Evolution

Evolution

  • Giuseppe Laquidara added an answer:
    Richard Dawkins and his idea of an individual affected by Down's Syndrome. The "moral choice" [to abort him] on the part of his parents.

    What is the scientific conscience? Now, imagine [together with sir Dawkins] that the smallest unit of measurement of the human being is not even an embryo, that is too complex for him on the evolutionary scale. Imagine that the smallest unit of measure of a human being is: One Gene. Or maybe even less.
    An atomic value, worthy of singular respect, endowed of the faculties of choice and judgment: of categories of good and evil.
    For "good" - according to Dawkins - the Gene deems his evolutionary selfish, a rational monad who "must" evolve, with no escape. For natural mold.

    What is the value of a child at this point, given his late stage of existence if compared with a gene? According to Dawkins, it seems to have a value very limited: if the genes composed a "wrong" embryo of a human being, that child is to be deleted. His parents have the "moral obligation" to eliminate him from the evolutive stair of human life.

    So, please: how deep was placed today the scientific conscience?

    Giuseppe Laquidara · Independent Researcher

    I see, but I don't agree, in principle. The fact is that an inverse and controversial phenomenon is running on the social networks, similar to SIR mechanisms for spread. Two kinds of "contagion" are relevant in the current epoch: the very visible and the very sneaky ones. An example for the former typology, is the ice bucket initiative — something so viral that we could consider its paradigm as "definitive", and crucial for the social networking 4.0 [Epidemic-like process for contents: relevant/fresh + attractive/contagious + convenient/efficient + emotional/depressive]. For the latter, Dawkins' statement(s) is perfect — and ours [our loose reaction] too: the message rises vertically as an aerostat balloon through some atmosphere heights of the global consciousness, than suddenly disappears. It will gravitate over our heads, out of the critical control.

    Obviously I agree: it was a personal opinion, not verified at all, and "not representative" — in classical scientific terms.

    —g

  • What is the limit of DNA evolution in any trend?

    Every cell and organism depending on the exposed environment, are in a continuous process of evolution, is there any limit.If yes what are those factors.

    Olesya Anatolyevna Astakhova · Lomonosov Moscow State University

    Do you mean the norm of reaction of genes? Genes (located in the DNA of the chromosomes of cells) for each species of organisms have a limit to the operation (function) and it characterizes the species in its external and internal qualities. For example, human DNA differs from the DNA of animals, because they have different norms of reaction of genotypes (i.e. genotypes work differently, have different norms, formed in the process of evolution). Well, now also there is the transition (development) from one norm of genes to another norm for each species separately.

  • Neeraja Sankaran added an answer:
    Any discussion of biological evolution applied to life beyond Earth preceding Wallace in 1903?

    A quick question about history of science. Alfred Wallace's 1903 book "Man's Place in the Universe" is usually considered the earliest precursor of contemporary astrobiology, since it applies the Darwinian (-Wallacean :o)) theory of biological evolution to life at large, beyond the boundaries of our planet. However, I wonder was there any previous discussion of it in the 1859-1903 period? After all, those were more than 4 decades of very vigorous scientific activity and speculation in the time when most educated people believed in life and intelligence beyond Earth. Do you know of any such reference? (I'm interested in specifically evolutionary discussions, not just any mention of extraterrestrial life, channels on Mars, etc. there were many of those.)

    Neeraja Sankaran · Ashoka University

    Am not sure about specific works, but I do think searching for material on the history of pangenesis might help ?

  • Andrea Gazzola added an answer:
    What kind of relation is there between the Hutchinson Niche Concept and norm of reaction for phenotypic plasticity?
    The Hutchinson niche is an n-dimensional hypervolume, where the dimensions are environmental conditions and resources, that define the requirements of an individual or a species to practice its way of life. The pattern of phenotypes produced by a given genotype under different environmental conditions is the norm of reaction.
    Andrea Gazzola · University of Pavia

    Great! Could you share any Idea on how this issue should be tackled?

  • Vincent Ranwez added an answer:
    Does gene duplication and polyploidy provide a mechanism for evolution?

    Please make it  simple and brief.

    Vincent Ranwez · Montpellier SupAgro

    I assume that part of the question is related to fitness and adaptation. Both polyploidy and duplication induce a redundancy in the genome that is assumed to facilitate adaptation. Roughly speaking, if a gene is in single copy then mutations on this gene often result in a non functionnal/non optimal protein and are hence counter selected. On the other hand, if the gene is in multiple copies, mutations can occur on one copy while an other copy remain unchanged to ensure the original function and the mutated copy can eventually turn to be useful for a variant of the original protein function.

    We recently published an article on this subject in BMC plant: "Impact of recurrent gene duplication on adaptation of plant genomes"

    http://www.biomedcentral.com/1471-2229/14/151

    The introduction of this article provides further details and bibliographic references on the impact of multiple copies: "Gene duplication creates an unstable state of functional redundancy, which in most cases will disappear by loss of one copy through accumulation of degenerative mutations, recombination and/or genetic drift. But sometimes both copies are long-term preserved due to functional changes reducing their redundancy and making the loss of one copy disadvantageous [14]. Although the respective roles of adaptive versus non-adaptive processes in the maintenance of gene duplicates have been much debated (for general reviews see [15-18]), gene duplication should increase the occurrence of adaptation for several reasons. First, it can allow the fixation of beneficial mutations on one copy, leading to neofunctionalization, while the other copy ensures the ancestral function [16,19]. Second, it can free the genome from an “adaptive conflict” if the different functions of an ancestral (single) gene cannot be improved independently [20-22]. Third, even when adaptation is not involved in the initial conservation of duplicates, the presence of two (or more) copies is expected to increase the adaptation rate under certain conditions. Duplication increases the number of gene copies, hence the rate of appearance of beneficial mutations."

    I hope this will help,

    sincerely,

  • Anek R Sankhyan asked a question:
    How should we rate the significanace of Deinotherium in hominoid evolution?

    contemporaneity and ecology

  • Anton Fuerlinger added an answer:
    How do you introduce evolution to children?
    What is your practice of your first explanation or teaching with children (<10 years old) ? I mean the very first sentences.

    I'm quite sure that adults, even biologists, don't take evolution serious.

    Very few are able to do a journey down the evolutionary ladder across the human border, to apes, monkeys, to fourlegged forerunners, they cannot imagine how early mammals could have lived, how their environment was like, because they are unaware of J.v. Uexkuells notion of species-specific "Umwelt"

    Uexkuell used a very low organism to show how radically different "world views" can be - e.g. the three triggers for behavior for a successful tick's life are "move anti-gravity, then detect buturic acid, then look for a place with 37°" - no eyes are needed for a tick to find blood!

    I think evolutionary thinking needs a lot of imagination to envisage life other than ours..and the hard problem is abstracting from our universal, indispensable anthropomorphic world-view.

  • Alexander Sadykov added an answer:
    Should we expect demographic transition in non-human population?

    It is usually assumed that the demographic transition (major intrinsic changes in fertility / mortality and life expectancy) is a purely human population phenomenon.  There are several explanatory theories that suggest the next causes: (1) social development [Condorcet, 1794], (2) economical/technological changes [Galor,O. 2011], (3) evolutionary change [Clark, G. 2007].
     However, these factors (in some degrees) operate within non-human populations. Moreover, some of the eco-evolutionary models indicate that the demographic transition may be a common consequence of co-selection adaptation of individual to each others within group) in hierarchically structured populations.

    There are several (not all) cases in which demographic transition can be suspected:

    1. Regular extinction/ reemerging of local populations without apparent external reasons.
    2. Pronounced long-term demographic changes, which cannot be explained by environment variations or inbreeding depression. 
    3. Sudden appearance of unusually old or unusually big individuals in populations. 
    4. Sadden epidemic outbreaks of previously limited infections. 
    5. Visible absence of equilibrium size (carrying capacity); variations of population size weakly correlated with environment factors. 
    6. Fusion/split of local populations.

    So, is a demographic transition in the non-human populations? I would be very grateful if you share your thoughts or maybe data that will help answer this question.

    Alexander Sadykov · University of Oslo

    It has not been published. 

  • Romain Studer added an answer:
    Is there any example of a study with amino acid sites under positive selection (dN/dS) that have been tested in vitro (confirmatory or not)?
    Is there any example of a study on amino acid sites under positive selection (dN/dS) that have been tested in vitro (confirmatory or not)?

    By dN/dS, I mean any amino acid sites in any species that have been detected with CodeML, either the site models (M2a, M8), or the branch-site model. Or any other similar methods that aims to identify sites that could favour adaptation during the evolutionary course.

    By in vitro, I mean that these sites have been mutated in vitro and tested to see if they yield a different phenotype, or if the targeted protein exhibit different biochemical properties.


    ===> I have the impression that there are plenty of studies that identify such amino acids under positive selection in a large-scale manner, i.e.:

    More genes underwent positive selection in chimpanzee evolution than in human evolution
    http://www.pnas.org/content/104/18/7489.full

    Patterns of Positive Selection in Six Mammalian Genomes
    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000144

    Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
    http://genome.cshlp.org/content/18/9/1393.short

    Patterns of Positive Selection in Seven Ant Genomes
    http://mbe.oxfordjournals.org/content/early/2014/05/06/molbev.msu141.abstract



    ===> There are many studies that analyse these sites in silico by mapping them on the 3D structures, i.e.:

    Patterns of Positive Selection in Six Mammalian Genomes
    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000144

    Adaptive Divergence of Ancient Gene Duplicates in the Avian MHC Class II β
    http://mbe.oxfordjournals.org/content/27/10/2360

    Evolution of Genes Involved in Gamete Interaction: Evidence for Positive Selection, Duplications and Losses in Vertebrates
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0044548


    ===> A few of them identifies the effect on protein stability, i.e.:

    Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
    http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002929

    Stability-activity tradeoffs constrain the adaptive evolution of RubisCO
    http://www.pnas.org/content/111/6/2223.long


    ===> But I have difficulties finding studies that actually tested these sites in vitro. I found these ones:

    Adaptive evolution of multicolored fluorescent proteins in reef-building corals.
    http://link.springer.com/article/10.1007%2Fs00239-005-0129-9

    Structural and Functional Evolution of Positively Selected Sites in Pine Glutathione S-Transferase Enzyme Family
    http://www.jbc.org/content/288/34/24441.full


    But I would like to know if there are other similar studies?
    Romain Studer · EMBL-EBI

    I found another one, quite recent:

    Functional Consequence of Positive Selection Revealed through Rational Mutagenesis of Human Myeloperoxidase

    http://mbe.oxfordjournals.org/content/29/8/2039.full

    "Taken together, our data provide further support for the in silico predictions of positive selection and highlight the correlation between positive selection and functional divergence. Our data demonstrate that directly probing the functional importance of positive selection can provide important insights into understanding protein evolution."

  • Rainer R Schoch 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.

    Rainer R Schoch · State Museum of Natural History Stuttgart

    Dear Mark,

    I remember various discusions with Dolf Seilacher and his student Wolf Reif on the constraint topic. Seilacher was most interested in "principles" of construction, arguing like an architect rather than an evolutionist. He was influenced by engineers of Stuttgart university. Reif, on the other hand, was the one who emphasized the constraints aspect more, but I presume his influence on Gould was limited, as they lived in different worlds of thought. So, in sum, I believe it was Seilacher who had influence on Gould, albeit in a rather superficial, general way.

    To be honest, I think Gould had a rather fuzzy view of constraints, his definitons changed over time, were sometimes contradictory. Gould was more focused on contingency, rather than physical laws constraining evolution and potentially constraining the power of selection. This is why he emphasized "historical constraints" so often, a concept that I find problematic. Nevertheless, the spandrels paper was very important, and as so often, gained more attention than the earlier papers by Seilacher (1970, 1972) and Reif (1975), especially because these were mostly written in German.

  • Douglas C Youvan added an answer:
    Can you please help proof read this complex figure on the structure of the genetic code?

    http://commons.wikimedia.org/wiki/File:Hydropathy_Molar_Volume_Genetic_Code_2.png

    From the Wikipedia Genetic Code article its summary figure gets 600,000 hits per year, and no one has ever proof read it as I work alone.

    The summary figure in the actual article had a horrible typo in it, and no one said a thing.

    Several times, a group from The Netherlands has tried to delete either me or this figure from Wikipedia.  I don't understand why.  They must be under the impression that a structured code is inconsistent with Darwinian evolution.  But as you know, the appearance of order does not disprove randomness:  A random number generator can spit out 50 digits of Pi on its first demonstration run - and have nothing wrong with it.  See page 82 of "The Golden Ticket" for an old Dilbert cartoon on this subject.

    Douglas C Youvan · Youvan Foundation

    Thank you all for your help.  I will incorporate this into a revision.

  • Hussin Jose Hejase added an answer:
    Darwin's Theory of Evolution: How to reconcile religious teaching with evolution? What is your view on this?
    Charles Robert Darwin (1809–1882) was a British naturalist and geologist, famous for his contributions to the theory of evolution. Darwin recognized that all living species have descended from common ancestors in a timely manner. Together with Alfred Russel Wallace, he released a joint publication in which he introduced his scientific theory that stipulates that such a branching pattern of evolution has been ensued from a process that he named “natural selection”.

    In 1859, Darwin published his Theory of Evolution in his famous book “On the Origin of Species”, overcoming the scientific rejection pertaining to earlier concepts of transmutation of species. In the 1870s much of the scientific community and the majority of the general public had accepted evolution as a fact. However, it was not until the emergence of the modern evolutionary synthesis when a broad consensus developed, between the 1930s to the 1950s, and in which natural selection was accepted as the basic mechanism of evolution.

    Charles Robert Darwin’s Theory of Evolution – How to reconcile religious teaching with evolution?
    Hussin Jose Hejase · American University of Science and Technology Lebanon

    Very interesting comments and views. I agree with my colleagues, it is a complex issue to look for reconciliation.

    Heidi, I like your spirit.

  • Gang Wang added an answer:
    Any software that could infer stages of hybridization, aside from NewHybrids?
    I am currently studying hybridization between 2 plant species using dominant genetic markers (ISSR markers), and would like to infer the stages of hybridization (infer with confidence that a certain individual is an F1 hybrid, F2, or backcross). So far the only one I have found is NewHybrids by Anderson and Thompson 2002 (http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm). Does anyone know if there are other softwares that could do a similar job, probably with a different model or inference method?
    Gang Wang · Chinese Academy of Sciences

    Hi Dr Wei, I am also looking for a way to discriminate the hybrid status with Structure software. I found some one did it (POLLINATOR-MEDIATED REPRODUCTIVE ISOLATION AMONG DIOECIOUS FIG SPECIES (FICUS, MORACEAE) http://dx.doi.org/10.1111/j.1558-5646.2012.01727.x). They calculated the posterior probabilities of the F1, F2 and no-hybrid individual that should be you wanted. However, I  couldn't get that result form with described method. I hope you can get it and share with us. Thanks.

  • Yuri Alves added an answer:
    Could anyone help me with papers about  evolution of Tethys ocean, since early Jurassic to Late Cretaceous? 

    Tethys evolution

    Yuri Alves · Rio de Janeiro State University

    Hi Guys, tethys atlas:

    maps:https://www.dropbox.com/s/3ufydwart1cnuhs/2000%20Dercourt%20et%20al%20Atlas%20Peri-Tethys.pdf

    explanatory notes: https://www.dropbox.com/s/1mhgpprpnuqy56q/2000%20Dercout%20et%20al%20atlas.pdf

  • Olena Peregrym added an answer:
    Is there a way to combine molecular and morphological data for phylogenetic analysis?
    Recently, I've been working on the evolutionary relationships of a plant family in Sri Lanka (Zingiberaceae). During my field explorations, I could not collect some of the species that had been described from Sri Lanka (they have possibly gone extinct; no record for more than 100 years). However, I've coded the morphological characters of those species from herbaria. I've the molecular data (DNA seq) only for the collected species, yet I need to get all the species into a single phylogenetic tree. Is this possible?
    Olena Peregrym · M.G.Kholodny Botany Institute

    Did somebody use the Mesquite for combining molecular and morphological data? Do you know a algorithm  for doing that?

  • Juan L Cantalapiedra added an answer:
    Does anyone have an idea of the supposed ancestral feeding strategy —faunivorous, omnivorous or herbivorous— of the crown living birds?
    Is there any phylogenetic-based reconstruction —or something similar—of the ancestral feeding mode of living birds? Any related paper?
    Juan L Cantalapiedra · The National Museum of Natural Sciences

    Thanks Ana! This seems like a very nice work on bird evolution!!

    Best regards!

  • Myroslav Sparavalo asked a question:
    My Post #1 on Linked-In

    I invite all the members of the ResearchGate community to discuss my recent post on  Linked-In titled "The Role of Mathematical Modeling in Future Evolution of Modern Civilization: Part 1 - Topicality".

  • Maria Constanza Gariboldi added an answer:
    What is the differences between Tajima´sD and Fu Fs?
    I did a neutralities tests (Tajima´s D and FU FS). It is a population with 10 individuals and 5 haplotypes of mitochondrial DNA (4 of them are similar and 2 are very different). Tajima´s D was significant and Fu FS was not. I know FU FS is more powerful than Tajima´s D, but I can't explain why FU FS was not statistically significant. Thank you!
    Maria Constanza Gariboldi · Universidad Maimónides
    Thank you Bárbara!
  • Angela Stanton added an answer:
    What are your thoughts about Darwin's theory of evolution?
    old theory with new insights, how about chromosomal variations among species?

    typo: pain=pair... why can't we edit? It does not seem to function...

  • Steven Vidovic added an answer:
    Is it possible to use linear measurements of long bones for calculating biological distance in human populations?
    Knowing the influence of environmental factors, I wonder if it is correct/possible to estimate biological relatedness from the morphology of these bones.
    Steven Vidovic · University of Portsmouth

    There are a variety of methods that could be used for such a study, many of them can be found in Hammer and Harper 2006 "Paleontological data analysis". I would suggest canonical variates for multiple 'groups', or discriminant function analysis for two 'groups'. Be aware that the number of variables you can study is equal to the smallest population sampled in one of your 'groups'.

    Also, you have to be careful that even if you do find a statistically significant separation this is not due to some other biological pressure, such as nutrition, or average age sampled etc.

  • Stephan A. Frye 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.
    Stephan A. Frye · Oslo University Hospital

    Have a look at Compare2Trees (http://www.mas.ncl.ac.uk/~ntmwn/compare2trees/index.html).

  • Kishore Kumar Krishnan asked a question:
    Fuzzy graph theory

    Has anyone got pdfs or materials for learning fuzzy graph theory evolution and fundamentals.

  • P.F. Zabrodskii added an answer:
    Evolution. How natural selection creates amazing things?

    Evolution. Natural selection creates amazing things. Probability theory. What is the probability of occurrence in the nature of a moth that looks like the muzzle of a cat or other animal? This probability can be calculated?   

    P.F. Zabrodskii · Saratov State Medical University

    I thought about how there are new kinds,  the evolution  ...

    Something I have enough for a clear understanding of this amazing process.

    And I do not represent  how life arose on Earth!

  • John Jennings added an answer:
    Is it worth of making a phylogenetic tree with morphological characters if molecular data are not available?
    I am working on nematodes and I had formalin fixed and glycerol dehydrated samples samples along with taxonomy I also want to do phylogeny, but I don't have molecular data. Is it still possible to make a tree on the basis of morphological characters, and should I make it and is it publishable?
    John Jennings · University of Adelaide

    In most of the hymenopteran groups I work on, there are generally only old museum specimens (often 50++ years) available and no fresh or freshly preserved specimens we can use to extract DNA. We often have to rely on morphology.

  • Kees Hulsman added an answer:
    What are the theoretical reasons why complexity should increase over uninterrupted evolutionary time?
    The concept of complexity increasing over uninterrupted evolutionary time is an area of dispute in the literature. The evidence for it seems to be mixed. Since theory can help reduce uncertainty, I was wondering about the range of theoretical reasons that have been proposed to explain why complexity appears to increase over evolutionary time.
    Kees Hulsman · Griffith University

    Hi Emily thanks for that. I use Holling et al.'s Panarchy Theory to help my understanding of ecological systems at different levels of organisation ,i.e. different temporal and spatial scales. That having been said, Panarchy does not explain why systems become more complex over uninterrupted evolutionary time. It does explain why disturbance does decrease complexity. 

  • Esma Buluş Kırıkkaya added an answer:
    Can anyone suggest any good children's books on geoscience and evolution in Arabic and Turkish?
    I was recently asked by a staff member of our city library if I had any suggestions for their kid's corner. They have a bit of money to spend on new books. I browsed the multilingual sections and saw that there is a shocking lack of arabic and turkish kid's books about natural sciences in general and geoscience and evolution especially.

    I would greatly appreciate some good book recommendations, presenting the science of evolution and geology in an easily understandable way and without creationism. So please no recommendations of Harun Yahya books.
    Esma Buluş Kırıkkaya · Kocaeli University

    I can suggest some books.
    Richard Dawkins is the author of "The Blind Watchmaker".and translator Feryal Halatçı.


    by Jared Diamond wrote "Guns, Germs and Steel", TÜBİTAK Science Publications.

  • Seth M. White added an answer:
    Is there any data on the effect of anthropogenic disturbance on fish social behaviour?
    I'm interested in assessing the impact of human activity on fish social systems, namely sexual systems including sex ratio adjustments ect. Does anyone know if there is any pre existing data concerning this question or any suitable methodologies that might be applied?
    Thanks
    Seth M. White · Columbia River Inter-Tribal Fish Commission

    Dear Harry, I recently wrote a review of "fish behaviorscapes" (see attached) which to some small degree addresses your questions. Perhaps some of the references cited will help.

  • Miquel A. Gonzàlez-Meler 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.
    Miquel A. Gonzàlez-Meler · University of Illinois at Chicago

    great study Frank. Thanks. 

    We have extended work on the relationships between plant photosynthesis and soil respiration, including a couple of recent  reviews in New Phytologist (Hopkins et al., 2013 and Chen et al., 2014). I hope you can find those papers also informative.

    Miquel

  • Dola Bhattacharjee added an answer:
    What is Evolution Stratergies?

    Whether this strategy can apply in MANET routing?

    Dola Bhattacharjee · Government of India

    http://comunidad.udistrital.edu.co/malzate/files/2011/12/AGameTheoreticTrustModelOfCooperation.pdf

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