Gregor Johann Mendel



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Gregor Johann Mendel

  • Gregor Johann Mendel
  • Born to a peasant family in Brno (then Brunn) in Moravia
  • Showed promise in school
  • Studied at the University of Vienna, but could not get a degree, because of a psychiatric condition (exams made him nervous)
  • Returned home, taught high school physics school
  • Became an abbot at a monastery
  • Bred peas for 8 years
  • Presented the findings to his local “nature lovers” society
  • Wrote to the leading authority of his time on plant hybridization, had his findings rejected as incorrect
  • Died unknown, and remained so for 35 years
  • Stands in history next to Newton, Darwin, and Einstein

Observable phenomena, explainable and not

  • Gravity.
  • The color of the sky.
  • Heredity.
  • “It’s All in the Genes”
  • New York Times, 5/2/04

“An SCN9A channelopathy causes congenital inability to experience pain” Nature Dec. 14, 2006

  • “The index case for the present study was a ten-year-old child, well known to the medical service after regularly performing 'street theatre'. He placed knives through his arms and walked on burning coals, but experienced no pain. He died before being seen on his fourteenth birthday, after jumping off a house roof.”
  • Fig. 2.11

BASEBALL; Blood, Sweat and Type O” NYT 12-15-06 In the end, the Red Sox apparently decided to spend more than $100 million to get the Japanese pitcher Daisuke Matsuzaka in a Boston uniform for the next six seasons, For intrigued baseball fans in the United States, Matsuzaka's relevant statistics are no-brainers: 26 years old, 6 feet, 187 pounds and a 108-60 record with a 2.95 earned run average in eight seasons with the Seibu Lions. But what many fans, the Red Sox front office and even Matsuzaka's determined agent, Scott Boras, may not realize is that in the eyes of the Japanese, Matsuzaka's most revealing statistic might be his blood type, which is Type O. By Japanese standards, that makes Matsuzaka a warrior and thus someone quite capable of striking out Alex Rodriguez, or perhaps Derek Jeter, with the bases loaded next summer.

  • BASEBALL; Blood, Sweat and Type O” NYT 12-15-06 In the end, the Red Sox apparently decided to spend more than $100 million to get the Japanese pitcher Daisuke Matsuzaka in a Boston uniform for the next six seasons, For intrigued baseball fans in the United States, Matsuzaka's relevant statistics are no-brainers: 26 years old, 6 feet, 187 pounds and a 108-60 record with a 2.95 earned run average in eight seasons with the Seibu Lions. But what many fans, the Red Sox front office and even Matsuzaka's determined agent, Scott Boras, may not realize is that in the eyes of the Japanese, Matsuzaka's most revealing statistic might be his blood type, which is Type O. By Japanese standards, that makes Matsuzaka a warrior and thus someone quite capable of striking out Alex Rodriguez, or perhaps Derek Jeter, with the bases loaded next summer.
  • In Japan, using blood type to predict a person's character is as common as going to McDonald's and ordering a teriyaki burger. The association is akin to the equally unscientific use of astrological signs by Americans to predict behavior, only more popular. It is widely believed that more than 90 percent of Japanese know their blood type. ''In everyday life in Japan, blood type is used as a kind of a social lubricant, a conversation starter,'' said Theodore Bestor, a professor of Japanese studies and anthropology at Harvard University. ''It's a piece of information that supposedly gives you some idea of what that person is like as a human being.
  • ''Japanese tend to have a fairly strong kind of inherent belief that genetics and biology really matter in terms of people's behavior. So I think Japanese might be much more predisposed to thinking about a kind of genetic basis for personality than most Americans would.'' Japanese popular culture has been saturated by blood typology for decades. Dating services use it to make matches. Employers use it to evaluate job applicants. Blood-type products -- everything from soft drinks to chewing gum to condoms -- have been found all over Japan.
  • A person can have one of four blood types, A, B, AB or O, and while the most common blood type in Japan is Type A, many of the more prominent Japanese players are like Matsuzaka, Type O. That group includes Hideki Matsui of the Yankees, Kazuo Matsui of the Colorado Rockies (and formerly of the Mets, with whom he was a huge disappointment) and Tadahito Iguchi of the Chicago White Sox. Sadaharu Oh, the great Japanese home run hitter? He is type O, too, as is Kei Igawa, the 27-year-old Hanshin Tigers left-hander who has until Dec. 28 to sign with the Yankees.
  • In Japan, people with Type O are commonly referred to as warriors because they are said to be self-confident, outgoing, goal-oriented and passionate. According to Masahiko Nomi, a Japanese journalist who helped popularize blood typology with a best-selling book in 1971, people with Type O make the best bankers, politicians and -- if you are not yet convinced -- professional baseball players.

In order for people with type O blood group to also be “self-confident, outgoing, goal-oriented and passionate” – what has to be the case?

  • Each of these “traits” has to be controlled by a single gene.
  • All of those genes have to be tightly linked to the ABO gene on chr. 9q.34.
  • The specific allele of all of those hypothetical genes that makes a person “self-confident, outgoing, goal-oriented and passionate” has to be the one linked to the “O” allele of the ABO gene, whereas the “A” and “B” alleles of the blood group gene have to be linked to the “lacking self-confidence, reclusive, couch-potato, and frigid” alleles of those genes, respectively.
  • All of the above.
  • None of the above.

Heredity: “blending inheritance”?

  • President W.J. Clinton Senator H.R. Clinton Their daughter, Chelsea

Phenomenon  explanation of mechanism

  • “Just so stories” (i.e., making up an explanation that “makes sense”). Encouraging (rare) example: Francis Crick’s invention of tRNA. Discouraging (overhwelmingly so, in numbers) examples: theories of heredity before Mendel/C-T-dV.
  • Scientific method.

Just So Stories (R. Kipling)

  • How the elephant got its trunk
  • How the camel got its hump
  • Etc.
  • R. Lewontin

“Accusers All; Going Negative: When It Works” New York Times 8-22-04

  • “THIS was supposed to be the positive campaign. Late last fall, Democrats and Republicans alike predicted that a new campaign rule requiring candidates to appear in their own advertisements and take credit for them would discourage them from making negative ads. Yet it's not even Labor Day and President Bush has spent the majority of the more than $100 million he has spent on television advertisements attacking his Democratic opponent, Senator John Kerry. Mr. Kerry and the other Democratic primary contenders seemed to spend the fall and early winter in a contest to see who could jibe Mr. Bush the most.”

“Accusers All; Going Negative: When It Works” New York Times 8-22-04 ctd

  • “Political consultants cite a strikingly consistent pattern when it comes to darker, more confrontational commercials. ''Focus groups will tell you they hate negative ads and love positive ads,'' said Steve McMahon, a Democratic strategist. ''But call them back four days later and the only thing they can remember are the negative ones.''
  • And studies have shown that not only are people more likely to remember attacks, it also takes fewer airings to remember them.
  • ''There appears to be something hard-wired into humans that gives special attention to negative information,'' said Kathleen Hall Jamieson, director of the Annenberg Public Policy Center at the University of Pennsylvania. ''I think it's evolutionary biology. It was the wariness of our ancestors that made them more likely to see the predator and hence to prepare. The one who was cautious about strange new food probably didn't eat it, they sat back and watched other people die. There's a reason to be hesitant about that which is vaguely menacing.''

Scientific method

  • Observe phenomenon.
  • Come up with an explanation for what accounts for it (=a hypothesis).
  • Test the hypothesis by doing something (=perform an experiment).
  • Look at the data from the experiment.
  • Determine, whether the data are …
    • … consistent with the hypothesis being true  1
    • … consistent with the hypothesis being wrong  2
    • … inconclusive  3
  • Note: if you are unable to cross the red line, go give an interview to a newspaper. Journalists love conjecture.

Problems 2.2 and 2.3 – required (write out the answer in essay form)

  • 2.2 During the millennia in which selective breeding was practiced, why did breeders fail to uncover the principle that traits are governed by discrete units of inheritance (that is, by genes)? (required reading – Cobb, Heredity Before Genetics: a History).
  • 2.3 Describe the characteristics of the garden pea that made it a good organism for Mendel’s analysis of the basic principles of inheritance. Evaluate, how easy or difficult it would be to make a similar study of inheritance in humans by considering the same attributes you described for the pea.

Before Mendel

  • 5,000 B.C. - ~1650 A.D. – “just so stories”
  • 1650 – 1760: flawed experiments
  • 1760 – 1856: better experiments (Joseph Kölreuter, Carl Gärtner, but with flaws in experimental design, and deep flaws in interpretation); heuristic successes in breeding (Robert Blakewell).
  • 1856-1866: Mendel’s experiments.

The significance of the “reverse cross”

  • “Whatever the case, for the most recent part of humanity's history — that which has occurred since the rise of civilization — the involvement of both males and females in producing new life has been taken as a given. That did not mean, however, that the two sexes were considered to make complementary contributions, or that there was thought to be any consistent observable relation between parents and offspring. A classic assumption — which persists in much folklore today — turned the apparent prehistoric focus on women on its head, producing a male-centred view. Semen — the only immediately apparent product of copulation — was thought to be 'seed' ('semen' means seed in Greek); parents still talk to children about 'Daddy planting a seed in Mummy's tummy'.”
  • Cobb NGR 7: 953.

“The Ancient Greeks came up with two contrasting views of human generation: Hippocrates argued that each sex produced 'semen', which then intermingled to produce the embryo, whereas Aristotle claimed that the woman provided the 'matter', in the shape of her menstrual blood, with the father's semen providing the 'form', shaping the female contribution in some unknown way. The great physician Galen, whose approach was to dominate European and Arab medicine for around 1,500 years, adopted many of Hippocrates ideas, including his 'two-semen' theory of generation.

  • “The Ancient Greeks came up with two contrasting views of human generation: Hippocrates argued that each sex produced 'semen', which then intermingled to produce the embryo, whereas Aristotle claimed that the woman provided the 'matter', in the shape of her menstrual blood, with the father's semen providing the 'form', shaping the female contribution in some unknown way. The great physician Galen, whose approach was to dominate European and Arab medicine for around 1,500 years, adopted many of Hippocrates ideas, including his 'two-semen' theory of generation.
  • The ideas of Aristotle and Hippocrates dominated Western (including Islamic) ideas about generation for over 1,500 years. On the other side of the planet, Chinese thinking about generation did not try to locate functions in structures, but instead focused on the 'generative vitality' of each sex, defined in terms of the energy flows of organ networks
  • Cobb NRG 7: 953.
  • 1677

Surprisingly to the modern eye, no one in the seventeenth century argued that eggs and sperm represented complementary elements that made equivalent contributions to the offspring. Instead, the next 150 years were dominated by either 'ovist' or 'spermist' visions of what eventually became known as 'reproduction' (the term was coined only in 1745) (Ref. 7). Each view considered that only one of the two parental components provided the stuff of which new life was made, with the other component being either food (as the spermists saw the egg), or a force that merely 'awoke' the egg (as the ovists saw the spermatozoa).

  • Surprisingly to the modern eye, no one in the seventeenth century argued that eggs and sperm represented complementary elements that made equivalent contributions to the offspring. Instead, the next 150 years were dominated by either 'ovist' or 'spermist' visions of what eventually became known as 'reproduction' (the term was coined only in 1745) (Ref. 7). Each view considered that only one of the two parental components provided the stuff of which new life was made, with the other component being either food (as the spermists saw the egg), or a force that merely 'awoke' the egg (as the ovists saw the spermatozoa).
  • There were many reasons underlying this apparent scientific dead end. For example, in chickens, the two elements did not seem to be equivalent at all: there was a single enormous egg, which was apparently passive, whereas the 'spermatic animals' were microscopic, incredibly active, and present in mind-boggling numbers. Ultimately, however, the reason that late seventeenth-century thinkers did not realize what to us seems blindingly obvious — that both eggs and sperm make equal contributions to the future offspring — was that there was no compelling evidence to make them appreciate this. Worse, such evidence could (and would) come only from the study of something that, at the time, was not even recognized to exist: consistency in the relations between parents and offspring, or heredity.
  • The problem was not that thinkers did not look for similarities between the generations, but that they did, and were understandably confused by what they saw. Human families provided striking, highly contradictory and apparently inconsistent evidence — children sometimes looked like one parent, sometimes a mixture of the two, sometimes like neither and sometimes like their grandparents. Harvey perceptively summed up the difficulties in his 1651 work, De Generatione Animalium ('On the Generation of Animals') (Fig. 2). Harvey mused: "...why should the offspring at one time bear a stronger resemblance to the father, at another to the mother, and, at a third, to progenitors both maternal and paternal, farther removed?"
  • Victor Hartmann
  • -- the drawing that inspired
  • Mussorgsky to write the
  • “Ballet of the Unhatched Chicks”
  • from Pictures at an Exhibition
  • Cobb NRG 7: 953.

In a rare experimental study of resemblance, Leeuwenhoek provided yet another example of the way characters appeared in each generation, and added to the prevailing perplexity. Using what could have been a tractable model — rabbits — Leeuwenhoek was surprised to find that a grey male wild rabbit could give rise to only grey offspring. But Leeuwenhoek argued that spermatozoa were the sole source of the future animal, so his strange finding from rabbits became "...a proof enabling me to maintain that the foetus proceeds only from the male semen and that the female only serves to feed and develop it."9 In other words, there was no relation between both parents and the offspring, but simply between father and offspring, which was represented by the little animal in the male semen. The father was grey, so the offspring were inevitably grey, thought Leeuwenhoek.

  • In a rare experimental study of resemblance, Leeuwenhoek provided yet another example of the way characters appeared in each generation, and added to the prevailing perplexity. Using what could have been a tractable model — rabbits — Leeuwenhoek was surprised to find that a grey male wild rabbit could give rise to only grey offspring. But Leeuwenhoek argued that spermatozoa were the sole source of the future animal, so his strange finding from rabbits became "...a proof enabling me to maintain that the foetus proceeds only from the male semen and that the female only serves to feed and develop it."9 In other words, there was no relation between both parents and the offspring, but simply between father and offspring, which was represented by the little animal in the male semen. The father was grey, so the offspring were inevitably grey, thought Leeuwenhoek.
  • It is tempting to imagine that if he had done the reciprocal cross, using a grey female wild rabbit, or if he had studied the grandchildren of his grey male, Leeuwenhoek might have paused for thought and the course of science might have been changed.
  • Cobb NRG 7: 953.

At the heart of agricultural practice is the assumption that, as Thomas Blundeville, an author with an interest in horse breeding, mathematics and navigation, put it in 1566: "...it is naturally geven to every beast for the moste parte to engender hys lyke."17 However, as Blundeville indicated, this was not always the case, and until the seventeenth-century studies on generation, it was not even clear that it applied to all organisms. More surprisingly, until the second half of the eighteenth century, there does not seem to have been any explicit attempt to exploit this phenomenon; selective breeding, in terms of a conscious decision to manipulate the stock of a domesticated organism, was not widespread, nor was it transformed into a theory. Breeders' 'knowledge' that like bred like was partial and entirely heuristic: they were concerned with what worked, not why18.

  • At the heart of agricultural practice is the assumption that, as Thomas Blundeville, an author with an interest in horse breeding, mathematics and navigation, put it in 1566: "...it is naturally geven to every beast for the moste parte to engender hys lyke."17 However, as Blundeville indicated, this was not always the case, and until the seventeenth-century studies on generation, it was not even clear that it applied to all organisms. More surprisingly, until the second half of the eighteenth century, there does not seem to have been any explicit attempt to exploit this phenomenon; selective breeding, in terms of a conscious decision to manipulate the stock of a domesticated organism, was not widespread, nor was it transformed into a theory. Breeders' 'knowledge' that like bred like was partial and entirely heuristic: they were concerned with what worked, not why18.
  • The difficulty with the breeders' basic assumption that like breeds like was that it was not always true. As Nicholas Russell has pointed out, when seventeenth-century English horse breeders tried to import animals from Arabia, the horses generally failed to flourish and rarely reproduced all the qualities that had made them attractive in the first place. As a result of many such experiences, "...most authors believed that the virtue of horses from exotic locations was only transmissible over generations while they remained in these places."18 Far from seeing the characters of their animals as having an innate, constitutional basis that could pass from one generation to another, breeders — like Aristotle and other thinkers — accepted that local conditions had a decisive role in shaping characters.
  • From the seventeenth-century, breeders tended to use the term 'blood' to describe the quality that apparently lay behind the characters of an animal. But, as with a royal 'bloodline', this was a vague, semi-mystical view of the power of an imprecise quality, rather than a recognition of the hereditary transmission of characters. This confusion was translated into practice: eighteenth-century racehorse breeders would not cross two successful racehorses, creating a 'thoroughbred' stock, but would instead cross racing stallions with local mares18.
  • Secretariat – to fans of horse racing,
  • the analog of Ted Willams and
  • Michael Jordan

Word of the day: heuristic

  • “A method based on empirical information that has no explicit rationalization
  • “A computational method that uses trial and error methods to approximate a solution for computationally difficult problems”
  • “involving or serving as an aid to learning, discovery, or problem-solving by experimental and especially trial-and-error methods <heuristic techniques> heuristic assumption>; also : of or relating to exploratory problem-solving techniques that utilize self-educating techniques (as the evaluation of feedback) to improve performance heuristic computer program>”

“Grrrrr”

  • Buffon was interested in the problem of hybrids, but chose to work with quadrupeds. It turned out to be difficult to do a controlled cross. For instance, during an attempt to mate a wolf with a dog, the female wolf ate the dog she was supposed to mate to, and then mauled the coachman.
  • Georges-Louis LECLERC,
  • comte de BUFFON (1707-1788) One of the great naturalists of all time
  • Canis lupus
  • R. Olby Origins of Mendelism

Joseph Kölreuter (1761)

  • Plant hybridization: 500 different hybridizations involving 138 species.
  • “The experimental study of genetics may be said to date from the work which Koelreuter described it.
  • Studied both F1 and F2 plants in crosses.
  • “When Kolreuter compared them, he found a striking contrast. F1 hybrids for any given cross were alike, and in most of their characters were intermediate between the two parental species. F2 and back-crossed hybrids were all different, and they tended to be less like their parental hybrids and more like one or other of the originating species.”
  • R. Olby Origins of Mendelism

1761 - 1900

  • “The contrast between the two generations remained an enigma until 1900 when Mendel’s explanation was made generally known. Whereas Mendel explained the enigma on cytological and statistical grounds, Koelreuter explained it on bases which may be described as theological and alchemical. [He] looked upon the wonderful uniformity and exact intermediacy of F1 hybrids as evidences of Nature’s perfection. The same cross repeated no matter how many times gave the same result. What caused the breakdown in the second generation? Surely, he reasoned, it must be man. Nature never intended that species should be crossed and to prevent it she had placed closely related forms far apart. Then came man mixing up nature’s careful arrangement and cramming into the confines of his little garden species which formerly were separated by thousands of miles. … The strange motley of forms in the F2 generation was thus the direct result of tampering with nature.”
  • R. Olby Origins of Mendelism

Gregor Mendel

The garden in Brno

Mendel’s most famous words

  • Those who survey the work done in this department will arrive at the conviction that among all the numerous experiments made, not one has been carried out to such an extent and in such a way as to make it possible to determine the number of different forms under which the offspring of the hybrids appear, or to arrange these forms with certainty according to their separate generations, or definitely to ascertain their numerical relations to each other.
  • (note: thank you, Christian Doppler)
  • Wer die Arbeiten auf diesem Gebiete überblickt, wird zu der Ueberzeugung gelangen, dass unter den zahlreichen Versuchen keiner in dem Umfange und in der Weise durchgeführt ist, dass es möglich wäre, die Anzahl der verschiedenen Formen zu bestimmen, unter welchen die Nachkommen der Hybriden auftreten, dass man diese Formen mit Sicherheit in den einzelnen Generationen ordnen und die gegenseitigen numerischen Verhältnisse feststellen könnte.
  • http://www.mendelweb.org/CollText/homepage.html

Newton, Darwin, Mendel, Einstein

  • The simplicity, clarity, elegance, rigor, and power of Mendel’s experimental approach to the problem of heredity. (ii) The influence of his work on subsequent development of science.
  • What is Mendel proposing to do?
  • Let’s generate hybrids, and after having done so, determine, how many different types of children (progeny) appear in the crosses.
  • Let us do this analysis generation-by-generation, in other words, analyze the parents, their children, and their grandchildren SEPARATELY.
  • Let us DETERMINE THE RATIOS: if, in a given generation, there is more than one type of child, let us ask, what proportion of the whole each type is.

Scientific reductionism

  • Put together – intelligently – an experimental setup that “isolates” a particular component of a phenomenon for study. One attempts to “reduce” a problem to its simplest possible form.
  • All previous hybridists – including such titans as Carl Linnaeus, the first Homo sapiens, and Charles Darwin himself! – looked at the transmission through generations of all the traits for a given species, or multiple traits at once.

Why?

  • It requires indeed some courage to undertake a labor of such far–reaching extent; this appears, however, to be the only right way by which we can finally reach the solution of a question the importance of which cannot be overestimated in connection with the narrative of how living beings develop.
  • Es gehört allerdings einiger Muth dazu, sich einer so weit reichenden Arbeit zu unterziehen; indessen scheint es der einzig, richtige Weg zu sein, auf dem endlich die Lösung einer Frage erreicht werden kann, welche für die Entwicklungs-Geschichte der organischen Formen von nicht zu unterschätzender Bedeutung ist.
  • http://www.mendelweb.org/CollText/homepage.html

Gasp #1

  • One might ask – why did Mendel spend 8 corageous, lonely years in backbreaking, painstaking work, planting peas, dissecting their flowers, crosspolinating them, tracking their progeny, counting seeds, replanting those, etc etc?
  • The answer, in part, seems to be: he was convinced that he was studying not an obscure phenomenon in an irrelevant setting (seed color in peas). He thought he would discover a key mechanism that operates in all living things!

Words to live by

  • The value and utility of any experiment are determined by the fitness of the material to the purpose for which it is used, and thus in the case before us it cannot be immaterial what plants are subjected to experiment and in what manner such experiment is conducted.
  • Der Werth und die Geltung eines jeden Experimentes wird durch die Tauglichkeit der dazu benützten Hilfsmittel, sowie durch die zweckmässige Anwendung derselben bedingt. Auch in dem vorliegenden Falle kann es nicht gleichgiltig sein, welche Pflanzenarten als Träger der Versuche gewählt und in welcher Weise diese durchgeführt wurden.
  • http://www.mendelweb.org/CollText/homepage.html

A universally applicable statement

  • Will your experiment generate data that will be of any use?
  • Well, a key determining factor in that is whether you chose the right material to do the experiment with.
  • Is the object of your study optimally suited to answer the question you are interested in?

What plant to pick

  • “The selection of the plant group which shall serve for experiments of this kind must be made with all possible care if it be desired to avoid from the outset every risk of questionable results.
  • The experimental plants must necessarily:
  • Possess constant differentiating characteristics.
  • The hybrids of such plants must, during the flowering period, be protected from the influence of all foreign pollen, or be easily capable of such protection.”
  • http://www.mendelweb.org/CollText/homepage.html

Useful piece of experimental guidance for a geneticist

  • “Accidental impregnation by foreign pollen, if it occurred during the experiments and were not recognized, would lead to entirely erroneous conclusions.”
  • Experimental genetics – from Mendel’s days and to this day – heavily relies on crosses. It is critical, therefore, that the cross be a controlled one, i.e., that it occur between specific organisms as per the experimental plan.
  • The problem, of course, is most organisms on Earth mate naturally, and uncontrollably.

Nature, March 24, 2005: “Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis” S. Lolle, R. Pruitt.

  • Nature, March 24, 2005: “Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis” S. Lolle, R. Pruitt.
  • Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene HOTHEAD (HTH) can inherit allele-specific DNA sequence information that was not present in the chromosomal genome of their parents but was present in previous generations.
  • (in other words, hh plants, when crossed “to themselves,” yield a surprisingly high frequency of Hh plants,)
  • “This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined and therefore seems to be a general mechanism for extra-genomic inheritance of DNA sequence information. We postulate that these genetic restoration events are the result of a template-directed process that makes use of an ancestral RNA-sequence cache.”

hh plant and its non-Mendelian offspring

“Startling Scientists, Plant Fixes Its Flawed Gene” – NYT 3/23/06

  • In a startling discovery, geneticists at Purdue University say they have found plants that possess a corrected version of a defective gene inherited from both their parents, as if some handy backup copy with the right version had been made in the grandparents' generation or earlier.
  • The finding implies that some organisms may contain a cryptic backup copy of their genome that bypasses the usual mechanisms of heredity. If confirmed, it would represent an unprecedented exception to the laws of inheritance discovered by Gregor Mendel in the 19th century. Equally surprising, the cryptic genome appears not to be made of DNA, the standard hereditary material.

Nature. 2006 Sep 28;443(7110):E8;

  • Nature. 2006 Sep 28;443(7110):E8;
  • Plant genetics: increased outcrossing in hothead mutants. Peng P, Chan SW, Shah GA, Jacobsen SE.
  • Lolle et al. report that loss-of-function alleles of the HOTHEAD (HTH) gene in Arabidopsis thaliana are genetically unstable, giving rise to wild-type revertants. On the basis of the reversion of many other genetic markers in hth plants, they suggested a model in which a cache of extragenomic information could cause genes to revert to the genotype of previous generations. In our attempts to reproduce this phenomenon, we discovered that hth mutants show a marked tendency to outcross (unlike wild-type A. thaliana, which is almost exclusively self-fertilizing). Moreover, when hth plants are grown in isolation, their genetic inheritance is completely stable. These results may provide an alternative explanation for the genome wide non-mendelian inheritance reported by Lolle et al.

The cross (a “self”)_:

  • The cross (a “self”)_:
  • hh gg x hh gg
  • Find 10 plants that are phenotypically G (i.e., “reverted” to wild-type).
  • Genotype those.
  • Observe that they are Gg (one allele “reverted”).
  • As a control, analyze the Hothead locus in those Gg plants.
  • Remarkably, find that ALL of them are also Hh.
  • Pull out Occam’s razor.

I’m sorry, whose razor?

  • Occam's razor (also spelled Ockham's razor) is a principle attributed to the 14th-century English logician and Franciscan friar William of Ockham. (A heuristic maxim that advises economy, parsimony, or simplicity in scientific theories. Occam's razor states that the explanation of any phenomenon should make as few assumptions as possible, eliminating, or "shaving off", those that make no difference in the observable predictions of the explanatory hypothesis or theory. In short, when given two equally valid explanations for a phenomenon, one should embrace the less complicated formulation. The principle is often expressed in Latin as the lex parsimoniae (law of succinctness): “entia non sunt multiplicanda praeter necessitatem.” (which translates to: entities should not be multiplied beyond necessity.)
  • This is often paraphrased as "All things being equal, the simplest solution tends to be the best one." In other words, when multiple competing theories are equal in other respects, the principle recommends selecting the theory that introduces the fewest assumptions and postulates the fewest hypothetical entities.

Why the pea?

  • “At the very outset special attention was devoted to the Leguminosae on account of their peculiar floral structure. Experiments which were made with several members of this family led to the result that the genus Pisum was found to possess the necessary qualifications.
  • Some thoroughly distinct forms of this genus possess characters which are constant, and easily and certainly recognizable, and when their hybrids are mutually crossed they yield perfectly fertile progeny.
  • Furthermore, a disturbance through foreign pollen cannot easily occur, since the fertilizing organs are closely packed inside the keel and the anthers burst within the bud, so that the stigma becomes covered with pollen even before the flower opens. This circumstance is especially important. As additional advantages worth mentioning, there may be cited the easy culture of these plants in the open ground and in pots, and also their relatively short period of growth. Artificial fertilization is certainly a somewhat elaborate process, but nearly always succeeds. For this purpose the bud is opened before it is perfectly developed, the keel is removed, and each stamen carefully extracted by means of forceps, after which the stigma can at once be dusted over with the foreign pollen.”
  • http://www.mendelweb.org/CollText/homepage.html

The garden pea (Pisum sativum) – a powerful “model system” for genetic experimentation

  • Can cross two organisms of defined phenotypes.
  • Cross an organism “to itself” (“a self-cross”) – “selfing.”
  • “Invert the direction of the cross” (take male gametes from a plant carrying trait A, and fertilize an ovum from a plant carrying trait A’ – and then do the inverse, i.e., male A’ crossed to female A).

The starting material

  • “In all, 34 more or less distinct varieties of Peas were obtained from several seedsmen and subjected to a two year's trial. All the … varieties yielded perfectly constant and similar offspring; at any rate, no essential difference was observed during two trial years. For fertilization 22 of these were selected and cultivated during the whole period of the experiments. They remained constant without any exception.”
  • http://www.mendelweb.org/CollText/homepage.html

“Pure-breeding line”

  • An awkward phrase that is best retired, but never will be.
  • It refers to an organism that exhibits a particular trait (e.g., seed color), and all progeny of that organism (whether it is selfed, or outcrossed to another such organism) also exhibit that trait.
  • Pure-breeding lines are best made by selfing, or brother-sister crosses (like Nefertiti).

The power of consanguineous marriages (+homework)

William Ernest Castle – founder of mouse genetics (UCB 1936-1962)

  • Inbreeding as a tool for making genetically uniform strains of mice that are homozygous for every allele in the genome.
  • Brother-sister matings – makes 12.5% of all loci in the genome homozygous (Clarence Little).
  • Why?
  • After 40 generations of brother-sister mating, >99.98% of genome is homozygous. By F60, mice are considered genetically identical to one another.

Back to Mendel: what traits to pick?

  • “Experiments which in previous years were made with ornamental plants have already affording evidence that the hybrids, as a rule, are not exactly intermediate between the parental species. With some of the more striking characters, those, for instance, which relate to the form and size of the leaves, the pubescence of the several parts, etc., the intermediate, indeed, is nearly always to be seen; in other cases, however, one of the two parental characters is so preponderant that it is difficult, or quite impossible, to detect the other in the hybrid.”
  • http://www.mendelweb.org/CollText/homepage.html

The reaffirmation of a known phenomenon

  • Mendel is pointing out the distinction between two “types” of traits.
  • The hybrid plant is “intermediate” in phenotype between two parents. For instance, the offspring of a tall and a short plant would be intermediate in height.
  • The hybrid plant has the phenotype like one of the parents. For instance a green x yellow cross yields only yellow-seeded plants.
  • Mendel chose to study “type 2 traits” – a judicious decision. We now know that the laws he discovered in doing so also apply to “type 1” traits, but that fact is considerably more difficult to observe.

The genesis of the famous term

  • “This is precisely the case with the Pea hybrids. In the case of each of the 7 crosses the hybrid-character resembles that of one of the parental forms so closely that the other either escapes observation completely or cannot be detected with certainty. This circumstance is of great importance in the determination and classification of the forms under which the offspring of the hybrids appear. Henceforth in this paper those characters which are transmitted entire, or almost unchanged in the hybridization, and therefore in themselves constitute the characters of the hybrid, are termed the dominant, and those which become latent in the process recessive. The expression "recessive" has been chosen because the characters thereby designated withdraw or entirely disappear in the hybrids, but nevertheless reappear unchanged in their progeny, as will be demonstrated later on.”
  • http://www.mendelweb.org/CollText/homepage.html


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