Gray worked extensively on a phenomenon that is now called the "Asa Gray disjunction", namely, the surprising morphological similarities between many eastern Asian and eastern North American plants. In fact, Gray felt the flora of eastern North America is more similar to the flora of "Japan than it is to the flora of western North America, but more recent studies have shown this is not so. While Gray was not the first botanist to notice this (it was first noticed in the early 18th century), beginning in the early 1840s he brought scientific focus to the issue. He was the first scientist in the world to possess the requisite knowledge set to do so as he had intimate knowledge of the northeast and southeast United States as well as eastern Asia – due to several contacts he had there. The phenomenon involves about 65 genera and is not limited to plants, but also includes fungi, arachnids, millipedes, insects, and freshwater fishes. It was believed that each pair of species might be international "sister species, but it is now known that this is not generally the case; the species involved are less closely related to one another. Today, botanists suggest three possible causes for the observed morphological similarity, which probably developed at different times and via different pathways; the species pairs are: (1) the products of similar environmental conditions, (2) Neogene, which is not the "early Tertiary", and relics of species that were formerly widely distributed but diversified later, probably during the "Miocene, (3) not as morphologically similar as was previously believed. Gray's work in this area gave significant support to Darwin's theory of evolution and is one of the hallmarks of Gray's career. In 1880 "David P. Penhallow was accepted by Gray as a research assistant. Penhallow aided in Gray's work regarding the distribution of northern hemisphere plants, and in 1882 Gray recommended Penhallow as a lecturer to "Sir John Dawson of "McGill University in "Montreal, Quebec, Canada.
Despite no longer having the burden of his professorial and garden duties, by the late 1870s the burden of maintaining himself as the pillar of American botany prevented Gray from the progress he desired on Synoptical Flora of North America, the follow-on to Flora of North America. This burden consisted of the fact that other scientists often only accepted Gray's word on a botanical matter, and the number of incoming specimens to identify was increasing vastly: numbers had to be assigned to them, collectors needed to be corresponded with, and preliminary papers had to be published. By the early 1880s, Gray's home was the center of everything to do with botany in America. Every aspiring botanist came to see him, even if just to look at him through his window.
After turning over his non-research duties to Sargent, Goodale, Farlow, and Watson, Gray concentrated more on research and writing, especially on "plant taxonomy, as well as lecturing around the country, largely promoting Darwinian ideas. Many of his lectures during this time were given at the "Yale Divinity School. "Liberty Hyde Bailey worked as Gray's herbarium assistant for two years during 1883–1884.
In spring 1887 Gray and his wife made their last trip to Europe, this one for six months from April–October, primarily to see Hooker.
Gray received the following advanced degrees: honorary degree of Master of Arts (1844) and Doctor of Laws (1875) from Harvard, and Doctor of Laws from "Hamilton College (New York) (1860), "McGill University (1884), and the University of Michigan (1887).
Prior to 1840, besides what he had discovered during his trip to Europe, Gray's knowledge of the flora of the "American West was limited to what he could learn from "Edwin James, who had been on the expedition to the West of Major "Stephen Harriman Long, and from "Thomas Nuttall, who had been on an expedition to the Pacific coast with "Nathaniel Jarvis Wyeth. In the latter half of 1840, Gray met the German-American botanist and physician "George Engelmann in New York City. Engelmann took frequent trips to explore the American West and northern Mexico. The two remained close friends and botanical collaborators. Engelmann would send specimens to Gray, who would classify them and act as a sales agent. Their collaborations greatly enhanced botanical knowledge of those areas. Another German-American botanist, "Ferdinand Lindheimer, collaborated with both Engelmann and Gray, focusing on collecting plants in "Texas, hoping to find specimens with "no Latin names". Another long-term and productive collaboration was with "Charles Wright, who collected in Texas and "New Mexico on two separate expeditions in 1849 and 1851–1852. These trips resulted in publication of the two-volume Plantae Wrightianae in 1852–1853.
Gray traveled to the American West on two separate occasions, the first in 1872 by train, and then again with "Joseph Dalton Hooker, son of "William Hooker, in 1877. His wife accompanied him on both trips. Both times his goal was botanical research, and he avidly collected plant specimens to bring back with him to Harvard. On his second trip through the American West, he and Hooker reportedly collected over 1,000 specimens. Gray's and Hooker's research was reported in their joint 1880 publication, "The Vegetation of the Rocky Mountain Region and a Comparison with that of Other Parts of the World," which appeared in volume six of Hayden's Bulletin of the United States Geological and Geophysical Survey of the Territories.
On both trips he climbed "Grays Peak, one of Colorado's many "fourteeners. His wife climbed Grays Peak with him in 1872. This mountain was named after Gray by the botanist and explorer of the Rocky Mountains "Charles Christopher Parry.
Prior to the 1870s, collecting in the western part of the country required slow horses, wagons, and often military escorts. But by this time, permanent settlements and railroads resulted in so many specimens coming in that Gray alone could not keep up with them. One of the post-war collectors who worked extensively with Gray was "John Gill Lemmon, husband of fellow botanist "Sara Plummer Lemmon. Gray named a new genus Plummera, now called "Hymenoxys, in Sara's honor. 
Gray and "Joseph Dalton Hooker went to visit "Richard Owen at London's "Hunterian Museum in January 1839. Gray met "Charles Darwin during lunch that day at "Kew Gardens, apparently introduced by Hooker. Darwin found a kindred spirit in Gray, as they both had an "empirical approach to science, and first wrote to him in April 1855. During 1855–1881 they exchanged about 300 letters. Darwin then wrote to Gray requesting information about the distribution of various species of American flowers, which Gray provided, and which was helpful for the "development of Darwin's theory. This was the beginning of an extensive lifelong correspondence.
Gray, Darwin, and Hooker became lifelong friends and colleagues, and Gray and Hooker conducted research on Darwin's behalf in 1877 on their "Rocky Mountain expedition. After Hooker returned to England and reported to Darwin on their adventure, Darwin wrote back to Gray: "I have just ... heard prodigies of your strength & activity. That you run up a mountain like a cat!"
By the early 1850s Gray had clearly defined his concept that the "species is the basic unit of taxonomy. This was partly the result of the 1831–1836 voyage during which Darwin discovered the differentiation of species among the various "Galápagos Islands. Gray was opposed to the idea of "transmutation of species, in which simpler forms naturally become more complex over time. Local geography could produce variances, like in the Galápagos and Hawaii (which Gray did not get to study in depth as he had wanted) but Gray was insistent that a genetic connection must exist between all members of a species, that like begat like. This concept was critical to Darwin's theories.
When Darwin received "Alfred Russel Wallace's paper that described "natural selection, Hooker and "Charles Lyell arranged for a joint reading of papers by Darwin and Wallace to the "Linnean Society on July 1, 1858. Since Darwin had nothing prepared, the reading included excerpts from his 1844 Essay and from a letter he had sent to Asa Gray in July 1857 outlining his theory on the origin of species. By that time, Darwin had begun writing his book "On the Origin of Species. The correspondence with Gray was thus a key piece of evidence in establishing Darwin's intellectual priority with respect to the "theory of evolution by natural selection. Neither Darwin nor Wallace attended the meeting. The papers were published by the society as "On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection. By summer 1859 it was obvious to Gray and others working with Darwin that On the Origin of Species would be a ground-breaking book.
Darwin published On the Origin of Species on November 24, 1859. The first printing was 1,250 copies, with some having been sent to America via ship; one of those was for Gray. Gray's copy arrived just before Christmas, and he read it between Christmas and New Year's. Since there was no international "copyright law at the time, Gray worked to protect the book from publishing piracy. According to American law at the time, a copyright could only be secured by an American edition being published by an American citizen, and "royalties were not required to be paid to the author. Gray arranged the first American edition of On the Origin of Species and was able to negotiate royalties on Darwin's behalf. Gray took a 5% royalty from the publisher, and Darwin was so grateful for Gray's efforts that he offered Gray some of his royalties. Darwin held Gray in high esteem: he dedicated his book "Forms of Flowers (1877) to Gray, and he wrote in 1881, "there is hardly any one in the world whose approbation I value more highly than I do yours." Seeing the "unity we perceive in nature", Gray strongly objected to the idea of transmutation of species (that simple forms become more complex over time), and also to "special creation (which did not allow for evolution). Perceiving law in the universe, he saw regarding all species "that they not only had a Creator but have a Governor." Gray and Agassiz strongly disagreed; Agassiz was adamantly opposed to the idea of evolution, whereas Gray was a staunch supporter. As the debate raged over Darwin's theories, the rift between Gray and Agassiz grew deeper, and they were estranged by December 1863, when Gray was elected president of the American Academy of Arts and Sciences, which also marked Agassiz' increasing isolation within the scientific community. Gray showed little interest in scientific politics and resigned from the National Academy of Sciences in 1867. In late 1866 Agassiz apologized to Gray and the two were at least civil to one another again.
Gray, considered by Darwin to be his friend and "best advocate", also attempted to convince Darwin in his letters that "design was inherent in all forms of life, and to return to his faith. Gray saw nature as filled with "unmistakable and irresistible indications of design" and argued that "God himself is the very last, irreducible causal factor and, hence, the source of all evolutionary change." Darwin agreed that his theories were "not at all necessarily atheistical" but was unable to share Gray's belief. "I feel most deeply that the whole subject is too profound for the human intellect. A dog might as well speculate on the mind of "Newton," he wrote. Gray was a Christian, but he was a staunch supporter of Darwin in America. He collected together a number of his own writings to produce an influential book, "Darwiniana (1876); these essays argued for a conciliation between Darwinian evolution and the tenets of "theism, at a time when many on both sides perceived the two as mutually exclusive. Gray denied that investigation of physical causes stood opposed to the theological view and the study of the harmonies between mind and Nature, and thought it "most presumable that an intellectual conception realized in Nature would be realized through natural agencies". The result of all this is that Gray distanced himself from "Social Darwinism. Gray is a critical link in the history of American intellectualism, and his writings that explain how religion and science were not necessarily mutually exclusive have been considered his supreme accomplishment; thereby providing a way for believers in "Creationism to consider Darwin's ideas.
In 1868 Gray had a year's leave of absence and visited Darwin in England – the first time they had met since they started their correspondence. Darwin had Gray in mind when he wrote, "It seems to me absurd to doubt that a man may be an ardent theist & an evolutionist." Darwin dedicated his 1877 book "The Different Forms of Flowers on Plants of the Same Species to Gray "as a small tribute of respect and affection". One area where Darwin and Gray disagreed was Darwin's theory of "pangenesis. The Grays traveled to Europe again during 1880–1881, including a final visit to "Down House, Darwin's home. He spent a year in Europe this time studying. Darwin died in 1882.
Gray became engaged to Jane Lathrop[c] Loring of "Boston in May 1847. Two of Gray's younger brothers, George and Joseph, were students at Harvard in the late 1840s and lived with Gray. During his junior year, George caught "typhoid fever in late 1847 and died on January 9, 1848, in the Loring house in Boston. This is part of the reason Gray's marriage was delayed from fall 1847 to spring 1848. Gray and Jane Loring married on May 4, 1848. Her parents were Charles Greely Loring, a member of the "Harvard Corporation and a lawyer, and Anna Pierce (Brace) Loring. Her family was "Unitarian, like most faculty and staff of Harvard at the time. Both of them kept to their separate religious denominations yet seem to have had no difficulties over it. They had no children. Jane Gray accompanied her husband on most of his expeditions. Gray was a devout "Presbyterian and was a member of First Church in Cambridge, a "Congregational church, where he served as a "deacon. He was also an ardent "empiricist in the tradition of "John Locke and "John Stuart Mill. When the congregation moved into its present building in 1872, at 11 Garden Street, Gray planted two Kentucky yellowwood trees, "Cladrastis kentukea, in front of the church. They stood until October 2014.
On Monday, November 28, 1887, Gray's hand and arm became paralyzed while he was coming down the stairs for breakfast. Even though the paralysis worsened, he was able to address two letters. On Thursday he lost the ability to speak in a steady rhythm. He lay speechless and quiet for two months, and died on January 30, 1888. He was buried at "Mount Auburn Cemetery. He did not want anything fancy on his gravestone, so his wife had it engraved with a cross and "Asa Gray 1810–1888". The cemetery's Asa Gray Garden, with a central fountain and numerous unusual tree varieties, is named in his honor.
In addition to the "Asa Gray disjunction", one of Gray's greatest achievements was the vast network of scientists he built who all communicated with one another and exchanged ideas. He is considered the preeminent American botanist of the 19th century.
The Asa Gray Award, awarded by the "American Society of Plant Taxonomists, was established in 1984 to honor a living botanist for career achievements.
"Grayanotoxin is named after him.
Gray has two namesake buildings at Harvard University: the "Asa Gray House, which is a National Historic Landmark, and the "Gray Herbarium.
"William Hooker named the genus "Grayia after Gray.
A residential building is named after him on the "Stony Brook University campus.
Two mountain peaks are named after him: "Gray Peak in New York and "Grays Peak in Colorado. The latter is near "Torreys Peak, named after his mentor and friend "John Torrey.
In 2011 the US Postal Service released an Asa Gray first-class postage stamp as part of its American Scientists series, along with "Melvin Calvin, "Maria Goeppert-Mayer, and "Severo Ochoa. This was the third volume of this series. It features "Shortia galacifolia, a flowering plant that fascinated Gray.
A street named after Asa Gray is home to the University Commons of the "University of Michigan in "Ann Arbor, Michigan.
Asa Gray Park in "Lake Helen, Florida, is named in his honor.
On Gray's 75th birthday, botanists led by editors of the "Botanical Gazette presented Gray with a silver vase with the inscription "1810, November eighteenth, 1885. Asa Gray, in token of the universal esteem of American Botanists." An accompanying silver "salver had the inscription "Bearing the greetings of one hundred and eighty botanists of North America to Asa Gray on his 75th birthday, Nov. 18, 1885."
Also received on his 75th birthday was a poem by "James Russell Lowell:
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