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## Summary#

Systems compel the individuals within them to act within the rules of the system rather than by a globally optimal set of rules.

Related:

## Notes#

### I#

See Howl.

A lot of the commentators say Moloch represents capitalism. This is definitely a piece of it, even a big piece. But it doesn’t quite fit. Capitalism, whose fate is a cloud of sexless hydrogen? Capitalism in whom I am a consciousness without a body? Capitalism, therefore granite cocks?

Moloch is introduced as the answer to a question – C. S. Lewis' question in Hierarchy Of Philosophers – what does it? Earth could be fair, and all men glad and wise. Instead we have prisons, smokestacks, asylums. What sphinx of cement and aluminum breaks open their skulls and eats up their imagination?

And Ginsberg answers: Moloch does it.

There’s a passage in the Principia Discordia where Malaclypse complains to the Goddess about the evils of human society. “Everyone is hurting each other, the planet is rampant with injustices, whole societies plunder groups of their own people, mothers imprison sons, children perish while brothers war.”

The Goddess answers: “What is the matter with that, if it’s what you want to do?”

Malaclypse: “But nobody wants it! Everybody hates it!”

Goddess: “Oh. Well, then stop.”

The implicit question is – if everyone hates the current system, who perpetuates it? And Ginsberg answers: “Moloch”. It’s powerful not because it’s correct – nobody literally thinks an ancient Carthaginian demon causes everything – but because thinking of the system as an agent throws into relief the degree to which the system isn’t an agent.

Bostrom makes an offhanded reference of the possibility of a dictatorless dystopia, one that every single citizen including the leadership hates but which nevertheless endures unconquered. It’s easy enough to imagine such a state. Imagine a country with two rules: first, every person must spend eight hours a day giving themselves strong electric shocks. Second, if anyone fails to follow a rule (including this one), or speaks out against it, or fails to enforce it, all citizens must unite to kill that person. Suppose these rules were well-enough established by tradition that everyone expected them to be enforced.

So you shock yourself for eight hours a day, because you know if you don’t everyone else will kill you, because if they don’t, everyone else will kill them, and so on. Every single citizen hates the system, but for lack of a good coordination mechanism it endures. From a god’s-eye-view, we can optimize the system to “everyone agrees to stop doing this at once”, but no one within the system is able to effect the transition without great risk to themselves.

### Examples#

#### Fish farming story#

As a thought experiment, let’s consider aquaculture (fish farming) in a lake. Imagine a lake with a thousand identical fish farms owned by a thousand competing companies. Each fish farm earns a profit of $1000/month. For a while, all is well. But each fish farm produces waste, which fouls the water in the lake. Let’s say each fish farm produces enough pollution to lower productivity in the lake by$1/month.

A thousand fish farms produce enough waste to lower productivity by $1000/month, meaning none of the fish farms are making any money. Capitalism to the rescue: someone invents a complex filtering system that removes waste products. It costs$300/month to operate. All fish farms voluntarily install it, the pollution ends, and the fish farms are now making a profit of $700/month – still a respectable sum. But one farmer (let’s call him Steve) gets tired of spending the money to operate his filter. Now one fish farm worth of waste is polluting the lake, lowering productivity by$1. Steve earns $999 profit, and everyone else earns$699 profit.

Everyone else sees Steve is much more profitable than they are, because he’s not spending the maintenance costs on his filter. They disconnect their filters too.

Once four hundred people disconnect their filters, Steve is earning $600/month – less than he would be if he and everyone else had kept their filters on! And the poor virtuous filter users are only making$300. Steve goes around to everyone, saying “Wait! We all need to make a voluntary pact to use filters! Otherwise, everyone’s productivity goes down.”

Everyone agrees with him, and they all sign the Filter Pact, except one person who is sort of a jerk. Let’s call him Mike. Now everyone is back using filters again, except Mike. Mike earns $999/month, and everyone else earns$699/month. Slowly, people start thinking they too should be getting big bucks like Mike, and disconnect their filter for \$300 extra profit…

A self-interested person never has any incentive to use a filter. A self-interested person has some incentive to sign a pact to make everyone use a filter, but in many cases has a stronger incentive to wait for everyone else to sign such a pact but opt out himself. This can lead to an undesirable equilibrium in which no one will sign such a pact.

#### Malthusian trap#

Suppose you are one of the first rats introduced onto a pristine island. It is full of yummy plants and you live an idyllic life lounging about, eating, and composing great works of art (you’re one of those rats from The Rats of NIMH).

You live a long life, mate, and have a dozen children. All of them have a dozen children, and so on. In a couple generations, the island has ten thousand rats and has reached its carrying capacity. Now there’s not enough food and space to go around, and a certain percent of each new generation dies in order to keep the population steady at ten thousand.

A certain sect of rats abandons art in order to devote more of their time to scrounging for survival. Each generation, a bit less of this sect dies than members of the mainstream, until after a while, no rat composes any art at all, and any sect of rats who try to bring it back will go extinct within a few generations.

In fact, it’s not just art. Any sect at all that is leaner, meaner, and more survivalist than the mainstream will eventually take over. If one sect of rats altruistically decides to limit its offspring to two per couple in order to decrease overpopulation, that sect will die out, swarmed out of existence by its more numerous enemies. If one sect of rats starts practicing cannibalism, and finds it gives them an advantage over their fellows, it will eventually take over and reach fixation.

If some rat scientists predict that depletion of the island’s nut stores is accelerating at a dangerous rate and they will soon be exhausted completely, a few sects of rats might try to limit their nut consumption to a sustainable level. Those rats will be outcompeted by their more selfish cousins. Eventually the nuts will be exhausted, most of the rats will die off, and the cycle will begin again. Any sect of rats advocating some action to stop the cycle will be outcompeted by their cousins for whom advocating anything is a waste of time that could be used to compete and consume.

For a bunch of reasons evolution is not quite as Malthusian as the ideal case, but it provides the prototype example we can apply to other things to see the underlying mechanism. From a god’s-eye-view, it’s easy to say the rats should maintain a comfortably low population. From within the system, each individual rat will follow its genetic imperative and the island will end up in an endless boom-bust cycle.

#### Capitalism#

Imagine a capitalist in a cutthroat industry. He employs workers in a sweatshop to sew garments, which he sells at minimal profit. Maybe he would like to pay his workers more, or give them nicer working conditions. But he can’t, because that would raise the price of his products and he would be outcompeted by his cheaper rivals and go bankrupt. Maybe many of his rivals are nice people who would like to pay their workers more, but unless they have some kind of ironclad guarantee that none of them are going to defect by undercutting their prices they can’t do it.

#### Two-income trap#

It theorized that sufficiently intense competition for suburban houses in good school districts meant that people had to throw away lots of other values – time at home with their children, financial security – to optimize for house-buying-ability or else be consigned to the ghetto.

From a god’s-eye-view, if everyone agrees not to take on a second job to help win their competition for nice houses, then everyone will get exactly as nice a house as they did before, but only have to work one job. From within the system, absent a government literally willing to ban second jobs, everyone who doesn’t get one will be left behind.

### II#

A basic principle unites all of the multipolar traps above. In some competition optimizing for X, the opportunity arises to throw some other value under the bus for improved X. Those who take it prosper. Those who don’t take it die out. Eventually, everyone’s relative status is about the same as before, but everyone’s absolute status is worse than before. The process continues until all other values that can be traded off have been – in other words, until human ingenuity cannot possibly figure out a way to make things any worse.

### III#

But not only have we not yet reached the sea, but we also seem to move uphill surprisingly often. Why do things not degenerate more and more until we are back at subsistence level? I can think of three bad reasons – excess resources, physical limitations, and utility maximization – plus one good reason – coordination.

I know that “capitalists sometimes do bad things” isn’t exactly an original talking point. But I do want to stress how it’s not equivalent to “capitalists are greedy”. I mean, sometimes they are greedy. But other times they’re just in a sufficiently intense competition where anyone who doesn’t do it will be outcompeted and replaced by people who do. Business practices are set by Moloch, no one else has any choice in the matter.

(from my very little knowledge of Marx, he understands this very very well and people who summarize him as “capitalists are greedy” are doing him a disservice)

For example, ever-increasing prison terms are unfair to inmates and unfair to the society that has to pay for them. Politicans are unwilling to do anything about them because they don’t want to look “soft on crime”, and if a single inmate whom they helped release ever does anything bad (and statistically one of them will have to) it will be all over the airwaves as “Convict released by Congressman’s policies kills family of five, how can the Congressman even sleep at night let alone claim he deserves reelection?”. So even if decreasing prison populations would be good policy – and it is – it will be very difficult to implement.

(Moloch the incomprehensible prison! Moloch the crossbone soulless jailhouse and Congress of sorrows! Moloch whose buildings are judgment! Moloch the stunned governments!)

[…] government can easily solve the pollution problem with fish farms. The best known solution to the Prisoners' Dilemma is for the mob boss (playing the role of a governor) to threaten to shoot any prisoner who defects. The solution to companies polluting and harming workers is government regulations against such. Governments solve arm races within a country by maintaining a monopoly on the use of force, and it’s easy to see that if a truly effective world government ever arose, international military buildups would end pretty quickly.

The two active ingredients of government are laws plus violence – or more abstractly agreements plus enforcement mechanism. Many other things besides governments share these two active ingredients and so are able to act as coordination mechanisms to avoid traps.

[…]

But these institutions not only incentivize others, but are incentivized themselves. These are large organizations made of lots of people who are competing for jobs, status, prestige, et cetera – there’s no reason they should be immune to the same multipolar traps as everyone else, and indeed they aren’t. Governments can in theory keep corporations, citizens, et cetera out of certain traps, but as we saw above there are many traps that governments themselves can fall into.

### IV#

So I agree with Robin Hanson: This is the dream time. This is a rare confluence of circumstances where the we are unusually safe from multipolar traps, and as such weird things like art and science and philosophy and love can flourish.

As technological advance increases, the rare confluence will come to an end. New opportunities to throw values under the bus for increased competitiveness will arise. New ways of copying agents to increase the population will soak up our excess resources and resurrect Malthus' unquiet spirit. Capitalism and democracy, previously our protectors, will figure out ways to route around their inconvenient dependence on human values. And our coordination power will not be nearly up to the task, assuming somthing much more powerful than all of us combined doesn’t show up and crush our combined efforts with a wave of its paw.

Contract Drafting Em

The last value we have to sacrifice is being anything at all, having the lights on inside. With sufficient technology we will be “able” to give up even the final spark.

(Moloch whose eyes are a thousand blind windows!)

Everything the human race has worked for – all of our technology, all of our civilization, all the hopes we invested in our future – might be accidentally handed over to some kind of unfathomable blind idiot alien god that discards all of them, and consciousness itself, in order to participate in some weird fundamental-level mass-energy economy that leads to it disassembling Earth and everything on it for its component atoms.

(Moloch whose fate is a cloud of sexless hydrogen!)

We will break our back lifting Moloch to Heaven, but unless something changes it will be his victory and not ours.

### VII#

The opposite of a trap is a garden. The only way to avoid having all human values gradually ground down by optimization-competition is to install a Gardener over the entire universe who optimizes for human values.

And the whole point of Bostrom’s Superintelligence is that this is within our reach. Once humans can design machines that are smarter than we are, by definition they’ll be able to design machines which are smarter than they are, which can design machines smarter than they are, and so on in a feedback loop so tiny that it will smash up against the physical limitations for intelligence in a comparatively lightning-short amount of time. If multiple competing entities were likely to do that at once, we would be super-doomed. But the sheer speed of the cycle makes it possible that we will end up with one entity light-years ahead of the rest of civilization, so much so that it can suppress any competition – including competition for its title of most powerful entity – permanently. In the very near future, we are going to lift something to Heaven. It might be Moloch. But it might be something on our side. If it’s on our side, it can kill Moloch dead.

And if that entity shares human values, it can allow human values to flourish unconstrained by natural law.

### VIII#

The Universe is a dark and foreboding place, suspended between alien deities. Cthulhu, Gnon, Moloch, call them what you will.

Somewhere in this darkness is another god. He has also had many names. In the Kushiel books, his name was Elua. He is the god of flowers and free love and all soft and fragile things. Of art and science and philosophy and love. Of niceness, community, and civilization. He is a god of humans.

The other gods sit on their dark thrones and think “Ha ha, a god who doesn’t even control any hell-monsters or command his worshippers to become killing machines. What a weakling! This is going to be so easy!”

But somehow Elua is still here. No one knows exactly how. And the gods who oppose Him tend to find Themselves meeting with a surprising number of unfortunate accidents.

There are many gods, but this one is ours.

[…]

The question everyone has after reading Ginsberg is: what is Moloch?

My answer is: Moloch is exactly what the history books say he is. He is the god of child sacrifice, the fiery furnace into which you can toss your babies in exchange for victory in war.

He always and everywhere offers the same deal: throw what you love most into the flames, and I can grant you power.

As long as the offer’s open, it will be irresistible. So we need to close the offer. Only another god can kill Moloch. We have one on our side, but he needs our help. We should give it to him.

## References#

Alexander, Scott. 2014. “Meditations On Moloch.” Slate Star Codex. https://slatestarcodex.com/2014/07/30/meditations-on-moloch/.


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# How to accelerate replacing of matrix rows in a loop as quickly as possible?

I am working with a very large sparse matrix (for example) given in what follows:

m = 50; n = 40; o = 30; size = m*n*o;
B = SparseArray[{
{i_, i_} -> RandomReal[], {size, size - 1} ->
2., {i_, j_} /; Abs[i - j] == 5 ->
1., {i_, j_} /; Abs[3 i - j] == 2 -> 2.
}, {size, size}, 0.]

This is a matrix of the size $60000\times 60000$ as a simple instance (in practice I have several of such matrices of higher sizes).

I wish to replace many rows of the matrix $B$ with special rows (here with zero rows) coming from boundary conditions. My list of rows' numbers are given by

index1 = Flatten[Table[{i, j, k}, {i, 1, m}, {j, 1, n}, {k, 1, o}], 2];
Table[ind = index1[[l]];
If[ind[[1]] == 1 || ind[[2]] == n, var[l] = 0, var[l] = l], {l,
Length@index1}];
bounindex = Table[var[l], {l, Length@index1}];

And my zero row is produced by

vector1 = SparseArray@ConstantArray[0, size];

Now for doing the replacement only for the 0 numbers obtained in bounindex, I write the following replacing rule in a loop as simply as possible:

Table[Which[bounindex[[i]] == 0, B[[i]] = vector1], {i,
size}]; // AbsoluteTiming

This works OK but it takes a tremendous time (in my real problem I have larger sizes)! So I am wondering if there is a speed-up technique to replace the special rows of the matrix $B$ with appropriate rows (that I want).

I would be thankful if some hints for accelerating such a replacement be given.

## 3 Answers

(updated)

For later comparisons, I will store the value of B:

B0 = B;

Original post

Set all the rows to zero at once. First, use Pick to find the rows to be zeroed:

delete = Pick[Range[60000], bounindex, 0];
len = Length[delete]

2670

Here is the number of nonzero values before zeroing out rows:

Length @ B["NonzeroValues"]

219989

Next, use Part to set all of the rows to 0:

B[[delete]] = SparseArray[{}, {len, 60000}]; //AbsoluteTiming

{0.00192, Null}

Here is the number of nonzero values after zeroing out rows:

Length @ B["NonzeroValues"]

208689

Update

The OP asked about replacements with a more complicated RHS (in his example the RHS could be constructed from an appropriate Dot product of a sparse matrix with B). Here is an example with a random, but fairly sparse RHS:

sub = SparseArray @ RandomChoice[{.9999,.0001} -> {0, 1}, {2670, 60000}];

Using the same procedure as before:

B = B0;
Length @ B["NonzeroValues"]
B[[delete]] = sub; //AbsoluteTiming

219989

{0.009667, Null}

Check:

Length @ sub["NonzeroValues"]
Length @ B["NonzeroValues"]

%-%%

16024

224713

208689

The timing above depends heavily on the sparsity of the substitute matrix.

One final note. @george2079 tried multiplying 2 sparse matrices as an alternative. A similar idea is to multiply a sparse array with a spare vector. This is also quite fast, but not as flexible (one can only zero out rows, not replace rows with some other desired row):

B = B0;
Length @ B["NonzeroValues"]

B = B SparseArray @ Clip @ bounindex; //AbsoluteTiming
Length @ B["NonzeroValues"]

219989

{0.006694, Null}

208689

• tricky use of sparsearray! – Ulrich Neumann Dec 28 '17 at 20:58
• This is cool in my viewpoint. Now, I have an inquiry to see if it is possible to extend your response. Is there a way to generalize this way by a way at which several rows are replaced by a combination of some other rows? For instance, in the following piece of code: Table[B[[i]] = (2 B[[i - 2 (n*o)]] + 4 B[[i - (n*o)]]), {i, size, size - (n*o) + 1, -1}]; // AbsoluteTiming – Fazlollah Dec 28 '17 at 21:00
• @Fazlollah I'm afk for a bit, but the rhs looks like a dot product of a matrix with 2s and 4s in the right place with B. If this matrix is Sparse, then the Dot product will be sparse, and then the same kind of Part assignment should work. – Carl Woll Dec 28 '17 at 21:09
• This response is great and fruitful for anyone solves high dimensional PDEs and wishes to impose the boundaries directly into the coefficient matrix. Thanks a lot. – Fazlollah Dec 30 '17 at 16:18

Perhaps ReplacePart[] is the answer you are looking for:

index0 = Position[bounindex, 0];
Bnew=ReplacePart[B, index0 -> vector1];

It is as fast as the Table-version...

• Does this do the replacement properly? Please re-check it. – Fazlollah Dec 28 '17 at 20:53
• ReplacePart command doesn't change B, Bnew(see my edit/answer is the 'replaced' matrix! – Ulrich Neumann Dec 29 '17 at 11:03

Edit no this is not good. It seems the matrix multiplication expands the sparse arrays ( evidenced by memory usage).

--

I dont know if this is good performance wise or not, but here is a simple idea:

construct a 1-base sparse array with a zero row and multiply:

B = B SparseArray[ {3, i_} -> 0, Dimensions[base] , 1]

format: plain


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# Cylinder Calculator

Enter the Height = units

Volume of the Cylinder = cubic units

Curved Surface Area of the Cylinder = square units

Total Surface Area of the Cylinder = square units

The Cylinder Calculator an online tool which shows Cylinder for the given input. Byju's Cylinder Calculator is a tool
which makes calculations very simple and interesting. If an input is given then it can easily show the result for the given number.

#### Practise This Question

What is the probability of getting a sum of 13 when rolling a pair of dice?


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# What are some of the best books on complex systems?

I'm rather interested in getting my feet wet at the interface of complex systems and emergence. Can anybody give me references to some good books on these topics? I'm looking for very introductory technical books.

-
@Dilaton. Perhaps it would be better to create one post for book recommendations of complex systems, and a separate post for book recommendations of information theory? It might not be constructive to keep them together. Also please crosscheck with the book recommendation topics that Phys.SE (and sister sites) already have. –  Qmechanic Oct 13 '12 at 14:18
–  Dimensio1n0 Sep 18 '13 at 9:10

Maybe these three lectures about emergence could be interesting to get a first overview of the topic. Therein Prof. De Deo explains for example that emergence has a lot to to with what new phenomena can occurre when coarse graining (or renormalizing) microscopic degrees of freedom of a large system to obtain an effective (possibly including emergent phenomena) macroscopic description.

Background material to understand and deepen the wisdom about the concepts presented in these lectures can be found here. Among these resources is this book titled "Statistical Physics: Statics, Dynamics and Renormalization". It explains not only the statistical mechanics basics, but from the authors "interdisciplinery" point of view it includes topics such as renormalization, self-organized criticality complexity, and other things which are useful and important to understand emergence (as explained in the video lectures).

I've just read some chapters of this book, it is slightly technical and very accessible, and the style of writing makes me wanting to read the whole thing.

-

James P. Sethna is one of the leading figure in this area. You can refer to his book without any doubt. http://www.lassp.cornell.edu/sethna/

-

I like the book Energy Landscapes by David Wales. It deals with various classes of complex systems (clusters, glasses, proteins) in the context of chemistry.

I want to add - emergence is fraught with flaky ideas; a lot of appeals to ignorance are rooted from the idea of irreducible complexity. So because we can't, say, predict the weather from $F=ma$, this means that God makes it happen.

If you're interested in something "bigger" than the chemistry of complex systems, I like the work of David Bohn (say, The Undivided Universe).

-


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Bayesian Mortality Modeling

library(StanMoMo)

Introduction: Bayesian Lee-Carter with Stan

First, we explain how to estimate the Lee-Carter model using the lc_stan function in the StanMoMo package.

For illustration, the package already includes the object FRMaleData containing deaths (FRMaleData$Dxt) and central exposures (FRMaleData$Ext) of French males for the period 1816-2017 and for ages 0-110 extracted from the Human Mortality Database. In this example, we focus on ages 60-90 and the period 1980-2010. This can be obtained via:

ages.fit<-60:90
years.fit<-1980:2010
deathFR<-FRMaleData$Dxt[formatC(ages.fit),formatC(years.fit)] exposureFR<-FRMaleData$Ext[formatC(ages.fit),formatC(years.fit)]

As a reminder, the Lee-Carter model assumes that the log death rates are given by $\log \mu_{xt}=\alpha_x+\beta_x \kappa_t$ To ensure identifiability of the model, we assume that $\sum_x \beta_x=1,\kappa_1=0$

Moreover, we assume that the period parameter follows a random walk with drift: $\kappa_t \sim \mathcal{N}(c+ \kappa_{t-1},\sigma)$ The choice of priors for each parameter can be found in the documentation of each function.

Bayesian Estimation

All the parameters can be estimated either under a Poisson model with argument family = "poisson" or under a Negative-Binomial model which includes an additional overdispersion parameter $$\phi$$ with argument family="nb": $D_{xt} \sim Poisson (e_{xt}\mu_{xt}) \text{ or } D_{xt} \sim NB (e_{xt}\mu_{xt},\phi)$ Given the matrix of deaths deathFR and the matrix of central exposures exposureFR, we can infer the posterior distribution of all the parameters and obtain death rates forecasts for the next 10 years under a Poisson model by a simple call to the lc_stan function:

fitLC=lc_stan(death = deathFR,exposure=exposureFR, forecast = 10, family = "poisson",chains=1,iter=1000,cores=1)
##
## SAMPLING FOR MODEL 'leecarter' NOW (CHAIN 1).
## Chain 1:
## Chain 1: Gradient evaluation took 0 seconds
## Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
## Chain 1:
## Chain 1:
## Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
## Chain 1: Iteration: 100 / 1000 [ 10%]  (Warmup)
## Chain 1: Iteration: 200 / 1000 [ 20%]  (Warmup)
## Chain 1: Iteration: 300 / 1000 [ 30%]  (Warmup)
## Chain 1: Iteration: 400 / 1000 [ 40%]  (Warmup)
## Chain 1: Iteration: 500 / 1000 [ 50%]  (Warmup)
## Chain 1: Iteration: 501 / 1000 [ 50%]  (Sampling)
## Chain 1: Iteration: 600 / 1000 [ 60%]  (Sampling)
## Chain 1: Iteration: 700 / 1000 [ 70%]  (Sampling)
## Chain 1: Iteration: 800 / 1000 [ 80%]  (Sampling)
## Chain 1: Iteration: 900 / 1000 [ 90%]  (Sampling)
## Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
## Chain 1:
## Chain 1:  Elapsed Time: 10.791 seconds (Warm-up)
## Chain 1:                3.464 seconds (Sampling)
## Chain 1:                14.255 seconds (Total)
## Chain 1:

Internally, the sampling is performed through the rstan::sampling function. By default, Stan samples four Markov chains of 2000 iterations. For each chain, there are 1000 warmup iterations (hence, 4000 post warm-up draws in total). Moreover, by default, Stan uses 1 core but we recommend using as many processors as the hardware and RAM allow (up to the number of chains). All this can be set using the following additional arguments : for instance, if one wants to sample 2 chains of 3000 iterations with 1000 warm-up samples, one can add chains=2,iter=3000,warmup=1000.

The output is an object of class stanfit (cf. the rstan package) which contains, among others, posterior draws, posterior summary statistics and convergence diagnostics.

The easiest way to extract the posterior draws is to call the rstan::extract function which returns a list with named components corresponding to the model parameters.

#Extract model parameters from the fitted model
params<-rstan::extract(fitLC)
print(names(params))
##  [1] "a"       "b"       "c"       "ks"      "sigma"   "k"       "phi"
##  [8] "k_p"     "mufor"   "log_lik" "pos"     "pos2"    "pos3"    "lp__"

Among these parameters, we find

• a : $$\alpha_x$$.
• b : $$\beta_x$$.
• k : $$\kappa_t$$.
• k_p : forecasts of $$\kappa_t$$.
• mufor : forecasts of death rates $$\mu_{xt}$$.
• log_lik : log-likelihoods.
• phi : overdispersion parameter for the NB model.
• c and sigma : drift and standard deviation of the random walk with drift.

The user can have access to an interface for interactive MCMC diagnostics, plots and tables helpful for analyzing posterior samples through the shinystan package (fore more details, you can check the shinystan web page)

library(shinystan)
launch_shinystan(fitLC)

Note: you need to close the shiny app before continuing in R.

Moreover, the package also includes functions to represent boxplots of the posterior distribution as well as fan plots for death rates predictions based on the ggplot2 and ggfan packages.

For instance, boxplots for the parameters from the Lee-Carter model can be obtained via:

boxplot_post_dist(fitLC, "a", ages.fit, years.fit)

boxplot_post_dist(fitLC, "b", ages.fit, years.fit)

boxplot_post_dist(fitLC, "k", ages.fit, years.fit)

Forecasting

All forecast death rates $$\mu_{xt}$$ are stored in the output mufor. We point out that the output mufor is a matrix of dimension $$N$$ $$\times$$ $$(A . M)$$ where the number of rows $$N$$ is the posterior sample size and the number of columns $$A.M$$ is the product of $$A$$ the age dimension and $$M$$ the number of forecast years.

Predictions of death rates for the next 10 years for ages 65, 75 and 85 with prediction intervals can be obtained as follows via

forecasting_plot(fitLC,ages.fit,years.fit,deathFR,exposureFR,c(65,75,85))

Other models

In a similar fashion, the models RH, APC, CBD and M6 can be estimated with the following functions:

Model Predictor
LC $$\log \mu_{xt} = \alpha_x + \beta_x\kappa_t$$
RH $$\log \mu_{xt} = \alpha_x + \beta_x\kappa_t+\gamma_{t-x}$$
APC $$\log \mu_{xt} = \alpha_x + \kappa_t +\gamma_{t-x}$$
CBD $$\log \mu_{xt} = \kappa_t^{(1)} + (x-\bar{x})\kappa_t^{(2)}$$
M6 $$\log \mu_{xt} = \kappa_t^{(1)} + (x-\bar{x})\kappa_t^{(2)}+\gamma_{t-x}$$
fitRH=rh_stan(death = deathFR,exposure=exposureFR, forecast = 10, family = "poisson",cores=4)
fitAPC=apc_stan(death = deathFR,exposure=exposureFR, forecast = 10, family = "poisson",cores=4)
fitCBD=cbd_stan(death = deathFR,exposure=exposureFR, age=ages.fit, forecast=10,family = "poisson",cores=4)
fitM6=m6_stan(death = deathFR,exposure=exposureFR, age=ages.fit,forecast = 10, family = "poisson",cores=4)

For information, the estimated parameters $$\kappa_t^{(1)}$$, $$\kappa_t^{(2)}$$ and $$\gamma_{t-x}$$ are respectively stored in the variables k,k2 and g. The forecast parameters are respectively stored in the variables k_p,k2_p and g_p.

You can check the next vignette to know more about model averaging techniques based on leave-future-out validation.


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$$\require{cancel}$$

# 7.2: Lorenz and Poincaré Invariance

One of the most common continuous symmetries of a relativistic theory is Lorentz invariance, i.e., the dynamics is the same in any Lorentz frame. The group of Lorentz transformations can be decomposed into two parts:

• Boosts, where we go from one Lorentz frame to another, i.e., we change the velocity.
• Rotations, where we change the orientation of the coordinate frame.

There is a slightly larger group of symmetries, called the Poincaré group, obtained when we add translations to the set of symmetries – clearly the dynamics doesn’t care where we put the orbit of space. The set of conserved quantities associated with this group is large. Translational and boost invariance implies conservation of four momentum, and rotational invariance implies conservation of angular momentum.

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# Gradientless Descent: High-Dimensional Zeroth-Order Optimization

ICLR 2020 (2020)

## Abstract

Zeroth-order optimization is the process of minimizing an objective $f(x)$ given oracle access to evaluations at adaptively chosen inputs $x$. In this paper, we present two simple yet powerful GradientLess Descent (GLD) algorithms that do not rely on an underlying gradient estimate and are numerically stable. We analyze our algorithm from a novel geometric perspective and we derive two invariance properties of our algorithm: monotone and affine invariance. Specifically, for {\it any monotone transform} of a smooth and strongly convex objective with latent dimension $k$, then we present a novel analysis that shows convergence within an $\epsilon$-ball of the optimum in $O(kQ\log(n)\log(R/\epsilon))$ evaluations, where the input dimension is $n$, $R$ is the diameter of the input space and $Q$ is the condition number. Our rates are the first of its kind to be both 1) poly-logarithmically dependent on dimensionality and 2) invariant under monotone transformations. From our geometric perspective, we can further show that our analysis is optimal. We emphasize that monotone and affine invariance are key to the empirical success of gradientless algorithms, as demonstrated on BBOB and MuJoCo benchmarks.


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## Jess Roberts

June 26th, 2017

Roberts, J. (2016). “hear the bird”: Sarah Piatt and the Dramatic Monologue. In A. Socarides & J. Putzi (Eds.), A History of Nineteenth-Century American Women’s Poetry (pp. 345-358). Cambridge: Cambridge University Press.

Abstract: For much of the latter half of the nineteenth century, American poet Sarah Piatt wrote and published poems that gave voice to women and children, that grieved the loss of loved ones and moral certainty, and that revealed an unnerving inclination for self-conscious complexity. Some of the most culturally influential periodicals of her time – Atlantic Monthly, Harper’s Weekly, Scribner’s – circulated hundreds of her poems, as well as reviews of the many collections of these poems in book form. These reviews were, by turns, delighted and discomfited by what they called Piatt’s “distinctiveness,” heralding her as one of America’s geniuses even as they cautioned her against apparently unbecoming subtlety and obscurity.

Among the things that distinguished Piatt was her obvious interest in the contextual dynamism of spoken language and the poetic genre that seemed particularly well suited to capitalize on and examine it: the dramatic monologue. Over the course of her career, Piatt wrote more dramatic monologues than any other nineteenth-century American poet. Though many Piatt scholars have addressed dramatic monologues in the context of essays about Piatt’s irony or ambivalence, and in terms of her place among Confederate poets or in postbellum magazine culture, no one has yet read her dramatic monologues primarily through the lens of genre. That is what I do here. In the pages that follow, I describe the generic conventions of the dramatic monologue that are integral to Piatt’s experiments with it, building an interpretive framework out of the doubleness inherent to the genre. I ground that analysis in Piatt’s fifth collection, Dramatic Persons and Moods (1879), because it provides the poems I address with a shared print context, the very title of which directs the reader’s eye to genre. What emerges is a clear picture of how Piatt manipulated the particular conventions of the dramatic monologue in order to anatomize the way women maintained and disrupted the very conventions that restricted their range of experience and expression in their roles as mothers and daughters, readers and writers.

## Nicolle Zellner

June 23rd, 2017

Zellner, N. E. B. (2017). Cataclysm No More: New Views on the Timing and Delivery of Lunar Impactors. Origins of Life and Evolution of Biospheres, 1-20.

Abstract: If properly interpreted, the impact record of the Moon, Earth’s nearest neighbour, can be used to gain insights into how the Earth has been influenced by impacting events since its formation ~4.5 billion years (Ga) ago. However, the nature and timing of the lunar impactors – and indeed the lunar impact record itself – are not well understood. Of particular interest are the ages of lunar impact basins and what they tell us about the proposed “lunar cataclysm” and/or the late heavy bombardment (LHB), and how this impact episode may have affected early life on Earth or other planets. Investigations of the lunar impactor population over time have been undertaken and include analyses of orbital data and images; lunar, terrestrial, and other planetary sample data; and dynamical modelling. Here, the existing information regarding the nature of the lunar impact record is reviewed and new interpretations are presented. Importantly, it is demonstrated that most evidence supports a prolonged lunar (and thus, terrestrial) bombardment from ~4.2 to 3.4 Ga and not a cataclysmic spike at ~3.9 Ga. Implications for the conditions required for the origin of life are addressed.

## Greg Saltzman

June 23rd, 2017

Saltzman, G. M. (2016). Contested Terrain:  Developments in Labor Law Affecting Higher Education Since 2012. In H. S. Wechsler (Ed.), NEA 2016 Almanac of Higher Education (Washington:  National Education Association (pp. 31-38).

## Vicki Baker

June 22nd, 2017

Baker, V. (2017). Organizational Contexts & Formal Mentoring Programs: Aligning Individual and Organizational Outcomes. In D. A. Clutterbuck, F. K. Kochan, L. Lunsford, N. Dominguez & J. Haddock-Millar (Eds.), The SAGE Handbook of Mentoring: SAGE Publishing.

## Christopher Rohlman

June 22nd, 2017

Rohlman, C. E., Blanco, M. R., & Walter, N. G. (2016). Putting Humpty-Dumpty Together: Clustering the Functional Dynamics of Single Biomolecular Machines Such as the Spliceosome. In M. Spies & Y. R. Chemla (Eds.), Single-Molecule Enzymology: Fluorescence-Based and High-Throughput Methods (Vol. 581, pp. 257-283).

Abstract: The spliceosome is a biomolecular machine that, in all eukaryotes, accomplishes site-specific splicing of introns from precursor messenger RNAs (pre-mRNAs) with high fidelity. Operating at the nanometer scale, where inertia and friction have lost the dominant role they play in the macroscopic realm, the spliceosome is highly dynamic and assembles its active site around each pre-mRNA anew. To understand the structural dynamics underlying the molecular motors, clocks, and ratchets that achieve functional accuracy in the yeast spliceosome (a long-standing model system), we have developed single-molecule fluorescence resonance energy transfer (smFRET) approaches that report changes in intra-and intermolecular interactions in real time. Building on our work using hidden Markov models (HMMs) to extract kinetic and conformational state information from smFRET time trajectories, we recognized that HMM analysis of individual state transitions as independent stochastic events is insufficient for a biomolecular machine as complex as the spliceosome. In this chapter, we elaborate on the recently developed smFRET-based Single-Molecule Cluster Analysis (SiMCAn) that dissects the intricate conformational dynamics of a pre-mRNA through the splicing cycle in a model-free fashion. By leveraging hierarchical clustering techniques developed for Bioinformatics, SiMCAn efficiently analyzes large datasets to first identify common molecular behaviors. Through a second level of clustering based on the abundance of dynamic behaviors exhibited by defined functional intermediates that have been stalled by biochemical or genetic tools, SiMCAn then efficiently assigns pre-mRNA FRET states and transitions to specific splicing complexes, with the potential to find heretofore undescribed conformations. SiMCAn thus arises as a general tool to analyze dynamic cellular machines more broadly.

## Andy Boyan

June 8th, 2017

Sherry, J. L., Boyan, A., Knight, K., Edwards, C., & Hao, Q. (2017). Multiplayer games as the ultimate communication lab and incubator: A multi-media study. In R. Kowert & T. Quandt (Eds.), New Perspectives on the Social Aspects of Digital Gaming: Multiplayer 2. New York: Routledge.

May 31st, 2017

Mor-Vaknin, N., Saha, A., Legendre, M., Carmona-Rivera, C., Amin, M. A., Rabquer, B. J., et al. (2017). DEK-targeting DNA aptamers as therapeutics for inflammatory arthritis. Nature Communications, 8, 14252.

Abstract: Novel therapeutics are required for improving the management of chronic inflammatory diseases. Aptamers are single-stranded RNA or DNA molecules that have recently shown utility in a clinical setting, as they can specifically neutralize biomedically relevant proteins, particularly cell surface and extracellular proteins. The nuclear chromatin protein DEK is a secreted chemoattractant that is abundant in the synovia of patients with juvenile idiopathic arthritis (JIA). Here, we show that DEK is crucial to the development of arthritis in mouse models, thus making it an appropriate target for aptamer-based therapy. Genetic depletion of DEK or treatment with DEK-targeted aptamers significantly reduces joint inflammation in vivo and greatly impairs the ability of neutrophils to form neutrophil extracellular traps (NETs). DEK is detected in spontaneously forming NETs from JIA patient synovial neutrophils, and DEK-targeted aptamers reduce NET formation. DEK is thus key to joint inflammation, and anti-DEK aptamers hold promise for the treatment of JIA and other types of arthritis.

## Holger Elischberger, Eric Hill and Lynn Verduzco-Baker

May 25th, 2017

Elischberger, H. B., Glazier, J. J., Hill, E. D., & Verduzco-Baker, L. (2017). Attitudes Toward and Beliefs about Transgender Youth: A Cross-Cultural Comparison Between the United States and India. Sex Roles, 76, 1-19.

Abstract: Using an internet-based survey, we examined attitudes toward transgender youth in the United States and India, two cultures with differences in conceptualizations of gender and treatment of transgender individuals in society, law, and religion. We found generally positive attitudes toward transgender youth in our U.S. (n = 218), but moderately negative ones in our Indian (n = 217), sample. Consistent with the literature on prejudice against transgender adults in many Western societies, general social conservatism in the form of religious beliefs and political ideology, gender-specific conservatism in the form of gender binary belief, and endorsement of environmental rather than biological causes of transgender identity were the best predictors of U.S. participants’ attitudes, although personal contact with gender and sexual minorities also played a role at the bivariate level. These findings suggest that the processes underlying prejudice against transgender youth are similar to those that foster adult-directed transphobia in that cultural context. In contrast, religion-based disapproval and environmental causal attributions were the best predictors of Indian respondents’ attitudes, whereas gender binary belief played only a minor role, and political conservatism and personal contact no role at all. Our regression analyses accounted for considerably more of the variability in U.S. than in Indian participants’ attitudes, highlighting the need for additional (qualitative) work to identify the factors that promote transprejudice in India. We discuss these findings in light of cross-cultural differences between the two countries in terms of our predictors and consider implications for efforts to reduce prejudice against transgender youth.

Albion College Student Co-Author: Jessica Glazier, ’16

## David Seely

May 18th, 2017

Seely, D. G., Andrianarijaona, V. M., Wulf, D., Morgan, K., McCammon, D., Fogle, M., et al. (2017). Line ratios for soft-x-ray emission following charge exchange between ${\mathrm{O}}^{8+}$ and Kr. Physical Review A, 95(5), 052704.

Abstract: Lyman spectra and line ratios are reported for soft-x-ray emissions following the charge exchange process in 293, 414, 586, and 1256 km/s O8+ and Kr collisions. Lyman series from Ly-α to Ly-ɛ were resolved for the O7+ ion using a high-resolution x-ray quantum microcalorimeter detector. It is found that the observed line ratios are dependent on the nl distribution of the captured electron, and the Ly-α and Ly-β x-ray emissions are enhanced. Moreover, by comparing the measured line ratios to the constructed theoretical single charge exchange line ratios for O8+ +H, it is suggested that autoionizing double capture plays a significant role in the enhancement of Ly-α and Ly-β emissions for the present system.

## Vicki Baker

May 18th, 2017

Baker, V. L., Greer, J., Lunsford, L. G., Pifer, M. J., & Ihas, D. (2017). Documenting the Aspiration Gap in Institutional Language About Undergraduate Research, Scholarship, and Creative Work. Innovative Higher Education, 42(2), 127-143.

Abstract: We conducted a content-analysis of the websites of 100 institutional members of the Council of Undergraduate Research in order to examine the relationship between messages communicated on websites as compared to messages expressed within institutional procedures and policies. Findings show that public research institutions were more likely than baccalaureate institutions to have an Office of Undergraduate Research. Further incentives and supports provided by such offices are predominantly directed to students. Lastly, our analysis of promotion and tenure policies reveals that only 14 institutions out of the 100 in our sample explicitly mentioned mentoring undergraduate researchers in the evaluation criteria for faculty members. We offer implications for research and practice.

## Cliff Harris

May 18th, 2017

Kambhu, A., Gren, M., Tang, W., Comfort, S., & Harris, C. E. (2017). Remediating 1,4-dioxane-contaminated water with slow-release persulfate and zerovalent iron. Chemosphere, 175, 170-177.

Abstract: 1,4-dioxane is an emerging contaminant that was used as a corrosion inhibitor with chlorinated solvents. Metal-activated persulfate can degrade dioxane but reaction kinetics have typically been characterized by a rapid decrease during the first 30 min followed by either a slower decrease or no further change (i.e., plateau). Our objective was to identify the factors responsible for this plateau and then determine if slow-release formulations of sodium persulfate and Fe0 could provide a more sustainable degradation treatment. We accomplished this by conducting batch experiments where Fe0-activated persulfate was used to treat dioxane. Treatment variables included the timing at which the dioxane was added to the Fe0-persulfate reaction (T = 0 and 30 min) and including various products of the Fe0-persulfate reaction at T = 0 min (Fe2+, Fe3+, and SO42−). Results showed that when dioxane was spiked into the reaction at 30 min, no degradation occurred; this is in stark contrast to the 60% decrease observed when added at T = 0 min. Adding Fe2+ at the onset (T = 0 min) also severely halted the reaction and caused a plateau. This indicates that excess ferrous iron produced from the Fe0-persulfate reaction scavenges sulfate radicals and prevents further dioxane degradation. By limiting the release of Fe0 in a slow-release wax formulation, degradation plateaus were avoided and 100% removal of dioxane observed. By using 14C-labeled dioxane, we show that ∼40% of the dioxane carbon is mineralized within 6 d. These data support the use of slow-release persulfate and zerovalent iron to treat dioxane-contaminated water.

## Roger Albertson

May 11th, 2017

Strunov, A., Schneider, D. I., Albertson, R., & Miller, W. J. (2017). Restricted distribution and lateralization of mutualistic Wolbachia in the Drosophila brain. Cellular Microbiology, 19(1).

Abstract: Microbial symbionts are universal entities of all living organisms that can significantly affect host fitness traits in manifold ways but, even more fascinating, also their behaviour. Although better known from parasitic symbionts, we currently lack any cases where ‘neurotrophic’ symbionts have co-evolved mutualistic behavioural interactions from which both partners profit. By theory, most mutualistic associations have originated from ancestral parasitic ones during their long-term co-evolution towards a cost-benefit equilibrium. To manipulate host behaviour in a way where both partners benefit in a reciprocal manner, the symbiont has to target and remain restricted to defined host brain regions to minimize unnecessary fitness costs. By using the classic Drosophila paulistorum model system we demonstrate that (i) mutualistic Wolbachia are restricted to various Drosophila brain areas, (ii) form bacteriocyte-like structures within the brain, (iii) exhibit strictly lateral tropism, and (iv) finally propose that their selective neuronal infection affects host sexual behaviour adaptively.

## Lynn Verduzco-Baker

May 10th, 2017

Verduzco-Baker, L. (2017). “I Don’t Want Them to Be a Statistic”: Mothering Practices of Low-Income Mothers. Journal of Family Issues, 38(7), 1010-1038.

Abstract: U.S. discourse on low-income mothers frames them as social problems and this presumption of deficiency is reflected in studies of parenting logics and practices. Scholars often underestimate the sophistication of low-income mothers’ parenting logic and do not recognize that these mothers work as hard as and use (appropriately) different parenting logics than those of middle-class mothers. I investigate parenting logics of African American and White low-income mothers. These women demonstrate a logic that follows many of the same premises of middle-class parenting strategies but additionally seeks to address obstacles that prevent low-income youth from reaching goals: addiction, drug dealing, pregnancy, and the street. This logic leads to strategies that may appear to be inexpensive adaptations of middle-class practices, however, analysis of mothers’ narratives reveals they are not derivative but are intended to prepare children to avoid perils of their social context. This study illuminates a previously misunderstood version of intensive mothering.

## Carrie Menold

May 4th, 2017

Sievers, N. E., Menold, C. A., Grove, M., & Coble, M. A. (2017). White mica trace element and boron isotope evidence for distinctive infiltration events during exhumation of deeply subducted continental crust. International Geology Review, 59(5-6), 621-638.

Abstract: Previous study of subducted continental crust within the Luliang Shan terrane in Northwest China has documented metasomatic formation of thick, hydrated phengite + garnet-rich selvages at the interface between mafic eclogite blocks and quartzofeldspathic host gneiss. Whole rock concentrations of Cs and Ba within the selvage are enriched by two orders of magnitude relative to the eclogite blocks and host gneiss. We performed in situ ion microprobe analyses of Li, Be, B, Rb, Sr, Cs and Ba and δ11B of phengite within the Luliang Shane terrane to better constrain the source(s) of the infiltrating fluid. The phengite within the selvage are enriched in Li, Cs and Ba and yield δ11B values between ?30? and ?9?, values that are lower than mantle values. High Ba/Rb, Cs/Rb coupled with low B/Be, B/Li and highly negative δ11B values indicate that the high-pressure fluid that formed the selvage was derived from highly devolatilized rocks within the subduction channel. In contrast, muscovite, which crystallized in the adjacent host gneiss during a subsequent lower pressure phase of fluid infiltration at approximately 0.9 GPa depths, has much lower Li, Cs and Ba relative to the high-pressure phengite. These retrograde muscovite have very high concentrations of B (up to 5500 ppm) and Be (up to 50 ppm) and high (?2 to +8?) δ11B values that are consistent with crystallization from a fluid derived from shallower and less devolatilized regions of the subduction zone. Additional host gneiss samples, regionally distributed and kilometres away from the studied area lack the B-rich signature and indicate that the late stage fluids were likely localized to the region near the studied traverse.

## Andy Boyan

May 4th, 2017

Bowman, N. D., Hallett, J., Boyan, A., & Groskopf, J. (2017). Squid or Chalkie? The Role of Self-identify and Selective Perception in Processing Tendentious “Hillbilly” Humor. Ohio Communication Journal, 55, 16-28.

## Heather Jordon

March 23rd, 2017

Jordon, H., & Morris, J. (2017). Cyclic m-cycle systems of complete graphs minus a 1-factor. Australasian Journal of Combinatorics, 67(2), 304–326.

Abstract: In this paper, we provide necessary and sufficient conditions for the existence of a cyclic m-cycle system of Kn − I when m and n are even and m | n.

## Craig Streu

March 15th, 2017

Streu, C. N., Reif, R. D., Neiles, K. Y., Schech, A. J., & Mertz, P. S. (2016). Drug Synthesis and Analysis on a Dime: A Capstone Medicinal Chemistry Experience for the Undergraduate Biochemistry Laboratory. Journal of Chemical Education, 93(12), 2084-2088.

Abstract: Integrative, research-based experiences have shown tremendous potential as effective pedagogical approaches. Pharmaceutical development is an exciting field that draws heavily on organic chemistry and biochemistry techniques. A capstone drug synthesis/analysis laboratory is described where biochemistry students synthesize azo-stilbenoid compounds and test the biological activity of those compounds as well as a known inhibitor on mushroom tyrosinase using UV/vis-based kinetic assays. In this paper, three such successful azo-stilbenoid inhibitors of tyrosinase, representative student generated data, technical aspects of the experiments, and an interpretation of student feedback on the project as a whole are presented.

## Vicki Baker

March 9th, 2017

Lunsford, L. G., & Baker, V. L. (2016). Great Mentoring in Graduate School: A Quick Start Guide for Protégés. Washington, DC: Council of Graduate Schools.

Abstract: Great Mentoring in Graduate School: A quick start guide for protégés provides a practical, student-oriented perspective informed by the authors’ experience and research on mentoring. The guide includes helpful advice and tips on a range of topics such as identifying a mentor, engaging with mentors to develop a professional identify, cultivating networks, and serving as a mentor to others.

March 9th, 2017

Chase, B., Ajithprasad, P., & Rajesh, S. V. (2016). The Identification of Diversity: Material Culture and Social Practice in Harappan Gujarat. In V. Widorn, U. Franke & P. Latschenberger (Eds.), Contextualizing Material Culture in South and Central Asia in Pre-Modern Times (pp. 111-124). Turnhout, Belgium: Brepols.

## Lynne Chytilo

March 9th, 2017

Chytilo, L. (Artist). (2016). Memory through the Senses. 100 Sculptors – 100 Sculptures Exhibit, Ella Sharp Museum of Art, Jackson, MI, November 12, 2016 – January 28, 2017.

## Glenn Deutsch

March 9th, 2017

Deutsch, G. (2016). So Big Like That. Post Road Magazine, 30.

## Karla McCavit and Nicolle Zellner

March 2nd, 2017

McCavit, K., & Zellner, N. E. B. (2016). Persistence of physics and engineering students via peer mentoring, active learning, and intentional advising. European Journal of Physics, 37(6), 065702.

Abstract: Albion College, a private, undergraduate-only, liberal arts college in Michigan, USA, has developed and implemented a low-cost peer-mentoring programme that blends personal and academic support to help students achieve academic success in the introductory courses required for the Physics Major or the Dual-Degree Program in Engineering. This enhanced mentoring programme provides much-needed assistance for undergraduate students to master introductory physics and mathematics coursework, to normalise the struggle of learning hard material, and to accept their identity as physics or engineering students (among other goals). Importantly, this programme has increased retention among entering science, technology, engineering and mathematics students at Albion College as they move through the introductory classes, as shown by a 20% increase in retention from first-semester to third-semester physics courses compared to years when this programme was not in place.

## Jess Roberts

February 22nd, 2017

Roberts, J. (2016). Teaching Patsy Yaeger. South: a scholarly journal, 48(2), 184-191.

February 22nd, 2017

Mani, R. S., Amin, M. A., Li, X., Kalyana-Sundaram, S., Veeneman, B. A., Wang, L., Rabquer, B. L., et al. (2016). Inflammation-Induced Oxidative Stress Mediates Gene Fusion Formation in Prostate Cancer. Cell Reports, 17(10), 2620-2631.

Abstract: Approximately 50% of prostate cancers are associated with gene fusions of the androgen-regulated gene TMPRSS2 to the oncogenic erythroblast transformation-specific (ETS) transcription factor ERG. The three-dimensional proximity of TMPRSS2 and ERG genes, in combination with DNA breaks, facilitates the formation of TMPRSS2-ERG gene fusions. However, the origins of DNA breaks that underlie gene fusion formation in prostate cancers are far from clear. We demonstrate a role for inflammation-induced oxidative stress in the formation of DNA breaks leading to recurrent TMPRSS2-ERG gene fusions. The transcriptional status and epigenetic features of the target genes influence this effect. Importantly, inflammation-induced de novo genomic rearrangements are blocked by homologous recombination (HR) and promoted by non-homologous end-joining (NHEJ) pathways. In conjunction with the association of proliferative inflammatory atrophy (PIA) with human prostate cancer, our results support a working model in which recurrent genomic rearrangements induced by inflammatory stimuli lead to the development of prostate cancer.

## Vicki Baker

December 20th, 2016

Pifer, M. J., & Baker, V. L. (2016). Professional, Personal, and Relational: Exploring the Salience of Identity in Academic Careers. Identity, 16(3), 190-205.

Abstract: This article explores the role of identity in lived experiences within the professoriate. While scholarship has given some attention to professional identity and personal identity, little in the literature has attempted to present a holistic view of identity and the complex ways that it defines and influences academic careers. The authors present findings from their analysis of interview data from 50 participants across career stages, from doctoral students to full professors. These findings suggest that three distinct but related, and potentially synergistic, components of identity are salient in shaping perceptions of and experiences within academic careers. The authors offer future directions for research centered on a rich conceptualization of identity as critical for understanding faculty development, experiences, and needs.

## Craig Streu

December 19th, 2016

Mertz, P., & Streu, C. (2015). Writing Throughout the Biochemistry Curriculum: Synergistic Inquiry-Based Writing Projects for Biochemistry Students. Biochemistry and Molecular Biology Education, 43(6), 408-416.

Abstract: This article describes a synergistic two-semester writing sequence for biochemistry courses. In the first semester, students select a putative protein and are tasked with researching their protein largely through bioinformatics resources. In the second semester, students develop original ideas and present them in the form of a research grant proposal. Both projects involve multiple drafts and peer review. The complementarity of the projects increases student exposure to bioinformatics and literature resources, fosters higher-order thinking skills, and develops teamwork and communication skills. Student feedback and responses on perception surveys demonstrated that the students viewed both projects as favorable learning experiences.

## Ian MacInnes

December 19th, 2016

MacInnes, I. (2016). Response: Fabulous or Spectral? Early Modern Culture, 11.

## Holger Elischberger, Eric Hill and Lynn Verduzco-Baker

December 9th, 2016

Elischberger, H. B., Glazier, J. J., Hill, E. D., & Verduzco-Baker, L. (2016). “Boys Don’t Cry”—or Do They? Adult Attitudes Toward and Beliefs About Transgender Youth. Sex Roles, 1-18.

Abstract: The present survey study examined the attitudes of U.S. adults toward transgender children and adolescents, as well as their behavioral intentions, in two hypothetical scenarios involving gender variant youth. Participants recruited online (N = 281) reported generally favorable attitudes toward transgender minors, but expressed some hesitation to allow a transgender child to use the restroom aligned with their gender as opposed to their birth sex or to share a room with same gender peers on a school trip, possibly due to conflating gender identity with sexual orientation in these situations. Attitudes were less positive in respondents who reported a religious affiliation, conservative social political views, and stronger conformity to certain traditional gender norms—particularly in men. Even after controlling for these factors, stronger belief in environmental versus biological causes of transgender identity was linked to more negative attitudes. Participants’ behavioral intentions were driven partly by their attitudes and causal attributions, but also by their age and, at least for women, personal connections to the transgender community. We discuss implications for the discourse surrounding transgender youth and the need for educating the public on the development of gender identity as well as the difference between gender identity and sexual orientation.

Albion College Student Co-Author: Jessica Glazier, ’16

## Abigail Cahill

November 22nd, 2016

Danovaro, R., Carugati, L., Berzano, M., Cahill, A. E., Carvalho, S., CHENUIL, A., et al. (2016). Implementing and innovating marine monitoring approaches for assessing marine environmental status. Frontiers in Marine Science, 3(213).

Abstract: Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labour intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine monitoring and design monitoring networks. This can be achieved by developing and testing innovative and cost-effective monitoring systems, as well as indicators of environmental status. Here, we present several recently developed methodologies and technologies to improve marine biodiversity indicators and monitoring methods. The innovative tools are discussed concerning the technologies presently utilized as well as the advantages and disadvantages of their use in routine monitoring. In particular, the present analysis focuses on: (i) molecular approaches, including microarray, Real Time quantitative PCR (qPCR), and metagenetic (metabarcoding) tools; (ii) optical (remote) sensing and acoustic methods; and (iii) in situ monitoring instruments. We also discuss their applications in marine monitoring within the MSFD through the analysis of case studies in order to evaluate their potential utilization in future routine marine monitoring. We show that these recently-developed technologies can present clear advantages in accuracy, efficiency and cost.

## Vicki Baker

November 17th, 2016

Pifer, M. J., Baker, V. L., & Lunsford, L. G. (2016). Local Cultures in Institutional Contexts: The Functions of Academic Departments in Liberal Arts Colleges. Journal for the Study of Postsecondary and Tertiary Education, 1, 233-252.

Abstract: The academic department remains understudied as a context of faculty work, particularly in institutional settings beyond the research university. In this article, we report findings from a study of faculty experiences within academic departments in liberal arts colleges, through analysis of interviews with 55 faculty members representing a 13-member consortium of liberal arts institutions in the mid-western U.S. Through inductive analysis and deductive coding from existing models, we identified five functions of departments in liberal arts colleges, including: (a) faculty hiring, retention, and promotion; (b) new faculty socialization; (c) informal interactions, mentoring, and network-building; (d) establishing and communicating institutional and departmental policies, practices, and procedures; and (e) the structuring of academic work. Findings suggest that departmental functions in liberal arts colleges are generally the same as those in other institution types, but play out differently and thus have different consequences for academic careers. Across functions, liberal arts colleges seem to be undergoing an evolution, or perhaps revolution, that has implications for academic work in such contexts.


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# New Scalar Field Quartessence

Tuesday, 18 September, 2018

## Published in:

arXiv:1809.07409

We propose a cosmological scenario involving a single scalar field, \varphi, that is a source of Dark Matter as well as Dark Energy. The Lagrangian density of \varphi contains a second field \chi, for simplicity assumed to be a scalar. For fixed values of \chi, the potential of \varphi decays exponentially at large positive \varphi-values. While \varphi is not coupled to Standard Model fields, \chi is assumed to couple to them. Hence, the Green functions of \chi depend on the temperature of the local equilibrium in the expanding universe. We assume that the coupling of \chi to \varphi is such that, at temperatures larger than some critical temperature Tc, \varphi is trapped near the origin, and excitations of \varphi about the origin form Dark Matter. After a phase transition at the temperature Tc, the trapping force disappears and \varphi rolls towards large field values. A homogenous component of \varphi appears and acts as Dark Energy. Within overdense regions, such as galaxies and galaxy clusters, the kinetic temperature is sufficiently high such that the phase transition does not occur. Thus, at the present time, \varphi can decribe both Dark Energy and Dark Matter.

## Author(s):

Robert Brandenberger
Rodrigo R. Cuzinatto
Jürg Fröhlich
Ryo Namba


text:
# Law of Sines

Law of Sines
Field: Geometry
Image Created By: Richard Scott

Law of Sines

The law of sines is a tool commonly used to help solve arbitrary triangles. It is a formula that relates the sine of a given angle to its opposite side length.

# Basic Description

In any triangle, there is a relationship between the measures of the angles and the lengths of the sides: the largest angle is opposite the longest side, the second-largest angle is opposite the second-longest side, and the smallest angle is opposite the shortest side.

The law of sines is an equation that more precisely expresses this relationship between the angles of a triangle and the length of their opposite sides. The law of sines states that the ratio between a length of one side of a triangle and the sine of its opposite angle is equal for all three sides. Specifically:

Given a triangle with side lengths $a, b, c$ and opposite angles $A, B, C$,

$\frac{a}{\sin A} = \frac{b}{\sin B} = \frac{c}{\sin C}$

The law of sines is used to find all of the lengths of the sides and the angle measures for an arbitrary triangle given only some of this information. This process is called solving a triangle. To use the law of sines in solving triangles, at least three elements of a triangle must be known. Whenever a side length and two angles are given, the law of sines can be used to solve the triangle.

In some cases, the law of sines can provide multiple solutions to a triangle. If two adjacent side lengths are given with one of the opposite angles, the law of sines cannot definitively determine the triangle, but instead offers zero, one, or two possible solutions in what is known as the ambiguous case.

The law of sines does not help with solving a triangle in several cases. With two known side lengths and the measure of the angle between, there is no way to use the law of sines to solve the triangle because no pair of opposite angle measure and side length is provided. The law of sines by itself is also not able to provide solutions when three side lengths are provided. Instead, the law of cosines is often used for solving triangles in these cases.

# A More Mathematical Explanation

## Two Derivations

There are at least two different ways to derive the law of sines: using the area [...]

## Two Derivations

There are at least two different ways to derive the law of sines: using the area formula and using the definition of sine.

### Using Area

The formula for area of a triangle uses the lengths of the base and height. By using these lengths and the angle measures of a triangle, we can derive the law of sines.

A triangle can be oriented so that any one side can be used as the base. Depending on which side is chosen as the base of the triangle, the height may be different. Let $h_{a}$ be the height when the side of length $a$ is the base. When $a$ is the base, $h_{a}$ is the distance from a vertex to the opposite side, such that $h_{a}$ is perpendicular to the side. When $b$ is oriented as the base of the triangle, $h_{b}$ runs perpendicular to side $b$ and is the distance from side $b$ to the vertex $B$.

First, we must determine the height of the triangle for each orientation of the base.

When $b$ is oriented as the base,

$\sin A = \frac{h_{b}}{c}$

$h_{b} = c \sin A$

When $a$ is oriented as the base,

$\sin B = \frac{h_{a}}{c}$

$h_{a} = c \sin B$

In any triangle,

$\text{Area} = \frac{\text{base} \times \text{height}}{2}$

Since the area of the triangle is the same no matter how the triangle is oriented, the area of the triangle with $b$ as the base is the same as the area of the triangle with $a$ as the base.

$\text{Area}_{\text{base} = b} = \text{Area}_{\text{base} = a}$

Substituting the formula for the area of a triangle,

$\frac{b h_{b}}{2} = \frac{a h_{a}}{2}$

Both $h_{b}$ and $h_{a}$ can be written in terms of side lengths $a, b, c$ and angles $A, B, C$ as shown in the "More on Height" section. Therefore, we can substitute ${(c\sin A)}$ for $h_{b}$ and ${(c\sin B)}$ for $h_{a}$, giving us

$\frac{b(c\sin A)}{2} = \frac{a(c\sin B)}{2}$

Multiplying both sides by $2$ and dividing by $c$ gives us

$b \sin A = a \sin B$

Then, rearranging once more gives us our equation in its most common form,

$\frac{a}{\sin A} = \frac{b}{\sin B}$

Since we can orient the base differently and go through the same process with other variables, we know that $\frac{b}{\sin B} = \frac{c}{\sin C}$, so

$\frac{a}{\sin A} = \frac{b}{\sin B} = \frac{c}{\sin C}$

which is the law of sines.

### Using the Definition of Sine

We know that, in a right triangle,

$\sin A =\frac{\text{opposite}}{\text{hypotenuse}}$

Letting $h$ represent height and $a, b$ represent the lengths of the sides opposite $A, B$, respectively, plug in the appropriate measures to solve for $\sin A, \sin B$.

$\sin A = \frac{h}{b}$

Clearing the fractions,

$b \sin A = h$

$\sin B = \frac{h}{a}$

Clearing the fractions,

$a \sin B = h$

Set both equations for $h$ equal to each other to get

$b \sin A = a \sin B$

Divide both sides by $\sin A, \sin B$ for

$\frac{a}{\sin A} = \frac{b}{\sin B}$

Since we can go through the same process using a different angle and different variables, we know that $\frac{b}{\sin B} = \frac{c}{\sin C}$, so

$\frac{a}{\sin A} = \frac{b}{\sin B} = \frac{c}{\sin C}$

## A Geometric Extension

For every triangle, there is some circle for which the vertices of the triangle lay on the circumference. This triangle is known as an inscribed triangle, and the circle is known as the circumcircle or circumscribed circle.

By the extended law of sines,

$\frac{a}{\sin A} = \frac{b}{\sin B} = \frac{c}{\sin C} = 2r$

where $r$ is the radius of the circumcircle.

### Proof

Let there be two inscribed triangles on a circle of radius $r$. Let $\vartriangle ABD$ be a triangle that has a hypotenuse that goes through the center of the circle. Let $\vartriangle ABC$ be an oblique triangle that shares $\overline{AB}$ with $\vartriangle ABD$.

For $\vartriangle ABD$,

$\sin D = \frac{\overline{AB}}{ \ \overline{AD} \ }$

Angle $C$ is equal to angle $D$ because they are both inscribed angles that cut the same arc. According to properties of inscribed angles, two inscribed angles that cut the same arc in circles of the came radius are equal. Since $\angle{C}$ and $\angle{D}$ are the same, so are $\sin C$ and $\sin D$.

Substituting $\sin C$ for $\sin D$ gives us

$\sin C = \frac{\overline{AB}}{ \ \overline{AD} \ }$

Solving for $\overline{AD}$ gives us

$\overline{AD} = \frac{\overline{AB}}{\sin C}$

Since $\overline{AD}$ is the diameter, $\overline{AD} = 2r$

$2r = \frac{\overline{AB}}{\sin C}$

or equivalently,

$2r = \frac{c}{\sin C}$

since $c$ is the length of the side opposite $\angle{C}$.

By the law of sines, we know that

$\frac{c}{\sin C}= \frac{a}{\sin A} = \frac{b}{\sin B}$

and therefore by the transitive property,

$\frac{a}{\sin A} = \frac{b}{\sin B} = \frac{c}{\sin C} = 2r$

## Example Problem

Solve the triangle. Find all of its parts, $\vartriangle ABC$, given $b = 10$, $A = 60^\circ$,$B = 30^\circ$.

### Solution

Since all of the angle measures in a triangle add up to $180^\circ, C = 90^\circ$

$\frac{a}{\sin A} = \frac{b}{\sin B} = \frac{c}{\sin C}$

$\frac{a}{\sin 60^\circ} = \frac{10}{\sin 30^\circ}$

Cross-multiplying gives us

$a \sin 30^\circ = (10) \sin 60^\circ$

Since $\sin 30^\circ= \frac{1}{2}$ and $\sin 60^\circ= \frac{\sqrt{3}}{2}$,

$a \left( \frac{1}{2} \right) = (10) \left( \frac{\sqrt{3}}{2} \right)$

$a = 10 \sqrt{3}$

$\frac{c}{\sin 90^\circ} = \frac{10}{\sin 30^\circ}$

Cross-multiplying gives us

$c \sin 30^\circ = (10) \sin 90^\circ$

Since $\sin 30^\circ= \frac{1}{2}$ and $\sin 90^\circ= 1$,

$c \left( \frac{1}{2} \right) = (10) (1)$

$c = 20$

If the above problem asked to find the radius of the circumcircle of $\vartriangle ABC$, the law of sines could help to find the diameter.

$\frac{a}{\sin A} = \frac{b}{\sin B} = \frac{c}{\sin C} = 2r$

$\frac{b}{\sin B} = 2r$

Substituting the values for $b, B$,

$\frac{10}{\sin 30^\circ} = 2r$

Since $\sin 30^\circ= \frac{1}{2}$,

$\cfrac{10}{\left( \frac{1}{2} \right)} = 2r$

$20 = 2r$
$10 = r$

# References

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#### Problem 1CC

1. Write an expression for the slope of the tangent line to the curve $y=f(x)$ at the point $(a, f(a))$.