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Scotland's place in Europe

Published: 5 Jan 2016 18:23
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PMs announcement means Scotland’s voice is more important than ever.

Commenting on the Prime Minister's statement to the House of Commons today on the recent European Council summit and his announcement that UK Government ministers will be able to campaign on both sides in the forthcoming referendum on EU membership, Europe Minister Humza Yousaf said:

"The Prime Minister's announcement today that he will permit his own ministers to campaign on either side in the coming EU referendum campaign is deeply worrying and could potentially move the UK closer to the EU exit door. It means whatever the outcome of the renegotiation the UK Government will not be making a unified case for remaining in the European Union.

"That is hugely significant, and means that it is more important than ever that those who do support Scotland and the UK's continued EU membership make the case as strongly as possible.

"The Scottish Government will be at the forefront of that argument in the coming months. We believe Scotland benefits enormously from being part of the EU - a vital export market accounting for almost half of Scottish exports in 2013, worth £12.9 billion and directly or indirectly supporting more than 300,000 Scottish jobs.

"The Scottish Government has not been consulted on the detail of the Prime Minister's renegotiations despite our repeated calls for Scotland to have a full and formal voice in the process to ensure our interests are properly considered and represented. Mr Cameron should share details of his proposals while there is still time, so we can be confident Scotland's views will be considered and our vital interests protected.

"Exit from the EU would pose a direct threat to jobs, investment and international influence. That is why the Scottish Government is determined to do all we can to secure a vote which keeps Scotland and the rest of the UK in the EU, and protect the benefits we all derive from our place in Europe."


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Feds shut down Megaupload, call it an international organized crime ring

As the internet pats itself on the back for protesting SOPA and changing the minds of a handful of U.S. Senators, file-sharing site Megaupload has been brought down in one of the largest copyright infringement cases of all time.

Seven individuals and two international corporations have been charged in the United States with running an international organized crime ring dealing exclusively in piracy of copyrighted material.

The U.S. Department of Justice accuses Megaupload.com of a conspiracy to traffic pirated movies, music, television programs, e-books, and software on a massive scale for the last five years, causing damages in excess of $500 million to copyright holders.

Investigation of Megaupload started with the FBI at the National Intellectual Property Rights Coordination Center (IPR Center) and extended to include the U.S. Immigration and Customs Enforcement’s Homeland Security Investigations.
This case is being led by the Department of Justice Task force on Intellectual Property, and being prosecuted by the U.S. Attorney’s Office for the Eastern District of Virginia and the Computer Crime & Intellectual Property Section in the Justice Department’s Criminal Division.

These are the same bodies that led the seizure of 150 domains from companies selling counterfeit professional sports attire, and the prosecution of warez FTP user Michael Uszakow in early 2011.

The department alleges that Megaupload's entire business model is based on the trade of popular copyrighted works, and that it rewarded users for doing so.

The indictment says Megaupload did not terminate the accounts of users who had uploaded works of copyright infringement, and "selectively complied with their obligations to remove copyrighted materials from their servers." The department says that when Megaupload was hit with a takedown notice, it would disable only a single link to the file, but leave the infringing content available through different links.

We will update with selections from actual text of the indictment shortly.

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TGIF: Spooktacular Reads

October 28, 2011

*sneaks in* Boo!

Ok, I know. You may all insert an eyeroll. But I had to!

This week the incredibly lovely Ginger at GReadsBook has asked:

Spooktacular Reads: Which books do you consider festive Halloween reads? Which stories have chilled you to the bone?

Oh this is gonna be long-winded! I tend to like books that are pretty dark and have a high creep/WTF-factor. But, I’m not necessarily into horror books. Because they give me nightmares. If you want straight up horror, check out Midnyte Reader. Anyway, I’ve divided my picks up a bit. Here’s my recent list:

No one who knows me will be surprised by this, but Maureen Johnson’s (LOVE HER) The Name of the Star is a really great ghost story.

The most haunting book I’ve read so far this year has to be Fury by Elizabeth Miles. It’s not necessarily scary, but GEEZ does it have some creepy moments.

The book with the most HOLY WTF?! is hands-down The Unbecoming of Mara Dyer by the super-fab Michelle Hodkin.

If you’d like a series to dive into, then definitely Kimberly Derting’s The Body Finder

Also, ANYTHING by Neil Gaiman. He’s a bad-ass.

And now for the kickin’ it old school list!:

Be warned! Mary Shelley’s Frankenstein is quite sad in addition to being creepy.

Washington Irving’s The Legend of Sleepy Hollow (I work down the street from Sleepy Hollow and am going on the Sleepy Hollow cemetery lantern tour TONIGHT!!!!!)

Bram Stoker’s Dracula. Duh.

Y’all, there are so many great book with high creep factors. SO. MANY. I’m sure I’ve left gaping holes in this list and y’all who are well-versed in horror are laughing at me, but . . . I tried.

Now I have a question for y’all. Have any of you read The Hollow series by Jessica Verday? It’s been on my radar for a bit, but I can’t find the damn books anywhere and I don’t like buying books I haven’t already read. So! If any of you can definitely tell me that they’re worth the monies, I will buy them. 🙂

Happy Halloween
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I was talking with some of my pupils about a question they were struggling with. This started me thinking about how the way a question is written and the language used can often distract the students from what the question is asking.

We were looking at shapes and the language of shapes by building complex shapes (like bottles and packaging) from simple ones.

MarmiteI talked to them about what they could find out in the question, and what they could work out from what they knew. But what they were struggling with (or distracted by) was the word Marmite.

The issue that had stopped them working was not a technical one, as I would see it. It was superficial to the lesson, but it was causing a blockage.

They had started talking about what it was, and stopped thinking about the language of shape.

One started calling it a bottle of Marmit.
“No”, said another, “it’s Mar-MITE.”
“Yes”, I said, “because of the magic e?”
“It’s not a magic e,” they said, “it’s a split digraph.”

So they all knew what a split digraph was, but they all could not read the word. And at the time I was annoyed about it. I wasn’t really sure why, but I was cross. Not cross because I had not heard of the phrase ‘split digraph’ before and they knew something I did not. But cross because they knew it, but could not use it. Why do we bother telling them it’s called a ‘split digraph’ when actually ‘magic e’ is just as likely to be useful? Does using the complex term make it easier to use it?

Later on, I thought about my own subject, where those short cuts are used all the time.

For example:
Over the magic fairy = bridge and changes sides or 2 negatives make a positive because the 2 lines cross

That sort of thing makes me cross when I hear it in my subject, and I wonder why they bothered to teach them those short cuts at all. So why am I expecting student not to use the specific language in English?

And that got me thinking about the elements that students need to be able to read the words that they need to access the work they are doing.

They are required to understand something (ie change the sound of the 1st e) on a sequencing or concrete level, to then be able to apply that to the abstract and unfamiliar situation, make links and spell Marmite.

And that is exactly what I don’t want for my subject. Students should not be distracted from making progress because they can’t read words or know what words mean, if those words are just a distraction. We should be careful in the words we use, and I should find out more about KS1 English!

Sometimes I’m guilty of thinking that if a pupil knows the name of the process, then they understand the process.

We want to make sure that the question is testing or developing their maths not distracting them with language they don’t understand or references that don’t have any relevance. So I’m going to try to make sure my new resources do that.


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Friday, June 5, 2009

Tempest in a nonspatial entity

Reply to Eric Reitan's defense of Goetz and Taliaferro

I've been honored by the attention of the author of the book "Is God a Delusion?", one of the many replies to Richard Dawkins and the new atheists. Eric Reitan is a philosopher and professor at Oklahoma State, and blogs at The piety that lies between, whose title is a reference to Plutarch, as well as to one founder of liberal theology, Friedrich Schleiermacher.

He expresses some appreciation and differences with my post on the spiritual atheist, on my post against theology, and most incisively, on my review of the book Naturalism by Stewart Goetz and Charles Taliaferro (G&T) which defends the idea of a supernatural soul. I'll reply to his points about this book here, to bring this discussion to a higher level, as it deserves.

I'll grant that I did not fathom all the jargon swirling within this book. I quoted three instances of what I believed to be egregious nonsense, and Reitan maintains that it is just when the jargon gets thickest that the work is most lucid. Seeing as he believes the purpose of the book is to "jar academics back to work", it should to be accessible to them- not just to specialists, but especially to the naturalists who wear the supposed blinders that predispose them against supernaturalism, such as myself, for instance.

I would not represent myself as a philosopher but as an educated layperson and scientist, capable of dealing with considerable thickets of jargon. I also labor under not having the book at hand, having borrowed it from the library (but will make some use of G&T's responses online). All the same, I think I can still say that G&T were egregiously unclear in an area that is, frankly, not rocket science.

To propose supernatural entities is to free oneself from any logical bounds: whether point-like or distributed, whether intuitive or counter-intuitive, there is no restriction at all on one's theorizing in this area, other than the points at which it contacts reality- the presumed interactions that the nonspatial entity (soul) has with our brains- causal, confined to one individual, confined in time, etc. I do not think one can point to any necessary condition of G&T's supernatural model that is not necessitated by empirical facts. Logic can not create bounds in this sphere- the nonspatial entity could be any size, any where, have any properties whatsoever, as long as it does not violate the empirically evident consciousness functions.

I could just as well propose that Peter Pan pushes around the earth's tectonic plates. There is no end of jargon I could devise to "clarify" how this might take place. But without engaging in the science at the reality-based end of this interaction, (as G&T do not do in the case of neuroscience), I would have no logical bounds on my models, and would be free to write another book about how I now think it is not Peter Pan after at all, but Poseidon who is responsible.

The basic point is that there is a reason to take the naturalist position- it eschews fantasy in deference to reality. That humans (especially children) are congenitally prone to jump to conclusions (or assumptions), including the wide-open field of supernatural conclusions, is no reason to give them philosophical credence. G&T in their web responses reiterate that "This commitment drives the naturalist’s world view and leads naturalists to question and deny the reality of how things appear to ordinary human beings." As mentioned in my original review, this is no philosophical justification for their premise, despite the smoothly expressed "reality" of this ordinary view. Ordinary human beings regard the sun as travelling through the sky and species as fixed types. Ordinary understanding does need to be explained (and corrected), but it is not a source of explanation, especially when conflicting so flagrantly with other logic and observation.

So the claim of doing "metaphysics" is not helpful in freeing the philosopher from dealing with reality. Either the system proposed agrees with reality, or it is an idea untethered from it. The test is empirical (defining "truthiness", to put it in lay terms), and every empirical indication we have is that when you chop off someone's head, their mind disappears promptly as well. Ditto for countless smaller interventions by drugs, lesions, strokes, electricity, etc. that affect aspects of consciousness.

Mathematics has a similar flexibility- one can make a mathematics of any assumptions one likes, and then strive to create a self-consistent system out of it. If that system is truly self-consistent (by way of proofs, etc.), then it stands a chance of describing aspects of the real world, since the real world is by necessity self-consistent. But that alone is no guarantee, the final test still being empirical. If the assumptions one gives oneself are completely free and without bound, however, then one is quite likely to end up in a morass of meaningless, or at any rate unnecessary, jargon and tangled thought, counting angels on the head of a pin.

Jargon aside, I think the first quote I pointed to from the book remains indefensible:
Hence, it does not seem the least bit implausible to say that a soul's thinking, choosing, experiencing pain, etc., are explainable in terms of its having the power to think and choose and exercising them, and its having the capacity to experience pain and its being actualized. (p.69).
Reitan calls the thinking behind this "neo-Aristotelian" and a "'causal ontology' that depends on a metaphysics of 'substances' with powers that derive from their 'natures'--thematically attuned to an older scholastic metaphysics". Why don't we use Aristotelian assumptions and scholastic metaphysics in modern thought outside of theology? Because they are completely vacuous. Why were the scholastics barren in their natural philosophy over hundreds of years? Because these assumptions don't productively work for anything having to do with outer reality, however closely they may cleave to psychological reality.

The basic point is that one can not just grant oneself assumptions. One has to examine, test, and judge one's assumptions at the deepest possible level. The naturalist shies from accepting a premise that is not reality-based and logic-based. The supernaturalist accepts "common understanding", causal open-ness, non-necessity of evidence, god, and other positions as starting points, each of which is philosophically impeachable. While this may count as just another pair of interpretive glasses in Reitan's book, there seems little reason to go down that path if the glasses are known to be mirrors instead of lenses. Putting on questionable or extravagant assumptions may be appropriate when exploring and teaching philosophical history, but it is no way to do philosophy.

For example, basic thermodynamics necessitates causal closure. The first law of thermodynamics about the conservation of energy is not just an assumption about reality, it is an observation that energy, in the forms of mass, energy, and information, can not be created from nothing and is interconvertable. There are no exceptions in the form of perpetual motion machines, etc. drawing data, energy, mass, etc. from outside reality (possibly excepting the origin of the universe itself, about which we are as yet profoundly ignorant). Thus to breezily propose causal open-ness and souls as supernatural entities that interact with brains, tell us what to do, etc. flies in the face of the most basic bedrock of physics, both theoretical and observed. The naturalist presupposition in this instance is not an option on the metaphysical smorgasbord, but a rather hard-won piece of empirical data.

Let me turn to some more specific notes Reitan provides on G&T:

For example, it is argued (by Sosa and others) that in order for A to causally influence B, A must first stand in a NONcausal relation with B that explains how and why A affects B as it does rather than something else (or nothing at all).
My understanding of this was that the non-causal relation was perhaps a term for a conceptual relation- one in our heads by which we make sense of the two entities in some narrative or model about their relationship which is causal in the real world. I may very well be wrong about this ... hard to tell. But it seems axiomatic that if there is a causal relation to physical objects, it should be empirically detectable, and that this would be the locus of investigation and controversy, not the armchair science that G&T offer. To reiterate, as far as the non-spatial, supernatural sphere of speculation goes, there are no intrinsic limits- the relations of A and B have no possible bounds or preconditions, interacting magically as far as we know.

[PS- After posting, I realized that I had mistaken this argument. Put concretely, two gears need to be physically close (noncausal relation) before they can induce movement in each other (causal relation). For the case of a nonspatial entity with no physical properties, one would be using purely fictive resources to describe these relations, especially if one failed to even attempt to account concretely for how the brain physically receives the signal. One might just as well resort to Star Trek tech-talk and claim that the soul and body interact over subspace (noncausal relation) by exchanging tachion pulses (causal relation).]

The passages you call gibberish all have the following in common: they presuppose their alternative metaphysical assumptions, in terms of causal powers rooted in a thing's nature. These alternative assumptions are in an important sense at odds with the assumptions that shape contemporary naturalism, assumptions which seek to understand things not in terms of a 'nature' conceived in Aristotelian terms (invoking the idea that a thing is a combination of FORM and MATTER, and that the nature of a thing is given by its FORM), but in terms of the interaction and organization of constituent physical parts--that is, reductionistically and spatio-temporally.
Right- I recognize that, but as above, it is worthwhile to analyze these assumptions at point blank, however deep and "embedded" they may be. Is thermodynamics correct? That is what naturalists assume, based not on scripture or common understanding, but on empiricism. Conversely, do we have reliable access to supernatural phenomena of any kind, or to things called "forms"? Not outside of our intuition, (aka "common understanding"), whose defects and predilections are all too obvious to the student of art, psychology, and comparative religion. Indeed the naturalistic world view and scientific method were primarily a psychological achievement, withdrawing the many projections elaborated in theology and prior philosophy and substituting for them critique by experiment and reason.

If you bring this latter metaphysic TO G&T's arguments, you are not merely begging the question but wearing a set of interpretive lenses which make it impossible to understand WHAT they are saying (and hence impossible to even begin the process of adequately assessing it).
I would be happy to grant that given all their assumptions, they make perfect, if extremely convoluted, sense. What their argument boils down to is that, given the assumption that we have souls and that super-nature exists, then we have souls with indeterminate properties and naturalism begins to look pretty silly. The argument is not at all whether their conclusions follow from their assumptions, but whether their assumptions make any sense, by the metric I hope we all share, which is congruence with reality, critically considered.

Here is a quote from web responses by G&T:
"We respectfully beg to differ. We never said that we posit the existence of the soul to fill an explanatory gap. Rather, we argued that there must be an explanatory gap in the physical world, given the existence of the soul and its choices to act. We are first convinced that the soul exists and makes libertarian choices for purposes and then go on to explain to our readers that the soul’s existence and causal activity implies that there must be a gap in the physical explanatory story."

I think it is pretty clear that they are going about this backwards. It is no surprise that if you posit souls, then the regular order of natural explanation leaves something to be desired. It is they who are not examining their assumptions, other than to lamely claim that they are following "common understandings".

The inescapable premise, it seems to me, is that science cannot discern whether there is more to reality than science can discern.

So, if we want to figure out what overarching metaphysics we should adopt, we need other considerations besides the scientific facts.
Here I have to disagree. The statement implies that reality can be defined in a way that exceeds "facts". But what would that difference be? G&T try to treat our common intuitions as facts of the highest order, from which we can conclude the existence of super-nature. But what of all the other facts that belie that same conclusion? Isn't this simply the privileging of one set of selected observations over a much more rigorous set of observations, based on their intimacy and affect?

In my view, their achievement lies in something else: reminding us that there is a research program here, and that a comprehensive worldview should be assessed not merely in terms of its 'fit' with science but with the totality of human experience, including the experience of ourselves as agents who act for reasons.
Indeed, this is where a truly scientific research program on human reasoning and volition will tell a great deal. My take on that research is that the intuitive ideas we have about will and authorship are being (or have already been) replaced by a paradigm that will explain them in a productive fashion- not explaining them away, but giving concrete accounts of their origin, mechanism, and role without impairing their subjective enjoyment. Thus one more long-cherished intuitive idea will go the way of so many before.

With that, I'll finish and return to the original topic of love and agree that the mystical religious experience generates in us love for the world, which is now so desperately needed. We needn't ask whether it loves us back- it might have a hard time doing so at this moment of ecological peril. In that respect the atheist may even agree with the doctrine of original sin- regarded as a perpetual duty we as conscious beings have to safeguard the unconscious source of our being from harm- especially including that harm caused by our own existence. Our consciousness is also our main hope, however- an expensive, hard-fought, rare, and precious achievement which may yet be of greater benefit to ourselves and our fellow creatures.

  1. "not explaining them away, but giving concrete accounts of their origin, mechanism, and role without impairing their subjective enjoyment."

    Good point. Cries of "reductionism!" are not the result of observation, but of the attitude of the offended. Observation reduces nothing. In the same vein, however, a scientist might maintain the same approach to religion as they would to humor, art, sports or sex. Giving ever more detailed descriptions of their mechanism and role, "without impairing their subjective enjoyment."

    I tend to agree with you regarding naturalism. Logic is wholly contingent on the inter-connectedness of all things (naturalism).

    However, as a "religion-friendly" naturalist, I would ask a scientist - Is it possible to fully measure the lake while we're swimming in it?

  2. "Is it possible to fully measure the lake while we're swimming in it?"

    Yes, it is, if one asks one's friendly surveyor to do so. Scientists do not as a rule study their own brains, but those of others, and coming up with a description of how consciousness works is going to rely on this approach too, for all the millennia spent in introspection. What it will mean to describe the subjective experience in such terms is not clear yet, but in the case of the sun circling the earth, the experience remains the same- we only have a new (larger) conceptual frame by which to intellectually interpret it.

  3. I'm not so sure I agree, but I think it's a worthy goal.

    We are a part of the universe. Even the act of observation becomes a player in affecting outcomes.

    Once again, it is a worthy goal that we should strive for, but I think there will always be room for intuitive searching and introspection in the pursuit of knowledge.

  4. I should add that "intuitive searching" is dangerous when it seeks to supersede observation. But respect for observation does not mean that intuitive searching should be done away with. How would a scientist find the motivation to formulate a hypothesis without it?

  5. Hi, Steven- I agree completely. I have the deepest respect for meditation, art, introspection, psychology .. the study of man. And creativity is critical to all science too, as you. say. Introspection tells us what it is like to be us in all its subjective richness and diversity, yet it does not tell us what the mechanism behind that being is- it simply can't.

    For one thing, our design is strongly outer-directed. We have great sense organs for sight, smell, etc, but poor ones for internal states. For all the complexity of our construction and workings, hunger amounts to the vaguest sensation- it is never going to tell us how the stomach works. All the introspection in the world won't tell us how the brain works either. It just isn't built that way.

    So cultivated consciousness comes in two quite complementary forms- the didactic, intellectual consciousness of how the world works and our place in it, complemented by subjective consciousness of the range of human experience, of empathy for others and spirituality, of how to get along with one's own unconscious, however it works. Both are deeply valuable and valid in their appropriate ways.

    Perhaps this is an alternate formulation of the "overlapping magisteria" idea in a way makes a little more sense to me than Gould's original one, returning to a basic subjective/objective distinction.

  6. Woops- make that "non-overlapping"!

  7. Excellent! I agree completely. 3rd person (objective) and 1st person(subjective) experience can complement each other and keep each other in check. Balance.

    I use 1st and 3rd person because I feel that they don't have the connotation that "subjective" and "objective" have - namely that they are possible states to completely achieve. The terminology I prefer implies (to me at least) that one is just taking precedence, not that the other is completely absent.

    And please understand that my feeling that complete 3rd person mastery of the universe is impossible, because we are 1st person players, is not a critique of 3rd person study. Heck no. We need 3rd person, critical thinking desperately.

    One reason I invoke the term "god" is because of the 1st person side of things. After a "deep" experience, or meditation or whatnot, I feel the term "god" more rightly describes the experience because of the personal sense of the word.

    Stepping back from the word "god" to me is casting my 1st person experience into a 3rd person light. That's not to say everyone needs "god". What is IS. But how do I describe the warm, overflowing feelings? The hope and feeling that all will be well? A 3rd person discussion is totally fine with me (serotonin, neurology, psychology, etc.), but it doesn't negate the 1st person experience (god).

    Dropping "god" for me is kind of like trying to score with your wife by discussing the mating habits of humans from the perspective of an evolutionary biologist. It might work in the classroom, but not in the bedroom!

  8. "So cultivated consciousness comes in two quite complementary forms- the didactic, intellectual consciousness of how the world works and our place in it, complemented by subjective consciousness of the range of human experience, of empathy for others and spirituality, of how to get along with one's own unconscious, however it works. Both are deeply valuable and valid in their appropriate ways."

    Have you read "The Universe in a Single Atom" by the Dalai Lama? This is quite similar to his thesis.

  9. My thoughts in response to this post are now on my blog. Since I don't know how to create a link when writing a comment on another blog, I will simply offer the url:


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Why is NGS read alignment so slow (fast)?

Modern sequencing machines produce a wealth of information. Unfortunately, it comes in the form of a jumble of millions of short sequence fragments (“reads”), for which we don’t know where on the genome they originated from. The job of read alignment tools like Bowtie2, BWA, or STAR is to bring order to chaos and tell us the likely location of a read on a reference genome.

Even if we have access to a high performance computer cluster, the alignment step is computationally expensive and thus rate-limiting in many next-generation sequencing pipelines. In perfect wet-lab biologist jargon, I have heard it referred to as the “overnight step”. Why does it take so long to determine the location of a short fragment to a reference sequence?

The bioinformatician’s question of how to map a read to a genome translates to the computer scientist’s question of how to match a pattern to a string. Luckily, the latter is a well-studied problem.

A naive approach

The simplest solution would be to take a read (the “pattern”) and slide it along the genomic sequence (the “string”) and compare at each position whether the read matches the genome. This “brute force” approach is perfectly valid and works just fine. Let’s take a look at some numbers to see if it is feasible in our context.

The human genome has approximately 3 billion bases, the typical length of a read is around 100 bases, and a typical experiment has about 10 million reads per sample. This means that a single read has roughly 3 billion possible position and for each position we would have to make 100 comparisons. Those 300 billion comparisons must be made for each of the 10 million reads, so we would end up with the fantastically large number of 3 quintillion comparisons per sample. Usually we have more than one sample. If we allow for even a single mismatch, things get completely out of hand. The brute force approach is clearly not an option.

Note that this is the worst case scenario and that there are better ways of searching a short pattern in a string. Even so, the major problem why the the brute force approach is slow remains: It makes many unnecessary comparisons. In other words, it searches for matches in areas where there is no chance of finding anything useful.

The power of indexing

When phones still had cords, people used to either memorize numbers or look them up in a phone book. If your friend’s last name started with an “S”, you wouldn’t look for his or her number in the “T” section. The implicit assumption was that all last names were ordered alphabetically and there was no chance that Mrs. Smith was to be found next to Mr. Taylor. By listing the names of people in alphabetical order, a phone book effectively limits the search space and allows you to find any number relatively quickly. A structure that facilitates lookup of large volumes of data using keys is called an “index“.

Like phone books, suffix arrays are structures that are designed for efficient searching of large bodies of text. To construct a suffix array, you sort all substrings of the original string that contain the last character (“suffixes”) in lexicographical order and record the positions relative to the unsorted suffixes. The effect is similar to a phone book. Suffixes starting with the identical character end up next to each other in the array. With a suffix array to guide the search looking up the location of a pattern in a string is extremely fast because every occurrence of the pattern is equivalent to locating the suffixes that begin with the pattern. Two binary searches for the start and end positions of the pattern within the suffix array result in the location of the pattern within the string. There are two problems, however.

The first issue is that we need to invest time to construct the suffix array from the original sequence of characters. Usually that’s not a serious problem because there exist algorithms to build suffix arrays that scale well to extremely long strings such as the human genome. On top, re-use of the index for multiple sequencing experiments will amortize the cost in time that went into building the index.

The second problem is more serious. It takes multiple times the space of the raw string to store a suffix array. This remains true even if we only implicitly store the order of the suffixes rather than the suffixes themselves. The memory footprint of the raw sequence of the human genome is on the order of several gigabytes. Working with a suffix array multiple times that size becomes troublesome if we want to keep it in RAM. This is a good examples that besides accuracy and speed, memory consumption is also an important consideration when determining how useful an algorithm or data structure is.

What we are looking for is a data structure that combines the fast lookup times of a suffix array with the low memory footprint of the brute-force approach.

The Burrows-Wheeler transform

The Burrows-Wheeler transform (BWT) is a reversible permutation of a sequence of characters that is more “compressible” than the original sequence. The BWT involves lexicographical sorting of all permutations of a string so that identical characters end up next to each other. This facilitates compact encoding as a sequence of ten A’s can be stored as “AAAAAAAAAA” or “10A” without loss of information.

There are important similarities between the suffix array and the BWT. Recall that a suffix array involves lexicographical sorting of all suffixes of a string. The BWT is the last column of a matrix of all lexicographical sorting of all permutations of a string. As the suffixes are necessarily contained in the string permutations and both are lexicographically sorted, the order of the elements in a suffix array and the Burrows-Wheeler permutation matrix must be identical. In fact, the BWT can be efficiently calculated from a suffix array and the BWT implicitly encodes a suffix array.

The BWT allows for a compact representation of the original string but it is by itself not very well suited for fast lookup of the location of a pattern. By augmenting the BWT with a table of ranks of each character in the BWT and a partial suffix arrays, we obtain a data structure that gets very close to the fast pattern matching found in suffix arrays while maintaining a memory footprint close to the raw string. Such a data structure is called an FM-index and is the basis of alignment tools like Bowtie2 and BWA (Burrows-Wheeler Aligner). The commands “bowtie2-build” and “bwa index” build the respective software-specific FM-indices that are used for running the alignment.

How to handle mismatches?

The FM-index based mapping of reads to the genome is only fast for exact matches. In practice, read mapping must be tolerant to mismatches. Mismatches can occur due to technical reasons such as PCR artifacts or incorrect base calling during the sequencing process. Conversely, true variations between sequences (SNPs, CNV, Indels) are among the most interesting biological results we have obtained from having sequenced thousands of human genomes. We definitely do not want an alignment tool to discard all reads with mismatches by default just because they aren’t perfect matches to the reference genome.

One strategy that is used in modern sequence alignment tools like Bowtie2 is to split the reads into “seeds”. Exact matches of seeds to the genome are found using the FM-index and then extended using variants of more sensitive sequence alignment algorithms like Needleman-Wunsch or Smith-Waterman. In this way, Bowtie2 balances the speed of finding the exact location of reads on the genome with a certain error tolerance that allows the identification of possibly interesting sequence variants.

What constitutes a valid alignment and how it scores can be tuned by the user with the help of command line arguments such as the number of allowed mismatches and gap penalties. This is where the biggest differences between alignment tools is observed. Which alignment tool to use is ultimately a matter of personal preference. In general, BWA is thought to have higher precision and is thus favored in variant calling, while Bowtie2 appears to be faster and more sensitive but may lack some of BWA’s precision.

The development of fast and accurate read alignment tools was an essential contribution to the current boom in genomics research. Without decades of research and algorithm development in computer science, we would be waiting for days or weeks for our read alignments to finish. So what are a few hours?

Other posts on next-generation sequence analysis:

Why we use the negative binomial distribution to model sequencing reads?

Why is NGS read alignment so slow (fast)?

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The Future Is As Bright As The Promises Of God

Posts tagged ‘happiness’

Help Yourself To Happiness

Everybody, everywhere
seeks happiness, it’s true,
But finding it and keeping it
seem difficult to do.
Difficult because we think
that happiness is found
Only in the places where
wealth and fame abound.
And so we go on searching
in palaces of pleasure
Seeking recognition
and monetary treasure,
Unaware that happiness
is just a state of mind
Within the reach of everyone
who takes time to be kind.
For in making others happy
we will be happy, too.
For the happiness you give away
returns to shine on you.
Helen Steiner Rice

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Posted by: birdsandsquirrels | August 7, 2008

waiting again

I’m about halfway through the two week wait, either 7 or 8 dpo according to TCOYF and Fertilty Friend. So far I haven’t been obsessing really, or getting my hopes up. I’m fully expecting to have to call the doctor’s office next Thursday to ask for more clomid, and psyching myself up for an hsg, and trying to figure out when to schedule S’s semen analysis. Today I had a little bit of spotting, and while I know that could potentially maybe possibly be implantation spotting, I’m not getting invested. My temps have gone up another .2 degrees, so if I was obsessing, it could be the start of a triphasic pattern. I felt a little nauseous last night and I had a hell of a time sleeping. I was so hot and couldn’t get comfortable. I’ve felt a little cramping too. Somehow, this cycle, I have so far been able to be stay emotionally distant from my hopes and expectations. I’ve been using the natural progesterone cream after ovulation this cycle, and perhaps that’s the cause of the higher temps.

I’m feeling like my entire life is focused on trying to get pregnant. I’ve become a boring person, and I can’t even talk to anyone about this stuff, except S, who is sick and tired of ‘talking about babies’. Several weeks ago, I applied for a job that I really wanted and was extremely perfectly qualified for, and I got a disappointing email yesterday saying that I was “Not selected – pursuing other candidate”. It’s total bullshit. There is no way that I wasn’t qualified enough to at least get an interview. It was a job that I would have really liked too. I’ve been in this state for nearly two years now, and while I know I’ve been picky, and have only been applying to jobs I actually want, I’ve only gotten called for one interview out of dozens of jobs I’ve applied for. And that happened right before I was going out of state for our wedding and honeymoon, so that didn’t even work out. I’m angry. On one hand, I know that I am an excellent employee, hard working, conscientious, smart, capable, and all that, but on the other hand, I keep getting rejection after rejection, in both the job search front and the baby making front. I’m depressed. I’m exhausted. I feel useless. I feel like shit all around. Wow this is a cheery post.

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Mid-Week Edition! “She Gained Automatic Salary Increase…” Click To Discover How and More!

…………….Read This Powerful Testimony Below!…………….

“I just thank You Man of God for the anointing thats over your life and this ministry. I give God the glory for my pay increase! I had started a new job about 4 months ago the pay wasn’t good but I took the job as it was nearer to my home, it was more easier for childcare too. I remembered the teaching from the Professionals meeting about how to cut corners and get your own way in your career. Something told me to call in work as I wanted to check in on the clinical lead to see how they were doing. As I called they said they was thinking of me and they have spoken to head office, since I’ve implemented good changes working here. They decided to give me a pay rise which is just for me and in full effect from last month!” S.P, London

Hi Church,

What shall we say the kingdom of heaven is like? The Kingdom of heaven is like a mustard seed, we all are seeds planted in the ground and we have time to be nurtured and to grow. Whatever your facing you may be in your season of being prepared but I declare as your planted in the ground you will shoot up out of nowhere and surprise all of your enemies and people around you. God has seen your heart and he wants you to conquer in every situation so remain firmly planted in Him. This week and this month may The Lord God make you more fruitful and profitable . I see your coast been enlarged in and to every area. I see more Testimonies, more breakthrough, more miracles coming to you. (1 Chro 4:10) If You believe shout ” I will BUILD! I Will PROSPER! I will FINISH and I will PROFIT it!”

– Bishop Climate Irungu

Its time for YOU to BUILD, PROSPER & FINISH IT! If You Don’t Have The Part 1-2 Teaching Of I will Build, I will Prosper & I will Finish Click Below Now to get your Live Audio Copy!

Part 1 BPF Live Audio Teaching & Part 2 BPF Live Audio Teaching You can also call NOW to order on UK: 0207-738-3668 Outside UK: 0044 131 555 2290

You have heard the Miracles, You have seen the testimonies, Click Here to Invest in your Prophetic Miracle Pen Now! Use this point of contact to change your situation or change your fate, According to Matthew 18:19 Bishop Climate will agree with you that whatsoever you cancel using this Miracle pen will be cancelled here on earth and in Heaven, whatsoever you accept with Miracle pen God will cause it to be accepted!

Look out for our weekend in pictures out Now! and Also view Kingdom Principles Our weekly Kingdom Principles segment by Prophetess Beryl Nelson Brand new Out Today EVERY WEDNESDAY! on our TKC London FB Page!

This Week At TKC London 4th – 8th September 2013!

Tonight join us for our Mid Week Boost ( 3 in 1) service of Bible Study, Intercession and Deliverance this is a service you don’t want to miss to reenergise you for the week.

Tomorrow is our Singles Clinic! Come and hear teachings on the preparation of marriage, issues in relationships and more!

Friday 6th September don’t miss our Miracle, Healing and Deliverance Service at 7:30pm. If you need any special healing, laying of hands  this is the place to be many testimonies of instant healing taken place right here! This is not a service you want to miss!

Saturday 24th August Join us at Kingdom Professionals Meeting at 4pm -6pm! Are you looking to excel in your business, in your career? Looking how to shoot to the top of your career ladder in the right way? Come and discover Biblical Principles on how you can walk in the spirit of excellence no matter what type of career or business you are in!

8-9AM it’s Morning Glory! Join us to start your Sunday in prayer!

9-10AM Prophetic Hour with the man of God no appointment needed, just be sure to turn up early as limited spaces are available.

11AM Word Service:  Is spiritual growth your purpose? Do you want to live a successful and winning lifestyle? Do you want to be a disciple of Jesus? Then Come hear the word, Grow and glow spiritually!

3PM Miracle Prophetic Service:– Are you believing God for a quick breakthrough, Personal word of Knowledge? Do you want to face Monday with a High gear , full of energy and power? Then this service is for you!

Our Prayer Lines are open and available 24/7 If you have any need, seeking spiritual guidance through Prayer and Deliverance:

Call Now +44 207 738 3668 For UK

Call Now 1-732-444-7074 For North America (USA & CANADA)

– Greetings From Bishop Climate & Bishop Climate Ministries Team

One comment

  1. Everyone loves it when people come together and share views.
    Great blog, stick with it!

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Major Darknet Marketplace Alphabay Goes Down, Exit Scam Speculations Arise

Major Darknet Marketplace Alphabay Goes Down, Exit Scam Speculations Arise

Major anonymous free market, Alphabay, has been reported to have been offline since Tuesday. The detection of a large sum of bitcoin being moved from a wallet believed to be owned by Alphabay and scant official statements regarding the outage has led to speculations that the dark market may be attempting to conduct an exit scam – despite a lack of hard evidence to support the claim.

Also Read: 1 in 4 UK Drug Users Have Purchased Narcotics via Dark Web Marketplaces in the Last Year

Sponsored Links

Alphabay Employee ‘Trappy’ Posted on Reddit This Morning but No Reason was Given for the Site’s Downtime

Major Darknet Marketplace Alphabay Goes Down, Exit Scam Speculations Arise

Alphabay, a leading anonymous dark market, has reportedly been offline since Tuesday. Alphabay failed to issue an official statement (see below) until 28 hours after the outage was first reported, leading to speculation that the anonymous free market may be attempting to conduct an ‘exit scam’ – in which the marketplace suddenly disappears, keeping the bitcoin and cryptocurrency stored in their users’ accounts.

A user named ‘Trappy’, who is believed to be employed with Alphabay, posted on Reddit this morning, warning the website’s users that the downtime may result in an increase in phishing sites, but no reason was given for the site’s downtime. So far, Trappy’s post is the sole “official” acknowledgment that has been made regarding Alphabay’s downtime.

The outage comes weeks after Alphabay announced that it would be integrating Zcash payments, citing high fees and uncertainty surrounding bitcoin’s upcoming hard-fork as the principal catalysts for decision. Some have suggested the outage may be a consequence of the Zcash integration, which could have caused unexpected security vulnerabilities – and may explain the unwillingness of Alphabay to provide detail regarding the cause of its outage.

Despite Widespread Speculation, the Causes Behind Alphabay’s Outage Is Currently Unknown

Major Darknet Marketplace Alphabay Goes Down, Exit Scam Speculations Arise

Speculations that Alphabay may be trying to exit with its customer’s cryptocurrency began to grow following the discovery that 1,479.03904709 bitcoin has been moved from an account associated with Alphabay, valued at approximately 3.8 million USD. Suggestions have been made that Alphabay may be attempting to sell their bitcoin before bitcoin’s upcoming hard-fork – which could be true irrespective of if the funds in question once belonged to the dark market’s users.

The darknet markets have witnessed several exit scams in previous years. In May 2017, prominent anonymous dark market, Outlaw, abruptly ceased operations without refunding users’ bitcoins – citing an unsubstantiated hack as the catalyst. In 2015 the then leading dark marketplace, Evolution, disappeared with $12 millions USD worth of bitcoin. The seizure of The Silk Road and arrest of Ross Ulbricht also served as the catalyst for several early anonymous markets to close shop and flee with their users’ bitcoin.

Despite widespread speculation, the causes behind Alphabay’s outage is at the time of writing unknown.

Do you think that Alphabay is attempting to conduct an exit scam? Or do you think the dark marketplace will return to operations? Share your thoughts in the comments section below!

Images courtesy of Shutterstock

At all comments containing links are automatically held up for moderation in the Disqus system. That means an editor has to take a look at the comment to approve it. This is due to the many, repetitive, spam and scam links people post under our articles. We do not censor any comment content based on politics or personal opinions. So, please be patient. Your comment will be published.

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God Bless You

I composed this piece for the second edition of Gwaith Sŵn’s Sonic Darts radio show, broadcast on 3 July 2015 on Resonance104.4fm. As the theme for the show was one based around conspiracy theories, I began this piece with a recording of a rather deranged American Christian shortwave radio broadcast that I had picked up in the middle of a Finnish forest. But rather than highlight the insane ramblings of the preacher, who claimed that the end of the world was indeed nigh, I was instead drawn to the desperate and fearful phone calls of the listeners…

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Fried zucchini and eggplant sandwiches

2016 Food Blog August-0626What is it about summer and fried food? It doesn’t make sense. Why would we want, on the hottest of afternoons, foods at nuclear temperatures encased inside hot, thick, sometimes greasy breading that, should we make them ourselves, require rivulets of sweat and a pot of shimmering, toe-endangering oil? Is it the hazy memory of a thousand state and county fairs of collective childhood, studded with corn dogs and funnel cake and battered oreos? Is it the only kind of seafood we would eat for lunch as kids, and thus required for a beach day? Is it just that green tomatoes are only really worth eating when they are lovingly smothered by a cornmeal crust?

2016 Food Blog August-05902016 Food Blog August-0606I’ve done this height-of-summer-frying thing before, and here I am again, dunking breaded vegetables in hot oil to create a sandwich inspired by Disneyland and babaganoush (there’s an unexpected pairing, eh?), that ticks all the flavor marks including that deep, primal urge for crisp coated, meltingly soft centered fried food, on a sun-streaming, fan-screaming kind of week.

2016 Food Blog August--22016 Food Blog August-0613I said Disneyland and babaganoush, and that truly is how the sandwich was imagined. A few months ago on a trip to that happiest of places, I ordered a fried green tomato sandwich. It was good – the tomatoes were tangy and sharp, and the sandwich format made creamy, fatty remoulade a requirement – but I thought it could be more. Instead of just the green tomatoes, there could be zucchini. There could be eggplant. There could be, rather than a mayonnaise based sauce, something with yogurt, with herbs, with lemon. There could be tahini.

2016 Food Blog August-With the addition of that idea of sesame, I was suddenly in babaganoush territory, that lovely roasted eggplant dip, soft and pulpy and aromatic.* From there, all links to green tomatoes were cleanly severed, and I was daydreaming Mediterranean and Middle Eastern flavor combinations.

2016 Food Blog August-0616The sandwich we ended up with – the one that ticks every box (or perhaps every taste bud) – has the crunch-into-barely-resistant-softness of panko-coated fried vegetables, a tangy, rich spread of yogurt and tahini lightened with lemon and a mixture of herbs, and a shower of tangy crumbled goat cheese. It has pickled onions for a sour astringency, and the sticky sweet coup de grace of a drizzle of pomegranate molasses. You don’t want too much of it, but this wouldn’t be the same sandwich if you left it off. The bread is lightly toasted, and the breading for the vegetables carries a light dusting of cayenne pepper for a suggestion of heat. What’s more, you can eat the leftovers – if there are any – without the sandwich: stacked up kindling style and sprinkled and drizzled with the extras, the vegetables shine even more brightly. I had them for lunch this way the day after our sandwiches, and I’m kicking myself for not taking a photo or two before I plunged in.

2016 Food Blog August-0617A few notes: the pomegranate molasses can certainly be purchased if you don’t want to make it yourself – look for a Middle Eastern grocery store – but it’s pretty easy (and much cheaper) to make if you don’t mind taking the time. You will probably wind up with extra, which could be drizzled over everything from salad to grilled poultry to ice cream. Because it takes a while, to speed up the dinner prep you could make the molasses the day before, and store it in a glass jar in the fridge, where it will thicken considerably overnight. A minute or two before you are ready to assemble the sandwiches, immerse your jar of pomegranate molasses in a bowl of very hot water. It will warm and liquefy enough to be pourable again. As for the bread, we ended up with ciabatta rolls, but I think something seeded might also be nice for these sandwiches – perhaps these shaped like hot dog buns instead of full loaves. In any case if you use a roll or a bun instead of sliced bread, you’ll want to dig out the soft center so there’s room in the middle to stack up plenty of the vegetable slices.

2016 Food Blog August-06202016 Food Blog August-0622* I realize not all babaganoush contains tahini, but the ones I’ve liked do, along with lemon, and some herbs, and a shower of pomegranate seeds.

2016 Food Blog August-0628

Fried Zucchini and Eggplant Sandwiches
Quantities listed are for two sandwiches, but are easily doubled
About 45 minutes
Pomegranate molasses:
1 cup pomegranate juice (I like the POM brand)
Tahini yogurt spread:
2 tablespoons tahini paste
4 tablespoons (¼ cup) greek yogurt
1-2 teaspoons lemon zest (about 1 lemon)
1 tablespoon lemon juice
1 tablespoon finely chopped fresh chives
2 tablespoons finely chopped fresh parsley
1 tablespoon finely chopped fresh mint
¼ – ½ teaspoon salt, to taste
1 cup vegetable oil
2 zucchini, cut into long planks
1 Chinese or Japanese eggplant, cut into long planks
¾ cups all-purpose flour
1 teaspoon salt + more for post-frying sprinkling
½ teaspoon cayenne pepper
2 eggs, beaten
2 cups panko breadcrumbs
¼ cup crumbled goat cheese
2 tablespoons pickled onions or to taste
2 sandwich rolls of your choice about 6-8 inches in length; we used ciabatta

  • Begin with the pomegranate molasses, as this takes the longest: pour the pomegranate juice into a small pot and boil over medium heat until you have only about 2 tablespoons left; 20-25 minutes. The juice will have a slightly thicker viscosity, and you’ll know it’s seconds from being done when the whole thing seems to be a frantic stack of bubbles. Set it aside to cool – it will thicken into a syrup. (You can also refrigerate overnight – see note above.)
  • While the pomegranate juice reduces, make the tahini yogurt spread. In a small bowl, whisk together the tahini and yogurt with the lemon zest and juice. Add the herbs and the salt, whisk again to thoroughly combine, and taste for seasoning. Adjust quantities of salt and lemon juice as desired. Set aside.
  • For the sandwich filling, set up a three-part breading station: you will need three plates or shallow bowls. Pie plates work very well. On the first plate/bowl, combine the flour with the salt and cayenne, mixing well with a fork or a small whisk. Spread out the flour mixture in an even layer across the plate. In the second plate/bowl, crack the eggs and beat well to combine. In the third plate/bowl, dump 2 cups of the panko and spread out in an even layer.
  • In a large, deep skillet with straight sides, heat the oil to about 350F. While it warms up, bread the vegetables. First coat each slice of eggplant and zucchini in a light layer of flour. Then transfer to the egg and coat again, being sure all dry flour is covered. Finally, press lightly into the panko on both sides. Set each slice on a separate plate or a wire cooling rack until the oil is ready. Set another wire rack over a baking tray and place in an oven set for 300F. This is to keep the finished slices warm and crisp while the rest are frying.
  • When the oil hits 350F, begin adding the vegetable slices. Carefully place them into the oil individually, only adding four or five at a time to avoid crowding the skillet – the more you put in there, the lower the oil temperature gets, which can lead to a greasy end product. Fry over medium to medium-high heat until the panko coating is nicely browned and crisp, about 3 minutes per side. As the slices are finished frying, sprinkle them lightly with salt and add them to the wire rack set-up in the warm oven until you are ready to assemble and serve. Repeat until all slices are fried.
  • Split the sandwich rolls lengthwise and dig out most of the interior, leaving a thin layer of crust on all sides (you can keep the hunks you dug out for bread crumbs). Lightly toast the remaining crust in the oven with your fried vegetables or in a toaster oven, just until it is warm and slightly crisp on the outside.
  • To assemble, smear a tablespoon or two of tahini yogurt spread on each side of the sandwich rolls. Stack a few slices of vegetables onto the bottom of the roll, being sure you have both zucchini and eggplant on your sandwich. Strew on a few slices of pickled onion, about 2 tablespoons of crumbled goat cheese, and drizzle over about a tablespoon of pomegranate molasses. Clamp on the top of the roll, cut the sandwich in half with a serrated knife for easier eating, and serve immediately.

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same-sex, different status

Q: Wait, are you from portland Maine, or portland Oregon?
A: The gay one, not the hipster one

On Wednesday, May 6th, Maine became the most recent state to allow same-sex marriage and the second state, after Vermont, to do so through legislative means.

this is an update of a post from April 7th, 2009, featured below, only with a new, stellar, somewhat less hate-spangled map!

Last week Iowa, and now Vermont. I gotta share some maps of this tomfoolery snail-paced progress:

There will be a reason other than apples, maple syrup, and the leaves changing to visit Vermont this fall. Vermont legislators voted in equal marriage!

In an historic move, just moments ago this morning the Vermont House of Representatives voted 100-49 to override Gov. Jim Douglas’s veto, following this morning’s earlier vote of 23-5 by the Senate. Vermont is the first state to recognize marriage for same-sex couples through the legislative process. The law goes into effect Sept 1.

which leaves us where…

Laws Regarding Same-Sex Partnerships in the United States

=D ██ Purple: Same sex marriages
;^) ██ Green: Unions granting rights similar to marriage
:0) ██ Greyish-Indigo: Unions granting limited/enumerated rights
:/ ██ Light Blue: Foreign same-sex marriages recognized
:l ██ Essential Grey: No specific prohibition or recognition of same-sex marriage/ unions
=( ██ Yellow: Statute bans same-sex marriage
😡 ██ Orange: State Constitution bans same-sex marriage
X-0 ██ Red: State Constitution bans same-sex marriage and other kinds of same-sex unions

Woot! This is in no way a walkback of my Valumtimes Day post, but ya know… poco a poco

The World is Yrs,
Sunshine Superboy

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Listen to free music by Alicia Keys

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Becuadro Alicia keys – Doncha Know (Sky is Blue) (reblip)
Clair_De_Lunar Hope you're well! @redangel Alicia Keys – New Day

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Cristel Alicia Keys – Girl On Fire
Clair_De_Lunar good morning, great morning to be alive its only going up to 28 degrees tho, smdh. @knowtheledge: "Mornin! @Clair_De_Lunar: "Alicia Keys – New Day"" (reblip)

Alicia KeysNew Day

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ellendiane strong-bold black coffee and a fluffy electric blue robe :)- some good tunes. . . then workout time... my recipe for warm:)x @bluescat
Clair_De_Lunar Alicia Keys – New Day (Live on Letterman)

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Blip.fm is internet radio made social. It's easy to search for, play, and discover free music recommended by real people. Join today to create your own free station and start listening to @marienie.

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Geared clock measures time linearly

Arduino TeamApril 4th, 2017

Jonathan Odom, a full-time designer at Instructables who goes by the name “JON-A-TRON,” decided to make a clock illustrating time’s linearity.  What he came up with was a beautifully crafted (robotically manufactured at the Pier 9 workshop, that is) clock that uses two rack and pinion assemblies to move a line of numbers for hours on top of another line signifying minutes.

The minute “hand” is divided up into five-minute intervals, which seems to him to feel less neurotic than being precise down to the exact minute. Magnifying glasses are used to magnify an hour and minute number, reminding onlookers to focus on the present.

The clock is actuated using an Arduino Uno with a motor driver, controlling a stepper motor for each “hand.” It’s an incredible build, and nicely illustrated. Whether or not you have access to the tools needed to recreate this exact clock, perhaps this concept will inspire something similar!

Be sure to check out Odom’s clock Instructables write-up here and see a demo of it below!

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Homemade Natural 10-Minute Jewelry Cleaner

Cleaning your jewelry is the perfect way to give an older piece a fresh, new look. I have certain pieces that I wear almost every day, and I never realize how tarnished they’ve become until I give them a nice cleaning. Today I have a recipe for a homemade jewelry cleaner that can be made with materials that you’re likely to already have in your home. It’s incredible how well this cleaner actually works, and it only takes 10 minutes! I would recommend sticking to solely using this on metals, just in case the ingredients could react unfavorably on precious stones or gems.

Shop jewelry.

Homemade Natural Jewelry Cleaner

Baking pan
Aluminum foil
1 cup boiling water
½ cup white vinegar
1 tablespoon salt
1 tablespoon baking soda

1. Line your pan with foil, shiny side up. Lay your jewelry in the pan, making sure all parts are in contact with the foil.

How to clean jewelry

2. Mix water, salt, and baking soda together, and slowly pour into the pan.

3. Slowly add the vinegar into the pan. You will see lots of bubbles form as the mixture does its work!

Natural jewelry cleaner bubbling

4. Let everything sit for 5-10 minutes, using a spoon, if necessary, to reposition the jewelry and to stir the mixture.

5. Rinse your jewelry with cold water, and then dry. Easy peasy!

Clean Jewelry

With a cleaner this easy, there’s no excuse for me to wear a tarnished piece ever again! Do you have any other recipes for a homemade jewelry cleaner? Let us know!

Shop jewelry.

Follow FP Brigette on Twitter.

  1. I just purchased a gorgeous really old/vintage squash blossom necklace. I was scared to use anything abraisive as it is pretty black with patina. I used toothpaste and a toothbrush to clean the front areas of the necklace but Im not sure if I should clean all the history off of it? any suggestions on what or if you are meant to take off the patina on these old treasures. By the way, toothpaste works brilliantly.

  2. Melinda- my boyfriend used to sell Native jewelry here in Santa Fe, both vintage & new. He says concerning antique squashblossoms removing the vintage patina can lower the “value” of the piece. He says there are two basic types, those that have a “hammered” or “rough” finish, & those that have a sandcast “smooth” finish. Only the smooth finish are polished with any regularity, but even those if they have a patina on them should be left that way until sold. :)

  3. hello! is this only to clean “real jewelry” or can it be used for cheap, store-bought jewelry that have been tarnished and brassy as well? Thank You :)

  4. Hah.. did you know that coca-cola can do the same? Of course Pepsi as well. Just leave your silver jewelry in cola for a little while and it will spark.

  5. In the case of the lion ring pictured: it looks like you actually just rubbed the patina out of the recesses. Patina is intentionally applied to give metal an antique finish.

  6. I am using connisseurs jewellery cleaner . My ring is of ruby and diamonds. Is it ok to dip in the cleaner every day? It is also mentioned on the back of the container that that this cleaner can remove light scratces? Is this true.

  7. There are things that can help on a daily basis, just to clean your jewellery a little. But if you want your jewellery to look like new, take it to a local jeweller, and ask for a clean & polish.

  8. Subwoofers could possibly be purchased separately, includes the satellite speakers.
    Make sure that you simply do your research well at home appliance stores with
    your area or possibly, read some reviews online to find out the very best
    theater to invest on. The most essential much of this product
    is its home audio speakers, which can be responsible to the sound output from the system.

  9. Wow! I had no idea that I can clean my silver jewellery at home! So cool! Thanks a lot for the article! I will try this method immediately! Cowley Carpet Cleaners Ltd.

  10. Here is a trick I learned from a colleague in our cleaning company . Take a small piece of aluminum foil, about 1″ square, and put it in the bottom of a coffee cup. Add about a T of baking soda. Pour boiling water over it and dunk your jewelry. You can drop it in and swirl it around, or you can just dunk it a few times and it cleans any tarnish off in seconds. I like to put a twist tie or string on the jewelry and then just dunk it. When I pull it out, sometimes there are some little dark spots. I just rub them out with my finger. This works well on tarnished silver dishes or tableware as well.

  11. Great tip! I just found my favorite silver necklace is tarnished, but I have no time to take it to a jeweler. It just needs to be cleaned a little, so as I see I can do it at home. Thanks for the good idea!

  12. Most of the time i go to jewellery store to cleaned my all gold and silver jewellery as they are much precious but now a days i am very busy so i was looking for home made jewellery cleaning stuff on internet so got your website blog.Below tips are very helpful and time saving.

  13. There was somebody on this site mentioned Windex for cleaning jewellery. I poured some in a bowl and filled it with winded. I put a fair amount of jewellery in the bowl and immediately could see them get silver. It is the most amazing cleaner I have ever used and I think I used them all but not with these results. Whoever posted it thank you.I used Bebbington glass cleaner that I purchase from Bebbigton on Wright avenue in Dartmouth. I buy it by the gallon so I fix and make jewellery and this will save me lots of money and get the most amazing results ever.

  14. I tried the recipe and, for the most part, on the front of my dime size sterling silver pendant or charm is much cleaner. The back only removed a small bright silver spot. The rest of it still is tarnished. I tried the recipe in newer batches, let it soak longer, then made the paste. Nothing. Any other ideas?

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What do all great online instructors do?

We know that running an online class has several challenges not always faced by those that meet in a physical classroom on campus. Barbara A. Popp, the director of curriculum, instruction, and professional development for New Jersey’s Manville School District, lists out the top practices for online instructors to help guide the way. Among her advice, she suggests helping students with their time management and organization, crucial skills that often fall to the wayside because many students incorrectly assume online classes don’t take as much time and effort as their other classes. Another point she makes includes the fact that presenting material in different ways (videos, notes, discussion boards, etc.) engages students more profoundly.

Check out the eSchool News article here.

Popp, Barbara A. “10 things all great online educators do.” eSchool Media. eSchool News, 8 Oct. 2015. Web. 8 Oct. 2015.

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Preservation, Road Trips

The McOuat building

The McOuat (Mi-COO-it) building was a blight. Few buildings in downtown Indianapolis looked this bad.

Blighted, not blighted

But a renovation completed in 2010 brought this 1901 building back to life. It’s now stores and apartments.

This building stands on Washington Street and is on both the National and Michigan Roads. I took the first photo above when I toured the Michigan Road in 2008. Much of this block was blighted then. But in the years that followed, Washington Street resurged. Buildings were renovated, businesses moved in — and now it’s a destination again.

10 thoughts on “The McOuat building

    • We do like redemption stories, don’t we?! Downtown Indianapolis is undergoing a rebirth of sorts, slowly. I wonder if it’s because the millennial generation wants to live downtown. Whatever the reason, I love to see it. Secretly, I’d love to live downtown someday.

    • I remember when I used to come Downtown 25 years ago, visiting from Terre Haute. This place was a dump. It’s astonishing how much work they’ve done to make Downtown a real destination since then.

  1. Bob Dungan says:

    Nice to see it has been redone. I think Goverment should encourage reuse of existing buildings and discourage gobbling up farm land to build new buildings. Urban sprawl has gotten out of control in our area.

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/ Nginx

WordPress on Nginx

Running WordPress on server with Nginx is not a problem. However getting “pretty” permalinks can be a challenge.

What you need to do, is to add an extra directive to your vhost setting for the domain you host your blog on. Depending on how you’ve set up your blog the way varies. If you’ve done it the hard core way in terminal using wget, tar and vi – you probably already know what to do…

If you are using software like ISPConfig, you need to edit the nginx Directives part under options for your vhost.

If you don’t use any software to manage your server, you have to manually edit your vhost file. On a Ubuntu/Debian box this is located in /etc/nginx/sites-available/.

Add the following directive to that file. If you are unfamiliar with editing vhost files, just place it at the bottom.

try_files $uri $uri/ /index.php?$args;

If you have your WordPress install under a folder like blog, you have to make sure the directive is placed under that location, like this;

location /blog/ { try_files $uri $uri/ /index.php?$args; }

Remember to either reload or restart the nginx service for the changes to take effect.

Now you can change the permalinks to your heart’s content!


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Archive for the ‘Slate’ tag

Want to Help Shape the Future? Get Involved With Science—No Ph.D. Required. (

By September 6th, 2017 at 9:24 am | Comment

Here’s an excerpt from a piece I coauthored with Jay Lloyd, my colleague at Arizona State University’s School for the Future of Innovation in Society.

Want to Help Shape the Future? Get Involved With Science—No Ph.D. Required.

Imagining what the world will be like in a decade or two can feel like flipping through a catalog of dystopian visions rooted in today’s dismaying headlines. Will smartphones make our children depressed and lonely? Are we on the brink of making the world nearly uninhabitable for humans? Will hacking and cyberterrorism lead to real-world warfare? Can bioterrorists use precision gene-editing to kill millions of people? Will technological innovations produce mass unemployment?

That many of these anxieties are connected to scientific advances and technological breakthroughs is no coincidence. The forces of science and technology that drive large parts of today’s economy catalyze vast social changes. Innovations emerge from corporations, universities, and laboratories that are remote from most people’s everyday experiences. Understanding them often requires specialized knowledge and training. And while these innovations can be enormously beneficial, they often come with tradeoffs. For example, social media platforms offer greater connectedness, but they can also allow information to be weaponized as a tool of asymmetric warfare.

 It can sometimes feel like professional researchers and technologists are pushing us into a future that may not be one we envision for ourselves and our communities. Technological innovation can feel more like a natural disaster than the result of human decisions if youstruggle to make a living or deal with toxic electronics waste. We fear losing control, ceding our agency to algorithms and tech companies and research scientists.
One way to help alleviate some of the concerns is greater public involvement in scientific research and technological innovation—no Ph.D. required.  Read the full article here.

Categories: In the News

Citizen Science Isn’t Just About Collecting Data

By August 16th, 2016 at 11:19 am | Comment

Nonscientists should take part in discussions about research priorities and more.
This article, Citizen Science Isn’t Just About Collecting Data, originally appeared in Slate AUG. 15 2016 7:31 AM
The earthquake near Washington, D.C., five years ago in August 2011—the one that damaged the Washington Monument and the National Cathedral but had little other noticeable impact—caught me by surprise. Sitting in an office on the 12th floor of a building downtown, I thought it might have been an improbably large truck on the street below, until a co-worker suggested we probably ought to leave the building. We spent the rest of that sunny afternoon milling around with other office workers before calling it a day and heading to happy hour.

What I did not do, but really wish that I had, was enter a description of my experience into the U.S. Geological Survey’s crowdsourcing initiative, Did You Feel It? The system collects data from people who have felt tremors to determine the extent and intensity of earthquakes in near-real time. The submitted data are used in the USGS ShakeMaps, which help organizations like the Federal Emergency Management Agency prepare for and respond to earthquakes.
Read the full article here.

Categories: In the News

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Defining the Millennial organisation

After a night’s sleep, it occurred to me that it might not have been clear what I meant by a “Millennial organisation” in my last post. Here are some thoughts.

We have heard a lot recently about people in Generation Y and how they feel about work. (Here, via David Gurteen, is an example from Teresa Wu that generated spectacular amounts of heat and little light — check some of the trackbacks, especially this rather grumpy one.) What if businesses change in the same way? What would a Generation Y organisation look like? Before suggesting some answers, it is worth briefly summarising why organisations might need to change.

  • Climate change is still with us. It may have been pushed off the front pages, but it is still a reality. It will affect many business models directly, and many more indirectly.
  • The economy is front page news. The collapse of many shared assumptions about growth and prosperity should make us take stock and possibly re-focus.
  • Technology is facilitating many more interesting interactions. 5-10 years ago businesses learnt that they could not survive without at least a brochure-ware website. Now it is becoming essential to identify where and how your market is conducting its conversations online, and join in.
  • People’s expectations are changing. This is not just a Generation Y thing — customers of all generations are challenging their suppliers in ways that were impossible to predict just a short time ago. Employee profiles are also changing — the products of the baby boom are starting to retire in large numbers, potentially leaving a significant gap in the workforce.

That’s a lot of potential for disruption, and there is probably more (I haven’t even touched on globalisation, for example). What will an organisation that deals effectively with all those challenges look like? How might it behave? I can see at least six things, which correspond roughly to the six points made by Teresa Wu.

  • Millennial organisations will support and promote talent, wherever it arises. In doing so, they will need to be able to identify it first.
  • They will take seriously the work started by Ted Levitt in asking the question “what business are you really in?” They will not be afraid to re-invent themselves. (Compare Ford’s and Toyota’s approach to diversification into prefabricated housing, and consider the health of those businesses now.)
  • They will generate a sense of community and common purpose in their people by encouraging them to share and communicate what they know.
  • They will tend to have a flatter hierarchy than traditional organisations, and the leadership will actively involve people from across the organisation in key decision-making processes.
  • They will engage more actively with their clients or customers, in whatever way best suits the client or customer. (Because, as Jordan Furlong makes clear, the market does not care: “You have no right to make money from every problem or opportunity clients face, and the humility that comes from approaching clients that way matters.”)
  • They will encourage their people to bring a sense of commitment to the work that they do, to create better-quality work and a better-quality workplace. This means that badly behaved high-achievers will be tolerated less than they are at present, as will clients who make people’s lives a misery. (Bob Sutton is the guru for this one.)

An organisation with these characteristics will not be frightened of unapproved chaotic information — instead it will recognise the inevitability of the existence of such fragments and seek ways of bringing them to wider attention. It will also be constantly aware of the need to respond to changing markets by changing itself as often as necessary. (I wonder whether this also means that they will have to be smaller in size than they are now.) It probably won’t behave like the firms in Jordan Furlong’s article “The failure of billable-hour compensation“, which describes with alarming clarity “an under-publicized way in which the billable hour poisons the [legal] profession.”

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Easy Email Marketing Automation Dubai – 1000 Soluciones y Herramientas de marketing digital para incrementar sus Ventas Rápidamente

Easy Email Marketing Automation Dubai

Why Email Marketing & Social network Are Like Peas in a Hull

When it involves digital marketing, most successful brands attain their standing because they offer a all natural client experience– one that brings all the branches of their marketing strategy with each other. When various methods on various systems function seamlessly together, the outcome offers a a lot more cohesive user viewpoint. Uniformity is the cornerstone of constructing a solid, trusted brand– without it, your advertising and marketing initiatives could have the other effect to the one wanted.
If your service uses numerous online marketers, it comes to be particularly challenging to run smooth campaigns, unless each understands what the other is dealing with. Email advertising and social media are two such offenders. They could complement each other magnificently, or they could enter entirely various directions. If you\’re currently struggling to offer the seamless digital experience that customers expect, below\’s how you can deal with integrating your e-mail as well as social networks advertising and marketing initiatives.
Your prime material advertising channels
Material advertising and marketing– the art of producing and also dispersing beneficial, appropriate material to your clients and audience– is presently one of the most efficient forms of digital marketing. While the goal is to attract business, content advertising supplies real value that notifies or amuses its audience, instead of being an obvious advertisement. Great web content comes in several kinds, from blog site posts and also whitepapers to video clips, infographics and also presentations.
Developing web content is one point: then you have distribution. There are many ways to disperse content online ( neighborhood groups, forums, podcasts), but 2 of the most efficient are e-mail e-newsletters as well as social networks. Both allow you to get to as wide (or as slim) an audience as you wish. With e-mail advertising and marketing, you have an efficient method to interact with your existing client base (or those who have actually signed up), to distribute content, and to discreetly promote your business. But with around 75% of American adults making use of social media sites systems, these networks are additionally important. Social network customers often tend to be open to interaction and also are a lot more interactive with the companies they take pleasure in compared to they made use of to be. Usage social media sites well, as well as you could expect abundant shares as well as engagement ( given you\’ve been creative with your material marketing). Even far better– learn how to incorporate the two.

email marketing automation Easy – Number 1

One can advertise the various other, and also vice versa

Email and also social media marketing are on the same team, so they need to support one another. On the one hand, e-mail advertising and marketing could assist to improve your initiatives on social networks by advising your e-mail subscribers that your brand name has a humming social neighborhood they could get associated with. Use your e-mails to advertise your social web pages with buttons and clickthroughs. At the beginning, you may locate it less complicated to concentrate on promoting just one social media network– whichever gets the very best involvement– so clients don\’t feel overwhelmed voluntarily.
Similarly, you can likewise urge your social networks fans to sign up for your subscriber list. There are a number of excellent ways to do this– if you\’re making use of Twitter, think about utilizing Twitter Cards, which let individuals sign up without leaving the system. Your Facebook web page can additionally be made use of to advertise email signups by including a \’subscribe\’ type– learn the best ways to do this right here. Post regular pointers of the awesome deals that you\’re sending out via email and also enjoy your email checklist expand.
Re-engaging inactive customers
Did you understand that you can conveniently publish your email data source to Facebook and Twitter? Just what\’s more, by following your e-mail clients and getting to recognize them, you might also obtain more followers while doing so. You could use Twitter Advertising and Facebook \’Custom Audience\’ to publish your clients to your social data source and also promote straight to your e-mail list through social platforms– excellent for retargeting objectives. Exactly what\’s more, you could retarget those who in fact clicked and also opened your emails, using a tool like Perfect Audience.
Facebook marketing is one method to increase your retargeting efforts– here\’s a overview of Facebook advertising that you might find valuable. Yet it could likewise be costly, so it is necessary to recognize the most effective method of alloting your funds. If you retarget those who you understand are currently thinking about your offering, you\’re most likely to obtain much better conversion rates. Try sending out an e-mail to clients that leads them via to your website– then you can especially target social ads to appear only to individuals that followed that link via.

Easy email marketing automation – Number 2

Utilizing social channels to grow your e-mail checklist

If you\’re obtaining interest in your brand name on social media, after that chances are this audience would be interested in receiving email e-newsletters as well. It\’s about getting your energetic social complying with to take activity– as well as making it extremely simple for them to authorize up. First off, you should allow your followers know that you have a e-newsletter in the first area. It it\’s not evident, they will not understand. So the primary step is to supply a clear web link from your social profiles to your email sign-up web page. At the very same time, you should be clear concerning the advantages they will obtain: attempt making use of rewards such as unique discounts as well as email-only deals.
As mentioned previously, you can likewise make use of Twitter\’s list building cards as well as Facebook\’s personalized tabs– the advantage which being that customers never ever have to leave the social system they\’re presently on. The less effort called for from them, the far better.
Digital marketers are discovering numerous means to with ease wed their e-mail as well as social media efforts. Do you have some experience around? We would certainly like to speak with you about exactly how your team uses e-mail and also social in tandem to achieve success.

Autor: Patrick Foster: Ecommerce Expert.

How To Earn Commission From Internet Marketing

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