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Monthly Archives: May 2022
Gemara: The Essence of the Talmud | My Jewish Learning
Posted: May 11, 2022 at 11:26 am
The teachings transmitted by the rabbis in the centuries following the destruction of the Second Temple formed the core of what has come to be known as rabbinic Judaism, which still provides the framework for the various types of Judaism practiced today. The most widely studied of these rabbinic teachings are known collectively as the Talmud, which has two parts: Mishnah and Gemara.
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The Mishnah is the earlier work, compiled from the teachings of sages living at the end of the Second Temple period and in the century following the destruction of the Temple.
A study book of laws and value statements that express the classical rabbis vision of Judaism, the Mishnahs preoccupation is promotion of a religious and legal tradition both continuous with the past and practical for life in the post-destruction Diaspora. The Mishnah contains multiple opinions on many laws and does not often suggest which is the most authoritative. The plurality of Jewish practice is preserved in the text.
Sages in both Babylonia (modern-day Iraq) and the Land of Israel continued to study traditional teachings, including the Mishnah, describing the teachings as having been passed down from Moses at Sinai (either literally or figuratively). The oral discussions were preserved, either by memorization or notation, and later edited together in a manner that places generations of sages in conversation with one another. These teachers were interested in bringing greater harmonization between biblical and rabbinic traditions, largely by providing proof-texts for known laws and explaining differences between the biblical and rabbinic versions of laws. This is the origin of the Gemara.
There are actually two works known as Gemara the Babylonian Gemara (referred to as Bavli in Hebrew) and the Palestinian (or Jerusalem) Gemara (referred to as Yerushalmi). The term Gemara itself comes from the Aramaic root g.m.r (equivalent to l.m.d, in Hebrew), giving it the meaning teaching.
Although the Yerushalmi was completed earlier (with material spanning roughly 200-500 C.E.), it was eclipsed by the much longer Bavli (200-600 C.E.). The Bavlis popularity may be due to the work of the Gaonim of Babylonia, who cited that work in the legal judgements (responsa) that they sent to communities throughout the Diaspora. Both Gemaras were written in a combination of Hebrew and Aramaic dialects and share the teachings of sages known by the term Amoraim (in the singular, Amora).
Hevruta study at Pardes, a nondenominational yeshiva in Jerusalem. (Courtesy of Pardes Institute of Jewish Studies, http://www.pardes.org.il)
Gemara encompasses several literary genres, and subject matter ranges from the sacred to the profane. While it is often misrepresented as merely a commentary on the laws of the Mishnah, the Gemara has an intricate relationship with the Mishnah and a far greater scope. Although it is organized in accordance with the structure of the six orders of the Mishnah, mishnaic teachings are, for the Gemara, the launch pad for diverse topics: prayer, holy days, agriculture, sexual habits, contemporary medical knowledge, superstitions, criminal and civil law.
The Gemara contains both halakhah (legal material) and aggadah (narrative material). Aggadah includes historical material, biblical commentaries, philosophy, theology, and wisdom literature. Stories reveal information about life in ancient times, among Jews and between Jews and their neighbors, and folk customs. All of these genres are blended together with the halakhic material, in what is sometimes described as a stream-of-consciousness fashion filled with meaningful tangents and digressions.
In dealing with the teachings of the Mishnah, the Gemara has multiple functions. It explains unclear words or phrasing. It also provides precedents or examples to assist in application of the law and offers alternative opinions from sages of the Mishnah and their contemporaries (known as Tannaim). Whereas the Mishnah barely cites biblical verses, the Gemara for nearly every law discussed introduces these connections between the biblical text and the practices and legal opinions of its time. It also extends and restricts applications of various laws, and even adds laws on issues left out of the Mishnah entirely (for example, the key observances of Hanukkah). Multiple opinions of sages are weighed against one another, often without presenting a conclusion.
Talmudic teachings have been most often studied in groups or pairs among masters and students and/or between two partners in learning. A pair of study partners is called a havruta. The havruta-style provides a challenging, lively, and intimate environment in which to explore the rich spiritual and intellectual depths of the Talmud.
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History of the Jews of Yemen – aish.com – Aish
Posted: at 11:26 am
An ancient Jewish community that survived all odds and came home.
A lone Jewish person remains in Yemen, down from seven in February, according to a new United Nations report about the treatment of religious minorities in conflict zones. (Gabby Deutch, Jewish Insider March 14, 2022) In the early 20th century, Jews in Yemen numbered over 50,000; today, there is one Jew left. There are reportedly a handful of hidden Jews in Yemen who have converted to Islam but secretly practice Judaism.
Yemenite Jews have a unique religious tradition that separates them from Ashkenazi, Sephardi, and other Jewish groups. The roots of the Jews in YemenTeiman in Hebrew can be traced back to Biblical times. Yemen is mentioned in Jewish scriptures in various places. It is noted as the place of origin of Jobs friend Eliphaz. Additionally, the famed Queen of Sheba, discussed in the Book of Kings where she visits King Solomon, is said to have heard about King Solomon from Jews in Yemen, which was located near the kingdom of Sheba.
Al Ajar, Hadan, 1984, Photo: Miryam Tangi
Although the province is not mentioned in the Mishna or the Talmud, there is an assumed reference in Josephuss book, The Jewish War. Josephus states that he had informed the remotest Arabians regarding the destruction, and the assumption is that he is referring to the Jews of Yemen.
The immigration of the majority of Jews into Yemen appears to have taken place at the beginning of the 2nd century. In the ancient Jewish cemetery at Beth Shearim, there is an inscription in one of the rooms, describing those buried there as people of Himyar (the Yemenite Kingdom). The assumption is that their bodies were sent from Yemen for burial in Israel, not that they died while visiting Israel, just as many people today ask to be buried in the Land of Israel.
There are fascinating legends regarding how the Jewish community in Yemen was founded.
One local Yemenite Jewish tradition says that Jews came to the Arabian Peninsula at the time of King Solomon. Some say this was because King Solomon sent Jewish merchants to Yemen to prospect for gold and silver to use for the Temple in Jerusalem. Others say Jewish artisans were sent to the region when they were requested by the Queen of Sheba, during that same time period.
Al Ajar, Hadan, 1984, Photo: Miryam Tangi
Another tradition, that of the Jews of Saana, states that their ancestors settled in Yemen 42 years before the destruction of the First Temple. It is also said that in the time of the prophet Jeremiah approximately 75,000 Jews, including Kohanim and Levites, traveled to Yemen.
The tradition of the Jews of Habban (southern Yemen) is that they are the descendants of the tribe of Judah that belonged to a brigade dispatched by Herod the Great to assist the Roman legions fighting in the region. The tradition is that they arrived in the area before the destruction of the Second Temple, and did not return to the Land of Israel.
Jews that lived in the Arabian Peninsula before the Roman period concentrated mainly in two areas Yemen and Hejaz (today's Northwest Saudi Arabia).
There is a fascinating story regarding the King of Himyar and the Jews. Apparently, King Abu-Kariba Assad laid siege to Yathrib (modern-day Medina) to avenge the death of his son who had been killed by the inhabitants of the city. During the siege, the king became deathly ill and two medically knowledgeable Jews from Yathrib, Kaab, and Assad, entered the enemy camp and saved his life. After hearing the king, they pleaded with him to lift the siege and make peace with the city.
Al Ajar, Hadan, 1983. Photo: Miryam Tangi
Not only did the king end the war, but he was also so impressed with the Jews that he embraced Judaism, along with his entire army. Upon his return home, he brought two Jews back with him to teach the populace and insisted that all his people convert to Judaism. The conversions, however, were not total, and there remained as many pagans as Jews in the land. There is also debate whether he converted out of genuine belief or out of political expedience. It is clear though that Judaism flourished in Himyar at this time, and many inscriptions with Jewish terms (God of Israel) are found dating to the 6th and 7th centuries.
The size of the Jewish population of Yemen for the first five centuries C.E. remained steady at about 3,000. The Jews were scattered throughout the country but carried on extensive commerce with other locations, and thus the Jews possessed many Jewish texts, and were knowledgeable of their heritage, although there were few scholars at that time.
In 628 CE, some of non-Jewish Yemenite leaders and tribes converted to Islam. Shortly afterward, Mohammed sent his cousin Ali to Sana'a to create a strong Islamic central authority in Yemen.
During this period of Muslim rule, the Jews were designated as Ahl al-Kitab, protected People of the Book. They were granted freedom of religion conditional on their paying Jizya, a poll tax. Active Muslim persecution of the Jews began in full force under the Shiite-Zaydi clan (the sect currently followed by the fanatical anti-Semitic Houthis in Yemen), when they seized power from the more tolerant Sunni Muslims early in the 10th century.
Under the Zaydi rule, which lasted nearly 1,000 years, Jews were treated as second-class citizens and were oppressed by the rulers and population. They were considered impure, and could not touch a Muslims food, had to walk on a Muslims left side, could not build houses higher than a Muslim's or ride a camel or horse, and when riding on a mule or a donkey, they had to sit sideways. Upon entering the Muslim quarter, a Jew had to take off his footgear and walk barefoot. If attacked with stones or fists by Islamic youth, a Jew was not allowed to defend himself.
Al Ajar, Hadan, 1983. Photo: Miryam Tangi
The Orphans Decree was a law that if a father died, his children were to be taken by the state and forcibly converted to Islam. Although this law was largely ignored during Ottoman rule, during the period of Imam Yahya (19181948) in 1922, the cruel law was enforced with strictness. Orphaned Jews were abducted from the community, and neither pleas nor bribes were accepted to release them. The community and relatives of the orphans searched for ways to save the children from this tragedy, and at times were able to prevent the forced conversion by marrying off the children quickly, as a married person was considered an adult and not able to be taken by the state. Sometimes the children were able to be moved to a large city and hidden with a Jewish family and other times they were taken out of the country.
In the late 12th Century, a false prophet arose in Yemen and proclaimed that Judaism and Islam were now one and the same. He used quotes from the Torah to prove his claim, and since the majority of the population was not that learned, he was very influential. The greatest Torah scholar of Yemen, Yaakov ben Natanel al-Fayyumi, wrote to the Rambam (Maimonides) in 1172 to ask for his response. The Rambam responded with the soon-to-be-famous Iggeret Teiman, Letter to Yemen, elaborating on the answer and clarifying the foundations of Jewish belief. This letter made such an impression on the Jews of Yemen that they included the name of Rambam in the addish prayer, praying that he live a long life and his name be blessed.
Following his Letter to Yemen, the rabbis of Yemen would send letters to the Rambam, and he would teach through the letters he sent. He also sent them a copy of his Mishneh Torah the codified Jewish law, and this magnum opus was copied meticulously in Yemen. In the Geniza in Cairo, many letters from the 12th century and onward were found, demonstrating the close connection between the Cairo community and the rabbis in Yemen that began with the Rambam.
Despite their geographic isolation, the Yemenite Jews maintained contact with important Jewish centers, particularly with Egypt and Babylonia. Throughout their history, they had great scholars.
In the 14th century, Rabbi Nathanael ben Isaiah wrote an Arabic commentary on the Bible. In the second half of the 15th century, Rabbi Saadia ben David al-Adani was the author of a commentary on the Bible, and Rabbi Abraham ben Solomon wrote on the Prophets.
Study in the mufredj while the father is making tsitsit, Beit Sinan, Arhab, 1986. Photo: Miryam Tangi
Rabbi Shlomo Adani (born 1567) was also a native of Yemen and is considered one of the greatest commentators on the Mishna. He was born in Sana'a, Yemen to Rabbi Yeshua Adani, a leading rabbi of the city. The family immigrated to the land of Israel in 1571, where he completed his book entitled Melechet Shlomo in 1624. His work is considered a classic and is partially printed in most of the editions of the Mishna with commentaries. There are also streets in Jerusalem, Beersheba, and other Israeli cities named after Rabbi Shlomo Adani.
Rabbi Shalom Sharabi, born in Yemen in 1720, is considered the father of all contemporary Sephardic kabbalists. After he was miraculously saved from a difficult situation, he fulfilled his vow to go to the Holy Land of Israel and to live in Jerusalem.
When travel became easier with the opening of the Suez Canal in 1869, Jews began to emigrate from Yemen to then-Palestine. Many of the Jews that moved during this time, which was approximately 10 percent of the population, settled in Jerusalem, Jaffa, or in agricultural settlements.
In 1922, when the government of Yemen began to harshly enforce the Orphan's Decree, as discussed in this article, even more Jews sought to immigrate.
Following the partition vote of 1947 in which the UN voted to split then-Palestine and give a country to Jews, Arab Muslims in Yemen, assisted by the local police force, began rioting and murdering, killing 82 Jews in Aden and destroying hundreds of Jewish homes. This paralyzed the Jewish community financially and frightened the Jews regarding their future in Yemen.
This increasingly perilous situation led to the emigration of virtually the entire Yemenite Jewish community between June 1949 and September 1950 in Operation Magic Carpet. During this period, over 50,000 Jews emigrated to Israel.
A more minor, continuous migration was allowed to continue until 1962 when a civil war put an abrupt halt to any further Jewish exodus.
Today the overwhelming majority of the half a million Jews worldwide of Yemenite descent live in Israel. They are the legacy of 2,000 years of Yemenite Jewry.
With thanks to the photographer Miryam Tangi for granting permission to use her photos. Click here to read her article about Yemenite Jews.
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Rabbi Denker reflects on 38 years in the rabbinate – Cleveland Jewish News
Posted: at 11:26 am
For Rabbi Steven L. Denker, one of the first stops in retirement will be Cuyahoga Community College, where he is enrolled as a student in automotive technology.
Other than that, spending more time with family is on the horizon, Denker told the Cleveland Jewish News May 6 in an online interview.
By way of explanation, Denker, 70, shrugged and said, Ive always loved cars, adding hes enrolled now in his first hands-on class, a survey course. Depending on the season, he drives a Subaru Impreza hatchback or a Honda S2000.
Hes already taken a math course and a course on management of an automotive facility.
Denker has been a rabbi for 38 years and has spent the last 18 as spiritual leader at Temple Emanu El in Orange, first as interim and for most of those years as its permanent rabbi.
One of Denkers first tasks was to help Temple Emanu El think through its next steps in 2004.
He said that required many meetings, including with focus groups, discussions and with stakeholders.
It was necessary. It wasnt easy. Those kinds of changes for any congregation are never easy, Denker said, adding many of Clevelands synagogues have relocated. There are very few congregations that stay in the same spot for their entire history.
Denker has led several trips to Israel at Temple Emanu El and for other congregations. In previous posts, he has also led congregational trips to Jewish Spain, Morocco and Cuba.
One of his favorite quotations from Pirkei Avot, also known as Ethics of the Fathers, is Your associates honor should be dearer to you than your own.
Of the recent rise in antisemitism, Denker said it has always been there, but below the surface.
It has surfaced in recent years because it has become fashionable in some circles, he said and because of the extreme nature of public discourse that we are in the middle of, not just in the United States but worldwide.
Denker was born in New York City, attended public schools in Brooklyn and became a bar mitzvah at Talmud Torah of Flatbush.
He graduated from Brooklyn Technical High School and holds a Bachelor of Arts degree from City University of New York, a Master of Hebrew Letters and an honorary Doctor of Divinity degree from Hebrew Union College-Jewish Institute of Religion in New York.
Prior to entering rabbinical training, he was director of community relations for the New York City chapter of the American Jewish Committee and served on the staff of the late U.S. Rep. Stephen J. Solarz.
He started rabbinical school at age 29, attending HUC-JIR, spending his first year in Jerusalem and the rest of his time at the New York City campus.
In his second year, he was invited to dinner at then-cantorial student Alane Simons (now Katzew). Another guest at the table was Lisa Arlyn Lowe, whom Katzew hoped to set up with Denker.
It was a match, and the couple has been married nearly 40 years. Lowe is a lawyer at Meyers, Roman, Friedberg & Lewis in Woodmere.
Denkers first rabbinical post was as assistant, then associate rabbi at Temple Sholom in Chicago. After doing some teaching and part-time work, he served at Congregation Kol Ami in Chicagos Water Tower Place, as its rabbi for 10 years.
It was time for me to look beyond Kol Ami, Denker said of his decision to approach the Central Conference of American Rabbis placement commission.
The Temple Emanu El interim position was suggested, which Denker accepted for one year. He stayed on a second year with permission from the placement commission.
In that second year, I saw that things were coming together to make the physical move, which was necessary in my opinion for the congregation to have a future, said Denker, who sought and received permission to apply for the permanent position at Temple Emanu El. So altogether, its been 18 years.
Denker said there were certain things that attracted him to want to stay.
I saw the enthusiasm of the members and the commitment of the members and the viability of the congregation, he said. And also the opportunity to help a congregation really be reborn, which is pretty much what happened.
In his time in Cleveland, Denker said he has enjoyed taking part in changing the landscape of the Jewish community in Cleveland.
People drive by Brainard and Emory, Denker said. And they think theres been a synagogue there since Moses, which is not quite the case.
Characterizing the congregation, Denker said, Emanu Els got a wonderful group of people for whom a mid-size congregation middle of the road Reform congregation is appropriate.
When they moved to Cleveland, Denker and Lowes older son, David, was about to start college. Alexander was 15 and graduated from Solon High School. David now lives in Jerusalem with his wife, A.J. Bruce, and their daughter, Nava; Alexander lives in Washington, D.C.
In December, Denker and Lowe relocated from Solon to Beachwood in what he called a typical downsizing.
Reflecting, Denker said among his greatest joys has been watching a generation grow up and to be part of peoples lives and have the extreme honor of having people learn Torah with me.
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Rabbi Denker reflects on 38 years in the rabbinate - Cleveland Jewish News
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No, Rabbi Boteach, the death penalty is barbarian, and hate is idolatry and dumb – The Times of Israel
Posted: at 11:26 am
About Anger, Hate, Revenge, and Capital Punishment
Ive written against the death penalty over and over again, both from the perspective of Jewish Law and from a psychological perspective. I hate to repeat myself, but I must address the subject, now one of Americas most famous rabbis has raised the issue and has written a book on Kosher Hate.
In short: hes almost completely mistaken.
Rabbi Boteach started out very nicely outside of the box. Being Gay was not against the Torahhow could what you ARE be a sin? He did suggest that Gay-Jewish men should marry Jewish women because they will make such nice husbands and fathers, and otherwise, so many Jewish women would numerically be forced to stay single, but hey, no one is perfect.
He stressed that sex is a positive thing in Judaism, and charmed many Gentiles, even on television, with the wisdom of the Sages and the Rabbis about sex and about relationships. He did a lot of good work. Past tense.
His friend Michael Jackson, suspected (and then confirmed) as a serial pedophile, he advised marrying a woman. He never apologized for that.
Lately, hes really on a slippery slope. He started an election campaign as a Republican. He wasnt elected but, in the process, wrote a lot of unwarranted apologetics for right-wing political deceit. He did write that the GOP should rid itself of its anti-sexuality campaigns: anti-abortion, anti-Gay, anti-marriage equality, etc. It would just go downhill from there.
Boteach chose to debate Evangelicals. I warned that he would lose doing so, and so would all Jews. He went anyway. He flattered them and got nowhere. He didnt castigate them, in the stern fashion that Christians got used to over the ages, about Antisemitism in the churches, and their missionary assault and dreams on the Jews, etc. He had to be lovely.
He wrote a book Kosher Jesus. It has a 15-chapter section: Why the Jews Cannot Accept Jesus, instead of: Why Jews Have no Need for Jesus.
It didnt stop there. He then started campaigning against the fake turning the other cheek and loving ones enemy. He was right that that advice was unfit for humans and that the Christian bloodbath through the ages proved that. But, that doesnt mean that hating is holy and anger is redemptive.
Yes, there is a place for anger and hatein therapy. But, funerals of Jewish-Israeli victims of local Antisemitism are so uplifting because people cry, praise the murdered, and praise G^d. While, funerals of (would-be) terrorists are often marred by screams and threats of hatred and revenge. If one needs to die, its so much better to die a victim than a victimizer. Its so easy and primitive to hate, so elevated and elevating to focus on life.
The good rabbi didnt stop there. Today, he wrote he wants the death penalty for terrorists who murdered Jews in Israel, claiming that is Jewish.
Hes so off the derech (Jewish way). First of all, this is assimilation to the worst of the culture surrounding him. One of the ways the US is backward (besides a lack of universal health care) is capital punishment. All of the trial, incarceration (often for decades), and execution procedures are nothing Jewish Law could agree with. Its plain, stupid, hate-filled revenge and cruelty. Trying to prove the value of human life by killing humans.
On a side note, why does he reserve the word innocent for Jews? Are there no innocent Muslims? He sees The conflicting value systems of the two opposing camps. That is so reminiscent of Christian Dualism (not Monotheism): Evil against Good. The Talmud explains: Theres no sinning but in an attack of folly. Had you thought about it some longer, youd not have done it. There are no inherently evil people. If their nature was bad, theyd be innocent. His anger betrays he thinks they do have free will.
This is on top of Christians saying for 2,000 years that they have God and the Testament of love and Jews have the Testament and God of hatred. International press agencies always call Israels deterrence: revenge.
No terrorist who takes that many lives should be permitted to live. Does He still believe in G^d? Why do we say: May G^d revenge their blood?
He is right that Judaism allows for some revenge and feeling of vengeance but only in very limited fashion (compare the avenger of blood). So, we can find Hebrew Bible verses and Rabbinic comments about revenge, but they pale in comparison to G^ds Advice to forgo this. They were highlighted by father and son Kahane, may G^d revenge their blood. But they almost became a caricature when ignoring the multitude of texts preaching peace.
The summary of the Hebrew Bible is: Dont do unto others which you dont want others to do to you. All the Rabbis agree that An eye for an eye means we must financially compensate, not permission to take revenge.
When we must hurt of stop others, doing so angerly makes it a very grave sin (Jacob protecting Dinah against Esav, Shimon and Levi in Shechem, Shimon and Joseph). Not everyone is as calm and holy as Phinehas.Life in jail stands for: unacceptable deeds AND one can always repent.
The Talmud says that a Rabbinic Court that awards the death penalty more than once in 7 years is a bunch of murderers. Some say: once in 70 years! Here, we sometimes have multiple antisemitic murderers per day.
Besides that, research shows that the death penalty doesnt deter. Plus, in this case, its especially meaningless. These Jew-hating Muslims are not afraid to die. What use is to kill or promise to kill them? House demolitions and withdrawing entry permits of close family somewhat seem to work.
And, is he willing to kill them, or is the dirty work for someone else?
His rationalization for his revenge is that mass murderers who rot in jail could become bargaining chips for hostage-takers. Too easy! Does the rabbi have a donor card to facilitate becoming an organ donor after death? He could add another one, that he doesnt want to be exchanged for any murderer and the like if taken captive. I have. Jonathan Pollard did.
He must do some serious soul searching, including asking his best friends how he got into this assimilated mess. And, consult a real therapist.
But possibly the worst thing he wrote today was about others like Eichmann. You got to be kidding. He must ask forgiveness for this false Holocaust comparison. Even Arafat could not stand in the shadow of Eichmann.
But, I cant recall he ever said he was wrong, Im not holding my breath. Sad. Let him prove me wrong. Reb Shlomo always said: You never know.
MM is a prolific and creative writer and thinker, previously a daily blog contributor to the TOI. He often makes his readers laugh, mad, or assume he's nutsclose to perfect blogging. As a frontier thinker, he sees things many don't yet. He's half a prophet. Half. Let's not exaggerate. He doesn't believe that people observe and think in a vacuum. He, therefore, wanted a broad bio that readers interested can track a bit what (lack of) backgrounds, experiences, and educations contribute to his visions. * This year, he will prioritize getting his unpublished books published rather than just blog posts. Next year, he hopes to focus on activism against human extinction. To find less-recent posts on a subject XXX among his over 1500 archived ones, go to the right-top corner of a Times of Israel page, click on the search icon and search "zuiden, XXX". One can find a second, wilder blog, to which one may subscribe, here: https://mmvanzuiden.wordpress.com/ or by clicking on the globe icon next to his picture on top. * Like most of his readers, he believes in being friendly, respectful, and loyal. However, if you think those are his absolute top priorities, you might end up disappointed. His first loyalty is to the truth. He will try to stay within the limits of democratic and Jewish law, but he won't lie to support opinions or people when don't deserve that. (Yet, we all make honest mistakes, which is just fine and does not justify losing support.) He admits that he sometimes exaggerates to make a point, which could have him come across as nasty, while in actuality, he's quite a lovely person to interact with. He holds - how Dutch - that a strong opinion doesn't imply intolerance of other views. * Sometimes he's misunderstood because his wide and diverse field of vision seldomly fits any specialist's box. But that's exactly what some love about him. He has written a lot about Psychology (including Sexuality and Abuse), Medicine (including physical immortality), Science (including basic statistics), Politics (Israel, the US, and the Netherlands, Activism - more than leftwing or rightwing, he hopes to highlight reality), Oppression and Liberation (intersectionally, for young people, the elderly, non-Whites, women, workers, Jews, LGBTQIA+, foreigners and anyone else who's dehumanized or exploited), Integrity, Philosophy, Jews (Judaism, Zionism, Holocaust and Jewish Liberation), the Climate Crisis, Ecology and Veganism, Affairs from the news, or the Torah Portion of the Week, or new insights that suddenly befell him. * Chronologically, his most influential teachers are his parents, Nico (natan) van Zuiden and Betty (beisye) Nieweg, Wim Kan, Mozart, Harvey Jackins, Marshal Rosenberg, Reb Shlomo Carlebach, and, lehavdil bein chayim lechayim, Rabbi Dr. Natan Lopes Cardozo, Rav Zev Leff, and Rav Meir Lubin. This short list doesn't mean to disrespect others who taught him a lot or a little. * He hopes that his words will inspire and inform, and disturb the comfortable and comfort the disturbed. He aims to bring a fresh perspective rather than harp on the obvious and familiar. When he can, he loves to write encyclopedic overviews. He doesn't expect his readers to agree. Rather, original minds should be disputed. In short, his main political positions are among others: anti-Trumpism, for Zionism, Intersectionality, non-violence, anti those who abuse democratic liberties, anti the fake ME peace process, for original-Orthodoxy, pro-Science, pro-Free Will, anti-blaming-the-victim, and for down-to-earth, classical optimism, and happiness. Read his blog on how he attempts to bridge any tensions between those ideas or fields. * He is a fetal survivor of the pharmaceutical industry (https://diethylstilbestrol.co.uk/studies/des-and-psychological-health/), born in 1953 to his parents who were Dutch-Jewish Holocaust survivors who met in the largest concentration camp in the Netherlands, Westerbork. He grew up a humble listener. It took him decades to become a speaker too, and decades more to admit to being a genius. But his humility was his to keep. And so was his honesty. Bullies and con artists almost instantaneously envy and hate him. He hopes to bring new things and not just preach to the choir. * He holds a BA in medicine (University of Amsterdam) is half a doctor. He practices Re-evaluation Co-counseling since 1977, is not an official teacher anymore, and became a friendly, powerful therapist. He became a social activist, became religious, made Aliyah, and raised three wonderful kids. Previously, for decades, he was known to the Jerusalem Post readers as a frequent letter writer. For a couple of years, he was active in hasbara to the Dutch-speaking public. He wrote an unpublished tome about Jewish Free Will. He's a strict vegan since 2008. He's an Orthodox Jew but not a rabbi. * His writing has been made possible by an allowance for second-generation Holocaust survivors from the Netherlands. It has been his dream since he was 38 to try to make a difference by teaching through writing. He had three times 9-out-of-10 for Dutch at his high school finals but is spending his days communicating in English and Hebrew - how ironic. G-d must have a fine sense of humor. In case you wonder - yes, he is a bit dyslectic. If you're a native English speaker and wonder why you should read from people whose English is only their second language, consider the advantage of having an original peek outside of your cultural bubble. * To send any personal reaction to him, scroll to the top of the blog post and click Contact Me.
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Why Saying This Short Prayer Before Bed Lightens Your Psychic Load – aish.com – Aish
Posted: at 11:26 am
How to have a better sleep -- and a better life.
Theres a prayer I try to say before I go to sleep at night.
Creator of the World.I hereby forgivewhoever has angered or humiliated me,And whoever has done meany wrong;Whether it wason purpose or by accident,Whether it wasdone by word or by deed,in this incarnationor in previous ones.
Please let no onebe punished on my account.
The idea for the prayer came from the Talmudic sage, Rabbi Nehunya ben HaKana who, when asked the secret of his longevity, replied, Before I go to sleep I make sure to forgive anyone who vexed me.
Why am I drawn to this prayer?
For one, its a great soporific, way better than any sleeping pill. The unconscious has a way of collecting the various slights and aggravations it experienced that day. You know, the co-worker who said goodbye to everyone in the office except you, the creepy dog-owner who in the dead of night brings his Labrador specifically to your lawn to deposit whatever it wants, that sort of thing. By the time Im ready for bed, my mind is fairly churning with grievances, whether I know it or not.
Instead of rehashing what I wouldve, couldve, shouldve said, instead of nursing my grudge, I can give a cosmic shout out: Youre all forgiven!
Instead of rehashing what I wouldve, couldve, shouldve said, instead of nursing my grudge, I can give a cosmic shout out: Youre all forgiven! And with my bucket of slights thus emptied, I go peacefully to sleep.
Wait a minute. Did I really forgive them?
What about that friend who stood you up and never bothered to call to explain what happened? I dont know if I can forgive them all so easily or so fast. But at least Im feeling a bit more open toward these vexers in my life. First, the prayer has introduced the possibility of accidental. As the saying goes, half of what we think is malice could simply be attributed to stupidity. Suddenly I start wondering about the persons backstory, the hard stuff of his or her life, the things I dont know about that mightve made it virtually impossible for the friend to call and apologize.
And even if the Labrador owner has no excuse for his behavior, do I really want to incur divine wrath upon his head? The prayer makes me come into contact with my own primitive need for getting-back, getting even or revenge, and then I can say: Hey, I dont want it.
Then its only a matter of time before I begin to reflect: Who did I insult, ignore, underestimate, misjudge, shove past, or bang into in my rush to do what I considered so important? The Jewish term for this practice is cheshbon hanefesh a taking stock or an accounting of ones soul. Maybe I can improve here, make a tweak there for the next time Im in that situation. This soul accounting makes my day feel purposeful. Im not simply drifting obtusely through a life that happens to be mine, but consciously shaping my world and my self.
Lastly, the prayer lifts me up to a higher reality, of fourth, fifth, sixth, possibly infinite dimensions. Whether in this incarnationgilgulor another Whoa. Did I just read about the transmigration of the soul in a standard non-mystical Jewish prayer book? Whoa! Ive always believed in recycling on a physical plane. Our atoms and cells and bacteria dont die with us, but keep on living in an altered form. So doesnt it make sense that a soul wouldnt evaporate entirely, either, but get reprocessed into someone else?
Imagine if we could look at our neighbors, friends, co-workers, police officers, and all the people who dont think or vote like I do with fresh, grudge-free eyes?
Gilgul, reincarnation the idea of a soul spinning through various bodies over the generations, has a way of putting my peeves or other peoples aggressive behavior into perspective. Why did that guy cut me off like a jerk on the highway? I dont know. Like Sara Rigler wrote in Ive Been Here Before, were all just chapters in a book, and we dont know which chapter came before and which one comes after, which, for me, takes the heat and intensity off any obnoxious encounter.
The best part about that prayer is waking up with a psychic load way lighter.
Try the prayer sometime. Imagine if one night, the entire world, before going to bed, recited the prayerand meant it?
What would our country be like if we could look at our neighbors, friends, co-workers, intimates, police officers, meter maids, and all the people who dont think or vote like I do (the right way), with fresh, grudge-free eyes?
Is it really possible? Can I open my heart just a hairsbreadth to the neighbor who psychotically curses whoever steps on a blade of her manicured lawn?
I have my doubts. But if the Talmudic sage Rabbi Nehunya thought it was within our human range, maybe, just maybe I can.
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Hedges: Jesus, Endless War, and the Rise of American Fascism – Scheerpost.com
Posted: at 11:26 am
The Democratic Party is hoping to thwart an election rout by running against the expected Supreme Court decision on abortion. This is depressingly all that is left of its political capital.
By Chris Hedges / Original to ScheerPost
The Democratic Party which had 50 years to writeRoe v Wadeinto law with Jimmy Carter, Bill Clinton, and Barack Obama in full control of the White House and Congress at the inception of their presidencies is banking its electoral strategy around the expected Supreme Court decision to lift the judicial prohibition on the ability of states to enact laws restricting or banning abortions.
I doubt it will work.
The Democratic Partys hypocrisy and duplicity is the fertilizer for Christian fascism. Its exclusive focus on the culture wars and identity politics at the expense of economic, political, and social justice fueled a right-wing backlash and stoked the bigotry, racism, and sexism it sought to curtail. Its opting for image over substance, including its repeated failure to secure the right to abortion, left the Democrats distrusted and reviled.
The Biden administration invited Amazon Labor Union president Christian Smalls and union workers from Starbucks and other organizations to the White House at the same time it re-awarded a $10 billion contract to the union-busting Amazon and the National Security Agency (NSA) for cloud computing. The NSA contract is one of 26 federal cloud computing contracts Amazon has with the U.S. Army and Air Force, the Department of Health and Human Services, the Department of Homeland Security, the Department of the Interior, and the Census Bureau. Withholding the federal contracts until Amazon permitted free and open union organizing would be a powerful stand on behalf of workers, still waiting for the $15 minimum wage Joe Biden promised as a candidate. But behind the walls of the Democratic Partys Potemkin village stands the billionaire class. Democrats have failed to address the structural injustices that turned America into an oligarchic state, where the obscenely rich squabble like children in a sandbox over multibillion-dollar toys. The longer this game of political theater continues, the worse things will get.
The Christian fascists have coalesced in cult-like fashion around Donald Trump. They are bankrolled by the most retrograde forces of capitalism. The capitalists permit the stupidities of the Christian fascists and their self-destructive social and cultural wars. In exchange, the billionaire class gets corporate monopolies, union busting, privatized state, and municipal services, including public education, revoked government regulations, especially environmental regulation, and can engage in a virtual tax boycott.
The war industry loves the Christian fascists who turn every conflict from Iraq to Ukraine into a holy crusade to crush the latest iteration of Satan. The Christian fascists believe military power, and the manly virtues that come with it, are blessed by God, Jesus, and the Virgin Mary. No military budget is too big. No war waged by America is evil.
These Christian fascists make up perhaps 30 percent of the electorate, roughly equivalent to the percentage of Americans who believe abortion is murder. They are organized, committed to a vision, however perverse, and awash in money. John Roberts, Samuel Alito, Amy Coney Barrett, Clarence Thomas, Neil Gorsuch and Brett Kavanaugh, mediocre jurists and Federalist Society ideologues who carry the banner of Christian fascism, control the Supreme Court.
Establishment Republicans and Democrats, like George Armstrong Custer on Last Stand Hill, have circled the wagons around the Democratic Party in a desperate bid to prevent Trump, or a Trump mini-me, from returning to the White House. They, and their allies in Silicon Valley, are using algorithms and overt de-platforming to censor critics from the left and the right, foolishly turning figures like Trump, Alex Jones, and Marjorie Taylor Greene into martyrs. This is not a battle over democracy, but the spoils of power waged by billionaires against billionaires. No one intends to dismantle the corporate state.
The ruling class in both parties told lies about NAFTA, trade deals, reforming welfare, abolishing financial regulations, austerity, the Iraq war, and neoliberalism that did far more damage to the American public than any lie told by Trump. The reptilian slime oozes out of every pore of these politicians, from Nancy Pelosi and Chuck Schumer to Biden, who backed the 1976 Hyde Amendment banning federal funding of abortions and in 1982 voted to support a constitutional amendment that would allow states to overturnRoe v Wade. Their hypocrisy is not lost on the public, even with their armies of consultants, pollsters, courtiers in the press, public relations teams and advertising agencies.
Marjorie Taylor Greene is clueless and unhinged. She claims Hillary Clinton was involved in a child mutilation and a pedophilia ring and several high-profile school shootings were staged. But weaponized, like Trump, she is a political cruise missile aimed straight at the heart of the discredited centers of traditional power.
Hate is the fuel of American politics. No one votes for who they want. They vote against those they hate. Black and brown marginal communities have suffered worse assaults than the white working class, but they have been defanged politically with militarized police that function as internal armies of occupation. The erosion of due process, the worlds largest prison system and the stripping away of all rights, including often voting rights because of felony convictions, as well as a loss of access to most social services and jobs, reduced them to a subsistence level on the lowest rung of Americas caste system. They are also the primary targets of Republican-sponsored voter suppression and redistricting.
The glue holding this Christianized fascism together is not prayer, although we will get a lot of that, but war. War is the raison dtre of all systems of totalitarianism. War justifies a constant search for internal enemies. It is used to revoke basic civil liberties and impose censorship. War demonizes those in the Middle East, Russia, or China, who are blamed for the economic and social debacles that inevitably get worse. War diverts the rage engendered by a dysfunctional state towards immigrants, people of color, feminists, liberals, artists, anyone who does not identify as a heterosexual, the press, antifa, Jews, Muslims, Russians, or Asians. Take your pick. It is a bigots smorgasbord. Every item on the menu is fair game.
I spent two years with the Christian right reporting and researching my bookAmerican Fascists: The Christian Right and the War on America.These Christian fascists have never hidden their agenda or their desire to create a Christian nation, any more than Adolf Hitler hid his demented vision for Germany in Mein Kampf. They prey, like all fascists, on the despair of their followers. They paint gruesome portraits of the end times when the longed-for obliteration of non-believers presages the glorious return of Jesus Christ. The battle at Armageddon, they believe, will be launched from the Antichrists worldwide headquarters in Babylon once the Jews again have control of Israel. The closer we get to Armageddon, the giddier they become.
These people believe this stuff, as they believe in QAnon or the election fraud that supposedly put Biden in office. They are convinced that a demonic, secular-humanist ideology propagated by the media, the United Nations, elite universities, the American Civil Liberties Union, the National Association for the Advancement of Colored People, the NationalOrganization for Women, Planned Parenthood, the Trilateral Commission along with the US State Department and major foundations are seeking to destroy them.
Violence is embraced as a cleansing agent, a key component of any fascist movement. The Christian fascists do not fear nuclear war. They welcome it. The insane provocations of Russia by the Biden administration, including the decision to provide $33 billion in assistance to Ukraine, target ten Russian generals for assassination and pass on to Ukraine the intelligence to sink the Moskva, the guided missile cruiser that was the flagship of the Russian Black Sea fleet, supercharges the ideology of the Christian right. The marriage of the war industry, determined to make war forever, with the Christian fascists yearning for the apocalypse is terrifying. Biden is sleepwalking us into a war with Russia and perhaps China. The Christian fascists will accelerate the bloodlust.
The political deformities we have spawned are not unique. They are the product of a society and government that no longer functions on behalf of the citizenry, one that has been seized by a tiny cabal, in our case corporate, to serve its exclusive interests. The airy promises politicians make, including the announcement by candidate Barack Obama that the first thing he would do in office was sign the Freedom of Choice Act, which during his eight years as president he never got around to doing, are worthless. The scheduled vote next week in the Senate on a bill asserting that abortions are legal in the United States, which is expected to be blocked by the Republicans use of the filibuster, a Senate procedural rule that requires 60 votes to advance most legislation in the 100-member chamber, is another empty gesture.
We saw the consequences of this dysfunction in Weimar Germany and Yugoslavia, a conflict I covered forThe New York Times. Political stagnation and economic misery breeds rage, despair, and cynicism. It gives rise to demagogues, charlatans, and con artists. Hatred drives political discourse. Violence is the primary form of communication. Vengeance is the highest good. War is the chief occupation of the state. It is the vulnerable and weak who pay.
NOTE TO SCHEERPOST READERS :There is now no way left for me to continue to write a weekly column for ScheerPost and produce my weekly television show without your help.The walls are closing in, with startling rapidity, on independent journalism, with the elites, including the Democratic Party elites, clamoring for more and more censorship. Bob Scheer, who runs ScheerPost on a shoestring budget, and I will not waver in our commitment to independent and honest journalism, and we will never put ScheerPost behind a paywall, charge a subscription for it, sell your data or accept advertising. Please, if you can, sign up atchrishedges.substack.comso I can continue to post my now weekly Monday column on ScheerPost and produce my weekly television show, The Chris Hedges Report.
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Abbas Saves Bennett’s Hide: We’ll Give the Coalition Another Chance – The Jewish Press – JewishPress.com
Posted: at 11:26 am
The Raam party has decided to give another chance to the coalition and the government, party chairman Mansour Abbas announced Wednesday afternoon, following another discussion of the Islamist Shura council. Today we are returning to a political partnership for the benefit of Arab society, he explained. We have stabilized the political system and exercised our citizenship. We decided to freeze our membership following the events on the Temple Mount, and we have now decided to give another chance and return to the coalition agreements.
In an angry aside, Abbas noted: Netanyahu is back to inciting against us. Its the same Netanyahu with whom we had relations in the previous government and coalition negotiations which are documented on my phone well probably have to get it out.
For a while now, Abbas and the Bennett coalition have been claiming that the Raam chairman was then-Prime Minister Benjamin Netanyahus guest four different times in his official residence on Balfour Street in Jerusalem when the PM was courting him in hope of adding the four-MK Islamist party to his coalition government. Likud members have been denying the claim, calling Abbas a liar.
On May 10, 2021, Ynets Moran Azulai reported: Prime Minister Benjamin Netanyahu and Raam Chairman Mansour Abbas met last Saturday in Balfour at Netanyahus request. Despite the statements of Likud members in recent days that there were no contacts between the Likud and Raam, the prime minister asked Abbas to not join the Bennett-led government. The Likud refused to comment.
MK Itamar Ben Gvir cut into the Raam chairmans statement and slammed Abbas: You are the greatest danger. Abbas replied, You are a convicted terrorist. Then Raam MK Mazen Ghanaim screamed at Ben Gvir: You killed Rabin.
He didnt.
Following the Abbas announcement, the opposition withdrew its proposed bill to dissolve the Knesset and will likely try again in the near future.
Prime Minister Naftali Bennett refused to answer a question about what had been promised to Raam in exchange for returning to the coalition, and said: We are a government of doing and of goodwill and moving away from the things that do not contribute.
As we reported earlier (Islamist Party Delays Decision on Staying in Coalition Citing Jazeera Reporters Death), Raam presented Bennett with a five-item ultimatum to come back to the fold:
1. Preservation of the status quo in the Al-Aqsa Mosque (they mean the entire Temple Mount DI) and prevention of the establishment of Jewish Talmudic prayers and rituals in the mosques courtyards. Thats davening to you and me.2. An agreement signed by all the leaders of the coalition for the implementation of the economic five-year plan and the transfer of its budgets within a year.3. Implementation of government decisions in the Negev and recognition of illegal villages within six months.4. A written commitment by the Prime Minister to soften Interior Minister Ayelet Shakeds rigid stance on burning issues in Arab society, especially planning and construction (yes, they really did demand this).5. Increasing the collection of unlicensed weapons in Arab society and expanding the program to combat violence and crime.
Well keep you posted as to which of the above demands will be met soon. The most likely are items 2 and 3.
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Susan Slotnick: And they wound up here – Hudson Valley One
Posted: at 11:25 am
The family enjoying spring in New Paltz.
On August 30, the Americans left Afghanistan. On August 31, Taliban operatives attacked the home of the father, his wife and their three children ages 2, 4 and 9. To hide, he rushed his family into the basement. That same day the Taliban terrorized the neighborhood starting from 1 a.m. until 4 a.m. Cars were stolen, houses demolished, screams were heard.
He was forced to leave the family dog in the house, since a barking dog would alert the ten Taliban ransacking his home where they were hiding. When he risked emerging from the basement, bullet holes were in the walls, furnishings were smashed, their car was seized. Worst of all, the beloved family dog shot and killed. They fled.
His crime was having service contracts with the Americans and other international companies.
After a short stay with his wifes family, they escaped to Mazar-i-Sharif where they hid for three months without leaving their dwelling. There was almost no food. Health care was non-existent. Separated from friends and family, loneliness and fear for loved ones was a constantinternal panic. Without a way to leave, their two daughters would never be educated, the fathers income non-existent, they could be murdered. Life, with the happiness they knew, was gone forever.
Hope came from a phone call alerting him the border with Pakistan was open. A sliver of time might be available for the family to flee.
At the border 40,000 other humans were waiting to leave. From 5 a.m. to 2 p.m. the multitudes were so tightly packed together they could not sit down. The children had no food or water. The Taliban were also there trying to scare the citizenry. A bullet landed an inch from his wifes shoe. Other bullets shot into the crowd found their mark.
The next time the border was open they tried to flee again. This time, having sold all of his wifes jewelry, they had some money. Their first night in Pakistan they stayed up all night in a park. After not eating for a long time they found a Burger King near the park and were able to feed the children and find shelter in a small hotel for five nights. The room had only one twin bed, so the parents slept on the floor.
In Pakistan, the police confiscated their passports, visas and registration papers to be returned only after the family paid hefty bribes. Next, the family flew to Mexico City where they received help for one month from the International Rescue Committee. When the month was over, they were out on the street with no help whatsoever.
After calling a taxi requesting transportation into the United States, they were told the only option was to hire illegal coyotes costing thousands of dollars, the remainder of all their assets.
The father said, A very old woman with white hair, short and very strong with a mask on so we could not identify her, came to see us and helped us get to America. The day after her visit a car arrived to drive us to the border. Ten people with all their possessions were driven to the wall. One by one, using pulleys, each person was pulled to the top of the 18-foot barrier. A person stationed at the top to carry us over and another person on the USA side to help us down.
The family walked for hours until the Border Patrol found them. They were taken to a US jail, fingerprinted, separated by gender and imprisoned for five days. In the fathers cell, 80 men languished without a bathroom or water, packed too tightly to lie down. With no window, the father did not know if it was day or night. Worst of all, without water to wash, he could not say his prayers. His wifes hijab was confiscated, robbing her of her already-compromised identity.
By then months had passed since leaving Kabul, but it would be another several months longer before finding respite.
Many refugees are relocated to Buffalo, New York, a designated sanctuary city, but due to an influx of Ukrainians, Russians and Bangladeshis, displaced persons services were over-burdened. The familys papers legitimizing their status were rejected and once again the father pleaded for help to no avail.
For many years I have taught my students all change for the good of humanity starts with each persons individual consciousness. One principled person with a conscience, local artist and activist Robert Sabuda, a God sent, called the family and offered them shelter here in New Paltz. When the family arrived at the Poughkeepsie Amtrak Station, they were greeted by members of New Paltz for Refugees Committee
For two hours I interviewed the father without him showing emotion. Once the words New Paltz were introduced into the narrative, he put his hand on his heart and wept, from joy and happiness. For the remainder of his chronicle, the crying continued, tears of relief coming from gratitude. His children, his wife and he survived. The worst of his travails were over. The familys new life was beginning and it was because New Paltz is filled with conscious people who joined forces to provide shelter, food, education, healthcare, transportation,friendship, hospitality and love.
Maybe conscious intentions to make a better world grows on the magnificent spring trees around here, but money doesnt. So many open-hearted people making donations have saved this family. Another family arrived here last week That makes three families, 14 souls. So much more is needed to continue to make New Paltz a safe haven, a light of kindness in this overwhelming world full of need. As the Talmud says, If you save one person, its as if you saved the whole world. Wont you please help? To make a donation, visit https://www.newpaltz4refugees.org/
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Autism and the complete human genome: Q&A with Evan Eichler | Spectrum – Spectrum
Posted: at 11:24 am
Evan Eichler
Professor, University of Washington
It has been more than 20 years since scientists announced the completion of the Human Genome Project even though the $3 billion effort to sequence the 3 billion bases of human DNA was not, in fact, complete. Technological limitations meant that roughly 8 percent of the genome remained a mystery.
In April, the Telomere-to-Telomere Consortium closed nearly all the gaps, adding roughly 200 million bases of genetic information that codes for more than 1,900 genes.
This new treasure trove of data, detailed in six papers in Science, stands to advance autism research, says Evan Eichler, professor of genome sciences at the University of Washington in Seattle.
Spectrum spoke with Eichler, who was part of the Human Genome Project and the Telomere-to-Telomere Consortium, about what secrets may emerge from once-murky regions of the genome.
This interview has been edited for length and clarity.
Spectrum: How will having a more complete human genome affect autism research?
Evan Eichler: Because our reference genome was incomplete, some gene sequences were not correctly mapped to their place in the genome. So when we would find a variant in an autism genome that was missing from the reference genome, we didnt always know where it was or which gene or genes it affected. This new telomere-to-telomere draft improves mapping across the board. The sequences we gather from people with autism are now more likely to be mapped to the right place.
One phenomenon often associated with autism is the deletion or duplication of DNA, known as copy number variation (CNV). In our recent paper in Science, we analyzed the new telomere-to-telomere data and found that it was a better predictor of true copy number 9 times out of 10 when compared with the old reference. That means were in a much better position to assess CNVs, which we know to contribute to autism, than with the old reference that was full of holes.
S: How was this updated human genome sequence produced differently from previous ones?
EE: We typically sequence autism genomes with short reads, which are just a few hundred bases long. When we do this, were missing genetic variation that occur over long stretches of DNA, particularly structural variation such as large deletions, duplications and rearrangements of DNA. We have previously shown that about 75 percent of all structural variation in the human genome goes undetected if we rely only on short-read data. Roughly 10 percent of autism cases stem from known structural variation in DNA. If we can sequence the genomes of autism families with long reads, many thousands of bases long, we can explore the 75 percent of structural variation that was previously undetected and potentially find more genetic causes of autism.
S: Are there potentially new autism-linked genes in the more complete genome?
EE: About 500 genes have been mapped to complex regions of the new reference genome that were previously excluded from sequencing studies because our techniques didnt reliably map there. Among those genes are ones important for brain function, such as SRGAP2C. The number of copies of this gene influences where, how and when dendrites form during development, which influences the density and strength of synaptic connections. Its a gene incredibly important to brain function, whose duplicate copies we couldnt reliably detect with short reads.
Another gene, ARHGAP11B on chromosome 15, was previously found to be deleted in two people with autism and intellectual disability. Its known to increase neuronal stem cell division during development. That gene is typically not studied in autistic people because it was mapped to very repetitive regions of the genome that previous genome-sequencing techniques skipped over entirely.
S: What could we learn about autism from the dark regions of the human genome that do not code for proteins?
EE: DNA that makes up the short arms of human chromosomes, called acrocentric DNA, may be important in autism. Those stretches were only sequenced in the last year or so of the Telomere-to-Telomere project.
There are gene families in acrocentric DNA that encode rDNA, which helps form the ribosomes that produce proteins in cells. We know autism is often linked with having too many or too few copies of genes; acrocentric DNA is another category of DNA we can now analyze for the same problem. If we can compare the rDNA of people with autism with that of neurotypical individuals, any differences we see may help us understand the chances of developing autism.
S: Now that we have a new reference genome, will some autism studies need to be repeated?
EE: Yes, well need to run all autism genomes against this new, more complete reference genome. Im particularly interested in looking for variations in genes on the X chromosome, which is linked with sex. There are significant sex differences in boys versus girls when it comes to autism, with boys four times more likely to be autistic than girls. Now, with the new reference genome, we can detect copy number variations and other genetic variation better than before, including on the X chromosome.
We would also like to look at unsolved cases of autism those not linked to any known rare genetic variants and those without high polygenic risk scores, which reflect common genetic variants associated with the condition. These unsolved cases account for a very large fraction of kids with autism. Maybe in the dark regions of the genome, or in genes not characterized before, we can find answers especially with long-read sequences of Mom, Dad and unaffected siblings to shed light on how these unsolved cases are genetically distinct or similar to their family members.
S: What about methylated DNA DNA with chemical tags called methyl groups on top. There is evidence that these epigenetic tags, which influence gene activity, play a role in autism.
EE: With new long-read sequencing techniques such as nanopore sequencing, we can distinguish methylated sequences without having to amplify or convert the DNA beforehand, as was necessary with prior techniques. There might be differences in epigenetic modifications of DNA between people with and without autism that we missed before, which could help address some of the unsolved cases of autism.
S: How feasible is it for researchers to conduct long-read sequencing, or for families to access it?
EE: The major limitation is the cost. Sequencing and assembling a genome well with long reads costs about $10,000, compared with about $1,000 with short reads. Most insurance companies are not going to pay for long-read sequencing. Theres also the issue of throughput. Since it started in 2016, the SPARK project has aimed to look at 50,000 families using exome sequences, which capture only the protein-coding regions of the genome. In that same time, we could look at just 50 families with long-read whole-genome sequencing. [SPARK is funded by the Simons Foundation,Spectrumsparent organization.]
But costs always come down with time. I think that long reads will replace short reads in 10 years. I think every family deserves to have their genomes fully sequenced and characterized, to help them make decisions such as what the best care for their children should be. We just have to get the technology to a cost-effective point.
S: The newly sequenced parts of the genome often contain highly repetitive DNA. Autism has been linked to the presence of such repetitive regions. What might these new regions tell us about autism?
EE: The short answer is we dont know yet. But there is evidence that those regions are very relevant to autism. Two common genetic causes of autism include duplications on chromosome 15q, which account for about 1.5 percent of autism cases, and deletions on 16p11.2, which account for just under 1 percent of autism cases. We know that repetitive regions are hotspots for chromosomal damage that can lead to deletions and duplications, but they werent precisely mapped. Now we can precisely map these regions of genomic instability and gain insights on how breaks occur there and potentially lead to autism.
S: Does anything else come to mind with this new work?
EE: One thing thats still a puzzle is that the same genetic variation strongly linked with autism can have very different outcomes in one kid versus another. Some children may be mildly affected, whereas others may be severely affected. I dont think the odyssey of this work ends with finding the primary genetic causes of autism. We need to understand the background in which these variations lie the way they interact with other genetic variation to understand their true outcome.
Another thing I have reflected on more recently is how most of the innovations we see with this new project were driven by scientists a full generation younger than me. I think that bodes well for the future, to have so many young people interested in solving these difficult problems. The future of human genetics research is in good hands.
Cite this article: https://doi.org/10.53053/GPXL5356
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Study probes the relationship between genetics, proteins, and disease risk – The Hub at Johns Hopkins
Posted: at 11:24 am
ByAnnika Weder
A nearly 40-year-old study is the basis for new groundbreaking collaborative research identifying the relationship between genetics, proteins, and disease risk, while shedding light on racial health disparities in the process.
The new study, the results of which have been published in a paper in Nature Genetics, has provided a wealth of information that will allow the research community to test the ways in which proteins affect health outcomes, such as the risk for developing various types of cancer or heart disease or contracting COVID-19. The work could also lead to the development or repurposing of therapeutic drugs to treat human disease. The researchers hope the study will increase the understanding of the genetic basis of disease, in particular because the diversity of study participants will unlock new information about the links between proteins and disease.
The makings of this comprehensive study date back to the mid-1980s, when the Atherosclerosis Risk in Communities study was launched with Josef Coresh from the Department of Epidemiology in the Bloomberg School of Public Health as a principal investigator. ARIC, for which Johns Hopkins is a key field center, investigated causes of atherosclerosisa disease characterized by the build-up of fats, cholesterol, and other substances in the walls of arteriesand measured how cardiovascular risk factors, medical care, and outcomes vary by race, sex, place, and time.
The study was notable in two critical ways: it followed individuals for decades, collecting biological samples at regular intervals; and it included Americans of European ancestry as well as Americans of African ancestry. Beginning in 1987, more than 10,000 participants regularly received physical examinations and follow-up phone calls to maintain contact and to assess the health status of the cohort. Data collected include participants' medical history, demographics, health behaviors, and genetic information. The ARIC study has become a valuable resource, resulting in over 2,500 publications to date. Many independent research projects have used ARIC data for a range of topics including the study of heart disease, kidney disease, diabetes, and cognitive decline.
When Nilanjan Chatterjee, Bloomberg Distinguished Professor of biostatistics and genetic epidemiology, learned through graduate students he was co-advising with Coresh that ARIC also collected participants' proteomic datainformation about the proteins present in organismshe realized the immense untapped potential this resource held.
Image caption: Nilanjan Chatterjee
Image credit: CHRIS HARTLOVE
Proteins have a central role in many biological functions, supporting the structure, function, regulation, and repair of organs, tissues, and cells. Proteins support muscle contraction and movement, for example. They transmit signals to coordinate processes between different organs and move essential molecules around the body. Antibodies that support immune function, hormones that help coordinate bodily function, and enzymes that carry out chemical reactions such as digestion are all proteins. Because proteins control many of the mechanisms critical to an organism's health, diseases can often trace their origins to mutations in proteins.
Proteomics, the systemic analysis of proteins, gathers information about the proteome, the complete set of proteins produced by a given cell, organ, or organism. It falls under a class of disciplines collectively referred to as omics, which aim to collectively characterize the groups of biological molecules that translate into the structure, function, and dynamics of an organism. Other examples of omics studies include genomics, the study of an organism's full genetic information; epigenomics, the study of the supporting structure of the genome; and transcriptomics, the study of the set of all RNA molecules.
"ARIC is an incredibly unique data source, both because of the amount of genetic, proteomic, and other omic data they have on such a large number of study individuals, and because of its inclusion of individuals from European and African ancestries," says Chatterjee. "Diverse ancestry data is completely lacking in many omics studies. ARIC had a wealth of proteomic data that had not been analyzed, so we were very happy to take advantage of this incredible resource available to us right here at Johns Hopkins."
For their study, the researchers first analyzed genetic variants that correlate with protein levels in individuals to identify protein quantitative trait loci, or pQTL, portion of DNA. They then developed machine learning-based models that can predict information about an individual's proteinsinformation that is not always collectedbased on genetic information, which is often more accessible in large-scale studies.
Nilanjan Chatterjee
Bloomberg Distinguished Professor of biostatistics and genetic epidemiology
This model in turn will allow scientists to identify links between the levels of certain proteins in an organism and its corresponding disease risk. Knowing which proteins to target in order to prevent development of a disease is crucial for developing new drug therapies or repurposing existing drug therapies, as many drugs work by targeting the body's proteins.
To demonstrate how the model works, the team applied it to proteome-wide association studies for two related traits: gout, a common form of arthritis, and its closely related biomarker, uric acid. The results showed that an existing drug could be repurposed to combat gout.
"'Omics' innovations have made multi-disciplinary collaborations necessary, exciting, and productive," says Coresh. "The lived experience of over 10,000 participants in the ARIC cohort, combined with data on nearly 5,000 protein levels in their blood, allowed for the development of tools that are broadly applicable to human health and disease. We have already seen more than a half a dozen new investigations using the tools and the methods will be even more broadly applicable."
For Chatterjee, the study's powerful models and insightful findings underlined the importance of using diverse populations in genetic and omics studies.
"African populations in particular have a lot more genetic variation because the population is older," Chatterjee says. "Excluding people of African ancestry means we miss out on a large fraction of genetic variations and how it impacts health outcomes. Taking results from a genome-wide association study done with only individuals of European ancestry and trying to apply the results to other populations does not work as well for understanding disease risk, which is not surprising. To best serve all patients, diversity in omics studies is imperative."
Josef Coresh
Epidemiologist and principal investigator on the ARIC study
In addition, the team found that information garnered from populations of African ancestry added incredible value for interpreting results from study participants overall.
"Because European populations are newer, their genes are more confoundedmany variants always come together, and it is difficult to determine which genetic variant is causally related to a trait," Chatterjee explains. "African populations are older, and over more generations, the tight linkage among variants have broken down and it becomes possible to identify which variants are most likely to be the causal variant for a trait."
Looking forward, for Chatterjee, an exciting aspect of this project was the immense potential for impact these models have. Chatterjee hopes that a multi-omics approach in a multi-ancestry study will unlock a more comprehensive understanding of the genetic basis of complex disease and how that genetic basis arises. Next steps may include developing and improving statistical and machine learning models to combine data from populations of multiple ancestries, data from other types of -omics studies, and extending analysis to rare variants.
The authors emphasize that the study would not be possible without the strong partnerships and collaborations across Johns Hopkins and beyond, including the sophisticated data analysis led by Department of Biostatistics PhD student Jingning Zhang and post-doctoral fellow Diptavo Dutta.
Given the collaborative nature of the undertaking, it was important to the team to make the resources and models they developed available to others. They have made the models available online.
"Anyone can download these models for use in their own study to test for the effect of proteins on whichever traits they are investigating," Chatterjee explains. "Our work has already generated ideas for many follow-up studies using proteomic data, and it has been exciting to see that, in fact, people have already started using the models in their own protein association studies."
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