实际上，“T单倍型组”（T haplogroup）根本就不是什么“一段……特殊序列”，而是一种“指纹特征”。原来，英国科学家在1998年使用DNA指纹技术来确定杰弗逊与其女奴赫明斯后裔的亲缘关系。具体地说，就是要通过对Y染色体不同位点进行DNA扩增，然后比较个体之间的异同。一般来说，DNA指纹分析所根据的标记（DNA片段）越多，得出的结果越可靠。并且，标记之间，也需要具有一定的物理距离。这组科学家在Y染色体上进行了19个标记物的分析，它们之间的距离，至少有两千万个碱基（～20 Mb，见下图DYS393与DYS392）的距离。这种跨越了大半个染色体的DNA，还能够算是“一段”吗？请问方博士，“研究人员”是怎么“分析”这“段”“特殊序列”的啊？
方分子遗传学家不仅对分子遗传学懵懵懂懂，他对美国历史也是迷迷糊糊。比如，他说杰弗逊“死时留下遗嘱，卖掉部分土地和黑奴还债。”事实是，杰弗逊死时留下的遗嘱，除了给外孙留下的财产之外，将全部财产用于偿还债务（I subject all my other property to the payment of my debts in the first place
"The amalgamation of whites with blacks produces a degradation to which no lover of his country, no lover of excellence in the human character, can innocently consent." (E. M. Halliday. Understanding Thomas Jefferson. HarperCollins 2002. p.153)
"The improvement of the blacks in body and mind, in the first instance of their mixture with the whites, has been observed by every one, and proves that their inferiority is not the effect merely of their condition in life." (同上，p.151)
如果说假冒伪劣方分子遗传学家不懂分子遗传学，假冒伪劣方美国通不通美国历史还情有可原的话，那么这个说着一口字正腔圆福建云霄英语的“将马到死”奖获得者翻译英语也能出错，就让人难以原谅。原来，根据方舟子照抄的维基百科辞条，“杰斐逊和赫明斯”的“不正当关系”一直保持了近40年（lasted nearly four decades），或38年（Jefferson had a long-term intimate liaison with Hemings for 38 years），但是，方舟子却说：
“In 1968 the historian Winthrop Jordan noted that Jefferson was at Monticello "nine months prior to each birth" of Hemings' children, during a 13-year period when he was often away for months at a time”（1968年，历史学家乔丹发现在一段13年的时间中，杰弗逊经常长期在外，但在赫明斯每次生产之前的九个月，杰弗逊都在蒙蒂切罗。）
In 1773, the year after Jefferson married the young widow Martha Wayles Skelton, her father died. She and Jefferson inherited his estate, including 11,000 acres, 135 slaves, and £4,000 of debt.
Sally Hemings was three-fourths white and is believed to be a half-sister to Jefferson's late wife, as her father was likely John Wayles. As a widower, Wayles had six children by his 12-year liaison with his mulatto slave Betty Hemings; the youngest was Sally.
Sally Hemings was three-quarters white, described as "mostly white" and "decidedly attractive", and was the half sister of Jefferson's beloved wife.
Hemings' children were seven-eighths European in ancestry and legally white according to Virginia law of the time. Of the four who survived to adulthood: William Beverley, Harriet Hemings, Madison Hemings and Eston Hemings, all but Madison eventually identified as white and lived as adults in white communities.
Since 1998 and the DNA study, most historians have accepted that the widower Jefferson had a long intimate relationship with Hemings, and fathered six children with her, four of whom survived to adulthood.
He allowed Beverley (male) and Harriet to "escape" in 1822 at ages 23 and 21, although Jefferson was already struggling financially and would be $100,000 in debt at his death.
In his 1826 will, Jefferson freed the younger brothers Madison and Eston Hemings, who were approaching the age of 21.
For instance, Madison Hemings' account was supported by the fact that Jefferson freed all of Sally Hemings' children, although he was deeply in debt. Hers was the only family whose members were all freed; Sally's daughter Harriet was the only female slave he ever freed.
Most importantly, Jefferson freed all the Hemings children; theirs was the only slave family to all go free from Monticello, they were the only slaves freed as they came of age, and Harriet Hemings was the only female slave he ever freed.
Jefferson also freed three older males related to Sally Hemings; they had each served him for decades.
In 1827 the remaining 130 slaves at Monticello were sold to pay the debts of Jefferson's estate.
Jefferson made no public comment on the matter,
"she [Hemings] had children which resembled Mr. Jefferson so closely that it was plain that they had his blood in their veins.... He [Randolph] said in one instance, a gentleman dining with Mr. Jefferson, looked so startled as he raised his eyes from the latter to the servant behind him, that his discovery of the resemblance was perfectly obvious to all."
According to an 1868 letter by Jefferson biographer Henry Randall to the historian James Parton, Jefferson's grandson, Thomas Jefferson Randolph, said that Jefferson's daughter, Martha, stated on her deathbed, that Jefferson had been away from Monticello for 15 months before one of Hemings' children was born, so could not be the father.
Martha Randolph, Jefferson's daughter, had made a deathbed claim that Jefferson was away for a 15-month period during which one of the Hemings' children was conceived.
Jefferson's grandson, Thomas Jefferson Randolph, told a historian in the 1850s that the late Peter Carr, a nephew of Jefferson's, had fathered Hemings' children.
Randolph then told Randall that the late Peter Carr, Jefferson's nephew and a married man at the time, had fathered Hemings' children, as explanation for the 'startling' close resemblance that every visitor to Monticello could see.
In the 1970s, as part of his six-volume biography of Jefferson, Malone was the first to publish a letter by Ellen Randolph Coolidge, Randolph's sister, who claimed the late Samuel Carr (also a married man), rather than his brother Peter, had fathered Hemings' children.
Historians generally asserted this denial for nearly 180 years.
In addition, they determined he would not have had such a relationship because of his expressed antipathy to blacks and miscegenation in his writings, combined with his perceived moral character.
In 1953 Jefferson's Farm Book was published, after having been rediscovered. Its records of slave births, deaths, purchases and sales provided researchers with considerable data about the lives of slaves at Monticello.
In 1968 the historian Winthrop Jordan noted that Jefferson was at Monticello "nine months prior to each birth" of Hemings' children, during a 13-year period when he was often away for months at a time. Fawn McKay Brodie also used this information in her biography of Jefferson, which contributed to her conclusion that he had fathered Hemings' children. The source for the birth dates of the children is Jefferson's Farm Book.
Researchers tested Y-chromosomal DNA from living male claimed descendants of Jefferson and Hemings.
In 1998 Dr. Eugene Foster with researchers at the University of Leicester tested the Y-DNA of male descendants of the Jefferson, Carr and Eston Hemings lines in an attempt to determine whether Thomas Jefferson or one of the Carrs had fathered Sally Hemings' children.
Because most of the Y chromosome is passed unchanged from father to son, apart from occasional mutations, DNA analysis of the Y chromosome can reveal whether or not individuals are likely to be male-line relatives. （Foster, EA, et al. (1998). "Jefferson fathered slave's last child
Jefferson had no acknowledged male descendant
Wayles-Jefferson descendants declined to have Thomas Jefferson's remains disturbed.
Thomas Jefferson did not have a surviving son from his marriage to Martha Wayles Skelton and thus did not have an acknowledged direct male descendant as a positive control. The team located male-line descendants of Thomas Jefferson's paternal uncle, Field Jefferson, who had the same Y-chromosomal DNA. Five such descendants (J41, J42, J47, J49, and J50) were located and their DNA was analyzed.
The five descendants of Field Jefferson (which are proxies for Thomas Jefferson) have nearly identical Y-chromosome DNA alleles, except for a single difference at J50.
The team located a male-line descendant of Sally Hemings' youngest son Eston Hemings Jefferson for genealogical DNA testing, as the other sons were not known to have direct male-line descendants.
Three Carr male descendants of Peter and Samuel Carr, the nephews in question, were tested. The results showed a consensus Carr haplotype for the male line. It was conclusively different from that of the Hemings descendant and the Jefferson male line. Foster said, "The simplest and most probable explanations for our molecular findings are that Thomas Jefferson, rather than one of the Carr brothers, was the father of Eston Hemings Jefferson. . ."
Because of mid-19th c. family testimony by Jefferson's grandchildren that one of his nephews, Peter or Samuel Carr, was the biological father of Hemings' children, historians had long asserted this. To test this tradition, researchers tested three male-line descendants (C27, C29, and C31) of Samuel and Peter Carr.
The three Carr descendants studied in the DNA analysis have "closely related haplotypes, with one (C29) showing a single microsatellite unit difference at one locus and a single MSY1 unit difference", probably due to mutation. Their consensus haplotype "differs substantially from the Jefferson family haplotype, even showing a biallelic marker difference, and thus the two families are readily distinguished." They are distinctly different from the Hemings and Woodson descendants. Thus, the Carrs were disproved as the ancestor of the Eston Hemings descendant, and the focus returned to Thomas Jefferson, as other historic evidence supported his paternity.
While another Jefferson male from his line would have had the same DNA as Thomas Jefferson, no other candidate from his male line had ever been identified as a possible father during the nearly 200 years of the historic controversy.
Because the Jefferson male line was found to be the K2 haplogroup (since 2008 referred to as haplogroup T (Y-DNA)), relatively rare in Europe, researchers in 2007 did additional studies to determine if it was represented among other Jefferson-surname males in England. As it was found among other Jefferson males unrelated to Jefferson's family, they concluded that the haplotype had likely become "indigenous" to England after some random, ancient migration.
The descendant of Eston Hemings has the same set of Y-chromosome DNA alleles as the Jefferson male line (simply, he "carries the Jefferson family haplotype."). This supports the claim that Thomas Jefferson could have been the father of Eston Hemings. It is impossible to prove absolutely that no other Jefferson fathered the child. (1) That would be proving a negative, and (2) any male who had the same Y-chromosome as Thomas Jefferson (other descendants of a common male ancestor) could have been the father, provided that this person had relations with Sally Hemings nine months before the birth of Eston Hemings. But, there is no historical evidence that Hemings had more than one partner.
The Scholars Commission Report (2001) and other scholars argue against Jefferson's paternity; they generally favor his younger brother Randolph Jefferson as a candidate as father of Hemings' children, although he was never seriously proposed before the results of the DNA study.
The study team acknowledged the historical body of evidence and said that the simplest explanation was that Thomas Jefferson was most likely the father. For instance, he was documented at Monticello at the time of each of Sally Heming's conceptions, and she never conceived when he was not there. Other circumstantial evidence supports his paternity (see historiography discussion above).
In 1968 the historian Winthrop Jordan noted that Jefferson was at Monticello "nine months prior to each birth" of Hemings' children, during a 13-year period when he was often away for months at a time.
He is believed to have had a relationship with Sally Hemings that lasted nearly four decades, until his death, and six children by her.
This confirmed the body of historical evidence, and most historians believe that Jefferson had a long-term intimate liaison with Hemings for 38 years, and fathered her six children of record, four of whom lived to adulthood.
As a widower, Wayles had six children by his 12-year liaison with his mulatto slave Betty Hemings; the youngest was Sally. As the historians Philip D. Morgan and Joshua D. Rothman have noted, this was one of numerous interracial relationships in the Wayles-Hemings-Jefferson families, which were also common in Virginia and the Upper South.