Saturday, July 07, 2007

CIEL colloquium on the Divine Office, 2006

CIEL speakers say Divine Office is another victim of liturgical revolution

Brian Mershon
October 3, 2006

From the October 5 issue of The Wanderer.

Oxford, UK — The prayers of the Church that every priest prays daily, the Divine Office, have been stripped of much of their theological content and ruined, according to several academics speaking at the CIEL 2006, the 11th International Colloquium of historical, canonical, and theological studies on the Roman Catholic liturgy. The colloquium was held at Merton College, Oxford, September 13-16.

Previous attendees and speakers have included the late Michael Davies, teacher, writer, and former president of International Federation of Una Voce (FIUV), Joseph Cardinal Ratzinger, and Dario Cardinal Castrillon Hoyos.

This key finding, little known to many Catholics, but mentioned repeatedly by the presenters, was but one of the academic highlights of this conference with more than 160 delegate attendees, of which 29 were priests, with nine religious, two deacons, and two Anglican clergyman. Ten countries outside of the UK were represented, with 24 participants from the United States.

Priests from the Priestly Fraternity of St. Peter, Canons Regular of the New Jerusalem, the Institute of Christ the King Sovereign Priest, the Sovereign Military Order of Malta, Society of St. John Cantius Canons, Ignatian Social Justice, as well as diocesan priests and monsignors, were among the attendees.

Dr. László Dobszay teaches at Hungarian Academy of Sciences in Budapest, Hungary. During his paper presentation "Music Proper to the Roman Liturgy," he gave his assessment of the Divine Liturgy. He is also the author of The Bugnini Liturgy and the Reform of the Reform.

"No one speaks of the ruination of the Divine Office," he said. "The Church knows that one of the keys to understanding Sacred Scripture is by reading the psalms every day. The psalms reflect on the orations [in the liturgy] and vice-versa; they are linked."

The Rev. Dr. Michael Lang is the author of Turning Towards the Lord, published by Ignatius Press. He resides at the London Oratory of St. Philip Neri, and he was ordained a priest in 2004.

Fr. Lang moderated many of the academic talks, and he echoed the results of Dr. Dobszay's research: "The destruction of the Roman breviary began with [the reforms] of Pope St. Pius X," he said. "It is no longer the Roman breviary."

Archbishop Ranjith, the secretary of the Congregation for Divine Worship and the Discipline of the Sacraments, gave a presentation April 27, 2006 in Rome as an introductory presentation to Fr. Lang's "important study" Turning Towards the Lord. At this presentation, Archbishop Ranjith said, "In fact, in the foreword to this book, His Holiness Pope Benedict XVI...affirms that 'to the ordinary churchgoer, the two most obvious effects of the liturgical reform of the Second Vatican Council seem to be the disappearance of Latin and the turning of the altars towards the people. Those who read the relevant texts will be astonished to learn that neither is in fact found in the decrees of the council'."

And in an impassioned, illuminating conclusion to the 12 academic papers delivered over the three and one-half day colloquium at Merton College, the Rev. Dr. Laurence Hemming of Heythrop College in London, said, "The breviary of 1911 is a truncated version" of the Roman breviary.

"Even the 1568 breviary was a truncation," indicating that significant modifications to the daily prayer book of the Church have been made over the past 400 years, of questionable spiritual value.

The Rev. Dr. Alcuin Reid, London, spoke on "Sacrosanctum Concilium and the Organic Development of the Liturgy." Dr. Reid is most known in academic circles in the Church as the author of The Organic Development of the Liturgy, published by St. Michael's Abbey Press.

The then-Cardinal Ratzinger wrote a long and glowing review of this book. In it, he said: "At the end of his book, the author enumerates some principles for proper reform: This should keep being open to development, and continuity with the Tradition, in a proper balance; it includes awareness of an objective liturgical tradition, and therefore takes care to ensure a substantial continuity."

Cardinal Ratzinger continued, "The author then agrees with the Catechism of the Catholic Church in emphasizing that 'even the supreme authority in the Church may not change the Liturgy arbitrarily, but only in the obedience of faith and with religious respect for the mystery of the Liturgy' (CCC, n. 1125)."

For instance, Dr. Reid said that a "juridical positivism" by Pope Paul VI gave us new eucharistic prayers. "The liturgical positivism concept was very important to the reformers," he said. He also explained how one of the council fathers in an interview said, "The liturgy is not to become a cut-and-paste plaything of pastors, liturgists, and other experts."

These three new eucharistic prayers drafted by the liturgical commission and approved by Pope Paul VI have since multiplied to at least 13 approved by the Holy See, at last count.

"Cuckoo eggs were placed in the middle of the Roman liturgy," he said. "Let me make it clear: they are valid, but that is not enough." Dr. Reid said.

The Rev. Dr. Hemming of Heythrop College in London, during his paper "Theological Perspectives on the Traditional Liturgy," affirmed this balanced understanding of the liturgy.

"How it is done matters! Every single action and word [of the priest] really matters!"

This blind obedience and understanding of the Holy Father as having supreme fiat over everything helped create this chaos as much as anything. Indeed, Fr. Lang repeated our current Pope's own words in a talk he gave prior to taking possession of St. John Lateran after his election. He quoted Pope Benedict XVI as saying, "The Pope is the humble servant of Tradition and nothing more."

In other words, theological, philosophical, and juridical positivism, especially when it comes to the sacred liturgy, is outside the scope of his jurisdiction. His vocation is to "hand on" what he has been given.

Caution Against Unjust Labels

In Dr. Reid's paper, he also cautioned Catholics against stereotyping and making unfair accusations about those attached to the Latin liturgical traditions.

"Traditionalists are often portrayed as unfaithful," Dr. Reid said. "It is time to abandon these uncritical assessments of such Catholics."

He did, however, set the boundaries of two perspectives he called untenable to faithful Catholics. "One is to claim that no further development from the 1962 missal or calendar is possible."

However, Dr. Reid did state that it was his personal opinion that the vast liturgical calendar changes such as the suppression of Septuagesima, ember days, and many other such innovations cannot be substantiated by the texts of Sacrosanctum Concilium, nor from the intentions of the council fathers.

While the uncountable and drastic changes to the liturgy from 1970 to the present are indeed a rupture with true organic development, many Catholics attached to the classical Roman rite (Traditional Latin rite) do not realize that Pope Pius XII and many of his Predecessors made selective, but noticeable, changes to the liturgy during their pontificates, Reid said.

For instance, the entire Holy Week underwent substantial reform during the pontificate of Pope Pius XII. While the Missal of 1962 and that of Pope St. Pius V remain, in essence, the same, there were still changes made.

"Two, to claim to accept Pope Paul VI's reforms uncritically" is also untenable to faithful Catholics. In other words, those Catholics who uncritically accept the entirety of reforms from Pope Paul VI and thereafter and call into question Catholics who are more critical, is not a reasonable and tenable position, according to Dr. Reid.

He went on to address a question of how and when he personally thought any future reforms of the 1962 missal would or should occur by stating that potential "developments" of the 1962 calendar are currently a severe pastoral concern.

"Lots of people are bruised, but I think it [the 1962 missal] needs to be left alone for a while. We certainly don't want to scandalize some people even more nor disrupt possible reconciliation with others," he said.

"The Roman rite has suffered severe damage and its urgent repair is required."

Keys To The Texts

Dr. Reid outlined what he considers to be the proper hermeneutics of interpreting Sacrosanctum Concilium, the Constitution on the Sacred Liturgy — the hermeneutical "keys" or lens from which we should adjust the resulting liturgical reform.

He noted that the first chapter's "General Principles" approved by the council fathers was the first starting point. From here, we go to paragraph numbers 14 through 19, especially the often misinterpreted, "Mother Church earnestly desires that all the faithful should be led to that fully conscious, and active participation in liturgical celebrations which is demanded by the very nature of the Liturgy."

Dr. Reid rightly points out that actuoso participatio, the Latin original, might be better translated as "actual participation" due to the fact that modern man views the word "active" to mean gestures, singing, or responding only, and often omits, silence, meditation, and contemplation, which, of course, are integral to Christian prayer, and are indeed "actual participation."

In fact, others who have dealt with this key terminology and its deeper spiritual and theological understanding say that "actual contemplative participation" in the sacred liturgy is perhaps an even higher spiritual goal than merely going through rote gestures without any idea or concept of the fundamental meaning behind them.

And Dr. Reid also explained the importance of paragraphs 15 through 19, which speak of the necessity for a renewed liturgical formation for all, especially the clergy. Without a true and thorough historical, theological, and philosophical education and formation of the clergy based upon sound liturgical theology, any true renewal is far in the future.

Dr. Hemming delved deeply into this education and formation of the clergy in his talk on the theological perspectives of the liturgy. Sacrosanctum Concilium, n. 16, reads, "The study of Sacred Liturgy is to be ranked among the compulsory and major courses in seminaries and religious houses of studies; in theological faculties it is to rank among the principal courses. It is to be taught under its theological, historical, spiritual, pastoral, and juridical aspects."

In other words, since "The Eucharist is the 'source and summit of the Christian life'" (CCC, n. 1342) and "As does the whole of the Christian life, the moral life finds its source and summit in the Eucharistic Sacrifice" (CCC, n. 2031), all theological and pastoral disciplines should be ordered to, by, and from a proper liturgical theological foundation.

"You cannot have the liturgy as the linchpin of the Church, and then say that a deformed liturgical reform had no effect," Dr. Hemming said.

Sacrosanctum Concilium emphasizes this point again within paragraph n. 16. "Moreover, other professors, while striving to expound the mystery of Christ and the history of salvation from the angle proper to each of their own subjects, must nevertheless do so in a way which will clearly bring out the connection between their subjects and the liturgy, as also the unity which underlies all priestly training. This consideration is especially important for professors of dogmatic, spiritual, and pastoral theology and for those of Holy Scripture."

Liturgical Theology Is Foundation

Dr. Hemming said, "Liturgical theology means theology from which every other theological study takes its life and meaning; theology has no other home without its foundation in the sacred liturgy." Many Benedictines especially, and other monastics have known and taught this for years, and Dr. Hemming highlighted during his talk, "Sacred Scripture's true and proper place is within the home of the sacred liturgy."

Dr. Hemming referenced Fr. Aidan Nichols' book, Looking at the Liturgy: A Critical Look at its Contemporary Form (Ignatius Press, 1996) where the theologian sees an overemphasis on the reformers rationalizing the liturgy in an attempt to make it more understandable or more comprehensible, especially to modern man. Dr. Hemming identifies the primary philosophical flaw of this perhaps excessive rationalism of the sacred mysteries.

"This caused confusion," he said. "The confusion that arose was as to who was supposed to be the center of the liturgical reform — man or God?"

People will often complain about not being able to understand what is happening at Mass, Hemming said, which confirms the experience of many Catholics who attend both the modern and classical Roman rite. To some, it appears to be incomprehensible, he said.

"But we must remember that incomprehension is part of divine worship. The liturgy is the unfolding of intelligibility of what faith is made known by God."

In other words, it is a mystery. That is why they are called "the sacred mysteries." "Mysterium" is a Greek word equivalent to the Latin word sacramentum. By definition, a mystery, in theological terms, is something of which we can ponder and explore the depths, but can never completely comprehend nor fathom.

"In other words, this subject, the rationality and the mystery of the liturgy, has become the center of the question of the liturgy," Hemming said.

"God is the center of worship."

"More Inclusive"

Dr. Sheridan Gilley from Durham University presented a paper on "Roman Liturgy and Popular Piety." Dr. Gilley emphasized that prior to the liturgical revolution, the priest was obliged to celebrate Mass in a certain way, but the faithful were free to participate in the Mass in any way they liked; whereas nowadays the priest is free to choose how he wishes to celebrate, but the faithful are forced to participate in a very particular way.

"The old rite made for a more inclusive Church." According to Dr. Gilley, prior to the 1970 liturgical reforms, there was a book published called 30 Ways to Hear Mass, and there was only one way for the priest to say Mass. Now, there are a myriad number of ways for the priest to say Mass, but the lay faithful are all coerced into one way of hearing it.

Dr. Sheridan's research showed that the popular piety of Catholics, particularly in Ireland in the 1800s, included rosaries, pilgrimages, sodalities, exposition and benediction of the Blessed Sacrament, jubilees, triduums, shrines, and retreats, often with organized spiritual direction given by their priests.

Catholicism was in the very fabric of their being, and this use of sacraments and devotions sprang from their rich liturgical life.

This parish-based sacramental system carried the faith and the liturgy into their daily lives. It was part of their very culture.

Fr. Joseph Santos of Holy Name of Jesus Parish in Providence, R.I., gave a paper on the history of the Rite of Braga (Portugal), which showed one example of the multiple variations of the Roman rite that have flourished in the Church for centuries. The rite of Braga is almost 1,400 years old in its current state and it is almost exactly the same.

Pristas' Work Read By Curia

Dr. Lauren Pristas, Caldwell College, New Jersey, presented a paper entitled "The Development of the Roman Calendar." Fr. Lang introduced Pristas and said that a senior curial official called her work "a bombshell."

She is the author of The Collects of the Roman Missal: A Study of the Liturgical Reform. Her work has been published in Communio and other academic publications, and she systematically compares the changes in the wording and theology of the orations of the missal of 1970 with those of the 1962 missal from an academic historical perspective.

In her talk at the CIEL Colloquium, she explained the early history of the development of the liturgical calendar. She said research shows the development of the liturgical calendar began very early, before AD 325, and that the celebration of Christmas appears around AD 354.

"There is no such thing as history nor future for God or from the divine perspective," Pristas said. "Eternity is the ever-present now from a divine perspective."

Therefore, for human beings who are incarnate living in a material world, the cycle of the liturgical years assists us in living life more closely in union with God and His angels and His saints than mere daily living according to secular calendars, Dr. Pristas said.

"The liturgical year works through the participation in the sacred mystery itself, not principally through imitation, prayer, and meditation," Pristas said. "Even the non-baptized can imitate and meditate.

"These [methods of prayer] are helpful, but they are not the principal ways of appropriating Christ's mysteries." By living the liturgical calendar and participating as often as possible in the divine mysteries, we become more attuned to God and His will and plan for our lives and for the world.

"The spiritual participation in the mystery of salvation comes through the living out of the feast itself, not principally through imitation, meditation, nor even contemplation," Dr. Pristas said. We must live and appropriate the liturgical calendar. Spiritual reading and prayer and silence and devotions are helpful, but all must be tied back to the Church's liturgical year, in which we can most fully partake of the sacred mysteries.

Latin In The Liturgy

The Rev. Dr. Lang presented a paper entitled, "The Early Development of Christian Latin as a Liturgical Language." He traced the development of the use of Greek to Latin as the primary language in the early Church, and despite the popular historical revisionism within much of the U.S. Church, Fr. Lang said that vulgar Latin was never used in the liturgy. He said it was a much higher prose like British liturgical language found in the Anglican Book of Common Prayer, for instance.

"Stylized Christian Latin was used, but not the vulgar tongue," Fr. Lang said. He also informed us that research points to the fact that the baptismal formula was solidified in Latin in the second century.

As examples of a richer prose being used, he said that even for the Homeric epics The Iliad and The Odyssey, a specific type of language was used for these stories when told orally. It was not the language of everyday use, he said.

Today, the words "Hosanna," "Alleluia," and "Amen" are preserved in their original language in order to maintain their solemn character, Fr. Lang said. They are more expressions of sentiments and exclamations than they are denotative in nature.

Fr. Lang said, that by using biblical terminology, in the very early Church, there was a controlled freedom in the content and style of the early anaphoras, or eucharistic prayers, within the bounds of orthodoxy, of course. However, as the rite developed and the Church spread, the formulation of the anaphoras and other prayers gradually became more fixed.

From AD 360 to 380, the transition from the use of Greek to Latin was almost complete, Fr. Lang said, primarily for the eucharistic prayer. The Kyrie, of course, was maintained in Greek.

After Constantine allowed freedom to Christianity, Christian feasts replaced pagan festivals, thereby becoming holy days or holidays, Fr. Lang concluded.

Brian Mershon is a commentator on cultural issues from a classical Catholic perspective. His trade is in media relations, and his vocation is as a husband to his beloved wife Tracey and father to his six living children. He attempts to assist his family and himself in attaining eternal salvation through frequent attendance at the Traditional Latin rite of Mass, homeschooling, and building Catholic culture in the buckle of the Bible Belt of Greenville, South Carolina.

Friday, July 06, 2007

Genome transplant in bacteria

ScienceDaily: Scientists transplant DNA in bacteria
Creation of artificial life brought a step closer by DNA ...
Scientists Swap Genes in Bacteria -

June 29, 2007
Scientists Transplant Genome of Bacteria
Correction Appended

Scientists at the institute directed by J. Craig Venter, a pioneer in sequencing the human genome, are reporting that they have successfully transplanted the genome of one species of bacteria into another, an achievement they see as a major step toward creating synthetic forms of life.

Other scientists who did not participate in the research praised the achievement, published yesterday on the Web site of the journal Science. But some expressed skepticism that it was as significant as Dr. Venter said.

His goal is to make cells that might take carbon dioxide out of the atmosphere and produce methane, used as a feedstock for other fuels. Such an achievement might reduce dependency on fossil fuels and strike a blow at global warming.

“We look forward to having the first fuels from synthetic biology certainly within the decade and possibly in half that time,” he said.

Richard Ebright, a molecular biologist at Rutgers University, said the transplantation technique, which leads to the transferred genome’s taking over the host cell, was “a landmark accomplishment.”

“It represents the complete reprogramming of an organism using only a chemical entity,” Dr. Ebright said.

Leroy Hood, a pioneer of the closely related field of systems biology, said Dr. Venter’s report was “a really marvelous kind of technical feat” but just one of a long series of steps required before synthetic chromosomes could be put to use in living cells.

“It’s a really worthy accomplishment, but I hope it doesn’t get hyped to be more than it is,” Dr. Hood said.

One reason for Dr. Venter’s optimism is that he says his institute is close to synthesizing from simple chemicals an entire genome, 580,000 DNA units in length, of a small bacterium, Mycoplasma genitalium. If that genome can be made to take over a bacterium using the method announced today, Dr. Venter should be able to claim that he has made the first synthetic life form. The bacterium would be identical to nature’s version, but would demonstrate how precise control could be achieved over every aspect of the machinery of living cells.

Biologists have long been able to move useful genes into bacteria and other organisms in a process called genetic engineering. The idea of synthetic biology is to carry out genetic engineering in a more extensive and systematic way.

Synthetic biologists, who held their third annual meeting in Zurich, Switzerland, this week, hope to create biochemical processes and then choose the gene sequences that will direct these processes and build the DNA from scratch. The scientists’ goal is to select and reorder the genetic machinery developed by evolution just as an engineer might assemble an efficient circuit board from existing components.

Dr. Venter hopes to lay the basis for a new approach to synthetic biology by first synthesizing whole genomes in the laboratory and then making them take control of, or “boot up,” a living cell. His new report accomplishes the second of the two steps, at least in Mycoplasma. His team, which includes a distinguished biologist, Hamilton Smith, purified the full DNA from one kind of Mycoplasma and showed that it could take control of another, making the host cell switch over to producing proteins specified by the inserted DNA. Dr. Smith said he was not sure whether the inserted genome destroyed the host genome or just made the cell divide, assigning the two genomes to different daughter cells.

Booting up cells with new genomes is a major limitation in synthetic biology, Dr. Venter said. With that hurdle now crossed, it will be possible to “design cells in future to manufacture new types of fuel and break our dependency on oil and do something about carbon dioxide going into the atmosphere.”

Dr. Hood, co-founder of the Institute for Systems Biology in Seattle, said the next step on Dr. Venter’s agenda, putting a functional synthetic genome into an organism, would be more significant.

“Synthesizing a whole chromosome and getting it to function will be a really remarkable step that will be much closer to the golden vision of creating new organisms,” he said.

George Church, a leading systems biologist at the Massachusetts Institute of Technology, said that the new report was “good science” but that it had been achieved in an organism, Mycoplasma, that is unsuitable for industrial uses. As for Dr. Venter’s assertion that his result is “an enabling technique,” Dr. Church said, “The door to synthetic biology is already wide open, and people are pouring through it.”

Dr. Church agreed with Dr. Venter’s forecast that synthetic biologists could produce fuels within 10 years. He noted that LS9 Inc. in San Carlos, Calif., was producing laboratory amounts of petroleumlike fuels in bacteria.

Dr. Venter is more colorful and less publicity shy than most academic biologists. But he has many solid achievements to his credit. They have so far been in sequencing, or decoding, genomes.

He pioneered methods for sequencing the first bacterium, Haemophilus influenzae, and raced the government to a draw in sequencing a draft version of the human genome in June 2000. Though unable to produce a complete version because he was forced out of Celera, the company he headed, Dr. Venter devised a better method than his government-supported rivals, one that has become the standard way to sequence genomes.

Dr. Venter has always sought academic credit by publishing his results in scientific journals and now directs a nonprofit research laboratory in Rockville, Md., the J. Craig Venter Institute. But he has another foot firmly planted in the commercial world. He has set up, and the Venter Institute largely owns, Synthetic Genomics, whose goal is to make alternative fuels to oil and coal. He has also applied for far-reaching patents on the uses of synthetic life forms.

The report today may be less significant if his research team is unable to repeat the success in more useful organisms than the Mycoplasma bacterium. Dr. Church said a quite similar experiment with Escherichia coli, a standard laboratory organism, was accomplished in 1958 by two French scientists, François Jacob and E. L. Wollman.

Dr. Venter’s next goal, creating the first synthetic bacterium, could have broader interest. At the Zurich meeting this week, his colleague Dr. Smith reported progress in synthesizing a Mycoplasma genome from scratch saying, according to a Nature blog, that he had already constructed it in the form of 101 long DNA fragments. When stuck together, they would comprise the whole genome.

Dr. Venter said Dr. Smith had traveled at least that far.

“We are weeks to months away from booting up that chromosome,” Dr. Venter said.

The longest piece of DNA synthesized so far, he explained, is 35,000 units long, whereas the Mycoplasma genome or chromosome is 580,000 units.

The synthetic Mycoplasma, if the Venter team is successful, would be identical to the natural kind and should present no conceivable hazard. But synthetic biology is a technique with potentially far-reaching consequences like environmental effects and misappropriation by terrorists. In addition, the ability to synthesize living organisms may provoke philosophical comment.

Scientists have taken the initiative in assessing the effects with the hope of staying far enough ahead of events to avoid regulation. A report on the possible dangers of synthetic biology is being prepared for the Sloan Foundation by scientists at M.I.T., the Venter Institute and the Center for Strategic and International Studies.

Dr. Venter said that he was filing for many more patents and that his team was trying to scale up methods of synthesizing DNA and “watermarking chromosomes in fun ways to make it unequivocal they are manmade.” He said he had no plans to use Mycoplasma as a production organism and was developing other bacteria.

“This is an area where things will happen at an exponential pace,” he said. “Once people know you can do chromosomal transplants, that will trigger new approaches.”

Others may already have raced ahead using old-fashion genetic engineering to put new genes into standard microbes. Steve delCardayre, vice president for research at LS9, said it had developed a strain of standard industrial microorganism that produced hydrocarbons from treated agricultural waste.

The present strain, which Dr. delCardayre called adolescent, is “very close to meeting an economic threshold” and will be tested in a pilot plant early next year. The youthful microbe already produces an ethanol-like product, at 65 percent of the cost of corn-derived ethanol, Dr. delCardayre said. LS9 fuels, he added, will meet the same diverse needs as petroleum does, can be transported in existing pipelines and be used in existing vehicles.

Correction: June 30, 2007

A picture caption yesterday with a front-page article about a scientific advance in the effort to create synthetic life forms misidentified the scientist pictured. He is J. Craig Venter, who directs the institute that made the breakthrough, not Hamilton Smith, a biologist who worked on the project. The article also misstated the educational affiliation of George Church, a biologist who commented on the research. He is at Harvard Medical School, not M.I.T.

New Method For Reading DNA Sheds Light On How Cells Define Themselves

New Method For Reading DNA Sheds Light On How Cells Define Themselves

Science Daily — As a fertilized egg develops into a full grown adult, mammalian cells make many crucial decisions -- closing doors of opportunity as they adopt careers as liver cells, skin cells, or neurons. One of the most fundamental mysteries in biomedicine is how cells make such different career decisions despite having exactly the same DNA. By using a new kind of genomic technology, a new study unveils a special code -- not within DNA, but within the so-called "chromatin" proteins surrounding it -- that could unlock these mysterious choices underlying cell identity.

A research team led by scientists at the Broad Institute of Harvard and MIT and the Massachusetts General Hospital has created genome-wide chromatin maps for embryonic stem (ES) cells and two cell types derived from them, by applying a powerful new technology for sequencing DNA. The work, published in the July 1st advance online edition of Nature, provides a framework for mapping the complete chromatin landscape of almost any kind of cell. One of the most surprising findings suggests that cells contain an explicit chromatin-based code that reveals the developmental choices they have already made as well as those decisions that lie ahead.

"Unraveling the mysteries of chromatin holds great promise for understanding how cells in the body -- with nearly identical DNA -- assume such different forms and functions," said co-senior author Bradley Bernstein, an associate member at the Broad Institute and an assistant professor at Massachusetts General Hospital and Harvard Medical School. "By applying a new technology for sequencing DNA, we have been able to look across the genome at chromatin, with greater resolution and efficiency than ever before."

Chromatin proteins are more than just packing material for the genome. By virtue of different chemical groups fastened to them, these proteins influence which parts of the double helix are open -- or not -- to the cellular machinery, thus controlling which genes get turned on or off.

To decipher this "epigenetic" code requires ways of determining precisely which chromatin proteins sit at which locations along a cell's DNA. In principle, scientists could infer the locations by using specialized DNA chips. In practice, though, the technique has proven slow and expensive to construct genome-wide maps of mammalian chromatin. But now, a new method of massively parallel DNA sequencing has given rise to a powerful approach for readily churning out whole-genome maps of chromatin structure. The technology -- based on single-molecule sequencing -- makes it possible to read billions of DNA letters simultaneously. "Single molecule-based methods for decoding DNA are now throwing open the doors to a plethora of unexplored questions in chromatin, epigenetics and many other areas of biology," said Bernstein.

Empowered by this new technology, the researchers set out to study chromatin in cells with drastically different behaviors. They analyzed an assortment of chromatin proteins, each with a distinct chemical tag that switches genes either on or off. The scientists examined these proteins in mouse ES cells -- known for their unusual ability to form nearly any tissue -- as well as two other types of descendant cells that are more limited in the developmental paths they can choose.

One of the most remarkable findings involves a way of using chromatin to look into a cell's past to determine the developmental decisions it has already made, and to peer into the future to read its potential choices. The fortuneteller lies in a unique form of modified chromatin known as a "bivalent domain", which marks the control regions of important genes. Such domains merge both activating and repressive chemical tags, keeping genes quiet yet poised for later activity.

Bivalent domains had been noted for their role in ES cells, helping keep these cells' developmental options wide open. But with the new genome-wide chromatin data, the scientists discovered that these domains also function in more specialized kinds of stem cells. In neural stem cells, for example, bivalent domains sit near genes important to various types of brain cells, but are notably absent from genes that would be active only in, say, skin cells or blood cells.

"Looking at a cell through a microscope often cannot tell you what kind of cell it is, or more importantly, what it has the potential to become," said first author Tarjei Mikkelsen, a Broad Institute researcher and a Harvard-MIT Health Sciences and Technology graduate student. "But by decoding its chromatin on a genomic scale, we can now begin to systematically address such questions."

"Our understanding of the basis of cell identity -- the way that a liver cell knows that it is different from a skin cell -- has been rather vague, much like our understanding of heredity was prior to our knowledge of DNA," said Broad Institute director Eric Lander, a co-senior author of the study. "The chromatin maps suggest that it may be possible to directly read out a complete description of all of a cell's past commitments and its future potential. If true, this would have enormous implications for our understanding of developmental biology and for guiding regenerative medicine."

In addition to shedding light on key developmental decisions, chromatin maps also contain other sorts of new biological information. One type of chromatin modification marks not the control regions of genes, but their "bodies" -- from where genes first begin to where they end. The scientists found that these "body" marks identify not only typical genes -- that is, the ones that encode proteins -- but also so-called "non-coding" genes that only produce RNAs. These marks could provide a practical handle for precisely mapping all of the genes in the genome, a task that has proven quite challenging by other methods.

Reference: Mikkelsen et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature; DOI:10.1038/nature06008

Note: This story has been adapted from a news release issued by Broad Institute of MIT and Harvard.

Tuesday, July 03, 2007

Fr. Seraphim Rose, Nihilism

Nihilism by Fr. Seraphim Rose

I'll have to read it; I don't know the quality of it. He is respected by many American Orthodox as a mystic; in the past I have found some of his writings dealing with "intellectual history" to be overreaching...

Franz Michel William

The latest from Sandro Magister: Franz Michel Willam, the Theologian the Pope Has Rescued from Oblivion