Post your questions for Lynn Margulis!

The following essay comes from Lynn Margulis‘ new book, “Luminous Fish.” Lynn has agreed to swing around today to answer any questions you might have for her, whether they be related to this post or other topics you’d like her to weigh in on. Please post your questions in the comments section below. If you’re curious to see what she has discussed on previous stops of her blog tour, check out this post on Pharyngula.

Mas tira un pelito the Spaniards have been saying for centuries que cien bueyes: a pubic hair pulls more forcefully than a hundred oxen. The lure of science and knowledge is very strong but is often outmatched by the lure of pelitos. That human attractions for each other have enduring effects on the great course of scientific inquiry is perhaps underappreciated by readers of literature. Myriad original analyses and observations by hundreds of quietly obsessed scientists profoundly, if circuitously, influence the “civilized” world. But how does the private life of some obscure researcher alter public “progress” or inspire technological “revolution”? How might the sex life of the chief of medicine at the urban research hospital impede (or accelerate) the newest medical “miracle” that saves (or destroys) the reproductive organs of his young mistress . . . and of hundreds of other anonymously sterile women who are ready to pay?

How does the direct study of nature in nature, say of the night sky by an awkward and shy teenage astronomer, directly affect the probability of a lander to Mars and its return to Earth in 2025? Will the private dramas of two geologists—say, a petrologist and a geomorphologist—influence verification that magnetotactic bacteria, rod-shaped cells with tiny aligned magnets, were common inhabitants of our red, dusty, and today, entirely barren neighboring planet? Perhaps. Or maybe not. In this era where the majority of well-read, highly educated gentry ignore the wetness of nature in which we are all embedded, the consequences are as numerous as they are obscure.

Perhaps my rude exposure of the personal lives of real people (J. Robert Oppenheimer and Kitty, Phylis and Philip Morrison) as well as the fictional characters [in Luminous Fish], all of whom have little in common except passionate preoccupations with first-hand generation of scientific truths, helps to answer these questions.

A small decision (say, whether to study Geology 101 or Chemistry 101 on Mondays and Wednesdays where the schedule has an opening) may have huge consequences to the future scientist. When a student elects chemistry, she is likely not to be aware of her invisible commitment to retorts, distillation apparatus, laboratory organics, heavy metals, weekends inside a deserted brick laboratory rather than fieldwork on the Triassic slopes of Mt. Sugarloaf or in the tin fields of Malaysia. How do the textbooks, computer programs, educational magazines obtain their “facts”?

A very few dedicated loners generate the “scientific truths” that the rest of us must accept on authority. The curious investigator himself fills up with doubt and self-criticism; when he reads the oversimplification or exaggeration attributed to him, he is usually embarrassed. He is dismayed by distortion of his work; he knows he never meant to contribute to problems of human health or environmental degradation. He knows in his heart of hearts what I know and what all my very best colleagues know: The continuous underlying international story of science may exist in some platonic sense, but it can never be told. Not only does no one even know the whole story from end to end but no one even can know it, in principle.

Glimpses accompany flashing insights. One fish at a time, Photoblepharon scintillates. The school reveals patchiness as the swarming swimmers expose their bacterial light in the dark waters of the Gulf of Aqaba. They illuminate and then darken the scuffling sediments below to provide an occasional glimpse. The dazzling flashes sparkle amidst the dullness of routine. I have modeled my prose after these denizens of the deep.

Nature, as we see, yields only with great reluctance and to very few who attempt to engage her. All spread of new knowledge is complicated by the lure of the pelitos and the warm, scented bait of the newborn. But science, in spite of its ignorant detractors, continues to spin its narrative, the big story of our natural history and the probable future of mankind. Potential young scientists and aged returnees in the scientific enterprise are not excluded, at least in principle, by the luck of their village of origin, the shape of their eyelids, or the hue of their skin.

“Science,” as Stewart Brand says, “is the only news. Everything else is ‘he said, she said.’” How, in spite of all diversions, selection pressures, and scarcities, science successfully describes a very few scenes illuminated by a very few fish is what I intend to bring to you. We remind each other that deep inside each flashlight fish, apparently without foresight or intention, when the density of trapped and healthily growing bacteria reaches some 10 million per teaspoon, the cold light abruptly turns on. The drab, now white-bellied fish becomes luminous to lead itself and its glow-in-the-dark symbionts to choice food and safe haven. Unplanned and unprayed-for nature just does it. And we are the beneficiaries.

Rebecca Watson

Rebecca is a writer, speaker, YouTube personality, and unrepentant science nerd. In addition to founding and continuing to run Skepchick, she hosts Quiz-o-Tron, a monthly science-themed quiz show and podcast that pits comedians against nerds. There is an asteroid named in her honor. Twitter @rebeccawatson Mastodon Instagram @actuallyrebeccawatson TikTok @actuallyrebeccawatson YouTube @rebeccawatson BlueSky

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  1. Hi Lynn, I'd like to ask you a few questions about your new book! I haven't read it yet, but I enjoyed the excerpt you posted here. It reminds me of writings by Alan Lightman and Richard Powers, two of my favorite authors.

    I love the idea of writing about how love intersects with and, possibly, changes the scientific life and, ultimately, science itself. I know this was true for me and in my case, alas, had unfortunate results. When I was 14, I fell in love with a boy in a fundamentalist Christian church. Over the next 10 years, when I could have been studying science, instead I was getting a virtual degree in fundamentalism. Although I eventually shed the superstion, I never fully returned to my childhood love of science. Without giving too much away, can you tell us about your own experiences at the intersection of love and science and how they play into this book?

    The descriptions of Luminous Fish from amazon mentions both fiction and essays. Did you create a new type of blending of the two genres?

    What made you decide to include fictional stories?

    In your post you say, "the majority of well-read, highly educated gentry ignore the wetness of nature in which we are all embedded." I'm not certain I agree but I find this intriguing. Can you give some specific examples?

    Well, I could post another 10 questions easily but I'll let some others chime in with their queries.


    SkepLit Reading Group Editor

  2. There are minutiae in all lives, some of which have no effect, some of which are catastrophic. Whether one leaves the house at 07:30 or 07:31 may be the difference between catching , or missing, a green light which is being simultaneously jumped by a fuel tanker, or between meeting or missing the future Mr. or Mrs. X

    Golden lads and chimney sweepers come to dust, but some get rich first.

    Why would scientists be any different?

  3. Hi! So… what's the problem with the 3 divisions view of life (eukaryotes, archaeabacteria, eubacteria)? It seems to be a more natural and internally consistent view of biological evolutionary relationships, or do you think otherwise? Thanks!

  4. What evidence would prove or disprove a causal relationship between HIV and AIDS? Has such evidence been discovered?

  5. In "symbiotic planet" you seemed to indicate that symbioses might be the driving factor behind speciation and novelty in life history. However, in many cases, you seem to restrict your arguments to the origin of eukaryotes and other microorganisms. I'm personally more curious in the application of these ideas in present biology. Do we know the mechanisms of symbiotic establishments in the wild? What interesting symbioses have we observed, and what mechanisms were involved? Scott Gilbert has done some interesting reviews of biological phenomena in predator/prey relationships, where, during development, a prey can detect its predator in the environment and develop accordingly. Has any such mechanism been established for symbiotic relationships?

  6. Sorry, my brace hit the key and saved that before I finished. You wrote, "A very few dedicated loners generate the “scientific truths” that the rest of us must accept on authority."

    As skepchicks, we are generally leery of accepting anything "on authority." I don't know if believing what scientists say is actually accepting things on authority, but rather that we understand the scientific method and are able to check on the original papers and research of these few scientists whenever we want. So we trust the process more than the authority. Do you disagree with that summation? Can you comment on the difference between the two?



    P.S. I'm interested in what you have to say about HIV/AIDS too, because I think it's quite irresponsible to the point of perhaps being immoral to say things that might make people stop taking their meds and, hence, die.

  7. For Dr. Margulis:

    You don't think it's appropriate to think of bacteria as constituting multiple separate species. Wouldn't it be appropriate to consider them analogous to ring species in eukaryotes? Ring species have a continuous flow of genetic material but still, in some or most geographic circumstances, they constitute more than one species.


  8. I certainly hope that Ms. Watson and her compatriots over at the Skeptics Guide to the Universe will grill Prof. Margulis about her support for Prof. Duesberg.

  9. Dr Margulis,

    You have gone on record as stating that most pregnant women test positive for HIV.

    Can you give a published reference for this ridiculous statement?

    Thank you,


  10. What made you decide to include fictional stories?

    Donna: Nice to meet you in spite of the on-line nature of our introduction. These stories were written from the fifties through about 2005, rejected for GOOD reason by my critical family and others. I kept improving them as a back-burner hobby. Why? Because I loved the unconstrained opportunity to write what I wished. (This NEVER happens in science) and I wanted to show the specific case of what the second questioner here mentions> How small acts can amplify and thousands of unsuspecting can be deeply affected, even scarred. Sorry to be so late, I worked all day and, in spite of Jon Mikel's help, actually forgot about blog-time. LM

  11. Why would scientists be any different?

    Scientists aren't different but the situations in which they operate can be extremely different. Read Horace Freeland Judson's factual books (8th Day of Creation, the book on Fraud) if this interests you. I want to show the interior truths of the people whose lives and acts he describes.

    Alan Lightman, btw, is a terrific writer and person but I am not fmiliar with the other author Donna mentions above.

  12. Ike:

    What’s the problem with the 3 divisions view of life (eukaryotes, archaeabacteria, eubacteria)?

    No problem per se, just that this classification uses a single criterion 16-18S rRNA and thus gives only a single measuring stick for one small aspect of the whole organism phylogeny. As a "partial phylogeny" it is useful but should not be extraolated to say, plants that all have at least 3 different 16-18SrRNA (nucleocytoplasm, mitochondria, plastid, at least.) All symbioses are ignored and from 2000 to 50,000 other (genes/cell) are also ignored. For those of us interested in the history of life we know t hat all semes (characters of evolutionary significance) need consideration. We are now doing the 4th edition of Five Kingdoms, illustrated guide to phyla of life on Earth (Academic Press) and we are very careful to explain these point. We are interested in not just the body of any orgianism but its fossil history, life cycle and life histroy, genetic system the classical evolutionists were ..but we do not underestimate the power (and of course limitations) of the new technoques. Take a look at 5lkingdoms 3rd ed. and see what we are trying to update now. Thanks for asking. LM

  13. nowoo

    What evidence would prove or disprove a causal relationship between HIV and AIDS? Has such evidence been discovered?

    The criteria for evidence are well-established (Koch's postulates).. The" disease agent" 1. must have identity (detectable presence of the agent itself. 2. It must correlated entirely with the symptom(s) of the disease. (3) the disease agent should be cultivable (growable, reproduce) under conditions where nothing else is present in the growth medium (so called "pure culture".). 4. After a certain number of these identified agents are in the culture tube when added to the animal the symptoms reappear (i.e., correlation of the symptoms with an identifiable so-called disease agent).

    These postulates were shown by Pasteur for anthrax, by Salk and Sabin for polio virus, for measiles, rubella, chicken pox. mumps, Rocky Mt Spoted fever and other tick and flea borne illnesses, for malaria, yellow fever….the list goes on. The scientific community is in general good agreement. For AIDS (a syndrome, by definition, a set of symptoms that not everyone shows and not all of the time) there is no identity of the HIV virus, the tests differ in the USA, UK, and Australia, etc. We have requested from the CDC and other one or a few SCIENTIFIC PAPERS that show as much as possible that this virus behaves like other known viruses. We have never seen any remotely adequate answers. We have been called names for simply asking proper scientific questions. We find Peter Duesberg is the only researcher who behaves like a scientist as he has published all of his work that is relevant and discussed it comprehensibly.

    See Rebecca Culshaw "Why I quit AIDS", Harvey Bialy's book about the scientific life of Duesberg, George Miklos' (the only one of these people I know, he is an exemplary colleague) review of Bialy's book, Andrew Maniotis (Chicago) various statements of what they do to him when he attempts to tell the t ruth clearly..but the best writing, and the scariest and most coherent is Celia Farber's article in Harper's magazine (Mar 06?) about the AIDs tests. See for yourself. Gallo's office called me. Mario Stephenson of the Worcester Med school "wants to astraighten me out". I am happy to talk to them if we can record their conversation and if they submit what it is they want to t alk to me about first. I realized how unscientific the entire morass is when I heard Lettvin (?) talk about how mutable (changeable) the virus the reason for the inability to make vaccine. At that moment I realized, and then verified, that there are no consisten criteria foridentity: What does the virus look like? How many particles per cell are there. What is the correlation between those with symptoms and those who test poistive with no symptoms? Etc. No correlation, no evidence. The term "HIV-AIDS" is a sham and should never be used. "ID" stands for not Intelligent Design but for Immunodeficiency. But incessant use of antibiotics, including in milk and other foods lead to immunodeficiency. ETC. In fact I'm sick of this discussion as I have no special knowledge just a need to have scientific data, not propaganda. LM

  14. Professor Margulis,

    As someone who deals with sex — in its so many forms, how did you find it to write about humans and "genital friction"?

  15. Joanthan Bartlett

    Do we know the mechanisms of symbiotic establishments in the wild? What interesting symbioses have we observed, and what mechanisms were involved?

    I never say anything "is interesting"..except to me or a colleague, family member of friend, but I love your question anyway.

    First: Bacteria, including archabacteria, can mate either by cell to cell contact or by dropping one's DNA into the wetness to be taken up by the other. All bacteria will rather mate than die when that is the coice. Since you can put them in the refrigerator in the evenig and make them be another species by morning I agree with Sorin Sonea (book: Prokaryotology, Universite Montreal Press) that they have no species in the sense nucleated organisms have..Then we work with speciated protists that have no sexual life histories but surely that have species identity.

    Jonathan, there is a fine literature dating back to the mod 19thC that has been summarized in several books: Evolution by ASsociation, History of Symbiosis research (Jan Sapp) our book Acquiring Genomes: A Theory of the origins (s, plural) of species (Margulis and Sagan, 2002 Basic Books) and now we found that most of the classical well studied cases were known to Boris Kozo Polyanski in his book A new Principle of Biology (he meant evolution by symbiogenesis) in 1926. This book is nearly all translated by Vicot Fet, a biol. prof at Marshall univ in Huntiington W V.

    By no means are these ideas only in the microcosm. What is a cow (or a bison) unable to eat grass? A starved cow. What is a subterranean termite unable to eat and digest wood? A dead termite. Both these types of animals owe their existence to great communities of highly specific symbionts that digest their foodstuffs, make them change their bodies (over time, of course). The rumen, the hindgut. The literature is vast and so detailed that in 1924-26 K-P wrote a book eplaining this..he united Darwins "natural selection (which only ELIMINATES life forms, does not create them) with SYMBIOGENESIS that does create new species in the same genus. Other modes of species change include: polyploidy in plants, hybridization in marine larvae, karyotypic fissioning (centromere reprouction) in mammals and several other modes. All are far more significant for the generation of new species than "random mutation". Of course random mutations hone and refine the bigger hereditary processes but there is no evidence I know of that proves that random mutation GENERATES evolutionary novelty..i.e. new species. All this is detailed in the books I mentioned and see the ISS (International Symbiosis Society) and its journal called Symbiosis.

  16. So we trust the process more than the authority. Do you disagree with that summation?

    Donna: I entirely agree with everything you said but of course even a workcoholic scientist like me has to derive most of the information (inclduing absolutely the methods and the logic) from others because of lack of time money and because we have to do our own thing. Every day the amount to learn goes up and all of us suffer from too much to do.

    An extremely important aspect of scientific evidence is that it be open to inquiry and criticism, explicable (sometimes that takes work to learn vocabulary and details of course) and that no scientific point be argued on authority alone, ever. Note it is also a social activity with a writing and other forms of communication component. I have never k nown a practicing scientist who is reluctant to speak about his work and who doesn't w elcome criticism. I think very little is more important than a fine, knowledgeable critic.The proper critic is of immense value. Why, because attempts to answer valid criticism lead to better explanation, new observations, new search for evidence, new colleagues and, in general better science. This is what happened during all these years with Luminous Fish. I thank all those people how rejcted immature forms of this book because, in my tries to see their criticism the ms improved greatly. It is now publishable. I hope we (Chelsea Green) will be able to put it into paperback next year or so. LM

  17. Jimmymac:

    As someone who deals with sex — in its so many forms, how did you find it to write about humans and “genital friction”?

    My recent silence was due to my mistaken opening of your web page and the loss entirely of skepchick. I had not seen Hot Sand web page. Nice, I guess. I'll have to go back to it.

    Now by the time we wrote What is SEX? (Dorion Sagan and I) we (with Lorraine Olendzenski) had submitted a paper at a symposium at the MBL Woods Hole Ma about the nature of sex. On the basis of this paper Richard Dawkins and Mark Ridkey asked for a chapter in their book about origins of sex, the Gustavus Adolpho Nobel program had sponsored an entire annual program on sex in general (we wrote a paper for HarperCollins for their book) and then we wrote Origin of Sex. This fascinated me because it gave me more than permission, license, I might say, to read the literature on bacterial sexuality, genetic repair, and photoreactivation, parasexuality in fungi, origin of meiosis by L R Cleveand and myriad books about insect penises and eating of ones mates (usually the female eats the male), parthenogeneisis in anolis lizards, gender change in wrasse (fish), sperm competion (gorillas have small testes and garner their females by bodies, chimps have relatively huge testes and the sperm does compete, more like people ETC. Most of the animal books are confused because they think sex is the only mode of reproduction (as it is in mammals etc.) Some of the books moralized.

    Anyway, the "origins of sex" ms was an eye opener. Sexual life histories are so embedded in the evolution of various groups that it was easy to see that sex of the meiosis-fertilization sort typical of many protoctists and virtually all fungi plants and animals had evolved along with the eukaryptic cell in protoctists, probably in Proterozoic seas. The variation in sex, reproduction and gender determination in the 50+ phyla of protoctists is astounding by a measure that makes animals, plants and fungi all look alike. I found that tje older careful scientists who never did any of this work for money, only to learn the answers (e.g., HF Kirby, LR Cleveland)

    All of this to say that by the time we did What is Sex? for Nevraumont we had all the problems solved on an academic level and only needed to gather more illustrations and examples.

    In Mystery Dance, the origin of human sexuality book we performed the evolutionary striptease, As the make-up and fashionable clothes come off a body is revealed that advertizes readiness to mate (tight pink pants, big boobs, etc.) Striping, we realized, was descending into history as the sex act itself occurs between two protoctist-like cells: swimming sperm and large egg. But the publisher insisted we not be sexist and w e had to make the stripteaser hermaphroditic. It was downhill from there.

    To be more explicit, with repect to sex humans are just one of thousands of similar mamalian examples. Smell the pheromone, visually excite, loosen the hormones, fill erectile tissue with blood, come to climax and rest afterwards. The only deviation from stallions and mares, dogs and bitches, tomcats and their females is what John Donne wrote centuries ago:" Sir: More than kisses letters mingle soules"…or perhaps what Emily D, our neighbor said "For each exstatic instant we must an anguish pay, in keen and quiverling ration to the ecstacy". Talking, real communication, can excite.

    But from the broad view there is nearly nothing radically different about humans at all (cf with 50,000 different genders in Schizophyllum-a fungus- or 93per cent of the genes thrown away during maturation in the ciliate called Stylonychia that go to do meiotic sex, or the lethality of sex in stentor, environmental changes and their induction of behavior that leads to mating etc. I guess I'm really more interested in the way the need to survive lead to the establishment and cannonization of sex in early lineages, in the ways sex became linked to death and the ways sex occurs without morphological manifestation of it (parasexuality). There are many things on heaven and Earth that we have not dreamed about (Horatio) and that is why in the end, Nature's non-fiction is far richer than human fiction, and friction. LM

  18. Lynn,

    I don't know if you're going to post any more answers or if you're done, but I'm packing it in for the night. Thanks for letting Skepchick host your blog tour today, and for discussing your new book — and other topics — with us. I, for one, look forward to reading Luminous Fish. It sounds fascinating.


  19. Wouldn’t it be appropriate to consider them analogous to ring species in eukaryotes?

    Brian Schmidt: Thanks for your question, sorry to take so long to answer. My problem is that I don't know the term "ring species". Are these "clines" in populations? Please give 2 or 3 examples to help explain.

    In Acq Genomes we define species (keep it within eukaryotes) and note the concept of origin by symbiogenesis. Organsms that share the same set of integrated former symbionts belong to the same speccies. Witness green animals (Placobranchus, Elysia). They have close relatives, ineviably with different names, who lack the photosynththetic entity. Indeed, check out the leignathid fishes with luminour bacterial colonies under their eyes in "light organs", Like photoblepharon in the Luminous Fish book. LM

  20. “the majority of well-read, highly educated gentry ignore the wetness of nature in which we are all embedded.” I’m not certain I agree but I find this intriguing. Can you give some specific examples?

    One example should suffice. We have take over 40% of the araable land surface to feed people. In so doing we have caused huge numbers of non-human planetmate species fo extinguish. Do you think we could cover 80 persent of the land with corn, rice, wheat etc. See Vaclav Snel's MIT press book, The Earth's Biosphere" . As Mark Twain noted, "The world was made for Man? I dunno"

  21. You have gone on record as stating that most pregnant women test positive for HIV.

    I have listed my sources in another see Celia Farber's Harper Maga (March 2006??) article for this one. Thanks. If there are no new questions I give myelf up to morpheus.

  22. You have gone on record as stating that most pregnant women test positive for HIV. an you give a published reference for this ridiculous statement?

    Thank you,

    Try Celia Farber's comprehensive Harper's Magazine article, I think it was published Mar 06? The other refs I wrote before, etc.

    I've been up since before 06:00 today and reluctantly give myself up to morpheus now. Good night. Thanks again.

  23. Dr Margulis,

    Your original quote on Pharyngula was that the “HIV tests are nearly always positive for pregnant women”.

    When I asked for evidence for this unbelievable claim, you cited Celia Farber’s March 2006 article in Harper’s Magazine (“Out of Control”).

    This article is merely an opinion piece by a journalist who is a self-confessed disbeliever of the orthodox view that HIV exists and can cause AIDS. The article itself contains not one scientific reference, and it is not a scientific publication.

    I was rather hoping that as a scientist you would be able to point me towards some peer-reviewed publication in the scientific literature to back up your claim, and am sorry you are unable to do so.

    I have tried on your behalf, but comprehensively failed to find any evidence to support your statement. I have found numerous references to the sensitivity and specificity of HIV antibody tests in various conditions, and I am aware that false positive results may occur, as with every single laboratory test known to science. You might consider the analogy of say a pregnancy test itself; – these are usually very accurate, but conditions do exist when they may give misleading results (and the fact that this can occur does not cast doubt on the existence of pregnancy!).

    You imply that pregnancy will cause all tests to be [false] positive, yet the reported incidence of a false positive test occurring when screening a low prevalence population is in the order of 1 in 25 000 tests (see refs). Quite clearly HIV tests are not “nearly always positive” in pregnant women.

    It is quite possible that you are misunderstanding the underlying principles of testing and confusing the true/false positivity with the concept of predictive values that rely on an understanding of the underlying disease prevalence.

    If one tests a very low HIV prevalence population where you would expect the overwhelming majority of individuals NOT to have HIV infection, then you might well find that most of those who actually DO test positive are NOT infected. (Continuing the analogy, if you did the aforementioned pregnancy tests in 1000 nuns, you might well find that the 3 nuns who test positive are not pregnant).

    In areas with high HIV prevalence, like Southern Africa, there will be relatively very few false positive HIV tests. (The analogy here is might be in performing pregnancy tests in a group of 1000 women whose periods were late – the vast majority of positive pregnancy tests here will be true positives (say, 200), and there will be proportionately very, very few false positives (3 out of 200).

    I hope this clarifies the concept for you, and makes you consider carefully the sources you cite. You are a high profile scientist, and people pay attention to what you say. It is beholden upon you to ensure what you say is accurate and evidence based, and not merely regurgitate misleading opinions gleaned from unreliable sources as “fact”.




  24. In an attempt to steer this back toward topics that Lynn is more interested in, I recommend that Lynn read the book _Viral Sex_ by Jaap Goudsmit ( ). And also some papers on the taxonomy and nomenclature of viruses, which spell out why it does seem possible to identify distinctive clades of very highly related viruses[1,2]. Most people agree with Lynn's idea that it makes little sense to think of Genus and Species, in bacteria and viruses that do not have the type of sexual reproduction that many eukaryotes use. The taxonomy and nomenclature of living things is still very useful for humans, and we can use terms like "species", "type", "serotype", "strain" and "isolate" if we agree on what they mean within the system of set of systems we are studying, even if they do not align perfectly with the same terms used in other systems.

    Retroviruses all package 2 copies of the viral genome. Most often, this is two copies from the same parental genome. In some cases, the host cell can be dually infected with two different virions. If the two infecting viruses then are expressed at the same time, the budding viral particles can sometimes package one genome from each of the two parental infecting viruses.

    The reverse transcriptase of retroviruses uses template switching between the two packaged RNA genomes in the virion, to produce the first DNA strand, known as cDNA (complimentary DNA). So if the virion happens to be one of these with two different parental genomes packaged, the resulting cDNA is a hybrid, with some regions of the genome copied from one parent, and other regions of the same new genome copied from the other.

    Retroviruses also sometimes transduce a cellular gene into their genomes. This is fairly rare, but the result is sometimes highly detectable by humans. So these rare but detectable viruses have gotten a lot of attention over the years, beginning with the Rous Sarcoma Viruses, which cause sarcomas in domestic chicken flocks, and continuing with mouse tumor viruses, such as the Moloney strain of murine Leukemia virus (Mo-MuLV).

    It seems that not all retroviruses can recombine with all others, even if they can infect the same cell line. For one thing, the region of the Gag protein that is responsible for binding the Psi element of the viral genome, is rather specific. If there was not this specificity, the viruses would very often package some random messenger RNA instead of the viral RNA genome.

    Many other restrictions on viral recombination, or restrictions on the viability of the resulting recombinant genome can exist. For example in the lentiviruses (a "genus" in the retrovirus "family", we agree that these terms are not exactly analogous to their eukaryotic counterparts, but they are still apparently useful for categorizing related groups of organisms), the TAR element in the long terminal repeat, must interact with the Tat protein encoded by the virus. So, for example, the Tat protein must recognize the TAR element in the RNA genome [3]. Even if the Tat protein and TAR elements are compatible, the Tat protein also has to interact with several cellular proteins which can vary between host species [4,5].

    Given all of this, "reproductive isolation" can occur between retroviruses that are due to either host factors, virus factors, geographic isolation and other mechanisms. The end result, is groups of very highly related "strains" or "isolates" of viruses which may be said to be equivalent to a "species" [1,2].


    1: Fauquet CM, Stanley J.

    Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors.

    Arch Virol. 2005 Oct;150(10):2151-79. Epub 2005 Aug 19. Review.

    PMID: 16132185

    2: Koenig R, Verhoeven JT, Fribourg CE, Pfeilstetter E, Lesemann DE.

    Evaluation of various species demarcation criteria in attempts to classify ten new tombusvirus isolates.

    Arch Virol. 2004 Sep;149(9):1733-44.

    PMID: 15593416

    3: Chen H, He J, Fong S, Wilcox G, Wood C.

    Jembrana disease virus Tat can regulate human immunodeficiency virus (HIV) long terminal repeat-directed gene expression and can substitute for HIV Tat in viral replication.

    J Virol. 2000 Mar;74(6):2703-13.

    PMID: 10684286

    4: Maury WJ, Carpenter S, Graves K, Chesebro B.

    Cellular and viral specificity of equine infectious anemia virus Tat transactivation.

    Virology. 1994 May 1;200(2):632-42.

    PMID: 8178449

    5: Endo-Munoz L, Warby T, Harrich D, McMillan NA.

    Phosphorylation of HIV Tat by PKR increases interaction with TAR RNA and enhances transcription.

    Virol J. 2005 Feb 28;2:17.

    PMID: 15737233

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