Evolution

Evolution

  • Andrey Luchnik added an answer:
    How did the genetic code evolve?
    I attached a page of a thought provoking book written by A. E. Wilder-Smith and published in 1981. Does anyone know, if his criticism is still valid?
    Are there any convincing models, why the genetic code (in the nucleus) of all cells is almost always the same.
    Shouldn't it evolve based on currently accepted models? If it does not evolve anymore, how did it evolve in the first place?
    Andrey Luchnik · Russian Academy of Sciences

    Dear Reinhard!

    You write: "Random mutation cannot create a code". That is true. So how it could be created? By whom? 

    I discuss this question in my popular articles written in Russian. They can be found in Internet. But Russian is most flexible among all Indoeuropean languages, all originating from south Urals. So I  can understand West European languages, even Sanscrit because I am Russian. But not vice versa. 

    Interesting, that agglutinative languages such as Turkish, Basks, Shumeric all originate from South Urals. German language bears some traits of ancient Urals agglutinative language. But it is flexible like all other Indoeuropean languages including Russian.

    Return to genetic code. It could not be born by itself (himself). The only plausible hypothesis considered nowadays is panspermia from other planets:

    Crick F.H.C., Orgel L.E. "Directed panspermia", Icarus 19, 341-346 (1973)

    But question arises: If it is brought from another planet, then it is brought from yet another plant to this particular 'another planet' . And so on to eternity. 

    Is DNA an eternal molecule ubiquitous in the Universe? As young and eternal as Universe? Challenging questions...

  • Fangluan Gao added an answer:
    How to do extended Bayesian skyline plot analyses?
    I want to use BEAST to do EBSP analyses with two loci. I open two "input.nex" files in BEAUti to generate a "output.xml" file (In the Trees panel select Extended Bayesian skyline plot for the tree prior), and then run BEAST. I do not know if this is right and I do not know what to do next. I can not construct the trend of demographic history in Tracer just like BSP. I got one log file but two trees files (for each locus), and I do not know how to import both tree files into Tracer.
    Fangluan Gao · Fujian Agriculture and Forestry University

    Hi Yong Shi,

    I got it. Thank you for your help.

  • Shian-Loong Bernard Lew added an answer:
    Can pollution trigger evolution in some species?
    We are all aware of the evils of pollution and its impact on ecology. Among all the destruction it causes, is there any chance that it may actually lead to evolution of some species? Are there any examples?
    Shian-Loong Bernard Lew · Taylor's University

    If evolution implies increased complexity, then the answer is No. If evolution implies fitness to an inferior target, then the answer is Yes. As advanced by devolution hypotheses. Because genetic entropy may "discount" evolution's selection for the fittest (measured to a prior yardstick) due to pollution:

    Following from which info-centric views of genetics and evolution may be used to explain:

    • Pollution causing mutation in frog -devolution
    • The link between pesticides and Alzheimer's-devolution

    Just because somethings thrive tells us little of its fitness-.Especially if that fitness is a moving target. If we eat "heavy metal tuna" and become cognitively- impaired how fit are we compared to our ancestors, even though our average life expectancy is higher? Where are we on the global fitness landscape?

  • Janine Wonnacott added an answer:
    Is the war an adaptive behaviour for men?
    Is the war a way to rationalize the natural human violence ?

    You don't have to interpret the "posture / submit" response as a result of man's good nature.

    For wolves, it is in the best interest of the pack that all wolves be healthy and uninjured.  If conflict and issues of rank and dominance can be settled through posturing rather than fighting, that's better for the group.  Fighting can mean injury, even for the victor, which weakens the pack.

  • Timothy A. Dickinson added an answer:
    Is there a software that can compare two phylogenetic trees to each othe (face to face comparison)?
    I want to compare the results I obtained using two different phylogenetic trees. I would like to have some lines between the species in the two trees.The phylogenetic trees or the dendograms are constructed using molecular markers.
    Timothy A. Dickinson · Royal Ontario Museum

    Janos Podani's Syn-Tax 2000 package (https://www.exetersoftware.com/cat/syntax/syntax.html; http://ramet.elte.hu/~podani/) implements methods for comparing two or more trees, as described here: Podani, J., and Dickinson, T.A. 1984. Comparison of dendrograms: a multivariate approach. Canadian Journal of Botany 62(12): 2765-2778. See also Podani, J. 2000. Simulation of random dendrograms and comparison tests: some comments. J. Classif. 17:123-142 and Podani, J., A. Engloner and A. Major. 2009. Multilevel comparison of dendrograms: A new method with an application for genetic classifications. Statistical Applications in Genetics and Molecular Biology 8(1): Article 22. DOI: 10.2202/1544-6115.1443. 

  • Timothy D Smith added an answer:
    What is the state of current evidence about the existence of a vomero-nasal organ in birds?
    The literature on whether birds have vomero-nasal organs (VNO) in birds is confusing, with little hard evidence supporting the presence of the organ, but equally few firm rejections of its presence. The situation regarding dinosaurs is equally confusing; Tyrannosaurus rex apparently did not have a VNO, but some pterosaurs might have had one (at least, they have two currently unexplained palatal fossae). Is there any recognised definitive literature on this matter?
    Timothy D Smith · Slippery Rock University of Pennsylvania

    The question of living birds possessing a VNS is one for histological research. This is so because of the microscopic size of the elements. In the periphery, one hopes to find a neuroepithelium in the form of a duct or patch, and Kurt summarizes the necessary evidence on the accessory olfactory bulb. So the very nice images provided above on the grey parrot and other birds are simply too macroscopic for the job.

    A pitfall in the search for vomeronasal structures is that serial histological sections are needed because sampling regions can lead to falsely proclaiming a VNS structure is absent (when in fact it remains hidden in unsampled regions).  So, there may well be birds that have not been studied thoroughly enough. See the literature on the VNO in primates and bats to get a sense of the enormity of the task. 

    That said, I would definitely agree with Kurt that a VNS in birds is highly unlikely. What seems possible though, is that some vestige of the peripheral receptor organ (the VNO) may remain in at least some birds, as is the case for some mammals. 

  • Peter Salonius added an answer:
    What does it mean to you that the global conc. of atmospheric CO2 crossed 400 ppm mark for the first time in recorded history?
    What would be the consequence? Practically is there any way out? Soliciting inputs from the experts.
    Peter Salonius · Natural Resources Canada, Retired

    What type of climate change are you worried about?
     
    You are probably concerned with the catastrophic human produced climate warming projected by the IPCC and Global Climate Models that have not been validated, and that have failed to match observations (no climate warming during the last 2 decades in spite of rising atmospheric concentrations of carbon containing greenhouse gases.)
     
    One of many papers showing that CLIMATE WARMING CAUSES INCREASED ATMOSPHERIC CO2 CONCENTRATIONS suggests  that the IPCC thesis and the assumptions of Global Climate Models ----------- that that assume CLIMATE WARMING
    IS CAUSEDBY ATMOSPHERIC CO2 CONCENTRATIONS ----------------- are in serious error.... see: 
     
     
    http://www.clim-past.net/8/1213/2012/cp-8-1213-2012.html
     
    The IPCC thesis and the assumptions of Global Climate Models that that assume that
    CLIMATE WARMING IS CAUSED BY  INCREASED ATMOSPHERIC CO2 CONCENTRATIONS ..........has been the basis for taxpayer funded and enormously misguided government policies and regulations designed to curb human emissions of CO2.
     

     ------------------------------------------------------------------------


    QUOTING from the FULL TEXT of the paper (with somewhat 'iffy' English) concerning the dominance of the Sun's influence on the Earth's CYCLICAL warming and cooling ................. available at:

     http://www.doiserbia.nb.rs/Article.aspx?id=0354-98361500018A&AspxAutoDetectCookieSupport=1#.VRbMQPnF-ah
     
     
     
    "The start of the Grand Minimum of TSI is anticipated approximately in cycle 27±1 approximately in 2043±11 and the beginning of the phase of deep cooling of the 19th Little Ice Age (of the Maunder Minimum type) in the past 7,500 years approximately in 2060±11, with possible duration of 45-65 years "
     
    "The Sun is controlling and practically totally determining the mechanism of quasi-bicentennial cyclic alternations of climate changes from warming to Little Ice Age and set corresponding time-scales for practically all physical processes taking place in the Sun-Earth system. The current long practically stable levels of World Ocean and of temperature additionally reflects the current state of global warming during past 17 years, which are under the direct control of the quasi-bicentennial decrease of TSI. Approximately in the end of 2014 we begin the descent into 19th Little Ice Age in the past 7,500 years " 
     

    Peter Salonius
     

  • Georgi Gladyshev added an answer:
    Can somebody advise a big, widely used and comprehensive resource on studies related to origin of life?
    Can somebody advise a big, widely used and comprehensive resource on studies related to origin of life? Or maybe there are some institutions/individuals constantly working on that problem?
    And another question is what happened to Eigen and Schuster's Hypercycle Theory? Is it a fundamental for today's understanding of the basic realisation of inorganic-->organic transition concept?
    Georgi Gladyshev · Russian Academy of Sciences

    Georgi P. Gladyshev (2015) Natural Selection and Thermodynamics of Biological Evolution. Natural Science, 2015, 7, 117-126 Published Online March 2015 Pub. Date: March 9, 2015
    DOI: 10.4236/ns.2015.73013 http://dx.doi.org/10.4236/ns.2015.73013

    Abstract The author of this article proposes that the representation of Charles Darwin and Alfred Wallace’s theory on “variation and selection” in the living world is a reflection of the action of hierarchical thermodynamics...

  • Ashley W. Poust added an answer:
    Can someone recommend books or articles with information on mammalian evolution?
    I am currently doing my presentation on mammals and their evolution, I would like to have books where I could get information.
    Ashley W. Poust · University of California, Berkeley

    I think one of the best books to think about evolution in mammals is GG Simpson's 1953 Condon lecture "Evolution and Geography, An essay on Historical Biogeography with special reference to Mammals".

    You'll have to take it with a grain of salt - this was written before phylogenetics or plate tectonics caught on. And to echo other authors it depends on the level you are looking. Simpson's paper is amazing if you want to start thinking about how evolution happens, but it is not just a retelling of the history of mammal evolution. For that look for books by Prothero, Kurten, DR Wallace, or for more general books on the history of life and turn to the last few chapters (almost invariably mammals are at the end).

  • Sundaresan Muthuswamy added an answer:
    Is consciousness giving human beings an evolutionary advantage?
    While having the concept of Self as opposed to others or to the environment seems good for focusing the organism functions on survivability and on DNA spreading, is there any evidence that consciousness has an evolutionary advantage?

    To elaborate further, here I'm talking about consciousness as the first person experience. And for "first person experience" I'm not talking about "experience OF first person": conversly, I'm specifically addressing the "experience IN first person MODALITY" (as a corollary to this question, I'm proposing that the word "consciousness" refers to too many concepts). In this view, I consider self-consciousness "experience of first person in first person modality".
    If we embrace the assumption that consciousness is always consciousness of something, we still lack an explanation for the nature and the purpose ("what is/what's for" rather than "how is it") of the first person experience, and as such why evolution favored it.

    In a lot of other Q/A about self and consciousness people are talking about consctructs that may function even without consciousness. Two examples:
    -self: a neural network comprising semantic concepts about the world could very well include the concept of self as a non-other or non-environment, or even a concept of self as an independent organism with such and such features; why do we need consciousness to conceptualize it? Would a machine decoding all the concepts coming across the node of (or the distributed knowledge about) self be considered conscious? We do not have to attribute consciousness to the machine to explain the machine processing its concept of self.
    -thinking: processing is certainly different from consciously elaborate something, as all the studies on automatic and subconscious processing show. On the other hand, this point address the free will problem: when we consciously elaborate something, does it mean we are voluntarly doing so? Or are we just experiencing a first person "show" of something already happened subconsciously (as Libet's studies suggest)? Without touching upon the ad infinitum regression problems, this poses the question if consciousness is useful without free will: if the conscious experience is just a screen on which things are projected, no free will is needed and thus what's the whole point of consciousness? As such, do we also need free will for accepting consciousness? If we are working with the least number of assumptions, it seems unlikely the we can accept consciousness.

    It seems to me that the general attitude of cognitive theories in a biological information processing/computational theory of mind framework is to try to explain everything without putting consciousness in the equation. And indeed it seems to me that no one is actually putting consciousness in the equation, when explaining cognition or behaviour (at least in modern times).

    All in all, it seems to me that all the above reasonings bring the suggestion that consciousness is not needed and has no evolutionary advantage over automatic non-conscious entities. Or that we should make more and more assumptions (such as accepting free will) to make sense of consciousness.
    I think that asking why we have consciousness could lead us to understand it better.
    Sundaresan Muthuswamy · ACE colle of engineering and Technology, Thiruvellum.

    SOME THOUGHTS:-

    When one dreams the living consciousness is able to identify itself as the experiencer and many weird or meaningful dreams seem to be real and only when waking up one realizes it is after all a dream. Even pain can be experienced  during the dream which is not real and is benign though the physical heartbeat pounds more. This virtual pain really looks real and is to be felt and observed. All these happen in the dream state. While we wake up that is in the waking state we feel various emotions amongst which the most prominent being that of joy and pain.It is the feeling of pain which predominantly drives man or women into contemplation and finally   to seek the higher powers visible and invisible. Happiness is such an experience which if it is open ended or endless would perhaps spell anarchy in this manifest world  . However happiness is our prime goal and perhaps can be said as a natural instinct to make us  feel comfortable.

    Both these qualities are of the mind and its domain being  the consciousness is just the witnesser. It is the capacity of the mind to  make us feel and see the universe and  nearby surroundings. When the mind has the capacity to make us feel even the pain which is false and unconnected, how long or for that matter what prevents it  to create in us an illusion of the Universe? If man can create virtual 2-D,    and 3-D images why not is it possible for Nature to create a real life 6-D and more.... real looking and living objects and we all being the actors forced to act?

    The Gigantic Universe with its solid and gaseous content cannot be born from nothing, and at the same time it is practically and humanely inconceivable to feel and ever Create such an happening. This answer will never ever be done by any human be it a scientist or otherwise. Hence in the ultimate analyses in Vedantic  literature and spiritual pursuits the concept of Total mind enters into the picture of our life frame and eventually it says it is just a mental   aberration of the Cosmic Mind which creates a real life like and seemingly real existence.The Consciousness of the Total Mind Which is also  the Experiencer is the    entire Universe with we earthlings  also being a part of It.

    However  and whatever theories we may make and prove the simple existence of this seemingly extensive Universe and the Source of creation can never be physically explained. This being so no amount of boasting or basking in the  name and glory of science can ever match  even  a small length or boundary of Truth of the universal existence and its cause.

    Hence Consciousness is a very big term to comprehensively define and understand fully. Somehow men of great stature have found an easy way out namely discovering  the term called Universal Love   with humility being its trademark that  can allow humans to have a genuine feel of Consciousness and Its ways.

    The definition of science coined by man is essentially to make inroads towards the betterment of the human race and not for labelling  it as the ultimate tool as most budding scientists and the new generations  have started to express nowadays

  • Brian Thomas Foley added an answer:
    Are you teaching evolution using Evolutionary Analysis?

    (4th or 5th edition) I would like to create a forum for the exchange of ideas, questions, and teaching experiences. What works, in your teaching? What doesn't work? Have you used any "active learning" methods in your course? Do you use virtual laboratory exercises (such as those from SimBio) in your course?

    Brian Thomas Foley · Los Alamos National Laboratory

    For molecular evolution and phylogenetic analysis, the Phyobabble group is very nice.  http://phylobabble.org/  It is well organized and has a lot of experts in phylogenetic analysis.  For data sets, and looking for interesting data and stories of evolution, the TreeBase is pretty interesting.  http://treebase.org/treebase-web/home.html

    For looking at "the tree of life" I really like the OneZoom site. http://www.onezoom.org/  the tutorial there is really worth taking, for example to learn that you can switch between common names of the organisms and Latin names.

    In GOOGLE+ (google plus) there are a lot of "communities" for sharing thoughts, ideas, resources for studying evolution.  https://plus.google.com/communities/108054924267127040453 for one example.

    On YouTube, COncOrdance and AronRa have done some very nice videos:  https://www.youtube.com/user/C0nc0rdance   https://www.youtube.com/results?search_query=aronra+evolution

  • Are "sex pheromones" really produced by insects?
    I had previously asked a question "Can bacteria mediate "mating" in insects?" for which i had received wonderful answers from my peers. Taking all answers and reference into consideration we performed certain experiments to ascertain our hypothesis. We cultured a germ-free line (GFL) of B. dorsalis females. Virgin males were given a dual-choice between GFL and Non-GFL B. dorsalis females in a customized olfactometer. We were astonished as males were significantly (P < 0.0001) attracted to non-GFL B. dorsalis females.

    We had previously identified 9 bacteria from the reproductive organ of the females and each bacteria was checked for their attractiveness. Two out of nine were attractive to virgin males. Is there a possibility that these bacteria produce "sex pheromones" that attract male towards female flies? Further work is under-process.
    Iuliana Vasian (born Budae) · Babeş-Bolyai University

    Nice work. Good look

  • Craig Dremann added an answer:
    Conservation biology: a fixist view of life?

    All too often, people talking about biodiversity or ecosystem preservation (be it in the frame of climate/global change or of mitigation of other human activities, like agriculture or urbanisation) convey a message that we should basically maintain the current state, implying that any change would be for the worse and that human actions can only damage nature, not improve it. This somehow ignores the very principle of evolution - which means (in Darwin's words) change through descent with modification. There are attempts in conservation biology to use evolutionary processes (like in the dynamic management of genetic ressources used for some agricultural species), but these are marginal compared to the dominant 'preservation as identical' position. Aren't we missing the whole point of life evolution and of man being part of it when advocating to preserve the current status, rather than allow nature to evolve with us?

    Craig Dremann · The Reveg Edge

    I think we can divide the planet into the human-habitat and the natural habitat, which in generally is divided into a 90:10 split.  And until recently we believed that we could have it all, but we may be coming to the conclusion that we need more than 10% to remain, to maintain the other 90% for us--like providing the annual rainfall that we need to survive.  

    My guess is that we need to set aside and restore at least 35% of the natural areas as Ecological Restoration Preserves, that is what I am asking at https://www.researchgate.net/post/Do_we_need_to_set_aside_35_of_the_planet_as_Ecological_Restoration_Preserves?

    So biodiversity and conservation as independent considerations are not the issue, but how much of the natural world do we need to keep around us, so that we can maintain our human-portion of the planet?

  • John Grehan added an answer:
    How much influence would you say Dolf Seilacher had on Gould and Lewontin's "spandrels" paper, particularly on their critique of 'panadapationism'?

    See Hallam's obituary for Seilacher in the Geoscientist 24(7):28.

    I would agree that Gould had a fuzzy view of constraints, and more I would say very fuzzy as much of his thinking about evolution lacked an integrated coherence. As to the impact of his paper, given his prominence his paper received similar prominence - at least in the English speaking world. But whether it was much of a paper is another matter. It was not very deep in its analysis, far less than potential influences such as Leon Croizat whom Gould read, but never cited even though he seems to have borrowed on Croizat;s work in this respect.

    John Grehan

  • Brenden S Holland added an answer:
    Exotic plants or animals evolving into new species?

    In California we have over 1,000 exotic plants that have become naturalized and exotic animals like the Argentine ant in California, lives a very different lifestyle than in its original country.   Anybody looking into the possibility that these exotic plants and exotic animals may be evolving into new species, in the new lands they now live in?

    Brenden S Holland · University of Hawaiʻi at Mānoa

    Well yes if we want to consider insular islands as natural examples of how, and how fast species evolve to become unique entities from their "parental" lineages, the Hawaiian Islands are rife with  examples, and a rich literature, as to  how lineages phyletically evolve in reproductive isolation (due first to major GEOGRAPHIC ISOLATION) from source populations.

    So given sufficient time, habitat diversity, and starting genetic variation, multiple lineages can arise from a single introduction event. Silverswords are a great example, as well as hundreds of species within the Hawaiian Drosophila, the case-building Hyposmocoma (micromoths with maybe 400 species), Tree Snails (endemic subfamily Achatinellinae with 100 species), and an entire family of snails with diverse biology, morphology, habitat preferences and around 350 endemic species called the Amastridae.  This is in fact the only endemic FAMILY in Hawaii.  So yes, certainly, deeper taxa than species can evolve following colonization/introduction events, given the right set of conditions!

  • Simon Dellicour added an answer:
    A quantitative measurement of group assignment using mtDNA sequences, any advice?
    I'm working with two species using the mitochondrial cytb sequences from several localities and I want to obtain a continuous measurement of species assignation (i.e., one value for specimen/haplotype). I thought in use the program STRUCTURE to get the values of Q. But as far I know this approach could have several assumptions problems about LD and loci independence. Do you know another approach to get some estimator as Q from Structure? What about Geneland?
    Simon Dellicour · University of Oxford

    If you have a mono-locus dataset (for DNA sequences), I would recommend to try the SAMOVA clustering method of Dupanloup et al. (2002; doi:10.1046/j.1365-294X.2002.01650.x). This procedure assigns populations to groups based on geographical vicinity and sequence similarity. The most likely structure corresponds to the partition of populations that maximized among-group variation measured by the AMOVA ΦCT statistic (Excoffier et al. 1992; in Genetics).

  • Mohit Sharma added an answer:
    Is there any article on Relationship between DNA Methylation and Human Evolution?

    DNA methylation was involved in the evolution of duplicate genes, gene expression, miRNA network stability. Question, Is there any great article to discuss The Relationship between DNA Methylation and Human Evoluation?

    Best regards,

    Mohit Sharma · I.T.S Centre for Dental Studies & Research

    In this manner methylation by turning off or on certain genes, could affect the fitness of an organism.... Probably evolution could operate in an organism in this manner without causing heritage changes? 

  • Björn L.D.M. Brücher added an answer:
    Wildest theory in Carcinogenesis: cancer formation as speciation. What do others think?
    Peter Deusberg proposed in an article in Cell that Carcinogenesis can most appropriately be described as a form of speciation. His argument exploits common characteristics of cancer cells to show that these cells have headed down the evolutionary pathway to speciation. These hallmarks include:

    1. Specie specific autonomy
    2. Karyotypic and phenotype individuality
    3. Flexibility by Karyotypic variations within stable margins of autonomy
    4. Immortality by replacing defective Karyotypes.
    5. Low probability of alterations in Karyotype generating autonomous species.

    Questions:

    Is carcinogenesis speciation?

    If so, how will this alter further cancer biology research?
    Björn L.D.M. Brücher · Theodor Billroth Academy

    Reality is different:

    Cancer is causatively triggered in:

    1) 5-10 by mutations
    2) 15% by infection and
    3) 80% are sporadic, meaning from an unknown cause.

    Unfortunately, for several decades the primary proposal from 1928, that cancer could be based by mutations with its modification to Knudson's 1-hit and later on the 2-hit-theory during the 1970s mutated from an opinion into a dogma, although only some 5% of cancers have been proven to be caused by such mutations to date.

    The NCI website states that ?mutations occur during carcinogenesis.? This, and the prior statement, that mutations cause cancer, has not been proven for more than an estimated 10% of cancers.

    The fact that mutations are observed in advanced cancers should not be synonymous with the notion that mutations are responsible for the development of cancer itself or that they are a prerequisite for carcinogenesis; an observation should primarily be an observation and not a conclusion.

    We presume that by ignoring citations of original references (on which peer-reviewers also have an influence) together with a kind of receptive reading (or better: over-reading) has resulted in the fact that an opinion (i.e., ?mutations cause cancer?) was transformed into a ?dogma? during the past five or so decades.

    Scientifically, it is even incorrect to state that mutations are "the" cause for cancer development and by this it is more than justified, that mutations are increasingly questioned [Rosenfeld S: Are the somatic mutation and tissue organization field theories of carcinogenesis incompatible? Cancer Inform 2013, 12:221?229; Versteeg R: Cancer: tumours outside the mutation box. Nature 2014,506(7489):438?439].

    We propose a new and more plausible cancer hypothesis for the majority of cancers and its underlying biochemical and physiological explanation as published in the past year at:

    http://www.biomedcentral.com/1471-2407/14/331

    http://www.nature.com/nature/journal/v517/n7536/full/517563a.html#comments

  • C. S. Mukhopadhyay added an answer:
    What is the difference between positive and negative selection pressure?

    How do we differentiate between positive and negative selection. These two terms sound like they are complementary to each other.

    C. S. Mukhopadhyay · Guru Angad Dev Veterinary and Animal Sciences University

    @Dr Andrea Gazolla, thanks for the note.

  • Sandra Lorena Ament added an answer:
    Assessing convergence using AWTY or TRACER?
    Can anyone offer any helpful tips on using these programs to assess convergence or determine how long to run an analysis for?
    Sandra Lorena Ament · University of Zurich

    Hi there. I assume you got what you needed by now, but I put this for future readers of the question. This fantastic blog helped me understand a bit more about convergence and AWTY. People like Dan Rabosky participate, so the comments and discussions are awesome:

    http://treethinkers.blogspot.ch/2008/05/are-we-there-yet-redux.html

    http://treethinkers.blogspot.ch/2009/05/for-this-unauthorized-installment-of.html

  • Michael Buchwitz added an answer:
    Does "Big history" as an exhibition/ education concept work for natural history or mixed museums?

    Do you have any experience with big history/ universal history exhibitions as well as courses for high school classes, especially:
    - comparison of natural and cultural processes which work at different time scales (from years to billions of years)
    - look at historical events (e.g. political turnovers, economical crises) from different points of view, i.e. study of written reports vs natural archives/ scientific data
    - evolution as a (meta)concept that includes biological evolution, but also evolution of the universe, planetary evolution, abiogenesis, cultural evolution, evolution of mind
    - answer to the question whether and to what degree history is determined by changes in environmental conditions (e.g. climatic forcing)
    - transition from humans as minor constituents of land ecosystems to humans as ecosystem modellers and from early artefacts to written language

    BTW: Is "big history" already out of fashion due to certain weak points (i.e. re-introduction of anthropocentrism and historicism into scientific discourse)?

    Michael Buchwitz · Museum für Naturkunde Magdeburg

    @Daniel R. Brooks: Do you refer to the permanent exhibition at the Vienna museum or the special exhibition named "Time trips – wie kann man zeit zeigen [how to make time tangible]"?

    The NHM in Vienna has got the advantage that it includes an anthropology and prehistory section - so it can offer at least some continuity between natural and human (cultural) history in its permanent exhibition. What I had in mind is something concise, i.e. a special exhibition like "Time trips" that illustrates the history of everything without crucial points getting lost under the weight of information.

    @Björn Berning: Holistic approaches of presenting a certain topic can be often fruitful and rewarding, especially in the context of museums (which are not constrained by school board plans).

    In a way "big history" is related to certain ideas of holism but perhaps the most critical point of big history is bridging the gap between natural history and cultural history (as noted by Andrew Sampson).

    @Jens: Yes, especially in the geosciences there are certain university courses that try to provide the larger picture.

    At high school level children get taught some isolated parts of the whole picture in the history, biology, geography and astronomy classes but usually not a comprehensive overview. So an aim of museums could be to teach the link between these parts (as a mind-expanding journey).

    @Andrew Sampson: Macquarie University has of course the benefit of David Christian and the Big History Institute:

    http://www.mq.edu.au/research/centres_and_groups/big_history_institute/

    You can log in as a high school teacher and get lots of teaching materials - in English, though, which is a certain threshold for teachers from non-English-speaking countries.

    A special exhibition like the one you mentioned is what I had in mind and, based thereupon, a piece of teaching for high schools that can be swallowed in two hours.

    @Nelson Orringer: Everyone knows Mt. Rushmore but I wonder about its suitability for big history classes - the monument and its surroundings arguably offer enough objects for the study of both, nature and history, but to address nature and history in a somehow unified way (such as a time scale?) could be challenging.

  • Azubuike Victor Chukwuka added an answer:
    What could be the potential drivers for the evolution of "extreme" sexual dimorphisms in isopods and other crustaceans?
    Sexual dimorphisms can be strongly pronounced in some groups of deep-sea isopods, e.g. in Macrostylidae. In these, not only primary and secondary sexual organs are affected by sexual dimorphisms but also for example the walking legs, the pleotelson shape and in some cases the whole body. In the past and potentially still today, these dimorphisms lead to taxonomic error. I am interested in the evolution of those dimorphisms and their meaning in the context of a deep-sea environment with low abundances.
    Azubuike Victor Chukwuka · University of Ibadan

    Sexual dimorphism is strongly driven by ecological factors. an important factor that can result in extreme dimorphism between sexes is the ecological preferences of each sex.

    For instance the dietary requirement for the female may differ from that of the male for reproductive reasons. thus an environment that is healthy enough to sustain the variety of resources will allow for morphological and physiological specializations suitable to efficiently harness this resource.

    In essence sexual dimorphism will never be expressed in extreme forms unless it confers an ecological advantage on the species and its population as a whole.

  • Leandro R. Jones added an answer:
    Does anyone know of any clear cases of molecular convergence?

    In my teaching I discuss the importance of convergence in evolutionary studies. Of course we can use cases of convergence to discover the selection pressure(s) responsible for particular adaptations, so convergence is our “friend.” But convergence is also our “enemy” because it can make taxonomy more difficult: Do taxa share a trait due to convergence or common ancestry?  I tell my students they don't have to worry about convergence distorting their taxonomies if they use traits below the level of the surface phenotype, e.g., molecular structures such as amino acid sequences or (ideally) A-C-T-G sequences. Since it's good to doubt one's claims, does anyone know any clear cases of molecular convergence?

  • James R Knaub added an answer:
    Is the scientific method natural to humans, or does it require a special effort? What about other animals?
    Take the average person you meet - how do they make decisions? What about evolution - has the scientific method ever had any influence on genetic mutation, or has any other aspect of evolution had any influence on living beings?
    James R Knaub · N/A

    Edward -

    The "What about other animals?" caught my attention, and reading through the other answers first, I think that Aliza came closest to what I was thinking. You do see the basics of experimentation by other animals. A lot if it had to be accidental at first, like a large bird dropping a clam on a rock to open it, or just having fun, like a parrot or similar bird I saw had taught itself to use a peanut shell as a bucket from which it drank. But other primates use tools, and some examples of basic elements of scientific methodology have to be found in large numbers in other animals.

    Perhaps the disappointment we feel is that humans have learned something about 'perfecting' the scientific method, yet often seem to avoid it. However, I think that many use it more than they realize. Someone who didn't want to take high school algebra may claim for the rest of their lives that they "never used it," without being fully conscious of the many thousands of subtle uses of logic they made that may have been inspired by abilities they honed in that experience with algebra. However, you could say this is more related to the Ancient Greek Philosophy of logic, which fell short of full science or they would possible have gone beyond the 'four elements.' But it is something and it gave modern science a start.

    However, it is true that there is a great deal of interference with science in modern society. I heard or read that in North Carolina, the legislature decided that climate change was not to be considered in official documents, due to its inconvenience, so in effect it was outlawed. At one point the US Bureau of the Census, trying to avoid undercounting minorities, was criticized by Congress, at least one member going so far as to say that "sampling" was some kind of magic, not to be trusted. As a statistician, I was very embarrassed for the US. I've seen office politics that I had to struggle with and often lose against while trying to take the most clearly correct actions. The foolishness, irrationality, and too often selfish and hateful nature of humans can sometimes drown rational and socially progressive views, which you would think would contradict the evolutionary progress that was part of the inquiry Edward made. But perhaps we are just overreacting when we see it that way. Perhaps when we see irrational behavior (or otherwise disappointing behavior that I realize I mixed in here) we weigh that too heavily, and do not give enough credit to the scientific nature that is present in humans and other animals. It isn't perfect, but it's there.

    Jim 

  • Louis Brassard added an answer:
    When do you think art first developed?
    The 40,800 year old cave paintings from El Castillo cave in Spain are the oldest examples of human painting. Shells containing 100,000 year old pigments possibly used for body painting have been found in Southern Africa. 200,000 year old ostrich shell jewelry was found in Librya. Older still, a 350,000 year old rose quartz hand axe was found in a burial pit in Spain. This seems to be the oldest example of symbolism in a human species. But when did art first appear? Captive great apes and monkeys--young and old--have shown a facility for painting (they even have color preferences). However, no wild individuals have ever been shown to do art in their natural habitats. This is most likely because it does not give them any type of survival advantage. They obviously have more important things to deal with in their daily lives. But since humans and chimps have a capacity for art, this means our last common ancestor probably had it as well. It's possible unambiguous expressions of art probably didn't come about until an increase in our brain size gave us greater cognitive abilities. A friend of mine has speculated that art sprung forth from our need to pass on learned information that did not come naturally to us. I would say art was closely tied to spirituality early on. Now the question is whether art first developed in the genus Homo or sometime earlier?

    David,

    I personally think that our primate ancestors had almost all that we have to become us but did not had conscious access to it.  The communal practice that gave them access to what I call self-enactment was communal singing-dancing: our first religion and from that first communal art all others came.  All these self-enactments already existed for our primate but where used subconsciously as part of their perceptual processes.  Pre-music self-enactment was developed early in mammalian brain for interpreting animal sounds and in order to do that they harnessed their motor control system by self-enacting it for maching sound to the type of rythms that they used to move their own body.  Birds and some marine mammals went further and used this pre-music self-enactment for communal emotional control with musical expression and body movement and for female courtship etc. Dance is intimatly linked to it.  The history of the use of music in cinema, in animation re-discovered the importance of music for us to understand emotionally and for us to really perceive movement.  Walt Disney had understood that it was critical for his animation movie for the whale.  Look at all these shamanic dancing practices all around the world and singing and dancing as it used to be is well alive. And all the major social revolutionary movement are centered on communal dancing singing together. So it is as true today as when it created us. The story is getting too long.   Regards

  • Leonard Greenfield added an answer:
    Why did we develop different from other species?

    There are many theories about homo sapiens development compared to others. And I know why but it´s not so easy to Google I have notice.

    So my question is how many know this, and is logically simple but it´s not so easy like we learned to use tools.

    THERMAL ENERGY, AND WE GET MORE TIME  TO DO OTHER THING´S.

    Leonard Greenfield · Temple University

    The simplest answer to your question is that every population and species evolves  differently, genetically and phenotyically,  from other populations and  species once natural interbreeding ceases. Each of the isolated  populations, if they are humans or apes  have approximately 66,000 nuclear DNA loci  (estimating 22,000 promoters, 22,000 operators, and 22, 000 protein coding)  any of which can base pair mutate into many thousands of permutations.  Thus, first , there is guaranteed to be different mutations occurring in each isolate each generation. Second, the environments in which the populations live, including the members of each population who are genetically and behaviorally unique,   are also going to be different - thus, without gene flow, there is a natural tendency for all populations and later their descendant species,  to go unique ways.

    Now, trying to identify more than just a skeleton (pun intended, lol) of a sequence of the   unique events in our lineage over the past 6 million years will be a great challenge. The enormity and depth of this  real sequence will probably never be known sufficiently enough to use the discovered fraction as the basis for causal explanations. You would have to have god-like omnicience to have access to this knowledge  and, we do not yet understand  the machinations of even  a  single human  brain. 

  • Marc Verhaegen added an answer:
    Are there evolutionary advantages to having mild schizophrenia?
    If so, what are they and why might they arise?
    Marc Verhaegen · Study Center Anthropology

    The late David Horrobin wrote a whole book (very readable, but speculative) on this: "The madness of Adam & Eve - How shcizophrenia shaped humanity" (Bantam Press 2001), partly based on human waterside evolution.

  • David Peris added an answer:
    Is there a convenient software package for drawing minimum spanning networks for phylogenetic studies?
    I have struggled to do this with Powerpoint, but am sure that there must be simpler, better, more efficient software programmes for this purpose. Any suggestions? How have others done this? This is a good examples: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146880/pdf/1471-2148-11-172.pdf
    David Peris · University of Wisconsin, Madison

    I've found an interesting software, developed by Jessica W. Leigh: popART (http://popart.otago.ac.nz/index.shtml).

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