what part of the feather he was looking at and could not scan the scope across a feather with a traveling stage and get an overall view. He also concentrated his main effort of the smaller parts of the feather such as the barbules and barbicels and largely ignored the larger parts such as rachis and barbs. In his paper he states concerning a blue feather that “In the barb the pigment is restricted entirely to the apex. The lateral sheets of cortex are altogether without pigment and the medullary cells, richly supplied with pigment in black or duns, are entirely without pigment.” I can not understand how he could possibly have drawn this conclusion. In picture 2 I show a single barb with its attached barbules and barbicels. The barb is the large black central shaft in this picture that goes clear from the bottom to the top of the view.

It is obvious that when Cole wrote his paper he simply relied on what Lloyd-Jones was telling him could be seen with a microscope. So Cole decided that black was due to some genetics that resulted in distributing the exact same pigment granules spread uniformly though the feather parts. Lloyd-Jones had also looked at such birds and reported the feathers were colored in all parts. That was the origin of the word spread. It is curious that Cole seems to have ignored entirely Lloyd-Jones observation that pigment granules varied in size in some cases and granules in blue feathers were gigantic compared to granules in a spread black pigeon. In fact it is clear that by the time Lloyd-Jones published his paper a year after Cole’s paper he was not at all comfortable with Cole’s interpretation. In particular Lloyd-Jones did not like Cole’s use of the word spread at all. He wrote “It seems wise to the writer to retain the symbol S in the genetic formula for pigeons, but with this modification, that we consider it a factor for ‘stopping’ rather than for ‘spreading.’” It is clear that Lloyd-Jones realizes that a great deal more than simply pigment distribution within the feather is involved in turning blue into black, including the fact that blacks simply having a great deal more total pigment and a different size of pigment granule.

The conflicts between these two workers is rather surprising as they were obviously communicating their findings to each other. I can only surmise that Cole did not give Lloyd-Jones the courtesy of reviewing his paper before publication. Had this happened a lot of future confusion that has continued to this day might have been avoided. Namely that clumping of pigment granules had something to do with production of what we call the blue color of pigeon feathers. Still, they would not have gotten the story right as they missed all the pigment in the barb shaft itself and concentrated their effort looking at the wrong part of the feather.

More recently we have the quantitative data on amount of pigment present in blue vs. black. Sell, et all⁴ report that the blue part of a feather in a spread blue has nearly ten times as much total pigment as a blue pigeon. It seems reasonable that ten times as much pigment would make the feather much blacker in color. In fact, this should have a great deal larger impact on color than spreading granules from groups where they are not even close to touching, from an optical light standpoint, to some more uniform distribution.

At the start of this paper I showed picture 1 as an example of two blue feathers. These are secondary flight feathers and one appears to be barred and the other barless. The barless feather is the result of an interesting accident. For another microscopy project I needed to look at the barbules and barbicels of some feathers. The problem was some of the feathers had so little pigment I simply could not see some things and getting photos was impossible. So, I decided to dye those feathers. But before using up feathers of interest to the project I experimented with dying recessive white feathers. The dye I used was obtained from a local shop that supplies all kinds of hair treatment products for women. If you want pink or green hair they had the products. I picked a Proctor and Gamble product, Clairol, Beautiful Collection, Jet Black, shade B22D. This is a semi permanent dye and is applied to damp hair simply by spreading it on the hair, waiting 20 minutes for human hair, rinsing well and drying. To dye a feather I wet the feather out using Palm Olive dish washing detergent and rinsed the detergent completely from the feather. I damp dried the feather with absorbent tissue paper, spread the dye on both sides of the damp feather with a tooth pick and waited various lengths of time up to three hours. I then rinsed any free dye from the feather under running water and air dried the feather. In no case did the feather end up any place close to black. The deepest color was about equal to a fairly dark dirty blue. In the case of the feather shown in picture 1 the dye exposure time was 10 minutes. In picture 3 I show a single barb and attached barbules from this dyed feather.

Picture 3. Barb and attached barbules of a black dyed recessive white feather

Again the barb is the large central shaft that runs from the bottom to the top of the view. As can clearly be seen nearly all the dye taken up by the feather is concentrated in the barb itself and very little is deposited in the barbules. Most of the dye that is deposited in the barbules is all towards the end 1/3 of the barbule on only one side of the barb. The barbules on the other side of the barb are for practical purposes nearly dye free. It is plainly obvious that the blue color we see in both a natural blue feather and a white feather dyed with black dye is the result of both pigment and dye being mainly found in the barb shaft itself where pigment and dye are both uniformly distributed. There is no clumping in the barb. The barbules are for practical purposes near white.

Thus the last 95 years of nonsense about blue having something to do with the non uniform distribution of pigment in the barbules should be put to its final rest as a totally failed and disproved idea.

1. Leon J. Cole, Studies on Inheritance in Pigeons: I. Hereditary Relations of the Principal Colors. Bulletin 158, Agricultural Experiment Station of the Rhode Island State College, pages 311-385, 1914

2. Orren Lloyd-Jones, Studies on Inheritance in Pigeons: II. A Microscopical and Chemical Study on the Feather Pigments, The Journal of Experimental Biology, 18, 453-509, 1915

3. Richard Cryberg, Microscopic Examination of the Pigment Found on Wild Type C. livia, https://www.angelfire.com/ga/huntleyloft/Pigment.html

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The Blue Question

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