Page 1 Of 20 Joseph T: Fill & Download for Free

As someone who does research on atheism, I would offer that I'm relatively highly qualified to answer this question.The question was why atheism is increasing (and I will limit my response to the American case), not whether or not it is. The data across multiple sources would show that it is, in fact, increasing, although slowly; I would consider this a point that does not need to be argued (although it could be demonstrated rather easily).But as for why, no one knows why atheism is increasing in America, or if the trend will continue. There are various theories; in fact, a contrary case could also be made that religion is simply changing, or that other indicators evince increasing vitality for religion or that secular growth is not strong/will not last [1; 19, chapter 3].I can offer you five theoretical reasons, backed by research. Bear in mind that these explanations are not necessarily either mutually inclusive or exclusive, nor is this list meant to be exhaustive; I was trying not to make this entry so long that people wouldn't read it.No.1 Political Backlash (Values Conflict)Offered initially by Hout and Fischer in a 2002 paper [2], this view implies that the increase in atheists is likely part of the larger increase in those who have “No Religion”, referred to as the “Nones”. Because they find that the shift from a religious preference to no religious preference does not characterize political conservatives, but only political moderates and liberals, they offer that the larger shift to no religion is a political response to the Religious Right. I infer that the growth of atheism becomes more plausible inside the political atmosphere which drove the rise in Nones (see reason number 5). Robert Putnam (mentioned further below) also noted in his co-authored volume American Grace [3] that a values conflict that emerged across 1960 to 1990 is responsible for multiple “shocks” across American society that result in the rise of the Nones as well; these shocks, in this case, are centered on conflict over social values, particularly as they relate to sex, sexuality, and drug use.Hout and Fischer also refer to delays in marriage. One of the conventional pieces of wisdom in the sociology of religion is that data often show a “return” to religion or church for those young couples who bear children; this is referred to as a “life cycle” effect and depends upon demography. Because modern American populations are putting off marriage and childbearing until later, we are seeing a lag with respect to return to religion. However, taking the political backlash into account, it is possible that more and more people will not return to religion or the church even after marrying and having children, as the lag means them spending more time outside of institutionalized religion (see also point number 5, about generational displacement, which keys into this).No. 2: Broad Social DisengagementIn 2001, Harvard sociologist Robert Putnam published Bowling Alone: The Collapse and Revival of American Community [3]. His central thesis meant to show the key indicators of the strength of American community and civil life had weakened over time (e.g. number of social ties to other people). In 2005, sociologist William Bainbridge published an article examining the social ties of atheists [4]. His abstract read:Data from a large, four-language web-based questionnaire, supplemented with data from the General Social Survey, allow us to explore possible sources of Atheism, notably the hypothesis that lack of social obligations encourages disbelief in God. The analysis is rooted in the compensator theory of religion, first proposed twenty-five years ago, but it incorporates a recent addition: the distinction between primary and secondary compensation. Social obligations make secondary compensation important, because it substitutes a compensator for a reward that a person is obligated to provide to another person. The data show that Atheism is indeed more common among people whose social obligations are weak. The analysis also traces connections between Atheism and the demographic fertility collapse that has been occurring in most advanced industrial nations, suggesting that secularization might best be understood in the context of declining social obligations.This analysis has been contradicted since its publication [18], yet it is still worth considering when we wonder about the rise of atheism.No. 3: SecularizationSecularization has a long and conflicted history in the sociology of religion, with a research focus dating back to the 1950s [5]; it has also gone under a great number of revisions and caveats along the way. In a crude way, it can be summarized as saying that modernity is antithetical to religion. Immediately we can see that whether this relationship is true will depend upon how we define and/or measure “modernity” (and “religion” for that matter).[As an important side note, secularization theory was highly contested by the rise of Rational Choice Theory of religion, inaugurated by Rodney Stark and William Bainbridge in 1987 [6]; it was contested prior to 1987 by other theorists and researchers, but RCT largely is a response to the various inadequacies of secularization theory when it comes to explaining religious change.]In 2004, Norris and Inglehart published Sacred and Secular: Religion and Politics Worldwide [7], which introduced what came to be known as the Existential Security Thesis (also sometimes called the existential security framework; closely related to the personal security hypothesis/uncertainty hypothesis). The linchpin observation made from this book was that the countries which tended to perform well on indices of societal well-being also tended to be lower down on religiosity spectrums, and vice versa (i.e. poor societal well-being, high religiosity). EST was essentially a modified, updated version of secularization theory. It posited two axioms: a security axiom, and a cultural traditions axiom. George Brian Nicholson, in his Master’s thesis on EST [8], provides the following sufficient description:The security axiom reflects the idea that “societies around the world differ greatly in their levels of economic and human development and socioeconomic equality—and consequently, in the extent to which they provide their people with a sense of existential security” (Norris and Inglehart, 2004, p.217). Facing more illness, disease, higher child mortality rates, political unrest, and providing less education, for example, marks these societies. The divide between rich and poor countries continues to increase. Thus, countries with less security will have more of a need for religion. The cultural traditions axiom reflects the underlying influence of a country’s religious or cultural heritage on the ideological views of the citizens. This adds a qualitative entity to their secularization theory...the authors summarize their overall secularization argument: “The theory … argues that the erosion of religious values, beliefs, and practices is shaped by long-term changes in existential security, a process linked with human development and socioeconomic equality, and with each society’s cultural legacy and religious traditions” (Norris and Inglehart, 2004, p.53).Any attempt to examine societal or state health and its relationship to indicators of religiosity falls into the scope of EST.Another poster here mentioned the EST work of Gregory Paul. He published an article supporting EST in 2005 [9]; his article’s claims and conclusions were rebutted to some extent in the same journal the following year [10], with the article’s authors saying:This rejoinder addresses Paul’s thesis, analysis, and conclusions in terms of the various methodological assumptions and frameworks used to deploy his study. It is the opinion of the authors that once all of the methodological issues are considered, Paul’s findings and conclusions are rendered ineffectual. In closing, various suggestions are offered in the hopes of advancing Paul’s hopes for “future research and debate on the issue” of comparative analysis of religiosity, secularism, and democratic social health.Furthermore, Gregory Paul also does not have any credentials that would regard him as a social scientist, social theorist, or even as a researcher of religion. He is manifestly an anti-theist [11], which renders his work suspect.No. 4: Internet UseCheyne and Britton, in an unpublished manuscript ostensibly dated 2010 [12], say:The internet has changed many things, including the world of atheists and other nontheists. Prior to the advent of the internet, such people were relatively isolated, possibly able to find a few books such as Bertrand Russell’s “Why I am not a Christian” at the local library, but with little material to stimulate any incipient irreligion unless they lived in major centres. It is likely the internet, even more than works by Dawkins, Hitchens, and the others or, rather, the interaction between the two that has created what has been called, for better or worse, the “new atheism.” Much has been written about the characteristics of the new atheists and much of this has been based on the writings of a few highly visible atheists. Little is known about the depth or breadth of such views. In addition to the direct effects of such writings, it is the chatter on the internet about such books and the rise of atheist blogs such as Atheist Planet, Pharyngula, and many others that is creating a sense of community among nonbelievers, doubters, and sceptics. Hence, we thought it timely to investigate the characteristics of the people connected, however peripherally, to this new internet communityAnd then there is Downey's popular paper about the relationship between Internet use and no religion [13], which would show how Internet use contributes to a decline in religious affiliation, although this is very likely not a direct effect on disaffiliation itself but co-occurs with other factors that perhaps are. See also Smith and Cimino's 2012 article [17] which discusses specifically the role of the Internet, online atheist communities, activism, and identity formation.See also new work by Paul McClure [20], who finds that “internet use is associated with increases in being religiously unaffiliated and decreases in religious exclusivism. At the same time, I find that television viewing is linked to decreases in religious attendance and other time-related religious activities, but these outcomes are not impacted by Internet use. To explain these disparate findings, I argue that the Internet is fundamentally different from previous technologies like television and thus impacts religious beliefs and belonging but not time-related religious activities.”No. 5: Generational DisplacementMerino’s work [14] suggests that a cohort effect is in play; the rising number of atheists is explained mostly by the generational increases via demography. This would comport well with the fact that the increase in the number of atheists has been slow and gradual.​​However, other research [15] would show that the nonreligious, including atheists, compared to religious denominations and traditions, demographically perform poorly when it comes to generating/retaining their numbers across time. Still, counterbalancing for these two items might yet allow for atheism to increase slowly over many years.​​In summary, many things contribute to the rise in atheism. Phil Zuckerman, despite his association with Gregory Paul and his own manifest anti-theism, has produced some work worthy of consideration. Notably, apostasy and "no religion" are not to be equated with atheism per se, however, some apostates do go on to become atheists. Below is a quote from my own work, referencing Zuckerman's book Faith No More: Why People Reject Religion [16]:Zuckerman (2011, chapter 10, pp. 151-169) interviewed 87 apostates (individuals who had left or rejected their previous religious tradition or affiliation but who may or may not have become atheists/agnostics), some of whom eventually became atheists, and pinpointed “the nine most typical, most pervasive, or most often mentioned reasons given by apostates in accounting for their rejection of religion (p. 153).” These reasons broadly fell into the following categories: parents; education; misfortune; other cultures/other religions; friends, colleagues, lovers; politics; sex; Satan and hell; and malfeasance of religious associates. Zuckerman, adding the caveat that “reasons are not necessarily causes”, distinguishes between subjective reasons and objective causes; that is, any one of the various factors may increase the likelihood of apostasy but would not be, in and of itself, a cause for the rejection of one’s religion. He concludes that “a variety of life circumstances, personal experiences, and/or social dynamics (p. 165)” underlie the likelihood of apostasy.EDIT (April 27, 2017). A few months ago, Richard Flory had a piece in Observer, about factors driving the nonreligious rise. It was so compelling, I had to add his insights here. To summarize:First, traditional authority structures, including religious ones, have been flattened through access to knowledge. As a result, everyone and no one is an authority, which reduces the need for traditional authorities of any sort.Second, fewer Americans view important social institutions – such as religious organizations, corporations and government – as having a positive impact in society.Third, religion has a bad brand. From sex scandals across different religious traditions to the increasing association between evangelical Christianity and the political right, religion per se has taken a beating.[I think this one is especially important] Fourth, increasing competition for people’s attention from work, family responsibilities, social media and other activities means that religion loses out to more pressing commitments.Finally, personal choice is a bedrock feature of American culture. Individuals choose professional affiliations, diets, club memberships and myriad other associations, with religion being one more affiliation that is “chosen” by adherents.__________[1] Stark, R. (2015). The triumph of faith: Why the world is more religious than ever. Open Road Media.[2] Hout, M., & Fischer, C. S. (2002). Why more Americans have no religious preference: Politics and generations. American Sociological Review, 165-190.[3] Putnam, R. D., Campbell, D. E., & Garrett, S. R. (2012). American grace: How religion divides and unites us. Simon and Schuster.[4] Bainbridge, W. S. (2005). Atheism. Interdisciplinary Journal of Research on Religion, 1.[5] Page on iasc-culture.org[6] Stark, R., & Bainbridge, W. S. (1987). A theory of religion (Vol. 2). New York: Lang.[7] Norris, P., & Inglehart, R. (2011). Sacred and secular: Religion and politics worldwide. Cambridge University Press.[8] Nicholson, G. B. (2006). Cultural Zones and Existential Security: A Cross-national Examination of Secularization Theory (Master's Thesis, University of Georgia).[9] Paul, G. (2005). Cross-national correlations of quantifiable societal health with popular religiosity and secularism in the prosperous democracies. Journal of Religion & Society 1(7).[10] Mach, T. S., Moreno-Riano, G., & Smith, M. C. (2006). Religiosity, Secularism, and Social Health: A Research Note. Journal of Religion and Society, 8.[11] THE SCIENCE OF RELIGION by Gregory S. Paul[12] Page on arts.uwaterloo.ca[13] [1403.5534] Religious affiliation, education and Internet use[14] Merino, S. M. (2013). Irreligious socialization? The adult religious preferences of individuals raised with no religion. Secularism and Nonreligion, 1, 1-16.[15] Page on pewforum.org[16] Zuckerman, P. (2011). Faith no more: Why people reject religion. Oxford University Press.[17] Smith, C., & Cimino, R. (2012). Atheisms unbound: The role of the new media in the formation of a secularist identity. Secularism and Nonreligion, 1(1), 17-31.[18] Hunter, L. A. (2010). Explaining atheism: Testing the secondary compensator model and proposing an alternative. Interdisciplinary Journal of Research on Religion, 6.[19] Hood Jr, R. W., Spilka, B., Hunsberger, B., & Gorsuch, R. (1996). The psychology of religion: An empirical approach. New York: Guilford Press.[20] McClure, P. K. (2017). Tinkering with Technology and Religion in the Digital Age: The Effects of Internet Use on Religious Belief, Behavior, and Belonging. Journal for the Scientific Study of Religion. DOI. 10.1111/jssr.12365

I can prove it if you believe the people who knew him best. Josiah Quincy III, who was a U.S. Congressman, Mayor of Boston, and Harvard University President gave his observations about Joseph Smith after meeting Joseph Smith and spending considerable time with him. He said:It is by no means improbable that some future textbook, for the use of generations yet unborn, will contain a question something like this:What historical American of the nineteenth century has exerted the most powerful influence upon the destinies of his countrymen?And it is by no means impossible that the answer to that interrogatory may be thus written: Joseph Smith, the Mormon Prophet. And the reply, absurd as it doubtless seems to most men now living, may be an obvious common-place to their descendants.History deals in surprises and paradoxes quite as startling as this. The man who established a religion in this age of free debate, who was and is today accepted by hundreds of thousands as a direct emissary from the Most High—such a rare human being is not to be disposed of by pelting his memory with unsavory epithets.Fanatic, impostor, charlatan, he may have been; but these hard names furnish no solution to the problem he presents to us. Fanatics and impostors are living and dying every day, and their memory is buried with them; but the wonderful influence which this founder of a religion exerted and still exerts throws him into relief before us, not as a rogue to be criminated, but as a phenomenon to be explained.The most vital questions Americans are asking each other today have to do with this man and what he has left us. A generation other than mine must deal with these questions. Burning questions they are, which must give a prominent place in the history of the country to that sturdy self-asserter whom I visited at Nauvoo.Joseph Smith, claiming to be an inspired teacher, faced adversity such as few men have been called to meet, enjoyed a brief season of prosperity such as few men have ever attained, and finally, forty-three days after I saw him, went cheerfully to a martyr's death. When he surrendered his person to Governor Ford, in order to prevent the shedding of blood, the Prophet had a presentiment of what was before him. "I am going like a lamb to the slaughter," he is reported to have said; "but I am as calm as a summer's morning. I have a conscience void of offense, and shall die innocent."I have no theory to advance respecting this extraordinary man. I shall simply give the facts of my intercourse with him. At some future time they may be found to have some bearing upon the theories of others who are more competent to make them. Ten closely written pages of my journal describe my impressions of Nauvoo, and of its Prophet, mayor, general and judge.I recommend that you read those ten pages at Josiah Quincy's Narrative About Joseph Smith.Of particular note are his closing words:I have endeavored to give the details of my visit to the Mormon Prophet with absolute accuracy. If the reader does not know just what to make of Joseph Smith, I cannot help him out of the difficulty. I myself stand helpless before the puzzle.Joseph Fielding McConkie pointed out that, "Many a pretender to the prophetic office has claimed to entertain angels or to have spoken with God, but who other than Joseph Smith introduced his angels to others? Joseph Smith introduced Moroni to Oliver Cowdery, David Whitmer, and Martin Harris (Testimony of the 3 Witnesses - https://www.lds.org/scriptures/bofm/three?lang=eng). He was never alone when priesthood or keys were restored.... He and Sydney Rigdon received the revelation on the degrees of glory together. Together they saw legions of angels, along with the Father and the Son (see D&C 76:21-23 - https://www.lds.org/scriptures/dc-testament/dc/76?lang=eng). Oliver Cowdery was with Joseph Smith when John the Baptist came to restore the Aaronic Priesthood (https://www.lds.org/scriptures/dc-testament/dc/13?lang=eng), and when Peter, James, and John came to restore the Melchizedek Priesthood (https://www.lds.org/scriptures/pgp/js-h/1?lang=eng). Oliver was also with Joseph Smith when Christ came to accept the dedication of the Kirtland Temple, and Moses, Elias, and Elijah restored their keys, powers, and authorities (D&C 110 - https://www.lds.org/scriptures/dc-testament/dc/110?lang=eng)." (Sons and Daughters of God, pp. 194-195)Jesus spoke of both true and false prophets in the latter days but cautioned that true prophets could be identified from false ones by their fruit (Matt. 7:15-20; 12:33; Luke 6:43-45). The fruit of the prophet Joseph Smith are:a. A strong faith in God and his Son, Jesus Christ, and their divinity (lst Article of Faith; 2 Nephi 25:23, 25, 26, 28; 31:18, 21)b. Church members who believe in Christ's sacrificial atonement and are striving to follow in his footsteps (1 Pet. 2:21; 2 Nephi 2:7; 31:16; 3rd and 13th Article of Faith)c. A membership that is unified in its beliefs and doctrines (1 Cor. 1:10; Mosiah 18:21)d. Members who are rearing strong, loving families (D&C 68:25-28; Mosiah 4:14-15)e. Members who believe in the power of God to do miracles today (7th Article of Faith; D&C 35:8-9)f. Members who have a love for the scriptures and are striving to live by every word that proceeds forth out of the mouth of God (8th Article of Faith; Deut. 8:3; Matt. 4:4; Moroni 7:25; D&C 1:29-32)g. Members who are a law-abiding people (12th Article of Faith; D&C 101:76-101)h. Members who give unselfishly not only tithes and offerings but also of their time and talents to further the Lord's work (D&C 64; Mosiah 18:8-9)i. A well educated Church (D&C 88:118; 90:15; 93:36; 109:7)j. A healthy people who abstain from using alcohol, tobacco, and other substances harmful to their bodies (1 Cor. 6:19; D&C 89)k. Members who are clean in speech (D&C 63:61-64)l. A missionary Church (Matt 28:19; D&C 1; 4; 18)m. A people who are actively participating in service to the community, state, and nation (D&C 134)n. A Church that insists that its members obey all of the Ten Commandments including keeping the Sabbath day holy (D&C 59; 68:29)o. A people who practice charity for those both inside and outside the LDS Church (D&C 121:45; 2 Cor. 9:7)p. Members who actively participate in Church services and leadership most often without monetary compensation (D&C 84:103-110)q. A belief in the importance of temples and in salvation for our ancestors (D&C 124:22-44; 127; 128)r. A belief that all people are spiritual brothers and sisters and children of our Heavenly Father (D&C 93) and as such have great worth to God and the potential to become like him (Matt. 5:48; 1 Jn. 3:2; D&C 132:19-20)s. A belief in the Holy Ghost's power to witness and justify (D&C 46)t. Members who believe in the biblical standards of morality, marriage, and family and oppose abortion and all sexual sins (D&C 42:18-25)u. A Church, which accepts truth from any source whether secular or religious (D&C 93:23-40)v. A Church which has a rational claim to the divine authority given by the Savior (D&C 13; Jos. Smith-Hist. 1:68-75)w. An organization, which is led through revelation from Jesus Christ and thus holds that the Savior is the head and foundation of the Church (Helaman 5:12)x. A Church which is founded upon apostles and prophets with Jesus Christ being the chief cornerstone (Eph. 2:20)y. Members who covenant with God and strive to honor those covenants (Mosiah 18:10, 13; Doctrine and Covenants 22:1, 3; Doctrine and Covenants 132:4, 6-7, 15, 18-19, 26-27, 41-42, 51)z. Members who renew their covenants on a weekly basis (Moroni 4-5; D&C 20)If, as Jesus taught, a corrupt tree cannot bring forth good fruit (Matt. 7:18), how can the good fruit of the Church Joseph Smith founded be explained? (see Eph. 5:8-10; Titus 2:14; Rev. 14:12-13). In defending Peter and John, Gamaliel reasoned “...if this counsel or this work be of men, it will come to naught; but if it be of God, ye cannot overthrow it." (Acts 5:38-39) I believe that this is also true of Joseph Smith.

Human ViromeThe human virome (representing human viral communities) presents greater technical challenges (1) for identification and enumeration compared to the microbiome.Technical difficulties with characterizing the human viromeWe identify bacteria in the human microbiome using conserved genomic sequences (16S rRNA). Lacking such conserved genomic regions, viral genomic sequences from human samples are compared to known virus reference sequence databases. Drawback is such databases don't include sequences from novel viruses (2) while the human virome likely harbors as-yet-undiscovered viruses and viral relics.Viruses have small genomes, and are proportionally fewer compared to bacteria. Thus, viral nucleic acids are proportionally minuscule in the total derived from human microbial communities. To detect them, we need to enrich viral nucleic acids before sequence analysis. In turn, enrichment methods could be unwittingly selective, bias against certain viruses, and lead to loss of low-abundance viruses (3).From 4The human virome constitutes viral communities all over the human body. They run the gamut from viral relics such as HERVs (Human Endogenous Retroviruses), retroviral genes internalized millions of years ago during evolution, to tissue-resident viruses such as CMV (Cytomegalovirus) in the respiratory tract. Contribution of these viral communities also runs the gamut from most essential such as HERV-W genes, necessary for placental development, to HERV-K, the most recent integrant, implicated in neurological diseases such as schizophrenia, cancers such as breast and prostate, and autoimmune diseases such as MS (multiple sclerosis), RA (rheumatoid arthritis) and SLE (systemic lupus erythematosus).Figure 1 from 5HERVs (Human Endogenous Retroviruses)Viral genetic material is either DNA or RNA. Retroviruses have RNA but use it to produce DNA, the reverse, 'retro', of the norm. When inserted into host DNA, this viral DNA replicates every time host DNA replicates. When retroviruses infect germline (eggs and sperm) cells, they acquire a vastly greater capacity to replicate. Now endogenous retroviruses (ERV), they are present not just in each and every cell of that host but also get passed on to each and every cell of the host's descendants.ERVs represent 8% of the human genome (6).How do we know we harbor such retroviral relics? By their striking structural genomic similarity consisting of gag, pro, pol and env genes flanked by two identical-at-integration non-coding long terminal repeats (LTRs), which contain the signal for transcription initiation and regulation.Over evolutionary time (~35 million years), ERVs accumulated mutations (insertions, deletions, substitutions) and/or epigenetic modifications (for e.g., DNA methylation) at the same rate as the host genome (7, 8, 9, 10), rendering them non-functional, i.e. unable to produce infectious viral particles.Recombinations between the two flanking LTRs removed the internal coding region leaving a single LTR and inactivating ERVs, which are 10–100 times more numerous than their full length counterparts (11), and many of these insertions are fixed in the host population.To date, no active ERVs have been discovered in humans. The human genome has ~100,000 ERV loci resulting from proliferations of ~50 independent invasions of the genome from free-living (exogenous) retroviruses (12, 13).Figure 2 from 14HERV classification is still a work-in-progress. Magiorkinis et al (15) classify HERV families as the typical, HERV-T; the old, HERV-L; the abundant, HERV-H; the indispensable, HERV-W; the last but not the least, HERV-K.HERV-K(HML2) or HK2, the most recent, is the only ERV lineage to still replicate in the human population within the last few million years.~1,000 HK2 loci in the human reference genome, apparently integrated over the last ~35 million years. Continuously replicating over this long period, most full-length integrated ERV loci (proviruses) converted to relics by recombination. Remainder acquired premature stop codons and/or frameshifts. All reference genome HK2 loci are therefore replication defective, and only 24 loci retain full-length open reading frames (ORFs) in at least one of their genes (16).RNA transcription and protein expression of HK2 and other ERVs are elevated in many cancers, some autoimmune/inflammatory diseases, and HIV infection, leading to a long and unresolved search for a causal role in disease (17, 18, 19). More recently, disease-associated elevation of HERV protein expression has driven research into their potential as immunotherapy targets for cancer and HIV treatment (20).HERV-W, the indispensable HERVs in the Placenta: Genes Syncytins 1 and 2The emergence of placentation during evolution is fundamental to human evolution.Indispensable for human fetus growth, the placenta is composed of multiple unique cell types called extravillous and villous trophoblasts. The latter differentiate into multinucleated cells called syncytiotrophoblasts, which secrete human chorionic gonadotropin (hCG) and human placental lactogen (hPL), products that help optimize mother-fetus nutrient and hormone exchange.Viral relics in the form of specific HERVs are essential for placental development (14, 21, 22).Viruses were long suspected present in placenta with virus-like particles observed in human placenta (23, 24, 25, 26). These observations faded from memory until the discovery of the Syncytin genes in the late 1990s.Two Env proteins, Syncytin-1 and Syncytin-2 proteins, encoded by two different ERV loci, i.e., ERVW-1 and ERVFRD-1, located on chromosome 7 and 6, respectively, are expressed in the placenta. Independently co-opted numerous times among placental mammals and expressed in the placenta, these genes play a crucial role in the formation of the syncytiotrophoblast, a key function that sustains the highly dynamic and metabolically demanding placenta (27, 28, 29, 30, 31, 32, 33, 34, 35).Figure 1 from 36.- Viral genes like these may actually have been central in the emergence of placental mammals from egg-laying animals (29, 37, 38, 39, 40).Box from 36.In vitro studies (41) and reduced expression in pre-eclampsia (42, 43, 44, 45, 46, 47, 48, 49) suggest these retroviral-origin genes are important in human placentation. Pre-eclampsia, 'toxemia of pregnancy', includes hypertension, liver and kidney toxicity, and if untreated, can lead to eclampsia, i.e. seizures, threatening the life of mother and child. These multiple, independent studies thus suggest that human placental syncytin expression is crucial for normal placental function and ensuing normal pregnancy.Mouse syncytin gene knockouts provide more definitive proof. Syncytin-1 knockout mouse: growth retardation, altered placental strcuture, death in utero (50). Syncytin-2 knockout mouse: impaired syncytiotrophoblasts (51).Serving a similar purpose in placentation of eutherian mammals, syncytin genes are thus a most extreme and powerful example of convergent evolution, having evolved independently multiple times through co-option of HERV genes.HERVs in the brain: No definitive proof of disease causation. Lot of correlative data for neurological diseases,Table 1 from 52.especially for schizophrenia.Tables 1 and 2 from 53HERVs and cancerHow to be sure something causes cancer? Likely causes are so numerous ranging from genetic predisposition to numerous environmental factors that pinning one or few down as causative agents is akin to the proverbial needle in a haystack. In 1965 Austin Bradford Hill proposed the famous Hill's criteria (54), essential in helping ascribe causality, as in the link between smoking and lung cancer. How does that pan out with HERVs (55, 56, 57)?Consistency of association: HERVs consistently expressed in many tumors (breast, ovarian, lymphoma, melanoma, sarcoma, bladder, prostate).Strength of association: HERVs rarely expressed in normal tissues.Temporal association: Environmental factors as in exogenous such as chemicals, UV radiation, smoking, viruses, and endogenous as in hormones and cytokines help drive HERV expression.Biological plausibility: no clear evidence yet.Experimental evidence: no clear evidence yet in humans (some mouse model data exists).Clearly work-in-progress.HERV-Breast Cancer link: 58, 59; HERV-Melanoma link: 60; HERV-prostate cancer link: 61.HERVs and autoimmunity (62, 63): MS (multiple sclerosis; 64, 65), RA (rheumatoid arthritis: 66, 67), SLE (systemic lupus erythematosus: 68), Sjogren's syndrome, Graves Disease.Association data; no causal data yet.Certain HERVs and herpes viruses associated with MS.Circulating anti-HERV antibodies present in >50% of SLE in some studies.Those with anti-HERV antibodies more likely to have active clinical SLE.Location-wise identity of Viruses in Human bodyHuman StoolStable over time (69), unsurprisingly healthy gut virome is influenced by diet (70).Abundance of food-related (plant) viruses (71).Eneteropathogenic viruses (72) found in both healthy and in those with GI tract illnesses (73).Novel bacteriophages encode genes for antibiotic resistance and bacterial metabolic pathways (69, 70, 74). More diverse in adults, much less so in a 1-week old infant stool sample (75). Clearly, we dynamically acquire a gut bacteriophage community over time.Novel viruses. Viruses from the new genus Gyrovirus in the Circoviridae family (76) are found in both chicken meat and human samples. Open questions: Do they replicate in humans, i.e. capable of cross-species transmission, or are they harmless?Diarrhea was associated with novel viruses such as astrovirus (77), cosavirus and bocavirus (78).Human SkinPersistent colonization by papillloma, polyoma, and circoviruses(79, 80). Innocuous for the most part. Exception is Merkel cell polyomavirus associated with severe skin carcinoma (81).Human circulatory systemAnelloviridae are ubiquitous in human populations (82, 83).An intriguing heart and lung transplant study (84) tracked circulating plasma virome months post-transplant, and found circulating virome changed with post-transplant treatment. Low dose of anti-viral (valganciclovir) and immunosuppressant (tacrolimus): Herpesvirales and Caudovirales dominate; high dose, Anelloviridae dominate.Graphical Abstract from 84.LiverFlavivirus GBVC (or Hepatitis virus G), a surprising partner in human health, delays HIV disease progression (85).LungInfluenza (flu), Corona and other less well-characterized viruses (86).Bocavirus found in both healthy and in those with respiratory tract illnesses (87).Bacteriophages: Cystic Fibrosis (CF) patients have bacteriophages similar to each other while those in healthy adults are unique to each individual (88). In this study, spouse of one CF patient and an asthmatic control shared some viral genomes found in CF patients. This suggests environment strongly influences human viral genome since shared environment was associated with shared viruses between spouses, and chronic pathologies that are very different, as CF and asthma are, could still lead to establishment of similar viral communities, perhaps because they both cause impaired airway clearance of microbes.CMV (Cytomegalovirus)CMV, a herpes virus, infects majority of the world’s population.In the US, ~60% prevalence in >6 years of age and ~>90% in >80 years of age in the years 1988-1994 (89).It's usually, but not always, benign (90).Associated with immunosenescence (immune aging) in the elderly (91).CMV-schizophrenia link: In a study of >1000 subjects, 15% carried a particular benign variant of a gene involved in the stabilization of neuronal connections and in synaptic plasticity, essential to learning and memory. 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Translational psychiatry 2.12 (2012): e201. Page on nature.com.Leboyer, Marion, et al. "Human endogenous retrovirus type W (HERV-W) in schizophrenia: A new avenue of research at the gene-environment interface." The World Journal of Biological Psychiatry 14.2 (2013): 80-90.Thanks for the A2A, Matt Chanoff. I'll answer about the human mycobiome (fungal communities of the human body) separately.