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1.
Here we address three misconceptions stated by Rice et al. in their observations of our article Paz-y-Mi?o and Espinosa (Evo
Edu Outreach 2:655–675, 2009), published in this journal. The five authors titled their note “The Theory of Evolution is Not an Explanation for the Origin of Life.” First, we argue that it is fallacious to believe that because the formulation of the theory of evolution, as conceived
in the 1800s, did not include an explanation for the origin of life, nor of the universe, the concept of evolution would not
allow us to hypothesize the possible beginnings of life and its connections to the cosmos. Not only Stanley Miller’s experiments
of 1953 led scientists to envision a continuum from the inorganic world to the origin and diversification of life, but also
Darwin’s own writings of 1871. Second, to dismiss the notion of Rice et al. that evolution does not provide explanations concerning
the universe or the cosmos, we identify compelling scientific discussions on the topics: Zaikowski et al. (Evo Edu Outreach
1:65–73, 2008), Krauss (Evo Edu Outreach 3:193–197, 2010), Peretó et al. (Orig Life Evol Biosph 39:395–406, 2009) and Follmann and Brownson (Naturwissenschaften 96:1265–1292, 2009). Third, although we acknowledge that the term Darwinism may not be inclusive of all new discoveries in evolution, and also that creationists and Intelligent Designers hijack the
term to portray evolution as ideology, we demonstrate that there is no statistical evidence suggesting that the word Darwinism
interferes with public acceptance of evolution, nor does the inclusion of the origin of life or the universe within the concept
of evolution. We examine the epistemological and empirical distinction between the theory of evolution and the concept of evolution and conclude that, although the distinction is important, it should not compromise scientific logic. 相似文献
2.
Menshutkin VV 《Zhurnal obshche? biologii》2003,64(4):328-336
The computer model of two alternative variants of biological evolution is proposed. The first variant supposes random while the second--directed change of individual features, thus corresponding to the Darwinian and non-Darwinian evolution. The evolution of fish communities in fresh waters serves as a particular example. The model is executed using object-oriented method of programming and mathematical apparatus of fuzzy logics. The investigation of the model showed that process of Darwinian evolution is connected with significantly greater species diversity and variability of evolutionary process trajectories than non-Darwinian one. On the other hand, non-Darwinian type of evolution provides fast achievement of high individual fitness, especially under conditions of constant environment. Non-Darwinian type evolution failed in big evolutionary alteration (for example, transition to predation); while the Darwinian evolution under the same conditions can produce such alterations though it took more time and many extinct species. Phylogenetic tree of Darwinian evolution is always more complex than of non-Darwinian one under the same conditions. 相似文献
3.
Meiotic prophase serves as an arena for the interplay of two important cellular activities, meiotic recombination and synapsis of homologous chromosomes. Synapsis is mediated by the synaptonemal complex (SC), originally characterized as a structure linked to pairing of meiotic chromosomes (Moses (1958) J Biophys Biochem Cytol 4:633–638). In 1975, the first electron micrographs of human pachytene stage SCs were presented (Moses et al. (1975) Science 187:363–365) and over the next 15 years the importance of the SC to normal meiotic progression in human males and females was established (Jhanwar and Chaganti (1980) Hum Genet 54:405–408; Pathak and Elder (1980) Hum Genet 54:171–175; Solari (1980) Chromosoma 81:315–337; Speed (1984) Hum Genet 66:176–180; Wallace and Hulten (1985) Ann Hum Genet 49(Pt 3):215–226). Further, these studies made it clear that abnormalities in the assembly or maintenance of the SC were an important contributor to human infertility (Chaganti et al. (1980) Am J Hum Genet 32:833–848; Vidal et al. (1982) Hum Genet 60:301–304; Bojko (1983) Carlsberg Res Commun 48:285–305; Bojko (1985) Carlsberg Res Commun 50:43–72; Templado et al. (1984) Hum Genet 67:162–165; Navarro et al. (1986) Hum Reprod 1:523–527; Garcia et al. (1989) Hum Genet 2:147–53). However, the utility of these early studies was limited by lack of information on the structural composition of the SC and the identity of other SC-associated proteins. Fortunately, studies of the past 15 years have gone a long way toward remedying this problem. In this minireview, we highlight the most important of these advances as they pertain to human meiosis, focusing on temporal aspects of SC assembly, the relationship between the SC and meiotic recombination, and the contribution of SC abnormalities to human infertility.The synaptonemal complex–50 years 相似文献
4.
Kevin Brosnan 《Biology & philosophy》2011,26(1):51-64
According to some recent arguments, (Joyce in The evolution of morality, MIT Press, Cambridge, 2006; Ruse and Wilson in Conceptual issues in evolutionary biology, MIT Press, Cambridge, 1995; Street in Philos Studies 127: 109–166, 2006) if our moral beliefs are products of natural selection, then we do not have moral knowledge. In defense of this inference,
its proponents argue that natural selection is a process that fails to track moral facts. In this paper, I argue that our
having moral knowledge is consistent with, (a) the hypothesis that our moral beliefs are products of natural selection, and
(b) the claim (or a certain interpretation of the claim) that natural selection fails to track moral facts. I also argue that
natural selection is a process that could track moral facts, albeit imperfectly. I do not argue that we do have moral knowledge.
I argue instead that Darwinian considerations provide us with no reason to doubt that we do, and with some reasons to suppose
that we might. 相似文献
5.
Gap-junctional coupling is an important way of communication between neurons and other excitable cells. Strong electrical
coupling synchronizes activity across cell ensembles. Surprisingly, in the presence of noise synchronous oscillations generated
by an electrically coupled network may differ qualitatively from the oscillations produced by uncoupled individual cells forming
the network. A prominent example of such behavior is the synchronized bursting in islets of Langerhans formed by pancreatic
β-cells, which in isolation are known to exhibit irregular spiking (Sherman and Rinzel, Biophys J 54:411–425, 1988; Sherman and Rinzel, Biophys J 59:547–559, 1991). At the heart of this intriguing phenomenon lies denoising, a remarkable ability of electrical coupling to diminish the
effects of noise acting on individual cells. In this paper, building on an earlier analysis of denoising in networks of integrate-and-fire
neurons (Medvedev, Neural Comput 21 (11):3057–3078, 2009) and our recent study of spontaneous activity in a closely related model of the Locus Coeruleus network (Medvedev and Zhuravytska,
The geometry of spontaneous spiking in neuronal networks, submitted, 2012), we derive quantitative estimates characterizing denoising in electrically coupled networks of conductance-based models
of square wave bursting cells. Our analysis reveals the interplay of the intrinsic properties of the individual cells and
network topology and their respective contributions to this important effect. In particular, we show that networks on graphs
with large algebraic connectivity (Fiedler, Czech Math J 23(98):298–305, 1973) or small total effective resistance (Bollobas, Modern graph theory, Graduate Texts in Mathematics, vol. 184, Springer, New
York, 1998) are better equipped for implementing denoising. As a by-product of the analysis of denoising, we analytically estimate the
rate with which trajectories converge to the synchronization subspace and the stability of the latter to random perturbations.
These estimates reveal the role of the network topology in synchronization. The analysis is complemented by numerical simulations
of electrically coupled conductance-based networks. Taken together, these results explain the mechanisms underlying synchronization
and denoising in an important class of biological models. 相似文献
6.
Saziye Bayram Tracy L. Stepien E. Bruce Pitman 《Bulletin of mathematical biology》2009,71(6):1482-1506
This paper presents a mathematical model of a system of many coupled nephrons branching from a common cortical radial artery,
and accompanying analysis of that system. This modeling effort is a first step in understanding how coupling magnifies the
tendency of nephrons to oscillate owing to tubuloglomerular feedback. Central to the present work is the single nephron integral
model (as in Pitman et al., The IMA Volumes in Mathematics and Its Applications, vol. 129, pp. 345–364, 2002 and in Zaritski, Ph.D. Dissertation, 1999) which is a simplification of the single nephron PDE model of Layton et al. (Am. J. Physiol. 261, F904–F919, 1991). A second principal idea used in the present model is a coupling of model nephrons, generalizing the work of Pitman et al.
(Bull. Math. Biol. 66, 1463–1492, 2004) who proposed a model of two coupled nephrons. In this study, we couple nephrons through a nearest neighbor interaction.
Speaking generally, our results suggest that a series of similar nephrons coupled to their nearest neighbors are more prone
to be found in an oscillatory mode, relative to a single nephron with the same properties. More specifically, we show analytically
that, for N coupled identical nephrons, the region supporting oscillatory solutions in the time delay–gain parameter plane increases
with N. Numerical simulations suggest that, if N nephrons have gains and time delays that do not differ by much, the system is, again, more prone to oscillate, relative to
a single nephron, and the oscillations tend to be approximately synchronous and in-phase. We examine the effect of parameters
on bifurcation. We also examine alternative models of coupling; this analysis allows us to conclude that the increased propensity
of coupled nephrons to oscillate is a robust finding, true for several models of nephron interaction. 相似文献
7.
Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist
approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental
molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out)
and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computational and
experimental strategy was formally proposed in mid 1990s leading to the re-emergence of Systems Biology. However, soon it
became clear that natural systems were far more complex than expected. A new strategy to address biological complexity was
proposed at MIT (Massachusetts Institute of Technology) in June 2004, when the first meeting of synthetic biology was held.
Though the term ‘synthetic biology’ was proposed during 1970s (Szybalski in Control of gene expression, Plenum Press, New
York, 1974), the usage of the original concept found an experimental proof in 2000 with the demonstration of a three-gene circuit called
repressilator (Elowitz and Leibler in Nature, 403:335–338, 2000). This encouraged people to think of forward engineering biology from a set of well described parts. 相似文献
8.
The Protein Kinase C family of enzymes is a group of serine/threonine kinases that play central roles in cell-cycle regulation,
development and cancer. A key step in the activation of PKC is translocation to membranes and binding of membrane-associated
activators including diacylglycerol (DAG). Interaction of novel and conventional isotypes of PKC with DAG and phorbol esters
occurs through the two C1 regulatory domains (C1A and C1B), which exhibit distinct ligand binding selectivity that likely
controls enzyme activation by different co-activators. PKC has also been implicated in physiological responses to alcohol
consumption and it has been proposed that PKCα (Slater et al. J Biol Chem 272(10):6167–6173, 1997; Slater et al. Biochemistry 43(23):7601–7609, 2004), PKCε (Das et al. Biochem J 421(3):405–413, 2009) and PKCδ (Das et al. J Biol Chem 279(36):37964–37972, 2004; Das et al. Protein Sci 15(9):2107–2119, 2006) contain specific alcohol-binding sites in their C1 domains. We are interested in understanding how ethanol affects signal
transduction processes through its affects on the structure and function of the C1 domains of PKC. Here we present the 1H, 15N and 13C NMR chemical shift assignments for the Rattus norvegicus PKCδ C1A and C1B proteins. 相似文献
9.
10.
The problem of how often to disperse in a randomly fluctuating environment has long been investigated, primarily using patch
models with uniform dispersal. Here, we consider the problem of choice of seed size for plants in a stable environment when
there is a trade off between survivability and dispersal range. Ezoe (J Theor Biol 190:287–293, 1998) and Levin and Muller-Landau (Evol Ecol Res 2:409–435, 2000) approached this problem using models that were essentially deterministic, and used calculus to find optimal dispersal parameters.
Here we follow Hiebeler (Theor Pop Biol 66:205–218, 2004) and use a stochastic spatial model to study the competition of different dispersal strategies. Most work on such systems
is done by simulation or nonrigorous methods such as pair approximation. Here, we use machinery developed by Cox et al. (Voter
model perturbations and reaction diffusion equations 2011) to rigorously and explicitly compute evolutionarily stable strategies. 相似文献
11.
Bryant D 《Bulletin of mathematical biology》2009,71(2):339-351
The Hadamard transform (Hendy and Penny, Syst. Zool. 38(4):297–309, 1989; Hendy, Syst. Zool. 38(4):310–321, 1989) provides a way to work with stochastic models for sequence evolution without having to deal with the complications of tree
space and the graphical structure of trees. Here we demonstrate that the transform can be expressed in terms of the familiar
P[τ]=e
Q[τ] formula for Markov chains. The key idea is to study the evolution of vectors of states, one vector entry for each taxa; we
call this the n-taxon process. We derive transition probabilities for the process. Significantly, the findings show that tree-based models
are indeed in the family of (multi-variate) exponential distributions. 相似文献
12.
Tarnow E 《Cognitive neurodynamics》2010,4(4):367-376
Theories of short term memory often include a limited capacity “buffer”. Such a buffer contains items which do not decay at
all but are overwritten by new data. I show that one of the experiments that fueled the buffer concept, the free recall experiments
by Murdock (J Exp Psychol 64(5):482–488, 1962), does not contain such a buffer. 相似文献
13.
14.
Temperature controls a latitudinal gradient in the proportion of watershed nitrogen exported to coastal ecosystems 总被引:5,自引:4,他引:1
Increased export of biologically available nitrogen (N) to the coastal zone is strongly linked to eutrophication, which is
a major problem in coastal marine ecosystems (NRC (2000) Clean Coastal Waters: Understanding and Reducing the Effects of Nutrient Pollution. National Academy Press, Washington,
DC; Bricker et al. (1999) National Estuarine Eutrophication Assessment. Effects of nutrient enrichment in the nation’s estuaries. NOAA-NOS Special
Projects Office, Silver Spring, MD). However, not all of the nitrogen input to a watershed is exported to the coast (Howarth
et al. (1996) Biogeochemistry 35:75–139; Jordan and Weller (1996) Bioscience 46:655–664). Global estimates of nitrogen export to coasts have been taken to be 25% of watershed input, based
largely on northeastern U.S. observations (Galloway et al. (2004) Biogeochemistry 70:153–226; Boyer et al. (2006) Global Biogeochem Cycle 20:Art. No. GB1S91). We applied the N budgeting methodology developed for the International SCOPE
Nitrogen project (Howarth et al. (1996) Biogeochemistry 35:75–139; Boyer et al. (2002) Biogeochemistry 57:137–169) to 12 watersheds in the southeastern U.S., and compared them with estimates of N export for
16 watersheds in the northeastern U.S. (Boyer et al. (2002) Biogeochemistry 57:137–169). In southeastern watersheds, average N export was only 9% of input, suggesting the need for
downward revision of global estimates. The difference between northern and southern watersheds is not a function of the absolute
value of N inputs, which spanned a comparable range and were positively related to export in both cases. Rather, the proportion
of N exported was significantly related to average watershed temperature (% N export = 58.41 e−0.11 * temperature; R
2 = 0.76), with lower proportionate nitrogen export in warmer watersheds. In addition, we identified a threshold in proportionate
N export at 38°N latitude that corresponds to a reported breakpoint in the rate of denitrification at 10–12°C. We hypothesize
that temperature, by regulating denitrification, results in increased proportionate N export at higher latitudes. Regardless
of the mechanism, these observations suggest that temperature increases associated with future climate change may well reduce
the amount of nitrogen that reaches estuaries, which will have implications for coastal eutrophication. 相似文献
15.
16.
Yasuhiro Fukushima Minoru Tsukada Ichiro Tsuda Yutaka Yamaguti Shigeru Kuroda 《Cognitive neurodynamics》2007,1(4):305-316
To clarify how the information of spatiotemporal sequence of the hippocampal CA3 affects the postsynaptic membrane potentials
of single pyramidal cells in the hippocampal CA1, the spatio-temporal stimuli was delivered to Schaffer collaterals of the
CA3 through a pair of electrodes and the post-synaptic membrane potentials were recorded using the patch-clamp recording method.
The input–output relations were sequentially analyzed by applying two measures; “spatial clustering” and its “self-similarity”
index. The membrane potentials were hierarchically clustered in a self-similar manner to the input sequences. The property
was significantly observed at two and three time-history steps. In addition, the properties were maintained under two different
stimulus conditions, weak and strong current stimulation. The experimental results are discussed in relation to theoretical
results of Cantor coding, reported by Tsuda (Behav Brain Sci 24(5):793–847, 2001) and Tsuda and Kuroda (Jpn J Indust Appl Math 18:249–258, 2001; Cortical dynamics, pp 129–139, Springer-Verlag, 2004). 相似文献
17.
Agarwal B 《Journal of bioenergetics and biomembranes》2011,43(3):299-310
ATP, the ‘universal biological energy currency’, is synthesized by utilizing energy either from oxidation of fuels or from
light, via the process of oxidative and photo-phosphorylation respectively. The process is mediated by the enzyme F1F0-ATP synthase, using the free energy of ion gradients in the final energy catalyzing step, i.e., the synthesis of ATP from
ADP and inorganic phosphate (Pi). The details of the molecular mechanism of ATP synthesis are among the most important fundamental issues in biology and
hence need to be properly understood. In this work, a role for anions in making ATP has been found. New experimental data
has been reported on the inhibition of ATP synthesis at nanomolar concentrations by the potent, specific anion channel blockers
4,4′-diisothiocyanostilbene-2, 2′-disulphonic acid (DIDS) and tributyltin chloride (TBTCl). Based on these inhibition studies,
attention has been drawn to anion translocation (in addition to proton translocation) as a requirement for ATP synthesis.
The type of inhibition has been quantified and an overall kinetic scheme for mixed inhibition that explains the data has been
evolved. The experimental data and the type of inhibition found have been interpreted in the light of the torsional mechanism
of energy transduction and ATP synthesis (Nath J Bioenerg Biomembr 42:293–300, 2010a; J Bioenerg Biomembr 42:301–309, 2010b). This detailed and unified mechanism resolves long-standing problems and inconsistencies in the first theories (Slater Nature
172:975–978, 1953; Williams J Theor Biol 1:1–17, 1961; Mitchell Nature 191:144–148, 1961; Mitchell Biol Rev 41:445–502, 1966), makes several novel predictions that are experimentally verifiable (Nath Biophys J 90:8–21, 2006a; Process Biochem 41:2218–2235, 2006b), and provides us with a new and fruitful paradigm in bioenergetics. The interpretation presented here provides intelligent
answers to the unexplained existing results in the literature. It is shown that mechanistic interpretation of the experimental
data requires substantial addition to available conceptual foundations such that present concepts, theories, and mechanisms
must be revised. 相似文献
18.
Zachary Cooper Michael Greenwood Borbala Mazzag 《Bulletin of mathematical biology》2009,71(7):1543-1579
We investigate the role of heterogeneous expression of IP3R and RyR in generating diverse elementary Ca2+ signals. It has been shown empirically (Wojcikiewicz and Luo in Mol. Pharmacol. 53(4):656–662, 1998; Newton et al. in J. Biol. Chem. 269(46):28613–28619, 1994; Smedt et al. in Biochem. J. 322(Pt. 2):575–583, 1997) that tissues express various proportions of IP3 and RyR isoforms and this expression is dynamically regulated (Parrington et al. in Dev. Biol. 203(2):451–461, 1998; Fissore et al. in Biol. Reprod. 60(1):49–57, 1999; Tovey et al. in J. Cell Sci. 114(Pt. 22):3979–3989, 2001). Although many previous theoretical studies have investigated the dynamics of localized calcium release sites (Swillens
et al. in Proc. Natl. Acad. Sci. U.S.A. 96(24):13750–13755, 1999; Shuai and Jung in Proc. Natl. Acad. Sci. U.S.A. 100(2):506–510, 2003a; Shuai and Jung in Phys. Rev. E, Stat. Nonlinear Soft Matter Phys. 67(3 Pt. 1):031905, 2003b; Thul and Falcke in Biophys. J. 86(5):2660–2673, 2004; DeRemigio and Smith in Cell Calcium 38(2):73–86, 2005; Nguyen et al. in Bull. Math. Biol. 67(3):393–432, 2005), so far all such studies focused on release sites consisting of identical channel types. We have extended an existing mathematical
model (Nguyen et al. in Bull. Math. Biol. 67(3):393–432, 2005) to release sites with two (or more) receptor types, each with its distinct channel kinetics. Mathematically, the release
site is represented by a transition probability matrix for a collection of nonidentical stochastically gating channels coupled
through a shared Ca2+ domain. We demonstrate that under certain conditions a previously defined mean-field approximation of the coupling strength
does not accurately reproduce the release site dynamics. We develop a novel approximation and establish that its performance
in these instances is superior. We use this mathematical framework to study the effect of heterogeneity in the Ca2+-regulation of two colocalized channel types on the release site dynamics. We consider release sites consisting of channels
with both Ca2+-activation and inactivation (“four-state channels”) and channels with Ca2+-activation only (“two-state channels”) and show that for the appropriate parameter values, synchronous channel openings within
a release site with any proportion of two-state to four-state channels are possible, however, the larger the proportion of
two-state channels, the more sensitive the dynamics are to the exact spatial positioning of the channels and the distance
between channels. Specifically, the clustering of even a small number of two-state channels interferes with puff/spark termination
and increases puff durations or leads to a tonic response. 相似文献
19.
20.
Osvaldo Borges Pinto-Júnior Luciana Sanches Francisco de Almeida Lobo Adilson Amorim Brandão José de Souza Nogueira 《International journal of biometeorology》2011,55(2):109-118
Leaf area index (LAI) is an important ecophysiological variable because leaves are the organs responsible for gas exchange
between plants and the atmosphere. This variable can be calculated from primary values of leaf area assessed by destructive
or non-destructive methods, which is relatively easy when crop species are investigated, but is not the case when the focus
is on natural wood plants communities. In this paper, we analyze the seasonality of LAI estimated by three different methods
in the Amazonia-savannah transitional forest, located 50 km north-east of Sinop city, Mato Grosso, Brazil. In the first method,
we combine Monsi and Saekis' original method [Monsi M, Saeki T (1953) Jpn J Bot 14:22–52], which measures LAI using the Beer-Lambert extinction law, and the proposition of Goudriaan [Goudriaan
J (1988) Agric For Meteorol 43:155–169] to estimate the extinction coefficient from solar height. The second method differed from
the first only in the way in which the daily fraction of intercepted photosynthetic active radiation (FPAR) was calculated,
as proposed by Charles-Edwards and Lawn (Charles-Edwards DA, Lawn RJ (1984) Plant Cell Environ 7:247–251]. In the third method, we used a remote sensing technique [MOD15_BU-collection 4, produced
and distributed by EROS Data Center Distributed Active Archive Center (EDC DAAC)]. We found that the first and the second
methods revealed the expected LAI dynamics, which increased during the dry–wet transition and wet season, and decreased during
the wet–dry transition and dry season. From 20 randomly distributed sets in a 1.0 ha area, only 3 showed significant differences
in LAI estimated from the first two methods; conversely, LAI was overestimated by the third method. 相似文献