text:
\section{Introduction}

In systems  composed of many elements, rich and complex behavior can emerge from simple interactions.  Indeed, for many systems studied by physicists and chemists, we can understand almost everything by thinking just about interactions between pairs of elements.  Sometimes this is an essentially exact statement:  (almost) all the complexity of chemical bonding and reactivity has its origins in the Coulomb interactions among electrons and protons, and the total energy associated with this interaction is a sum over pairs of particles.  Alternatively, the pairwise description might not be microscopically exact, but could still be a very good approximation, as in the description of many different kinds of magnets (ferromagnets, antiferromagnets, spin glasses) using only interactions between pairs of spins.   In fact, pairwise interactions can generate essentially unlimited complexity, since finding the ground state of a model magnet with arbitrary pairwise interactions among the spins is an NP--complete problem \cite{barahona_82}.

Could models based on pairwise interactions be powerful enough to capture the behavior of biological systems?   One the one hand we know that pairwise interactions can provide considerable explanatory power, but on the other hand restricting our description to pairwise interactions is an enormous simplification.  The tension between the physicists' desire for simplification and the biologists' appreciation of complexity is the subject of well known jokes \cite{horse}.
Jokes aside, biological systems often have many elements with no obvious geometrical arguments for simplification, and certainly there are many cases where the elements (bases along DNA, amino acids along a single protein chain, proteins, cells,  ...) have many opportunities to interact in combinatorial fashion as they generate biological function.   Two recent streams of work have led to a re--examination of these issues.

Consider, for example, a protein with $N$ amino acids.  The structure and function of the protein is determined by its sequence, but these often are robust to small changes in sequence.   More profoundly, a large family of proteins may share essential structural and functional features while having widely divergent sequences.  We would like to have a description of this ensemble of sequences, ideally being able to write down the probability distribution out of which functional sequences are drawn.  Recent work argues that an effective description of this sequence ensemble for a protein family can be obtained by taking account of pairwise correlations among amino acids at different sites, but ignoring all higher order effects \cite{socolich+al_05,russ+al_05}.  Although this work does not provide an explicit construction of the underlying distribution, it does provide a Monte Carlo procedure for generating new sequences that are consistent with the pairwise correlations in known families, and sequences generated in this way have been proven experimentally to be fully functional.

What seems like a very different problem is provided by networks of neurons.  If we look in a small window of time, then each neuron either does or does not generate an action potential (spike).  For two cells chosen at random out of a densely connected collection of neurons, one typically finds that pairwise correlations are weak but statistically significant.  Recently it has been suggested that the full pattern of correlations among all the neurons in such a network can be described by the maximum entropy model \cite{jaynes_57,schneidman+al_03} that is consistent with the observed pairwise correlations, and this approach has been shown to provide successful predictions for the combinatorial patterns of activity in the vertebrate retina as it responds to natural movies \cite{schneidman+al_06,tkacik+al_06}.  These maximum entropy models in fact are Ising models with pairwise interactions, which have long been discussed as schematic models for neural networks \cite{hopfield_82,amit_89}; here the Ising model emerges directly as the least structured model consistent with the experimentally measured patterns of coincident spiking among pairs of cells.

These two different examples represent two very different implementations of the idea that complex structures can emerge from pairwise interactions.  It is important to note that in neither case is there any hope that the pairwise description is microscopically exact.  Thus the apparent success of the pairwise approximation provides a first hint that these systems, despite their complexity, are simpler than they might have been.  This idea has been reinforced by yet more recent application of the pairwise, maximum entropy models to other neural systems \cite{shlens+al_06,cosyne07,other_neurons_2}, to a kinase cascade network \cite{tkacik_07}, and to the patterns of gene expression in yeast \cite{psu_group}.

Biochemical, genetic and neural networks all have different structures, and the `networks'   of amino acids in a protein are yet more different.  The mathematical approaches taken in Refs \cite{lockless+ranganathan_99,socolich+al_05,russ+al_05} and \cite{schneidman+al_06,tkacik+al_06}  also are very different, although the theme of pairwise correlations runs through both analyses.  Here we show that the mathematical differences are only differences of emphasis:  In the relevant limit, the Monte Carlo methods of Refs \cite{lockless+ranganathan_99,socolich+al_05,russ+al_05} generate samples drawn out of the maximum entropy probability distribution that would be constructed using the methods of Refs \cite{schneidman+al_06,tkacik+al_06}.  Thus we have a unified framework for exploring the potential of pairwise interactions to tame the complexity of these and other biological systems.  Within this framework we identify some open problems, and comment on the implicit analogies between neural networks and proteins.

\section{Setting up the problem}

Let the system we are studying be described by variables $\sigma_{\rm i}$ that are associated with each element or site ${\rm i}$, where ${\rm i} = 1, 2, \cdots, N$.  For a network of neurons, $\rm i$ can label the individual cells, and $\sigma_{\rm i}$ marks whether that cell generated an action potential in a small window of time; taken together, the set $\sigma_1, \sigma_2 , \cdots , \sigma_N \equiv \{\sigma_{\rm i}\}$ defines the pattern of spiking and silence across the whole network.  For a protein, ${\rm i}$ is an index into the amino acid sequence, and $\sigma_{\rm i}$ indicates which amino acid is found at site ${\rm i}$ along this sequence; the full sequence is defined by $\{\sigma_{\rm i}\}$ \cite{AAnote}.

We will phrase our discussion in terms of  ``operators'' $\hat O_\mu  (\{\sigma_{\rm i}\})$ on the set of variables $\{\sigma_{\rm i}\}$. The simplest operators are the variables $\sigma_{\rm i}$ themselves. For neurons, knowing the expectation values $\langle \sigma_{\rm i}\rangle$ means that we know the probability of cell $\rm i$ generating an action potential in a small window of time---the ``firing rate'' of the cell.  For a protein, knowing $\langle\sigma_{\rm i}\rangle$ means that we know the probability of finding each of the twenty possible amino acids at position $\rm i$ in the sequence.  The next most complicated operators involve pairs of variables; knowing the expectation values of these operators corresponds to knowing the probability of two cells generating synchronous action potentials, or the joint probabilities of finding two amino acids at particular locations along the protein sequences.  The central claim of the recent work reviewed above is that knowledge of  the expectation values $\langle \hat O_\mu\rangle$ for these ``one body'' and ``two body'' operators is sufficient to describe, at least to a good approximation, the functional biological system.

One approach to using knowledge of the expectation values $\langle \hat O_\mu\rangle$ is to construct a  probability distribution for the states of the system,
$P(\{\sigma_{\rm i}\})$ that is consistent with this knowledge but otherwise is as random or unstructured as possible; this is the maximum entropy distribution \cite{jaynes_57}. The form of this distribution is given by
\begin{equation}
P(\{\sigma_{\rm i}\}) = {1\over{Z(\{g_\mu\})}}\exp\left[ -\sum_{\mu=1}^K g_\mu \hat O_\mu  (\{\sigma_{\rm i}\})\right],
\label{Pmaxent}
\end{equation}
where the partition function $Z$ serves to normalize the distribution;
\begin{equation}
Z(\{g_\mu\}) = \sum_{\{\sigma_{\rm i}\}} \exp\left[ -\sum_{\mu=1}^K g_\mu \hat O_\mu  (\{\sigma_{\rm i}\})\right] .
\label{Z}
\end{equation}
By analogy with statistical mechanics it is useful to define the free energy
\begin{equation}
F(\{g_\mu\}) = -\ln Z (\{g_\mu\}).
\end{equation}
Note that there is no real temperature in this problem, or equivalently we have chosen units in which $k_B T = 1$.
The coupling constants $g_\mu$ have to be chosen so that the expectation values in this distribution are equal to their known values, which is equivalent to solving the equations
\begin{equation}
{{\partial F}\over{\partial g_\mu}} = \langle \hat O_\mu \rangle .
\label{fix_avgs}
\end{equation}
This maximum entropy approach is the one used in recent work on the analysis of correlations in networks of neurons \cite{schneidman+al_06,tkacik+al_06}.

As an alternative to the maximum entropy construction, imagine that we create $M$ copies of the system, with variables $\{\sigma_{\rm i}^{(1)}\}, \{\sigma_{\rm i}^{(2)}\}, \cdots , \{\sigma_{\rm i}^{(M)}\}$.  We can evaluate the empirical expectation values of the operators $\hat O_\mu$ across these $M$ copies,
\begin{equation}
\langle \hat O_\mu \rangle_{\rm emp} = {1\over M}\sum_{n=1}^M \hat O_\mu (\{\sigma_{\rm i}^{(n)}\}) .
\end{equation}
Given each of these empirical expectation values, we can try to form a measure of how close these $M$ systems are to being representative of the true expectation values.  Consider
\begin{equation}
\chi^2 = {1\over 2} \sum_{\mu=1}^K W_\mu [\langle \hat O_\mu \rangle_{\rm emp} - \langle \hat O_\mu \rangle]^2 ,
\label{chisq}
\end{equation}
where the $W_\mu$ are weights, expressing how seriously we take deviations in each of the individual operators.  Notice that $\chi^2$ is  a function of all $M\times N$ variables
$\{\sigma_{\rm i}^{(1)},  \sigma_{\rm i}^{(2)} , \cdots ,  \sigma_{\rm i}^{(M)}\} $.  We can try to force these variables to be representative of the expectation values $\langle \hat O_\mu \rangle$ by drawing from the probability distribution
\begin{equation}
P(\{\sigma_{\rm i}^{(1)},  \sigma_{\rm i}^{(2)} , \cdots ,  \sigma_{\rm i}^{(M)}\} )
= {1\over{{\cal Z}_M}} \exp\left[ - {1\over T} \chi^2 \right] ,
\label{Pannealing}
\end{equation}
and then letting $T\rightarrow 0$; again, ${\cal Z}_M$ is a partition function that serves to normalize the distribution. This annealing procedure is the one used in recent work on the synthesis of artificial proteins \cite{lockless+ranganathan_99,socolich+al_05,russ+al_05}.

\section{Mathematical equivalence of the two methods}

Our goal is to show that the probability distribution for $M$ copies, Eq (\ref{Pannealing}), really is equivalent to the maximum entropy distribution, Eq (\ref{Pmaxent}), in the limit $T\rightarrow 0$ and $M\rightarrow\infty$.  Interestingly, we will see that in this limit the precise values of the weights $W_\mu$ which enter the definition of $\chi^2$ are irrelevant.

To understand the predictions of the annealing method, we need to calculate the partition function ${\cal Z}_M$,
\begin{equation}
{\cal Z}_M = \sum_{\{\sigma_{\rm i}^{(n)}\}}
\exp\left[ -{1\over T} \chi^2 \right] .
\end{equation}
It will be useful near the end of our discussion to define another free energy $G = -\ln {\cal Z}_M$.  Note that this free energy depends on the expectation values $\{\langle \hat O_\mu\rangle\}$, whereas the free energy $F$ depends on the coupling constant $\{g_\mu\}$.

To make progress we use the standard approach of introducing auxiliary fields $\phi_\mu$ to unpack the quadratic terms in the exponential:
\begin{widetext}
\begin{eqnarray}
\exp\left[ -{1\over T} \chi^2 \right] &=&
\exp\left[ - {1\over {2T}} \sum_{\mu=1}^K W_\mu [\langle \hat O_\mu \rangle_{\rm emp} - \langle \hat O_\mu \rangle]^2 \right]\\
&=&
\left[\prod_{\mu=1}^K \left(
{T\over{2\pi W_\mu}}\right)^{1/2}\right]
\int d\phi_1 \int d\phi_2  \cdots\int d\phi_ K
\exp\left[
-\sum_{\mu=1}^K {{T\phi_\mu^2}\over{2W_\mu}}
+ i \sum_{\mu=1}^K \phi_\mu \langle \hat O_\mu \rangle_{\rm emp}
- i \sum_{\mu=1}^K \phi_\mu \langle \hat O_\mu \rangle
\right]
\nonumber\\
&&\\
&=&
\left[\prod_{\mu=1}^K \left(
{T\over{2\pi W_\mu}}\right)^{1/2}\right]
\int d^K\phi
\exp\left[
-\sum_{\mu=1}^K {{T\phi_\mu^2}\over{2W_\mu}}
- i \sum_{\mu=1}^K \phi_\mu \langle \hat O_\mu \rangle
\right]
\exp\left[ + {i\over M} \sum_{n=1}^M\sum_{\mu=1}^K \phi_\mu  \hat O_\mu (\{\sigma_{\rm i}^{(n)}\})
\right] .
\nonumber\\
&&
\end{eqnarray}
Note that only the last term under the integral depends on the variables $\{\sigma_{\rm i}^{(n)}\}$.
Thus when we compute the partition function we can take the sum over these variables under the integral and write
\begin{eqnarray}
{\cal Z}_M &=& \sum_{\{\sigma_{\rm i}^{(n)}\}}
\exp\left[ -{1\over T} \chi^2 \right] \nonumber\\
&=&
\left[\prod_{\mu=1}^K \left(
{T\over{2\pi W_\mu}}\right)^{1/2}\right]
\int d^K\phi
\exp\left[
-\sum_{\mu=1}^K {{T\phi_\mu^2}\over{2W_\mu}}
- i \sum_{\mu=1}^K \phi_\mu \langle \hat O_\mu \rangle
\right]
\sum_{\{\sigma_{\rm i}^{(n)}\}}
\exp\left[ + {i\over M} \sum_{n=1}^M\sum_{\mu=1}^K \phi_\mu  \hat O_\mu (\{\sigma_{\rm i}^{(n)}\})
\right] .
\nonumber\\
&&
\end{eqnarray}
The crucial piece of this equation is the sum over all possible states of the $M$ copies of the system, but since the $M$ copies are independent given $\{\phi_\mu\}$, we can simplify:
\begin{equation}
\sum_{\{\sigma_{\rm i}^{(n)}\}}
\exp\left[ + {i\over M} \sum_{n=1}^M\sum_{\mu=1}^K \phi_\mu  \hat O_\mu (\{\sigma_{\rm i}^{(n)}\})
\right]
=
\left(\sum_{\{\sigma_{\rm i}\}}
\exp\left[ + {i\over M} \sum_{\mu=1}^K \phi_\mu  \hat O_\mu (\{\sigma_{\rm i}\})
\right]\right)^M .
\end{equation}
Now we notice that the sum over states in this expression is just the partition function of the maximum entropy distribution, Eq (\ref{Z}), if we identify $-i\phi_\mu/M = g_\mu$.
In this way we can relate the partition function for the annealing problem to an integral over the partition function of the maximum entropy problem,
\begin{equation}
{\cal Z}_M =
\left[\prod_{\mu=1}^K \left(
{T\over{2\pi W_\mu}}\right)^{1/2}\right]
\int d^K\phi
\exp\left[
-\sum_{\mu=1}^K {{T\phi_\mu^2}\over{2W_\mu}}
- i \sum_{\mu=1}^K \phi_\mu \langle \hat O_\mu \rangle
\right]
\left[ Z(\{ g_\mu = -i\phi_\mu/M\}) \right]^M .
\label{int3}
\end{equation}

The form of Eq (\ref{int3}) suggests that we change variables from $\phi_\mu$ to the coupling constants $g_\mu$, and, recalling that  $Z(\{g_\mu\}) = \exp[-F(\{g_\mu\})]$, we obtain
\begin{eqnarray}
{\cal Z}_M &=&
\left[\prod_{\mu=1}^K \left(
{T\over{2\pi W_\mu}}\right)^{1/2}\right]
(iM)^K
\int d^K g
\exp\left[
+\sum_{\mu=1}^K {{M^2T g_\mu^2}\over{2W_\mu}}
+M  \sum_{\mu=1}^K g_\mu \langle \hat O_\mu \rangle
-M F(\{g_\mu\})
\right]
\\
&=&
\left[\prod_{\mu=1}^K \left(
{{\tilde T}\over{2\pi MW_\mu}}\right)^{1/2}\right]
(iM)^K
\int d^K g
\exp\left[ -M {\cal F}(\{g_\mu\}; \{W_\mu\}; {\tilde T})\right] ,
\label{int5}
\end{eqnarray}
\end{widetext}
where the effective free energy
\begin{equation}
{\cal F}  =
F(\{g_\mu\}) - \sum_{\mu=1}^K g_\mu \langle \hat O_\mu \rangle
- \sum_{\mu=1}^K {{{\tilde T} g_\mu^2}\over{2W_\mu}} ,
\end{equation}
and ${\tilde T} = MT$.
The partition function of the annealing problem involves an integral over coupling constants, and the integrand is the exponential of $M$ times a free energy that is of order unity as the number of copies $M$ becomes large.  Thus, as $M\rightarrow\infty$, the integral should be dominated by the saddle point where $\partial {\cal F}/\partial g_\mu = 0$ for all $\mu$, or equivalently by values of the coupling constants such that
\begin{equation}
{{\partial F}\over{\partial g_\mu}} = \langle\hat O_\mu \rangle + {{\tilde T}\over{W_\mu}}g_\mu .
\end{equation}
If we consider the limit ${\tilde T}\rightarrow 0$, then this equation is exactly the same as Eq (\ref{fix_avgs}) which sets the values of the coupling constants in the maximum entropy approach.  Thus we can write the saddle point approximation to ${\cal Z}_M$ as
\begin{equation}
{\cal Z}_M \approx A \exp\left[ -M F(\{g_\mu^*\} ) +M \sum_{\mu=1}^K g_\mu^* \langle O_\mu\rangle \right] ,
\end{equation}
where $\{g_\mu^*\}$ are the coupling constants which provide the solution to Eq (\ref{fix_avgs}), and $A$ is a constant that does not depend on $M$.
Finally, we can extract the large $M$ behavior of the free energy $G = -\ln {\cal Z}_M$,
\begin{equation}
\lim_{M\rightarrow\infty} {1\over M} G(\{ \langle \hat O_\mu\rangle\})
=  F(\{g_\mu^*\} ) - \sum_{\mu=1}^K g_\mu^* \langle O_\mu\rangle .
\label{ans}
\end{equation}

To understand the result in Eq (\ref{ans}), we should step back to our original formulation of the two methods.  The free energy $G$ in the annealing method refers to $M$ copies of the system, so it is not surprising that it is proportional to $M$; once we take out this factor we {\em almost} get the free energy $F$ from the maximum entropy method.  The difference is that in the maximum entropy formulation the behavior of the system is a function of the coupling constants $g_\mu$, while in the annealing method the free energy is explicitly a function of the expectation values $\langle\hat O_\mu\rangle$.  This is exactly the situation for the Helmholtz and Gibbs free energies in thermodynamics---the Helmholtz free energy is a function of the volume, and the Gibbs free energy is a function of the pressure.  More generally, whenever we have conjugate variables (pressure and volume, particle number and chemical potential, ... ), we  use the Legendre transformation to connect descriptions based on one or the other member of the conjugate pair \cite{callen_60}.

For the example of pressure and volume, we have
$G(T,p) = F + pV$ and hence the familiar differential relations
\begin{eqnarray}
{{\partial F(T,V)}\over{\partial V} } &=& -p\\
{{\partial G(T,p)}\over{\partial p} } &=& V.
\end{eqnarray}
Crucially, $F$ and $G$ are descriptions of the same physical system.  More strongly, for large systems (here, $M\rightarrow \infty$) we know that constant pressure and constant volume ensembles are equivalent.
For our problem, the analogous equations are
\begin{eqnarray}
{{\partial F(\{g_\mu\})}\over{\partial g_\mu} } &=& \langle \hat O_\mu\rangle\\
{1\over M}{{\partial G(\{\langle \hat O_\mu\rangle\})}\over{\partial \langle \hat O_\mu\rangle} } &=& -g_\mu.
\end{eqnarray}
The conclusion is that the annealing method, in the $M\rightarrow\infty$, ${\tilde T}\rightarrow 0$ limit, describes $M$ independent copies of the maximum entropy model.

\section{Should we be surprised?}

The derivation above is a bit circuitous, although it does make the connections between the two approaches explicit.  We can make a somewhat shorter, if less constructive, argument.

The probability distribution used in the annealing calculations, Eq (\ref{Pannealing}), is a Boltzmann distribution and hence a maximum entropy distribution.  More precisely, it is the maximum entropy distribution consistent with some average value of $\chi^2$ between the observed and simulated expectation values; as usual $\langle\chi^2\rangle$ is set by the value of $T$.  When we let $T\rightarrow 0$, the expectation value of $\chi^2$ must approach its minimum value, which is zero, unless there is something very odd about the structure of the phase space.  Thus in the $T\rightarrow 0$ limit, the annealing method generates samples from a maximum entropy distribution in which the expectation values computed from the $M$ simulated copies of the system are exactly equal to the observed values.  Finally, if we let $M\rightarrow\infty$, then what we are simulating is an ensemble of samples in which the selected expectation values exactly match their experimental values, but otherwise the distribution of samples has maximum entropy.    That is, we have drawn samples out of the maximum entropy distribution consistent with the observed expectation values.

The subtlety of this argument, which we hope justifies the longer calculation above, concerns the combination of the limits $M\rightarrow\infty$ and $T\rightarrow 0$ and the role of the weights $W_\mu$ in defining $\chi^2$.  The careful calculation shows that we actually need $\tilde T = MT \rightarrow 0$, which is stronger than one might have thought, and that in this limit the weights are irrelevant.

\section{Finite sample size}

Our discussion thus far has assumed that the expectation values $\langle \hat O_\mu (\{\sigma_{\rm i}\}) \rangle$ are known.    In fact we never know these expectation value exactly, since our inferences are based on a finite data set.  For networks of neurons, if we define our variables $\sigma_{\rm i}$ as the presence or absence of a spike from cell $\rm i$ in a small window $\Delta \tau = 10-20\,{\rm ms}$, then an experiment of $\sim 1\,{\rm hr}$ provides more than $10^5$ samples of the state $\{\sigma_{\rm i}\}$, although of course not all these samples are independent \cite{schneidman+al_06,tkacik+al_06}.
With these relatively large sample sizes, it is plausible that we can approximate expectation values, e.g. of the pairwise correlations among neurons $C_{\rm ij} = \langle \sigma_{\rm i}\sigma_{\rm j}\rangle - \langle \sigma_{\rm i}\rangle\langle\sigma_{\rm j}\rangle$, by the corresponding time averages over the experiment, although of course with very large networks the number of pairs can become comparable to the number of samples and we should be careful.  For proteins, in contrast, we have only a few families with $\sim 10^3$ known sequences, and in many cases one must work from fewer than $100$ examples \cite{lockless+ranganathan_99,socolich+al_05,russ+al_05}.  Correspondingly the question of how to treat the issues of statistical significance in the estimation of of $\langle \hat O_\mu\rangle$ has been much more at the center of the discussion of the protein data.

Taken at face value, the construction of $\chi^2$ in Eq (\ref{chisq}) gives our estimates of different operators different weights $W_\mu$.  One plausible choice for these weights (by analogy with usual construction of $\chi^2$) is to set $W_\mu$ equal to the inverse of the variance in our estimates of $\langle \hat O_\mu\rangle$.  This might suggest that the distribution in Eq (\ref{Pannealing}) really does represent the probability of finding the empirical averages $\langle \hat O_\mu \rangle_{\rm emp}$, with $T$ inversely proportional to the number of independent samples $N_{\rm samp}$  in our original database.  But from the maximum entropy distribution we can compute the expected variance in our estimates of the expectation values, and this is
\begin{equation}
\overline {\left[ \delta\langle \hat O_\mu\rangle_{\rm est} \right]^2}
= {1\over{N_{\rm samp}}} {{\partial^2 F(\{g_\mu\})}\over{\partial g_\mu^2}} .
\end{equation}
Unfortunately, the same arguments can be used to show that errors in the estimates of the different operators in general are not independent, since
\begin{equation}
\overline {\left[ \delta\langle \hat O_\mu\rangle_{\rm est} \delta\langle \hat O_\nu\rangle_{\rm est} \right]}
= {1\over{N_{\rm samp}}} {{\partial^2 F(\{g_\mu\})}\over{\partial g_\mu\partial g_\nu}} .
\end{equation}
Thus, while the construction of $\chi^2$ provides a convenient heuristic, it can't really represent the likelihood of measuring empirical expectation values given the true expectation values.  Conveniently, in the limit $M\rightarrow \infty, T\rightarrow 0$, all these concerns disappear and even the precise values of the $W_\mu$ are irrelevant.

But if the construction of $\chi^2$ doesn't capture the statistical significance of our estimated expectation values correctly, what should we do instead?    Once we know that we are looking for the maximum entropy distribution consistent with a certain set of expectation values, we know that the {\em form} of the distribution is given by Eq (\ref{Pmaxent}), and our task is to infer the parameters $\{g_\mu\}$.  If we imagine that we have $N_{\rm samp}$ independent samples, with states $\{\sigma_\mu^{(1)} , \sigma_\mu^{(2)} , \cdots , \sigma_\mu^{(N_{\rm samp})}\}$, then the probability of observing these data is given by
\begin{widetext}
\begin{equation}
P(\{\sigma_\mu^{(1)} , \sigma_\mu^{(2)} , \cdots , \sigma_\mu^{(N_{\rm samp})}\})
= \left[ {1\over{Z(\{g_\mu\})}}\right]^{N_{\rm samp}}
\exp\left[ -\sum_{\mu=1}^K g_\mu \sum_{n=1}^{N_{\rm samp}} \hat O_\mu  (\{\sigma_{\rm i}^{(n)}\})\right] .
\end{equation}
Now if we try to find the parameters $\{g_\mu\}$ by maximizing this probability (maximum likelihood estimation),  we find
\begin{eqnarray}
0 =
{{\partial \ln P(\{\sigma_\mu^{(1)} , \sigma_\mu^{(2)} , \cdots , \sigma_\mu^{(N_{\rm samp})}\})}\over{\partial g_\mu}}
&=& -N_{\rm samp} {{\partial \ln Z(\{g_\mu\})}\over{\partial g_\mu}}
-  \sum_{n=1}^{N_{\rm samp}} \hat O_\mu  (\{\sigma_{\rm i}^{(n)}\})\\
&=&  N_{\rm samp} {{\partial F(\{g_\mu\})}\over{\partial g_\mu}}
-  \sum_{n=1}^{N_{\rm samp}} \hat O_\mu  (\{\sigma_{\rm i}^{(n)}\})\\
{1\over{N_{\rm samp}}} \sum_{n=1}^{N_{\rm samp}} \hat O_\mu  (\{\sigma_{\rm i}^{(n)}\})
&=& {{\partial F(\{g_\mu\})}\over{\partial g_\mu}} .
\end{eqnarray}
\end{widetext}
We see that this is the same as Eq (\ref{fix_avgs}) if we identify the ``known'' expectation values with the averages over our finite set of samples.  Thus, the maximum entropy construction can be viewed as maximum likelihood inference within a specified class of models, and in this framework many questions about the consequences of finite sample size can be seen as part of the more general problem of learning probabilistic models from data \cite{Hinton,note_samps}.

In  a Bayesian framework, we can construct a probability distribution for the parameters $\{g_\mu\}$ given the data $\{\sigma_\mu^{(n)}\}$.  Exploring this distribution, e.g. by Monte Carlo in parameter space \cite{kinney+al_07}, allows us to assign rigorous errors to our parameter estimates.  More importantly, within a Bayesian framework we can integrate over parameters to determine the likelihood that a given {\em class} of models generates the data  \cite{vijay,mackay_03}; this allows us to compare models in which all interactions are possible with those in which some interactions have been set exactly to zero.
In the context of protein structure, if most interactions can be set to zero then we can envision the crucial amino acids as forming limited networks rather than being distributed throughout the protein \cite{lockless+ranganathan_99,suel+al_03}.  In biochemical, genetic and neural networks, setting many interactions to zero would mean describing these networks by a sparsely interconnected graph.    It should be emphasized that the absence of statistically significant correlations between variables $\sigma_{\rm i}$ and $\sigma_{\rm j}$ does not mean that there is no interaction between these variables.  Although this program has not been carried out in any of the systems studied thus far, the Bayesian approach to model selection should provide a rigorous method for deciding on the number of significant interactions \cite{note_bayes}.

\section{Discussion}

As we collect more and more quantitative data on biological systems, it becomes increasingly urgent to find a theoretical framework within which these data can be understood. In many cases, one approach to this problem involves writing down a probability distribution that describes some network of interacting variables:
\begin{itemize}
\item In the context of protein evolution, we would like to write down the probability that any particular amino acid sequence will arise as a functional protein in a certain family.
\item In the context of neural networks, we would like to write down the probability that the network will exhibit any particular pattern of spiking and silence.
\item In the context of genetic networks, we would like to write down the probability that a cell will exhibit any particular combination of gene expression levels, either under a fixed set of conditions or averages over its lifetime.
\end{itemize}

One might object that such probabilistic descriptions are not consistent with the search for a more `rule based' understanding; surely, for example, some sequences form functional proteins and some do not.  Without entering into a philosophical discussion about whether degrees of functionality can be mapped into probabilities, we note that as the systems we are studying become large, our intuition from statistical mechanics is that the difference between a  description in which states are assigned probabilities (the canonical ensemble) and one in which some states are allowed and the rest are not (the microcanonical ensemble) becomes vanishingly small.    Thus, even if we start with a probabilistic description, once we think about proteins with many amino acids or networks constructed from many neurons or genes, we expect that our descriptions will converge to one in which there is a sharp distinction between allowed and disallowed combinations of the underlying variables.

The fact that we are interested in networks with many variables makes the task of constructing a probabilistic description quite daunting.  With $N$ elements, there are $\sim \exp(\alpha N)$ possible combinations of the underlying variables, where $\alpha$ typically is of order unity.  Obviously no experiment will exhaustively explore this configuration space, just as no experiment exhaustively explores the configuration space of the spins in even a small magnetic grain.  For the magnetic grain, however, there is a limited set of natural macroscopic variables to measure---such as the magnetization, specific heat, and susceptibility---that seem to provide a good characterization of the states available to the system.  Can we hope for some analogous simplification in the context of biological networks?

Quantities such as the magnetization and susceptibility can be written as averages over the Boltzmann distribution.  More precisely, the magnetization describes the average behavior of individual spins, and the susceptibility describes the average behavior of pairs of spins (two--point correlations).    The analogous idea, then, is that our description of biological systems might be simplified by focusing on correlations between pairs of elements, rather than allowing for arbitrarily complex combinatorial interactions among many elements.  This is precisely the strategy adopted in recent work on protein sequences \cite{lockless+ranganathan_99,socolich+al_05,russ+al_05} and on networks of real neurons \cite{schneidman+al_06,tkacik+al_06}.  In each case, although the focus on pairwise interactions was implemented differently, the approach was surprisingly successful, accounting for data far beyond the measured correlations.  What we have shown here is that the approaches which arose in different contexts really are the same, so we have a single strategy for simplifying our description of biological systems that seems to be working at very different levels of organization, from single molecules \cite{lockless+ranganathan_99,socolich+al_05,russ+al_05} to biochemical and genetic networks \cite{tkacik_07,psu_group} up to small chunks of the brain \cite{schneidman+al_06,tkacik+al_06,shlens+al_06,cosyne07,other_neurons_2}.  While much remains to be done to test the limits of this approach, this is a very exciting development.

The annealing approach which was used in the analysis of protein sequences allows us to generate directly new samples from the simplified probabilistic model, without actually constructing the model explicitly.  For proteins, these samples are new molecules that can be synthesized, and this has been the path to experimental test of the focus on pairwise correlations.  One could imagine using the same method for neurons to generate new patterns of spiking and silence in the network, and one could then check that the higher--order correlations in these patterns (beyond the pairwise correlations which are matched exactly) agree with experiment.

The explicit construction of the maximum entropy model, as has been done in the analysis of neurons, allows us to explore the ``thermodynamics'' of the system.  Questions one can address include whether the space of configurations breaks into multiple basins, and whether the parameters of the biological system are in any sense special, e.g. because they are near a critical point.  Perhaps the most direct question we can address given a maximum entropy model for the distribution of states concerns the entropy itself.  In the context of neurons, this entropy sets the capacity for the system to convey information, whether about the external sensory inputs or about some internal variables such as memories and intentions.  In the context of proteins, this entropy measures the number of possible sequences that are consistent with membership in the particular family of functional proteins that we are studying.  An explicit model for the distribution of sequences within a family  is also the proper tool for assessing the likelihood that a previously uncharacterized protein belongs to this family, a practical problem of central importance in analyzing the growing body of sequence data.

\acknowledgments{We thank E Schneidman, GJ Stephens, and G Tka\v{c}ik for helpful discussions.  WB is grateful to C \& R Miller for providing an excuse to visit Texas.  Work in Princeton was supported in part by NIH Grant P50 GM071508
and by NSF Grants IIS--0613435 and PHY--0650617.
Work in Dallas was supported in part by the HHMI.}

redpajama_set_name: RedPajamaArXiv


This data was created from original field work or complied from existing geologic map data. ESRI Personal and File Geodatabase formats. Digital geologic map and compilation data intended for non-site-specific investigations. Geologic map database of north Idaho. Feature data set includes feature classes: attitudes (point), contacts, map units, dikes, faults, fold axes, linears (point), loess and more. This is a work in progress. Most mapping at 1:24,000. Dataset includes an ArcMap mxd file (relative paths). Data compiled using IGS Geologic Map Data Model. Includes the following 30 x 60 minute tiles of geologic map data: St. Maries, Coeur d' Alene, Potlatch, Orofino, Elk City, Kooskia, Nez Perce Pass, Missoula West, and Hamilton. Available only as a download.


text:
from google.appengine.api import users
from google.appengine.api.logservice import logservice
from webapp2_extras import sessions

# Libraries
import webapp2

#
# Login with your Google Account
# @author Johann du Toit
#
class LoginHandler(webapp2.RequestHandler):
	def get(self):

		# Normal Google User Account
		self.redirect(users.create_login_url('/'))

#
# Logout from your Google Account
# @author Johann du Toit
#
class LogoutHandler(webapp2.RequestHandler):
	def get(self):

		# Send to logout
		self.redirect(users.create_logout_url('/'))

redpajama_set_name: RedPajamaGithub


« Sermon: CCOG Q&A: Cremation, Garner Ted Armstrong, Abraham: Jew or Hebrew?
While technology could benefit humans a great deal, Hawking wrote, researchers need to focus on making sure we avoid the risks that come with it. In the near future, artificial intelligence could increase economic equality and prosperity through job automation. But one day, the same systems could take over our financial markets, manipulate our leaders, and control our weapons, Hawking said.
While China is actually working on aspects of that, biblical prophecy indicates that China will not emerge as the 'victor' in AI as Google CEO Eric Schmidt (and others) think. Now, perhaps I should add that Eric Schmidt is correct that major AI developments could be in place by 2030 (for information on years, check out the articles Does God Have a 6,000 Year Plan? What Year Does the 6,000 Years End? and When Will the Great Tribulation Begin? 2018, 2019, or 2020?).
Matthew Maavek did correctly opine that AI is likely to morph into an Orwellian control tool.
While Elan Musk fears the rise of an Immortal dictator, the Bible shows that a mortal, European, dictator will rise up (Revelation 17:12-13).
Notice they had one language, but God changed that. One of the reasons He said He did that was because humans would be able to do things that they purposed. The language barrier has been a factor in slowing down aspects of intellectual progress, as well as intellectual foolishness. But now with computers, software, and many of the world's educated understanding the English language, we should expect faster development.
With machine learning (a process that creates AI), researchers are seeking alternative data sources, such as content structure, keyword use, headline choice, and engagement to rank the validity of news articles. Current results signal more training data is still needed, but as such data increases, so will the accuracy.
Bible prophecy shows that a militaristic European dictator will arise, will apparently use something like AI.
But this dictator will NOT be immortal, nor will he be Chinese.
This entry was posted on Saturday, October 20th, 2018 at 7:45 am	and is filed under Prophecy.
BibleNewsProphecy: Crowdsourcing and Artificial Intelligence to solve "wicked problems"?


text:
Police: officer shoots dog after being attacked
A St. George Police Department was bit by a K-9 while responding to a domestic dispute call. The dog was shot and ran away.
Police: officer shoots dog after being attacked A St. George Police Department was bit by a K-9 while responding to a domestic dispute call. The dog was shot and ran away. Check out this story on thespectrum.com: https://www.thespectrum.com/story/news/2018/10/23/police-dog-loose-st-george-after-biting-officer-being-shot/1739403002/
Emily Havens, St. George Spectrum & Daily News Published 11:23 a.m. MT Oct. 23, 2018 | Updated 4:53 p.m. MT Oct. 23, 2018
A potentially dangerous, injured dog is on the loose after it bit an officer and took several shots early Tuesday morning. Residents are instructed to keep their distance and call dispatch if they come across the K-9.(Photo: Spectrum & Daily News file photo)Buy Photo
A St. George police officer shot a dog Tuesday after the animal allegedly escaped through a window and attacked him.
The incident occurred on the block of 1100 North and 1100 West around 3 a.m. while St. George Police officers were responding to a family dispute call. According to SGPD officer Tiffany Atkin, officers had responded to the same residence several hours earlier.
Atkin said the individuals who were involved in the dispute owned the dog, possibly a Pit Bull-Labrador mix, and that it was chained up outside when the officers arrived on scene.
"The owners asked if they could move the dog into the house," Atkin said.
The officers told the owners they could put their dog in the house as long as they did so safely, Atkin said. After the dog was inside, it escaped from a rear-facing window and attacked one of the officers on scene.
"There was little time for him to react," Atkin said. "He was backpedaling, trying to get away from the dog."
Atkin said the dog bit the officer in the forearm and latched on, violently shaking as it held its grip.
The officer drew his firearm and fired at the dog, according to police. Atkin said the shots are accounted for, as in none hit any other individuals or buildings, but they're unsure how many shots actually struck the dog.
The dog ceased attacking the officer and ran away, Aktin said, and it has yet to be found.
The officer who was bit is receiving medical treatment, and Atkin said he was released from the hospital and is expected to make a full recovery.
Kevin Graham (Photo: Purgatory Correctional Facility)
St. George resident Kevin Graham was charged with one B-misdemeanor count of simple assault in light of the domestic dispute incident.
Once the dog is located, Atkin said the dog will received medical treatment, and its fate will be determined after an investigation is completed.
"We're saddened for everyone involved," Atkin said. "We would never want this to happen to the officer or the dog, and we feel bad for the family also. It's an unfortunate incident that we wish we could have avoided."
Follow reporter Emily Havens on Twitter, @EmilyJHavens, and find her on Facebook at facebook.com/emilyjhavens. Call her at 435-674-6214 or email her at ehavens@thespectrum.
Plane crash-lands in Hurricane; incident under investigation
Weekend storms bring almost inch of rain to parts of Southern Utah
Read or Share this story: https://www.thespectrum.com/story/news/2018/10/23/police-dog-loose-st-george-after-biting-officer-being-shot/1739403002/
Crimson Cliffs High preps to open for first time
Body recovered in Grand Canyon
BYU updates honor code following criticism
Red Rock Canyon School to close after investigations

redpajama_set_name: RedPajamaCommonCrawl


text:
Manuel Pailos
Manuel Pailos was active/lived in Uruguay. Manuel Pailos is known for constructivist painting, sculpture and ceramics.
Auction Records (299)
Selected works (247)
Charts / Record Price
Manuel Pailós (Galicia, Spain, May 24, 1918-Montevideo, 2004) was a Uruguayan painter, sculptor and ceramist who stood out as one of the main figures of the torresgarciana current in Uruguay, a country that he arrived with his parents with few years of age and who later became a Uruguayan legal citizen.
His training took place in the Círculo de Bellas Artes with Guillermo Laborde and José Cúneo Perinetti, and from 1942 with Joaquín Torres García, in whose workshop he remained until the moment of its closure in 1967.
He directed the Torres García Workshop in its last years of operation, and was part of each of the exhibitions that were organized there.
Pailós' painting responded to the constructivist diagram, endo ... Displaying 750 of 3390 characters.
Subscriber Members, please Sign In for artist biographies and for all services. Others, full text is available on Fridays.
If you are not currently a member, please See Details about membership, which includes biography access, auction records, and many other features available to our day, month, or yearly Subscriber Members!
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About Manuel Pailos
Born: 1918 - Galicia, Spain
Died: 2004 - Montevideo, Uruguay
Known for: constructivist painting, sculpture and ceramics


text:
Q: Difference between random.randint and random.sample I have read the documentation for each and find it a bit hard to comprehend the differences here. I wrote this code using random.sample:
import random

print "Welcome to the guessing game."

number_of_guesses = 1
correct_number = random.sample(range(1,101),1)

while number_of_guesses < 999:

    user_choice = int(input("Guess a number between 1 and 100: "))

    if user_choice == correct_number:
        print "You guessed the number in %s tries." % number_of_guesses

    elif user_choice < correct_number:
        print "Too low, guess again."
        number_of_guesses += 1

    elif user_choice > correct_number:
        print "Too high, guess again."
        number_of_guesses += 1

When i run this code and enter a number i get "Too low, guess again." regardless of what number I enter, yet when i use random.randomint it works correctly.  Can anyone explain why this happens?

A: random.sample(range(1,101),1) will return a singleton list containing an integer, whereas random.randint(1,100) will directly return the integer itself. Note that random.randint is an inclusive bound (i.e. it can return either of the endpoints)
You could also use random.choice(range(1, 101)) to get the integer. In any case, I'd assume that randint is the fastest option.

redpajama_set_name: RedPajamaStackExchange


text:
<resources>
    <string name="app_name">Implicit Intent Demo</string>
    <string name="empty_text_error_message">Text can not be empty!</string>
    <string name="title_share_chooser">Share Text</string>
    <string name="error_msg_activity_not_found">No activity available to support this action!</string>
</resources>


text:
Observe and record the behaviour of land species
ClimateWatch is a national program developed by Earthwatch Australia, Bureau of Meteorology and the University of Melbourne to better understand how climate change is affecting our wildlife. The first continental phenology project in the Southern Hemisphere, ClimateWatch enables every Australian to become a citizen scientist, by collecting and recording data that will help shape the country's scientific response to climate change.
ClimateWatch is based on phenology, the study of periodic plant and animal life cycle events and how these are influenced by seasonal and interannual variations in climate. Terrestial species range from native, like the Sturt's Desert Pea, to introduced, like the Jacaranda Tree.
The behavioural information that you record will be publicly available through the Atlas of Living Australia. This information will then help policy-makers at the state and federal level to make informed decisions about climate change adaptation response and our natural environment.
Download the ClimateWatch app or our field guides to start recording on ClimateWatch species.
Who can get involved?
ClimateWatch is for everyone! You can ClimateWatch on your own or in groups, any time of the year. For secondary school teachers and university groups, we have lesson plans and activities that align with the national science curriculum. Click here for more details.
We also run workplace volunteering days where you can learn about climate change science and its impacts on the environment. You get to spend a day climatewatching, collecting data in the botanical gardens and we work with you to identify changes you can make in your life to reduce your environmental footprint to become a Climate Champion. Contact us to find out more.
Where can you ClimateWatch?
You can ClimateWatch just about anywhere. It is as easy as looking out your window and recording when your local jacaranda tree is flowering or by recording the presence of butterflies when walking the dog.
You can even ClimateWatch at night by listening for the echo of the white-striped free tail bat!
We have set up lots of ClimateWatch trails across the country. Why not grab a picnic and spend the afternoon outside and teach others about climatewatching in your local botanical garden? If you are interested in creating your own trail, contact us.
To start Climatewatching click here.
"Changes in rainfall and temperature across Australia are already triggering changes in the established flowering times, breeding cycles, migrations and distributions of the country's flora and fauna, both native and introduced. Citizen scientists play a very important role as we do not have enough dedicated scientists to monitor different areas."
Dr Lynda Chambers, ClimateWatch Science and Technical Advisor and Senior Researcher at Centre for Australian Weather and Climate Research
About ClimateWatch
Scientist Q and A - Dr Tim Entwisle
Conservation Week and 25 new WA indicator species.
Frog talks to computer!
Confessions of a Nuytsia floribunda spotting addict
Start monitoring pines in Tasmania
Phenology in the north, challenges in the south
Phenology and Citizen Science in the USA
Bees put to test over climate change
ClimateWatch report published
An Interview with ClimateWatch scientists Dr Lynda Chambers and Dr Marie Keatley


text:
Q: sudo apt install libgtk-3-dev : The following packages have unmet dependencies: libpcre2-dev for new flutter 3.0 installation on linux requires libgtk-3-dev
When i try sudo apt install libgtk-3-dev following dependencies error getting.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libpcre2-dev : Depends: libpcre2-8-0 (= 10.39-3build1) but 10.39-3+ubuntu21.10.1+deb.sury.org+2 is to be installed

A: You need downgrade the libpcre2-8-0 to version 10.39-3build1 :
sudo apt-get install libpcre2-8.0=10.39-3build1
And then install libgtk-3-dev:
sudo apt install libgtk-3-dev


WordPress Maintenance in Sacramento – A SNAP!
Here Are 2 Top-Quality Website Hosting Companies In Sacramento In my humble and yet incredibly awesome opinion CABizHost.com and IMarkHosting.com are first-class web host companies in the Sacramento area. These are well suited for small businesses that need to market online and they are also very newbie friendly. CABizHost.com has been providing quality Sacramento Web Hosting since 1987. Yup, since the BBS days. They Have no long-term contracts. Their multi-site facilities include redundant Internet connections, battery powered backup and standby power generation….


Endless Solutions is a network of experienced and licensed real estate, financial, and business professionals dedicated to serving our community by providing high quality, comprehensive endless solutions.
We provide specialized consultation to individuals, families, and businesses. Our holistic planning approach is a combination of information, education, and implementation strategies that direct our clients toward their desired financial goals.
Through our various strategic alliances with well established firms and professionals, we are able to provide our clients with a unique variety of products and services tailored to meet all of their specific real estate, financial, and business needs.


I have never taken my children to watch Sunderland Airshow - despite it being probably the largest free attraction in our region, I have always been a little bit scared of braving the crowds with three very active children and remember huge queues for the park and ride when I was a child so when DFDS Seaways asked if we'd like to blog about our visit of course we jumped at the chance. I loved the idea of a hassle free way to watch the show without any stress.
Saturday 25th July arrived and although it was cloudy it wasn't too chilly as we boarded KING Seaways and left the mouth of the Tyne. We headed straight up to the mermaid bar on level 10 which I think offers the best best views as you set sail. Harry, Heidi and Jack were entertained with balloon modelling and face painting (all included with our ticket) as I enjoyed a drink with my mum who was accompanying us on the trip.
We stopped for lunch in the 7 Seas restaurant where we filled our plates with spaghetti bolagnese, chicken curry with rice and lasagne and salad before some delicious lemon cheesecake. The timing was perfect as they announced it was time for the show to start just as we were leaving the restaurant.
We headed out to deck where there was plenty of space to gain a wonderful view of the spectacular stunts, amazing dips and dives and super fast action with plenty of gasps from the crowd as various aircraft flew right above our heads and in front of us.
As the typhoon flew right above our heads the noise really was piercing but luckily we could quickly dive inside and watch through the window without missing anything.
Two hours was certainly enough for me and my children did start to get a little bored towards the end so I was thankful we could head inside for some entertainment before sailing home. Some people have commented you miss half the show if you watch it from a DFDS day sailing and although I can see their point, 2 hours was more than adequate for us. If you would like to watch the whole of the airshow, a day sailing probably isn't for you. However if like us you would like to see some of the highlights from a fantastic viewpoint in a hassle and stress free manner, then a DFDS Seaways Airshow trip could definitely be for you and is something to consider for 2016.
We headed into the lounge as our ship headed back to North Shields and were entertained by a pretty decent live band and disco as we enjoyed a drink in the bar. There was a real family party atmosphere with lots of people up dancing and singing along together.
Before we knew it we were home and were sad to leave KING Seaways until next time. We couldn't leave without a quick cuddle from our favourite pirate parrot.
We have made a 2 minute video of our trip below featuring our highlights - I'd love to hear what you think. Visit http://www.dfdsseaways.co.uk/ to keep up to date with other DFDS Seaways day sailings.
A three course lunch is included with the price of your ticket however drinks in the restaurant are not and they are very pricey ( 4E for a can of coke, 6.5E for 1 litre of water). Drinks in the bars were not as expensive (£10 for five soft drinks).
There is free entertainment on board before and after the show including face painting, balloon modelling, wildlife spotting and talks, live singers, discos......make the most of it!
I really want to go to the Airshow but the thought of all the crowds does put me off. Seeing it from a boat seems like the perfect alternative to me, such a great idea!
Dont bother you are not at the air show that long and every single bar but one is shut during the whole journey even the shop.
This as we should have been in Tunisia. I'm sad we missed out because I too am not good in the size of crowd that the airshow attracts!
You are there for a short amount of time and everything on the ship is shut for the whole journey. There is a soft play but it is very small. Drinks in the restaurant are very expensive. £4 for a pint of coke. Scandalous. If i were you i would take your own drinks as no one checks once you are on board.
What a great way to see the air show - perfect for little ones. Shame we missed it - coming up to the north east soon to visit my family there.
So many things to keep the children busy! Nice way to watch the air show!!


text:
Demand for London offices remains steady despite Brexit uncertainty
Demand for London offices remains close to the 10-year average Credit: Dominic Lipinski/PA Wire
Rhiannon Curry
Demand for London office space appears not to have been hit by the looming European Union referendum as take-up in the first quarter of the year remained only marginally below the 10-year average, new figures have shown.
According to real estate adviser CBRE, 3.1m sq ft of the capital's office space was snapped up by companies in the first three months of the year – just 100,000 sq ft less than the 10-year average of 3.2m sq ft.
This was despite fears that economic headwinds and the possibility of Britain leaving the EU could dampen demand as companies delayed making decisions about their office needs until after the June 23 vote.
The total figure was helped by a major move by media company Thomson Reuters, which took 315,400 sq ft for a new office in Canary Wharf, lifting overall take-up.
The Shard also bagged two more tenants in the period, with online clothing retailer Matches Fashion and digital marketing agency Jellyfish both due to move in.
The amount of office space currently under offer – moves which have been agreed in principle but not completed – remains unchanged from the previous quarter at 3m sq ft, having been above the 10-year average of 2.8m sq ft since the beginning of 2014.
Thomson Reuters' move within Canary Wharf was the biggest deal of the quarter Credit: Paul Brown/REX/Shutterstock
Emma Crawford, head of central London leasing at CBRE, said the fact that companies were still continuing to choose to base themselves in London "speaks volumes" for the city's attractiveness as a global hub.
"Between a weak outlook for global economic growth and an upcoming vote on EU membership, businesses have had to contend with a heightened level of uncertainty," she said.
She added that CBRE anticipates a more subdued second quarter as the vote draws closer, but if the UK votes to remain in the EU, activity is expected to bounce back in the second half of the year.
If the country votes to leave on June 23, a two-year period of negotiations around the terms of the exit is expected. In this case, businesses who might have considered moving offices could choose to renew their lease in an existing building instead.
In extreme cases, some global companies might move their European headquarters out of London in the event of an exit, although it is more likely that they will grow more strongly elsewhere, rather than leaving the UK altogether, experts have said.
Brexit: The arguments for and against the EU
Addison Lee scrambles to find a buyer as competition from Uber pushes it off course


text:
const mongoose = require('mongoose'),
      Schema = mongoose.Schema;

const bookingSchema = new Schema({
  roomId: { type: Schema.Types.ObjectId },
  date: { type: Date },
  timeslots: [{
    type: String
  }]
});

//add indexing

module.exports = mongoose.model('Booking', bookingSchema);


Share the love this winter with you and yours in Blowing Rock at Appalachian Ski Mtn. during the resort's Valentine's Day Family Weekend bash.
Appalachian Ski Mtn. has a plethora of activities going on including free kids ice skating, a bonfire with s'mores, 2-for-1 deals, cookouts, pig pickin', free family ski portraits, moonlight skating, midnight skiing and snowboarding and more.
ASM has celebrated Valentine's Day weekend bash since its 50th anniversary five years ago, according to ASM General Manager Brad Moretz, who added that it's been quite popular over the years.
The weather will also be wintery, which is significant considering how November and December were so warm and snowless, aside from a couple dustings.
"We'll have winter weather, which is great. Hopefully nobody will be golfing," Moretz joked.
Dragon Go Big or Go Home ATP Event at 7 p.m.
S'Mores Bonfire Party from 7 to 9 p.m.
Free Junior Ice Skating from 9:30 to 11:30 a.m.
Free Family Ski Portrait from 11 a.m. to 3 p.m.
Pig Pickin' and Fixins Cooked, Served at Slopeside 11 a.m. to 3 p.m.


text:
The government has failed to protect the human rights of children
The UK has plummeted from 11th position to 156th in global ranking for meeting its children's rights obligations in the space of just a year. The UK now ranks among the bottom 10 global performers in the arena of improving the human rights of the child, after it achieved the lowest possible score across all six available indicators in the domain of Child Rights Environment (CRE), according to the KidsRights Index 2017.
The Index gathers data from Unicef and the United Nations Committee on the Rights of the Child (UNCRC) to identify global trends in the arena of children's rights protection. It comprises a ranking for all UN member states that have ratified the UN Convention on the Rights of the Child, a total of 165 countries.
The report says that a nation's prosperity does not always guarantee children's rights. Interestingly, economically better performing countries are not necessarily doing a better job when it comes to safeguarding the rights of children.
This year's overall worst performing countries are the United Kingdom, Papua New Guinea, New Zealand, Guinea-Bissau, Equatorial Guinea, Chad, Vanuatu, Sierra Leone, Afghanistan and Central African Republic.
Very serious concerns have been raised about structural discrimination in the UK. Muslim children are facing increased discrimination following recent anti-terrorism measures, and a rise in discrimination against gypsy and refugee children in recent years.
The KidsRights Index is comprised of 5 domains:
1. Right to Life
2. Right to Health
3. Right to Education
4. Right to Protection
5. Enabling Environment for Child Rights
Marc Dullaert, founder and chairman of the KidsRights Foundation, has urged the UK government to treat non-discrimination as a policy priority, and to speed up the process of aligning its child protection laws with the Convention on the Rights of the Child at both the national and devolved levels, as well as in all crown dependencies.
He said: "Discrimination against vulnerable groups of children and youths is severely hampering opportunities for future generations to reach their full potential."
"Following the general election, the new government should demonstrate to the world that it will not allow the retreat from the EU to adversely affect the rights and opportunities of its children."
In light of the findings, Lord Philip Hunt, shadow deputy leader of the House of Lords and shadow health spokesperson, accused the Government of "inactivity" and "inadequate service provision", urging it to do more to protect the rights of the child.
He said: "This report exposes the inactivity of the current UK government and inadequate service provision in this most important area of policy making; rights of the child."
"The UK is the sixth largest economy globally and therefore has the resources at its disposal to ensure that our children are adequately protected and cared for across multiple disciplines. Our children are our future and the barometer of our approach to social justice and the state of our society."
Although many states have adopted new children's rights policies in recent years, the Index reveals that implementation is often not evident, and many new policies fail to fully comply with the principles and provisions of the Convention on the Rights of the Child.
The Index rates and ranks the extent to which a country has implemented the general principles of the Convention on the Rights of the Child while taking into account the basic infrastructure for making and implementing children's rights policies. Portugal is this year's global top ranking nation, with France, Norway, Sweden, Finland and Spain also ranking in the top ten.
The Index methodology means that extremely poor performances in one domain cannot be compensated by higher scores in other domains, as all of areas children's rights are deemed to be equally important.
The report concluded that many industrialised nations, and especially the UK, are falling far short of allocating sufficient budgets towards creating a stable environment for children's rights, by neglecting their leadership responsibilities and failing to invest in the rights of children to the best of their abilities.
Human rights and the impact of childhood poverty
Earlier this month, another damning report published by the Royal College of Paediatrics, Child Health (RCPCH) and Child Poverty Action Group (CPAG) revealed that more than two-thirds of paediatricians believe poverty and low income contribute "very much" to the ill health of children that they work with.
The report – Poverty and child health: views from the frontline – is based on a survey of more than 250 paediatricians across the country, whose comments provide an insight into the grave reality of life for the millions of UK children living in poverty.
Latest figures show that more than one in four (nearly 4 million) children in the UK live in poverty – with projections suggesting this could rise to 5 million by the end of the decade.
The report explores number of areas including food insecurity, poor housing and worry, stress and stigma – and the effect of these issues on the health of children.
The report reveals that:
more than two-thirds of paediatricians surveyed said poverty and low income contribute 'very much' to the ill health of children they work with
housing problems or homelessness were a concern for two-thirds of respondents.
more than 60% said food insecurity contributed to the ill health amongst children they treat 3
40% had difficulty discharging a child in the last 6 months because of concerns about housing or food insecurity
more than 50% of respondents said that financial stress and worry contribute 'very much' to the ill health of children they work with
Alison Garnham, Chief Executive of the Child Poverty Action Group, said:
"Day in, day out doctors see the damage rising poverty does to children's health. Their disquiet comes through in the survey findings and should sound alarms for the next government. Low family incomes, inadequate housing and cuts to support services are jeopardising the health of our most vulnerable children.
"We can and must do better to protect the well-being of future generations. reinstating the UK's poverty-reduction targets would be an obvious place to start."
Professor Russell Viner, Officer for Health Promotion at the Royal College of Paediatrics and Child Health, said:
"Poverty has a devastating effect on child health and this report makes disturbing reading. The health impact on children living in poverty is significant – whether that's increased likelihood of respiratory problems, mental ill-health or obesity – than children living in more affluent areas.
"Worryingly, almost half of those surveyed feel the problem is getting worse, with the combination of increasing poverty, housing problems and cuts to services meaning more families are struggling."
The RCPCH and CPAG are calling on whoever forms the next Government to tackle poverty urgently through:
the restoration of binding national targets to reduce child poverty, backed by a national child poverty strategy
the adoption of a 'child health in all policies' approach to decision making and policy development, with Her Majesty's Treasury disclosing information about the impact of the Chancellor's annual budget statement on child poverty and inequality
the reversal of public health cuts to ensure universal early years services, including health visiting and school nursing, are prioritised and supported financially, with additional targeted help for children and families experiencing poverty
the reversal of cuts to universal credit which will leave the majority of families claiming this benefit worse off.
As one survey respondent said: "We cannot expect to have a healthy future for the UK if we leave children behind. Poverty makes children sick."
There were 3.9 million children living in "relative poverty" in 2014-15, up from 3.7 million a year earlier, according to figures from the Department for Work and Pensions (DWP).
The report follows the release of figures from the DWP which revealed one in four (nearly four million) children in the UK live in poverty – with projections suggesting this could rise to five million by the end of the decade.
It's not as if the government have been unaware of the consequences of their policies and the implications of a consistent failure to uphold the UK's human rights obligations towards children. In 2014, the Children's Commissioner warned that the increasing inequality resulting from the austerity cuts, and in particular, the welfare reforms, means that Britain is now in breach of the United Nations Convention on the Rights of the Child, which is supposed to protect children from the adverse effects of government economic measures.
In 2015, the Children's Commissioner criticised the Conservative's tax credit cuts and called for measures to reduce the impact that the changes will have on the poorest children. Anne Longfield, who took up her role on 1 March 2015, called on the government to exempt 800,000 children under five from tax credit cuts and to offer additional support to families with a child under five-years-old.
The role of Children's Commissioner was established under Labour's Children Act in 2004 to be the independent voice of children and young people and to champion their interests and bring their concerns and views to the national arena. The Commissioner's work must take regard of children's rights (the United Nations Convention on the Rights of the Child) and seek to improve the wellbeing of children and young people.
However, the government rejected the findings of what they deemed the "partial, selective and misleading" Children's Commissioner report. The Commissioner wrote to the Chancellor to call for children in the poorest families aged under five to be protected from the cuts.
However, George Osborne shamefully remained brazenly unrepentant.
A damning joint report written by the four United Kingdom Children's Commissioners for the UN Committee on the Rights of the Child's examination of the UK's Fifth Periodic Report under the UN Convention on the Rights of the Child (UNCRC), dated 14 August 2015, says, in its overall assessment of the UK's record:
"The Children's Commissioners are concerned that the UK State Party's response to the global economic downturn, including the imposition of austerity measures and changes to the welfare system, has resulted in a failure to protect the most disadvantaged children and those in especially vulnerable groups from child poverty, preventing the realisation of their rights under Articles 26 and 27 UNCRC.
The best interests of children were not central to the development of these policies and children's views were not sought.
Reductions to household income for poorer children as a result of tax, transfer and social security benefit changes have led to food and fuel poverty, and the sharply increased use of crisis food bank provision by families. In some parts of the UK there is insufficient affordable decent housing which has led to poorer children living in inadequate housing and in temporary accommodation.
Austerity measures have reduced provision of a range of services that protect and fulfil children's rights including health and child and adolescent mental health services; education; early years; preventive and early intervention services; and youth services.
The Commissioners are also seriously concerned at the impact of systematic reductions to legal advice, assistance and representation for children and their parents/carers in important areas such as prison law; immigration; private family law; and education. This means that children are denied access to remedies where their rights have been breached.
The Commissioners are also concerned at the future of the human rights settlement in the United Kingdom due to the UK Government's intention to repeal the Human Rights Act 1998 (HRA) which incorporates the European Convention on Human Rights (ECHR) into domestic law; replace it with a British Bill of Rights (the contents of which are yet to be announced), and 'break the formal link between British courts and the European Court of Human Rights'.
The HRA has been vital in promoting and protecting the rights of children in the United Kingdom and the European Court of Human Rights has had an important role in developing the protection offered to children by the ECHR.The Commissioners are concerned that any amendment or replacement of the HRA is likely to be regressive."
In another regressive and punitive policy move by the government, from April 6 2017, child tax credits and universal credit across the UK will be restricted to the first two children in a family. This measure will affect all households with two or more children that have an additional child after this date.
Analysis by consultancy Policy in Practice revealed a low-income family whose third or additional child is born before midnight on the day before the policy came into force would qualify for up to £50,000 in tax credit support over 18 years whereas a similar family whose third child is born on April 6 will miss out.
The government says it wants to save money and make the tax credit system "fairer". It intends the two-child restriction to "influence the behaviour" of less well-off families by making them "think twice" about having a third child. But it also accepts there is no evidence to suggest this will happen.
This is an extremely regressive eugenic policy, with its emphasis being on social class. Eugenics was discredited following its terrible escalation and consequences in Nazi Germany.
The two children only policy also a reflects a politically motivated form of crude behaviourism – behaviour modification through the use of financial punishments. It's probably true that all authoritarians and tyrants are behaviourists of sorts.
Critics say that at current birth rates, 100,000 third or subsequent children will not qualify for tax credit support over the next 12 months, inflating child poverty figures by at least 10% by 2020.
Social Darwinism is linked closely with eugenic ideas – a view that society and economics will naturally "check" the problem of dysgenics if no welfare policies are in place.
The Conservative government has steadily dismantled the welfare state over the past seven years, so that now, there is no longer adequate support provision for people both in work and out of work, to meet their basic living needs.
The current retrogressive, draconian approach to poverty needs to radically change if we are to be a nation that respects and upholds the human rights of all its citizens.
I don't make any money from my work. I am disabled because of illness and have a very limited income. But you can help by making a donation to help me continue to research and write informative, insightful and independent articles, and to provide support to others. The smallest amount is much appreciated – thank you.
May 18, 2017 May 18, 2017 · Posted in Human Rights, Political ideology, Welfare "reforms" · Tagged 2 child policy, Anne Longfield, Childhood Poverty, Children's Act 2004, Children's Commissioner, Convention on the Rights of the Child, DWP, Eugenics, health poverty, KidsRights Index, Lord Philip Hunt, Marc Dullaert, Russell Viner, Social Darwinism, Tax credit cuts, UNCRC, UNICEF ·
14 thoughts on "The government has failed to protect the human rights of children"
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gonna take a while to get through such a long blog – but I get the gist! Appalling.
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sdbast says:
Reblogged this on sdbast.
Kilburn Unemployed says:
Hi, Kitty
As I'm moving home this weekend and just dealing with my e-mail Inbox at this time, I don't really have time to 'get into this matter' but to refer those who are interested to a 'starter blog post' I did last month, or at least made a start on: National Society for Prevention of Cruely to Children and 'Crown Immunity' over Department for Work & Pensions neglect.
Alan Wheatley — aka 'Dude Swheatie of Kwug'
truthaholics says:
Reblogged this on | truthaholics and commented:
"Austerity measures have reduced provision of a range of services that protect and fulfil children's rights including health and child and adolescent mental health services; education; early years; preventive and early intervention services; and youth services. "
finolamoss says:
Not surprising but appalling.
Billions go in profit for the Privatised Child Protection industry; minimum £30,000 per adoption, average £600 per week fostering, experts, courts and to Childrens Charities for widening definitions of 'neglect' in birth families but not in foster care/adoption.
Record numbers torn without a say from their families and placed in care with poor outcomes.
The local authority asking Parliament to exempt them from child protection liability so they can proceed with full for profit non accountable services.
More than ever children on prescribed drugs, and Cameron proclaims a quarter have mental disorders to make money for pharma and the mental health industry, with 375 Disorders to choose from, and more children in real poverty.
Yes, children are seen as cash cows only. It shows the UK we now live in.
Childcare Proceedings Exposed says:
Reblogged this on Child Care Proceedings Exposed.
This is one of the worst failures a government can have. If they can't help our children, who are supposed to be the hope of the future, then they aren't worth much as a government!
PLease vote carefully in the election – it's your children who ultimately pay the price! 😦
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Mandatory reconsiderations and the rule of law
Vote Labour to uphold the rights of disabled people – our letter to the Guardian


text:
Say Yes to Nukes
In Essence | Summer 2011
THE SOURCE: "Thinking About the Unthinkable, Again" by Mark Helprin, in Claremont Review of Books, Winter 2010–Spring 2011.
For decades, the world has lived with the threat of nuclear war, but the dreaded mushroom clouds haven't appeared. Now the Obama administration is seeking to dispel the threat completely, by reducing and perhaps eventually abolishing altogether America's nuclear arsenal.
This is exactly the wrong thing to do, argues Mark Helprin, a senior fellow at the Claremont Institute. Getting rid of all of America's nuclear weapons will increase the likelihood of a catastrophic nuclear, biological, or chemical attack—and of conventional wars, too, he says. That's because deterrence—the threat of retaliation that has maintained international equilibrium since the end of World War II—will disappear. In a nuke-free world, the threshold of conflict between major powers would be "vastly lowered."
Furthermore, abolition can't work unless all parties know definitively that it is universal. That's impossible. Even today, no one has a complete inventory of the world's nuclear weapons. And disarmed nations will always have the knowledge to secretly rebuild their nuclear arsenals.
Well, then, the conventional wisdom goes, if abolition isn't immediately practical, let's diminish the threat of nuclear war by severely reducing the number of warheads in our arsenal. Wrong again, says Helprin. Under the New Strategic Arms Reduction Treaty (NSTART), which came into force this year, countries including the United States, Russia, and China will shrink their arsenals to achieve an agreed-upon parity. But parity is a pipe dream, Helprin says. The strategic balance constantly shifts as new alliances are formed and countries that once were unarmed join the game. Stability isn't attainable.
In the past, the superpowers possessed such a vast advantage that it made no sense for other countries to compete. At most, they might build a nuclear weapons arsenal sufficient to deter opponents. Today, with the number of warheads dwindling and technological advances deliberately frozen, "anyone, no matter how small, can get in the game, and will." And that, Helprin points out, is proliferation—the opposite of what treaties such as NSTART are seeking to achieve.
Reducing the number of warheads also puts small and rogue states on more equal footing with great nuclear powers, Helprin points out. This invites "lesser state adventurism," as would-be aggressors (for example, Iran) are tempted to start regional wars and use a nuclear threat to prevent outside intervention.
Helprin characterizes the idea that fewer nukes means a safer world as a "careless orthodoxy." Diminished nuclear stockpiles could actually invite trigger-happy nations to launch a first strike, he says. That's because they would have a better chance of taking out enough of an opponent's arsenal to preclude retaliation. At the Cold War's end, Helprin writes, an enemy would have had to factor in more than a thousand U.S. land-based missile targets and 17 nuclear-armed submarines. In the near future, an aggressor will need to take out only 89 fixed land targets and six submarine targets.
To make matters worse, the United States is weakening its conventional forces, Helprin says, increasing the likelihood that it might have to resort to nuclear weapons in a crisis. And the Obama administration is seeking to blunt U.S. ballistic missile defenses. Such a system can't be completely effective, but it can preserve the country's capacity to retaliate, and thus provides significant deterrence.
What should the United States do instead? Helprin recommends that it (1) continue to develop safety measures such as open-ocean tar-geting systems designed to guide launched missiles into water rather than onto inhabited land, (2) maintain missile shields, and (3) focus on keeping weapons out of the hands of "dictatorships, crazy states, lunatics, and medieval theocracies," using force if necessary.
American officials, Helprin concludes, need to carefully consider the complex doctrines and practices that have prevented "even a single detonation either in anger or by accident" in more than 60 years before casting them aside.
Photo: Tsar Bomba hydrogen bomb detonation
No Small Wonder
The Origins of the Sunni Awakening
Comparing the Tippy Tops
India's Vulture Void


text:
using System;
using System.Xml.Serialization;

namespace Aop.Api.Domain
{
    /// <summary>
    /// AlipayOpenMiniModelQueryModel Data Structure.
    /// </summary>
    [Serializable]
    public class AlipayOpenMiniModelQueryModel : AopObject
    {
        /// <summary>
        /// 内容:app_info表最新更新时间,格式:时间戳
        /// </summary>
        [XmlElement("app_info_modified")]
        public string AppInfoModified { get; set; }

        /// <summary>
        /// 内容:app_version表最新更新时间,格式:时间戳
        /// </summary>
        [XmlElement("app_version_modified")]
        public string AppVersionModified { get; set; }

        /// <summary>
        /// 内容:deploy_package表最新更新时间,格式:时间戳
        /// </summary>
        [XmlElement("deploy_package_modified")]
        public string DeployPackageModified { get; set; }

        /// <summary>
        /// 内容:deploy_window表最新更新时间,格式:时间戳
        /// </summary>
        [XmlElement("deploy_window_modified")]
        public string DeployWindowModified { get; set; }

        /// <summary>
        /// 是否为压测流量,true为是,默认false
        /// </summary>
        [XmlElement("load_test")]
        public string LoadTest { get; set; }

        /// <summary>
        /// APPID
        /// </summary>
        [XmlElement("mini_app_id")]
        public string MiniAppId { get; set; }

        /// <summary>
        /// 内容:mini_app_version表最新更新时间,格式:时间戳
        /// </summary>
        [XmlElement("mini_app_version_modified")]
        public string MiniAppVersionModified { get; set; }
    }
}


text:
General Honduras News · Honduran Culture
Plan for Retraining of Honduran Police
November 15, 2010 by Catracha Hondurena No Comments
The Security Ministry launched a comprehensive plan for re-training some 14,000 police officers, according to the director of the Institute of Police Technology (ITP), Commissioner César Augusto Mendoza.
The initiative is promoted strongly by the Security Minister, Oscar Álvarez, the Director General of the Police, Commissioner José Luis Muñoz Licona, and the rector of the Police Education System, Commissioner Mario Leonel Zepada Espinoza, said Mendoza.
It also has the support of the Ministry of Education under an agreement signed with the Ministry of Security. This will help those enrolled in primary education to continue until at least the ninth grade, or otherwise finish high school, in any discipline of police science, said Mendoza.
The director of the ITP reported that those enrolled in March whose training would be concluded in early December, will be the first 500 elite special services staff trained in prevention, criminal investigation, special issues and transit. He stressed that most of this group are teachers, graduates and business experts highly educated by the institution in police techniques.
He said that for next year, starting in January 2011, the ITP has already received over 1,400 applications from candidates with an educational background, but only the top 500 will be chosen to follow the curricula.
The new line is eminently civilian police with emphasis on respect for human rights.
As minimum requirements, said the police chief, applicants must submit their title for Education Media or Certificate from ninth grade, identity card, proof of criminal and police clearance, in addition to testing for drugs, HIV and Chagas disease. Between the group applying, and the graduating class, there are recorded 69 females.
Mendoza said the course will last six to eight months, and during their stay, the student will receive a pension of two thousand lempiras from the government. Upon graduation, they will join the National Police with a minimum wage, plus all the benefits of any public employee (social security, vacations, bonuses, life insurance, etc.) "More than a salary, the most important thing that the police will have is the immense satisfaction of protecting the weak, for me that is the most satisfying," said Mendoza.
In the case of service agents that will be submitted to the "recycling", the courses will begin next year with groups of 300 agents to complete the ultimate goal.
Training for both new, and for serving officers, includes courses in basic English, according to branch, and a complete training in handling "civilians", i.e. respect for human rights under the motto "to serve, protect, and ultimately suppress, but with the law and not with another crime," explained the director of ITP, based in the city of La Paz.
Mendoza believes that society will feel the changes in the police because the project is complemented by plans for the upper ranks of the University of the National Police of Honduras (UNPH) (graduate), National Police Academy (ANAP) (undergraduate) and the NCO School of Honduras, who graduate to assist the head administrative officers.


text:
Q: Can't activate conda env from shell script I've tried everything I've seen on SO to get this to work, but so far everything fails. Using macOS Big Sur 11.6, bash in Terminal (not zsh).
I'm trying to create a setup file and execute with sh setup.sh that will setup the env, install python, and then activate it. Nothing fancy. Doing it manually works fine, but once I put it in a shell script, it won't work. I'm running this script from inside an empty project folder.
Current script:
conda create -n MASTER python=3.8.5 -y

conda activate MASTER

Yeah, it's that simple to start with. I commented out the other pip installs until this works properly.
I tried running: bash -i setup.sh but it still does not activate. I get no errors but I'm still stuck in (base).
I tried using source: source /opt/anaconda3/etc/profile.d/conda.sh at beginning of script and/or before activate, still doesn't work. No errors again, but stuck in (base).
I tried using: eval $(conda shell.bash hook) at the start of script and before I try to activate the env, but it fails. This time I get the error:
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

But if I run conda init bash (in Terminal or in the script itself), it outputs:
no change     /opt/anaconda3/condabin/conda
no change     /opt/anaconda3/bin/conda
no change     /opt/anaconda3/bin/conda-env
no change     /opt/anaconda3/bin/activate
no change     /opt/anaconda3/bin/deactivate
no change     /opt/anaconda3/etc/profile.d/conda.sh
no change     /opt/anaconda3/etc/fish/conf.d/conda.fish
no change     /opt/anaconda3/shell/condabin/Conda.psm1
no change     /opt/anaconda3/shell/condabin/conda-hook.ps1
no change     /opt/anaconda3/lib/python3.8/site-packages/xontrib/conda.xsh
no change     /opt/anaconda3/etc/profile.d/conda.csh
no change     /Users/liquidRock/.bash_profile
No action taken.

I tried doing /opt/anaconda3/bin/conda activate MASTER which also prompts me to do conda init bash.
Even tried adding #!/bin/bash to the top of the file just in case, but no dice.

A: Thanks to @fravadona for the simplest of solutions.
Simply executing the script with source instead of sh. ♂
Final setup.sh script (with my preliminary pip installs):
# env & python
conda create -n MASTER python=3.8.5 -y
conda activate MASTER

# pip installs
pip install cmake
pip install --upgrade pip setuptools wheel
pip install opencv-python==4.2.0.32
pip install argparse
pip install datetime
pip install colorama
pip install python-dotenv
pip install python-dotenv[cli]

Executed thusly:
$ source setup.sh

Anaconda creates the env, installs python and dependencies, activates the env, then pip installs the additional dependencies.
Still not sure why it won't work by adding other things to the shell script, but this is still a great, simple solution. And yes, I am a novice with this stuff.


text:
<Picture this
Ghost in the machine>
Architecture & Design, Design
Design Perspective: Richard Malone
November 19, 2015 /Comments closed
[slider_pro id="162″]
From IAR Summer Edition
The exaggerated silhouettes of Richard Malone, created by shrinking and oversizing garments are references he draws from everyday people and the idiosyncrasies of style. He is continuously inspired by his hometown of Wexford and draws on his experience of coming of age in Ardcaven. Unkempt kids in school uniforms and ill-fitting parochial fashions are transformed through his original eye. Commenting on his process the designer notes, 'These very mundane and ordinary garments become fantastical through the way we describe them, fascinating even. It's like an extreme ordinariness that throws you, that sparks something and creates
an interest.'
Malone's working-class upbringing is central to his distinctive vision and set him apart from his peers at the prestigious Central Saint Martins in London. His collection was selected to open the press show for his graduating class in 2014 generating immediate attention from the industry's top fashion editors. He has received major international awards from LVMH and Deutsche Bank, both firsts for an Irish designer. This is an incredible period for Irish fashion talent with the recent stellar collections from Simone Rocha and JW Anderson and now with Malone refocusing attention on Ireland. Recently selected by the BBC as one of the UK's top five artists under the age of 25, Malone's upward trajectory is set to continue.
For any emerging designer, visibility on an international stage is crucial, yet Malone sees opportunity to develop his brand from home and on his own terms, taking creative refuge in his father's shed in Wexford and producing his collections from sustainable sources. He chooses to reuse end of roll fabrics and cheaper materials like pleather, manipulating them into high-end creations finished with skilled techniques. This contrast of low-end and luxury, achieved with such humour and vibrancy, is what is elevating the Wexford-born designer above the noise.
Malone's practice often involves the written word, film, performance art and installations. Figurative drawing is at the heart of his research and this summer he will exhibit a collection of his watercolour studies and sketches in a small intimate gallery in Wexford. Many of his subjects are local people and he looks forward to sharing this private process behind his work.
Malone embraces diversity in life and invites his audience to challenge conventional fashion. In July 2015, a limited selection of exclusive pieces and one-offs was available from Brown Thomas as part of their Create project supporting Irish design.
Aisling Farinella is Editor and Fashion Director of Thread magazine.
In the current edition of the Irish Arts Review, Autumn 21: 150 years since the birth of Jack B Yeats, Hilary Pyle considers the concept of memory embedded in his work. Jack B Yeats: Painting & Memory, @NGIreland - 4 September - 22 February 2021pic.twitter.com/f3HcfIWpPi
Artists On View - threadstories @MolesworthGall until 30 Sept In the @IrishArtsReview Stephanie McBride discovers that, like Banksy & French music duo Daft Punk, threadstories is using her own masked identity and anonymity as a riff on celebrity status, or an inversion of itpic.twitter.com/EVeilIF7FV
Art exhibitions: Merlin James @KerlinGallery Sept 4 - 9 Oct Merlin James revisits the rural scenes & architectural features that have captivated his practice. His works showing are often pierced, cropped or heavily overpainted, refining ideas of genre and narrative.pic.twitter.com/eDZ8gq0pyp


For, is not fatigue indistinguishable, when the spirits are high.
Insignificant before the thousands already under way.
And keeping quiet till your achievements can speak.
You are sure, the top of the stairs isn't far away.
And far above, the first tinkle of success's bells you hear.
Neither contentment nor disappointment, absolutely no sound.
You are already through that now receding moment.
Back to active blogging after a sabbatical of exactly one year!!!!!!!!!!!!! This one was promised a year ago to Meghna and is dedicated to her. The last one year has been a thrilling roller-coaster ride plunging more to newer depths and never quite scaling new heights. What matters is i have managed to come out in a single piece and am back to blogging. So Meghna enjoy being a Beacon again.