重點就是倒數第二頁的一小段，顏院報道了數據收集和結構確定的過程 （DATA COLLECTION AND STRUCTURE DETERMINATION）。 我來給大家總結濃縮一下：
第一步，收集了數據，這沒什麽可說的（The initial phases of D-xylose-bound XylE were obtainedfrom the Hg-derivative crystals by single anomalous diffraction (SAD) using the program ShelxC/D/E）。
第二步，用一個軟件從晶體數據中算出了一個粗結構（The electron density shows that there is one molecule in each asymmetry unit. Then a crude helical model was built manually using the program COOT）。
我們都知道水銀這種物質特別重，X射線轟擊這樣的物質，會在感光底片上留下格外特別的印記，這個水銀原子就像如天書一般的結構衍射圖中的一參照物。最後，純體蛋白的衍射雲圖，和被水銀標記的蛋白圖一比較疊加，相位問題大為改善，整個蛋白分子結構就浮出海麵了（With this partial model as input, the identified Hg atom positions were refined and phases were recalculated using the PHASER SAD experimental phasing module）。
4. 剩下的步驟，就如同釣魚收杆一樣，整個蛋白分子的結構如魚咬鉤被拉出海麵，這個魚鉤就是這個水銀標記分子。文章用的術語就是：原始的粗結構用XXXX軟件得以重建和細化（With the improved map, the crude model was rebuilt using COOT and refined with PHENIX）。
我看了顏院確定結構的步驟和參考文獻，她闡述了他們課題組獨立地根據晶體衍射雲圖推導出葡萄糖轉運子的結構，引經據典，無懈可擊，用個英語詞講就叫“BY THE BOOK”。
另外，你如果仔細讀顏院文章摘要裏的文字，有這麽一句話：盡管有大量（前人）的工作，葡萄糖受體的結構信息，依然在很大程度上是未知的（Despite rigorous efforts, the structural information for GLUT1–4 or their homologues remains largely unknown）。 什麽叫做“很大程度上未知”（largely），這個詞的解讀，恐怕有很大的伸縮空間。否則為什麽不叫“完全未知”呢？
可是罵歸罵，你還不能真正去指控巴爾違反了什麽規條，因為這個人所作的一切，完全是在規章製度之內，“by the book”！
這個規章製度是什麽呢？根據司法部的“特別檢察官法”，穆勒報告是提交給司法部長的一份“保密”材料，原文如下：At the conclusion of the Special Counsel's work, he or she shall provide the Attorney General with a confidential report explaining the prosecution or declination decisions reached by the Special Counsel。
如果不是漏看，而是有意忽略的話，那動機就好解釋了。顏院文章的取勝之處在於機理和結構一把抓，一舉突破了半個世紀的自然之謎，於是得到了NATURE的青睞。然而，如果說成是靠結構研究證實了某某人20年前老文章裏的分子機理，就成了拾人牙慧了，NATURE主編可能要建議她們轉投《結構生物學雜誌》（Journal of Structual Biology）這樣的二流期刊。
Your description of William Barr is neither relevant nor correct. He published the full (redacted as stipulated by law) Mueller report immediately after his summary for everyone to see. What conclusion can a group of experienced attorneys draw that would be different from that of Barr?
nightrider 發表評論於
回複 'cng' 的評論 :
Informative article.
However, your explanation of the phase problem in response to gx123 is incorrect. The detector of diffracted x-ray captures the temporal average of the electromagnetic power (Poynting vector) of the incoming light. The averaging process erases the phase information. The phase information is erased even when there is only one atom. The interference is irrelevant to the phase loss. If the phase information of the incoming light is not lost but determined, it is precisely the interference (in phase) or the superposition that submits the diffraction to the power of the Fourier analysis.
The Uptake of Hexose Phosphates (Uhp) is a protein system found in bacteria. It is a type of two-component sensory transduction pathway which helps bacteria react to their environment.
The uhp system is composed of UhpA, UhpB, UhpC, and UhpT. UhpB and UhpC are both transmembrane proteins which form a complex with each other. UhpA is a signal protein found in the cytoplasm.[2] UhpT is a transporter protein which facilitates the uptake of phosphorylated hexose molecules into the cell.
JessAB 發表評論於 2019-05-14 14:47:43
2. In 2012 Nieng’s Nature paper, she actually referenced Pao's 1998 review paper where Pao cited Yan’s 1993 and 1995 papers, which means Nieng indeed cited R. Yan's papers indirectly.
I believe that similar incidents happened more than once in academia. To safeguard one's results and credit, the only way is to build up on them, keeping publishing papers on that topic till people can't ignore them. If this is just one paper and the author moves on to something else, well who knows what's gonna happen.
但是，IT IS EASIER SAID THAN DONE. 從晶格電子密度圖到衍射斑點，丟失了很多信息。舉一個例子，你在感光片上看到一個比較弱的感光點，它有可能是一個較弱（振幅小）的X波擊中了底片；而另一種可能是有兩束很強的X波，由於他們的相位可能差了180度，一個X波的波峰，剛好碰到了另一個X波的峰底，結果，兩個相反的強振幅反而互相抵消了，所以在底片上留下的也是一個弱感光點。
After reading previous blogs about this topic, I am wondering what is the point of arguing why Nieng did not mention Yan’s work on her papers.
1. Nieng’s two papers were about crystal structures determined by X-ray which no one ever reported before although R. Yan had studied in the similar field before.
2. In 2012 Nieng’s Nature paper, she actually referenced Pao's 1998 review paper where Pao cited Yan’s 1993 and 1995 papers, which means Nieng indeed cited R. Yan's papers indirectly.
3. I think there is no requirement to reference directly every related paper especially when it was 20 years old.
Don’t get me wrong I have tremendous respect for the work R. Yan did 20 years ago.
(I can only type English on my computer)
北佛風光 發表評論於
“如果不是漏看，而是有意忽略的話，那動機就好解釋了。顏院文章的取勝之處在於機理和結構一把抓，一舉突破了半個世紀的自然之謎，於是得到了NATURE的青睞。然而，如果說成是靠結構研究證實了某某人20年前老文章裏的分子機理，就成了拾人牙慧了，NATURE主編可能要建議她們轉投《結構生物學雜誌》（Journal of Structual Biology）這樣的二流期刊。”
重點就是倒數第二頁的一小段，顏院報道了數據收集和結構確定的過程 （DATA COLLECTION AND STRUCTURE DETERMINATION）。 我來給大家總結濃縮一下：
第一步，收集了數據，這沒什麽可說的（The initial phases of D-xylose-bound XylE were obtainedfrom the Hg-derivative crystals by single anomalous diffraction (SAD) using the program ShelxC/D/E）。
第二步，用一個軟件從晶體數據中算出了一個粗結構（The electron density shows that there is one molecule in each asymmetry unit. Then a crude helical model was built manually using the program COOT）。
我們都知道水銀這種物質特別重，X射線轟擊這樣的物質，會在感光底片上留下格外特別的印記，這個水銀原子就像如天書一般的結構衍射圖中的一參照物。最後，純體蛋白的衍射雲圖，和被水銀標記的蛋白圖一比較疊加，相位問題大為改善，整個蛋白分子結構就浮出海麵了（With this partial model as input, the identified Hg atom positions were refined and phases were recalculated using the PHASER SAD experimental phasing module）。
4. 剩下的步驟，就如同釣魚收杆一樣，整個蛋白分子的結構如魚咬鉤被拉出海麵，這個魚鉤就是這個水銀標記分子。文章用的術語就是：原始的粗結構用XXXX軟件得以重建和細化（With the improved map, the crude model was rebuilt using COOT and refined with PHENIX）。
我看了顏院確定結構的步驟和參考文獻，她闡述了他們課題組獨立地根據晶體衍射雲圖推導出葡萄糖轉運子的結構，引經據典，無懈可擊，用個英語詞講就叫“BY THE BOOK”。
另外，你如果仔細讀顏院文章摘要裏的文字，有這麽一句話：盡管有大量（前人）的工作，葡萄糖受體的結構信息，依然在很大程度上是未知的（Despite rigorous efforts, the structural information for GLUT1–4 or their homologues remains largely unknown）。 什麽叫做“很大程度上未知”（largely），這個詞的解讀，恐怕有很大的伸縮空間。否則為什麽不叫“完全未知”呢？
可是罵歸罵，你還不能真正去指控巴爾違反了什麽規條，因為這個人所作的一切，完全是在規章製度之內，“by the book”！
這個規章製度是什麽呢？根據司法部的“特別檢察官法”，穆勒報告是提交給司法部長的一份“保密”材料，原文如下：At the conclusion of the Special Counsel's work, he or she shall provide the Attorney General with a confidential report explaining the prosecution or declination decisions reached by the Special Counsel。
如果不是漏看，而是有意忽略的話，那動機就好解釋了。顏院文章的取勝之處在於機理和結構一把抓，一舉突破了半個世紀的自然之謎，於是得到了NATURE的青睞。然而，如果說成是靠結構研究證實了某某人20年前老文章裏的分子機理，就成了拾人牙慧了，NATURE主編可能要建議她們轉投《結構生物學雜誌》（Journal of Structual Biology）這樣的二流期刊。
