DNA Buried 7,000 Centuries Is Retrieved
By NICHOLAS WADE
The genome is 10 times as old as any retrieved so far, and scientists
now say that DNA should be recoverable from animals that lived a million
years ago.
Once a Rebel, McCain Walks the Party Line
By JENNIFER STEINHAUER
Senator John McCain of Arizona appears to have entered Version 3 of his
long and multipronged career in the upper chamber — partisan warrior and
party stalwart.
中央研究院生物多樣性中心特聘研究員兼主任李文雄院士，以其傑出的遺傳學與演化論的學術貢獻，於13日榮獲英國遺傳學會（Genetics Society）頒授2009年孟德爾獎章（Mendel Medal），成為第一位獲此殊榮的亞洲科學家。
He believes genetics is “what China really wants”. Despite the small size of the British industry Mr Jackson says it is a world leader. “Even America comes to us to buy genetics, mainly pigs but also sheep and cattle.” Genetics improves pig economics, he says. British pigs can be fattened up for the kill in just three months but Chinese pigs take a year – or about 260 additional days of 6kg of cereal-based feed for half-a-billion animals. “Take that away and you can see how the genetics industry can do such a wonderful job for planet Earth,” said Mr Jackson.
他認為，基因才是“中國真正想要的”。傑克遜表示，儘管英國養豬產業規模小，卻是全球的佼佼者。 “連美國人都跑過來向我們購買基因，主要是豬的基因，不過也有牛羊。”他表示，基因可以改善養豬經濟。英國豬隻要3個月就能養夠膘，屠宰，但中國豬要用1年——即中國的5億頭豬，每頭要用6千克穀物飼料多餵養260天左右。傑克遜表示：“減去這些額外投入，你會發現基因工業可以給行星地球帶來如此美妙的變化。”
I.B.M. Joins Pursuit of $1,000 Personal Genome
By JOHN MARKOFF One of the oldest names in computing is vying for a high-tech piece of the personalized medicine puzzle.
Scientists and Philosophers Find That ‘Gene’ Has a Multitude of Meanings
Right, Rick Friedman for The New York Times
Evelyn Fox Keller, left, a science historian, calls the language of molecular biology “historical baggage,” while Eric S. Lander of the Broad Institute says he is not worried about any confusion that may arise in references to “genes.”
I owe an apology to my genes. For years I offhandedly blamed them for certain personal defects conventionally associated with one’s hereditary starter pack — my Graves’ autoimmune disease, for example, or my hair, which looks like the fibers left behind on the rim of an aspirin bottle after the cotton ball has been removed, only wispier.
Skip to next paragraph
This Week's Podcast
Related
Multimedia
David Corcoran, a science editor, explores some of the topics addressed in this week’s Science Times. This Week's PodcastRelated
Now it turns out that genes, per se, are simply too feeble to accept responsibility for much of anything. By the traditional definition, genes are those lineups of DNA letters that serve as instructions for piecing together the body’s proteins, and, I’m sorry, but the closer we look, the less instructive they seem, less a “blueprint for life” than one of those disappointing two-page Basic Setup booklets that comes with your computer, tells you where to plug it in and then directs you to a Web site for more information.
Scientists have learned that the canonical “genes” account for an embarrassingly tiny part of the human genome: maybe 1 percent of the three billion paired subunits of DNA that are stuffed into nearly every cell of the body qualify as indisputable protein codes. Scientists are also learning that many of the gene-free regions of our DNA are far more loquacious than previously believed, far more willing to express themselves in ways that have nothing to do with protein manufacture.
In fact, I can’t even make the easy linguistic transition from blaming my genes to blaming my whole DNA, because it’s not just about DNA anymore. It’s also about DNA’s chemical cousin RNA, doing complicated things it wasn’t supposed to do. Not long ago, RNA was seen as a bureaucrat, the middle molecule between a gene and a protein, as exemplified by the tidy aphorism, “DNA makes RNA makes protein.” Now we find cases of short clips of RNA acting like DNA, transmitting genetic secrets to the next generation directly, without bothering to ask permission. We find cases of RNA acting like a protein, catalyzing chemical reactions, pushing other molecules around or tearing them down. RNA is like the vice presidency: it’s executive, it’s legislative, it’s furtive.
furtive Show phonetics
adjective
(of people) behaving secretly so that other people do not notice them, or (of actions) done secretly and often quickly so that people do not notice:
I saw him cast a furtive glance at the woman at the table to his right.
He made one or two furtive phone calls.
There was something furtive about his behaviour and I immediately felt suspicious.
furtively Show phonetics
adverb
As she turned away I saw him sniff furtively under his arm.
For many scientists, the increasingly baroque portrait of the genome that their latest research has revealed, along with the muddying of molecular categories, is to be expected. “It’s the normal process of doing science,” said Jonathan R. Beckwith of Harvard Medical School. “You start off simple and you develop complexity.” Nor are researchers disturbed by any linguistic turbulence that may arise, any confusion over what they mean when they talk about genes. “Geneticists happily abuse ‘gene’ to mean many things in many settings,” said Eric S. Lander of the Broad Institute. “This can be a source of enormous consternation to onlookers who want to understand the conversation, but geneticists aren’t bothered.”
In Dr. Lander’s view, the “kluges upon kluges” are an occupational hazard. “We’re trying to parse an incredibly complex system,” he said. “It’s like the U.S. economy. What are your functional units? Employees and employers? Consumers and producers? What if you’re a freelancer with multiple employers? Where do farmers’ markets and eBay map onto your taxonomy?”
“You shouldn’t be worried about the fact that you have to layer on other things as you go along,” he said. “You can never capture something like an economy, a genome or an ecosystem with one model or one taxonomy — it all depends on the questions you want to ask.”
Dr. Lander added: “You have to be able to say, this is Tuesday’s simplification; Wednesday’s may be different, because incredible progress has been made by those simplifications.”
For other researchers, though, the parlance of molecular biology is desperately in need of an overhaul, starting with our folksy friend, gene. “The language is historical baggage,” said Evelyn Fox Keller, a science historian and professor emeritus at M.I.T. “It comes from the expectation that if we could find the fundamental units that make stuff happen, if we could find the atoms of biology, then we would understand the process.”
“But the notion of the gene as the atom of biology is very mistaken,” said Dr. Keller, author of “The Century of the Gene” and other books. “DNA does not come equipped with genes. It comes with sequences that are acted on in certain ways by cells. Before you have cells you don’t have genes. We have to get away from the underlying assumption of the particulate units of inheritance that we seem so attached to.”
Dr. Keller is a big fan of the double helix considered both in toto and in situ — in its native cellular setting. “DNA is an enormously powerful resource, the most brilliant invention in evolutionary history,” she said. “It is a far richer and more interesting molecule than we could have imagined when we first started studying it.”
Still, she said, “it doesn’t do anything by itself.” It is a profoundly relational molecule, she said, and it has meaning only in the context of the cell. To focus endlessly on genes, she said, keeps us stuck in a linear, unidirectional and two-dimensional view of life, in which instructions are read out and dutifully followed.
“What makes DNA a living molecule is the dynamics of it, and a dynamic vocabulary would be helpful,” she said. “I talk about trying to verb biology.” And to renoun it as well. Writing last year in the journal PloS One, Dr. Keller and David Harel of the Weizmann Institute of Science suggested as an alternative to gene the word dene, which they said could be used to connote any DNA sequence that plays a role in the cell. So far, Dr. Keller admits, it has yet to catch on.
Complex as our genome is, it obviously can be comprehended: our cells do it every day. Yet as the physician and essayist Lewis Thomas once noted, his liver was much smarter than he was, and he would rather be asked to pilot a 747 jet 40,000 feet over Denver than to assume control of his liver. “Nothing would save me or my liver, if I were in charge,” he wrote.
In a similar vein, we may never understand the workings of our cells and genomes as comfortably and cockily as we understand the artifacts of our own design. “We have evolved to solve problems,” Dr. Keller said. “Those do not include an understanding of the operation of our own systems — that doesn’t have much evolutionary advantage.” It’s quite possible, she said, that biology is “irreducibly complex,” and not entirely accessible to rational analysis. Which is not to say we’re anywhere near being stymied, she said: “Our biology is stretching our minds. It’s another loop in the evolutionary process.”
And if canonical genes are too thin a gruel to explain yourself to yourself, you can always reach for the stalwart of scapegoats. Blame it all on your mother, who surely loved you too much or too little or in all the wrong ways.
現代人的起源問題一直是一個備受爭論的話題，現今「走出非洲」理論是多數人普遍接受的主流理論。2012年5月美國DNA譜系科學院Anatole A. Klyosov重新審視了「走出非洲」論和歐羅巴人種的起源，認為人類並非起源於非洲，並使用“Walk through Y”項目的數據證明了這一觀點。研究結果發表在科研出版社英文期刊《Advances in Anthropology》(人類學進展)上(點擊閱讀原文)。
在過去的二十年裡，「走出非洲」論已經人盡皆知，但它卻從未被直接證明過。然而，對於許多專家來說，這一理論仍然具有著令人信服的吸引力。這一理論 主要基於這樣一個前提：最古老的人群顯示出最大的多樣性，而非洲人是多樣性最大的人群。其實這並不是一個強有力的論點，因為不同DNA的混合也會導致高的 多樣性。
作者從解剖學角度研究了現代人類的起源，根據人類遺傳學和DNA系統發育的分類發展，針對男性Y染色體單倍型，提出了一個歐羅巴人種(白種人又稱歐亞人種或高加索人種)起源的時間表，確定其在今天已知的所有單倍群中的位置，提供證據重新審視「走出非洲」論的正確性。
作者在非洲人Y染色體單倍型中發現了一個重大的多樣性，是幾個非常遙遠的血統的混合結果，而且其中一些不一定是來自非洲人，證明歐羅巴人種不包含「非洲」單核苷酸多態性(單倍型類群A或B)。這些重要的發現削弱了眾所周知的「走出非洲」的理論。
17個主要單倍型類群中46個進化亞枝的7556種單倍型，按照它們祖先的單倍型和與共同祖先的時間間隔，設計了一個時間平衡單倍型類群樹，發現非 洲單倍型類群A起源於距今132000±12000年前，來自於所有的其他有著單獨共同祖先的單倍群，我們稱其為β單倍群，起源於 64000±6000年前。一個單倍群A和β單倍群下游的共同祖先，創造了α單倍群，起源於160000±12000年前。
α單倍群和β單倍群的起源是未知的，但是最有可能的是它們是一個巨大的三角關係，從西方歐洲中部延伸通過俄羅斯平原東部到黎凡特南部。單倍群B是β單倍群可能是在距今46000年遷移到非洲。
研究證明，歐羅巴人種單倍群並非起源於「非洲」的單倍型類群A或B，事實支持歐羅巴人種以及所有非非洲人的單倍型類群，並未攜帶單核苷酸多態性 M91、P97、M31、P82、M23、M114、P262 、M32、M59、P289、P291、P102、M13、M171、M118 (單倍型類群A及其進化亞枝單核苷酸多態性)或M60 、M181、P90(單倍型類群B)，這是最近在“Walk through Y”FTDNA項目中，幾百個來自各種單倍群的人顯示的結果。
2013年11月澳洲墨爾本考爾菲德南部國際岩石藝術聯合會(IFRAO) Robert G. Bednarik也在科研出版社英文期刊《Advances in Anthropology》(人類學進展)發表的一篇文章中，從多個角度分析反駁了「走出非洲」理論，認為「走出非洲」理論是一個騙局(點擊閱讀原文)。（新聞來源：科研出版社／爾灣閱讀）
Re-Examining the "Out of Africa" Theory and the Origin of Europeoids (Caucasoids) in Light of DNA Genealogy
Author(s)
Anatole A. Klyosov, Igor L. Rozhanskii
Seven thousand five hundred fifty-six (7556) haplotypes
of 46 subclades in 17 major haplogroups were considered in terms of
their base (ancestral) haplotypes and timespans to their common
ancestors, for the purposes of designing of time-balanced haplogroup
tree. It was found that African haplogroup A (originated 132,000 ±
12,000 years before present) is very remote time-wise from all other
haplogroups, which have a separate common ancestor, named β-haplogroup,
and originated 64,000 ± 6000 ybp. It includes a family of Europeoid
(Caucasoid) haplogroups from F through T that originated 58,000 ± 5000
ybp. A downstream common ancestor for haplogroup A and β-haplogroup,
coined the α-haplogroup emerged 160,000 ± 12,000 ybp. A territorial
origin of haplogroups α- and β-remains unknown; however, the most likely
origin for each of them is a vast triangle stretched from Central
Europe in the west through the Russian Plain to the east and to Levant
to the south. Haplogroup B is descended from β-haplogroup (and not from
haplogroup A, from which it is very distant, and separated by as much as
123,000 years of “lat- eral” mutational evolution) likely migrated to
Africa after 46,000 ybp. The finding that the Europeoid haplogroups did
not descend from “African” haplogroups A or B is supported by the fact
that bearers of the Europeoid haplogroups, as well as all non-African
haplogroups do not carry either SNPs M91, P97, M31, P82, M23, M114,
P262, M32, M59, P289, P291, P102, M13, M171, M118 (haplogroup A and its
subclades SNPs) or M60, M181, P90 (haplogroup B), as it was shown
recently in “Walk through Y” FTDNA Project (the reference is
incorporated therein) on several hundred people from various
haplogroups.
haplography
- 音節
- hap • log • ra • phy
- 発音
- hæplɑ'grəfi | -lɔ'g-
Haplogroup - Wikipedia, the free encyclopedia
en.wikipedia.org/wiki/Haplogroup
In molecular evolution, a haplogroup (from the Greek: ἁπλούς, haploûs, "onefold, single, simple") is a group of similar haplotypes that share a common ancestor ...genome
Syllabification: (ge·nome)
Pronunciation: /ˈjēˌnōm/
Definition of genome
noun
Biologyhaploid
- 音節
- hap • loid
- 発音
- hǽplɔid
- haploidの変化形
- haploids (複数形)
[形]
1 単一の.
2 《生物》半数（性）の, 単数（性）の. ⇒DIPLOID
━━[名]《生物》半数体, 単数体：一組だけの染色体を有する生物体［細胞］.Derivatives
genome
- 音節
- ge • nome, -nom
- 発音
- dʒíːnoum, -nɑm | -nɔm
- レベル
- 社会人必須
- genomeの変化形
- genomes (複数形)
stalwart[stal・wart]
- レベル：社会人必須
- 発音記号[stɔ'ːlwərt]
[形]
1 〈支持者などが〉忠誠心のあつい, 熱烈な.
2 ((形式))〈特に男性が〉屈強な.
━━[名]
1 （党・組織の）熱烈な支持者.
2 屈強な人.
stal・wart・ly
[副]autoimmune
Autoimmunity is the system of immune responses of an organism against its own cells and tissues. Any disease that results from such an aberrant immune response is termed an autoimmune disease.
1 則留言:
in toto (in TO-to)
adverb: Totally; as a whole.
Etymology
From Latin totus (total). First recorded use: 1639.
Usage
"Garcia opposes lifting the embargo in toto." — Tim Padgett; Florida's 25th District; Time (New York); Sep 27, 2010.
張貼留言