Alternate views

@misc{lamarck1809zoological2,
    author = "Lamarck, J. B",
    title = "Zoological Philosophy",
    year = "1809",
    howpublished = "Translated into English by H. Elliott, 1914. Macmillan \& Co., New York",
    note = "talkorigins\_source = {true}; raw\_reference = {Lamarck, J. B., 1809, Zoological Philosophy. Translated into English by H. Elliott, 1914. Macmillan \& Co., New York.}"
}

@book{medawar1967mathematical3,
    author = "Medawar, P",
    title = "Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution",
    year = "1967",
    publisher = "Philadelphia, Wistar Institute Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Medawar, P., 1967, Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution: Philadelphia, Wistar Institute Press.}"
}

@techreport{wright1967comments5,
    author = "Wright, S",
    title = "Comments on the Preliminary Working Papers of Eden and Waddington, in Moorehead, P. S., and Kaplan, M. M., eds., Mathematical Challenges to the Neo-Darwinian Theory of Evolution, 5 of Wistar Institute Symposium",
    year = "1967",
    howpublished = "Philadelphia, Wistar Institute, p. 117-120",
    note = "talkorigins\_source = {true}; raw\_reference = {Wright, S., 1967, Comments on the Preliminary Working Papers of Eden and Waddington, in Moorehead, P. S., and Kaplan, M. M., eds., Mathematical Challenges to the Neo-Darwinian Theory of Evolution, 5 of Wistar Institute Symposium: Philadelphia, Wistar Institute, p. 117-120.}"
}

@incollection{hotton1980an1,
    author = "Hotton, N",
    editor = "Thomas, D. K. and Olson, E. C.",
    title = "An Alternative to Dinosaur Endothermy: The Happy Wanderers",
    year = "1980",
    booktitle = "A Cold Look at the Warm Blooded Dinosaurs",
    publisher = "Washington, D.C., American Association for the Advancement of Science, p. 311-350",
    note = "talkorigins\_source = {true}; raw\_reference = {Hotton, N., 1980, An Alternative to Dinosaur Endothermy: The Happy Wanderers, in Thomas, D. K., and Olson, E. C., eds., A Cold Look at the Warm Blooded Dinosaurs: Washington, D.C., American Association for the Advancement of Science, p. 311-350.}"
}

@incollection{rechenberg1984the,
    author = "Rechenberg, Ingo",
    title = "The Evolution Strategy. A Mathematical Model of Darwinian Evolution",
    year = "1984",
    booktitle = "Springer Series in Synergetics",
    url = "https://doi.org/10.1007/978-3-642-69540-7\_13",
    doi = "10.1007/978-3-642-69540-7\_13",
    openalex = "W23797105",
    pages = "122-132",
    references = "doi101002fedr4910860506, doi1010160378475482901173, doi1023072581158, openalexw1514875444"
}

Bruce D. Smith, American Colonial Monetary Regimes: The Failure of the Quantity Theory and Some Evidence in Favour of an Alternate View, The Canadian Journal of Economics / Revue canadienne d'Economique, Vol. 18, No. 3 (Aug., 1985), pp. 531-565

@article{doi102307135018,
    author = "Smith, Bruce D.",
    title = "American Colonial Monetary Regimes: The Failure of the Quantity Theory and Some Evidence in Favour of an Alternate View",
    year = "1985",
    journal = "Canadian Journal of Economics/Revue canadienne d économique",
    abstract = "Bruce D. Smith, American Colonial Monetary Regimes: The Failure of the Quantity Theory and Some Evidence in Favour of an Alternate View, The Canadian Journal of Economics / Revue canadienne d'Economique, Vol. 18, No. 3 (Aug., 1985), pp. 531-565",
    url = "https://doi.org/10.2307/135018",
    doi = "10.2307/135018",
    openalex = "W2063346774",
    references = "doi10100797813490628432, doi101086260266, doi1021034sr44, doi1023071052825, doi1023071055721, doi1023072278872, doi1023943princeton97806911587090030003, doi104159harvard9780674067851c4, openalexw1586286259, openalexw358016813"
}

@misc{ostrom1986the4,
    author = "Ostrom, J. H",
    title = "The Cursorial Origin of Avian Flight, in Padian, K., ed., The Origin of Birds and the Evolution of Flight",
    year = "1986",
    howpublished = "San Francisco, California Academy of Sciences, p. 75-81",
    note = "talkorigins\_source = {true}; raw\_reference = {Ostrom, J. H., 1986, The Cursorial Origin of Avian Flight, in Padian, K., ed., The Origin of Birds and the Evolution of Flight: San Francisco, California Academy of Sciences, p. 75-81.}"
}

@article{doi1023074449090,
    author = "Stewart, Jim and Hafner, Bob and Dale, Michael",
    title = "Students' Alternate Views of Meiosis",
    year = "1990",
    journal = "The American Biology Teacher",
    url = "https://doi.org/10.2307/4449090",
    doi = "10.2307/4449090",
    openalex = "W2326898059",
    references = "doi101002sce3730670408, doi101002sce3730720211"
}

These contrasting perspectives on teaching provide a convenient point of departure for my response to Kagan's review. How researchers frame teaching inevitably colors both the questions they choose to study and the models they create for teacher preparation. Kagan proposes a model of learning to teach that reflects the importance she places on mastery of procedural routines. Another body of research, either specifically excluded or otherwise omitted from her review, depicts teaching as centrally concerned with helping all students learn worthwhile content, within the context of a multicultural and pluralistic society. These studies do not necessarily support Kagan's developmental model; their findings complicate the narrative constructed by Kagan and cast doubt on the adequacy of her recommendations for teacher education. The existing literature on learning to teach does not lead inexorably towards Kagan's conclusions, nor is the evidence across competing discourse communities of researchers on teacher education as clear and convincing as she suggests. Kagan's review reflects one sector of the teacher education community. But there are other sectors. Some researchers on teacher education see the process of learning to teach through the lens of subject matter; others view teaching and learning to teach from an explicitly moral and ethical stance. The evidence, when considered in its entirety, is mixed. Ultimately, discussions of teacher education are informed as much by normative concerns as by empirical findings. The vision for teacher education held by many researchers differs from Kagan's. Many see teacher education as preparing prospective teachers not to adapt to existing conditions but to challenge current practices and to work for change. To claim, however, that research supports a developmental model, while excluding studies that challenge this model, misrepresents the full body of research on professional growth among preservice teachers.

@article{doi10310200346543062002171,
    author = "Grossman, Pamela L.",
    title = "Why Models Matter: An Alternate View on Professional Growth in Teaching",
    year = "1992",
    journal = "Review of Educational Research",
    abstract = "These contrasting perspectives on teaching provide a convenient point of departure for my response to Kagan's review. How researchers frame teaching inevitably colors both the questions they choose to study and the models they create for teacher preparation. Kagan proposes a model of learning to teach that reflects the importance she places on mastery of procedural routines. Another body of research, either specifically excluded or otherwise omitted from her review, depicts teaching as centrally concerned with helping all students learn worthwhile content, within the context of a multicultural and pluralistic society. These studies do not necessarily support Kagan's developmental model; their findings complicate the narrative constructed by Kagan and cast doubt on the adequacy of her recommendations for teacher education. The existing literature on learning to teach does not lead inexorably towards Kagan's conclusions, nor is the evidence across competing discourse communities of researchers on teacher education as clear and convincing as she suggests. Kagan's review reflects one sector of the teacher education community. But there are other sectors. Some researchers on teacher education see the process of learning to teach through the lens of subject matter; others view teaching and learning to teach from an explicitly moral and ethical stance. The evidence, when considered in its entirety, is mixed. Ultimately, discussions of teacher education are informed as much by normative concerns as by empirical findings. The vision for teacher education held by many researchers differs from Kagan's. Many see teacher education as preparing prospective teachers not to adapt to existing conditions but to challenge current practices and to work for change. To claim, however, that research supports a developmental model, while excluding studies that challenge this model, misrepresents the full body of research on professional growth among preservice teachers.",
    url = "https://doi.org/10.3102/00346543062002171",
    doi = "10.3102/00346543062002171",
    openalex = "W2108065459",
    references = "doi10172261032, doi1017763haer571j463w79r56455411, doi1023071175860, doi1023072576192, doi10310200028312006002207, doi1031020013189x015002004, doi10310200346543062002129, doi105860choice290440, doi105860choice411685, openalexw612243507"
}

TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TreeView runs as a native application on either MacOS or Windows computers, enables the user to use the standard fonts installed on their machine, their printer, and supports the relevant native graphics format (PICT and Windows metafile) for either creating graphics files or pasting pictures to other applications via the clipboard. The program also supports standard file operations, such as 'drag and drop' whereby dragging a file's icon onto the program opens that file. TreeView can read a range of tree file formats (see below) and can display trees in a range of styles (Fig. 1). Additional information, such as edge lengths and internal node labels can also be displayed. The order of the terminal taxa in the tree can be altered, and the tree can be rerooted. If the tree file contains more than one tree the user can view each tree in turn. The program can also save trees in a variety of file formats, so that it can be used to move trees between programs that use different file formats.

@article{doi101093bioinformatics124357,
    author = "Page, Roderic",
    title = "Tree View: An application to display phylogenetic trees on personal computers",
    year = "1996",
    journal = "Computer applications in the biosciences",
    abstract = "TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TreeView runs as a native application on either MacOS or Windows computers, enables the user to use the standard fonts installed on their machine, their printer, and supports the relevant native graphics format (PICT and Windows metafile) for either creating graphics files or pasting pictures to other applications via the clipboard. The program also supports standard file operations, such as 'drag and drop' whereby dragging a file's icon onto the program opens that file. TreeView can read a range of tree file formats (see below) and can display trees in a range of styles (Fig. 1). Additional information, such as edge lengths and internal node labels can also be displayed. The order of the terminal taxa in the tree can be altered, and the tree can be rerooted. If the tree file contains more than one tree the user can view each tree in turn. The program can also save trees in a variety of file formats, so that it can be used to move trees between programs that use different file formats.",
    url = "https://doi.org/10.1093/bioinformatics/12.4.357",
    doi = "10.1093/bioinformatics/12.4.357",
    openalex = "W2150297520",
    references = "doi101093bioinformatics10141, doi101093nar21133021, doi101093nar22224673, doi105860choice392183"
}

There has been an apparent increase in the frequency and duration of El Niño–Southern Oscillation events in the last two decades relative to the prior period of record. Furthermore, 1990–95 was the longest period of sustained high Darwin sea level pressure in the instrumental record. Variations in the frequency and duration of such events are of considerable interest because of their implications for understanding global climatic variability and also the possibility that the climate system may be changing due to external factors such as the increased concentration of greenhouse gases in the atmosphere. Nonparametric statistical methods for time series analysis are applied to a 1882 to 1995 seasonal Darwin sea level pressure (DSLP) anomaly time series to explore the variations in El Niño–like anomaly occurrence and persistence over the period of record. Return periods for the duration of the 1990–95 event are estimated to be considerably smaller than those recently obtained by using a linear ARMA model with the same time series. The likelihood of a positive anomaly of the DSLP, as well as its persistence, is found to exhibit decadal- to centennial-scale variability and was nearly as high at the end of the last century as it has been recently. The 1990–95 event has a much lower return period if the analysis is based on the 1882–1921 DSLP data. The authors suggest that conclusions that the 1990–95 event may be an effect of greenhouse gas–induced warming be tempered by a recognition of the natural variability in the system.

@article{doi1011751520044219970102351aeoaav20co2,
    author = "Rajagopalan, Balaji and Lall, Upmanu and Cane, Mark A.",
    title = "Anomalous ENSO Occurrences: An Alternate View*",
    year = "1997",
    journal = "Journal of Climate",
    abstract = "There has been an apparent increase in the frequency and duration of El Niño–Southern Oscillation events in the last two decades relative to the prior period of record. Furthermore, 1990–95 was the longest period of sustained high Darwin sea level pressure in the instrumental record. Variations in the frequency and duration of such events are of considerable interest because of their implications for understanding global climatic variability and also the possibility that the climate system may be changing due to external factors such as the increased concentration of greenhouse gases in the atmosphere. Nonparametric statistical methods for time series analysis are applied to a 1882 to 1995 seasonal Darwin sea level pressure (DSLP) anomaly time series to explore the variations in El Niño–like anomaly occurrence and persistence over the period of record. Return periods for the duration of the 1990–95 event are estimated to be considerably smaller than those recently obtained by using a linear ARMA model with the same time series. The likelihood of a positive anomaly of the DSLP, as well as its persistence, is found to exhibit decadal- to centennial-scale variability and was nearly as high at the end of the last century as it has been recently. The 1990–95 event has a much lower return period if the analysis is based on the 1882–1921 DSLP data. The authors suggest that conclusions that the 1990–95 event may be an effect of greenhouse gas–induced warming be tempered by a recognition of the natural variability in the system.",
    url = "https://doi.org/10.1175/1520-0442(1997)010<2351:aeoaav>2.0.co;2",
    doi = "10.1175/1520-0442(1997)010<2351:aeoaav>2.0.co;2",
    openalex = "W2121192614",
    references = "doi101002qj49708837511, doi101007bf00204745, doi10102995gl03602, doi10108001621459198810478639, doi101126science24048571293, doi101126science264515572, doi1011751520046919950520293ialtts20co2, doi1011751520047719900710988roicci20co2, doi1011751520049319841120326svnits20co2, doi1023072347366"
}

Darwinian Evolution. Anthony Flew. New Brunswick, NJ: Transaction Publishers, 1997.150 pp.

@article{bowler1998darwinian,
    author = "Bowler, Peter J.",
    title = "Darwinian Evolution",
    year = "1998",
    journal = "American Anthropologist",
    abstract = "Darwinian Evolution. Anthony Flew. New Brunswick, NJ: Transaction Publishers, 1997.150 pp.",
    url = "https://doi.org/10.1525/aa.1998.100.3.806",
    doi = "10.1525/aa.1998.100.3.806",
    number = "3",
    openalex = "W4230133078",
    pages = "806-807",
    volume = "100"
}

Presbyterian Center for Pain Medicine, Presbyterian Orthopedic Hospital, Charlotte, North Carolina, and Tufts University Medical School, Boston, Massachusetts, U.S.A. This article was adapted from an article by Gerald M. Aronoff, "Clinical Presentation and Differential Diagnosis of Myofascial Pain Syndrome," originally published by Discovery International (Deerfield, Illinois) in a syllabus for the symposium "Contemporary Management of Myofascial Pain Syndrome," October 19, 1996, Beverly Hills, California. Address correspondence and reprint requests to Dr. Gerald M. Aronoff, Medical Director, Presbyterian Center for Pain Medicine, Presbyterian Orthopedic Hospital, 1901 Randolph Road, Charlotte, NC 28207, U.S.A.

@article{doi1010970000250819980300000011,
    author = "Aronoff, Gerald M.",
    title = "Myofascial Pain Syndrome and Fibromyalgia: A Critical Assessment and Alternate View",
    year = "1998",
    journal = "Clinical Journal of Pain",
    abstract = {Presbyterian Center for Pain Medicine, Presbyterian Orthopedic Hospital, Charlotte, North Carolina, and Tufts University Medical School, Boston, Massachusetts, U.S.A. This article was adapted from an article by Gerald M. Aronoff, "Clinical Presentation and Differential Diagnosis of Myofascial Pain Syndrome," originally published by Discovery International (Deerfield, Illinois) in a syllabus for the symposium "Contemporary Management of Myofascial Pain Syndrome," October 19, 1996, Beverly Hills, California. Address correspondence and reprint requests to Dr. Gerald M. Aronoff, Medical Director, Presbyterian Center for Pain Medicine, Presbyterian Orthopedic Hospital, 1901 Randolph Road, Charlotte, NC 28207, U.S.A.},
    url = "https://doi.org/10.1097/00002508-199803000-00011",
    doi = "10.1097/00002508-199803000-00011",
    openalex = "W2312693617",
    references = "doi101001jama257202782, doi101002art1780330203, doi101016000293439290265d, doi101016s0033318290722128, doi101016s1058913905800786, doi1010970000250819911200000013, doi1010970000250819931200000003, doi1010970000684219860500000002, doi101136bmj12246117, openalexw1577205491"
}

Research favoring the so-called bottom-up and top-down classes of explanations for reversible figures that dominated the literature in last half of the 20th century is reviewed. Two conclusions are offered. First, any single-process model is extremely unlikely to be able to accommodate the wide array of empirical findings, suggesting that the "final" explanation will almost certainly involve a hybrid conceptualization of interacting sensory and cognitive processes. Second, the utility of distinguishing between 2 components of the observer's experience with reversible figures is emphasized. This distinction between the observer's ability to access multiple representations from the single stimulus pattern (ambiguity) and the observer's phenomenal experience of oscillation between those representations (reversibility) permits the literature to be segregated into useful categories of research that expose overlapping but distinctive cortical processes.

@article{doi101037003329091305748,
    author = "Long, Gerald M. and Toppino, Thomas C.",
    title = "Enduring Interest in Perceptual Ambiguity: Alternating Views of Reversible Figures.",
    year = "2004",
    journal = "Psychological Bulletin",
    abstract = {Research favoring the so-called bottom-up and top-down classes of explanations for reversible figures that dominated the literature in last half of the 20th century is reviewed. Two conclusions are offered. First, any single-process model is extremely unlikely to be able to accommodate the wide array of empirical findings, suggesting that the "final" explanation will almost certainly involve a hybrid conceptualization of interacting sensory and cognitive processes. Second, the utility of distinguishing between 2 components of the observer's experience with reversible figures is emphasized. This distinction between the observer's ability to access multiple representations from the single stimulus pattern (ambiguity) and the observer's phenomenal experience of oscillation between those representations (reversibility) permits the literature to be segregated into useful categories of research that expose overlapping but distinctive cortical processes.},
    url = "https://doi.org/10.1037/0033-2909.130.5.748",
    doi = "10.1037/0033-2909.130.5.748",
    openalex = "W2048560552",
    references = "doi1010160010028577900123, doi101037009634451092160, doi101037h0049612, doi10108000335558008248231, doi101113jphysiol1959sp006308, doi101113jphysiol1969sp008862, doi1023072103010, doi1043249781410612403, openalexw1641311894, openalexw3091830901"
}

Most people agree that local police should continue to place a high priority on responding to violent and other felony crime. At the same time, departments are increasingly asked to assume more service-related responsibilities within the community, creating a situation of thinly spread resources. Some nonemergency problems might be handled in an alternate way to increase efficiency in the delivery of police services. To measure community perceptions of alternate reporting methods, we mailed a survey to 6,000 urban residents in Kansas City. Most citizens embraced phone reporting, but were less willing to use mail-in reporting and the Internet. Policy implications are discussed.

@article{alarid2008citizens,
    author = "Alarid, Leanne F. and Novak, Kenneth J.",
    title = "Citizens' Views on Using Alternate Reporting Methods in Policing",
    year = "2008",
    journal = "Criminal Justice Policy Review",
    abstract = "Most people agree that local police should continue to place a high priority on responding to violent and other felony crime. At the same time, departments are increasingly asked to assume more service-related responsibilities within the community, creating a situation of thinly spread resources. Some nonemergency problems might be handled in an alternate way to increase efficiency in the delivery of police services. To measure community perceptions of alternate reporting methods, we mailed a survey to 6,000 urban residents in Kansas City. Most citizens embraced phone reporting, but were less willing to use mail-in reporting and the Internet. Policy implications are discussed.",
    url = "https://doi.org/10.1177/0887403407308289",
    doi = "10.1177/0887403407308289",
    number = "1",
    openalex = "W1968793981",
    pages = "25-39",
    volume = "19",
    references = "doi101093bjcazi096, doi101111j174591251994tb01149x, doi101111j174591252002tb00967x, doi1011770022427894031001002, doi1011770022427898035003005, doi1011771098611103258955, doi1011771098611104271105, doi1023071143749, doi1023071318956, doi105860choice372223"
}

E‐governance comprises the use of information and communication technologies (ICTs) to support public services, government administration, democratic processes, and relationships among citizens, civil society, the private sector, and the state. Developed over more than two decades of technology innovation and policy response, the evolution of e‐governance is examined in terms of five interrelated objectives: a policy framework, enhanced public services, high‐quality and cost‐effective government operations, citizen engagement in democratic processes, and administrative and institutional reform. This summary assessment of e‐governance in U.S. states and local governments shows that the greatest investment and progress have been made in enhanced public services and improved government operations. Policy development has moved forward on several fronts, but new policy issues continually add to an increasingly complex set of concerns. The least progress appears to have occurred in enhancing democracy and exploring the implications of e‐governance for administrative and institutional reform. ICT‐enabled governance will continue to evolve for the foreseeable future providing a dynamic environment for ongoing learning and action.

@article{doi101111j15406210200800981x,
    author = "Dawes, Sharon S.",
    title = "The Evolution and Continuing Challenges of E‐Governance",
    year = "2008",
    journal = "Public Administration Review",
    abstract = "E‐governance comprises the use of information and communication technologies (ICTs) to support public services, government administration, democratic processes, and relationships among citizens, civil society, the private sector, and the state. Developed over more than two decades of technology innovation and policy response, the evolution of e‐governance is examined in terms of five interrelated objectives: a policy framework, enhanced public services, high‐quality and cost‐effective government operations, citizen engagement in democratic processes, and administrative and institutional reform. This summary assessment of e‐governance in U.S. states and local governments shows that the greatest investment and progress have been made in enhanced public services and improved government operations. Policy development has moved forward on several fronts, but new policy issues continually add to an increasingly complex set of concerns. The least progress appears to have occurred in enhancing democracy and exploring the implications of e‐governance for administrative and institutional reform. ICT‐enabled governance will continue to evolve for the foreseeable future providing a dynamic environment for ongoing learning and action.",
    url = "https://doi.org/10.1111/j.1540-6210.2008.00981.x",
    doi = "10.1111/j.1540-6210.2008.00981.x",
    openalex = "W2162776220"
}

(2009). Leveling with Lagrange: An Alternate View of Constrained Optimization. Mathematics Magazine: Vol. 82, No. 3, pp. 186-196.

@article{doi1010800025570x200911953617,
    author = "Kalman, Dan",
    title = "Leveling with Lagrange: An Alternate View of Constrained Optimization",
    year = "2009",
    journal = "Mathematics Magazine",
    abstract = "(2009). Leveling with Lagrange: An Alternate View of Constrained Optimization. Mathematics Magazine: Vol. 82, No. 3, pp. 186-196.",
    url = "https://doi.org/10.1080/0025570x.2009.11953617",
    doi = "10.1080/0025570x.2009.11953617",
    openalex = "W2017137553",
    references = "doi1010079781461262787, doi1010079789401589031, doi1010160164070484900119, doi10108000029890197311993409, doi1023073008903, openalexw1482444097, openalexw1537593861, openalexw1541105928, openalexw3142069444, openalexw3164053048"
}

These results, coupled with the recent proposed placement of Strepsiptera sister to Coleoptera, suggest that while the phylogenetic neighborhood of Strepsiptera has been identified, unequivocal placement to a specific branch within Neuropteroidea will require additional study.

@article{doi101371journalpone0011887,
    author = "McKenna, Duane D. and Farrell, Brian D.",
    title = "9-Genes Reinforce the Phylogeny of Holometabola and Yield Alternate Views on the Phylogenetic Placement of Strepsiptera",
    year = "2010",
    journal = "PLoS ONE",
    abstract = "These results, coupled with the recent proposed placement of Strepsiptera sister to Coleoptera, suggest that while the phylogenetic neighborhood of Strepsiptera has been identified, unequivocal placement to a specific branch within Neuropteroidea will require additional study.",
    url = "https://doi.org/10.1371/journal.pone.0011887",
    doi = "10.1371/journal.pone.0011887",
    openalex = "W2134966375",
    references = "doi10108010635150701472164, doi101093bibbbn013, doi101093bioinformatics149817, doi101093bioinformatics178754, doi101093bioinformaticsbtg180, doi101093oxfordjournalsmolbeva026334, doi101093sysbio274401, doi1023072412923, openalexw1900040508, openalexw2994240441"
}

@article{más2010unfinished,
    author = "Más, Antonio and López-Galíndez, Cecilio and Cacho, Isabel and Gómez, Jordi and Martínez, Miguel Angel",
    title = "Unfinished Stories on Viral Quasispecies and Darwinian Views of Evolution",
    year = "2010",
    journal = "Journal of Molecular Biology",
    url = "https://doi.org/10.1016/j.jmb.2010.02.005",
    doi = "10.1016/j.jmb.2010.02.005",
    number = "4",
    openalex = "W2045919763",
    pages = "865-877",
    volume = "397",
    references = "doi101007bf00623322, doi1010160004698180901493, doi101016s0140673601053211, doi101038243290a0, doi101038nature05610, doi101038nrc1299, doi101126science28454181318, doi101126science959840, doi101146annurevmi41100187002251, openalexw1510546584"
}

@incollection{crossref2011darwinian,
    title = "Darwinian Evolution",
    year = "2011",
    booktitle = "Encyclopedia of Astrobiology",
    url = "https://doi.org/10.1007/978-3-642-11274-4\_2318",
    doi = "10.1007/978-3-642-11274-4\_2318",
    openalex = "W4250848644",
    pages = "409-409"
}

Abstract This book presents new ideas for why the acceptance and understanding of evolution and related concepts is so difficult for both children and adults. Drawing from diverse fields, the contributors include the foremost researchers and practitioners in the study of children’s cognitive development, science education, teaching of evolution, and the design and evaluation of formal and informal instruction of evolution. The book brings together a unique collection of researchers, educators, and practitioners, who met and discussed many of the ideas incorporated in this volume at regional and national meetings funded by the National Science Foundation. The chapters and the overall book integrate cutting edge ideas that emerged from these meetings.

@book{doi101093acprofoso97801997304210010001,
    title = "Evolution Challenges",
    year = "2012",
    booktitle = "Oxford University Press eBooks",
    abstract = "Abstract This book presents new ideas for why the acceptance and understanding of evolution and related concepts is so difficult for both children and adults. Drawing from diverse fields, the contributors include the foremost researchers and practitioners in the study of children’s cognitive development, science education, teaching of evolution, and the design and evaluation of formal and informal instruction of evolution. The book brings together a unique collection of researchers, educators, and practitioners, who met and discussed many of the ideas incorporated in this volume at regional and national meetings funded by the National Science Foundation. The chapters and the overall book integrate cutting edge ideas that emerged from these meetings.",
    url = "https://doi.org/10.1093/acprof:oso/9780199730421.001.0001",
    doi = "10.1093/acprof:oso/9780199730421.001.0001",
    openalex = "W89888216",
    references = "doi101002tea20027, doi101007s1119100992164, doi101007s1205200800618, doi10108009500690210145716, doi1015365joce1601602013, openalexw1569351806"
}

The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 "polymorphic" SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.

@article{doi101073pnas1519556112,
    author = "Ling, Shaoping and Hu, Zheng and Yang, Zuyu and Yang, Fang and Li, Yawei and Lin, Pei and Chen, Ke and Dong, Lili and Cao, Lihua and Tao, Yong and Hao, Lingtong and Chen, Qingjian and Gong, Qiang and Wu, Dafei and Li, Wenjie and Zhao, Wenming and Tian, Xiuyun and Hao, Chunyi and Hungate, Eric A. and Catenacci, Daniel V.T. and Hudson, Richard R. and Li, Wen‐Hsiung and Lu, Xuemei and Wu, Chung‐I",
    title = "Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 "polymorphic" SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.},
    url = "https://doi.org/10.1073/pnas.1519556112",
    doi = "10.1073/pnas.1519556112",
    openalex = "W2177689130",
    references = "doi101038nature12213, doi101038scientificamerican117998, doi101056nejmoa1113205, doi101093bioinformaticsbtg412, doi101093bioinformaticsbtp324, doi101093bioinformaticsbtp352, doi101093oxfordjournalsmolbeva040454, doi101126science1235122, doi101126science959840, doi101146annurevgenom082908150129, doi105962bhltitle27468"
}

The various positions that Muslim scholars have adopted vis-à-vis Darwin’s theory of evolution since its inception in 1859 are here reviewed with an eye on the theological arguments that are embraced, whether explicitly or implicitly. A large spectrum of views and arguments are thus found, ranging from total rejection to total acceptance, including “human exceptionalism” (evolution is applicable to all organisms and animals but not to humans). The two main theological arguments that are thus extracted from Muslim scholars’ discussions of evolution are: 1) Is God excluded by the evolutionary paradigm or does the term “Creator” acquire a new definition? 2) Does Adam still exist in the human evolution scenario, and how to include his Qur’anic story in the scientific scenario? Additional, but less crucial issues are sometimes raised in Islamic discussions of evolution: a) Does the extinction of innumerable species during the history of life on earth conflict with the traditional view of God’s creation? b) Is theodicy (“the problem of evil”) exacerbated or explained by evolution? c) Are “species” well-defined and important biological entities in the Islamic worldview? d) Can the randomness that seems inherent in the evolutionary process be reconciled with a divine creation plan? These questions are here reviewed through the writings and arguments of Muslim scholars, and general conclusions are drawn about why rejectionists find it impossible to address those issues in a manner that is consistent with their religious principles and methods, and why more progressive, less literalistic scholars are able to fold those issues within a less rigid conception of God and the world.

@misc{guessoum2016islamic,
    author = "Guessoum, Nidhal",
    title = "Islamic Theological Views on Darwinian Evolution",
    year = "2016",
    booktitle = "Oxford Research Encyclopedia of Religion",
    abstract = "The various positions that Muslim scholars have adopted vis-à-vis Darwin’s theory of evolution since its inception in 1859 are here reviewed with an eye on the theological arguments that are embraced, whether explicitly or implicitly. A large spectrum of views and arguments are thus found, ranging from total rejection to total acceptance, including “human exceptionalism” (evolution is applicable to all organisms and animals but not to humans). The two main theological arguments that are thus extracted from Muslim scholars’ discussions of evolution are: 1) Is God excluded by the evolutionary paradigm or does the term “Creator” acquire a new definition? 2) Does Adam still exist in the human evolution scenario, and how to include his Qur’anic story in the scientific scenario? Additional, but less crucial issues are sometimes raised in Islamic discussions of evolution: a) Does the extinction of innumerable species during the history of life on earth conflict with the traditional view of God’s creation? b) Is theodicy (“the problem of evil”) exacerbated or explained by evolution? c) Are “species” well-defined and important biological entities in the Islamic worldview? d) Can the randomness that seems inherent in the evolutionary process be reconciled with a divine creation plan? These questions are here reviewed through the writings and arguments of Muslim scholars, and general conclusions are drawn about why rejectionists find it impossible to address those issues in a manner that is consistent with their religious principles and methods, and why more progressive, less literalistic scholars are able to fold those issues within a less rigid conception of God and the world.",
    url = "https://doi.org/10.1093/acrefore/9780199340378.013.36",
    doi = "10.1093/acrefore/9780199340378.013.36",
    openalex = "W2480734908",
    references = "doi101017cbo9780511676345008"
}

Judgement, as one of the core tenets of medicine, relies upon the integration of multilayered data with nuanced decision making. Cancer offers a unique context for medical decisions given not only its variegated forms with evolution of disease but also the need to take into account the individual condition of patients, their ability to receive treatment, and their responses to treatment. Challenges remain in the accurate detection, characterization, and monitoring of cancers despite improved technologies. Radiographic assessment of disease most commonly relies upon visual evaluations, the interpretations of which may be augmented by advanced computational analyses. In particular, artificial intelligence (AI) promises to make great strides in the qualitative interpretation of cancer imaging by expert clinicians, including volumetric delineation of tumors over time, extrapolation of the tumor genotype and biological course from its radiographic phenotype, prediction of clinical outcome, and assessment of the impact of disease and treatment on adjacent organs. AI may automate processes in the initial interpretation of images and shift the clinical workflow of radiographic detection, management decisions on whether or not to administer an intervention, and subsequent observation to a yet to be envisioned paradigm. Here, the authors review the current state of AI as applied to medical imaging of cancer and describe advances in 4 tumor types (lung, brain, breast, and prostate) to illustrate how common clinical problems are being addressed. Although most studies evaluating AI applications in oncology to date have not been vigorously validated for reproducibility and generalizability, the results do highlight increasingly concerted efforts in pushing AI technology to clinical use and to impact future directions in cancer care.

@article{doi103322caac21552,
    author = "Bi, Wenya Linda and Hosny, Ahmed and Schabath, Matthew B. and Giger, Maryellen L. and Birkbak, Nicolai J. and Mehrtash, Alireza and Allison, Tavis and Arnaout, Omar and Abbosh, Christopher and Dunn, Ian F. and Mak, Raymond H. and Tamimi, Rulla M. and Tempany, Clare M. and Swanton, Charles and Hoffmann, Udo and Schwartz, Lawrence H. and Gillies, Robert J. and Huang, Raymond Y. and Aerts, Hugo J.W.L.",
    title = "Artificial intelligence in cancer imaging: Clinical challenges and applications",
    year = "2019",
    journal = "CA A Cancer Journal for Clinicians",
    abstract = "Judgement, as one of the core tenets of medicine, relies upon the integration of multilayered data with nuanced decision making. Cancer offers a unique context for medical decisions given not only its variegated forms with evolution of disease but also the need to take into account the individual condition of patients, their ability to receive treatment, and their responses to treatment. Challenges remain in the accurate detection, characterization, and monitoring of cancers despite improved technologies. Radiographic assessment of disease most commonly relies upon visual evaluations, the interpretations of which may be augmented by advanced computational analyses. In particular, artificial intelligence (AI) promises to make great strides in the qualitative interpretation of cancer imaging by expert clinicians, including volumetric delineation of tumors over time, extrapolation of the tumor genotype and biological course from its radiographic phenotype, prediction of clinical outcome, and assessment of the impact of disease and treatment on adjacent organs. AI may automate processes in the initial interpretation of images and shift the clinical workflow of radiographic detection, management decisions on whether or not to administer an intervention, and subsequent observation to a yet to be envisioned paradigm. Here, the authors review the current state of AI as applied to medical imaging of cancer and describe advances in 4 tumor types (lung, brain, breast, and prostate) to illustrate how common clinical problems are being addressed. Although most studies evaluating AI applications in oncology to date have not been vigorously validated for reproducibility and generalizability, the results do highlight increasingly concerted efforts in pushing AI technology to clinical use and to impact future directions in cancer care.",
    url = "https://doi.org/10.3322/caac.21552",
    doi = "10.3322/caac.21552",
    openalex = "W2911605224",
    references = "doi101016jcell201701018"
}

@incollection{crossref2021darwinian,
    title = "Darwinian Evolution",
    year = "2021",
    booktitle = "A Philosopher Looks at Human Beings",
    url = "https://doi.org/10.1017/9781108907057.004",
    doi = "10.1017/9781108907057.004",
    openalex = "W4249678390",
    pages = "48-74"
}