Slashdot Mirror

A single finished genome is not the problem. It is the raw data.

The problem is that any time you sequence a new individual's genome for a species that already has a genome assembly, you need minimum 5x coverage across the genome to reliably find variation. Because of variation in coverage, that means you may have to shoot for >20x coverage to find all the variation. The problem is more complex when you are trying to de novo assemble a genome for a species that does NOT have a genome assembly. In this case, you often have to aim for at least 40x coverage (and in the 100x range may be better).

To get the data, we use next-gen sequencing. To give you an idea of the data output, a single Illumina HiSeq 2000 run produces 3 billion reads. Each "read" is a pair of genomic fragments 100 bases long. That means 600,000,000,000 bases are produced in a single run. The run is stored as a .fastq file, meaning that each base is stored as an ASCII character, and has an associated quality score stored as another ASCII character. So that's 1.2 trillion ASCII characters for a single run, or about 1.09 terabytes uncompressed. This does not include the storage for the (uncompressable) images taken by the sequencing machine in order to call the bases. They can be an order of magnitude larger. A single experiment may involve dozens of such runs.

There is an expectation that these runs will be made available in a public repository when an analysis is published. That puts great stress on places like NIH, where 1.7 quadrillion raw bases have been uploaded in about the last four years:
http://www.ncbi.nlm.nih.gov/Traces/sra/

You are correct when you say that computational power is a bigger problem, but again, this is not related to the three billion bases of the genome, which is trivial in size. Once again, the problem is the raw data. When assembling a new species' genome from scratch, you somehow have to reassemble those 3 billion pairs of 100-base reads. The way that is done is by hashing every single read into pieces about 21 nucleotides long, then storing them all, creating a de Bruijin graph, and navigating through it. The amount of RAM required for this is absolutely insane.

Storage is not the problem. Computational power is.

Each genetic sequence is ~3GB but since sequences between individuals are very similar it is possible to compress them by only recording the differences from a reference sequences making each genome ~20 MB. This means you could store a sequences for everybody in the world in ~132 PB or 0.05% or total worldwide data storage (295 exabytes)

Now the real challenge is more in having enough computational power to read and process the 3 billion letters genetic sequence and designing effective algorithms to process this data.

More info on compression of genomic sequences
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074166/

Said gut inflammation nearly all of the time comes from highly concentrated sugar/starch.

Exactly what happens to your teeth/mouth, happens to the rest of your digestive system too. The predominant bacteria change, and grow massively and uncontrolled, because of the huge amount of ready-made/predigested energy.

I'm not saying anything about the cancer link myself. But more and unusual bacteria... over decades (of eating stuff not fit for human consumption)... draw your own conclusions...

If you are dealing with cancer recovery, some ideas:

"Ketogenic Diet May Be Key to Cancer Recovery"
http://articles.mercola.com/sites/articles/archive/2013/03/10/ketogenic-diet.aspx
"The premise is that since cancer cells need glucose to thrive, and carbohydrates turn into glucose in your body, then cutting out carbs literally starves the cancer cells."

People who live in traditional societies eating a traditional vegetable heavy diet and getting lots of sunlight and exercise also seem to have less lung cancer even when they smoke.
"Eat For Health - The Anti-Cancer Diet"
http://www.drfuhrman.com/library/article24.aspx

Also look into vitamin D:
http://www.naturalnews.com/036597_vitamin_D_anti-cancer_drug.html
http://www.grassrootshealth.net/

And iodine:
http://theiodineproject.webs.com/cancerandiodine.htm

Making these sorts of changes is not quite the same as an Android body btw, mentioned in Star Trek episode "I, Mudd" as something Uhura wants), but at least it might help get to the point where you could have one if you wanted -- related to out other conversation:
http://slashdot.org/comments.pl?sid=3892785&threshold=0&commentsort=0&mode=thread&cid=44082521

I can see you project an optimistic sense of humor about it all, which can be a healthful thing:
http://www.humorproject.com/bookstore/
http://www.ncbi.nlm.nih.gov/pubmed/10116744
"Laughter has many clinical benefits, promoting beneficial physiological changes and an overall sense of well-being. Humor even has long-term effects that strengthen the effectiveness of the immune system."

So, laughing is probably better healthwise than a buzz from a "droud"? :-)
http://laughteryoga.org/
http://www.youtube.com/watch?v=yXEfjVnYkqM

For nerve damage, vitamin B12 and omegas 3s. See also my comments here on mercury and herbs:
http://aaronwinborn.com/blogs/aaron/monday-was-my-46th-birthday-and-likely-my-last-anything-awesome-i-should-try-after-i-die

Yeah, stairs can be a real life-saver for many -- to get some regular exercise, which moves the lymph around, which boosts the immune system and the body's natural self-cleaning mechanisms. Walking outside in the sunshine helps, too (although of course how you need to manage your DVT and clot risks however competent doctors recommend):
http://www.bluezones.com/

For some inspiration, a movie that is up for free on YouTube for a while for the two year anniversary (again, adjusted for DVT):
http://www.fatsickandnearlydead.com/
http://www.rebootwithjoe.com/

And also, here is a movie (and book) on how clogged arteries can limit blood flow to the body's cells, creating a huge variety of health issues from that common cause (perhaps the root cause of most chronic illnesses in the US today as "diseases of affluence" such as you may be experiencing):
http://www.ravediet.com/

Also ask, "What Color is Your Diet?"
http://www.amazon.com/W

700 MB?? I think you can compress that to 4MB: http://www.ncbi.nlm.nih.gov/pubmed/18996942

You citation needed folks get on my nerves, but in my line of work the saying is "show me the data." I have alot of free time so I went ahead and googled it for you. Now most of the studies are behind paywalls and the wiki articles all allude to the problem. You however went ahead and thought you were being clever by quantifying anything over 100Hz. As I said, most of the wiki document alluding to it were behind paywalls but I did find ONE that has a number in it. It's a PDF and it is on slide 2. Go read that and holler back at me. Once you have your revelation, you can accept it as a fact that doesn't mean the end of all physics, or you can move your goalposts some more.

From the DOE
Also for your perusal Go to the lighting section.
Here is one of the offending paywall studies. The synopsis says there is some negative effects but it didn't have that magical 100Hz mentioned and I'm not paying to find out- I already know.

BT resistance: Medline lists over 900 papers when searching for "bt resistance" and Medline doesn't even index a lot of entomology or agricultural journals.

Hell, it's even a higher chance of getting struck by lightning than getting killed by a terrorist...

Chance of getting struck by lightning in a year 1 in 1000000 ( http://en.wikipedia.org/wiki/Lightning_strike )
Chance of getting killed by a terrorist 1 in 20000000 ( http://swampland.time.com/2013/05/06/chances-of-dying-in-a-terrorist-attack-number/ )

Some more statistics on helthcare-risks http://www.washingtonsblog.com/wp-content/uploads/2013/04/CDC-Mortality-CHart.jpg

http://terrorism.about.com/od/issuestrends/a/EconomicImpact.htm :

The US alone now spends about US $500 billion annually--20 percent of the US federal budget--on departments directly engaged in combating or preventing terrorism, most notably Defense and Homeland Security. The Defense budget increased by one-third, or over $100 billion, from 2001 to 2003 in response to the heightened sense of the threat of terrorism – an increase equivalent to 0.7 per cent of US GDP. Expenditures on defense and security are essential for any nation, but of course they also come with an opportunity cost; those resources are not available for other purposes, from spending on health and education to reductions in taxes. A higher risk of terrorism, and the need to combat it, simply raises that opportunity cost.

Estimated cost of NSA per year ~$4 Billion
Amount spent on cancer research by US goverment per year ~$5.6 Billion ( http://report.nih.gov/categorical_spending.aspx )
Amount needed to end world hunger ~$30 Billion per year.
Amount needed for universal healthcare in the US ~$200 Billion ( http://truecostblog.com/2009/05/13/how-much-would-universal-healthcare-cost/ )

Supposedly this is more than made up for by the fact they can live the rest of their life how they feel they should be.

Maybe. There are people that do regret it. If you do, there's no magic reset available. On this earth you will never fully be again what you once were.

Are sex change operations justified?

Sex changes are not effective, say researchers

'I will never be able to have sex again. Ever'

But what worries other psychiatrists is the mounting evidence that surgery may not actually improve the lives of those who feel they were born with the wrong body. A review of more than 100 international studies of post-operative transsexuals by the University of Birmingham found there was no scientific evidence that surgery was effective and, in many cases, patients were left feeling more distressed. Baltimore's Johns Hopkins University — which housed one of the pioneer gender clinics — no longer performs sex-change surgery due to such concerns.

A recent British review found suicide rates of up to 18 per cent among people who had undergone gender reassignment surgery. Doctors from London's Portman Clinic say they see many patients who feel trapped in "no-man's land" after surgery, finding themselves with a body which is no longer recognisable as male or female. Psychotherapy, the experts believe, may have saved them from such a fate but few gender clinics offer it. -- more

Long-term follow-up of transsexual persons undergoing sex reassignment surgery

It's a difficult issue for all concerned.

Anyway my outcomes will be better by having a gun.

Statistically speaking, you are more likely to kill yourself in moment of depression, a family member in the heat of anger, or a family member in an accident, rather than a criminal seeking to do you harm.

Fact: If you have a gun, everybody in your home is more likely than your non-gun-owning neighbors and their families to die in a gun-related accident, suicide or homicide.

Citation: http://www.ncbi.nlm.nih.gov/pubmed/9715182
Citation: http://pediatrics.aappublications.org/content/105/4/888.full
Citation: http://ajl.sagepub.com/content/early/2011/02/01/1559827610396294

Saying my argument is retarded is ignoring the clear and well establishing science. Rejecting the evidence with anger and namecalling does nothing to support your side that you will react with calm rationality in all situations, and never snap.

What if a company makes and patents a cDNA that is later found to also exist naturally?

Have we sequenced every variant of every species?

Case in point, Monsato make GM crops that resist herbicides. What if the parts they are patenting, have analouges in some other plant in the wild?

Monsanto is, in part, doing exactly what you suggested. The genetic element that grants their crops resistance to glyphosate (Round-Up) was discovered in microbes growing in waste runoff containing glyphosate. The patent is on the plants that have been transformed / engineered to contain this naturally occurring resistance gene in their genome and express it to garner resistance to the herbicide.

The cDNA argument is much worse to ludicrous. The only thing one could imagine is patentable surrounding the issue of cDNA is the technique involved in its generation, but that ship has sailed long ago. The entire process of generating cDNA is by using materials all found in nature. The RNA template that is used to generate cDNA in these cases of naturally occurring genes is obviously naturally occurring* and the technology to even create cDNA in the first place is using a naturally occurring enzyme, reverse transcriptase (found in retroviruses like HIV to catalyze the conversion of their genomic RNA to DNA). Because all these elements exist in the natural world, it is certainly possible in say HIV infected humans that random gene mRNA molecules have been converted to cDNA, thus negating the argument of generating something that does not exist in the natural world. More importantly, the only facet of this whole process of generating cDNA that is artificial is placing the materials in a tube together, NOT inventing any novel chemicals or enzymes to catalyze the process!

* In cells, mRNA molecules are heavily modified, sections spliced out, nucleotides edited, the 5' end capped, the 3' end poly-adenylated, so with the arguments placed forth concerning cDNA, one can imagine in vitro transcription of a gene creates an RNA molecule that doesn't exist in nature and can therefore be patented. Ridiculous, right?

..... comparative genomics really only teaches us about evolution. It's not relevant to medicine, outside of predicting the evolution of pathogens. We're not benefiting human medicine by sequencing, say, red pandas or sea turtles, although these things are certainly important for other reasons. There are occasionally exceptional genomes, like the naked mole rat (immune to cancer), but these are rare.

Comparative genomics are of enormous importance to the field of cisgenesis/intragenesis. Somewhat inbetween traditional plant breeding and inter-species genetic engineering, intragenics seeks to modify a target organism by transferring genes from related organisms. When applied to agriculture, there are practical savings in resources expended when trying to create new cultivars of existing crops. For more see: http://www.ncbi.nlm.nih.gov/pubmed/17692557

Making a car safer to drive because accidents becmoe more survivable is not the same thing as making accidents less likely, which is what we've been discussing. Those two cars will of course behave differently. Do you think that the presence of an airbag or a seat belt materially affects the car's handling? Of course not. The differences are due to a litany of other changes to cars over time.

As for that limb you're on. Don't look down:
https://news.uns.purdue.edu/html4ever/2006/060927ManneringOffset.html
http://www.ncbi.nlm.nih.gov/pubmed/8198694?dopt=Abstract
http://john-adams.co.uk/wp-content/uploads/2006/failure%20of%20seatbelt%20legislation.pdf
http://www.smithsonianmag.com/science-nature/Presence-of-Mind-Buckle-Up-And-Behave.html

And it's not limited to cars:
http://www.youtube.com/watch?v=7IB2xRfRHOA
http://gregmankiw.blogspot.com/2006/07/peltzman-effect.html
http://www.damninteresting.com/the-balance-of-risk/
http://www.thelancet.com/journals/lancet/article/PIIS0140673607603134/abstract
http://www.washingtonpost.com/wp-dyn/content/article/2009/03/27/AR2009032702825.html
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(07)61755-3/fulltext?_eventId=login
http://web.williams.edu/Economics/wp/Wilson_Circumcision.pdf
https://en.wikipedia.org/wiki/Risk_compensation

There's been other similar prior work. For example, there's evidence that gamers can quickly allocate their attention in an efficient fashion. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680769/ and that gamers have faster reaction times for a large variety of tasks http://cdp.sagepub.com/content/18/6/321.short.

No, no, no.

We all know that gaming is the work of the devil and teaches our chillin' nothing good.

Both Fox News and the Pastor told me so.

This "research" must be suppressed.

There's been other similar prior work. For example, there's evidence that gamers can quickly allocate their attention in an efficient fashion. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680769/ and that gamers have faster reaction times for a large variety of tasks http://cdp.sagepub.com/content/18/6/321.short.

Indeed, I'd have modded you up if I'd have mod points.

This study is yet another one showing these effects, but is by far not the first. The effects of video-game playing, in particular action video-game playing, on various part of the decision making process have been studied extensively. The whole research was kicked off by the publication of

Green, C.S. & Bavelier, D. (2003). Action video games modify visual selective attention. Nature, 423, 534-537

with more publications related to that topic available on the lab page of Daphne Bavelier.

Disclaimer: I was working in the same department as the above-mentioned lab some years ago

There's been other similar prior work. For example, there's evidence that gamers can quickly allocate their attention in an efficient fashion. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680769/ and that gamers have faster reaction times for a large variety of tasks http://cdp.sagepub.com/content/18/6/321.short.

According to that site, eating = impaired driving as well: http://www.ncbi.nlm.nih.gov/pubmed/22931176

Also the first wiki link calls it distracted driving, which is different from impaired, so lets stick with that.

You can educate yourself on why you're a horrible driver at: http://www.distraction.gov/

http://www.ncbi.nlm.nih.gov/pubmed/23332329 you go first, I see none.

Anyways, it makes sense that air quality is worse in areas with less trees leading to higher rates of lung disease, but we didn't need this study to affirm that. Just drive in a major city on a hot afternoon and check out the smog.

Of course I meant it to be a flippant remark but I'll reply to you seriously.

Hasn't the pro side already "denied" global warming enough to rename it "climate change"?

It was climate change before it was global warming. For instance this paper [PDF] published in October 1970 by George Benton titled "Carbon Dioxide and its Role in Climate Change".

Don't just assume that the causes of climate change now has to be the same as historical causes. According to paleoclimatologists what we're seeing now doesn't match up very well with what happened in the past. The closest is probably the PETM 55 million years ago but the rise in carbon and temperature were much slower (~20,000 years) than now (probably less than 300 years if we don't do something).

The Earth and life will certainly recover and keep going until the Sun gets too hot. The question is how much of human civilization will survive?

Trust me, you don't want to sound like BLAST at parties...unless it's a geeky party, that is.

And yes, I'm a neuroscientist FWIW.

A neuroscientist that's at least 20 years out of date.
http://en.wikipedia.org/wiki/Neurogenesis#Occurrence_in_adults
http://www.ncbi.nlm.nih.gov/pubmed/8338665
http://pubs.niaaa.nih.gov/publications/arh27-2/197-204.htm
http://web.mit.edu/9.013/www/lectures/07_PG_Neurogenesis_Migration.pdf

And yes, I'm a neuroscientist FWIW.

A neuroscientist that's at least 20 years out of date.
http://en.wikipedia.org/wiki/Neurogenesis#Occurrence_in_adults
http://www.ncbi.nlm.nih.gov/pubmed/8338665
http://pubs.niaaa.nih.gov/publications/arh27-2/197-204.htm
http://web.mit.edu/9.013/www/lectures/07_PG_Neurogenesis_Migration.pdf

In a 2004 study on this very subject, it was determined that the mean latency period for thyroid cancer to appear after radiation exposure was over 30 years. Some appear sooner, of course, but many appeared much later than that. What is the point of this report? At best, the proclamation of not causing any noticeable immediate harm is premature. But saying that the exposure is "unlikely to be able to attribute any health effects in the future" borders on irresponsible, and seems driven by an agenda.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356259/

It's annoying, but it's rapidly changing. A decade ago, I'm not sure open-access was a thing most researchers had ever heard of. Today, any biomedical research funded by the NIH has to be open access within a year of publication. I agree, it's time to cut the buggy whip makers out, but realize that is in fact happening right now.

It's a good thing then that the decision is predicated on the finding that CODIS scans for 13 non-coding segments of DNA that are not medically relevant.

Citation needed. At least the THO1 marker is associated with a disease [1, 2].

It's a good thing then that the decision is predicated on the finding that CODIS scans for 13 non-coding segments of DNA that are not medically relevant.

Citation needed. At least the THO1 marker is associated with a disease [1, 2].

Woah, woah, hold up. First of all, there is absolutely no way that all SNPs can contribute to diseases. The average difference between two people is something like 3 million SNPs; that is, at 3 million out of 3.1 billion positions in a human genome, two people of the same sex will have different values. Most of those differences are insignificant because the genome is built to be resilient to changes: (a) several amino acids have multiple representations that prevent some of the most common mutations from affecting their sequence, (b) the exact value of many amino acids is insignificant because they merely provide structural filler, making some codon missense mutations irrelevant, (c) many RNA elements have similar nonspecificity, (d) variation in function of either DNA, RNA, or protein elements may not amount to a detectable difference, (e) despite the recent discovery by the ENCODE project that as much as 80% of the genome may have some function, much of that appears to be extremely non-sequence-specific anyway; a significant chunk of the genome just provides scaffolding so that more important parts are easily accessible for transcription.

Second, it only takes a handful of rapidly-changing features to uniquely identify people. Seven billion people require just over 32 bits of information to specify; accounting for redundancy you can get a very small error rate with about half that. Given that we know of millions upon millions of SNPs, the probability of selecting 32 SNPs that are linked to actual disease is infinitesimal.

Third, I got it wrong; CODIS uses a different genetic marker called a short tandem repeat, which is a form of mutation that flips particularly frequently because the DNA replication machinery finds it very repetitive and has a high chance of slipping forward or backward while duplicating it. These regions are even less likely to be of medical importance because of their common variability. As it stands, the likelihood of a wrongful CODIS identification is non-zero, even between two families, because they only use 13 markers consistently. The one known case where one marker was linked to a disease was, quite simply, very unlikely. As an example, the VWA marker exists in a gene associated with a rare disease but has nothing to do with it.

Woah, woah, hold up. First of all, there is absolutely no way that all SNPs can contribute to diseases. The average difference between two people is something like 3 million SNPs; that is, at 3 million out of 3.1 billion positions in a human genome, two people of the same sex will have different values. Most of those differences are insignificant because the genome is built to be resilient to changes: (a) several amino acids have multiple representations that prevent some of the most common mutations from affecting their sequence, (b) the exact value of many amino acids is insignificant because they merely provide structural filler, making some codon missense mutations irrelevant, (c) many RNA elements have similar nonspecificity, (d) variation in function of either DNA, RNA, or protein elements may not amount to a detectable difference, (e) despite the recent discovery by the ENCODE project that as much as 80% of the genome may have some function, much of that appears to be extremely non-sequence-specific anyway; a significant chunk of the genome just provides scaffolding so that more important parts are easily accessible for transcription.

Second, it only takes a handful of rapidly-changing features to uniquely identify people. Seven billion people require just over 32 bits of information to specify; accounting for redundancy you can get a very small error rate with about half that. Given that we know of millions upon millions of SNPs, the probability of selecting 32 SNPs that are linked to actual disease is infinitesimal.

Third, I got it wrong; CODIS uses a different genetic marker called a short tandem repeat, which is a form of mutation that flips particularly frequently because the DNA replication machinery finds it very repetitive and has a high chance of slipping forward or backward while duplicating it. These regions are even less likely to be of medical importance because of their common variability. As it stands, the likelihood of a wrongful CODIS identification is non-zero, even between two families, because they only use 13 markers consistently. The one known case where one marker was linked to a disease was, quite simply, very unlikely. As an example, the VWA marker exists in a gene associated with a rare disease but has nothing to do with it.

I've already read enough comments of people not knowing what or how schizophrenia is - it's not just voices (or always involving voices in general). The National Institute for Mental Health has this nice little bit to get you all up to a half-educated level:

- What are the symptoms of schizophrenia?
The symptoms of schizophrenia fall into three broad categories: positive symptoms, negative symptoms, and cognitive symptoms.

- Positive symptoms
Positive symptoms are psychotic behaviors not seen in healthy people. People with positive symptoms often "lose touch" with reality. These symptoms can come and go. [...] They include the following:
Hallucinations are things a person sees, hears, smells, or feels that no one else can see, hear, smell, or feel. "Voices" are the most common type of hallucination in schizophrenia. Many people with the disorder hear voices. [...]

Delusions are false beliefs that are not part of the person's culture and do not change. The person believes delusions even after other people prove that the beliefs are not true or logical. People with schizophrenia can have delusions that seem bizarre, such as believing that neighbors can control their behavior with magnetic waves. [...]

Thought disorders are unusual or dysfunctional ways of thinking. One form of thought disorder is called "disorganized thinking." This is when a person has trouble organizing his or her thoughts or connecting them logically. They may talk in a garbled way that is hard to understand. Another form is called "thought blocking. [...]

- Negative symptoms
Negative symptoms are associated with disruptions to normal emotions and behaviors. These symptoms are harder to recognize as part of the disorder and can be mistaken for depression or other conditions.

These symptoms include the following:
- "Flat affect" (a person's face does not move or he or she talks in a dull or monotonous voice)
- Lack of pleasure in everyday life
- Lack of ability to begin and sustain planned activities
- Speaking little, even when forced to interact.

People with negative symptoms need help with everyday tasks. They often neglect basic personal hygiene. This may make them seem lazy or unwilling to help themselves, but the problems are symptoms caused by the schizophrenia.

- Cognitive symptoms
Cognitive symptoms are subtle. Like negative symptoms, cognitive symptoms may be difficult to recognize as part of the disorder. Often, they are detected only when other tests are performed. Cognitive symptoms include the following:
- Poor "executive functioning" (the ability to understand information and use it to make decisions)
- Trouble focusing or paying attention
- Problems with "working memory" (the ability to use information immediately after learning it).

Edited down, for some brevity. Full text here
Cognitive symptoms often make it hard to lead a normal life and earn a living. They can cause great emotional distress.

So, there are almost twice as many violent schizophrenics per the population than other people?

No, 5% of schizophrenics are violent, however people suffering from schizophrenia only make up < 1% of the general population.

The illness occurs in 1 percent of the general population

Source: NIMH General Information on Schizophrenia

This irritated me enough to do a quick look for pubmed and Cochrane articles:
http://www.ncbi.nlm.nih.gov/pubmed/20088678

I'm going to quote from the Cochrane Review:
http://onlinelibrary.wiley.com/doi/10.1002/14651858.CD005186.pub3/pdf
"Description of the condition In England, 8.2%of patients admitted to hospital develop healthcare-associated infections (HAIs) (Hospital Infection Society 2007). HAIs cause 5,000 deaths and cost £930 million annually (National Audit Office 1998). In the United States (US), an estimated 5% of patients develop HAIs, at a cost of 4.5 billion USD per year. This translates to an estimated two million cases of HAIs per annum, accounting for nearly 100,000 deaths (Klevens 2007). In Canada, an estimated 220,000 HAIs occur each year, with 8,000 related deaths (Zoutman 2003). Infection control experts everywhere are working to identify and correct factors that contribute to these rates. Although hand hygiene has long been regarded as the most effective preventive measure (Teare 1999), numerous studies over the past few decades have demonstrated that compliance with hand hygiene recommendations is poor and interventions are not effective long term."

I suggest you spend some time learning what Cochrane is *before* responding, to ensure you don't make an even bigger public fool of yourself.

There are animals, such as the puffer fish, where parts are edible but other parts are poisonous. Many people have died from incorrectly prepared fugu

The toxin in puffer fish/fugu (and the other species that contain tetrodotoxin) probably isn't produced by those animals, but by a bacteria or plankton in their diet. Possibly with some processing by the host animal, but almost certainly not synthesized by the animal. More likely just concentrated in a highly specific biological filter.

OK, but why do Ferrets get used preferentially for influenza studies?
I hope this doesn't come off as know-it-all, but there's a classic example of how picking test animals in medical studies really gave some erronious results and delayed recognizing a major health problem - Thalidomide.
Most of the lab animals used to test Thalidomide have zero incidence of birth defects under the doses normally used (even if these are proportionately dozens of times human doses). After reports of stunted limb growth and related syndromes started showing up, mostly in Europe, American researchers retested the drug on a much wider variety of animals, and after seeing several new test animal types with no negative effects, found the problem also occured in horses (and if memory serves, even tested it on a couple of elephants and found it occured there too). Horses were not generally considered major animal test subjects because of expense, and were sometimes not considered good for pregnancy related testing because of their long gestation times.
          So the broader question should be, what are the arguments for using ferrets for influenza studies? Is it a matter of cost? Has somebody sequenced the parts of ferret DNA that explain how the flu might affect them and found it has particular similarities to human DNA? Did ferret results translate to a good prediction about human epedemics in the past? This article doesn't really say why, so I see why even people who read more than the summary aren't comfortable with some of the conclusions.
          I followed through on my own questions here, so as not to just be nitpicking:

http://www.ncbi.nlm.nih.gov/pubmed/19412910
        This is just a short abstract, but it indicates that ferrets get the same broad set of symptoms as humans when they contract a flu. It also mentions that some of the more common lab animals, such as rats and guinea pigs are still quite useful for flu research.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180220/
        A much longer article. It discusses why mice don't work as well as larger rodents, and why even cotton rats (which ARE used) are not ideal. (You learn something every day - today I learned Cotton Rats don't have a sneeze reflex).

OK, but why do Ferrets get used preferentially for influenza studies?
I hope this doesn't come off as know-it-all, but there's a classic example of how picking test animals in medical studies really gave some erronious results and delayed recognizing a major health problem - Thalidomide.
Most of the lab animals used to test Thalidomide have zero incidence of birth defects under the doses normally used (even if these are proportionately dozens of times human doses). After reports of stunted limb growth and related syndromes started showing up, mostly in Europe, American researchers retested the drug on a much wider variety of animals, and after seeing several new test animal types with no negative effects, found the problem also occured in horses (and if memory serves, even tested it on a couple of elephants and found it occured there too). Horses were not generally considered major animal test subjects because of expense, and were sometimes not considered good for pregnancy related testing because of their long gestation times.
          So the broader question should be, what are the arguments for using ferrets for influenza studies? Is it a matter of cost? Has somebody sequenced the parts of ferret DNA that explain how the flu might affect them and found it has particular similarities to human DNA? Did ferret results translate to a good prediction about human epedemics in the past? This article doesn't really say why, so I see why even people who read more than the summary aren't comfortable with some of the conclusions.
          I followed through on my own questions here, so as not to just be nitpicking:

http://www.ncbi.nlm.nih.gov/pubmed/19412910
        This is just a short abstract, but it indicates that ferrets get the same broad set of symptoms as humans when they contract a flu. It also mentions that some of the more common lab animals, such as rats and guinea pigs are still quite useful for flu research.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180220/
        A much longer article. It discusses why mice don't work as well as larger rodents, and why even cotton rats (which ARE used) are not ideal. (You learn something every day - today I learned Cotton Rats don't have a sneeze reflex).

Everyone already considers mistakes done as a toddler irrelevant, and most do so for mistakes done as a preteen as well. This will just push the age limit for acceptability of "sins of youth" further.

As well it should. Reputable scientific studies demonstrate that full adult maturity doesn't arrive until the mid-20s. Specifically, "the frontal cortex areaâ"which governs judgment, decision-making and impulse controlâ"doesnâ(TM)t fully mature until around age 25."

The statistics back this up. If you look at who is committing violent crime and other serious antisocial behavior, it's almost always young males aged 14 to 25.

probably less than 5% of obese people are obese from the above listed medical conditions. The rest are obese from too much eating.

http://endocrine.niddk.nih.gov/pubs/Hypothyroidism/

http://www.annualreviews.org/doi/abs/10.1146/annurev.publhealth.29.020907.090954

Funny you should mention that. The majority of obese people I come across happen to be smokers. And here's mention of a study that seems to agree.
Also weight problems and heavy smoking both are more prevalent in schizophrenics.

No such condition can result in obesity. All they affect is feeling of hunger. Ie, it's somewhat harder to control yourself but it physically can't make you fat.

Sorry, but you're wrong:

Prednisolone: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0011824/?report=details#side_effects
Possible side effects: ...Rapid weight gain ...Swelling in your hands, ankles, or feet ...Gaining weight around your neck, upper back, breast, face, or waist ...Increased appetite ...Unusually full or round face

Methylprednisolone: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0011173/?report=details#side_effects
Possible side effects: ...Swelling in your hands, ankles, or feet, rapid weight gain ...Weight gain, increased hair growth, roundness or swelling of your face, thinning skin.

Synthetic corticosteroids cause weight gain, pretty much "period".

No such condition can result in obesity. All they affect is feeling of hunger. Ie, it's somewhat harder to control yourself but it physically can't make you fat.

Sorry, but you're wrong:

Prednisolone: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0011824/?report=details#side_effects
Possible side effects: ...Rapid weight gain ...Swelling in your hands, ankles, or feet ...Gaining weight around your neck, upper back, breast, face, or waist ...Increased appetite ...Unusually full or round face

Methylprednisolone: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0011173/?report=details#side_effects
Possible side effects: ...Swelling in your hands, ankles, or feet, rapid weight gain ...Weight gain, increased hair growth, roundness or swelling of your face, thinning skin.

Synthetic corticosteroids cause weight gain, pretty much "period".

Unfortunately (or fortunately, depending on your outlook), given the limited amount of time and money to diagnose such issues, it is far more sensible to "think horses, not zebras".

I have no sympathy for you regarding the doctor's diagnosis. Are you aware of the fact that obesity has been shown to have an impact on the occurence and severity of IgA nephropathy?

Your doctor was right. Losing weight would have helped.

I have a theory: playing football outside trains your peripheral motion perception (1) and reading trains your foveal motion perception. I'll leave it as an exercise to the reader to figure out how these activities might correlate with intelligence.

Full text, btw: http://www.bcs.rochester.edu/people/Duje/papers/13_Melnick_IQ_CB.pdf

Mtb is an intracellular pathogen. It invades our cells, the very same cells that are supposed to kill bacteria (the macrophages). This is why treatment of TB takes six months. Vitamin C, at a dosage lethal for Mtb as described in the article, cannot be used to kill the bacteria in our cells. The importance of the article is that it identifies a potentially intereseting difference between Mtb and other bacteria.

As for vitamin C, this is not some kind of a miraculous drug; it is just a co-enzyme required for a few particular reactions in our metabolic pathways. We, humans, are mutants, we lack the ability to synthetise vitamin C -- along with our cousins, the monkeys, although most animals do synthetise it on their own. Lack of vitamin C impedes the metabolism. However, only little of the co-enzyme is needed, and once vitamin C is no longer a limiting factor, it has barely an effect.

Think about that in terms of a network. If your wireless router is extremely slow, buying a new one will increase the speed of your connection. But what good is a super fast wifi router, if the outgoing connection runs at 10Mbit?

Vitamin C is also an antioxidant, and this is why some people (quite incorrectly) think that taking large doses of vitamin C are beneficial. However, there are two forms of this compound, L-ascorbate (vitamin C) and D-ascorbate; both are antioxidative, but only one is a co-enzyme. D-ascorbate, however, shows no beneficial effects.

Big pharma has not much interest in preventing the use of vitamin C in Mtb treatment. Mtb drugs are cheap, generic, and effective; the main reason why Mtb is a problem for much of the world is lack of fast and cheap diagnostic tools. You see, 2 billions (2e9, one third of worlds population) are infected with Mtb, and of these, only 10% will develop tuberculosis during their lifetime. However, we don't know which, why, and when. Also, when a person falls ill, it is not a quick process like a flu; rather than that, a person starts feeling unwell, caughing and becomes infectious over weeks before she finally decides to see a doctor. Here is a review article I wrote on TB and biomarkers: http://www.ncbi.nlm.nih.gov/pubmed/23181737 (full text behind a paywall, unfortunately).

Pauling believed that taking large doses of vitamines will prevent cancer and took large amounts of vitamin C throughout his life. In 1994, he died of prostate cancer.

Citation needed. Where are articles or information about these studies or their conclusion?

Seriously? Take five minutes and start searching medical journals. There are literally HUNDREDS of studies (maybe thousands) on vaccine side effects and effectiveness. There are DOZENS of metastudies that have tried and failed to find evidence of a link between autism and vaccines.

If you want just one example, take this study, which compiled data on 14.7 MILLION children who had been given MMR vaccines.

The authors actually are actually really negative about the way side effects are reported for vaccines, and they encourage more rigorous studies with better reporting.

Nevertheless, among the many studies with good data they looked at, they conclusively said that there is no evidence of a link between MMR vaccine and autism.

Why would a group of authors ready to chastise the medical establishment for not being more clear about possible side effects try to hide an autism link? They even identify and specifically discuss a number of known actual side effects to the vaccine.

This is just one. There are dozens of other review studies like it, and hundreds of individual studies on vaccine effectiveness and side effects. I'm terribly sorry for your son and your family, but there's absolutely no evidence of the link you suggest. A few hours looking at actual medical journals and studies, rather than at random websites promoting unjustified links, could easily demonstrate that.

"But there is no real relationship between these agents and the kinds of antibiotics that come in pills."

Wrong.

http://www.ncbi.nlm.nih.gov/pubmed/16922622

Only the ignorant hypochondriacs. The better informed ones are more concerned about triclosan affecting their epigenetics and giving them multiple drug resistant hand-ebola bacteria.

Source: I am an over-informed hypochondriac. I cringe when I have to touch receipts.

Ok did the research, she "invented" the wheel, they have been using this method since at least 2007. Her method uses "a novel core-shell nanorod electrode with hydrogenated TiO2 (H-TiO2) core and polyaniline shell. H-TiO2 acts as the double layer electrostatic core. "
http://www.usc.edu/CSSF//History/2013/Projects/S0912.pdf

Not so novel: "Incorporating the utilization of carbon nanotubes cathode and TiO2 nanotubes anode in energy storage, a nonaqueous hybrid supercapacitor was developed in order to significantly increase the energy density of the supercapacitor."
http://www.ncbi.nlm.nih.gov/m/pubmed/18019169/

Also dr yat li which she claims was "supervising" her seems to think he invented it a year ago without her help. Notice his name is on this article with other doctors but her name is missing: "Hydrogenated TiO2 Nanotube Arrays for Supercapacitors"
http://pubs.acs.org/doi/abs/10.1021/nl300173j

She basically did a chemistry experiment that had already been done and published, she invented nothing

Hey cool! I know the mechanism behind this! Garden cress are of the family Brassicaceae and many of that family are incredibly sensitive to a type of plasticizer called phthalates

I've worked in research horticulture for some years and research staff who focus on Brassica spp are incredibly careful about the components used in things like planthouses and controlled growth chambers

Not all plastics and plasticizers contain these compounds ( I've been told it is only in cheap plastics but I can't confirm this ). But if you're spending +50K on a controlled growth environment for your Brassica spp you want written confirmation from your supply company that no phthalates are used anywhere in it's construction as it negatively affects growth, including germination in some species. This include no phthalates in the circuitry, wiring and shrinkwrap where their outgassing could get into the growth chamber, even indirectly

I haven't read more than the abstracts of the articles below but they provide a useful starting point

Trace gases generated in closed plant cultivation systems and their effects on plant growth. https://www.ncbi.nlm.nih.gov/pubmed/11541892

Growth inhibition in Chinese cabbage (Brassica rapa var. chinensis) growth exposed to di-n-butyl phthalate. https://www.ncbi.nlm.nih.gov/pubmed/18678443

Hey cool! I know the mechanism behind this! Garden cress are of the family Brassicaceae and many of that family are incredibly sensitive to a type of plasticizer called phthalates

I've worked in research horticulture for some years and research staff who focus on Brassica spp are incredibly careful about the components used in things like planthouses and controlled growth chambers

Not all plastics and plasticizers contain these compounds ( I've been told it is only in cheap plastics but I can't confirm this ). But if you're spending +50K on a controlled growth environment for your Brassica spp you want written confirmation from your supply company that no phthalates are used anywhere in it's construction as it negatively affects growth, including germination in some species. This include no phthalates in the circuitry, wiring and shrinkwrap where their outgassing could get into the growth chamber, even indirectly

I haven't read more than the abstracts of the articles below but they provide a useful starting point

Trace gases generated in closed plant cultivation systems and their effects on plant growth. https://www.ncbi.nlm.nih.gov/pubmed/11541892

Growth inhibition in Chinese cabbage (Brassica rapa var. chinensis) growth exposed to di-n-butyl phthalate. https://www.ncbi.nlm.nih.gov/pubmed/18678443

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2509604/

Our findings add to the literature on child labor violations. In 2003, the US Department of Labor Wage and Hour Division identified 7228 minors employed in violation of the FLSA.37 In the same year, a survey of state labor departments carried out by the National Consumers League identified 4755 minors (in 30 states) who were illegally employed.14 Kruse and Mahoney used data from the US Bureau of Labor Statistics Current Population Survey to estimate that as many as 295 800 15- to 17-year-olds working in nonagricultural industries are illegally employed annually.4

Our resultsâ"which were derived from self-reported practices that we independently classified as being in violation or complianceâ"revealed that a substantial proportion of US adolescents working in the retail or service sector were employed in violation of the child labor laws. Extrapolating our findings to the roughly 2.4 million 16- and 17-year-old workersâ"a group for which the US Bureau of Labor Statistics reports employment data and who mostly work in retail and service2,3,7â"we estimate that as many as 264000 of these youths may be employed in violation of the FLSAâ(TM)s night work provisions and as many as 888 000 may be employed in violation of the hazardous orders each year.

And...

http://stopchildlabor.org/?cat=66

Young Worker Deaths & Injuries

Accidents are the leading cause of death for children between the ages of 10 and 19. Teenagers are particularly vulnerable to accidents at work. A 2006 survey found that 1 in 13 youth had been injured on the job. In 2008, 34 workers under 18 died in the workplace.

This is in the U.S. WITH child labor laws.

Social network size and artistic creativity.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079404/

It corresponds with social behaviour towards family and tribe. And fear of the outsider. Fear of immigration. Racism. And other such fears of people being different.

If you look at a more general coverage of the functions of the Amygdala you'll find lots of references to it being the centre of the fear response, and precious little about creativity. The only reference to creativity here is the possibility as an explanation for "unique responses" to the Rorschach ink-blot test.
http://en.wikipedia.org/wiki/Amygdala
An explanation that fits in better with what else we know about the amygdala is that the "unique responses" were seeing images of mad axe-murderers, where most people would see butterflies.

(As for "fairness", grow up.)

There is nothing childish about preferring things that are fair to things that are unfair. Indeed, if you feel that, you're just revealing you're a nasty self-serving person.