Crunching Codon Data in the Browser

Yesterday I talked about my favorite technique of crunching data in the browser. Generally, I try to get my data in tab-delimited form and then save it in a plain old text file. I open the text file in Chrome, use Control-Shift-J to pop open the console window, then load the data into a variable with

allData = document.getElementsByTagName("pre")[0].innerHTML;

What if your data is not tab-delimited? Well, think about it this way: All data is delimited. The only question is what the delimitation scheme is and whether it's consistent all the way through. JavaScript offers many ways to parse data. You're limited only by your understanding of the data, and of JavaScript. Bottom line, all data can be parsed. It's a matter of finding patterns.

Let's go through a quick example using some bio-data. The other day I talked about pulling codon tables down from genomevolution.org. I eventually stuffed a bunch of data into a text file. The data looked like this:

CCA(P) 0.47%CCG(P) 0.83%CCT(P) 1.39%CCC(P) 0.23%CGA(R) 0.14%CGG(R) 0.12%CGT(R) 0.47%CGC(R) 0.21%CAA(Q) 0.60%CAG(Q) 1.65%CAT(H) 1.07%CAC(H) 0.31%CTA(L) 0.40%CTG(L) 1.21%CTT(L) 3.64%CTC(L) 0.58%GCA(A) 2.68%GCG(A) 0.82%GCT(A) 2.12%GCC(A) 1.08%GGA(G) 2.87%GGG(G) 0.69%GGT(G) 2.02%GGC(G) 1.22%GAA(E) 5.15%GAG(E) 2.61%GAT(D) 4.10%GAC(D) 1.53%GTA(V) 2.82%GTG(V) 1.18%GTT(V) 2.16%GTC(V) 0.48%ACA(T) 2.12%ACG(T) 0.47%ACT(T) 1.48%ACC(T) 1.13%AGA(R) 2.00%AGG(R) 0.93%AGT(S) 1.31%AGC(S) 1.00%AAA(K) 4.85%AAG(K) 3.71%AAT(N) 3.78%AAC(N) 1.47%ATA(I) 3.83%ATG(M) 2.77%ATT(I) 3.30%ATC(I) 1.14%TCA(S) 1.45%TCG(S) 0.48%TCT(S) 1.23%TCC(S) 0.64%TGA(*) 0.06%TGG(W) 0.82%TGT(C) 0.72%TGC(C) 0.43%TAA(*) 0.20%TAG(*) 0.06%TAT(Y) 3.22%TAC(Y) 0.98%TTA(L) 1.90%TTG(L) 1.16%TTT(F) 3.52%TTC(F) 0.98% CCA(P) 1.09%CCG(P) 0.74%CCT(P) 1.51%CCC(P) 1.70%CGA(R) 1.15%CGG(R) 1.02%CGT(R) 0.90%CGC(R) 1.25%CAA(Q) 3.39%CAG(Q) 2.64%CAT(H) 1.52%CAC(H) 0.72%CTA(L) 1.46%CTG(L) 2.22%CTT(L) 1.19%CTC(L) 1.74%GCA(A) 1.77%GCG(A) 1.29%GCT(A) 2.33%GCC(A) 2.88%GGA(G) 1.50%GGG(G) 1.52%GGT(G) 1.78%GGC(G) 1.90%GAA(E) 3.51%GAG(E) 2.26%GAT(D) 3.64%GAC(D) 1.60%GTA(V) 0.87%GTG(V) 2.03%GTT(V) 1.82%GTC(V) 1.74%ACA(T) 1.01%ACG(T) 1.17%ACT(T) 1.33%ACC(T) 2.26%AGA(R) 0.57%AGG(R) 0.31%AGT(S) 1.29%AGC(S) 1.12%AAA(K) 2.56%AAG(K) 1.75%AAT(N) 2.37%AAC(N) 1.36%ATA(I) 0.55%ATG(M) 1.93%ATT(I) 3.46%ATC(I) 2.00%TCA(S) 0.96%TCG(S) 0.59%TCT(S) 1.45%TCC(S) 1.17%TGA(*) 0.09%TGG(W) 1.53%TGT(C) 0.63%TGC(C) 0.48%TAA(*) 0.16%TAG(*) 0.11%TAT(Y) 1.94%TAC(Y) 0.91%TTA(L) 2.18%TTG(L) 2.24%TTT(F) 2.70%TTC(F) 1.17%

Plus much more like the above. Lots and lots of codon tables for lots and lots of organisms. How to parse it all? Since there's a carriage return at the end of each table (but not at the end of each line in the table), getting an array of tables just requires

codonTables = allTheText.split( "\n" );

If you're not a biogeek, here's a big chunk of molecular biology in a nutshell: DNA is a four-letter language (A,G,C,T) for spelling three-letter words called codons. If you do the math, there are 64 possible codons. Each codon corresponds to an amino acid (of which there are 20 in living organisms). The fact that there are 64 codons but only 20 amino acids means some amino acids have more than one codon. But also: three of the 64 codons have a special meaning. The codons TAG, TGA, and TAA are so-called stop codons. They don't code for any amino acid. Instead they tell RNA polymerase when to stop making protein.

The codon table for an organism tells you the usage frequency for each of the 64 possible codons. The frequencies (as you can see above) vary a lot, not only within a single codon table (for a single organism) but across organisms. Some organisms have DNA that's unusually high in G (guanine) and C (cytosine). Those organisms tend, not surprisingly, to use codons containing mostly G and C. Other organisms, like C. botulinum (yes, that botulinum), have DNA that contains hardly any G or C and hence use the codon AAA (which stands for lysine) a good deal more than, say, GCG (alanine).

If we know (as we do, from the above tables) the frequencies of occurrence of codons that contain 'A' (such as CAA, CCA, AAA, AAT, AGA, etc.), then it's a simple matter to sum all the 'A' frequencies to get the total frequency of occurrence of A in the organism's DNA (or at least in the coding regions of its DNA). We can do that also for C, G, and T to get their frequencies. Here's a routine that looks at a codon table's 64 entries and derives A, G, C, and T compositions for the DNA:

function getBaseComposition( table ) {

   var codons = table.split("%"); // parse table into individual codons & freqs
   codons.pop();  // get rid of empty final item

   var bases = new Object( );

   bases.A = 0;
   bases.G = 0;
   bases.T = 0;
   bases.C = 0;
   
   function analyze( item ) { 
      var percent = item.split(/\s/)[1] * .01; // get that percentage
      var codon = item.substring(0,3); // get the actual codon
      bases[ codon[0] ]+= percent; // base 1
      bases[ codon[1] ]+= percent; // base 2
      bases[ codon[2] ]+= percent; // "wobble" base
   }

   codons.forEach( analyze ); // loop over all codons

   bases.A /= 3;  // normalize the frequencies
   bases.G /= 3;
   bases.T /= 3;
   bases.C /= 3;
   
   return bases;
}

The line codons = table.split("%") chops the codon table up into a bunch of pieces that look like CCA(P) 0.47 (that is: a codon, followed by one-letter amino-acid abbreviation in parens, followed by a frequency number). The "%" character happens to be convenient to parse on, but the  presence of a % at the end of the table also means split("%") creates an empty item at the end of the array, which we don't want. We get rid of the empty item with .pop().

Parsing CCA(P) 0.47 into a codon and a frequency number is easy. To get the codon, take the first three characters of the string, by using  item.substring(0,3). To get the number at the end, just split at the space using item.split(/\s/)[1] The bracketed 1 on the end means give me the second item in the array that was created by split(). The first item in the array (at index 0) would of course be CCA(P).

Note that we have to normalize frequencies (divide by 3) toward the end, because we're looking at 64 frequency percentages (that add up to 1.0) but we're counting 3 bases per frequency number (because codons have 3 bases each), hence if we don't normalize, we're going to end up with 300% total base content instead of 100%.

The internal method analyze( ) is a callback. We give it to the forEach( ) method of the codons array. In case you didn't realize it, JavaScript now has a built-in forEach( ) method as part of every Array object, and most modern browsers support it.

If we run this code against the first codon table shown further above (which happens to be for an organism named Abiotrophia defectiva strain ATCC 49176), we get back an object with fields A, G, T, and C containing the overall frequencies of occurrence of those bases in A. defectiva DNA (or at least the parts of its DNA that code for protein, which is well over 90%). What I got in Chrome's console looked like this:

Object {A: 0.34040000000000004, G: 0.22683333333333336, T: 0.28150000000000003, C: 0.15116666666666664}

The G+C percentage for this organism comes to 0.378 (or 37.8%). To me, what's more interesting than the G+C number is that no two base compositions match. G does not equal C (not even close, in fact) and A does not equal T. In theory, G should equal C (and A=T) according to Chargaff's second parity rule, which applies to single-stranded DNA. (Remember, that's what we're dealing with here: ssDNA. We're looking at codon values that correspond to sequences on the RNA-synonymous strand of the organism's DNA.) Obviously, Chargaff's second parity rule doesn't hold in this case, because G is almost twice C, and A is 150% of T! Moreover, A+G equals 0.5672, meaning the purine content is 56.72%. According to Chargaff's second rule, purines and pyrimidines should be 50% each. That's not the case here.

Things get really fun when it comes time to graph the data you crunch in the console window. If you're thinking "Google Charts," think again. There's a much easier and more powerful way to graph data (and no, it does not involve Excel). I'll tell you all about it in my next post.

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John Lennon in The Collective Consciousness Being Real

Lennon - in the Collective Consciousness - Being Real.

I started looking up John Lennon quotes on Goodreads - which helped inspire me to write this article. I only realised a day later that it was the anniversary of his tragic death - when I saw that a lot of my friends had also been looking him up and replaying his music. I don't think it was just a co-incidence that I made that connection, I do think that his spirit is still very much with us in our attempts to find better ways of being at peace with ourselves, and living more in harmony with the planet.

As I co-administrate a facebook open group called "Back to The Garden" some of his quotes were particularly relevant - such as "I'm not really a career person; I'm a gardener, basically." Also, "The thing the sixties did was to show us the possibilities and the responsibility that we all had. It wasn't the answer. It just gave us a glimpse of the possibility." Our group is already named "Back to The Garden" because of the 60's song "Woodstock" which says "We are stardust, we are golden, and we've got to get ourselves back to the garden". Our aim is to share information to help us try to live sustainable lives by creating supportive local communities, and to participate in global meditation link-ups to help influence the collective consciousness towards achieving this. We also share our creativity to help express our ideas.

My article shows why I think John is such a great example to us all - of how to truly be ourselves.

John Lennon was such a thoroughly REAL person. His quotes reflect all sides of human nature, from the sad and withdrawn, to the desperately painful, to the angry, to the loving and celebratory, and from the arrogant to the humble, as well as from the serious to the exuberant humour-filled sheer absolutes of expression. We all have many sides to our nature but we tend to try to pretend that we don't, mostly because we are afraid to show some of it. Does society make us think that if we remain on a bland even-keel we are more agreeable to others? Surely we are more interesting if we share what we truly feel? It's perfectly possible to be honest without being horrid. Why can't we just accept all of it and be this real? Okay, we don't all need to be huge public characters, but we can be quietly firm about who and how we choose to be.

Another quote of John's which is staggeringly beautiful in its stark honesty is "When you're drowning you don't think I would be incredibly pleased if someone would notice I'm drowning and come and rescue me. You just scream."

If you are facing a period of 'depression', why not allow that to simply be for a while? I generally have 3 days of it every now and again. I learnt from a very early age to manage it. You could say it was artistic temperament, but it isn't just that - we all have natural cycles energetically and physically, which affect us emotionally, and I believe we are better off listening to these than trying to deny them. (Of course, you should look after yourself with good nutrition, exercise, and the right amount of sleep, because imbalance in these areas can exacerbate or oven trigger such periods.) I basically I give myself permission to let it happen and actually explore it - I write or paint myself through it. I don't do anything I don't want to - I just live with it. Okay, so I don't usually publish what I've written at such times - but I do learn from it - and I am well aware that I am processing emotion, dealing with it - not trying to suppress it. I know that after the 3 days it will go again because I have given it the space to play through. Often I make positive changes in my life after these stages - so they are like transition phases. I seem to gather strength and insight from actually allowing them to really work through, and somehow grow from the experience. Perhaps by allowing the darker side its space, I then get recompense by gaining access to more of the light, because sometimes it is straight after one of these periods that I produce my best work. Maybe if we looked at it as if we are like snakes shedding skins so that we have room to grow some more, we could learn to process these phases naturally, we could all deal with them. Maybe they wouldn't hang around then - we could trust ourselves to get through them - not let them overwhelm us, or leave us stuck half in half out - we could go into them fully and come out the other side. I think it is healthy to allow ones-self to honestly explore all sides of your nature, as that is probably the only way you can truly get to know and trust yourself. I think that is why I love John Lennon so much - he trusted himself to be real - and he told the truth.

Of course, John Lennon isn't the only one who has dared to be so real, there are many other people who have been a great example to us in this way, and most of these have left great quotations we can continue to draw on for inspiration. I list loads of them on my Goodreads (Jay Woodman) page, and also share some on my Radiance-Solutions website.

Art of any form - music, writing, painting, are the most obvious ones, but there are many more, (and we don't have to be 'artistic' to express ourselves, you could just write letters you may never post, or notes to yourself) - any of this helps us to truly face the world and explore it and the human psyche. We may begin with ambivalence, but we soon become fearless if we explore thoroughly enough. We become powerful in ourselves because we are learning to understand ourselves. We can't ever really hope to understand everything around us, but we can learn to understand ourselves in relation to anything else. If we know what we stand for and how we feel about things - then that never changes no matter what else changes around you - you become like a rock, yet at the same time feel floatingly free. (Of course if you do learn from new information and experiences or learn to respond differently to situations, your outlook does evolve, but you are still the floating rock that is you growing as part of the conscious universe.)

You know we need variety in life to make it interesting. There has to be variety to even enable us to exist as individuals. So you stop blocking it off - you accept your curiosity and begin to explore, and the more you do this, the more you tend to then celebrate and appreciate the variety. You also accept your vulnerability, yet at the same time feel incredibly strong because you have opened fully to life. Life feels magical - even in its madness and confusion - it is staggeringly intoxicating.

So let's grasp the bull by the horns and dare to be real - you'll be amazed how great it will feel.... Not to be sucked in any more, not be afraid any more. You will feel powerful, filled with energy, draw yourselves up, and take control of who you want to be.

Neale Donald Walsch said "You are all in the process of defining yourselves. Every act is an act of self definition. "

Ralph Waldo Emerson said "To be yourself in a world that is constantly trying to make you something else is the greatest accomplishment."

And Shakespeare said "To thine own self be true, and it must follow, as the night the day, thou canst not then be false to any man."

John Lennon also said "There are two basic motivating forces: fear and love. When we are afraid, we pull back from life. When we are in love, we open to all that life has to offer with passion, excitement, and acceptance. We need to learn to love ourselves first, in all our glory and our imperfections. If we cannot love ourselves, we cannot fully open to our ability to love others or our potential to create. Evolution and all hopes for a better world rest in the fearlessness and open-hearted vision of people who embrace life."

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But wait a minute, just as with Lennon (and many others) - those in power don't want us to be real do they? They want us to go on consuming their goods (with poisons in them), and watching TV (with all the pap they'd like us to believe). They want us to feel powerless so that they can continue to lead us blindly into wars and other money making schemes, and so that we accept their laws and judgements, instead of questioning them or standing up for ourselves and our rights. If we are real then we become a threat to them, and they feel a need to deal with us - exactly, you got it - but now there are too many of us, and things are going to have to change. If we stop listening to them, if we stop using their systems, and simply walk away - that is all that is needed.

Then we will look after each other at community level - ensure we are can access healthy food, work together at projects that sustain us - not them - keep things local - it makes much more sense. Trade our skills, make things that last, that don't waste raw materials and fuel, things that are truly useful - not junk to make profit out of others. We can take back everything they have been trying to take away from us completely, bit by bit, over centuries, sneakily.

Marianne Williamson said "Do you really not know what to do? Or do you just lack the courage to do it?"

And Ghandi said "Be the change you wish to see in the world."

And Van Morrison said "You can't stop us on the road to freedom, you can't keep us 'cause our eyes can see."

And John Lennon said "You may say I'm a dreamer, but I'm not the only one. I hope some day you'll join us, and the world will live as one."

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Another thing Lennon taught us was never to be sucked into trying to fight those trying to exert power over us at their own game. He said "If you want peace, you won't get it with violence." And "There's no separation. We're all one. Give peace a chance, not Shoot people for peace. All you need is love. I believe it. It's damn hard, but I absolutely believe it."

So don't allow yourself to be diverted - firstly it infects you with their level of thinking, secondly it takes your power away. Save your power for doing the good stuff, dismiss the rest as insignificant. As long as you remain complete in who you want to be, you will keep your absolute power. The minute you slip into something else - you lose some of it to them. Don't give it away, keep you power quietly to yourself, and you will always be free, they cannot defeat you. No matter what they do, your power remains yours - they do not get a jot of it. Look at how we remember the great people like John Lennon - that's because they never lost anything at all. He has become untouchable, and yet we can all touch him and his dreams, and help make them as real as he believed they could be. He said "A dream you dream alone is only a dream, a dream you dream together is reality." And "Peace is not something you wish for; It's something you make, Something you do, Something you are....."

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More notes regarding depression.

Cognitive Dissonance[1] [1] might arise when you begin to realise there are things wrong in the world but can't see the whole picture so your bits don't fit or make sense, or you might be disappointed by the difference between your expectations and what has happened, or of people. As Lennon said "The more real you get the more unreal the world gets."

So you need to re-adjust. Surely allowing ourselves the time to do this rather than try to fight it is actually healthy? Look closely at how you are feeling and thinking. Express how you feel through safe means - artistically, or by speaking to a friend, therapist, or to an inanimate object or imaginary person, or by writing letters or notes. Even ask rhetorical questions, or ask for what you want to happen - it helps you clarify things and you might even find answers. Recognise your autonomy - you can seek clarification in your understanding, or you can actually just choose to change the way you want to feel or do things.

Medication obviously is useful in that it can give you the break to rest and steady yourself, before beginning to explore what is happening. If you view it as a tool to get back up a few steps, not as an excuse to just lie down at the bottom - then it is a positive and empowering act rather than something you are succumbing to. You should ideally always have a plan with your doctor to ensure that you are helped to withdraw carefully and gradually as you take back your power. You do sometimes need to be firm with your doctor about this, take responsibility for your own best interests, but never try to do it completely on your own.

Khalil Gibran wrote that "Your pain is the breaking of the shell that encloses your understanding."

Plug into the umbilical cord of power through meditation and recharge yourself. Connect with the beautiful energy of the planet too. You are a rock between the earth and the reeling stars. Stand there feeling it deeply. Reach out your arms, dance if you want to, swim in the moonlight, sing or shout. Feel the processes in yourself re-adjusting, and renewing - and you will emerge with magic keys - re-enter life in the next stage of growing.

Remember your connection with the harmonics of the universe. You are one aspect of the one life force, manifested as human consciousness - everything else is a distraction. Focus on your relationship with the life force and yourself - who you are being - how you want to be. Other worries often pale into insignificance when you look at the bigger picture. You begin to realise that none of that small stuff can stop you from choosing exactly who you want to be. When you appreciate the astonishing variety of life around you, you tend to just find it easier to allow other things and people to just be as they are> Reasoning doesn't matter so much anymore, even forgiving doesn't matter much anymore - because you see that there is no need, you just let go of the small stuff and walk on deep into the wonder of being fully alive.

As John Lennon said: "Limitless undying love - which shines around me like a million suns - it calls me on and on across the universe."

FOOTNOTE:

1 - Festinger's (1957) cognitive dissonance theory suggests that we have an inner drive to hold all our attitudes and beliefs in harmony and avoid disharmony (or dissonance).

Cognitive dissonance refers to a situation involving conflicting attitudes, beliefs or behaviors. This produces a feeling of discomfort leading to an alteration in one of the attitudes, beliefs or behaviours to reduce the discomfort and restore balance etc.

Julia Woodman - Life Coach, Self Esteem Counsellor, Artist, Poet - of Radiance-Solutions.co.uk and offering phone and email advice and support.

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Common Drugs of Abuse - Cut off Concentrations and their Detection Periods (Drugteststrips)

Drug abuse is widespread and is one of the top health concerns in many countries. Drug abuse causes multiple problems to the abuser, his/her family and the immediate society. Physical and mental effects are quite obvious in the drug abuser. Drug abusers cannot function as normal citizens of the society. They neglect their families, become poor socially and economically and may also involve in crimes. It is very important to detect the drug abusers using drug tests to make them stay away from harmful drugs. Here we will look at some of the common drugs of abuse, their detection periods and cut-off concentrations in different drug testing samples.

Common Drugs of Abuse
National Survey on Drug Use and Health (NSDUH) recently stated that about 22 million Americans were abusing illicit drugs in 2009. Some of the commonly used illicit and prescribed drugs are Marijuana, Methamphetamine, Phencyclidine (PCP), Cocaine and Opiates.

Marijuana
Marijuana is the most commonly abused drug in America with almost 16.7 million users. Marijuana is a psychoactive drug. The immediate effects of marijuana include relaxation, euphoria, and hallucinations. However, marijuana addiction leads to problems such as short-term memory impairment, red conjunctiva, and increased heart rate and blood pressure.

Methamphetamine
There were more than 500,000 methamphetamine users in America in 2009. Methamphetamine is also a stimulant that causes euphoria, mood elevation, and appetite suppression. High doses of the drug lead to restlessness, anxiety, irritability, tremors, and paranoia. It may also result in fixed and dilated pupils, and heart and brain dysfunction.

Phencyclidine (PCP):
Around 45,000 people started using Phencyclidine in 2009. PCP, a "dissociative" drug, stimulates central nervous system. Short-term effects of PCP addiction are drowsiness, lethargy, and disorganized thoughts. PCP abuse causes visual, tactile, and auditory misperceptions; slurred speech; and sweating. Severe psychological effects are seen among PCP drug abusers.

Cocaine:
There were 1.6 million Cocaine users in United States in 2009. Cocaine is a powerful nervous system stimulant. Cocaine enhances euphoria, alertness, energy and motor activity. High dosage cocaine abuse leads to convulsions, tremors and increased body temperature. Drug tests for cocaine detection check for presence of Benzoylecgonine which is the main metabolite of the drug.

Opiates:
Opiates including morphine, codeine, and heroin are derivatives of opium. High dosage of opium consumption causes depression of central nervous system leading to dizziness, lethargy, and drowsiness. Liver diseases, respiratory depression, and spontaneous abortion are caused by long-term use of opiates. Morphine and Morphine Glucuronides are the metabolites of opiates that are detected in drug tests.

Drug detection
Urine, saliva, and hair are the common samples taken to perform a drug test in order to detect the elevate levels of the above mentioned drugs. Detection period and cut-off concentrations of various drugs vary based on the type of test. The drug cut off concentration level is defined as the minimum level of drug or metabolite concentration in the specimen, which can be considered as a positive result. Amount of drugs that can be detected is based on several factors such as drug detection time, frequency of use, metabolism, specimen type, methods of drug testing, and others.

Urine Tests
Most of the illicit drug abusers are commonly tested by using urine tests. Urine drug test kits are available in the market for on-site tests or laboratory analysis. Urine drug tests are least expensive compared to all other types.

The cut off level for marijuana in urine is 50 ng/ml and can be detected between 2 to 4 days of consumption. Habitual marijuana use can be detected up to 30 days in urine. Cut off level for methamphetamine is 1000 ng/ml and can be detected between 3 to 5 days. PCP 25 ng/ml and detection period is 3 to 7 days. Cocaine 150 ng/ml and can be detected between 4 to 5 days. The cut-off level for opiates earlier was 300ng/ml. However, in order to reduce possibility of false positives, it is increased to 2000ng/ml. Opiates such as heroin, codeine or morphine can be detected for 2-4 days.

Hair Drug Tests:
Hair drug tests are accurate and can detect any type of drugs for 90 days. A hair sample of 1.5 inches of length is enough to conduct hair drug tests.
The cut off concentrations of common drugs of abuse using hair drug tests are: Cocaine (Benzoylecgonine) - 0.5 ng/mg, Amphetamines (Amphetamine) - 0.5 ng/mg, Marijuana - 0.005 ng/mg, Opiates (Morphine) - 0.2 ng/mg, Phencyclidine (Phencyclidine) - 0.3 ng/mg.

Saliva Drug Tests:
More recent drug use can be detected by saliva drug tests. These are more expensive than urine tests and less expensive than hair tests. They are easy to use and the chances of adulteration are very less. Detection period of saliva tests is not known for some drugs. However, methamphetamine and PCP can be detected for 1-3 days.

The cutoff concentrations for the above mentioned drugs using saliva tests are Cocaine - 20 ng/ml, Amphetamines (d-Amphetamine) - 50 ng/ml, Marijuana (THC-COOH) - 12 ng/ml, Opiates (Morphine) - 40 ng/ml, Phencyclidine (Phencyclidine) - 10 ng/ml.

Whatever the test may be, the cut-off concentration is a crucial parameter to detect the presence of drugs in order to provide accurate results.

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What is the payoff structure of gold?

In an excellent new post, John Cochrane corrects some of Greg Mankiw's points on gold as an investment, writing:

In any case, Greg shouldn't have phrased the question, "how much gold should I hold according to mean variance analysis, presuming I'm smarter than everyone else and can profit at their expense by looking in this crystal ball?" He should have phrased the question, "how much more or less than the market average should I hold?" And "what makes me different from average to do it?"... 

As Greg points out, gold is a tiny fraction of [global] wealth. So it should be at most a tiny fraction of a portfolio.

Quite so. But even if one would not personally choose to make one-way directional bets on an asset, one might want to specify the asset's full state-contingent payoff structure, for those who do choose to speculate or to use the asset to hedge their idiosyncratic risks.

In other words, when does gold pay off? Cochrane tosses out a possible answer:

There is all this bit about gold, guns, ammo and cans of beans. If you think about gold that way, you're thinking about gold as an out of the money put option on calamitous social disruption, including destruction of the entire financial and monetary system. That might justify a different answer.

This idea is pretty common. But is it true? Would gold really pay off in the event of a calamitous social disruption? I'm really not sure that it would.

The basic idea here is that fiat money's value rests on the stability of governments; remove governmental stability, and people will go back to using gold as money (or at least to using gold-backed money), as in days of yore. If that happened, it would be handy to have stocked up a whole bunch of the suddenly back-in-use medium of exchange.

But I seriously question whether this would ever happen. See, both technology and the structure of governance have really changed since the days when gold was used for money. The assumption that the end of the Recent System (fiat money) would make us revert to the Old System (gold-backed money or gold as money) does not seem well-founded to me.

First of all, gold has always had a lot of limitations as a medium of exchange. Most notably, it is relatively easy to steal. To realize this, all you have to do is look at games like World of Warcraft, Diablo, Dungeons and Dragons, or the original Final Fantasy. In those games, gold is the money, and you often get gold not by doing an honest day's work, but by running around and beating people up and taking their gold. In other words, the entire world of modern fantasy role-playing is a subtle joke on gold's unsuitability as a medium of exchange.

Now in the past, people just sucked it up and dealt with this, spending large amounts of money and effort to guard their gold. But in the modern day, better alternatives are available. In particular, electronic security is cheaper than physical security. It's easier to guard digits than lumps of gold. In fact, in the case of gold-backed money (rather than physical gold money), you'd need electronic security in addition to guards at Fort Knox. Non-gold-backed digital currency is always cheaper to use than gold-backed digital currency.

So if fiat systems collapsed but electronic networks remained intact, it seems to me that we'd move to some sort of Bitcoin-type artificially scarce digital currency, rather than gold. Not Bitcoin itself, but some electronic currency managed by an institution with lots of staying power and respect. I'd put my money on ToyotaBucks.

OK, but what about a calamity so huge that electronic networks collapsed? In that case, wouldn't we have to go back to using physical money?

Maybe, but it wouldn't be gold. In the days when people carried around gold doubloons and whatnot as money, you had a global political system characterized by pockets of stability (the Spanish Empire, or the Chinese Empire, or whatever) scattered among large areas of anarchy. Those stable centers minted and gave out the gold coins. But in the event of a massive modern global catastrophe that brought widespread anarchy, the gold bars buried in your backyard would not be swappable for eggs or butter at the corner store. You'd need some big organization to turn the gold bars into coins of standard weights and purity. And that big organization is not going to do that for you as a free service. More likely, that big organization will simply kill you and take your gold bars, Dungeons and Dragons style.

In other words, I think gold is never coming back as a medium of exchange, under any circumstances. It is no more likely than a return of the Holy Roman Empire. Say goodbye forever to gold money.

So when does gold actually pay off? Well, remember that stories do not have to be true for people to believe them. Lots and lots of people believe that gold or gold-backed money in the event of a global social  disruption. And so when this story becomes more popular (possibly with the launching of websites like Zero Hedge?), or when large-scale social disruption seems more likely while holding the popularity of the story constant, gold pays off. Gold is like a credit default swap backed by an insolvent counterparty - it has no hope of actually being redeemed, but you can keep it around forever, and it goes up in price whenever people get scared.

In other words, gold pays off when there is an outbreak of goldbug-ism. Gold is a bet that there will be more goldbugs in the future than there are now. And since the "gold will be money again" story is very deep and powerful, based as it is on thousands of years of (no longer applicable) historical experience, it is highly likely that goldbug-ism will break out again someday. So if you're the gambling type, or if you plan to start the next Zero Hedge, or if your income for some reason goes down when goldbug-ism breaks out, well, go ahead and place a one-way bet on gold.

The only way gold will never pay off again is if practically everyone reads and believes this blog post. Not much chance of that happening!

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Easy Data-Crunching in the Browser

When I have data-crunching to do, I like to do it in the browser. Excel gives me a headache. Teaching myself how to write Excel macros doesn't leave me with a transferable skill (a skill that can be used outside of Excel); it just makes me an expert at Excel. Which I don't want to be.

At least if I crunch data with JavaScript, I learn JavaScript skills that I can apply to web-page design, AJAX programming, Scalable Vector Graphics programming, Canvas programming, and lots of other scenarios.

What do I mean by crunching data in the browser? Say you have a text file containing some data. Open the text file in Chrome or Firefox, then use Control-Shift-J to get to the browser's  JavaScript console. There you are. You're ready to crunch data.

How? Let's say your text file contains a table. (Perhaps you took an OpenOffice table and used the table-to-text menu command to render the table as tab-delimited text.) Presumably there's a tab separating each columnar data item and a hard return at the end of each line. Perfect. You're ready to program.

Use Control-A to Select All of the table. (Or; Highlight the whole thing by swiping across the page with the mouse.) In the JS console, type

myTable = getSelection( ).toString( );

Now you have the whole table in one variable.

Alternatively, instead of selecting all, you could grab the entire text file programmatically this way:

wholePage = document.getElementsByTagName("pre")[0].innerHTML;

When you open a text file in a browser, it always puts the text in a <pre> element. The method getElementsByTagName( ) always returns an array, even if there's just one item in it (as in this case). To get the one and only item in the array, use index zero: [0]. To get the text of the element, use innerHTML.

To get the rows from your table:

rows = myTable.split("\n");   

By splitting on every newline (carriage return), you get an array of table tows. To get the columns for row 7 (which is actually at index 6 in the array):

columns = rows[6].split("\t");  

By splitting on tabs, you've created an array of column items. When you want to display something in the console, do

console.log( columns[ 0 ] );

In this case we've chosen to display the first column item (which is at index zero).

This is all familiar enough stuff to experienced JS users. I'm showing the basics here for those who might be new to programming. If you're new to programming, you need to be reminded (arguably) that array items are indexed in zero-based fashion: the first item is at index zero, the second item is at index one, the final item is always at length-minus-one.

If you're new to the Chrome JavaScript console (Control-Shift-J opens the console; plus be sure the Console tab is selected), you'll want to take note that you need to use Shift-Enter to type new lines in the console. Just hitting Enter executes whatever code is in the console. Write a line of code, then Shift-Enter to continue writing on a new line.

To recap: A quick way to crunch data is to put your data in a text file, open the text file with your browser, select all content, then use getSelection().toString() to load the selected content into a variable. Alternatively, load the whole text page with document.getElementsByTagName("pre")[0].innerHTML. From there, you can parse and crunch at will. 

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The Way to Get Him Or Her Boyfriend Last 6 Simple Actions

A partnership could get into a stalemate at one point or another. It would happen to anyone. However, many people wouldn't like to accept under any circumstances your situation and vehemently refuse the resignation. Driven by feelings which may have not really written the storyplot along with the feelings that flowed halfway, we go back to earlier times to try to recapture the that they who gave us life the wrong way up. But are these claims possible? I'd personally agree. Allow me to share 6 simple actions which can be used to get your boyfriend back.

Provide him with space. Tend not to will hysterically call him or her boyfriend as soon as you left each other, just to suffer that you just cannot bear to stay away from him. Everything is carried out with calm and patience. If your breakup left nowhere, the top should be to allow your ex that will put his thoughts as a way and realize his feelings. If you try to choke him, he'll almost certainly feel only constrained and may back off for the land seeking freedom regardless of the sort.Phone him constantly after a fortnight. A timescale of two weeks is plenty on your ex to comprehend clearly what he wants from life, and as a consequence within you. Consequently, you'll be able to call and inquire of him bed mattress he doing and discover if he accepts selecting a face-to-face meeting. Direct communication is the foremost in these cases. If he doesn't feel yet willing to view you, then allow understand you are ready, then when he feels the demand he or she call you. However, don't seem desperate at any moment, as they will use this.If you meet him, likely be operational and honest. It is vital to never dispute past. Just let yourself use whatever you decide and feel. It doesn't mean to leap on him and declare him eternal love. Try, however, to utilize behavior plus your words to generate him understand, that with your heart, she has an exclusive place and you are clearly offered to develop this relationship. Do your best, get forced out on him to talk his feelings. If according to him he needs added time to concentrate, tend not to rush and never press him to offer the result immediately. It's very important to indicate them that you are a mature individual that accepts life as it's and continues going. Slacken him the sense that you just feel weak in their absence.Tend not to play detective. Since you have given him some slack to take into consideration your relationship, you may get a possibility to follow him everywhere and discover who he links with. As a result you're only wasting your some time to killing any trace of passion that could have existed between two of you. Nobody would rather be controlled in daily life in depth. And quite a few certainly, if, after a fortnight of thinking, he still won't phone you and reject your messages or calls, it's pretty obviously for any person what is going on.Arrange yourself. Now inside your should imply to them what he lost by breaking up with you. Have your very best self possible shape if you meet him, but convert it into a meeting between friends and zip more. You already know adequately that no man would rather go to a woman demolished, with dark circles, hair everywhere as well as a broken heart. No malice on his or her part, the fear that they can may cause more pain. Thus, rather select joy, optimism as well as a "fresh" air, that are more attractive qualities and that provide you higher probability of success.Do not attempt to generate him jealous. Although you are able to that every men suffer terribly whenever they know that their "love of his lifeIn . is assaulted by other conquerors, in such cases it will be foolish from a side to present him this impression. Besides the reality that he or she catch you're just scheming to make him jealous, he or she also start assuming that you're easily impressed and puzzled by your heartaches.

Follow these advices, and you should increase considerably the likelihood to meet up with him or her boyfriend again. Furthermore, you'll turned into a more aged person, since you already experienced being dumped.

The whole website is the blog which is aimed to help people to get ex back . Rate this Article

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Zhu Honglin has published 8 articles. Article submitted on May 04, 2013. Word count: 729

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jQuery for Bioinformatics

I've been using JavaScript for almost two decades now, but somehow I've managed to avoid learning jQuery until just recently, mostly out of laziness but also because of a lingering yet torrid love-hate relationship with "syntax sugar" programming patterns. The best thing I can say about jQuery is that it has a seductively compact and powerful syntax. The worst thing I can say about jQuery is this.repeat(previousStatement).

For better or worse, I've had to begin dabbling in jQuery recently to save myself from the horror of old-school bare-knuckle DOM parsing. You know what I'm talking about: Nested loops with lots of calls to getElementsByTagName( ) followed up with hand-parsing of innerHTML. Who wants to do all that when you can use the oh-so-cute $(selector).each( ) construction?

The trouble with cute/compact syntax (as any recovering Perl user will gladly tell you in return for a bottle of cheap sherry) is that it's write-only. When you go back to look at something a week later and see 15 lines' worth of JS functionality rolled up into a shockingly crisp (yet thoroughly opaque) jQuery one-liner, you often wish you'd gone ahead and written those 15 homely lines of JavaScript in the first place, instead of giving in to that one irresistibly sexy, powerful line of jQuery that's oh yeah BTW also self-obfuscating.

Nonetheless, if you do a lot of page-scraping (as I do when visiting bioinformatics sites), the time savings of being able to parse a page with jQuery can be formidable. Who can resist grabbing all rows of a table with $("tr")? Who can resist iterating over them with .each()?

I tend to use the online apps at genomevolution.org quite heavily. The great folks who maintain that site have a nice way of serving up prodigious amounts of data in easy-to-use interactive forms, but sometimes you just want to harvest the data from a table and be done with it. Take the page I created at http://genomevolution.org/r/9726, which is based on a list of 100 unique bacterial species in the group known as Alphaproteobacteria. If you go to that page and scroll over to the far right, you'll see a column header labeled "Codon Usage." Underneath that label is a "Get All Codon Tables" link. Click that link and be prepared to wait about two minutes as the codon data loads for each organism. It's worth the wait, because when you're done, you're looking at color-coded codon usage frequencies for all 64 codons, for all 100 organisms.

Suppose you just want the codon data in text form, to analyze later? Scraping the raw data out of the HTML page is a royal bitch, because whether you know it or not, that page has tables embedded in tables embedded in tables. Parsing the DOM by hand is (shudder, wince) well nigh unthinkable.

Go to http://genomevolution.org/r/9726 and click "Get All Codon Tables" under the "Codon Usage" column heading. Allow a minute or two for codon data to load. Meanwhile, Control-Shift-J opens the Chrome console. (Select the Console tab at the top of the window if it's not already selected.) Paste the following code into the console. Hit Enter. Savor the power.

codonData = [];

function process( ) {

    var CODONS_COLUMN  = 15;

    var rowdata =  jQuery( 'td', this );
    var codonUsage = rowdata[ CODONS_COLUMN ].textContent.split(/(?=CCA)/)[1]; 
    codonData.push( codonUsage ); 
}

$('tr[id^=gl]').each( process ); // oh jQuery, must you tease me so?

console.log( codonData.join("\n") );

All of this was originally a single statement, with an inline callback function (in typical jQuery fashion). I decided to unroll it into more verbose, easier to understand form, lest my head explode two weeks from now trying to re-read and re-figure-out the code.

This bit of code does some pretty typical jQuery things, such as grab all rows of a table with $('tr'), except that in this case I most certainly do not want all rows of all tables in the HTML page (which would be hundreds of rows of extraneous stuff). The rows I need happen to have an "id" attribute with a value that begins with "gl." The construction $('tr[id^=gl]') is jQuery's syntax for selecting table rows that have an id-attribute that begins with "gl."  (The ^= here means "begins with." You could signify "ends with" using $= instead of ^=.)

The process() callback fetches all table columns for the current row using the jQuery( 'td', this ) construction, which means gives me a jQuery object representing all "td" elements under the DOM node represented by this. In the callback context, this refers to the current jQuery node, not the window object or Function object. If you choose (as I did not) to declare your callback with arguments, as in function myCallback( argA, argB), then argA will be the index of the current item and argB will be this.

If you're wondering about the regex /(?=CCA)/, I need this because ordinarily the codon data would look like this:

Codon Usage: The Bacterial and Plant Plastid Code (transl_table=11) CCA(P) 1.18%CCG(P) 1.58%CCT(P) 1.17%CCC(P) 1.37%CGA(R) 0.32%CGG(R) 1.32%CGT(R) 1.82%CGC(R) 2.54%CAA(Q) 1.07%CAG(Q) 2.84%CAT(H) 1.59%CAC(H) 0.89%CTA(L) 0.48%CTG(L) 4.58%CTT(L) 1.96%CTC(L) 0.84%GCA(A) 2.94%GCG(A) 2.14%GCT(A) 2.31%GCC(A) 3.90%GGA(G) 0.90%GGG(G) 1.74%GGT(G) 2.11%GGC(G) 3.23%GAA(E) 3.92%GAG(E) 1.36%GAT(D) 3.76%GAC(D) 1.49%GTA(V) 1.08%GTG(V) 3.01%GTT(V) 2.19%GTC(V) 0.81%ACA(T) 1.82%ACG(T) 1.49%ACT(T) 0.57%ACC(T) 1.83%AGA(R) 0.30%AGG(R) 0.31%AGT(S) 0.61%AGC(S) 1.33%AAA(K) 2.01%AAG(K) 1.60%AAT(N) 1.39%AAC(N) 1.64%ATA(I) 0.59%ATG(M) 2.56%ATT(I) 2.88%ATC(I) 1.59%TCA(S) 0.65%TCG(S) 0.47%TCT(S) 1.37%TCC(S) 1.34%TGA(*) 0.14%TGG(W) 1.47%TGT(C) 0.46%TGC(C) 0.70%TAA(*) 0.14%TAG(*) 0.03%TAT(Y) 1.47%TAC(Y) 0.90%TTA(L) 0.61%TTG(L) 1.67%TTT(F) 2.41%TTC(F) 1.22%

Notice that first line ("Codon usage: The Bacterial [blah blah]"). I just want the codon data, not the leader line. But how to split off the codon data? Answer: Use a lookahead regular expression that doesn't consume the match. If you split on /CCA/ (the first codon) you will of course consume the CCA, never to be seen again. Instead, use (?=CCA), with parentheses (absolutely essential!) and the parser will look ahead to find an upcoming CCA, then stop and match the spot right before the CCA without consuming the CCA.

I'm sure a true jQuery expert can rewrite the foregoing code in a much more elegant, compact manner. For me, elegant and compact aren't always optimal. I've learned to value readable and self-documenting over elegant and opaque. Cute/sexy isn't always best. I'll take homely and straightforward any day.

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Excellent Hypnosis Training in Singapore

Hypnosis, a mental state which is produced by a scientific technique known as hypnotic induction. A combined process of various suggestions which produces a state of heightened suggestibility. In this case a person has high mental concentration, they may not be fully aware and they will feel extremely physically relaxed.

This therapy is used in a variety of medical fields to help people attain physical and mental well being. A tested and a proven means for treating many personal and emotional disorders which is basically has a potential to place back on track in their life. This is all about reading someone else's mind. It's a technique in which you have to learn the required information through CD audio programs, or you can go for a personal trainer that can help you study the complete course of hypnosis in Singapore. With the help of these resources one can easily start his training. Apply all the basics that you will learn from your training. Make your good foundation to start with.

Human brain is a complex system combination of neurons and chemical reactions assuming that once the person is under hypnotism, the subconscious mind is the one talking to them. There are many levels of dream-wake that the mind can regress to and sometimes the defenses which are still up and the subconscious mind remains hidden and casual to the efforts of the hypnotists.

Trust and cooperation is a major part followed in the procedure. As long you give focus, you should be able to do your job easily with creditability. All you have learned from your training, will take you far at the top, master the skill and for that you have to practice. All the skills that you have learned through hypnosis training will allow you to help others, molds you when certain situations arises and can help you gain some recognized qualifications. Get certified by various bodies which makes you a certified therapist. Apply different tricks of hypnotism with your friends and family, make it clear that you need complete honesty from them regarding training experience.

People will begin to show interest in learning hypnosis and bear in mind that it would take more time in becoming a expert in this skill. You can teach others what you have learnt from your training, you also have to follow the advice and instructions from people who have been already practicing. Just be sure to start with facts so that there is no confusion remains in the end.

Author works as a hypnotists in one of the well known center providing Hypnosis Certification . Get certified training through Hypnosis Singapore.

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Peter Schiff trolls Sargent and Sims

Some people on Twitter sent me this video of Peter Schiff, self-described "Austrian" and one of the world's most powerful EconoTrolls, ridiculing the two 2011 Economics Nobel winners, Tom Sargent and Chris Sims:

Schiff spends the first 9 minutes of the 11-minute video lambasting Sargent and Sims for (supposedly) not being able to answer the "poignant question" (sic) of what economic policy steps America should be taking. He repeatedly claims that Sargent and Sims can't answer this question because they don't "actually [understand] any economics". He contrasts this with himself, saying "I have real solutions based on a real knowledge of economics. I may not have a Nobel prize, but I got some street smarts."

Except Schiff's entire rant is pretty clearly just a hatchet job. Sargent and Sims didn't really fail to answer the question! Schiff just edited out the parts where they gave their answers!

Around the 9:30 mark, Schiff admits that Sims actually did give policy recommendations, and that these recommendations were very mainstream - monetary easing, short-term deficits, and long-term fiscal consolidation!

As for Sargent, Schiff doesn't cut him a break at all, but Sargent also answered the question. His full answer can be seen here. He basically says that the federal government needs to cut spending. (Update: As CA points out in the comments, Sargent might just be saying that we need to clarify which programs we're going to cut, since spending cuts are inevitable.)

So here's the question: Why does Schiff perform this unfair hatchet job on the Nobel Prize winners?

Of course I don't know the answer for certain. But it seems fairly clear that Schiff is trying to pump up his own credentials. He continually repeats that he knows more about economics than the Nobel Prize winners. And the fact that Sargent's answer dovetails with Schiff's well-known policy preferences means that Schiff either didn't understand Sargent (entirely possible), or else deliberately ignored the fact that Sargent agrees with him. That suggests self-glorification, at the expense of famous people, was Schiff's main objective.

Why would Schiff want to do this? It could be simply for fun! Being grandiose and self-congratulatory is fun (for some more than others). Or maybe it's a part of Schiff's business. As the head of a money management firm (Euro Pacific Capital), and as a seller of newsletters and writer of books about the coming collapse of the American economy, Schiff could always use some macro cred. Convincing investors that Schiff's everyman "street smarts" convey a superior understanding of the macroeconomy, while the bumbling know-nothing ivory-tower academics play with their irrelevant mathematical models, might make those investors more likely to stick with Schiff even as his repeated inflation predictions fail to pan out.

A sort of anti-intellectual folksy charm seems to be exactly what Schiff is going for. Notice how at around 9:06 he mispronounces Bernanke's name as "Bernacky". He then repeats this mispronunciation several more times (a quick search through older Schiff videos confirms that he often, though not always, mispronounces it this way). Now at first it might seem insane to hand one's wealth over to a macro investor who doesn't even know how to say the Fed Chairman's name. But who knows? Maybe there are deeply conservative people out there for whom handing a small sliver of their life's savings to Schiff is worth it purely for the sake of political affinity, as a sort of protest vote against Obama and the socialist money-printers. Or maybe Schiff just wants to signal his utter contempt for all things Fed. Or maybe after getting burned by repeated widowmaker trades, investors who buy into the "Austrian" schtick can console themselves that "Bernacky" just cheated, and went against the fundamentals of God and Market, but that that high-and-mighty bearded technocrat will get his comeuppance in the end! 

OK, I admit I really have no idea what's going on in this Austrian/Fox Business/right-wing-radio/macro-derp-herping world. At this point I'm just taking random swings for humor value. SORRY. Sorry.

But anyway, it occurs to me that the life of the Austrian investment guru is a tough one. Not only do you have to convince people that you know better economics than Tom Sargent and Chris Sims, but you have to fight rear-guard actions against others of your own kind, to prove you're The One True Austrian Guru. In 2009, a guy named Mish Shedlock, who runs his own money management business, called Schiff out on some failed exchange rate predictions and on the poor performance of one of Schiff's funds during and after the crisis. This is a bit funny, since Shedlock himself is a self-professed subscriber to "Austrian" ideas; his fund's name even sounds like Schiff's ("Sitka Pacific Capital Management" vs. "Euro Pacific Capital"). But his all-out attack on Schiff precipitated one of the great EconoTroll Battles of all time. 

Schiff quickly whirled to deal with the attack from behind. He gave Shedlock a brutal taste of his own medicine, pointing out Shedlock's own poor performance and mocking Shedlock's small amount of Assets Under Management. In response, Shedlock went for the jugular, calling out Schiff on his hyperinflation predictions and challenging Schiff to a debate. Schiff very wisely avoided debating someone with far less fame than himself, and stuck to dissing Shedlock harshly on his radio show. The highly entertaining three-year feud shows no signs of abating.

Anyway, what's the upshot of all my Schiff-trolling? The upshot is: If you see some guy making fun of top academic economists, fine. Maybe he has a good point! But if the alternative he's offering consists of a long string of failed macro predictions, loosely justified by hand-waving references to "the Austrian School" and seasoned with right-wing politics and folksy charm, beware. Chances are he's just pulling your leg. And if the top academic economists are reluctant to wade into political war zones, and unwilling to overstate the certainty afforded by their theories, well, that's probably to their credit rather than a reason to ridicule them.

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Book Review: The Quants

If you want a fun, non-technical history of quantitative finance, this is your book. It traces the development of quant models, from Ed Thorp and Black-Scholes-Merton all the way through David X. Li. It explains trading strategies like statistical arbitrage in layman's terms, and offers insight into what it's like to run a trading operation, day to day. And it narrates the three-decade-long run-up to the epic finance-industry meltdown of 2007-8, including "warm-ups" like Black Monday and the fall of Long Term Capital Management. The author, Scott Patterson, writes in an accessible, engaging style, making it difficult to put the book down at times. It also does a good job of profiling some of the colorful personalities of the quant world - Peter Muller and Cliff Asness being the most colorful of the bunch.

So I definitely recommend The Quants.

Like (almost) all books, The Quants is not without its flaws. Chief among these is that the book mostly fails to deliver on one of the promises in its subtitle - it fails to give a detailed account of the quants that nearly destroyed Wall Street.

Why was Wall Street almost destroyed? The general story that I buy goes something like this:

1) Wall Street firms, by creating securitized mortgage-backed financial products, increased the demand for housing, which along with other factors helped fuel a nationwide housing bubble.

(Note: This assumes that some initial rapid price increase is needed to "jump-start" a bubble, leading to a spiral of self-reinforcing price increases, either through speculation, herd behavior, or the mistaken inference of underlying structural change, or some combination thereof. That may not be how bubbles really work, but it's currently my best guess, from what I've seen in the lab and read in the literature.)

2) Wall Street firms priced these securities using quantitative models that were fundamentally flawed, leading them to understate the risk of the mortgage-backed securities and derivatives based on these securities. Some of the flaws included eternally rising national house prices, non-time-varying correlations, thin-tailed (less risky) stochastic processes, and omission of counterparty risk.

3) These models lead banks to hold way too many of the aforementioned securities, and to borrow way too much money (leverage) to buy them. Complacent (and possibly captured) regulators and ratings agencies did nothing to stop this.

4) When the bubble popped and prices fell and correlations spiked, banks collapsed.

This story is very similar to the one given in The Quants. So Patterson does, in my view, get the crisis correct.

But four of the six people profiled in The Quants were operators of independent hedge funds - Ed Thorp of Princeton Newport, Ken Griffin of Citadel, Cliff Asness of AQR, and Jim Simons of Renaissance. Though big by historical hedge fund standards, these firms were not nearly as big (or, for the most part, as leveraged) as the banks that were at the center of the crisis - Goldman Sachs, Bank of America, Lehman, etc. And though most of the quant hedge funds suffered in the great 2008 crash, the specter of their collapse did not really threaten the system itself. In fact, as The Quants recounts, the quant hedge funds suffered their own meltdown a year earlier, in the summer of 2007, but this caused far fewer problems for the economy than the near-collapse of the big banks in 2008. Notably, none of the independent quant hedge funds were bailed out by the U.S. government in 2008 - some because they were not in danger, others because they simply weren't systematically important enough to warrant bailouts.

This is not to say that quant hedge funds can't be dangerous to the financial system; Long Term Capital Management clearly was. It's simply the case that this time, in 2008, independent hedge funds were not at the center of the crisis. They mostly sat on the sidelines, watching the carnage and hoping that they didn't die. One of the funds Patterson profiles, Renaissance Technologies, was using strategies so different from the big banks that it gained 80% in 2008. (Disclosure: The founder and some ex-employees of Renaissance Technologies have made large donations to the university where I work!)

The Quants also profiled two men who headed internal hedge funds within big banks - Peter Muller of Morgan Stanley, and Boaz Weinstein of Deutsche Bank. Weinstein's group appears to have bought lots of mortgage-backed securities, and to have lost a lot of money for the firm in the 2008 crash. But this means that only one out of the six protagonists of The Quants could plausibly be described as having "almost destroyed Wall Street".

Personally, I would have liked to have seen The Quants tell the stories of the "pricing quants" and "risk quants" within the big banks, whose models were instrumental in convincing regulators, ratings agencies, and bank executives themselves that mortgage-backed products were safe. Patterson does briefly tell the story of two such quants, Fischer Black  David X. Li, but I'd like to have seen a lot more about these guys, and about academics like Myron Scholes and Robert Merton.

Did the quants within big banks know that their models were wrong? Did they try to warn the executives not to apply the models? Did they simply shut up and take a paycheck as greedy, reckless executives misused and over-applied their models? Or did they actively promote blanket and widespread use of the flawed models, encouraging the heavy use of leverage and the holding of huge amounts of mortgage-backed products? I wish The Quants had answered this question, but it did not.

I also think The Quants displays a little too much fear of the unknown. Patterson definitely seems to regard the black-box strategies of companies like Renaissance as creepy and inherently suspicious. But I think this fear is mostly unwarranted. Any assumptions can be wrong, so any algorithm can blow up. No quant model is riskless or foolproof, and none will ever be. But that applies just as much to the intuitive trades of "shoot-from-the-hip" human traders, or to any other investing mechanism. No spooky supercomputers or secretive mathematicians were needed in order to blow up the Japanese financial system in 1989, or the U.S. financial system in 1929.

The key, as Ed Thorp is quoted as saying in the book, is in limiting leverage, so that collapses don't bring down the whole system. Limiting the systemic risk caused by "too big to fail" institutions also seems to be important. The mundane factors of leverage and bigness seem much more scary, to me, than the opacity of quant trading strategies.

Nevertheless, it is a really good book, and if you have any interest in the history of finance, you should check it out.

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Step-by-Step Concerning How to Hypnotize Someone Without Them Knowing

If you'd prefer governing the lives of other folks then learning to hypnotize someone without them knowing might allow you to accomplish what you need to accomplish. A lot of people have no idea that performing such a cute thing is achievable however it is about producing the best from life, able to find the partner you need, the sort of life you need and making the most effective from your chances got for all. To perform something, initially you must develop a space at heart for possibilities ahead of turning out perfectly into a reality. Furthermore, understand that you can not get visitors to do something. As an example, you can not hypnotize somebody to leap away from a window or anything for these. As there are deeper hardwired endurance mechanisms, which are made to safeguard our everyday life as opposed to what hypnosis will get to.

You can find three main steps of hypnotizing someone and reduce costs is always to stimulate an unclear state of awareness. This is essential since they shall be disposed in your hypnotic commands, and lowers their psychological defenses. Basically, it indicates causing them to be feel comfortable plus more relaxed in a really positive way. Communicate in the relaxed tone, which can be in accord making use of their breathing patterns as well as the subject needs to be about relaxing things like vacation something like that for these, using anchoring techniques and embedded commands so they can take deeper states of trance. Besides, the niche needs to be in times they are centering on what you may are telling them. It's also advisable to choose a place where you must acknowledge. The spot must comfortable and clear of noise.

One other step is always to embed wishes and concepts within their brain discreetly, to produce hypnotic tips to their unconscious mind. Consequently, it is extremely significant to comprehend hypnotic language guides. These represent the linguistic structures it is possible to connect with lsquoprogram' other folk's feelings and thoughts. A great tricky language guide is named lsquostacked presuppositions' in places you just presume various things within your sentences in order that their marbles are kept busy. Let them have a flatter. Praise them, be operational and they're going to become to be controlled by what you may being a hypnotist says. Praises create a place of reliance. You can even learn to nod your mind gradually when telling them your hypnotic command. As soon as you try this, they are going to also nod their heads as a possible agreement of what you may are letting them know.

The next and last step is always to close all of it and get rid of it. Once you place them in circumstances of state of hypnosis and effectively embedded ideas, you ought to make certain that they perform these suggestions when they recover their normal state of consciousness. As an example, it is possible to let them visualize that they perform certain actions in the future, in addition to how great they are going to feel when they finish hypnotizing your thinking, making some great benefits of the proceedings you need them to obtain specific. These are the basic main tips and guides of the way to hypnotize someone without them knowing, which can be proven and possess did wonders.

The author of the article like studying the hypnotize tips and have a blog, click here to visit the website.

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Want to Manage Stress? - Avoid Unhealthy Habits (Drugteststrips)

Stress is common in today's busy lifestyle. Many people are resorting to harmful habits like smoking, drinking, substance abuse, etc. to deal with stress. These habits may give temporary relief by taking the mind away from the situation causing stress. But in long run, they create new problems and destroy the individual's life.

Many people are struggling with stress:
Stress became a part of our regular life today. It could be due to financial problems, problems at work, an argument with children or spouse, health issues like diabetes, arthritis or a heart disease. Look around and you can see many people in stress for some reason or the other. Whether the problem is big or small, whether it is caused by external factors or internal perceptions, the ultimate result will be anxiety and stress.

People are turning to unhealthy habits:
Many of us are blessed with enough emotional strength and self-esteem to deal with regular stress in life. However, some people, who are not mentally strong enough, turn to unhealthy activities that may provide an instant relief. As they feel better for that moment, they simply turn to unhealthy habits every now and then to confront stress. Thus, it turns into a habit and eventually an addiction.

Avoid unhealthy habits:
Smoking, alcohol and drug abuse are common unhealthy habits adopted by people to beat the stress. However, you wouldn't know when these unhealthy stress relieving habits have turned into stress-causers, making you weaker mentally. Not only will they add up to your stress, they will also start impacting your health adversely, making you unhealthy both physically and mentally.

Smoking: Though many people are aware of the fact that smoking is injurious to health, they find it to be a better option to deal with stress. Tobacco contains a psychoactive drug, called nicotine, which creates an illusion in the human brain. The brain will not be able to understand the adverse effects on body like increased blood pressure, increased heart rate, tensed muscles, constricted blood vessels, etc. By smoking you are just transferring you stress from brain to body.

Excessive drinking: Many studies reported that alcohol abuse is many times related to stress caused by economic struggle, job issues or marital discord. A drink or two may not matter much, but excessive drinking can simply land you in troubles. Long term excessive drinking may lead to chronic mental disorders apart from causing physical harm including liver and cardiovascular diseases, cancer, etc.

Illegal drug use: Many theories of addiction claim that stress leads to increased drug use. Illicit drug abuse is highly addictive and may cause more mental disorders like post-traumatic stress disorder, depression, etc. Adverse physical effects are obvious due to drug abuse. Drug abusing person may also face economic and social problems.

Inculcate healthy habits:
Overeating or under-eating, procrastination, prescription drug abuse, too much sleeping, etc. are other common unhealthy habits embraced by people to deal with stress. Like alcohol or substance abuse, they also exacerbate the stress levels. Stress will always be there; the path you choose to manage it makes the difference.

There are many ways to manage stress effectively. Inculcating healthy habits such as regular physical exercise, yoga or meditation, intake of nutrient-rich food, etc. can help a lot in managing stress. Healthy habits not only protect you from harmful effects of stress, but also help you build physical strength and mental confidence to manage stress causing situations.

Practicing unhealthy habits may seem to be an easy way to deal with stress compared to adopting healthy lifestyle, but it will most probably lead to destruction.

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Help Understand Bipolar Disorder Symptoms

Male depression - what exactly does it mean, and how to males experience it differently from women? It comes as a surprise to many people to learn that men and women actually experience it very differently, often feeling very different symptoms and displaying different behaviours. It can be particularly difficult for men as the symptoms of male depression are often quite far from the common conceptions people have developed about how clinical depression looks. The words used can be very confusing, because although the word depression suggests a consistently low and 'sad' mood, it can often manifest in males in the form of agitation and anger.

Depression in men can be particularly hard to diagnose for these reasons, and very often men don't even recognise that they may be suffering from it. This is why it's so important to ensure a wider understanding of how the disorder manifests in men, how it can be controlled and how to find a way through it.

However, although the disorder can show different symptoms in men it's important to keep in mind that what most people think of as 'typical' symptoms are generally still present and dominant in most cases - for example, a loss of enthusiasm for formerly enjoyable activities, loss of interest in sex and consistently 'down' moods, along with recurring thoughts of death and suicide.

So how can you help someone you know who may be suffering from depression - or what can you do if you're a man and you think you might have depression? It's important that if a friend of family member may be suffering, you approach the situation cautiously, as some men may go into denial over having a problem. This denial can sometimes take on an angry form and cause the person to withdraw from you. It's important to broach the subject carefully and be prepared to explain how their behaviour lines up with common symptoms if necessary.

If you believe you might be suffering from depression you should talk to your doctor about potential treatment paths for you, which typically involve some therapy work and often medication (although that's not always the case). In the meantime, it's a good idea to try to avoid stressful situations if possible - while there are often many underlying factors that cause it, being put under pressure can trigger an episode.

Click here to learn more about bipolar disorder symptoms.

Richard Atchison, raised in New Zealand, graduated in 2002 from Auckland High School. A Presidential Scholar, he entered Auckland State University that autumn as an English major, with an emphasis in Literary Studies. Presently, an article contributor for various sites. bipolar disorder symptoms

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Infrastructure skeptics take a hit

Via Barry Ritholtz and Mark Thoma comes the following chart by McKinsey:



This chart simultaneously debunks not one, but TWO of the biggest talking points of the anti-infrastructure derpers:

Derp 1: "It's just civil engineers angling for pork!"

This is one I hear a lot. The American Society of Civil Engineers released an "infrastructure report card" that gave the U.S. a "D+". In response, anti-infrastructure people often throw up their hands and say "Of course a bunch of civil engineers want us to spend more money on civil engineering!" But now McKinsey says the same thing. The chart above cites the McKinsey Global Institute's own in-house analysis. If you think McKinsey itself is in the tank for a bunch of gold-digging civil engineers,you're...well, it sounds pretty silly when you say it out loud, doesn't it?

As an aside, the McKinsey report also cites independent figures from the World Economic Forum, the Army Corps of Engineers, and the Federal Transit Authority. Everyone agrees that the U.S. needs more infrastructure spending.


Derp 2: "Oh yeah? What about Japan in the 90s?"

A lot of anti-infrastructure people bring up Japan's infrastructure splurge in the 1990s. Japan built bridges to nowhere (I drove across one, once; "nowhere" is not an exaggeration), concreted over riverbeds and parks and beaches, and generally committed an epic waste of money, labor, and concrete. We'd commit the same error if we spent more on roads and bridges, right?

Wrong. As the McKinsey report shows, Japan still spends much more on infrastructure than it needs to (and this, btw, is after a dramatic reduction in spending in the '00s). That is in stark contrast to most other countries. So this report clearly says that we are not Japan. We are on the opposite side of the optimal point. They need less, we need more.


In conclusion, McKinsey just killed two of the main anti-infrastructure arguments. Increasingly, all the anti-infrastructure people have left is their derp. At a time when interest rates are super-low and millions are out of work, there is no good case against a big blast of infrastructure spending. Let's do it right now.

Update: Numbers! We need to spend an additional $1 trillion (that's 1000 $billion) dollars on infrastructure over the next 5 years. or about 1% of GDP.

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Enhance Your Life Through Online Counselling

The world is a place of innovation, creativity, excitement, and wonder. The unfortunate reality of it all is that many people do not experience those feelings in their lives. Instead, they suffer from the negative feelings that are in the world including despair, depression, sadness, and hopelessness. Nobody wants to live a life that way, but because of circumstances that are often out of their control, many people are forced into those feelings. Through online counselling, individuals can learn to overcome harsh feelings and gain new hope in their lives, giving them the motivation to move on, feel the excitement, and begin to wonder. The following are three ways in which an online life coach could enhance your life.

The first way that online counselling could enhance your life is if you suffer from depression. People who suffer from depression often have a hard time getting up in the morning. They may feel like what they do will not make a difference in the world and they would rather not get up to do it. With an online life coach, they will not have to get out of bed. They can simply switch the computer on for their session. The counselor can work with the individual to help them cope with the feelings they are having. The coach can help the individual to see why their life is worth living and give them hope for the future.

The next way that online counselling could enhance someone's life is if they are going through a hard family situation. This could be the death of a loved one, a divorce, dealing with a difficult child, etc. Through an online session, the individual can learn how to deal with their family member. They can confide in the counselor and get real ideas, real techniques, and real comfort from the counselor so that they are better equipped to get through their hard times.

The last way that online counselling could enhance a person's life is if they were the victim of abuse. Many abuse victims are afraid to go and talk to someone, fearing that their abuser will see them, or that other people will look down on them. With an online life coach, they will not have to let their secret out. They can complete their counseling sessions, work through the pain that came from the abuse, learn how to get out of the abuse cycle, and can become stronger without anyone suspecting that is what they are doing. When they feel that they are strong enough, they can confront the abuse and move on in life without it.

Whether you have chronic depression, have suffered the loss of a family member, or have been abused, an online counselor is just what you might need in order to get through the difficult times you are facing.

Caroline Bronte have worked as a successful Counsellor Online Counselling and Telephone Counselling Please click on the links for further information and how to get in touch.

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Beginner's Guide Concerning How to Hypnotize an Individual

Maybe you have considered hypnotizing someone and managing his unconscious mind? It is obvious that hypnosis is an efficient method of getting use of one's mind which will help battle several problems of tension, addiction along with other disorders. However, the best question to think about when conversing relating to this art of putting someone into trance is the fact that regardless if you are doing the work together with his permission or otherwise. While hypnotizing a willing individual is easy, practicing it on candidates without informing could be a tough task.

Basics of utilizing Hypnosis

For novices who are prepared to discover the tips and tricks of methods to hypnotize an individual, taking the help of a skilled and expertise professional is definitely recommended. You may also bank on several books and guidelines which supports you will get adequate knowledge and knowledge about the very best of hypnotizing techniques effortlessly and effectiveness. To master your art of hypnosis, it is crucial that you take action for a lot of days to obtain effective results and treatments for unconscious minds.

Tips of Hypnosis for novices

If you're a beginner who's prepared to discover the basics of the extremely intriguing and exciting approach to progressive relaxation, given several simple tips and aspects that should be considered rightly.

Like a first timer, you need to know that to hypnotize somebody that is unwilling could be a tough job because it needs extreme concentration and expertise practice. Hence, it is strongly recommended that you ought to initially opt for those who are unbiased and liberal relating to this process. Try you techniques and tricks on the willing person which not just helps get result but additionally contributes to oneself confidence.

Secondly, you have to maintain an authoritative position when experiencing the skill of hypnosis. Regardless if you are attempting to hypnotize an individual or many, always keep to possess proper confidence and convincing capacity to assure your candidate. Using various objects, added with hand movements, high pitched sounds and much more also help create a highly effective and suitable atmosphere.

Rather than relaxing in a stiff and uncomfortable manner, enable your candidate sit inside a relaxed position which supports you hypnotize him easily. Use ways of voice modulation to get in touch with his inner mind with complete focus and a focus. Help each body pat of the subject get relaxed, beginning with his legs to back and top while you move upward. Ensure that you continue doing this technique twice to possess him thoroughly relaxed and distracted, thus having complete charge of the unconscious mind.

You need to consider signs and symbols for example breathing, relaxed posture and rhythmic response to make sure that your candidate is totally hypnotized. Only once you are confident and assured of the success, make use of your voice to direct his unconscious mind with assistance of advanced techniques.

Always keep that hypnosis is really a skill which must be practiced properly to get beneficial and good results at its best.

Click here to get more info about how to do hypnosis , and the blog can help you become a hypnosism sooner or later!

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Getting Started in Desktop Bioinformatics

I've spent about four months now exploring do-it-yourself desktop bioinformatics. Overall, I'm excited by what I've been able to do and I'm optimistic about the prospects for other do-it-yourself desktop-science geeks, because there are tons of great online tools for doing bio-sci and lots of important scientific questions yet to be fleshed out. So I thought I'd share some of what I've learned, and provide some pointers for anyone who might want to try his or her hand at this sort of "citizen science."

It helps to have the benefit of a science education (in particular, a bio education) before beginning, but one of the great things about do-it-yourself desktop science is that you can (and will!) learn as you go. For example, you might have only a bare-bones basic understanding of enzymology before you begin, but as you move deeper into a particular research quest, you'll find yourself wanting to learn more about this or that aspect of an enzyme. So you'll hit Google Scholar and bring yourself up-to-date on this or that detail of a particular subject. That's a Good Thing.

When I first plunged into DNA analysis, I have to admit my knowledge of mitochondria was weak. I knew they had their own DNA, for example, but it wasn't obvious to me (until I started digging) that mitochondrial DNA is pathetically small, whereas the mitochondrial proteome (the superset of all products that go into making up a functioning mitochondrion) is large. In other words, most "mitochondrial genes" are not in mtDNA. They're in nuclear DNA. There are a couple of online databases of nuclear mitochondrial genes (NUMTs, as they're known), but by and large this is an area in dire need of more research. Someone needs to put together a database or reference set of yeast NUMTs, for example. We also need a database for algal NUMTs, another for protozoan NUMTs, another for rice or corn or Arabidopsis NUMTs, etc. Maybe you'll be the one to move such a project along?

So. How can you get started in desktop bioinformatics? I recommend familiarizing yourself with the great tools at genomevolution.org, which is powered by iPlant, which (in turn) is funded by the National Science Foundation Plant Cyberinfrastructure Program here in the U.S. In particular, I recommend you set aside an evening to run through some of the tutorials at genomevolution.org. That'll give you an idea of what's possible with their tools.

Many organisms have genes for flagellum proteins,
but not all such organisms actually make a flagellum.
(The flagellum is the whiplike appendage that gives the
cell motility. Above: Bdellovibrio, a bacterium with a
powerful flagellum.)

If you go to this page and scroll down, you'll find some really interesting short videos showing how to use some of the genomevolution.org tools. They're fun to watch and should stimulate your imagination.

What kinds of problems need investigating by desktop biologists? The sky's the limit. One quest that lends itself to citizen science is looking for examples of horizontal gene transfer (HGT). This requires that you first teach yourself a little bit about BLAST searches. (BLAST searches are sequence-similarity searches that let you compare DNA against DNA or amino-acid sequence against amino-acid sequence.) The strategies involved here can range from simple and brute force to sophisticated; and the great thing is, you can invent your own heuristics. It's a wide-open area. I recently found good evidence (90%+ similarity of DNA sequences) for bacterial gene transfer into rice, which I'll write about in a later post. I'm confident there are thousands of examples of horizontal gene transfer (whether from bacteria to bacteria, bacteria to plant, bacteria to insect, or whatever) waiting to be discovered. You could easily be the next discoverer of one of these gene transfers.

Here are some other ideas for desktop-science explorations:

• Find and characterize flagellar genes in organisms that lack motility. If you dig into the literature, you'll find that there are many examples of supposedly immotile organisms (like the intracellular parasite Buchnera, which lives inside aphids) that not only harbor flagellum genes but express some of them—yet have no external flagellum. Obviously, organisms that retain flagellum genes but actually don't make a flagellum (that little whip-like tail that makes single-celled organisms swim around) must be retaining those genes for a reason. The gene products must be doing something. But what? Also: Paramecium and diatoms and other eukaryotes make flagella and/or cilia. Most animals also make cilia. (Ever get a tickle deep in your throat or bronchia? It was probably something tangling with the cilia lining your bronchial system.) What's the relationship between cilia gene products in Paramecium, say, and cilia in animals? Do any plants conceal cilia genes? If so, how are they related phylogenetically to lower-organism cilia?
• Migration of genes from parasites to host DNA. A general pattern that seems to happen in nature is: a bacterium or other invader takes up residency inside an animal or plant cell, becoming an endosymbiont; then some of its genes (the symbiont's genes) move to the nucleus of the host cell. Which genes? What do the genes do? That's up to you to try to find out. 
• Bidirectionally ("bidi") transcribed genes: While rare, there are examples of genes in which each strand of DNA is transcribed into mRNA. (The genome for Rothia mucilaginosa contains many putative examples of this.) Find organisms that contain bidi genes. Try to determine if both strands are actually transcribed. Examine sister-species organisms to see if one strand is transcribed in one organism and the other gene (on the other strand) is transcribed in the other organism.
• Phylogenetics of plasmid and viral genes. Try to determine the ancestry of a virus gene. There are good tree-making services online that do all the hard work for you, including protein-sequence alignments. All you have to do is cut and paste Fasta files.
• Codon analysis. There are many plants (rice is one) and higher organisms in which DNA is more or less equally divided into high-GC-content genes and low-GC-content genes. Surely the codon usage patterns for each class of gene(s) varies. But how? What are the codon adaptation indexes (CAI values) for the various genes? Create a few histograms of CAI values. Use CAIs and other techniques to try to determine which genes are highly expressed. Are HEGs (highly expressed genes) mostly high-GC? Low-GC? Both? Run some histograms on the genes' purine (A+G) content, G+C content, G+C content by codon position.
• Many organisms (and organelles) have extremely GC-poor genomes. Some have bizarre codon usage patterns (where, say, the codon AAA is used 12 times more than the average codon). Some use 56 or fewer codons (out of 64 possible). Find the organelle or organism that uses the fewest codons. See if there's an organism or organelle that uses fewer than 20 amino acids. Which amino acid(s) get(s) left out? 
• Characterize the DNA repairosome of an aerobic and an anerobic archeon. Compare and contrast the two.
• Find all the genes in a particular organism that have mitochondrial-targeting presequences in their DNA. 
• Pick two closely related organisms. Try to figure out how many million years ago they diverged. Use mitochondrial DNA analysis as well as cytoplasmic protein analysis. 
• Find the bacterium that has more secretion-protein, permease, and protein-translocation genes than any other. Compare it to its closest relative. 
• Find an organism that is pathogenic (to humans, animals, or plants). Find its closest non-pathogenic relative. Compare genomes. Determine which genes are most likely to be involved in virulence. 
• Some seemingly simple organisms (amoebae) have more DNA than a human. Why? What's all that DNA doing there? Does it contain horizontally transferred genes from plants, bacteria, archeons, animals? Are amoebas and other super-large-genome organisms "DNA hoarders"? Are they DNA curationists? Characterize the genes (enumerate by category, first) of these organisms. How many are expressed? How many are junk? What's the energy cost of maintaining that much junk DNA? Can it all be junk? Is an amoeba actually a devolved higher life form that forgot how to do morphogenesis and can no longer develop into a tadpole or whatever?
• [ insert your own project here! ]

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